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Rescooped by hunter chen from Plant pathogens and pests
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Frontiers | Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance | Plant Biotechnology

Frontiers | Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance | Plant Biotechnology | Biotech | Scoop.it
Plant viruses infect many economically important crops, including wheat, cotton, maize, cassava, and other vegetables. These viruses pose a serious threat to agriculture worldwide, as decreases in cropland area per capita may cause production to fall short of that required to feed the increasing world population. Under these circumstances, conventional strategies can fail to control rapidly evolving and emerging plant viruses. Genome-engineering strategies have recently emerged as promising tools to introduce desirable traits in many eukaryotic species, including plants. Among these genome engineering technologies, the CRISPR (clustered regularly interspaced palindromic repeats)/CRISPR-associated 9 (CRISPR/Cas9) system has received special interest because of its simplicity, efficiency, and reproducibility. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. Here, we briefly describe the biology of the CRISPR/Cas9 system and plant viruses, and how different genome engineering technologies have been used to target these viruses. We further describe the main findings from recent studies of CRISPR/Cas9-mediated viral interference and discuss how these findings can be applied to improve global agriculture. We conclude by pinpointing the gaps in our knowledge and the outstanding questions regarding CRISPR/Cas9-mediated viral immunity.

Via Christophe Jacquet
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Genome editing comes of age - Nature Protocols

Genome editing comes of age - Nature Protocols | Biotech | Scoop.it

Kim 2016,

Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)–Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). I specifically highlight the key advances that set the foundation for the rapid and widespread implementation of CRISPR–Cas9 genome editing approaches that has revolutionized the field.


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Ingrid M's curator insight, August 11, 2016 10:34 AM
While there may be many corrective and beneficial uses for gene editing, there are few scarier prospects of science-gone-wrong.

Rescooped by hunter chen from Plant-microbe interaction
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Current Biology: Pathogen Tactics to Manipulate Plant Cell Death (2016)

Current Biology: Pathogen Tactics to Manipulate Plant Cell Death (2016) | Biotech | Scoop.it

Programmed cell death (PCD) is a conserved process among eukaryotes that serves a multitude of functional roles during an organism’s natural life cycle. PCD involves the tightly regulated process of cell death cued by specific spatiotemporal stimuli, which confer survival benefits. In eukaryotes, PCD is an essential process involved in senescence, aging, embryo development, cell differentiation, and immunity. In animal systems, morphologically distinct forms of PCD have been described (Figure 1) [1, 2]. Type I, or apoptotic cell death, is the best understood form of PCD and is defined by cell shrinkage, nuclear condensation and fragmentation, and eventual disintegration of the cell into apoptotic bodies that are digested by phagocytes. Type II cell death is an autophagic process that is induced during nutrient deprivation and chronic stress. Autophagic cell death is characterized by the rupture of the lysosome and subsequent release of toxic chemicals that degrade the cell contents. Unlike type I and type II, type III PCD is distinguished by the swelling of organelles and subsequent rupture of the plasma membrane. A programmed necrosis or necroptosis was initially believed to be an uncontrolled process of necrosis, but has been recently reclassified as type III form of cell death. Finally, pyroptosis is another recently categorized form of cell death that is mediated by caspase-1 activity. Morphologically, pyroptotic cells share characteristics of both apoptosis and necrosis [1]. Noteworthy, necroptosis and pyroptosis are pro-inflammatory forms of PCD activated by microbial infections and diverse environmental stimuli.

 

In plants, PCD is less rigorously classified (Figure 1). One difficulty in distinguishing the forms of PCD in plants and animals comes as a result of the different cellular morphology in plant cells — most notably the presence of the cell wall and chloroplasts. Unlike the plasma membrane, the degradation of the cell wall is not a universal feature of PCD in plants. Additionally, the formation of apoptotic bodies is not observed in plant cells, as there are no circulating phagocytes to engulf them [3]. Instead, plant cells committed to PCD release autolytic compounds stored in the vacuole that degrade cell contents. In these cases, the cell wall may develop perforations for the absorption and recycling of cellular components by neighboring cells. Although not as well characterized as the mitochondria, the chloroplasts have been shown to induce light-dependent PCD through singlet oxygen species (1O2) that may function in parallel to mitochondrial-mediated PCD at an early step in initiating the rupture of the vacuole [3].

