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John E Carlson
Chonnam National University, Gwangju, Gwangju, South Korea
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Available from: Kelli Hoover
Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles.
Erin D Scully
Scott M Geib
, John E Carlson,
Ming Tien
Duane McKenna
Kelli Hoover
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Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages. Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids. A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants. The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles' unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning.
The Camelina aquaporin CsPIP2;1 is regulated by phosphorylation at Ser273, but not at Ser277, of the C-terminus and is involved in salt- and drought-stress responses
Ha-Young Jang
Jiye Rhee
, John E. Carlson,
Sung-Ju Ahn
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Aquaporin (AQP) proteins are involved in water homeostasis in cells at all taxonomic levels of life. Phosphorylation of some AQPs has been proposed to regulate water permeability via gating of the channel itself. We analyzed plasma membrane intrinsic proteins (PIP) from Camelina and characterized their biological functions under both stressful and favorable conditions. A three-dimensional theoretical model of the Camelina AQP proteins was built by homology modeling which could prove useful in further functional characterization of AQPs. CsPIP2;1 was strongly and constitutively expressed in roots and leaves of Camelina, suggesting that this gene is related to maintenance of homeostasis during salt and drought stresses. CsPIP2s exhibited water channel activity in Xenopus oocytes. We then examined the roles of CsPIP2;1 phosphorylation at Ser273 and Ser277 in the regulation of water permeability using phosphorylation mutants. A single deletion strain of CsPIP2;1 was generated to serve as the primary host for testing AQP expression constructs. A Ser277 to alanine mutation (to prevent phosphorylation) did not change CsPIP2;1 water permeability while a Ser273 mutation to alanine did affect water permeability. Furthermore, a CsPIP2;1 point mutation when ectopically expressed in yeast resulted in lower growth in salt and drought conditions compared with controls, and confirmation of Ser273 as the phosphorylation site. Our results support the idea that post-translational modifications in the Ser273 regulatory domains of the C-terminus fine tune water flux through CsPIP2;1.
Journal of Plant Physiology 09/2014; DOI:10.1016/j.jplph.2014.06.009
· 2.77 Impact Factor
Available from: Daniela Thomazella
Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.
Lyndel W Meinhardt
Gustavo Gilson Costa
Daniela Pt Thomazella
Paulo José Teixeira
Marcelo Falsarella Carazzolle
Stephan C Schuster
, John E Carlson,
Mark J Guiltinan
Piotr Mieczkowski
Andrew Farmer
Thiruvarangan Ramaraj
Jayne Crozier
Robert E Davis
Jonathan Shao
Rachel L Melnick
Gonçalo Ag Pereira
Bryan A Bailey
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The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease.
BMC Genomics 02/2014; 15(1):164. DOI:10.1186/1471-2164-15-164
· 4.04 Impact Factor
Available from: Kelli Hoover
Midgut transcriptome profiling of anoplophora glabripennis, a lignocellulose degrading cerambycid beetle.
Erin D Scully
Kelli Hoover
, John E Carlson,
Ming Tien
Scott M Geib
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Wood-feeding insects often work in collaboration with microbial symbionts to degrade lignin biopolymers and release glucose and other fermentable sugars from recalcitrant plant cell wall carbohydrates, including cellulose and hemicellulose. Here, we present the midgut transcriptome of larval Anoplophora glabripennis, a wood-boring beetle with documented lignin-, cellulose-, and hemicellulose- degrading capabilities, which provides valuable insights into how this insect overcomes challenges associated with feeding in woody tissue. Transcripts from putative protein coding regions of over 9,000 insect-derived genes were identified in the A. glabripennis midgut transcriptome using a combination of 454 shotgun and Illumina paired-end reads. The most highly-expressed genes predicted to encode digestive-related enzymes were trypsins, carboxylesterases, beta-glucosidases, and cytochrome P450s. Furthermore, 180 unigenes predicted to encode glycoside hydrolases (GHs) were identified and included several GH 5, 45, and 48 cellulases, GH 1 xylanases, and GH 1 beta-glucosidases. In addition, transcripts predicted to encode enzymes involved in detoxification were detected, including a substantial number of unigenes classified as cytochrome P450s (CYP6B) and carboxylesterases, which are hypothesized to play pivotal roles in detoxifying host tree defensive chemicals and could make important contributions to A. glabripennis' expansive host range. While a large diversity of insect-derived transcripts predicted to encode digestive and detoxification enzymes were detected, few transcripts predicted to encode enzymes required for lignin degradation or synthesis of essential nutrients were identified, suggesting that collaboration with microbial enzymes may be required for survival in woody tissue. A. glabripennis produces a number of enzymes with putative roles in cell wall digestion, detoxification, and nutrient extraction, which likely contribute to its ability to thrive in a broad range of host trees. This system is quite different from the previously characterized termite fermentation system and provides new opportunities to discover enzymes that could be exploited for cellulosic ethanol biofuel production or the development of novel methods to control wood-boring pests.
