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Rescooped by Olivier ANDRE from Plant immunity and legume symbiosis
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Natural Variations and Genome-Wide Association Studies in Crop Plants

Natural Variations and Genome-Wide Association Studies in Crop Plants | biotechnology | Scoop.it

In eukaryotic RNA silencing, RNase-III classes of enzymes in the Dicer family process double-stranded RNA of cellular or exogenous origin into small-RNA (sRNA) molecules. sRNAs are then loaded into effector proteins known as ARGONAUTEs (AGOs), which, as part of RNA-induced silencing complexes, target complementary RNA or DNA for silencing. Plants have evolved a large variety of pathways over the Dicer–AGO consortium, which most likely underpins part of their phenotypic plasticity. Dicer-like proteins produce all known classes of plant silencing sRNAs, which are invariably stabilized via 2′-O-methylation mediated by HUA ENHANCER 1 (HEN1), potentially amplified by the action of several RNA-dependent RNA polymerases, and function through a variety of AGO proteins. Here, we review the known characteristics and biochemical properties of the core silencing factors found in the model plant Arabidopsis thaliana. We also describe how interactions between these core factors and more specialized proteins allow the production of a plethora of silencing sRNAs involved in a large array of biological functions. We emphasize in particular the biogenesis and activities of silencing sRNAs of endogenous origin.


Via Christophe Jacquet
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Rescooped by Olivier ANDRE from Plant roots and rhizosphere
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Root architecture and root and tuber crop productivity

Root architecture and root and tuber crop productivity | biotechnology | Scoop.it

It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.


Via Christophe Jacquet
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Rescooped by Olivier ANDRE from The Plant Microbiome
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BMC Bioinformatics: a website for visualization and analysis of microbial population structures

BMC Bioinformatics: a website for visualization and analysis of microbial population structures | biotechnology | Scoop.it

The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105-108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators' private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.


Via Stéphane Hacquard
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Scooped by Olivier ANDRE
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Cells Go Solo (science 2013)

Cells Go Solo (science 2013) | biotechnology | Scoop.it

The scientific literature contains an enormous body of work in which large numbers of cells have been broken open and homogenized to prepare samples for biochemical characterization and, certainly, much has been learned from such studies. But more recently, it has become possible to monitor events in single cells, thus allowing investigators to test whether existing “averaged” readings of the state of many cells from traditional large-scale assays accurately represent the behavior of the individual cells being studied. Such single-cell measurements are providing a wealth of information—sometimes unanticipated and often previously obscured—about how cells respond to perturbations or signals. In this special issue, three Reviews provide examples of fundamental insights into cellular regulation that are revealed when it is possible to measure enzymatic activity, transcriptional responses, or the metabolic state in individual cells

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Scooped by Olivier ANDRE
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Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells (Nature biotechnology 2013)

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells (Nature biotechnology 2013) | biotechnology | Scoop.it

Genome sequencing of single cells has a variety of applications, including characterizing difficult-to-culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and their genetic material is simultaneously amplified for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated, nanoliter-scale reactors, facilitating the de novo assembly of near-complete microbial genomes from single Escherichia coli cells. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1- to 2-Mb resolution. MIDAS can potentially further the characterization of genomic diversity in many heterogeneous cell populations

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Rescooped by Olivier ANDRE from Plant microbe interactions
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PLOS Genetics: The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters

PLOS Genetics: The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters | biotechnology | Scoop.it
Changes in chromatin structure are required for time- and tissue-specific gene regulation. How exactly these changes are mediated is under intense scrutiny. The interplay between activating histone modifications, e.g. H3K4me, and the silencing H3K27me3 mark has been recognized as critical to orchestrate differentiation and development in plants and animals. Here we show that filamentous fungi, exemplified by the cereal pathogen Fusarium graminearum, can use H3K27 methylation to generate silenced, facultative heterochromatin, covering more than a third of the genome, much more than the 5–8% of Neurospora or metazoan genomes. Removal of the silencing mark by mutation of the methyltransferase subunit of the PRC2 silencing complex resulted in activation of more than 1,500 genes, 14% of the genome. We show that generation of facultative heterochromatin by H3K27 methylation is an ancestral process that has been lost in certain lineages (e.g. at least some hemiascomycetes, the genus Aspergillus and some basidiomycetes). Our studies will open the door to future precise “epigenetic engineering” of gene clusters that generate bioactive compounds, e.g. putative mycotoxins, antibiotics and industrial feedstocks. Availability of tractable fungal model systems for studies of the control and function of H3K27 methylation may accelerate mechanistic research
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Advanced genetic tools for plant biotechnology (Nature Reviews Genetics 2013)

Advanced genetic tools for plant biotechnology (Nature Reviews Genetics 2013) | biotechnology | Scoop.it

Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.

