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Core Holes At Vale Hot Springs Area (Combs, Et Al., 1999) | Open...
Open Energy Info (EERE)
Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal...
Core Holes At Newberry Caldera Area (Combs, Et Al., 1999) | Open...
Slim Holes At Steamboat Springs Area (Combs, Et Al., 1999) |...
X-ray imaging for environmental science Chris Jacobsen
E-Print Network (OSTI)
at CNM, Electron Microscopy Center, plus computation. 16 #12;Ultrafast imaging of fuel injector sprays, Chris Jacobsen, Robert Towers. Not shown: Sue Wirick, Chris Peltzer. Phase contrast and fluorescence
Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And
Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Report: Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration Details Activities (27) Areas (8) Regions (0) Abstract: No abstract prepared. Author(s): Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik Published: Geothermal Technologies Legacy Collection, 1999 Document Number: Unavailable DOI: Unavailable Source: View Original Report Acoustic Logs At Newberry Caldera Area (Combs, Et Al., 1999) Acoustic Logs At Steamboat Springs Area (Combs, Et Al., 1999) Core Analysis At Fort Bliss Area (Combs, Et Al., 1999)
Injectivity Test At Newberry Caldera Area (Combs, Et Al., 1999) | Open
Newberry Caldera Area (Combs, Et Al., 1999) Newberry Caldera Area (Combs, Et Al., 1999) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Injectivity Test At Newberry Caldera Area (Combs, Et Al., 1999) Exploration Activity Details Location Newberry Caldera Area Exploration Technique Injectivity Test Activity Date Usefulness useful DOE-funding Unknown Notes After circulating the mud out of the hole and replacing it with clear water, we attempted two injection tests; one into the open hole section (51 16'- 5360') below the HQ liner, and one into the annulus outside the uncemented part (2748' - -4800') of the liner. References Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration
Acoustic Logs At Newberry Caldera Area (Combs, Et Al., 1999) | Open Energy
Acoustic Logs At Newberry Caldera Area (Combs, Et Al., 1999) Acoustic Logs At Newberry Caldera Area (Combs, Et Al., 1999) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Acoustic Logs At Newberry Caldera Area (Combs, Et Al., 1999) Exploration Activity Details Location Newberry Caldera Area Exploration Technique Acoustic Logs Activity Date Usefulness could be useful with more improvements DOE-funding Unknown Notes The acoustic borehole televiewer (BHTV) was run twice in the wellbore with limited success. There were several problems with the tool's fimctions, but images were successfully obtained over the interval from 2748' to 3635'. References Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration
Slimhole Handbook- Procedures and Recommendations for Slimhole Drilling and
Slimhole Handbook- Procedures and Recommendations for Slimhole Drilling and Slimhole Handbook- Procedures and Recommendations for Slimhole Drilling and Testing in Geothermal Exploration Jump to: navigation, search OpenEI Reference LibraryAdd to library Report: Slimhole Handbook- Procedures and Recommendations for Slimhole Drilling and Testing in Geothermal Exploration Abstract No abstract prepared. Authors Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen and Gene Polik Organization Sandia National Laboratories Published Geothermal Technologies Legacy Collection, 1999 Report Number SAND99-1976 DOI Not Provided Check for DOI availability: http://crossref.org Online Internet link for Slimhole Handbook- Procedures and Recommendations for Slimhole Drilling and Testing in Geothermal Exploration Citation
Slim Holes At International Geothermal Area, Japan (Combs, Et Al., 1999) |
Japan (Combs, Et Al., 1999) Japan (Combs, Et Al., 1999) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Slim Holes At International Geothermal Area, Japan (Combs, Et Al., 1999) Exploration Activity Details Location International Geothermal Area Japan Exploration Technique Slim Holes Activity Date Usefulness useful DOE-funding Unknown Notes Based on personal relationships between Maxwell scientists and Japanese geothermal developers, production and injection data from 64 slim holes and 79 large-diameter wells (see table below) at four Japanese geothermal fields (Oguni, Sumikaw~ Takigarni, and Kirishirna) have been obtained. References Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And
Injectivity Test At Steamboat Springs Area (Combs, Et Al., 1999) | Open
Steamboat Springs Area (Combs, Et Steamboat Springs Area (Combs, Et Al., 1999) Exploration Activity Details Location Steamboat Springs Area Exploration Technique Injectivity Test Activity Date Usefulness not indicated DOE-funding Unknown Notes Part of the injection testing used downhole packers for isolating various zones and evaluating their permeability. By running the packers into the hole on N-rod ( 2.75"+K610 OD), the annulus was roughly the same cross-sectional area as the inside of the pipe. It was then possible to inject into either the zone above the packer or the one below, and compare the infectivity of those intervals. References Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration
Modeling-Computer Simulations (Combs, Et Al., 1999) | Open Energy
Modeling-Computer Simulations (Combs, Et Al., 1999) Modeling-Computer Simulations (Combs, Et Al., 1999) Exploration Activity Details Location Unspecified Exploration Technique Modeling-Computer Simulations Activity Date Usefulness useful DOE-funding Unknown Notes Various models/simulations used to analyze data obtained from slimhole drilling. References Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration Retrieved from "http://en.openei.org/w/index.php?title=Modeling-Computer_Simulations_(Combs,_Et_Al.,_1999)&oldid=387232" Category: Exploration Activities What links here Related changes Special pages Printable version Permanent link Browse properties
Static Temperature Survey At Steamboat Springs Area (Combs, Et Al., 1999) |
Steamboat Springs Area Steamboat Springs Area (Combs, Et Al., 1999) Exploration Activity Details Location Steamboat Springs Area Exploration Technique Static Temperature Survey Activity Date Usefulness not indicated DOE-funding Unknown Notes Numerous temperature logs were taken with Sandia'splatinum-resistance-thermometer (PRT) tool which along with a Sandia logging truck remained on-site for the entire project. Static temperature logs (no flow in hole) were done with this tool before each series of productiotilnjection tests. References Jim Combs, John T. Finger, Colin Goranson, Charles E. Hockox Jr., Ronald D. Jacobsen, Gene Polik (1999) Slimhole Handbook- Procedures And Recommendations For Slimhole Drilling And Testing In Geothermal Exploration Retrieved from "http://en.openei.org/w/index.php?title=Static_Temperature_Survey_At_Steamboat_Springs_Area_(Combs,_Et_Al.,_1999)&oldid=511162"
Jasen Jacobsen The MITRE Corporation
Science Conference Proceedings (OSTI)
... CPE for affected platforms and products �Generator use CPE Major Revision Possibilities 2 ... All Rights Reserved. BACKUP SLIDES 30 Page 32. ...
Douglas Jacobsen! NERSC Bioinformatics Computing Consultant
NLE Websites -- All DOE Office Websites (Extended Search)
Running Jobs on Running Jobs on Genepool --- 1 --- February 1 2, 2 013 Structure of the Genepool System --- 2 --- compute n odes gpint n odes high p riority & interac6ve nodes fpga web services database services login n odes filesystems ssh genepool.nersc.gov h=p://...jgi---psf.org User A ccess C ommand L ine S cheduler S ervice Types of Jobs on genepool * Batch - S cheduled ( compute n odes, f pga) - 8,320 c ores f or 7 2,953,280 c ompute h ours p er y ear i n g enepool - use " qsub" t o s ubmit a j ob * Interac@ve - S cheduled (compute n odes s ubset) - 80 c ores p resently, i ncreasing s ize - use " qlogin" t o s ubmit a j ob * Interac@ve - U nscheduled (login n odes, g pints) - 4 login nodes, 27 gpint n odes - ssh t o t he h ost, d irect---use * Services - U nscheduled ( login n odes, g pints, -
Douglas Jacobsen! NERSC User Services Group
Services Group Services Group Using Modules at NERSC --- 1 --- September 10, 2013 NERSC Supported Software * NERSC p rovides a w ide r ange o f s cien=fic a nd c omputer programming s o@ware t o u sers - Scien)fic A pplica)ons: V ASP, A mber, N AMD, ABySS, ... - Compilers: p gi, i ntel, g cc, c ray - Scrip)ng L anguages: perl, p ython, R * and p ackages f or e ach! - SoIware L ibraries: b las/lapack ( MKL), b oost, h df5, n etcdf, ... - U)li)es: gnuplot, g it, m ercurial, 7 zip, c make, . .. - Debuggers & P rofilers: C rayPat, D DT, TotalView, g db, M AP, darshan - Visualiza)on: V isit, P araView, V MD, ... * See complete list: - hVp://www.nersc.gov/users/soIware/ --- 2 --- Software is Managed by Modules * NERSC p rovides m any v ersions o f m any s o@ware packages - To s upport d iverse w orkload o n s ystems * Maintaining
ridEngine - qs NERSC - isjobcomplete NERSC - NERSC g enepool w ebsite * Inves@ga@ng c ompleted j obs - qacct Univa G ridEngine - qqacct NERSC - qqacct w ith q...
l ong r unning c onnec6ons a live through fi rewalls a nd s uch Options for command line work on gpints * Problem: i nterac@ve w ork i s l ost w hen t erminal closed t o g o h...
Aging gene
Aging gene Name: Linda S Martinez Location: NA Country: NA Date: NA Question: Have the aging gene or genes been located on the human chromosomes, and, if yes, will removing that...
Douglas Jacobsen, Yushu Yao! NERSC User Services Group
* * * *** Password: --- 6 --- Prompt o n l ocal s ystem No-fica-on o f a cceptable...
Trichoderma genes
DOE Patents (OSTI)
Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.
Foreman, Pamela (Los Altos, CA); Goedegebuur, Frits (Vlaardingen, NL); Van Solingen, Pieter (Naaldwijk, NL); Ward, Michael (San Francisco, CA)
Gene Frequency
Gene Frequency Gene Frequency Name: donna Location: N/A Country: N/A Date: N/A Question: If six fingers is a dominant human trait why do we have only five? Replies: This is simple. There are just not many genes in the human population for six fingers. Steve Sample Look in any high school biology book for what is known as Hardy-Weinberg equilibrium. These two scientists (separately) said that gene frequencies do not change much unless something in the environment selects them over other genes. In other words, unless 6 fingers somehow becomes an advantage, and five-fingered people have less of an advantage, the frequency of six fingered people in the population will not necessarily increase. This is the same reason that recessive traits don't disappear from the population. Also, six fingers is not considered attractive and they may not get as many mates. Also, more people are born with six fingers than you might imagine but just have them amputated shortly after birth.
Proto-genes and de novo gene birth
Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described. ...
Carvunis, Anne-Ruxandra
Human and Gorilla Genes
Human and Gorilla Genes Name: Eileen B Status: NA Age: NA Location: NA Country: NA Date: NA Question: What are the differences between the genetic mechanisms which affect...
Microfluidic gene synthesis
The ability to synthesize custom de novo DNA constructs rapidly, accurately, and inexpensively is highly desired by researchers, as synthetic genes and longer DNA constructs are enabling to numerous powerful applications ...
Kong, David Sun, 1979-
Evolution of Genes and Gene Networks in Filamentous Fungi
The Pezizomycotina, commonly known as the filamentous fungi, are a diverse group of organisms that have a major impact on human life. The filamentous fungi diverged from a common ancestor approximately 200 � 700 million years ago. Because of the diversity and the wealth of biological and genomic tools for the filamentous fungi it is possible to track the evolutionary history of genes and gene networks in these organisms. In this dissertation I focus on the evolution of two genes (lolC and lolD) in the LOL secondary metabolite gene cluster in Epichlo� and Neotyphodium genera, the evolution of the MAP kinase-signaling cascade in the filamentous fungi, the regulation of the gene networks involved in asexual development in Neurospora crassa, and the identification of two genes in the N. crassa asexual development gene network, acon-2 and acon-3. I find that lolC and lolD originated as an ancient duplication in the ancestor of the filamentous fungi, which were later recruited in the LOL gene cluster in the fungal endophyte lineage. In the MAP kinase-signaling cascade, I find that the MAPK component is the most central gene in the gene network. I also find that the MAPK signaling cascade originated as three copies in the ancestor to eukaryotes, an arrangement that is maintained in filamentous fungi. My observations of gene expression profiling during N. crassa asexual development show tissue specific expression of genes. Both the vegetative mycelium and the aerial hyphae contribute to the formation of macroconidiophores. Also, with the help of genomic tools recently developed by researchers in the filamentous fungal community, I identified NCU00478 and NCU07617 as the genes with mutations responsible for two aconidial strains of N. crassa, acon-2 and acon-3 respectively.
Greenwald, Charles Joaquin
Traits and Multiple Genes
Traits and Multiple Genes Traits and Multiple Genes Name: Frank Location: N/A Country: N/A Date: N/A Question: Please, could you give me an example of how human traits are controlled by more than one pair of alleles? Replies: Your question is just a bit vague, there are different answers depending on just what your question is. I will answer it in terms of polygenic traits also known as additive alleles. When you think of traits such as skin color, hair color and eye color, or traits where there is a wide range of phenotypes they are usually under the control of more than one pair of alleles. These alleles can even be on different chromosomes! Each pair of additive alleles adds to the phenotype. For instance in the case of skin color, scientists now believe that 3 genes control skin color. You then get 3 sets from your mother and 3 from your father for 6 possibilities. If all 6 of the alleles are for dark skin, you will have the darkest possible skin. If you have 5 dark alleles and one light, you will have very dark skin. If you have all 6 light alleles then you will have the lightest skin possible. Is it possible to have a child that is light skinned when both parents are dark-skinned? Well, not if both have all 6 dark alleles, but if they have some light alleles and the child inherits all of the possible light alleles available, then yes, the child could have lighter skin than either parent. It is now believed that eye color is not simply brown being dominant over blue because how many people do you know that have the same shade of brown or blue eyes? Eye color must also be polygenic.
GeneDistiller�Distilling Candidate Genes from Linkage Intervals
Background: Linkage studies often yield intervals containing several hundred positional candidate genes. Different manual or automatic approaches exist for the determination of the gene most likely to cause the disease. While the manual search is very flexible and takes advantage of the researchers � background knowledge and intuition, it may be very cumbersome to collect and study the relevant data. Automatic solutions on the other hand usually focus on certain models, remain ��black boxes� � and do not offer the same degree of flexibility. Methodology: We have developed a web-based application that combines the advantages of both approaches. Information from various data sources such as gene-phenotype associations, gene expression patterns and protein-protein interactions was integrated into a central database. Researchers can select which information for the genes within a candidate interval or for single genes shall be displayed. Genes can also interactively be filtered, sorted and prioritised according to criteria derived from the background knowledge and preconception of the disease under scrutiny. Conclusions: GeneDistiller provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. A typical query takes less than two seconds, thus allowing an interactive and explorative approach to the hunt for the candidate gene.
Dominik Seelow; Jana Marie Schwarz; Markus Schuelke
Recessive and Dominant Gene Action
Recessive and Dominant Gene Action Recessive and Dominant Gene Action Name: Katie Location: N/A Country: N/A Date: N/A Question: What Causes some genes to be ressesive and other genes to be dominant? Replies: Think about the fact that genes code for directions for making proteins. There are many different kinds of proteins in our body-enzymes for regulating metabolism, structural proteins for building our bodies, hormones for regulating processes etc. If the gene for the protein is structural, then it is important to have the right kind and the right amount. If the gene is defective (usually recessive genes are defective, but not always) the right protein will not be made and the structure will either be defective and won't work at all or there won't be enough to maintain the structure. Sometimes you need both genes to be working to get enough of the structure. So a homozygous person will have the strongest structure. A heterozygote would have one gene that is working a may produce enough of the protein to maintain the structure, but maybe not. So in some cases, just having one copy of the dominant (working) gene is enough. If it is a trait for something like eye color, this is not going to cause a defect, just a difference. In this case, being heterozygous or homozgyous for the dominant trait produces the same color of eye. In the case of sickle cell anemia, the recessive gene changes the protein structure of the shape of the red blood cell. If you have one good copy and one bad copy of the gene, some of your cells will be normal and some will be sickle cells. One good copy of the gene gives you enough normal red blood cells to stay healthy. But if you don't have a normal copy, all of your cells have the capability to sickle under certain conditions and this can be fatal. So think of dominant and recessive genes in terms of what they produce and what that protein is supposed to do and then think of what would happen if the dominant gene was able to overtake the effect of the recessive gene.
The Honorable Gene Dean
Office of Legacy Management (LM)
Energy' .' Energy' .' Washington, DC 20585 DE! 14 1gg4 The Honorable Gene Dean \ P.O. Box 1659~ L Huntington, West Virginia 25717 _ ',.. : Dear Mayor Dean: Secretary of Energy Hazel O'Leary has'announced,a new approach ,to openness in the'Department of Energy (DOE) and its communications with the public. In support of this in.itiative, we are pleased,to forward the..enclosed information related to the former Reduction Pilot Plant sitein your jurisdiction that performed work for DOE predecessor agencies. This information is provided.for your information, use,.band retention., DDE's Formerly Utilized Sites Remedial.Action Program is responsible for identification of sitesused by DOE's predecessor agencies, determini,ng theirs current radiological condition and, where it has authority, performing
GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes
We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.
Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D.; Lykidis, Athanasios; Kyrpides, Nikos C.
What is the morphology of a gene?
of as structural, operator, and regulatory genes." - Dorland's Illustrated Medical Dictionary, 27th ed. So, in terms of morphology, a gene is a specific sequence of nucleotide in...
Prodigal: Microbial Gene Prediction Software
Screenshot Screenshot Artemis Screenshot of Prodigal Results Compared with Curated Annotations and other Computational Genefinders for Anaeromyxobacter dehalogenans 2CP-C (Click to enlarge) Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include: Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less. Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very
Gene order computation using Alzheimer's DNA microarray gene expression data and the ant colony optimisation algorithm
As Alzheimer's Disease (AD) is the most common form of dementia, the study of AD-related genes via biocomputation is an important research topic. One method of studying AD-related gene is to cluster similar genes together into a gene order. Gene ...
Chaoyang Pang; Gang Jiang; Shipeng Wang; Benqiong Hu; Qingzhong Liu; Youping Deng; Xudong Huang
Metazoan Gene Families from Metazome
DOE Data Explorer (OSTI)
Metazome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst metazoans. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of version 2.0.4, Metazome provides access to twenty-four sequenced and annotated metazoan genomes, clustered at nine evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, Ensembl, and JGI are hyper-linked and searchable. The included organisms (by common name) are: Human, Mouse, Rat, Dog, Opossum, Chicken, Frog, Stickleback, Medaka, Fugu pufferfish; Zebrafish, Seasquirt - savignyi, Seasquirt - intestinalis, Amphioxus, Sea Urchin, Fruitfly, Mosquite, Yellow Fever Mosquito, Silkworm, Red Flour Beetle, Worm, Briggsae Worm, Owl limpet (snail), and Sea anemone. [Copied from Metazome Overview at http://www.metazome.net/Metazome_info.php
THE JOURNAL OF GENE MEDICINE RESEARCH ARTICLE J Gene Med 2008; 10: 583592.
-transduction with the two types of viral vectors provided doxycycline- regulated transgene expression in a neuron gene transfer; tetracycline-regulated gene expression; CNS; lentiviral vectors; doxycycline; cell
Bristol, University of
Gene expression by software mechanisms
This paper describes the molecular interactions and coordination of cell processes using computer operating system concepts related to synchronization and communication. We argue that in molecular biology, the genes and their chromatin context provide ... Keywords: cell biology, modules, operating systems, pipe, process communication, signals
Gabriel Ciobanu; Bogdan Tanasa
Enhanced polymeric nanoparticles for gene delivery
The potential of gene therapy to treat disease and improve human health is tremendous. The failure of viral gene therapy clinical trials due to toxicity, immunogenicity, and carcinogenicity has been tragic and strongly ...
Green, Jordan Jamieson
Uses of antimicrobial genes from microbial genome
We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.
Sorek, Rotem; Rubin, Edward M.
Method for determining gene knockouts
A method for determining candidates for gene deletions and additions using a model of a metabolic network associated with an organism, the model includes a plurality of metabolic reactions defining metabolite relationships, the method includes selecting a bioengineering objective for the organism, selecting at least one cellular objective, forming an optimization problem that couples the at least one cellular objective with the bioengineering objective, and solving the optimization problem to yield at least one candidate.
Maranas, Costas D. (Port Matilda, PA); Burgard, Anthony R. (State College, PA); Pharkya, Priti (State College, PA)
Human gene sequencing makes advances
SciTech Connect
The Human Genome Project is a federal project that is on the scale of the Manhattan Project of the 1940s. The focus of this project is to map and sequence the 100,000 plus genes and 3 billion base pairs that comprise the human genome. This effort has made two recent advances. First, two of the major companies involved in this project formed a strategic alliance that will pump up to 125 million dollars into this project. Second, researchers at Argonne National Lab. have tested a new sequencing technique that could identify 100 million base pairs a day when fully implemented.
Alper, J.
QB1 - Stochastic Gene Regulation
Summaries of this presentation are: (1) Stochastic fluctuations or 'noise' is present in the cell - Random motion and competition between reactants, Low copy, quantization of reactants, Upstream processes; (2) Fluctuations may be very important - Cell-to-cell variability, Cell fate decisions (switches), Signal amplification or damping, stochastic resonances; and (3) Some tools are available to mode these - Kinetic Monte Carlo simulations (SSA and variants), Moment approximation methods, Finite State Projection. We will see how modeling these reactions can tell us more about the underlying processes of gene regulation.
Munsky, Brian [Los Alamos National Laboratory
Methods for monitoring multiple gene expression
The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.
Berka, Randy; Bachkirova, Elena; Rey, Michael
Berka, Randy (Davis, CA); Bachkirova, Elena (Davis, CA); Rey, Michael (Davis, CA)
Bayesian survival analysis using gene expression.
??This thesis developed and applied Bayesian models for the analysis of survival data. The gene expression was considered as explanatory variables within the Bayesian survival� (more)
Thamrin, Sri Astuti
Nano-vesicles for gene delivery.
??Gene therapy was considered an important modality for the potential treatment of cancer. It aimed to correct diseases through the delivery of genetic material encoding� (more)
Tan, Karen Li Ping.
Microarray gene expression classification with few genes: Criteria to combine attribute selection and classification methods
Microarray data classification is a task involving high dimensionality and small samples sizes. A common criterion to decide on the number of selected genes is maximizing the accuracy, which risks overfitting and usually selects more genes than actually ... Keywords: Efficient classification with few genes, Feature selection, Machine learning, Microarray data classification
Carlos J. Alonso-Gonz�lez; Q. Isaac Moro-Sancho; Arancha Simon-Hurtado; Ricardo Varela-Arrabal
Gene therapy in alcoholic rats
70 70 Sept. 9, 2001 Gene Therapy Reduces Drinking in "Alcoholic" Rats UPTON, NY - Scientists at the U.S. Department of Energy's Brookhaven National Laboratory have shown that increasing the level of a brain protein important for transmitting pleasure signals can turn rats that prefer alcohol into light drinkers, and those with no preference into near teetotalers. The findings, published in the first September 2001 issue of the Journal of Neurochemistry (Vol. 78, No. 5), may have implications for the prevention and treatment of alcoholism in humans. "This is a preliminary study, but when you see a rat that chooses to drink 80 to 90 percent of its daily fluid as alcohol, and then three days later it's down to 20 percent, that's a dramatic drop in alcohol intake - a very clear change in behavior," said Panayotis Thanos, the lead researcher. "This gives us great hope that we can refine this treatment for future clinical use."
Graph theoretic approach to parallel gene assembly
We study parallel complexity of signed graphs motivated by the highly complex genetic recombination processes in ciliates. The molecular gene assembly operations have been modeled by operations of signed graphs, i.e., graphs where the vertices have a ... Keywords: Double-split graphs, Gene assembly, Local complement, Parallel assembly, Perfect matching, Signed graphs, Split graphs
Tero Harju; Chang Li; Ion Petre
Scalable Time Warp on Blue Gene Supercomputers
n this paper we illustrate scalable parallel performance for the TimeWarp synchronization protocol on the L and P variants of the IBM BlueGene supercomputer. Scalable Time Warp performance for models that communicate a large percentage of the event population ... Keywords: Time Warp, Blue Gene Supercomputer
David W. Bauer Jr.; Christopher D. Carothers; Akintayo Holder
Noise minimization in eukaryotic gene expression
All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or noise. Several recent studies in Saccharomyces cerevisiae and Escherichia coli have investigated the relationship between transcription and translation rates and stochastic fluctuations in protein levels, or more generally, how such randomness is a function of intrinsic and extrinsic factors. However, the fundamental question of whether stochasticity in protein expression is generally biologically relevant has not been addressed, and it remains unknown whether random noise in the protein production rate of most genes significantly affects the fitness of any organism. We propose that organisms should be particularly sensitive to variation in the protein levels of two classes of genes: genes whose deletion is lethal to the organism and genes that encode subunits of multiprotein complexes. Using an experimentally verified model of stochastic gene expression in S. cerevisiae, we estimate the noise in protein production for nearly every yeast gene, and confirm our prediction that the production of essential and complex-forming proteins involves lower levels of noise than does the production of most other genes. Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection.
Fraser, Hunter B.; Hirsh, Aaron E.; Giaever, Guri; Kumm, Jochen; Eisen, Michael B.
Gene coding for the E1 endoglucanase
The gene encoding Acidothermus cellulolyticus E1 endoglucanase is cloned and expressed in heterologous microorganisms. A new modified E1 endoglucanase enzyme is produced along with variants of the gene and enzyme. The E1 endoglucanase is useful for hydrolyzing cellulose to sugars for simultaneous or later fermentation into alcohol. 6 figs.
Thomas, S.R.; Laymon, R.A.; Himmel, M.E.
Induction and selection of the most interesting Gene Ontology based multiattribute rules for descriptions of gene groups
A rules induction algorithm dedicated to describe groups of genes with similar expression profiles by means of Gene Ontology terms is discussed in the paper. The presented algorithm takes into consideration information contained in the Gene Ontology ... Keywords: Decision rules, Gene Ontology, Gene groups descriptions, Rough sets, Rule interestingness measures
Marek Sikora; Aleksandra Gruca
Tissue-Specific Gene Delivery via Nanoparticle Coating
The use of biomaterials for gene delivery can potentially avoid many of the safety concerns with viral gene delivery. However, the efficacy of polymeric gene delivery methods is low, particularly in vivo. One significant ...
Harris, Todd J.
Identification of candidate genes in Arabidopsis and Populus...
in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database, and additional genes were identified as...
Science at LLNL with IBM Blue Gene/Q
Lawrence Livermore National Laboratory (LLNL) has a long history of working with IBM on Blue Gene� supercomputers. Beginning in November 2001 with the joint announcement of a partnership to expand the Blue Gene research project (including Blue Gene�/L ...
B. Carnes, B. Chan, E. W. Draeger, J.-L. Fattebert, L. Fried, J. Glosli, W. D. Krauss, S. H. Langer, R. McCallen, A. A. Mirin, F. Najjar, A. L. Nichols, T. Oppelstrup, J. A. Rathkopf, D. Richards, F. Streitz, P. M. Vranas, J. J. Rice, J. A. Gunnels, V. Gurev, C. Kim, J. Magerlein, M. Reumann, H.-F. Wen
Algorithms for Gene Clustering Analysis on Genomes
The increased availability of data in biological databases provides many opportunities for understanding biological processes through these data. As recent attention has shifted from sequence analysis to higher-level analysis of genes across multiple genomes, there is a need to develop efficient algorithms for these large-scale applications that can help us understand the functions of genes. The overall objective of my research was to develop improved methods which can automatically assign groups of functionally related genes in large-scale data sets by applying new gene clustering algorithms. Proposed gene clustering algorithms that can help us understand gene function and genome evolution include new algorithms for protein family classification, a window-based strategy for gene clustering on chromosomes, and an exhaustive strategy that allows all clusters of small size to be enumerated. I investigate the problems of gene clustering in multiple genomes, and define gene clustering problems using mathematical methodology and solve the problems by developing efficient and effective algorithms. For protein family classification, I developed two supervised classification algorithms that can assign proteins to existing protein families in public databases and, by taking into account similarities between the unclassified proteins, allows for progressive construction of new families from proteins that cannot be assigned. This approach is useful for rapid assignment of protein sequences from genome sequencing projects to protein families. A comparative analysis of the method to other previously developed methods shows that the algorithm has a higher accuracy rate and lower mis-classification rate when compared to algorithms that are based on the use of multiple sequence alignments and hidden Markov models. The proposed algorithm performs well even on families with very few proteins and on families with low sequence similarity. Apart from the analysis of individual sequences, identifying genomic regions that descended from a common ancestor helps us study gene function and genome evolution. In distantly related genomes, clusters of homologous gene pairs serve as evidence used in function prediction, operon detection, etc. Thus, reliable identification of gene clusters is critical to functional annotation and analysis of genes. I developed an efficient gene clustering algorithm that can be applied on hundreds of genomes at the same time. This approach allows for large-scale study of evolutionary relationships of gene clusters and study of operon formation and destruction. By placing a stricter limit on the maximum cluster size, I developed another algorithm that uses a different formulation based on constraining the overall size of a cluster and statistical estimates that allow direct comparisons of clusters of different size. A comparative analysis of proposed algorithms shows that more biological insight can be obtained by analyzing gene clusters across hundreds of genomes, which can help us understand operon occurrences, gene orientations and gene rearrangements.
Yi, Gang Man
Sustainability Assessment of Workforce Well-Being and Mission Readiness
Energy.gov (U.S. Department of Energy (DOE))
Presentation by Dr. Jodi Jacobsen, Associate Professor, University of Maryland, Baltimore 2008, September
Characterization of the mouse thrombospondin 2 gene
The authors have characterized the exon/intron organization, complete 3[prime] untranslated region (3[prime]-UTR), and approximately 2.5 kb of the promoter/5[prime] flanking region of the mouse thrombospondin 2 (TSP2) gene. The sizes of exons and the pattern of interruption of the reading frame by introns are highly conserved in mouse TSP2 in comparison with mouse or human TSP1, a finding that suggests a close evolutionary relationship between the two genes. The TSP2 and TSP1 genes are also similar in that the 3[prime]-UTRs of both genes contain multiple TATT and ATTT(A) motifs that might function as mediators of mRNA stability. However, the sequences of the promoter regions in TSP1 and TSP2 are very different; in particular, the TSP2 gene lacks the serum response element and the NF-Y binding site that have been implicated in the serum response of the human TSP1 gene. The structure of the TSP2 gene is consistent with emerging evidence supporting the view that TSP1 and TSP2 perform overlapping but distinct functions. 41 refs., 4 figs., 1 tab.
Tetsuji Shingu; Bornstein, P. (Univ. of Washington, Seattle (United States))
Single, Key Gene Discovery Could Streamline Production of Biofuels...
Single, Key Gene Discovery Could Streamline Production of Biofuels Single, Key Gene Discovery Could Streamline Production of Biofuels August 11, 2011 - 3:51pm Addthis WASHINGTON,...
The specificity and evolution of gene regulatory elements
The regulation of gene expression underlies the morphological, physiological, and functional differences between human cell types, developmental stages, and healthy and disease states. Gene regulation in eukaryotes is ...
Friedman, Robin Carl
Visualizing Gene Expression In Situ
Visualizing bacterial cells and describing their responses to the environment are difficult tasks. Their small size is the chief reason for the difficulty, which means that we must often use many millions of cells in a sample in order to determine what the average response of the bacteria is. However, an average response can sometimes mask important events in bacterial physiology, which means that our understanding of these organisms will suffer. We have used a variety of instruments to visualize bacterial cells, all of which tell us something different about the sample. We use a fluorescence activated cell sorter to sort cells based on the fluorescence provided by bioreporter genes, and these can be used to select for particular genetic mutations. Cells can be visualized by epifluorescent microscopy, and sensitive photodetectors can be added that allow us to find a single bacterial cell that is fluorescent or bioluminescent. We have also used standard photomultipliers to examine cell aggregates as field bioreporter microorganisms. Examples of each of these instruments show how our understanding of bacterial physiology has changed with the technology.
Burlage, R.S.
Radiation-induced gene responses
In the process of identifying genes that are differentially regulated in cells exposed to ultraviolet radiation (UV), we identified a transcript that was repressed following the exposure of cells to a combination of UV and salicylate, a known inhibitor of NF-kappaB. Sequencing this band determined that it has identify to lactate dehydrogenase, and Northern blots confirmed the initial expression pattern. Analysis of the sequence of the LDH 5` region established the presence of NF-kappaB, Sp1, and two Ap-2 elements; two partial AP- 1; one partial RE, and two halves of E-UV elements were also found. Electromobility shift assays were then performed for the AP-1, NF- kappaB, and E-UV elements. These experiments revealed that binding to NF-kappaB was induced by UV but repressed with salicylic acid; UV did not affect AP-1 binding, but salicylic acid inhibited it alone or following UV exposure; and E-UV binding was repressed by UV, and salicylic acid had little effect. Since the binding of no single element correlated with the expression pattern of LDH, it is likely that multiple elements govern UV/salicylate-mediated expression.
Woloschak, G.E.; Paunesku, T.; Shearin-Jones, P.; Oryhon, J.
with 0, 50 or 200 cGy gamma-rays and the cells harvested for RNA 48 hours post irradiation. The RNA was hybridized to RAE 230A Affymetrix microarrays and differences in gene...
Affymetrix White Paper: GeneChip
Affymetrix® White Paper: GeneChip® 3' IVT Express Kit May 14, 2009 P/N WH105 Page 1 of 9 White and optimized reagents that enable lower RNA input and increased ease of use. In this white paper, we describe, and the plastic consumables needed to run the assay. #12;Affymetrix® White Paper: GeneChip® 3' IVT Express Kit May
Wandless, Tom
Mutations of the GREAT gene cause cryptorchidism
DDBJ/EMBL/GenBank accession no. AF453828 In humans, failure of testicular descent (cryptorchidism) is one of the most frequent congenital malformations, affecting 1�3 % of newborn boys. The clinical consequences of this abnormality are infertility in adulthood and a significantly increased risk of testicular malignancy. Recently, we described a mouse transgene insertional mutation, crsp, causing high intraabdominal cryptorchidism in homozygous males. A candidate gene Great (G-protein-coupled receptor affecting testis descent), was identified within the transgene integration site. Great encodes a seven-transmembrane receptor with a close similarity to the glycoprotein hormone receptors. The Great gene is highly expressed in the gubernaculum, the ligament that controls testicular movement during development, and therefore may be responsible for mediating hormonal signals that affect testicular descent. Here we show that genetic targeting of the Great gene in mice causes infertile bilateral intraabdominal cryptorchidism. The mutant gubernaculae fail to differentiate, indicating that the Great gene controls their development. Mutation screening of the human GREAT gene was performed using DHPLC analysis of the genomic DNA from 60 cryptorchid patients. Nucleotide variations in GREAT cDNA were found in both the patient and the control populations. A unique missense mutation (T222P) in the ectodomain of the GREAT receptor was identified in one of the patients. This mutant receptor fails to respond to ligand stimulation, implicating the GREAT gene in the etiology in some cases of cryptorchidism in humans.
Ivan P. Gorlov; Aparna Kamat; Natalia V. Bogatcheva; Eric Jones; Dolores J. Lamb; Anne Truong; Colin E. Bishop; Ken Mcelreavey; Er I. Agoulnik
PRediction IMprovement Pipeline for Amrita Pati 1 , NataliaGene Prediction IMprovement Pipeline, http://geneprimp.jgi-based post-processing pipeline that identifies erroneously
Pati, Amrita
Post transcriptional regulation of chloroplast gene expression by nuclear encoded gene products
DOE Green Energy (OSTI)
Many individual chloroplast genes require the products of a collection of nuclear genes for their successful expression. These nuclear gene products apparently work with great specificity, each committed to the expression of a single chloroplast gene. We have chosen as a model nuclear mutants of Chlamydomonas affected in different stages in the expression of the chloroplast encoded Photosystem II polypeptide, D2. We have made the progress in understanding how nuclear gene products affect the translation of the D2 encoding MRNA. Two nuclear genes are required for this process which have been mapped genetically. In contrast to other examples of nuclear control of translation in the chloroplast, these nuclear gene products appear to be required either for specific stages in translation elongation or for the post-translational stabilization of the nascent D2 protein. Pseudoreversion analysis has led us to a locus which may be directly involved in D2 expression. We have made considerable progress in pursuing the molecular basis of psbd MRNA stabilization. psbD 5' UTR specific transcripts have been synthesized in vitro and used in gel mobility shift assays. UV-crosslinking studies are underway to identify the transacting factors which bind to these sequences. The continued examination of these mutants will help us to understand how nuclear gene products work in this specific case of chloroplast gene expression, and will elucidate how two distinct genomes can interact generally.
Kuchka, M.R.
Gene for ataxia-telangiectasia complementation group D (ATDC)
Disclosed herein is a new gene, an AT gene for complementation group D, the ATDC gene and fragments thereof. Nucleic acid probes for said gene are provided as well as proteins encoded by said gene, cDNA therefrom, preferably a 3 kilobase (kb) cDNA, and recombinant nucleic acid molecules for expression of said proteins. Further disclosed are methods to detect mutations in said gene, preferably methods employing the polymerase chain reaction (PCR). Also disclosed are methods to detect AT genes from other AT complementation groups.
Murnane, John P. (San Francisco, CA); Painter, Robert B. (Burlingame, CA); Kapp, Leon N. (San Rafael, CA); Yu, Loh-Chung (Redwood City, CA)
Disclosed herein is a new gene, an AT gene for complementation group D, the ATDC gene and fragments thereof. Nucleic acid probes for the gene are provided as well as proteins encoded by the gene, cDNA therefrom, preferably a 3 kilobase (kb) cDNA, and recombinant nucleic acid molecules for expression of the proteins. Further disclosed are methods to detect mutations in the gene, preferably methods employing the polymerase chain reaction (PCR). Also disclosed are methods to detect AT genes from other AT complementation groups. 30 figs.
Murnane, J.P.; Painter, R.B.; Kapp, L.N.; Yu, L.C.
Soft computing methods to predict gene regulatory networks: An integrative approach on time-series gene expression data
To unravel the controlling mechanisms of gene regulation, in this paper we present the application of sophisticated soft computing methods applied on an important problem from Bioinformatics-inferring gene regulatory networks (GRN) from time series gene ... Keywords: Automatic model building, Gene regulatory network, LARS, Reverse-engineering, Schizosaccharomyces pombe, Time series microarray data, Yeast
Zeke S. H. Chan; Ilkka Havukkala; Vishal Jain; Yingjie Hu; Nikola Kasabov
A Rule-Based Framework for Gene Regulation Pathways Discovery
We present novel approach to discover the rules that govern gene regulation mechanisms. The method is based on supervised machine learning and is designed to reveal relationships between transcription factors and gene promoters. As the representation of the gene regulatory circuit we have chosen a special form of IF-THEN rules associating certain features (a generalized idea of a Transcription Factor Binding Site) in gene promoters with specific gene expression profiles.
Wilczynski, B; Hvidsten, T; Kryshtafovych, A; Stubbs, L; Komorowski, J; Fidelis, K
Pathogenicity island mobility and gene content.
Key goals towards national biosecurity include methods for analyzing pathogens, predicting their emergence, and developing countermeasures. These goals are served by studying bacterial genes that promote pathogenicity and the pathogenicity islands that mobilize them. Cyberinfrastructure promoting an island database advances this field and enables deeper bioinformatic analysis that may identify novel pathogenicity genes. New automated methods and rich visualizations were developed for identifying pathogenicity islands, based on the principle that islands occur sporadically among closely related strains. The chromosomally-ordered pan-genome organizes all genes from a clade of strains; gaps in this visualization indicate islands, and decorations of the gene matrix facilitate exploration of island gene functions. A %E2%80%9Clearned phyloblocks%E2%80%9D method was developed for automated island identification, that trains on the phylogenetic patterns of islands identified by other methods. Learned phyloblocks better defined termini of previously identified islands in multidrug-resistant Klebsiella pneumoniae ATCC BAA-2146, and found its only antibiotic resistance island.