BMC Genomics 12/2013; 14(1):850. DOI:10.1186/1471-2164-14-850
· 4.04 Impact Factor
Available from: PubMed Central
Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing.
Sandra A Owusu
Margaret Staton
Tara N Jennings
Scott Schlarbaum
Mark V Coggeshall
Jeanne Romero-Severson
, John E Carlson,
Oliver Gailing
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Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies. Methods and Results: Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent. Conclusions: Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species.
12/2013; 1(12). DOI:10.3732/apps.1300050
Available from: Chung-Jui Tsai
Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide.
Yi Xu
Chin-Fu Chen
Tina P Thomas
Parastoo Azadi
Brett Diehl
Chung-Jui Tsai
Nicole Brown
, John E Carlson,
Ming Tien
Haiying Liang
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Our study has identified pathways and gene candidates that may be associated with the greater flexibility and digestibility of the poplar cell walls. With the goal of facilitating lignin removal during the utilization of woody biomass as a biofuel feedstock, we previously transformed a hybrid poplar clone with a partial cDNA sequence encoding a tyrosine- and hydroxyproline-rich glycoprotein from parsley. A number of the transgenic lines released more polysaccharides following protease digestion and were more flexible than wild-type plants, but otherwise normal in phenotype. Here, we report that overexpression of the tyrosine-rich peptide encoding sequence in these transgenic poplar plants did not significantly alter total lignin quantity or quality (S/G lignin ratio), five- and six-carbon sugar contents, growth rate, or susceptibility to a major poplar fungal pathogen, Septoria musiva. Whole-genome microarray analysis revealed a total of 411 differentially expressed transcripts in transgenic lines, all with decreased transcript abundance relative to wild-type plants. Their corresponding genes were overrepresented in functional categories such as secondary metabolism, amino acid metabolism, and energy metabolism. Transcript abundance was decreased primarily for five types of genes encoding proteins involved in cell-wall organization and in lignin biosynthesis. The expression of a subset of 19 of the differentially regulated genes by qRT-PCR validated the microarray results. Our study has identified pathways and gene candidates that may be the underlying cause for the enhanced flexibility and digestibility of the stems of poplar plants expressing the TYR transgene.
Plant Cell Reports 09/2013; DOI:10.1007/s00299-013-1496-0
· 2.94 Impact Factor
Available from: Kelli Hoover
Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.
Erin D Scully
Scott M Geib
Kelli Hoover
Ming Tien
Susannah G Tringe
Kerrie W Barry
Tijana Glavina Del Rio
Mansi Chovatia
Joshua R Herr
, John E Carlson
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The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a reservoir of novel enzymes to enhance industrial cellulosic biofuels production or targets for novel control methods for this invasive and highly destructive insect.
PLoS ONE 09/2013; 8(9):e73827. DOI:10.1371/journal.pone.0073827
· 3.53 Impact Factor
Available from: Xiao Han
Populus euphratica: the transcriptomic response to drought stress.
Sha Tang
Haiying Liang
Donghui Yan
Ying Zhao
Xiao Han
, John E Carlson,
Xinli Xia
Weilun Yin
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Populus euphratica Olivier is widely established in arid and semiarid regions but lags in the availability of transcriptomic resources in response to water deficiency. To investigate the mechanisms that allow P. euphratica to maintain growth in arid regions, the responses of the plant to soil water deficit were analyzed at a systems level using physiological and pyrosequencing approaches. We generated 218,601 and 287,120 reads from non-stressed control and drought-stressed P. euphratica leaves respectively, totaling over 200 million base pairs. After assembly, 24,013 transcripts were yielded with an average length of 1,128 bp. We determined 2,279 simple sequence repeats, which may have possible information for understanding drought adaption of woody plants. Stomatal closure was inhibited under moderate drought to maintain a relatively high rate of CO2 assimilation and water transportation, which was supposed to be important for P. euphratica to maintain normal growth and develop vigorous root systems in an adverse environment. This was accompanied by strong transcriptional remodeling of stress-perception, signaling and transcription regulation, photoprotective system, oxidative stress detoxification, and other stress responsive genes. In addition, genes involved in stomatal closure inhibition, ascorbate-glutathione pathway and ubiquitin-proteasome system that may specially modulate the drought stress responses of P. euphratica are highlighted. Our analysis provides a comprehensive picture of how P. euphratica responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants.
Plant Molecular Biology 07/2013; 83(6). DOI:10.1007/s11103-013-0107-3
· 4.07 Impact Factor
Two aquaporins of Jatropha are regulated differentially during drought stress and subsequent recovery.
