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Full-Text Articles in Life Sciences
Perturbation Of Brachypodium Distachyon Cellulose Synthase A4 Or 7 Results In Abnormal Cell Walls, Pubudu P. Handakumbura, Dominick A. Matos, Karen S. Osmont, Michael J. Harrington, Kyuyoung Heo, Kabindra Kafle, Seong H. Kim, Tobias I. Baskin, Samuel P. Hazen
Perturbation Of Brachypodium Distachyon Cellulose Synthase A4 Or 7 Results In Abnormal Cell Walls, Pubudu P. Handakumbura, Dominick A. Matos, Karen S. Osmont, Michael J. Harrington, Kyuyoung Heo, Kabindra Kafle, Seong H. Kim, Tobias I. Baskin, Samuel P. Hazen
Samuel P Hazen
Background: Cellulose is an integral component of the plant cell wall and accounts for approximately forty percent of total plant biomass but understanding its mechanism of synthesis remains elusive. CELLULOSE SYNTHASE A (CESA) proteins function as catalytic subunits of a rosette-shaped complex that synthesizes cellulose at the plasma membrane. Arabidopsis thaliana and rice (Oryza sativa) secondary wall CESA loss-of-function mutants have weak stems and irregular or thin cell walls. Results: Here, we identify candidates for secondary wall CESAs in Brachypodium distachyon as having similar amino acid sequence and expression to those characterized in A. thaliana, namely CESA4/7/8. To functionally characterize …
Functional Characterization Of Cinnamyl Alcohol Dehydrogenase And Caffeic Acid O-Methyltransferase In Brachypodium Distachyon, Gina M. Trabucco, Dominick A. Matos, Scott J. Lee, Aaron J. Saathoff, Henry D. Priest, Todd C. Mockler, Gautam Sarath, Samuel P. Hazen
Functional Characterization Of Cinnamyl Alcohol Dehydrogenase And Caffeic Acid O-Methyltransferase In Brachypodium Distachyon, Gina M. Trabucco, Dominick A. Matos, Scott J. Lee, Aaron J. Saathoff, Henry D. Priest, Todd C. Mockler, Gautam Sarath, Samuel P. Hazen
Samuel P Hazen
Background: Lignin is a significant barrier in the conversion of plant biomass to bioethanol. Cinnamyl alcohol dehydrogenase (CAD) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the pathway of lignin monomer biosynthesis. Brown midrib mutants in Zea mays and Sorghum bicolor with impaired CAD or COMT activity have attracted considerable agronomic interest for their altered lignin composition and improved digestibility. Here, we identified and functionally characterized candidate genes encoding CAD and COMT enzymes in the grass model species Brachypodium distachyon with the aim of improving crops for efficient biofuel production. Results: We developed transgenic plants overexpressing artificial microRNA designed …
Transcriptional Regulation Of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up With Arabidopsis Thaliana, Pubudu P. Handakumbura, Samuel P. Hazen
Transcriptional Regulation Of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up With Arabidopsis Thaliana, Pubudu P. Handakumbura, Samuel P. Hazen
Samuel P Hazen
Secondary cell wall synthesis occurs in specialized cell types following completion of cell enlargement. By virtue of mechanical strength provided by a wall thickened with cellulose, hemicelluloses, and lignin, these cells can function as water-conducting vessels and provide structural support. Several transcription factor families regulate genes encoding wall synthesis enzymes. Certain NAC and MYB proteins directly bind to the SNBE and AC elements upstream of structural genes and other transcription factors. The most detailed model of this regulatory network is established predominantly for a eudicot, Arabidopsis thaliana. In grasses, both the patterning and the composition of secondary cell walls are …
Biological Conversion Assay Using Clostridium Phytofermentans To Estimate Plant Feedstock Quality, Scott J. Lee, Thomas A. Warnick, Sivakumar Pattahil, Jesus G. Alvelo-Maurosa, Michelle J. Serapiglia, Heather Mccormick, Virginia Brown, Naomi F. Young, Danny J. Schnell, Lawrence B. Smart, Michael G. Hahn, Jeffrey F. Pedersen, Susan B. Leschine, Samuel P. Hazen
Biological Conversion Assay Using Clostridium Phytofermentans To Estimate Plant Feedstock Quality, Scott J. Lee, Thomas A. Warnick, Sivakumar Pattahil, Jesus G. Alvelo-Maurosa, Michelle J. Serapiglia, Heather Mccormick, Virginia Brown, Naomi F. Young, Danny J. Schnell, Lawrence B. Smart, Michael G. Hahn, Jeffrey F. Pedersen, Susan B. Leschine, Samuel P. Hazen
