Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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Of Bacteria and Men: Plant pathogen focus: Pierce's disease and the vineyards of California (2013)

Of Bacteria and Men: Plant pathogen focus: Pierce's disease and the vineyards of California (2013) | Plant Gene Seeker -PGS | Scoop.it

Xylella fastidiosa  is not your ordinary kind of bug. It made it to the list of the most wanted plant pathogenic bacteria in 2012! This is well deserved: X. fastidiosa can infect over a hundred species (grapevine, oleander, citrus, almonds,…), and it causes severe symptoms that can kill the infected plant. TheXylella bacteria colonize the xylem vessels, and by doing so they block the transport of water in the plant. The water-deprived leaves dry and scorch, until finally they drop to the ground.

 

Check also the video on the glassy-winged sharpshooter leafhopper.


Via Kamoun Lab @ TSL, Mary Williams
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Hao-Xun Chang's comment, February 16, 2013 10:11 AM
I love your blog!!! I'm also study plant pathology~ I'll keep following.
Kamoun Lab @ TSL's comment, February 20, 2013 10:44 PM
Thanks for the kind comments :)
Diana Rivera's curator insight, March 4, 2013 6:08 PM

This type of pathogen can be very dangerous to any grower.  The Xylella Fastidiosa can whip out an entire harvest of crops, and some people might not understand how dangerous they can be to society.  By taking out feilds of crops they are putting our natural resource in danger.  Everyone needs to eat nutricious foods, but these pathogens are threating our health.

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Scientists Identify Genetic Mechanism That Contributed to Irish Famine

Scientists Identify Genetic Mechanism That Contributed to Irish Famine | Plant Gene Seeker -PGS | Scoop.it
February 6, 2013: Research by UC Riverside plant pathologists is the first to show that RNA silencing regulates plant defense against the notorious Phytophthora pathogens.
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Current Opinion in Plant Biology - Symbiosis and the social network of higher plants

Current Opinion in Plant Biology - Symbiosis and the social network of higher plants | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

In the Internet era, communicating with friends and colleagues via social networks constitutes a significant proportion of our daily activities. Similarly animals and plants also interact with many organisms, some of which are pathogens and do no good for the plant, while others are beneficial symbionts. Almost all plants indulge in developing social networks with microbes, in particular with arbuscular mycorrhizal fungi, and emerging evidence indicates that most employ an ancient and widespread central ‘social media’ pathway made of signaling molecules within what is called the SYM pathway. Some plants, like legumes, are particularly active recruiters of friends, as they have established very sophisticated and beneficial interactions with nitrogen-fixing bacteria, also via the SYM pathway. Interestingly, many members of the Brassicaceae, including the model plant Arabidopsis thaliana, seem to have removed themselves from this ancestral social network and lost the ability to engage in mutually favorable interactions with arbuscular mycorrhizal fungi. Despite these generalizations, recent studies exploring the root microbiota of A. thalianahave found that in natural conditions, A. thaliana roots are colonized by many different bacterial species and therefore may be using different and probably more recent ‘social media’ for these interactions. In general, recent advances in the understanding of such molecular machinery required for plant–symbiont associations are being obtained using high throughput genomic profiling strategies including transcriptomics, proteomics and metabolomics. The crucial mechanistic understanding that such data reveal may provide the infrastructure for future efforts to genetically manipulate crop social networks for our own food and fiber needs.

Highlights

► Most plants associate with arbuscular mycorrhizal fungi using an ancient and highly conserved SYM pathway. ► Most of this pathway has been lost in some plant families including the Brassicaceae. ► This SYM pathway has been usurped by some plant families such as the legumes to instead also associate with nitrogen-fixing bacteria. ► The possibility of manipulating this SYM pathway to engineer more efficient associations between nonleguminous crops and nitrogen-fixing bacteria is discussed.

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Current Opinion in Plant Biology - Plant hormone signaling during development: insights from computational models

Current Opinion in Plant Biology - Plant hormone signaling during development: insights from computational models | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Recent years have seen an impressive increase in our knowledge of the topology of plant hormone signaling networks. The complexity of these topologies has motivated the development of models for several hormones to aid understanding of how signaling networks process hormonal inputs. Such work has generated essential insights into the mechanisms of hormone perception and of regulation of cellular responses such as transcription in response to hormones. In addition, modeling approaches have contributed significantly to exploring how spatio-temporal regulation of hormone signaling contributes to plant growth and patterning. New tools have also been developed to obtain quantitative information on hormone distribution during development and to test model predictions, opening the way for quantitative understanding of the developmental roles of hormones.