Williams, Kelly Porter
The mouse angiogenin gene family: Structures of an angiogenin-related protein gene and two pseudogenes
Angiogenin, a homologue of pancreatic ribonuclease, is a potent inducer of blood vessel formation. As an initial step toward investigating the in vivo functional role of this protein via gene disruption, we undertook the isolation of the angiogenin gene (Ang) from the 129 strain mouse, which will be used for generating targeting constructs. Unexpectedly, screening of a genomic library with an Ang gene probe obtained previously from the BALB/c strain yielded two new genes closely similar to Ang rather than Ang itself. One of these encodes a protein with 78% sequence identity to angiogenin and is designated {open_quotes}Angrp{close_quotes} for {open_quotes}angiogenin-related protein.{close_quotes} The ribonucleolytic active site of angiogenin, which is critical for angiogenic activity, is completely conserved in Angrp, whereas a second essential site, thought to bind cellular receptors, is considerably different. Thus, the Angrp product may have a function distinct from that of angiogenin. The second gene obtained by library screening is a pseudogene, designated {open_quotes}Ang-ps1,{close_quotes} that contains a frame shift mutation in the early part of the coding region. Although the Ang gene was not isolated from this library, it was possible to amplify this gene from 129 mouse genomic DNA by the polymerase chain reaction (PCR). Sequence analysis showed that the 129 strain Ang gene is identical to the BALB/c gene throughout the coding region. PCR cloning also yielded a second Ang-like pseudogene, designated {open_quotes}Ang-ps2.{close_quotes} Southern blotting of genomic DNA confirmed the presence of Ang, Angrp, and at least one of the pseudogenes in an individual mouse and suggested that the mouse Ang gene family may contain more than the four members identified here. 31 refs., 4 figs., 1 tab.
Brown, W.E.; Nobile, V.; Shapiro, R. [Harvard Medical School, Boston, MA (United States)] [and others
Localized atomic basis set in the projector augmented wave method A. H. Larsen, M. Vanin, J. J. Mortensen, K. S. Thygesen, and K. W. Jacobsen
for different basis sets. This error is defined as ELCAO - Egrid = Emol LCAO - atoms Eatoms LCAO - Emol grid
Thygesen, Kristian
(for Gene Recognition Analysis Internet Link),
5 6/1/2011 5 6/1/2011 6.6 Speeding Up the Process of Gene Discovery The human genome contains information that could be used to prevent birth defects and treat or cure devastating diseases, but it is written in a language that scientists are only beginning to understand. To help decipher the code, Ed Uberbacher and colleagues at Oak Ridge National Laboratory combined cutting- edge computer technology with their knowledge of human biology to develop GRAIL (for Gene Recognition Analysis Internet Link), a "thinking" computer program that imitates the human learning process as it searches for genetic meaning. GRAIL and successor software programs can rapidly identify key instructions in genes from within vast stretches of DNA that appear to be meaningless-a critical contribution to the
Regulation of methane genes and genome expression
At the start of this project, it was known that methanogens were Archaeabacteria (now Archaea) and were therefore predicted to have gene expression and regulatory systems different from Bacteria, but few of the molecular biology details were established. The goals were then to establish the structures and organizations of genes in methanogens, and to develop the genetic technologies needed to investigate and dissect methanogen gene expression and regulation in vivo. By cloning and sequencing, we established the gene and operon structures of all of the �methane� genes that encode the enzymes that catalyze methane biosynthesis from carbon dioxide and hydrogen. This work identified unique sequences in the methane gene that we designated mcrA, that encodes the largest subunit of methyl-coenzyme M reductase, that could be used to identify methanogen DNA and establish methanogen phylogenetic relationships. McrA sequences are now the accepted standard and used extensively as hybridization probes to identify and quantify methanogens in environmental research. With the methane genes in hand, we used northern blot and then later whole-genome microarray hybridization analyses to establish how growth phase and substrate availability regulated methane gene expression in Methanobacterium thermautotrophicus ?H (now Methanothermobacter thermautotrophicus). Isoenzymes or pairs of functionally equivalent enzymes catalyze several steps in the hydrogen-dependent reduction of carbon dioxide to methane. We established that hydrogen availability determine which of these pairs of methane genes is expressed and therefore which of the alternative enzymes is employed to catalyze methane biosynthesis under different environmental conditions. As were unable to establish a reliable genetic system for M. thermautotrophicus, we developed in vitro transcription as an alternative system to investigate methanogen gene expression and regulation. This led to the discovery that an archaeal protein, designated TFE, that had sequences in common with the eukaryotic general transcription factor TFIIE, stimulated archaeal transcription initiation and that the archaeal TATA-box binding protein (TBP) remained attached to the promoter region whereas the transcription factor TFB dissociated from the template DNA following initiation. DNA sequences that directed the localized assembly of archaeal histones into archaeal nucleosomes were identified, and we established that transcription by an archaeal RNA polymerase was slowed but not blocked by archaeal nucleosomes. We developed a new protocol to purify archaeal RNA polymerases and with this enzyme and additional improvements to the in vitro transcription system, we established the template requirements for archaeal transcription termination, investigated the activities of proteins predicted to be methane gene regulators, and established how TrpY, a novel archaeal regulator of expression of the tryptophan biosynthetic operon functions in M. thermautotrophicus. This also resulted in the discovery that almost all M. thermautotrophicus mutants isolated as spontaneously resistant to 5-methyl tryptophan (5MTR) had mutations in trpY and were therefore 5MTR through de-repressed trp operon expression. This established a very simple, practical procedure to determine and quantify the DNA sequence changes that result from exposure of this Archaeon to any experimental mutagenesis protocol. Following the discovery that the Thermococcus kodakaraensis was amenable to genetic manipulation, we established this technology at OSU and subsequently added plasmid expression, a reporter system and additional genetic selections to the T. kodakaraensis genetic toolbox. We established that transcription and translation are coupled in this Archaeon, and by combining in vitro transcription and in vivo genetics, we documented that both TFB1 and TFB2 support transcription initiation in T. kodakaraensis. We quantified the roles of ribosome binding sequences and alternative initiation codons in translation initiation, established that polarity e
John N. Reeve
Gene Expression in the Stallion Testes
Understanding the genes that regulate spermatogenesis and steroidogenesis in the testis is critical for enhancement of stallion fertility. Stallion testicular samples were used to identify candidate genes by cDNA microarrays that simultaneously assessed expression levels of 9132 genes. First, gene expression was compared between light (spermatogenically active) and dark (spermatogenically inactive) testis tissue of 1.5-year-old horses (n = 3). Ninety-three genes were differentially expressed (35 light specific, 58 dark specific) in matched paired samples. Second, gene expression was compared between testicular tissue of two mature stallions, one with normal quality semen (fertile) and one with poor quality semen (subfertile). A total of 233 genes were differentially expressed (122 in fertile tissue, 111 in subfertile tissue). Of these, phosphodiesterase 3B (PDE3B), steroidogenic acute regulatory (StAR) protein, and outer dense fiber of sperm tails 2 (ODF2) mRNAs, were localized and quantified by in situ hybridization (ISH) in mature stallions and/or in unilateral cryptorchids. ISH revealed differences (P < 0.05) among mature stallions (n = 10) for PDE3B (localized to seminiferous tubules) and StAR protein (localized to interstitial spaces) mRNAs. A positive correlation coefficient (r = .556, p = .025) was found between StAR protein mRNA and plasma concentration of testosterone. Additionally, both gene products were evaluated in 1-year-old (n = 3) and 3-year-old (n = 3) unilateral cryptorchid stallions. Expression of both PDE3B and StAR protein gene was significantly higher in mature, descended testes compared to mature, retained testes and the descended and retained testes of immature, cryptorchid stallions. StAR protein gene demonstrated significantly higher expression in immature retained testes compared to immature descended testes. A precision-cut tissue slice (PCTS) in vitro culture system was evaluated as a potential tool to study equine testes function. Testes from immature stallions (n = 3) were cut into slices (mean slice weight = 13.85 +/- 0.20 mg; mean slice thickness = 515.00 +/- 2.33 ?m) and exposed to medium containing ovine luteinizing hormone (oLH) at concentrations of 0, 5, 50 and 500 ng/ml for 6 h at 32 degrees C. Medium content of testosterone and estradiol was increased 500% and 120%, respectively, by addition of oLH versus that observed for the testis tissue slices treated with 0 ng oLH (control). An oLH concentration-dependent increase in StAR protein mRNA in tissue slices was detected by in situ hybridization; whereas, differences for PDE3B and ODF2 mRNAs were not observed. Collectively, these results demonstrate that the stallion is an excellent model for studying male fertility due to the initiation of spermatogenesis, frequency of cryptorchidism, and routine castration providing useful tissue to use for studying gene expression.
Laughlin, Andy M.
The plant mitochondrial mat-r gene/nad1 gene complex. Progress report
The authors have completed sequencing the segments (totalling 19 kb, both complementary strands) of the maize mtDNA molecule that encode the entire NADH dehydrogenase subunit (nadl) gene. They have identified nucleotides in mature transcripts of the nadl gene that are edited and have generated clones of cDNAs of entire mature (fully spliced) nadl transcripts. They have examined the relative rates of splicing in transcripts of the four nadl gene group II introns and begun examining nadl intron cDNAs to determine the extent and distribution of RNA edits in introns, in order to evaluate the possibility that intron excision and exon splicing might be editing independent.
Wolstenholme, D.R.
Gene encoding acetyl-coenzyme A carboxylase
A DNA encoding an acetyl-coenzyme A carboxylase (ACCase) from a photosynthetic organism and functional derivatives are disclosed which are resistant to inhibition from certain herbicides. This gene can be placed in organisms to increase their fatty acid content or to render them resistant to certain herbicides. 5 figs.
Roessler, P.G.; Ohlrogge, J.B.
Information Retrieval meets Gene Analysis Hagit Shatkay
Information Retrieval meets Gene Analysis Hagit Shatkay Celera Genomics 45 West Gude Drive, based on probabilistic information retrieval, which uses the lit- erature to establish functional-related publications. This wealth of information presents a major data-analysis challenge. An ultimate goal is to under
Shatkay, Hagit
Mechanisms of radiation-induced gene responses
In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.
Woloschak, G.E.; Paunesku, T.
Molecular Cell Control of Proinflammatory Gene
-depen- dent erasure of H4K20me3 is required for effective gene activation and is achieved by NF-kB-depen- dent such as nuclear factor-k B (NF-kB), activator protein 1 (AP1), and interferon regulatory factor (IRFs
Higgins, Darren
Book Review Bayesian Inference for Gene Expression
Book Review Bayesian Inference for Gene Expression and Proteomics. Edited by Kim-Anh Do, Peter Mu for a long time. This book is a timely publication entirely devoted to cutting-edge Bayesian methods in their own biological research. Moreover, the book calls for more methodological and theoretical research
Vannucci, Marina
RAS Gene Hot-Spot Mutations in
Point mutations in the cellular homologues HRAS, KRAS2, and NRAS of the viral Harvey and Kirsten rat sarcoma virus oncogenes are commonly involved in the onset of malignancies in humans and other species such as dog, mouse, and rat. Most often, three particular hot-spot codons are affected, with one amino acid exchange being sufficient for the induction of tumor growth. While RAS genes have been shown to play an important role in canine tumors such as non-small lung cell carcinomas, data about RAS mutations in canine fibrosarcomas as well as KRAS2 mutations in canine melanomas is sparse. To increase the number of tumors examined, we recently screened 13 canine fibrosarcomas and 11 canine melanomas for point mutations, particularly within the mutational hot spots. The results were compared to the already existing data from other studies about these tumors in dogs. A family of genes often involved in human tumors are the well-characterized RAS genes, which comprise HRAS, KRAS2, and NRAS, coding for closely related, small, 189 amino acid, 21 kDa, membrane-bound, intracellular proteins. The human cellular HRAS and KRAS2 genes were identified to be homologues of the Harvey and Kirsten rat sarcoma
Canine Neoplasias; J. Bullerdiek
Integrating gene expression profiling and clinical data
We propose a combination of machine learning techniques to integrate predictive profiling from gene expression with clinical and epidemiological data. Starting from BioDCV, a complete software setup for predictive classification and feature ranking without ... Keywords: BioDCV, Biomarkers, Classification, DNA microarray, Feature selection, Functional genomics, SVM, Statistical learning
Silvano Paoli; Giuseppe Jurman; Davide Albanese; Stefano Merler; Cesare Furlanello
Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression
Variable expressivity of mutant phenotypes in genetically identical individuals is a phenomenon widely reported but poorly understood. For example, mutations in the gene encoding the transcription factor ALR-1 in Caenorhabditis ...
Topalidou, Irini
Abnormal Gene Expression of Four Genes in Cells from Family Members of
Abnormal Gene Expression of Four Genes in Cells from Family Members of Abnormal Gene Expression of Four Genes in Cells from Family Members of Hereditary-type Retinoblastoma Patients relative to Normal Individuals Chin-Yu Wang, 1 Yuanlin Peng, 1 Zhonghui Yang, 2 Chuan-Yuan Li, 2 Hatsumi Nagasawa, 1 Markus M. Fitzek, 3 John B. Little, 4 Joel S. Bedford, 1 and Eric Y. Chuang 5 1 Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado; 2 Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina; 3 Department of Radiation Oncology, Tufts-New England Medical Center; 4 Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts; and 5 Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
Gene family evolution by duplication, speciation and loss - CECM
increase of the lower bound. Let S = {S1,...,Sk} be a set .... (expected number of event by million years) and a gene loss rate of 0.02. We chose a gene gain/loss�...
Account Request Form | IBM Blue Gene Parallel Supercomputer,...
(check all that apply) Please make at least one selection Brookhaven Blue GeneQ Argonne Leadership Computing Facility (based on Blue GeneQ) What is the name of the code? Do you...
Mediator and cohesin connect gene expression and chromatin architecture
Transcription factors control cell-specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound ...
Kagey, Michael H.
Distal chromatin structure influences local nucleosome positions and gene expression
The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene ...
Jansen, An
Cross-regulation and interaction between eukaryotic gene regulatory processes
Regulation of genes is fundamental to all living processes and can be exerted at many sequential steps. We studied several eukaryotic gene regulatory mechanisms with an emphasis on understanding the interplay between ...
Spies, Noah (Noah Walter Benjamin)
Performance Analysis of Enhanced Clustering Algorithm for Gene Expression Data
Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively used to make proteins. This method is used to analysis the gene expression, an important task in bioinformatics research. Cluster analysis of gene expression data has proved to be a useful tool for identifying co-expressed genes, biologically relevant groupings of genes and samples. In this paper we applied K-Means with Automatic Generations of Merge Factor for ISODATA- AGMFI. Though AGMFI has been applied for clustering of Gene Expression Data, this proposed Enhanced Automatic Generations of Merge Factor for ISODATA- EAGMFI Algorithms overcome the drawbacks of AGMFI in terms of specifying the optimal number of clusters and initialization of good cluster centroids. Experimental results on Gene Expression Data show that the proposed EAGMFI algorithms could identify compact clus...
Chandrasekhar, T; Elayaraja, E
Casein genes of Bos taurus. II. Isolation and characterization of the /beta/-casein gene
The expression of the casein genes in the cells of the mammary gland is regulated by peptide and steroid hormones. In order to study the controlling mechanisms we have isolated and characterized the /beta/-casein gene. The gene is 8.6 kb long and exceeds by a factor of 7.8 the length of the corresponding mRNA which is encoded by nine exons. The genomic clones incorporate in addition 8.5 kb and 4.5 kb of the 5/prime/- and 3/prime/-flanking regions. We have determined the sequence of the 5- and 3-terminals of the gene and have performed a comparative analysis of the corresponding regions of the rat /beta/-casein gene. Furthermore we have identified the conversed sequences identical or homologous to the potential sections of binding to the nuclear factor CTF/NF-1 by glucocorticoid and progesterone receptors. The regulatory region of the bovine casein gene contains two variants of the TATA signal, flanking the duplication section in the promoter region.
Gorodetskii, S.I.; Tkach, T.M.; Kapelinskaya, T.V.
Ataxia-telangiectasia: mutations in the ATM gene
The invention is related to ataxia-telangiectasia, specifically, mutations in the ataxia-telangiectasia mutated gene.
Gatti, Richard A. (3835 Longridge Ave., Sherman Oaks, CA 91243); Concannon, Patrick J. (5335 old Mill Rd. NE., Bainbridge Island, WA 98110)
Functional visualisation of genes using singular value decomposition
Progress in understanding core pathways and processes of cancer requires thorough analysis of many coding regions of the genome. New insights are hampered due to the lack of tools to make sense of large lists of genes identified using high throughput ... Keywords: gene ontology, genes, singular value decomposition, visualisation
Hamid Ghous, Paul J. Kennedy, Nicholas Ho, Daniel R. Catchpoole
Parametric spectral analysis of malaria gene expression time series data
Spectral analysis of DNA microarray gene expressions time series data is important for understanding the regulation of gene expression and gene function of the Plasmodium falciparum in the intraerythrocytic developmental cycle. In this paper, ... Keywords: autoregressive model, microarray time series analysis, plasmodium falciparum, singular spectrum analysis, spectral estimation
Liping Du; Shuanhu Wu; Alan Wee-Chung Liew; David Keith Smith; Hong Yan
The ribosomal protein genes and Minuteloci of Drosophila melanogaster
necessary, D. mela- nogaster genes were named or renamed according to the standard metazoan RP gene nomenclature proposed by Wool and colleagues [5,58,59] and approved by the HUGO Gene Nomenclature Committee [18], whilst still conforming to Fly- Base [60...
Marygold, Steven J; Roote, John; Reuter, Gunter; Lambertsson, Andrew; Ashburner, Michael; Millburn, Gillian; Harrison, Paul; Yu, Zhan; Kenmochi, Naoya; Kaufman, Thomas C; Leevers, Sally J; Cook, Kevin R
Classification of co-expressed genes from DNA regulatory regions
The analysis of non-coding DNA regulatory regions is one of the most challenging open problems in computational biology. In this paper we investigate whether we can predict functional information about genes by using information extracted from their ... Keywords: Combinatorial and machine learning methods integration, Gene classification, Gene expression and bio-sequence data integration, Motif extraction and selection
Giulio Pavesi; Giorgio Valentini
Synthetic gene design with a large number of hidden stops
Hidden stops are nucleotide triples TAA, TAG and TGA that appear on the second and third reading frames of a protein coding gene. Recent studies suggested the important role of hidden stops in preventing misread of mRNA. We study the problem of designing ... Keywords: back translation, bioinformatics, codons, gene design, hidden stops, mRNA, protein coding genes, synthetic biology
Vinhthuy Phan; Sudip Saha; Ashutosh Pandey; Tit-Yee Wong
In vitro circadian ANP secretion by gene transferring cells encapsulated in polycaprolactone tubes: gene chronotherapy
A new insofar as chronobiologic therapeutic approach by atrial natriuretic peptide (ANP) for hypertension and/or congestive heart failure (CHF) is based on the release of ANP from ANP cDNA transfected Chinese Hamster Ovary (CHO) cells encapsulated in polycaprolactone (PCL) tubes. ANP secretion was maintained for at least 6 months. The encapsulated cells remained viable during culturing. Control cells without transferred ANP cDNA were negative. ANP secretion is circadian periodic, peaking around 04:18, shifted to around 07:56 by melatonin treatment. The encapsulation technique, based on principles of chronotherapy, may provide a more efficient gene therapy, applicable for eventual human implantation of gene transferred cells.
Zhengrong Wang A; Liguo Chen A; Chaomin Wan A; Yiqu A; G. Corn�lissen B; F. Halberg B
Metagenomic gene annotation by a homology-independent approach
Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.
Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin
Molecular characterization of a maize regulatory gene
Based on initial bombardment studies we have previously concluded that promoter diversity was responsible for the diversity of naturally occurring R alleles. During this period we have found that R is controlled at the level of translation initiation and intron 1 is alternatively spliced. The experiments described in Sections 1 and 2 sought to quantify these effects and to determine whether they contribute to the tissue specific expression of select R alleles. This study was done because very little is understood about the post-transcriptional regulation of plant genes. Section 3 and 4 describe experiments designed to identify important structural components of the R protein.
Wessler, S.R.
Gene expression in physically impeded maize roots
Two approaches were used to search for genes which respond to physical impedance. First, cDNA clones induced by mechanical stress or drought stress of other plant species were hybridized to mRNA from maize root tips. The results showed that only two clones, TCH1 induced by wind stress in Arabidopsis, and LP2 induced by drought stress in pine, had high homology with the RNA in maize root tips, but they did not reveal an inducible pattern of expression in the impeded maize roots tips. Second, a cDNA library was constructed from mMRNA from a 10 min physical impedance treatment of maize roots tips and was differentially screened with radioactive labeled cDNA probes synthesized using mRNA extracted from stressed and non-stressed maize roots tips. Three clones, PIIGI, pIIG2, and pIRG3, were identified as responding to a 10 min physical impedance stress. The first two cDNA clones (PIIGI and pIIG2), whose expressions were induced in a 10 min physical impedance treatment, were characterized further. cDNA PIIGI contains 678 hp with an open reading frame which specifies a polypeptide of 129 amino acid residues which showed 97% similarity at the nucleic acid level to maize root cortical cell delineating protein. Northern analysis with cDNA PIIGI as a probe showed that the expression was strongly induced by the 10 min physical impedance treatment and genomic Southern analysis showed that a relatively conserved gene family exists in maize. The CDNA pIIG2 has a nucleotide sequence of 830 bp with an open reading frame which specifies a polypeptide of 210 amino acid residues, but in a search of the GENBANK database it did not show significant homology with any identified gene of known function. Genomic Southern hybridization using cDNApIIG2 found duplicated loci in maize but single loci in rice. The third cDNA clone pIRG3, 800 bp, whose expression was reduced about 33% by 10 to 30 min physical impedance, is identical to the partial sequence of maize "calreticulin!' gene by GENBANK search.
Huang, Ying-Fei
Surface enhanced Raman gene probe and methods thereof
The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.
Vo-Dinh, T.
IBM Blue Gene Parallel Supercomputer, Brookhaven National Laboratory, (BNL)
L L Overview Simple Example: Compile, Link, Run Compiler Invocation Compile and Link Tips Batch Job Submission Applications Support Math Libraries MPI Version IBM Fortran Blue Gene & Linux Manuals (IBM Redbooks) Much of the info you need will be in the Linux manual, but there is also some Blue Gene-specific info in the Blue Gene manual. Current Fortran compiler version number can be determined on fen by typing: ls /opt/ibmcmp/xlf/bg, will be highest number listed. IBM C/C++ Blue Gene & Linux Manuals (IBM Redbooks) Much of the info you need will be in the Linux manual, but there is also some Blue Gene-specific info in the Blue Gene manual. Linux Manual: Go to XL C/C++ for Linux, choose the Product Library link, then select current version number in tab at page top. (Current C/C++
How to Login How to Login Please note, New York Blue/L has been decommissioned and these web pages have not yet been updated to reflect its removal from service. The New York Blue/P is now one rack and remains in service. The BNL Blue Gene/Q also remains in service. Introduction Accessing the Blue Gene SSH Gateways Accessing the Blue Gene Front-End Nodes Accessing the Visualization Cluster Accessing the CSC GPU Cluster SSH Tunneling Introduction The only way to access Blue Gene computing resources remotely (outside the Blue Gene network enclave) is through the Blue Gene ssh gateways. Even users connecting from inside the BNL campus network need to go through the gateways. Outside the BNL campus the gateways are known as: ssh.bluegene.bnl.gov Inside the BNL campus they are known as: ssh.bluegene.bnl.local
Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations with OWL
, Shneiderman B: Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 2004, 5:84. 8. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP...
Gene Geracao Eolica Do Nordeste | Open Energy Information
Do Nordeste Place Brazil Sector Wind energy Product Aims to manufacture and commercialize wind turbines generators between 3 and 10kW. Incubated by Padetec. References Gene -...
Universal Gene Transfer Technology for Gram Positive Bacteria
research �DNA Gene therapy holds great promise to cure cancer, HIV, and other hereditary and contagious diseases � Genetic engineering has been widely ...
Genomics, Gene Expression and Other Studies in Soybean Rust
Joint Genome Institute Genomics, Gene Expression and otherRust Martha Luc�a Posada-Buitrago Ph.D Genomics DivisionEvolutionary Genomics DOE- Joint Genome Institute Lawrence
Posada-Buitrago, Martha Lucia
Regulation of the chitinase gene expression in suspension-cultured ...
Plant Molecular Biology 39: 907�914, 1999. � 1999 Kluwer Academic Publishers . Printed in the Netherlands. 907. Regulation of the chitinase gene expression�...
Available Technologies: Library of Plasmids to Control Gene ...
A scientist wishing to differentially express a set of genes can query the database, choose the most appropriate vectors for the desired expression levels, ...
Alterations in mitochondrial gene copy numbers following irradiation...
Alterations in mitochondrial gene copy numbers following irradiation in radiosensitive mice Sumita Raha Northwestern University Abstract We have developed a quantitative real-time...
Alterations in mitochondrial gene copy numbers following irradiation in radiosensitive mice. Sumita Raha, Qiong Wang, Emily Mirkin, M. Beau Wanzer, Tatjana Paunesku and Gayle...
Formal models of gene clusters - CECM - Simon Fraser University
The detection of conserved gene clusters is a challenge for both the biologi- ..... depending on both the combinatorial nature of the considered data (strings or.
Post transcriptional regulation of chloroplast gene expression by nuclear encoded gene products. Progress report, June 1, 1990--June 30, 1992
Many individual chloroplast genes require the products of a collection of nuclear genes for their successful expression. These nuclear gene products apparently work with great specificity, each committed to the expression of a single chloroplast gene. We have chosen as a model nuclear mutants of Chlamydomonas affected in different stages in the expression of the chloroplast encoded Photosystem II polypeptide, D2. We have made the progress in understanding how nuclear gene products affect the translation of the D2 encoding MRNA. Two nuclear genes are required for this process which have been mapped genetically. In contrast to other examples of nuclear control of translation in the chloroplast, these nuclear gene products appear to be required either for specific stages in translation elongation or for the post-translational stabilization of the nascent D2 protein. Pseudoreversion analysis has led us to a locus which may be directly involved in D2 expression. We have made considerable progress in pursuing the molecular basis of psbd MRNA stabilization. psbD 5` UTR specific transcripts have been synthesized in vitro and used in gel mobility shift assays. UV-crosslinking studies are underway to identify the transacting factors which bind to these sequences. The continued examination of these mutants will help us to understand how nuclear gene products work in this specific case of chloroplast gene expression, and will elucidate how two distinct genomes can interact generally.
Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph
Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression: The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression: N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression: Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin, and diffusion protein OmpC were expressed to higher levels under Fe limitation. N. europaea has a high Fe requirement and under Fe limiting conditions (0.2 {micro}M), is capable to assimilate up to 70% of the available Fe without the ability to produce siderophores.
Daniel J. Arp
Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression. The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression. N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression. Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin, and diffusion protein OmpC were expressed to higher levels under Fe limitation. N. europaea has a high Fe requirement and under Fe limiting conditions (0.2 ?M), is capable to assimilate up to 70% of the available Fe without the ability to produce siderophores.
Daniel J Arp
Evolutionary analyses of nonfamily genes in plants
73 73 © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd Received Date : 11-May-2012 Revised Date : 16-Oct-2012 Accepted Date : 07-Nov-2012 Article type : Original Article Evolutionary analyses of non-family genes in plants Chu-Yu Ye 1,2,3,4 , Ting Li 1,3,4 , Hengfu Yin 1 , David J. Weston 1 , Gerald A. Tuskan 1,2 , Timothy J. Tschaplinski 1,2 , Xiaohan Yang 1,2,* 1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 2 BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 3 Present addresses: Beijing Forestry University, Beijing 100083, China (C.-Y.Y.); Pioneer Hi- Bred International, Johnston, IA 50131, USA (T.L.) 4 These authors contributed equally to this work. * Corresponding author:
Text analysis of MEDLINE for discovering functional relationships among genes: evaluation of keyword extraction weighting schemes
One of the key challenges of microarray studies is to derive biological insights from the gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the functional links among genes. However, ... Keywords: BEA-PARTITION, DNA microarray lists, MEDLINE, bioinformatics, clustering analysis, data mining, gene clustering, gene expression patterns, information extraction, keyword association, keyword extraction, keyword weighting, text analysis
Ying Liu; Shamkant B. Navathe; Alex Pivoshenko; Venu G. Dasigi; Ray Dingledine; Brian J. Ciliax
Detecting reliable gene interactions by a hierarchy of Bayesian network classifiers
The main purpose of a gene interaction network is to map the relationships of the genes that are out of sight when a genomic study is tackled. DNA microarrays allow the measure of gene expression of thousands of genes at the same time. These data constitute ... Keywords: Bayesian network classifiers, DNA microarrays, Gene interactions, Knowledge discovery, Robust arc identification
Rub�n Arma�anzas; I�aki Inza; Pedro Larra�aga
Early Experience on the Blue Gene/Q Supercomputing System
The Argonne Leadership Computing Facility (ALCF) is home to Mira, a10 PF Blue Gene/Q (BG/Q) system. The BG/Q system is the third generation in Blue Gene architecture from IBM and like its predecessors combines system-on-chip technology with a proprietary ... Keywords: supercomputing, performance, multi-core, scalability, applications
Vitali Morozov, Kalyan Kumaran, Venkatram Vishwanath, Jiayuan Meng, Michael E. Papka
Petascale Debugging via Allinea DDT for IBM Blue Gene /P
@allinea.com> Senior Systems Engineer, Allinea Software Inc. ALCF L2P Workshop, May 23, 2012 #12;Outline ExperienceArchitecture #12;Current Status IBM Blue Gene /P Acceptance testing at ALCF (Allinea DDT 3.1) Scale (Allinea DDT 3.2) Early access for IBM Blue Gene /Q expected July 2012 ALCF requirement Scale for Mira
Kemner, Ken
Gene identification in Phytophthora capsici through expressed sequence tags
Expressed Sequence Tags (ESTs) are a rich source of information for gene discovery. In this paper, we describe the annotation of ESTs of Phytophthora capsici whose complete genome is not yet available. P. capsici is an Oomycete plant pathogen ... Keywords: Phytophthora capsici, expressed sequence tags, gene functional annotation
N. Reena; A. Chandrasekar; A. Riju; P. L. Nima; S. J. Eapen; M. Anandaraj
Predicting Gene Structures from Multiple RT-PCR Tests
Predicting Gene Structures from Multiple RT-PCR Tests (Extended Abstract) Jakub Kov´ac1 , Tom RT-PCR experiments in gene finding. We present hardness results and practical algorithms for several variants of the problem. We also apply our methods to a real RT-PCR data set in the Drosophila genome. We
Vinar, Tomas
Parallel volume rendering on the IBM Blue Gene/P
Parallel volume rendering is implemented and tested on an IBM Blue Gene distributed-memory parallel architecture. The goal of studying the cost of parallel rendering on a new class of supercomputers such as the Blue Gene/P is not necessarily to achieve ...
Tom Peterka; Hongfeng Yu; Robert Ross; Kwan-Liu Ma
Scaling properties of transcription profiles in gene networks
Here we show that the transcriptional noise is an emergent property with scale invariance from genome level to the level of small Transcriptional Regulatory Genetic Networks (TRGN). We show that a small set of 9-12 genes reproduces the geometric ... Keywords: TRGN, behavioural variability, bioinformatics, gene networks, genome size, housekeeping functions, regulatory networks, scale invariance, transcription profiles, transcriptional noise, transcriptional regulatory genetic networks
Renata C. Ferreira; Francisco Bosco; Marcelo R. S. Briones
BlueGene/L applications: Parallelism On a Massive Scale
BlueGene/L (BG/L), developed through a partnership between IBM and Lawrence Livermore National Laboratory (LLNL), is currently the world's largest system both in terms of scale, with 131,072 processors, and absolute performance, with a peak rate of ... Keywords: BlueGene/L, application scalability, massively parallel architectures, performance study and optimization
Bronis R. De Supinski; Martin Schulz; Vasily V. Bulatov; William Cabot; Bor Chan; Andrew W. Cook; Erik W. Draeger; James N. Glosli; Jeffrey A. Greenough; Keith Henderson; Alison Kubota; Steve Louis; Brian J. Miller; Mehul V. Patel; Thomas E. Spelce; Frederick H. Streitz; Peter L. Williams; Robert K. Yates; Andy Yoo; George Almasi; Gyan Bhanot; Alan Gara; John A. Gunnels; Manish Gupta; Jose Moreira; James Sexton; Bob Walkup; Charles Archer; Francois Gygi; Timothy C. Germann; Kai Kadau; Peter S. Lomdahl; Charles Rendleman; Michael L. Welcome; William Mclendon; Bruce Hendrickson; Franz Franchetti; Stefan Kral; J�rgen Lorenz; Christoph W. �berhuber; Edmond Chow; �mit �ataly�rek
Prediction of epigenetically regulated genes in breast cancer cell lines
Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes. Therefore, using high-throughput microarrays to measure CpG island methylation will lead to better understanding of tumor pathobiology and progression, while revealing potentially new biomarkers. We have examined a recently developed high-throughput technology for measuring genome-wide methylation patterns called mTACL. Here, we propose a computational pipeline for integrating gene expression and CpG island methylation profles to identify epigenetically regulated genes for a panel of 45 breast cancer cell lines, which is widely used in the Integrative Cancer Biology Program (ICBP). The pipeline (i) reduces the dimensionality of the methylation data, (ii) associates the reduced methylation data with gene expression data, and (iii) ranks methylation-expression associations according to their epigenetic regulation. Dimensionality reduction is performed in two steps: (i) methylation sites are grouped across the genome to identify regions of interest, and (ii) methylation profles are clustered within each region. Associations between the clustered methylation and the gene expression data sets generate candidate matches within a fxed neighborhood around each gene. Finally, the methylation-expression associations are ranked through a logistic regression, and their significance is quantified through permutation analysis. Our two-step dimensionality reduction compressed 90% of the original data, reducing 137,688 methylation sites to 14,505 clusters. Methylation-expression associations produced 18,312 correspondences, which were used to further analyze epigenetic regulation. Logistic regression was used to identify 58 genes from these correspondences that showed a statistically signifcant negative correlation between methylation profles and gene expression in the panel of breast cancer cell lines. Subnetwork enrichment of these genes has identifed 35 common regulators with 6 or more predicted markers. In addition to identifying epigenetically regulated genes, we show evidence of differentially expressed methylation patterns between the basal and luminal subtypes. Our results indicate that the proposed computational protocol is a viable platform for identifying epigenetically regulated genes. Our protocol has generated a list of predictors including COL1A2, TOP2A, TFF1, and VAV3, genes whose key roles in epigenetic regulation is documented in the literature. Subnetwork enrichment of these predicted markers further suggests that epigenetic regulation of individual genes occurs in a coordinated fashion and through common regulators.
Loss, Leandro A; Sadanandam, Anguraj; Durinck, Steffen; Nautiyal, Shivani; Flaucher, Diane; Carlton, Victoria EH; Moorhead, Martin; Lu, Yontao; Gray, Joe W; Faham, Malek; Spellman, Paul; Parvin, Bahram
BESC Submits 32 Gene Disclosures for Patents | ORNL
News Careers Work with ORNL About ORNL Visiting ORNL Events and Conferences Highlights Success Stories Contact Us Index Home | ORNL | Highlights SHARE BESC submits 32 gene disclosures for future patents July 01, 2012 Plant geneticist Wellington Muchero examines phenotypic traits of Populus transgenic lines grown in a greenhouse. The Bioenergy Science Center (BESC) at Oak Ridge National Laboratory (ORNL) is preparing invention disclosures for 32 different genes that can help improve the yield of ethanol from cellulosic biomass. These genes or their variants function to overcome recalcitrance-difficulty in breaking down cellulosic biomass to release sugars. Several members of ORNL's Biosciences Division are submitting disclosures: 16 genes by Wellington Muchero, 10 genes by Udaya Kalluri, and
Table of Contents
... are based on the reference Leachman, JW, Jacobsen, RT, Lemmon, EW, and Penoncello, SG �Fundamental Equations of ... Handbook 44 � 2013 ...
1999 Macmillan Magazines Ltd letters to nature
. Spector and C. Jacobsen for developing the zone plates, with support from the NSF. The NSLS is supported
Beichner, Robert J.
Danish Modern, Then and Now -- The AIA Committee on Design, Historic Resources Committee [Forum
assaulted by a crass �gas station from everywhere,� whichcanopy of another gas station, designed by Jacobsen, just a
Lyndon, Donlyn FAIA
CARBON TECHNOLOGY: III: Anode Production/Performance
ANODE PROPERTY DEVELOPMENT DURING HEAT TREATMENT: Mona Jacobsen, Department of Thermal Energy and Hydro Power, the Norwegian Institute�...
A study of mammalian microRNA-mediated repression of gene expression by ribosome profiling
All cells in a multicellular organism carry the same genes, yet these same genes direct the differentiation of many different cell types. This is facilitated by differential gene expression, the control of which can be ...
Guo, Huili
The synthetic multivulva genes and their suppressors regulate opposing cell fates through chromatin remodeling
The synthetic multivulva (synMuv) genes act redundantly to inhibit vulval fates in Caenorhabditis elegans. These genes are grouped into three classes called A, B and C. The class A genes encode putative transcription ...
Andersen, Erik C
Transposon-induced nuclear mutations that alter chloroplast gene expression
The goal of this project is to use mutant phenotypes as a guide to nuclear genes that determine the timing and localization of chloroplast development The immediate goals are to identify nuclear mutants with defects in chloroplast gene expression from maize lines harboring active Mu transposons; characterize their phenotypes to determine the precise defect in gene expression; clone several of the most interesting mutations by exploiting the transposon tag; and use the clones to further define the roles of these genes in modulating chloroplast gene expression. Three mutants were described earlier that had global defects in chloroplast gene expression. We have found that two of these mutations are allelic. Both alleles have global defects in chloroplast translation initiation, as revealed by the failure to assemble chloroplast mRNAs into polysomes. We have isolated and characterized three new mutants from Mu lines that have novel defects in chloroplast RNA metabolism. We are now ready to begin the task of cloning several of these genes, by using the Mu transposon tag.
Barkan, A.
Gene expression profiles of microdissected pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) remains an important cause of malignancy-related death and is the eighth most common cancer with the lowest overall 5-year relative survival rate. To identify new molecular markers and candidates for new therapeutic regimens, we investigated the gene expression profile of microdissected cells from 11 normal pancreatic ducts, 14 samples of PDAC, and 4 well-characterized pancreatic cancer cell lines using the Affymetrix U133 GeneChip set. RNA was extracted from microdissected samples and cell lines, amplified, and labeled using a repetitive in vitro transcription protocol. Differentially expressed genes were identified using the significance analysis of microarrays program. We found 616 differentially expressed genes. Within these, 140 were also identified in PDAC by others, such as Galectin-1, Galectin-3, and MT-SP2. We validated the differential expression of several genes (e.g., CENPF, MCM2, MCM7, RAMP, IRAK1, and PTTG1) in PDAC by immunohistochemistry and reverse transcription polymerase chain reaction. We present a whole genome expression study of microdissected tissues from PDAC, from microdissected normal ductal pancreatic cells and pancreatic cancer cell lines using highdensity microarrays. Within the panel of genes, we identified novel differentially expressed genes, which have not been associated with the pathogenesis of PDAC before.