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RNAi Animation (Nature Reviews Genetics)

RNAi Animation (Nature Reviews Genetics) | biotechnology | Scoop.it

RNA interference (RNAi)

RNA interference (RNAi) is an important pathway that is used in many different organisms to regulate gene expression. This animation introduces the principles of RNAi involving small interfering RNAs (siRNAs) and microRNAs (miRNAs). We take you on an audio-visual journey through the steps of gene expression and show you an up-to-date view of how RNAi can silence specific mRNAs in the cytoplasm.

The accompanying slideshow provides further information about RNAi and small RNAs.

When the video is streamed, the resolution will adjust to match the speed of your internet connection. To view the animation in full-screen mode, please click the icon showing the square with arrows.

To expand the slideshow, please click the icon showing the square and an arrow.

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European Parliament votes to limit crop-based biofuels : Nature News Blog

European Parliament votes to limit crop-based biofuels : Nature News Blog | biotechnology | Scoop.it

The European Union Parliament voted today to limit Europe’s use of biofuels based on crops such as palm oil and soya beans, years after scientists pointed out that making fuel from food crops can do more harm than good to the environment.

The vote shows that politicians want to slow the use of conventional crop-based biofuels, after a decade of encouraging their expansion.

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Rescooped by Olivier ANDRE from Plant & Evolution
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Synthetic biology approaches to engineering the nitrogen symbiosis in cereals

Synthetic biology approaches to engineering the nitrogen symbiosis in cereals | biotechnology | Scoop.it

Nitrogen is abundant in the earth’s atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical fertilizers. The chemical reduction of nitrogen for this purpose consumes large amounts of energy and the reactive nitrogen released into the environment as a result of fertilizer application leads to greenhouse gas emissions, as well as widespread eutrophication of aquatic ecosystems. The environmental impacts are intensified by injudicious use of fertilizers in many parts of the world. Simultaneously, limitations in the production and supply of chemical fertilizers in other regions are leading to low agricultural productivity and malnutrition. Nitrogen can be directly fixed from the atmosphere by some bacteria and Archaea, which possess the enzyme nitrogenase. Some plant species, most notably legumes, have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering cereal crops with the capability to fix their own nitrogen could one day address the problems created by the over- and under-use of nitrogen fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the cereal crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. While potentially transformative, these biotechnological approaches are challenging; however, with recent advances in synthetic biology they are viable long-term goals. This review discusses the possibility of these biotechnological solutions to the nitrogen problem, focusing on engineering the nitrogen symbiosis in cereals.


Via Jean-Michel Ané, Pierre-Marc Delaux
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Rescooped by Olivier ANDRE from ROOTBOARD
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CurrOpinPlantBiol: DNA assembly for plant biology: techniques and tools

CurrOpinPlantBiol: DNA assembly for plant biology: techniques and tools | biotechnology | Scoop.it

Via Mary Williams, ROOTSPROUT
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Scooped by Olivier ANDRE
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Accelerating plant breeding (Trends in Plant Science 2014)

Accelerating plant breeding (Trends in Plant Science 2014) | biotechnology | Scoop.it

The growing demand for food with limited arable land available necessitates that the yield of major food crops continues to increase over time. Advances in marker technology, predictive statistics, and breeding methodology have allowed for continued increases in crop performance through genetic improvement. However, one major bottleneck is the generation time of plants, which is biologically limited and has not been improved since the introduction of doubled haploid technology. In this opinion article, we propose to implement in vitro nurseries, which could substantially shorten generation time through rapid cycles of meiosis and mitosis. This could prove a useful tool for speeding up future breeding programs with the aim of sustainable food production.