Highlights

► Plant hormone signaling pathways exhibit complex topologies. ► Computational models predict the dynamics of hormone signaling. ► Modeling provides key insights on the role of hormones during growth and development. ► New tools allow for a quantitative understanding of hormone signaling.

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PLOS ONE: A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules

PLOS ONE: A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Andres Zurita's insight:

Short regulatory RNA-s have been identified as key regulators of gene expression in eukaryotes. They have been involved in the regulation of both physiological and pathological processes such as embryonal development, immunoregulation and cancer. One of their relevant characteristics is their high stability, which makes them excellent candidates for use as biomarkers. Their number is constantly increasing as next generation sequencing methods reveal more and more details of their synthesis. These novel findings aim for new detection methods for the individual short regulatory RNA-s in order to be able to confirm the primary data and characterize newly identified subtypes in different biological conditions. We have developed a flexible method to design RT-qPCR assays that are very sensitive and robust. The newly designed assays were tested extensively in samples from plant, mouse and even human formalin fixed paraffin embedded tissues. Moreover, we have shown that these assays are able to quantify endogenously generated shRNA molecules. The assay design method is freely available for anyone who wishes to use a robust and flexible system for the quantitative analysis of matured regulatory RNA-s.

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Rooting plant development - what's new since Dolan et al 1993 published "Cellular organisation of the Arabidopsis thaliana root"?

Rooting plant development - what's new since Dolan et al 1993 published "Cellular organisation of the Arabidopsis thaliana root"? | Plant Gene Seeker -PGS | Scoop.it

Here's a nice two page summary of the state-of-the field in 1993, what we've learned, and where we're going.


Via Mary Williams
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Andres Zurita's comment, February 13, 2013 7:14 AM
great analysis, unfortunately I couldn't break the paywall :)
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PLOS Genetics: A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Ge...

PLOS Genetics: A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Ge... | Plant Gene Seeker -PGS | Scoop.it
PLOS Genetics is an open-access
Andres Zurita's insight:

An important issue in understanding mechanisms of eukaryotic transcriptional regulation is how members of large transcription-factor families, with conserved DNA–binding domains (such as the 162-member Arabidopsis bHLH family), discriminate between target genes. However, the specific question of whether, and to what extent, closely related sub-family members, with potential overlapping functional redundancy (like the quartet of Phytochrome (phy)-Interacting bHLH transcription Factors (PIF1, 3, 4, and 5) studied here), share regulation of target genes through shared binding to promoter-localized consensus motifs does not appear to have been widely investigated. Here, using ChIP–seq analysis, we have identified genes that bind PIF3 to conserved, sequence-specific sites in their promoters; and, using RNA–seq, we have identified those genes displaying altered expression in various pif mutants. Integration of these data identifies those genes that are likely direct targets of transcriptional regulation by PIF3. Our data suggest that the PIF quartet members share directly in transcriptional activation of numerous target genes, potentially via redundant promoter occupancy, in a manner that varies quantitatively from gene to gene. This finding suggests that these PIFs function collectively as a signaling hub, selectively partitioning common upstream signals from light-activated phys at the transcriptional-network interface.

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Trends in Biotechnology - Plant genetic engineering and agricultural biotechnology 1983–2013


Via Plant Breeding and Genomics News
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From ozone depletion to agriculture: understanding the role of UV radiation in sustainable crop production - Wargent - 2013 - New Phytologist - Wiley Online Library

From ozone depletion to agriculture: understanding the role of UV radiation in sustainable crop production - Wargent - 2013 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Largely because of concerns regarding global climate change, there is a burgeoning interest in the application of fundamental scientific knowledge in order to better exploit environmental cues in the achievement of desirable endpoints in crop production. Ultraviolet (UV) radiation is an energetic driver of a diverse range of plant responses and, despite historical concerns regarding the damaging consequences of UV-B radiation for global plant productivity as related to stratospheric ozone depletion, current developments representative of a range of organizational scales suggest that key plant responses to UV-B radiation may be exploitable in the context of a sustainable contribution towards the strengthening of global crop production, including alterations in secondary metabolism, enhanced photoprotection, up-regulation of the antioxidative response and modified resistance to pest and disease attack. Here, we discuss the prospect of this paradigm shift in photobiology, and consider the linkages between fundamental plant biology and crop-level outcomes that can be applied to the plant UV-B response, in addition to the consequences for related biota and many other facets of agro-ecosystem processes.

