Cesar Medina
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Rescooped by César Augusto Medina Culma from Publications
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Plant Methods: Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system (2013)

Plant Methods: Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system (2013) | Cesar Medina | Scoop.it
Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) methods to improve crop plants. Until recently, available tools for introducing site-specific double strand DNA breaks were restricted to zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs). However, these technologies have not been widely adopted by the plant research community due to complicated design and laborious assembly of specific DNA binding proteins for each target gene. Recently, an easier method has emerged based on the bacterial type II CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) immune system. The CRISPR/Cas system allows targeted cleavage of genomic DNA guided by a customizable small noncoding RNA, resulting in gene modifications by both non-homologous end joining (NHEJ) and homology-directed repair (HDR) mechanisms. In this review we summarize and discuss recent applications of the CRISPR/Cas technology in plants.
Via Kamoun Lab @ TSL
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Rescooped by César Augusto Medina Culma from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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#NGS Developments in next generation sequencing – a visualisation

#NGS Developments in next generation sequencing – a visualisation | Cesar Medina | Scoop.it
With this post I present a figure I’ve been working on for a while now. With it, I try to summarise the developments in (next generation) sequencing, or at least a few aspects of it. I’...

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Rescooped by César Augusto Medina Culma from Plants and Microbes
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PLOS Pathogens: A Pathogen Type III Effector with a Novel E3 Ubiquitin Ligase Architecture (2013)

PLOS Pathogens: A Pathogen Type III Effector with a Novel E3 Ubiquitin Ligase Architecture (2013) | Cesar Medina | Scoop.it

Type III effectors are virulence factors of Gram-negative bacterial pathogens delivered directly into host cells by the type III secretion nanomachine where they manipulate host cell processes such as the innate immunity and gene expression. Here, we show that the novel type III effector XopL from the model plant pathogen Xanthomonas campestris pv. vesicatoriaexhibits E3 ubiquitin ligase activity in vitro and in planta, induces plant cell death and subverts plant immunity. E3 ligase activity is associated with the C-terminal region of XopL, which specifically interacts with plant E2 ubiquitin conjugating enzymes and mediates formation of predominantly K11-linked polyubiquitin chains. The crystal structure of the XopL C-terminal domain revealed a single domain with a novel fold, termed XL-box, not present in any previously characterized E3 ligase. Mutation of amino acids in the central cavity of the XL-box disrupts E3 ligase activity and prevents XopL-induced plant cell death. The lack of cysteine residues in the XL-box suggests the absence of thioester-linked ubiquitin-E3 ligase intermediates and a non-catalytic mechanism for XopL-mediated ubiquitination. The crystal structure of the N-terminal region of XopL confirmed the presence of a leucine-rich repeat (LRR) domain, which may serve as a protein-protein interaction module for ubiquitination target recognition. While the E3 ligase activity is required to provoke plant cell death, suppression of PAMP responses solely depends on the N-terminal LRR domain. Taken together, the unique structural fold of the E3 ubiquitin ligase domain within the Xanthomonas XopL is unprecedented and highlights the variation in bacterial pathogen effectors mimicking this eukaryote-specific activity.


Via Kamoun Lab @ TSL
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Liberians to Invest in the Soil Launches Major Rice and Cassava Project

Liberians to Invest in the Soil Launches Major Rice and Cassava Project | Cesar Medina | Scoop.it
Vice President Joseph N. Boakai has admonished Liberians, regardless of status or background, to consider rice and cassava as a national concern and a...
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Rescooped by César Augusto Medina Culma from Plant pathogenic fungi
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Nature: Plant biology: Electric defence (2013)

