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Wood secondary cell wall organisation and formation by glycomic and transcriptomic approaches
Curated by Guy COSTA
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Plants perform molecular maths

Plants perform molecular maths | SylvaLIM | Scoop.it
“Arithmetic division guides plants' use of energy at night.”
Via Sakis Koukouvis
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Cat Perrin's comment, July 12, 2013 6:12 AM
Plants are so incredible!!!
Yamuna Flaherty's curator insight, September 25, 2013 2:19 PM

Whoa!

robyns tut's curator insight, October 14, 2013 1:08 PM

This is an interesting science piece. You can research how this happens and whether research is going into learning how to replicate this in other objets.

-Tanah

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Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates 

Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates  | SylvaLIM | Scoop.it
The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.

Via Francis Martin
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Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates 

Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates  | SylvaLIM | Scoop.it
The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.

Via Francis Martin
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BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes | SylvaLIM | Scoop.it

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, February 7, 2016 9:39 PM

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.

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Secondary ion mass spectrometry imaging and multivariate data analysis reveal co-aggregation patterns of Populus trichocarpa leaf surface compounds on a micrometer scale

Secondary ion mass spectrometry imaging and multivariate data analysis reveal co-aggregation patterns of Populus trichocarpa leaf surface compounds on a micrometer scale | SylvaLIM | Scoop.it
“ Spatially resolved analysis of a multitude of compound classes has become feasible with the rapid advancement in mass spectrometry imaging strategies. In this study, we present a protocol that combines high lateral resolution time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging with a multivariate data analysis (MVA) approach to probe the complex leaf surface chemistry of Populus trichocarpa. Here, epicuticular waxes (EWs) found on the adaxial leaf surface of P. trichocarpa were blotted on silicon wafers and imaged using TOF-SIMS at 10 μm and 1 μm lateral resolution. Intense M+● and M−● molecular ions were clearly visible, which made it possible to resolve the individual compound classes present in EWs. Series of long-chain aliphatic saturated alcohols (C21–C30), hydrocarbons (C25–C33) and wax esters (WEs; C44–C48) were clearly observed. These data correlated with the 7Li-chelation matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, which yielded mostly molecular adduct ions of the analyzed compounds. Subsequently, MVA was used to interrogate the TOF-SIMS dataset for identifying hidden patterns on the leaf's surface based on its chemical profile. After the application of principal component analysis (PCA), a small number of principal components (PCs) were found to be sufficient to explain maximum variance in the data. To further confirm the contributions from pure components, a five-factor multivariate curve resolution (MCR) model was applied. Two distinct patterns of small islets, here termed ‘crystals’, were apparent from the resulting score plots. Based on PCA and MCR results, the crystals were found to be formed by C23 or C29 alcohols. Other less obvious patterns observed in the PCs revealed that the adaxial leaf surface is coated with a relatively homogenous layer of alcohols, hydrocarbons and WEs. The ultra-high-resolution TOF-SIMS imaging combined with the MVA approach helped to highlight the diverse patterns underlying the leaf's surface. Currently, the methods available to analyze the surface chemistry of waxes in conjunction with the spatial information related to the distribution of compounds are limited. This study uses tools that may provide important biological insights into the composition of the wax layer, how this layer is repaired after mechanical damage or insect feeding, and which transport mechanisms are involved in deploying wax constituents to specific regions on the leaf surface.”
Via Francis Martin
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Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae

Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae | SylvaLIM | Scoop.it
“ BMC Genomics is an open access journal publishing original peer-reviewed research articles in all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work. BMC series - open, inclusive and trusted.”
Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, January 24, 2016 3:54 PM
Background

Micro RNAs are a class of small non coding RNAs of 20–24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing.

Results

In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.

Conclusions

The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

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Genome Biology - Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity

Genome Biology - Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity | SylvaLIM | Scoop.it

Background

Microbe-associated molecular patterns, such as those present in bacterial flagellin, are powerful inducers of the innate immune response in plants. Successful pathogens deliver virulence proteins, termed effectors, into the plant cell where they can interfere with the immune response and promote disease. Engineering the plant immune system to enhance disease resistance requires a thorough understanding of its components.