Ha-Young Jang
Seong-Wook Yang
, John E Carlson,
Yang-Gyu Ku
Sung-Ju Ahn
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Jatropha has potential to be an important bio-fuel crop due to such advantages as high seed oil content and the ability to grow well on marginal lands less suited for food crops. Despite its ability to grow on marginal land, Jatropha is still susceptible to high salt and drought stresses, which can significantly reduce plant growth, stomatal conductance, sap-flow rate, and plant sap volume. This study was undertaken to collect basic knowledge of the physiological and molecular aspects of Jatropha response to salt and drought stresses, and to elucidate how Jatropha recovers from stress. From these studies we identified candidate genes that may be useful for the development of Jatropha cultivars that will grow efficiently in arid and barren lands. Of particular interest, two plasma membrane intrinsic proteins were identified: Jatropha plasma membrane intrinsic protein 1 (JcPIP1) and Jatropha plasma membrane intrinsic protein 2 (JcPIP2). The expression levels of JcPIP1 were dramatically increased in roots, stems, and leaves during the recovery from stress, whereas the JcPIP2 gene transcripts levels were induced in roots and stems during the water deficit stress. The protein levels of JcPIP1 and JcPIP2 were consistent with the gene expression patterns. Based on these results, we hypothesized that JcPIP1 plays a role in the recovery events from water stresses, while JcPIP2 is important in early responses to water stress. Virus induced gene silencing technology revealed that both JcPIP1 and JcPIP2 have positive roles in response to water deficit stresses, but have antagonistic functions at the recovery stage. We suggest that both JcPIP1 and JcPIP2 may play important roles in responses to water deficit conditions and both have potential as targets for genetic engineering.
Journal of plant physiology 03/2013; DOI:10.1016/j.jplph.2013.03.001
· 2.50 Impact Factor
Cold stress causes rapid but differential changes in properties of plasma membrane H(+)-ATPase of camelina and rapeseed.
Hyun-Sung Kim
Jung-Min Oh
Sheng Luan
, John E Carlson,
Sung-Ju Ahn
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Camelina (Camelina sativa) and rapeseed (Brassica napus) are well-established oil-seed crops with great promise also for biofuels. Both are cold-tolerant, and camelina is regarded to be especially appropriate for production on marginal lands. We examined physiological and biochemical alterations in both species during cold stress treatment for 3 days and subsequent recovery at the temperature of 25°C for 0, 0.25, 0.5, 1, 2, 6, and 24h, with particular emphasis on the post-translational regulation of the plasma membrane (PM) H(+)-ATPase (EC184.108.40.206). The activity and translation of the PM H(+)-ATPase, as well as 14-3-3 proteins, increased after 3 days of cold stress in both species but recovery under normal conditions proceeded differently. The increase in H(+)-ATPase activity was the most dramatic in camelina roots after recovery for 2h at 25°C, followed by decay to background levels within 24h. In rapeseed, the change in H(+)-ATPase activity during the recovery period was less pronounced. Furthermore, H(+)-pumping increased in both species after 15min recovery, but to twice the level in camelina roots compared to rapeseed. Protein gel blot analysis with phospho-threonine anti-bodies showed that an increase in phosphorylation levels paralleled the increase in H(+)-transport rate. Thus our results suggest that cold stress and recovery in camelina and rapeseed are associated with PM H(+)-fluxes that may be regulated by specific translational and post-translational modifications.
Journal of plant physiology 02/2013; DOI:10.1016/j.jplph.2013.01.007
· 2.50 Impact Factor
Available from: Maria del Mar Jimenez-Gasco
Phylogenetic Analysis of Fusarium solani Associated with the Asian Longhorned Beetle, Anoplophora glabripennis
Scott M Geib
Erin D Scully
Mar Jimenez-Gasco
, John E Carlson,
Ming Tien
Kelli Hoover
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Culture-independent analysis of the gut of a wood-boring insect, Anoplophora glabripennis (Coleoptera: Cerambycidae), revealed a consistent association between members of the fungal Fusarium solani species complex and the larval stage of both colony-derived and wild A. glabripennis populations. Using the translation elongation factor 1-alpha region for culture-independent phylogenetic and operational taxonomic unit (OTU)-based analyses, only two OTUs were detected, suggesting that genetic variance at this locus was low among A. glabripennis-associated isolates. To better survey the genetic variation of F. solani associated with A. glabripennis, and establish its phylogenetic OPEN ACCESS Insects 2012, 3 142 relationship with other members of the F. solani species complex, single spore isolates were created from different populations and multi-locus phylogenetic analysis was performed using a combination of the translation elongation factor alpha-1, internal transcribed spacer, and large subunit rDNA regions. These analyses revealed that colony-derived larvae reared in three different tree species or on artificial diet, as well as larvae from wild populations collected from three additional tree species in New York City and from a single tree species in Worcester, MA, consistently harbored F. solani within their guts. While there is some genetic variation in the F. solani carried between populations, within-population variation is low. We speculate that F. solani is able to fill a broad niche in the A. glabripennis gut, providing it with fungal lignocellulases to allow the larvae to grow and develop on woody tissue. However, it is likely that many F. solani genotypes could potentially fill this niche, so the relationship may not be limited to a single member of the F. solani species complex. While little is known about the role of filamentous fungi and their symbiotic associations with insects, this report suggests that larval A. glabripennis has developed an intimate relationship with F. solani that is not limited by geographic location or host tree.