Robert Gr�tzmann; Christian Pilarsky; Ole Ammerpohl Y; Jutta L�ttges Z; Bence Sipos Z; Melanie Foerder; Ingo Alldinger; Beatrix Jahnke; Hans Konrad Schackert; Holger Kalthoff Y; Bernd Kremer B; Hans Detlev Saeger
Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism
Cyanophages infecting the marine cyanobacteria Prochlorococcus and Synechococcus encode and express genes for the photosynthetic light reactions. Sequenced cyanophage genomes lack Calvin cycle genes, however, suggesting ...
Thompson, Luke Richard
Powered by NERSC, A Database of Billions of Genes and Counting...
the news" Home News & Publications News Center News Powered by NERSC, a Database of Billions of Genes and Counting Powered by NERSC, a Database of Billions of Genes...
The human VH3b gene subfamily is highly polymorphic
The authors have previously shown that human antibody (Ab) directed against the capsular polysaccharide of the important bacterial pathogen, Haemophilus influenzae type b (Hib) is encoded by a small group of VH3 gene family members. The majority of anti-Hib PS Ab use members of the smaller VH3b subfamily. To examine directly the available human VH3 repertoire, they have used PCR to amplify and clone candidate germ-line VH3b H chain V region genes from two unrelated subjects from whom anti-Hib polysaccharide mAb had been previously obtained. A single functional VH3b germ-line gene was obtained from one subject. This gene is identical throughout the coding region to the previously identified gene 9.1. Twelve distinct VH3b germ-line sequences, 87.6-99.8% homologous to one another, were obtained from the second subject. One of these genes, LSG1.1, is also identical to the 9.1 germ-line gene, and a second, LSG6.1 is identical to a previously reported cDNA, M85. These germ-line VH3b genes are 82.7-94.1% homologous to rearranged anti-Hib PS VH3b segments obtained from these subjects. These findings further demonstrate that considerable polymorphism of VH segments exists in the human population. Despite the presence of very highly homologous VH elements in the germ line, particular genes are highly conserved within the outbred human population. 52 refs., 4 figs.
Adderson, E.E.; Carroll, W.L. (Univ. of Utah, Salt Lake City, UT (United States)); Azmi, F.H.; Wilson, P.M.; Shackelford, P.G. (Washington Univ., St. Louis, MO (United States))
Sorghum bioenergy genotypes, genes and pathways
Sorghum (Sorghum bicolor [L.] Moench) is the fifth most economically important cereal grown worldwide and is a source of food, feed, fiber and fuel. Sorghum, a C4 grass and a close relative to sugarcane, is adapted to hot, dry adverse environments and this plant is a potentially important bioenergy crop for Texas. The diversity of the twelve high biomass sorghum genotypes was analyzed using 50 simple sequence repeats (SSR) markers with genome coverage. The accumulation of biomass during sorghum development was studied in BTx623, an elite grain sorghum genotype. Genetic similarity analysis showed that the twelve high biomass genotypes were quite diverse and different from most current grain sorghum genotypes. The ratio of leaf/stem biomass accumulation was higher early in the vegetative phase during rapid canopy development and lower later in this phase when stem growth rate increased. This resulted in an increasing ratio of stem to leaf dry weight during development. Numerous cellulose sythase genes have been putatively identified in the sorghum genome. The relative level of Ces5 RNA in leaves decreased during vegetative phase of development by ~32 fold. There was no change in the relative abundance of Ces5 RNA in stems. Also there was no change in the relative abundance of Ces3 RNA in either stem or leaves during the vegetative stage. The knowledge gained in this study may contribute to the development of sorghum bioenergy hybrids that accumulate more biomass and that are modified in composition to make them more amenable to biofuels production.
Plews, Ian Kenneth
Research and Development U.S. Army Corps of Engineers
graphs, with applications to planar graph colourings Andrea Bedini1,2 and Jesper Lykke Jacobsen3 1-mail: firstname.lastname@example.com, firstname.lastname@example.com Abstract. Combining tree decomposition and transfer, Combin. Probab. Comput. 6, 497506 (1997). [37] A. Bedini and J.L. Jacobsen, in preparation. hal-00466411
US Army Corps of Engineers
Pattern Recognition 41 (2008) 3092 --3103 Contents lists available at ScienceDirect
Pelachaud, Catherine
Gene network and pathway generation and analysis: Editorial
The past decade has witnessed an exponential growth of biological data including genomic sequences, gene annotations, expression and regulation, and protein-protein interactions. A key aim in the post-genome era is to systematically catalogue gene networks and pathways in a dynamic living cell and apply them to study diseases and phenotypes. To promote the research in systems biology and its application to disease studies, we organized a workshop focusing on the reconstruction and analysis of gene networks and pathways in any organisms from high-throughput data collected through techniques such as microarray analysis and RNA-Seq.
Zhao, Zhongming; Sanfilippo, Antonio P.; Huang, Kun
The RCg2 promoter was identified in a search for root-specific genes to combat the rice water weevil (RWW) but expressed at low frequency (~10%). Spatial expression of RCg2 was investigated using two reporter constructs YXA (RCg2-gus-ocs) and YXB (RCg2-gus-RCg2) that included 1.6 kb of the RCg2 5' sequence fused to the ?-glucuronidase (gus) coding region. YXB plants were generated via Agrobacterium-mediated transformation but only 8 of 158 plants analyzed showed strong GUS activity despite the presence of an intact construct. Reactivation of RCg2 gene in rice was investigated by treatment of R0 and R1 of YXB transgenic plants with 5-azacytidine. Reactivation of RCg2-gus was observed in some transgenic plants indicating different mechanisms involved in the gene silencing of the YXB lines. DNA methylation analysis, northern blotting, RT-PCR and small RNA analysis supported the conclusion that PTGS and TGS are present in the silenced plants. Promoter analysis in silico and using promoter deletion assays predicted that the RCg2 promoter contains a complex region that includes miRNA homologs, MITEs and repetitive sequences. The high frequency of promoter-related silencing suggests functional interactions of these elements of the transgene and the homologous endogenous gene. To identify key elements contributing to the root-preferential expression of RCg2 and the high frequency of silencing observed in transgenic (YXB) lines, several RCg2 promoter deletion constructs were designed. These include 5' deletions MC1, MC2, MC4, MC7 and MC8 and internal deletions MC5, MC11, MC12 and MC13. The frequency with which silencing was encountered in populations of the deletion mutants was used to characterize the effects of various promoter elements. Deletion of the region from -406 to -208 (compared MC11 to YXB, and MC13 to MC1) revealed that region contains a negative element. Among 36 independent transformants, 33% with MC11 expressed GUS and 85% with MC13 showed GUS expression. Comparing MC7 transgenic plants to MC1 revealed that the region ?888 to ?729 is another negative regulatory element, and comparing MC11 to MC12, the proportion of expression of transgenic plants indicated the region ?729 to ?406 is a positive regulatory element.
Shi, Xiangyu
Single, Key Gene Discovery Could Streamline Production of Biofuels |
Energy.gov (U.S. Department of Energy (DOE)) Indexed Site
Single, Key Gene Discovery Could Streamline Production of Biofuels Single, Key Gene Discovery Could Streamline Production of Biofuels Single, Key Gene Discovery Could Streamline Production of Biofuels August 11, 2011 - 3:51pm Addthis WASHINGTON, DC -- A team of researchers at the Department of Energy's BioEnergy Science Center (BESC) have pinpointed the exact, single gene that controls ethanol production capacity in a microorganism. This discovery could be the missing link in developing biomass crops that produce higher concentrations of ethanol at lower costs. "The Department of Energy relies on the scientific discoveries of its labs and research centers to improve the production of clean energy sources," said Energy Secretary Steven Chu. "This discovery is an important step in developing biomass crops that could increase yield of
Expression of Genes Linked to NOx Detoxification in Aerobic Bacteria
operons referred to as the nif cluster. This suite of genesgenes not found in the nif clusters of K. pneumoniae (i.e.is high conservation among nif gene organization based on
Cua, Lynnie
Gene and translation initiation site prediction in metagenomic sequences
Motivation: Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce ...
Doug Hyatt; Philip F. LoCascio; Loren J. Hauser; Edward C. Uberbacher
A Model for the Dynamics of Gene Networks
In this work we propose a model for gene expression based on the theory of random dynamical systems (RDS) and show that it has a "modularity property" in the following sense: given any collection of genes that are linked in a transcriptional network, if each of them is individually described by a certain class of RDS then there is a natural, and essentially unique, prescription for coupling them together, respecting the network topology, in such a way that the collective system formed by all genes is a RDS as well. Moreover, the class of RDS used to describe the individual genes is flexible enough to account for a wide range of stochastic behaviors within the realm of stationary processes.
Fernando Antoneli; Renata C. Ferreira; Francisco Bosco; Marcelo R. S. Briones
Auxiliary metabolic genes in viruses infecting marine cyanobacteria
Marine viruses shape the diversity and biogeochemical role of their microbial hosts. Cyanophages that infect the cyanobacteria Prochlorococcus and Synechococcus often carry metabolic genes not found in other bacteriophages. ...
Leveraging high-throughput datasets for studies of gene regulation
In this thesis, I leveraged computational methods on biological data to better understand gene regulation and development of the human body, as well as of the model organisms mouse and yeast. Firstly, I tackled biological ...
Yen, Angela
Zebrafish promoter microarrays identify actively transcribed embryonic genes
We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation ...
Wardle, Fiona C
Molecular geomicrobiology: genes and geochemical cycling Jennifer Macalady 1
Frontiers Molecular geomicrobiology: genes and geochemical cycling Jennifer Macalady 1 , Jillian F occurs. Yet, the field of molecular geomicrobiology remains in its infancy. In the foreseeable future, merging of modern biogeochemistry with molecularly resolved ecological studies will inspire
Macalady, Jenn
Motif discovery through predictive modeling of gene regulation
We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites PSSMs by incorporating promoter sequence and transcriptome gene expression data. We use a modern large-margin machine learning approach, based on ...
Manuel Middendorf; Anshul Kundaje; Mihir Shah; Yoav Freund; Chris H. Wiggins; Christina Leslie
Context-specific Bayesian clustering for gene expression data
The recent growth in genomic data and measurement of genome-wide expression patterns allows to examine gene regulation by transcription factors using computational tools. In this work, we present a class of mathematical models that help in understanding ...
Yoseph Barash; Nir Friedman
New Perspectives on Gene Family Evolution - CECM - Simon Fraser ...
PLoS ONE 1, e85 (2006). 12. Doyon, J.-P., Chauve, C., Hamel, S.: Algorithms for exploring the space of gene tree/species tree reconciliations. In: Nelson, C.E.�...
Single-Molecule Approaches to Stochastic Gene Expression
Both the transcription of mRNAs from genes and their subsequent translation into proteins are inherently stochastic biochemical events, and this randomness can lead to substantial cell-to-cell variability in mRNA and protein ...
Raj, Arjun
Deterministic Ensemble Forecasts Using Gene-Expression Programming
A method called gene-expression programming (GEP), which uses symbolic regression to form a nonlinear combination of ensemble NWP forecasts, is introduced. From a population of competing and evolving algorithms (each of which can create a ...
Atoossa Bakhshaii; Roland Stull
Genome Enabled Discovery of Carbon Sequestration Genes in Poplar
The goals of the S.H. Strauss laboratory portion of 'Genome-enabled discovery of carbon sequestration genes in poplar' are (1) to explore the functions of candidate genes using Populus transformation by inserting genes provided by Oakridge National Laboratory (ORNL) and the University of Florida (UF) into poplar; (2) to expand the poplar transformation toolkit by developing transformation methods for important genotypes; and (3) to allow induced expression, and efficient gene suppression, in roots and other tissues. As part of the transformation improvement effort, OSU developed transformation protocols for Populus trichocarpa 'Nisqually-1' clone and an early flowering P. alba clone, 6K10. Complete descriptions of the transformation systems were published (Ma et. al. 2004, Meilan et. al 2004). Twenty-one 'Nisqually-1' and 622 6K10 transgenic plants were generated. To identify root predominant promoters, a set of three promoters were tested for their tissue-specific expression patterns in poplar and in Arabidopsis as a model system. A novel gene, ET304, was identified by analyzing a collection of poplar enhancer trap lines generated at OSU (Filichkin et. al 2006a, 2006b). Other promoters include the pGgMT1 root-predominant promoter from Casuarina glauca and the pAtPIN2 promoter from Arabidopsis root specific PIN2 gene. OSU tested two induction systems, alcohol- and estrogen-inducible, in multiple poplar transgenics. Ethanol proved to be the more efficient when tested in tissue culture and greenhouse conditions. Two estrogen-inducible systems were evaluated in transgenic Populus, neither of which functioned reliably in tissue culture conditions. GATEWAY-compatible plant binary vectors were designed to compare the silencing efficiency of homologous (direct) RNAi vs. heterologous (transitive) RNAi inverted repeats. A set of genes was targeted for post transcriptional silencing in the model Arabidopsis system; these include the floral meristem identity gene (APETALA1 or AP1), auxin response factor gene (ETTIN), the gene encoding transcriptional factor of WD40 family (TRANSPARENTTESTAGLABRA1 or TTG1), and the auxin efflux carrier (PIN-FORMED2 or PIN2) gene. More than 220 transgenic lines of the 1st, 2nd and 3rd generations were analyzed for RNAi suppression phenotypes (Filichkin et. al., manuscript submitted). A total of 108 constructs were supplied by ORNL, UF and OSU and used to generate over 1,881 PCR verified transgenic Populus and over 300 PCR verified transgenic Arabidopsis events. The Populus transgenics alone required Agrobacterium co-cultivations of 124.406 explants.
Filichkin, Sergei; Etherington, Elizabeth; Ma, Caiping; Strauss, Steve
Activation of the human beta interferon gene by the adenovirus type 12 E1B gene
The transcription of endogenous beta interferon mRNA was activated in human embryo kidney (HEK) cells infected with adenovirus 12 (Ad12) but was activated only inefficiently or not at all in HEK cells infected with Ad5 and rc-1 (Ad5 dl312 containing the Ad12 E1A region). The analysis with Ad12 mutants showed that Ad12 E1B products, especially the 19K protein, were important for the expression of the endogenous beta interferon gene and Ad12 E1A products were not involved in the expression. The expression of exogeneously transfected pIFN-CAT (a hybrid plasmid having the human beta interferon promoter fused with the CAT gene) was activated in HEK and chicken embryo fibroblast (CEF) cells infected with either Ad12 or Ad5. The analysis of cotransfection of CEF cells with pIFN-CAT and plasmids containing fragments of Ad12 or Ad5 DNA showed that Ad12 or Ad5 E1B (possibly the 19K protein) was and E1A was not involved in the expression of the exogenous pIFN-CAT.
Shiroki, K.; Toth, M.
Organization and control of genes encoding catabolic enzymes in Rhizobiaceae
Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the [beta]-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novel regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate [beta]-carboxy-cis,cis-muconate. [beta]-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for [beta]-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to [beta]-carboxy-cis,cis-muconate.
Parke, D.; Ornston, L.N.
Genome-enabled Discovery of Carbon Sequestration Genes
The fate of carbon below ground is likely to be a major factor determining the success of carbon sequestration strategies involving plants. Despite their importance, molecular processes controlling belowground C allocation and partitioning are poorly understood. This project is leveraging the Populus trichocarpa genome sequence to discover genes important to C sequestration in plants and soils. The focus is on the identification of genes that provide key control points for the flow and chemical transformations of carbon in roots, concentrating on genes that control the synthesis of chemical forms of carbon that result in slower turnover rates of soil organic matter (i.e., increased recalcitrance). We propose to enhance carbon allocation and partitioning to roots by 1) modifying the auxin signaling pathway, and the invertase family, which controls sucrose metabolism, and by 2) increasing root proliferation through transgenesis with genes known to control fine root proliferation (e.g., ANT), 3) increasing the production of recalcitrant C metabolites by identifying genes controlling secondary C metabolism by a major mQTL-based gene discovery effort, and 4) increasing aboveground productivity by enhancing drought tolerance to achieve maximum C sequestration. This broad, integrated approach is aimed at ultimately enhancing root biomass as well as root detritus longevity, providing the best prospects for significant enhancement of belowground C sequestration.
Tuskan, Gerald A [ORNL; Tschaplinski, Timothy J [ORNL; Kalluri, Udaya C [ORNL; Yin, Tongming [ORNL; Yang, Xiaohan [ORNL; Zhang, Xinye [ORNL; Engle, Nancy L [ORNL; Ranjan, Priya [ORNL; Basu, Manojit M [ORNL; Gunter, Lee E [ORNL; Jawdy, Sara [ORNL; Martin, Madhavi Z [ORNL; Campbell, Alina S [ORNL; DiFazio, Stephen P [ORNL; Davis, John M [University of Florida; Hinchee, Maud [ORNL; Pinnacchio, Christa [U.S. Department of Energy, Joint Genome Institute; Meilan, R [Purdue University; Busov, V. [Michigan Technological University; Strauss, S [Oregon State University
Stripe Forming Architecture of the Gap Gene System
In this report, we show that gap genes encode exactly one set of pair-rule stripes, which occur in the native even-skipped position. The core of this work is a detailed analysis that shows how this conclusion follows from the arrangement of gap domains in the embryo. This analysis shows that: (1) pattern forming information is transmitted from gap to pair-rule genes by means of a nonredundant set of morphogenetic gradients, and (2) the stripe forming capability of the gap genes is constrained by the arrangement of these gradients and by the fact that each gap domain consists of a pair of correlated gradients. We also show that in the blastoderm, the regulatory sign of a transcriptional regulator is unlikely to change in a concentration dependent manner. The principal analytic tool used to establish these results is the gene circuit method. Here, this method is applied to examine hybrid data sets consisting of real gene expression data for four gap genes and hypothetica...
John Reinitz David; David Kosman; Carlos E. Vanario-alonso; David H. Sharp
Plants utilize carbon by partitioning the reduced carbon obtained through photosynthesis into different compartments and into different chemistries within a cell and subsequently allocating such carbon to sink tissues throughout the plant. Since the phytohormones auxin and cytokinin are known to influence sink strength in tissues such as roots (Skoog & Miller 1957, Nordstrom et al. 2004), we hypothesized that altering the expression of genes that regulate auxin-mediated (e.g., AUX/IAA or ARF transcription factors) or cytokinin-mediated (e.g., RR transcription factors) control of root growth and development would impact carbon allocation and partitioning belowground (Fig. 1 - Renewal Proposal). Specifically, the ARF, AUX/IAA and RR transcription factor gene families mediate the effects of the growth regulators auxin and cytokinin on cell expansion, cell division and differentiation into root primordia. Invertases (IVR), whose transcript abundance is enhanced by both auxin and cytokinin, are critical components of carbon movement and therefore of carbon allocation. Thus, we initiated comparative genomic studies to identify the AUX/IAA, ARF, RR and IVR gene families in the Populus genome that could impact carbon allocation and partitioning. Bioinformatics searches using Arabidopsis gene sequences as queries identified regions with high degrees of sequence similarities in the Populus genome. These Populus sequences formed the basis of our transgenic experiments. Transgenic modification of gene expression involving members of these gene families was hypothesized to have profound effects on carbon allocation and partitioning.
Detecting disease genes based on semi-supervised learning and protein-protein interaction networks
Objective: Predicting or prioritizing the human genes that cause disease, or ''disease genes'', is one of the emerging tasks in biomedicine informatics. Research on network-based approach to this problem is carried out upon the key assumption of ''the ... Keywords: Disease gene neighbours, Disease-causing gene prediction, Multiple data resources integration, Protein-protein interaction network, Semi-supervised learning
Thanh-Phuong Nguyen; Tu-Bao Ho
Isolation and characterization of resistance gene analogs (RGAs) in sorghum
The largest group of plant disease resistance (R) genes that share similar structures contains a predicted nucleotide-binding site (NBS) domain. NBS domains of this class of R genes show highly conserved amino acid motifs, which makes it possible to isolate resistance gene analogs (RGAs) by PCR with degenerate primers and homology searches from public databases. Multiple combinations of degenerate primers were designed from three conserved motifs (one motif was used for a subgroup-specific primer design) in the NBS regions of R genes of various plants. All combinations of primer pairs were used to amplify genomic DNA from sorghum. TIR-specific primer combinations showed no PCR amplification in sorghum. Homology searches identified many NBS-encoding sequences among the expressed or genomic molecular database entries for sorghum. Motif analysis of the sorghum NBS sequences that were identified in this study revealed eight major conserved motifs plus two additional highly conserved motifs, but no TIR-specific motifs. Phylogenetic analysis of sorghum NBS sequences showed tree topology typical of NBS-LRR genes, including clustered nodes and longbranch lengths. Eleven distinct families of NBS sequences, representing a highly diverse sample, were isolated from Sorghum bicolor. With two exceptions, sorghum RGA families appeared to be closely related in sequence to at least one R-gene cloned from other species. In addition, deduced amino acid sequences of sorghum RGAs showed strong sequence similarity to almost all known non-TIR (Toll/Interleukin 1 Receptor)- type R-genes. Mapping with sorghum RGA markers revealed one linkage group containing four out of ten randomly selected markers, suggesting non-random distribution of NBS sequences in the sorghum genome. Rice sequences homologous to sorghum NBS sequences were found from two-way BLAST searches. Some of them were shown to be orthologs, when determined by using phylogenetic approaches which combined five different evolution models and tree-building methods.
Cho, Jae-Min
Low doses of neutrons induce changes in gene expression
Studies were designed to identify genes induced following low-dose neutron but not following {gamma}-ray exposure in fibroblasts. Our past work had shown differences in the expression of {beta}-protein kinase C and c-fos genes, both being induced following {gamma}-ray but not neutron exposure. We have identified two genes that are induced following neutron, but not {gamma}-ray, exposure: Rp-8 (a gene induced by apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency (HIV). Rp-8 mRNA induction was demonstrated in Syrian hamster embryo fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.5 cGy/min) and at high dose rate (12 cGy/min). The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measures of CAT activity and CAT transcripts following irradiation demonstrated an unresponsiveness to {gamma} rays over a broad range of doses. Twofold induction of the HIV-LTR was detected following neutron exposure (48 cGy) administered at low (0.5 cGy/min) but not high (12 cGy/min) dose rates. Ultraviolet-mediated HIV-LTR induction was inhibited by low-dose-rate neutron exposure.
Woloschak, G.E.; Chang-Liu, C.M. [Argonne National Lab., IL (United States); Panozzo, J.; Libertin, C.R. [Loyola Univ., Maywood, IL (United States)
Studies were designed to identify genes induced following low-dose neutron but not following [gamma]-ray exposure in fibroblasts. Our past work had shown differences in the expression of [beta]-protein kinase C and c-fos genes, both being induced following [gamma]-ray but not neutron exposure. We have identified two genes that are induced following neutron, but not [gamma]-ray, exposure: Rp-8 (a gene induced by apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency (HIV). Rp-8 mRNA induction was demonstrated in Syrian hamster embryo fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.5 cGy/min) and at high dose rate (12 cGy/min). The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measures of CAT activity and CAT transcripts following irradiation demonstrated an unresponsiveness to [gamma] rays over a broad range of doses. Twofold induction of the HIV-LTR was detected following neutron exposure (48 cGy) administered at low (0.5 cGy/min) but not high (12 cGy/min) dose rates. Ultraviolet-mediated HIV-LTR induction was inhibited by low-dose-rate neutron exposure.
Woloschak, G.E.; Chang-Liu, C.M. (Argonne National Lab., IL (United States)); Panozzo, J.; Libertin, C.R. (Loyola Univ., Maywood, IL (United States))
Reconstruction of Gene Networks of Iron Response in Shewanella oneidensis
It is of great interest to study the iron response of the -proteobacterium Shewanella oneidensis since it possesses a high content of iron and is capable of utilizing iron for anaerobic respiration. We report here that the iron response in S. oneidensis is a rapid process. To gain more insights into the bacterial response to iron, temporal gene expression profiles were examined for iron depletion and repletion, resulting in identification of iron-responsive biological pathways in a gene co-expression network. Iron acquisition systems, including genes unique to S. oneidensis, were rapidly and strongly induced by iron depletion, and repressed by iron repletion. Some were required for iron depletion, as exemplified by the mutational analysis of the putative siderophore biosynthesis protein SO3032. Unexpectedly, a number of genes related to anaerobic energy metabolism were repressed by iron depletion and induced by repletion, which might be due to the iron storage potential of their protein products. Other iron-responsive biological pathways include protein degradation, aerobic energy metabolism and protein synthesis. Furthermore, sequence motifs enriched in gene clusters as well as their corresponding DNA-binding proteins (Fur, CRP and RpoH) were identified, resulting in a regulatory network of iron response in S. oneidensis. Together, this work provides an overview of iron response and reveals novel features in S. oneidensis, including Shewanella-specific iron acquisition systems, and suggests the intimate relationship between anaerobic energy metabolism and iron response.
Yang, Yunfeng [ORNL; Harris, Daniel P [ORNL; Luo, Feng [Clemson University; Joachimiak, Marcin [Clemson University; Wu, Liyou [University of Oklahoma; Dehal, Paramvir [Lawrence Berkeley National Laboratory (LBNL); Jacobsen, Janet [Lawrence Berkeley National Laboratory (LBNL); Yang, Zamin Koo [ORNL; Gao, Haichun [University of Oklahoma; Arkin, Adam [Lawrence Berkeley National Laboratory (LBNL); Palumbo, Anthony Vito [ORNL; Zhou, Jizhong [University of Oklahoma
A functional gene array for detection of bacterial virulence elements
We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.
Jaing, C
The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A{sup vy}) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure (radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in animals and humans needs to be defined.
Randy Jirtle
Studies were designed to identify genes induced in fibroblasts after exposure to low-dose neutron radiation but not after {gamma} rays. Our past work had shown similar modulation of transcripts for {alpha}-tubulin, {beta}- and {gamma}-actins, ornithine decarboxylase and interleukin 1 after exposure to either neutrons or {gamma} rays. However, differences in the expression of {beta}-protein kinase C and c-fos genes were observed, with both being induced after exposure to {gamma} rays but not neutrons. Recently, we have identified two genes that are induced after exposure to neutrons but not {gamma} rays: Rp-8 (a gene associated with apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency virus (HIV). Induction of Rp-8 mRNA was demonstrated in Syrian hamster embryo (SHE) fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.005 Gy/min) and high dose rate (0.12 Gy/min). No induction of other genes associated with apoptosis such as Rp-2, bcl-2 and Tcl-30 was observed. The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measurements of CAT activity and CAT transcripts after irradiation demonstrated an unresponsiveness to {gamma} rays over a broad range of doses (0.1-3 Gy). Twofold induction of the HIV-LTR was detected after exposure to neutrons (0.48 Gy) administered at low (0.05 Gy/min) but not high (0.12 Gy/min) dose rates. Ultraviolet-mediated HIV-LTR induction, however, was inhibited by exposure to low-dose-rate neutron irradiation. These results are interesting in light of reports that Rp-8 is induced during apoptosis and that HIV causes apoptosis. 17 refs., 3 figs., 1 tab.
Woloschak, G.E.; Chang-Liu, C.M. [Argonne National Lab., IL (United States); Panozzo, J.; Libertin, C.R. [Loyola Univ. of Chicago, Maywood, IL (United States)
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks
Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.
Makarova, Kira S.; Omelchenko, Marina V.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Vasilenko, Alexander; Zhai, Min; Lapidus, Alla; Copeland, Alex; Kim, Edwin; Land, Miriam; Mavrommatis, Konstantinos; Pitluck, Samuel; Richardson, Paul M.; Detter, Chris; Brettin, Thomas; Saunders, Elizabeth; Lai, Barry; Ravel, Bruce; Kemner, Kenneth M.; Wolf, Yuri I.; Sorokin, Alexander; Gerasimova, Anna V.; Gelfand, Mikhail S.; Fredrickson, James K.; Koonin, Eugene V.; Daly, Michael J.
Divinyl ether synthase gene and protein, and uses thereof
The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.
Howe, Gregg A. (East Lansing, MI); Itoh, Aya (Tsuruoka, JP)
Identification of a novel gene family that includes the interferon-inducible human genes 6�16and ISG12
Response Elements (ISREs) and the 9 nt GAS elements for type I and type II IFNs, respectively. Most ISGs code for proteins whose biochemical and cellular roles are either well understood (e.g the genes for RNA-dependent protein kinase PKR [6,7], 2... that the ISG12 motif occurs in simple eukary- otes suggests that not all ISG12 genes in higher organisms have necessarily been incorporated into the IFN response. We therefore looked at the number and fidelity of Inter- feron Stimulated Response Elements (ISREs...
Parker, Nadeene; Porter, Andrew C G
ORIGINAL ARTICLE Regulation of nif gene expression and the
ORIGINAL ARTICLE Regulation of nif gene expression and the energetics of N2 fixation over the diel importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus ecotypes, NifH subunit and nitrogenase activity over the diel cycle in the microbial mat of an alkaline hot
Performance Analysis on Blue Gene Q with HPCToolkit
for performance analysis of OpenMP · Next steps · Using HPCToolkit on Blue Gene/Q at ALCF 3 #12;4 Rice University -- within and across nodes 18 #12;HPCToolkit at ALCF · ALCF systems -- /soft/perftools/hpctoolkit/pkgs/hpctoolkit · Man pages -- /soft/perftools/hpctoolkit/pkgs/hpctoolkit/share/man · ALCF guide to HPCToolkit -- http://www.alcf
Data mining and genetic algorithm based gene/SNP selection
Objective: Genomic studies provide large volumes of data with the number of single nucleotide polymorphisms (SNPs) ranging into thousands. The analysis of SNPs permits determining relationships between genotypic and phenotypic information as well as ... Keywords: Data mining, Drug effectiveness, Feature selection, Genes, Genetic algorithm, Intersection approach, Single nucleotide polymorphisms (SNPs)
Shital C. Shah; Andrew Kusiak
Information Retrieval meets Gene Analysis Hagit Shatkay \\Lambda
Information Retrieval meets Gene Analysis Hagit Shatkay \\Lambda Celera Genomics 45 West Gude Drive, based on probabilistic information retrieval, which uses the lit erature to establish functionalrelated publications. This wealth of information presents a major dataanalysis challenge. An ultimate goal is to under
Low Dose Radiation Research Program: Gene Expression Profile...
human cDNA clones, we focused on differential gene expression for a low-dose x-ray irradiation at 2cGy and its comparison with high-dose at 4Gy. Four time points were studied at...
Overview of the Blue Gene/L system architecture
The Blue Gene�/L computer is a massively parallel supercomputer based on IBM system-on-a-chip technology. It is designed to scale to 65,536 dual-processor nodes, with a peak performance of 360 teraflops. This paper describes the project objectives ...
A. Gara; M. A. Blumrich; D. Chen; G. L.-T. Chiu; P. Coteus; M. E. Giampapa; R. A. Haring; P. Heidelberger; D. Hoenicke; G. V. Kopcsay; T. A. Liebsch; M. Ohmacht; B. D. Steinmacher-Burow; T. Takken; P. Vranas
Review: Clustering of high throughput gene expression data
High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is ... Keywords: Bioinformatics, Clustering, Gene expression data, High throughput data, Microarrays
Harun Pirim; Burak Ek?Io?Lu; Andy D. Perkins; �Etin Y�Ceer
Human Diversity: Our Genes Tell Where we Live
Human Diversity: Our Genes Tell Where we Live Dispatch Laurent Excoffier A detailed genetic. The novelty of the recent work of Rosenberg et al. [7] is precisely that they have checked the validity of the analysis of a cell-line panel of 52 worldwide popu- lations [9] managed by the French Center for the Study
Rosenberg, Noah
Characterization of candidate genes in English cocker spaniel hereditary nephritis
Six different isoforms of Type IV collagen (colIV?1-6) have been identified. The individual isoforms of colIV are termed alpha chains and are translated from six different COLIV genes (COLIVA1-A6). Collagen Type IV gene products compose the structural framework of basement membranes. The glomerular basement membrane (GBM) is a specialized basement membrane involved in the ultrafiltration processes of the kidney. The colIV?1-?5 chains are expressed in the human GBM while the colIV ?1-?6 chains are expressed in the canine GBM. Many inherited diseases of the kidney have been reported and mutations in genes regulating kidney function have been identified. Alport syndrome (AS) is the most common form of human hereditary nephritis (HN). AS is defined as an inherited progressive kidney disorder associated with sensoneural deafness and is characterized by extensive thickening and multilamminar splitting of the GBM when examined by electron microscopy. AS has both X-linked (XLAS) and autosomal (ARAS) modes of inheritance. Mutations in the COLIVA5 gene are responsible for XLAS. A form of HN with characteristic splitting of the GBM with X-linked inheritance has been described in Samoyed dogs. A specific mutation in the COLIVA5 gene has been identified in Samoyed dogs affected with HN. Mutations in the COLIVA3 and COLIVA4 genes are responsible for ARAS. A form of HN has been identified in English cocker spaniel dogs (ECS) that has been described as autosomal in inheritance and includes GBM abnormalities including extensive lammination characteristic of ARAS. Both ARAS and ECS-HN show loss of the colIVA3 and colIVA4 chains in the GBM when examined with monoclonal anitibodies. ECS-HN has been hypothesized to have the same molecular basis of disease as ARAS. As such, we have isolated and characterized canine COLIVA3 and COLIVA4 sequences from normal dogs and ECS dogs affected with HN and compared the coding regions of these candidate genes.
Camacho, Zenaido
Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats
Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In ...
Shi, Yanmei, Ph. D. Massachusetts Institute of Technology
Cloning and sequencing of the alcohol dehydrogenase II gene from Zymomonas mobilis
The alcohol dehydrogenase II gene from Zymomonas mobilis has been cloned and sequenced. This gene can be expressed at high levels in other organisms to produce acetaldehyde or to convert acetaldehyde to ethanol.
Ingram, Lonnie O. (Gainesville, FL); Conway, Tyrrell (Gainesville, FL)
Cancer classification through gene expression data analysis has recently emerged as an active area of research. This paper applies Genetic Algorithms (GA) for selecting a group of relevant genes from cancer microarray data. Then, the popular classifiers, ...
Jinn-Yi Yeh
Multimodality imaging of reporter gene expression using a novel fusion vector in living cells and animals
Novel double and triple fusion reporter gene constructs harboring distinct imagable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.
Gambhir, Sanjiv (Portola Valley, CA); Pritha, Ray (Mountain View, CA)
Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus
Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.
Yang, Xiaohan [ORNL; Jawdy, Sara [ORNL; Tschaplinski, Timothy J [ORNL; Tuskan, Gerald A [ORNL
Gene RAD58(XRS4): Mapping to the right arm of chromosome XIII
This report presents the results of mapping of Saccharomyces cerevisiae gene RAD58(XRS4) to the right arm of chromosome XIII at a distance of 48 cM proximal to the gene ADE4. 10 refs., 1 tab.
Kozhin, S.A.; Chepurnaya, O.V.; Korolev, V.G. [Konstantinov Institute of Nuclear Physics, Gatchina (Russian Federation)
Sumoylation strategies in regulated repression by nuclear receptors and in function of tumor metastasis suppressor genes
links gene expression by NF-kB and ?-amyloid precursorinteracts with and inhibits NF-kB in human colon and breastby KAI1. Since KAI1 is a NF-kB target gene, its message
Cai, Ling
SATB1 packages densely-looped, transciptionally-active chromatin for coordinated expression of cytokine genes
T. Loss of silent- chromatin looping and impaired imprintingT. SATB1 targets chromatin remodelling to regulate genesS.T. & Fisher, A.G. Chromatin structure and gene regulation
Cai, Shutao; Lee, Charles C.; Kohwi-Shigematsu, Terumi
Tissue-engineered liver microreactor as an in vitro surrogate assay for gene delivery
The lack of correlation between in vitro and in vivo gene delivery experiments presents a significant obstacle in the progress of gene therapy studies by preventing the extrapolation of successful cell culture results into ...
Kalezi, Artemis
A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory
Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast Mingzhou (Joe) Song1 significantly expressed genes in response to bioethanol conversion inhibitor 5-hydroxymethylfurfural in detoxification for bioethanol conversion by yeast. 1 Introduction Computational modeling of gene regulatory
Song, Joe
Identification of new genes and pathways that act to delay C. elegans aging
Aging of an organism is determined by both stochastic and genetic components. The importance of genes is illustrated by the discovery of single gene mutations that alter lifespans of species ranging from invertebrates C. ...
Berdichevsky, Alina
The chosen genes : Jews, genetics, and the future of ethnic medicine
All humans have certain genes that cause or predispose them to various diseases. In the ideal medical future, scientists will have hyperfast gene analyzers able to sequence anyone's DNA in a matter of minutes. In that ...
Anthes, Emily Kennedy
Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system
The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease ...
Zhang, Feng
Novel double and triple fusion reporter gene constructs harboring distinct imageable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.
Gambhir; Sanjiv (Portola Valley, CA), Pritha; Ray (Mountain View, CA)
DCGene: a novel predicting approach of the disease related genes on functional annotation
Disease Candidate Genes (DCGene) is an advanced system for predicting the disease related genes, It is a novel computational approach by using the GO annotation information. The performance of the DCGene is evaluated in a set containing 1057 test samples, ...
Yuan Fang; Hui Wang
The fission yeast stress MAPK cascade regulates the pmp3+ gene that encodes a highly conserved plasma membrane protein.
transcription factor in fission yeast. Genes Dev. Degols, G.stress-activated kinase in fission yeast. Genes Dev. 12,MAP kinase pathway in fission yeast. Genes Dev. 10, 2289-
Wang, Ling-yu; Shiozaki, Kazuhiro
The fission yeast stress MAPK cascade regulates the pmp3(+) gene that encodes a highly conserved plasma membrane protein
Spectral analysis of microarray gene expression time series data of Plasmodium falciparum
We propose a new strategy to analyse the periodicity of gene expression profiles using Singular Spectrum Analysis (SSA) and Autoregressive (AR) model based spectral estimation. By combining the advantages of SSA and AR modelling, more ... Keywords: SSA, autoregressive spectral estimation model, bioinformatics, drug discovery, gene expression profiles, gene target, microarray time series analysis, plasmodium falciparum, singular spectrum analysis
Liping Du; Shuanhu Wu; Alan Wee-Chung Liew; David K. Smith; Hong Yan
An effective density-based hierarchical clustering technique to identify coherent patterns from gene expression data
We present an effective tree-based clustering technique (Gene ClusTree) for finding clusters over gene expression data. GeneClusTree attempts to find all the clusters over subspaces using a tree-based density approach by scanning the whole database in ... Keywords: coherent patterns, maximal space cluster, p-value, reduced space cluster, z-score
Sauravjyoti Sarmah; Rosy Das Sarmah; Dhruba Kumar Bhattacharyya
Independent arrays or independent time courses for gene expression time series data analysis
In this paper we apply three different independent component analysis (ICA) methods, including spatial ICA (sICA), temporal ICA (tICA), and spatiotemporal ICA (stICA), to gene expression time series data and compare their performance in clustering genes ... Keywords: DNA microarray, Gene expression data, Independent component analysis, Principal component analysis
Sookjeong Kim; Jong Kyoung Kim; Seungjin Choi
Analysis of mammary specific gene locus regulation in differentiated cells derived by somatic cell fusion
The transcriptional regulation of a gene is best analysed in the context of its normal chromatin surroundings. However, most somatic cells, in contrast to embryonic stem cells, are refractory to accurate modification by homologous recombination. We show here that it is possible to introduce precise genomic modifications in ES cells and to analyse the phenotypic consequences in differentiated cells by using a combination of gene targeting, site-specific recombination and somatic cell fusion. To provide a proof of principle, we have analysed the regulation of the casein gene locus in mammary gland cells derived from modified murine ES cells by somatic cell fusion. A {beta}-galactosidase reporter gene was inserted in place of the {beta}-casein gene and the modified ES cells, which do not express the reporter gene, were fused with the mouse mammary gland cell line HC11. The resulting cell clones expressed the {beta}-galactosidase gene to a similar extent and with similar hormone responsiveness as the endogenous gene. However, a reporter gene under the control of a minimal {beta}-casein promoter (encompassing the two consensus STAT5 binding sites which mediate the hormone response of the casein genes) was unable to replicate expression levels or hormone responsiveness of the endogenous gene when inserted into the same site of the casein locus. As expected, these results implicate sequences other than the STAT5 sites in the regulation of the {beta}-casein gene.