 

A specialized form of plant cell death called hypersensitive response (HR) is initiated as a defense response to pathogen infection. HR shares morphological features and molecular mechanisms reminiscent of both pyroptosis and necroptosis [4]. Moreover, HR is unique in that it induces a signaling cascade to propagate immunity in neighboring cells as well as priming distal tissues for potential pathogen challenge, a phenomenon known as systemic acquired resistance [5]. Here we will briefly describe diverse plant disease resistance pathways, early molecular events during pathogen perception, and downstream signaling components. We will thoroughly discuss how pathogens have evolved strategies to circumvent and/or suppress diverse immune responses, in particular plant cell death. While many of these mechanisms involve indirect disabling of upstream immune responses to avoid cell death, direct manipulation of PCD regulators by pathogen effectors has not been extensively explored in the literature, and will be the focal point of this article.


Via Kamoun Lab @ TSL, Suayib Üstün
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Rakesh Yashroy's curator insight, July 27, 2016 10:06 PM
Good description of APOPTOSIS in animal and plant cells. Gram negative pathogens like Salmonella use their outer membrane vesicles to signal hijacking and apoptosis in defense macrophages in animal body @ http://s3.amazonaws.com/academia.edu.documents/33932139/1211.pdf?AWSAccessKeyId=AKIAJ56TQJRTWSMTNPEA&Expires=1469674971&Signature=0HXlHa3eNfInsWTE0YqGOgD6HTA%3D&response-content-disposition=inline%3B%20filename%3DYashRoy_R_C_2007_Mechanism_of_infection.pdf
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BioEssays: Pathogen perception by NLRs in plants and animals: Parallel worlds

BioEssays: Pathogen perception by NLRs in plants and animals: Parallel worlds | Biotech | Scoop.it
Intracellular NLR (Nucleotide-binding domain and Leucine-rich Repeat-containing) receptors are sensitive monitors that detect pathogen invasion of both plant and animal cells. NLRs confer recognition of diverse molecules associated with pathogen invasion. NLRs must exhibit strict intramolecular controls to avoid harmful ectopic activation in the absence of pathogens. Recent discoveries have elucidated the assembly and structure of oligomeric NLR signalling complexes in animals, and provided insights into how these complexes act as scaffolds for signal transduction. In plants, recent advances have provided novel insights into signalling-competent NLRs, and into the myriad strategies that diverse plant NLRs use to recognise pathogens. Here, we review recent insights into the NLR biology of both animals and plants. By assessing commonalities and differences between kingdoms, we are able to develop a more complete understanding of NLR function.

Via Christophe Jacquet, Jim Alfano
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Plant Aquaporin AtPIP1;4 Links Apoplastic H2O2 Induction to Disease Immunity Pathways

Plant Aquaporin AtPIP1;4 Links Apoplastic H2O2 Induction to Disease Immunity Pathways | Biotech | Scoop.it
Hydrogen peroxide (H2O2) is a stable component of reactive oxygen species, and its production in plants represents the successful recognition of pathogen infection and pathogen-associated molecular patterns (PAMPs). This production of H2O2 is typically apoplastic but is subsequently associated with intracellular immunity pathways that regulate disease resistance, such as systemic acquired resistance and PAMP-triggered immunity. Here, we elucidate that an Arabidopsis (Arabidopsis thaliana) aquaporin (i.e. the plasma membrane intrinsic protein AtPIP1;4) acts to close the cytological distance between H2O2 production and functional performance. Expression of the AtPIP1;4 gene in plant leaves is inducible by a bacterial pathogen, and the expression accompanies H2O2 accumulation in the cytoplasm. Under de novo expression conditions, AtPIP1;4 is able to mediate the translocation of externally applied H2O2 into the cytoplasm of yeast (Saccharomyces cerevisiae) cells. In plant cells treated with H2O2, AtPIP1;4 functions as an effective facilitator of H2O2 transport across plasma membranes and mediates the translocation of externally applied H2O2 from the apoplast to the cytoplasm. The H2O2-transport role of AtPIP1;4 is essentially required for the cytoplasmic import of apoplastic H2O2 induced by the bacterial pathogen and two typical PAMPs in the absence of induced production of intracellular H2O2. As a consequence, cytoplasmic H2O2 quantities increase substantially while systemic acquired resistance and PAMP-triggered immunity are activated to repress the bacterial pathogenicity. By contrast, loss-of-function mutation at the AtPIP1;4 gene locus not only nullifies the cytoplasmic import of pathogen- and PAMP-induced apoplastic H2O2 but also cancels the subsequent immune responses, suggesting a pivotal role of AtPIP1;4 in apocytoplastic signal transduction in immunity pathways.

