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Translation initiation in Drosophila melanogaster is reduced by mutations upstream of the AUG initiator codon
The importance to in vivo translation of sequences immediately upstream of the Drosophila alcohol dehydrogenase (Adh) start codon was examined at two developmental stages. Mutations were introduced into the Adh gene in vitro, and the mutant gene was inserted into the genome via germ line transformation. An A-to-T substitution at the [minus]3 position did not affect relative translation of ADH at the adult stage. A second mutant gene, containing five mutations in the region [minus]1 to [minus]9, was designed to completely block translation initiation. However, transformant lines bearing these mutations still exhibit detectable ADH, albeit at substantially reduced levels. The average fold reduction at the second-instar larval stage was 5.9, while at the adult stage a 12.5-fold reduction was observed.
Feng, Yue; Gunter, L.E.; Organ, E.L.; Cavener, D.R. (Vanderbilt University, Nashville, TN (United States))
Efficient translation initiation dictates codon usage at gene start
The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5–10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate. PMID:23774758
Bentele, Kajetan; Saffert, Paul; Rauscher, Robert; Ignatova, Zoya; Blüthgen, Nils
ABC50 mutants modify translation start codon selection.
ATP-binding cassette 50 (ABC50; also known as ABCF1) binds to eukaryotic initiation factor 2 (eIF2) and is required for efficient translation initiation. An essential step of this process is accurate recognition and selection of the initiation codon. It is widely accepted that the presence and movement of eIF1, eIF1A and eIF5 are key factors in modulating the stringency of start-site selection, which normally requires an AUG codon in an appropriate sequence context. In the present study, we show that expression of ABC50 mutants, which cannot hydrolyse ATP, decreases general translation and relaxes the discrimination against the use of non-AUG codons at translation start sites. These mutants do not appear to alter the association of key initiation factors to 40S subunits. The stringency of start-site selection can be restored through overexpression of eIF1, consistent with the role of that factor in enhancing stringency. The present study indicates that interfering with the function of ABC50 influences the accuracy of initiation codon selection. PMID:25597744
Stewart, Joanna D; Cowan, Joanne L; Perry, Lisa S; Coldwell, Mark J; Proud, Christopher G
Why has nature invented three stop codons of DNA and only one start codon?
We examine the standard genetic code with three stop codons. Assuming that the synchronization period of length 3 in DNA or RNA is violated during the transcription or translation processes, the probability of reading a frameshifted stop codon is higher than if the code would have only one stop codon. Consequently, the synthesis of RNA or proteins will soon terminate. In this way, cells do not produce undesirable proteins and essentially save energy. This hypothesis is tested on the AT-rich Drosophila genome, where the detection of frameshifted stop codons is even higher than the theoretical value. Using the binomial theorem, we establish the probability of reading a frameshifted stop codon within n steps. Since the genetic code is largely redundant, there is still space for some hidden secondary functions of this code. In particular, because stop codons do not contain cytosine, random C ? U and C ? T mutations in the third position of codons increase the number of hidden frameshifted stops and simultaneously the same amino acids are coded. This evolutionary advantage is demonstrated on the genomes of several simple species, e.g. Escherichia coli. PMID:22483666
K?ížek, Michal; K?ížek, Pavel
Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes
Summary: The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5? end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an "open" conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a "closed" conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the "P" site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded "landing pad" for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site. PMID:21885680
Hinnebusch, Alan G.
Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers
Technology Transfer Automated Retrieval System (TEKTRAN)
Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...
Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism
Technology Transfer Automated Retrieval System (TEKTRAN)
In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic dive...
Structural Changes Enable Start Codon Recognition by the Eukaryotic Translation Initiation Complex
Summary During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Ĺ resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2?, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon. PMID:25417110
Hussain, Tanweer; Llácer, Jose L.; Fernández, Israel S.; Munoz, Antonio; Martin-Marcos, Pilar; Savva, Christos G.; Lorsch, Jon R.; Hinnebusch, Alan G.; Ramakrishnan, V.
Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism.
In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation. PMID:24779012
Que, Youxiong; Pan, Yongbao; Lu, Yunhai; Yang, Cui; Yang, Yuting; Huang, Ning; Xu, Liping
Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism
In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation. PMID:24779012
Que, Youxiong; Pan, Yongbao; Lu, Yunhai; Yang, Cui; Yang, Yuting; Huang, Ning; Xu, Liping
Conserved residues in yeast initiator tRNA calibrate initiation accuracy by regulating preinitiation complex stability at the start codon.
Eukaryotic initiator tRNA (tRNAi) contains several highly conserved unique sequence features, but their importance in accurate start codon selection was unknown. Here we show that conserved bases throughout tRNAi, from the anticodon stem to acceptor stem, play key roles in ensuring the fidelity of start codon recognition in yeast cells. Substituting the conserved G31:C39 base pair in the anticodon stem with different pairs reduces accuracy (the Sui(-) [suppressor of initiation codon] phenotype), whereas eliminating base pairing increases accuracy (the Ssu(-) [suppressor of Sui(-)] phenotype). The latter defect is fully suppressed by a Sui(-) substitution of T-loop residue A54. These genetic data are paralleled by opposing effects of Sui(-) and Ssu(-) substitutions on the stability of methionylated tRNAi (Met-tRNA(i)) binding (in the ternary complex [TC] with eIF2-GTP) to reconstituted preinitiation complexes (PICs). Disrupting the C3:G70 base pair in the acceptor stem produces a Sui(-) phenotype and also reduces the rate of TC binding to 40S subunits in vitro and in vivo. Both defects are suppressed by an Ssu(-) substitution in eIF1A that stabilizes the open/P(OUT) conformation of the PIC that exists prior to start codon recognition. Our data indicate that these signature sequences of tRNA(i) regulate accuracy by distinct mechanisms, promoting the open/P(OUT) conformation of the PIC (for C3:G70) or destabilizing the closed/P(IN) state (for G31:C39 and A54) that is critical for start codon recognition. PMID:24589778
Dong, Jinsheng; Munoz, Antonio; Kolitz, Sarah E; Saini, Adesh K; Chiu, Wen-ling; Rahman, Hafsa; Lorsch, Jon R; Hinnebusch, Alan G
Discrimination of 5?-terminal start codons by translation initiation factor 3 is mediated by ribosomal protein S1
The interrelation between ribosomal protein S1 and IF3 in recognition\\/discrimination of 5?-terminal start codons by 30S ribosomes has been studied using in vitro toeprinting. The study has been performed with two naturally occurring leaderless mRNAs, ? cI and phage r1t rro mRNA, as well as with an artificial leaderless mRNA derived from the E. coli ompA gene. We show that
Isabella Moll; Armin Resch; Udo Bläsi
NSDL National Science Digital Library
In this activity, "write" a secret message in genetic code as beads on a string. Learners use an amino acid codon table to determine the DNA sequences that correspond to the one-letter amino acid abbreviations that make up their secret word(s). Learners also use start and stop codons in their sequences and follow a color key for the bases. Learners can trade strands with a friend to see if they can decode their secret message.
Julie Yu
C-terminal domain of eukaryotic initiation factor 5 promotes start codon recognition by its dynamic interplay with eIF1 and eIF2?
SUMMARY Recognition of the proper start codon on mRNAs is essential for protein synthesis, which requires scanning and involves eukaryotic initiation factors (eIFs) eIF1, eIF1A, eIF2 and eIF5. The carboxyl-terminal domain (CTD) of eIF5 stimulates 43S preinitiation complex (PIC) assembly; however, its precise role in scanning and start codon selection has remained unknown. Using nuclear magnetic resonance (NMR) spectroscopy, we identified the binding sites of eIF1 and eIF2? on eIF5-CTD and find that they are partially overlapped. Mutating select eIF5 residues in the common interface specifically disrupts interaction with both factors. By abrogating eIF5-CTD binding to eIF2?, genetic and biochemical evidence indicate that these eIF5-CTD mutations impair start codon recognition and impede eIF1 release from the PIC. This study provides mechanistic insight into the novel role of eIF5-CTD's dynamic interplay with eIF1 and eIF2? in switching PICs from an open to closed state at start codons. PMID:22813744
Luna, Rafael E.; Arthanari, Haribabu; Hiraishi, Hiroyuki; Nanda, Jagpreet; Martin-Marcos, Pilar; Markus, Michelle A.; Akabayov, Barak; Milbradt, Alexander G.; Luna, Lunet E.; Seo, Hee-Chan; Hyberts, Sven G.; Farmy, Amr; Reibarkh, Mikhail; Miles, David; Hagner, Patrick R.; O'Day, Eilzabeth M.; Yi, Tingfang; Marintchev, Assen; Hinnebusch, Alan; Lorsch, Jon; Asano, Katsura; Wagner, Gerhard
Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents.
Hexaploid tritordeum (H(ch)H(ch)AABB; 2n?=?42) results from the cross between Hordeum chilense (H(ch)H(ch); 2n?=?14) and cultivated durum wheat (Triticum turgidum ssp. durum (AABB; 2n?=?28). Morphologically, tritordeum resembles the wheat parent, showing promise for agriculture and wheat breeding. Start Codon Targeted (SCoT) polymorphism is a recently developed technique that generates gene-targeted markers. Thus, we considered it interesting to evaluate its potential for the DNA fingerprinting of newly synthesized hexaploid tritordeums and their respective parents. In this study, 60 SCoT primers were tested, and 18 and 19 of them revealed SCoT polymorphisms in the newly synthesized tritordeum lines HT27 and HT22, respectively, and their parents. An analysis of the presence/absence of bands among tritordeums and their parents revealed three types of polymorphic markers: (i) shared by tritordeums and one of their parents, (ii) exclusively amplified in tritordeums, and (iii) exclusively amplified in the parents. No polymorphism was detected among individuals of each parental species. Three SCoT markers were exclusively amplified in tritordeums of lines HT22 and HT27, being considered as polyploidization-induced rearrangements. About 70% of the SCoT markers of H. chilense origin were not transmitted to the allopolyploids of both lines, and most of the SCoTs scored in the newly synthesized allopolyploids originated from wheat, reinforcing the potential use of tritordeum as an alternative crop. PMID:24733248
Cabo, Sandra; Ferreira, Luciana; Carvalho, Ana; Martins-Lopes, Paula; Martín, António; Lima-Brito, José Eduardo
Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions.
Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT) markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB) of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) showed that genetic variation was greater within geographical regions (50.99%) than between them (49.01%). Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions. PMID:25853316
Zhang, Junchao; Xie, Wengang; Wang, Yanrong; Zhao, Xuhong
Analysis of diversity and relationships among orchardgrass (Dactylis glomerata L.) accessions using start codon-targeted markers.
Orchardgrass, or cocksfoot, is an important perennial forage grass worldwide. The comprehensive understanding of orchardgrass accessions will benefit germplasm collection and breeding progress, and it will enhance efforts to improve forage yield and quality. Therefore, 24 novel, simple, polymorphic, and reliable start codon-targeted (SCoT) markers were used to analyze the diversity and genetic relationships among 95 orchardgrass accessions. In total, 273 polymorphic bands were detected with an average of 11.4 bands per primer. The average polymorphic rate for the species was 83.4%, suggesting a high discriminating ability of the SCoT technique for orchardgrass. The molecular variance analysis revealed that 69.13 and 30.87% of variation resided within and among groups, respectively, demonstrating that the orchardgrass germplasms had a higher level of genetic diversity within groups than among geographical regions and distributions. The distinct geographical divergence of orchardgrass was revealed between North America and Oceania. The unweighted pair-group method with arithmetic mean dendrogram revealed a separation of 7 main clusters between 95 accessions according to the geographical origin. Furthermore, each cluster was divided into subgroups mainly according to the origin of its state. The genetic divergence of orchardgrass might be influenced by the ecogeographical conditions, climatic types, breeding systems and gene flow with variations in cultures, bird migration, and breeder selection. These results could facilitate orchardgrass germplasm collection, management, and breeding worldwide. PMID:25036346
Jiang, L F; Qi, X; Zhang, X Q; Huang, L K; Ma, X; Xie, W G
Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA.
The foot-and-mouth disease virus (FMDV) RNA contains two in-frame AUG codons separated by 84 nt that direct translation initiation of the viral polyprotein. The mechanism of initiation at the IRES-proximal AUG codon (AUG1) has been previously analyzed, whereas no data on factor requirements for AUG2 have been reported. Here, using the method of 48S translation initiation complex reconstitution, we show that eIF1 is indispensable in forming the 48S initiation complex at AUG2. In contrast, it reduces the assembly of this complex at AUG1. Stabilization of a stem-loop between the initiation triplets induces a small decrease in the toeprint intensity at AUG2, accompanied by an increase in the AUG1/AUG2 ratio as well as a moderate reduction of protein synthesis initiated at AUG2 in transfected cells. PTB and ITAF45 exerted an additive positive effect on the 48S complex at AUG2, although a substantial reconstitution on both AUGs occurs on omission of either of these proteins. Relative to the beta-globin mRNA, the 48S complex formation at AUG1 and AUG2 is slow and occurs with the same kinetics as revealed by the "kinetic" toeprint assay. Mutation of AUG1 to AUA does not abrogate protein synthesis in transfected cells, and has no effect on the rate of the 48S complex formation at AUG2. We conclude that the AUG2 initiation region is selected independently of 48S complex formation at the upstream AUG1. The kinetic toeprint assay also shows that cap-dependent assembly of the 48S complex in vitro occurs faster than the FMDV IRES-mediated complex assembly. PMID:17592045
Andreev, Dmitri E; Fernandez-Miragall, Olga; Ramajo, Jorge; Dmitriev, Sergey E; Terenin, Ilya M; Martinez-Salas, Encarna; Shatsky, Ivan N
Osteogenesis Imperfecta Type I Caused by a Novel Mutation in the Start Codon of the COL1A1 Gene in a Korean Family.
Osteogenesis imperfecta (OI) comprises a heterogeneous group of disorders characterized by susceptibility to bone fractures ranging in severity from perinatal death to a subtle increase in fracture frequency. We report the case of a patient who appeared healthy at birth and did not experience any fractures until 12 months of age. We observed blue sclera, frequent fractures without commensurate trauma, nearly normal stature, the absence of dentinogenesis imperfecta, no bony deformity, and no limitation of mobility in the patient - all characteristics suggestive of OI Type I. The patient's mother also had blue sclera and a history of frequent fracture episodes until the age of 15 years. A novel COL1A1 missense mutation (c.2T>G) disrupting the start codon of the gene (ATG to AGG (Met1Arg)) was found in the patient and his mother. PMID:25696019
Cho, Sung Yoon; Lee, Ji-Ho; Ki, Chang-Seok; Chang, Mi Sun; Jin, Dong-Kyu; Han, Heon-Seok
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
Upstream ORFs (uORFs) are mRNA elements defined by a start codon in the 5? UTR that is out-of-frame with the main coding sequence. Although uORFs are present in approximately half of human and mouse transcripts, no study ...
Calvo, Sarah E.
Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species.
Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement. PMID:25750860
Satya, Pratik; Karan, Maya; Jana, Sourav; Mitra, Sabyasachi; Sharma, Amit; Karmakar, P G; Ray, D P
Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species
Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement. PMID:25750860
Satya, Pratik; Karan, Maya; Jana, Sourav; Mitra, Sabyasachi; Sharma, Amit; Karmakar, P.G.; Ray, D.P.
Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA
The foot-and-mouth disease virus (FMDV) RNA contains two in-frame AUG codons separated by 84 nt that direct translation initiation of the viral polyprotein. The mechanism of initiation at the IRES-proximal AUG codon (AUG1) has been previously analyzed, whereas no data on factor requirements for AUG2 have been reported. Here, using the method of 48S translation initiation complex reconstitution, we show
A new 34-kilodalton isoform of human fibroblast growth factor 2 is cap dependently synthesized by using a non-AUG start codon and behaves as a survival factor.
Four isoforms of human fibroblast growth factor 2 (FGF-2) result from alternative initiations of translation at three CUG start codons and one AUG start codon. Here we characterize a new 34-kDa FGF-2 isoform whose expression is initiated at a fifth initiation codon. This 34-kDa FGF-2 was identified in HeLa cells by using an N-terminal directed antibody. Its initiation codon was identified by site-directed mutagenesis as being a CUG codon located at 86 nucleotides (nt) from the FGF-2 mRNA 5' end. Both in vitro translation and COS-7 cell transfection using bicistronic RNAs demonstrated that the 34-kDa FGF-2 was exclusively expressed in a cap-dependent manner. This contrasted with the expression of the other FGF-2 isoforms of 18, 22, 22.5, and 24 kDa, which is controlled by an internal ribosome entry site (IRES). Strikingly, expression of the other FGF-2 isoforms became partly cap dependent in vitro in the presence of the 5,823-nt-long 3' untranslated region of FGF-2 mRNA. Thus, the FGF-2 mRNA can be translated both by cap-dependent and IRES-driven mechanisms, the balance between these two mechanisms modulating the ratio of the different FGF-2 isoforms. The function of the new FGF-2 was also investigated. We found that the 34-kDa FGF-2, in contrast to the other isoforms, permitted NIH 3T3 cell survival in low-serum conditions. A new arginine-rich nuclear localization sequence (NLS) in the N-terminal region of the 34-kDa FGF-2 was characterized and found to be similar to the NLS of human immunodeficiency virus type 1 Rev protein. These data suggest that the function of the 34-kDa FGF-2 is mediated by nuclear targets. PMID:9858574
Arnaud, E; Touriol, C; Boutonnet, C; Gensac, M C; Vagner, S; Prats, H; Prats, A C
Eukaryotic translation initiation factor eIF5 promotes the accuracy of start codon recognition by regulating Pi release and conformational transitions of the preinitiation complex
eIF5 is the GTPase activating protein (GAP) for the eIF2·GTP·Met-tRNAiMet ternary complex with a critical role in initiation codon selection. Previous work suggested that the eIF5 mutation G31R/SUI5 elevates initiation at UUG codons by increasing GAP function. Subsequent work implicated eIF5 in rearrangement of the preinitiation complex (PIC) from an open, scanning conformation to a closed state at AUG codons, from which Pi is released from eIF2·GDP·Pi. To identify eIF5 functions crucial for accurate initiation, we investigated the consequences of G31R on GTP hydrolysis and Pi release, and the effects of intragenic G31R suppressors on these reactions, and on the partitioning of PICs between open and closed states. eIF5-G31R altered regulation of Pi release, accelerating it at UUG while decreasing it at AUG codons, consistent with its ability to stabilize the closed complex at UUG. Suppressor G62S mitigates both defects of G31R, accounting for its efficient suppression of UUG initiation in G31R,G62S cells; however suppressor M18V impairs GTP hydrolysis with little effect on PIC conformation. The strong defect in GTP hydrolysis conferred by M18V likely explains its broad suppression of Sui? mutations in numerous factors. We conclude that both of eIF5's functions, regulating Pi release and stabilizing the closed PIC conformation, contribute to stringent AUG selection in vivo. PMID:25114053
Saini, Adesh K.; Nanda, Jagpreet S.; Martin-Marcos, Pilar; Dong, Jinsheng; Zhang, Fan; Bhardwaj, Monika; Lorsch, Jon R.; Hinnebusch, Alan G.
Eukaryotic translation initiation factor eIF5 promotes the accuracy of start codon recognition by regulating Pi release and conformational transitions of the preinitiation complex.
eIF5 is the GTPase activating protein (GAP) for the eIF2 · GTP · Met-tRNAi (Met) ternary complex with a critical role in initiation codon selection. Previous work suggested that the eIF5 mutation G31R/SUI5 elevates initiation at UUG codons by increasing GAP function. Subsequent work implicated eIF5 in rearrangement of the preinitiation complex (PIC) from an open, scanning conformation to a closed state at AUG codons, from which Pi is released from eIF2 · GDP · Pi. To identify eIF5 functions crucial for accurate initiation, we investigated the consequences of G31R on GTP hydrolysis and Pi release, and the effects of intragenic G31R suppressors on these reactions, and on the partitioning of PICs between open and closed states. eIF5-G31R altered regulation of Pi release, accelerating it at UUG while decreasing it at AUG codons, consistent with its ability to stabilize the closed complex at UUG. Suppressor G62S mitigates both defects of G31R, accounting for its efficient suppression of UUG initiation in G31R,G62S cells; however suppressor M18V impairs GTP hydrolysis with little effect on PIC conformation. The strong defect in GTP hydrolysis conferred by M18V likely explains its broad suppression of Sui(-) mutations in numerous factors. We conclude that both of eIF5's functions, regulating Pi release and stabilizing the closed PIC conformation, contribute to stringent AUG selection in vivo. PMID:25114053
Saini, Adesh K; Nanda, Jagpreet S; Martin-Marcos, Pilar; Dong, Jinsheng; Zhang, Fan; Bhardwaj, Monika; Lorsch, Jon R; Hinnebusch, Alan G
N- and C-terminal residues of eIF1A have opposing effects on the fidelity of start codon selection
Translation initiation factor eIF1A stimulates preinitiation complex (PIC) assembly and scanning, but the molecular mechanisms of its functions are not understood. We show that the F131A,F133A mutation in the C-terminal tail (CTT) of eIF1A impairs recruitment of the eIF2-GTP-Met-tRNAiMet ternary complex to 40S subunits, eliminating functional coupling with eIF1. Mutating residues 17–21 in the N-terminal tail (NTT) of eIF1A also reduces PIC assembly, but in a manner rescued by eIF1. Interestingly, the 131,133 CTT mutation enhances initiation at UUG codons (Sui? phenotype) and decreases leaky scanning at AUG, while the NTT mutation 17–21 suppresses the Sui? phenotypes of eIF5 and eIF2? mutations and increases leaky scanning. These findings and the opposite effects of the mutations on eIF1A binding to reconstituted PICs suggest that the NTT mutations promote an open, scanning-conducive conformation of the PIC, whereas the CTT mutations 131,133 have the reverse effect. We conclude that tight binding of eIF1A to the PIC is an important determinant of AUG selection and is modulated in opposite directions by residues in the NTT and CTT of eIF1A. PMID:17332751
Fekete, Christie A; Mitchell, Sarah F; Cherkasova, Vera A; Applefield, Drew; Algire, Mikkel A; Maag, David; Saini, Adesh K; Lorsch, Jon R; Hinnebusch, Alan G
Amino-terminal extension generated from an upstream AUG codon is not required for mitochondrial import of yeast N2,N2-dimethylguanosine-specific tRNA methyltransferase.
The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The DNA sequence of the TRM1 locus and the 5' ends of mRNAs expressed from this gene have been determined. The majority of the 5' ends map within a large open reading frame between two in-frame ATGs at positions +1 and +49. A small fraction of the 5' ends are located upstream of the first ATG. Both AUGs of the TRM1 mRNAs are used to initiate translation, and two forms of N2,N2-dimethylguanosine-specific tRNA methyltransferase, which differ by an amino-terminal extension of 16 amino acids, are made. Mitochondrial tRNAs are modified when the initiation of translation is limited to one or the other of the AUGs, suggesting that the amino-terminal extension is not necessary for import of the protein into mitochondria. Mitochondrial targeting information must, therefore, be located in a region of N2,N2-dimethylguanosine-specific tRNA methyltransferase that is found in both forms of the enzyme. Images PMID:3299379
Ellis, S R; Hopper, A K; Martin, N C
Problem-Solving Test: The Effect of Synonymous Codons on Gene Expression
ERIC Educational Resources Information Center
Terms to be familiar with before you start to solve the test: the genetic code, codon, degenerate codons, protein synthesis, aminoacyl-tRNA, anticodon, antiparallel orientation, wobble, unambiguous codons, ribosomes, initiation, elongation and termination of translation, peptidyl transferase, translocation, degenerate oligonucleotides, green…
Szeberenyi, Jozsef
Tuning gene expression with synthetic upstream open reading frames
We engineered short ORFs and used them to control the expression level of recombinant proteins. These short ORFs, encoding a two-amino acid peptide, were placed upstream of an ORF encoding a protein of interest. Insertion of these upstream ORFs (uORFs) resulted in suppression of protein expression. By varying the base sequence preceding the uORF, we sought to vary the translation initiation rate of the uORF and subsequently control the degree of this suppression. Using this strategy, we generated a library of RNA sequence elements that can specify protein expression over a broad range of levels. By also using multiple uORFs in series and non-AUG start codons, we were able to generate particularly low expression levels, allowing us to achieve expression levels spanning three orders of magnitude. Modeling supported a mechanism where uORFs shunt the flow of ribosomes away from the downstream protein-coding ORF. With a lower translation initiation rate at the uORF, more ribosomes "leak" past the uORF; consequently, more ribosomes are able to reach and translate the downstream ORF. We report expression control by engineering uORFs and translation initiation to be robust, predictable, and reproducible across all cell types tested. We propose control of translation initiation as a primary method of choice for tuning expression in mammalian systems. PMID:23798422
Ferreira, Joshua P.; Overton, K. Wesley; Wang, Clifford L.
Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
Background Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species. Result RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, especially in 'Molecular function' category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. Conclusion A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species. PMID:24160180
We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general. PMID:2644621
Murray, E E; Lotzer, J; Eberle, M
Site-specific codon bias in bacteria
Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between two codons utilizing the same tRNA. Statistical
J. Maynard Smith; N. H. Smith
C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site
The EcoO109I restriction-modification system, which recognizes 5˘-(A\\/G)GGNCC(C\\/T)-3˘, has been cloned, and contains convergently transcribed endonuclease and methylase. The role and action mechanism of the gene product, C.EcoO109I, of a small open read- ing frame located upstream of ecoO109IR were investigated in vivo and in vitro. The results of dele- tion analysis suggested that C.EcoO109I acts as a positive regulator of
Keiko Kit; Junko Tsuda; Shin-ya Nakai
Single nucleotide polymorphism creating a variable upstream open reading frame regulates glucocorticoid receptor expression.
The glucocorticoid and mineralocorticoid receptors are known to play a crucial role in cellular responses to acute and chronic stress conditions. However, the influence of genetic variants and regulatory mechanisms within the glucocorticoid and mineralocorticoid receptor genes NR3C1 and NR3C2 is still incompletely understood. We therefore investigated putative upstream open reading frames, a motif regulating gene expression, from the 5' untranslated regions of the predominant human glucocorticoid receptor gene NR3C1 isoform alpha variant 1 and from the human mineralocorticoid receptor NR3C2 variants 1 and 2. The in silico analysis displayed one SNP (rs10482612), being present heterozygously in about 1.2% of the world population and 1.8% of the European population (according to the NCBI database), whose minor allele 'A' creates an upstream start codon. Our functional analysis performed by reporter gene assay and quantitative real-time PCR confirmed that the minor allele 'A' of the SNP rs10482612 can indeed alter protein activity of the subsequent gene during baseline conditions and cellular stress by creating a functional uORF in the 5'UTR of the NR3C1 transcript variant 1. PMID:25771224
Marceca, Claudia; Pfob, Martina; Schelling, Gustav; Steinlein, Ortrud K; Eggert, Marlene
Sequence analysis of the transcription control region upstream of the human FGF-3 gene.
With the purpose of studying the transcriptional regulation of the human FGF-3 gene, we have cloned and determined the nucleotide sequence of the 11-kbp region flanking its 5' end. Analysis of the sequence disclosed the presence of multiple repetitive elements. Remarkably, all of them were found to have inserted in the same orientation as the FGF-3 gene, suggesting that the whole upstream region could play a role in the control of its transcription. Unique regions within the sequence were scanned for the presence of transcriptional regulatory elements. A potential "Initiator" sequence preceded by several motifs homologous to binding sites for transcription factors pinpointed a putative promoter, 6 kbp upstream of the ATG codon for the FGF-3 protein. A 250-nt sequence stretch surrounding the "Initiator" was found to display punctate homology with the first (P1) of the three promoters (P1, P2 and P3) of the mouse Fgf-3/int-2 gene, specifically in the region of the transcriptional start sites. These data should be useful in studying the mechanisms of regulation of the FGF-3 transcription unit. PMID:10727086
Djenabi, S; Brison, O; Galdemard, C; Lavialle, C
Since the Mach number of the solar wind increases with increasing heliocentric distance, the ratio of thermal to magnetic pressure, or beta, of the Uranian magnetosheath is expected to be much higher than in the terrestrial magnetosheath. Consistent with this expectation the magnetosheath is observed to be extremely turbulent, and one may expect many particles to leak back upstream into
C.T. Russell; R. P. Lepping; C. W. Smith
Missouri River Looking Upstream
This is a comparison between the top photo taken on September 27, 2006 and the bottom photo taken June 8, 2011. These photos where both taken from the Double Ditch Indian Village, Bismarck, ND. This is the Missouri River at Double Ditch Indian Village looking north, upstream. Due to the flooding of ...
Biotechnology: Upstream Processing Associate
NSDL National Science Digital Library
In this 2:31 video excerpted from Pathways to Technology, youâ??ll learn about the role biotechnology plays in the fight against cancer. Roya Dirin is an upstream processing associate who works with cells, looking for proteins that can help treat cancer. Her first career was as a midwife, but she decided to switch fields because she wanted to help cure diseases. Roya explains how her community college biotechnology degree is just the first step in her new career. The video is accompanied by a background essay, standards alignment, and discussion questions. Users who sign up for a free account can download the video as well.
Site-specific codon bias in bacteria
Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between two codons utilizing the same tRNA. Statistical analyses, based on conclusions reached in an accompanying paper, show that the use of an unfavored codon at a given site in different genera is not due to common descent and must therefore be caused either by sequence-specific mutation or sequence-specific selection. Reasons are given for thinking that sequence-specific mutation cannot be responsible. We are unable to explain the preference between synonymous codons ending in C or T, but synonymous choice between A and G at third sites is largely explained by avoidance of AG-G (where the hyphen indicates the boundary between codons). We also observed that the preferred codon for proline in Enterobacter cloacea has changed from CCG to CCA. 27 refs., 7 tabs.
Smith, J.M.; Smith, N.H. [Univ. of Sussex, Brighton (United Kingdom)
Phylogenetic inference with weighted codon evolutionary distances.
We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates. PMID:19308635
Criscuolo, Alexis; Michel, Christian J
Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy.
Effects on translation in vivo by modification deficiencies for 2-methylthio-N6-isopentenyladenosine (ms2i6A) (Escherichia coli) or 2-methylthio-N6-(4-hydroxyisopentenyl)adenosine (ms2io6A) (Salmonella typhimurium) in tRNA were studied in mutant strains. These hypermodified nucleosides are present on the 3' side of the anticodon (position 37) in tRNA reading codons starting with uridine. In E. coli, translational error caused by tRNA was strongly reduced in the case of third-position misreading of a tryptophan codon (UGG) in a particular codon context but was not affected in the case of first-position misreading of an arginine codon (CGU) in another codon context. Misreading of UGA nonsense codons at two different positions was codon context dependent. The efficiencies of some tRNA nonsense suppressors were decreased in a tRNA-dependent manner. Suppressor tRNA which lacks ms2i6A-ms2io6A becomes more sensitive to codon context. Our results therefore indicate that, besides improving translational efficiency, ms2i6A37 and ms2io6A37 modifications in tRNA are also involved in decreasing the intrinsic codon reading context sensitivity of tRNA. Possible consequences for regulation of gene expression are discussed. PMID:3086285
Bouadloun, F; Srichaiyo, T; Isaksson, L A; Björk, G R
Codon Compression Algorithms for Saturation Mutagenesis.
Saturation mutagenesis is employed in protein engineering and genome-editing efforts to generate libraries that span amino acid design space. Traditionally, this is accomplished by using degenerate/compressed codons such as NNK (N = A/C/G/T, K = G/T), which covers all amino acids and one stop codon. These solutions suffer from two types of redundancy: (a) different codons for the same amino acid lead to bias, and (b) wild type amino acid is included within the library. These redundancies increase library size and downstream screening efforts. Here, we present a dynamic approach to compress codons for any desired list of amino acids, taking into account codon usage. This results in a unique codon collection for every amino acid to be mutated, with the desired redundancy level. Finally, we demonstrate that this approach can be used to design precise oligo libraries amendable to recombineering and CRISPR-based genome editing to obtain a diverse population with high efficiency. PMID:25303315
Pines, Gur; Pines, Assaf; Garst, Andrew D; Zeitoun, Ramsey I; Lynch, Sean A; Gill, Ryan T
Transfer RNA misidentification scrambles sense codon recoding
Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids. It requires an unused or rarely used codon, and an orthogonal tRNA synthetase:tRNA pair with the complementary anticodon. Mycoplasma capricolum contains only 6 CGG arginine codons without a dedicated tRNAArg. We wanted to reassign this codon to pyrrolysine by providing M. capricolum with pyrrolysyl-tRNA synthetase, a synthetic tRNA with a CCG anticodon (tRNAPylCCG), and the genes for pyrrolysine biosynthesis. Here we show that tRNAPylCCG is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry reveals that in the presence of tRNAPylCCG, CGG codons are translated as arginine. This result is not unexpected as most tRNA synthetases use the anticodon as a recognition element. The data suggest that tRNA misidentification by endogenous aminoacyl-tRNA synthetases needs to be overcome for sense codon recoding. PMID:24000185
Krishnakumar, Radha; Prat, Laure; Aerni, Hans; Ling, Jiqiang; Merryman, Chuck
A Major Controversy in Codon-Anticodon Adaptation Resolved by a New Codon Usage Index
Two alternative hypotheses attribute different benefits to codon-anticodon adaptation. The first assumes that protein production is rate limited by both initiation and elongation and that codon-anticodon adaptation would result in higher elongation efficiency and more efficient and accurate protein production, especially for highly expressed genes. The second claims that protein production is rate limited only by initiation efficiency but that improved codon adaptation and, consequently, increased elongation efficiency have the benefit of increasing ribosomal availability for global translation. To test these hypotheses, a recent study engineered a synthetic library of 154 genes, all encoding the same protein but differing in degrees of codon adaptation, to quantify the effect of differential codon adaptation on protein production in Escherichia coli. The surprising conclusion that "codon bias did not correlate with gene expression" and that "translation initiation, not elongation, is rate-limiting for gene expression" contradicts the conclusion reached by many other empirical studies. In this paper, I resolve the contradiction by reanalyzing the data from the 154 sequences. I demonstrate that translation elongation accounts for about 17% of total variation in protein production and that the previous conclusion is due to the use of a codon adaptation index (CAI) that does not account for the mutation bias in characterizing codon adaptation. The effect of translation elongation becomes undetectable only when translation initiation is unrealistically slow. A new index of translation elongation ITE is formulated to facilitate studies on the efficiency and evolution of the translation machinery. PMID:25480780
Xia, Xuhua
19 CFR 351.523 - Upstream subsidies.
Code of Federal Regulations, 2010 CFR
...2010-04-01 2010-04-01 false Upstream subsidies. 351.523 Section 351.523 Customs...Identification and Measurement of Countervailable Subsidies § 351.523 Upstream subsidies. (a) Investigation of upstream...
Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes.
AGA and AGG codons for arginine are the least used codons in Escherichia coli, which are encoded by a rare tRNA, the product of the dnaY gene. We examined the positions of arginine residues encoded by AGA/AGG codons in 678 E. coli proteins. It was found that AGA/AGG codons appear much more frequently within the first 25 codons. This tendency becomes more significant in those proteins containing only one AGA or AGG codon. Other minor codons such as CUA, UCA, AGU, ACA, GGA, CCC and AUA are also found to be preferentially used within the first 25 codons. The effects of the AGG codon on gene expression were examined by inserting one to five AGG codons after the 10th codon from the initiation codon of the lacZ gene. The production of beta-galactosidase decreased as more AGG codons were inserted. With five AGG codons, the production of beta-galactosidase (Gal-AGG5) completely ceased after a mid-log phase of cell growth. After 22 hr induction of the lacZ gene, the overall production of Gal-AGG5 was 11% of the control production (no insertion of arginine codons). When five CGU codons, the major arginine codon were inserted instead of AGG, the production of beta-galactosidase (Gal-CGU5) continued even after stationary phase and the overall production was 66% of the control. The negative effect of the AGG codons on the Gal-AGG5 production was found to be dependent upon the distance between the site of the AGG codons and the initiation codon. As the distance was increased by inserting extra sequences between the two codons, the production of Gal-AGG5 increased almost linearly up to 8 fold. From these results, we propose that the position of the minor codons in an mRNA plays an important role in the regulation of gene expression possibly by modulating the stability of the initiation complex for protein synthesis. Images PMID:2109307
Chen, G F; Inouye, M
CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition
The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer's combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses. PMID:19378146
Zaneveld, Jesse; Hamady, Micah; Sueoka, Noboru; Knight, Rob
Hand gesture recognition by analysis of codons
NASA Astrophysics Data System (ADS)
The problem of recognizing gestures from images using computers can be approached by closely understanding how the human brain tackles it. A full fledged gesture recognition system will substitute mouse and keyboards completely. Humans can recognize most gestures by looking at the characteristic external shape or the silhouette of the fingers. Many previous techniques to recognize gestures dealt with motion and geometric features of hands. In this thesis gestures are recognized by the Codon-list pattern extracted from the object contour. All edges of an image are described in terms of sequence of Codons. The Codons are defined in terms of the relationship between maxima, minima and zeros of curvature encountered as one traverses the boundary of the object. We have concentrated on a catalog of 24 gesture images from the American Sign Language alphabet (Letter J and Z are ignored as they are represented using motion) [2]. The query image given as an input to the system is analyzed and tested against the Codon-lists, which are shape descriptors for external parts of a hand gesture. We have used the Weighted Frequency Indexing Transform (WFIT) approach which is used in DNA sequence matching for matching the Codon-lists. The matching algorithm consists of two steps: 1) the query sequences are converted to short sequences and are assigned weights and, 2) all the sequences of query gestures are pruned into match and mismatch subsequences by the frequency indexing tree based on the weights of the subsequences. The Codon sequences with the most weight are used to determine the most precise match. Once a match is found, the identified gesture and corresponding interpretation are shown as output.
Ramachandra, Poornima; Shrikhande, Neelima
Use of molecular beacons to probe for messenger RNA release from ribosomes during 5'-translational blockage by consecutive low-usage codons in Escherichia coli
NASA Astrophysics Data System (ADS)
In `5'-translational blockage,' significantly reduced yields of proteins are synthesized in Escherichia coli when consecutive low-usage codons are inserted near translation starts of messages (with reduced or no effect when these same codons are inserted downstream). We tested the hypothesis that ribosomes encountering these low-usage codons prematurely release the mRNA. RNA from polysome gradients was fractionated into pools of polysomes, monosomes and ribosomes-free. New hybridization probes, called `molecular beacons,' and standard slot-blots, were used to detect test messages containing either consecutive low-usage AGG (arginine) or synonymous high-usage CGU insertions near the 5' end. The results show an approximately twofold increase in the ratio of free to bound mRNA when the low-usage codons were present compared to high-usage codons. In contrast, there was no difference in the ratio of free to bound mRNA when consecutive low-usage CUA or high-usage CUG (leucine) codons were inserted, or when the arginine codons were inserted near the 3' end. These data indicate that at least some mRNA is released from ribosomes during 5'-translational blockage by arginine but not leucine codons, and they support proposals that premature termination of translation can occur in some conditions in vivo in the absence of a stop codon.
Gao, Wenwu; Tyagi, Sanjay; Kramer, Fred R.; Goldman, Emanuel
Characterization of the porcine epidemic diarrhea virus codon usage bias.
Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree. PMID:25239728
Chen, Ye; Shi, Yuzhen; Deng, Hongjuan; Gu, Ting; Xu, Jian; Ou, Jinxin; Jiang, Zhiguo; Jiao, Yiren; Zou, Tan; Wang, Chong
Codon Usage Domains over Bacterial Chromosomes
introduce a clustering method based on information theory, specifically designed to cluster genes according of sulphur limitation, the most abundant proteins of the cyanobacterium Calothrix are encoded so as to reduce their sulphur requests. More recently, Elf et al. [8] have shown that when the codon reading is part
Kent, University of
Single-stranded genomic architecture constrains optimal codon usage.
Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts' codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes. PMID:22334868
Cardinale, Daniel J; Duffy, Siobain
Single-stranded genomic architecture constrains optimal codon usage
Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts' codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes. PMID:22334868
Cardinale, Daniel J.; Duffy, Siobain
Codon Usage in Higher Plants, Green Algae, and Cyanobacteria 1
Codon usage is the selective and nonrandom use of synonymous codons by an organism to encode the amino acids in the genes for its proteins. During the last few years, a large number of plant genes have been cloned and sequenced, which now permits a meaningful comparison of codon usage in higher plants, algae, and cyanobacteria. For the nuclear and organellar genes of these organisms, a small set of preferred codons are used for encoding proteins. Codon usage is different for each genome type with the variation mainly occurring in choices between codons ending in cytidine (C) or guanosine (G) versus those ending in adenosine (A) or uridine (U). For organellar genomes, chloroplastic and mitochrondrial proteins are encoded mainly with codons ending in A or U. In most cyanobacteria and the nuclei of green algae, proteins are encoded preferentially with codons ending in C or G. Although only a few nuclear genes of higher plants have been sequenced, a clear distinction between Magnoliopsida (dicot) and Liliopsida (monocot) codon usage is evident. Dicot genes use a set of 44 preferred codons with a slight preference for codons ending in A or U. Monocot codon usage is more restricted with an average of 38 codons preferred, which are predominantly those ending in C or G. But two classes of genes can be recognized in monocots. One set of monocot genes uses codons similar to those in dicots, while the other genes are highly biased toward codons ending in C or G with a pattern similar to nuclear genes of green algae. Codon usage is discussed in relation to evolution of plants and prospects for intergenic transfer of particular genes. PMID:16667228
Campbell, Wilbur H.; Gowri, G.
Selection Conflicts, Gene Expression, and Codon Usage Trends in Yeast
Synonymous codon usage in yeast appears to be influenced by natural selection on gene expression, as well as regional variation in compositional bias. Because of the large number of potential targets of selection (i.e., most of the codons in the genome) and presumed small selection coefficients, codon usage is an excellent model for studying factors that limit the effectiveness of
Richard M. Kliman; Naheelah Irving; Maria Santiago
A common periodic table of codons and amino acids
A periodic table of codons has been designed where the codons are in regular locations. The table has four fields (16 places in each) one with each of the four nucleotides (A, U, G, C) in the central codon position. Thus, AAA (lysine), UUU (phenylalanine), GGG (glycine), and CCC (proline) were placed into the corners of the fields as the
J. C. Biro; B. Benyo; C. Sansom; Á Szlávecz; G Fördös; T Micsik; Z Benyó
Codon optimization of genes for efficient protein expression in mammalian cells by selection of only preferred human codons.