12/2012; 3(3):141-160. DOI:10.3390/insects3010141
Available from: Megan Monsanto
A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map
Guang-Chen Fang
Barbara P Blackmon
Margaret E Staton
C Dana
Thomas L Kubisiak
Bode A Olukolu
David Henry
Tatyana Zhebentyayeva
Christopher A Saski
Chun-Huai Cheng
Megan Monsanto
Stephen Ficklin
Michael Atkins
Laura L Georgi
Abdelali Barakat
Nicholas Wheeler
, John E Carlson,
Ronald Sederoff
Albert G Abbott
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Three Chinese chestnut bacterial artificial chromo-some (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was
Available from: Olga Pechanova
Overexpression of Constans Homologs CO1 and CO2 Fails to Alter Normal Reproductive Onset and Fall Bud Set in Woody Perennial Poplar.
Chuan-Yu Hsu
Joshua P Adams
Kyoungok No
Haiying Liang
Richard Meilan
Olga Pechanova
Abdelali Barakat
, John E Carlson,
Grier P Page
Cetin Yuceer
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CONSTANS (CO) is an important flowering-time gene in the photoperiodic flowering pathway of annual Arabidopsis thaliana in which overexpression of CO induces early flowering, whereas mutations in CO cause delayed flowering. The closest homologs of CO in woody perennial poplar (Populus spp.) are CO1 and CO2. A previous report [1] showed that the CO2/FLOWERING LOCUS T1 (FT1) regulon controls the onset of reproduction in poplar, similar to what is seen with the CO/FLOWERING LOCUS T (FT) regulon in Arabidopsis. The CO2/FT1 regulon was also reported to control fall bud set. Our long-term field observations show that overexpression of CO1 and CO2 individually or together did not alter normal reproductive onset, spring bud break, or fall dormancy in poplar, but did result in smaller trees when compared with controls. Transcripts of CO1 and CO2 were normally most abundant in the growing season and rhythmic within a day, peaking at dawn. Our manipulative experiments did not provide evidence for transcriptional regulation being affected by photoperiod, light intensity, temperature, or water stress when transcripts of CO1 and CO2 were consistently measured in the morning. A genetic network analysis using overexpressing trees, microarrays, and computation demonstrated that a majority of functionally known genes downstream of CO1 and CO2 are associated with metabolic processes, which could explain their effect on tree size. In conclusion, the function of CO1 and CO2 in poplar does not appear to overlap with that of CO from Arabidopsis, nor do our data support the involvement of CO1 and CO2 in spring bud break or fall bud set.
PLoS ONE 09/2012; 7(9):e45448. DOI:10.1371/journal.pone.0045448
· 3.53 Impact Factor
Available from: Antoine Kremer
Genomics of Fagaceae
Antoine Kremer
Albert G. Abbott
, John E. Carlson,
Paul S. Manos
Christophe Plomion
Paul Sisco
Margaret E. Staton
Saneyoshi Ueno
Giovanni G. Vendramin
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An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8–10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak).
Tree Genetics & Genomes 06/2012; 8(3). DOI:10.1007/s11295-012-0498-3
· 2.44 Impact Factor
A petiole-galling insect herbivore decelerates leaf lamina litter decomposition rates
Christopher J. Frost
Jennifer M. Dean
Erica C. Smyers
Mark C. Mescher
, John E. Carlson,
Consuelo M. De Moraes
John F. Tooker
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1. Herbivore-mediated changes in leaf-litter chemistry are often considered responsible for altering litter decomposition rates, but such chemical changes often co-occur with other factors such as physical alteration of leaf material that also influence decomposition rates. We attempted to disentangle these effects using the poplar petiole gall moth (Ectoedemia populella Brusk), which forms galls on petioles at the base of the leaf lamina but does not alter leaf morphology. Thus, differences in leaf decomposition rates between galled and ungalled leaves should be explained by gall-mediated changes in leaf chemistry. 2. Petiole galling decelerated leaf lamina litter decomposition in two Populus host species, but in temporally distinct ways. In Populus granidentata, galling decelerated decomposition by 7% after 4 months. After 12 and 18 months, Populus tremuloides litter decomposition rates were 12% and 17% lower, respectively, in lamina tissue whose petiole had been galled relative to ungalled. On average, the petiole galler increased leaf lamina nitrogen concentrations by 17%, decreased tannin concentrations from 37% to 53% and decreased tannin-binding capacity by 11% and 37% in P. grandidentata and P. tremuloides, respectively. These changes would be expected to increase, rather than decrease, decomposition rates. 3. Unlike other insect herbivores guilds that have variable effects on litter decomposition in direction and magnitude, all gall insects studied to date have decelerated leaf-litter decomposition. This consistent effect of galling on decomposition provides a framework for deciphering a fundamental aspect of insect herbivory on a critical ecosystem process. 4. We used a gall-inducing moth with a distinctive natural history to confirm the role of herbivore-mediated litter chemistry in leaf-litter decomposition dynamics. Moreover, we advance the hypothesis that gall-induced defensive manipulations that protect a host plant from injury by other herbivores lead to decelerated litter decomposition.