Robinson, Claire [Molecular Recognition Group, Hannah Research Institute, Ayr KA6 5HL (United Kingdom); Kolb, Andreas F. [Molecular Recognition Group, Hannah Research Institute, Ayr KA6 5HL (United Kingdom)], E-mail: firstname.lastname@example.com
Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase activities from Cyclotella cryptica
The present invention relates to a cloned gene which encodes an enzyme, the purified enzyme, and the applications and products resulting from the use of the gene and enzyme. The gene, isolated from Cyclotella cryptica, encodes a multifunctional enzyme that has both UDP-glucose pyrophosphorylase and phosphoglucomutase activities. 8 figs.
Jarvis, E.E.; Roessler, P.G.
Finding genes in DNA using decision trees and dynamic programming
{ salz berg,xchendhndrsn}:~cs.jhu.edu,kewf~gdb.org This study demonstrates the use of decision tree classifiers as the basis for a general gene-finding system. The system uses a dynamic programming algorithm that. finds the optimal segmentation of a DNA sequence into coding and noncoding regions (exons and introits).]�he optimality property is dependent oll a separate scoring function that takes a subsequence and assigns to it a score reflecting the probability that the sequence is an exon. In this study, the scoring functions were sets of decision trees and rules that were combined to give the probability estimate. Experimental results on a newly collected database of human DNA sequences are encouraging, and some new observations about the structure of classifiers for tile gene-finding problem have emerged from this study. We also provide descriptions of a new probability chain model that produces very accurate filters to find donor and acceptor sites.
Steven Salzberg; Xin Chen; John Henderson; Kenneth Fasman
Manipulating Genes with Hidden TALENs | Advanced Photon Source
A New Discovery Answers an Old Question A New Discovery Answers an Old Question Peering into the Interfaces of Nanoscale Polymeric Materials Ironing Out the Details of the Earth's Core Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Manipulating Genes with Hidden TALENs FEBRUARY 10, 2012 Bookmark and Share X-ray studies carried out at APS and computer modeling of the data reveal how TALEN intimately winds itself into the major groove of target DNA to form a protein-DNA complex just 60 Å x 60 Å x 90 Å. From Amanda Nga-Sze Mak et al., Science 335(6069), 716 (10 February, 2012). A better understanding of gene function in model plant and animal systems could be used to develop useful traits in livestock and crop plants, and
Cloning of the canine glucose-6-phosphatase gene
Two Maltese puppies with massive hepatomegaly and failure to thrive were found to have a markedly reduced Glucose-6-phosphatase (G-6-Pase) activity in the liver and kidney. Deficiency of G-6-Pase activity causes type 1a glycogen storage disease in humans. To further study the mutation responsible for the disease in dog, we cloned G-6-Pase canine cDNA from normal mixed breed dog liver RNA using reverse transcriptase and PCR amplification using primers derived from the published murine G-6-Pase gene sequence. Sequencing revealed an open reading frame of 1071 nucleotides that encodes a predicted 357 amino acid polypeptide in the canine G-6-Pase gene, same as mouse and human. We found more than 90% sequence homology between dog and human G-6-Pase sequence. Hydropathy analysis of the deduced canine G-6-Pase polypeptide shows six transmembrane-spanning segments similar to those seen in human and mouse. Endoplasmic reticulum (ER) localization is similarly predicted by the presence of the ER protein retention signal KK positioned 3 and 4 amino acids from the carboxy terminal. Potential asparagine-linked glycosylation sites are identified at positions 96, 203, and 276. Northern blot analysis revealed increased G-6-Pase mRNA in the deficient dog liver compared to control. This could possibly reflect upregulation of transcription due to the persistent hypoglycemic state. Further studies are directed at the identification of the mutation involved in this deficient dog strain. Characterization of the G-6-Pase gene and protein in the deficient dog model can pave the way for new understanding in the pathophysiology of this disease and for the trials of novel therapeutic approaches including gene therapy.
Kishnani, P.; Bao, Y. [Duke University Medical Center, Durham, NC (United States); Brix, A.E. [and others
Gene flow and the genealogical history of Heliconius heurippa
that H. heurippa is a distinct species and not simply a geographic race of H. cydno; H. heurippa is considerably more differentiated than any other geo- graphic populations of H. melpomene or H. cydno sampled in Panama, Colombia and Venezuela [26... ). It seems likely that there is a hybrid zone between these species somewhere in the Andes between Villavicencio (Colombia) and San Cristobal (Venezuela; Linares Pers. Obs.), which would explain the observed levels of gene flow. Allele networks for nuclear...
Salazar, Camilo; Jiggins, Chris D; Taylor, Jesse E; Kronforst, Marcus R; Linares, Mauricio
Probing cell-free gene expression noise in femtoliter volumes
Cell-free systems offer a simplified and flexible context that enables important biological reactions while removing complicating factors such as fitness, division, and mutation that are associated with living cells. However, cell-free expression in unconfined spaces is missing important elements of expression in living cells. In particular, the small volume of living cells can give rise to significant stochastic effects, which are negligible in bulk cell-free reactions. Here, we confine cell-free gene expression reactions to cell relevant 20 fL volumes (between the volumes of E. coli and S. cerevisiae), in polydimethylsiloxane (PDMS) containers. We demonstrate that expression efficiency varies widely at this volume, and we analyze gene expression noise. Noise analysis reveals signatures of translational bursting while noise dynamics suggest that overall cell-free expression is limited by a diminishing translation rate. In addition to offering a unique approach to understanding noise in gene circuits, our work contributes to a deeper understanding of the biophysical properties of cell-free expression systems, thus aiding efforts to harness cell-free systems for synthetic biology applications.
Karig, David K [ORNL; Jung, Seung-Yong [ORNL; Srijanto, Bernadeta R [ORNL; Collier, Pat [ORNL; Simpson, Michael L [ORNL
Compositions and methods for detecting gene rearrangements and translocations
Disclosed is a series of nucleic acid probes for use in diagnosing and monitoring certain types of leukemia using, e.g., Southern and Northern blot analyses and fluorescence in situ hybridization (FISH). These probes detect rearrangements, such as translocations involving chromosome band 11q23 with other chromosomes bands, including 4q21, 6q27, 9p22, 19p13.3, in both dividing leukemic cells and interphase nuclei. The breakpoints in all such translocations are clustered within an 8.3 kb BamHI genomic region of the MLL gene. A novel 0.7 kb BamH1 cDNA fragment derived from this gene detects rearrangements on Southern blot analysis with a single BamHI restriction digest in all patients with the common 11q23 translocations and in patients with other 11q23 anomalies. Northern blot analyses are presented demonstrating that the MLL gene has multiple transcripts and that transcript size differentiates leukemic cells from normal cells. Also disclosed are MLL fusion proteins, MLL protein domains and anti-MLL antibodies.
Rowley, Janet D. (Chicago, IL); Diaz, Manuel O. (Chicago, IL)
Ayuda:Imágenes | Open Energy Information
Imágenes Imágenes Jump to: navigation, search Esta página trata en detalle la sintaxis de la imagen al momento de editar una página wiki. Usted o algún otro usuario deberá comúnmente cargar una imagen antes de que esta sea visible en la página. Contents 1 Sintaxis 2 Formato 3 Alineación 3.1 Alineación vertical 4 Tamaño y cuadro 5 Detener del movimiento de texto 6 Galería de Imágenes 6.1 Parámetros 7 Enlaces 7.1 Enlace a la página de descripción 7.2 Enlazar directamente al archivo 8 Requisitos 9 Archivos en otras páginas web Sintaxis La sintaxis necesaria para mostrar una imagen: [[Image:{nombre_archivo}|{opciones}]] Donde las opciones que se señalan a continuación, separadas por barras verticales, pueden oscilar entre cero o más: border, frame, thumb, o frameless: Determina el proceso de formato
A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database
We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.
Dehal, Paramvir S.; Boore, Jeffrey L.
MicroSyn: A user friendly tool for detection of microsynteny in a gene family
O O F T W A R E Open Access MicroSyn: A user friendly tool for detection of microsynteny in a gene family Bin Cai 1,2 , Xiaohan Yang 3,4 , Gerald A Tuskan 3,4 and Zong-Ming Cheng 1,2,4* Abstract Background: The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes. Results: We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene
Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown function, or wrongly or vaguely annotated. Many of these 'unknown' proteins are common to prokaryotes and plants. We accordingly set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction is integrative, coupling the extensive post-genomic resources available for plants with comparative genomics based on hundreds of microbial genomes, and functional genomic datasets from model microorganisms. The early phase is computer-assisted; later phases incorporate intellectual input from expert plant and microbial biochemists. The approach thus bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is much more powerful than purely computational approaches to identifying gene-function associations. Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) are conserved between plants and prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology .. independent characteristics associated in the SEED database with the prokaryotic members of each family, specifically gene clustering and phyletic spread, as well as availability of functional genomics data, and publications that could link candidate families to general metabolic areas, or to specific functions. In-depth comparative genomic analysis was then performed for about 500 top candidate families, which connected ~55 of them to general areas of metabolism and led to specific functional predictions for a subset of ~25 more. Twenty predicted functions were experimentally tested in at least one prokaryotic organism via reverse genetics, metabolic profiling, functional complementation, and recombinant protein biochemistry. Our approach predicted and validated functions for 10 formerly uncharacterized protein families common to plants and prokaryotes; none of these functions had previously been correctly predicted by computational methods. The functions of five more are currently being validated. Experimental testing of diverse representatives of these families combined with in silica analysis allowed accurate projection of the annotations to hundreds more sequenced genomes.
09/13/2007 08:42 PMTweaking Genes Could Extend ALS Survival Page 1 of 1http://health.usnews.com/usnews/health/healthday/070913/tweaking-genes-could-extend-als-survival.htm
09/13/2007 08:42 PMTweaking Genes Could Extend ALS Survival Page 1 of 1http://health.usnews.com/usnews/health/healthday/070913/tweaking-genes-could-extend-als-survival.htm Tweaking Genes Could Extend ALS Survival Mouse study.S. scientists say they've spotted genes that influence survival in mice with amyotrophic lateral sclerosis (ALS
Engelhardt, John F.
Gene Expression and Association Analyses of Stress Responses in Loblolly Pine (Pinus taeda L.)
The molecular mechanisms underlying disease-resistance and drought-resistance in forest trees are not well understood. Linking variation in gene expression with genetic polymorphisms and with variations in disease- and drought-resistance phenotypes can provide information about these complex traits. We used real-time quantitative polymerase chain reaction (PCR) to detect variations in the expression of 88 disease- and drought-responsive genes within an association population of 354 loblolly pine trees (Pinus taeda L.). Using association genetics approaches, we then linked 3,938 single nucleotide polymorphisms (SNPs) in candidate genes with gene expression phenotypes to identify novel disease- and drought-responsive genes. To further examine differences in gene expression induced by drought, Fusarium circinatum (responsible for pitch canker disease), and drought F. circinatum, the expression of 114 genes identified through comparative and association genetics approaches was analyzed on a subset of 24 loblolly pine trees possessing a range of pitch canker- and drought-resistance phenotypes. Significant differences in the uninduced expression of all 88 genes measured on the association population were observed among loblolly pine trees. Principal component analysis showed that some variation within the association population could be accounted for by population substructure of geographic origin. Hierarchical clustering of genes based on uninduced expression did not consistently group together functionally similar genes probably because expression was collected on unstressed stem tissue. This was supported in the smaller expression study as correlations between expression values of genes in the same functional networks were usually stronger when induced by a treatment compared with correlations between the uninduced expression of genes in the control group. Gene expression frequently changed by up to 4-fold in response to one or more treatments, but PtMYB12 was the only gene that exhibited a statistically significant change in response to treatments. ANOVA analyses of gene expression controlling for pitch canker resistance and for water use efficiency phenotypes identified differentially expressed genes suggesting that they may be contributing to these phenotypes. Finally, association genetics approaches detected 101 significant associations between SNPs in 94 candidate genes potentially involved in stress responses and 27 gene expression phenotypes.
Seeve, Candace Marie
Structural comparison and chromosomal localization of the human and mouse IL-13 genes
The genomic structure of the recently described cytokine IL-13 has been determined for both human and mouse genes. The nucleotide sequence of a 4.6-kb DNA segment of the human gene is described. The human IL-13 gene (IL 13) occurs as a single copy in the haploid genome and maps to human chromosome 5. A 4.3-kb DNA fragment of the mouse IL-13 gene (Il 13) has been sequenced and found to occur as a single copy, mapping to mouse chromosome 11. Intrachromosomal mapping studies revealed that both genes contain four exons and three introns and show a high degree of sequence identify throughout their length. Potential recognition sequences for transcription factors that are present in the 5'-flanking region and are conserved between both genes include IFN-responsive elements, binding sites for AP-1, AP-2, and AP-3, an NF-lL 6 site, and a TATA-like sequence. Both genes map to chromosomal locations adjacent to genes encoding other cytokines, including IL-3, GM-CSF, IL-5, and IL-4 suggesting that IL-13 is another member of this cytokine gene family that may have arisen by gene duplication. 26 refs., 5 figs., 3 tabs.
McKenzie, A.N.J.; Sato, A.; Doyle, E.L.; Zurawski, G. (DNAX Research Institute of Cellular and Molecular Biology, Palo Alto, CA (United States)); Li, X.; Milatovich, A.; Francke, U. (Stanford Univ. Medical School, CA (United States)); Largaespada, D.A.; Copeland, N.G.; Jenkins, N.A. (National Cancer Institute, Frederick, MD (United States))
(Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata)
In prior support periods we identified, cloned and sequenced three genes involved in the regulation of nif gene expression in Rhodobacter capsulatus. These were called nifRI, nifR2 and nifR4; they turn out to be homologue of the ntrC, ntrB and ntrA genes of enterobacteria. We subsequently found that mutations in an additional gene, nifR5. render R. capsulatus nif genes constitutive with respect to ammonia. The nifR5 gene was shown to be similar to glnB of enteric bacteria, encoding the regulatory protein PII, and furthering the intersection of the glutamine synthetase adenylylation cascade with the control of nif gene transcription. In pursuit of the mechanism of 0{sub 2} control of nif gene expression, we constructed and analyzed the topology of a small plasmid in R. capsulatus as a function of 0{sub 2} concentration. We also cloned and obtained partial sequence data for two genes encoding the B subunit of DNA gyrase. The nucleotide sequence of the rpoB gene encoding RNA polymerase was nearly completed. A method for isolation of genes expressed differentially, developed for cyanobacteria, was applied successfully to R. capsulatus. Several genes that depend on nifR4 for their transcription were isolated. A transcription start site for a nifA gene was identified and the promoter sequence was analyzed. A physical map of the R calsulatus SB1003 chromosome was prepared, based on pulsed-field electrophoresis of XbaI and AseI fragments and hybridization with a gridded cosmid library, using a device that permits 864 cosmids to be hybridized at one time with a labeled chromosomal fragment.
Not Available
Imaging gene expression in real-time using aptamers
Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (F�rster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging microscopy). Real-time transcription was measured by FLIM-FRET, which was detected by the decrease in donor lifetime resulting from ligand binding to IMAGEtags that were newly synthesized from the activated GAL1 promoter. The FRET signal was specific for transcribed IMAGEtags.
Shin, Il Chung
Genome-wide discovery of missing genes in biological pathways of prokaryotes
Genome-wide Genome-wide discovery of missing genes in biological pathways of prokaryotes Yong Chen 1,3,4,5 , Fenglou Mao 1,2 , Guojun Li 1,3 , Ying Xu 1,2,6* From The Ninth Asia Pacific Bioinformatics Conference (APBC 2011) Incheon, Korea. 11-14 January 2011 Abstract Background: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem. Methods: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping,
A hierarchy of ECM-mediated signalling tissue-specific gene expression regulates tissue-specific gene expression
A dynamic and reciprocal flow of information between cells and the extracellular matrix contributes significantly to the regulation of form and function in developing systems. Signals generated by the extracellular matrix do not act in isolation. Instead, they are processed within the context of global signalling hierarchies whose constituent inputs and outputs are constantly modulated by all the factors present in the cell's surrounding microenvironment. This is particularly evident in the mammary gland, where the construction and subsequent destruction of such a hierarchy regulates changes in tissue-specific gene expression, morphogenesis and apoptosis during each developmental cycle of pregnancy, lactation and involution.
Roskelley, Calvin D; Srebrow, Anabella; Bissell, Mina J
Sequence of the dog immunoglobulin alpha and epsilon constant region genes
The immunoglobulin alpha (IGHAC) and epsilon (IGHEC) germline constant region genes were isolated from a dog liver genomic DNA library. Sequence analysis indicates that the dog IGHEC gene is encoded by four exons spread out over 1.7 kilobases (kb). The IGHAC sequence encompasses 1.5 kb and includes all three constant region coding exons. The complete exon/intron sequence of these genes is described. 28 refs., 2 figs., 2 tabs.
Patel, M.; Selinger, D.; Mark, G.E.; Hollis, G.F.; Hickey, G.J. [Merck Research Labs., Rathway, NJ (United States)
Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)
Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when applied to the manually curated training set. Applying this method to the data representing around a quarter of the fraction space for water soluble proteins in D. vulgaris, we obtained 854 reliable pair wise interactions. Further, we have developed algorithms to analyze and assign significance to protein interaction data from bait pull-down experiments and integrate these data with other systems biology data through associative biclustering in a parallel computing environment. We will 'fill-in' missing information in these interaction data using a 'Transitive Closure' algorithm and subsequently use 'Between Commonality Decomposition' algorithm to discover complexes within these large graphs of protein interactions. To characterize the metabolic activities of proteins and their complexes we are developing algorithms to deconvolute pure mass spectra, estimate chemical formula for m/z values, and fit isotopic fine structure to metabolomics data. We have discovered that in comparison to isotopic pattern fitting methods restricting the chemical formula by these two dimensions actually facilitates unique solutions for chemical formula generators. To understand how microbial functions are regulated we have developed complementary algorithms for reconstructing gene regulatory networks (GRNs). Whereas the network inference algorithms cMonkey and Inferelator developed enable de novo reconstruction of predictive models for GRNs from diverse systems biology data, the RegPrecise and RegPredict framework developed uses evolutionary comparisons of genomes from closely related organisms to reconstruct conserved regulons. We have integrated the two complementary algorithms to rapidly generate comprehensive models for gene regulation of understudied organisms. Our preliminary analyses of these reconstructed GRNs have revealed novel regulatory mechanisms and cis-regulatory motifs, as well asothers that are conserved across species. Finally, we are supporting scientific efforts in ENIGMA with data management solutions and by integrating all of the algorithms, software and data into
Nitin S. Baliga
Gene Brooks and His Contributions to the American Choral Directors Association.
?? In his thirty years as Executive Director of ACDA, Dr. Gene Brooks has demonstrated his passion for choral music through his work in the� (more)
Zamer, Craig
Over-expressing a barley ZIP gene doubles grain zinc content in barley (Hordeum vulgare)
the ZRT, IRT-related protein (ZIP) family have recently beenover-expressing a barley ZIP gene, HvZIP7 to evaluate its
Tiong, Jingwen; Genc, Yusuf; McDonald, Glenn K; Langridge, Peter; Huang, Chun Y Dr
An efficient method for exploring the space of gene tree ... - CECM
Apr 20, 2011 ... To compute the posterior probability distribution of a subset of .... synthetic gene trees generation process we followed is based on several�...
Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology
B, �man P, Jansson C. Starch branching enzymes in sorghum (Sorghum bicolor) and barley (Hordeum vulgare): Comparativethe sbeIIb genes in sorghum (Sorghum bicolor) and barley (
Sun, Chuanxin
Circadian oscillation of starch branching enzyme gene expression in the sorghum endosperm
B, Aman P, Jansson C. Starch branching enzymes in sorghum (Sorghum bicolor) and barley (Hordeum vulgare): Comparativethe sbellb genes in sorghum (Sorghum bicolor) and barley (
Mutisya, J.
Gene copy number studies in archived and fresh mouse tissue samples
sections from archived samples were used for DNA isolation and quantitative real time PCR amplification that revealed variations in mitochondrial gene copy numbers in different...
Major genes and QTL influencing wool production and quality: a review
Abstract � The opportunity exists to utilise our knowledge of major genes that influence the economically important traits in wool sheep. Genes with Mendelian inheritance have been identified for many important traits in wool sheep. Of particular importance are genes influencing pigmentation, wool quality and the keratin proteins, the latter of which are important for the morphology of the wool fibre. Gene mapping studies have identified some chromosomal regions associated with variation in wool quality and production traits. The challenge now is to build on this knowledge base in a cost-effective way to deliver molecular tools that facilitate enhanced genetic improvement programs for wool sheep.
Ian William Purvis; Ian Robert Franklin
The role of sequence, gene orientation, and intergenic distance in chromatin structure and function
Bernstein BE (2008) Chromatin state maps: new technologies,histone modifications and chromatin remodeling. Proc Natladdress biases associated with chromatin structure or gene
Langley, Sasha A.
for gene function in plant biology Chuanxin Sun 1 , HaileDepartment of Plant Biology & Forest Genetics, UppsalaJansson, Department of Plant Biology & Forest Genetics, The
Gene Repression and Cell Cycle Regulation by PU.1 in Acute Myeloid Leukemia.
??Acute myeloid leukemia (AML) is associated with mutations or chromosomal translocations in genes encoding transcription factors. PU.1 is a transcription factor that is required for� (more)
Ziliotto, Rachel GH
Id-1 and Id-2 genes and products as markers of epithelial cancer
A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.
Desprez, Pierre-Yves (El Cerrito, CA); Campisi, Judith (Berkeley, CA)
Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics
Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.
Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Bisaria, Anjali [ORNL; Tuskan, Gerald A [ORNL; Kalluri, Udaya C [ORNL
Performance Evaluation of Gene Expression Programming for Hydraulic Data Mining
Abstract: Predication is one of the fundamental tasks of data mining. In recent years, Artificial Intelligence techniques are widely being used in data mining applications where conventional statistical methods were used such as Regression and classification. The aim of this work is to show the applicability of Gene Expression Programming (GEP), a recently developed AI technique, for hydraulic data prediction and to evaluate its performance by comparing it with Multiple Linear Regression (MLR). Both GEP and MLR were used to model the hydraulic jump over a roughened bed using very large series of experimental data that contain all the important flow and roughness parameters such as the initial Froude number, the height of roughness ratio, the length of roughness ratio, the initial length ratio (from the gate) and the roughness density. The results show that GEP is a promising AI approach for hydraulic data prediction.
Khalid Eldr; Abdel-azim Negm
Recombinant cells that highly express chromosomally-integrated heterologous genes
Recombinant host cells are obtained that comprise (A) a heterologous, polypeptide-encoding polynucleotide segment, stably integrated into a chromosome, which is under transcriptional control of an endogenous promoter and (B) a mutation that effects increased expression of the heterologous segment, resulting in enhanced production by the host cells of each polypeptide encoded by that segment, relative to production of each polypeptide by the host cells in the absence of the mutation. The increased expression thus achieved is retained in the absence of conditions that select for cells displaying such increased expression. When the integrated segment comprises, for example, ethanol-production genes from an efficient ethanol producer like Zymomonas mobilis, recombinant Escherichia coli and other enteric bacterial cells within the present invention are capable of converting a wide range of biomass-derived sugars efficiently to ethanol. 13 figs.
Ingram, L.O.; Ohta, Kazuyoshi; Wood, B.E.
Recombinant host cells are obtained that comprise (A) a heterologous, polypeptide-encoding polynucleotide segment, stably integrated into a chromosome, which is under transcriptional control of an endogenous promoter and (B) a mutation that effects increased expression of the heterologous segment, resulting in enhanced production by the host cells of each polypeptide encoded by that segment, relative to production of each polypeptide by the host cells in the absence of the mutation. The increased expression thus achieved is retained in the absence of conditions that select for cells displaying such increased expression. When the integrated segment comprises, for example, ethanol-production genes from an efficient ethanol producer like Zymomonas mobilis, recombinant Escherichia coli and other enteric bacterial cells within the present invention are capable of converting a wide range of biomass-derived sugars efficiently to ethanol.
Ingram, Lonnie O. (Gainesville, FL); Ohta, Kazuyoshi (Gainesville, FL); Wood, Brent E. (Gainesville, FL)
Identification of human gene core promoters in silico
Identification of the 5�-end of human genes requires identification of functional promoter elements. In silico identification of those elements is difficult because of the hierarchical and modular nature of promoter architecture. To address this problem, I propose a new stepwise strategy based on initial localization of a functional promoter into a 1-2 kb (extended-promoter) region from within a large genomic DNA sequence of 100 kb or larger, and further localization of a Transcriptional Start Site (TSS) into a 50-100 bp (core-promoter) region. Using positional dependent 5-tuple measures, a Quadratic Discriminant Analysis (QDA) method has been implemented in a new program- CorePromoter. Our experiments indicate that when given a 1-2 kb extended promoter, CorePromoter will correctly localize the TSS to a 100 bp interval approximately 60 % of the time.
Michael Q. Zhang
A2 Processor User's Manual for Blue Gene/Q
A2 Processor A2 Processor User's Manual for Blue Gene/Q Note: This document and the information it contains are provided on an as-is basis. There is no plan for providing for future updates and corrections to this document. October 23, 2012 Version 1.3 Title Page ® Copyright and Disclaimer © Copyright International Business Machines Corporation 2010, 2012 Printed in the United States of America October 2012 IBM, the IBM logo, and ibm.com are trademarks or registered trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. Other product and service names might be trademarks of IBM or other compa- nies. A current list of IBM trademarks is available on the Web at "Copyright and trademark information" at www.ibm.com/legal/copytrade.shtml.
Cold, Salty and Promiscuous-Gene-shuffling Microbes Dominate
September 30, 2013 September 30, 2013 Cold, Salty and PromiscuousGene-shuffling Microbes Dominate Antarcticas Deep Lake Sequestered in Antarctica's Vestfold Hills, Deep Lake became isolated from the ocean 3,500 years ago by the Antarctic continent rising, resulting in a saltwater ecosystem that remains liquid in extreme cold, and providing researchers a unique niche for studying the evolution of the microbes that now thrive under such conditions. Deep Lake's microscopic inhabitants are dominated by haloarchaea, microbes that require high salt concentrations to grow and are naturally adapted to conditions - at minus 20°C - that would prove lethally cold to other organisms. In a detailed analysis published online the week of September 30, 2013 in the journal Proceedings
Microsoft PowerPoint - gene_kight_panelist_presentation
Fossil Energy R&D Fossil Energy R&D American Recovery & Reinvestment Act Projects 10 th Annual U.S. Department of Energy Small Business Conference Small Businesses Leading the Way to Recovery and Reinvestment Gene Kight Director, Finance and Procurement Office of Fossil Energy August 12, 2009 2 Small Businesses Leading the Way to Recovery and Reinvestment Expand and Extend Clean Coal Power Initiative (CCPI) Round 3 (Additional available CCPI funds total >$600 million) Industrial Carbon Capture and Storage Geologic Sequestration Site Characterization Geologic Sequestration Training & Research Carbon Capture and Storage (FutureGen Re-start) FE Program Direction $800 million $1.52 billion $50.0 million $20.0 million $1.0 billion
A novel approach to determine normal variation in gene expression data
Animal models for human diseases are of crucial importance for studying gene expression and regulation. In the last decade the development of mouse models for cancer, diabetes, neuro-degenerative and many other diseases has been on steady rise. Microarray ... Keywords: gene expression, hypertension, immune response, mouse models, normal variance, principal component analysis, replicates
Vinay Nadimpally; Mohammed J. Zaki
An integrated algorithm for gene selection and classification applied to microarray data of ovarian cancer
Objective: The type of data in microarray provides unprecedented amount of data. A typical microarray data of ovarian cancer consists of the expressions of tens of thousands of genes on a genomic scale, and there is no systematic procedure to analyze ... Keywords: Gene selection, Genetic algorithm, Microarray data, Ovarian cancer, Particle swarm optimization, Support vector machine
Zne-Jung Lee
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively in an algorithm that allows us to bypass the gene trees and compute species tree likelihoods directly from
Plasmids containing the gene for DNA polymerase I from Streptococcus pneumoniae
A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of /und Streptococcus/ /und pneumoniae/. Plasmid pSM22, the vector containing the pneumococcal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme. 1 fig., 1 tab.
Lacks, S.A.; Martinez, S.; Lopez, P.; Espinosa, M.
Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina
Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina States of America Abstract Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found anaconda population structure (IBD), and important for gene flow, although genetic distances were
Shaffer, H. Bradley
Independent component analysis: Mining microarray data for fundamental human gene expression modules
As public microarray repositories rapidly accumulate gene expression data, these resources contain increasingly valuable information about cellular processes in human biology. This presents a unique opportunity for intelligent data mining methods to ... Keywords: Data mining, Gene modules, Independent component analysis, Microarrays, Parthenolide
Jesse M. Engreitz; Bernie J. Daigle, Jr.; Jonathan J. Marshall; Russ B. Altman
A heuristic for gene selection and visual prediction of sample type
In this paper, we introduce a heuristic method for gene selection. We target this method, coupled with RadViz visualisation, to the visual prediction of tissue samples which may exist in normal and disease states. As a result of this coupling, the gene ...
Jianping Zhou; Georges Grinstein; Kenneth Marx
Selective gene silencing in activated leukocytes by targeting siRNAs to the integrin lymphocyte
to suppress gene expression and cell proliferation only in activated lymphocytes. The siRNA-fusion proteinSelective gene silencing in activated leukocytes by targeting siRNAs to the integrin lymphocyte are resistant to lipid-based transfection in vitro and are difficult to target in vivo. We show here
Lieberman, Judy
Ah receptor represses acute-phase response gene expression without binding to its cognate response
Repression of the nuclear factor-kB (NF-kB) pathway has been extensively researched because of its pivotal NF-kB regulated-gene expression, especially acute-phase genes, such as serum amyloid A (Saa). Using of transcription factors, such as nuclear factor-kB (NF-kB), signal transducer and activator of transcription-3
Perdew, Gary
Genomic analysis of 12-oxo-phytodienoic acid reductase genes of Zea mays
The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes of the octadecanoid pathway which converts linolenic acid to a phytohormone, jasmonic acid. Bioinformatics analysis of ESTs and genomic sequences from available private and public databases revealed that the maize genome encodes eight different OPR genes. This number of maize OPR genes has been independently confirmed by Southern blot analysis and by mapping of individual OPR genes to maize chromosomes using oat maize chromosome addition lines. Survey of massively parallel signature sequencing (MPSS) assays revealed that transcripts of each OPR gene accumulate differentially in diverse organs of maize plants. This data suggested that individual OPR genes may have a distinct function in development. Similarly, RNA blot analysis revealed that distinct OPR genes are differentially regulated in response to stress hormones, wounding or pathogen infection. ZmOPR1 and ZmOPR2 appear to have important functions in defense responses to pathogens because they are transiently induced by salicylic acid (SA), chitooligosaccharides and by infection with Cochliobolus carbonum, Bipolaris maydis and Fusarium verticillioides and not by wounding. In contrast to these two genes, ZmOPR6 and ZmOPR7/8 are highly induced by wounding and treatments with wound-associated signaling molecules jasmonic acid, ethylene and abscisic acid. ZmOPR6 and ZmOPR7/8 are not induced by SA treatments or pathogen infections suggesting their specific involvement in wound-induced defense responses. Possible functions of specific OPR genes are discussed.
Zhang, Jinglan
An ant colony optimization based algorithm for identifying gene regulatory elements
It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences. Most of the existing algorithms for identifying regulatory elements are inclined to converge into a local optimum, and have high time complexity. ... Keywords: Ant colony optimization, Gene regulatory elements, Motif identification
Wei Liu, Hanwu Chen, Ling Chen
A database-centric approach to system managemant in the blue gene/L supercomputer
In designing the management system for Blue Gene/L, we adopted a database-centric approach, All configuration and operational data for a particular Blue Gene/L system are stored in a relational database that is kept in the system's service node. The ...
Ralf Bellofatto; Paul G. Crumley; David Darrington; Brant knudson; Mark Megerian; Jos� E. Moreira; Alda S. Ohmacht; John Orbeck; Don Reed; Greg Stewart
Analyses of humanchimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging
Analyses of humanchimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging Joa Abstract Compared to chimpanzees (Pan troglodytes), the onset of aging appears to be delayed in the human acting on genes associated with aging in different model systems, which allowed us to explore
Church, George M.
The improvement of breast cancer prognosis accuracy from integrated gene expression and clinical data
Predicting the accurate prognosis of breast cancer from high throughput microarray data is often a challenging task. Although many statistical methods and machine learning techniques were applied to diagnose the prognosis outcome of breast cancer, they ... Keywords: Breast cancer prognosis, Cancer classification, Clinical data, Gene expression, Gene selection, Genetic algorithm, Support vector machine
Austin H. Chen; Chenyin Yang
Plasimids containing the gene for DNA polymerase I from Streptococcus pneumoniae
A method is disclosed for cloning the gene which encodes a DNA polymerase-exonuclease of Streptococcus pneumoniae. Plasmid pSM22, the vector containing the pneumocccal polA gene, facilitates the expression of 50-fold greater amounts of the PolI enzyme.
Lacks, Sanford A. (Brookhaven, NY); Martinez, Susana (Sound Beach, NY); Lopez, Paloma (Madrid, ES); Espinosa, Manuel (Madrid, ES)
Blue Gene/L compute chip: control, test, and bring-up infrastructure
The Blue Gene�/L compute (BLC) and Blue Gene/L link (BLL) chips have extensive facilities for control, bring-up, self-test, debug, and nonintrusive performance monitoring built on a serial interface compliant with IEEE Standard 1149.1. Both the ...
R. A. Haring; R. Bellofatto; A. A. Bright; P. G. Crumley; M. B. Dombrowa; S. M. Douskey; M. R. Ellavsky; B. Gopalsamy; D. Hoenicke; T. A. Liebsch; J. A. Marcella; M. Ohmacht
FUNCTIONAL ANNOTATION OF OIL PALM GENES USING AN AUTOMATED BIOINFORMATICS APPROACH 35 FUNCTIONAL ANNOTATION OF OIL PALM GENES USING AN AUTOMATED BIOINFORMATICS APPROACH LAURA B WILLIS*; PHILIP A LESSARDBank, and duplicate entries were eliminated by pairwise BLAST searches, resulting in a collection of unique oil palm
Sinskey, Anthony J.
Scaling physics and material science applications on a massively parallel Blue Gene/L system
Blue Gene/L represents a new way to build supercomputers, using a large number of low power processors, together with multiple integrated interconnection networks. Whether real applications can scale to tens of thousands of processors (on a machine like ... Keywords: Blue Gene/L, MPI, applications, scalability, supercomputers
George Almasi; Gyan Bhanot; Alan Gara; Manish Gupta; James Sexton; Bob Walkup; Vasily V. Bulatov; Andrew W. Cook; Bronis R. de Supinski; James N. Glosli; Jeffrey A. Greenough; Francois Gygi; Alison Kubota; Steve Louis; Thomas E. Spelce; Frederick H. Streitz; Peter L. Williams; Robert K. Yates; Charles Archer; Jose Moreira; Charles Rendleman
New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes
Algorithmic methods for gene prediction have been developed and successfully applied to many different prokaryotic genome sequences. As the set of genes in a particular genome is not homogeneous with respect to DNA sequence composition features, the GeneMark.hmm program utilizes two Markov models representing distinct classes of protein coding genes denoted "typical" and "atypical". Atypical genes are those whose DNA features deviate significantly from those classified as typical and they represent approximately 10% of any given genome. In addition to the inherent interest of more accurately predicting genes, the atypical status of these genes may also reflect their separate evolutionary ancestry from other genes in that genome. We hypothesize that atypical genes are largely comprised of those genes that have been relatively recently acquired through lateral gene transfer (LGT). If so, what fraction of atypical genes are such bona fide LGTs? We have made atypical gene predictions for all fully completed prokaryotic genomes; we have been able to compare these results to other "surrogate" methods of LGT prediction.
Borodovsky, M.
Regulation of adenovirus transcription by an Ela gene in microinjected Xenopus laevis oocytes
The regulation of adenovirus type 5 gene expression by the E1a gene product was examined in microinjected Xenopus laevis oocytes. Chimeric genes were constructed which included the promoter region of early adenovirus type 5 gene 3 and the structural sequence which codes for the bacterial enzyme chloramphenicol-3-O-acetyltransferase (CAT). A plasmid containing this chimeric gene as well as plasmids containing the E1a gene were coinjected into oocyte nuclei. The presence of the E1a gene was shown to increase CAT activity by up to 8.5-fold over basal levels. Synthesis of the functional product from the E1a gene requires the removal of intron sequences by RNA splicing. The E1a gene and a derivative that precisely lacks the intron were equally effective in increasing CAT activity, suggesting that splicing of the primary E1a transcript is efficiently accomplished in the oocyte nucleus. This was confirmed by directly examining the E1a mRNAs by the S1 mapping procedure. A protein extract from adenovirus type 5-infected HeLa cells enriched for the E1a protein may supplant the E1a plasmid in enhancing CAT activity. Synthesis of the CAT enzyme after gene injection is invariant in oocytes from the same frog, but oocytes from different frogs show a high degree of variability in their ability to synthesize the CAT enzyme. Microinjected X. laevis oocytes appear to be an extremely useful system to study the effects of protein elements on transcription.
Jones, N.C.; Richter, J.D.; Weeks, D.L.; Smith, L.D.
The comparative genomics of salinispora and the distribution and abundance of secondary metabolite genes in marine plankton
rplB smpB Comparative genomics Gene gain Gene loss Totalbiology and comparative genomics. BMC Bioinformatics 10(1):Intersection of Evolution and Genomics. Science 300(5626):
Penn, Kevin Matthew
Rb pathway and chromatin remodeling genes that antagonize let-60 Ras signaling during C. elegans vulval development
The synthetic multivulva (synMuv) class A and class B genes act redundantly to regulate Ras-mediated vulval cell fate specification in the nematode Caenorhabditis elegans. The class B synMuv gene lin-35 encodes a protein ...
Ceol, Craig J. (Craig Joseph), 1971-
Using the Cre-loxP system to randomize target gene expression states and generate diverse phenotypes
Modifying the expression of multiple genes enables both deeper understanding of their function and the engineering of complex multigenic cellular phenotypes. However, deletion or overexpression of multiple genes is typically ...
Niesner, Bradley (Bradley Joseph)
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
Background: Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding ...
Gordan, Raluca
Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network
Contemporary high-throughput technologies permit the rapid identification of transcription factor (TF) target genes on a genome-wide scale, yet the functional significance of TFs requires knowledge of target gene expression ...
Busser, Brian W.