A simple design method for codon optimization of genes to express a heterologous protein in mammalian cells is described. Codon optimization was performed by choosing only codons preferentially used in humans and with over 60% GC content, and the method was named the "preferred human codon-optimized method." To test our simple rule for codon optimization, the preferred human codon-optimized genes for six proteins containing photoproteins (aequorin and clytin II) and luciferases (Gaussia luciferase, Renilla luciferase, and firefly luciferases from Photinus pyralis and Luciola cruciata) were chemically synthesized and transiently expressed in Chinese hamster ovary-K1 cells. All preferred human codon-optimized genes showed higher luminescence activity than the corresponding wild-type genes. Our simple design method could be used to improve protein expression in mammalian cells efficiently. PMID:25665506
Inouye, Satoshi; Sahara-Miura, Yuiko; Sato, Jun-Ichi; Suzuki, Takahiro
Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation
Ribosome profiling data report on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation. PMID:25538139
Pop, Cristina; Rouskin, Silvi; Ingolia, Nicholas T; Han, Lu; Phizicky, Eric M; Weissman, Jonathan S; Koller, Daphne
Genome-wide analysis of codon usage bias in Ebolavirus.
Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species. The interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system and evolution. In the present study, we performed comprehensive analyses of codon usage and composition of ZEBOV. Effective number of codons (ENC) indicates that the overall codon usage among ZEBOV strains is slightly biased. Different codon preferences in ZEBOV genes in relation to codon usage of human genes were found. Highly preferred codons are all A-ending triplets, which strongly suggests that mutational bias is a main force shaping codon usage in ZEBOV. Dinucleotide composition also plays a role in the overall pattern of ZEBOV codon usage. ZEBOV does not seem to use the most abundant tRNAs present in the human cells for most of their preferred codons. PMID:25445348
Cristina, Juan; Moreno, Pilar; Moratorio, Gonzalo; Musto, Héctor
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
Background Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. Results Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts. Conclusion Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes.
Mitreva, Makedonka; Wendl, Michael C; Martin, John; Wylie, Todd; Yin, Yong; Larson, Allan; Parkinson, John; Waterston, Robert H; McCarter, James P
Analysis of synonymous codon usage pattern in duck circovirus.
Duck circovirus (DuCV) disease causes a long-term immunosuppressive and multiple secondary infection in ducks. In this study, relative synonymous codon usage (RSCU) values, nucleotide contents and effective number of codon (ENC) values were calculated and compared among open reading frames (ORFs) of 53 DuCV genomes. The results reveal that most of the codons are ended with C and the overall bias is not remarkable in DuCV. A comparative analysis of codon contents and ENC values indicates that mutation pressure is the most significant factor responsible for the evolutional processes of codon usage bias in DuCV. However, other factors, such as composition constraints, translation selection, hydrophobicity and aromaticity should not be ignored. Finally principal component analysis (PCA) and hierarchical clustering method were performed based on RSCU. The significant difference of codon usage bias exists in DuCV-1 and DuCV-2 genotypes, but codon usage pattern of DuCV from the different epidemic areas or subtypes fails to influence the formation of codon usage bias. Analysis of the relationship of synonymous codon usage variation based on the two genotypes suggests that DuCV-2 is more conservative than DuCV-1, which may because of recombination events. Moreover, there are distinct differences in the degree of codon usage pattern evolution in different function genes, rep and cap. Therefore, the genotypes, subtypes and different functional genes also relate to the pattern of synonymous codon usage. The main objective of this study is to provide some sight into synonymous codon usage characteristics and the evolutionary relationship of DuCV. PMID:25497833
Xu, Yu; Jia, Renyong; Zhang, Zhilong; Lu, Yanyan; Wang, Mingshu; Zhu, Dekang; Chen, Shun; Liu, Mafeng; Yin, Zhongqiong; Cheng, Anchun
Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus
BACKGROUND: The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of
Emily HM Wong; David K Smith; Raul Rabadan; Malik Peiris; Leo LM Poon
Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding
Rapid cell growth demands fast protein translational elongation to alleviate ribosome shortage. However, speedy elongation undermines translational accuracy because of a mechanistic tradeoff. Here we provide genomic evidence in budding yeast and mouse embryonic stem cells that the efficiency–accuracy conflict is alleviated by slowing down the elongation at structurally or functionally important residues to ensure their translational accuracies while sacrificing the accuracy for speed at other residues. Our computational analysis in yeast with codon resolution suggests that mRNA secondary structures serve as elongation brakes to control the speed and hence the fidelity of protein translation. The position-specific effect of mRNA folding on translational accuracy is further demonstrated experimentally by swapping synonymous codons in a yeast transgene. Our findings explain why highly expressed genes tend to have strong mRNA folding, slow translational elongation, and conserved protein sequences. The exquisite codon-by-codon translational modulation uncovered here is a testament to the power of natural selection in mitigating efficiency–accuracy conflicts, which are prevalent in biology. PMID:25051069
Yang, Jian-Rong; Chen, Xiaoshu; Zhang, Jianzhi
Complex Codon Usage Pattern and Compositional Features of Retroviruses
Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition. PMID:24288576
RoyChoudhury, Sourav; Mukherjee, Debaprasad
Analysis of synonymous codon usage bias in Chlamydia.
Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexually transmitted diseases, and are associated with cardiovascular diseases. The analysis of codon usage may improve our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of target genes to improve their expression for gene therapy. Here, we analyzed the codon usage of C. muridarum, C. trachomatis (here indicating biovar trachoma and LGV), C. pneumoniae, and C. psittaci using the codon usage database and the CUSP (Create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). The results show that the four genomes have similar codon usage patterns, with a strong bias towards the codons with A and T at the third codon position. Compared with Homo sapiens, the four chlamydial species show discordant seven or eight preferred codons. The ENC (effective number of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained by the G+C content, while translational selection and gene length exert relatively weaker influences. Moreover, mutational pressure appears to be the major determinant of the codon usage variation among the chlamydial genes. In addition, we compared the codon preferences of C. trachomatis with those of E. coli, yeast, adenovirus and Homo sapiens. There are 23 codons showing distinct usage differences between C. trachomatis and E. coli, 24 between C. trachomatis and adenovirus, 21 between C. trachomatis and Homo sapiens, but only six codons between C. trachomatis and yeast. Therefore, the yeast system may be more suitable for the expression of chlamydial genes. Finally, we compared the codon preferences of C. trachomatis with those of six eukaryotes, eight prokaryotes and 23 viruses. There is a strong positive correlation between the differences in coding GC content and the variations in codon bias (r=0.905, P<0.001). We conclude that the variation of codon bias between C. trachomatis and other organisms is much less influenced by phylogenetic lineage and primarily determined by the extent of disparities in GC content. PMID:15645075
Lü, Hui; Zhao, Wei-Ming; Zheng, Yan; Wang, Hong; Qi, Mei; Yu, Xiu-Ping
Cloning and characterization of 5'-upstream region of human phospholipase C-beta2 gene.
5'-upstream region of the phospholipase C-beta2 gene, 810 bp, was cloned and characterized. S1 nuclease mapping and primer extension analyses revealed that a single transcriptional start site locates at 284 nucleotides upstream from the beginning of translation. The 5-upstream region lacks both TATA motif and typical initiator sequence, but retains GC-rich segment. Two putative regulatory regions, a negative region (-636/-588) and a positive region (-98/ -13) were identified in the upstream region of PLC-beta2 gene. We suggest that the transcription of PLC-beta2 may be regulated by binding of regulatory proteins to the negative and/or positive regulatory regions located in the upstream of the gene. PMID:11460885
Yun, E S; Lee, S J; Kim, M J; Ryu, S H; Suh, P G
Directional next-generation RNA sequencing and examination of premature termination codon mutations in endoglin/hereditary haemorrhagic telangiectasia.
Hereditary haemorrhagic telangiectasia (HHT) is a disease characterised by abnormal vascular structures, and most commonly caused by mutations in ENG, ACVRL1 or SMAD4 encoding endothelial cell-expressed proteins involved in TGF-? superfamily signalling. The majority of mutations reported on the HHT mutation database are predicted to lead to stop codons, either due to frameshifts or direct nonsense substitutions. The proportion is higher for ENG (67%) and SMAD4 (65%) than for ACVRL1 (42%), p < 0.0001. Here, by focussing on ENG, we report why conventional views of these mutations may need to be revised. Of the 111 stop codon-generating ENG mutations, on ExPASy translation, all except one were premature termination codons (PTCs), sited at least 50-55 bp upstream of the final exon-exon boundary of the main endoglin isoform, L-endoglin. This strongly suggests that the mutated RNA species will undergo nonsense-mediated decay. We provide new in vitro expression data to support dominant negative activity of stable truncated endoglin proteins but suggest these will not generate HHT: the single natural stop codon mutation in L-endoglin (sited within 50-55 nucleotides of the final exon-exon boundary) is unlikely to generate functional protein since it replaces the entire transmembrane domain, as would 8 further natural stop codon mutations, if the minor S-endoglin isoform were implicated in HHT pathogenesis. Finally, next-generation RNA sequencing data of 7 different RNA libraries from primary human endothelial cells demonstrate that multiple intronic regions of ENG are transcribed. The potential consequences of heterozygous deletions or duplications of such regions are discussed. These data support the haploinsufficiency model for HHT pathogenesis, explain why final exon mutations have not been detected to date in HHT, emphasise the potential need for functional examination of non-PTC-generating mutations, and lead to proposals for an alternate stratification system of mutational types for HHT genotype-phenotype correlations. PMID:23801935
Govani, F S; Giess, A; Mollet, I G; Begbie, M E; Jones, M D; Game, L; Shovlin, C L
Association of DRD4 uVNTR and TP53 codon 72 polymorphisms with schizophrenia: a case-control study
Background The tumour supressor gene TP53 is thought to be involved in neural apoptosis. The polymorphism at codon 72 in TP53 and the\\u000a long form variants of the upstream variable number of tandem repeats (uVNTR) polymorphism in the dopamine D4 receptor (DRD4)\\u000a gene are reported to confer susceptibility to schizophrenia.\\u000a \\u000a \\u000a \\u000a \\u000a Methods We recruited 934 patients with schizophrenia and 433 healthy individuals, and
For-Wey Lung; Bih-Ching Shu; Wei-Tsung Kao; C Nathan Chen; Yu-Chi Ku; Dong-Sheng Tzeng
ERIC Educational Resources Information Center
Discusses the importance of early interest in science and how effective it is on career choice in adult stages of life. Recommends starting mathematics and science activities in preschool and kindergarten. Describes how to create a career-oriented learning center in the classroom with examples of kitchen chemistry, nutrition/botany, zoology,…
Rubin, Penni
Genome Landscapes and Bacteriophage Codon Usage Julius B. Lucks1
Genome Landscapes and Bacteriophage Codon Usage Julius B. Lucks1 , David R. Nelson1,2 , Grzegorz R and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E of bacteriophages. Citation: Lucks JB, Nelson DR, Kudla GR, Plotkin JB (2008) Genome Landscapes and Bacteriophage
Plotkin, Joshua B.
[Codon usage bias in the straw mushroom Volvariella volvacea].
We analyzed the whole genome coding sequence of Volvariella volvacea to study the pattern utilization of codons by Codon W 1.4.2. As results, 24 optimal codons were identified. Moreover, the frequency of codons usage was calculated by CUSP program. We compared the frequency of codons usage of V. volvacea with other organisms including 6 modal value species (Homo sapiens, Saccharomys cerevisiae, Arabidopsis thalian, Mus musculus, Danio rerio and Drosophila melanogaster) and 4 edible fungi (Coprinopsis cinerea, Agaricus bisporus, Lentinula edodes and Pleurotus ostreatus). We found that there were less differences in 3 edible fungi (excluding Pleurotus ostreatus) than 6 modal value species, comparing with the frequency of codons usage of V. volvacea. With software SPSS16.0, cluster analysis which showed differences in the size of codon bias, reflects the evolutionary relationships between species, which can be used as a reference of evolutionary relationships of species. This was the first time for analysis the codon preference among the whole coding sequences of edible fungi, serving as theoretical basis to apply genetic engineering of V. volvacea. PMID:25720157
Jiang, Wei; Lü, Beibei; He, Jianhua; Wang, Jinbin; Wu, Xiao; Wu, Guogan; Bao, Dapeng; Chen, Mingjie; Zhang, Jinsong; Tan, Qi; Tang, Xueming
Positional requirements for the function of nif -specific upstream activator sequences
The upstream activator sequence (UAS) found in Klebsiella pneumoniae nif promoters and required for the activation of transcription by nifA, is absent from the nifF-nifL intergenic region, but is present downstream from the nifLA transcription start at+59. To determine whether nif upstream activator sequences can function in a 3' position, the nifH UAS was cloned downstream from the NifH transcription
Martin Buck; Joanna Woodcock; Wendy Cannon; Lesley Mitchenall; Martin Drummond
NSDL National Science Digital Library
Before starting any of the activities in this guide, we strongly recommend that you read the information in this section. Here we cover the critically important issues of how to handle amphibians and reptiles, and safety issues concerning these animals and field activities in general. We also discuss permits and regulations relating to the collecting, handling, and raising of herps. This free selection also includes the Table of Contents, Preface, and Introduction.
Marianne E. Krasny
NASA Astrophysics Data System (ADS)
This level sets the stage for the design philosophy called "Triadic Game Design" (TGD). This design philosophy can be summarized with the following sentence: it takes two to tango, but it takes three to design a meaningful game or a game with a purpose. Before the philosophy is further explained, this level will first delve into what is meant by a meaningful game or a game with a purpose. Many terms and definitions have seen the light and in this book I will specifically orient at digital games that aim to have an effect beyond the context of the game itself. Subsequently, a historical overview is given of the usage of games with a serious purpose which starts from the moment we human beings started to walk on our feet till our contemporary society. It turns out that we have been using games for all kinds of non-entertainment purposes for already quite a long time. With this introductory material in the back of our minds, I will explain the concept of TGD by means of a puzzle. After that, the protagonist of this book, the game Levee Patroller, is introduced. Based on the development of this game, the idea of TGD, which stresses to balance three different worlds, the worlds of Reality, Meaning, and Play, came into being. Interested? Then I suggest to quickly "press start!"
Harteveld, Casper
A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype
The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27KIP1, an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27KIP1 expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5?UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF–encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27KIP1 expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27KIP1 activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27KIP1 activity can also be modulated by an uORF and mutations affecting uORF could change p27KIP1 expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases. PMID:23555276
Occhi, Gianluca; Regazzo, Daniela; Trivellin, Giampaolo; Boaretto, Francesca; Ciato, Denis; Bobisse, Sara; Ferasin, Sergio; Cetani, Filomena; Pardi, Elena; Korbonits, Márta; Pellegata, Natalia S.; Sidarovich, Viktoryia; Quattrone, Alessandro; Opocher, Giuseppe; Mantero, Franco; Scaroni, Carla
NSDL National Science Digital Library
A person, place, or thing is what usually sparks those first memorable childhood impressions. Of course, we often do not study our newfound interests from the time of our personal enlightenment to adulthood, but early childhood interests are strong and they can have a powerful hold on us. Children usually show interest in many areas, though one interest usually resurfaces as they get older. Often, it seems this interest--usually one from childhood--is the one that leads to a profession. This free selection from Start Young! Early Childhood Science Activities also includes a Contents, Introduction, and Index section, along with a Quick Reference Chart.
Penni Rubin
Ecological Adaptation in Bacteria: Speciation Driven by Codon Selection
In bacteria, physiological change may be effected by a single gene acquisition, producing ecological differentiation without genetic isolation. Natural selection acting on such differences can reduce the frequency of genotypes that arise from recombination at these loci. However, gene acquisition can only account for recombination interference in the fraction of the genome that is tightly linked to the integration site. To identify additional loci that contribute to adaptive differences, we examined orthologous genes in species of Enterobacteriaceae to identify significant differences in the degree of codon selection. Significance was assessed using the Adaptive Codon Enrichment metric, which accounts for the variation in codon usage bias that is expected to arise from mutation and drift; large differences in codon usage bias were identified in more genes than would be expected to arise from stochastic processes alone. Genes in the same operon showed parallel differences in codon usage bias, suggesting that changes in the overall levels of gene expression led to changes in the degree of adaptive codon usage. Most significant differences between orthologous operons were found among those involved with specific environmental adaptations, whereas "housekeeping" genes rarely showed significant changes. When considered together, the loci experiencing significant changes in codon selection outnumber potentially adaptive gene acquisition events. The identity of genes under strong codon selection seems to be influenced by the habitat from which the bacteria were isolated. We propose a two-stage model for how adaptation to different selective regimes can drive bacterial speciation. Initially, gene acquisitions catalyze rapid ecological differentiation, which modifies the utilization of genes, thereby changing the strength of codon selection on them. Alleles develop fitness variation by substitution, producing recombination interference at these loci in addition to those flanking acquired genes, allowing sequences to diverge across the entire genome and establishing genetic isolation (i.e., protection from frequent homologous recombination). PMID:22740635
Retchless, Adam C.; Lawrence, Jeffrey G.
Synonymous codon usage in chloroplast genome of Coffea arabica
Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A3, T3, G3, C3, GC3) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC3 plot grouped majority of the analyzed genes on or just below the left side of the expected GC3 curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica. PMID:23251044
Nair, Rahul R; Nandhini, Manivasagam B; Monalisha, Elango; Murugan, Kavitha; Sethuraman, Thilaga; Nagarajan, Sangeetha; Rao, Nayani Surya Prakash; Ganesh, Doss
In the paper experimental measurements of the time-dependent velocity and density perturbations upstream of obstacles in linearly stratified flow are presented. Attention is concentrated on obstacles which generate turbulent separated wakes at Froude numbers, based on velocity an...
Swimming Upstream: How to Reduce Homelessness in
Swimming Upstream: How to Reduce Homelessness in Tempe's Emerging Urban Setting David V. Summers of the Tempe First United Methodist Church, provides vital support services to homeless and working poor people
Zhang, Junshan
Evidence of efficient stop codon readthrough in four mammalian genes
Stop codon readthrough is used extensively by viruses to expand their gene expression. Until recent discoveries in Drosophila, only a very limited number of readthrough cases in chromosomal genes had been reported. Analysis ...
Loughran, Gary
Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast
Recent analysis of genomic signatures in mammals, flies, and worms indicates that functional translational stop codon readthrough is considerably more abundant in metazoa than previously recognized, but this analysis ...
Jungreis, Irwin
Towards reassigning the rare AGG codon in Escherichia coli.
The rare AGG codon in Escherichia coli has been reassigned to code non-canonical amino acids (ncAAs) by using the PylRS-tRNA(Pyl)(CCU) pair. When N(?) -alloc-lysine was used as a PylRS substrate, almost quantitative occupancy of N(?) -alloc-lysine at an AGG codon site was achieved in minimal medium. ncAAs can be potentially incorporated at the AGG codon with varying efficiencies, depending on their activities towards corresponding enzymes. As AGG is a sense codon, the approach reported here resolves the typical low ncAA incorporation issue that has been associated with ncAA mutagenesis and therefore allows bulk preparation of proteins with site-selectively incorporated ncAAs for applications such as therapeutic protein production. PMID:25044341
Zeng, Yu; Wang, Wei; Liu, Wenshe R
Whistler waves observed upstream from collisionless shocks
Waves in the frequency range 0.5-4. Hz have been studied in the region upstream of the earth's bow shock with data from the flux-gate magnetic field experiment on Imp 6. Such waves are invariably detected adjacent to the shock, persisting upstream for intervals often less than a minute but occasionally of the order of many hours. Analysis of 150 examples
D. H. Fairfield
Damping and spectral formation of upstream whistlers
NASA Astrophysics Data System (ADS)
Previous studies have indicated that damping rates of upstream whistlers strongly depend on the details of the electron distribution function. Moreover, detailed analysis of Doppler shift and the whistler dispersion relation indicate that upstream whistlers propagate obliquely in a finite band of frequencies. In this paper we present results of a kinetic calculation of damping lengths of wideband whistlers using the sum of seven drifting bi-Maxwellian electron distributions as a best fit to the ISEE 1 electron data. For two cases, when upstream whistlers are observed, convective damping lengths derived from ISEE magnetic field and ephemeris data are compared with theoretical results. We find that the calculated convective damping lengths are consistent with the data and that upstream whistlers remain marginally stable. We also show that the slope of plasma frame spectra of upstream whistlers, obtained by direct fitting of the observed spectra, is between 5 and 7. The overall spectral, wave, and particle characteristics, proximity to the shock, as well as propagation and damping properties indicate that these waves cannot be generated locally. Instead, the observed upstream whistlers arise in the shock ramp, most likely by a variety of cross-field drift and/or anisotropy driven instabilities.
Orlowski, D. S.; Russell, C. T.; Krauss-Varban, D.; Omidi, N.; Thomsen, M. F.
The empirical codon mutation matrix as a communication channel
Background A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino acids or codons derive one protein sequence from its ancestral sequence during evolution. In this paper, we regard the Empirical Codon Mutation (ECM) Matrix as a communication channel and compute the corresponding channel capacity. Results The channel capacity of 4.1875 bit, which is needed to preserve the information determined by the amino acid distribution, is obtained with an exponential factor of 0.26 applied to the ECM matrix. Additionally, we have obtained the optimum capacity achieving codon distribution. Compared to the biological distribution, there is an obvious difference, however, the distribution among synonymous codons is preserved. More importantly, the results show that the biological codon distribution allows for a "transmission" at a rate very close to the capacity. Conclusion We computed an exponential factor for the ECM matrix that would still allow for preserving the genetic information given the redundancy that is present in the codon-to-amino acid mapping. This gives an insight how such a mutation matrix relates to the preservation of a species in an information-theoretic sense. PMID:24655606
Properties and determinants of codon decoding time distributions
Background Codon decoding time is a fundamental property of mRNA translation believed to affect the abundance, function, and properties of proteins. Recently, a novel experimental technology--ribosome profiling--was developed to measure the density, and thus the speed, of ribosomes at codon resolution. Specifically, this method is based on next-generation sequencing, which theoretically can provide footprint counts that correspond to the probability of observing a ribosome in this position for each nucleotide in each transcript. Results In this study, we report for the first time various novel properties of the distribution of codon footprint counts in five organisms, based on large-scale analysis of ribosomal profiling data. We show that codons have distinctive footprint count distributions. These tend to be preserved along the inner part of the ORF, but differ at the 5' and 3' ends of the ORF, suggesting that the translation-elongation stage actually includes three biophysical sub-steps. In addition, we study various basic properties of the codon footprint count distributions and show that some of them correlate with the abundance of the tRNA molecule types recognizing them. Conclusions Our approach emphasizes the advantages of analyzing ribosome profiling and similar types of data via a comparative genomic codon-distribution-centric view. Thus, our methods can be used in future studies related to translation and even transcription elongation. PMID:25572668
The Upstream Detectors of the FIRST Experiment at GSI
NASA Astrophysics Data System (ADS)
FIRST (FragmentationofIonsRelevantforSpaceandTherapy)isanexperimentdevotedtoaprecise measurementofion fragmentation for space radiation protection and hadron therapyapplications. Afirst run dedicated to the fragmentation of fully stripped 12Cions on a thin graphite target has been already performed during August 2011 at GSI. The experiment is composed of already existing detectors complemented by a newly designed interaction region, including the so -called Upstream Detectors: a Start Counter and a Beam Monitor. The Start Counter is used to trigger the beam and to give a precise time reference for time of flight measurements, while the Beam Monitor is needed to track ions before their interaction in the target. In this paper we present their description and the results of the tests performed on different beams to validate their performances before the installation at GSI.
Paoloni, A.; Anelli, M.; Iarocci, E.; Patera, V.; Piersanti, L.; Sarti, A.; Sciubba, A.
A Model of Proto-Anti-Codon RNA Enzymes Requiring L-Amino Acid Homochirality
A Model of Proto-Anti-Codon RNA Enzymes Requiring L-Amino Acid Homochirality Albert Erives Received natural amino acid units of polypeptides using a universal scheme of triplet nucleotide ``codons) the absence of any codons for D-amino acids; (ii) the odd combination of alternate codon patterns for some
Erives, Albert J.
Analysis of synonymous codon usage patterns in different plant mitochondrial genomes.
Codon usage in mitochondrial genome of the six different plants was analyzed to find general patterns of codon usage in plant mitochondrial genomes. The neutrality analysis indicated that the codon usage patterns of mitochondrial genes were more conserved in GC content and no correlation between GC12 and GC3. T and A ending codons were detected as the preferred codons in plant mitochondrial genomes. The Parity Rule 2 plot analysis showed that T was used more frequently than A. The EN(C)-plot showed that although a majority of the points with low EN(C) values were lying below the expected curve, a few genes lied on the expected curve. Correspondence analysis of relative synonymous codon usage yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggest that natural selection is likely to be playing a large role in codon usage bias in plant mitochondrial genomes, but not only natural selection but also other several factors are likely to be involved in determining the selective constraints on codon bias in plant mitochondrial genomes. Meantime, 1 codon (P. patens), 6 codons (Z. mays), 9 codons (T. aestivum), 15 codons (A. thaliana), 15 codons (M. polymorpha) and 15 codons (N. tabacum) were defined as the preferred codons of the six plant mitochondrial genomes. PMID:19005776
Zhou, Meng; Li, Xia
Backup Agreements in Fashion Buying---The Value of Upstream Flexibility
We focus on backup agreements between a catalog company and manufacturers---a scheme to provide upstream sourcing flexibility for fashion merchandise. A backup agreement states that if the catalog company commits to a number of units for the season, the manufacturer holds back a constant fraction of the commitment and delivers the remaining units before the start of the fashion season.
Gary D. Eppen; Ananth. V. Iyer
Whistler waves observed upstream from collisionless shocks
NASA Technical Reports Server (NTRS)
Waves in the frequency range 0.5 - 4 Hz were studied in the region upstream of the earth's bow shock using data from the fluxgate magnetic field experiment on IMP-6. Analysis of 150 examples of these waves during a three month interval indicates that amplitudes are generally less than 1 or 2 gammas and propagation directions generally make angles of between 20 and 40 degrees with the field direction. The waves as measured in the spacecraft frame of reference are either left or right hand polarized with respect to the average field direction. It is concluded that the observed waves are right handed waves in the plasma frame of reference with wavelengths of approximately 100 km propagating upstream in the whistler mode. Doppler shifting reduces the observed frequencies in the spacecraft frame and reverses the observed polarization for those waves propagating more directly upstream. Similar waves are seen ahead of most interplanetary shocks.
Fairfield, D. H.
Patterns of codon usage bias in Silene latifolia.
Patterns of codon usage bias (CUB) convey useful information about the selection on synonymous codons induced by gene expression and contribute to an understanding of substitution patterns observed at synonymous sites. They can also be informative about the distinctive evolutionary properties of sex chromosomes such as genetic degeneration of the Y chromosome, dosage compensation, and hemizygosity of the X chromosome in males, which can affect the selection on codon usage. Here, we study CUB in Silene latifolia, a species of interest for studying the early stages of sex chromosome evolution. We have obtained a large expressed sequence tag data set containing more than 1,608 sequence fragments by 454 sequencing. Using three different methods, we conservatively define 21 preferred codons. Interestingly, the preferred codons in S. latifolia are almost identical to those in Arabidopsis thaliana, despite their long divergence time (we estimate average nonsynonymous site divergence to be 0.216, and synonymous sites are saturated). The agreement suggests that the nature of selection on codon usage has not changed significantly during the long evolutionary time separating the two species. As in many other organisms, the frequency of preferred codons is negatively correlated with protein length. For the 43 genes with both exon and intron sequences, we find a positive correlation between gene expression levels and GC content at third codon positions, but a strong negative correlation between expression and intron GC content, suggesting that the CUB we detect in S. latifolia is more likely to be due to natural selection than to mutational bias. Using polymorphism data, we detect evidence of ongoing natural selection on CUB, but we find little support for effects of biased gene conversion. An analysis of ten sex-linked genes reveals that the X chromosome has experienced significantly more unpreferred to preferred than preferred to unpreferred substitutions, suggesting that it may be evolving higher CUB. In contrast, numbers of substitutions between preferred and unpreferred codons are similar in both directions in the Y-linked genes, contrary to the expectation of genetic degeneration. PMID:20855431
Qiu, Suo; Bergero, Roberta; Zeng, Kai; Charlesworth, Deborah
Modular innovations in upstream fish passage
This project examined design alternatives for the construction, equipping and operation of upstream fish passage facilities suitable for installation at small hydropower sites being developed or re-developed. These alternatives were examined for technical feasibility and economic viability with the object of providing alternative means of meeting the biological requirements of an upstream fish passage in a more cost-effective manner than strictly traditional methods. An overview is presented of the fish passage design process in a project formation flowchart and design data checklist. The design features, materials and equipment specifically considered in this study are described with information on the characteristics, advantages, and applicability of each item.
Truebe, J.; Drooker, M.
Dual functions of codons in the genetic code
The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3'-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code. PMID:20446809
Lobanov, Alexey V.; Turanov, Anton A.; Hatfield, Dolph L.; Gladyshev, Vadim N.
Model for Codon Position Bias in RNA Editing
NASA Astrophysics Data System (ADS)
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.
Liu, Tsunglin; Bundschuh, Ralf
A model for codon position bias in RNA editing
NASA Astrophysics Data System (ADS)
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.
Bundschuh, Ralf; Liu, Tsunglin
Translational Control via Protein-Regulated Upstream
Translational Control via Protein-Regulated Upstream Open Reading Frames Jan Medenbach,1 Markus of the regulation of msl-2 mRNA by Sex lethal (SXL), which is critical for dosage compensa- tion in Drosophila, has reading frames (uORFs), and interaction sites for RNA-binding proteins. We show that SXL binding
Bedwell, David M.
Estimating Selection on Synonymous Codon Usage from Noisy Experimental Data
A key goal in molecular evolution is to extract mechanistic insights from signatures of selection. A case study is codon usage, where despite many recent advances and hypotheses, two longstanding problems remain: the relative contribution of selection and mutation in determining codon frequencies and the relative contribution of translational speed and accuracy to selection. The relevant targets of selection—the rate of translation and of mistranslation of a codon per unit time in the cell—can only be related to mechanistic properties of the translational apparatus if the number of transcripts per cell is known, requiring use of gene expression measurements. Perhaps surprisingly, different gene-expression data sets yield markedly different estimates of selection. We show that this is largely due to measurement noise, notably due to differences between studies rather than instrument error or biological variability. We develop an analytical framework that explicitly models noise in expression in the context of the population-genetic model. Estimates of mutation and selection strength in budding yeast produced by this method are robust to the expression data set used and are substantially higher than estimates using a noise-blind approach. We introduce per-gene selection estimates that correlate well with previous scoring systems, such as the codon adaptation index, while now carrying an evolutionary interpretation. On average, selection for codon usage in budding yeast is weak, yet our estimates show that genes range from virtually unselected to average per-codon selection coefficients above the inverse population size. Our analytical framework may be generally useful for distinguishing biological signals from measurement noise in other applications that depend upon measurements of gene expression. PMID:23493257
Wallace, Edward W.J.; Airoldi, Edoardo M.
Nutrient regime regulates complex transcriptional start site usage within a Pseudoalteromonas chitinase gene cluster.
The chitinase gene cluster of the marine bacterium Pseudoalteromonas sp. S91, chiABC, which produces the major chitinases of this sp., was transcribed as an operon and from each individual gene. chiA, chiB and chiC were found to possess multiple transcriptional start points (TSPs), the use of which was determined by the nutrient regime used for S91 growth. In minimal medium containing glutamate, chiA, chiB and chiC each used 3, 1 and 1 TSP, respectively. Upon the addition of the chitin monomer N-acetylglucosamine, the number of chiA TSPs was unaffected. However, chiB used an additional 4 TSPs, and chiC used four new TSPs excluding the TSP used in glutamate only. In addition, the cluster was transcribed as an operon from TSP A1 of chiA. All TSPs were potentially associated with either a sigma(70)- or sigma(54)-dependent promoter. Under the growth conditions used, no TSPs were detected for chiB or chiC in S91CX, a chiA transposon mutant. The transcription of the S91 chiABC gene cluster produced at least four polycistronic mRNAs. In addition, the occurrence of operon transcription of chiABC, and identification of an additional 12 putative TSPs within the gene cluster, gave an indication that each gene appeared to be transcribed from more than one promoter region upstream of each in-frame translation start codon. Questions arose regarding the reason for this complexity of transcription within the gene cluster, leading to a re-evaluation of the Chi protein domains. By bioinformatic review, ChiA, ChiB and ChiC were found to potentially possess additional putative domains. PMID:19458654
Delpin, Marina W; Goodman, Amanda E
Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization
Individual mRNAs are translated by multiple ribosomes that initiate translation with a few seconds interval. The ribosome speed is codon dependant, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modelling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations per sec) and the time (1 sec) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translational efficiency.
Namiko Mitarai; Kim Sneppen; Steen Pedersen
All-codon scanning identifies p53 cancer rescue mutations
,2 , Linda V. Hall1 , Kirsty Salmon1 , G. Wesley Hatfield1,3,4 , Richard H. Lathrop1,2,5, * and Peter Kaiser6 of Microbiology and Molecular Genetics, 4 Department of Chemical Engineering and Materials Science, 5 Department with modified properties. We describe the fast and simple All- Codon Scanning (ACS) strategy that creates
Lathrop, Richard H.
Codon engineering for improved antibody expression in mammalian cells
While well established in bacterial hosts, the effect of coding sequence variation on protein expression in mammalian systems is poorly characterized outside of viral proteins or proteins from distant phylogenetic families. The potential impact is substantial given the extensive use of mammalian expression systems in research and manufacturing of protein biotherapeutics. We are studying the effect of codon engineering on
Jill M. Carton; Tina Sauerwald; Pam Hawley-Nelson; Barry Morse; Nancy Peffer; Heena Beck; Jin Lu; Adam Cotty; Bernard Amegadzie; Ray Sweet
Upstream urbanization exacerbates urban heat island effects
NASA Astrophysics Data System (ADS)
Urban Heat Island (UHI) effects adversely impact weather, air quality, and climate. Previous studies have attributed UHI effects to localized, surface processes. Based on an observational and modeling study of an extreme UHI (heat wave) episode in the Baltimore metropolitan region, we find that upstream urbanization exacerbates UHI effects and that meteorological consequences of extra-urban development can cascade well downwind. Under southwesterly wind, Baltimore, MD, experienced higher peak surface temperatures and higher pollution concentrations than did the larger urban area of Washington, DC. Ultra-high resolution numerical simulations with National Land Cover Data (NLCD) of 2001 show a nonlocal, dynamical contribution to UHI effects; when the upstream urban area is replaced by natural vegetation (in the model) the UHI effects could be reduced by more than 25%. These findings suggest that judicious land-use and urban planning, especially in rapidly developing countries, could help alleviate UHI consequences including heat stress and smog.
Zhang, Da-Lin; Shou, Yi-Xuan; Dickerson, Russell R.
Admissible upstream conditions for slender compressible vortices
NASA Technical Reports Server (NTRS)
The influence of the compressibility on the flow in slender vortices is being studied. The dependence of the breakdown of the slender-vortex approximation on the upstream conditions is demonstrated for various Reynolds numbers and Mach numbers. Compatibility conditions, which have to be satisfied if the vortex is to remain slender, are discussed in detail. The general discussions are supplemented by several sample calculations.
Liu, C. H.; Krause, E.; Menne, S.
Upstream reciprocity and the evolution of gratitude.
If someone is nice to you, you feel good and may be inclined to be nice to somebody else. This every day experience is borne out by experimental games: the recipients of an act of kindness are more likely to help in turn, even if the person who benefits from their generosity is somebody else. This behaviour, which has been called 'upstream reciprocity', appears to be a misdirected act of gratitude: you help somebody because somebody else has helped you. Does this make any sense from an evolutionary or a game theoretic perspective? In this paper, we show that upstream reciprocity alone does not lead to the evolution of cooperation, but it can evolve and increase the level of cooperation if it is linked to either direct or spatial reciprocity. We calculate the random walks of altruistic acts that are induced by upstream reciprocity. Our analysis shows that gratitude and other positive emotions, which increase the willingness to help others, can evolve in the competitive world of natural selection. PMID:17254983
Nowak, Martin A; Roch, Sébastien
Selection pressures on codon usage in the complete genome of bacteriophage T7
Summary We searched the complete 39,936 base DNA sequence of bacteriophage T7 for nonrandomness that might be attributed to natural selection. Codon usage in the 50 genes of T7 is nonrandom, both over the whole code and among groups of synonymous codons. There is a great excess of purineany base-pyrimidine (RNY) codons. Codon usage varies between genes, but from the
Paul M. Sharp; Mark S. Rogers; David J. McConnell
Summary DNA methylation and deamination increases the C?T mutation rate in CpG dinucleotides, especially in vertebrate genomes. This has profound effect on codon usage in heavily vertebrate genomes, and may obscure the effect of other factors on codon usage bias. We have classified the sense codons into three groups: those decreased by DNA methylation (i.e., CpG-containing codons), those increased by
Xuhua Xia
Reselection of a Genomic Upstream Open Reading Frame in Mouse Hepatitis Coronavirus 5?-Untranslated-Region Mutants
An AUG-initiated upstream open reading frame (uORF) encoding a potential polypeptide of 3 to 13 amino acids (aa) is found within the 5? untranslated region (UTR) of >75% of coronavirus genomes based on 38 reference strains. Potential CUG-initiated uORFs are also found in many strains. The AUG-initiated uORF is presumably translated following genomic 5?-end cap-dependent ribosomal scanning, but its function is unknown. Here, in a reverse-genetics study with mouse hepatitis coronavirus, the following were observed. (i) When the uORF AUG-initiating codon was replaced with a UAG stop codon along with a U112A mutation to maintain a uORF-harboring stem-loop 4 structure, an unimpaired virus with wild-type (WT) growth kinetics was recovered. However, reversion was found at all mutated sites within five virus passages. (ii) When the uORF was fused with genomic (main) ORF1 by converting three in-frame stop codons to nonstop codons, a uORF-ORF1 fusion protein was made, and virus replicated at WT levels. However, a frameshifting G insertion at virus passage 7 established a slightly 5?-extended original uORF. (iii) When uAUG-eliminating deletions of 20, 30, or 51 nucleotides (nt) were made within stem-loop 4, viable but debilitated virus was recovered. However, a C80U mutation in the first mutant and an A77G mutation in the second appeared by passage 10, which generated alternate uORFs that correlated with restored WT growth kinetics. In vitro, the uORF-disrupting nondeletion mutants showed enhanced translation of the downstream ORF1 compared with the WT. These results together suggest that the uORF represses ORF1 translation yet plays a beneficial but nonessential role in coronavirus replication in cell culture. PMID:24173235
Wu, Hung-Yi; Guan, Bo-Jhih; Su, Yu-Pin; Fan, Yi-Hsin
Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses
Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment. PMID:24595095
Tong, Yigang
A General Model of Codon Bias Due to GC Mutational Bias
BackgroundIn spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a
Gareth A. Palidwor; Theodore J. Perkins; Xuhua Xia; Dov Joseph Stekel
Evidence for codon bias selection at the pre-mRNA level in eukaryotes
for unequal usage of synon- ymous codons (codon bias) [1] is the mutation-selection balance [2]. UnderRNA molecules, is the most widely accepted selective mechanism. Because selection for codon usage is likely to be weak, its effects are detectable in simple organisms with large population sizes, where the effects
Majewski, Jacek
Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations
Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical prediction in prokaryotic genomes based on a set of three physicochemical characteristics of codons--by codon
Jayaram, Bhyravabotla
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic Hong Qin*,1
1 Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes Hong Qin*,1 distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis pattern using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias
Wu, Wei-Biao
The Starting Early Starting Smart Story.
ERIC Educational Resources Information Center
Starting Early Starting Smart (SESS) is an early childhood public/private initiative designed to identify new, empirical knowledge about the effectiveness of integrating substance abuse prevention, addictions treatment, and mental health services with primary health care and childcare service settings (e.g., Head Start, day care, preschool) to…
Casey Family Programs, Seattle, WA.
The Highly Conserved Codon following the Slippery Sequence Supports ?1 Frameshift Efficiency at the HIV-1 Frameshift Site
HIV-1 utilises ?1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating ?1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon') contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules—eRF1 protein or a cognate suppressor tRNA—were able to access and decode the intercodon prior to ?1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted) ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1. PMID:25807539
Mathew, Suneeth F.; Crowe-McAuliffe, Caillan; Graves, Ryan; Cardno, Tony S.; McKinney, Cushla; Poole, Elizabeth S.; Tate, Warren P.
KRAS codon 61, 146 and BRAF mutations predict resistance to cetuximab plus irinotecan in KRAS codon 12 and 13 wild-type metastatic colorectal cancer
Background:KRAS codons 12 and 13 mutations predict resistance to anti-EGFR monoclonal antibodies (moAbs) in metastatic colorectal cancer. Also, BRAF V600E mutation has been associated with resistance. Additional KRAS mutations are described in CRC.Methods:We investigated the role of KRAS codons 61 and 146 and BRAF V600E mutations in predicting resistance to cetuximab plus irinotecan in a cohort of KRAS codons 12
F Loupakis; A Ruzzo; C Cremolini; B Vincenzi; L Salvatore; D Santini; G Masi; I Stasi; E Canestrari; E Rulli; I Floriani; K Bencardino; N Galluccio; V Catalano; G Tonini; M Magnani; G Fontanini; F Basolo; A Falcone; F Graziano
Upstream basin circulation of rotating, hydraulically controlled flows
Upstream basin circulation of rotating, hydraulically controlled flows Adele Morrison Australian in the overturning motivates an improved understanding of the overflows and the associated upstream basin circulation-critical transitions [4]. A feature of hydraulically controlled flows is that the stratification in the basin upstream
Lebovitz, Norman
Manufacturing Technician-Upstream: John Condosta
NSDL National Science Digital Library
This online video in Windows Media (wmv) format is a brief lecture from a biopharmaceutical manufacturing operator about his job experience. John Condosta was a microbiology major in college and now enjoys working 12-hour days in upstream processing. He gives advice about job searching, resumes, and how to interview before taking questions from the audience. He describes his typical day working with fermentation or purification. Everyday is a new learning experience for him due to new products and new processes. This video would be useful for college or technical students who are interested in hearing a firsthand account of the work-life in the field of biopharmaceutics and bio-manufacturing.