Functional Ecology 06/2012; 26(3):628-636. DOI:10.2307/23258544
· 4.86 Impact Factor
Available from: Gustavo Gilson Lacerda Costa
The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao
Gustavo G L Costa
Odalys G Cabrera
Ricardo A Tiburcio
Francisco J Medrano
Marcelo F Carazzolle
Daniela P T Thomazella
Stephen C Schuster
, John E Carlson,
Mark J Guiltinan
Bryan A Bailey
Piotr Mieczkowski
Gonçalo A G Pereira
Lyndel W Meinhardt
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In this study, we report the sequence of the mitochondrial (mt) genome of the Basidiomycete fungus Moniliophthora roreri, which is the etiologic agent of frosty pod rot of cacao (Theobroma cacao L.). We also compare it to the mtDNA from the closely-related species Moniliophthora perniciosa, which causes witches' broom disease of cacao. The 94 Kb mtDNA genome of M. roreri has a circular topology and codes for the typical 14 mt genes involved in oxidative phosphorylation. It also codes for both rRNA genes, a ribosomal protein subunit, 13 intronic open reading frames (ORFs), and a full complement of 27 tRNA genes. The conserved genes of M. roreri mtDNA are completely syntenic with homologous genes of the 109 Kb mtDNA of M. perniciosa. As in M. perniciosa, M. roreri mtDNA contains a high number of hypothetical ORFs (28), a remarkable feature that make Moniliophthoras the largest reservoir of hypothetical ORFs among sequenced fungal mtDNA. Additionally, the mt genome of M. roreri has three free invertron-like linear mt plasmids, one of which is very similar to that previously described as integrated into the main M. perniciosa mtDNA molecule. Moniliophthora roreri mtDNA also has a region of suspected plasmid origin containing 15 hypothetical ORFs distributed in both strands. One of these ORFs is similar to an ORF in the mtDNA gene encoding DNA polymerase in Pleurotus ostreatus. The comparison to M. perniciosa showed that the 15 Kb difference in mtDNA sizes is mainly attributed to a lower abundance of repetitive regions in M. roreri (5.8 Kb vs 20.7 Kb). The most notable differences between M. roreri and M. perniciosa mtDNA are attributed to repeats and regions of plasmid origin. These elements might have contributed to the rapid evolution of mtDNA. Since M. roreri is the second species of the genus Moniliophthora whose mtDNA genome has been sequenced, the data presented here contribute valuable information for understanding the evolution of fungal mt genomes among closely-related species.
Fungal Biology 05/2012; 116(5):551-62. DOI:10.1016/j.funbio.2012.01.008
· 2.14 Impact Factor
Available from: Abdelali Barakat
Chestnut resistance to the blight disease: insights from transcriptome analysis
Abdelali Barakat
Meg Staton
Chun-Huai Cheng
Joseph Park
Norzawani Buang M Yassin
Stephen Ficklin
Chia-Chun Yeh
Fred Hebard
Kathleen Baier
William Powell
Stephan C Schuster
Nicholas Wheeler
Albert Abbott
, John E Carlson,
Ronald Sederoff
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A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified. Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.
BMC Plant Biology 03/2012; 12:38. DOI:10.1186/1471-2229-12-38
· 3.94 Impact Factor
Available from: Norzawani Buang
Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants
Abdelali Barakat
Norzawani Buang M Yassin
Joseph S Park
Alex Choi
Josh Herr
, John E Carlson
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The biosynthesis of monolignols, the main components of lignin, involves many intermediates and enzymes. The cinnamoyl-CoA reductase (CCR) enzyme catalyzes the conversion of cinnamoyl-CoAs to cinnamaldehydes, i.e. the first specific step in lignin synthesis. The CCR and CCR-like gene family was studied partially in several plant species. This is a comprehensive study of the CCR and CCR-like gene family including genome organization, gene structure, phylogeny across land plant species, and, expression profiling in Populus. Analysis of amino acid motifs enabled the identification of sequence variations in the CCR catalytic site and annotates CCR and CCR-like genes. CCR and CCR-like genes were distributed in three major phylogenetic classes of which one includes the bona fide CCR genes. The other two classes include CCR and CCR-like, of which several genes present a high similarity to cinnamyl alcohol dehydrogenase, or dihydroflavonol reductase (DFR) genes. All CCR, CCR-like, and DFR classes were deeply rooted in the phylogeny of land plants suggesting that their evolution preceded the evolution of lycophytes. Over two thirds of CCR and CCR-like Populus genes were physically distributed on duplicated regions. This suggests that these duplication/retention processes contributed significantly to the size of the CCR and CCR-like gene family. The Populus CCR and CCR-like genes showed six expression patterns in the tissues studied with a preferential expression of PoptrCCR12 in xylem. The other genes present divergent expression profiles with some preferentially expressed in leaves, bark, or both. Several CCR and CCR-like genes were induced or repressed under various abiotic stresses suggesting that their duplication was followed by the evolution of divergent expression profiles and divergence of functions.