Implementation of genomics and bioinformatics approaches for identification and characterization of tomato ripening-related genes
Initial activities were focused on isolation and characterization of fruit ripening-related genes from tomato. Screening of four tomato cDNA libraries at low stringency with 10 fruit development and ripening-related genes yielded ~3000 positives clones. Microarray expression analysis of half of these positives in mature green and breaker stage fruits resulted in eight ripening-induced genes. RNA gel-blot analysis and previously published data confirmed expression for seven of the eight. One novel gene, designated LeEREBP1, was chosen for further characterization. LeEREBP1 encodes an AP2/ERF-domain transcription factor and is ethylene inducible. The expression profiles of LeEREBP1 parallel previously characterized ripening-related genes from tomato. Transgenic plants with increased and decreased expression of LeEREBP1 were generated and are currently being characterized to define the function of LeEREBP1. A large public tomato EST dataset was mined to gain insight into the tomato transcriptome. By clustering genes according to the respective expression profiles of individual tissues, tissue and developmental expression patterns were generated and genes with similar functions grouped together. Tissues effectively clustered for relatedness according to their profiles confirming the integrity of the approach used to calculate gene expression. Statistical analysis of EST prevalence in fruit and pathogenesis-related libraries resulted in 333 genes being classified as fruit ripening-induced, 185 as fruit ripening-repressed, and 169 as pathogenesis-related. We performed a parallel analysis on public EST data for grape and compared the results for ripening-induced genes to tomato to identify similar and distinct ripening factors in addition to candidates for conserved regulators of fruit ripening. An online interactive database for tomato gene expression data - Tomato Expression Database (TED) was implemented. TED contains normalized expression data for approximately 12,000 ESTs over ten time points during fruit development. It also contains comprehensive annotation of each EST. Through TED, we provide multiple approaches to pursue analysis of specific genes of interest and/or access the larger microarray dataset to identify sets of genes that may behave in a pattern of interest. In addition, a set of useful data mining and data visualization tools were developed and are under continuing expansion.
Fei, Zhangjun
Rice Transformation as a Means to Study Gene Expression
An exceptionally effective transformation procedure has been established by using class I embryo-derived rice callus. Every treated callus clump yielded multiple independently transformed plants (average 40 plantlets). Analysis of genomic DNA blots and pollen expressing green fluorescent protein (GFP) from T0 plants revealed that 64% bore a single locus T-DNA insertion in which half had one T-DNA copy. Additive transgene expression was observed fromT0 plants with GFP driven by mUbi1 promoter. Transgenic plants could be rapidly characterized by analyzing GFP pollen from T0 plants without the need for further generations or genomic DNA blot analysis. Agrobacterium tumefaciens-mediated transformation of microspore-derived callus for generating large numbers of T-DNA haploid and doubled haploid(DH) plants has also been investigated. The established transformation procedure resulted in 100% transformation frequency for class I microspore-derived rice callus. Each callus typically yields multiple independent transgenic plants. Genomic DNA blot analysis suggested 98% of the transgenic plants are independent events. About half of the transgenic plants were identified as haploid plants, whereas half are DH hemizygous or homozygous transgenic plants. DH homozygous transgenic plants were obtained from T0plants and confirmed by pollen GFP expression and genomic blot analysis in T0transgenic DH plants. In this study, about 60% ofT0transgenic DH plants had a single locus T-DNA insertion of which 45% bore one T-DNA copy. Furthermore, in a population of over 2,000 haploid and doubled haploid T-DNA plants , about 25% showed phenotypic differences from non-transformed haploid plants. Approximately 5% were seriously phenotypically abnormal including lethal or semi-lethal mutants. This highly efficient transformation procedure using microspore-derived callus could be valuable in speeding up plant breeding and in new gene discovery. Diversification of the mUbi1 promoter led to a minimal promoter that has a similar function as the original mUbi1. Transient and stable transformation as measured from gene expression driven by the minimal promoter suggested that it has a similar function as the original wild type promoter.
Jiang, Yiming
Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles
The interactor normalization task (INT) is to identify genes that play the interactor role in protein-protein interactions (PPIs), to map these genes to unique IDs, and to rank them according to their normalized confidence. INT has two subtasks: gene ... Keywords: Data mining, feature evaluation and selection, mining methods and algorithms, text mining, scientific databases.
Hong-Jie Dai; Po-Ting Lai; Richard Tzong-Han Tsai
Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus
Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock.
Ranjan, Priya [ORNL; Yin, Tongming [ORNL; Zhang, Xinye [ORNL; Kalluri, Udaya C [ORNL; Yang, Xiaohan [ORNL; Jawdy, Sara [ORNL; Tuskan, Gerald A [ORNL
Self-assembled pentablock copolymers for selective and sustained gene delivery
The poly(diethylaminoethyl methacrylate) (PDEAEM) - Pluronic F127 - PDEAEM pentablock copolymer (PB) gene delivery vector system has been found to possess an inherent selectivity in transfecting cancer cells over non-cancer cells in vitro, without attaching any targeting ligands. In order to understand the mechanism of this selective transfection, three possible intracellular barriers to transfection were investigated in both cancer and non-cancer cells. We concluded that escape from the endocytic pathway served as the primary intracellular barrier for PB-mediated transfection. Most likely, PB vectors were entrapped and rendered non-functional in acidic lysosomes of non-cancer cells, but survived in less acidic lysosomes of cancer cells. The work highlights the importance of identifying intracellular barriers for different gene delivery systems and provides a new paradigm for designing targeting vectors based on intracellular differences between cell types, rather than through the use of targeting ligands. The PB vector was further developed to simultaneously deliver anticancer drugs and genes, which showed a synergistic effect demonstrated by significantly enhanced gene expression in vitro. Due to the thermosensitive gelation behavior, the PB vector packaging both drug and gene was also investigated for its in vitro sustained release properties by using polyethylene glycol diacrylate as a barrier gel to mimic the tumor matrix in vivo. Overall, this work resulted in the development of a gene delivery vector for sustained and selective gene delivery to tumor cells for cancer therapy.
Zhang, Bingqi
Organization and transfer of heterologous chloramphenicol and tetracycline resistance genes in pneumococcus
The cat and tet genes of chloramphenicol- and tetracycline-resistant clinical isolates of Streptococcus pneumuoniae from Paris and Japan were shown to be contained in adjacent heterologous insertions into the chromosome. The two insertions transformed laboratory strains at frequencies that were low, unequal, and, for tet, very sensitive to the length of the donor deoxyribonucleic acid strand. In contrast, the transforming activity of cat was relatively stable. There was an unusual asymmetric cotransfer, in that a majority of the tet transformants also acquired cat, whereas only a few of the cat transformants also acquired tet. The evidence for chromosomal insertion came from genetic data showing linkage of cat to a chromosomal gene and from cosedimentation of cat with chromosomal markers in both velocity and dye-buoyancy experiments. Genes on a known plasmid introduced into pneumococcus from Streptococcus faecalis showed very different physical behavior. Most of the transformation properties of these genes can be readily accounted for by analogy to transformation of deletions of normal genes. Whether transposition contributes any of the transfers remains to be determined. The presence of one of the genes in the recipient promoted the integration of the other, demonstrating enhanced accumulation of heterologous genes by a process that did not involve plasmids in the species of concern.
Shoemaker, N.B.; Smith, M.D.; Guild, W.R.
Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation
It has been long recognized that a significant fraction of the radiation-induced genetic damage to cells are caused by secondary oxidative species. Internal cellular defense systems against oxidative stress play significant roles in countering genetic damage induced by ionizing radiation. The role of the detoxifying enzymes may be even more prominent in the case of low-dose, low-LET irradiation, as the majority of genetic damage may be caused by secondary oxidative species. In this study we have attempted to decipher the roles of the superoxide dismutase (SOD) genes, which are responsible for detoxifying the superoxide anions. We used adenovirus vectors to deliver RNA interference (RNAi or siRNA) technology to down-regulate the expression levels of the SOD genes. We have also over-expressed the SOD genes by use of recombinant adenovirus vectors. Cells infected with the vectors were then subjected to low dose ?-irradiation. Total RNA were extracted from the exposed cells and the expression of 9000 genes were profiled by use of cDNA microarrays. The result showed that low dose radiation had clear effects on gene expression in HCT116 cells. Both over-expression and down-regulation of the SOD1 gene can change the expression profiles of sub-groups of genes. Close to 200 of the 9000 genes examined showed over two-fold difference in expression under various conditions. Genes with changed expression pattern belong to many categories that include: early growth response, DNA-repair, ion transport, apoptosis, and cytokine response.
Eric Y. Chuang
Barbara McClintock, Jumping Genes, and Transposition
Barbara McClintock and Transposable Genetic Elements McClintock Honored · Woman of Science · Educational Material · Resources with Additional Information Barbara McClintock's remarkable life spanned the history of genetics in the twentieth century. ... [T]he science of genetics, to which McClintock made seminal contributions both experimental and conceptual, has come to dominate all of the biological sciences, from molecular biology, through cell and developmental biology, to medicine and agriculture. ... Barbara McClintock Courtesy of the Cold Spring Harbor Laboratory Archives McClintock made her first significant contribution as a graduate student, developing cytological techniques that allowed her to identify each of the ten maize chromosomes. These early experiments laid the groundwork for a remarkable series of cytogenetic discoveries ... [for which] McClintock was the intellectual driving force ... . These include identification of maize linkage groups with individual chromosomes, the well-known cytological proof of genetic crossing-over, evidence of chromatid crossing-over, cytological determination of the physical location of genes within chromosomes, identification of the genetic consequences of nonhomologous pairing, establishment of the causal relationship between the instability of ring-shaped chromosomes and phenotypic variegation, discovery that the centromere is divisible, and identification of a chromosomal site essential for the formation of the nucleolus. ...
Mapping our genes: The genome projects: How big, how fast
For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.
and Performance Engineering Team Early Experience on the Blue Gene/Q Supercomputing System Mira P erformance B oot C amp Argonne, M ay 2 1, 2 013 Argonne L eadership C ompuDng F acility Argonne N aDonal L aboratory, A rgonne, I L 2 Outline Introduc+on - Argonne L eadership C ompu+ng F acility - From B G/P t o B G/Q BG/Q S ystem C haracteris+cs - Memory S ubsystem - Computa+on C apabili+es - Interconnect a nd C ommunica+on P roper+es - Power C onsump+on a nd E fficiency BG/Q S pecific F eatures - QPX --- 4 ---way S IMD V ector U nit - Prefetching U nit a nd L ist P refetching Applica+on S tudies - GTC, G FMC, D NS3D ALCF @ Argonne 3 Produc'on S ystems: Mira - B G/Q s ystem - 49,152 nodes / 786,432 cores - 786 TB of memory - Peak fl op r ate: 1 0 P F - Linpack fl op r ate: 8 .1 P F Intrepid
Mutations of the Apc gene in experimental colorectal carcinogenesis induced by azoxymethane in F344 rats
Summary We investigated in the rat the role of the Apc gene, which is mutated in familial adenomatous polyposis and sporadic colon cancer in the process leading from normal colonic mucosa to aberrant crypt foci (ACF) and finally to adenomas and adenocarcinomas. We analysed mutations in exon 15 of the rat Apc gene using in vitro synthesized protein assay in 66 ACF and in 28 colon tumours induced by azoxymethane. No Apc mutations were found in ACF, whereas five mutations were found in the tumours. The data suggest that mutations of the Apc gene are associated with the transition from ACF to adenoma and adenocarcinoma and not from normal mucosa to ACF.
G Caderni; M Bazzicalupo; C Briani; A Giannini; M Fazi; P Dolaral
A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland
Motivation: The identification of functional cis-acting DNA regulatory elements is a crucial step towards understanding gene regulation. Ab initio motif detection algorithms have been extensively used in search of regulatory elements. ...
Shahar Alon; Eli Eisenberg; Jasmine Jacob-Hirsch; Gideon Rechavi; Gad Vatine; Reiko Toyama; Steven L. Coon; David C. Klein; Yoav Gothilf
Biomedical data retrieval utilizing textual data in a gene expression database by Richard Lu, MD.
Background: The commoditization of high-throughput gene expression sequencing and microarrays has led to a proliferation in both the amount of genomic and clinical data that is available. Descriptive textual information ...
Lu, Richard, M.D
Endogenous control of stochastic gene expression in the development of Caenorhabditis elegans
Studies in the past decade have established gene expression as an inherently variable process. Accompanying this exciting finding is a fundamental question: how do physiological events, such as cell fate specification, ...
Ji, Ni, Ph. D. Massachusetts Institute of Technology
MOLECULAR THERAPY Vol. 4, No. 2, August 2001 Copyright The American Society of Gene Therapy
that a plasmid car- rying the full SERPINA1 on a 19-kb genomic fragment and the EBV gene EBNA1 and its family] and Liu [5] have developed a simple hydro- dynamic procedure for efficient transfection of liver cells
Ford, James
Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen (2010 JGI User Meeting)
Director Eddy Rubin on "Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen" on March 25, 2010 at the 5th Annual DOE JGI User Meeting
Rubin, Eddy
The Antioxidant Vitamins C & EChapter 15 Vitamin E and Selenium Effects on Differential Gene
The Antioxidant Vitamins C & E Chapter 15 Vitamin E and Selenium Effects on Differential Gene Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry Press Downloadable pdf of Chapter 15 Vitam
An Efficient Method for Exploring the Space of Gene Tree/Species ...
Jan 19, 2010 ... If one is interested in the posterior probability distribution of a subset of .... loss rates along each branch of S, the generation of a gene tree starts.
Quantitative analysis of non-viral gene therapy in primary liver culture systems
Gene therapy has the potential to cure thousands of diseases caused by genetic abnormalities, provide novel combination therapies for cancers and viral infections, and offer a new and effective platform for next generation ...
Tedford, Nathan C
Rewriting game theory as a foundation for state-based models of gene regulation
We present a game-theoretic foundation for gene regulatory analysis based on the recent formalism of rewriting game theory. Rewriting game theory is discrete and comes with a graph-based framework for understanding compromises and interactions ...
Chafika Chettaoui; Franck Delaplace; Pierre Lescanne; Mun�delanji Vestergaard; Ren� Vestergaard
Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene
Background: Phages infecting marine picocyanobacteria often carry a psbA gene, which encodes a homolog to the photosynthetic reaction center protein, D1. Host encoded D1 decays during phage infection in the light. Phage ...
Chisholm, Sallie (Penny)
The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants
We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution
Grigoriev, Igor V.; Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; dePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cedric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin-ichi; Murata, Takashi; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sorensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theilsen, Gunter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing-Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loque, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel
Modified cellulose synthase gene from Arabidopsis thaliana confers herbicide resistance to plants
Cellulose synthase ("CS"), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl)phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.
Somerville, Chris R. (Portola Valley, CA); Scheible, Wolf (Golm, DE)
Drug-loaded nanoparticles induce gene expression in human pluripotent stem cell derivatives
typically contain few functional groups for further chemical modification. Doxycycline (DXC), a potent small complex spatiotemporal control of gene expression and cell transitions.8 Doxycycline (DXC) is a small
Saha, Krishanu
Effects of melatonin and age on gene expression in mouseCNS using microarray analysis
gene contains an activation site for NF-kB (Cowland et al. ,and levels of activated NF-kB increase in murine cortex withThus, increased levels of NF-kB activation in the aged brain
Bondy, Stephen Bondy C
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
We recently showed that the mammalian genome encodes >1,000 large intergenic noncoding (linc)RNAs that are clearly conserved across mammals and, thus, functional. Gene expression patterns have implicated these lincRNAs in ...
Presser, Aviva
A role for the Spemann organizer gene, Goosecoid, in tumor metastasis
The process of invasion and metastasis during tumor progression is often reminiscent of cell migration events occurring during embryonic development. I hypothesized that genes controlling cellular changes in the Spemann ...
Hartwell, Kimberly A. (Kimberly Ann)
Polylipid Nanoparticle, a Novel Lipid-Based Vector for Liver Gene Transfer
for Liver Gene Transfer Yahan Fan and Jian Wu Additionalapplicable for in vivo � 2013 Fan and Wu; licensee InTech.Award (321 Plan). Yahan Fan is the recipient of China
Fan, Yahan; Wu, Jian
Molecular Biology, Pathobiology, and Genetics Intrinsic Gene Expression Profiles of Gliomas Are a Better
Molecular Biology, Pathobiology, and Genetics Intrinsic Gene Expression Profiles of Gliomas distinct molecular subgroups that correlate with survival. These include two favorable prognostic subgroups with poor prognosis (median survival, molecular subtypes
Analysis of metazoan DNA replication initiation using Drosophila gene amplification as a model system
Gene amplification in Drosophila follicle cells is an excellent model to study origin specification and developmental regulation of DNA replication in vivo. We mapped all follicle cell amplicons using a comparative genomic ...
Kim, Jane Christina
BMP7 Gene Transfer via Gold Nanoparticles into Stroma Inhibits Corneal Fibrosis In Vivo
This study examined the effects of BMP7 gene transfer on corneal wound healing and fibrosis inhibition in vivo using a rabbit model. Corneal haze in rabbits was produced with the excimer laser performing -9 diopters ...
Tandon, Ashish
Coevolution of languages and genes on the island of Sumba, eastern Indonesia
Coevolution of languages and genes on the island of Sumba, eastern Indonesia J. Stephen Lansing Angeles, CA 90095; and Eijkman Institute for Molecular Biology, Diponegoro 69, Jakarta 10430, Indonesia
Watkins, Joseph C.
Evolution of Hox gene expression and function and the effect on limb specification in arthropods
In Nature, pp. 661-665. Grenier, J. K. , and Carroll, S.101, 577-580. Carroll, S. , Grenier, J. and Weatherbee, S. (sets of target genes (Grenier and Carroll, 2000). Moreover,
Hsia, Cheryl Chih-Jui
Computational prediction of RNA-based gene regulatory mechanisms in human and Tetrahymena
The diversity and profound impact of gene regulation mediated by small RNAs (sRNAs) is just beginning to come into focus. RNA interference (RNAi) pathways have been shown to mediate processes such as genomic rearrangement ...
Kitzman, Jacob O
miRNAminer: a tool for homologous microRNA gene search
Background MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental ...
Artzi, Shay
Differential Gene Expression Pre-processing: from CEL files to ExpressionSet
different between mutants and wild types Install Libraries and Load Data > source-processing: from CEL files to ExpressionSet Gene Annotation Visualize Expression Profile using Heatmap Produce
Qiu, Weigang
Exploring the specificity and mechanisms of siRNA-mediated gene silencing in mammalian cells
Complementary short interfering RNAs (siRNAs) are routinely used to knockdown gene expression. siRNAs bind to their target sequence and guide transcript cleavage and subsequent degradation. This type of silencing is ...
Alem�n, Lourdes Maria
Powered by NERSC, A Database of Billions of Genes and Counting!
Powered by NERSC, a Powered by NERSC, a Database of Billions of Genes and Counting! Powered by NERSC, a Database of Billions of Genes and Counting! With More than a Billion Microbial genes, IMG/M Breaks a Record January 26, 2012 | Tags: Joint Genome Institute Linda Vu, email@example.com, +1 510 495 2402 IMG/M team celebrates the recording of 1 billionth gene. Microbes are microscopic organisms that live in every nook and cranny of our planet. Without them, plants wouldn't grow, garbage wouldn't decay, humans wouldn't digest food, and there would literally be no life on Earth, or at least as we know it. By examining the genetic makeup of these "bugs," scientists hope to understand how they work, and how they can be used to solve a variety of important problems like identifying new
The effects of transcription factor competition on gene regulation
Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies investigated the influence of the cellular environment on the facilitated diffusion mechanism and, in particular, the influence of `other' DNA binding proteins competing with the TF molecules for DNA space. Molecular crowding on the DNA is likely to influence the association rate of TFs to their target site and the steady state occupancy of those sites, but it is still not clear how it influences the search in a genome-wide context, when the model includes biologically relevant parameters (such as: TF abundance, TF affinity for DNA and TF dynamics on the DNA). We performed stochastic simulations of TFs performing the facilitated diffusion mechanism, and considered various abundances of cognate and non-cognate TFs. We show that, for both obstacles that move on the DNA and obstacles that are fixed on the DNA, changes in search time are not statistically significant in case of biologically relevant crowding levels on the DNA. In the case of non-cognate proteins that slide on the DNA, molecular crowding on the DNA always leads to statistically significant lower levels of occupancy, which may confer a general mechanism to control gene activity levels globally. When the `other' molecules are immobile on the DNA, we found a completely different behaviour, namely: the occupancy of the target site is always increased by higher molecular crowding on the DNA. Finally, we show that crowding on the DNA may increase transcriptional noise through increased variability of the occupancy time of the target sites.
Nicolae Radu Zabet; Boris Adryan
Assignment of the cysteinyl-tRNA synthetase gene (CARS) to 11p15. 5
The attachment of each of the 20 naturally occurring amino acids to their cognate tRNA isoaccepting families is catalyzed by a specific aminoacyl-tRNA synthetase. The structural genes encoding 10 of these enzymes have been assigned to specific human chromosomes. The HARS, LARS, RARS, and TARS genes, encoding histidyl-, leucyl-, arginyl-, and threonyl-tRNA synthetases, respectively, are all located on chromosome 5( 1, 5, 7, 9, 14). The MARS (methionyl-tRNA synthetase), NARS (asparaginyl-tRNA synthetase), VARS (valyl-tRNA synthetase), and WARS (tryptophanyl-tRNA synthetase) genes have been assigned to chromosomes 12, 18, 6, and 14, respectively (3, 4, 6, 8). A gene originally identified as encoding glutaminyl-tRNA synthetase was mapped to chromosome 1q32-q42 (10). However, a recent study suggests that the product of this gene is, in fact, a multifunctional enzyme with both glutamyl- and prolyl-tRNA synthetase activities (2). The fact that 4 of the 10 aminoacyl-tRNA synthetase genes already mapped are located on chromosome 5 may be fortuitous but might also indicate an evolutionary or regulatory relatedness. It is therefore, of interest to map genes encoding other aminoacyl-tRNA synthetases to determine if additional examples of synteny exist. The recent isolation of cDNA and genomic DNA clones for human cysteinyl-tRNA synthetase has now enabled us to map the CARS gene to segment p15.5 on chromosome 11 by fluorescence in situ hybridization.
Cruzen, M.E.; Bengtsson, U.; McMahon, J.; Wasmuth, J.J.; Arfin, S.M. (Univ. of California, Irvine (United States))
Snapshot of iron response in Shewanella oneidensis by gene network reconstruction
Background: Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis. Results: We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. Conclusions: Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.
Yang, Yunfeng; Harris, Daniel P.; Luo, Feng; Xiong, Wenlu; Joachimiak, Marcin; Wu, Liyou; Dehal, Paramvir; Jacobsen, Janet; Yang, Zamin; Palumbo, Anthony V.; Arkin, Adam P.; Zhou, Jizhong
Status of clinical gene sequencing data reporting and associated risks for information loss
Clinical gene sequencing is growing in importance and cost-effectiveness. In the past two years, the number of genes associated with disease has grown by roughly 25%. Knowledge of genetic variations will soon guide drug selection and dosages, predict ... Keywords: Algorithms, Automatic data processing, Computational biology, Computer-assisted, DNA/Analysis, Diagnosis, Diagnostic use, Genetics, Genome, Human, Information storage and retrieval, Variation (genetics)
Douglas R. Mitchell; Joyce A. Mitchell
Risk haplotype pattern discovery for gene mapping by recursive partitioning method based on weighted classification trees
In this paper, we present a combinatorial approach based on recursive weighted longest prefix trees (RWLPT) for mining a massive genetic marker data. Given a case and a control chromosome dataset, we develop a fast recursive permutation algorithm ... Keywords: combinatorial optimisation, disease susceptibility genes, gene mapping, genetic markers, haplotype clusters, haplotype-disease association, multilocus SNP analysis, non-numerical algorithms, recursive partitioning, risk haplotype pattern discovery, weighted classification trees
Tran Trang; Hoang Ngoc Minh
A comparative method for identification of gene structures and alternatively spliced variants
Motivation: Alternative splicing (AS) serves as a mechanism to create diversity of functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures. Results: A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on EST-to-genome and genome-to-genome comparisons and is implemented in two steps: sequence alignment and a series of post-alignment processes, including progressive signal extracting and patching. For gene identification, these post-alignment processes serve as noise filters and enable PSEP to eliminate approximately 88 % of potential overprediction. The overall accuracy of PSEP is better or comparable to that of other well-known cross-species gene prediction programs, including the ROSETTA program, TWINSCAN, SGP-1/-2, and SLAM, when tested on three benchmark data sets (the ELN gene region, the HoxA cluster, and the ROSETTA set). In addition, 76.2 % and 76.0 % of multiple-exon genes in the ROSETTA data set and human chromosome 20, respectively, are found to have AS forms. Approximately 23 % of the 210 elementary alternatives identified in the ROSETTA data set are not conserved between the human and mouse genomes, and all of the 210 transcripts are not found in the RefSeq annotation. With its dual functions in cross-species conserved sequence analysis and AS analysis, PSEP is highly suitable for studying the evolution of AS patterns and for finding unidentified gene expression features. Availability: The programs of PESP as well as the visualization tool required to build the proposed annotation scheme is available at
Trees-juen Chuang; Feng-chi Chen; Meng-yuan Chou
Organization and control of genes encoding catabolic enzymes in Rhizobiaceae. Progress report, March 1993
Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the {beta}-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novel regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate {beta}-carboxy-cis,cis-muconate. {beta}-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for {beta}-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to {beta}-carboxy-cis,cis-muconate.
The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE)
The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE) will be held June 8-12, 2005 at the University of Texas at Austin. Exciting new and ongoing discoveries show significant regulation of gene expression occurs after transcription. These post-transcriptional control events in plants range from subtle regulation of transcribed genes and phosphorylation, to the processes of gene regulation through small RNAs. This meeting will focus on the regulatory role of RNA, from transcription, through translation and finally degradation. The cross-disciplinary design of this meeting is necessary to encourage interactions between researchers that have a common interest in post-transcriptional gene expression in plants. By bringing together a diverse group of plant molecular biologist and biochemists at all careers stages from across the world, this meeting will bring about more rapid progress in understanding how plant genomes work and how genes are finely regulated by post-transcriptional processes to ultimately regulate cells.
Karen S. Browning; Marie Petrocek; Bonnie Bartel
Repression of the Drosophila proliferating-cell nuclear antigen gene promoter by zerknuellt protein
A 631-bp fragment containing the 5{prime}-flanking region of the Drosophila melanogaster proliferating-cell nuclear antigen (PCNA) gene was placed upstream of the chloramphenicol acetyltransferase (CAT) gene of a CAT vector. A transient expression assay of CAT activity in Drosophila Kc cells transfected with this plasmid and a set of 5{prime}-deletion derivatives revealed that the promoter function resided within a 192-bp region. Cotransfection with a zerknuellt (zen)-expressing plasmid specifically repressed CAT expression. However, cotransfection with expression plasmids for a nonfunctional zen mutation, even skipped, or bicoid showed no significant effect on CAT expression. RNase protection analysis revealed that the repression by zen was at the transcription step. The target sequence of zen was mapped within the 34-bp region of the PCNA gene promoter, even though it lacked zen protein-binding sites. Transgenic flies carrying the PCNA gene regulatory region fused with lacZ were established. These results indicate that zen indirectly represses PCNA gene expression, probably by regulating the expression of some transcription factor(s) that binds to the PCNA gene promoter.
Yamaguchi, Masamitsu; Hirose, Fumiko; Nishida, Yasuyoshi; Matsukage, Akio (Aichi Cancer Center Research Inst., Nagoya (Japan))
SATB1 tethers multiple gene loci to reprogram expression profiledriving breast cancer metastasis
Global changes in gene expression occur during tumor progression, as indicated by expression profiling of metastatic tumors. How this occurs is poorly understood. SATB1 functions as a genome organizer by folding chromatin via tethering multiple genomic loci and recruiting chromatin remodeling enzymes to regulate chromatin structure and expression of a large number of genes. Here we show that SATB1 is expressed at high levels in aggressive breast cancer cells, and is undetectable in non-malignant breast epithelial cells. Importantly, RNAi-mediated removal of SATB1 from highly-aggressive MDA-MB-231 cells altered the expression levels of over 1200 genes, restored breast-like acinar polarity in three-dimensional cultures, and prevented the metastastic phenotype in vivo. Conversely, overexpression of SATB1 in the less-aggressive breast cancer cell line Hs578T altered the gene expression profile and increased metastasis dramatically in vivo. Thus, SATB1 is a global regulator of gene expression in breast cancer cells, directly regulating crucial metastasis-associated genes, including ERRB2 (HER2/NEU), TGF-{beta}1, matrix metalloproteinase 3, and metastasin. The identification of SATB1 as a protein that re-programs chromatin organization and transcription profiles to promote breast cancer metastasis suggests a new model for metastasis and may provide means of therapeutic intervention.
Han, Hye-Jung; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi
Analysis of the human [alpha]-globin gene cluster in transgenic mice
A 350-bp segment of DNA associated with an erythroid-specific DNase I-hypersensitive site (HS -40), upstream of the [alpha]-globin gene cluster, has been identified as the major tissue-specific regulator of the [alpha]-globin genes. However, this element does not direct copy number-dependent or developmentally stable expression of the human genes in transgenic mice. To determine whether additional upstream hypersensitive sites could provide more complete regulation of [alpha] gene expression, the authors have studied 17 lines of transgenic mice bearing various DNA fragments containing HSs -33, -10, -8, and -4, in addition to HS -40. Position-independent, high-level expression of the human [zeta]- and [alpha]-globin genes was consistently observed in embryonic erythroid cells. However, the additional HSs did not confer copy-number dependence, alter the level of expression, or prevent the variable down-regulation of expression in adults. These results suggest that the region upstream of the human [alpha]-globin genes is not equivalent to that upstream of the [beta] locus and that although the two clusters are coordinately expressed, there may be differences in their regulation.
Sharpe, J.A.; Vyas, P.; Higgs, D.R.; Wood, W.G. (Univ. of Oxford, Oxford (United Kingdom)); Wells, D.J. (Royal Veterinary College, Royal College Street, London (United Kingdom)); Whitelaw, E. (Univ. of Sydney, Sydney (Australia))
Mathematical modeling and information theoretical analysis of DevR regulated genes in Mycobacterium tuberculosis
The DevR-DevS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several downstream genes in a complex manner. In the present work we have developed a mathematical model to show the role of binding sites in the DevR mediated gene expression. Through modeling it has been shown the individual and collective role of the binding sites in regulating the DevR mediated gene expression. The objective of the present work is two fold. First, to describe qualitatively the temporal dynamics of wild type genes and their known mutants. Based on these results we propose that DevR controlled gene expression follows a specific pattern which is efficient in describing other DevR mediated gene expression. Second, to analyze the behavior of the system from the information theoretical point of view. Using the tools of information theory we have calculated the molecular efficiency of the system and have shown that it is close to the maximum limit of isothermal efficiency.
Arnab Bandyopadhyay; Soumi Biswas; Alok Kumar Maity; Suman K Banik
Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata: Progress report for the period June 5, 1986-June 4, 1987
This document describes research conducted between June 1986 and June 1987. Results dealing with the organization and regulation of genes in the photosynthetic bacterium Rhodobacter capsulatus includes cloning, sequencing, and demonstrating characterizing the products of genes that regulate expression of nitrogen fixation genes; the connection between DNA supercoiling mediated by DNA gyrase and nif gene expression; and mapping the entire chromosome of R. capsulatus.
Haselkorn, R.
[Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata]. Progress report, [June 5, 1989--June 4, 1991
A molecular genetic analysis of carotenoid biosynthesis and the effects of carotenoid mutations on other photosynthetic genes in Rhodobacter capsulatus
The nine known R. capsulatus carotenoid genes are contained within the 46 kilobase (kb) photosynthesis gene cluster. An 11 kb subcluster containing eight of these genes has been cloned and its nucleotide sequence determined. A new gene, crtK, has been located in the middle of the subcluster. The carotenoid gene cluster contains sequences homologous to Escherichia coli ..omega../sup 70/ promoters, rho-independent transcription terminators, and prokaryotic transcriptional factor binding sites. The phenotypes and genotypes of ten transposon Tn5.7 insertion mutations within the carotenoid gene cluster have been analyzed, by characterization of the carotenoids accumulated and high resolution mapping of the Tn5.7 insertions. The enzymatic blockages in previously uncharacterized early carotenoid mutants have been determined using a new in vitro synthesis system, suggesting specific roles for the CrtB and CrtE gene products. The expression of six of the eight carotenoid genes in the cluster is induced upon the shift from dark chemoheterotrophic to anaerobic photosynthetic growth. The magnitude of the induction is equivalent to that of genes encoding structural photosynthesis polypeptides, although the carotenoid genes are induced earlier after the growth shift. Different means of regulating photosynthesis genes in R. capsulatus are discussed, and a rationale for the temporal pattern of expression of the carotenoid genes during photosynthetic adaptation is presented. Comparison of the deduced amino acid sequences of the two dehydrogenases of the R. capsulatus carotenoid biosynthesis pathway reveals two regions of strong similarity. The effect of carotenoid mutations on the photosynthetic phenotype has been studied by examining growth rates, pigments, pigment-protein complexes and gene expression for a complete set of carotenoid mutants. 161 refs.
Armstrong, G.A.
Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus
Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.
Burke-Agueero, D.H.
Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.
Role of Morphological Growth State and Gene Expression in Desulfovibrio africanus strain Walvis Bay Mercury Methylation
The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)- reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating -proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production, but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. While no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles.
Moberly, James G [ORNL; Miller, Carrie L [ORNL; Brown, Steven D [ORNL; Biswas, Abir [ORNL; Brandt, Craig C [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL
Activation of endothelial-leukocyte adhesion molecule 1 (ELAM-1) gene transcription
Leukocyte adherence to endothelium is in part mediated by the transient expression of endothelial-leukocyte adhesion molecule 1 (ELAM-1) on endothelial surfaces stimulated by tumor necrosis factor {alpha} (TNF), interleukin (IL) 1, or bacterial lipopolysaccharide (LPS). The intracellular factors controlling induction of ELAM-1 mRNA and protein are unknown. In nuclear runoff experiments with cultured human umbilical vein endothelial cells (HUVEC), the authors demonstrate that transcriptional activation of the ELAM-1 gene occurs following stimulation with TNF. Sequence analysis of the 5{prime} flanking region of the ELAM-1 gene reveals consensus DNA-binding sequences for two known transcription factors, NF-{kappa}B and AP-1. Gel mobility shift assays demonstrate that TNF, IL-1, or LPS induces activation of NF-{kappa}B-like DNA binding activity in HUVEC. Phorbol 12-myristate 13-acetate, a known activator of protein kinase C (PKC), weakly induces NF-{kappa}B-like activity, ELAM-1 mRNA, and ELAM-1 surface expression in HUVEC. However, TNF, IL-1, and LPS do not activate PKC in HUVEC at doses that strongly induce NF-{kappa}B-like protein activation and ELAM-1 gene expression. PKC blockade with H7 does not inhibit activation of these NF-kB-like proteins but does inhibit ELAM-1 gene transcription. They conclude that PKC-independent activation of NF-{kappa}B in HUVEC with TNF, IL-1, or LPS is associated with, but not sufficient for, activation of ELAM-1 gene transcription.
Montgomery, K.F.; Tarr, P.I.; Bomsztyk, K.; Harlan, J.M.; Pohlman, T.H. (Univ. of Washington, Seattle (United States)); Osborn, L.; Hession, C.; Tizard, R.; Goff, D.; Vassallo, C.; Lobb, R. (Biogen, Inc., Cambridge, MA (United States))
Regulation of hepatic PPAR{gamma}2 and lipogenic gene expression by melanocortin
The central melanocortin system regulates hepatic lipid metabolism. Hepatic lipogenic gene expression is regulated by transcription factors including sterol regulatory element-binding protein 1c (SREBP-1c), carbohydrate responsive element-binding protein (ChREBP), and peroxisome proliferator-activated receptor {gamma}2 (PPAR{gamma}2). However, it is unclear if central melanocortin signaling regulates hepatic lipogenic gene expression through the activation of these transcription factors. To delineate the molecular mechanisms by which the melanocortin system regulates hepatic lipid metabolism, we examined the effect of intracerebroventricular injection of SHU9119, a melanocortin receptor antagonist, on hepatic expression levels of genes involved in lipid metabolism in mice. SHU9119 treatment increased hepatic triglyceride content and mRNA levels of lipogenic genes, SREBP-1c, and PPAR{gamma}2, whereas it did not cause any changes in hepatic ChREBP mRNA levels. These findings suggest that reduced central melanocortin signaling increases hepatic lipid deposition by stimulating hepatic lipogenic gene expression at least partly through the activation of SREBP-1c and PPAR{gamma}2.
Poritsanos, Nicole J.; Wong, Davie [Department of Physiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, R3E 3J7 (Canada); Vrontakis, Maria E. [Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB, R3E 3J7 (Canada); Mizuno, Tooru M. [Department of Physiology, University of Manitoba, 730 William Avenue, Winnipeg, MB, R3E 3J7 (Canada)], E-mail: firstname.lastname@example.com
Gene Expression of ANP, BNP and ET-1 in the Heart of Rats during Pulmonary Embolism
Aims: Atrial natriuretic petide (ANP), brain natriuretic peptide (BNP) and endothelin-1 (ET-1) may reflect the severity of right ventricular dysfunction (RVD) in patients with pulmonary embolism (PE). The exact nature and source of BNP, ANP and ET-1 expression and secretion following PE has not previously been studied. Methods and Results: Polystyrene microparticles were injected to induce PE in rats. Gene expression of BNP, ANP and ET-1 were determined in the 4 cardiac chambers by quantitative real time polymerase chain reaction (QPCR). Plasma levels of ANP, BNP, ET-1 and cardiac troponin I (TNI) were measured in plasma. PE dose-dependently increased gene expression of ANP and BNP in the right ventricle (RV) and increased gene expression of ANP in the right atrium (RA). In contrast PE dosedependently decreased BNP gene expression in both the left ventricle (LV) and the left atrium (LA). Plasma levels of BNP, TNI and ET-1 levels dose-dependently increased with the degree of PE. Conclusion: We found a close correlation between PE degree and gene-expression of ANP, and BNP in the cardiac chambers with a selective increase in the right chambers of the heart. The present data supports the idea of natriuretic peptides as
Henrik Gutte; Jytte Oxb�l; Ulrik Sloth Kristoffersen; Jann Mortensen; Andreas Kj�r
In silico analysis of motifs in promoters of Differentially Expressed Genes in rice (Oryza sativa L.) under anoxia
The aim of this study was to characterise the molecular mechanisms of transcriptional regulation of Differentially Expressed Genes (DEGs) in rice coleoptiles under anoxia by identifying motifs that are common in the promoter region of co-regulated ... Keywords: AREs, DEGs, Oryza sativa, anaerobic response elements, anoxia, bioinformatics, consensus promoter motif, differentially expressed genes, eukaryotic promoters, gene promoters, in silico motifs, in-silico motifs, microarrays, molecular mechanisms, motif detection, promoter motifs, rice, transcriptional regulation
Ashutosh Kumar; Shuchi Smita; Neeti Sahu; Vivekanand Sharma; Shankaracharya; Ambarish S. Vidyarthi; Dev Mani Pandey
DFCI Gene Index Project: Genomic Databases for Plants, Animals, Protist, and Fungi from the Dana-Farber Cancer Institute
The DFCI Gene Index Project creates databases for specific organisms. The goal for these databases is to provide an analysis of publicly available Expressed Sequence Transcripts (ESTs). ESTs are fragments of genes that were, at some time, copied from DNA to RNA. and gene sequence data to identify transcrips. The databases are in zipped files and free for download. The website also provides software and tools for use with the data, along with instructions from the website on how to link to background resources. The Gene Indices are organized into four categories: Animals, Plants, Protist, and Fungi.