KRAS codon 12 mutations occur very frequently in pancreatic adenocarcinomas
DNAs from human pancreatic adenocarcinomas were analyzed for the presence of mutations in codons 12, 13 and 61 of the NRAS, KRAS and HRAS gene. Formalin-fixed and paraffin-embedded tissue was used directly in an in vitro amplification reaction to expand the relevant RAS sequences. The mutations were detected by selective hybridization using mutation-specific synthetic oligonucleotides. In 28 of the 30 patients the authors found a mutation in codon 12 of the KRAS gene. This result confirms findings that KRAS mutations occur frequently in adenocarcinomas of the exocrine pancreas. The mutations are predominantly G-T transversions, in contrast to the KRAS mutations in colon tumors which are mainly G-A transitions. Furthermore, in a portion of the tumors the mutation appears to be homozygous.
Smit, V.T.H.B.M.; Boot, A.J.M.; Smits, A.M.M.; Fleuren, G.J.; Cornelisse, C.J.; Bos, J.L. (State Univ. of Leiden (Netherlands))
Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach.
Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of synonymous codons. Also, we built a multinomial logistic regression statistical model for codon usage, which considers the effect of patterns on codon usage. This model justifies the observed codon usage preference better than the classic organism dependent codon usage. Our results showed that the codon usage plays a role in controlling protein levels, for genes that participate in a specific biological function. This is the first time that this phenomenon is reported. PMID:25409941
Foroughmand-Araabi, Mohammad-Hadi; Goliaei, Bahram; Alishahi, Kasra; Sadeghi, Mehdi; Goliaei, Sama
The Distribution of Synonymous Codon Choice in the Translation Initiation Region of Dengue Virus
Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti) was estimated by a novel formula. Finally, the synonymous codon usage preference for the translation initiation region of this virus was also analyzed. The result indicates that the general trend of the 59 synonymous codon usage of the four genotypes of DENV are similar to each other, and this pattern has no link with the geographic distribution of the virus. The effect of codon usage pattern of Aedes albopictus and Aedes aegypti on the formation of codon usage of DENV is stronger than that of the two primates. Turning to the codon usage preference of the translation initiation region of this virus, some codons pairing to low tRNA copy numbers in the two primates have a stronger tendency to exist in the translation initiation region than those in the open reading frame of DENV. Although DENV, like other RNA viruses, has a high mutation to adapt its hosts, the regulatory features about the synonymous codon usage have been 'branded' on the translation initiation region of this virus in order to hijack the translational mechanisms of the hosts. PMID:24204777
Zhou, Jian-hua; Zhang, Jie; Sun, Dong-jie; Ma, Qi; Chen, Hao-tai; Ma, Li-na; Ding, Yao-zhong; Liu, Yong-sheng
Recent Selection on Synonymous Codon Usage in Drosophila
. Evidence from a variety of sources indicates that selection has influenced synonymous codon usage in Drosophila. It has generally been difficult, however, to distinguish selection that acted in the distant past from ongoing selection.\\u000a However, under a neutral model, polymorphisms usually reflect more recent mutations than fixed differences between species\\u000a and may, therefore, be useful for inferring recent selection.
Richard M. Kliman
KRAS codon 12 mutations occur very frequently in pancreatic adenocarcinomas
DNAs from human pancreatic adenocarcinomas were analyzed for the presence of mutations in codons 12, 13 and 61 of the NRAS, KRAS and HRAS gene. Formalin-fixed and paraffin-embedded tissue was used directly in an in vitro amplification reaction to expand the relevant RAS sequences. The mutations were detected by selective hybridization using mutation-specific synthetic oligonucleotides. In 28 of the 30
Vincent T. H. B. M. Smit; Angelina J. M. Boot; Alida M. M. Smits; Gert Jan Fleuren; Cees J. Cornelisse; Johannes L. Bos
Codon Optimisation Is Key for Pernisine Expression in Escherichia coli
Background Pernisine is an extracellular serine protease from the hyperthermophilic Archaeon Aeropyrum pernix K1. Low yields from the natural host and expression problems in heterologous hosts have limited the potential applications of pernisine in industry. Methodology/ Principal Findings The challenges of pernisine overexpression in Escherichia coli were overcome by codon preference optimisation and de-novo DNA synthesis. The following forms of the pernisine gene were cloned into the pMCSGx series of vectors and expressed in E. coli cells: wild-type (pernisinewt), codon-optimised (pernisineco), and codon-optimised with a S355A mutation of a predicted active site (pernisineS355Aco). The fusion-tagged pernisines were purified using fast protein liquid chromatography equipped with Ni2+ chelate and gel filtration chromatography columns. The identities of the resultant proteins were confirmed with N-terminal sequencing, tandem mass spectrometry analysis, and immunodetection. Pernisinewt was not expressed in E. coli at detectable levels, while pernisineco and pernisineS355Aco were expressed and purified as 55-kDa proforms with yields of around 10 mg per litre E. coli culture. After heat activation of purified pernisine, the proteolytic activity of the mature pernisineco was confirmed using zymography, at a molecular weight of 36 kDa, while the mutant pernisineS355Aco remained inactive. Enzymatic performances of pernisine evaluated under different temperatures and pHs demonstrate that the optimal enzymatic activity of the recombinant pernisine is ca. 100°C and pH 7.0, respectively. Conclusions/ Significance These data demonstrate that codon optimisation is crucial for pernisine overexpression in E. coli, and that the proposed catalytic Ser355 has an important role in pernisine activity, but not in its activation process. Pernisine is activated by autoproteolytical cleavage of its N-terminal proregion. We have also confirmed that the recombinant pernisine retains the characteristics of native pernisine, as a calcium modulated thermostable serine protease. PMID:25856104
Šnajder, Marko; Miheli?, Marko; Turk, Dušan; Ulrih, Nataša Poklar
Corporation-induced Diseases, Upstream Epidemiologic Surveillance, and Urban Health
Corporation-induced diseases are defined as diseases of consumers, workers, or community residents who have been exposed to disease agents contained in corporate products. To study the epidemiology and to guide expanded surveillance of these diseases, a new analytical framework is proposed. This framework is based on the agent–host–environment model and the upstream multilevel epidemiologic approach and posits an epidemiologic cascade starting with government-sanctioned corporate profit making and ending in a social cost, i.e., harm to population health. Each of the framework's levels addresses a specific level of analysis, including government, corporations, corporate conduits, the environment of the host, and the host. The explained variable at one level is also the explanatory variable at the next lower level. In this way, a causal chain can be followed along the epidemiologic cascade from the site of societal power down to the host. The framework thus describes the pathways by which corporate decisions filter down to disease production in the host and identifies opportunities for epidemiologic surveillance. Since the environment of city dwellers is strongly shaped by corporations that are far upstream and several levels away, the framework has relevance for the study of urban health. Corporations that influence the health of urban populations include developers and financial corporations that determine growth or decay of urban neighborhoods, as well as companies that use strategies based on neighborhood characteristics to sell products that harm consumer health. Epidemiological inquiry and surveillance are necessary at all levels to provide the knowledge needed for action to protect the health of the population. To achieve optimal inquiry and surveillance at the uppermost levels, epidemiologists will have to work with political scientists and other social scientists and to utilize novel sources of information. PMID:18437580
Translational redefinition of UGA codons is regulated by selenium availability.
Incorporation of selenium into ~25 mammalian selenoproteins occurs by translational recoding whereby in-frame UGA codons are redefined to encode the selenium containing amino acid, selenocysteine (Sec). Here we applied ribosome profiling to examine the effect of dietary selenium levels on the translational mechanisms controlling selenoprotein synthesis in mouse liver. Dietary selenium levels were shown to control gene-specific selenoprotein expression primarily at the translation level by differential regulation of UGA redefinition and Sec incorporation efficiency, although effects on translation initiation and mRNA abundance were also observed. Direct evidence is presented that increasing dietary selenium causes a vast increase in ribosome density downstream of UGA-Sec codons for a subset of selenoprotein mRNAs and that the selenium-dependent effects on Sec incorporation efficiency are mediated in part by the degree of Sec-tRNA([Ser]Sec) Um34 methylation. Furthermore, we find evidence for translation in the 5'-UTRs for a subset of selenoproteins and for ribosome pausing near the UGA-Sec codon in those mRNAs encoding the selenoproteins most affected by selenium availability. These data illustrate how dietary levels of the trace element selenium can alter the readout of the genetic code to affect the expression of an entire class of proteins. PMID:23696641
Howard, Michael T; Carlson, Bradley A; Anderson, Christine B; Hatfield, Dolph L
Inducible suppression of global translation by overuse of rare codons.
Recently, artificial gene networks have been developed in synthetic biology to control gene expression and make organisms as controllable as robots. Here, I present an artificial posttranslational gene-silencing system based on the codon usage bias and low tRNA content corresponding to minor codons. I engineered the green fluorescent protein (GFP) gene to inhibit translation indirectly with the lowest-usage codons to monopolize various minor tRNAs (lgfp). The expression of lgfp interfered nonspecifically with the growth of Escherichia coli, Saccharomyces cerevisiae, human HeLa cervical cancer cells, MCF7 breast cancer cells, and HEK293 kidney cells, as well as phage and adenovirus expansion. Furthermore, insertion of lgfp downstream of a phage response promoter conferred phage resistance on E. coli. Such engineered gene silencers could act as components of biological networks capable of functioning with suitable promoters in E. coli, S. cerevisiae, and human cells to control gene expression. The results presented here show general suppressor artificial genes for live cells and viruses. This robust system provides a gene expression or cell growth control device for artificially synthesized gene networks. PMID:25636849
Kobayashi, Hideki
Computational codon optimization of synthetic gene for protein expression
Background The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression. Results In this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU. Conclusions The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology. PMID:23083100
Inducible Suppression of Global Translation by Overuse of Rare Codons
Recently, artificial gene networks have been developed in synthetic biology to control gene expression and make organisms as controllable as robots. Here, I present an artificial posttranslational gene-silencing system based on the codon usage bias and low tRNA content corresponding to minor codons. I engineered the green fluorescent protein (GFP) gene to inhibit translation indirectly with the lowest-usage codons to monopolize various minor tRNAs (lgfp). The expression of lgfp interfered nonspecifically with the growth of Escherichia coli, Saccharomyces cerevisiae, human HeLa cervical cancer cells, MCF7 breast cancer cells, and HEK293 kidney cells, as well as phage and adenovirus expansion. Furthermore, insertion of lgfp downstream of a phage response promoter conferred phage resistance on E. coli. Such engineered gene silencers could act as components of biological networks capable of functioning with suitable promoters in E. coli, S. cerevisiae, and human cells to control gene expression. The results presented here show general suppressor artificial genes for live cells and viruses. This robust system provides a gene expression or cell growth control device for artificially synthesized gene networks. PMID:25636849
Analyses of clinicopathological, molecular, and prognostic associations of KRAS codon 61 and codon 146 mutations in colorectal cancer: cohort study and literature review
Background KRAS mutations in codons 12 and 13 are established predictive biomarkers for anti-EGFR therapy in colorectal cancer. Previous studies suggest that KRAS codon 61 and 146 mutations may also predict resistance to anti-EGFR therapy in colorectal cancer. However, clinicopathological, molecular, and prognostic features of colorectal carcinoma with KRAS codon 61 or 146 mutation remain unclear. Methods We utilized a molecular pathological epidemiology database of 1267 colon and rectal cancers in the Nurse's Health Study and the Health Professionals Follow-up Study. We examined KRAS mutations in codons 12, 13, 61 and 146 (assessed by pyrosequencing), in relation to clinicopathological features, and tumor molecular markers, including BRAF and PIK3CA mutations, CpG island methylator phenotype (CIMP), LINE-1 methylation, and microsatellite instability (MSI). Survival analyses were performed in 1067 BRAF-wild-type cancers to avoid confounding by BRAF mutation. Cox proportional hazards models were used to compute mortality hazard ratio, adjusting for potential confounders, including disease stage, PIK3CA mutation, CIMP, LINE-1 hypomethylation, and MSI. Results KRAS codon 61 mutations were detected in 19 cases (1.5%), and codon 146 mutations in 40 cases (3.2%). Overall KRAS mutation prevalence in colorectal cancers was 40% (=505/1267). Of interest, compared to KRAS-wild-type, overall, KRAS-mutated cancers more frequently exhibited cecal location (24% vs. 12% in KRAS-wild-type; P?0.0001), CIMP-low (49% vs. 32% in KRAS-wild-type; P?0.0001), and PIK3CA mutations (24% vs. 11% in KRAS-wild-type; P?0.0001). These trends were evident irrespective of mutated codon, though statistical power was limited for codon 61 mutants. Neither KRAS codon 61 nor codon 146 mutation was significantly associated with clinical outcome or prognosis in univariate or multivariate analysis [colorectal cancer-specific mortality hazard ratio (HR)?=?0.81, 95% confidence interval (CI)?=?0.29-2.26 for codon 61 mutation; colorectal cancer-specific mortality HR?=?0.86, 95% CI?=?0.42-1.78 for codon 146 mutation]. Conclusions Tumors with KRAS mutations in codons 61 and 146 account for an appreciable proportion (approximately 5%) of colorectal cancers, and their clinicopathological and molecular features appear generally similar to KRAS codon 12 or 13 mutated cancers. To further assess clinical utility of KRAS codon 61 and 146 testing, large-scale trials are warranted. PMID:24885062
Moving stormwater P management upstream (Invited)
NASA Astrophysics Data System (ADS)
Reducing stormwater phosphorus loading using current approaches, which focus on treatment at the end of the pipe, is unlikely to reduce P loads enough to restore nutrient-impaired urban lakes. An indication of this is that of the nearly 150 nutrient impaired lakes in the Twin Cities region, only one has been restored. We hypothesize that substantial reduction of eutrophication will require reductions of P inputs upstream from storm drains. Developing source reduction strategies will required a shift in thinking about system boundaries, moving upstream from the storm drain to the curb, and from the curb to the watershed. Our Prior Lake Street Sweeping Project, a 2-year study of enhanced street sweeping, will be used to illustrate the idea of moving the system boundary to the curb. This study showed that P load recovery from sweeping increases with both sweeping frequency and overhead tree canopy cover. For high canopy streets, coarse organic material (tree leaves; seed pods, etc.) comprised 42% of swept material. We estimate that P inputs from trees may be half of measured storm P yields in 8 urban catchments in St. Paul, MN. Moreover, the cost of removing P during autumn was often < 100/pound P, compared with > 1000/lb P for stormwater ponds. We can also move further upstream, to the watershed boundary. P inputs to urban watersheds that enter lawns include lawn fertilizer, polyphosphates added to water supplies (and hence to lawns via irrigation), and pet food (transformed to pet waste). Minnesota enacted a lawn P fertilizer restriction in 2003, but early reductions in stormwater P loads were modest, probably reflecting reduction in direct wash-off of applied fertilizer. Because urban soils are enriched in P, growing turf has continued to extract available soil P. When turf is mowed, cut grass decomposes, generating P in runoff. As soil P becomes depleted, P concentrations in lawn runoff will gradually decline. Preliminary modeling suggests that substantial reductions in P export from lawns may take a decade or more. Our Twin Cities Household Ecosystem Project has shown that with the P fertilizer law in effect, the main source of P to lawns is now pet wastes left on lawns. Among lawns, P export to streets is likely highly disproportionate, depending on both social factors such as fertilization rates (even for N) and mulching; and biophysical factors such as slope and soil texture. Modeling these fluxes at the lawn scale could be used to target high-risk sites and tailor messages to homeowners that match their lawn management goals. In summary, urban ecologists and engineers are rethinking strategies for reducing urban P inputs to surface waters. As we develop better understanding of flowpaths of P through urban watersheds, we can use this knowledge to move P reduction strategies upstream, shifting the focus from removing P from stormwater to preventing it from entering stormwater in the first place.
Baker, L. A.; Hobbie, S. E.; Finlay, J. C.; Kalinosky, P.; Janke, B.
Upstream open reading frame in 5'-untranslated region reduces titin mRNA translational efficiency.
Titin is the largest known protein and a critical determinant of myofibril elasticity and sarcomere structure in striated muscle. Accumulating evidence that mRNA transcripts are post-transcriptionally regulated by specific motifs located in the flanking untranslated regions (UTRs) led us to consider the role of titin 5'-UTR in regulating its translational efficiency. Titin 5'-UTR is highly homologous between human, mouse, and rat, and sequence analysis revealed the presence of a stem-loop and two upstream AUG codons (uAUGs) converging on a shared in frame stop codon. We generated a mouse titin 5'-UTR luciferase reporter construct and targeted the stem-loop and each uAUG for mutation. The wild-type and mutated constructs were transfected into the cardiac HL-1 cell line and primary neonatal rat ventricular myocytes (NRVM). SV40 driven 5'-UTR luciferase activity was significantly suppressed by wild-type titin 5'-UTR (? 70% in HL-1 cells and ? 60% in NRVM). Mutating both uAUGs was found to alleviate titin 5'-UTR suppression, while eliminating the stem-loop had no effect. Treatment with various growth stimuli: pacing, PMA or neuregulin had no effect on titin 5'-UTR luciferase activity. Doxorubicin stress stimuli reduced titin 5'-UTR suppression, while H2O2 had no effect. A reported single nucleotide polymorphism (SNP) rs13422986 at position -4 of the uAUG2 was introduced and found to further repress titin 5'-UTR luciferase activity. We conclude that the uAUG motifs in titin 5'-UTR serve as translational repressors in the control of titin gene expression, and that mutations/SNPs of the uAUGs or doxorubicin stress could alter titin translational efficiency. PMID:25264194
Cadar, Adrian G; Zhong, Lin; Lin, Angel; Valenzuela, Mauricio O; Lim, Chee C
Expression of Human nPTB Is Limited by Extreme Suboptimal Codon Content
Background The frequency of synonymous codon usage varies widely between organisms. Suboptimal codon content limits expression of viral, experimental or therapeutic heterologous proteins due to limiting cognate tRNAs. Codon content is therefore often adjusted to match codon bias of the host organism. Codon content also varies between genes within individual mammalian species. However, little attention has been paid to the consequences of codon content upon translation of host proteins. Methodology/Principal Findings In comparing the splicing repressor activities of transfected human PTB and its two tissue-restricted paralogs–nPTB and ROD1–we found that the three proteins were expressed at widely varying levels. nPTB was expressed at 1–3% the level of PTB despite similar levels of mRNA expression and 74% amino acid identity. The low nPTB expression was due to the high proportion of codons with A or U at the third codon position, which are suboptimal in human mRNAs. Optimization of the nPTB codon content, akin to the "humanization" of foreign ORFs, allowed efficient translation in vivo and in vitro to levels comparable with PTB. We were then able to demonstrate that all three proteins act as splicing repressors. Conclusions/Significance Our results provide a striking illustration of the importance of mRNA codon content in determining levels of protein expression, even within cells of the natural host species. PMID:18335065
Robinson, Fiona; Jackson, Richard J.; Smith, Christopher W. J.
Measurement of average decoding rates of the 61 sense codons in vivo
Most amino acids can be encoded by several synonymous codons, which are used at unequal frequencies. The significance of unequal codon usage remains unclear. One hypothesis is that frequent codons are translated relatively rapidly. However, there is little direct, in vivo, evidence regarding codon-specific translation rates. In this study, we generate high-coverage data using ribosome profiling in yeast, analyze using a novel algorithm, and deduce events at the A- and P-sites of the ribosome. Different codons are decoded at different rates in the A-site. In general, frequent codons are decoded more quickly than rare codons, and AT-rich codons are decoded more quickly than GC-rich codons. At the P-site, proline is slow in forming peptide bonds. We also apply our algorithm to short footprints from a different conformation of the ribosome and find strong amino acid-specific (not codon-specific) effects that may reflect interactions with the exit tunnel of the ribosome. DOI: http://dx.doi.org/10.7554/eLife.03735.001 PMID:25347064
Gardin, Justin; Yeasmin, Rukhsana; Yurovsky, Alisa; Cai, Ying; Skiena, Steve; Futcher, Bruce
Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development
Background Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed. Results We performed a comprehensive codon usage analysis of 310 IAV strains from the pandemic of 2009. Highly biased codon usage for Ala, Arg, Pro, Thr and Ser were found. Codon usage is strongly influenced by underlying biases in base composition. When correspondence analysis (COA) on relative synonymous codon usage (RSCU) is applied, the distribution of IAV ORFs in the plane defined by the first two major dimensional factors showed that different strains are located at different places, suggesting that IAV codon usage also reflects an evolutionary process. Conclusions A general association between codon usage bias, base composition and poor adaptation of the virus to the respective host tRNA pool, suggests that mutational pressure is the main force shaping H1N1 pdm IAV codon usage. A dynamic process is observed in the variation of codon usage of the strains enrolled in these studies. These results suggest a balance of mutational bias and natural selection, which allow the virus to explore and re-adapt its codon usage to different environments. Recoding of IAV taking into account codon bias, base composition and adaptation to host tRNA may provide important clues to develop new and appropriate vaccines. PMID:23134595
Potential Autoregulation of Transcription Factor PU.1 by an Upstream Regulatory Element
Regulation of the hematopoietic transcription factor PU.1 (Spi-1) plays a critical role in the development of white cells, and abnormal expression of PU.1 can lead to leukemia. We previously reported that the PU.1 promoter cannot induce expression of a reporter gene in vivo, and cell-type-specific expression of PU.1 in stable lines was conferred by a 3.4-kb DNA fragment including a DNase I hypersensitive site located 14 kb upstream of the transcription start site. Here we demonstrate that this kb ?14 site confers lineage-specific reporter gene expression in vivo. This kb ?14 upstream regulatory element contains two 300-bp regions which are highly conserved in five mammalian species. In Friend virus-induced erythroleukemia, the spleen focus-forming virus integrates into the PU.1 locus between these two conserved regions. DNA binding experiments demonstrated that PU.1 itself and Elf-1 bind to a highly conserved site within the proximal homologous region in vivo. A mutation of this site abolishing binding of PU.1 and Elf-1 led to a marked decrease in the ability of this upstream element to direct activity of reporter gene in myelomonocytic cell lines. These data suggest that a potential positive autoregulatory loop mediated through an upstream regulatory element is essential for proper PU.1 gene expression. PMID:15767686
Okuno, Yutaka; Huang, Gang; Rosenbauer, Frank; Evans, Erica K.; Radomska, Hanna S.; Iwasaki, Hiromi; Akashi, Koichi; Moreau-Gachelin, Francoise; Li, Youlin; Zhang, Pu; Göttgens, Berthold; Tenen, Daniel G.
Distinguishable codon usage and amino acid composition patterns among substrates of leaderless secretory pathways from proteobacteria
The combined set of codon usage frequencies (61 sense codons) from the 111 annotated sequences of leaderless secreted type\\u000a I, type III, type IV, and type VI proteins from proteobacteria were subjected to the forward and backward selection to obtain\\u000a a combination of most effective predictor variables for classification\\/prediction purposes. The group of 24 codon frequencies\\u000a displayed a strong discriminatory
In?ra Kampenusa; P?teris Zikmanis
Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1
Two species of the DNA virus Torque teno sus virus (TTSuV), TTSuV1 and TTSuV2, have become widely distributed in pig-farming countries in recent years. In this study, we performed a comprehensive analysis of synonymous codon usage bias in 41 available TTSuV2 coding sequences (CDS), and compared the codon usage patterns of TTSuV2 and TTSuV1. TTSuV codon usage patterns were found to be phylogenetically conserved. Values for the effective number of codons (ENC) indicated that the overall extent of codon usage bias in both TTSuV2 and TTSuV1 was not significant, the most frequently occurring codons had an A or C at the third codon position. Correspondence analysis (COA) was performed and TTSuV2 and TTSuV1 sequences were located in different quadrants of the first two major axes. A plot of the ENC revealed that compositional constraint was the major factor determining the codon usage bias for TTSuV2. In addition, hierarchical cluster analysis of 41 TTSuV2 isolates based on relative synonymous codon usage (RSCU) values suggested that there was no association between geographic distribution and codon bias of TTSuV2 sequences. Finally, the comparison of RSCU for TTSuV2, TTSuV1 and the corresponding host sequence indicated that the codon usage pattern of TTSuV2 was similar to that of TTSuV1. However the similarity was low for each virus and its host. These conclusions provide important insight into the synonymous codon usage pattern of TTSuV2, as well as better understangding of the molecular evolution of TTSuV2 genomes. PMID:24303050
Dai, Dingzhen
Estimating the fraction of invariable codons with a capture-recapture method
A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of
Arend Sidow; Trang Nguyen; Terence P. Speed
Why Are Translationally SubOptimal Synonymous Codons Used in Escherichia coli ?
. Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms\\u000a to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force,\\u000a so there is a balance between mutation, selection, and drift; (2) at some
Nick G. C. Smith; Adam Eyre-Walker
Codon optimization of the major antigen encoding genes of diverse strains of influenza a virus
A large number of influenza A virus outbreaks and mortality occurred in the world recently, an urgent attention to develop\\u000a effective and sufficient quantity of vaccines are needed. Vaccines are generally protein with immunogenic properties and are\\u000a not expressed in sufficient quantity because of the codon bias, so it is necessary to optimize its codon in the expression\\u000a host. Codon
Indra Mani; Vijai Singh; Dharmendra Kumar Chaudhary; Pallavi Somvanshi; M. P. S. Negi
3. Credit JTL Long distance view looking upstream towards New ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
3. Credit JTL Long distance view looking upstream towards New Hampshire; commercial structures in foreground. - Bellows Falls Arch Bridge, Spanning Connecticut River, North Walpole, Cheshire County, NH
Codon 219 polymorphism of PRNP in healthy caucasians and Creutzfeldt-Jakob disease patients
A number of point and insert mutations of the PrP gene (PRNP) have been linked to familial Creutzfeldt-Jakob disease (CJD) and Gerstmann-Straussler-Scheinker disease (GSS). Moreover, the methionine/valine homozygosity at the polymorphic codon 129 of PRNP may cause a predisposition to sporadic and iatrogenic CJD or may control the age at onset of familial cases carrying either the 144-bp insertion or codon 178, codon 198, and codon 210 pathogenic mutations in PRNP. In addition, the association of methionine or valine at codon 129 and the point mutation at codon 178 on the same allele seem to play an important role in determining either fatal familial insomnia or CJD. However, it is noteworthy that a relationship between codon 129 polymorphism and accelerated pathogenesis (early age at onset or shorter duration of the disease) has not been seen in familial CJD patients with codon 200 mutation or in GSS patients with codon 102 mutation, arguing that other, as yet unidentified, gene products or environmental factors, or both, may influence the clinical expression of these diseases. 17 refs.
Petraroli, R.; Pocchiari, M. [Instituto Superiore di Sanita, Rome (Italy)
Analysing codon usage bias of cyprinid herpesvirus 3 and adaptation of this virus to the hosts.
The codon usage patterns of open reading frames (ORFs) in cyprinid herpesvirus 3 (CyHV-3) have been investigated in this study. The high correlation between GC12 % and GC3 % suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base component in the CyHV-3, while mutational pressure effect results from the high correlation between GC3 % and the first principal axis of principle component analysis (Axis 1) on the relative synonymous codon usage (RSCU) value of the viral functional genes. However, the interaction between the absolute codon usage bias and GC3 % suggests that other selections take part in the formation of codon usage, except for the mutational pressure. It is noted that the similarity degree of codon usage between the CyHV-3 and goldfish, Carassius auratus (L.), is higher than that between the virus and common carp, Cyprinus carpio L., suggesting that the goldfish plays a more important role than the common carp in codon usage pattern of the CyHV-3. The study of codon usage in CyHV-3 can provide some evidence about the molecular evolution of the virus. It can also enrich our understanding about the relationship between the CyHV-3 and its hosts by analysing their codon usage patterns. PMID:25491502
Ma, Y P; Liu, Z X; Hao, L; Ma, J Y; Liang, Z L; Li, Y G; Ke, H
Analysis of synonymous codon usage in FAD7 genes from different plant species.
In this study, the codon bias of the FAD7 genes among 10 different plant species was analyzed to identify general patterns of codon usage in the FAD7 genes. Our results showed that U-ended or A-ended codons were preferentially used in FAD7 for dicots, whereas G-ended or C-ended codons were preferentially used in FAD7 for monocots. An ENC-plot showed that some other factors may influence the codon usage of FAD7, except mutation bias in plant species. A correlation analysis between the codon adaptation index and GC or GC3s contents demonstrated that the codon usage bias of the FAD7 gene in plant species could be influenced by the gene expression level. The cluster analysis of relative synonymous codon usage values and phylogenetic trees of protein sequences for FAD7 genes confirm that the codon preference of FAD7 is influenced by genetic relationships. Moreover, Arabidopsis thaliana and Nicotiana tabacum were predicted to be the most appropriate expression hosts for the FAD7 genes from dicots, and Zea mays may be suitable for the expression of the FAD7 genes from monocots. Our results provide useful insights into the evolutionary relationships of plant species. PMID:25730080
Ma, Q P; Li, C; Wang, J; Wang, Y; Ding, Z T
Non-optimal codon usage affects expression, structure and function of clock protein FRQ.
Codon-usage bias has been observed in almost all genomes and is thought to result from selection for efficient and accurate translation of highly expressed genes. Codon usage is also implicated in the control of transcription, splicing and RNA structure. Many genes exhibit little codon-usage bias, which is thought to reflect a lack of selection for messenger RNA translation. Alternatively, however, non-optimal codon usage may be of biological importance. The rhythmic expression and the proper function of the Neurospora FREQUENCY (FRQ) protein are essential for circadian clock function. Here we show that, unlike most genes in Neurospora, frq exhibits non-optimal codon usage across its entire open reading frame. Optimization of frq codon usage abolishes both overt and molecular circadian rhythms. Codon optimization not only increases FRQ levels but, unexpectedly, also results in conformational changes in FRQ protein, altered FRQ phosphorylation profile and stability, and impaired functions in the circadian feedback loops. These results indicate that non-optimal codon usage of frq is essential for its circadian clock function. Our study provides an example of how non-optimal codon usage functions to regulate protein expression and to achieve optimal protein structure and function. PMID:23417067
Zhou, Mian; Guo, Jinhu; Cha, Joonseok; Chae, Michael; Chen, She; Barral, Jose M; Sachs, Matthew S; Liu, Yi
Lung cancer risk in relation to TP53 codon 47 and codon 72 polymorphism in Bangladeshi population.
The objective of this study was to determine whether p53 codon 47 and codon 72 polymorphisms are associated with increased risk of lung cancer in Bangladeshi population. We carried out a case-control study and examined the genotype distribution Pro47Ser and Arg72Pro single-nucleotide polymorphisms along with tobacco smoking in the predisposition of lung cancer by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach. The study included 106 lung cancer patients and 116 control subjects from Bangladesh. Lung cancer risk was estimated as odds ratio (OR) and 95 % confidence interval (CI) using conditional logistic regression models adjusting for age, sex, and smoking. No significant association was found between Pro47Ser SNP and lung cancer. The frequencies of p53 codon 72 polymorphisms (Arg/Arg, Arg/Pro, and Pro/Pro) in lung cancer were 25.5, 37.7, and 36.8 %, respectively; frequencies in the controls were 53.4, 30.2, and 16.4 %, respectively (p?0.01). The Arg/Pro and Pro/Pro genotype were significantly associated with increased risk of lung cancer (OR?=?2.51, 95 % CI?=?1.38-4.82 and OR?=?4.62, 95 % CI?=?2.31-9.52, respectively) compared with the Arg/Arg genotype. The combined frequency of Arg/pro and Pro/Pro genotype was also found to be associated with elevated risk of lung cancer (OR?=?3.36, 95 % CI?=?1.90-5.94, p?0.01). However, no significant relationship was found between age, sex, and histological subtypes of lung cancer with p53 codon 72 genotype distributions. When classified by smoking status, the effects of Arg72Pro polymorphism on lung cancer risk was only found to be significant (? (2) ?=?33.94, p?=?0.00000004) in case of heavy smokers (40 packs per year or more). We conclude that not Pro47Ser SNP but Arg72Pro SNP is involved in susceptibility to developing lung cancer, at least in Bangladeshi population. PMID:25034526
Mostaid, Md Shaki; Ahmed, Maizbha Uddin; Islam, Mohammad Safiqul; Bin Sayeed, Muhammad Shahdaat; Hasnat, Abul
Premature Stop Codon in MMP20 Causing Amelogenesis Imperfecta
Proteolytic enzymes are necessary for the hardening of dental enamel during development, and mutations in the kallikrein 4 (KLK4) and enamelysin (MMP20) genes cause autosomal recessive amelogenesis imperfecta (ARAI). So far, only one KLK4 and two MMP20 mutations have been reported. We have identified an ARAI-causing point mutation (c.l02G>A, g.l02G>A, and p.W34X) in exon 1 of MMP20 in a proband with autosomal recessive hypoplastic-hypomaturation amelogenesis imperfecta. The G to A transition changes the tryptophan (W) codon (TGG) at amino acid position 34 into a translation termination (X) codon (TGA). No disease-causing sequence variations were detected in KLK4. The affected enamel is thin, with mild spacing in the anterior dentition. The enamel layer is hypomineralized, does not contrast with dentin on radiographs, and tends to chip away from the underlying dentin. An intrinsic yellowish pigmentation is evident even during eruption. The phenotype supports current ideas concerning the function of enamelysin. PMID:18096894
Papagerakis, P.; Lin, H-K.; Lee, K. Y.; Hu, Y.; Simmer, J. P.; Bartlett, J. D.; Hu, J. C-C
ERIC Educational Resources Information Center
The task for the National Data Management Project is to share technological capabilities with the Head Start Community in order to implement improved services for children and families involved in Head Start. Many Head Start programs have incorporated technology into their programs, including word processing, database management systems,…
Maryland Univ., College Park. Univ. Coll.
ERIC Educational Resources Information Center
A quality Head Start facility should provide a physical environment responsive both to the needs of the children and families served and to the needs of staff, volunteers, and community agencies that share space with Head Start. This manual is a tool for Head Start grantees and delegate agencies for assessing existing facilities, making…
Research Assessment Management, Inc., Silver Spring, MD.
A Study of the purine\\/pyrimidine codon occurrence with a reduced centered variable and an evaluation compared to the frequency statistic
With the three-letter alphabet {R,Y,N} (R = purine, Y = pyrimidine, N= R or Y), there are 26 codons (NNN being excluded): RNN, . ,NNY (six codons at two unspecified bases N), RRN,. ,NYY (12 codons at one unspecified base N), RRR ,.._, YYY (eight specified codons). A statistical methodology that uses the codon frequency and a reduced centered variable
Prion protein gene analysis in three kindreds with fatal familial insomnia (FFI): Codon 178 mutation and codon 129 polymorphism
Fatal familial insomnia (FFI) is a disease linked to a GAC(Asp) [yields] AAC(Asn) mutation in codon 178 of the prion protein (PrP) gene. FFI is characterized clinically by untreatable progressive insomnia, dysautonomia, and motor dysfunctions and is characterized pathologically by selective thalamic atrophy. The authors confirmed the 178[sup Asn] mutation in the PrP gene of a third FFI family of French ancestry. Three family members who are under 40 years of age and who inherited the mutation showed only reduced perfusion in the basal ganglia on single photon emission computerized tomography. Some FFI features differ from the clinical and neuropathologic findings associated with 178[sup Asn] reported elsewhere. However, additional intragenic mutations accounting for the phenotypic differences were not observed in two affected individuals. In other sporadic and familial forms of Creutzfeldt-Jakob disease and Gerstmann-Straeussler syndrome, Met or Val homozygosity at polymorphic codon 129 is associated with a more severe phenotype, younger age at onset, and faster progression. In FFI, young and old individuals at disease onset had 129[sup Met/Val]. Moreover, of five 178[sup Asn] individuals who are above age-at-onset range and who are well, two have 129[sup Met] and three have 129[sup Met/Val], suggesting that polymorphic site 129 does not modulate FFI phenotypic expression. Genetic heterogeneity and environment may play an important role in inter- and intrafamilial variability of the 178[sup Asn] mutation. 32 refs., 5 figs., 1 tab.
Medori, R.; Tritschler, H.J. (Universita di Bologna (Italy))
Expression of Human Hemojuvelin (HJV) Is Tightly Regulated by Two Upstream Open Reading Frames in HJV mRNA That Respond to Iron Overload in Hepatic Cells.
The gene encoding human hemojuvelin (HJV) is one of the genes that, when mutated, can cause juvenile hemochromatosis, an early-onset inherited disorder associated with iron overload. The 5' untranslated region of the human HJV mRNA has two upstream open reading frames (uORFs), with 28 and 19 codons formed by two upstream AUGs (uAUGs) sharing the same in-frame stop codon. Here we show that these uORFs decrease the translational efficiency of the downstream main ORF in HeLa and HepG2 cells. Indeed, ribosomal access to the main AUG is conditioned by the strong uAUG context, which results in the first uORF being translated most frequently. The reach of the main ORF is then achieved by ribosomes that resume scanning after uORF translation. Furthermore, the amino acid sequences of the uORF-encoded peptides also reinforce the translational repression of the main ORF. Interestingly, when iron levels increase, translational repression is relieved specifically in hepatic cells. The upregulation of protein levels occurs along with phosphorylation of the eukaryotic initiation factor 2?. Nevertheless, our results support a model in which the increasing recognition of the main AUG is mediated by a tissue-specific factor that promotes uORF bypass. These results support a tight HJV translational regulation involved in iron homeostasis. PMID:25666510
Onofre, Cláudia; Tomé, Filipa; Barbosa, Cristina; Silva, Ana Luísa; Romăo, Luísa
Why Are Translationally Sub-Optimal Synonymous Codons Used in Escherichia coli?
Why Are Translationally Sub-Optimal Synonymous Codons Used in Escherichia coli? Nick G.C. Smith, Adam Eyre-Walker Centre for the Study of Evolution and School of Biological Sciences, University still be referred to as a sub-optimal codon.Correspondence to: N.G.C. Smith; email: n.g.c.smith
Eyre-Walker, Adam
Lie superalgebras and the multiplet structure of the genetic code. I. Codon representations
for the storage and transfer of genetic information. DNA is a macromolecule in the form of a double helix whichLie superalgebras and the multiplet structure of the genetic code. I. Codon representations Michael that the degeneracy of the genetic code, i.e., the phenomenon that different codons base triplets of DNA
Forger, Frank Michael
Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius
Technology Transfer Automated Retrieval System (TEKTRAN)
We have previously identified the mycobacterial high G+C codon usage bias as a limiting factor in heterologous expression of MAP proteins from Lb.salivarius, and demonstrated that codon optimisation of a synthetic coding gene greatly enhances MAP protein production. Here, we effectively demonstrate ...
Codon Usage Bias and Effective Population Sizes on the X Chromosome versus the Autosomes in
: John H. McDonald Abstract Codon usage bias (CUB) in Drosophila is higher for X-linked genes than in Drosophila melanogaster Jose L. Campos,*,1 Kai Zeng,2 Darren J. Parker,3 Brian Charlesworth,1 and Penelope R on the McDonaldKreitman test. Key words: Drosophila melanogaster, codon usage, effective population size
Two-nucleotide codon change in a hemoglobin polymorphism of the Celebes black ape ( Macaca nigra )
A hemoglobin polymorphism involving variant ß-chains was demonstrated in the Celebes black ape, Macaca nigra. Fingerprinting and amino acid analysis of the tryptic peptides from the two chain types have shown that they differ by a single amino acid substitution, between lysine and aspartic acid, which requires a two-nucleotide change in the corresponding codon. Another substitution in the same codon
Mitsuo Murata; Peter E. Thompson
The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage
Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C?T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C?T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages. PMID:24583580
Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua
Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus
Background Equine infectious anemia virus (EIAV) is an important animal model for understanding the relationship between viral persistence and the host immune response during lentiviral infections. Comparison and analysis of the codon usage model between EIAV and its hosts is important for the comprehension of viral evolution. In our study, the codon usage pattern of EIAV was analyzed from the available 29 full-length EIAV genomes through multivariate statistical methods. Finding Effective number of codons (ENC) suggests that the codon usage among EIAV strains is slightly biased. The ENC-plot analysis demonstrates that mutation pressure plays a substantial role in the codon usage pattern of EIAV, whereas other factors such as geographic distribution and host translation selection also take part in the process of EIAV evolution. Comparative analysis of codon adaptation index (CAI) values among EIAV and its hosts suggests that EIAV utilize the translational resources of horse more efficiently than that of donkey. Conclusion The codon usage bias in EIAV is slight and mutation pressure is the main factor that affects codon usage variation in EIAV. These results suggest that EIAV genomic biases are the result of the co-evolution of genome composition and the ability to evade the host's immune response. PMID:24359511
Factors affecting mito-nuclear codon usage interactions in the OXPHOS system of Drosophila melanogaster
Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation (OXPHOS) is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes
Zheng Sun; Liang Ma; Robert W. Murphy; Xiansheng Zhang; Dawei Huang
Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus
Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus, 2003) Although the surface proteins of human influenza A virus evolve rapidly and continually produce the sequence evolution of three influenza A genes over the past two decades. We study codon usage
Plotkin, Joshua B.