Samuel P Hazen
Background - There is currently considerable interest in developing renewable sources of energy. One strategy is the biological conversion of plant biomass to liquid transportation fuel. Several technical hurdles impinge upon the economic feasibility of this strategy, including the development of energy crops amenable to facile deconstruction. Reliable assays to characterize feedstock quality are needed to measure the effects of pre-treatment and processing and of the plant and microbial genetic diversity that influence bioconversion efficiency. Results - We used the anaerobic bacterium Clostridium phytofermentans to develop a robust assay for biomass digestibility and conversion to biofuels. The assay utilizes the …
Brachypodium As A Model For The Grasses: Today And The Future, Jelena Brkljacic, Erich Grotewold, Randy Scholl, Todd Mockler, David F. Garvin, Philippe Vain, Thomas Brutnell, Richard Sibout, Michael Bevan, Hikmet Budak, Ana L. Caicedo, Caixia Gao, Yong Gu, Samuel P. Hazen, Ben F. Holt Iii, Shin-Young Hong, Antonio J. Manzaneda, Thomas Mitchell-Olds, Keiichi Mochida, Luis A. J. Mur, Chung-Mo Park, John Sedbrook, Michelle Watt, Shao Jian Zheng, John P. Vogel
Brachypodium As A Model For The Grasses: Today And The Future, Jelena Brkljacic, Erich Grotewold, Randy Scholl, Todd Mockler, David F. Garvin, Philippe Vain, Thomas Brutnell, Richard Sibout, Michael Bevan, Hikmet Budak, Ana L. Caicedo, Caixia Gao, Yong Gu, Samuel P. Hazen, Ben F. Holt Iii, Shin-Young Hong, Antonio J. Manzaneda, Thomas Mitchell-Olds, Keiichi Mochida, Luis A. J. Mur, Chung-Mo Park, John Sedbrook, Michelle Watt, Shao Jian Zheng, John P. Vogel
Samuel P Hazen
No abstract provided.
Exploring The Transcriptional Landscape Of Plant Circadian Rhythms Using Genome Tiling Arrays, Samuel P. Hazen, Felix Naef, Tom Quisel, Joshua M. Gendron, Huaming Chen, Joseph R. Ecker, Justin O. Borevitz, Steve A. Kay
Exploring The Transcriptional Landscape Of Plant Circadian Rhythms Using Genome Tiling Arrays, Samuel P. Hazen, Felix Naef, Tom Quisel, Joshua M. Gendron, Huaming Chen, Joseph R. Ecker, Justin O. Borevitz, Steve A. Kay
Samuel P Hazen
Background - Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome. Results - As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons, creating …
Development Of Genetic And Genomic Research Resources For Brachypodium Distachyon, A New Model System For Grass Crop Research, David F. Garvin, Yonb-Qiang Gu, Robert Hasterok, Samuel P. Hazen, Glyn Jenkins, Todd C. Mockler, Luis A J Mur, John P. Vogel
Development Of Genetic And Genomic Research Resources For Brachypodium Distachyon, A New Model System For Grass Crop Research, David F. Garvin, Yonb-Qiang Gu, Robert Hasterok, Samuel P. Hazen, Glyn Jenkins, Todd C. Mockler, Luis A J Mur, John P. Vogel
Samuel P Hazen
Grass crop genomics research frequently is hindered by large genome sizes and polyploidy. While rice is an attractive system for grass genomics due to its small genome size and available genome sequence, it is not particularly well-suited as a robust model system for all grass crops. The wild grass species Brachypodium distachyon (L.) P. Beauv. (Brachypodium) has recently gained favor as a new model system for grass crop genomics research because it possesses a suite of biological traits desired in a model system. Further, it is more closely related to the large and diverse group of cool season grass crops …
Network Discovery Pipeline Elucidates Conserved Time Of Day Specific Cis-Regulatory Modules, Samuel P. Hazen, T. P. Michael, T. C. Mocker, G. Brenton, C. Mcentee, A Byer, J. D. Trout, H. D. Priest, C. M. Sullivan, R. Shen, S. A. Givan, M. Yanovsky, F. Hong, S. A. Kay, J. A. Chory
Network Discovery Pipeline Elucidates Conserved Time Of Day Specific Cis-Regulatory Modules, Samuel P. Hazen, T. P. Michael, T. C. Mocker, G. Brenton, C. Mcentee, A Byer, J. D. Trout, H. D. Priest, C. M. Sullivan, R. Shen, S. A. Givan, M. Yanovsky, F. Hong, S. A. Kay, J. A. Chory
Samuel P Hazen
Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least …
Morning-Specific Phytohormone Gene Expression Program Underlying Rhythmic Plant Growth, Samuel P. Hazen, T. P. Michael, G. Breton, H. D. Priest, T. C. Mockler, S. A. Kay, J. A. Chory