Murine chromosomal location of five bHLH-Zip transcription factor genes
The genes for the bHLH-Zip transcription factors Tfap4, Mxi1, Tcfeb, Usf1, and Usf2 have been mapped in mouse by interspecific backcross analysis. Mxi1, Usf1, and Usf2 have been mapped previously by in situ hybridization, but their positions on the meiotic linkage map had not been determined. The other two genes have not previously been mapped in mouse. These transcription factors belong to a growing family of transcriptional regulators, some of which are known to form a complex network of interacting proteins that control cell proliferation and apoptosis. As expected, based on mapping studies of other bHLH-Zip genes, these loci were well distributed among mouse chromosomes. In addition, some of the probes used in this study detected multiple, independently segregating loci, suggesting the possible existence of additional family members or species-specific pseudogenes. 34 refs., 1 fig., 1 tab.
Steingrimsson, E.; Gilbert, D.J.; Copeland, N.G.; Jenkins, N.A. [Univ. of Texas, Houston, TX (United States)] [and others
Ionizing radiation downregulates ASPM, a gene responsible for microcephaly in humans
Microcephaly is a malformation associated with in utero exposed atomic bomb survivors and can be induced in mice by fetal exposure to ionizing radiation (IR). The pathogenesis of IR-induced microcephaly, however, has not been fully understood. Our analyses of high-coverage expression profiling (HiCEP) demonstrated that the abnormal spindle-like microcephaly associated gene (ASPM) was down-regulated in irradiated human diploid fibroblasts. ASPM was recently reported as the causative gene for MCPH-5, the most common type of congenital microcephaly in humans. Here, we show that the expression of the Aspm gene was significantly reduced by IR in various human and murine cells. Additionally, Aspm was found downregulated in the irradiated fetal mouse brain, particularly in the ventricular zones. A similar suppression was observed in the irradiated neurosphere cultures. This is the first report suggesting that the suppression of Aspm by IR could be the initial molecular target leading to the future microcephaly formation.
Fujimori, Akira [Cellular and Molecular Biology Team, National Institute of Radiological Sciences, Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan)], E-mail: firstname.lastname@example.com; Yaoi, Takeshi; Ogi, Hiroshi [Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Sciences, Kawaramachi Hirokoji, Kamigyo-ku, Kyoto 602-8566 (Japan); Wang Bing [National Institute of Radiological Sciences, Heavy-Ion Radiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Suetomi, Katsutoshi; Sekine, Emiko; Yu Dong; Kato, Takamitsu [Cellular and Molecular Biology Team, National Institute of Radiological Sciences, Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Takahashi, Sentaro [National Institute of Radiological Sciences, Heavy-Ion Radiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Okayasu, Ryuichi [Cellular and Molecular Biology Team, National Institute of Radiological Sciences, Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Itoh, Kyoko; Fushiki, Shinji [Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Graduate School of Medical Sciences, Kawaramachi Hirokoji, Kamigyo-ku, Kyoto 602-8566 (Japan)
Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data
Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila Transcription Network Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point-Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions. We address this challenge by linking PCX and Matlab via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.
Ruebel, Oliver; Keranen, Soile V.E.; Biggin, Mark; Knowles, David W.; Weber, Gunther H.; Hagen, Hans; Hamann, Bernd; Bethel, E. Wes
Cloning and expression of the gene for bacteriophage T7 RNA polymerase
This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the T7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.
Studier, F. William (Stony Brook, NY); Davanloo, Parichehre (Basel, CH); Rosenberg, Alan H. (Setauket, NY); Moffatt, Barbara A. (East Lansing, MI); Dunn, John J. (Bellport, NY)
This application describes a means to clone a functional gene for bacteriophage T7 RNA polymerase. Active T7 RNA polymerase is produced from the cloned gene, and a plasmid has been constructed that can produce the active enzyme in large amounts. T7 RNA polymerase transcribes DNA very efficiently and is highly selective for a relatively long promoter sequence. This enzyme is useful for synthesizing large amounts of RNA in vivo or in vitro, and is capable of producing a single RNA selectively from a complex mixture of DNAs. The procedure used to obtain a clone of the R7 RNA polymerase gene can be applied to other T7-like phages to obtain clones that produce RNA polymerases having different promoter specificities, different bacterial hosts, or other desirable properties. T7 RNA polymerase is also used in a system for selective, high-level synthesis of RNAs and proteins in suitable host cells.
Studier, F. William (Stony Brook, NY); Davanloo, Parichehre (Basel, CH); Rosenberg, Alan H. (Setauket, NY); Moffatt, Barbara A. (Waterloo, CA); Dunn, John J. (Bellport, NY)
Porting Charm++/NAMD to IBM Blue Gene/Q Wei Jiang Argonne Leadership Computing Facility
Porting Charm++/NAMD to IBM Blue Gene/Q Porting Charm++/NAMD to IBM Blue Gene/Q Wei Jiang Argonne Leadership Computing Facility 7 th , March NAMD_esp NAMD - Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems Portable to all popular supercomputing platforms Great scalability based on Charm++ parallel objects Scientific aims on Blue Gene/Q Ensemble run that launches large number of replicas concurrently - mainly for energetic simulation High throughput simulation for large scale systems ~100M atoms Requirements for charm++ New communication layer that supports parallel/parallel runs Enable charm++ programming paradigm on Parallel Active Messaging Interface (PAMI) Parallel Structure of NAMD Hybrid force/spatial decomposition Adaptive Overlap of Communication and Computation
Gene H. McCall, 1988 | U.S. DOE Office of Science (SC)
Office of Science (SC) Website
Gene H. McCall, 1988 Gene H. McCall, 1988 The Ernest Orlando Lawrence Award Lawrence Award Home Nomination & Selection Guidelines Award Laureates 2000's 1990's 1980's 1970's 1960's Ceremony The Life of Ernest Orlando Lawrence Contact Information The Ernest Orlando Lawrence Award U.S. Department of Energy SC-2/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-9395 E: firstname.lastname@example.com 1980's Gene H. McCall, 1988 Print Text Size: A A A RSS Feeds FeedbackShare Page National Security: For his pioneering work in the field of laser-driven inertial fusion and its application to nuclear weapon design and diagnostics, for his early, independent work on laser-plasma interactions and the role of electron heating, and for his work on hypervelocity particles and shockless acceleration to enable development of a new class
Easy preparation of a large-size random gene mutagenesis library in Escherichia coli
Easy preparation of a large-size random gene mutagenesis library in Easy preparation of a large-size random gene mutagenesis library in Escherichia coli Chun You, Y.-H. Percival Zhang PII: S0003-2697(12)00291-6 DOI: http://dx.doi.org/10.1016/j.ab.2012.05.022 Reference: YABIO 10976 To appear in: Analytical Biochemistry Received Date: 27 April 2012 Revised Date: 21 May 2012 Accepted Date: 22 May 2012 Please cite this article as: C. You, Y.-H. Percival Zhang, Easy preparation of a large-size random gene mutagenesis library in Escherichia coli, Analytical Biochemistry (2012), doi: http://dx.doi.org/10.1016/j.ab.2012.05.022 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency Qin Ma, Ying Xu PII: S1672-0229(13)00008-9 DOI: http://dx.doi.org/10.1016/j.gpb.2013.01.004 Reference: GPB 52 To appear in: Please cite this article as: Q. Ma, Y. Xu, Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency, (2013), doi: http://dx.doi.org/10.1016/j.gpb.2013.01.004 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon
Annotation Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon Ludmila Tyler 1,2 , Jennifer N Bragg 1† , Jiajie Wu 1,3† , Xiaohan Yang 4 , Gerald A Tuskan 4 , John P Vogel 1* Abstract Background: Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast- growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally
Variation in Telangiectasia Predisposing Genes Is Associated With Overall Radiation Toxicity
Purpose: In patients receiving radiotherapy for breast cancer where the heart is within the radiation field, cutaneous telangiectasiae could be a marker of potential radiation-induced heart disease. We hypothesized that single nucleotide polymorphisms (SNPs) in genes known to cause heritable telangiectasia-associated disorders could predispose to such late, normal tissue vascular damage. Methods and Materials: The relationship between cutaneous telangiectasia as a late normal tissue radiation injury phenotype in 633 breast cancer patients treated with radiotherapy was examined. Patients were clinically assessed for the presence of cutaneous telangiectasia and genotyped at nine SNPs in three candidate genes. Candidate SNPs were within the endoglin (ENG) and activin A receptor, type II-like 1 (ACVRL1) genes, mutations in which cause hereditary hemorrhagic telangiectasia and the ataxia-telangiectasia mutated (ATM) gene associated with ataxia-telangiectasia. Results: A total of 121 (19.1%) patients exhibited a degree of cutaneous telangiectasiae on clinical examination. Regression was used to examine the associations between the presence of telangiectasiae in patients who underwent breast-conserving surgery, controlling for the effects of boost and known brassiere size (n=388), and individual geno- or haplotypes. Inheritance of ACVRL1 SNPs marginally contributed to the risk of cutaneous telangiectasiae. Haplotypic analysis revealed a stronger association between inheritance of a ATM haplotype and the presence of cutaneous telangiectasiae, fibrosis and overall toxicity. No significant association was observed between telangiectasiae and the coinheritance of the candidate ENG SNPs. Conclusions: Genetic variation in the ATM gene influences reaction to radiotherapy through both vascular damage and increased fibrosis. The predisposing variation in the ATM gene will need to be better defined to optimize it as a predictive marker for assessing radiotherapy late effects.
Tanteles, George A. [Department of Genetics, University of Leicester, Leicester (United Kingdom) [Department of Genetics, University of Leicester, Leicester (United Kingdom); Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Murray, Robert J.S. [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Mills, Jamie [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom)] [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Barwell, Julian [Department of Genetics, University of Leicester, Leicester (United Kingdom) [Department of Genetics, University of Leicester, Leicester (United Kingdom); Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Chakraborti, Prabir [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom)] [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom); Chan, Steve [Department of Clinical Oncology, Nottingham University Hospitals NHS Trust, Nottingham (United Kingdom)] [Department of Clinical Oncology, Nottingham University Hospitals NHS Trust, Nottingham (United Kingdom); Cheung, Kwok-Leung [Division of Breast Surgery, University of Nottingham, Nottingham (United Kingdom)] [Division of Breast Surgery, University of Nottingham, Nottingham (United Kingdom); Ennis, Dawn [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom)] [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom); Khurshid, Nazish [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Lambert, Kelly [Department of Breast Surgery, University Hospitals of Leicester, Glenfield Hospital, Leicester (United Kingdom)] [Department of Breast Surgery, University Hospitals of Leicester, Glenfield Hospital, Leicester (United Kingdom); Machhar, Rohan; Meisuria, Mitul [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Osman, Ahmed; Peat, Irene [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom)] [Department of Cancer Studies and Molecular Medicine, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester (United Kingdom); Sahota, Harjinder [Department of Genetics, University of Leicester, Leicester (United Kingdom)] [Department of Genetics, University of Leicester, Leicester (United Kingdom); Woodings, Pamela [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom)] [Department of Clinical Oncology, Derby Hospitals NHS Foundation Trust, Derby (United Kingdom); Talbot, Christopher J., E-mail: email@example.com [Department of Genetics, University of Leicester, Leicester (United Kingdom); and others
Genomic structure of the choroideremia (CHM) gene and mutation analysis in CHM patients
We have isolated the complete open reading frame (ORF) of the choroideremia (CHM) gene and elucidated its exon-intron structure. The ORF of the CHM gene is located on 15 exons and encodes a protein of 653 amino acids. Among 75 CHM patients investigated for large structural abnormalities, 15 (20%) showed deletions of one or more exons of the gene. The deletions vary in size from a few kb spanning one exon to more than 10 megabases encompassing a large part of Xq21. In addition, we have positioned the X-chromosomal breakpoint in a CHM female with an X;7 translocation between exons 3 and 4. Fine mapping of the deletions indicates that there is no clustering of deletion breakpoints. Moreover, only 2 deletions are located entirely within the CHM gene, indicating that most deletions can be detected by PCR amplification of exons 1 and 15. From within the CHM gene we identified two microsatellite markers, a (CA){sub n}- and a [(TA){sub 4-12}C]{sub n}-like repeat, which should be very valuable for CHM diagnostics in clear-cut CHM families. In patients in which the diagnosis of choroideremia is less obvious, mutation analysis can be performed by PCR-SSCP analysis and direct sequencing. The feasibility of this approach was illustrated by the finding of 10 causative mutations in 12 Danish CHM families investigated. Interestingly, all CHM gene mutations detected thus far give rise to the introduction of a premature stop codon. Missense mutations thus far have not been found.
Bokhoven, H. van; Hurk, J. van den; Bogerd, L. [Univ. Hospital Nijmegen (Netherlands)] [and others
GWAS Meets Microarray: Are the Results of Genome- Wide Association Studies and Gene-Expression Profiling Consistent? Prostate Cancer as an Example
Background: Genome-wide association studies (GWASs) and global profiling of gene expression (microarrays) are two major technological breakthroughs that allow hypothesis-free identification of candidate genes associated with tumorigenesis. It is not obvious whether there is a consistency between the candidate genes identified by GWAS (GWAS genes) and those identified by profiling gene expression (microarray genes). Methodology/Principal Findings: We used the Cancer Genetic Markers Susceptibility database to retrieve single nucleotide polymorphisms from candidate genes for prostate cancer. In addition, we conducted a large meta-analysis of gene expression data in normal prostate and prostate tumor tissue. We identified 13,905 genes that were interrogated by both GWASs and microarrays. On the basis of P values from GWASs, we selected 1,649 most significantly associated genes for functional annotation by the Database for Annotation, Visualization and Integrated Discovery. We also conducted functional annotation analysis using same number of the top genes identified in the meta-analysis of the gene expression data. We found that genes involved in cell adhesion were overrepresented among both the GWAS and microarray genes. Conclusions/Significance: We conclude that the results of these analyses suggest that combining GWAS and microarray data would be a more effective approach than analyzing individual datasets and can help to refine the identification of
Ivan P. Gorlov; Gary E. Gallick; Olga Y. Gorlova; Christopher Amos; Christopher J. Logothetis
Chromosomal localization of the gene encoding the human DNA helicase RECQL and its mouse homologue
We have determined the chromosomal location of the human and mouse genes encoding the RECQL protein, a putative DNA helicase homologous to the bacterial DNA helicase, RecQ. RECQL was localized to human chromosome 12 by analysis of human-rodent somatic cell hybrid DNA, fine mapping of RECQL by fluorescence in situ hybridization revealed its chromosomal location to be 12p11-p12. The corresponding mouse gene, Recql, was mapped to the telomeric end of mouse chromosome 6 by analysis of DNA from an interspecific cross. 19 refs., 2 figs.
Puranam, K.L.; Kennington, E.; Blackshear, P.J. [Duke Univ., Durham, NC (United States)] [and others
Temperature, acetosyringone, virulence genes and wounding effects on Agrobacterium-mediated transformation efficiency
Several conditions were evaluated to determine their impact on Agrobacterium-mediated transformation efficiency. Temperature and acetosyringone (AS) effects were first studied in tobacco, as a plant model system and then applied to cotton transformation. In tobacco, AS significantly increased transformation rates that resulted in stable transformed plants. Four temperatures were evaluated during the cc-cultivation period to determine the most appropriate temperature for T-DNA transfer and integration into the plant genome. Even though 19�C was reported in the literature as the optimal temperature for Agrobacterium-mediated gene transfer, 25�C was statistically significantly different as compared to 15�C, 19�C or 32�C and produced the highest number of transgenic tobacco plants. The superior treatments established in tobacco transformation were applied to Agrobacterium-mediated transformation of the cotton shoot apex. Explant survival rates in selection medium were recorded and used to compare two temperatures (19�C and 25�C) and the effects of AS to induce the vir genes. After approximately 6-7 wk in selection medium, the percentage of surviving exhalants established that 25�C was the best temperature for cotton transformation, either with or without AS. Two wounding methods and the addition of a super-virulent plasmid were tested in cotton shoot apex transformation experiments. Their effects were evaluated using the green fluorescent protein (GFP) as an in vivo reporter gene to determine the early transformation patterns. Both removal of a leaf primordial and sanitation were examined. Transient GFP expression did not reveal any major benefit of the treatments on the transformation pattern. In contrast, when additional copies of virG and virE genes were inserted into Agrobacterium, a considerable increase in the number of fluorescence spots per exploit was evident. This was the first time GFP gene was used in cotton. Its expression was reliable, and the system was successfully established. Since GFP has several advantages as a reporter gene over the traditional GUS gene and herbicide resistance genes, it would allow the development of a more accurate selection process and therefore it would speed up the optimization of the shoot apex method.
Salas Fernandez, Maria Guadalupe
BioLattice: A framework for the biological interpretation of microarray gene expression data using concept lattice analysis
Motivation: A challenge in microarray data analysis is to interpret observed changes in terms of biological properties and relationships. One powerful approach is to make associations of gene expression clusters with biomedical ontologies and/or biological ... Keywords: Clustering, Concept analysis, Concept lattice, DNA microarray, Gene expression
Jihun Kim; Hee-Joon Chung; Yong Jung; Kack-Kyun Kim; Ju Han Kim
Use of bgaH as a reporter gene for studying translation initiation in the archaeon Haloferax volcanii
The bgaH gene isolated from Haloferax lucentensis codes for P-galactosidase. To study the function of initiator tRNAs in translation initiation in Haloferax volcanii, the initiator AUG codon of the bgaH gene was mutated ...
Sullivan, Eric L., S.M. Massachusetts Institute of Technology
Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies
The main objective of this study was to investigate the feasibility of using PharmGKB, a pharmacogenomic database, as a source of training data in combination with text of MEDLINE abstracts for a text mining approach to identification of potential gene ... Keywords: Gene-drug associations, Pathway-driven analysis, PharmGKB, Pharmacogenomics, Support vector machine, Text mining
S. Pakhomov; B. T. Mcinnes; J. Lamba; Y. Liu; G. B. Melton; Y. Ghodke; N. Bhise; V. Lamba; A. K. Birnbaum
Research article: Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast
Transcriptional regulation in eukaryotic genes generally requires combinatorial binding on DNA of multiple transcription factors. Though many analyses have been performed for identification of combinatorial patterns in promoter sequences, there are few ... Keywords: Introns, Ribosomal protein genes, Transcriptional regulation, Upstream regions, Yeast
Jun Hu; Huimin Li; Jing Zhang
Evaluation of alterations in gene expression in MCF-7 cells induced by the agricultural chemicals Enable and Diazinon
Steroid hormones, such as estrogen, are produced in one tissue and carried through the blood stream to target tissues in which they bind to highly specific nuclear receptors and trigger changes in gene expression and metabolism. Industrial chemicals, such as bisphenol A and many agricultural chemicals, including permethrin and fervalerate, are known to have estrogenic potential and therefore are estrogen mimics. Widely used agricultural chemicals, Enable (fungicide) and Diazinon (insecticide), were evaluated to examine their toxicity and estrogenicity. MCF-7 cells, an estrogen-dependent human breast cancer line, were utilized for this purpose. MCF-7 cells were treated with 0.033-3.3 ppb (ng/ml) of Enable and 0.3-67 ppm of Diazinon and gene expression was compared to that in untreated cells. Microarray analysis showed down-regulation of eight genes and up-regulation of thirty four genes in cells treated with 3.3 ppb of Enable, compared to untreated cells. Similarly, in cells treated with 67 ppm of Diazinon, there were three genes down-regulated and twenty seven genes up-regulated. For both chemicals, specific genes were selected for special consideration. RT-PCR confirmed results obtained from analysis of the microarray. These studies were designed to provide base-line data on gene expression-altering capacity of specific chemicals and will allow assessment of the deleterious effects caused by exposure to the aforementioned chemicals.
Mankame, Tanmayi Pradeep
A novel HMM-based clustering algorithm for the analysis of gene expression time-course data
A novel hidden Markov model (HMM) and clustering algorithm for the analysis of gene expression time-course data is proposed. The proposed model, called the profile-HMM, is specifically designed to explicitly take into account the dynamic nature of temporal ... Keywords: Clustering, Gene expression time-course data, Hidden Markov models, Temporal dependences, Time-series analysis
Yujing Zeng; Javier Garcia-Frias
Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice
), complement factor B (CFB), and complement component 2 (C2), Chemokine (C-X3-C motif) receptor 1 (CX3CR1), Age to permanent exposure to reactive oxygen species generated by the absorption of light. Genes involved in gene expression should reflect an adjustment of blood flow for the oxygen requirement of the retina
Dahlquist, Kam D.
Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies
The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. A major ... Keywords: Bioinformatics (genome or protein) databases, Clustering, classification, and association rules, Data and knowledge visualization, Data mining, Feature extraction or construction
George Lee; Carlos Rodriguez; Anant Madabhushi
Shrinkage-based regularization tests for high-dimensional data with application to gene set analysis
Traditional multivariate tests such as Hotelling's test or Wilk's test are designed for classical problems, where the number of observations is much larger than the dimension of the variables. For high-dimensional data, however, this assumption cannot ... Keywords: Feature selection, Gene set analysis, High dimensionality, MANOVA, Power, Regularization
Yanfeng Shen; Zhengyan Lin; Jun Zhu
In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise Mycobacterium tuberculosis
Che12 is a temperate Chennai phage infecting Mycobacterium tuberculosis. The nucleotide sequence of the 52,047bp linear double stranded DNA genome has a GC content of 62.9% with 70 putative ORFs identified. Functions are assigned to 24 genes based on ... Keywords: Bioinformatics, Mycobacterium tuberculosis, Temperate mycobacteriophage
N. S. Gomathi; H. Sameer; Vanaja Kumar; S. Balaji; V.N. Azger Dustackeer; P. R. Narayanan
Classical and dominance-based rough sets in the search for genes under balancing selection
Since the time of Kimura�s theory of neutral evolution at molecular level the search for genes under natural selection is one of the crucial problems in population genetics. There exists quite a number of statistical tests designed for it, however, ... Keywords: ATM, BLM, RECQL, WRN, balancing selection, classical rough sets approach, dominance-based rough sets approach, natural selection, neutrality tests
Krzysztof A. Cyran
Ethanol production by Escherichia coli strains co-expressing Zymomonas PDC and ADH genes
A novel operon and plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase activities of Zymomonas mobilis are described. Also disclosed are methods for increasing the growth of microorganisms or eukaryotic cells and methods for reducing the accumulation of undesirable metabolic products in the growth medium of microorganisms or cells.
Ingram, Lonnie O. (Gainesville, FL); Conway, Tyrrell (Lincoln, NE); Alterthum, Flavio (Gainesville, FL)
A light-weight virtual machine monitor for Blue Gene/P
In this paper, we present a light-weight, micro--kernel-based virtual machine monitor (VMM) for the Blue Gene/P Supercomputer. Our VMM comprises a small ?-kernel with virtualization capabilities and, atop, a user-level VMM component that manages virtual ...
Jan Stoess; Jonathan Appavoo; Udo Steinberg; Amos Waterland; Volkmar Uhlig; Jens Kehne
Design and implementation of message-passing services for the Blue Gene/L supercomputer
The Blue Gene�/L (BG/L) supercomputer, with 65,536 dual-processor compute nodes, was designed from the ground up to support efficient execution of massively parallel message-passing programs. Part of this support is an optimized implementation of ...
G. Alm�si; C. Archer; J. G. Casta�os; J. A. Gunnels; C. C. Erway; P. Heidelberger; X. Martorell; J. E. Moreira; K. Pinnow; J. Ratterman; B. D. Steinmacher-Burow; W. Gropp; B. Toonen
Engineering PFLOTRAN for Scalable Performance on Cray XT and IBM BlueGene Architectures
Engineering PFLOTRAN for Scalable Performance on Cray XT and IBM BlueGene Architectures Richard University, Raleigh, NC 27695-8206 3 Department of Civil, Construction, and Environmental Engineering, North the release of a hypothetical uranium plume at the Hanford 300 Area in southeastern Washington state
Diverse RNA processing pathways important for post-transcriptional gene regulation
Cis-acting elements in 3' untranslated regions (UTRs) of mRNAs are crucial to the regulation of gene expression. Animal microRNAs (miRNAs) each target hundreds of mRNAs, which are recognized by pairing to nucleotides 2-7 ...
Jan, Calvin H
Discovering genes-diseases associations from specialized literature using the grid
This paper proposes a novel method for text mining on the Grid, aimed at pointing out hidden relationships for hypothesis generation and suitable for semi-interactive querying. The method is based on unsupervised clustering and the outputs are visualized ... Keywords: Grid, genes-diseases association, knowledge discovery, text mining, unsupervised clustering
Alberto Faro; Daniela Giordano; Francesco Maiorana; Concetto Spampinato
Using feedback to regulate gene expression in a developmental control architecture
We present what we believe is the first attempt to physically reconstruct the exploratory mechanism of genetic regulatory networks. Feedback plays a crucial role during developmental processes and its mechanisms have recently become much clearer due ... Keywords: adaptation/self-adaptation, developmental processes, evolvable hardware, gene regulatory networks, signal processing
Kester Clegg; Susan Stepney; Tim Clarke
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
the increased computational load. Since all of these transactions are stored in the VAMPIRE database, no dataVAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data of analysis, collectively known as variance-modeled posterior inference with regional exponentials (VAMPIRE
In silico analysis of putative miRNAs and their target genes in sorghum Sorghum bicolor
MicroRNAs miRNAs are small endogenous genes regulators which regulate different processes underlying plant adaptation to abiotic stresses. To gain a deep understanding of role of miRNAs in plants, in the present study, we computationally analyzed different ...
Gobind Ram; Arun Dev Sharma
Validating candidate gene-mutation relations in MEDLINE abstracts via crowdsourcing
We describe an experiment to elicit judgments on the validity of gene-mutation relations in MEDLINE abstracts via crowdsourcing. The biomedical literature contains rich information on such relations, but the correct pairings are difficult to extract ... Keywords: annotation, crowdsourcing, mutations, text mining
John D. Burger; Emily Doughty; Sam Bayer; David Tresner-Kirsch; Ben Wellner; John Aberdeen; Kyungjoon Lee; Maricel G. Kann; Lynette Hirschman
Unsupervised gene/protein named entity normalization using automatically extracted dictionaries
Gene and protein named-entity recognition (NER) and normalization is often treated as a two-step process. While the first step, NER, has received considerable attention over the last few years, normalization has received much less attention. We have ...
Aaron M. Cohen
Discovery of Mineralization Predication Classification Rules by Using Gene Expression Programming Based on PCA
Classification is one of the fundamental tasks in geology field. In this paper, we propose an evolutionary approach for discovering classification rules of mineralization predication from distinct combinations of geochemistry elements by using gene expression ... Keywords: GEP, Principal Component Analysis, mineralization predication
Dongmei Zhang; Yue Huang; Jing Zhi
Modified cellulose synthase gene from 'Arabidopsis thaliana' confers herbicide resistance to plants
Cellulose synthase ('CS'), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl) phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.
Somerville, Chris R.; Scieble, Wolf
Towards isolation of the gene for X-linked retinitis pigmentosa (RP3)
Until recently the region of interest containing the gene for X-linked retinitis pigmentosa (RP3) was thought to lie between CYBB (Xp21.1) and the proximal end of the deletion in patient BB (JBBprox). This region was thought to span 100-150 kb. Here we present new mapping data to show that the distance between the 5{prime} (most proximal) end of CYBB and JBBprox is only 50 kb. Recently Roux et al. (1994) have described the isolation of a gene within this region but this showed no disease-associated changes. Further evidence from mapping the deletion in patient NF (who suffered from McLead`s syndrome and CGD but not RP) and from linkage analysis of our RP3 families with a new dinucleotide repeat suggests that the gene must extend proximally from JBBprox. In order to extend the region of search we have constructed a YAC contig spanning 800 kb to OTC. We are continuing our search for the RP3 gene using a variety of strategies including exon trapping and cDNA enrichment as well as direct screening of cDNA libraries with subclones from this region.
Dry, K.L.; Aldred, M.A.; Hardwick, L.J. [MRC Human Genetics Unit, Scotland (United Kingdom)] [and others
Control of Stochastic Gene Expression by Host Factors at the HIV Promoter
promoter contains cis- acting Sp1 and NF-kB elements that regulate gene expression via the recruitment lentivirus variants with mutations introduced in the Sp1 and NF-kB elements, we employed flow cytometry, m and reduction in the regulation of histone acetylation and deacetylation. Furthermore, the NF-kB sites exhibit
Schaffer, David V.
Gene Regulation in M Cell Lineages: In Vitro and In Vivo
LTbR agonist (Fig 2-1C). The NF-kB gene relB (Relb) has alsoof relB is regulated by NF-kB activation, and the LT?R andreceptors all signal through NF-kB activation, this finding
Wang, Jing
Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene
Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene transcription factors are critical in controlling motor neuron fates along the rostrocaudal axis, exemplified by the precise pattern of limb innervation by more than fifty Hox-dependent motor pools. The mechanisms by which
Gifford, David K.
Sp1 and CREB regulate basal transcription of the human SNF2L gene
Imitation Switch (ISWI) is a member of the SWI2/SNF2 superfamily of ATP-dependent chromatin remodelers, which are involved in multiple nuclear functions, including transcriptional regulation, replication, and chromatin assembly. Mammalian genomes encode two ISWI orthologs, SNF2H and SNF2L. In order to clarify the molecular mechanisms governing the expression of human SNF2L gene, we functionally examined the transcriptional regulation of human SNF2L promoter. Reporter gene assays demonstrated that the minimal SNF2L promoter was located between positions -152 to -86 relative to the transcription start site. In this region we have identified a cAMP-response element (CRE) located at -99 to -92 and a Sp1-binding site at -145 to -135 that play a critical role in regulating basal activity of human SNF2L gene, which were proven by deletion and mutation of specific binding sites, EMSA, and down-regulating Sp1 and CREB via RNAi. This study provides the first insight into the mechanisms that control basal expression of human SNF2L gene.
Xia Yu; Jiang Baichun; Zou Yongxin; Gao Guimin; Shang Linshan; Chen Bingxi; Liu Qiji [Key Laboratory for Experimental Teratology of the Ministry of Education and Institute of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong 250012 (China); Gong Yaoqin [Key Laboratory for Experimental Teratology of the Ministry of Education and Institute of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong 250012 (China)], E-mail: email@example.com
SATB1 packages densely-looped, transciptionally-active chromatinfor coordinated expression of cytokine genes
SATB1 is an important regulator of nuclear architecture that anchors specialized DNA sequences onto its cage-like network and recruits chromatin remodeling/modifying factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4, and Il13 from the 200kb cytokine gene cluster region of mouse chromosome 11 during T-helper 2 (Th2)-cell activation. We show that upon cell activation, SATB1 is rapidly induced to form a unique transcriptionally-active chromatin structure that includes the cytokine gene region. Chromatin is folded into numerous small loops all anchored by SATB1, is histone H3 acetylated at lysine 9/14, and associated with Th2-specific factors, GATA3, STAT6, c-Maf, the chromatin-remodeling enzyme Brg-1, and RNA polymerase II across the 200kb region. Before activation, the chromatin displays some of these features, such as association with GATA3 and STAT6, but these were insufficient for cytokine gene expression. Using RNA interference (RNAi), we show that upon cell activation, SATB1 is not only required for chromatin folding into dense loops, but also for c-Maf induction and subsequently for Il4, Il5, and Il13 transcription. Our results show that SATB1 is an important determinant for chromatin architecture that constitutes a novel higher-order, transcriptionally-active chromatin structure upon Th2-cell activation.
GeneBox: Interactive Visualization of Microarray Data Sets Nameeta Shah
led biologists to ask complex questions, which the existing, fully automated analyses are often and Differential Ex- pression Calculation of differential expression of a gene requires one to compare fluorescence phosphate conditions (low Pi) vs. high Pi; on the blue axis we show the differential expression of DBY7286
California at Davis, University of
Mining time-shifting co-regulation patterns from gene expression data
Previous work for finding patterns only focuses on grouping objects under the same subset of dimensions. Thus, an important bio-interesting pattern, i.e. time-shifting, will be ignored during the analysis of time series gene expression data. In this ...
Ying Yin; Yuhai Zhao; Bin Zhang; Guoren Wang
Discrete Dynamical System Modeling for Gene Regulatory Networks of HMF Tolerance for
Saccharomyces cerevisiae in response to 5-hydroxymethylfurfural, a bioethanol conversion inhibitor. The modeling) In the bioethanol conversion process, this system equation describes the ideal behavior of yeast gene expression in yeast during biomass conversion to ethanol. The Verhulst equation, a single- variable DDS model
Isolation and Characterization of Flowering Genes in Ryegrass (Lolium perenne L.)
ryegrass. In L. temulentum LD conditions also induces the LtCO expression peak with light and activates GAs with a concomitant production of GA20 floral bio-active GA5. In Arabidopsis CO activates FLOWERING LOCUS T (FT), which in turn activates the transcription of the floral meristem identity genes. FT belongs to a group
Functional analysis of the microRNA genes of C. elegans
MicroRNAs (miRNAs) were discovered in C. elegans during studies of the control of developmental timing. MicroRNAs are a large class of short non-coding RNAs found in many viruses, plants and animals that regulate gene ...
Alvarez-Saavedra, Ezequiel (Ezequiel Andr�s)
Effects of soil type and farm management on soil ecological functional genes and microbial activities
Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.
Reeve, Jennifer [Washington State University; Schadt, Christopher Warren [ORNL; Carpenter-Boggs, Lynne [Washington State University; Kang, S. [University of Oklahoma; Zhou, Jizhong [University of Oklahoma, Norman; Reganold, John P. [Washington State University
Designing a highly-scalable operating system: the Blue Gene/L story
Blue Gene/L is currently the world's fastest and most scalable supercomputer. It has demonstrated essentially linear scaling all the way to 131,072 processors in several benchmarks and real applications. The operating systems for the compute and I/O ...
Jos� Moreira; Michael Brutman; Jos� Casta�os; Thomas Engelsiepen; Mark Giampapa; Tom Gooding; Roger Haskin; Todd Inglett; Derek Lieber; Pat McCarthy; Mike Mundy; Jeff Parker; Brian Wallenfelt
Astronomical real-time streaming signal processing on a Blue Gene/L supercomputer
LOFAR is the first of a new generation of radio telescopes, that combines the signals from many thousands of simple, fixed antennas, rather than from expensive dishes. Its revolutionary design and unprecedented size enables observations in a frequency ... Keywords: Blue Gene/L, LOFAR, correlator, filtering
John W. Romein; P. Chris Broekema; Ellen van Meijeren; Kjeld van der Schaaf; Walther H. Zwart
Massively parallel genomic sequence search on the Blue Gene/P architecture
This paper presents our first experiences in mapping and optimizing genomic sequence search onto the massively parallel IBM Blue Gene/P (BG/P) platform. Specifically, we performed our work on mpiBLAST, a parallel sequence-search code that has been optimized ...
Heshan Lin; Pavan Balaji; Ruth Poole; Carlos Sosa; Xiaosong Ma; Wu-chun Feng
Genetic Background Modulates Gene Expression Profile Induced by Skin Irradiation in Ptch1 Mice
Purpose: Ptch1 germ-line mutations in mice predispose to radiation-induced basal cell carcinoma of the skin, with tumor incidence modulated by the genetic background. Here, we examined the possible mechanisms underlying skin response to radiation in F1 progeny of Ptch1{sup neo67/+} mice crossed with either skin tumor-susceptible (Car-S) or -resistant (Car-R) mice and X-irradiated (3 Gy) at 2 days of age or left untreated. Methods and Materials: We conducted a gene expression profile analysis in mRNA samples extracted from the skin of irradiated or control mice, using Affymetrix whole mouse genome expression array. Confirmation of the results was done using real-time reverse-transcriptase polymerase chain reaction. Results: Analysis of the gene expression profile of normal skin of F1 mice at 4 weeks of age revealed a similar basal profile in the nonirradiated mice, but alterations in levels of 71 transcripts in irradiated Ptch1{sup neo67/+} mice of the Car-R cross and modulation of only eight genes in irradiated Ptch1{sup neo67/+} mice of the Car-S cross. Conclusions: These results indicate that neonatal irradiation causes a persistent change in the gene expression profile of the skin. The tendency of mice genetically resistant to skin tumorigenesis to show a more complex pattern of transcriptional response to radiation than do genetically susceptible mice suggests a role for this response in genetic resistance to basal cell tumorigenesis.
Galvan, Antonella; Noci, Sara [Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale Tumori, Milan (Italy); Mancuso, Mariateresa; Pazzaglia, Simonetta; Saran, Anna [ENEA Laboratories, Rome (Italy); Dragani, Tommaso A. [Department of Experimental Oncology and Laboratories, Fondazione IRCCS Istituto Nazionale Tumori, Milan (Italy)], E-mail: firstname.lastname@example.com
Dynamic and collective analysis of membrane protein interaction network based on gene regulatory network model
Membrane protein interactions are vitally important for every process in a living cell. Information about these interactions can improve our understanding of diseases and provide the basis to revolutionize therapeutic treatments. However, current experimental ... Keywords: Bio-network, Dynamic and collective control, Gene regulatory network, Membrane protein interaction network, Robustness, Scale free distributing, Small-world network
Yong-Sheng Ding; Yi-Zhen Shen; Li-Hong Ren; Li-Jun Cheng
Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse Brain
Large scale gene expression studies in the mammalian brain offer the promise of understanding the topology, networks and ultimately the function of its complex anatomy, opening previously unexplored avenues in neuroscience. High-throughput methods permit ... Keywords: Bioinformatics (genome or protein) databases, Data mining, Registration, Segmentation, Information Visualization
Lydia Ng; Sayan Pathak; Chihchau Kuan; Chris Lau; Hong-wei Dong; Andrew Sodt; Chinh Dang; Brian Avants; Paul Yushkevich; James Gee; David Haynor; Ed Lein; Allan Jones; Mike Hawrylycz
Blue Gene/L compute chip: synthesis, timing, and physical design
As one of the most highly integrated system-on-a-chip application-specific integrated circuits (ASICs) to date, the Blue Gene�/L compute chip presented unique challenges that required extensions of the standard ASIC synthesis, timing, and physical ...