A General Model of Codon Bias Due to GC Mutational Gareth A. Palidwor1
. Principal Findings: In analyzing codon usage bias in hundreds of prokaryotic and plant genomes and in human in prokaryotes, plants and human respectively. When codons are grouped based on common GC content, 87%, 80% and 68% of the variation in usage is explained for prokaryotes, plants and human respectively
Xia, Xuhua
Synonymous Codon Usage in Drosophila melanogaster: Natural Selection and Translational Accuracy
I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the protein level. The frequency
Hiroshi Akashi
Translation efficiency is determined by both codon bias and folding energy
density | translation initiation Synonymous mutations (mutations that alter the coding DNA and RNATranslation efficiency is determined by both codon bias and folding energy Tamir Tullera,b,1 studies have suggested that codon bias is the most important determinant of translation efficiency
Ruppin, Eytan
Species Based Synonymous Codon Usage in Fusion Protein Gene of Newcastle Disease Virus
Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species. PMID:25479071
Kumar, Chandra Shekhar; Kumar, Sachin
The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens
The role of silent position in the codon on the protein structure is an interesting and yet unclear problem. In this paper, 563 Homo sapiens genes and 417 Escherichia coli genes coding for proteins with four different folding types have been analyzed using variance analysis, a multivariate analysis method newly used in codon usage analysis, to find the correlation between
Wanjun Gu; Tong Zhou; Jianmin Ma; Xiao Sun; Zuhong Lu
Catalytic Ignition and Upstream Reaction Propagation in a Platinum Tube
NASA Technical Reports Server (NTRS)
A challenge for catalytic combustion in monolithic reactors at elevated temperatures is the start-up or "light-off" from a cold initial condition. In this work, we demonstrate a concept called "back-end catalytic ignition that potentially can be utilized in the light-off of catalytic monoliths. An external downstream flame or Joule heating raises the temperature of a small portion of the catalyst near the outlet initiating a localized catalytic reaction that propagates upstream heating the entire channel. This work uses a transient numerical model to demonstrate "back-end" ignition within a single channel which can characterize the overall performance of a monolith. The paper presents comparisons to an experiment using a single non-adiabatic channel but the concept can be extended to the adiabatic monolith case. In the model, the time scales associated with solid heat-up are typically several orders of magnitude larger than the gas-phase and chemical kinetic time-scales. Therefore, the model assumes a quasi-steady gas-phase with respect to a transient solid. The gas phase is one-dimensional. Appropriate correlations, however, account for heat and mass transfer in a direction perpendicular to the flow. The thermally-thin solid includes axial conduction. The gas phase, however, does not include axial conduction due to the high Peclet number flows. The model includes both detailed gas-phase and catalytic surface reactions. The experiment utilizes a pure platinum circular channel oriented horizontally though which a CO/O2 mixture (equivalence ratios ranging from 0.6 to 0.9) flows at 2 m/s.
Struk, P. M.; Dietrich, D. L.; Mellish, B. P.; Miller, F. J.; T'ien, J. S.
ERIC Educational Resources Information Center
Smart Start is a comprehensive public-private initiative to help all North Carolina children enter school healthy and ready to succeed, and provides children from birth to age five access to high-quality and affordable child care, health care, and other critical services. This document comprises the first two issues of "Smart Start News," a…
Harris, Monica, Ed.
The Evolution of Codon Preferences in Drosophila: A Maximum-Likelihood Approach to Parameter Estimation and Hypothesis Testing
. Synonymous codon usage in related species may differ as a result of variation in mutation biases, differences in the overall\\u000a strength and efficiency of selection, and shifts in codon preference—the selective hierarchy of codons within and between\\u000a amino acids. We have developed a maximum-likelihood method to employ explicit population genetic models to analyze the evolution\\u000a of parameters determining codon
Gilean A. T. McVean; Jorge Vieira
Far upstream element binding protein 1: a commander of transcription, translation and beyond.
The far upstream binding protein 1 (FBP1) was first identified as a DNA-binding protein that regulates c-Myc gene transcription through binding to the far upstream element (FUSE) in the promoter region 1.5?kb upstream of the transcription start site. FBP1 collaborates with TFIIH and additional transcription factors for optimal transcription of the c-Myc gene. In recent years, mounting evidence suggests that FBP1 acts as an RNA-binding protein and regulates mRNA translation or stability of genes, such as GAP43, p27(Kip) and nucleophosmin. During retroviral infection, FBP1 binds to and mediates replication of RNA from Hepatitis C and Enterovirus 71. As a nuclear protein, FBP1 may translocate to the cytoplasm in apoptotic cells. The interaction of FBP1 with p38/JTV-1 results in FBP1 ubiquitination and degradation by the proteasomes. Transcriptional and post-transcriptional regulations by FBP1 contribute to cell proliferation, migration or cell death. FBP1 association with carcinogenesis has been reported in c-Myc dependent or independent manner. This review summarizes biochemical features of FBP1, its mechanism of action, FBP family members and the involvement of FBP1 in carcinogenesis. PMID:22926519
Zhang, J; Chen, Q M
Dual-Domain, Dual-Targeting Organellar Protein Presequences in Arabidopsis Can Use Non-AUG Start Codons
The processes accompanying endosymbiosis have led to a complex network of interorganellar protein traffic that originates from nuclear genes encoding mitochondrial and plastid proteins. A significant proportion of nucleus-encoded organellar proteins are dual targeted, and the process by which a protein acquires the capacity for both mitochondrial and plastid targeting may involve intergenic DNA exchange coupled with the incorporation of
Alan C. Christensen; Anna Lyznik; Saleem Mohammed; Christian G. Elowsky; Annakaisa Elo; Ryan Yule; Sally A. Mackenziea
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2. UPSTREAM SIDE OF DIVERSION DAM ON THE SNAKE RIVER, LOOKING SOUTH-SOUTHWEST. NOTE BANK REINFORCEMENT ON LEFT AND SPILLWAY ON RIGHT. - Snake River Ditch, Headgate on north bank of Snake River, Dillon, Summit County, CO
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OVERALL VIEW OF CASCADE CANAL COMPANY CRIB DAM, LOOKING UPSTREAM FROM DIRECTION OF KACHESS DAM. VIEW TO NORTH - Kachess Dam, 1904 Cascade Canal Company Crib Dam, Kachess River, 1.5 miles north of Interstate 90, Easton, Kittitas County, WA
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24. VIEW FROM EAST BANK, LOOKING UPSTREAM, SHOWING RECONSTRUCTED MAIN AND DIVERSION DAMS IN BACKGROUND WITH WATER-GATE AND BEGINNING OF HEAD-RACE IN LEFT FOREGROUND. - Forge Creek Dam-John Cable Mill, Townsend, Blount County, TN
Linking the impacts of upstream activities such as urban development to changes in downstream streamflow is critical to achieving a balance between economic development and environmental protection as a basis for sustainable watershed development. This paper presents a modeling a...
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4. VIEW SHOWING UPSTREAM FACE OF DAM, LOOKING NORTHEAST - High Mountain Dams in Upalco Unit, Kidney Lake Dam, Ashley National Forest, 4.7 miles North of Miners Gulch Campground, Mountain Home, Duchesne County, UT
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3. OVERALL VIEW OF DAM, SHOWING UPSTREAM FACE, LOOKING EAST - High Mountain Dams in Upalco Unit, Kidney Lake Dam, Ashley National Forest, 4.7 miles North of Miners Gulch Campground, Mountain Home, Duchesne County, UT
43. Photocopied August 1978. ICE RACK, VIEW FROM UPSTREAM, OCTOBER ...
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43. Photocopied August 1978. ICE RACK, VIEW FROM UPSTREAM, OCTOBER 9, 1902. NOTE TIMBERED FLOOR ABOVE RACK, THE UNTIMBERED FLOOR TO THE REAR. (284) - Michigan Lake Superior Power Company, Portage Street, Sault Ste. Marie, Chippewa County, MI
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DETAIL VIEW OF TOP OF DAM GATE STRUCTURE. UPSTREAM LOCK GATE AT RIGHT REAR. LOOKING WEST. - Illinois Waterway, La Grange Lock and Dam, 3/4 mile south of Country 795N at Illinois River, Versailles, Brown County, IL
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DOG HOUSE AT UPSTREAM LOCK GATE. ALSO SEEN AT LEFT IN PHOTO NO. IL-164-A-23. - Illinois Waterway, La Grange Lock and Dam, 3/4 mile south of Country 795N at Illinois River, Versailles, Brown County, IL
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3. AN IMAGE LOOKING SOUTH, TOWARD THE UPSTREAM SIDE OF THE CENTRAL PIER AND SHOWING THE SOUTHEAST ABUTMENT AND ERODED STARLING. - Cement Plant Road Bridge, Spanning Leatherwood Creek on County Road 50 South, Bedford, Lawrence County, IN
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5. A VIEW LOOKING WEST, TOWARD THE UPSTREAM SIDE OF THE PIER, SHOWING THE DETERIORATED SHEARWATER EDGE, THE NORTHEAST ABUTMENT AND WING WALL. - Cement Plant Road Bridge, Spanning Leatherwood Creek on County Road 50 South, Bedford, Lawrence County, IN
GPON upstream link utilization analysis with integrated network surveillance
We integrate physical layer surveillance concept into management system of GPON by allocating an unused time slot for network surveillance depending upon its availability in upstream GTC frame and analyze the link bandwidth utilization.
Hakjeon Bang; M. Thollabandi; Sungchang Kim; Dong-Soo Lee; Jongdeog Kim; Chang-Soo Park
1. Credit JTL General view looking upstream and towards New ...
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1. Credit JTL General view looking upstream and towards New Hampshire, unidentified 'crazy man' perched on top of arch. - Bellows Falls Arch Bridge, Spanning Connecticut River, North Walpole, Cheshire County, NH
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75. PALMDALE WATER COMPANY, LITTLEROCK DAM, EASTWOOD MULTIPLE-ARCHED TYPE: UPSTREAM ELEVATION, SHEET 2; OCTOBER 2, 1919. Littlerock Water District files. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA
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10. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: MISCELLANEOUS METAL DETAILS. Sheet A-22, November, 1940. File no. SA 342/31. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
41. Upstream end of emergency spillway excavation. Photographer unknown, 1929. ...
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41. Upstream end of emergency spillway excavation. Photographer unknown, 1929. Source: Arizona Department of Water Resources (ADWR). - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ
3. General view of upstream face, looking northwest. Spillway is ...
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3. General view of upstream face, looking northwest. Spillway is at the far end of the dam. The Antelope Valley is visible in center background. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA
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10. DETAIL OF UPSTREAM FACE OF NEW YORK CANAL HEADWORKS, SHOWING GATE LIFTING GEARS (TOP), WORM GEAR SHAFTS (CENTER) AND SLIDE GATES (BOTTOM). VIEW TO NORTHWEST. - Boise Project, Boise River Diversion Dam, Across Boise River, Boise, Ada County, ID
26. UPSTREAM VIEW OF DISCHARGE END OF OUTLET STRUCTURE.... Volume ...
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26. UPSTREAM VIEW OF DISCHARGE END OF OUTLET STRUCTURE.... Volume XVI, No. 17, September 29, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
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16. VIEW EASTERLY ALONG THE UPSTREAM SIDE OF THE OGEE SECTION OF THE SPILLWAY.... Volume XVIII, No. 13, January 29, 1940. - Prado Dam, Spillway, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
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7. VIEW WEST ALONG THE UPSTREAM SLOPE OF THE EMBANKMENT, SHOWING ROCK PAVING IN PROGRESS.... Volume XIX, No. 7, June 24, 1940. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
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22. UPSTREAM VIEW OF THE OUTLET CONTROL STRUCTURE AND THE PIER FOR THE SERVICE BRIDGE.... Volume XVIII, No. 12, January 29, 1940. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
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24. UPSTREAM VIEW OF A PORTION OF THE CLOSED CONDUIT SECTION OF OUTLET WORKS.... Volume XVI, No. 15, August 16, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
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8. VIEW OF UPSTREAM SIDE OF THE CONCRETE STOPLOG STRUCTURE NEAR THE MIDDLE OF THE SPILLWAY AT DAM 357, LOOKING SOUTHWEST - J. Clark Salyer National Wildlife Refuge, Dam 357, Along Lower Souris River, Kramer, Bottineau County, ND
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2. VIEW OF DAM 357, SHOWING UPSTREAM FACE OF THE DAM, LOOKING WEST FROM THE NEW MINIMUM FLOW CONTROL STRUCTURE - J. Clark Salyer National Wildlife Refuge, Dam 357, Along Lower Souris River, Kramer, Bottineau County, ND
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5. VIEW OF DAM 341, SHOWING THE UPSTREAM SIDE OF OUTLET WORKS FROM THE WEST SIDE, LOOKING NORTHEAST - J. Clark Salyer National Wildlife Refuge, Dam 341, Along Lower Souris River, Kramer, Bottineau County, ND
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10. VIEW OF MINIMUM FLOW CONTROL GATE STRUCTURE INSTALLED UPSTREAM FACE OF DAM 357 IN MID-1960s, LOOKING NORTHWEST - J. Clark Salyer National Wildlife Refuge, Dam 357, Along Lower Souris River, Kramer, Bottineau County, ND
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9. VIEW SHOWING UPSTREAM CONCRETE BULKHEAD FOR CONCRETE PIPE THROUGH THE DAM INSTALLED SHORTLY AFTER DAM 357 WAS COMPLETED, LOOKING NORTHEAST - J. Clark Salyer National Wildlife Refuge, Dam 357, Along Lower Souris River, Kramer, Bottineau County, ND
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23. VIEW LOOKING UPSTREAM FROM WEST BANK OF HEAD-RACE SHOWING RECONSTRUCTED MAIN AND DIVERSION DAMS; HEAD-RACE IS JUST OUT OF PICTURE AT LEFT. - Forge Creek Dam-John Cable Mill, Townsend, Blount County, TN
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11. DETAIL OF UPSTREAM FACE OF SLUICE GATE CONTROLS FROM CATWALK, SHOWING GATE LIFTING GEARS (TOP) AND GEAR SHAFTS (BOTTOM). VIEW TO SOUTHWEST. - Boise Project, Boise River Diversion Dam, Across Boise River, Boise, Ada County, ID
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WEST SIDE OF SUBSTATION, WITH SWITCH ROOM WING AND UPSTREAM (NORTH) FACADE OF POWERHOUSE (MI-100-B) VISIBLE AT RIGHT. VIEW TO EAST - Hardy Hydroelectric Plant, Substation, 6928 East Thirty-sixth Street, Newaygo, Newaygo County, MI
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18. VIEW OF SETTLING BASIN FROM UPSTREAM TRESTLE, SHOWING BULKHEAD ON RIGHT AND SAND BANK ON LEFT, LOOKING NORTHWEST - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA
7. Detail view of reinforced concrete archrings comprising dam's upstream ...
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7. Detail view of reinforced concrete arch-rings comprising dam's upstream face. Impressions of the wooden formwork used in construction are visible in the concrete. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA
1. View from the northwest of the bridge's northwest (upstream) ...
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1. View from the northwest of the bridge's northwest (upstream) elevation - Big Cottonwood River Bridge No. 246, Spanning Big Cottonwood River at Cottonwood Street (City Road No. 165), New Ulm, Brown County, MN
2. View from the north of the bridge's northwest (upstream) ...
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2. View from the north of the bridge's northwest (upstream) elevation - Big Cottonwood River Bridge No. 246, Spanning Big Cottonwood River at Cottonwood Street (City Road No. 165), New Ulm, Brown County, MN
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UPSTREAM LOCK GATE DETAIL AND DOG HOUSE. NOTE ARM AND GEARING FOR CONTROLLING LOCK GATE. LOOKING WEST SOUTHWEST. - Illinois Waterway, Brandon Road Lock and Dam , 1100 Brandon Road, Joliet, Will County, IL
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7. DETAIL CENTRAL PIER (SKEWBACK) WITH BREAKWATER, UPSTREAM (EAST) SIDE. NOTE FRACTURES ALONG BARREL ARCH EXTRADOS. - Roaring Creek Bridge, State Road 2005 spanning Roaring Creek in Locust Township, Slabtown, Columbia County, PA
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29. VIEW OF TWIN FALLS MAIN CANAL BRIDGE FROM UPSTREAM LOOKING DOWNSTREAM. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID
7. Chandler Falls, looking upstream (from north). Golf tee of ...
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7. Chandler Falls, looking upstream (from north). Golf tee of the Mesa Country Club on right. Photographer: Mark Durben, February 1989. Source: SRPA - Tempe Canal, South Side Salt River in Tempe, Mesa & Phoenix, Tempe, Maricopa County, AZ
Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.
Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts. PMID:23322170
Cardinale, Daniel J; DeRosa, Kate; Duffy, Siobain
High codon adaptation in citrus tristeza virus to its citrus host
Background Citrus tristeza virus (CTV), a member of the genus Closterovirus within the family Closteroviridae, is the causal agent of citrus tristeza disease. Previous studies revealed that the negative selection, RNA recombination and gene flow were the most important forces that drove CTV evolution. However, the CTV codon usage was not studied and thus its role in CTV evolution remains unknown. Results A detailed comparative analysis of CTV codon usage pattern was done in this study. Results of the study show that although in general CTV does not have a high degree of codon usage bias, the codon usage of CTV has a high level of resemblance to its host codon usage. In addition, our data indicate that the codon usage resemblance is only observed for the woody plant-infecting closteroviruses but not the closteroviruses infecting the herbaceous host plants, suggesting the existence of different virus-host interactions between the herbaceous plant-infecting and woody plant-infecting closteroviruses. Conclusion Based on the results, we suggest that in addition to RNA recombination, negative selection and gene flow, host plant codon usage selection can also affect CTV evolution. PMID:22698086
Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)
The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes. PMID:24454907
Chen, Haixia; Sun, Shichun; Norenburg, Jon L.; Sundberg, Per
A comparative analysis of synonymous codon usage bias pattern in human albumin superfamily.
Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life. Though the frequency of codon usage is not equal across species and within genome in the same species, the phenomenon is non random and is tissue-specific. Several factors such as GC content, nucleotide distribution, protein hydropathy, protein secondary structure, and translational selection are reported to contribute to codon usage preference. The synonymous codon usage patterns can be helpful in revealing the expression pattern of genes as well as the evolutionary relationship between the sequences. In this study, synonymous codon usage bias patterns were determined for the evolutionarily close proteins of albumin superfamily, namely, albumin, ?-fetoprotein, afamin, and vitamin D-binding protein. Our study demonstrated that the genes of the four albumin superfamily members have low GC content and high values of effective number of codons (ENC) suggesting high expressivity of these genes and less bias in codon usage preferences. This study also provided evidence that the albumin superfamily members are not subjected to mutational selection pressure. PMID:24707212
Mirsafian, Hoda; Mat Ripen, Adiratna; Singh, Aarti; Teo, Phaik Hwan; Merican, Amir Feisal; Mohamad, Saharuddin Bin
A Comparative Analysis of Synonymous Codon Usage Bias Pattern in Human Albumin Superfamily
Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life. Though the frequency of codon usage is not equal across species and within genome in the same species, the phenomenon is non random and is tissue-specific. Several factors such as GC content, nucleotide distribution, protein hydropathy, protein secondary structure, and translational selection are reported to contribute to codon usage preference. The synonymous codon usage patterns can be helpful in revealing the expression pattern of genes as well as the evolutionary relationship between the sequences. In this study, synonymous codon usage bias patterns were determined for the evolutionarily close proteins of albumin superfamily, namely, albumin, ?-fetoprotein, afamin, and vitamin D-binding protein. Our study demonstrated that the genes of the four albumin superfamily members have low GC content and high values of effective number of codons (ENC) suggesting high expressivity of these genes and less bias in codon usage preferences. This study also provided evidence that the albumin superfamily members are not subjected to mutational selection pressure. PMID:24707212
Mirsafian, Hoda; Mat Ripen, Adiratna; Singh, Aarti; Teo, Phaik Hwan; Merican, Amir Feisal; Mohamad, Saharuddin Bin
Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids
Background Different proteins are required in widely different quantities to build a living cell. In most organisms, transcription control makes a major contribution to differential expression. This is not the case in trypanosomatids where most genes are transcribed at an equivalent rate within large polycistronic clusters. Thus, trypanosomatids must use post-transcriptional control mechanisms to balance gene expression requirements. Results Here, the evidence for translational selection, the enrichment of 'favoured' codons in more highly expressed genes, is explored. A set of highly expressed, tandem-repeated genes display codon bias in Trypanosoma cruzi, Trypanosoma brucei and Leishmania major. The tRNA complement reveals forty-five of the sixty-one possible anticodons indicating widespread use of 'wobble' tRNAs. Consistent with translational selection, cognate tRNA genes for favoured codons are over-represented. Importantly, codon usage (Codon Adaptation Index) correlates with predicted and observed expression level. In addition, relative codon bias is broadly conserved among syntenic genes from different trypanosomatids. Conclusion Synonymous codon bias is correlated with tRNA gene copy number and with protein expression level in trypanosomatids. Taken together, the results suggest that translational selection is the dominant mechanism underlying the control of differential protein expression in these organisms. The findings reveal how trypanosomatids may compensate for a paucity of canonical Pol II promoters and subsequent widespread constitutive RNA polymerase II transcription. PMID:18173843
Horn, David
Gaining Insights into the Codon Usage Patterns of TP53 Gene across Eight Mammalian Species
TP53 gene is known as the "guardian of the genome" as it plays a vital role in regulating cell cycle, cell proliferation, DNA damage repair, initiation of programmed cell death and suppressing tumor growth. Non uniform usage of synonymous codons for a specific amino acid during translation of protein known as codon usage bias (CUB) is a unique property of the genome and shows species specific deviation. Analysis of codon usage bias with compositional dynamics of coding sequences has contributed to the better understanding of the molecular mechanism and the evolution of a particular gene. In this study, the complete nucleotide coding sequences of TP53 gene from eight different mammalian species were used for CUB analysis. Our results showed that the codon usage patterns in TP53 gene across different mammalian species has been influenced by GC bias particularly GC3 and a moderate bias exists in the codon usage of TP53 gene. Moreover, we observed that nature has highly favored the most over represented codon CTG for leucine amino acid but selected against the ATA codon for isoleucine in TP53 gene across all mammalian species during the course of evolution. PMID:25807269
Mazumder, Tarikul Huda; Chakraborty, Supriyo
NSDL National Science Digital Library
This is the first of several lessons on starting a small business. This class is intended for adults entrepreneurs who may be thinking of starting a business. This lesson gives economic information on small businesses. It also provides information to help the student determine whether they are ready to be a business owner and whether their particular business could succeed. QUESTION: If you were to start a small business or home occupation, what would it be? Create a document giving a brief description of a potential business idea. (You will not be required to share the information with class members.) LESSON: Please read the following articles. 1. Go to the ...
Sonya Duke
Emergence of Upstream Swimming via a Hydrodynamic Transition
NASA Astrophysics Data System (ADS)
We demonstrate that upstream swimming of sperm emerges via an orientation disorder-order transition. The order parameter, the average orientation of the sperm head against the flow, follows a 0.5 power law with the deviation from the critical flow shear rate (? -?c ). This transition is successfully explained by a hydrodynamic bifurcation theory, which extends the sperm upstream swimming to a broad class of near surface microswimmers that possess front-back asymmetry and circular motion.
Tung, Chih-kuan; Ardon, Florencia; Roy, Anubhab; Koch, Donald L.; Suarez, Susan S.; Wu, Mingming
Influence of a river valley constriction on upstream sedimentation
. Each of these processes generates relatively coarse deposits. A flood lake may occur upstream from the constriction when the width of the river exceeds the width of the constriction. The flood waters entering the lake undergo decreased velocity... and decreased competency resulting in the deposition of previously suspended river sediments. This process, similar to deltaic processes, deposits coarser materials on the upstream side of the flood lake and progressively finer material out into the flood...
Kinnebrew, Quin
Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus
Codon usage bias has been documented in a wide diversity of species, but the relative contributions of mutational bias and various forms of natural selection remain unclear. Here, we describe for the first time genome-wide patterns of codon bias at 4623 genes in the purple sea urchin, Strongylocentrotus purpuratus. Preferred codons were identified at 18 amino acids that exclusively used G or C at third positions, which contrasted with the strong AT bias of the genome (overall GC content is 36.9%). The GC content of third positions and coding regions exhibited significant correlations with the magnitude of codon bias. In contrast, the GC content of introns and flanking regions was indistinguishable from the genome-wide background, which suggested a limited contribution of mutational bias to synonymous codon usage. Five distinct clusters of genes were identified that had significantly different synonymous codon usage patterns. A significant correlation was observed between codon bias and mRNA expression supporting translational selection, but this relationship was driven by only one highly biased cluster that represented only 8.6% of all genes. In all five clusters preferred codons were evolutionarily conserved to a similar degree despite differences in their synonymous codon usage distributions and magnitude of codon bias. The third positions of preferred codons in two codon usage groups also paired significantly more often in stems than in loops of mRNA secondary structure predictions, which suggested that codon bias might also affect mRNA stability. Our results suggest that mutational bias has played a minor role in determining codon bias in S. purpuratus and that preferred codon usage may be heterogeneous across different genes and subject to different forms of natural selection. PMID:23637123
Kober, Kord M.; Pogson, Grant H.
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome.
Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains' genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins. PMID:25350396
Zhou, Jian-hua; Ding, Yao-zhong; He, Ying; Chu, Yue-feng; Zhao, Ping; Ma, Li-ya; Wang, Xin-jun; Li, Xue-rui; Liu, Yong-sheng
Suppressors of lysine codons may be misacylated lysine tRNAs.
We describe a novel class of missense suppressors that read the codons for lysine at two positions (211 and 234) in the trpA polypeptide of Escherichia coli. The suppressor mutations are highly linked to lysT, a gene for lysine tRNA. The results suggest that the suppressors are misacylated lysine tRNAs that carry glycine or alanine. The mutant codons are apparently suppressed better at position 211 than at position 234, indicating the existence of codon context effects in missense suppression. PMID:6415042
Murgola, E J; Pagel, F T
NSDL National Science Digital Library
Last month, Pediatrics, the official journal of the American Academy of Pediatrics (AAP), issued a formal policy statement concerning School Start Times for Adolescents (http://pediatrics.aappublications.org/content/early/2014/08/19/peds.2014-1697.abstract?sid=3f739b0e-a552-4a4a-bd0a-907809e20255). In essence, the AAP called for schools to start later, citing sleep deprivation among teenagers as â??an important public health issue.â?ť This site from Start School Later, a group advocating for â??health, safety and equity in education,â?ť provides good, if somewhat one-sided, information on the topic. If youâ??re unfamiliar, start with Research & Info, which provides links to a number of informative sites about adolescent sleep needs and the impact of early school start times. Success Stories takes readers to schools around the country that have experimented with, and benefited from, later start times. If you're inspired, you can also Get Involved. Whatever your position on the issue, this is an informative and interesting site.
UAG is a sense codon in several chlorophycean mitochondria.
The mitochondrial genetic code of those land plants and green algae that have been examined does not deviate from the universal one. A red alga, Chondrus crispus, is the sole reported example throughout the algae that uses a deviant (non-universal) mitochondrial genetic code (UGA=Trp). We have analyzed 366-bp DNA sequences of the gene for mitochondrial cytochrome oxidase subunit I (COXI) from ten chlorophyceaen algae, and detected 3-8 in-frame UAG codons in the sequences of five species. Comparisons of these sequences with those of other algae and land plants have shown that most of the UAG sites in Hydrodictyon reticulatum, Pediastrum boryanum and Tetraedron bitridens correspond to alanine, and those of Coelastrum microporum and Scenedesmus quadricauda to leucine. The three species in which UAG probably codes for alanine are characterized by zoospore formation in asexual reproduction and form a clade in the COXI phylogenetic tree. The two species in which UAG codes for leucine are known to form daughter coenobia and pair in the tree. This is the first report on a deviant mitochondrial genetic code in green algae. Mutational change(s) in the release factor corresponding to UAG would be involved in these code changes. No genetic code deviation has been found in five other species examined. PMID:8662206
Hayashi-Ishimaru, Y; Ohama, T; Kawatsu, Y; Nakamura, K; Osawa, S
Suppression of Premature Termination Codons as a Therapeutic Approach
In this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. A number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (PTCs; also known as nonsense mutations) in mammalian cells. We discuss efforts to utilize these drugs to suppress disease-causing PTCs that result in the loss of protein expression and function. In-frame PTCs represent a genotypic subset of mutations that make up ~11% of all known mutations that cause genetic diseases, and millions of patients have diseases attributable to PTCs. Current approaches aimed at reducing the efficiency of translation termination at PTCs (referred to as PTC suppression therapy) have the goal of alleviating the phenotypic consequences of a wide range of genetic diseases. Suppression therapy is currently in clinical trials for treatment of several genetic diseases caused by PTCs, and preliminary results suggest that some patients have shown clinical improvements. While current progress is promising, we discuss various approaches that may further enhance the efficiency of this novel therapeutic approach. PMID:22672057
Keeling, Kim M.; Wang, Dan; Conard, Sara E.; Bedwell, David M.
Pyrrolysine is not hardwired for cotranslational insertion at UAG codons
Pyrrolysine (Pyl), the 22nd naturally encoded amino acid, gets acylated to its distinctive UAG suppressor tRNAPyl by the cognate pyrrolysyl-tRNA synthetase (PylRS). Here we determine the RNA elements required for recognition and aminoacylation of tRNAPyl in vivo by using the Pyl analog N-?-cyclopentyloxycarbonyl-l-lysine. Forty-two Methanosarcina barkeri tRNAPyl variants were tested in Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNAPyl mutants were selected to determine in vivo binding to M. barkeri PylRS in a yeast three-hybrid system and to measure in vitro tRNAPyl aminoacylation. tRNAPyl identity elements include the discriminator base, the first base pair of the acceptor stem, the T-stem base pair G51:C63, and the anticodon flanking nucleotides U33 and A37. Transplantation of the tRNAPyl identity elements into the mitochondrial bovine tRNASer scaffold yielded chimeric tRNAs active both in vitro and in vivo. Because the anticodon is not important for PylRS recognition, a tRNAPyl variant could be constructed that efficiently suppressed the lac opal U4 mutation in E. coli. These data suggest that tRNAPyl variants may decode numerous codons and that tRNAPyl:PylRS is a fine orthogonal tRNA:synthetase pair that facilitated the late addition of Pyl to the genetic code. PMID:17360621
Ambrogelly, Alexandre; Gundllapalli, Sarath; Herring, Stephanie; Polycarpo, Carla; Frauer, Carina; Söll, Dieter
Barriers impede upstream spawning migration of flathead chub
Many native cyprinids are declining throughout the North American Great Plains. Some of these species require long reaches of contiguous, flowing riverine habitat for drifting eggs or larvae to develop, and their declining populations have been attributed to habitat fragmentation or barriers (e.g., dams, dewatered channels, and reservoirs) that restrict fish movement. Upstream dispersal is also needed to maintain populations of species with passively drifting eggs or larvae, and prior researchers have suggested that these fishes migrate upstream to spawn. To test this hypothesis, we conducted a mark–recapture study of Flathead Chub Platygobio gracilis within a 91-km reach of continuous riverine habitat in Fountain Creek, Colorado. We measured CPUE, spawning readiness (percent of Flathead Chub expressing milt), and fish movement relative to a channel-spanning dam. Multiple lines of evidence indicate that Flathead Chub migrate upstream to spawn during summer. The CPUE was much higher at the base of the dam than at downstream sites; the seasonal increases in CPUE at the dam closely tracked seasonal increases in spawning readiness, and marked fish moved upstream as far as 33 km during the spawning run. The upstream migration was effectively blocked by the dam. The CPUE of Flathead Chub was much lower upstream of the OHDD than at downstream sites, and <0.2% of fish marked at the dam were recaptured upstream. This study provides the first direct evidence of spawning migration for Flathead Chub and supports the general hypothesis that barriers limit adult dispersal of these and other plains fishes.
Walters, David M.; Zuellig, Robert E.; Crockett, Harry J.; Bruce, James F.; Lukacs, Paul M.; Fitzpatrick, Ryan M.
Amino Acid Deletion at Codon 67 and Thr-to-Gly Change at Codon 69 of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Confer Novel Drug Resistance Profiles
The potential roles of an amino acid deletion at codon 67 (?67) and a Thr-to-Gly change at codon 69 (T69G) in the reverse transcriptase of human immunodeficiency virus (HIV) type 1 in drug sensitivity and relative replication fitness were studied. Our results suggest that the ?67 and T69G changes can be categorized as mutations associated with multidrug resistance. The combination of both mutations with an L74I change (?67+T69G/L74I) leads to a novel 3?-azido-3?-deoxythymidine resistance motif and compensates for impaired HIV replication. PMID:11264389
Imamichi, Tomozumi; Murphy, Michael A.; Imamichi, Hiromi; Lane, H. Clifford
Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models
We develop novel methods for comparative genomics analysis of protein-coding genes using phylogenetic codon models, in pursuit of two main lines of biological investigation: First, we develop PhyloCSF, an algorithm based ...
Lin, Michael F. (Michael Fong-Jay)
Evidence of abundant stop codon readthrough in Drosophila and other Metazoa
While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions ...
Jungreis, Irwin
Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes
Background Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed genes are thought to experience stronger selection pressures on synonymous codons. This should result in codon usage bias even in species with relatively low effective population sizes, like mammals, where synonymous site selection is thought to be weak. Here we use phylogenetic codon-based likelihood models to explore patterns of codon usage bias in a dataset of 18 mammalian rhodopsin sequences, the protein mediating the first step in vision in the eye, and one of the most highly expressed genes in vertebrates. We use these patterns to infer selection pressures on key translational mechanisms including polypeptide elongation, protein folding, mRNA stability, and splicing. Results Overall, patterns of selection in mammalian rhodopsin appear to be correlated with post-transcriptional and translational processes. We found significant evidence for selection at synonymous sites using phylogenetic mutation-selection likelihood models, with C-ending codons found to have the highest relative fitness, and to be significantly more abundant at conserved sites. In general, these codons corresponded with the most abundant tRNAs in mammals. We found significant differences in codon usage bias between rhodopsin loops versus helices, though there was no significant difference in mean synonymous substitution rate between these motifs. We also found a significantly higher proportion of GC-ending codons at paired sites in rhodopsin mRNA secondary structure, and significantly lower synonymous mutation rates in putative exonic splicing enhancer (ESE) regions than in non-ESE regions. Conclusions By focusing on a single highly expressed gene we both distinguish synonymous codon selection from mutational effects and analytically explore underlying functional mechanisms. Our results suggest that codon bias in mammalian rhodopsin arises from selection to optimally balance high overall translational speed, accuracy, and proper protein folding, especially in structurally complicated regions. Selection at synonymous sites may also be contributing to mRNA stability and splicing efficiency at exonic-splicing-enhancer (ESE) regions. Our results highlight the importance of investigating highly expressed genes in a broader phylogenetic context in order to better understand the evolution of synonymous substitutions. PMID:24884412
Characterizing the Native Codon Usages of a Genome: An Axis Projection Approach
Codon usage can provide insights into the nature of the genes in a genome. Genes that are "native" to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias "typical" usage to a more biased "high-expression" usage characteristic of genes encoding abundant proteins. Genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. In this study, we present a method for characterizing the codon usages of native genes—both typical and highly expressed—within a genome. Each gene is evaluated relative to a half line (or axis) in a 59D space of codon usage. The axis begins at the modal codon usage, the usage that matches the largest number of genes in the genome, and it passes through a point representing the codon usage of a set of genes with expression-related bias. A gene whose codon usage matches (does not significantly differ from) a point on this axis is a candidate native gene, and the location of its projection onto the axis provides a general estimate of its expression level. A gene that differs significantly from all points on the axis is a candidate foreign gene. This automated approach offers significant improvements over existing methods. We illustrate this by analyzing the genomes of Pseudomonas aeruginosa PAO1 and Bacillus anthracis A0248, which can be difficult to analyze with commonly used methods due to their biased base compositions. Finally, we use this approach to measure the proportion of candidate foreign genes in 923 bacterial and archaeal genomes. The organisms with the most homogeneous genomes (containing the fewest candidate foreign genes) are mostly endosymbionts and parasites, though with exceptions that include Pelagibacter ubique and Beutenbergia cavernae. The organisms with the most heterogeneous genomes (containing the most candidate foreign genes) include members of the genera Bacteroides, Corynebacterium, Desulfotalea, Neisseria, Xylella, and Thermobaculum. PMID:20679093
Davis, James J.; Olsen, Gary J.
Characterization of codon usage bias in the gI gene of duck enteritis virus
The analysis on codon usage bias of gI gene of duck enteritis virus (DEV) may provide a basis for understanding the evolution and molecular characteristic of DEV, and for selecting appropriate host expression systems to improve the expression of target gene. A comparative analysis of the codon usage bias of the DEV gI gene and 22 other refrence herpesviruses gI-like
Lijuan Li; Anchun Cheng; Mingshu Wang; Shunchuan Zhang; Dekang Zhu; Renyong Jia; Qihui Luo; Yi Zhou; Zhengli Chen; Xiaoyue Chen
Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum
Here, the codon usage patterns of two Clostridium species (Clostridium perfringens and Clostridium acetobutylicum) are reported. These prokaryotes are characterized by a strong mutational bias towards A+T, a striking excess of coding sequences and purine-rich leading strands of replication, strong GC-skews and a high frequency of genomic rearrangements. As expected, it was found that the mutational bias dominates codon usage
Hector Musto; Hector Romero; Alejandro Zavala
Health and safety in small workplaces: refocusing upstream.
Small workplaces have particular injury risks and are enduringly difficult for the occupational health and safety (OHS) system to reach. This paper puts forward an "upstream" perspective on OHS in small workplaces that moves beyond the attributes of the workplace and those who work there. The paper draws on and synthesizes ideas and findings from emerging upstream OHS research, our own empirical investigations in Ontario and Quebec, and our collected research experience in small workplace health. Upstream structures and processes (regulations, policies, services, interventions, professional practices) are often misaligned with the conditions of work and social relations of small workplaces. Key upstream factors include regulatory exemption, subcontracting, unionization levels, the changing character of small enterprise, joint management, service and inspection constraints, competing institutional accountabilities, institutional orientation to large business, and inappropriate service and policy. Misalignment of the OHS system with the nature and practical realities of small workplaces can undermine prevention and the management of ill health and injury. To address such misalignments, the paper calls for: 1) restructuring of data collection and consultation processes to increase the visibility, voice and credibility of small workplaces; 2) "audits" of OHS-related legislation, policy and interventions to assess and address implications for small workplaces; 3) reflection on current terms and concepts that render workers invisible and capture poorly the essence and (increasing) diversity of these workplaces; and 4) extension of the upstream gaze to the global level. PMID:20629444
Eakin, Joan M; Champoux, Daničle; MacEachen, Ellen
Clustering in Large Networks Does Not Promote Upstream Reciprocity
Upstream reciprocity (also called generalized reciprocity) is a putative mechanism for cooperation in social dilemma situations with which players help others when they are helped by somebody else. It is a type of indirect reciprocity. Although upstream reciprocity is often observed in experiments, most theories suggest that it is operative only when players form short cycles such as triangles, implying a small population size, or when it is combined with other mechanisms that promote cooperation on their own. An expectation is that real social networks, which are known to be full of triangles and other short cycles, may accommodate upstream reciprocity. In this study, I extend the upstream reciprocity game proposed for a directed cycle by Boyd and Richerson to the case of general networks. The model is not evolutionary and concerns the conditions under which the unanimity of cooperative players is a Nash equilibrium. I show that an abundance of triangles or other short cycles in a network does little to promote upstream reciprocity. Cooperation is less likely for a larger population size even if triangles are abundant in the network. In addition, in contrast to the results for evolutionary social dilemma games on networks, scale-free networks lead to less cooperation than networks with a homogeneous degree distribution. PMID:21998641
Masuda, Naoki
Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights.
The purpose of this study was to investigate the balance between transfer ribonucleic acid (tRNA) supply and demand in retrovirus-infected cells, seeking the best targets for antiretroviral therapy based on the hypothetical tRNA Inhibition Therapy (TRIT). Codon usage and tRNA gene data were retrieved from public databases. Based on logistic principles, a therapeutic score (T-score) was calculated for all sense codons, in each retrovirus-host system. Codons that are critical for viral protein translation, but not as critical for the host, have the highest T-score values. Theoretically, inactivating the cognate tRNA species should imply a severe reduction of the elongation rate during viral mRNA translation. We developed a method to predict tRNA species critical for retroviral protein synthesis. Four of the best TRIT targets in HIV-1 and HIV-2 encode Large Hydrophobic Residues (LHR), which have a central role in protein folding. One of them, codon CUA, is also a TRIT target in both HTLV-1 and HTLV-2. Therefore, a drug designed for inactivating or reducing the cytoplasmatic concentration of tRNA species with anticodon TAG could attenuate significantly both HIV and HTLV protein synthesis rates. Inversely, replacing codons ending in UA by synonymous codons should increase the expression, which is relevant for DNA vaccine design. PMID:24151425
Frias, Diego; Monteiro-Cunha, Joana P; Mota-Miranda, Aline C; Fonseca, Vagner S; de Oliveira, Tulio; Galvao-Castro, Bernardo; Alcantara, Luiz C J
Pyrrolysine is not hardwired for cotranslational insertion at UAG codons.
Pyrrolysine (Pyl), the 22nd naturally encoded amino acid, gets acylated to its distinctive UAG suppressor tRNA(Pyl) by the cognate pyrrolysyl-tRNA synthetase (PylRS). Here we determine the RNA elements required for recognition and aminoacylation of tRNA(Pyl) in vivo by using the Pyl analog N-epsilon-cyclopentyloxycarbonyl-l-lysine. Forty-two Methanosarcina barkeri tRNA(Pyl) variants were tested in Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNA(Pyl) mutants were selected to determine in vivo binding to M. barkeri PylRS in a yeast three-hybrid system and to measure in vitro tRNA(Pyl) aminoacylation. tRNA(Pyl) identity elements include the discriminator base, the first base pair of the acceptor stem, the T-stem base pair G51:C63, and the anticodon flanking nucleotides U33 and A37. Transplantation of the tRNA(Pyl) identity elements into the mitochondrial bovine tRNA(Ser) scaffold yielded chimeric tRNAs active both in vitro and in vivo. Because the anticodon is not important for PylRS recognition, a tRNA(Pyl) variant could be constructed that efficiently suppressed the lac opal U4 mutation in E. coli. These data suggest that tRNA(Pyl) variants may decode numerous codons and that tRNA(Pyl):PylRS is a fine orthogonal tRNA:synthetase pair that facilitated the late addition of Pyl to the genetic code. PMID:17360621
Ambrogelly, Alexandre; Gundllapalli, Sarath; Herring, Stephanie; Polycarpo, Carla; Frauer, Carina; Söll, Dieter
Mechanism of controlling supersonic cavity oscillations using upstream mass injection
NASA Astrophysics Data System (ADS)
The mechanism of controlling supersonic cavity oscillations using upstream mass injection is investigated by implicit large-eddy simulations of a turbulent flow (M? = 2.0, ReD = 105) past a rectangular cavity with a length-to-depth ratio of 2. The mass injection is simulated by specifying a vertical velocity profile of a jet ejecting steadily through a slot placed at the upstream of the cavity leading edge. The results show that the steady upstream mass injection produces significant attenuation of the cavity oscillations, and two primary mechanisms are demonstrated to be directly responsible for the noise suppression: lifting up of the cavity shear layer, and damping of the shear-layer instability. It is found that the case of low mass flow injection investigated is more effective in stabilizing the cavity shear layer than the high mass flow injection. A transition stage might exist between two well-developed oscillating modes, but "mode-switching" is not observed.