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APSR1, a novel gene required for meristem maintenance, is negatively regulated by low phosphate availability- Plant Science

APSR1, a novel gene required for meristem maintenance, is negatively regulated by low phosphate availability- Plant Science | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:
Proper root growth is crucial for anchorage, exploration, and exploitation of the soil substrate. Root growth is highly sensitive to a variety of environmental cues, among them water and nutrient availability have a great impact on root development. Phosphorus (P) availability is one of the most limiting nutrients that affect plant growth and development under natural and agricultural environments. Root growth in the direction of the long axis proceeds from the root tip and requires the coordinated activities of cell proliferation, cell elongation and cell differentiation. Here we report a novel gene, APSR1 (Altered Phosphate Starvation Response1), involved in root meristem maintenance. The loss of function mutant apsr1-1 showed a reduction in primary root length and root apical meristem size, short differentiated epidermal cells and long root hairs. Expression of APSR1 gene decreases in response to phosphate starvation and apsr1-1 did not show the typical progressive decrease of undifferentiated cells at root tip when grown under P limiting conditions. Interestingly, APSR1 expression pattern overlaps with root zones of auxin accumulation. Furthermore,apsr1-1 showed a clear decrease in the level of the auxin transporter PIN7. These data suggest that APSR1is required for the coordination of cell processes necessary for correct root growth in response to phosphate starvation conceivably by direct or indirect modulation of PIN7. We also propose, based on its nuclear localization and structure, that APSR1 may potentially be a member of a novel group of transcription factors.

My Favourite Mutant by far!!!

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Science: Jack of All Trades, Master of Flowering

Science: Jack of All Trades, Master of Flowering | Plant Gene Seeker -PGS | Scoop.it

"Carbohydrates are thought to play a crucial role in the regulation of flowering, and trehalose-6-phosphate (T6P) has been suggested to function as a proxy for carbohydrate status in plants. The loss of TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) causes Arabidopsis thaliana to flower extremely late, even under otherwise inductive environmental conditions. This suggests that TPS1 is required for the timely initiation of flowering. We show that the T6P pathway affects flowering both in the leaves and at the shoot meristem, and integrate TPS1 into the existing genetic framework of flowering-time control. "


Via Mary Williams
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Mary Williams's curator insight, February 8, 2013 3:28 AM

Great! Trehalose-6-phophate is such an interesting molecule....

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The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Andres Zurita's insight:

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entitybranch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of theLEAFY (LFY) and terpene synthase (TPS) gene homologs.

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A Tripartite Growth Regulatory Cascade of Basic Helix-Loop-Helix Transcription Factors

A Tripartite Growth Regulatory Cascade of Basic Helix-Loop-Helix Transcription Factors | Plant Gene Seeker -PGS | Scoop.it

Plant growth is regulated by a multiplicity of factors, many of which are transduced via hormone signaling. However, how these hormone signals converge to affect growth is not entirely clear (reviewed in Depuydt and Hardtke, 2011). New work from Ikeda et al. (pages 4483–4497, November 2012) and Bai et al. (pages 4917–4929) demonstrates that the cell elongation component of growth is regulated by a mechanism involving groups of three basic helix-loop-helix (bHLH) transcription factors (some of which lack the basic domain).


