DougLIM
Follow
Find
28 views | +0 today
DougLIM
Research on plant cell wall
Curated by Guy COSTA
Your new post is loading...
Your new post is loading...
Rescooped by Guy COSTA from DougLIM
Scoop.it!

POMO - Plotting Omics analysis results for Multiple Organisms

“ Systems biology experiments studying different topics and organisms produce thousands of data values across different types of genomic data.”
Via Biswapriya Biswavas Misra, Guy COSTA
more...
No comment yet.
Rescooped by Guy COSTA from Plant Genetics, NGS and Bioinformatics
Scoop.it!

A universal RNA extraction protocol for land plants | RNA-Seq Blog

A universal RNA extraction protocol for land plants | RNA-Seq Blog | DougLIM | Scoop.it
“ New method will facilitate next-generation sequencing and comparative studies of gene expression RNA, a nucleic acid involved in protein synthesis, is widely”
Via Ali Taheri
more...
No comment yet.
Rescooped by Guy COSTA from Plant Pathogenomics
Scoop.it!

PLOS ONE: Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation (2013)

PLOS ONE: Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation (2013) | DougLIM | Scoop.it
Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum,Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. Thein silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.
Via Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

PLOS ONE: Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation (2013)

PLOS ONE: Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation (2013) | DougLIM | Scoop.it
Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum,Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. Thein silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.
more...
No comment yet.
Rescooped by Guy COSTA from Plant Genomics
Scoop.it!

Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways


Via Biswapriya Biswavas Misra
more...
No comment yet.
Rescooped by Guy COSTA from C@fé des Sciences
Scoop.it!

Pourquoi votre génome sera “pricé”

Pourquoi votre génome sera “pricé” | DougLIM | Scoop.it
“ Le Guardian Science a publié une tribune assez étrange sur l’exagération des craintes face au séquençage individuel de génomes.”
Via Goulu
more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

Genes' defense mechanism identified - San Francisco Chronicle

Genes' defense mechanism identified - San Francisco Chronicle | DougLIM | Scoop.it
Genes' defense mechanism identified San Francisco Chronicle The researchers looked at the effect of genistein-combined polysaccharide, or GCP, a proprietary extract made by a Japanese company, on prostate cancer cells in laboratory and animal...
more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

Roles of Predicted Glycosyltransferases in the Biosynthesis of the Rhizobium etli CE3 O Antigen.

The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer. The genetic regions required for its synthesis have been identified, and the nucleotide sequences are known. The structure of the O antigen has been determined, but the roles of specific genes in synthesizing this structure are relatively unclear. Within the known O-antigen genetic clusters of this strain, nine open reading frames (ORF) were found to contain a conserved glycosyltransferase domain. Each ORF was mutated, and the resulting mutant lipopolysaccharide (LPS) was analyzed. Tricine SDS-PAGE revealed stepwise truncations of the O antigen that were consistent with differences in mutant LPS sugar compositions and reactivity with O-antigen-specific monoclonal antibodies. Based on these results and current theories of O-antigen synthesis, specific roles were deduced for each of the nine glycosyltransferases, and a model for biosynthesis of the R. etli CE3 O antigen was proposed. In this model, O-antigen biosynthesis is initiated with the addition of N-acetyl-quinovosamine-phosphate (QuiNAc-P) to bactoprenol-phosphate by glycosyltransferase WreU. Glycosyltransferases WreG, WreE, WreS, and WreT would each act once to attach mannose, fucose, a second fucose, and 3-O-methyl-6-deoxytalose (3OMe6dTal), respectively. WreH then would catalyze the addition of methyl glucuronate (MeGlcA) to complete the first instance of the O-antigen repeat unit. Four subsequent repeats of this unit composed of fucose, 3OMe6dTal, and MeGlcA would be assembled by a cycle of reactions catalyzed by two additional glycosyltransferases, WreM and WreL, along with WreH. Finally, the O antigen would be capped by attachment of di- or tri-O-methylated fucose as catalyzed by glycosyltransferase WreB. Ojeda KJ, Simonds L, Noel KD. (2013). J Bacteriol. Feb 22. [Epub ahead of print]
more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

Glycogen metabolism

For more information, log on to- shomusbiology.weebly.com Download the study materials here- shomusbiology.weebly.com The overall reaction for the breakdown of glycogen to glucose-1-phosphate is: glycogen(n residues) + Pi is in equilibrium with...
more...
No comment yet.
Rescooped by Guy COSTA from PlantBioInnovation
Scoop.it!

POMO - Plotting Omics analysis results for Multiple Organisms

“ Systems biology experiments studying different topics and organisms produce thousands of data values across different types of genomic data.”
Via Biswapriya Biswavas Misra
Guy COSTA's insight:
Nice protocole for large scale data analysis
more...
No comment yet.
Rescooped by Guy COSTA from Plant Genomics
Scoop.it!

Bioinformatics for Glycobiology and Glycomics: An Introduction - UBlog

Bioinformatics for Glycobiology and Glycomics: An Introduction - UBlog | DougLIM | Scoop.it
“ The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the ...”
Via Biswapriya Biswavas Misra
more...
No comment yet.
Rescooped by Guy COSTA from Rhizobium Research
Scoop.it!