Li, Weipeng; Nonomura, Taku; Fujii, Kozo
QUICK START Installing Outlook
to set it up for the first time. First check that Outlook is installed but don't open it yet. From report that your e-mail account is configured. Tick the box to Manually configure server settings to download all of your mail the first time you use it. 1 2 Getting started Check that you are set up
Sussex, University of
ERIC Educational Resources Information Center
Through its signature initiative, Liberal Education and America's Promise (LEAP), the Association of American Colleges and Universities (AAC&U) is promoting a vision for learning that begins in school: Starting in School . . . Rigorous and rich curriculum focused on the essential learning outcomes; comprehensive, individualized, and…
Albertine, Susan
ERIC Educational Resources Information Center
Noting that many students' experiences with police officers is negative, Heartland Programs Head Start in Salina, Kansas, initiated the Cop Day Program to develop a positive image of law enforcement. Police officer participated in classroom activities at the teachers' discretion once a month. Teachers and administrators noticed improvement in…
Hoffman, Stephen M.
NSDL National Science Digital Library
Learners follow a three-step process to start their own rock collection. Learners will collect rocks, record information about each rock on a Rock Chart, observe and sort their rocks, and create a rock display. This activity also includes a book list with resources for rock classification.
An investment club is a group of people who learn about investments together and pool their money to purchase stocks or bonds. Learn how to start such a club, how to manage the tax aspects of joint investments, and how to benefit from club...
Johnson, Jason; Thompson, Bill; Polk, Wade
PAINTING CHECKLIST GETTING STARTED o Choose your colour scheme o Test colours using sample pots o Measure the area to be painted · Choose paint finish, matt, semi-gloss, gloss etc · Type of paint to use, water-based etc · State of repair of current surface · Painting over oil-based/gloss paint or wallpaper
Peters, Richard
NSDL National Science Digital Library
The StartMe application gives Internet users the opportunity to create their own personal browser startpage with their favorite bookmarks and RSS feeds. The drag and drop interface is user-friendly, particularly for computer neophytes. Visitors can also incorporate extensions for popular browsers or tweak the appearance of their startpage as they see fit. This version is compatible with all operating systems.
ERIC Educational Resources Information Center
Case studies of seven Home Start programs are given as the third section of an evaluation study. Communities involved are Huntsville, Alabama; Fairbanks, Alaska; Fort Defiance, Arizona; Dardanelle, Arkansas; Wichita, Kansas; Gloucester, Massachusetts; and Reno, Nevada. Although each study varies in format, each describes in detail the degree and…
High/Scope Educational Research Foundation, Ypsilanti, MI.
Development of GPON upstream physical-media-dependent prototypes
This paper presents three new gigabit-capable passive optical network (GPON) physical-media-dependent (PMD) prototypes: a burst-mode optical transmitter, an avalanche photodiode\\/transimpedance amplifier (APD-TIA), and a burst-mode optical receiver. With these, point-to-multipoint (P2MP) upstream transmission can be realized in a high-performance GPON at 1.25 Gb\\/s. Performance measurements on the new burst-mode upstream PMD modules comply with GPON uplink simulations. The laser transmitter
Xing-Zhi Qiu; Peter Ossieur; Johan Bauwelinck; Yanchun Yi; Dieter Verhulst; Jan Vandewege; Benoit De Vos; Paolo Solina
ISEE-3/IMP-8 observations of simultaneous upstream proton events
NASA Technical Reports Server (NTRS)
Upstream 50-200 keV proton events were observed simultaneously by the low energy proton detectors on ISEE-3 and IMP-8, and the gradient from the spin averaged fluxes at the two spacecraft was calculated. The dependence of that gradient upon the angular distributions at IMP-8 was investigated as well as the distance from IMP-8 to the bow shock. The pitch angle distributions are narrow at ISEE-3 and wide and often pancake-shaped at IMP-8 with a peak near 90 degrees. This implies the existence of a weak scattering region about 5-15 earth radii upstream of the earth's bow shock.
Sanderson, T. R.; Reinhard, R.; Wenzel, K.-P.; Mitchell, D. G.; Roelof, E. C.
Evidence that UGA is read as a tryptophan codon rather than as a stop codon by Mycoplasma pneumoniae, Mycoplasma genitalium, and Mycoplasma gallisepticum.
Molecular cloning and sequencing showed that Mycoplasma gallisepticum, like Mycoplasma capricolum, contains both tRNA(UCA) and tRNA(CCA) genes, while Mycoplasma pneumoniae and Mycoplasma genitalium each appear to have only a tRNA(UCA) gene. Therefore, these mycoplasma species contain a tRNA with the anticodon UCA that can translate both UGA and UGG codons. PMID:2104612
Inamine, J M; Ho, K C; Loechel, S; Hu, P C
[Comparative studies on codon usage bias of Ganoderma lucidum based on analysis of genomic and transcriptomic data].
Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain. PMID:25518336
Zhu, Xiao-Xuan; Zhu, Ying-Jie; Song, Jing-Yuan; Sun, Chao; Chen, Shi-Lin
Identification of eRF1 residues that play critical and complementary roles in stop codon recognition
The initiation and elongation stages of translation are directed by codon–anticodon interactions. In contrast, a release factor protein mediates stop codon recognition prior to polypeptide chain release. Previous studies have identified specific regions of eukaryotic release factor one (eRF1) that are important for decoding each stop codon. The cavity model for eukaryotic stop codon recognition suggests that three binding pockets/cavities located on the surface of eRF1's domain one are key elements in stop codon recognition. Thus, the model predicts that amino acid changes in or near these cavities should influence termination in a stop codon-dependent manner. Previous studies have suggested that the TASNIKS and YCF motifs within eRF1 domain one play important roles in stop codon recognition. These motifs are highly conserved in standard code organisms that use UAA, UAG, and UGA as stop codons, but are more divergent in variant code organisms that have reassigned a subset of stop codons to sense codons. In the current study, we separately introduced TASNIKS and YCF motifs from six variant code organisms into eRF1 of Saccharomyces cerevisiae to determine their effect on stop codon recognition in vivo. We also examined the consequences of additional changes at residues located between the TASNIKS and YCF motifs. Overall, our results indicate that changes near cavities two and three frequently mediated significant effects on stop codon selectivity. In particular, changes in the YCF motif, rather than the TASNIKS motif, correlated most consistently with variant code stop codon selectivity. PMID:22543865
Conard, Sara E.; Buckley, Jessica; Dang, Mai; Bedwell, Gregory J.; Carter, Richard L.; Khass, Mohamed; Bedwell, David M.
How to use Big Data technologies to optimize operations in Upstream Petroleum Industry
How to use Big Data technologies to optimize operations in Upstream Petroleum Industry Abdelkader generated by the Petroleum Industry and particularly its upstream segment? Upstream is no stranger to Big the desired outcomes? Keywords Big Data; Analytics; Upstream Petroleum Industry; Knowledge Management; KM
Paris-Sud XI, Université de
When to Start Antiretroviral Therapy
... circumstances. What factors influence the decision to start ART? The following factors influence the decision to start ... an important factor in deciding when to start ART? A CD4 count measures the number of CD4 ...
A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae
Background Heterologous gene expression is an important tool for synthetic biology that enables metabolic engineering and the production of non-natural biologics in a variety of host organisms. The translational efficiency of heterologous genes can often be improved by optimizing synonymous codon usage to better match the host organism. However, traditional approaches for optimization neglect to take into account many factors known to influence synonymous codon distributions. Results Here we define an alternative approach for codon optimization that utilizes systems level information and codon context for the condition under which heterologous genes are being expressed. Furthermore, we utilize a probabilistic algorithm to generate multiple variants of a given gene. We demonstrate improved translational efficiency using this condition-specific codon optimization approach with two heterologous genes, the fluorescent protein-encoding eGFP and the catechol 1,2-dioxygenase gene CatA, expressed in S. cerevisiae. For the latter case, optimization for stationary phase production resulted in nearly 2.9-fold improvements over commercial gene optimization algorithms. Conclusions Codon optimization is now often a standard tool for protein expression, and while a variety of tools and approaches have been developed, they do not guarantee improved performance for all hosts of applications. Here, we suggest an alternative method for condition-specific codon optimization and demonstrate its utility in Saccharomyces cerevisiae as a proof of concept. However, this technique should be applicable to any organism for which gene expression data can be generated and is thus of potential interest for a variety of applications in metabolic and cellular engineering. PMID:24636000
Synonymous Codon Usage Affects the Expression of Wild Type and F508del CFTR.
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel composed of 1480 amino acids. The major mutation responsible for cystic fibrosis results in loss of amino acid residue, F508 (F508del). Loss of F508 in CFTR alters the folding pathway resulting in endoplasmic-reticulum-associated degradation. This study investigates the role of synonymous codon in the expression of CFTR and CFTR F508del in human HEK293 cells. DNA encoding the open reading frame (ORF) for CFTR containing synonymous codon replacements was expressed using a heterologous vector integrated into the genome. The results indicate that the codon usage greatly affects the expression of CFTR. While the promoter strength driving expression of the ORFs was largely unchanged and the mRNA half-lives were unchanged, the steady-state levels of the mRNA varied by as much as 30-fold. Experiments support that this apparent inconsistency is attributed to nonsense mediated decay independent of exon junction complex. The ratio of CFTR/mRNA indicates that mRNA containing native codons was more efficient in expressing mature CFTR as compared to mRNA containing synonymous high-expression codons. However, when F508del CFTR was expressed after codon optimization, a greater percentage of the protein escaped endoplasmic-reticulum-associated degradation resulting in considerable levels of mature F508del CFTR on the plasma membrane, which showed channel activity. These results indicate that codon usage has an effect on mRNA levels and protein expression, for CFTR, and likely on chaperone-assisted folding pathway, for F508del CFTR. PMID:25676312
Shah, Kalpit; Cheng, Yi; Hahn, Brian; Bridges, Robert; Bradbury, Neil A; Mueller, David M
Upstream particle events close to the bow shock and 200 earth radii upstream - ISEE-1 and ISEE-3 observations
NASA Technical Reports Server (NTRS)
Two energetic particle events (28 keV - 145 keV) upstream of the earth's bow shock have been investigated with two identical experiments of the Max-Planck-Institut/University of Maryland on ISEE-1 and ISEE-3. Close to the bow shock the particle distribution is more or less isotropic and indicates strong scattering of these particles in the upstream wave field. At ISEE-3 the particles move essentially scatter-free from the general bow shock direction. The temporal evolution of the particle bursts is discussed in terms of the interplanetary magnetic field topology and the scattering conditions.
Scholer, M.; Hovestadt, D.; Klecker, B.; Ipavich, F. M.; Gloeckler, G.
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
72. VIEW OF UPSTREAM SIDE OF THE MAIN LOCK MITER GATE IN A CLOSED POSITION, SHOWING THE FIT OF CONTACT BLOCKS Photograph No. 50-398. November 28, 1950 - Upper Mississippi River 9-Foot Channel Project, Lock & Dam 27, Granite City, Madison County, IL
View of upstream face of the forebay dam of Grand ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
View of upstream face of the forebay dam of Grand Coulee Dam, looking west. Construction of the forebay dam, which replaced the eastern end of the original Grand Coulee Dam, was completed in 1974. - Columbia Basin Project, Grand Coulee Dam & Franklin D. Roosevelt Lake, Across Columbia River, Southeast of Town of Grand Coulee, Grand Coulee, Grant County, WA
Organized retailing in India: upstream channel structure and management
Purpose – This paper's aim is to identify structural and relational factors influencing the upstream channel management of organized retailers in India. Design\\/methodology\\/approach – In-depth interviews were conducted with 15 organized retailers and two manufacturers in India. Data were analyzed using the thematic network analysis technique from qualitative research. The authors use the framework of institutional theory to guide the
Chitra Srivastava Dabas; Brenda Sternquist; Humaira Mahi
63. Upstream face of Waddell Dam as viewed from the ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
63. Upstream face of Waddell Dam as viewed from the west abutment. Crane at center is used to service the penstock intake. Photographer Mark Durben. Source: Salt River Project. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ
43. View of log boom (upstream) protecting fish screens at ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
43. View of log boom (upstream) protecting fish screens at Dingle Basin, looking southwest from north side of basin. Photo by Brian C. Morris, PUget Power, 1989. - Puget Sound Power & Light Company, White River Hydroelectric Project, 600 North River Avenue, Dieringer, Pierce County, WA
45. View of upstream face of fish screens at Dingle ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
45. View of upstream face of fish screens at Dingle Basin, looking northwest from south side of basin. Photo by Brian C. Morris, Puget Power, 1989. - Puget Sound Power & Light Company, White River Hydroelectric Project, 600 North River Avenue, Dieringer, Pierce County, WA
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
10. VIEW UPSTREAM OF PIPELINE SECTION AT JUNCTION OF HUME CEMENT PIPE AND CAST-IRON (460'). NOTE CYLINDRICAL COLLAR OF CEMENT SECTIONS AND BELL JUNCTIONS OF IRON PIPE. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
PHOTO OF THE BOAT HOUSE, GATE HOUSE, UPSTREAM SIDE OF SPILLWAYS LOOKING EAST; WATER INTAKE AND LOG BOOMS ARE SEEN ON RESERVOIR. PHOTO BY JET LOWE, HAER, 1995. - Elwha River Hydroelectric System, Glines Hydroelectric Dam & Plant, Port Angeles, Clallam County, WA
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
9. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: REINFORCEMENT DETAILS OF VALVE CONTROL STRUCTURE. Sheet A-20, July, 1939. File no. SA 342/29. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters
Studies have shown that the bulk of eukaryotic genomes is transcribed. Transcriptome maps are frequently updated, but low-abundant transcripts have probably gone unnoticed. To eliminate RNA degradation, we depleted the exonucleolytic RNA exosome from human cells and then subjected the RNA to tiling microarray analysis. This revealed a class of short, polyadenylated and highly unstable RNAs. These promoter upstream transcripts
Pascal Preker; Jesper Nielsen; Susanne Kammler; Sřren Lykke-Andersen; Marianne S. Christensen; Christophe K. Mapendano; Mikkel H. Schierup; Torben Heick Jensen
12. Upstream view showing thelower log pond log chute in ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
12. Upstream view showing thelower log pond log chute in the main channel of the Hudson River. The log chute in the dam can be seen in the background. Facing southwest. - Glens Falls Dam, 100' to 450' West of U.S. Route 9 Bridge Spanning Hudson River, Glens Falls, Warren County, NY
10. View to west from Jacob Meyer Park, showing upstream ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
10. View to west from Jacob Meyer Park, showing upstream (east) side of truss span. Bend is visible in lower portion of damaged vertical compression member third from right. - Stanislaus River Bridge, Atchison, Topeka & Santa Fe Railway at Stanislaus River, Riverbank, Stanislaus County, CA
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
23. VIEW LOOKING UPSTREAM AND TOWARD LEFT ABUTMENT OF DAM. NOTE FORMS FOR LEFT GRAVITY ABUTMENT AT UPPER RIGHT CORNER OF PICTURE. ARCHES 3, 4, 5, AND 7 COMPLETED TO ELEVATION 1795. 5 OR 7.5 FEET BELOW TOP OF PARAPET WALL. November 29, 1938 - Bartlett Dam, Verde River, Phoenix, Maricopa County, AZ
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
25. UPSTREAM VIEW OF LOWER END OF OUTLET STRUCTURE SHOWING FORMS IN PLACE FOR GRAVITY WALL SECTIONS.... Volume XVI, No. 16, August 16, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
18. WAIKOLU STREAM CROSSING NO. 2, VIEW UPSTREAM. IRON PIPE RUNS WITHIN CONCRETE AND RUBBLE STRUCTURE AND CONTINUES BURIED UNTIL REACHING PIERS UNDER THE PALL. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
3. FORMER INTAKE DAM NO. 2, VIEW LOOKING UPSTREAM AT LEFT IS RUBBLE MASONRY COVERING INTERSECTION OF THE TWO IRON PIPES FROM NEW DAM ENTERING OLD INTAKE OPENING AT RIGHT IS BOX FLUME LEADING TO AERATOR. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
4. AERATOR AT 525, CONSTRUCTED 1937-1938, VIEW FROM UPSTREAM (TRASH SCREEN REMOVED FOR CLARITY), WATER FROM INTAKE FLOWS THROUGH FLUME, THEN DAMS, AND SPILLS OVER STEPS TO MIX WITH OXYGEN, THUS REDUCING ACIDITY LEVELS. ACID INDUCES FASTER CORROSION OF PIPES AND SPOILS TASTE. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI
9. Detail, typical bearing, upstream side of west end of ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
9. Detail, typical bearing, upstream side of west end of Bridge Number 301.85, view to east, 210mm lens with electronic flash fill. - Southern Pacific Railroad Shasta Route, Bridge No. 301.85, Milepost 301.85, Pollard Flat, Shasta County, CA
18. View to southwest. Detail, bearing shoe, upstream side of ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
18. View to southwest. Detail, bearing shoe, upstream side of east pier. Copy negative made from 35mm color transparency made with with 135mm lens by John Snyder, due to lack of sufficiently long lens for 4x5 camera. - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA
13. Detail, upper chord connection point on upstream side of ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
13. Detail, upper chord connection point on upstream side of truss, showing connection of upper chord, laced vertical compression member, knee-braced strut, counters, and laterals. - Red Bank Creek Bridge, Spanning Red Bank Creek at Rawson Road, Red Bluff, Tehama County, CA
Laser Doppler velocity measurements of swirling flows with upstream influence
NASA Technical Reports Server (NTRS)
Swirling flow in a rotating tube is studied by flow visualization at a moderate Reynolds number, and its velocity field is measured by laser-Doppler anemometry. The tube has constant diameter, and approximately uniform initial rigid rotation of the flow is assured by passing the flow through a rotating plug of porous metal before it enters the test section. At moderate swirl values, an object mounted on the tube centerline causes a closed bubble to form upstream of the obstacle, with a clearly defined stagnation point on the axis, and recirculating flow inside the bubble. The bubble length grows upstream as the swirl is increased, until it breaks up into a Taylor column reaching all the way upstream and downstream at swirl values above a certain critical value. A vortex jump (in the sense of Benjamin) occurs downstream of the obstacle except when the Taylor column is present. Using a laser-Doppler anemometer, axial and swirl velocity profiles are obtained at several stations upstream and downstream of the bubble, and in and around the bubble.
Rloff, K. L.; Bossel, H. H.
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
32. AERIAL VIEW OF TIETON DAM, UPSTREAM FACE OF DAM (Trashrack-structure for outlet at lower left in reservoir, spillway at upper left. Reservoir nearly empty due to drought.) - Tieton Dam, South & East of State Highway 12, Naches, Yakima County, WA
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
2. UPSTREAM SIDE OF DAM AND BRIDGE WITH ABANDONED SAN TAN FLOOD-WATER HEADGATE IN FOREGROUND. TAKEN FROM NORTH END OF DAM - San Carlos Irrigation Project, Sacaton Dam & Bridge, Gila River, T4S R6E S12/13, Coolidge, Pinal County, AZ
Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters
Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters Alexander Bolshoy1 of the distribution of predicted intrinsic curvature along all available complete prokaryotic genomes, the genomes were divided into two groups. Curvature distribution in all prokaryotes of the first group indicated
Bolshoy, Alexander
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
25. TWIN FALLS MAIN CANAL HEADWORKS FROM UPSTREAM LOOKING TOWARD THE WEST (DAM-TENDER RICHARD CARL ADJUSTING THE GATES TO ALLOW 3400 CFS THROUGH). - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID
Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates
NASA Astrophysics Data System (ADS)
It has been observed for several proteins that slowing down the rate at which individual codons are translated can increase their probability of cotranslational protein folding, while speeding up codon translation can decrease it. Here we investigate whether or not this inverse relationship between translation speed and the cotranslational folding probability is a general phenomenon or if other scenarios are possible. We first derive chemical kinetic equations that relate individual codon translation rates to the probability that a domain will fold, populate an intermediate or misfold, and examine the cotranslational folding scenarios that are possible within these models. We find that speeding up codon translation through misfolding-prone segments can, in some cases, increase the folding probability of a domain immediately before the nascent protein is released from the ribosome and decrease its chances of misfolding. Thus, for some proteins fast-translating codons could be as important as slow-translating codons in coordinating cotranslational protein folding.
O'Brien, Edward P.; Vendruscolo, Michele; Dobson, Christopher M.
A Start-up company to start your career
is not a `for-profit' business · But still must recoup costs · Harvard typically takes ~8% in equity · CompanyA Start-up company to start your career Professional Development Seminar March 6, 2013 #12;What is a start-up company? · Small, just started · Typically 1-5 years old · Often no products, no sales
Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection
. We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly\\u000a biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among\\u000a genes. At one end genes
Héctor Musto; Héctor Romero; Alejandro Zavala; Kamel Jabbari; Giorgio Bernardi
Nuclear factors specifically bind to upstream sequences of a Xenopus laevis ribosomal protein gene promoter.
The upstream region of the Xenopus laevis L14 ribosomal protein gene was deleted starting from the 5' extremity in order to define the promoter length necessary to express a linked reporter CAT gene. The functional analysis indicated that a sequence located between -63 and -49 from the capsite is important for an efficient promoter activity. Band shift and ExoIII protection assays evidenced the binding to this region of a factor, called XrpFI, present in the crude nuclear extract from X.laevis oocytes. Methylation interference analysis localized the contacts in the G residues belonging to a short box, 5' CTTCC 3', positioned between -53 and -49 from the capsite. An additional factor, XrpFII, makes contacts with the sequence 5'GCCTGTTCGCC 3' located between -27 and -17 from the capsite. The deletion mutant still containing this sequence is poorly transcribed, but resumes activity when a short fragment containing the binding site for factor XrpFI is cloned in an upstream position. Images PMID:2682523
Carnevali, F; La Porta, C; Ilardi, V; Beccari, E
Mean velocities and Reynolds stresses upstream of a simulated wing-fuselage juncture
NASA Technical Reports Server (NTRS)
Values of three mean velocity components and six turbulence stresses measured in a turbulent shear layer upstream of a simulated wing-fuselage juncture and immediately downstream of the start of the juncture are presented nd discussed. Two single-sensor hot-wire probes were used in the measurements. The separated region just upstream of the wing contains an area of reversed flow near the fuselage surface where the turbulence level is high. Outside of this area the flow skews as it passes around the body, and in this skewed region the magnitude and distribution of the turbulent normal and shear stresses within the shear layer are modified slightly by the skewing and deceleration of the flow. A short distance downstream of the wing leading edge the secondary flow vortext is tightly rolled up and redistributes both mean flow and turbulence in the juncture. The data acquisition technique employed here allows a hot wire to be used in a reversed flow region to indicate flow direction.
Mcmahon, H.; Hubbartt, J.; Kubendran, L. R.
A synonymous codon variant in two patients with autosomal recessive bestrophinopathy alters in vitro splicing of BEST1
Purpose Autosomal recessive bestrophinopathy (ARB) is a newly defined retinal dystrophy caused by biallelic mutations in bestrophin-1 (BEST1) and is hypothesized to represent the null bestrophin-1 phenotype in humans. The aim was to determine whether a synonymous BEST1 variant, c.102C>T, identified in two unrelated ARB patients, alters pre-mRNA splicing of the gene. Additionally a detailed phenotypic characterization of this distinctive condition is presented for both patients. Methods BEST1 was analyzed by direct sequencing. Patients underwent standard ophthalmic assessment. In silico and in vitro analysis using a minigene system was performed to assess whether a synonymous variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing of BEST1. Results Both ARB patients harbored either proven (patient 1; c.102C>T p.Gly34Gly and c.572T>C p.Leu191Pro) or presumed (patient 2; c.102C>T p.Gly34Gly and c.1470_1471delCA, p.His490GlnfsX24) biallelic mutations in BEST1 and were found to have phenotypes consistent with ARB. In vitro analysis of the synonymous variant, c.102C>T p.Gly34Gly, demonstrated it to introduce a cryptic splice donor site 52 nucleotides upstream of the actual splice donor site. Conclusions The novel BEST1 variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing in vitro and is potentially pathogenic. In vivo this splicing variant is predicted to lead to the production of an mRNA transcript with a premature termination codon (p.Glu35TrpfsX11) that is predicted to be degraded by NMD. PMID:21203346
Davidson, Alice E.; Sergouniotis, Panagiotis I.; Burgess-Mullan, Rosemary; Hart-Holden, Nichola; Low, Sancy; Foster, Paul J.; Manson, Forbes D.C.; Black, Graeme C.M.
Comparative study of codon substitution patterns in foot-and-mouth disease virus (serotype O)
We compared genetic variations in the VP1 gene of foot-and-mouth disease viruses (FMDVs) isolated since 2000 from various region of the world. We analyzed relative synonymous codon usage (RSCU) and phylogenetic relationship between geographical regions, and calculated the genetic substitution patterns between Korean isolate and those from other countries. We calculated the ratios of synonymously substituted codons (SSC) to all observed substitutions and developed a new analytical parameter, EMC (the ratio of exact matching codons within each synonymous substitution group) to investigate more detailed substitution patterns within each synonymous codon group. We observed that FMDVs showed distinct RSCU patterns according to phylogenetic relationships in the same serotype (serotype O). Moreover, while the SSC and EMC values of FMDVs decreased according to phylogenetic distance, G + C composition at the third codon position was strictly conserved. Although there was little variation among the SSC values of 18 amino acids, more dynamic differences were observed in EMC values. The EMC values of 4- and 6-fold degenerate amino acids showed significantly lower values while most 2-fold degenerate amino acids showed no significant difference. Our findings suggest that different EMC patterns among the 18 amino acids might be an important factor in determining the direction of evolution in FMDV. PMID:21825834
Ahn, Insung; Bae, Se-Eun
The effect of tRNA levels on decoding times of mRNA codons
The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (?0.38 to ?0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. PMID:25056313
Dana, Alexandra; Tuller, Tamir
Infrequent point mutations in codons 12 and 61 of ras oncogenes in human hepatocellular carcinomas.
DNA from human hepatocellular carcinomas (HCC) were analysed for the presence of mutations in codons 12 and 61 of the K-ras, H-ras and N-ras genes. The relevant ras sequences were amplified in vitro using the polymerase chain reaction and point mutations detected by selective hybridisation using mutation-specific synthetic oligonucleotides. In one of the 19 HCCs a mutation in codon 61 of the K-ras gene was detected, whilst in 3/19 HCCs a mutation was found in codon 61 of the N-ras gene. The mutations were all heterozygous A-T transversions and were found in HCCs arising in patients with underlying cirrhosis. In two of these patients where the corresponding normal tissue was available only the wild-type ras gene was detected, indicating that oncogenic activation of the ras gene was a consequence of somatic mutation. In another patient the same mutation in codon 61 of the N-ras gene was found in cirrhotic liver tissue and in all four patients the same mutation was also detected in formalin-fixed, paraffin-embedded liver biopsy HCC tissue obtained at diagnosis. These results indicate that mutational activation of the ras genes at codon 61 is an infrequent but possibly early event in the development of HCC in Britain. PMID:1323601
Challen, C; Guo, K; Collier, J D; Cavanagh, D; Bassendine, M F
p53 codon 72 polymorphism and breast cancer risk: A meta-analysis
p53 is a tumor suppressor gene and plays important roles in the etiology of breast cancer. Studies have produced conflicting results concerning the role of p53 codon 72 polymorphism (G>C) on the risk of breast cancer; therefore, a meta-analysis was performed to estimate the association between the p53 codon 72 polymorphism and breast cancer. Screening of the PubMed database was conducted to identify relevant studies. Studies containing available genotype frequencies of the p53 codon 72 polymorphism were selected and a pooled odds ratio (OR) with 95% confidence interval (CI) was used to assess the association. Sixty-one published studies, including 28,539 breast cancer patients and 32,788 controls were identified. The results suggest that variant genotypes are not associated with breast cancer risk (Pro/Pro + Arg/Pro vs. Arg/Arg: OR=1.016, 95% CI=0.931–1.11, P=0.722). The symmetric funnel plot, Egger's test (P=0.506) and Begg's test (P=0.921) were all suggestive of the lack of publication bias. This meta-analysis suggests that the p53 codon 72 Pro/Pro + Arg/Pro genotypes are not associated with an increased risk of breast cancer. To validate the association between the p53 codon 72 polymorphism and breast cancer, further studies with larger numbers of participants worldwide are required. PMID:23737888
NSDL National Science Digital Library
It would seem that more and more people are interested in developing their own business, and a number of websites are dedicated to helping these persons achieve that goal. One valuable website in that realm is StartUpNation. Created by Jeff and Rich Sloan, the site contains a well-designed homepage that includes links to sections dedicated to areas of interest to the prospective entrepreneur, including those that deal with customer service and creating strategic marketing plans. A good place to start is the â??Lean from the Expertsâ?ť area, located on the left-hand side of the homepage. Here, visitors can learn from successful individuals, such as Glenn Coggeshell of Black Dot Coffee. Along the same side, visitors can also read about how to choose a business for themselves and also how to plan to make this business a reality. In keeping with the times, the site also affords users the opportunity to sign up for RSS feeds and the ability to listen (and download) a number of podcasts.
Missouri: Early Head Start Initiative
ERIC Educational Resources Information Center
Missouri's Early Head Start/Child Care Partnership Project expands access to Early Head Start (EHS) services for children birth to age 3 by developing partnerships between federal Head Start, EHS contractors, and child care providers. Head Start and EHS contractors that participate in the initiative provide services through community child care…
Center for Law and Social Policy, Inc. (CLASP), 2012
Minnesota: Early Head Start Initiatiive
ERIC Educational Resources Information Center
Minnesota provides supplemental state funding to existing federal Head Start and Early Head Start (EHS) grantees to increase their capacity to serve additional infants, toddlers, and pregnant women. The initiative was started in 1997 when the state legislature earmarked $1 million of the general state Head Start supplemental funds for children…
Center for Law and Social Policy, Inc. (CLASP), 2012
Torque fluctuations caused by upstream mean flow and turbulence
NASA Astrophysics Data System (ADS)
A series of studies are in progress investigating the effects of turbine-array-wake interactions for a range of atmospheric boundary layer states by means of the EnFlo meteorological wind tunnel. The small, three-blade model wind turbines drive 4-quadrant motor-generators. Only a single turbine in neutral flow is considered here. The motor-generator current can be measured with adequate sensitivity by means of a current sensor allowing the mean and fluctuating torque to be inferred. Spectra of torque fluctuations and streamwise velocity fluctuations ahead of the rotor, between 0.1 and 2 diameters, show that only the large-scale turbulent motions contribute significantly to the torque fluctuations. Time-lagged cross-correlation between upstream velocity and torque fluctuations are largest over the inner part of the blade. They also show the turbulence to be frozen in behaviour over the 2 diameters upstream of the turbine.
Farr, T. D.; Hancock, P. E.
Vaccine production: upstream processing with adherent or suspension cell lines.
The production of viral vaccines in cell culture can be accomplished with primary, diploid, or continuous (transformed) cell lines. Each cell line, each virus type, and each vaccine preparation require the specific design of upstream and downstream processing. Media have to be selected as well as production vessels, cultivation conditions, and modes of operation. Many viruses only replicate to high titers in adherently growing cells, but similar to processes established for recombinant protein production, an increasing number of suspension cell lines is being evaluated for future use. Here, we describe key issues to be considered for the establishment of large-scale virus production in bioreactors. As an example upstream processing of cell culture-derived influenza virus production is described in more detail for adherently growing and for suspension cells. In particular, use of serum-containing, serum-free, and chemically defined media as well as choice of cultivation vessel are considered. PMID:24297427
Genzel, Yvonne; Rödig, Jana; Rapp, Erdmann; Reichl, Udo
Effect of sequence context at stop codons on efficiency of reinitiation in GCN4 translational control.
Translational control of the GCN4 gene involves two short open reading frames in the mRNA leader (uORF1 and uORF4) that differ greatly in the ability to allow reinitiation at GCN4 following their own translation. The low efficiency of reinitiation characteristic of uORF4 can be reconstituted in a hybrid element in which the last codon of uORF1 and 10 nucleotides 3' to its stop codon (the termination region) are substituted with the corresponding nucleotides from uORF4. To define the features of these 13 nucleotides that determine their effects on reinitiation, we separately randomized the sequence of the third codon and termination region of the uORF1-uORF4 hybrid and selected mutant alleles with the high-level reinitiation that is characteristic of uORF1. The results indicate that many different A+U-rich triplets present at the third codon of uORF1 can overcome the inhibitory effect of the termination region derived from uORF4 on the efficiency of reinitiation at GCN4. Efficient reinitiation is not associated with codons specifying a particular amino acid or isoacceptor tRNA. Similarly, we found that a diverse collection of A+U-rich sequences present in the termination region of uORF1 could restore efficient reinitiation at GCN4 in the presence of the third codon derived from uORF4. To explain these results, we propose that reinitiation can be impaired by stable base pairing between nucleotides flanking the uORF1 stop codon and either the tRNA which pairs with the third codon, the rRNA, or sequences located elsewhere in GCN4 mRNA. We suggest that these interactions delay the resumption of scanning following peptide chain termination at the uORF and thereby lead to ribosome dissociation from the mRNA. Images PMID:8264629
Grant, C M; Hinnebusch, A G
Start Smart: Steps to Starting a Business Workshop Registration The Start Smart workshop will cover
. ----------------------------------------------------------------------------------------------------------------------------------------------- START SMART REGISTRATION Name Daytime phone Address E-mail address City State Zip Optional: NameStart Smart: Steps to Starting a Business Workshop Registration The Start Smart workshop will cover and mail it with your check* or credit card information to: WSU Tri-Cities Business LINKS 2710 Crimson Way
Collins, Gary S.
12. Detail, lower chord connection point on upstream side of ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
12. Detail, lower chord connection point on upstream side of truss, showing pinned connection of lower chord eye bars, laced vertical compression member, diagonal eye bar tension members, turnbuckled diagonal counters, and floor beam. Note also timber floor stringers supported by floor beam, and exposed ends of timber deck members visible at left above lower chord eye bar. View to northwest. - Red Bank Creek Bridge, Spanning Red Bank Creek at Rawson Road, Red Bluff, Tehama County, CA
Steepened channels upstream of knickpoints: Controls on relict landscape response
NASA Astrophysics Data System (ADS)
The morphology of a relict landscape provides important insight into erosion rates and processes prior to base level fall. Fluvial knickpoints are commonly thought to form a leak-proof moving boundary between a rejuvenated landscape below and a relict landscape above. We argue that fluvial rejuvenation may leak farther upstream, depending on the rate and style of knickpoint migration. The outer margin of a relict landscape should therefore be used with caution in tectonic geomorphology studies, as channel steepening upstream of knickpoints could reduce the relict area. We explore the response of the Roan Plateau to knickpoint retreat triggered by late Cenozoic upper Colorado River incision. Multiple knickpoints (100-m waterfalls) separate a low-relief, upper landscape from incised canyons below. Two digital elevation model data sets (10-m U.S. Geological Survey and 1-m Airborne Laser Swath Mapping) indicate steeper channels above waterfalls relative to concave channels farther upstream. The steepened reaches are several kilometers long, correspond to doubling of slope, and exhibit channel narrowing and an increase in hillslope angle. We compare two mechanisms for generating steepened reaches. The first uses a recent model for erosion amplification due to flow acceleration at the waterfall lip. The second acknowledges that waterfall lips may be limited to the outcrop of a resistant formation. Subtle structural warping of the stratigraphy can lead to lowering of the waterfall lip as it retreats, thus lowering base level for upstream channels. Results of numerical modeling experiments suggest the latter mechanism is more consistent with our observations of long, mildly steepened reaches.
Berlin, Maureen M.; Anderson, Robert S.
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
8. SEDIMENTATION CHAMBER, VIEW UPSTREAM (PLANK COVER REMOVED FOR CLARITY). BOX FLUME DROPS SLIGHTLY INTO CHAMBER ON LEFT SIDE. CHAMBER IS A SERIES OF BAFFLES DESIGNED TO SLOW THE FLOW OF WATER. FLOW IS REDUCED TO ALLOW PARTICULATES TO SETTLE TO THE BOTTOM. TWO SCREENS (NOT SHOWN) FILTER LARGER DEBRIS. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI
Cooperative MIMO for alien noise cancellation in upstream VDSL
We present cooperative MIMO for alien noise cancellation (CoMAC): a per-tone, blind, low-complexity, linear, and adaptive noise whitening algorithm for alien crosstalk mitigation in upstream vectored VDSL systems. CoMAC directly acts on the residual errors of the vectored users after self-FEXT cancellation and frequency domain equalization, and thus, leverages the inherent alien-crosstalk-induced spatial correlation across users. CoMAC employs a low-complexity
Pravesh Biyani; Amitkumar Mahadevan; Patrick Duvaut; Shailendra Singh
Retail Zone Pricing and Simulated Price Effects of Upstream Mergers
Despite the oft?recognized reality of zone pricing by food retailers, this form of price discrimination has received very little attention within the context of upstream merger analysis. Promoting this issue to 'center stage', we relax the conventional merger simulation assumption of uniform pass?through by retailers. Relaxing this assumption allows us to explore the potential impacts of zone pricing on post?merger
Geoffrey M. Pofahl; ORAL CAPPS JR.; H. Alan Love
Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion
One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function – a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering. PMID:24433543
Bohlke, Nina; Budisa, Nediljko
START Background Report START, September 2013 1 BACKGROUND REPORT
START Background Report © START, September 2013 1 BACKGROUND REPORT Al-Shabaab Attack on Westgate evening, Sept. 24. Media sources report that Somali militant organization al-Shabaab has claimed deaths as of Sept. 25. START has developed this background report highlighting attacks attributed to al-Shabaab
Hill, Wendell T.
From Head Start to Sure Start: Reflections on Policy Transfer
ERIC Educational Resources Information Center
This article uses the history of debates over the US Head Start programme (1965), Early Head Start (1994) and the UK Sure Start initiative (1998), as a window on to policy transfer. In all the three, the aim was that early intervention could offer a means of boosting children's educational attainment and of countering the wider effects of poverty…
Welshman, John
PCR-RFLP to Detect Codon 248 Mutation in Exon 7 of "p53" Tumor Suppressor Gene
ERIC Educational Resources Information Center
Individual genome DNA was extracted fast from oral swab and followed up with PCR specific for codon 248 of "p53" tumor suppressor gene. "Msp"I restriction mapping showed the G-C mutation in codon 248, which closely relates to cancer susceptibility. Students learn the concepts, detection techniques, and research significance of point mutations or…
Ouyang, Liming; Ge, Chongtao; Wu, Haizhen; Li, Suxia; Zhang, Huizhan
Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients
BACKGROUND: Polymorphisms of the human prion protein gene (PRNP) contribute to the genetic determinants of Creutzfeldt-Jakob disease (CJD). Numerous polymorphisms in the promoter regions as well as the open reading frame of PRNP were investigated. Greater than 90% of Korean, Chinese, and Japanese carry the homozygote 129 MM codon. In Korea, polymorphisms have not been comprehensively studied, except codons 129
Bo-Yeong Choi; Su Yeon Kim; So-Young Seo; Seong Soo A An; SangYun Kim; Sang-Eun Park; Seung-Han Lee; Yun-Ju Choi; Sang-Jin Kim; Chi-Kyeong Kim; Jun-Sun Park; Young-Ran Ju
NASA Astrophysics Data System (ADS)
The first half of the 1982 water year (October 1, 1981-March 31, 1982) saw streamflow conditions across the country get off to a generally wet start, with almost 90% of the key index gaging stations reporting normal to above normal flows, according to the U.S. Geological Survey, Department of the Interior.USGS hydrologists said that the overall wet water picture was reflected in the nation's Big Five rivers—Mississippi, Missouri, St. Lawrence, Ohio, and Columbia—which averaged above normal for 4 of the first 6 months of the new water year. The water year used by hydrologists runs from October 1 to September 1 of the following calendar year and is designed to roughly follow the growing season and to begin and end during a period of generally low streamflow. Hydrologists use the Big Five, which together drain more than half of the conterminous United States, as a quick check on the status of the nation's water resources. Combined flow of the Big Five averaged 787 billion gallons a day (bgd) during the first half of the 1982 water year, 14% above normal.
Meeting Report: Moving Upstream—Evaluating Adverse Upstream End Points for Improved Risk Assessment and Decision-Making
Background Assessing adverse effects from environmental chemical exposure is integral to public health policies. Toxicology assays identifying early biological changes from chemical exposure are increasing our ability to evaluate links between early biological disturbances and subsequent overt downstream effects. A workshop was held to consider how the resulting data inform consideration of an "adverse effect" in the context of hazard identification and risk assessment. Objectives Our objective here is to review what is known about the relationships between chemical exposure, early biological effects (upstream events), and later overt effects (downstream events) through three case studies (thyroid hormone disruption, antiandrogen effects, immune system disruption) and to consider how to evaluate hazard and risk when early biological effect data are available. Discussion Each case study presents data on the toxicity pathways linking early biological perturbations with downstream overt effects. Case studies also emphasize several factors that can influence risk of overt disease as a result from early biological perturbations, including background chemical exposures, underlying individual biological processes, and disease susceptibility. Certain effects resulting from exposure during periods of sensitivity may be irreversible. A chemical can act through multiple modes of action, resulting in similar or different overt effects. Conclusions For certain classes of early perturbations, sufficient information on the disease process is known, so hazard and quantitative risk assessment can proceed using information on upstream biological perturbations. Upstream data will support improved approaches for considering developmental stage, background exposures, disease status, and other factors important to assessing hazard and risk for the whole population. PMID:19057713
Woodruff, Tracey J.; Zeise, Lauren; Axelrad, Daniel A.; Guyton, Kathryn Z.; Janssen, Sarah; Miller, Mark; Miller, Gregory G.; Schwartz, Jackie M.; Alexeeff, George; Anderson, Henry; Birnbaum, Linda; Bois, Frederic; Cogliano, Vincent James; Crofton, Kevin; Euling, Susan Y.; Foster, Paul M.D.; Germolec, Dori R.; Gray, Earl; Hattis, Dale B.; Kyle, Amy D.; Luebke, Robert W.; Luster, Michael I.; Portier, Chris; Rice, Deborah C.; Solomon, Gina; Vandenberg, John; Zoeller, R. Thomas
... for Kids for Teens Teens Home Body Mind Sexual Health Food & Fitness Diseases & Conditions Infections Q&A School & ... Anger When Will I Start Developing? KidsHealth > Teens > Sexual Health > Your Changing Body > When Will I Start Developing? ...