Plant Science 09/2011; 181(3):249-57. DOI:10.1016/j.plantsci.2011.05.012
· 4.11 Impact Factor
Australian Journal of Botany
Agnieszka Bagniewska-Zadworna
Maciej Zenkteler
Elżbieta Zenkteler
Maria K. Wojciechowicz
Abdelali Barakat
, John E. Carlson
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Embryos and plants from the crosses Salix viminalis L. as the female parent and Populus alba L., P. violascens Dode or P. tremula L. as the male parent were obtained by in vitro embryo rescue technique. F1 intergeneric progeny were obtained by overcoming post-zygotic barriers caused by the deficiency of endosperm as nutritive tissue during the first stage of embryo development. Ovules containing immature heart-stage embryos as well as early cotyledonary embryos were isolated and rescued in modified 1/2 MS medium supplemented with 3% sucrose to ensure maturity. Seedlings were cultured under in vitro conditions in 1/2 MS medium that contained 0.2 mg l–1 naphtaleneacetic acid and plantlets after rooting were transferred first into pots and subsequently to the experimental field in the Botanical Garden in Poznań, Poland. After 2 years, the putative hybrid nature of the plants was checked by analysing morphological characters and molecular markers. Scanning electron microscopy, flow cytometry and random amplification of polymorphic DNA screening of individuals confirmed the hybrid nature of the S. viminalis × P. alba and S. viminalis × P. violascens progeny and of 25% of the analysed plants from the cross S. viminalis × P. tremula. This study showed the feasibility of overcoming pre- and post-fertilisation barriers to achieve intergeneric hybrids between species from two genera of Salicaceae. The in vitro system to produce hybrids with characters of both parents could be of great importance for increasing biomass production. This study also opens new opportunities to improve other traits in trees, such as resistance to pathogens inherited from one parent.
Australian Journal of Botany 06/2011; 59,:382-392.
· 0.90 Impact Factor
Available from: Dawn S Luthe
FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar.
Chuan-Yu Hsu
Joshua P Adams
Hyejin Kim
Kyoungok No
Caiping Ma
Steven H Strauss
Jenny Drnevich
Lindsay Vandervelde
Jeffrey D Ellis
Brandon M Rice
Norman Wickett
Lee E Gunter
Gerald A Tuskan
Amy M Brunner
Grier P Page
Abdelali Barakat
, John E Carlson,
Claude W DePamphilis
Dawn S Luthe
Cetin Yuceer
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Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.
Proceedings of the National Academy of Sciences 06/2011; 108(26):10756-61. DOI:10.1073/pnas.1104713108
· 9.81 Impact Factor
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Abdelali Barakat
University of South Dakota
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Margaret E Staton
Clemson University
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Charles Addo-Quaye
Purdue University
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Jim Leebens-Mack
University of Georgia
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Hong Ma
Fudan University
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Chonnam National University
Gwangju, Gwangju, South Korea
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Worcester, Massachusetts, United States
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Seattle, Washington, United States
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By Irene Klotz CAPE CANAVERAL, Fla (Reuters) - A Russian Soyuz rocket blasted off from the Baikonur Cosmodrome in Kazakhstan on Friday, sending a U.S.-Russia crew to the International Space Station for a year-long flight, a NASA Television broadcast showed. Four Soviet-era cosmonauts lived on the now-defunct Mir space station for a year or longer, but the missions, which concluded in 1999, did not have the sophisticated medical equipment that will be used during International Space Station investigations, NASA said.
By Will Dunham WASHINGTON (Reuters) - A fossil site in the Canadian Rockies that provides a wondrous peek into life on Earth more than half a billion years ago has offered up the remains of an intriguing sea creature, a four-eyed arthropod predator that wielded a pair of spiky claws. Scientists said on Friday they unearthed nicely preserved fossils in British Columbia of the 508 million-year-old animal, named Yawunik kootenayi, that looked like a big shrimp with a bad attitude and was one of the largest predators of its time. The fossil beds in Kootenay National Park where it was found were in a previously unexplored area of the Burgess Shale rock formation that for more than a century has yielded exceptional remains from the Cambrian Period, when many of the major animal groups first appeared. Yawunik, whose name honors a mythical sea monster in the native Ktunaxa people's creation story, was a primitive arthropod, the highly successful group that includes shrimps, lobsters, crabs, insects, spiders, scorpions, centipedes and millipedes.