A. A. Bright; R. A. Haring; M. B. Dombrowa; M. Ohmacht; D. Hoenicke; S. Singh; J. A. Marcella; R. F. Lembach; S. M. Douskey; M. R. Ellavsky; C. G. Zoellin; A. Gara
Intrinsic and extrinsic regulation of type III secretion gene expression in Pseudomonas aeruginosa
Pseudomonas aeruginosa is an opportunistic pathogen that is particularly problematic in the healthcare setting where it is a frequent cause of pneumonia, bloodstream, and urinary tract infections. An important determinant of P. aeruginosa virulence is a type III secretion system (T3SS). T3SS-dependent intoxication is a complex process that minimally requires binding of P. aeruginosa to host cells, injection of the cytotoxic effector proteins through the host cell plasma membrane, and induction of T3SS gene expression. The latter process, referred to as contact-dependent expression, involves a well-characterized regulatory cascade that activates T3SS gene expression in response to host cell contact. Although host cell contact is a primary activating signal for T3SS gene expression, the involvement of multiple membrane-bound regulatory systems indicates that additional environmental signals also play a role in controlling expression of the T3SS. These regulatory systems coordinate T3SS gene expression with many other cellular activities including motility, mucoidy, polysaccharide production, and biofilm formation. The signals to which the organism responds are poorly understood but many seem to be coupled to the metabolic state of the cell and integrated within a master circuit that assimilates informational signals from endogenous and exogenous sources. Herein we review
Manisha R. Diaz; Jessica M. King; Timothy L. Yahr; J�rgen Heesemann; Max Von; Matthew C. Wolfgang; Timothy L. Yahr; Department Of
Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations
calculated solvation energies and flexibility of codon sequences as well as codon usage in genes and amino are typically very small in prokaryotic genomes. Usage of a genome-specific plane as opposed to a common energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid
Jayaram, Bhyravabotla
Software Note: Using probe secondary structure information to enhance Affymetrix GeneChip background estimates
High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed ... Keywords: Background correction, DNA microarray, Probe secondary structure
Raad Z. Gharaibeh; Anthony A. Fodor; Cynthia J. Gibas
Polymorphisms and haplotypes in folate-metabolizing genes and risk of non-Hodgkin lymphoma
) in the promoter region of the thymidylate synthase gene (TYMS 3R 3 2R) and variant alleles in the cytosolic serine in the development of lymphoma.8,9 For example, in agreement with our previous findings in adultALL, the TYMS 3R
California at Berkeley, University of
Hepatocyte-specific deletion of the keap1 gene activates Nrf2 and confers potent resistance against acute drug toxicity
Nrf2 is a key regulator of many detoxifying enzyme genes, and cytoplasmic protein Keap1 represses the Nrf2 activity under quiescent conditions. Germ line deletion of the keap1 gene results in constitutive activation of Nrf2, but the pups unexpectedly died before weaning. To investigate how constitutive activation of Nrf2 influences the detoxification system in adult mice, we generated mice bearing a hepatocyte-specific disruption of the keap1 gene. Homozygous mice were viable and their livers displayed no apparent abnormalities, but nuclear accumulation of Nrf2 is elevated. Microarray analysis revealed that, while many detoxifying enzyme genes are highly expressed, some of the typical Nrf2-dependent genes are only marginally increased in the Keap1-deficient liver. The mutant mice were significantly more resistant to toxic doses of acetaminophen than control animals. These results demonstrate that chronic activation of Nrf2 confers animals with resistance to xenobiotics without affecting the morphological and physiological integrity of hepatocytes.
Okawa, Hiromi [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan); Motohashi, Hozumi [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan); Kobayashi, Akira [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan); Aburatani, Hiroyuki [Research Center for Advance Science and Technology, University of Tokyo, Tokyo 153-8904 (Japan); Kensler, Thomas W. [Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205 (United States); Yamamoto, Masayuki [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan) and ERATO Environmental Response Project, Japan Science and Technology Corporation, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan)]. E-mail: email@example.com
Mutations in the consensus helicase domains of the Werner syndrome gene
Werner syndrome (WS) is an autosomal recessive disease with a complex phenotype that is suggestive of accelerated aging. WS is caused by mutations in a gene, WRN, that encodes a predicted 1,432-amino-acid protein with homology to DNA and RNA helicases. Previous work identified four WS mutations in the 3{prime} end of the gene, which resulted in predicted truncated protein products of 1,060-1,247 amino acids but did not disrupt the helicase domain region (amino acids 569-859). Here, additional WS subjects were screened for mutations, and the intron-exon structure of the gene was determined. A total of 35 exons were defined, with the coding sequences beginning in the second exon. Five new WS mutations were identified: two nonsense mutations at codons 369 and 889; a mutation at a splice-junction site, resulting in a predicted truncated protein of 760 amino acids; a 1-bp deletion causing a frameshift; and a predicted truncated protein of 391 amino acids. Another deletion is >15 kb of genomic DNA, including exons 19-23; the predicted protein is 1,186 amino acids long. Four of these new mutations either partially disrupt the helicase domain region or result in predicted protein products completely missing the helicase region. These results confirm that mutations in the WRN gene are responsible for WS. Also, the location of the mutations indicates that the presence or absence of the helicase domain does not influence the WS phenotype and suggests that WS is the result of complete loss of function of the WRN gene product. 63 refs., 1 fig., 5 tabs.
Yu, Chang-En; Oshima, Junko; Wijsman, E.M. [Univ. of Washington, Seattle, WA (United States)] [and others
Isolation, sequencing, and the genomic organization of the reduced folate carrier gene in the murine system
Defective closure of the neural tube during embryogenesis results in serious and common birth defects such as spina bifida and anencephaly. Neural tube defects (NTDS) occur at an average rate in the U.S. of 1 per 1000 live-births with selected ethnic groups having higher or lower prevalence rates. Several investigators have shown a marked decrease in the occurrence and recurrence rates of NTDs with the administration of periconceptional supplemental folic acid. Intracellular folates are believed to be responsible for the reduction in NTDs due to their role in facilitating single-carbon transfers in critical biochemical pathways leading to DNA synthesis. Alterations in the folate pathway could compromise DNA synthesis and cellular proliferation, potentially disrupting normal developmental events. To this end, the genetic regulation of folate internalization is being investigated. The reduced folate carrier (RFC) delivers 5-methyltetrahydrofolate from the folate receptors to the cytoplasm of the cell. As a first step in defining the relationship between NTDs and aberrant folate internalization, we isolated and partially sequenced the RFC gene in the mouse. Screening of a murine ES cell genomic library produced eight positive clones; three were selected for subcloning. An approximately 1OKb positive clone was subcloned into pbluescript and has been divided into smaller subclones. Utilizing each subc[one independently, and deriving sequencing primers from the known CDNA sequence of the gene, followed by chromosome walking, 5.6Kb of the genomic sequence was derived. The gene contains eight exons and seven introns. The gene forms at least four splicing variants with alternate exons located 5'of exons 1 and 5, and as an extension of exon 3a. Future studies will be initiated to determine the tissue specific expression of the RFC gene in relation to the folate binding proteins. The RFC variant expression will be localized and a knock-out mouse constructed. Utilizing this model system, correlations between altered RFC function, folate supplementation, and the occurrence of NTDs may be elucidated.
Greer, Kimberly Ann
The C. elegans class A synthetic multivulva genes inhibit ectopic RAS-mediated vulval development by tightly restricting expression of lin-3 EGF
The class A and B synthetic multivulva (synMuv) genes of C. elegans redundantly antagonize an EGF/Ras pathway to prevent ectopic vulval induction. The class B synMuv genes encode many proteins known to remodel chromatin ...
Saffer, Adam M
Transposon-induced nuclear mutations that alter chloroplast gene expression. Annual report, September 1, 1991--August 31, 1992
Comparative analysis of GT14/GT14-like family genes in Arabidopsis, Oryza, Populus, Sorghum and Vitis
Glycosyltransferase family14 (GT14) belongs to the glycosyltransferase (GT) superfamily that plays important roles in the biosynthesis of cell walls, the most abundant source of cellulosic biomass for bioethanol production. It has been hypothesized that DUF266 proteins are a new class of GTs related to GT14. In this study, we identified 62 GT14 and 106 DUF266 genes (named GT14-like herein) in Arabidopsis, Oryza, Populus, Sorghum and Vitis. Our phylogenetic analysis separated GT14 and GT14-like genes into two distinct clades, which were further divided into eight and five groups, respectively. Similarities in protein domain, 3D structure and gene expression were uncovered between the two phylogenetic clades, supporting the hypothesis that GT14 and GT14-like genes belong to one family. Therefore, we proposed a new family name, GT14/GT14-like family that combines both subfamilies. Variation in gene expression and protein subcellular localization within the GT14-like subfamily were greater than those within the GT14 subfamily. One-half of the Arabidopsis and Populus GT14/GT14-like genes were found to be preferentially expressed in stem/xylem, indicating that they are likely involved in cell wall biosynthesis. This study provided new insights into the evolution and functional diversification of the GT14/GT14-like family genes.
Ye, Chuyu [ORNL; Li, Ting [ORNL; Tuskan, Gerald A [ORNL; Tschaplinski, Timothy J [ORNL; Yang, Xiaohan [ORNL
Structure and chromosomal localization of the human gene of the phosphotyrosyl phosphatase activator (PTPA) of protein phosphatase 2A
The PTPA gene encodes a specific phosphotyrosyl phosphatase activator of the dimeric form of protein phosphatase 2A. PTPA, cloned from human genomic libraries, is encoded by one single-copy gene, composed of 10 exons and 9 introns with a total length of about 60 kb. The transcription start site was determined, and the 5{prime} flanking sequence was analyzed for its potential as a promotor. This region lacks a TATA sequence in the appropriate position relative to the transcription start, is very GC-rich, and contains upstream of the transcription start four Sp1 sites, a feature common to many TATA-less promotors. Based on the homology with DNA binding consensus sequences of transcription factors, we identified in this promotor region several putative DNA binding sites for transcription factors, such as NF-{kappa}B, Myb, Ets-1, Myc, and ATF. Transfection experiments with a construct containing the PTPA promotor region inserted 5{prime} of a luciferase reporter gene revealed that the 5{prime} flanking sequence of the PTPA gene indeed displayed promotor activity that seems to be cell-line dependent. By fluorescence in situ hybridization and G-banding, the PTPA gene was localized to the 9q34 region. The PTPA gene is positioned centromeric of c-abl in a region embracing several genes implicated in oncogenesis. 28 refs., 8 figs., 1 tab.
Van Hoof, C.; Cayla, X.; Merlevede, W.; Goris, J. [Katholieke Universiteit Leuven, Parish (France)] [and others] [Katholieke Universiteit Leuven, Parish (France); and others
Mysteries of the Deep: What happens inside of MPI on Blue Gene/Q and why it matters
Mysteries Mysteries of the Deep: What happens inside of MPI on Blue Gene/Q and why it matters Jeff Hammond Leadership Computing Facility Argonne National Laboratory March 5, 2013 Jeff Hammond PAMI and MPI on BGQ The view from the boat Jeff Hammond PAMI and MPI on BGQ A reason to dive Jeff Hammond PAMI and MPI on BGQ But not too deep Jeff Hammond PAMI and MPI on BGQ Blue Gene/P Communication architecture Jeff Hammond PAMI and MPI on BGQ Blue Gene/Q Communication architecture Jeff Hammond PAMI and MPI on BGQ MPI-3 on Blue Gene/Q There is no official plan to support MPI-3 on Blue Gene/Q but a subset of these features may be available at some point in the future. I have build MPICH-3.0.x on Blue Gene/Q and many things pass while others are completely broken, but this is not a supported usage and you should not do it unless you are l33t h4xz0r. Jeff Hammond PAMI and MPI on BGQ MPI-3 on Blue Gene/Q A portable implementation
Examination of dioxin and its alteration of gene expression via DNA Microarray Analysis
Endocrine disruptive chemicals are known to produce harmful developmental effects on humans and other animals. Since substantial quantities of these chemicals are concentrated in the fat reserves of their victims, it is reasonable to expect a correlation between chemical concentration and physical effect before and to research further into the actuality of the EDCs effects. Some health hazards that are suspected to result from chemical exposure in humans are cleft lip and palate problems, feminization of male offspring, extreme premature puberty in female offspring, neural tube defects, autism, ototoxity, fetal alcohol syndrome (FAS), fetal tobacco syndrome (FTS), Type II diabetes also known as Non Insulin Dependent Diabetes Mellitus (NIDDM), and ADD/ADHD. Little evidence has been available to demonstrate how dioxin specifically alters gene expression, both in developing embryos and adults. Recently, Texas A&M University has acquired several DNA Microarray Systems, which are revolutionizing the examination of research into gene expression alterations. A new cell line of human embryonic kidney cells (293T/17 epithelial) have been properly cultured, had the RNA successfully isolated, and patterns were interpreted for genetic change using DNA Microarray Analysis. Through a cDNA slide specifically spotted with DNA of approximately 1200 endocrine regulated genes, the RNA of these cells can be examined using the DNA Microarray System after being exposed to different concentrations of dioxin, estradiol, DMSO, combinations of chemicals, and finally a control line of unexposed cells. Specific altered genes of the human embryo are predicted to be represented as changed in the RNA of cells previously exposed to dioxin. A nearly undetectable amount of dioxin (10?? M), was introduced to these cells, and produced significant variation from the natural gene expression. These data suggest that major advances in the prevention of physical pain and deformities in both developmental and everyday lives of both humans and animals could be attained by reducing exposure to environmental chemicals. The genes that are altered by the effects of TCDD promise further research, investigation, and prevention of many disruptive diseases.
Wright, Justin Charles
Expression of Candidate Genes for Horn Growth in Early Bovine Development
Bovine horns develop primarily after birth and the presence or absence of horns is due to a single gene. It has been reported that the horn bud appears in the bovine embryo at d 60 of gestation. Our hypothesis is that the gene that determines the presence of horns is expressed in osteoprogenitor cells of the early fetus and will affect the expression of RUNX2, MSX1, MSX2, and/or TWIST1. To test this hypothesis, bovine fetal samples were collected from commercial females at the Caviness Packing Company in Hereford, Texas. Fetuses ranged from d 28 to d 80 of gestation. A survey of the expression of genes from the region on bovine chromosome 1 known to contain the locus that causes horns (IFNAR1 to SOD1), was conducted using qualitative and quantitative RT-PCR, and in situ hybridization. Genes with known roles in osteogenesis and chrondrogenesis (MSX1, TWIST1, RUNX2 and SOX9) were included as positive controls. With the exception of OLIG1, which was only expressed in the brain, all of the genes investigated were expressed in fetal frontal and parietal bones by qualitative RT-PCR. The level of expression of C21orf59, C21orf66, IL10RB, and SFRS15 increased in the frontal bone of horned samples from d 55 to d 70 of gestation. At d 60 of gestation, a change in the shape of the frontal bone was observed, which has been reported to be the developmental stage when the horn bud appears. At this time point, MSX1, TWIST1, RUNX2 and SOX9 were detected in frontal bone, in cells from the osteoblast lineage, as expected. Furthermore, C21orf59, C21orf62, C21or66 and SFRS15 from the polled interval were localized to developing mesenchyme, osteoblasts and/or osteoclasts of the frontal bone, suggesting that each of these genes has a role in intramembranous bone formation. In addition, gradients of expressed C21orf66 and SFRS15 were detected in developing endochondral bone. There was evidence of an antisense transcript of C21orf66 expressed in the same cell types as the sense transcript. Further characterization of this antisense transcript demonstrated that it covered the entire sense transcript. Based on observed expression in the mesenchyme, rather than just in mature osteoblasts or osteoclasts, C21orf66 and/or its antisense transcript become the most likely candidates for the polled locus.
Vitanza, Sarah M.
Integrated high-resolution physical and comparative gene maps in horses
High-resolution physically ordered gene maps for the horse (Equus caballus, ECA) are essential to the identification of genes associated with hereditary diseases and traits of interest like fertility, coat color, and disease resistance or susceptibility. Such maps also serve as foundations for genome comparisons across species and form the basis to study chromosome evolution. In this study seven equine chromosomes (ECA6, 7, 10, 15, 18, 21 and X) corresponding to human chromosomes (HSA) 2, 19 and X were selected for high-resolution mapping on the basis of their potential involvement in diseases and conditions of importance to horses. To accomplish this, gene- and sequence-specific markers were generated and genotyped on the TAMU 5000rad horse x hamster RH panel. Additionally, screening of a BAC library by overgoes and subsequent STS content mapping and fingerprinting approaches were used to assemble and verify a BAC contig along a ~5 Mb span on ECA21. Dense gene maps were generated for each of the seven equine chromosomes by adding 408 new markers (285 type I and 123 type II) to the current maps of these chromosomes, thereby greatly improving overall map resolution to one mapped marker every 960kb on average (range: 700 kb ��? 1.3 Mb). Moreover, the contig on ECA21 contained 47 markers (42 genes and 5 microsatellites) as well as 106 STS markers distributed along 207 BAC clones. Comparisons of these maps with other species revealed a remarkably high level of horse-human X chromosome conservation, as well as two evolutionary breakpoints unique to Perissodactyls or Equids for the equine homologues of HSA19 and HSA2, one of which has been more precisely localized by the ECA21 contig. Thus, high resolution maps developed for these chromosomes i) provide a basis to map traits of interest rapidly to specific chromosomal regions, ii) facilitate searches for candidate genes for these traits by fine comparisons of the equine regions with corresponding segments in other species, and iii) enable understanding the evolution of the chromosomes. Expansion of this work to the entire equine genome will be important for developing novel strategies for diagnosis, prevention, and treatment of equine diseases.
Brinkmeyer Langford, Candice Lea
Two structurally distinct {kappa}B sequence motifs cooperatively control LPS-induced KC gene transcription in mouse macrophages
The mouse KC gene is an {alpha}-chemokine gene whose transcription is induced in mononuclear phagocytes by LPS. DNA sequences necessary for transcriptional control of KC by LPS were identified in the region flanking the transcription start site. Transient transfection analysis in macrophages using deletion mutants of a 1.5-kb sequence placed in front of the chloramphenicol acetyl transferase (CAT) gene identified an LPS-responsive region between residues -104 and +30. This region contained two {kappa}B sequence motifs. The first motif (position -70 to -59, {kappa}B1) is highly conserved in all three human GRO genes and in the mouse macrophage inflammatory protein-2 (MIP-2) gene. The second {kappa}B motif (position -89 to -78, {kappa}B2) was conserved only between the mouse and the rat KC genes. Consistent with previous reports, the highly conserved {kappa}B site ({kappa}B1) was essential for LPS inducibility. Surprisingly, the distal {kappa}B site ({kappa}B2) was also necessary for optimal response; mutation of either {kappa}B site markedly reduced sensitivity to LPS in RAW264.7 cells and to TNF-{alpha} in NIH 3T3 fibroblasts. Although both {kappa}B1 and {kappa}B2 sequences were able to bind members of the Rel homology family, including NF{kappa}B1 (P50), RelA (65), and c-Rel, the {kappa}B1 site bound these factors with higher affinity and functioned more effectively than the {kappa}B2 site in a heterologous promoter. These findings demonstrate that transcriptional control of the KC gene requires cooperation between two {kappa}B sites and is thus distinct from that of the three human GRO genes and the mouse MIP-2 gene. 71 refs., 8 figs.
Ohmori, Y.; Fukumoto, S.; Hamilton, T.A. [Cleveland Clinic Foundation, Cleveland, OH (United States)
A human gene (DDX10) encoding a putative DEAD-box RNA helicase at 11q22-q23
A human gene encoding a putative RNA helicase, designated DDX10, was identified 400 kb telomeric to the ataxia-telangiectasia gene at chromosome 11q22-q23. The predicted amino acid sequence shows very high similarity to a subgroup of DEAD-box RNA helicases involved in ribosome biogenesis. This novel gene encodes a 3.2-kb transcript in a variety of human tissues. A processed pseudogene of DDX10 was detected at chromosome 9q21-q22. We observed a rare trinucleotide repeat length polymorphism within the coding sequence of DDX10. 39 refs., 5 figs.
Savitsky, K.; Ziv, Y.; Bar-Shira, A. [Tel Aviv Univ., Ramat Aviv (Israel)] [and others
The pKZ1 transgene as a sensitive passive gene expression reporter for low
pKZ1 transgene as a sensitive passive gene expression reporter for low pKZ1 transgene as a sensitive passive gene expression reporter for low dose radiation responses Pamela J Sykes Flinders University and Medical Centre Abstract After high radiation dose exposures, changes in a number of biological endpoints in vivo can be readily observed above the normal background variation that exists in any biological system. Where these responding biological endpoints can be tied to carcinogenic risk, for example, apoptosis, proliferation or chromosomal aberrations, the net effect of the radiation exposure on cancer risk can be surmised. If the biological changes are proportional to radiation dose, then at much lower doses, the biological responses will eventually fall within the range of normal inter-individual and temporal variation, making statistical proof of any
DOE Joint Genome Institute: Genes from Tiny Algae Shed Light on Big Role
April 9, 2009 April 9, 2009 Genes from Tiny Algae Shed Light on Big Role Managing Carbon in World's Oceans & Coping with Environmental Change WALNUT CREEK, CA-Scientists from two-dozen research organizations led by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Monterey Bay Aquarium Research Institute (MBARI) have decoded genomes of two algal strains, highlighting the genes enabling them to capture carbon and maintain its delicate balance in the oceans. These findings, from a team led by Alexandra Z. Worden of MBARI and published in the April 10 edition of the journal Science, will illuminate cellular processes related to algae-derived biofuels being pursued by DOE scientists. The study sampled two geographically diverse isolates of the photosynthetic
Characterization and regulation of the bovine stearoyl-CoA desaturase gene promoter
The bovine stearoyl-CoA desaturase (Scd) gene plays an important role in the bovine mammary gland where substrates such as stearic and vaccenic acids are converted to oleic acid and conjugated linoleic acid (CLA), respectively. Up to 90% of the CLA in bovine milk is formed due to the action of this enzyme in the mammary gland. The areas of the bovine promoter of importance in regulating this key enzyme were examined and an area of 36 bp in length was identified as having a critical role in transcriptional activation and is designated the Scd transcriptional enhancer element (STE). Electrophoretic mobility shift assay detected three binding complexes on this area in Mac-T cell nuclear extracts. Treatment of cells with CLA caused a significant reduction in transcriptional activity, with this effect being mediated through the STE region. The bovine Scd gene promoter was up-regulated by insulin and down-regulated by oleic acid.
Keating, Aileen F. [Department of Animal Science, University of Vermont, Burlington, VT 05405 (United States); Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1 (Canada); Kennelly, John J. [Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1 (Canada); Zhao Fengqi [Department of Animal Science, University of Vermont, Burlington, VT 05405 (United States)]. E-mail: email@example.com
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in U.S. history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared to outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep-sea. Various other microbial functional genes relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance, and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could play a significant role in biodegradation of oil spills in deep-sea environments.
Lu, Z.; Deng, Y.; Nostrand, J.D. Van; He, Z.; Voordeckers, J.; Zhou, A.; Lee, Y.-J.; Mason, O.U.; Dubinsky, E.; Chavarria, K.; Tom, L.; Fortney, J.; Lamendella, R.; Jansson, J.K.; D?haeseleer, P.; Hazen, T.C.; Zhou, J.
Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.
We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solely for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.
Yoshii, K.; Iskra, K.; Naik, H.; Beckman, P.; Broekema, P. C. (LCF); ( MCS); (Netherlands Inst. for Radio Astronomy)
A possible mechanism for the inhibition of ribosomal RNA gene transcription during mitosis
Abstract. When cells enter mitosis, RNA synthesis ceases. Yet the RNA polymerase I (pol I) transcription machinery involved in the production of pre-rRNA remains bound to the nucleolus organizing region (NOR), the chromosome site harboring the tandemly repeated rRNA genes. Here we examine whether rDNA transcription units are transiently blocked or "frozen " during mitosis. By using fluorescent in situ hybridization we were unable to detect nascent prerRNA chains on the NORs of mouse 3T3 and rat kangaroo PtK2 cells. Appropriate controls showed that our approach was sensitive enough to visualize, at the light microscopic level, individual transcriptionally active rRNA genes both in situ after experimental unfolding of nucleoli and in chromatin spreads ("Miller
Dieter Weisenberger; Ulrich Scheer
An antisense pectin methylesterase gene alters pectin chemistry and soluble solids in tomato fruit
Pectin methylesterase (PME, EC 3.1.11) demethoxylates pectins and is believed to be involved in degradation of pectic cell wall components by polygalacturonase in ripening tomato fruit. We have introduced antisense and sense chimeric PME genes into tomato to elucidate the role of PME in fruit development and ripening. Fruits from transgenic plants expressing high levels of antisense PME RNA showed plants was associated with an increased molecular weight and methylesterification of pectins and decreased levels of total and chelator soluble polyuronides in cell walls. The fruits of transgenic plants also contained higher levels of soluble solids than wild-type fruits. This trait was maintained in subsequent generations and segregated in normal Mendelian fashion with the antisense PME gene. These results indicate that reduction in PME enzyme activity in ripening tomato fruits had a marked influence on fruit pectin metabolism and increased the soluble solids content of fruits, but did not interfere with the ripening process.
Denise M. Tieman; Robert W. Harriman; G. Ramamohan; Avtar K. H
Cloning and structure of the human corticotrophin releasing factor-binding protein gene (CRHBP)
The human CRF-binding protein gene has been cloned and mapped to the distal region of chromosome 13 and loci 5q in the mouse and human genomes, respectively. The gene consists of 7 exons and 6 introns. The mature protein has 10 cysteines and 5 tandem disulfide bridges 4 of which are contained within exons 3, 5, 6, and 7. One bridge is shared by exons 3 and 4. The signal peptide and the first 3 amino acids of the mature protein were coded for by an extreme 5[prime] exon. Primer extension analyses revealed the transcriptional initiation site to be located 32 bp downstream from a consensus TATA box. The promoter sequence contained a number of putative promoter elements including an AP-1 site, three ER-half sites, the immunoglobulin enhancer elements NF-kB and INF-1, and the liver-specific enhancers LFA1 and LFB1. 26 refs., 5 figs., 1 tab.
Behan, D.P.; Potter, E.; Lewis, K.A.; Vale, W.W. (Salk Inst., La Jolla, CA (United States)); Jenkins, N.A.; Copeland, N. (Frederick Cancer Research and Development Center, MD (United States)); Lowry, P.J. (Reading Univ. (United Kingdom))
Moral obligation and the human germ-line gene therapy debate
genetic engineering, there are few arguments made for a positive moral obligation to genetic intervention. This is especially so with respect to human germ-line gene therapy. Burke. K. Zimmerman makes one of the few arguments that society and the medical profession have a moral obligation to develop and use human germ-line gene therapy. However, Zimmerman's arguments are vague, and he misses some important points. It is the point of this thesis to criticize and buttress Zimmerman's arguments, and to show that philosophers have an important role to play, in conjunction with scientists, in the ethical debate surrounding genetic engineering. In addition to making suggestions for improvement of Zimmerman's argument, I will argue that the argument succeeds.
Clark, Alan B
Co-Regulation among genes and pathways that are responsive to low-dose ionizing
Regulation among genes and pathways that are responsive to low-dose ionizing Regulation among genes and pathways that are responsive to low-dose ionizing radiation. Matthew A. Coleman 1 , Anya Krefft 1 , Francesca Pearson 1 , Leif E. Peterson 2 , Jian Jian Li 3 , Xiaowen Xin 1 , Terrence Critchlow 1 , Ilkay Altintas 4 , Bertram Ludaescher 5 and Andrew J. Wyrobek 6 . 1 Biosciences, LLNL, Livermore, CA, 94550, 2 Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, 77030, 3 School of Health Sciences, Purdue University, West Lafayette, IN, 47907. 4 San Diego Supercomputer Center, University of California, San Diego La Jolla, CA 92093. 5 Department of Computer Science, University of California, Davis, CA 95616. 6 Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA. 94706. Contact information: firstname.lastname@example.com
Expression of the three SBE genes, encoding starch branching enzymes, in the sorghum endosperm exhibited a diurnal rhythm during a 24-h cycle. Remarkably, the oscillation in SBE expression was maintained in cultured spikes after a 48-h dark treatment, also when fed a continuous solution of sucrose or abscisic acid. Our findings suggest that the rhythmicity in SBE expression in the endosperm is independent of cues from the photosynthetic source and that the oscillator resides within the endosperm itself.
Mutisya, J.; Sun, C.; Jansson, C.
Background Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, both at the whole-genome level and at the level of individual glycoside hydrolase families. Results We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. Examination of individual glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51) revealed both similarities and distinctions between monocots and dicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. Conclusions This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a monocot model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.
Tyler, Ludmila [USDA-ARS Western Regional Research Center; Bragg, Jennifer [USDA-ARS Western Regional Research Center; Wu, Jiajie [USDA-ARS Western Regional Research Center; Yang, Xiaohan [ORNL; Tuskan, Gerald A [ORNL; Vogel, John [USDA-ARS Western Regional Research Center
Viral vectors for gene modification of plants as chem/bio sensors.
Chemical or biological sensors that are specific, sensitive, and robust allowing intelligence gathering for verification of nuclear non-proliferation treaty compliance and detouring production of weapons of mass destruction are sorely needed. Although much progress has been made in the area of biosensors, improvements in sensor lifetime, robustness, and device packaging are required before these devices become widely used. Current chemical and biological detection and identification techniques require less-than-covert sample collection followed by transport to a laboratory for analysis. In addition to being expensive and time consuming, results can often be inconclusive due to compromised sample integrity during collection and transport. We report here a demonstration of a plant based sensor technology which utilizes mature and seedling plants as chemical sensors. One can envision genetically modifying native plants at a site of interest that can report the presence of specific toxins or chemicals. In this one year project we used a developed inducible expression system to show the feasibility of plant sensors. The vector was designed as a safe, non-infectious vector which could be used to invade, replicate, and introduce foreign genes into mature host plants that then allow the plant to sense chem/bio agents. The genes introduced through the vector included a reporter gene that encodes for green fluorescent protein (GFP) and a gene that encodes for a mammalian receptor that recognizes a chemical agent. Specifically, GFP was induced by the presence of 17-{beta}-Estradiol (estrogen). Detection of fluorescence indicated the presence of the target chemical agent. Since the sensor is a plant, costly device packaging development or manufacturing of the sensor were not required. Additionally, the biological recognition and reporting elements are maintained in a living, natural environment and therefore do not suffer from lifetime disadvantages typical of most biosensing platforms. Detection of the chem/bio agent reporter (GFP) can be detected only at a specific wavelength.
Manginell, Monica; Harper, Jason C.; Arango, Dulce C.; Brozik, Susan Marie; Dolan, Patricia L.
Human gene encoding prostacyclin synthase (PTGIS): Genomic organization, chromosomal localization, and promoter activity
The prostacyclin synthase gene isolated from human genomic libraries (PTGIS) consists of 10 exons spanning approximately 60 kb. All the splice donor and acceptor sites conform to the GT/AG rule. Genomic Southern blot and fluorescence in situ hybridization analyses revealed that the human prostacyclin synthase gene is present as a single copy per haploid genome and is localized on chromosome 20q13.11-q13.13. The 1.5-kb sequence of the 5{prime} of the translational initiation site contained both GC-rich and pyrimidine-rich regions and consensus sequences of the transcription factor recognition sites such as Sp1, AP-2, the interferon-{gamma} response element, GATA, NF-{kappa}B, the CACCC box, and the glucocorticoid response element. The core binding sequence (GAGACC) of the shear stress responsive element was also found in the 5{prime}-flanking region of the gene. The major product of the primer extension analysis suggested that the transcription of the gene started from the positions around 49 bp upstream of the translational initiation codon. Transient transfection experiments using human aortic and bovine arterial endothelial cells demonstrated that the GC-rich region (positions -145 to -10) possessed a significant promoter activity. The 6-kb downstream sequence of the translational termination codon contained multiple polyadenylation signals, Alu repeat sequences, and the consensus sequence of the primate-repetitive DNA element, MER1. Two sizes of the prostacyclin synthase mRNAs (approximately 6 and 3.3 kb) were detected with the human aorta and lung. RNA blot hybridization analysis using the 3{prime}-untranslated region as probe indicated that the sizes of the 3{prime}-flanking regions were different in the major 6-kb and minor 3.3-kb mRNAs. 54 refs., 7 figs.
Yokoyama, Chieko; Yabuki, Tomoko; Inoue, Hiroyasu [National Cardiovascular Center Research Institute, Osaka (Japan)] [and others] [National Cardiovascular Center Research Institute, Osaka (Japan); and others
Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB
A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.
DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.
Exploiting network-based approaches for understanding gene regulation and function
to their target genes, controlled by their cis-regulatory elements, form a complex and directional network of interactions. In contrast, functional linkage networks constructed in function prediction pipelines typically comprise of undirected networks where all... in the network that pass through a node of interest � the higher the number of paths that pass through a node, the more important it is. Average path length Average length of the shortest paths between all pairs of nodes in the network. Closeness Closeness...
Janga, Sarath Chandra
Lateral Transfer of a Lectin-Like Antifreeze Protein Gene in Fishes
Fishes living in icy seawater are usually protected from freezing by endogenous antifreeze proteins (AFPs) that bind to ice crystals and stop them from growing. The scattered distribution of five highly diverse AFP types across phylogenetically disparate fish species is puzzling. The appearance of radically different AFPs in closely related species has been attributed to the rapid, independent evolution of these proteins in response to natural selection caused by sea level glaciations within the last 20 million years. In at least one instance the same type of simple repetitive AFP has independently originated in two distant species by convergent evolution. But, the isolated occurrence of three very similar type II AFPs in three distantly related species (herring, smelt and sea raven) cannot be explained by this mechanism. These globular, lectin-like AFPs have a unique disulfide-bonding pattern, and share up to 85 % identity in their amino acid sequences, with regions of even higher identity in their genes. A thorough search of current databases failed to find a homolog in any other species with greater than 40 % amino acid sequence identity. Consistent with this result, genomic Southern blots showed the lectin-like AFP gene was absent from all other fish species tested. The remarkable conservation of both intron and exon sequences, the lack of correlation between evolutionary distance and mutation rate, and the pattern of silent vs non-silent codon changes make it unlikely that the gene for this AFP pre-existed but was lost from most branches of the teleost radiation. We propose instead that lateral gene transfer has resulted in the occurrence of the type II AFPs in herring, smelt and sea raven and
Laurie A. Graham; Stephen C. Lougheed; K. Vanya Ewart; Peter L. Davies
Molecular cloning and characterization of genomic sequence tags (GSTs) from the PHYA, PHYB, and HY5 gene families of cotton (Gossypium species)
The goals of this research project were to identify and characterize the cotton orthologs and paralogs of the Arabidopsis phytochrome genes and the cell elongation factor HY5. Based on close evolutionary relatedness between cotton and Arabidopsis, the similar genes to PHYA, PHYB and HY5 genes from Gossypium species have been identified. GSTs for two paralogous PHYA genes (PHYA1 and PHYA2) from diploid cottons have been cloned, sequenced and characterized. At least four PHYA genes: two PHYA1 and two PHYA2 genes (A&D-genome specific) have been determined in tetraploid cottons that were acquired from diploid ancestors. Cotton PHYA genes share 60-65% nucleotide identity with Arabidopsis PHYA gene. Approximately 80% nucleotide similarity between cotton PHYA1 and PHYA2 has been observed. Both cotton PHYA genes were actively expressed. The expression of A-genome PHYA1 and D-genome PHYA2 has been observed in G. hirsutum seedlings. A CAPS marker (BbvI) has been developed for PHYA1 gene, and a QTL locus that is closely linked (LOD = 4.13) to fiber length has been identified using the PHYA1 CAPS marker. In addition, GST for cotton PHYB gene has been cloned using the similar approach. Cloned cotton PHYB gene shows remarkable conservation within cotton species and shares 85% and 78% nucleotide sequence similarity with Arabidopsis PHYB and PHYD genes, respectively. GSTs for cotton HY5 gene have been cloned and characterized. Tetraploid cottons G. hirsutum and G. barbadense have two genes for HY5: HY5-A and HY5-B, which were acquired from wild diploid ancestors through polyploidization. The D-genome contributed HY5-A gene while the A-genome contributed HY5-B gene. Approximately 50-60% structural similarity between cotton and Arabidopsis HY5 loci has been observed. HY5-A gene was expressed in cotton seedlings while the expression of HY5-B was not observed. Using polymorphic sites in HY5-B genes, CAPS marker (RsaI) has been developed for HY5-B loci. However, no significant linkage was determined in QTL-mapping of an F? fiber length cotton population using HY5-B CAPS. Gossypium derived phytochrome and HY5 genes have the potential to be useful as molecular markers in marker-assisted cotton breeding, to improve cotton fiber quality, resistance to pathogens and insects, and tolerance to environmental adversities.
Abdurakhmonov, Ibrokhim Yulchievich
Arsenic-induced alteration in the expression of genes related to type 2 diabetes mellitus
Chronic exposure to high concentrations of arsenic in drinking water is associated with an increased risk for developing type 2 diabetes. The present revision focuses on the effect of arsenic on tissues that participate directly in glucose homeostasis, integrating the most important published information about the impairment of the expression of genes related to type 2 diabetes by arsenic as one of the possible mechanisms by which it leads to the disease. Many factors are involved in the manner in which arsenic contributes to the occurrence of diabetes. The reviewed studies suggest that arsenic might increase the risk for type 2 diabetes via multiple mechanisms, affecting a cluster of regulated events, which in conjunction trigger the disease. Arsenic affects insulin sensitivity in peripheral tissue by modifying the expression of genes involved in insulin resistance and shifting away cells from differentiation to the proliferation pathway. In the liver arsenic disturbs glucose production, whereas in pancreatic beta-cells arsenic decreases insulin synthesis and secretion and reduces the expression of antioxidant enzymes. The consequences of these changes in gene expression include the reduction of insulin secretion, induction of oxidative stress in the pancreas, alteration of gluconeogenesis, abnormal proliferation and differentiation pattern of muscle and adipocytes as well as peripheral insulin resistance.
Diaz-Villasenor, Andrea [Department of Genomic Medicine and Environmental Toxicology, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Circuito Escolar, Cd. Universitaria, Coyoacan 04510 Mexico, DF (Mexico)], E-mail: email@example.com; Burns, Anna L. [Department of Genomic Medicine and Environmental Toxicology, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Circuito Escolar, Cd. Universitaria, Coyoacan 04510 Mexico, DF (Mexico); Facultad de Medicina, Universidad Nacional Autonoma de Mexico (Mexico); Hiriart, Marcia [Department of Biophysics, Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico (Mexico); Cebrian, Mariano E. [Seccion Externa de Toxicologia, CINVESTAV, IPN (Mexico); Ostrosky-Wegman, Patricia [Department of Genomic Medicine and Environmental Toxicology, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Circuito Escolar, Cd. Universitaria, Coyoacan 04510 Mexico, DF (Mexico)
RAPID COMMUNICATION P Mutations Within the Piga Gene in Patients With Paroxysmal Nocturnal
is an acquired clonal hematologic disorder with protean clinical manifestations, including erythrocyte hemolysis, venous thrombosis, infections, and defective hematopoiesis.'.' The primary biochemical defect in PNH resides in the incomplete synthesis of glycosylphosphatidylinositol (GPI) anchors used to attach certain proteins to the cell ~urface.~' ~ In PNH, there is a deficiency of all GPI-linked surface proteins on the abnormal clone of hematopoietic cells, with clinical manifestations resulting from the absence of these proteins. In all patients tested to date, the defect occurs at the level of N-acetyl-glucosamine addition to the phosphatidylinositol acceptor molecule, an early step in GP1 anchor biosynthesi^.'.^ Using the nomenclature of GPI-deficient murine cell lines, " all PNH patients have a class A complementation defect.' Miyata et all ' recently cloned the Piga cDNA, which repairs the class A defect in a human GPI-deficient cell line. Named for its ability to repair a phosphatidylinositol glycan class A defect, Piga is a candidate gene for PNH. Genetic mutations within the Piga gene could cause incomplete GP1 anchor biosynthesis and abnormal expression of all GPIlinked surface proteins. Recently, a nucleotide deletion leading to a splicing defect in the Piga gene was reported in an Epstein-Barr virus (EBV)-transformed cell line derived from a patient with PNH, and confirmed in the patient's peripheral blood neutrophils.'' Using highly purified GPI-deficient granulocytes as a source of RNA, we have performed total RNA (Northern blot) and reverse transcriptase polymerase chain reaction
Aroxysmal Nocturnal Hemoglobinuria (pnh
Structure of the gene for the catalytic subunit of human DNA polymerase {delta} (POLD1)
We have isolated genomic DNA clones covering the gene for human DNA polymerase {delta} catalytic subunit (POLD1) and its 5{prime} flanking sequence. This gene is divided into 27 exons and is distributed over at least 32 kb of DNA. The exons and most of the introns are relatively small. The sizes of the exons range from 55 to 201 bp. Seven introns are smaller than 100 bp. Intron 1 is the largest intron, with a size of greater than 10 kb. All of the intron-exon junctions match well with the reported consensus sequence and the variable number of tandem repeats were found in several introns. Transcription of POLD1 appears to initiate at multiple sites. The major start site was 53 nucleotides upstream of the ATG start codon. The sequence of the promoter and upstream DNA is G+C rich and does not contain a TATA sequence. Several potential transcription factor-binding sites, including the AP2-, CTF-, Ets1-, GCF, MBF-1, NF-E1, and Sp1-binding sites, were found in this region. A 1.8-kb pol {delta} promoter DNA directed the expression of a luciferase reporter gene when transfected into HeLa cells. 69 refs., 4 figs., 3 tabs.