Morning-Specific Phytohormone Gene Expression Program Underlying Rhythmic Plant Growth, Samuel P. Hazen, T. P. Michael, G. Breton, H. D. Priest, T. C. Mockler, S. A. Kay, J. A. Chory
Samuel P Hazen
Most organisms use daily light/dark cycles as timing cues to control many essential physiological processes. In plants, growth rates of the embryonic stem (hypocotyl) are maximal at different times of day, depending on external photoperiod and the internal circadian clock. However, the interactions between light signaling, the circadian clock, and growth-promoting hormone pathways in growth control remain poorly understood. At the molecular level, such growth rhythms could be attributed to several different layers of time-specific control such as phasing of transcription, signaling, or protein abundance. To determine the transcriptional component associated with the rhythmic control of growth, we applied temporal …
A High-Resolution Map Of Arabidopsis Recombinant Inbred Lines By Whole-Genome Array Hybridization, Samuel P. Hazen, T. S. Singer, Y. Fan, H. S. Chang, T. Zhu, S. P. Briggs
A High-Resolution Map Of Arabidopsis Recombinant Inbred Lines By Whole-Genome Array Hybridization, Samuel P. Hazen, T. S. Singer, Y. Fan, H. S. Chang, T. Zhu, S. P. Briggs
Samuel P Hazen
Recombinant populations were the basis for Mendel's first genetic experiments and continue to be key to the study of genes, heredity, and genetic variation today. Genotyping several hundred thousand loci in a single assay by hybridizing genomic DNA to oligonucleotide arrays provides a powerful technique to improve precision linkage mapping. The genotypes of two accessions of Arabidopsis were compared by using a 400,000 feature exon-specific oligonucleotide array. Around 16,000 single feature polymorphisms (SFPs) were detected in ~8,000 of the ~26,000 genes represented on the array. Allelic variation at these loci was measured in a recombinant inbred line population, which defined …
Rapid Array Mapping Of Circadian Clock And Developmental Mutations In Arabidopsis, Samuel P. Hazen, J. O. Borevitz, F. G. Harmon, J. L. Pruneda-Paz, T. F. Schultz, M. J. Yanovsky, S. J. Liljegren, J. R. Ecker, S. A. Kay
Rapid Array Mapping Of Circadian Clock And Developmental Mutations In Arabidopsis, Samuel P. Hazen, J. O. Borevitz, F. G. Harmon, J. L. Pruneda-Paz, T. F. Schultz, M. J. Yanovsky, S. J. Liljegren, J. R. Ecker, S. A. Kay
Samuel P Hazen
Classical forward genetics, the identification of genes responsible for mutant phenotypes, remains an important part of functional characterization of the genome. With the advent of extensive genome sequence, phenotyping and genotyping remain the critical limiting variables in the process of map-based cloning. Here, we reduce the genotyping problem by hybridizing labeled genomic DNA to the Affymetrix Arabidopsis (Arabidopsis thaliana) ATH1 GeneChip. Genotyping was carried out on the scale of detecting greater than 8,000 single feature polymorphisms from over 200,000 loci in a single assay. By combining this technique with bulk segregant analysis, several high heritability development and circadian clock traits …
Quantitative Trait Loci And Comparative Genomics Of Cereal Cell Wall Composition, Samuel P. Hazen, R. M. Hawley, G. L. Davis, B. Henrissat, J. D. Walton
Quantitative Trait Loci And Comparative Genomics Of Cereal Cell Wall Composition, Samuel P. Hazen, R. M. Hawley, G. L. Davis, B. Henrissat, J. D. Walton
Samuel P Hazen
Quantitative trait loci (QTLs) affecting sugar composition of the cell walls of maize (Zea mays) pericarp were mapped as an approach to the identification of genes involved in cereal wall biosynthesis. Mapping was performed using the IBM (B73 × Mo17) recombinant inbred line population. There were statistically significant differences between B73 and Mo17 in content of xylose (Xyl), arabinose (Ara), galactose (Gal), and glucose. Thirteen QTLs were found, affecting the content of Xyl (two QTLs), Ara (two QTLs), Gal (five QTLs), Glc (two QTLs), Ara + Gal (one QTL), and Xyl + Glc (one QTL). The chromosomal regions corresponding to …
Cellulose Synthase-Like (Csl) Genes Of Rice, Samuel P. Hazen, J. S. Scott-Craig, J. D. Walton
Cellulose Synthase-Like (Csl) Genes Of Rice, Samuel P. Hazen, J. S. Scott-Craig, J. D. Walton
Samuel P Hazen
No abstract provided.