Results

We describe a high-throughput screen, using RNA-seq and virus-induced gene silencing, to identify tomato genes whose expression is enhanced by the flagellin microbe-associated molecular pattern flgII-28, but reduced by activities of the Pseudomonas syringae pv. tomato (Pst) type III effectors AvrPto and AvrPtoB. Gene ontology terms for this category of FLAGELLIN-INDUCED REPRESSED BY EFFECTORS (FIRE) genes showed enrichment for genes encoding certain subfamilies of protein kinases and transcription factors. At least 25 of the FIRE genes have been implicated previously in plant immunity. Of the 92 protein kinase-encoding FIRE genes, 33 were subjected to virus-induced gene silencing and their involvement in pattern-triggered immunity was tested with a leaf-based assay. Silencing of one FIRE gene, which encodes the cell wall-associated kinase SlWAK1, compromised the plant immune response resulting in increased growth of Pst and enhanced disease symptoms.

Conclusions

Our transcriptomic approach identifies FIRE genes that represent a pathogen-defined core set of immune-related genes. The analysis of this set of candidate genes led to the discovery of a cell wall-associated kinase that participates in plant defense. The FIRE genes will be useful for further elucidation of the plant immune system.

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Cette forêt urbaine dont rêvent les Français

Cette forêt urbaine dont rêvent les Français | SylvaLIM | Scoop.it
“ La ville idéale des Français ressemble à une forêt urbaine, selon un sondage mené par l’Ifop pour l’Union nationale des entreprises du paysage (Unep). L’Unep y voit un révélateur des attentes de l’opinion, plus ou moins satisfaites selon les villes.”
Via Francis Martin
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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
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A universal RNA extraction protocol for land plants | RNA-Seq Blog

A universal RNA extraction protocol for land plants | RNA-Seq Blog | SylvaLIM | 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
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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) | SylvaLIM | 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
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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) | SylvaLIM | 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.
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Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways


Via Biswapriya Biswavas Misra
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Being in Mysteries

Being in Mysteries | SylvaLIM | Scoop.it
For an audio version of 'Being in Mysteries' click the play button The petals are like stiff velvet against my fingers, and the entrancing colour of blood. There is something otherworldly about this parasitic species; they don’t seem to belong to the surrounding community of plants. They’re amongst the rarest flowers in Europe and yet…
Via Neelima Sinha
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Demystifying traditional herbal medicine with modern approach

Demystifying traditional herbal medicine with modern approach | SylvaLIM | Scoop.it
“ Plants have long been recognized for their therapeutic properties. For centuries, indigenous cultures around the world have used traditional herbal medicine to treat a myriad of maladies. By contrast, the rise of the modern pharmaceutical industry in the past century has been based on exploiting individual active compounds with precise modes of action. This surge has yielded highly effective drugs that are widely used in the clinic, including many plant natural products and analogues derived from these products, but has fallen short of delivering effective cures for complex human diseases with complicated causes, such as cancer, diabetes, autoimmune disorders and degenerative diseases. While the plant kingdom continues to serve as an important source for chemical entities supporting drug discovery, the rich traditions of herbal medicine developed by trial and error on human subjects over thousands of years contain invaluable biomedical information just waiting to be uncovered using modern scientific approaches. Here we provide an evolutionary and historical perspective on why plants are of particular significance as medicines for humans. We highlight several plant natural products that are either in the clinic or currently under active research and clinical development, with particular emphasis on their mechanisms of action. Recent efforts in developing modern multi-herb prescriptions through rigorous molecular-level investigations and standardized clinical trials are also discussed. Emerging technologies, such as genomics and synthetic biology, are enabling new ways for discovering and utilizing the medicinal properties of plants. We are entering an exciting era where the ancient wisdom distilled into the world's traditional herbal medicines can be reinterpreted and exploited through the lens of modern science.”
Via Loïc Lepiniec, Ali Taheri
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A SIMPLE Pipeline for Mapping Point Mutations