Calcium-Dependent Regulation of Genes for Plant Nodulation in Rhizobium leguminosarum Detected by iTRAQ Quantitative Proteomic Analysis - Journal of Proteome Research (ACS Publications)

Calcium-Dependent Regulation of Genes for Plant Nodulation in Rhizobium leguminosarum Detected by iTRAQ Quantitative Proteomic Analysis - Journal of Proteome Research (ACS Publications) | DougLIM | Scoop.it
Rhizobia, the nitrogen-fixing bacterial symbionts of legumes, represent an agricultural application of primary relevance and a model of plant–microbe molecular dialogues. We recently described rhizobium proteome alterations induced by plant flavonoids using iTRAQ. Herein, we further extend that experimentation, proving that the transient elevation in cytosolic calcium is a key signaling event necessary for the expression of the nodulation (nod) genes. Ca2+ involvement in nodulation is a novel issue that we recently flagged with genetic and physiological approaches and that hereby we demonstrate also by proteomics. Exploiting the multiple combinations of 4-plex iTRAQ, we analyzed Rhizobium leguminosarum cultures grown with or without the nod gene-inducing plant flavonoid naringenin and in the presence or absence of the extracellular Ca2+ chelator EGTA. We quantified over a thousand proteins, 189 of which significantly altered upon naringenin and/or EGTA stimulation. The expression of NodA, highly induced by naringenin, is strongly reduced when calcium availability is limited by EGTA. This confirms, from a proteomic perspective, that a Ca2+ influx is a necessary early step in flavonoid-mediated legume nodulation by rhizobia. We also observed other proteins affected by the different treatments, whose identities and roles in nodulation and rhizobium physiology are likewise discussed. J. Proteome Res., (2013). Publication Date (Web): September 16,
Via IvanOresnik
more...
No comment yet.
Rescooped by Guy COSTA from Space & Time
Scoop.it!

Cell Wall Assembly and Intracellular Trafficking in Plant Cells Are Directly Affected by Changes in the Magnitude of Gravitational Acceleration

Plants are able to sense the magnitude and direction of gravity. This capacity is thought to reside in selected cell types within the plant body that are equipped with specialized organelles called statoliths. However, most plant cells do not possess statoliths, yet they respond to changes in gravitational acceleration.
Via Michele Diodati
more...
No comment yet.
Rescooped by Guy COSTA from C@fé des Sciences
Scoop.it!

[Strange and Funky Animal Photographer] BIML

[Strange and Funky Animal Photographer] BIML | DougLIM | Scoop.it
“ BIML? Quoi t’est-ce? Et bien, derrière ce barbare sigle, ce cache le Laboratoire d’inventaire et de surveillance des abeilles (Bee Inventory and Monitoring Lab), extension de l’institut d’inspection géologique des Etats Unis (USGS).”
Via Goulu
more...
No comment yet.
Rescooped by Guy COSTA from DougLIM
Scoop.it!

Roles of Predicted Glycosyltransferases in the Biosynthesis of the Rhizobium etli CE3 O Antigen.

The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer. The genetic regions required for its synthesis have been identified, and the nucleotide sequences are known. The structure of the O antigen has been determined, but the roles of specific genes in synthesizing this structure are relatively unclear. Within the known O-antigen genetic clusters of this strain, nine open reading frames (ORF) were found to contain a conserved glycosyltransferase domain. Each ORF was mutated, and the resulting mutant lipopolysaccharide (LPS) was analyzed. Tricine SDS-PAGE revealed stepwise truncations of the O antigen that were consistent with differences in mutant LPS sugar compositions and reactivity with O-antigen-specific monoclonal antibodies. Based on these results and current theories of O-antigen synthesis, specific roles were deduced for each of the nine glycosyltransferases, and a model for biosynthesis of the R. etli CE3 O antigen was proposed. In this model, O-antigen biosynthesis is initiated with the addition of N-acetyl-quinovosamine-phosphate (QuiNAc-P) to bactoprenol-phosphate by glycosyltransferase WreU. Glycosyltransferases WreG, WreE, WreS, and WreT would each act once to attach mannose, fucose, a second fucose, and 3-O-methyl-6-deoxytalose (3OMe6dTal), respectively. WreH then would catalyze the addition of methyl glucuronate (MeGlcA) to complete the first instance of the O-antigen repeat unit. Four subsequent repeats of this unit composed of fucose, 3OMe6dTal, and MeGlcA would be assembled by a cycle of reactions catalyzed by two additional glycosyltransferases, WreM and WreL, along with WreH. Finally, the O antigen would be capped by attachment of di- or tri-O-methylated fucose as catalyzed by glycosyltransferase WreB. Ojeda KJ, Simonds L, Noel KD. (2013). J Bacteriol. Feb 22. [Epub ahead of print]

more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

Natural Variation in Grain Composition of Wheat and Related Cereals - Journal of Agricultural and Food Chemistry (ACS Publications)

Natural Variation in Grain Composition of Wheat and Related Cereals - Journal of Agricultural and Food Chemistry (ACS Publications) | DougLIM | Scoop.it
The wheat grain comprises three groups of major components, starch, protein, and cell wall polysaccharides (dietary fiber), and a range of minor components that may confer benefits to human health. Detailed analyses of dietary fiber and other bioactive components were carried out under the EU FP6 HEALTHGRAIN program on 150 bread wheat lines grown on a single site, 50 lines of other wheat species and other cereals grown on the same site, and 23–26 bread wheat lines grown in six environments. Principal component analysis allowed the 150 bread wheat lines to be classified on the basis of differences in their contents of bioactive components and wheat species (bread, durum, spelt, emmer, and einkorn wheats) to be clearly separated from related cereals (barley, rye, and oats). Such multivariate analyses could be used to define substantial equivalence when novel (including transgenic) cereals are considered.
more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium ... - 7thSpace Interactive (press release)

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium ...
more...
No comment yet.
Scooped by Guy COSTA
Scoop.it!

AGPs in Trithuria reproductive structures

AGPs in Trithuria reproductive structures | DougLIM | Scoop.it
Trithuria is the sole genus of Hydatellaceae, a family of the early-divergent angiosperm lineage Nymphaeales. In order to help determine the early evolution of angiosperm cell-wall structures, Cost...
more...
No comment yet.