HER2 Codon 655 Polymorphism and Risk of Breast Cancer in African Americans and Whites
Background. Several recent epidemiologic studies examined the association between breast cancer risk and an inherited, single-nucleotide polymorphism in the HER2 gene, codon 655 G to A, which leads to an amino acid substitution of Ile to Val. Results of previous studies have been mixed, with most studies showing no association but some suggesting an association in younger women or women
Robert Millikan; Allison Eaton; Kendra Worley; Lorna Biscocho; Elizabeth Hodgson; Wen-Yi Huang; Joseph Geradts; Mary Iacocca; David Cowan; Kathleen Conway; Lynn Dressler
Incorporating PCA and FCM into Organism Classification Based on Codon Usage
To recognize the DNA sequence and mine the hidden information to achieve the classification of organisms are viewed as a difficult work to biologists. As we known, the amino acids are the basic elements to construct DNA. Hence, if the codon usage of amino acids can be analyzed well, the useful information about classification of organisms may be obtained. However,
Kun-lin Hsieh; I-ching Yang; Cheng-chang Jeng; Chun-nan Lin
Role of PRNP codon 129 genotype in defining strain transmission properties of human transmissible spongiform encephalopathy
three codon 129 genotype mice are susceptible with a ranking of transmission efficiency of HuMM>HuMV>HuVV. HuMM mice develop the most widespread neuropathology with features similar to human vCJD. Subclinical infection was noted in each mouse line...
Bishop, Matthew T.
Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders Joshua T. Herbeck,1
Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders Joshua T. Herbeck,1 John: 10.1007/s00239-002-2437-7 Correspondence to: Joshua Herbeck, JBP Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA; email: firstname.lastname@example.com #12
Herbeck, Joshua
New LIC vectors for production of proteins from genes containing rare codons.
In the effort to produce proteins coded by diverse genomes, structural genomics projects often must express genes containing codons that are rare in the production strain. To address this problem, genes expressing tRNAs corresponding to those codons are typically coexpressed from a second plasmid in the host strain, or from genes incorporated into production plasmids. Here we describe the modification of a series of LIC pMCSG vectors currently used in the high-throughput (HTP) production of proteins to include crucial tRNA genes covering rare codons for Arg (AGG/AGA) and Ile (AUA). We also present variants of these new vectors that allow analysis of ligand binding or co-expression of multiple proteins introduced through two independent LIC steps. Additionally, to accommodate the cloning of multiple large proteins, the size of the plasmids was reduced by approximately one kilobase through the removal of non-essential DNA from the base vector. Production of proteins from core vectors of this series validated the desired enhanced capabilities: higher yields of proteins expressed from genes with rare codons occurred in most cases, biotinylated derivatives enabled detailed automated ligand binding analysis, and multiple proteins introduced by dual LIC cloning were expressed successfully and in near balanced stoichiometry, allowing tandem purification of interacting proteins. PMID:24057978
Eschenfeldt, William H; Makowska-Grzyska, Magdalena; Stols, Lucy; Donnelly, Mark I; Jedrzejczak, Robert; Joachimiak, Andrzej
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment. We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence. MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse. PMID:21949676
Ranwez, Vincent; Harispe, Sébastien; Delsuc, Frédéric; Douzery, Emmanuel J. P.
Effective population size does not predict codon usage bias in mammals
Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (Ne), with selection on CUB operating less efficiently in species with small Ne. Here, we specifically ask whether variation in Ne predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of Ne (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in Ne predicts variation in CUB. Second, across six mammalian species with genetic estimates of Ne (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), Ne and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in Ne does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between Ne and CUB. PMID:25505518
Kessler, Michael D; Dean, Matthew D
Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts
, and we propose a classification of phages with translationally biased hosts which is based on adaptation morphogenesis, host interaction and ssDNA binding are also affected by adaptive pressure. Adaptation affectsCodon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts Alessandra
Carbone, Alessandra
Oligonucleotide Design and Codon Optimization for PCR-based Gene Synthesis
by ligation or PCR; this thesis focuses on PCR-based methods. Many sets of oligonucleotides can be used protein-coding regions; because the genetic code is degenerate, a combinatorial number of di erent sequences can encode the same protein. If the primary concern is a protein sequence, codons can be changed
Williams, Brian C.
Is DNA Code Periodicity Only Due to CUF - Codons Usage Frequency?
The triplet code for proteins and functional RNA has been either from the universal pattern of ancient RNA (- HI) [1], with a key role of an uneven codon usage frequency (CUF) in the periodic patterns origination, or a reading frame monitoring device (RFMD -H2) [2- 4]. HI has lately been upheld [1] but in a single sequence sensitive way
Mariusz Zoltowski; Nicolaus Copernicus
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences
Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show
Iris Bahir; Menachem Fromer; Yosef Prat; Michal Linial
TGF-?1 codon 25 gene polymorphism is associated with cirrhosis in patients with hereditary hemochromatosis
Hereditary hemochromatosis (HHC) is an autosomal recessive disorder of iron metabolism with variable penetrance. Only a minority of C282Y homozygotes develop clinical overt disease and cirrhosis. The phenotypic heterogeneity of HHC may be due to host genetic factors influencing fibrogenesis such as cytokine gene polymorphisms. In this respect, we investigated the impact of functional genetic polymorphisms of TGF-?1 (codon 10
Christoph H. Österreicher; Christian Datz; Felix Stickel; Claus Hellerbrand; Melitta Penz; Harald Hofer; Fritz Wrba; Edward Penner; Detlef Schuppan; Peter Ferenci
Maryland Early Head Start Initiative
ERIC Educational Resources Information Center
Since 2000, Maryland has provided state supplemental funds to Head Start and Early Head Start (EHS) programs to improve access. Local EHS programs may use funds, through child care partnerships, to extend the EHS day or year. Maryland's approach to building on EHS includes: (1) Increase the capacity of existing Head Start and EHS programs to…
Center for Law and Social Policy, Inc. (CLASP), 2012
Influenza A Virus Attenuation by Codon Deoptimization of the NS Gene for Vaccine Development
ABSTRACT Influenza viral infection represents a serious public health problem that causes contagious respiratory disease, which is most effectively prevented through vaccination to reduce transmission and future infection. The nonstructural (NS) gene of influenza A virus encodes an mRNA transcript that is alternatively spliced to express two viral proteins, the nonstructural protein 1 (NS1) and the nuclear export protein (NEP). The importance of the NS gene of influenza A virus for viral replication and virulence has been well described and represents an attractive target to generate live attenuated influenza viruses with vaccine potential. Considering that most amino acids can be synthesized from several synonymous codons, this study employed the use of misrepresented mammalian codons (codon deoptimization) for the de novo synthesis of a viral NS RNA segment based on influenza A/Puerto Rico/8/1934 (H1N1) (PR8) virus. We generated three different recombinant influenza PR8 viruses containing codon-deoptimized synonymous mutations in coding regions comprising the entire NS gene or the mRNA corresponding to the individual viral protein NS1 or NEP, without modifying the respective splicing and packaging signals of the viral segment. The fitness of these synthetic viruses was attenuated in vivo, while they retained immunogenicity, conferring both homologous and heterologous protection against influenza A virus challenges. These results indicate that influenza viruses can be effectively attenuated by synonymous codon deoptimization of the NS gene and open the possibility of their use as a safe vaccine to prevent infections with these important human pathogens. IMPORTANCE Vaccination serves as the best therapeutic option to protect humans against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease cause by this important human respiratory pathogen. The nonstructural (NS) gene of influenza virus encodes both the multifunctional nonstructural protein 1 (NS1), essential for innate immune evasion, and the nuclear export protein (NEP), required for the nuclear export of viral ribonucleoproteins and for timing of the virus life cycle. Here, we have generated a recombinant influenza A/Puerto Rico/8/1934 (H1N1) (PR8) virus containing a codon-deoptimized NS segment that is attenuated in vivo yet retains immunogenicity and protection efficacy against homologous and heterologous influenza virus challenges. These results open the exciting possibility of using this NS codon deoptimization methodology alone or in combination with other approaches for the future development of vaccine candidates to prevent influenza viral infections. PMID:24965472
Nogales, Aitor; Baker, Steven F.; Ortiz-Riańo, Emilio; Dewhurst, Stephen; Topham, David J.
Genomic adaptation of the ISA virus to Salmo salar codon usage
Background The ISA virus (ISAV) is an Orthomyxovirus whose genome encodes for at least 10 proteins. Low protein identity and lack of genetic tools have hampered the study of the molecular mechanism behind its virulence. It has been shown that viral codon usage controls several processes such as translational efficiency, folding, tuning of protein expression, antigenicity and virulence. Despite this, the possible role that adaptation to host codon usage plays in virulence and viral evolution has not been studied in ISAV. Methods Intergenomic adaptation between viral and host genomes was calculated using the codon adaptation index score with EMBOSS software and the Kazusa database. Classification of host genes according to GeneOnthology was performed using Blast2go. A non parametric test was applied to determine the presence of significant correlations among CAI, mortality and time. Results Using the codon adaptation index (CAI) score, we found that the encoding genes for nucleoprotein, matrix protein M1 and antagonist of Interferon I signaling (NS1) are the ISAV genes that are more adapted to host codon usage, in agreement with their requirement for production of viral particles and inactivation of antiviral responses. Comparison to host genes showed that ISAV shares CAI values with less than 0.45% of Salmo salar genes. GeneOntology classification of host genes showed that ISAV genes share CAI values with genes from less than 3% of the host biological process, far from the 14% shown by Influenza A viruses and closer to the 5% shown by Influenza B and C. As well, we identified a positive correlation (p<0.05) between CAI values of a virus and the duration of the outbreak disease in given salmon farms, as well as a weak relationship between codon adaptation values of PB1 and the mortality rates of a set of ISA viruses. Conclusions Our analysis shows that ISAV is the least adapted viral Salmo salar pathogen and Orthomyxovirus family member less adapted to host codon usage, avoiding the general behavior of host genes. This is probably due to its recent emergence among farmed Salmon populations. PMID:23829271
Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum.
The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes are exceedingly A + T-rich, while those of the alpha gene are less so. All three genes have a relatively G + C-rich region 20 to 40 base-pairs in length, found approximately 200 base-pairs 5' to the messenger RNA start site. This G + C-rich region 5' to the beta and gamma genes is flanked by short inverted repeats. Within this region, there is an 11 base-pair exact homology between the alpha and gamma genes, and a less perfect homology between these genes and the beta gene. The homology is flanked at a short distance by interspersed G and T residues. The gamma gene is greater than 90% A + T for greater than 800 base-pairs upstream. Further upstream there is a G + C-rich region that is also found inverted approximately 3.5 X 10(3) base-pairs away. The gamma and beta genes are tandemly linked, and the entire approximately 500 base-pair intergene region between the 3' end of the gamma gene and the 5' end of the beta gene is A + T-rich (approximately 90%) with the exception of the homology region 5' to the gamma gene. We demonstrate also the presence of a discoidin I pseudogene fragment having only 139 base-pairs of discoidin homology with greater than 8% mismatch. It is flanked upstream by five 39 base-pair G + C-rich repeats, and downstream by sequences that are extremely A + T-rich. We discuss the possible significance of the conserved G + C-rich structures on discoidin I gene expression. PMID:6694210
Poole, S J; Firtel, R A
Identification of a novel first exon in the human dystrophin gene and of a new promoter located more than 500 kb upstream of the nearest known promoter
The dystrophin gene, which is muted in patients with Duchenne and Becker muscular dystrophies, is the largest known human gene. Five alternative promoters have been characterized until now. Here we show that a novel dystrophin isoform with a different first exon can be produced through transcription initiation at a previously-unidentified alternative promoter. The case study presented is that of patient with Duchenne muscular dystrophy who had a deletion extending from 5{prime} end of the dystrophin gene to exon 2, including all promoters previously mapped in the 5{prime} part of the gene. Transcripts from lymphoblastoid cells were found to contain sequences corresponding to exon 3, indicating the presence of new promoter upstream of this exon. The nucleotide sequence of amplified cDNA corresponding to the 5{prime} end of the new transcript indicated that the 5{prime} end of exon 3 was extended by 9 codons, only the last (most 3{prime}) of which codes for methionine. The genomic nucleotide sequence upstream from the new exon, as determined using inverse polymerase chain reaction, revealed the presence of sequences similar to a TATA box, an octamer motif and an MEF-2 element. The identified promoter/exon did not map to intron 2, as might have been expected, but to a position more than 500 kb upstream of the most 5{prime} of the previously-identified promoters, thereby adding 500 kb to the dystrophin gene. The sequence of part of the new promoter region is very similar to that of certain medium reiteration frequency repetitive sequences. These findings may help us understand the molecular evolution of the dystrophin gene.
Yanagawa, H.; Nishio, H.; Takeshima, Y. [Kobe Univ. School of Medicine (Japan)] [and others
Analysis of Serine Codon Conservation Reveals Diverse Phenotypic Constraints on Hepatitis C Virus Glycoprotein Evolution
Serine is encoded by two divergent codon types, UCN and AGY, which are not interchangeable by a single nucleotide substitution. Switching between codon types therefore occurs via intermediates (threonine or cysteine) or via simultaneous tandem substitutions. Hepatitis C virus (HCV) chronically infects 2 to 3% of the global population. The highly variable glycoproteins E1 and E2 decorate the surface of the viral envelope, facilitate cellular entry, and are targets for host immunity. Comparative sequence analysis of globally sampled E1E2 genes, coupled with phylogenetic analysis, reveals the signatures of multiple archaic codon-switching events at seven highly conserved serine residues. Limited detection of intermediate phenotypes indicates that associated fitness costs restrict their fixation in divergent HCV lineages. Mutational pathways underlying codon switching were probed via reverse genetics, assessing glycoprotein functionality using multiple in vitro systems. These data demonstrate selection against intermediate phenotypes can act at the structural/functional level, with some intermediates displaying impaired virion assembly and/or decreased capacity for target cell entry. These effects act in residue/isolate-specific manner. Selection against intermediates is also provided by humoral targeting, with some intermediates exhibiting increased epitope exposure and enhanced neutralization sensitivity, despite maintaining a capacity for target cell entry. Thus, purifying selection against intermediates limits their frequencies in globally sampled strains, with divergent functional constraints at the protein level restricting the fixation of deleterious mutations. Overall our study provides an experimental framework for identification of barriers limiting viral substitutional evolution and indicates that serine codon-switching represents a genomic "fossil record" of historical purifying selection against E1E2 intermediate phenotypes. PMID:24173227
Koutsoudakis, George; Urbanowicz, Richard A.; Mirza, Deeman; Ginkel, Corinne; Riebesehl, Nina; Calland, Noémie; Albecka, Anna; Price, Louisa; Hudson, Natalia; Descamps, Véronique; Backx, Matthijs; McClure, C. Patrick; Duverlie, Gilles; Pecheur, Eve-Isabelle; Dubuisson, Jean; Perez-del-Pulgar, Sofia; Forns, Xavier; Steinmann, Eike; Tarr, Alexander W.; Pietschmann, Thomas
Analysis of serine codon conservation reveals diverse phenotypic constraints on hepatitis C virus glycoprotein evolution.
Serine is encoded by two divergent codon types, UCN and AGY, which are not interchangeable by a single nucleotide substitution. Switching between codon types therefore occurs via intermediates (threonine or cysteine) or via simultaneous tandem substitutions. Hepatitis C virus (HCV) chronically infects 2 to 3% of the global population. The highly variable glycoproteins E1 and E2 decorate the surface of the viral envelope, facilitate cellular entry, and are targets for host immunity. Comparative sequence analysis of globally sampled E1E2 genes, coupled with phylogenetic analysis, reveals the signatures of multiple archaic codon-switching events at seven highly conserved serine residues. Limited detection of intermediate phenotypes indicates that associated fitness costs restrict their fixation in divergent HCV lineages. Mutational pathways underlying codon switching were probed via reverse genetics, assessing glycoprotein functionality using multiple in vitro systems. These data demonstrate selection against intermediate phenotypes can act at the structural/functional level, with some intermediates displaying impaired virion assembly and/or decreased capacity for target cell entry. These effects act in residue/isolate-specific manner. Selection against intermediates is also provided by humoral targeting, with some intermediates exhibiting increased epitope exposure and enhanced neutralization sensitivity, despite maintaining a capacity for target cell entry. Thus, purifying selection against intermediates limits their frequencies in globally sampled strains, with divergent functional constraints at the protein level restricting the fixation of deleterious mutations. Overall our study provides an experimental framework for identification of barriers limiting viral substitutional evolution and indicates that serine codon-switching represents a genomic "fossil record" of historical purifying selection against E1E2 intermediate phenotypes. PMID:24173227
Brown, Richard J P; Koutsoudakis, George; Urbanowicz, Richard A; Mirza, Deeman; Ginkel, Corinne; Riebesehl, Nina; Calland, Noémie; Albecka, Anna; Price, Louisa; Hudson, Natalia; Descamps, Véronique; Backx, Matthijs; McClure, C Patrick; Duverlie, Gilles; Pecheur, Eve-Isabelle; Dubuisson, Jean; Perez-del-Pulgar, Sofia; Forns, Xavier; Steinmann, Eike; Tarr, Alexander W; Pietschmann, Thomas; Ball, Jonathan K
Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study.
Phylogenomic analyses of ancient relationships are usually performed using amino acid data, but it is unclear whether amino acids or nucleotides should be preferred. With the 2-fold aim of addressing this problem and clarifying pancrustacean relationships, we explored the signals in the 62 protein-coding genes carefully assembled by Regier et al. in 2010. With reference to the pancrustaceans, this data set infers a highly supported nucleotide tree that is substantially different to the corresponding, but poorly supported, amino acid one. We show that the discrepancy between the nucleotide-based and the amino acids-based trees is caused by substitutions within synonymous codon families (especially those of serine-TCN and AGY). We show that different arthropod lineages are differentially biased in their usage of serine, arginine, and leucine synonymous codons, and that the serine bias is correlated with the topology derived from the nucleotides, but not the amino acids. We suggest that a parallel, partially compositionally driven, synonymous codon-usage bias affects the nucleotide topology. As substitutions between serine codon families can proceed through threonine or cysteine intermediates, amino acid data sets might also be affected by the serine codon-usage bias. We suggest that a Dayhoff recoding strategy would partially ameliorate the effects of such bias. Although amino acids provide an alternative hypothesis of pancrustacean relationships, neither the nucleotides nor the amino acids version of this data set seems to bring enough genuine phylogenetic information to robustly resolve the relationships within group, which should still be considered unresolved. PMID:22962005
Rota-Stabelli, Omar; Lartillot, Nicolas; Philippe, Hervé; Pisani, Davide
How to use Big Data technologies to optimize operations in Upstream Petroleum Industry
How to use Big Data technologies to optimize operations in Upstream Petroleum Industry Abdelkader for it to have value. But what about Big Data generated by the Petroleum Industry and particularly its upstream; Analytics; Upstream Petroleum Industry; Knowledge Management; KM; Business Intelligence; BI; Innovation
Boyer, Edmond
Langmuir waves upstream of interplanetary shocks: Dependence on shock and plasma parameters
Click Here for Full Article Langmuir waves upstream of interplanetary shocks: Dependence on shock for the production of upstream Langmuir waves and therefore to determine which shocks are likely to generate interplanetary Type II radio bursts. Of the 178 shocks included in this study, 43 produced upstream Langmuir
California at Berkeley, University of
Observations of low-frequency electromagnetic plasma waves upstream from the Martian shock
Observations of low-frequency electromagnetic plasma waves upstream from the Martian shock D. A of electromagnetic plasma waves upstream from the Martian bow shock. We discuss two recurring wave features of electromagnetic waves and disturbances upstream from the Martian shock [e.g., Riedler et al., 1989; Grard et al
California at Berkeley, University of
Increased risk of oesophageal adenocarcinoma among upstream petroleum workers
Objectives To investigate cancer risk, particularly oesophageal cancer, among male upstream petroleum workers offshore potentially exposed to various carcinogenic agents. Methods Using the Norwegian Registry of Employers and Employees, 24 765 male offshore workers registered from 1981 to 2003 was compared with 283 002 male referents from the general working population matched by age and community of residence. The historical cohort was linked to the Cancer Registry of Norway and the Norwegian Cause of Death Registry. Results Male offshore workers had excess risk of oesophageal cancer (RR 2.6, 95% CI 1.4 to 4.8) compared with the reference population. Only the adenocarcinoma type had a significantly increased risk (RR 2.7, 95% CI 1.0 to 7.0), mainly because of an increased risk among upstream operators (RR 4.3, 95% CI 1.3 to 14.5). Upstream operators did not have significant excess of respiratory system or colon cancer or mortality from any other lifestyle-related diseases investigated. Conclusion We found a fourfold excess risk of oesophageal adenocarcinoma among male workers assumed to have had the most extensive contact with crude oil. Due to the small number of cases, and a lack of detailed data on occupational exposure and lifestyle factors associated with oesophageal adenocarcinoma, the results must be interpreted with caution. Nevertheless, given the low risk of lifestyle-related cancers and causes of death in this working group, the results add to the observations in other low-powered studies on oesophageal cancer, further suggesting that factors related to the petroleum stream or carcinogenic agents used in the production process might be associated with risk of oesophageal adenocarcinoma. PMID:19858535
Kirkeleit, Jorunn; Riise, Trond; Bjřrge, Tone; Moen, Bente E; Brĺtveit, Magne; Christiani, David C
Differential expression of Myc1 and Myc2 isoforms in cells transformed by eIF4E: evidence for internal ribosome repositioning in the human c-myc 5?UTR
eIF4E is essential for translation initiation, but its overexpression causes malignant transformation. Recent work demonstrated that eIF4E\\/F participates in exposing and locating alternate translation start codons during scanning. Translation initiation of several important protooncogenes and growth-regulators, such as Myc and FGF-2, can start at CUG start codon(s) upstream of the normal open reading frame (ORF). The resulting amino-terminal extension alters
Peggy Sue Carter; Marta Jarquin-Pardo; Arrigo De Benedetti; A De Benedetti
Energetic Ions and Magnetic Fields Upstream From the Kronian Magnetosphere
NASA Astrophysics Data System (ADS)
The existence of energetic particle events to ~200 Rs upstream and ~1300 Rs downstream of Saturn was established during the Voyager 1, 2 flybys in 1980 and 1981, respectively. The origin of the events could not be determined with certainty because of lack of particle charge state and species measurements at lower (<300 keV) energies, which dominate the spectra. High sensitivity observations of energetic ion directional intensities, energy spectra, and ion composition were obtained by the Ion and Neutral Camera (INCA) of the MIMI instrument complement with a geometry factor of ~2.5 cm2 sr and some capability of separating light (H, He) and heavier (C, N, O) ion groups (henceforth referred to as "hydrogen" and "oxygen" respectively). Charge state information was provided where possible by the Charge-Energy-Mass-Spectrometer (CHEMS) over the range ~3 to 220 keV per charge, and magnetic field (IMF) data by the MAG instrument on Cassini. The observations revealed the presence of distinct upstream bursts of energetic hydrogen and oxygen ions whenever the IMF connected the spacecraft to the planetary bow shock, up to distances of 135 RS. The events exhibited the following characteristics: (1) Hydrogen ion bursts are observed in the energy range 3 to 220 keV (and occasionally to E > 220 keV) and oxygen ion bursts in the energy range 32 to -300 keV. (2) Particle onsets are nearly field-aligned, but the distribution tends to isotropize as the event progresses in time. (3) The duration of the ion bursts is several minutes up to 4 hrs. (4) The events are of varying composition, with some exhibiting significant fluxes of oxygen. (5) The bursts have a filamentary structure with some exhibiting distinct signatures of "velocity- filtering effects" at the edges of convecting IMF filaments. (6) Some ion bursts are accompanied by distinct diamagnetic field depressions and exhibit wave structures consistent with ion cyclotron waves for H+, and O+. Given the repeated magnetic field configuration during the detection of the events and that energetic ions trapped within the magnetosphere of Saturn are mostly H+ and O+ we conclude that O+-rich upstream events must be particles leaking from Saturn's magnetosphere under favorable IMF conditions. The spectral evolution of the upstream events and their anisotropy characteristics will be presented and discussed in the context of current models.
Krimigis, S. M.; Sarris, E.; Sergis, N.; Dialynas, K.; Mitchell, D. G.; Hamilton, D. C.; Dougherty, M.
Hybrid simulation codes with application to shocks and upstream waves
NASA Technical Reports Server (NTRS)
Hybrid codes in which part of the plasma is represented as particles and the rest as a fluid are discussed. In the past few years such codes with particle ions and massless, fluid electrons have been applied to space plasmas, especially to collisionless shocks. All of these simulation codes are one-dimensional and similar in structure, except for how the field equations are solved. The various approaches that are used (resistive Ohm's law, predictor-corrector, Hamiltonian) are described in detail and results from the various codes are compared with examples taken from collisionless shocks and low frequency wave phenomena upstream of shocks.
Winske, D.
2. View of Potomac River at Great Falls looking upstream ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
2. View of Potomac River at Great Falls looking upstream from Observation Tower. The majestic character of this wild and untrammeled spot is vividly shown. Scanty flow is evidenced by light colored normal water line markings on rock formation. Washington Agueduct Dam is shown in upper portion. Maryland on right and Virginia on left. Natives quoted as saying the water was as low or lower than during the drought conditions of 1930. Mr. Horyduzak, Photographer, 1943. - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA
The p53 tumor suppressor is a tetrameric transcription factor that is posttranslational modified at >20 different sites by phosphorylation, acetylation, or sumoylation in response to various cellular stress conditions. Specific posttranslational modifications, or groups of modifications, that result from the activation of different stress-induced signaling pathways are thought to modulate p53 activity to regulate cell fate by inducing cell cycle arrest, apoptosis, or cellular senescence. Here we review recent progress in characterizing the upstream signaling pathways whose activation in response to various genotoxic and non-genotoxic stresses result in p53 posttranslational modifications.
Sporadic—but Not Variant—Creutzfeldt-Jakob Disease Is Associated with Polymorphisms Upstream of PRNP Exon 1
Human prion diseases have inherited, sporadic, and acquired etiologies. The appearance of the novel acquired prion disease, variant Creutzfeldt-Jakob disease (vCJD), and the demonstration that it is caused by the same prion strain as that causing bovine spongiform encephalopathy, has led to fears of a major human epidemic. The etiology of classical (sporadic) CJD, which has a worldwide incidence, remains obscure. A common human prion-protein–gene (PRNP) polymorphism (encoding either methionine or valine at codon 129) is a strong susceptibility factor for sporadic and acquired prion disease. However, a quantitative-trait–locus study of prion incubation periods in mice has demonstrated an important factor that is close to Prnp but is independent of its coding sequence or that of the nearby prion-like doppel gene (Prnd). We have analyzed the PRNP locus for such tightly linked susceptibility factors. Fifty-six polymorphic sites have been identified within 25 kb of the PRNP open reading frame, including sites within the PRNP promoter and the PRNP 3? untranslated region. These have been characterized in 61 Centre d'Étude du Polymorphisme Humain (CEPH) families, demonstrating extensive linkage disequilibrium around PRNP and the existence of 11 major European PRNP haplotypes. Haplotype frequencies estimated in healthy U.K. control individuals were very similar to those deduced in the CEPH families. A common haplotype was overrepresented in patients with sporadic CJD (sCJD). Through use of a log-linear modeling approach to simultaneously model Hardy-Weinberg and linkage disequilibria, a significant independent association was found between sCJD and a polymorphism upstream of PRNP exon 1 (P=.005), in addition to the strong susceptibility conferred by codon 129 (P=2×10-8). However, although our sample size was necessarily small, no association was found between these polymorphisms and vCJD or iatrogenic CJD, in keeping with their having distinct disease mechanisms. In addition, there was no evidence of a PRNP founder effect in the first reported geographical cluster of vCJD. PMID:11704923
Mead, Simon; Mahal, Sukhvir P; Beck, John; Campbell, Tracy; Farrall, Martin; Fisher, Elizabeth; Collinge, John
Beta -Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon.
Previous work showed that human beta-globin mRNAs harboring a premature termination codon are degraded in the erythroid tissues of mice to products that lack sequences from the mRNA 5' end but contain a 5' cap-like structure. Whether these decay products are the consequence of endonucleolytic or 5'-to-3' exonucleolytic activity is unclear. We report that this beta-globin mRNA decay pathway is recapitulated in cultured mouse erythroleukemia (MEL) cells and targets nonsense-free mRNA to a lesser extent than nonsense-containing mRNA. S1 nuclease mapping and primer extension demonstrated that 70-80% of decay product 5' ends contain a UG dinucleotide. Detection of upstream counterparts of these decay products indicates that they are generated by endonucleolytic activity. Both crude and partially purified polysome extracts prepared from MEL cells contain an endonucleolytic activity that generates decay products comparable to those observed in vivo. These data suggest that an endonuclease with preference for UG dinucleotides is involved in the degradation of nonsense-containing and, to a lesser extent, nonsense-free human beta-globin mRNAs in mouse erythroid cells. PMID:12242335
Stevens, Audrey; Wang, Yang; Bremer, Kirsten; Zhang, Jing; Hoepfner, Robert; Antoniou, Michael; Schoenberg, Daniel R; Maquat, Lynne E
The Bastille Day Magnetic Clouds and Upstream Shocks: Near Earth Interplanetary Observations
NASA Technical Reports Server (NTRS)
The energetic charged particle, interplanetary magnetic field, and plasma characteristics of the 'Bastille Day' shock and ejecta/magnetic cloud events at 1 AU occurring over the days 14-16 July 2000 are described. Profiles of MeV (WIND/LEMT) energetic ions help to organize the overall sequence of events from the solar source to 1 AU. Stressed are analyses of an outstanding magnetic cloud (MC2) starting late on 15 July and its upstream shock about 4 hours earlier in WIND magnetic field and plasma data. Also analyzed is a less certain, but likely, magnetic cloud (MC1) occurring early on 15 July; this was separated from MC2 by its upstream shock and many heliospheric current sheet (HCS) crossings. Other HCS crossings occurred throughout the 3-day period. Overall this dramatic series of interplanetary events caused a large multi-phase magnetic storm with min Dst lower than -300 nT. The very fast solar wind speed (greater than or equal to 1100 km/s) in and around the front of MC2 (for near average densities) was responsible for a very high solar wind ram pressure driving in the front of the magnetosphere to geocentric distances estimated to be as low as approx. 5 R(sub E), much lower than the geosynchronous orbit radius. This was consistent with magnetic field observations from two GOES satellites which indicated they were in the magnetosheath for extended times. A static force free field model is used to fit the two magnetic cloud profiles providing estimates of the clouds' physical and geometrical properties. MC2 was much larger than MCI, but their axes were nearly antiparallel, and their magnetic fields had the same left-handed helicity. MC2's axis and its upstream shock normal were very close to being perpendicular to each other, as might be expected if the cloud were driving the shock at the time of observation. The estimated axial magnetic flux carried by MC2 was 52 x 10(exp 20) Mx, which is about 5 times the typical magnetic flux estimated for other magnetic clouds in the WIND data over its first 4 years and is 17 times the flux of MC1. This large flux is due to both the strong axially-directed field of MC2 (46.8 nT on the axis) and the large radius (R(sub 0) = 0.189 AU) of the flux tube. MC2's average speed is consistent with the expected transit time from a halo-CME to which it is apparently related.
Lepping, R. P.; Berdichevsky, D. B.; Burlaga, L. F.; Lazarus, A. J.; Kasper, J.; Desch, M. D.; Wu, C.-C.; Reames, D. V.; Singer, H. J.; Singer, H. J.; Vondrak, Richard R. (Technical Monitor)
A Large Eddy Simulation Study for upstream wind energy conditioning
NASA Astrophysics Data System (ADS)
The wind energy industry is increasingly focusing on optimal power extraction strategies based on layout design of wind farms and yaw alignment algorithms. Recent field studies by Mikkelsen et al. (Wind Energy, 2013) have explored the possibility of using wind lidar technology installed at hub height to anticipate incoming wind direction and strength for optimizing yaw alignment. In this work we study the benefits of using remote sensing technology for predicting the incoming flow by using large eddy simulations of a wind farm. The wind turbines are modeled using the classic actuator disk concept with rotation, together with a new algorithm that permits the turbines to adapt to varying flow directions. This allows for simulations of a more realistic atmospheric boundary layer driven by a time-varying geostrophic wind. Various simulations are performed to investigate possible improvement in power generation by utilizing upstream data. Specifically, yaw-correction of the wind-turbine is based on spatio-temporally averaged wind values at selected upstream locations. Velocity and turbulence intensity are also considered at those locations. A base case scenario with the yaw alignment varying according to wind data measured at the wind turbine's hub is also used for comparison. This reproduces the present state of the art where wind vanes and cup anemometers installed behind the rotor blades are used for alignment control.
Sharma, V.; Calaf, M.; Parlange, M. B.
Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion.
Codon-anticodon mismatches and tRNA misloadings cause translational amino acid misinsertions, producing dysfunctional proteins. Here I explore the original hypothesis whether mismatches tend to compensate misacylation, so as to insert the amino acid coded by the codon. This error compensation is promoted by the fact that codon-anticodon mismatch stabilities increase with tRNA misacylation potentials (predicted by 'tfam') by non-cognate amino acids coded by the mismatched codons for most tRNAs examined. Error compensation is independent of preferential misacylation by non-cognate amino acids physico-chemically similar to cognate amino acids, a phenomenon that decreases misinsertion impacts. Error compensation correlates negatively with (a) codon/anticodon abundance (in human mitochondria and Escherichia coli); (b) developmental instability (estimated by fluctuating asymmetry in bilateral counts of subdigital lamellae, in each of two lizard genera, Anolis and Sceloporus); and (c) pathogenicity of human mitochondrial tRNA polymorphisms. Patterns described here suggest that tRNA misacylation is sometimes compensated by codon-anticodon mismatches. Hence translation inserts the amino acid coded by the mismatched codon, despite mismatch and misloading. Results suggest that this phenomenon is sufficiently important to affect whole organism phenotypes, as shown by correlations with pathologies and morphological estimates of developmental stability. PMID:21470914
Seligmann, Hervé
Stress induced MAPK genes show distinct pattern of codon usage in Arabidopsis thaliana, Glycine max and Oryza sativa
Mitogen activated protein kinase (MAPK) genes provide resistance to various biotic and abiotic stresses. Codon usage profiling of the genes reveals the characteristic features of the genes like nucleotide composition, gene expressivity, optimal codons etc. The present study is a comparative analysis of codon usage patterns for different MAPK genes in three organisms, viz. Arabidopsis thaliana, Glycine max (soybean) and Oryza sativa (rice). The study has revealed a high AT content in MAPK genes of Arabidopsis and soybean whereas in rice a balanced AT-GC content at the third synonymous position of codon. The genes show a low bias in codon usage profile as reflected in the higher values (50.83 to 56.55) of effective number of codons (Nc). The prediction of gene expression profile in the MAPK genes revealed that these genes might be under the selective pressure of translational optimization as reflected in the low codon adaptation index (CAI) values ranging from 0.147 to 0.208. PMID:25187684
Singha, H Surachandra; Chakraborty, Supriyo; Deka, Himangshu
The human mitochondrial tRNAMet: Structure/function relationship of a unique modification in the decoding of unconventional codons
Human mitochondrial mRNAs utilize the universal AUG and the unconventional isoleucine AUA codons for methionine. In contrast to translation in the cytoplasm, human mitochondria use one tRNA, hmtRNAMetCAU, to read AUG and AUA codons at both the peptidyl- (P-), and aminoacyl-(A-) sites of the ribosome. The hmtRNAMetCAU has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position 34 (f5C34), and a cytidine substituting for the invariant uridine at position 33 of the canonical "U-turn" in tRNAs. The structure of the tRNA's anticodon stem and loop domain (hmtASLMetCAU), determined by NMR restrained molecular modeling, revealed how the f5C34 modification facilitates the decoding of AUA at the P- and A-sites. The f5C34 defined a reduced conformational space for the nucleoside, in what appears to have restricted the conformational dynamics of the anticodon bases of the modified hmtASLMetCAU. The hmtASLMetCAU exhibited a "C-turn" conformation that has some characteristics of the U-turn motif. Codon binding studies with both E. coli and bovine mitochondrial ribosomes revealed that the f5C34 facilitates AUA binding in the A-site and suggested that the modification favorably alters the ASL's binding kinetics. Mitochondrial translation by many organisms including humans sometimes initiates with the universal isoleucine codons AUU and AUC. The f5C34 enabled P-site codon binding to these normally isoleucine codons. Thus, the physicochemical properties of this one modification, f5C34, expand codon recognition from the traditional AUG to the non-traditional, synonymous codons AUU and AUC as well as AUA, in the reassignment of universal codons in the mitochondria. PMID:21168417
Bilbille, Yann; Gustilo, Estella M.; Harris, Kimberly A.; Jones, Christie N.; Lusic, Hrvoje; Kaiser, Robert J.; Delaney, Michael O.; Spremulli, Linda L.; Deiters, Alexander; Agris, Paul F.
Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.
The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. PMID:25623487
Wohlin, Ĺsa
Constraint on di-nucleotides by codon usage bias in bacterial genomes.
It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes. PMID:24333347
Satapathy, Siddhartha Sankar; Powdel, Bhes Raj; Dutta, Malay; Buragohain, Alak Kumar; Ray, Suvendra Kumar
Amino-acid substitutions at codon 13 of the N-ras oncogene in human acute myeloid leukaemia
NASA Astrophysics Data System (ADS)
DNAs from four out of five patients with acute myeloid leukaemia (AML) tested by an in vivo selection assay in nude mice using transfected mouse NIH 3T3 cells were found to contain an activated N-ras oncogene. Using a set of synthetic oligonucleotide probes, we have detected a mutation at codon 13 in all four genes. The same codon is mutated in an additional AML DNA that is positive in the focus-formation assay on 3T3 cells. DNA from the peripheral blood of one patient in remission does not contain a codon 13 mutation.
Bos, Johannes L.; Toksoz, Deniz; Marshall, Christopher J.; Verlaan-de Vries, Matty; Veeneman, Gerrit H.; van der Eb, Alex J.; van Boom, Jacques H.; Janssen, Johannes W. G.; Steenvoorden, Ada C. M.
START Background Report START, May 2014 1 BACKGROUND REPORT
START Background Report © START, May 2014 1 BACKGROUND REPORT Boko Haram Recent Attacks On Tuesday, April 15, 2014, the terrorist organization Boko Haram attacked a girls' school in Chibok, Borno state, in northern Nigeria, abducting between 250-300 young school girls. Boko Haram's leader, Abubakar Shekau
Hill, Wendell T.
START Background Report START, August 2013 1 BACKGROUND REPORT
(AQAP), using data from START's Global Terrorism Database (GTD). ATTACKS ON U.S. TARGETS ABROAD Between Terrorist Attacks against U.S. Targets Abroad, 1970-2012 Source: Global Terrorism Database #12;START building housing French paratroopers. These attacks were claimed by Islamic Jihad, a name used by Hezbollah
Hill, Wendell T.
Cloning and characterization of 5'-upstream sequence of the M32 gene for a mouse homologue of Drosophila heterochromatin protein 1 (HP1).
M32 [also termed chromatin modifier protein 2 (MOD2)] is a nuclear protein consisting of the condensed chromatin structure (heterochromatin) and considered one of the mammalian homologues of heterochromatin protein 1 (HP1), first isolated as one of the components of heterochromatin in Drosophila. This report presents the isolation and characterization of the 5'-upstream region of the mouse M32 gene containing a promoter region and 5'-untranslated region (5'-UTR) exon. The 5'-upstream region (approximately 0.27 kb starting from the 5' end of the 5'-UTR exon) of the M32 gene contained neither a TATA box nor a CCAAT box, but possessed potential binding sites for transcription factors such as Sp1, H4TF-1, PEA2, PEA3, GSG element and Egr-1, and was highly G/C-rich. The promoter activity of this 5'-upstream region was demonstrated by transfecting its fusion-construct with the E. coli beta-galactosidase gene into the F9 mouse teratocarcinoma cell line. The 5' ends of the mRNA were mapped to at least two positions in the 5'-upstream region. Interestingly, the 5'-upstream region exhibited a high degree of similarity to a portion of heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 gene, which is thought to play a role in RNA processing, located in the reverse orientation to the M32 gene, and also to several known ESTs and cDNAs. These findings suggest that the 5'-upstream region of the M32 gene consists of a multiple regulatory complex which probably plays important roles in nuclear function such as chromatin organization and RNA processing. PMID:11761715
Sato, M; Miyado, K; Kimura, M
[BIG-H3 protein: mutation of codon 124 and corneal amyloidosis].