Chang, Lon-Sheng; Zhao, Lingyun; Zhu, Longyun [Ohio State Univ., Columbus, OH (United States)] [and others] [Ohio State Univ., Columbus, OH (United States); and others
The unique glutathione reductase from Xanthomonas campestris: Gene expression and enzyme characterization
The glutathione reductase gene, gor, was cloned from the plant pathogen Xanthomonas campestris pv. phaseoli. Its gene expression and enzyme characteristics were found to be different from those of previously studied homologues. Northern blot hybridization, promoter-lacZ fusion, and enzyme assay experiments revealed that its expression, unlike in Escherichia coli, is OxyR-independent and constitutive upon oxidative stress conditions. The deduced amino acid sequence shows a unique NADPH binding motif where the most highly conserved arginine residue, which is critical for NADPH binding, is replaced by glutamine. Interestingly, a search of the available Gor amino acid sequences from various sources, including other Xanthomonas species, revealed that this replacement is specific to the genus Xanthomonas. Recombinant Gor enzyme was purified and characterized, and was found to have a novel ability to use both, NADPH and NADH, as electron donor. A gor knockout mutant was constructed and shown to have increased expression of the organic peroxide-inducible regulator gene, ohrR.
Loprasert, Suvit [Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210 (Thailand)]. E-mail: email@example.com; Whangsuk, Wirongrong [Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210 (Thailand); Sallabhan, Ratiboot [Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210 (Thailand); Mongkolsuk, Skorn [Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210 (Thailand); Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand)
Taxa-area Relationship (TAR) of Microbial Functional Genes with Long-TGerm Fertilization
Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that the turnover in space of microorganisms may be higher with long-term fertilization.
Liang, Yuting; Wu, Liyou; Clark, Ian; Xue, Kai; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Hirsch, Penny; Mcgrath, Steve; Zhou, Jizhong
Analysis of the function of the agouti gene in obesity and diabetes
This chapter discusses the agouti gene and dominant mutations in that gene that lead to agouti-induced obesity, and recent work with transgenic mice to elucidate the role of agouti in obesity. Agouti was cloned in 1992 by the lab of Rick Woychik at Oak Ridge National Laboratory, making it the first of many recently cloned mouse obesity genes. Sequence analysis predicted that mouse agouti is a secreted protein of 131 amino acids. The mature protein has a basic central region (lys57-arg85), a proline-rich domain (pro86-pro91) and a C-terminal region (cys 92-cys 13 1) containing 10 cysteine residues which form 5 disulfide bonds. The human homologue of agouti has also been cloned by the Woychik lab and maps to human chromosome 20q 11.2. Human agouti is 132 amino acids long and is 85% similar to the mouse agouti protein and is normally expressed in adipose tissue. The researchers have been able to recapitulate obesity, hyperinsulinemia, and hyperglycemia with the ubiquitous expression of agouti. Agouti expression in either liver and adipose tissue alone does not cause obesity, and there`s a dose-dependent effect of agouti on body weight, food efficiency, body temperature, and insulin and glucose levels.
Mynatt, R.L.; Miltenberger, R.J.; Klebig, M.L. [and others
Regulation and Systems Biology 2012:6 93-107 Regulation and Systems Biology 2012:6 93-107 doi: 10.4137/GRSB.S9357 This article is available from http://www.la-press.com. © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. OPEN ACCESS Full open access to this and thousands of other papers at http://www.la-press.com. Gene Regulation and Systems Biology O R I G I N A L R E S E A R C H Gene Regulation and Systems Biology 2012:6 93 Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA Michael R. Leuze 1, *, Tatiana V. Karpinets 2,3, *, Mustafa H. Syed 2 , Alexander S. Beliaev 4 and Edward C. Uberbacher 2 1 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Localization of CHl1-related helicase genes to human chromosome regions 12p11 and 12p13: Similarity between parts of these genes and conserved human telomeric-associated DNA
The helicase enzymes are essential components of a number of multi-protein complexes, including those that regulate transcription, splicing, translation, and DNA repair. These enzymes assist in the unwinding of double-stranded DNA and RNA as an essential part of their function. The yeast Chl1 gene encodes a putative helicase that appears to be essential for normal chromosome transmission. Human cDNAs related to this yeast gene, hCHLR1 and hCHLR2, were recently isolated and shown to encode products that localize to the nucleus. Two corresponding genes have now been partially characterized and localized to human chromosome regions 12p11 and 12p13, indicating that this gene is contained with a duplicated region localized to 12p. In addition, a comparison of the hCHLR gene sequences with available databases indicates that a large portion of these genes, including exons encoding two functional domains of the carboxyl-terminal region of these proteins, has been duplicated as part of a larger human teleomeric repeat sequence found on many human chromosomes. Our results suggest that duplication of a relatively large region of chromosome 12p containing this putative helicase gene has resulted in the creation of numerous pseudogenes as part of a subtelomeric repeat. The presence of these helicase pseudogenes, as well as pseudogenes for other genes such as the interleukin-9 receptor, within many subtelomeric regions support the possibility that the spread of this region is subject to exchange between different chromosomes and may have implications for elucidation of the mechanism of intra- and interchromosomal duplication events. 21 refs., 4 figs.
Amann, J.; Kidd, V.J.; Lahti, J.M.; Valentine, M. [St. Jude Children`s Research Hospital, Memphis, TN (United States)
Dopaminergic gene polymorphisms affect long-term forgetting in old age: Further support for the magnification hypothesis
Emerging evidence from animal studies suggests that suboptimal dopamine DA modulation may be associated with increased forgetting of episodic information. Extending these observations, we investigated the influence of DA-relevant genes on forgetting ...
Goran Papenberg; Lars B�ckman; Irene E. Nagel; Wilfried Nietfeld; Julia Schr�der; Lars Bertram; Hauke R. Heekeren; Ulman Lindenberger; Shu-Chen Li
An ABC transporter gene from Fusarium verticillioides, FvABC1, may confer tolerance to corn antimicrobial compounds.
??An ABC transporter gene, FvABC1, was cloned and sequenced from the corn pathogen Fusarium verticillioides in order to study non-degradative tolerance to corn antimicrobial compounds.� (more)
Palencia, Edwin Rene
The Consensus Coding Sequence (Ccds) Project: Identifying a Common Protein-Coding Gene Set for the Human and Mouse Genomes
Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but ...
Kellis, Manolis
Analysis of the murine Dtk gene identifies conservation of genomic structure within a new receptor tyrosine kinase subfamily
The receptor tyrosine kinase Dtk/Tyro 3/Sky/rse/brt/tif is a member of a new subfamily of receptors that also includes Axl/Ufo/Ark and Eyk/Mer. These receptors are characterized by the presence of two immunoglobulin-like loops and two fibronectin type III repeats in their extracellular domains. The structure of the murine Dtk gene has been determined. The gene consists of 21 exons that are distributed over 21 kb of genomic DNA. An isoform of Dtk is generated by differential splicing of exons from the 5{prime} region of the gene. The overall genomic structure of Dtk is virtually identical to that determined for the human UFO gene. This particular genomic organization is likely to have been duplicated and closely maintained throughout evolution. 38 refs., 3 figs., 1 tab.
Lewis, P.M.; Crosier, K.E.; Crosier, P.S. [Univ. of Auckland (New Zealand)] [and others] [Univ. of Auckland (New Zealand); and others
An Observational Study of Environmental Influences on the Intensity Changes of Typhoons Flo (1990) and Gene (1990)
The European Centre for Medium-Range Weather Forecasts Tropical Ocean�Global Atmosphere advanced analysis was used to study the mechanisms that affect the intensity of Typhoons Flo (1990) and Gene (1990). The outflow structure, eddy momentum flux ...
Chun-Chieh Wu; Hsiu-Ju Cheng
Gene amplification in Drosophila ovarian follicle cells as a developmental strategy and model for metazoan DNA replication
The process of gene amplification in Drosophila ovaries provides a means of increasing the amount of template for transcription, thus increasing the amount of protein that can be made over a short developmental period. At ...
Claycomb, Julie Michelle, 1977-
Search for major genes with progeny test data to accelerate the development of genetically superior loblolly pine. Technical progress report
This report details the progress of the three tasks of this project. The tasks are: (1) develop genetic models and analytical methods; (2) molecular confirmation of major gene segregation; and (3) develop strategies for marker-assisted breeding.
Designing Soybeans for the 21st Century MarketsChapter 6 Identification of Genes that Mediate Protection against Soybean Pathogens
Designing Soybeans for the 21st Century Markets Chapter 6 Identification of Genes that Mediate Protection against Soybean Pathogens Food Science Nutrition Biochemistry Processing Biofuels - Bioproducts eChapters Food Science & Technolo
Design, manufacture, and application of DNA microarrays to study gene expression phenotypes of lysine-producing Corynebacterium glutamicum
Corynebacterium glutamicum partial genome DNA microarrays were constructed that were capable of assaying the transcriptional profile of the genes of pathways involved in central carbon metabolism and lysine biosynthesis. ...
Roberge, Christopher (Christopher M.)
A Novel Mechanism for Regulation of Low Density Lipoprotein Receptor Gene Expression via a Stabilization of mRNA
From: Dietary Fats and Risk of Chronic Disease A Novel Mechanism for Regulation of Low Density Lipoprotein Receptor Gene Expression via a Stabilization of mRNA Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry PRESS
Genomic structure and chromosomal mapping of the human CD22 gene
The human CD22 gene is expressed specifically in B lymphocytes and likely has an important function in cell-cell interactions. A nearly full length human CD22 cDNA clone was used to isolate genomic clones that span the CD22 gene. The CD22 gene is spread over 22 kb of DNA and is composed of 15 exons. The first exon contains the major transcriptional start sites. The translation initiation codon is located in exon 3, which also encodes a portion of the signal peptide. Exons 4 to 10 encode the seven Ig domains of CD22, exon 11 encodes the transmembrane domain, exons 12 to 15 encode the intracytoplasmic domain of CD22, and exon 15 also contains the 3' untranslated region. A minor form of CD22 mRNA likely results from splicing of exon 5 to exon 8, skipping exons 6 and 7. A 4.6-kb Xbal fragment of the CD22 gene was used to map the chromosomal location of CD22 by fluorescence in situ hybridization. The hybridization locus was identified by combining fluorescent images of the probe with the chromosomal banding pattern generated by an Alu probe. The results demonstrate the CD22 is located within the band region q13.1 of chromosome 19. Two closely clustered major transcription start sites and several minor start sites were mapped by primer extension. Similarly to many other lymphoid-specific genes, the CD22 promoter lacks an obvious TATA box. Approximately 4 kb of DNA 5' of the transcription start sites were sequenced and found to contain multiple Alu elements. Potential binding sites for the transcriptional factors NF-kB, AP-1, and Oct-2 are located within 300 bp 5' of the major transcription start sites. A 400-bp fragment (bp -339 through +71) of the CD22 promoter region was subcloned into a pGEM-chloramphenicol acetyltransferase vector and after transfection into B and T cells was found to be active in both B and T cells. 45 refs., 7 figs., 2 tabs.
Wilson, G.L.; Kozlow, E.; Kehrl, J.H. (National Institutes of Health, Bethesda, MD (United States)); Najfeld, V. (Mount Sinai Medical Center, New York, NY (United States)); Menniger, J.; Ward, D. (Yale School of Medicine, New Haven, CT (United States))
Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata: Progress report, June 5, 1987-June 4, 1988
We have cloned a number of fragments of DNA containing genes necessary for nitrogen fixation from the photosynthetic bacterium Rhodobacter capsulatus. The nif genes are locally clustered but the clusters are on non-neighboring DNA restriction fragments. We sought to determine the physical linkage of these fragments, to determine their relationship with the corresponding nif genes of Klebsiella, and to determine the nucleotide sequence of some of the fragments. So far we have identified six or seven regulatory genes among these, using a nifH::lac fusion. Four of the regulatory genes are required for expression of nifH. Two of these, nifR1 and nifR2, have sequences homologous to ntrC and ntrB of enteric bacteria. A third, nifR4, has sequence homology, in the C-terminal region, to the ntrA genes of Rhizobium and Klebsiella. Constitutive expression of nifR4 in R. capsulatus, from a plasmid clone, complemented a nifR4 chromosomal mutant but not a nifR1 mutant. Moreover, both oxygen and ammonia regulation of nitrogenase were maintained under these conditions. These results are consistent with a model requiring both nifR1 and nifR4 for nitrogenase gene expression; they rule out our earlier suggestion that nifR1 is needed only to turn on nifR4. Current efforts are focused on the purification of RNA polymerase and the products of nifR1, nifR2, and nifR4 to study nif gene transcription in vitro, particularly with the goal of determining the role of DNA supercoiling in transcription.
Enhanced Hydrogen Production in Escherichia coli Through Chemical Mutagenesis, Gene Deletion, and Transposon Mutagenesis
We demonstrate that hydrogen production can be increased by random mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and that hydrogen production can be further increased in the chemically-mutagenized strain by targeted gene deletion and overexpression of genes related to formate metabolism. Chemical mutagenesis of Escherichia coli BW25113 hyaB hybC hycE::kan/pBS(Kan)-HycE to form strain 3/86 resulted in 109 +/- 0.5- fold more hydrogen; 3/86 lacks functional hydrogen uptake hydrogenases 1 and 2, has hydrogenproducing hydrogenase 3 inactivated from the chromosome, and has constitutively active hydrogenase 3 based on expression of the large subunit of hydrogenase 3 from a high copy number plasmid. Deleting fdoG, which encodes formate dehydrogenase O, (that diverts formate from hydrogen), from chemical mutagen 3/86 increased hydrogen production 188 +/- 0.50-fold (relative to the unmutagenized strain), and deletion of hycA, which encodes the repressor of formate hydrogen lyase (FHL), increased hydrogen production 232 +/- 0.50-fold. Deleting both fdoG and hycA increased hydrogen production 257 +/- 0.50-fold, and overexpressing fhlA along with the fdoG hycA mutations increased hydrogen 308 +/- 0.52-fold. Whole-transcriptome analysis of chemical mutagen 3/86 revealed 89 genes were induced and 31 genes were repressed. In an effort to identify chromosomal mutations in chemical mutagen 3/86, we performed comparative genome sequencing and identified two chromosomal loci with mutations in coding regions of ftnA and yebJ; however, neither gene was related to the increased hydrogen production as determined by the close vial (short) hydrogen assay. In addition, transposon mutagenesis, which is one of the most efficient strategies for creating random mutations in the genomic DNA, was performed in two different strains: E. coli BW25113 hyaB hybC hycA fdoG::kan/pCA24N-FhlA and E. coli MG1655 to identify beneficial mutations for hydrogen production. As a result of screening 461 E. coli BW25113 hyaB hybC hycA fdoG::kan/pCA24N-FhlA transformants and 1000 E. coli MG1655 transformants, three interesting mutations have been discovered in E. coli BW25113 hyaB hybC hycA fdoG::kan/pCA24N-FhlA transformants (gpsA, dipZ, glgP) and 1 beneficial mutation in E. coli MG1655 transformants (malT). When any of these genes gpsA, dipZ, or glgP is disrupted by Tn5 insertion, hydrogen production decreases 17, 3 and 8-fold, respectively. Additionally, when malT gene is disrupted by Tn5 insertion, hydrogen increases 3.4-fold.
Garzon Sanabria, Andrea Juliana
Real-Time Gene Expression Profiling of Live Shewanella Oneidensis Cells
The overall objective of this proposal is to make real-time observations of gene expression in live Shewanella oneidensis cells with high sensitivity and high throughput. Gene expression, a central process to all life, is stochastic because most genes often exist in one or two copies per cell. Although the central dogma of molecular biology has been proven beyond doubt, due to insufficient sensitivity, stochastic protein production has not been visualized in real time in an individual cell at the single-molecule level. We report the first direct observation of single protein molecules as they are generated, one at a time in a single live E. coli cell, yielding quantitative information about gene expression [Science 2006; 311: 1600-1603]. We demonstrated a general strategy for live-cell single-molecule measurements: detection by localization. It is difficult to detect single fluorescence protein molecules inside cytoplasm - their fluorescence is spread by fast diffusion to the entire cell and overwhelmed by the strong autofluorescence. We achieved single-molecule sensitivity by immobilizing the fluorescence protein on the cell membrane, where the diffusion is much slowed. We learned that under the repressed condition protein molecules are produced in bursts, with each burst originating from a stochastically-transcribed single messenger RNA molecule, and that protein copy numbers in the bursts follow a geometric distribution. We also simultaneously published a paper reporting a different method using ?-glactosidase as a reporter [Nature 440, 358 (2006)]. Many important proteins are expressed at low levels, inaccessible by previous proteomic techniques. Both papers allowed quantification of protein expression with unprecedented sensitivity and received overwhelming acclaim from the scientific community. The Nature paper has been identified as one of the most-cited papers in the past year [http://esi-topics.com/]. We have also an analytical framework describing the steady-state distribution of protein concentration in live cells, considering that protein production occurs in random bursts with an exponentially distributed number of molecules. This model allows for the extraction of kinetic parameters of gene expression from steady-state distributions of protein concentration in a cell population, which are available from single cell data obtained by fluorescence microscopy. [Phys. Rev. Lett. 97, 168302 (2006)]. A major objective in the Genome to Life (GtL) program is to monitor and understand the gene expression profile of a complete bacterial genome. We developed genetic and imaging methods for sensitive protein expression profiling in individual S. oneidensis cell. We have made good progress in constructing YFP-library with several hundred chromosomal fusion proteins and studied protein expression profiling in living Shewanella oneidensis cells. Fluorescence microscopy revealed the average abundance of specific proteins, as well as their noise in gene expression level across a population. We also explored ways to adapt our fluorescence measurement for other growth conditions, such as anaerobic growth.
Xiaoliang Sunney Xie
Regulation of E2F-1 gene expression in human breast cancer cells
17?-Estradiol induces E2F-1 gene expression in ZR-75 and MCF-7 human breast cancer cells. Analysis of the E2F-1 gene promoter in MCF-7 cells previously showed that hormone-induced transactivation required interactions between estrogen receptor ? (ER?)/Sp1 bound to upstream GC-rich sites and NFYA bound to downstream CCAAT sites within the -169 to -54 promoter region. This promoter region was also E2-responsive in ER?-positive ZR-75 cells; however, further analysis of the promoter showed that cooperative ER?/Sp1/NFY interactions were not necessary for hormone-induced transactivation in ZR-75 cells. The upstream GC-rich motifs are activated independently by ER?/Sp1 in ZR-75 but not MCF-7 cells, and the downstream CCAAT sites were also E2-responsive. E2 also induced reporter gene activity in ZR-75 cells transfected with an expression plasmid containing the yeast GAL4 DNA binding domain fused to pM-NFYA and a construct containing five tandem GAL4 response elements. Subsequent studies showed that hormonal activation of pE2F-1jm1 and pM-NFYA are dependent on non-genomic pathways in which E2 activates cAMP/protein kinase A. Hormone-dependent regulation of E2F-1 gene expression in ZR-75 and MCF-7 involves different mechanisms, demonstrating the importance of cell context on transactivation pathways, even among ER-positive breast cancer cell lines. TCDD inhibited ER?-mediated responses in MCF-7 and ZR-75 cells. E2- induced E2F-1protein and mRNA levels in MCF-7 and ZR-75 cells and this response was inhibited by TCDD. Constructs containing GC-rich sites alone or in combination with the downstream NFY sites were used in transactivation studies to investigate the mechanism of inhibitory AhR-ER? crosstalk. Although TCDD inhibited E2-induced mRNA, protein and reporter gene actitivity, it was not possible to determine if the inhibitory response was due to limiting ER? protein levels due to proteasome degradation since proteaome inhibitors alone blocke hormone-dependent responses. TCDD also inhibited the cAMP/PKA pathway by inhibiting adenyl cyclase activity. In Drosophila SL-2 cells cotransfected with the GC-rich -169 to -54 region, ER? and Sp1 plasmids E2 induced transactivation in cells cotransfected with AhR/Arnt expression plasmids suggesting that the AhR complex suppressed ER?/Sp1 action. These results demonstrate that TCDD inhibits E2-dependent activation of both non-genomic and genomic pathways of ER-mediated E2F-1 gene expression. 17?-Estradiol induces E2F-1 gene expression in ZR-75 and MCF-7 human breast cancer cells. Analysis of the E2F-1 gene promoter in MCF-7 cells previously showed that hormone-induced transactivation required interactions between estrogen receptor ? (ER?)/Sp1 bound to upstream GC-rich sites and NFYA bound to downstream CCAAT sites within the -169 to -54 promoter region. This promoter region was also E2-responsive in ER?-positive ZR-75 cells; however, further analysis of the promoter showed that cooperative ER?/Sp1/NFY interactions were not necessary for hormone-induced transactivation in ZR-75 cells. The upstream GC-rich motifs are activated independently by ER?/Sp1 in ZR-75 but not MCF-7 cells, and the downstream CCAAT sites were also E2-responsive. E2 also induced reporter gene activity in ZR-75 cells transfected with an expression plasmid containing the yeast GAL4 DNA binding domain fused to pM-NFYA and a construct containing five tandem GAL4 response elements. Subsequent studies showed that hormonal activation of pE2F-1jm1 and pM-NFYA are dependent on non-genomic pathways in which E2 activates cAMP/protein kinase A. Hormone-dependent regulation of E2F-1 gene expression in ZR-75 and MCF-7 involves different mechanisms, demonstrating the importance of cell context on transactivation pathways, even among ER-positive breast cancer cell
Ngwenya, Sharon Khethiwe
Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus
Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.
Induri, Brahma R [West Virginia University; Ellis, Danielle R [West Virginia University; Slavov, Gancho [West Virginia University; Yin, Tongming [ORNL; Muchero, Wellington [ORNL; Tuskan, Gerald A [ORNL; DiFazio, Stephen P [West Virginia University
Nidogen-1 regulates laminin-1-dependent mammary-specific gene expression
Nidogen-1 (entactin) acts as a bridge between the extracellular matrix molecules laminin-1 and type IV collagen, and thus participates in the assembly of basement membranes. To investigate the role of nidogen-1 in regulating cell-type-specific gene expression in mammary epithelium, we designed a culture microecosystem in which each component, including epithelial cells, mesenchymal cells, lactogenic hormones and extracellular matrix, could be controlled. We found that primary and established mesenchymal and myoepithelial cells synthesized and secreted nidogen-1, whereas expression was absent in primary and established epithelial cells. In an epithelial cell line containing mesenchymal cells, nidogen-1 was produced by the mesenchymal cells but deposited between the epithelial cells. In this mixed culture, mammary epithelial cells express b-casein in the presence of lactogenic hormones. Addition of either laminin-1 plus nidogen-1, or laminin-1 alone to mammary epithelial cells induced b- casein production. We asked whether recombinant nidogen-1 alone could signal directly for b-casein. Nidogen-1 did not induce b-casein synthesis in epithelial cells, but it augmented the inductive capacity of laminin-1. These data suggest that nidogen-1 can cooperate with laminin-1 to regulate b-casein expression. Addition of full length nidogen-1 to the mixed cultures had no effect on b-casein gene expression; however, a nidogen-1 fragment containing the laminin-1 binding domain, but lacking the type IV collagen-binding domain, had a dominant negative effect on b-casein expression. These data point to a physiological role for nidogen-1 in the basement membrane-induced gene expression by epithelial cells.
Pujuguet, Philippe; Simian, Marina; Liaw, Jane; Timpl, Rupert; Werb, Zena; Bissell, Mina J..
One pyrimidine dimer inactivates expression of a transfected gene in xeroderma pigmentosum cells
The authors have developed a host cell reactivation assay of DNA repair utilizing UV-treated plasmid vectors. The assay primarily reflects cellular repair of transcriptional activity of damaged DNA measured indirectly as enzyme activity of the transfected genes. They studied three plasmids (pSV2cat, 5020 base pairs; pSV2catSVgpt, 7268 base pairs; and pRSVcat, 5027 base pairs) with different sizes and promoters carrying the bacterial cat gene (CAT, chloramphenicol acetyltransferase) in a construction that permits cat expression in human cells. All human simian virus 40-transformed cells studied expressed high levels of the transfected cat gene. UV treatment of the plasmids prior to transfection resulted in differential decrease in CAT activity in different cell lines. With pSV2catSVgpt, UV inactivation of CAT expression was greater in the xeroderma pigmentosum group A and D lines than in the other human cell lines tested. The D0 of the CAT inactivation curve was 50 J X m-2 for pSV2cat and for pRSVcat in the xeroderma pigmentosum group A cells. The similarity of the D0 data in the xeroderma pigmentosum group A cells for three plasmids of different size and promoters implies they all have similar UV-inactivation target size. UV-induced pyrimidine dimer formation in the plasmids was quantified by assay of the number of UV-induced T4 endonuclease V-sensitive sites. In the most sensitive xeroderma pigmentosum cells, with all three plasmids, one UV-induced pyrimidine dimer inactivates a target of about 2 kilobases, close to the size of the putative CAT mRNA.
Protic-Sabljic, M.; Kraemer, K.H.
Binding motifs in bacterial gene promoters modulate transcriptional effect of global regulators
Bacterial gene regulation involves transcription factors (TFs) that influence the expression of many genes. Global regulators, including CRP (cAMP Receptor Protein), ArcA, and FNR, can modulate the transcriptional activity of multiple operons. The similarity of a regulatory element s sequence to a TF s consensus binding site (BS) and the position of the regulatory element in an operon promoter are considered the most important determinants of this TF s regulatory influence. In this study we explore the hypothesis that the number of TFBS half-sites (where a half-site is one half of the palindromic BS consensus sequence, which we shall refer to as a binding motif or a BM) of a global regulator in an operon s promoter plays an important role in the operon s transcriptional regulation. We examine empirical data from transcriptional profiling of the CRP regulon in Shewanella oneidenses MR 1 and Escherichia coli, and of the ArcA regulon in S. oneidenses MR 1. We compare the power of CRP BM counts and of full, symmetrical CRP TFBS characteristics, namely similarity to consensus and location, to predict CRP-induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full-length TFBS quality or location. Regression analysis indicates that IHF (Integration Host Factor) and ArcA have synergistic effects on CRP-induced gene transcription, positive and negative, respectively. Based on these results, we propose that the fine-tuning of bacterial transcriptional activity by CRP may involves not only the bending of the operon promoter, facilitated by CRP in cooperation with the histone-like protein IHF, but also the cumulative binding affinity of multiple weak BMs.
Leuze, Michael Rex [ORNL; Karpinets, Tatiana V [ORNL; Syed, Mustafa H [ORNL; Beliaev, Alexander S [ORNL; Uberbacher, Edward C [ORNL
Dissection of the erythroid-specific transcriptional promoter used by the gene encoding aminolevulinic acid dehydratase (ALAD)
The gene encoding delta-aminolevulinate dehydratase (ALAD), the second enzyme of the heme biosynthetic pathway, exists as a single gene in most mammalian genomes and we have sequenced over 12 kb from overlapping lambda clones containing the murine ALAD gene. The gene has a dual promoter driving expression of two different first exons; exon1A is expressed in all tissues and exon1B only in erythroid cells, where heme production is induced to exceptionally high levels for hemoglobin synthesis. Erythroid-specific expression of the ALAD gene is presumably accomplished by using the exon1B promoter which we hypothesize is responsive to erythroid-specific transcriptional activators. In order to test this, we have used gel mobility shift assays and DNase footprint analyses to dissect and identify the critical upstream regulatory elements. Nuclear extracts, prepared from murine erythroleukemia cells (MELC), human chronic myelogenous leukemia cell line (K562) and human fibroblast cell line (HeLa), were used as sources of proteins to analyze DNA binding sites in the ALAD erythroid-specific promoter from -307 to +1. In this region, there are three potential GATA1 sites, two CACCC boxes, a CCAAT box and a GGTGG box. NF-E2 sites were explored by using in vitro translation products of cloned p18 and p45, the two heterologous components of NF-E2, and successfully gel-shifted a 29 bp double-stranded oligo found at 2.6 kb in front of the ALAD gene. Thus, the ALAD gene utilizes both a housekeeping and a tissue-specific promoter.
Bishop, T.R.; Schaffer, T.; Pien, B. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)
Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida
The nucleotide sequence of the genes from Pseudomonas putida encoding oxidation of benzene to catechol was determined. Five open reading frames were found in the sequence. Four corresponding protein molecules were detected by a DNA-directed in vitro translation system. Escherichia coli cells containing the fragment with the four open reading frames transformed benzene to cis-benzene glycol, which is an intermediate of the oxidation of benzene to catechol. The relation between the product of each cistron and the components of the benzene oxidation enzyme system is discussed.
Irie, S.; Doi, S.; Yorifuji, T.; Takagi, M.; Yano, K.
Gene Expression in the Third Dimension: The ECM-nucleus Connection
Decades ago, we and others proposed that the dynamic interplay between a cell and its surrounding environment dictates cell phenotype and tissue structure. Whereas much has been discovered about the effects of extracellular matrix molecules on cell growth and tissue specific gene expression, the nuclear mechanisms through which these molecules promote these physiological events remain unknown. Using mammary epithelial cells as a model, the purpose of this review is to discuss how the extracellular matrix influences nuclear structure and function in a three-dimensional context to promote epithelial morphogenesis and function in the mammary gland.
Spencer, Virginia A; Xu, Ren; Bissell, Mina
Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC
, Bronte Park, Buckland and Fentonbury); 12 from West Pencil Pine, an area on the disease front; and 35 from the DFTD- free northwestern coast region. The deletion is most prevalent in the northwest (found in 54.8% of tested individuals), followed by West... genetically disparate populations in the north- west and that the incidence of disease in these popula- tions is much lower than in similar populations in the east [33]. This gene deletion may be advantageous for the following reasons. First, the loss of Saha...
Cheng, Yuanyuan; Stuart, Andrew; Morris, Katrina; Taylor, Robyn; Siddle, Hannah; Deakin, Janine; Jones, Menna; Amemiya, Chris T; Belov, Katherine
Mesoporous Silica Nanomaterials for Applications in Catalysis, Sensing, Drug Delivery and Gene Transfection
The central theme of this dissertation is represented by the versatility of mesoporous silica nanomaterials in various applications such as catalysis and bio-applications, with main focus on biological applications of Mesoporous Silica Nanospheres (MSN). The metamorphosis that we impose to these materials from catalysis to sensing and to drug and gene delivery is detailed in this dissertation. First, we developed a synthetic method that can fine tune the amount of chemically accessible organic functional groups on the pores surface of MSN by exploiting electrostatic and size matching between the cationic alkylammonium head group of the cetyltrimethylammonium bromide (CTAB) surfactant and various anionic organoalkoxysilane precursors at the micelle-water interface in a base-catalyzed condensation reaction of silicate. Aiming nature imitation, we demonstrated the catalytic abilities of the MSNs, We utilized an ethylenediamine functional group for chelating Cu{sup 2+} as a catalytic functional group anchored inside the mesopores. Thus, a polyalkynylene-based conducting polymer (molecular wire) was synthesized within the Cu-functionalized MSNs silica catalyst. For sensing applications, we have synthesized a poly(lactic acid) coated mesoporous silica nanosphere (PLA-MSN) material that serves as a fluorescence sensor system for detection of amino-containing neurotransmitters in neutral aqueous buffer. We exploited the mesoporosity of MSNs for encapsulating pharmaceutical drugs. We examined bio-friendly capping molecules such as polyamidoamine dendrimers of generations G2 to G4, to prevent the drug leaching. Next, the drug delivery system employed MSNs loaded with Doxorubicin, an anticancer drug. The results demonstrated that these nano-Trojan horses have ability to deliver Doxorubicin to cancer cells and induce their death. Finally, to demonstrate the potential of MSN as an universal cellular transmembrane nanovehicle, we anchored positively charged dendrimers on the surface of MSN and utilize them to complex cationic DNA. The p-EGFP-CI gene-coated MSN nanocomposite was able to transfect cancer cell lines, such as human HeLa and CHO cancer cell lines. The gene carrier ability of MSNs was further proved by transfecting primary cells and cotransfecting of two different genes in cancer cell lines. In sum, MSN are versatile partners in several types of applications.
Daniela Rodica Radu
Gene silencing in cancer cells using siRNA : genetic and functional studies
Sequence-specific small interfering RNA (siRNA) duplexes can be used for gene silencing in mammalian cells and as mechanistic probes for determining gene function. Transfection of siRNA for specificity protein 1 (Sp1) in MCF-7 or ZR-75 cells decreased Sp1 protein in nuclear extracts, and immunohistochemical analysis showed that Sp1 protein in transfected MCF-7 cells was barely detectable. Decreased Sp1 protein in MCF-7 was accompanied by a decrease in basal and estrogen-induced transactivation and cell cycle progression. These results clearly demonstrate the key role of Sp1 protein in regulating growth and gene expression of breast cancer cells. The aryl hydrocarbon (AhR) is a ligand-activated nuclear transcription factor. siRNA for the AhR decreased TCDD-induced CYP1A1 protein, CYP1A1dependent activity, and luciferase activity in cells transfected with an Ah-responsive construct. 17?-Estradiol (E2) induces proliferation of MCF-7 cells, and this response is inhibited in cells cotreated with E2 plus TCDD. The effects of TCDD on E2-induced cell cycle progression were partially blocked in MCF-7 cells transfected with siRNA for AhR. The decrease in AhR protein in MCF-7 cells was also accompanied by increased G0/G1 ? S phase progression. Surprisingly, TCDD alone induced G0/G1 ? S phase progression and exhibited estrogenic activity in MCF-7 cells transfected with siRNA for the AhR. In contrast, degradation of the AhR in HepG2 liver cancer cells resulted in decreased G0/G1 ? S phase progression, and this was accompanied by decreased expression of cyclin D1, cyclin E, cdk2 and cdk4. In the absence of ligand, the AhR exhibits growth inhibitory (MCF-7) and growth promoting (HepG2) activity that is cell context-dependent. Sp family proteins play a complex role in regulation of pancreatic cancer cells growth and expression of genes required for growth, angiogenesis and apoptosis. Sp1, Sp3 and Sp4 cooperatively activate VEGF promoter constructs in these cells; however, only Sp3 regulates cell proliferation. siRNA for Sp3 inhibits phosphorylation of retinoblastoma protein, blocks G0/G1 ? S phase progression of Panc-1 cells, and upregulates p27 protein/promoter activity. Thus, Sp3 plays a critical role in angiogenesis (VEGF upregulation) and the proliferation of Panc-1 cells by a novel mechanism of Sp3-dependent suppression of the cyclin-dependent kinase inhibitor p27.
Abdel Rahim, Ma'en Ahmad
Evaluating Zoltan for Static Load Balancing on BlueGene Architectures
The purpose of this TechBase was to evaluate the Zoltan load-balancing library from Sandia National Laboratories as a possible replacement for ParMetis, which had been the load balancer of choice for nearly a decade but does not scale to the full 64,000 processors of BlueGene/L. This evaluation was successful in producing a clear result, but the result was unfortunately negative. Although Zoltan presents a collection load-balancing algorithms, none were able to meet or exceed the combined scalability and quality of ParMetis on representative datasets.
Kumfert, G
Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases
ral ssBioMed CentBMC Genomics Open AcceResearch article Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases Lucas B Edelman1,2,6, Giuseppe Toia1,2, Donald Geman4, Wei Zhang5 and Nathan D Price*1,2,3 Address... : 1Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA, 2Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA, 3Department of Chemical and Biomolecular...
Edelman, Lucas B; Toia, Giuseppe; Geman, Donald; Zhang, Wei; Price, Nathan D
Regulation of expression of two Ly-6 family genes by intron retention and transcription induced chimerism.
in increasing proteome complexity, [1-3]. In relation to this, alterations of splic- ing patterns or mis-splicing of genes are involved in sev- eral pathologies, [4-6] including several genetic diseases such as spinal muscular atrophy (SMA), myotonic dystro- phy... and for LY6G5B were PR_1 and PR_5. Real-time RT-PCR for LY6G5B was performed by using SYBR� green PCR master mix and the ABI PRISM� 7700 sequence detection system (Applied Biosystems). Primers for real-time RT-PCR were designed for the differential...
Calvanese, Vincenzo; Mallya, Meera; Campbell, R Duncan; Aguado, Begona
Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data.
ral ssBioMed CentBMC Bioinformatics Open AcceMethodology article Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data Michael J Gilchrist*1, Mikkel B Christensen1, Richard Harland2, Nicolas Pollet3, James C... for Basic Biology, Okazaki, Aichi 444-8585, Japan and 5Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester, M13 9PT, UK Email: Michael J Gilchrist* - firstname.lastname@example.com; Mikkel B Christensen - mbc32...
Gilchrist, Michael J; Christensen, Mikkel B; Harland, Richard; Pollet, Nicolas; Smith, James C; Ueno, Naoto; Papalopulu, Nancy
Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes
in parents (P = 0.0012; excess homozygotes). Blast searches of the primer and probe sequences suggested that the assays should be specific, reducing the likelihood of deviation due to gene duplication. As the multilocus test does not assume HWE[8], we... test P-value was 0.90 (1,401 trios, ?102 = 4.9; see Additional file 8). ICSBP1 tag SNP analysis The resequencing of ICSBP1 in 32 T1D cases identified 42 polymorphisms, including one non-synonymous and fied were SNPs and two were DIPs; eight...
Morris, Gerard A J; Lowe, Christopher E; Cooper, Jason D; Payne, Felicity; Vella, Adrian; Godfrey, Lisa M; Hulme, John S; Walker, Neil M; Healy, Barry C; Lam, Alex C; Lyons, Paul A; Todd, John A
Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network
sex: playing voyeurs 50 years later. Science 2003, 301:802-803. 6. Thomas CM, Nielsen KM: Mechanisms of, and barriers to, hori- zontal gene transfer between bacteria. Nat Rev Microbiol 2005, 3:711-721. 7. Burrus V, Waldor MK: Shaping bacterial... cells under nutritional stress. Can J Microbiol 2006, 52:24-30. 24. Escobar-Paramo P, Giudicelli C, Parsot C, Denamur E: The evolu- tionary history of Shigella and enteroinvasive Escherichia coli revised. J Mol Evol 2003, 57:140-148. 25. Hartman AB...
Brilli, Matteo; Mengoni, Alessio; Fondi, Marco; Bazzicalupo, Marco; Lio, Pietro; Fani, Renato
Molecular characterization of a maize regulatory gene. Annual progress report, March 1990--November 1991
Reverse engineering a gene network using an asynchronous parallel evolution strategy
decay rate la for gene a. The half life of each protein is given by ln 2/la. The model takes account of cell division. The lengths of interphase and mitosis occur according to a well determined schedule [31], and are modelled using three rules: During... pipeline is used to extract per-nucleus concentrations and combine them into high-resolution time-series of integrated data. First, each embryo image is segmented; the posi- tion and extent of each nucleus are determined using a combination of watershed...
Jostins, Luke; Jaeger, Johannes
Molecular cloning and characterization of important stress and redox regulatory genes from Hydra vulgaris
In this research, important stress and redox regulatory genes present in Hydra vulgaris were isolated and characterized to facilitate our understanding of the evolution and mechanisms of stress response. H. vulgaris heat shock protein 70 (HvHSP70), extracellular copper zinc superoxide dismutase (HvECCuZnSOD), manganese superoxide dismutase (HvMnSOD), phospholipid peroxidase glutathione peroxidase (HvPHGPx) and monofunctional catalase (HvCatalase) were clone