Nature: Plant biology: Electric defence (2013) | Cesar Medina | Scoop.it
Herbivory and mechanical wounding in plants have been shown to elicit electrical signals — mediated by two glutamate-receptor-like proteins — that induce defence responses at local and distant sites. The mammalian nervous system can relay electrical signals at speeds approaching 100 metres per second. Plants live at a slower pace. Although they lack a nervous system, some plants, such as the mimosa (Mimosa pudica) and the Venus flytrap (Dionaea muscipula), use electrical signals to trigger rapid leaf movements. Signal propagation in these plants occurs at a rate of 3 centimetres per second — comparable to that observed in the nervous system of mussels. On page 422 of this issue, Mousavi et al. address the fascinating yet elusive issue of how plants generate and propagate electrical signals. The authors identify two glutamate-receptor-like proteins as crucial components in the induction of an electrical wave that is initiated by leaf wounding and that spreads to neighbouring organs, prompting them to mount defence responses to a potential herbivore attack. As sessile organisms, plants have evolved diverse strategies to combat herbivores. These include mechanical defences, such as the thorns found on rose bushes, and chemical deterrents, such as the insect-neurotoxic pyrethrins of the genus Chrysanthemum. However, some plants do not invest in continuous defensive structures or metabolites, relying instead on the initiation of defence responses on demand2. This strategy requires an appropriate surveillance system and rapid communication between plant organs. A key player in orchestrating these reactions is the lipid-derived plant hormone jasmonate, which rapidly accumulates in organs remote from the site of herbivore feeding. Mousavi et al. used thale cress (Arabidopsis thaliana) plants and Egyptian cotton leafworm (Spodoptera littoralis) larvae as a model of plant–herbivore interactions. The researchers placed the larvae on individual leaves and recorded changes in electrical potentials using electrodes grounded in the soil and on the surface of different leaves. The leaf-surface potential did not change when a larva walked on a leaf, but as soon as it started to feed, electrical signals were evoked near the site of attack and subsequently spread to neighbouring leaves at a maximum speed of 9 centimetres per minute. The relay of the electrical signal was most efficient for leaves directly above or below the wounded leaf. These leaves are well connected by the plant vasculature, which conducts water and organic compounds, and is a good candidate for the transmission of signals over long distances. Mousavi et al. http://www.nature.com/nature/journal/v500/n7463/full/nature12478.html
Via Kamoun Lab @ TSL, Steve Marek
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Rescooped by César Augusto Medina Culma from MutMap
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Plant J: QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations (2013)

Plant J: QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations (2013) | Cesar Medina | Scoop.it

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci: QTL). QTL mapping and isolation is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. Since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been however time consuming and labor intensive. Here we report a rapid identification of plant QTL by whole genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines (RILs) and F2 populations and successfully identified QTL for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTL over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.


Via Kamoun Lab @ TSL
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Teresa M. Nash's comment, November 28, 2013 1:23 AM
Nice.
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PLOS ONE: HrcQ Provides a Docking Site for Early and Late Type III Secretion Substrates from Xanthomonas

PLOS ONE: HrcQ Provides a Docking Site for Early and Late Type III Secretion Substrates from Xanthomonas | Cesar Medina | Scoop.it
Pathogenicity of many Gram-negative bacteria depends on a type III secretion (T3S) system which translocates bacterial effector proteins into eukaryotic cells. The membrane-spanning secretion apparatus is associated with a cytoplasmic ATPase complex and a predicted cytoplasmic (C) ring structure which is proposed to provide a substrate docking platform for secreted proteins. In this study, we show that the putative C ring component HrcQ from the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria is essential for bacterial pathogenicity and T3S. Fractionation studies revealed that HrcQ localizes to the cytoplasm and associates with the bacterial membranes under T3S-permissive conditions. HrcQ binds to the cytoplasmic T3S-ATPase HrcN, its predicted regulator HrcL and the cytoplasmic domains of the inner membrane proteins HrcV and HrcU. Furthermore, we observed an interaction between HrcQ and secreted proteins including early and late T3S substrates. HrcQ might therefore act as a general substrate acceptor site of the T3S system and is presumably part of a larger protein complex. Interestingly, the N-terminal export signal of the T3S substrate AvrBs3 is dispensable for the interaction with HrcQ, suggesting that binding of AvrBs3 to HrcQ occurs after its initial targeting to the T3S system.
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