In 1997, a group of hereditary corneal dystrophies was related to mutations in the TGFBI (BIGH3) gene. Within this group, some corneal dystrophies present particular biochemical features in that they are characterized by corneal amyloid deposition. Contrary to clinical and genetic knowledge, the biochemical characteristics of the encoded protein (Big-h3) and the mechanisms of its amyloid conversion remain unclear. We review the current knowledge on the Big-h3 protein and focus on the behavior of the codon 124 region. We discuss this protein's mechanisms of amyloid conversion from our results and previous reports as well as from other types of amyloidosis. These data provide a better understanding of the putative processes leading to the phenotypic variations linked with their respective codon 124 mutation. PMID:15179309
Schmitt-Bernard, C-F; Pouliquen, Y; Argilčs, A
Degradation of mRNAs that lack a stop codon: A decade of nonstop progress
Nonstop decay is the mechanism of identifying and disposing aberrant transcripts that lack in-frame stop codons. It is hypothesized that these transcripts are identified during translation when the ribosome arrives at the 3? end of the mRNA and stalls. Presumably the ribosome stalling recruits additional cofactors, Ski7 and the exosome complex. The exosome degrades the transcript using either one of is ribonucleolytic activities and the ribosome and the peptide are both released. Additional precautionary measures by the nonstop decay pathway may include translational repression of the nonstop transcript after translation, and proteolysis of the released peptide by the proteasome. This surveillance mechanism protects the cells from potentially harmful truncated proteins, but it may also be involved in mediating critical cellular functions of transcripts that are prone to stop codon read-through. Important advances have been made in the past decade as we learn that nonstop decay may have implications in human disease. PMID:22740367
Klauer, A. Alejandra; van Hoof, Ambro
SUMMARY Impulsivity, describing action without foresight, is an important feature of several psychiatric diseases, suicidality and violent behavior. The complex origins of impulsivity hinder identification of the genes influencing both it and diseases with which it is associated. We performed exon-centric sequencing of impulsive individuals in a founder population, targeting fourteen genes belonging to the serotonin and dopamine domain. A stop codon in HTR2B that is common (MAF >1%) but exclusive to Finns was identified. Expression of the gene in the human brain was assessed, as well as the molecular functionality of the stop codon that was associated with psychiatric diseases marked by impulsivity in both population and family-based analyses. Knockout of Htr2b increased impulsive behaviors in mice, indicative of predictive validity. Our study shows the potential for identifying and tracing effects of rare alleles in complex behavioral phenotypes using founder populations, and suggests a role for HTR2B in impulsivity. PMID:21179162
Bevilacqua, Laura; Doly, Stéphane; Kaprio, Jaakko; Yuan, Qiaoping; Tikkanen, Roope; Paunio, Tiina; Zhou, Zhifeng; Wedenoja, Juho; Maroteaux, Luc; Diaz, Silvina; Belmer, Arnaud; Hodgkinson, Colin A.; Dell'Osso, Liliana; Suvisaari, Jaana; Coccaro, Emil; Rose, Richard J; Peltonen, Leena; Virkkunen, Matti; Goldman, David
Lack of IRS-1 codon 513 and 972 polymorphism in Pima Indians
Insulin receptor substrate-1 (IRS-1), a 1242 amino acid protein, an endogenous substrate for the insulin receptor tyrosine kinase, mediates many or all of the metabolic actions of insulin. Recently, polymorphism at codons 513 and 972 of the IRS-1 gene resulting in 2 amino acid substitutions that were associated with type II diabetes were found in a Caucasian population. Using allele specific oligonucleotide (ASO) hybridization, we screened 242 diabetic and 190 nondiabetic Pima Indians, a population with a very high prevalence of type II diabetes. Neither of the two mutations was present in either diabetic or nondiabetic subjects. We conclude that polymorphism at codons 513 and 972 of the IRS-1 gene observed in certain Caucasian populations is very rare or absent in Pima Indians. 20 refs., 2 figs., 1 tab.
Celi, F.S.; Silver, K.; Walston, J. [and others] [and others
Could protein tertiary structure influence mammary transgene expression more than tissue specific codon usage?
Animal mammary glands have been successfully employed to produce therapeutic recombinant human proteins. However, considerable variation in animal mammary transgene expression efficiency has been reported. We now consider whether aspects of codon usage and/or protein tertiary structure underlie this variation in mammary transgene expression. Electronic supplementary material The online version of this article (doi:10.1007/s11248-010-9411-8) contains supplementary material, which is available to authorized users. PMID:20563642
He, Zuyong; Zhao, Yiqiang; Mei, Gui; Li, Ning
Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii
In unicellular species codon usage is determined by mutational biases and natural selection. Among prokaryotes, the influence of these factors is different if the genome is skewed towards AT or GC, since in AT-rich organisms translational selection is absent. On the other hand, in AT-rich unicellular eukaryotes the two factors are present. In order to understand if GC-rich genomes display
Hugo Naya; Héctor Romero; Nicola Carels; Alejandro Zavala; Héctor Musto
Solar wind flow upstream of the coronal slow shock
NASA Technical Reports Server (NTRS)
Slow shocks have been predicted to exist embedded in large coronal holes at low altitude. Two or more curved slow shocks may link together to form a composite discontinuity surface around the sun which may be called the coronal slow shock (CSS). Here a solar-wind model is studied under the assumption that a standing CSS exists and cororates with the sun at a constant angular velocity. A steady, axisymmetrical one-fluid model is introduced to study the expansion of solar wind in the open-field region upstream of the CSS. The model requires that the conditions downstream of the CSS near the equatorial plane can produce a solar wind agreeable with the observations made near the earth's orbit. The paper presents an illustrative calculation in which the polar caps within 60 deg of the polar angle are assumed to be the source region of the solar wind.
Whang, Y. C.
Upstream Structures and Their Effects on the Magnetosphere
NASA Technical Reports Server (NTRS)
Kinetic processes within the Earth's foreshock generate a profusion of plasma and magnetic field structures with sizes and durations ranging from the microscale (e.g. SLAMs, solitons, and density holes) to the mesoscale (e.g. foreshock cavities or boundaries, hot flow anomalies, and bubbles). Swept into the bow shock by the solar wind flow, the perturbations associated with these features batter the magnetosphere, driving a wide variety of magnetospheric effects, including large amplitude magnetopause motion, bursty reconnection and the generation of flux transfer events, enhanced pulsation activity within the magnetosphere, diffusion and energization of radiation belt particles, enhanced particle precipitation resulting in dayside aurora and riometer absorption, and the generation of field-aligned currents and magnetic impulse events in high-latitude ground magnetometers. This talk reviews the ever growing menagery of structures observed upstream from the bow shock, examines their possible interrelationships, and considers their magnetospheric consequences.
Sibeck, D. G.
SAP and life-cycle management in the upstream
Business relationships today depend more than ever on changing alliances and partnerships to leverage risk in a commodity market. SAP is a fully integrated, enterprise-wide software system that uses business processes tightly integrated around a common data model to facilitate these business relationships across the oil and gas supply chain. The SAP modules contain the business processes that are needed to handle the logistics and operations maintenance for operating an oil or gas field. Each industry has unique business-process requirements that the core SAP application set may not cover. In the oil and gas business, there are unique financial requirements in the upstream for working in joint ventures. In the downstream business segment, handling bulk hydrocarbons requires additional functionality.
Davis, B.
From Worker Health To Citizen Health: Moving Upstream
New rapid growth economies, urbanization, health systems crises and "big data" are causing fundamental changes in social structures and systems including health. These forces for change have significant consequences for occupational and environmental medicine and will challenge the specialty to think beyond workers and workplaces as the principal locus of innovation for health and performance. These trends are placing great emphasis on upstream strategies for addressing the complex systems dynamics of the social determinants of health. The need to engage systems in communities for healthier workforces is a shift in orientation from worker and workplace centric to citizen and community centric. This change for occupational and environmental medicine requires extending systems approaches in the workplace to communities which are systems of systems and which require different skills, data, tools and partnerships. PMID:24284749
Sepulveda, Martin-Jose
High-fidelity modeling of airfoil interaction with upstream turbulence
NASA Astrophysics Data System (ADS)
To supplement past research on low speed unsteady airfoil responses to upstream disturbances, this work proposes and investigates a method to generate a turbulent momentum source to be convected downstream and interact with an SD7003 airfoil in a high-fidelity numerical simulation. A perturbation velocity field is generated from a summation of Fourier harmonics and applied to the forcing function in the momentum terms of the Navier Stokes Equations. The result is a three-dimensional, divergence-free, convected turbulent gust with applied statistical parameters. A parametric study has been done in 2D and 3D comparing the resultant flow fields and airfoil interactions for various numerical and physical parameters.
Brodnick, Jacob
Hitchhiking behaviour in the obligatory upstream migration of amphidromous snails
Migratory animals endure high stress during long-distance travel in order to benefit from spatio-temporally fluctuating resources, including food and shelter or from colonization of unoccupied habitats. Along with some fishes and shrimps, nerite snails in tropical to temperate freshwater systems are examples of amphidromous animals that migrate upstream for growth and reproduction after a marine larval phase. Here I report, to my knowledge, the first example of 'hitchhiking' behaviour in the obligatory migration of animals: the nerite snail Neritina asperulata appears to travel several kilometres as minute juveniles by firmly attaching to the shells of congeneric, subadult snails in streams of Melanesian Islands, presumably to increase the success rate of migration. PMID:19411267
Kano, Yasunori
5. Looking west upstream, towards the location of the erstwhile ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
5. Looking west upstream, towards the location of the erstwhile intake flume into canal from the upper reaches of the Potomac River above the Great Falls, on the old Potowmack Canal built by George Washington. The plan contemplated canal navigation around the Great Falls of the Potomac River, located on the Virginia side of the Potomac, about 15 miles above Washington, D.C. The Company was organized in 1785, and by 1802, this and three or four smaller canals were substantially completed and raft-like boats began operation with materials from the west to the city of Georgetown. 'Although the canals and locks of the Potomac Canal were considered a great engineering accomplishment, the improvements to the river channel were inadequate. Disappointment ... - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA
Numerical analysis of supersonic combustion ramjet with upstream fuel injection
NASA Astrophysics Data System (ADS)
This paper describes possible fuel injection scheme for airbreathing engines that use hydrocarbon fuels. The basic idea is to inject fuel at the spike tip of the supersonic inlet to achieve mixing and combustion efficiency with a limited length combustion chamber. A numerical code, able to solve the full Navier-Stokes equations in turbulent and reacting flows, is employed to obtain numerical simulations of the thermo-fluidynamic fields at different scramjet flight conditions, at Mach numbers of M=6.5 and 8. The feasibility of the idea of the upstream injection is checked for a simple axisymmetric configuration and relatively small size. The results are discussed in connection with the potential benefits deriving from the use of new ultra high temperature ceramics (UHTC).
Savino, Raffaele; Pezzella, Giuseppe
Ensemble streamflow prediction adjustment for upstream water use and regulation
NASA Astrophysics Data System (ADS)
Hydrologic model forecasts are commonly biased in watersheds where water use and regulation activities cause flow alterations. Furthermore, direct accounting of such biases in forecast preparation is impractical as the information required is extensive and usually unavailable. This article introduces a new method to characterize the aggregate flow alteration biases and associated uncertainty in watersheds with important but largely undocumented water use and regulation activities. It also uses these assessments to adjust the ensemble streamflow predictions at downstream locations. The method includes procedures to (a) detect the presence of significant upstream regulation and water use influences; (b) correct the ensemble streamflow predictions and associated uncertainty for any biases in periods when such influences are detectable; and (c) assess the adjusted forecast reliability improvements. Applications in three watersheds of the American River in California demonstrate that the new method leads to significant forecast skill improvements and is also readily applicable to other regions.
Georgakakos, Aris P.; Yao, Huaming; Georgakakos, Konstantine P.
Upstream and downstream processing of recombinant IgA.
Immunoglobulin A (IgA) is the most abundant antibody class in the human body and has a unique role in mediating immunity. The ever-increasing knowledge about the potential of IgAs has renewed interest in this antibody class for therapeutic use against a variety of infectious and malignant diseases, and as a preventive agent for mucosal pathogens. Despite the considerable therapeutic potential of IgA the exploration thereof has often been hampered due to difficulties in producing and purifying desired quantities. Large amounts of pure IgA will be required for in vivo studies. This work reviews current achievements and bottlenecks in upstream and downstream processing of recombinant IgA from a biotechnological point of view. We also highlight recent accomplishments with diverse expression systems and presents different affinity techniques for the capture of recombinant IgA to compare their purification potential. PMID:25257601
Reinhart, David; Kunert, Renate
Upstream Swirl Effects on the Flow Inside a Labyrinth Seal
NASA Technical Reports Server (NTRS)
The flow field inside a seven cavity tooth on rotor labyrinth seal was measured using a 3D laser Doppler anemometer system. The seal was operated at a Reynolds number of 24,000 and a Taylor number of 6,600 using water as the working fluid. Swirl vanes were placed upstream of the seal to produce positive, negative, and no preswirl. It was found that the axial and radial velocities were minimally effected. The tangential velocity, both in the clearance region and the seal cavities on the rotor, were greatly altered by the preswirl. By applying negative preswirl, the tangential velocity was suppressed, even in the seventh cavity. The turbulence levels decreased as the preswirl varied from negative to positive.
Morrison, Gerald L.; Johnson, Mark C.
Maine: Early Head Start Initiatives
ERIC Educational Resources Information Center
Maine has two initiatives that build on Early Head Start (EHS). The first initiative, Fund for a Healthy Maine, has since 2001 provided tobacco settlement money to existing Head Start and EHS programs to expand the number of children who receive full-day, full-year services. Local programs have the option of using these funds for EHS, depending on…
Center for Law and Social Policy, Inc. (CLASP), 2012
Research Services START UP FUNDS
/compliance/chreb/ Conjoint Faculties Research Ethics Board New website: www.ucalgary.ca/research/ethics/cfreb Animal Care-up spending (prior to any recruitment of research participants or the acquisition of animals) and timeResearch Services START UP FUNDS www.ucalgary.ca/research START UP FUNDS From time to time some
de Leon, Alex R.
COMPONENT User's Guide Getting started
the files it will create a Program Manager group called COMPONENT. This group will display icons on the COMPONENT icon with the mouse. When COMPONENT starts your screen should look like this: Log window (a child the program starts a single child window titled Log is open on the desktop. This window is used by COMPONENT
Page, Roderic
Nebraska: Early Head Start Initiative
ERIC Educational Resources Information Center
Since 1999, Nebraska's Early Head Start Infant/Toddler Quality Initiative has supported Early Head Start (EHS) and community child care partnerships to improve the quality and professionalism of infant and toddler care. EHS programs apply to receive funding to establish partnerships with center-based or home-based child care.The initiative has…
Center for Law and Social Policy, Inc. (CLASP), 2012
Ingestion into the upstream wheelspace of an axial turbine stage
NASA Astrophysics Data System (ADS)
The upstream wheelspace of an axial air turbine stage complete with nozzle guide vanes (NGVs) and rotor blades (430 mm mean diameter) has been tested with the objective of examining the combined effect of NGVs and rotor blades on the level of mainstream ingestion for different seal flow rates. A simple axial clearance seal was used with the rotor spun up to 6650 rpm by drawing air through it from atmospheric pressure with a large centrifugal compressor. The effect of rotational speed was examined for several constant mainstream flow rates by controlling the rotor speed with an air brake. The circumferential variation in hub static pressure was measured at the trailing edge of the NGVs upstream of the seal gap and was found to affect ingestion significantly. The hub static pressure distribution on the rotor blade leading edges was rotor speed dependent and could not be measured in the experiments. The Denton three-dimensional CFD computer code was used to predict the smoothed time-dependent pressure field for the rotor together with the pressure distribution downstream of the NGVs. The level and distribution of mainstream ingestion, and thus, the seal effectiveness, was determined from nitrous oxide gas concentration measurements and related to static pressure measurements made throughout the wheelspace. With the axial clearance rim seal close to the rotor the presence of the blades had a complex effect. Rotor blades in connection with NGVs were found to reduce mainstream ingestion seal flow rates significantly, but a small level of ingestion existed even for very high levels of seal flow rate.
Green, T.; Turner, A. B.
Assessing upstream fish passage connectivity with network analysis.
Hydrologic connectivity is critical to the structure, function, and dynamic process of river ecosystems. Dams, road crossings, and water diversions impact connectivity by altering flow regimes, behavioral cues, local geomorphology, and nutrient cycling. This longitudinal fragmentation of river ecosystems also increases genetic and reproductive isolation of aquatic biota such as migratory fishes. The cumulative effects on fish passage of many structures along a river are often substantial, even when individual barriers have negligible impact. Habitat connectivity can be improved through dam removal or other means of fish passage improvement (e.g., ladders, bypasses, culvert improvement). Environmental managers require techniques for comparing alternative fish passage restoration actions at alternative or multiple locations. Herein, we examined a graph-theoretic algorithm for assessing upstream habitat connectivity to investigate both basic and applied fish passage connectivity problems. First, we used hypothetical watershed configurations to assess general alterations to upstream fish passage connectivity with changes in watershed network topology (e.g., linear vs. highly dendritic) and the quantity, location, and passability of each barrier. Our hypothetical network modeling indicates that locations of dams with limited passage efficiency near the watershed outlet create a strong fragmentation signal but are not individually sufficient to disconnect the system. Furthermore, there exists a threshold in the number of dams beyond which connectivity declines precipitously, regardless of watershed topology and dam configuration. Watersheds with highly branched configurations are shown to be less susceptible to disconnection as measured by this metric. Second, we applied the model to prioritize barrier improvement in the mainstem of the Truckee River, Nevada, USA. The Truckee River application demonstrates the ability of the algorithm to address conditions common in fish passage projects including incomplete data, parameter uncertainty, and rapid application. This study demonstrates the utility of a graph-theoretic approach for assessing fish passage connectivity in dendritic river networks assuming full basin utilization for a given species, guild, or community of concern. PMID:24147411
McKay, S Kyle; Schramski, John R; Conyngham, Jock N; Fischenich, J Craig
Relationship between p53 gene codon-72 polymorphisms and hypertrophic scar formation following caesarean section
The aim of the present study was to determine the relationship between p53 gene codon-72 polymorphisms and hypertrophic scar formation following caesarean section (CS). Blood samples from 260 female patients were collected one week following a CS for the detection of p53 gene polymorphisms using a molecular beacon-coupled quantitative polymerase chain reaction technique. Patients had follow-ups for 12–18 months to observe the scar formation. From these observations, the relationship between the p53 codon-72 polymorphisms and hypertrophic scar formation occurrence was investigated. Among the patients with the CCC/CCC genotype, nine patients had hypertrophic scars and 46 patients showed normal healing, which is a ratio of 0.19. However, the follow-up investigations indicated that the presence of a homozygous or heterozygous C-to-G alteration at the codon-72 site in gene p53 resulted in 13 patients with hypertrophic scars and 192 patients with normal healing, which is a ratio of 0.07. Therefore, these results indicate that patients with the CCC/CCC genotype had a higher risk of developing hypertrophic scars compared with that for patients with the CCC/CGC or CGC/CGC genotypes. PMID:24940419
New insights into stop codon recognition by eRF1
In eukaryotes, translation termination is performed by eRF1, which recognizes stop codons via its N-terminal domain. Many previous studies based on point mutagenesis, cross-linking experiments or eRF1 chimeras have investigated the mechanism by which the stop signal is decoded by eRF1. Conserved motifs, such as GTS and YxCxxxF, were found to be important for termination efficiency, but the recognition mechanism remains unclear. We characterized a region of the eRF1 N-terminal domain, the P1 pocket, that we had previously shown to be involved in termination efficiency. We performed alanine scanning mutagenesis of this region, and we quantified in vivo readthrough efficiency for each alanine mutant. We identified two residues, arginine 65 and lysine 109, as critical for recognition of the three stop codons. We also demonstrated a role for the serine 33 and serine 70 residues in UGA decoding in vivo. NMR analysis of the alanine mutants revealed that the correct conformation of this region was controlled by the YxCxxxF motif. By combining our genetic data with a structural analysis of eRF1 mutants, we were able to formulate a new model in which the stop codon interacts with eRF1 through the P1 pocket. PMID:25735746
Blanchet, Sandra; Rowe, Michelle; Von der Haar, Tobias; Fabret, Céline; Demais, Stéphane; Howard, Mark J.; Namy, Olivier
A model-independent approach to infer hierarchical codon substitution dynamics
Background Codon substitution constitutes a fundamental process in molecular biology that has been studied extensively. However, prior studies rely on various assumptions, e.g. regarding the relevance of specific biochemical properties, or on conservation criteria for defining substitution groups. Ideally, one would instead like to analyze the substitution process in terms of raw dynamics, independently of underlying system specifics. In this paper we propose a method for doing this by identifying groups of codons and amino acids such that these groups imply closed dynamics. The approach relies on recently developed spectral and agglomerative techniques for identifying hierarchical organization in dynamical systems. Results We have applied the techniques on an empirically derived Markov model of the codon substitution process that is provided in the literature. Without system specific knowledge of the substitution process, the techniques manage to "blindly" identify multiple levels of dynamics; from amino acid substitutions (via the standard genetic code) to higher order dynamics on the level of amino acid groups. We hypothesize that the acquired groups reflect earlier versions of the genetic code. Conclusions The results demonstrate the applicability of the techniques. Due to their generality, we believe that they can be used to coarse grain and identify hierarchical organization in a broad range of other biological systems and processes, such as protein interaction networks, genetic regulatory networks and food webs. PMID:20412602
A method for multi-codon scanning mutagenesis of proteins based on asymmetric transposons.
Random mutagenesis followed by selection or screening is a commonly used strategy to improve protein function. Despite many available methods for random mutagenesis, nearly all generate mutations at the nucleotide level. An ideal mutagenesis method would allow for the generation of 'codon mutations' to change protein sequence with defined or mixed amino acids of choice. Herein we report a method that allows for mutations of one, two or three consecutive codons. Key to this method is the development of a Mu transposon variant with asymmetric terminal sequences. As a demonstration of the method, we performed multi-codon scanning on the gene encoding superfolder GFP (sfGFP). Characterization of 50 randomly chosen clones from each library showed that more than 40% of the mutants in these three libraries contained seamless, in-frame mutations with low site preference. By screening only 500 colonies from each library, we successfully identified several spectra-shift mutations, including a S205D variant that was found to bear a single excitation peak in the UV region. PMID:22184456
Liu, Jia; Cropp, T Ashton
Evolution of Codon Usage in the Smallest Photosynthetic Eukaryotes and Their Giant Viruses
Prasinoviruses are among the largest viruses (>200 kb) and encode several hundreds of protein coding genes, including most genes of the DNA replication machinery and several genes involved in transcription and translation, as well as transfer RNAs (tRNAs). They can infect and lyse small eukaryotic planktonic marine green algae, thereby affecting global algal population dynamics. Here, we investigate the causes of codon usage bias (CUB) in one prasinovirus, OtV5, and its host Ostreococcus tauri, during a viral infection using microarray expression data. We show that 1) CUB in the host and in the viral genes increases with expression levels and 2) optimal codons use those tRNAs encoded by the most abundant host tRNA genes, supporting the notion of translational optimization by natural selection. We find evidence that viral tRNA genes complement the host tRNA pool for those viral amino acids whose host tRNAs are in short supply. We further discuss the coevolution of CUB in hosts and prasinoviruses by comparing optimal codons in three evolutionary diverged host–virus-specific pairs whose complete genome sequences are known. PMID:23563969
Michely, Stephanie; Toulza, Eve; Subirana, Lucie; John, Uwe; Cognat, Valérie; Maréchal-Drouard, Laurence; Grimsley, Nigel; Moreau, Hervé; Piganeau, Gwenaël
Environmental shaping of codon usage and functional adaptation across microbial communities
Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community. PMID:23921637
Roller, Maša; Luci?, Vedran; Nagy, István; Perica, Tina; Vlahovi?ek, Kristian
Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius
It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease. PMID:25237653
Johnston, Christopher D.; Bannantine, John P.; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D.
Self-catalytic DNA Depurination Underlies Human ?-Globin Gene Mutations at Codon 6 That Cause Anemias and Thalassemias*
The human ?-globin gene contains an 18-nucleotide coding strand sequence centered at codon 6 and capable of forming a stem-loop structure that can self-catalyze depurination of the 5?G residue of that codon. The resultant apurinic lesion is subject to error-prone repair, consistent with the occurrence about this codon of mutations responsible for 6 anemias and ?-thalassemias and additional substitutions without clinical consequences. The 4-residue loop of this stem-loop-forming sequence shows the highest incidence of mutation across the gene. The loop and first stem base pair-forming residues appeared early in the mammalian clade. The other stem-forming segments evolved more recently among primates, thereby conferring self-depurination capacity at codon 6. These observations indicate a conserved molecular mechanism leading to ?-globin variants underlying phenotypic diversity and disease. PMID:23457306
Alvarez-Dominguez, Juan R.; Amosova, Olga; Fresco, Jacques R.
Self-catalytic DNA depurination underlies human ?-globin gene mutations at codon 6 that cause anemias and thalassemias.
The human ?-globin gene contains an 18-nucleotide coding strand sequence centered at codon 6 and capable of forming a stem-loop structure that can self-catalyze depurination of the 5'G residue of that codon. The resultant apurinic lesion is subject to error-prone repair, consistent with the occurrence about this codon of mutations responsible for 6 anemias and ?-thalassemias and additional substitutions without clinical consequences. The 4-residue loop of this stem-loop-forming sequence shows the highest incidence of mutation across the gene. The loop and first stem base pair-forming residues appeared early in the mammalian clade. The other stem-forming segments evolved more recently among primates, thereby conferring self-depurination capacity at codon 6. These observations indicate a conserved molecular mechanism leading to ?-globin variants underlying phenotypic diversity and disease. PMID:23457306
Alvarez-Dominguez, Juan R; Amosova, Olga; Fresco, Jacques R
Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion
Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to 'statistical protein' that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNAPyl orthogonal pair cannot completely outcompete contamination by natural amino acids. PMID:23036644
O'Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U.; Ling, Jiqiang; Odoi, Keturah; Liu, Wenshe R.; Söll, Dieter
Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion.
Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to 'statistical protein' that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNA(Pyl) orthogonal pair cannot completely outcompete contamination by natural amino acids. PMID:23036644
O'Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U; Ling, Jiqiang; Odoi, Keturah; Liu, Wenshe R; Söll, Dieter
The Genetic Code Degeneration I: Rules Governing the Code Degeneration and the Spatial Organization of the Codon Informative Properties
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as dual entities characterized by its chemical type and the number of H bonds involved in the codon-anticodon interaction. A codon is characterized
Edmundo Rofman; Melina Rapacioli; Vladimir Flores
Apolipoprotein B48 is the Product of a Messenger RNA with an Organ-Specific In-Frame Stop Codon
The primary structure of human apolipoprotein (apo) B-48 has been deduced and shown by a combination of DNA excess hybridization, sequencing of tryptic peptides, cloned complementary DNAs, and intestinal messenger RNAs (mRNAs) to be the product of an intestinal mRNA with an in-frame UAA stop codon resulting from a C to U change in the codon CAA encoding Gln2153 in
San-Hwan Chen; Geetha Habib; Chao-Yuh Yang; Zi-Wei Gu; Bo Rong Lee; Shi-Ai Weng; Steven R. Silberman; Sheng-Jian Cai; J. P. Deslypere; Maryvonne Rosseneu; Antonio M. Gotto; Wen-Hsiung Li; Lawrence Chan
Trends in Codon and Amino Acid Usage in Human Pathogen Tropheryma Whipplei, the only Known Actinobacteria with Reduced Genome
The factors governing codon and amino acid usages in the predicted protein-coding sequences of Tropheryma whipplei TW08\\/27 and Twist genomes have been analyzed. Multivariate analysis identifies the replicational-transcriptional selection coupled with DNA strand-specific asymmetric mutational bias as a major driving force behind the significant inter-strand variations in synonymous codon usage patterns in T. whipplei genes, while a residual intra-strand synonymous
Sabyasachi Das; Sandip Paul; Chitra Dutta
Evolutionary Constraints on Codon and Amino Acid Usage in Two Strains of Human Pathogenic Actinobacteria Tropheryma whipplei
The factors governing codon and amino acid usages in the predicted protein-coding sequences of Tropheryma whipplei TW08\\/27 and Twist genomes have been analyzed. Multivariate analysis identifies the replicational-transcriptional selection\\u000a coupled with DNA strand-specific asymmetric mutational bias as a major driving force behind the significant interstrand variations\\u000a in synonymous codon usage patterns in T. whipplei genes, while a residual intrastrand synonymous
Sabyasachi Das; Sandip Paul; Chitra Dutta
Harvey ras Genes Transform without Mutant Codons, Apparently Activated by Truncation of a 5' Exon (Exon --1)
The hypothesis is tested that the ras gene of Harvey sarcoma virus (Ha-SV) and the proto-ras DNAs from certain tumor cells derive transforming function from specific codons in which they differ from normal proto-ras genes. Molecularly cloned Harvey proviral vectors carrying viral ras, normal rat proto-ras, and recombinant ras genes in which the virus-specific ras codons 12 and 59 were
Klaus Cichutek; Peter H. Duesberg
Glycine to Aspartic Acid Mutations at Codon 13 of the c-Ki-ras Gene in Human Gastrointestinal Cancers1
Point mutations of c-ras genes were analyzed in human gastrointestinal cancers. DNA obtained from the tissues was amplified by polymerase chain reaction and then analyzed by dot blot hybridization assay with oligonucleotide probes to detect mutations at codons 12, 13, and 61 of c- Ki-ras, c-Ha-ras, and c-N-ras. In two of 25 cases of stomach cancer point mutations at codon
Yasuhiko Nagata; Masumi Abe; Kohmei Kobayashi; Kuniko Yoshida; Tsunehisa Ishibashi; Tomoki Naoe; Eiichi Nakayama; Hiroshi Sliiktr
Sequence Elements Upstream of the Core Promoter Are Necessary for Full Transcription of the Capsule Gene Operon in Streptococcus pneumoniae Strain D39.
Streptococcus pneumoniae is a major bacterial pathogen in humans. Its polysaccharide capsule is a key virulence factor that promotes bacterial evasion of human phagocytic killing. While S. pneumoniae produces at least 94 antigenically different types of capsule, the genes for biosynthesis of almost all capsular types are arranged in the same locus. The transcription of the capsular polysaccharide (cps) locus is not well understood. This study determined the transcriptional features of the cps locus in the type 2 virulent strain D39. The initial analysis revealed that the cps genes are cotranscribed from a major transcription start site at the -25 nucleotide (G) upstream of cps2A, the first gene in the locus. Using unmarked chromosomal truncations and a luciferase-based transcriptional reporter, we showed that the full transcription of the cps genes not only depends on the core promoter immediately upstream of cps2A, but also requires additional elements upstream of the core promoter, particularly a 59-bp sequence immediately upstream of the core promoter. Unmarked deletions of these promoter elements in the D39 genome also led to significant reduction in CPS production and virulence in mice. Lastly, common cps gene (cps2ABCD) mutants did not show significant abnormality in cps transcription, although they produced significantly less CPS, indicating that the CpsABCD proteins are involved in the encapsulation of S. pneumoniae in a posttranscriptional manner. This study has yielded important information on the transcriptional characteristics of the cps locus in S. pneumoniae. PMID:25733517
Wen, Zhensong; Sertil, Odeniel; Cheng, Yongxin; Zhang, Shanshan; Liu, Xue; Wang, Wen-Ching; Zhang, Jing-Ren
Upstream migration of two pre-spawning shortnose sturgeon passed upstream of Pinopolis Dam, Cooper River, South Carolina
Two shortnose sturgeon were artificially passed above the Pinopolis Lock and Dam into the Santee-Cooper Lakes in order to simulate the use of a fish-passage mechanism. Movement patterns and spawning behavior were studied to determine the potential success of future shortnose sturgeon migrations if and when a fish-migration bypass structure is installed. In addition to movement patterns, water temperature was monitored in areas that shortnose sturgeons utilized. Shortnose sturgeon migrated through a large static system to a known shortnose sturgeon spawning area more than 160 km upstream where water temperatures were consistent with known shortnose sturgeon spawning temperatures. No specific movement patterns in the reservoir system were recorded during downstream migrations.
Finney, S.T.; Isely, J.J.; Cooke, D.W.
The START III bargaining space
The declining state of the Russian military and precarious Russian economic condition will give the US considerable advantages at the START III bargaining table. Taking the US-RF asymmetries into account, this paper discusses a menu of START III measures the US could ask for, and measures it could offer in return, in attempting to negotiate an equitable treaty. Measures the US might seek in a START III treaty include: further reductions in deployed strategic nuclear warheads, irreversibility of reductions through warhead dismantlement; beginning to bring theater nuclear weapons under mutual control, and increased transparency into the Russian nuclear weapons complex. The US may, however, wish to apply its bargaining advantages to attempting to achieve the first steps toward two long-range goals that would enhance US security: bringing theater nuclear weapons into the US-RF arms control arena, and increasing transparency into the Russian nuclear weapons complex. In exchange for measures relating to these objectives, the US might consider offering to Russia: Further strategic weapons reductions approaching levels at which the Russians believe they could maintain a degree of parity with the US; Measures to decrease the large disparities in potential deliver-system uploading capabilities that appear likely under current START II/START III scenarios; and Financial assistance in achieving START II/START III reductions as rapidly as is technically possible.
Karas, T.H.
78 FR 2038 - Notice of Availability of Proposed New Starts and Small Starts Policy Guidance
Federal Register 2010, 2011, 2012, 2013, 2014
...guidance to sponsors of New Starts and Small Starts projects, and inviting comment...apply in evaluating projects seeking New Starts and Small Starts funding...criteria required for New Starts and Small Starts projects. DATES: Comments...
Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid
While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (?GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. PMID:25200075
Babbitt, Gregory A.; Alawad, Mohammed A.; Schulze, Katharina V.; Hudson, André O.
Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags
Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (?10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid. PMID:23315666
Ahmad, Touqeer; Sablok, Gaurav; Tatarinova, Tatiana V.; Xu, Qiang; Deng, Xiu-Xin; Guo, Wen-Wu
Upstream regulatory regions required to stabilize binding to the TATA sequence in an adenovirus early promoter.
Of the five early adenovirus promoters, the early region 3 (E3) promoter is one of the most strongly induced by the E1A protein. To identify cellular proteins involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, DNase I footprinting using partially purified Hela cell extracts was performed. Four regions of the E3 promoter serve as binding domains for cellular proteins. These regions are found between -156 to -179 (site IV), -83 to -103 (site III), -47 to -67 (site II), and -16 to -37 (site I), relative to the start of transcription. Examination of the DNA sequences in each binding domain suggests that site III likely serves as a binding site for activator protein 1 (AP-1), site II for the cyclic AMP regulatory element binding protein (CREB), and site I for a TATA binding factor. The factors binding to either site II or III were sufficient to stabilize binding to the TATA sequence (site I). Mutagenesis studies indicated that both sites II and III, in addition to site I, are needed for complete basal and E1A-induced transcription. These results suggest that multiple cellular factors are involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, and that either of two upstream regions are capable of stabilizing factor binding to the TATA sequence. PMID:2959908
Garcia, J; Wu, F; Gaynor, R
Innovation and performance: The case of the upstream petroleum sector
NASA Astrophysics Data System (ADS)
This thesis investigates innovation in the upstream crude oil and natural gas sector, a strategic part of the Canadian economy and a vital industry for North American energy trade and security. Significant interest exists in understanding innovation in this sector from a private and public policy perspective. Interest in the sector has intensified recently due to concerns about world oil supply, Canada's oil sands development, and the potential that Canada may become an "energy superpower." The study examines the factors that drive companies involved in exploration, development, and production in the upstream petroleum sector to innovate and the impact of their innovation activities through major technologies on their performance. The thesis focuses on process innovation, which involves the adoption of new or significantly improved production processes, and is distinct from product innovation, which is based on the development and commercialization of a product with improved product characteristics to deliver new services to the consumer. The thesis provides a comprehensive review of the literature and develops an investigative model framework to examine the drivers of innovation and the impact of innovation on performance in the upstream petroleum sector. The research employs a survey questionnaire that was developed to obtain data and information, which was missing in the literature or not publicly available to test key relationships of innovation and performance indicators. In addition to the survey questionnaire, a number of knowledgeable experts in the industry were also interviewed. A total of 68 respondents completed the survey questionnaire, accounting for 40 percent of the firms in the industry. This percentage goes up to over 50 percent when account is taken of extremely small firms who could not fill out the survey. Further, the 68 respondents account for most of the industry revenues, production, and employment. The respondents include most of the key explorers, developers, and producers as well as the owners of the major projects and oil sands developments. Almost all firms in the industry with revenues above $1B with employees above 1000 responded to the survey. As well, many companies have joint project arrangements and farm-in agreements with other companies in the industry. Hence, this survey is considered highly representative of the industry. Industry associations were very helpful in providing advice, and in endorsing the circulation of the questionnaire. The results show that the sector relies more heavily on acquiring advanced machinery and equipment, processes and other external knowledge than on internal R&D. Advanced machinery and equipment includes embedded R&D. 3D and 4D seismic stand out as the most relied upon in exploration, horizontal wells in development activities, and field recovery in production. Increasing productive capacity, reducing costs and reducing environmental impact are the three main drivers of innovation. Collaboration is important to the sector and agreements with competitors and suppliers are ranked as most important. The main reason for collaboration is to gain access to external knowledge. Government tax incentives (e.g., the Scientific Research and Experimental Development) (SR&ED) tax credit and its fiscal framework are important in spurring R&D. Fiscal policies, on the other hand, are more important for acquiring advanced machinery and equipment, advanced processes, and other external knowledge. The study has several broad implications with respect to the application of technologies: (1) Without the adoption of major technologies, costs would have been substantially higher and productive capacity and productivity much lower. This study also contributes to the view that resources should not be treated as a fixed stock but as flow which can be improved. (2) The environment is an important driver of innovation, particularly environmental regulation. Providing the right mix of regulation and leaving firms to undertake innovation may result in fav
Persaud, A. C. Jai
Trainee: _________________________________ PI: _________________________________ Employee Start Date: ______________________
Trainee: _________________________________ PI: _________________________________ Employee Start Date: ______________________ SCIPP Laboratory-Specific Safety Training Checklist Prior to beginning&S Laboratory Safety Training 2. Read and understand the contents of the UCSC Lab Safety Manual (http
California at Santa Cruz, University of
Quantum Espresso Quick Start Introduction
Quantum Espresso Quick Start Introduction Quantum Espresso (http://www.quantum properties eg., phonon dispersion, NMR shifts and band structure to name a few. Quantum Espresso is available. Matter 21, 395502 (2009). Online Guide for QE : http://www.quantum
Bjørnstad, Ottar Nordal
Psychiatric Advance Directives: Getting Started
... Getting Started State by State Info FAQs Educational Webcasts Links Current Research In the News Legal Issues ... How to write a Psychiatric Advance Directive?" View webcast (15:04) What are Psychiatric Advance Directives? View ...
Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes
Background Accurate modelling of substitution processes in protein-coding sequences is often hampered by the computational burdens associated with full codon models. Lately, codon partition models have been proposed as a viable alternative, mimicking the substitution behaviour of codon models at a low computational cost. Such codon partition models however impose independent evolution of the different codon positions, which is overly restrictive from a biological point of view. Given that empirical research has provided indications of context-dependent substitution patterns at four-fold degenerate sites, we take those indications into account in this paper. Results We present so-called context-dependent codon partition models to assess previous empirical claims that the evolution of four-fold degenerate sites is strongly dependent on the composition of its two flanking bases. To this end, we have estimated and compared various existing independent models, codon models, codon partition models and context-dependent codon partition models for the atpB and rbcL genes of the chloroplast genome, which are frequently used in plant systematics. Such context-dependent codon partition models employ a full dependency scheme for four-fold degenerate sites, whilst maintaining the independence assumption for the first and second codon positions. Conclusions We show that, both in the atpB and rbcL alignments of a collection of land plants, these context-dependent codon partition models significantly improve model fit over existing codon partition models. Using Bayes factors based on thermodynamic integration, we show that in both datasets the same context-dependent codon partition model yields the largest increase in model fit compared to an independent evolutionary model. Context-dependent codon partition models hence perform closer to codon models, which remain the best performing models at a drastically increased computational cost, compared to codon partition models, but remain computationally interesting alternatives to codon models. Finally, we observe that the substitution patterns in both datasets are drastically different, leading to the conclusion that combined analysis of these two genes using a single model may not be advisable from a context-dependent point of view. PMID:21619569
Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression.
Roy et al. [Roy, A., Haziza, C. & Danchin, A. (1983) EMBO J. 2, 791-797] established that translation of Escherichia coli adenylate cyclase initiates at a UUG codon, and they suggested this might decrease the efficiency of translation. We investigated the effect of varying the initiation codon on the expression of the adenylate cyclase (cya) gene. Using oligonucleotide-directed mutagenesis, we changed the UUG initiation codon to GUG and the more common initiator AUG and assayed for cya gene expression in a number of ways. First, the GUG initiation codon, in place of UUG, doubled cya expression when cya was expressed from the dual cya P1/P2 promoters. The corresponding AUG codon construct was nonviable. Second, when the cya gene was placed under the transcriptional control of the thermoinducible phage lambda PL promoter, the relative amounts of cya gene product were 1:2:6 for the UUG, GUG, and AUG initiation codons, respectively. Finally, the cya P2 promoter, Shine-Dalgarno sequence, and the DNA corresponding to the first 86 codons of cya were fused to DNA encoding the E. coli galactokinase gene beginning at the second codon. The relative amounts of the fusion polypeptides, which had galactokinase activity, were 1:2:3 for the UUG, GUG, and AUG initiation codons, respectively. These results demonstrate that the cya UUG initiation codon limits cya expression at the level of translation. PMID:3898067
Reddy, P; Peterkofsky, A; McKenney, K
A study of the purine/pyrimidine codon occurrence with a reduced centered variable and an evaluation compared to the frequency statistic.
With the three-letter alphabet [R,Y,N] (R = purine, Y = pyrimidine, N = R or Y), there are 26 codons (NNN being excluded): RNN,...,NNY (six codons at two unspecified bases N), RRN,...,NYY (12 codons at one unspecified base N), RRR,...,YYY (eight specified codons). A statistical methodology that uses the codon frequency and a reduced centered variable leads to similar results for a codon occurrence study, regardless of gene function and regardless of a particular protein coding gene taxonomic population. Therefore, this variable can be considered a new codon usage index, whose use removes certain nonsignificant results found with the frequency statistic. This methodology identifies the common and rare codons (i.e., the codons having the highest and lowest occurrence) and leads to a model of codon evolution at three successive states: RNN, then RNY, and finally RYY. Some biological relations between this model and the YRY(N)6YRY preferential occurrence are also presented. PMID:2520209
Michel, C J
Statistical study of plasma properties upstream the Earth's bow shock
NASA Astrophysics Data System (ADS)
Observations of solar wind parameters at L1 are usually considered as a good measure for investigation of magnetospheric processes. On the other hand, several studies suggest observable changes of the solar wind speed in front of the bow shock. We use five years of THEMIS-ARTEMIS observations in the solar wind and compare the speed measured by these spacecraft with the Wind solar wind speed registered at L1 and propagated to their locations. We have found that the changes (decrease) of the solar wind speed in front of the bow shock are well correlated with the amplitude of upstream magnetic field fluctuations and/or with a content of accelerated ions. The effect is as large as 6% and it is notable up to 30 RE from the bow shock, i.e., at larger distances than previously reported. The released energy is spent partly on an acceleration of reflected particles and excitation of foreshock waves but a significant heating of the solar wind beam is also observed.