Olivier ANDRE's insight:

Highlights

We propose a concept for an in vitro nursery as a tool to reduce cycle time.Rapid cycles of meiosis and mitosis would enable multiple generations per year.In vitro production and fusion of artificial gametes is crucial for this method.Potential applications of rapid cycling are discussed.
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Scooped by Olivier ANDRE
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Evolution of crop species: genetics of domestication and diversification : Nature Reviews Genetics : Nature Publishing Group

Evolution of crop species: genetics of domestication and diversification : Nature Reviews Genetics : Nature Publishing Group | biotechnology | Scoop.it

Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

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Scooped by Olivier ANDRE
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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions (Nature biotechnology 2013)

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions (Nature biotechnology 2013) | biotechnology | Scoop.it

Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project. To address this problem, we need scalable, cost-effective methods to obtain assemblies with chromosome-scale contiguity. Here we show that genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres. To exploit this finding, we developed an algorithm that uses Hi-C data for ultra-long-range scaffolding of de novo genome assemblies. We demonstrate the approach by combining shotgun fragment and short jump mate-pair sequences with Hi-C data to generate chromosome-scale de novo assemblies of the human, mouse and Drosophila genomes, achieving—for the human genome—98% accuracy in assigning scaffolds to chromosome groups and 99% accuracy in ordering and orienting scaffolds within chromosome groups. Hi-C data can also be used to validate chromosomal translocations in cancer genomes.

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Scooped by Olivier ANDRE
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A proposal to use gamete cycling in vitro to improve crops and livestock ( nature biotechnology 2013)

A proposal to use gamete cycling in vitro to improve crops and livestock ( nature biotechnology 2013) | biotechnology | Scoop.it

The grand challenge of producing enough food, fiber and fuel for an ever-growing global population has benefited tremendously from genetic improvements in agriculturally important plants and animals over the past century. These genetic modifications have enabled billions more people to meet basic needs while using less arable land and providing good returns on research investment. Yet despite reductions in malnutrition-driven stunting and wasting, many humans remain undernourished. Satisfying these basic needs becomes more challenging with climate variability, constraints on productive farmland and limited availability of off-farm inputs (e.g., water, pesticides, phosphorus). Here, we outline the potential implications of an in vitro approach (thus far demonstrated in mice) for generating mature, fully functional female gametes from embryonic and induced pluripotent stem cells, as a means for rapidly breeding and introducing new traits into livestockand crops

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Scooped by Olivier ANDRE
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Emerging molecular mechanisms for biotechnological harnessing of heterosis in crops (Trends in Biotechnology 2013)

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Rescooped by Olivier ANDRE from Plant microbe interactions
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Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication

Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication | biotechnology | Scoop.it

 

production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground compartment and evolution of mutualistic strategy, are proposed in this opinion article. In this context, we argue that plant breeders have the opportunity to make use of native arbuscular mycorrhizal (AM) symbiosis in an innovative ecologically intensive agriculture.

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Scooped by Olivier ANDRE
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Cell picture show (Cell 2013)

Cell picture show (Cell 2013) | biotechnology | Scoop.it
What is the Cell Picture Show?

A place to showcase striking images in cell, developmental, and molecular biology; a place to learn about cutting-edge research with beautiful images.

Want to contribute?

Send us your lab's most artistic or interesting images obtained from your day-to-day research for consideration in an upcoming slideshow

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Olivier ANDRE's comment, September 23, 2013 1:28 AM
Beautiful !
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Zinc Fingers, TAL Effectors, or Cas9-Based DNA Binding Proteins: What’s Best for Targeting Desired Genome Loci?

Zinc Fingers, TAL Effectors, or Cas9-Based DNA Binding Proteins: What’s Best for Targeting Desired Genome Loci? | biotechnology | Scoop.it
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Rescooped by Olivier ANDRE from Plant-Microbe Symbiosis
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Biotechnological solutions to the nitrogen problem

Biotechnological solutions to the nitrogen problem | biotechnology | Scoop.it

The availability of nitrogen is one of the major limiting factors to crop growth. In the developed world, farmers use unsustainable levels of inorganic fertilisers to promote crop production. In contrast, in the developing world inorganic fertilisers are often not available and small-holder farmers suffer the resultant poor yields. Finding alternatives to inorganic fertilisers is critical for sustainable and secure food production. Bacteria and Archaea have evolved the capability to fix atmospheric nitrogen to ammonia, a form readily usable in biological processes. This capability presents an opportunity to improve the nutrition of crop plants, through the introduction into cereal crops of either the nitrogen fixing bacteria or the nitrogenase enzyme responsible for nitrogen fixation. While both approaches are challenging, recent advances have laid the groundwork to initiate these biotechnological solutions to the nitrogen problem.


Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, September 14, 2013 11:52 AM

No need to say that I agree with that!

Serenella A Sukno's comment, September 23, 2013 5:01 AM
cool!
Olivier ANDRE's comment, September 23, 2013 12:18 PM
Next green revolution ?