Via Jennifer Mach
Andres Zurita's insight:

A free Plant Cell paper

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Flavonoids: Their Structure, Biosynthesis and Role in the Rhizosphere, Including Allelopathy

Flavonoids: Their Structure, Biosynthesis and Role in the Rhizosphere, Including Allelopathy | Plant Gene Seeker -PGS | Scoop.it

Flavonoids are biologically active low molecular weight secondary metabolites that are produced by plants, with over 10,000 structural variants now reported. Due to their physical and biochemical properties, they interact with many diverse targets in subcellular locations to elicit various activities in microbes, plants, and animals. In plants, flavonoids play important roles in transport of auxin, root and shoot development, pollination, modulation of reactive oxygen species, and signalling of symbiotic bacteria in the legume Rhizobium symbiosis. In addition, they possess antibacterial, antifungal, antiviral, and anticancer activities. In the plant, flavonoids are transported within and between plant tissues and cells, and are specifically released into the rhizosphere by roots where they are involved in plant/plant interactions or allelopathy. Released by root exudation or tissue degradation over time, both aglycones and glycosides of flavonoids are found in soil solutions and root exudates. Although the relative role of flavonoids in allelopathic interference has been less well-characterized than that of some secondary metabolites, we present classic examples of their involvement in autotoxicity and allelopathy. We also describe their activity and fate in the soil rhizosphere in selected examples involving pasture legumes, cereal crops, and ferns. Potential research directions for further elucidation of the specific role of flavonoids in soil rhizosphere interactions are considered.

 

Weston LA, Mathesius U. (2013) J Chem Ecol. Feb 9. [Epub ahead of print]


Via IvanOresnik, Mary Williams
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Mary Williams's comment, February 14, 2013 3:00 AM
This issue of Chemical Ecology also has reviews of allelopathy and cereal crops - rice, rye, sorghum http://link.springer.com/journal/10886/onlineFirst/page/1
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Quinoa, a catalyst for innovation - CIRAD

Quinoa, a catalyst for innovation - CIRAD | Plant Gene Seeker -PGS | Scoop.it
Quinoa, a catalyst for innovation : As the International Year of Quinoa begins, Didier Bazile shows in this new issue of Perspective
how the supply chain can have a significant effect on territorial development, above and beyond i...
Andres Zurita's insight:

An Andean mother pseudo-cereal that might a represent an outstanding source of high quality proteins for food security.

And a super-tolerance plant model as well.

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Current Opinion in Plant Biology - Gene regulatory networks in the Arabidopsis root

Current Opinion in Plant Biology - Gene regulatory networks in the Arabidopsis root | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Thanks to the increasing use of high-throughput tools in genetics, genomics, proteomics and metabolomics, a tremendous amount of information has been generated in the recent years. How these genes, transcripts, proteins and metabolites are inter-connected in a spatiotemporal context is one of the most ambitious goals that fundamental biology needs to answer. Owing to high quality data that are available, Arabidopsis thalianahas become an ideal organism for the application of bioinformatics and systems biology studies. The radially symmetrical structure of the Arabidopsis root and the ability to track developmental time in constrained cell files make this organ the perfect model to investigate different types of biological networks at a cell type-specific level. In this review we present the latest findings in this field as well as our perspective on the future of root biological networks.

Highlights

► Root networks with feedforward and autoregulatory loops and mobile factors. ► Perspectives on how biological context can be inferred from existing networks. ► Cell type-specific signals and hormone models of the root meristem. ► Data types and integration needed to characterize root cell type networks.

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ScienceDirect.com - Current Opinion in Plant Biology - Dynamic models of epidermal patterning as an approach to plant eco-evo-devo

ScienceDirect.com - Current Opinion in Plant Biology - Dynamic models of epidermal patterning as an approach to plant eco-evo-devo | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Epidermal patterning in Arabidopsis thaliana leaves and root has become a model system for experimental and theoretical developmental studies, yielding well-characterized regulatory networks. We succinctly review the dynamic models proposed for this system and then argue that it provides an excellent instance to integrate and further study the role of non-genetic factors in plant development and evolution. Then, we set up to review the role of phytohormones and environmental stimuli in the regulation of cell-fate determination and patterning in this system. We conclude that dynamic modeling of complex regulatory networks can help understand the plasticity and variability of cellular patterns, and hence, such modeling approaches can be expanded to advance in the consolidation of plant Evolutionary and Ecological Developmental Biology (eco-evo-devo).