Via Christophe Jacquet
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Science stars of China

Science stars of China | Biotech | Scoop.it

From Nature, Science stars of China. Includes a profile of Caixia Gao: Crop engineer, "A gene-editing specialist seeks to make her mark by improving key agricultural plants.".


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Open access resources for genome-wide association mapping in rice : Nature Communications : Nature Publishing Group

Open access resources for genome-wide association mapping in rice : Nature Communications : Nature Publishing Group | Biotech | Scoop.it
Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

Via Yogesh Gupta, Jennifer Mach
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Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system

To reduce crop losses due to geminivirus infection, we targeted the bean yellow dwarf virus (BeYDV) genome for destruction with the CRISPR–Cas (clustered, regularly interspaced short palindromic repeats–CRISPR-associated proteins) system. Transient assays using BeYDV-based replicons revealed that CRISPR–Cas reagents introduced mutations within the viral genome and reduced virus copy number. Transgenic plants expressing CRISPR–Cas reagents and challenged with BeYDV had reduced virus load and symptoms, thereby demonstrating a novel strategy for engineering resistance to geminiviruses.


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Jennifer Mach's curator insight, October 6, 2015 2:58 PM

One of a pair of papers in Nature Plants on using CRISPR-Cas for immunity in plants.

Rescooped by hunter chen from Plant Biology Teaching Resources (Higher Education)
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With BioDirect, Monsanto Hopes RNA Sprays Can Someday Deliver Drought Tolerance and Other Traits to Plants on Demand | MIT Technology Review

With BioDirect, Monsanto Hopes RNA Sprays Can Someday Deliver Drought Tolerance and Other Traits to Plants on Demand | MIT Technology Review | Biotech | Scoop.it
Deep inside its labs, Monsanto is learning how to modify crops by spraying them with RNA rather than tinkering with their genes.

Via Mary Williams
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Anjali Misra's comment, August 20, 2015 8:49 PM
Is it going to be true, if so then we still need more trials...
Rescooped by hunter chen from Publications from The Sainsbury Laboratory
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BMC Research Notes: Broad application of a simple and affordable protocol for isolating plant RNA (2015)

BMC Research Notes: Broad application of a simple and affordable protocol for isolating plant RNA (2015) | Biotech | Scoop.it
Standard molecular biological methods involve the analysis of gene expression in living organisms under diverse environmental and developmental conditions. One of the most direct approaches to quantify gene expression is the isolation of RNA. Most techniques used to quantify gene expression require the isolation of RNA, usually from a large number of samples. While most published protocols, including those for commercial reagents, are either labour intensive, use hazardous chemicals and/or are costly, a previously published protocol for RNA isolation in Arabidopsis thaliana yields high amounts of good quality RNA in a simple, safe and inexpensive manner.

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Bioinformatics: bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby (2015)

Bioinformatics: bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby (2015) | Biotech | Scoop.it

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U.S.D.A. Approves Modified Potato. Next Up: French Fry Fans.

U.S.D.A. Approves Modified Potato. Next Up: French Fry Fans. | Biotech | Scoop.it
A potato genetically engineered to reduce the amounts of a potentially harmful ingredient in French fries and potato chips has been approved for commercial planting, the Department of Agriculture announced on Friday.

The potato’s DNA has been altered so that less of a chemical called acrylamide, which is suspected of causing cancer in people, is produced when the potato is fried.

The new potato also resists bruising, a characteristic long sought by potato growers and processors for financial reasons. Potatoes bruised during harvesting, shipping or storage can lose value or become unusable.