Urbar, Jaroslav; Nemecek, Zdenek; Safrankova, Jana; Jelinek, Karel; Prech, Lubomir
Rheotaxis facilitates upstream navigation of mammalian sperm cells
A major puzzle in biology is how mammalian sperm maintain the correct swimming direction during various phases of the sexual reproduction process. Whilst chemotaxis may dominate near the ovum, it is unclear which cues guide spermatozoa on their long journey towards the egg. Hypothesized mechanisms range from peristaltic pumping to temperature sensing and response to fluid flow variations (rheotaxis), but little is known quantitatively about them. We report the first quantitative study of mammalian sperm rheotaxis, using microfluidic devices to investigate systematically swimming of human and bull sperm over a range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions, and chirality of the flagellar beat leads to stable upstream spiralling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. A minimal mathematical model is presented that accounts quantitatively for the experimental observations. DOI: http://dx.doi.org/10.7554/eLife.02403.001 PMID:24867640
Kantsler, Vasily; Dunkel, Jörn; Blayney, Martyn; Goldstein, Raymond E
Rheotaxis facilitates upstream navigation of mammalian sperm cells
A major puzzle in biology is how mammalian sperm determine and maintain the correct swimming direction during the various phases of the sexual reproduction process. Whilst chemotaxis is assumed to dominate in the immediate vicinity of the ovum, it is unclear which biochemical or physical cues guide spermatozoa on their long journey towards the egg cell. Currently debated mechanisms range from peristaltic pumping to temperature sensing (thermotaxis) and direct response to fluid flow variations (rheotaxis), but little is known quantitatively about their relative importance. Here, we report the first quantitative experimental study of mammalian sperm rheotaxis. Using microfluidic devices, we investigate systematically the swimming behavior of human and bull sperm over the whole range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions and chirality of the flagellar beat leads to a stable upstream spiraling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. To rationalise these findings, we identify a minimal mathematical model that is capable of describing quantitatively the experimental observations. The combined experimental and theoretical evidence supports the hypothesis that the shape and beat patterns of mammalian sperm cells have evolved to optimally exploit rheotaxis for long-distance navigation.
Vasily Kantsler; Jörn Dunkel; Martyn Blayney; Raymond E. Goldstein
Large amplitude MHD waves upstream of the Jovian bow shock
NASA Technical Reports Server (NTRS)
Observations of large amplitude magnetohydrodynamics (MHD) waves upstream of Jupiter's bow shock are analyzed. The waves are found to be right circularly polarized in the solar wind frame which suggests that they are propagating in the fast magnetosonic mode. A complete spectral and minimum variance eigenvalue analysis of the data was performed. The power spectrum of the magnetic fluctuations contains several peaks. The fluctuations at 2.3 mHz have a direction of minimum variance along the direction of the average magnetic field. The direction of minimum variance of these fluctuations lies at approximately 40 deg. to the magnetic field and is parallel to the radial direction. We argue that these fluctuations are waves excited by protons reflected off the Jovian bow shock. The inferred speed of the reflected protons is about two times the solar wind speed in the plasma rest frame. A linear instability analysis is presented which suggests an explanation for many of the observed features of the observations.
Goldstein, M. L.; Smith, C. W.; Matthaeus, W. H.
Electron plasma waves upstream of the earth's bow shock
NASA Technical Reports Server (NTRS)
Electrostatic waves are observed around the plasma frequency fpe in the electron foreshock, together with electrons backstreaming from the bow shock. Using data from the sounder aboard ISEE 1, it is shown that this noise, previously understood as narrow band Langmuir waves more or less widened by Doppler shift or nonlinear effects, is in fact composed of two distinct parts: one is a narrow band noise, emitted just above fpe, and observed at the upstream boundary of the electron foreshock. This component has been interpreted as Langmuir waves emitted by a beam-plasma instability. It is suggested that it is of sufficiently large amplitude and monochromatic enough to trap resonant electrons. The other is a broad band noise, more impulsive than the narrow band noise, observed well above and/or well below fpe, deeper in the electron foreshock. The broad band noise has an average spectrum with a typical bi-exponential shape; its peak frequency is not exactly equal to fpe and depends on the Deybe length. This peak frequency also depends on the velocity for which the electron distribution has maximum skew. An experimental determination of the dispersion relation of the broad band noise shows that this noise, as well as the narrow band noise, may be due to the instability of a hot beam in a plasma.
Lacombe, C.; Mangeney, A.; Harvey, C. C.; Scudder, J. D.
Electron distributions upstream and downstream of ICME driven IP shocks
NASA Astrophysics Data System (ADS)
We study suprathermal electron distributions (E > 80 eV) in regions adjacent to interplanetary (IP) shocks driven by interplanetary coronal mass ejections (ICMEs). The shocks were observed by the two STEREO spacecraft during the years 2007-2010, hence during the minimum and at the beginning of the rising phase of the current solar cycle. All the ICMEs were isolated events, meaning that the shocks were produced only due to interactions of the ICMEs with the solar wind. We find that suprathermal electron pitch angle distributions (PADs) in regions adjacent to ICME driven IP shocks vary from shock to shock. At some shocks, these electrons show the "usual" isotropic halo and a narrow, field-aligned strahl. The PADs upstream and downstream of these shocks differ only in the width of the strahl, with the later being wider in the downstream regions. In other cases we observe unusual downstream conical distributions at intermediate angles (between 0 and 90 or 90 and 180° PA), counterstreaming electrons at the shock transitions and downstream PADs without the strahl component. Here we present two shocks from our sample with such unusual electrons distributions, not reported in the literature.
Kajdi?, P.; Blanco-Cano, X.; Opitz, A.; Sauvaud, J.-A.; Aguilar-Rodriguez, E.; Russell, C. T.; Luhmann, J. G.; Jian, L. K.; Rouillard, A. P.; Lavraud, B.
Upstream binding factor association induces large-scale chromatin decondensation
The function of upstream binding factor (UBF), an essential component of the RNA polymerase (pol) I preinitiation complex, is unclear. Recently, UBF was found distributed throughout ribosomal gene repeats rather than being restricted to promoter regions. This observation has led to the speculation that one role of UBF binding may be to induce chromatin remodeling. To directly evaluate the impact of UBF on chromatin structure, we used an in vivo assay in which UBF is targeted via a lac repressor fusion protein to a heterochromatic, amplified chromosome region containing lac operator repeats. We show that the association of UBF with this locus induces large-scale chromatin decondensation. This process does not appear to involve common remodeling complexes, including SWI/SNF and histone acetyltransferases, and is independent of histone H3 lysine 9 acetylation. However, UBF recruits the pol I-specific, TATA box-binding protein containing complex SL1 and pol I subunits. Our results suggest a working hypothesis in which the dynamic association of UBF with ribosomal DNA clusters recruits the pol I transcription machinery and maintains these loci in a transcriptionally competent configuration. These studies also provide an in vivo model simulating ribosomal DNA transactivation outside the nucleolus, allowing temporal and spatial analyses of chromatin remodeling and assembly of the pol I transcription machinery. PMID:15477594
Chen, Danyang; Belmont, Andrew S.; Huang, Sui
Resistance to MEK Inhibitors: Should We Co-Target Upstream?
NSDL National Science Digital Library
Aberrant activation of the ERK pathway is common in human tumors. This pathway consists of a three-tiered kinase module [comprising the kinases RAF, mitogen-activated protein kinase (MAPK) kinase (MEK), and extracellular signal–regulated kinase (ERK)] that functions as a negative feedback amplifier to confer robustness and stabilization of pathway output. Because this pathway is frequently dysregulated in human cancers, intense efforts are under way to develop selective inhibitors of the ERK pathway as anticancer drugs. Although promising results have been reported in early trials for inhibitors of RAF or MEK, resistance invariably occurs. Amplification of the upstream oncogenic driver of ERK signaling has been identified as a mechanism for MEK inhibitor resistance in cells with mutant BRAF or KRAS. Increased abundance of the oncogenic driver (either KRAS or BRAF in the appropriate cellular context) in response to prolonged drug treatment results in increased flux through the ERK pathway and restoration of ERK activity above the threshold required for cell growth. For patients with BRAF mutant tumors, the results suggest that the addition of a RAF inhibitor to a MEK inhibitor may delay or overcome drug resistance. The data thus provide a mechanistic basis for ongoing trials testing concurrent treatment with RAF and MEK inhibitors.
Poulikos I. Poulikakos (Memorial Sloan-Kettering Cancer Center; Program in Molecular Pharmacology and Chemistry REV)
Limitations of the 'ambush hypothesis' at the single-gene scale: what codon biases are to blame?
Ribosomal frameshifting, a translational error, catastrophically alters the amino acid composition of the nascent protein by shifting the reading frame from the intended contiguous trinucleotide reading. Frameshift events waste energy and resources, and peptide products have unpredictable cytotoxic effects. The 'Ambush Hypothesis' (Seligmann and Pollock 2004, DNA Cell Biol 23:701-5) suggests there is a selective pressure favouring the evolution of out-of-frame ('hidden') stop codons. Although this hypothesis has gained empirical support through whole-genome studies, it is presently unknown whether it can be applied at a single-gene scale. Herein, we report such an investigation using the gene, polyketide synthase (PKS), among species of fungi. Contrary to expectation, genes presented with significantly lower number of hidden stop codons than expected in a selection-neutral model (p < 0.0005), suggesting both non-adherence to the ambush hypothesis as well as suppression of hidden stop codon evolution. It is known that there are multiple adaptive considerations determining codon selection during evolution, and that the information-holding potential of the genetic code is finite. We hypothesize that the reason for low hidden stops in PKS genes is due to competing 'codon biases' that are prioritized over the selective pressure favouring the emergence of hidden stops. Future studies of the ambush hypothesis in the context of other drivers of codon bias may allow this hypothesis to be molded into a comprehensive genetic theory that can be integrated within the broader genetic theory of codon bias and applied to the genetic code at any scale of analysis. PMID:25307067
Bertrand, Robert L; Abdel-Hameed, Mona; Sorensen, John L
Upstream regulatory sequences of the yeast RNR2 gene include a repression sequence and an activation site that binds the RAP1 protein.
The small subunit of ribonucleotide reductase in Saccharomyces cerevisiae (RNR2) was induced 3- to 20-fold by a variety of DNA-damaging agents. Induction of the RNR2 transcript by at least one of these agents, methyl methanesulfonate, did not require protein synthesis. To identify sequences involved in the regulation of RNR2, we introduced deletions upstream of the transcription start site. Sequences required for induction were contained within a 200-base-pair region that could confer methyl methanesulfonate inducibility on the heterologous CYC1 promoter. This region contained a repression sequence and at least two positive activation sites. One of these activation sites bound RAP1, a protein known to associate with mating-type silencers and the upstream activation sequences of a number of genes. The behavior of deletions of the repression sequence suggests that induction of RNR2 may occur, at least in part, through relief of repression. Images PMID:2685560
Hurd, H K; Roberts, J W
Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine
Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409
Wang, Pei; Song, Fan; Cai, Wanzhi
Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization.
Human respiratory syncytial virus (RSV) is the most important viral agent of serious pediatric respiratory-tract disease worldwide. A vaccine or generally effective antiviral drug is not yet available. We designed new live attenuated RSV vaccine candidates by codon-pair deoptimization (CPD). Specifically, viral ORFs were recoded by rearranging existing synonymous codons to increase the content of underrepresented codon pairs. Amino acid coding was completely unchanged. Four CPD RSV genomes were designed in which the indicated ORFs were recoded: Min A (NS1, NS2, N, P, M, and SH), Min B (G and F), Min L (L), and Min FLC (all ORFs except M2-1 and M2-2). Surprisingly, the recombinant CPD viruses were temperature-sensitive for replication in vitro (level of sensitivity: Min FLC > Min L > Min B > Min A). All of the CPD mutants grew less efficiently in vitro than recombinant wild-type (WT) RSV, even at the typically permissive temperature of 32 °C (growth efficiency: WT > Min L > Min A > Min FLC > Min B). CPD of the ORFs for the G and F surface glycoproteins provided the greatest restrictive effect. The CPD viruses exhibited a range of restriction in mice and African green monkeys comparable with that of two attenuated RSV strains presently in clinical trials. This study provided a new type of attenuated RSV and showed that CPD can rapidly generate vaccine candidates against nonsegmented negative-strand RNA viruses, a large and expanding group that includes numerous pathogens of humans and animals. PMID:25157129
Le Nouën, Cyril; Brock, Linda G; Luongo, Cindy; McCarty, Thomas; Yang, Lijuan; Mehedi, Masfique; Wimmer, Eckard; Mueller, Steffen; Collins, Peter L; Buchholz, Ursula J; DiNapoli, Joshua M
Impact of TP53 Codon 72 and MDM2 SNP 309 Polymorphisms in Pancreatic Ductal Adenocarcinoma
Single-nucleotide polymorphisms (SNPs) of TP53 (codon 72, rs1042522) and MDM2 promoter (SNP 309, rs2279744) have been associated with risk for various human cancers. However, studies analyzing these polymorphisms in pancreatic ductal adenocarcinoma (PDAC) are lacking. We investigated TP53 codon 72 and MDM2 SNP 309 polymorphisms in 32 patients with PDAC, 16 patients with chronic pancreatitis (CP), and 32 normal controls, using formalin-fixed paraffin-embedded tissue. We also examined TP53 and MDM2 protein immunohistochemistry (IHC) to assess the involvement of these differences in malignant transformation and disease progression. TP53 Pro/Pro genotype was significantly more frequent in PDAC patients than in controls (65.6 vs. 15.6%, p < 0.001) and no significant difference was found between CP patients (37.5%) and controls. In MDM2 SNP 309, there were no significant differences among the three groups. Based on the Kaplan-Meier analysis, overall survival was significantly shorter in MDM2 G/G genotypes compared with other genotypes (G/T and T/T) (359 vs. 911 days, p = 0.016) whereas no significant differences in TP53 genotypes were observed (638 vs. 752 days, p = 0.471). Although TP53 IHC was frequent in PDAC patients (53.1%), TP53 and MDM2 protein expression was not correlated with polymorphisms. Our study demonstrated TP53 codon 72 polymorphism is potentially a genetic predisposing factor while MDM2 SNP 309 polymorphism might be useful in predicting survival outcome. PMID:25734904
Hori, Yasuki; Miyabe, Katsuyuki; Yoshida, Michihiro; Nakazawa, Takahiro; Hayashi, Kazuki; Naitoh, Itaru; Shimizu, Shuya; Kondo, Hiromu; Nishi, Yuji; Umemura, Shuichiro; Kato, Akihisa; Ohara, Hirotaka; Inagaki, Hiroshi; Joh, Takashi
Nonsense-mediated translational repression involves exon junction complex downstream of premature translation termination codon.
Human transforming growth factor-beta receptor type 2 (TGFbetaR2) mRNA harboring a premature translation termination codon (PTC) generated by frameshift mutation is targeted for nonsense-mediated translational repression (NMTR), rather than nonsense-mediated mRNA decay (NMD). Here we show that exon junction complex (EJC) downstream of a PTC plays an inhibitory role in translation of TGFbetaR2 mRNA. Translational repression by core EJC components occurs after formation of 80S ribosome complex, which is demonstrated using different types of internal ribosome entry sites (IRESes). Our findings implicate EJCs or core EJC components as negative regulators of translation. PMID:20067791
Lee, Hyung Chul; Oh, Nara; Cho, Hana; Choe, Junho; Kim, Yoon Ki
Deceleration of the solar wind upstream from the earth's bow shock and the origin of diffuse upstream ions
NASA Technical Reports Server (NTRS)
Observations with the Los Alamos Scientific Laboratory/Max-Planck-Institut crossed-fan solar wind ion experiment on ISEE I reveal that the solar wind is decelerated and deflected away from the direction of the earth's bow shock as it enters that portion of the upstream region populated by diffuse bow shock ions and long-period (10-60 s) waves. Typically, the average directed velocity vector changes by 7-10 km/s as it enters the wave region. At times, average speed changes as large as 25-40 km/s are observed. Superposed upon these changes in average flow speed are large amplitude (+ or - 15) fluctuations in flow speed associated with the waves themselves. The observations suggest that the solar wind deceleration is the result of momentum transfer from reflected bow shock ions to the wind via the long-period waves as the reflected ion beams go unstable. The broad angular distributions of the diffuse ions thus appear to be produced as a consequence of the disruption of reflected ion beams.
Bame, S. J.; Asbridge, J. R.; Feldman, W. C.; Gosling, J. T.; Paschmann, G.; Skopke, N.
"Upstream Thinking": the catchment management approach of a water provider
NASA Astrophysics Data System (ADS)
Human activities have large impacts on water quality and provision. Water companies throughout the UK are faced with the consequences of poor land management and need to find appropriate solutions to decreasing water quality. This is particularly true in the South West of England, where 93% of the drinking water is sourced from rivers and reservoirs: large areas of drained peatlands (i.e. Exmoor and Dartmoor National Parks) are responsible for a significant input of dissolved organic carbon (DOC) discolouring the water, whilst poorly managed farming activities can lead to diffuse pollution. Alongside the direct environmental implications, poor water quality is partly increasing water treatment costs and will drive significant future investment in additional water treatment, with further repercussions on customers. This highlights the need for water companies throughout the UK, and further afield, to be more involved in catchment management. "Upstream Thinking" is South West Water's (SWW) approach to catchment management, where working with stakeholders to improve water quality upstream aims to avoid increasingly costly solutions downstream. This approach has led the company to invest in two major areas of work: (1) The Farmland programme where problematic farm management practices and potential solutions are identified, typically 40% of the required investment is then offered in exchange for a legal undertaking to maintain the new farm assets in good condition for 25 years; (2) The Mires programme which involves heavy investment in peatland restoration through the blocking of open ditches in order to improve water storage and quality in the long term. From these two projects, it has been clear that stakeholder involvement of groups such as local farmers, the Westcountry Rivers Trust, the Exmoor National Park Authority, the Environment Agency, Natural England and the Exmoor Society is essential, first because it draws in catchment improvement expertise which is not directly held within the company, and second because it shows how local communities and groups are considered and valued by the company. Monitoring changes and providing a solid scientific base is also undertaken to prove the concept and justify any investment. The work carried out so far has highlighted that SWW's collaborative approach to catchment management is changing the relationship between private water suppliers in the UK and stakeholders or groups having an impact on water quality. This results in a progressive move from a situation where the polluter has to pay, to rewarding providers of clean water instead. The value of ecosystem payments of this kind is being discussed with the appropriate authorities (i.e. Natural England, and the Department for Environment, Food and Rural Affairs) so that it can form part of ensuring sustainable water supplies in future, with all the environmental and ecological benefits of clear raw waters in rivers, lakes and streams.
Grand-Clement, E.; Ross, M.; Smith, D.; Anderson, K.; Luscombe, D.; Le Feuvre, N.; Brazier, R. E.
Methods of upstream power backoff on very high speed digital subscriber lines
This article describes the near-far problem in the upstream direction of VDSL, which results when the lengths of VDSL loops in a binder vary significantly. Methods of upstream power backoff to mitigate the near-far problem are then described. Simulation results are presented, and the performances of the methods are discussed
Krista S. Jacobsen; Texas Instruments
The Benthos-Plankton Relationship Upstream and Downstream of a Blackwater Impoundment
The phytoplankton, zooplankton, and the macroinvertebrate snag communities of Black Creek, South Carolina, upstream and downstream of an impoundment were Investigated during 1982. Phytoplankton and zooplankton densities upstream of the impoundment were very low. The reservoir outflow contributed a large part of the zooplankton of all sizes to the stream immediately below the impoundment. Large copepods and cladocerans were almost
David D. Herlong; Michael A. Mallin
Direct Correlations of Large-Amplitude Waves with Suprathermal Protons in the Upstream Solar Wind
SUMMARY We present here the results of direct correlations of magnetometer, plasma wave detector, plasma probe, and Lepedea proton data taken simultaneously by experiments aboard Ogo 5 during a large upstream wave event, on March 10, 1968. Direct correlation of Lepedea fluxes with magnetometer fluctuations shows that the large upstream wave amplitudes occur when enhanced fluxes of protons with Ep
F. L. Scarf; R. W. Fredricks; L. A. Frank; C. T. Russell; P. J. Coleman; M. Neugebauer
Observational evidence on the origin of ions upstream of the earth's bow shock
The energies predicted by four different source hypotheses for ions observed upstream of the earth's bow shock are compared with observations of upstream field-aligned beams and gyrating ion events. A kinematic formalism in a frame of reference in which the motional electric field vanishes is used. Specular reflection of a fraction of the incident solar wind is found to be
M. F. Thomsen; S. J. Schwartz; J. T. Gosling
Energetic-ion acceleration and transport in the upstream region of Jupiter: Voyager 1 and 2
NASA Technical Reports Server (NTRS)
Long-lived upstream energetic ion events at Jupiter appear to be very similar in nearly all respects to upstream ion events at Earth. A notable difference between the two planetary systems is the enhanced heavy ion compositional signature reported for the Jovian events. This compositional feature has suggested that ions escaping from the Jovian magnetosphere play an important role in forming upstream ion populations at Jupiter. In contrast, models of energetic upstream ions at Earth emphasize in situ acceleration of reflected solar wind ions within the upstream region itself. Using Voyager 1 and 2 energetic ( approximately 30 keV) ion measurements near the magnetopause, in the magnetosheath, and immediately upstream of the bow shock, the compositional patterns are examined together with typical energy spectra in each of these regions. A model involving upstream Fermi acceleration early in events and emphasizing energetic particle escape in the prenoon part of the Jovian magnetosphere late in events is presented to explain many of the features in the upstream region of Jupiter.
Baker, D. N.; Zwickl, R. D.; Carbary, J. F.; Krimigis, S. M.; Lepping, R. P.
Simultaneous observations of energetic \\/keV\\/ upstreaming and electrostatic hydrogen cyclotron waves
A study is presented of upstreaming energetic ions in the kilovolt energy range and electrostatic hydrogen cyclotron (EHC) waves made using the ion mass spectrometer and plasma wave receiver sets for the first 1200 orbits of the S3-3 spacecraft. It was shown that the upstreaming ions are producing the EHC waves or that the EHC waves are heating the ions;
P. M. Kintner; M. C. Kelley; R. D. Sharp; A. G. Ghielmetti; M. Temerin; C. Cattell; P. F. Mizera; J. F. Fennell
Upstream method tailings dam c onstruction has been used throughout the world as an economic method for containm ent of slurry deposited tailin gs waste as hydraulic fill. These types of dams can be engineered to be stable in low seis micity zones of the world with c ontrol of the water pool away from the dam limits. Upstream method
Expressions of heparanase and upstream stimulatory factor in hepatocellular carcinoma
Background The expression of heparanase (HPSE) was associated with postoperative metastatic recurrence in patients with hepatocellular carcinoma (HCC). The six E-box binding sites in the core promoter of the HPSE gene suggested that transcription factors of E-box such as upstream stimulatory factor (USF) might regulate the transcription of the HPSE gene. The aim of our study is to measure the levels of HPSE and USF expression and investigate the relationship between USF expression and clinicopathological parameters in patients with HCC. Methods HPSE, USF1 and USF2 expressions in human HCC cell lines (BEL-7402, HepG2 and HCCLM3) and 15 fresh human HCC tissue samples were measured by real-time reverse transcriptase-PCR and Western blot analysis. The normal liver cell line QSG7701 or fresh normal liver tissue samples obtained from 15 additional surgical patients with hepatic rupture was used as a control. The protein expressions were determined by immunohistochemistry in paraffin-embedded human HCC tissues and corresponding non-neoplastic tumor surrounding tissues (NTST) of 57 patients. Results HPSE, USF1 and USF2 mRNA expressions were increased in HCC cell lines and HCC tissues compared with normal liver cell line and normal liver tissue. The protein expressions of HPSE, USF1 and USF2 in HCC cell lines and HCC tissues were also increased. Both USF1 and USF2 expressions were positively correlated with HPSE. USF1 and USF2 expressions were increased in patients with liver cirrhosis, worse tissue differentiation, advanced HCC stages and metastatic recurrence. Conclusions Increased USF in HCC is associated with HPSE expression. USF might be an important factor in regulating HPSE expression and act as a novel marker of metastatic recurrence of HCC patients. PMID:25149140
78 FR 49372 - Notice of Availability of New Starts and Small Starts Policy Guidance
Federal Register 2010, 2011, 2012, 2013, 2014
...commitment criteria for New Starts and Small Starts projects. The final...organizations, a private business, and an interested citizen...2013. Sponsors of New Starts and Small Starts projects...procedural changes made to the steps in the New Starts...
76 FR 37174 - Capital Investment Program-New Starts and Small Starts Program Funds
Federal Register 2010, 2011, 2012, 2013, 2014
...information on the New Starts, contact Eric Hu...gov mailto:, for project specific issues...Starts and Small Starts programs. After...amount allocated for New Starts and Small Starts...Agreement (FFGA) projects, four pending...
Targeted expression of redesigned and codon optimised synthetic gene leads to recrystallisation inhibition and reduced electrolyte leakage in spring wheat at sub-zero temperatures.
Antifreeze proteins (AFPs) adsorb to ice crystals and inhibit their growth, leading to non-colligative freezing point depression. Crops like spring wheat, that are highly susceptible to frost damage, can potentially be made frost tolerant by expressing AFPs in the cytoplasm and apoplast where ice recrystallisation leads to cellular damage. The protein sequence for HPLC-6 alpha-helical antifreeze protein from winter flounder was rationally redesigned after removing the prosequences in the native protein. Wheat nuclear gene preferred amino acid codons were used to synthesize a recombinant antifreeze gene, rAFPI. Antifreeze protein was targeted to the apoplast using a Murine leader peptide sequence from the mAb24 light chain or retained in the endoplasmic reticulum using C-terminus KDEL sequence. The coding sequences were placed downstream of the rice Actin promoter and Actin-1 intron and upstream of the nopaline synthase terminator in the plant expression vectors. Transgenic wheat lines were generated through micro projectile bombardment of immature embryos of spring wheat cultivar Seri 82. Levels of antifreeze protein in the transgenic lines without any targeting peptide were low (0.06-0.07%). The apoplast-targeted protein reached a level of 1.61% of total soluble protein, 90% of which was present in the apoplast. ER-retained protein accumulated in the cells at levels up to 0.65% of total soluble proteins. Transgenic wheat line T-8 with apoplast-targeted antifreeze protein exhibited the highest levels of antifreeze activity and provided significant freezing protection even at temperatures as low as -7 degrees C. PMID:16847628
Khanna, Harjeet K; Daggard, Grant E
Performance investigation and demonstration of colorless upstream transmission in ECDM-OFDM-PON.
This paper has experimentally demonstrated and analyzed the performance of 2.5-Gb/s × 3-channel upstream transmission in electrical code divided multiplexing-orthogonal frequency division multiplexing access (ECDM-OFDM) passive optical network (PON). The colorless upstream link can be realized in ECDM-OFDM-PON. The experimental results show that the performance degradation due to optical beating interference (OBI) noise can be well suppressed in this network when the three channels adopt the same upstream wavelength. Compared with the WDM-OFDM-PON upstream signals without ECDM, the error floor shows about three orders of magnitude improvement due to the code gain when the same wavelength is used for all upstream signals. PMID:21934818
Liu, Bo; Xin, Xiangjun; Zhang, Lijia; Yu, Jianjun
Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner
Upstream open reading frames (uORFs) are often found in the 5?-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression. PMID:25618853
Ebina, Isao; Takemoto-Tsutsumi, Mariko; Watanabe, Shun; Koyama, Hiroaki; Endo, Yayoi; Kimata, Kaori; Igarashi, Takuya; Murakami, Karin; Kudo, Rin; Ohsumi, Arisa; Noh, Abdul Latif; Takahashi, Hiro; Naito, Satoshi; Onouchi, Hitoshi
Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the "Gene Nursery" of Deltaretroviruses
A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes, e.g. by duplication or horizontal transfer. In contrast, many viruses generate protein-coding genes de novo, via the overprinting of a new reading frame onto an existing ("ancestral") frame. This mechanism is thought to play an important role in viral pathogenicity, but has been poorly explored, perhaps because identifying the de novo frames is very challenging. Therefore, a new approach to detect them was needed. We assembled a reference set of overlapping genes for which we could reliably determine the ancestral frames, and found that their codon usage was significantly closer to that of the rest of the viral genome than the codon usage of de novo frames. Based on this observation, we designed a method that allowed the identification of de novo frames based on their codon usage with a very good specificity, but intermediate sensitivity. Using our method, we predicted that the Rex gene of deltaretroviruses has originated de novo by overprinting the Tax gene. Intriguingly, several genes in the same genomic region have also originated de novo and encode proteins that regulate the functions of Tax. Such "gene nurseries" may be common in viral genomes. Finally, our results confirm that the genomic GC content is not the only determinant of codon usage in viruses and suggest that a constraint linked to translation must influence codon usage. PMID:23966842
Pavesi, Angelo; Magiorkinis, Gkikas; Karlin, David G.
Experience with the use of the Codonics Safe Label System(™) to improve labelling compliance of anaesthesia drugs.
The Codonics Safe Labeling System(™) (http://www.codonics.com/Products/SLS/flash/) is a piece of equipment that is able to barcode scan medications, read aloud the medication and the concentration and print a label of the appropriate concentration in the appropriate colour code. We decided to test this system in our facility to identify risks, benefits and usability. Our project comprised a baseline survey (25 anaesthesia cases during which 212 syringes were prepared from 223 drugs), an observational study (47 cases with 330 syringes prepared) and a user acceptability survey. The baseline compliance with all labelling requirements was 58%. In the observational study the compliance using the Codonics system was 98.6% versus 63.8% with conventional labelling. In the user acceptability survey the majority agreed the Codonics machine was easy to use, more legible and adhered with better security than the conventional preprinted label. However, most were neutral when asked about the likelihood of flexibility and customisation and were dissatisfied with the increased workload. Our findings suggest that the Codonics labelling machine is user-friendly and it improved syringe labelling compliance in our study. However, staff need to be willing to follow proper labelling workflow rather than batch label during preparation. Future syringe labelling equipment developers need to concentrate on user interface issues to reduce human factor and workflow problems. Support logistics are also an important consideration prior to implementation of any new labelling system. PMID:24967766
Ang, S B L; Hing, W C; Tung, S Y; Park, T
On the Importance of Oxidative Folding in the Evolution of Conotoxins: Cysteine Codon Preservation through Gene Duplication and Adaptation
Conotoxin genes are among the most rapidly evolving genes currently known; however, despite the well-established hypervariability of the intercysteine loops, the cysteines demonstrate significant conservation, with a site-specific codon bias for each cysteine in a family of conotoxins. Herein we present a novel rationale behind the codon-level conservation of the cysteines that comprise the disulfide scaffold. We analyze cysteine codon conservation using an internal reference and phylogenetic tools; our results suggest that the established codon conservation can be explained as the result of selective pressures linked to the production efficiency and folding of conotoxins, driving the conservation of cysteine at the amino-acid level. The preservation of cysteine has resulted in maintenance of the ancestral codon in most of the daughter lineages, despite the hypervariability of adjacent residues. We propose that the selective pressures acting on the venom components of cone snails involve an interplay of biosynthetic efficiency, activity at the target receptor and the importance of that activity to effective prey immobilization. Functional redundancy in the venom can thus serve as a buffer for the energy expenditure of venom production. PMID:24244311
Steiner, Andrew M.; Bulaj, Grzegorz; Puillandre, Nicolas
Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals
Translation of mRNA into a polypeptide chain is a highly accurate process. Many prokaryotic and eukaryotic viruses, however, use leaky termination of translation to optimize their coding capacity. Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms, a biological function for the resulting extended proteins has been elucidated only in very few cases. Here, we report that in human cells programmed stop codon readthrough is used to generate peroxisomal isoforms of cytosolic enzymes. We could show for NAD-dependent lactate dehydrogenase B (LDHB) and NAD-dependent malate dehydrogenase 1 (MDH1) that translational readthrough results in C-terminally extended protein variants containing a peroxisomal targeting signal 1 (PTS1). Efficient readthrough occurs at a short sequence motif consisting of a UGA termination codon followed by the dinucleotide CU. Leaky termination at this stop codon context was observed in fungi and mammals. Comparative genome analysis allowed us to identify further readthrough-derived peroxisomal isoforms of metabolic enzymes in diverse model organisms. Overall, our study highlights that a defined stop codon context can trigger efficient ribosomal readthrough to generate dually targeted protein isoforms. We speculate that beyond peroxisomal targeting stop codon readthrough may have also other important biological functions, which remain to be elucidated. PMID:25340584
Schink, Kay O.; Stehlik, Thorsten; Tillmann, Britta A. M.; Ast, Julia; Bölker, Michael
Getting Started: Study Abroad 101
Getting Started: Study Abroad 101 Education Abroad Virginia Tech 526 Prices Fork Rd., Room 131 www more aid to study abroad! · NOTE: FA works differently for non-VT and VT Direct programs: aid released graduation · 50% felt the overseas experience helped them get their first jobs · 84% felt that studying
Buehrer, R. Michael
Head Start Center Design Guide.
ERIC Educational Resources Information Center
This guide contains suggested criteria for planning, designing, and renovating Head Start centers so that they are safe, child-oriented, developmentally appropriate, beautiful, environmentally sensitive, and functional. The content is based on the U.S. General Services Administration's Child Care Center Design Guide, PBS-P140, which was intended…
Administration for Children, Youth, and Families (DHHS), Washington, DC. Head Start Bureau.
Rigor Made Easy: Getting Started
ERIC Educational Resources Information Center
Bestselling author and noted rigor expert Barbara Blackburn shares the secrets to getting started, maintaining momentum, and reaching your goals. Learn what rigor looks like in the classroom, understand what it means for your students, and get the keys to successful implementation. Learn how to use rigor to raise expectations, provide appropriate…
Blackburn, Barbara R.
ERIC Educational Resources Information Center
Starting where your students are means understanding how currencies are negotiated and traded in the classroom. Any behavior that students use to acquire the knowledge and skills needed in the classroom functions as currency. Teachers communicate the kinds of currencies they accept in their classrooms, such as getting good grades; students do…
Jackson, Robyn R.
Math Club Starting in Kindergarten
ERIC Educational Resources Information Center
Starting a math club as early as kindergarten and having a range of grade levels in attendance can be successful. With the help of the older students, the varied age groups are entertained and excited about attending math club. The purpose of the club is to enrich the classroom mathematics curriculum with hands-on activities and to have members…
Perry, Ann M.
Where innovation starts Dies Natalis
#12;Wim Schaefer Professor TU/e Architecture, Building and Planning department Sustainable urban: sustainable urban regions. This challenge to the cooperation of scientists, technical designers, industryWhere innovation starts Dies Natalis Sustainability 27 April 2012 Program for the Academic Ceremony
Franssen, Michael
Whitepaper: Starting a New Program
NSDL National Science Digital Library
This is a white paper on starting a geospatial educational program. The paper covers the growth of geospatial technology and introduces a model for creating a program in the field. Useful logic model templates are included to help educators going through the process. This paper would be a useful resource for educators and administrators creating a program from scratch at their institution.
Johnson, Ann B.
ERIC Educational Resources Information Center
Caring Start is a mobile-clinic program that provides prenatal care, well-baby clinics, childhood immunizations, counseling services, and contraceptives to rural poor families in northwest Pennsylvania. Before the mobile clinic, many rural women (mostly teenagers) went without prenatal health care due to lack of transportation. (LP)
Hoffman, Carl
Codon optimization, expression, and characterization of recombinant lumbrokinase in goat milk.
Lumbrokinase is an important fibrinolytic enzyme derived from earthworm. Although its cDNA has been isolated and sequenced, there is still no report on expression of the lumbrokinase due to unknown reasons. To determine the elements affecting the expression of lumbrokinase, two copies of a lumbrokinase cDNA(w) obtained by RT-PCR and a synthesized lumbrokinase cDNA(m) with optimized codons were cloned into a mammary-gland-specific expression vector pIbCP. The pIbCP-LK-LK vector preparations were directly injected in the lactating goat mammary glands. Results showed that both LK-w and LK-m were successfully expressed in goat milk. The fibrinolytic activity of the LK-w in milk was 225,000 +/- 13,200 tPA units/L, while that of the LK-m was 550,000 +/- 21,600 tPA units/L, indicating that the codon optimization plays an important role in improving the lumbrokinase expression. The molecular weight of the recombinant lumbrokinase is 31.8 kDa. The main physiochemical features of the recombinant lumbrokinase, including temperature stability, pH resistance, and sensitivity to pepsin, were also clarified. This is the first report on expression and characterization of a genetically engineered lumbrokinase. PMID:15294284
Hu, Rongliang; Zhang, Shoufeng; Liang, Huiying; Li, Ning; Tu, Changchun
Substrate-mediated Fidelity Mechanism Ensures Accurate Decoding of Proline Codons*
Aminoacyl-tRNA synthetases attach specific amino acids to cognate tRNAs. Prolyl-tRNA synthetases are known to mischarge tRNAPro with the smaller amino acid alanine and with cysteine, which is the same size as proline. Quality control in proline codon translation is partly ensured by an editing domain (INS) present in most bacterial prolyl-tRNA synthetases that hydrolyzes smaller Ala-tRNAPro and excludes Pro-tRNAPro. In contrast, Cys-tRNAPro is cleared by a freestanding INS domain homolog, YbaK. Here, we have investigated the molecular mechanism of catalysis and substrate recognition by Hemophilus influenzae YbaK using site-directed mutagenesis, enzymatic assays of isosteric substrates and functional group analogs, and computational modeling. These studies together with mass spectrometric characterization of the YbaK-catalyzed reaction products support a novel substrate-assisted mechanism of Cys-tRNAPro deacylation that prevents nonspecific Pro-tRNAPro hydrolysis. Collectively, we propose that the INS and YbaK domains co-evolved distinct mechanisms involving steric exclusion and thiol-specific chemistry, respectively, to ensure accurate decoding of proline codons. PMID:21768119
So, Byung Ran; An, Songon; Kumar, Sandeep; Das, Mom; Turner, Daniel A.; Hadad, Christopher M.; Musier-Forsyth, Karin
Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids.
The NADH dehydrogenase subunit A (ndhA) gene from maize chloroplasts encodes a highly conserved peptide, which at several positions could be restored to consensus sequences by potential C-to-U editing of the codons involved. This gene was, therefore, chosen for analysis of its mRNA sequence in the form of amplified cDNA. A comparison of this cDNA sequence with the plastome-encoded ndhA sequence reveals four C-to-U editing sites, thereby demonstrating as a novel finding that chloroplast editing can also affect internal mRNA positions. All the edited codons restore amino acids that are conserved in the ndhA-encoded peptides of other chloroplast species. Alignment with homologous mitochondrial NADH-ubiquinone reductase subunit 1 (nad1) sequences of plant and even nonplant species shows that two of the editing positions restore universally conserved amino acids and that one editing site is even shared with nad1 mRNA of plant mitochondria. No editing sites could be detected in the cDNA derived from transcripts of the maize chloroplast RNA polymerase alpha-subunit (rpoA) gene. PMID:1498612
Maier, R M; Hoch, B; Zeltz, P; Kössel, H
TP53 codon 72 polymorphism affects accumulation of mtDNA damage in human cells
Human TP53 gene is characterised by a polymorphism at codon 72 leading to an Arginine-to-Proline (R/P) substitution. The two resulting p53 isoforms have a different subcellular localisation after stress (more nuclear or more mitochondrial for the P or R isoform, respectively). p53P72 variant is more efficient than p53R72 in inducing the expression of genes involved in nuclear DNA repair. Since p53 is involved also in mitochondrial DNA (mtDNA) maintenance, we wondered whether these p53 isoforms are associated with different accumulation of mtDNA damage. We observed that cells bearing p53R72 accumulate lower amount of mtDNA damage upon rotenone stress with respect to cells bearing p53P72, and that p53R72 co-localises with polymerase gamma more than p53P72. We also analysed the in vivo accumulation of heteroplasmy in a 300 bp fragment of mtDNA D-loop of 425 aged subjects. We observed that subjects with heteroplasmy higher than 5% are significantly less than expected in the p53R72/R72 group. On the whole, these data suggest that the polymorphism of TP53 at codon 72 affects the accumulation of mtDNA mutations, likely through the different ability of the two p53 isoforms to bind to polymerase gamma, and may contribute to in vivo accumulation of mtDNA mutations. PMID:22289634
Altilia, Serena; Santoro, Aurelia; Malagoli, Davide; Lanzarini, Catia; Álvarez, Josué Adolfo Ballesteros; Galazzo, Gianluca; Porter, Donald Carl; Crocco, Paolina; Rose, Giuseppina; Passarino, Giuseppe; Roninson, Igor Boris; Franceschi, Claudio; Salvioli, Stefano
Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome
We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo5U34 and m6A37. In tRNAVal, these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem–loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo5U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome. PMID:22028366
Allnér, Olof; Nilsson, Lennart
Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences
NASA Astrophysics Data System (ADS)
Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic "pure" types of this model, observed in nature: "parallel triangles", "perpendicular triangles", degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/ ?zinovyev/7clusters .
Gorban, Alexander; Popova, Tatyana; Zinovyev, Andrey
Increased 2,3-butanediol production by changing codon usages in Escherichia coli.
The natural microorganism Escherichia coli without modification is not suitable for the efficient production of 2,3-butanediol (2,3-BD) on an industrial scale because of its poor metabolic performance. Metabolic capacities of E. coli have been improved to produce 2,3-BD efficiently, the performance of which is possible for producing such a product. Codon optimization with the ribosome-binding site for the efficient production of target genes (budA and budC) was achieved by molecular engineering, which allowed the metabolic engineering to proceed to the next level. As a result, comparing the productivity in 26 H, where the amount of p18COR was 1.04 g/L and that of p18WTR was 0.41 g/L, represents an approximate 60.6% increase in the productivity of the p18WTR with codon optimization. In other words, p18COR was 2.54-fold greater than p18WTR in the production of 2,3-BD. PMID:24527755
Park, Seo-Young; Kim, Borim; Lee, Soojin; Oh, Minkyu; Won, Jong-In; Lee, Jinwon