Highlights

► Network models proposed for epidermal patterning in the leaf and root of Arabidopsis thaliana have helped to integrate data, understand the dynamics behind this process, and generate novel predictions. ► Epidermal patterns are plastic and emerge from complex interactions in gene regulatory networks, that feedback with hormonal systems and environmental factors. ► Modeling epidermal patterning will help establish and address some of the basic questions in Ecological Developmental Biology.

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GigaScience: Crowdsourcing genomic analyses of ash and ash dieback -- power to the people (2013)

GigaScience: Crowdsourcing genomic analyses of ash and ash dieback -- power to the people (2013) | Plant Gene Seeker -PGS | Scoop.it

Ash dieback is a devastating fungal disease of ash trees that has swept across Europe and recently reached the UK. This emergent pathogen has received little study in the past and its effect threatens to overwhelm the ash populations. In response to this we have produced some initial genomics datasets and taken the unusual step of releasing them to the scientific for analysis without first performing our own. In this manner we hope to 'crowdsource' analyses and bring the expertise of the community to bear on this problem as quickly as possible. Our data has been released through our website at oadb.tsl.ac.uk and a public GitHub repository.


Via Kamoun Lab @ TSL
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PLOS ONE: A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

PLOS ONE: A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Andres Zurita's insight:
BackgroundTraditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of “reverse desertification”. Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.Methodology/Principal FindingsWe assessed the structure of the microbiome associated to the drought-sensitive pepper plant (Capsicum annuum L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. Bacillus spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by Klebsiella spp. (61% and 44% respectively). Most of the isolates (95%) presented in vitro multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for Bacillus and the rhizobacteria strains. We show that the C. annuumrhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress.Conclusions/SignificanceCrop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a “resource island” able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.
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Rescooped by Andres Zurita from Food Security
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Goldman Sachs accused of profiting from food crisis

Goldman Sachs accused of profiting from food crisis | Plant Gene Seeker -PGS | Scoop.it
Speculating on food prices saw investment banking firm Goldman Sachs pocket more than one billion pounds in 2012, reigniting the controversy surrounding banks profiting from the global food crisis.

Via CIMMYT, Int.
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Trends in Plant Science - Phloem-mobile signals affecting flowers: applications for crop breeding

Trends in Plant Science - Phloem-mobile signals affecting flowers: applications for crop breeding | Plant Gene Seeker -PGS | Scoop.it

Transport of endogenous macromolecules within and between tissues serves as a signaling pathway to regulate numerous aspects of plant growth. The florigenic FT gene product moves via the phloem from leaves to apical tissues and induces the flowering program in meristems. Similarly, short interfering RNA (siRNA) signals produced in source or sink tissues move cell-to-cell and long distance via the phloem to apical tissues. Recent advances in identifying these mobile signals regulating flowering or the epigenetic status of targeted tissues can be applicable to crop-breeding programs. In this review, we address the identity of florigen, the mechanism of allocation, and how virus-induced flowering and grafting of transgenes producing siRNA signals affecting meiosis can produce transgene-free progenies useful for agriculture.


Via Jennifer Mach
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ScienceDirect.com - Current Biology - Moderation of Arabidopsis Root Stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 Receptor Kinase Complexes

ScienceDirect.com - Current Biology - Moderation of Arabidopsis Root Stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 Receptor Kinase Complexes | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:
Background

The root system of higher plants originates from the activity of a root meristem, which comprises a group of highly specialized and long-lasting stem cells. Their maintenance and number is controlled by the quiescent center (QC) cells and by feedback signaling from differentiated cells. Root meristems may have evolved from structurally distinct shoot meristems; however, no common player acting in stemness control has been found so far.

Results

We show that CLAVATA1 (CLV1), a key receptor kinase in shoot stemness maintenance, performs a similar but distinct role in root meristems. We report that CLV1 is signaling, activated by the peptide ligand CLAVATA3/EMBRYO SURROUNDING REGION40 (CLE40), together with the receptor kinase ARABIDOPSIS CRINKLY4 (ACR4) to restrict root stemness. Both CLV1 and ACR4 overlap in their expression domains in the distal root meristem and localize to the plasma membrane (PM) and plasmodesmata (PDs), where ACR4 preferentially accumulates. Using multiparameter fluorescence image spectroscopy (MFIS), we show that CLV1 and ACR4 can form homo- and heteromeric complexes that differ in their composition depending on their subcellular localization.