The biotech tubers were developed by the J. R. Simplot Company, a privately held company based in Boise, Idaho, which was the initial supplier of frozen French fries to McDonald’s in the 1960s and is still a major supplier. The company’s founder, Mr. Simplot, who died in 2008, became a billionaire.
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Times Topic: Genetically Modified Food

The potato is one of a new wave of genetically modified crops that aim to provide benefits to consumers, not just to farmers as the widely grown biotech crops like herbicide-tolerant soybeans and corn do. The nonbruising aspect of the potato is similar to that of genetically engineered nonbrowning apples, developed by Okanagan Specialty Fruits, which are awaiting regulatory approval.

Via Christophe Jacquet, CP
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Infographic: 9 plant diseases that threaten your favorite foods–and how GM can help | Genetic Literacy Project

Infographic: 9 plant diseases that threaten your favorite foods–and how GM can help | Genetic Literacy Project | Biotech | Scoop.it

"Nature is relentless, challenging farmers with weeds, insects and diseases. Advances in genetic modification offer some unique tools that can help increase food production despite these challenges."


Via Mary Williams, Nicolas Denancé
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Rescooped by hunter chen from Plant Biology Teaching Resources (Higher Education)
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转基因食品探索之旅 | Understanding GMO: The Journey Begins

转基因食品是福是祸?留美学生踏上探索求知的旅程。愿这部科学界巨星云集、片长一小时的原创纪录片带你客观认识转基因食品,并成为社会理性探讨这个议题的起点。 Are GMO foods bless or curse? A group of Chinese students studying abroa

Via Mary Williams
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Nat Rev Immun: Regulation of pattern recognition receptor signalling in plants (2016)

Nat Rev Immun: Regulation of pattern recognition receptor signalling in plants (2016) | Biotech | Scoop.it

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The Sainsbury Lab's curator insight, August 1, 2016 7:34 AM
Recognition of pathogen-derived molecules by pattern recognition receptors (PRRs) is a common feature of both animal and plant innate immune systems. In plants, PRR signalling is initiated at the cell surface by kinase complexes, resulting in the activation of immune responses that ward off microorganisms. However, the activation and amplitude of innate immune responses must be tightly controlled. In this Review, we summarize our knowledge of the early signalling events that follow PRR activation and describe the mechanisms that fine-tune immune signalling to maintain immune homeostasis. We also illustrate the mechanisms used by pathogens to inhibit innate immune signalling and discuss how the innate ability of plant cells to monitor the integrity of key immune components can lead to autoimmune phenotypes following genetic or pathogen-induced perturbations of these components.
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PNAS: Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease (2013)

PNAS: Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease (2013) | Biotech | Scoop.it

We show that the genomes of maize, sorghum, and brachypodium contain genes that, when transformed into rice, confer resistance to rice blast disease. The genes are resistance genes (R genes) that encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains (NBS–LRR proteins). By using criteria associated with rapid molecular evolution, we identified three rapidly evolving R-gene families in these species as well as in rice, and transformed a randomly chosen subset of these genes into rice strains known to be sensitive to rice blast disease caused by the fungus Magnaporthe oryzae. The transformed strains were then tested for sensitivity or resistance to 12 diverse strains of M. oryzae. A total of 15 functional blast R genes were identified among 60 NBS–LRR genes cloned from maize, sorghum, and brachypodium; and 13 blast R genes were obtained from 20 NBS–LRR paralogs in rice. These results show that abundant blast R genes occur not only within species but also among species, and that the R genes in the same rapidly evolving gene family can exhibit an effector response that confers resistance to rapidly evolving fungal pathogens. Neither conventional evolutionary conservation nor conventional evolutionary convergence supplies a satisfactory explanation of our findings. We suggest a unique mechanism termed “constrained divergence,” in which R genes and pathogen effectors can follow only limited evolutionary pathways to increase fitness. Our results open avenues for R-gene identification that will help to elucidate R-gene vs. effector mechanisms and may yield new sources of durable pathogen resistance.