A SIMPLE Pipeline for Mapping Point Mutations | SylvaLIM | Scoop.it
“ A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient, as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost efficiency and ease of data production afforded by next-generation sequencing have created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user friendly, are complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next-generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes. The pipeline has been validated in Arabidopsis thaliana (Arabidopsis) and can be readily applied to other species, with the possibility of mapping either dominant or recessive mutations. * ### Glossary EMS : ethyl methanesulfonate NGS : next-generation sequencing SNP : single-nucleotide polymorphism”
Via Ali Taheri
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Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae

Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae | SylvaLIM | Scoop.it
“ BMC Genomics is an open access journal publishing original peer-reviewed research articles in all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work. BMC series - open, inclusive and trusted.”
Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, January 24, 2016 3:54 PM
Background

Micro RNAs are a class of small non coding RNAs of 20–24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing.

Results

In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.

Conclusions

The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

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Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases

Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases | SylvaLIM | Scoop.it
“ The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species.”
Via Francis Martin
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Transcriptome analysis of secondary cell wall development in Medicago truncatula

Transcriptome analysis of secondary cell wall development in Medicago truncatula | SylvaLIM | Scoop.it
“BackgroundLegumes are important to humans by providing food, feed and raw materials for industrial utilizations. Some legumes, such as alfalfa, are potential bioenergy crops due to their high biomass productivity. Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening in Arabidopsis, but such transcriptome data is lacking in legumes.ResultsA systematic microarray assay and high through-put real time PCR analysis of secondary cell wall development were performed along stem maturation in Medicago truncatula. More than 11,000 genes were differentially expressed during stem maturation, and were categorized into 10 expression clusters. Among these, 279 transcription factor genes were correlated with lignin/cellulose biosynthesis, therefore representing putative regulators of secondary wall development. The b-ZIP, NAC, WRKY, C2H2 zinc finger (ZF), homeobox, and HSF gene families were over-represented. Gene co-expression network analysis was employed to identify transcription factors that may regulate the biosynthesis of lignin, cellulose and hemicellulose. As a complementary approach to microarray, real-time PCR analysis was used to characterize the expression of 1,045 transcription factors in the stem samples, and 64 of these were upregulated more than 5-fold during stem maturation. Reverse genetics characterization of a cellulose synthase gene in cluster 10 confirmed its function in xylem development.ConclusionsThis study provides a useful transcriptome and expression resource for understanding cell wall development, which is pivotal to enhance biomass production in legumes.”
Via Jean-Michel Ané
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Cette forêt urbaine dont rêvent les Français

Cette forêt urbaine dont rêvent les Français | SylvaLIM | Scoop.it
“ La ville idéale des Français ressemble à une forêt urbaine, selon un sondage mené par l’Ifop pour l’Union nationale des entreprises du paysage (Unep). L’Unep y voit un révélateur des attentes de l’opinion, plus ou moins satisfaites selon les villes.”
Via Francis Martin
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"Computer Chips Can Now Be Made From Wood" | MSN News - Popular Science | 05/28/15

"Computer Chips Can Now Be Made From Wood" | MSN News - Popular Science | 05/28/15 | SylvaLIM | Scoop.it
“The woods are lovely, dark, deep, and filled with potential computer components. ”
Via Franklin Delano Williams
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Franklin Delano Williams's curator insight, May 28, 2015 9:44 AM

....When There Is A Will, There is A Way!! We Can Save The Planet From Our Trash!!

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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
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Nice protocole for large scale data analysis
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Bioinformatics for Glycobiology and Glycomics: An Introduction - UBlog

Bioinformatics for Glycobiology and Glycomics: An Introduction - UBlog | SylvaLIM | 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
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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) | SylvaLIM | 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
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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
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