Conclusions

We hypothesize that these homo- and heteromeric complexes may differentially regulate distal root meristem maintenance. We conclude that essential components of the ancestral shoot stemness regulatory system also act in the root and that the specific interaction of CLV1 with ACR4 serves to moderate and control stemness homeostasis in the root meristem. The structural differences between these two meristem types may have necessitated this recruitment of ACR4 for signaling by CLV1.

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Andres Zurita's comment, February 12, 2013 7:24 AM
excellent! thanks for scooping it¡
Mary Williams's comment, February 12, 2013 7:40 AM
My pleasure - the integration of signals at the root meristem is one of my favorite topics!
Andres Zurita's comment, February 12, 2013 7:54 AM
Great, my favorite is root development modulation by abiotic stress
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Request for a serious reconsideration of the paper by Seralini &al - Wager &al (2013) - Food Chem Toxicol

As you are undoubtedly aware, the use of molecular methods to improve crop plants, now known as GMOs, continues to be a highly controversial subject globally despite the absence of evidence, to date, of human, animal or environment harm. The paper by Seralini et al. makes claims that contradict a large body of literature on the subject, reviewed recently in your journal by Snell et al. (2012). This review, analyses by serious scientific bodies, including the U.S. National Academy of Sciences and the Royal Society, as well as the European Union’s recent overview of 25 years of biosafety research on GMOs, all conclude that there are no negative health impacts specifically attributable to the use of molecular methods of crop improvement. Moreover, the herbicide glyphosate, which affects an enzyme present in plants, but not animals, has a short residence time in the environment and a long history of safe use, as does the bacterium Bacillus thuringiensis, from which the so-called “Bt” gene was transferred to a number of crops to render them resistant to certain kinds of insect pests.

 

Seralini et al. make the extraordinary claim that rats fed GM corn, with or without added glyphosate, develop tumors earlier in life and die prematurely compared with controls, attributing enhanced morbidity and mortality to consumption of the GM corn and herbicide. Such extraordinary claims must be based on sound and extensive evidence, as they are guaranteed to cause – and indeed, have caused – widespread alarm. As detailed below, this study does not provide sound evidence to support its claims. Indeed, the flaws in the study are so obvious that the paper should never have passed review. This appears to be a case of blatant misrepresentation and misinterpretation of data to advance an anti-GMO agenda by an investigator with a clear vested interest. We find it appalling that a journal with the substantial reputation of FCT published such “junk” science so clearly intended to alarm and mislead...


Via Alexander J. Stein, Jean-Pierre Zryd
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STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes...

STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes... | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. Better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. Earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in the form of Hidden Markov models at promoter, untranslated and upstream regions of stress-up-regulated genes from expression analysis can help in elucidating various aspects of the stress response in Arabidopsis. In addition to the extensive content in the first version, STIFDB2 is now updated with 15 stress signals, 31 transcription factors and 5,984 stress-responsive genes from three species (Arabidopsis thaliana, Oryza sativa subsp. japonica and Oryza sativa subsp. indica). We have employed an integrated biocuration and genomic data mining approach to characterize the data set of transcription factors and consensus binding sites from literature mining and stress-responsive genes from the Gene Expression Omnibus. STIFDB2 currently has 38,798 associations of stress signals, stress-responsive genes and transcription factor binding sites predicted using the Stress-responsive Transcription Factor (STIF) algorithm, along with various functional annotation data. As a unique plant stress regulatory genomics data platform, STIFDB2 can be utilized for targeted as well as high-throughput experimental and computational studies to unravel principles of the stress regulome in dicots and gramineae. STIFDB2 is available from the URL:http://caps.ncbs.res.in/stifdb2

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Rescooped by Andres Zurita from World Environment Nature News
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Biodiversity helps protect nature against human impacts

Biodiversity helps protect nature against human impacts | Plant Gene Seeker -PGS | Scoop.it
New research suggests farmers and resource managers should not rely on seemingly stable but vulnerable single-crop monocultures. Instead they should encourage more kinds of plants in fields and woods as a buffer against sudden ecosystem disturbance.

Via Maria Nunzia @Varvera
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