Via Kamoun Lab @ TSL
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Annu Rev Phytopathology: Plant Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners (2016)

Annu Rev Phytopathology: Plant Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners (2016) | Biotech | Scoop.it

Plants possess large arsenals of immune receptors capable of recognizing all pathogen classes. To cause disease, pathogenic organisms must be able to overcome physical barriers, suppress or evade immune perception, and derive nutrients from host tissues. Consequently, to facilitate some of these processes, pathogens secrete effector proteins that promote colonization. This review covers recent advances in the field of effector biology, focusing on conserved cellular processes targeted by effectors from diverse pathogens. The ability of effectors to facilitate pathogen entry into the host interior, suppress plant immune perception, and alter host physiology for pathogen benefit is discussed. Pathogens also deploy effectors in a spatial and temporal manner, depending on infection stage. Recent advances have also enhanced our understanding of effectors acting in specific plant organs and tissues. Effectors are excellent cellular probes that facilitate insight into biological processes as well as key points of vulnerability in plant immune signaling networks.


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Maize Homologs of CCoAOMT and HCT, Two Key Enzymes in Lignin Biosynthesis, Form Complexes with the NLR Rp1 Protein to Modulate the Defense Response

Maize Homologs of CCoAOMT and HCT, Two Key Enzymes in Lignin Biosynthesis, Form Complexes with the NLR Rp1 Protein to Modulate the Defense Response | Biotech | Scoop.it
Disease resistance (R) genes encode nucleotide binding Leu-rich-repeat (NLR) proteins that confer resistance to specific pathogens. Upon pathogen recognition they trigger a defense response that usually includes a so-called hypersensitive response (HR), a rapid localized cell death at the site of pathogen infection. Intragenic recombination between two maize (Zea mays) NLRs, Rp1-D and Rp1-dp2, resulted in the formation of a hybrid NLR, Rp1-D21, which confers an autoactive HR in the absence of pathogen infection. From a previous quantitative trait loci and genome-wide association study, we identified genes encoding two key enzymes in lignin biosynthesis, hydroxycinnamoyltransferase (HCT) and caffeoyl CoA O-methyltransferase (CCoAOMT), adjacent to the nucleotide polymorphisms that were highly associated with variation in the severity of Rp1-D21-induced HR. We have previously shown that the two maize HCT homologs suppress the HR conferred by Rp1-D21 in a heterologous system, very likely through physical interaction. Here, we show, similarly, that CCoAOMT2 suppresses the HR induced by either the full-length or by the N-terminal coiled-coil domain of Rp1-D21 also likely via physical interaction and that the metabolic activity of CCoAOMT2 is unlikely to be necessary for its role in suppressing HR. We also demonstrate that CCoAOMT2, HCTs, and Rp1 proteins can form in the same complexes. A model is derived to explain the roles of CCoAOMT and HCT in Rp1-mediated defense resistance.

Via Christophe Jacquet
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MPMI: Focus on Noncoding RNA Regulation of Plant-Microbe Interactions (2016)

MPMI: Focus on Noncoding RNA Regulation of Plant-Microbe Interactions (2016) | Biotech | Scoop.it

Focus on Noncoding RNA Regulation of Plant-Microbe Interactions

John P. Carr and Steven A. Whitham

 

Noncoding RNAs of Plant Viruses and Viroids: Sponges of Host Translation and RNA Interference Machinery

W. Allen Miller, Ruizhong Shen, William Staplin, and Pulkit Kanodia

 

Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses

Qili Fei, Yu Zhang, Rui Xia, and Blake C. Meyers

 

Noncoding RNAs, Emerging Regulators in Root Endosymbioses

Christine Lelandais-Brière, Jérémy Moreau, Caroline Hartmann, and Martin Crespi

 

Satellite RNAs and Satellite Viruses

Peter Palukaitis

 

Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions

Qian-Hao Zhu, Wei-Xing Shan, Michael A. Ayliffe, and Ming-Bo Wang

 

Field Trial and Molecular Characterization of RNAi-Transgenic Tomato Plants That Exhibit Resistance to Tomato Yellow Leaf Curl Geminivirus

Alejandro Fuentes et al.

 


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Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants

CRISPR–Cas (clustered, regularly interspaced short palindromic repeats–CRISPR-associated proteins) is an adaptive immune system in many archaea and bacteria that cleaves foreign DNA on the basis of sequence complementarity. Here, using the geminivirus, beet severe curly top virus (BSCTV), transient assays performed in Nicotiana benthamiana demonstrate that the sgRNA–Cas9 constructs inhibit virus accumulation and introduce mutations at the target sequences. Further, transgenic Arabidopsis and N. benthamiana plants overexpressing sgRNA–Cas9 are highly resistant to virus infection.