By Laurence Frost and Gilles Guillaume PARIS (Reuters) - French auto parts maker Valeo plans to draw on drone software and other military technologies from partner Safran to offer self-driving vehicle platforms to carmakers by the end of the decade. While demonstrating an autonomous car and other prototype systems jointly developed with Safran, the French defense and aerospace group, Valeo said on Friday the first applications may reach carmaker clients within three years. "We realized very quickly that we had much more in common than we'd expected," Valeo innovation chief Guillaume Devauchelle told Reuters. "It turns out that an autonomous vehicle is really a terrestrial drone." Cars that complete whole journeys without human input are still many years away, but creeping automation is well underway, with models already on sale that can pilot themselves through slow traffic and hit the brakes when a pedestrian steps out.
By Andrea Shalal WASHINGTON (Reuters) - The U.S. Air Force overstepped its bounds as it worked to certify privately held SpaceX to launch military satellites, undermining the benefit of working with a commercial provider, an independent review showed on Thursday. The report cited a "stark disconnect" between the Air Force and SpaceX, or Space Exploration Technologies, about the purpose of the certification process and recommended changes. Air Force Secretary Deborah James ordered the review after the service missed a December deadline for certifying SpaceX to compete for some launches now carried out solely by United Launch Alliance, a joint venture of Lockheed Martin Corp and Boeing Co. The Pentagon is eager to certify SpaceX as a second launch provider, given mounting concerns in Congress about ULA's use of a Russian-built engine to power its Atlas 5 rocket.
The idea of bringing extinct animals back to life continues to reside in the realm of science fiction. Harvard geneticist George Church and his colleagues used a gene-editing technique known as CRISPR to insert mammoth genes for small ears, subcutaneous fat, and hair length and color into the DNA of elephant skin cells. Woolly mammoths (Mammuthus primigenius) have been extinct for millennia, with the last of the species dying out about 3,600 years ago. But we won't be seeing woolly mammoths prancing around anytime soon, "because there is more work to do," Church told U.K.'s The Times, according to Popular Science.

subset: commoncrawl


text:
Mustang 1909 Dark Brown Tortoise eyeglasses are cultivated and sophisticated. This timeless design is paired with a modern, light tortoise finish composed from handmade acetate into a distinct rectangular frame. The semi-transparent temples are accented by the sleek metal hinges and classic Mustang logo at the tips.Close
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Gargoyles Rover Tortoise eyeglasses are sleek and striking. This modern style comes in a prominent matte brown tortoise acetate, matched with rectangular lenses. The coordinating temples are modestly embedded with a brown metal Gargoyles logo.Close
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Geoffrey Beene 501 Tortoise eyeglasses are stark and contemplative. This distinguished style comes in a rich brown tortoise acetate and features sharp rectangular shaped lenses. The matching havana temples are engraved with Geoffrey Beene branding at the tips and complemented by the rustic, stylized hinges.Close
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There is a connection between summer and cars that remains in my mind.
"You must know half the people in Dawson County," friends have often remarked. "Every where we go, you are greeting someone."
They haven't asked me to write a gardening column for the paper, because my true gardening knowledge could be placed in a thimble with room to spare.
Over the past years, I have received many calls from people who have found snakes and/or snake skins around their home. I once had a lady try to sell me her house because she had found a snake skin in a hall closet.
Every year about this time I have someone ask me why they can't grow sweet onions that have the same mild, sweet flavor as the Vidalia onion.
We have more than one television in our house. In fact, there are about as many televisions as there are people.
I was surprised and delighted by the number of reactions to my column discussing the book about Greg Martenson's schools in Pakistan and Afghanistan - from a few who had read it and others who want to.
With recent rains, 2009 may be an excellent year for local vegetable gardens.
The people who make tissues will get some of my money this weekend. I'm going to try not to cry, but I know I will.
Each month I receive hundreds of calls from gardeners with questions ranging from how to keep deer out of a garden to disease control in a home lawn. A few questions you may have thought about, but never got around to asking are as follows:
We have a pretty kitchen at our house. We've got a big stove that has a convection oven. We haven't learned how to convect, but when we do, we supposedly have an oven that will do it.
It's a foregone conclusion; contrasts attract attention. It's also a possibility, though not necessarily so, that they engender new ways of looking at things.
Among flowering vines, few have flowers as spectacular as the clematis. It has been more than 150 years since this vine was first hybridized to improve flower size and color, and improvements continue to be made.
I think most people who have ever lost a loved one have thought or dreamed of having them back for just five minutes to catch up on your life and theirs.
Fescue is the most popular and widely used lawn grass in Dawson County. This is for good reason. Fescue is a cool season grass and loves the average temperatures of this region. Fescue grows rapidly in spring and fall but little during periods of extreme heat or cold.
Early March can be one of the blandest times in the landscape.
"Mama, is it bad that I am happy?"
I just finished sending out congratulatory messages across the globe to various women I have worked with through the decades.
Now is the time to start preparing your garden for potato plantings.
"So, how are Mama and Uncle Bobby doing without Granny?" my friend Renee asked as she took a seat across the table from me.
It must be open season on people who are overweight.
With all of the recent winter weather, a summer lawn may be the last thing on your mind. However, now is the time to start thinking about controlling summer annual weeds, such as crabgrass.
I sometimes think people have lost all sense of boundaries and personal decorum.
The winter storm of the past week has led to many shrubs and trees damaged in home landscapes.
I have often marveled how teachers could do it. Not just the keeping a classroom of children occupied or trying to keep track of how many kids have gone to the restroom, either. I have always been in awe of those good teachers who really inspire their students to learn.
I am not by any means a jewelry girl.
My "here" is quite different from what it was at the beginning of 2015.
No one listens to me.
Winter doesn't seem like a good time for insect control in your home orchard or landscape, does it? The frigid temperatures of February aren't conducive to much insect activity. However, right now insects are hiding out on your trees and shrubs waiting for the warm temperatures of spring to pop out and mess with your plants.
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TMS Lion cubs extend streak
The Tunica Middle School is now five and 0, with no signs of slowing down.
The young team met the Riverview Middle School Vikings of Memphis on Saturday, Sept. 17. Tunica came out on top 30-12, according to Head Coach Eiyessie Donald.
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Continuing my coverage of the [ IBM System x and System Storage Technical Symposium ]. Here is a recap of Day 2: IBM Storage Strategy in the Smarter Computing Era Since Clod Barrera introduced IBM's Smarter Computing initiative during...
Upcoming IBM Webinars for National Preparedness Month
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Last week, US President Barack Obama declared September 2011 as "National Preparedness Month". Here is an excerpt of the press release: Whenever our Nation has been challenged, the American people have responded with faith, courage, and...
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li { margin-bottom: 20px; } Continuing my week in Washington DC for the annual [ 2010 System Storage Technical University ], here is my quick recap of the keynote sessions presented Monday morning. Marlin Maddy, Worldwide Technical Events...


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Leviton 47606-AHT Advanced Home Telephone and Video Panel - White
Brand: Leviton Model: 47606-AHT Condition: New
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The Leviton Advanced Home Telephone and Video Panel - White (47606-AHT) combines a Telephone Line Distribution Module, Category 5e Voice and Data Board, and a 6-way 2 GHz Video Splitter in a dedicated plastic bracket for multi-line systems with video distribution. Provides two to four lines of service to up to 19 connections. Distribute Line 1 service to up to 12 different connections; distribute four-line service to up to eight different connections. Route voice and data services to up to 6 remote locations via Category 5e Voice and Data modules. Link with other distribution panels or modules to expand the system.
Features:• Provides two to four lines of telephone service to up to 19 connections when combined with other modules
• Routes video to 6 locations, and voice and data service to 6 remote locations via Category 5e Voice and Data Board
• Panel includes a plastic bracket, Telephone Line Distribution Module, Category 5e Voice and Data Board and a 6-Way 2 GHz Video Splitter
• Fits into any Leviton Structured Media enclosure or used as a stand-alone unit
• Offers multi-line systems with video distribution
Specifications:• Type: Full Size Pre-Configured Cabling Panel
• Description: Advanced Home Telephone and Video
• Height: 6.13 Inch
• Width: 13.3 Inch
• Depth: 2.28 Inch
• Cat 5e Voice Data Module: 1
• Telephone Line Distribution Module: 1
• 6-Way Video Splitter: 1
• Standards and Certifications: CULUS/FCC/TIA/EIA
• Warranty: 2 Year Limited
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Cory in the House
Cory Baxter, 15, and his father live in staff quarters at the White House.
Kyle Massey, Rondell Sheridan, Jason Dolley, Madison Pettis, Maiara Walsh, Jake Thomas, John D'aquino, Lisa Arch
Dennis Rinsler (Executive Producer), Marc Warren (Executive Producer)
|"Lip Service" Cory and his friends devise a kissing booth for the carnival, but there's a problem. (Repeat)
|"Who Let the Dolls Out" Cory and Sophie come up with a plan to make money, but Shophie is not happy with the results. (Repeat)
Since his dad, Victor, was named head chef to President Martinez, Cory Baxter now lives in Washington, D.C. Cory shares the staff quarters of the White House with his father and attends an exclusive private school. The president's young daughter, Sophie, is very clever for her age and likes to meddle. Meena, an ambassador's daughter, and Newt, heir to a political dynasty, become Cory's new friends.
Current cast
Kyle Massey as Cory Baxter
Rondell Sheridan as Victor Baxter
Jason Dolley as Newt Livingston
Madison Pettis as Sophie Martinez
Maiara Walsh as Meena Paroom
Jake Thomas as Jason Stickler
John D'aquino as President Richard Martinez
Lisa Arch as Samantha Samuels
TiVo subscribers who like "Cory in the House" also like...
Program data from Tribune Media Services, Inc.