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Jennifer Mach's curator insight, October 6, 2015 2:54 PM

One of a pair of papers in Nature Plants on using CRISPR-Cas for immunity in plants.

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How GMOs Offer Unexpected Salvation from a Potential Banana Apocalypse

How GMOs Offer Unexpected Salvation from a Potential Banana Apocalypse | Biotech | Scoop.it
There's more at stake than just fruit in the fight to stop a devastating agricultural disease.

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New Phytologist: Standards for plant synthetic biology: a common syntax for exchange of DNA parts (2015)

New Phytologist: Standards for plant synthetic biology: a common syntax for exchange of DNA parts (2015) | Biotech | Scoop.it

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.

 

Nicola J. Patron, Diego Orzaez, Sylvestre Marillonnet, Heribert Warzecha, Colette Matthewman, Mark Youles, Oleg Raitskin, Aymeric Leveau, Gemma Farré, Christian Rogers, Alison Smith, Julian Hibberd, Alex A. R. Webb, James Locke, Sebastian Schornack, Jim Ajioka, David C. Baulcombe, Cyril Zipfel, Sophien Kamoun, Jonathan D. G. Jones, Hannah Kuhn, Silke Robatzek, H. Peter Van Esse, Dale Sanders, Giles Oldroyd, Cathie Martin, Rob Field, Sarah O'Connor, Samantha Fox, Brande Wulff, Ben Miller, Andy Breakspear, Guru Radhakrishnan, Pierre-Marc Delaux, Dominique Loqué, Antonio Granell, Alain Tissier, Patrick Shih, Thomas P. Brutnell, W. Paul Quick, Heiko Rischer, Paul D. Fraser, Asaph Aharoni, Christine Raines, Paul F. South, Jean-Michel Ané, Björn R. Hamberger, Jane Langdale, Jens Stougaard, Harro Bouwmeester, Michael Udvardi, James A. H. Murray, Vardis Ntoukakis, Patrick Schäfer, Katherine Denby, Keith J. Edwards, Anne Osbourn, and Jim Haseloff


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The Sainsbury Lab's curator insight, July 14, 2015 12:25 PM

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.

Rescooped by hunter chen from Effectors and Plant Immunity
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Front. Plant Sci.: Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems (2015)

Front. Plant Sci.: Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems (2015) | Biotech | Scoop.it

Attempting to achieve long-lasting and stable resistance using uniformly deployed rice varieties is not a sustainable approach. The real situation appears to be much more complex and dynamic, one in which pathogens quickly adapt to resistant varieties. To prevent disease epidemics, deployment should be customized and this decision will require interdisciplinary actions. This perspective article aims to highlight the current progress on disease resistance deployment to control bacterial blight in rice. Although the model system rice−Xanthomonas oryzae pv. oryzae has distinctive features that underpin the need for a case-by-case analysis, strategies to integrate those elements into a unique decision tool could be easily extended to other crops.

 

Gerbert Sylvestre Dossa, Adam H. Sparks, Casiana Vera Cruz and Ricardo Oliva


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From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development

From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development | Biotech | Scoop.it
Highlights



Genome Wide Association Studies (GWASs) have been conducted in 22 plant species.


GWASs have uncovered novel mechanisms and genes underlying variation of growth and development.


GWASs frequently identify different sets of genes than those identified by mutant screening.


Phenotypic data for GWAS can be used to comprehend correlations and mechanistic links between traits.


Experimental design, conduct and analysis are keys for successful GWASs.

Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.

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Next generation sequencing shakes up genotype/phenotype correlation, disease discoveries

Next generation sequencing shakes up genotype/phenotype correlation, disease discoveries | Biotech | Scoop.it

With the ability to use next generation sequencing technology, researchers have a broadened understanding of the association of genetic changes and disease causation to a much greater resolution, driving new discoveries, said clinical geneticists...


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Arjen ten Have's curator insight, August 15, 2014 8:31 AM
An important IMO is that of how we will share all that information. How will dr watson in Nigeria know of it? Breast cancer for instance we know now, thanks to NGS, can often be divided in subtypes that all should be treated differently. Many MD proof databases will need to be developed.