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ScienceDirect.com - Trends in Biotechnology - Network analysis: tackling complex data to study plant metabolism

ScienceDirect.com - Trends in Biotechnology - Network analysis: tackling complex data to study plant metabolism | Plant-Microbe Interaction | Scoop.it

Incomplete knowledge of biochemical pathways makes the holistic description of plant metabolism a non-trivial undertaking. Sensitive analytical platforms, which are capable of accurately quantifying the levels of the various molecular entities of the cell, can assist in tackling this task. However, the ever-increasing amount of high-throughput data, often from multiple technologies, requires significant computational efforts for integrative analysis. Here we introduce the application of network analysis to study plant metabolism and describe the construction and analysis of correlation-based networks from (time-resolved) metabolomics data. By investigating the interactions between metabolites, network analysis can help to interpret complex datasets through the identification of key network components. The relationship between structural and biological roles of network components can be evaluated and employed to aid metabolic engineering.

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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Rice researchers redress retraction

Rice researchers redress retraction | Plant-Microbe Interaction | Scoop.it
Team that retracted its own papers finally finds elusive trigger of plant immune response.

Via Mary Williams
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Genera of Fungi database

Genera of Fungi database | Plant-Microbe Interaction | Scoop.it

The International Code of Nomenclature for algae, fungi, and plants (ICN; McNeill et al. 2012) provided for the development of lists of accepted names of fungi in all ranks that could be treated as conserved after examination and approval by the Nomenclature Committee for Fungi (NCF) and the General Committee (Art. 14.13). The Code also provided for the development of lists of names to be rejected (Art. 56.3).

As a first step towards the production of a List of Protected Generic Names for Fungi, a without-prejudice list is presented here as a basis for future discussion and the production of a List for formal adoption (at this stage only covering genera published before 1 January 2000, though this may still be expanded to include genera published up to 2013). We include 6995 generic names out of the 17072 validly published names proposed for fungi and invite comments from all interested mycologists by 31 March 2014. The selection of names for inclusion takes note of recent major publications on different groups of fungi, and further the decisions reached so far by international working groups concerned with particular families or genera. Changes will be sought in the Code to provide for this and lists at other ranks to be protected against any competing unlisted names, and to permit the inclusion of names of lichen-forming fungi. A revised draft will be made available for further discussion at the 10th International Mycological Congress in Bangkok in August 2014. A schedule is suggested for the steps needed to produce a list for adoption by the International Botanical Congress in August 2017. This initiative provides mycologists with an opportunity to place nomenclature at the generic level on a more secure and stable base.


Via Elsa Ballini
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Arabidopsis AZI1 family proteins mediate signal mobilization for systemic defence priming : Nature Communications : Nature Publishing Group

Arabidopsis AZI1 family proteins mediate signal mobilization for systemic defence priming : Nature Communications : Nature Publishing Group | Plant-Microbe Interaction | Scoop.it

Priming is a major mechanism behind the immunological ‘memory’ observed during two key plant systemic defences: systemic acquired resistance (SAR) and induced systemic resistance (ISR). Lipid-derived azelaic acid (AZA) is a mobile priming signal. Here, we show that the lipid transfer protein (LTP)-like AZI1 and its closest paralog EARLI1 are necessary for SAR, ISR and the systemic movement and uptake of AZA in Arabidopsis. Imaging and fractionation studies indicate that AZI1 and EARLI1 localize to expected places for lipid exchange/movement to occur. These are the ER/plasmodesmata, chloroplast outer envelopes and membrane contact sites between them. Furthermore, these LTP-like proteins form complexes and act at the site of SAR establishment. The plastid targeting of AZI1 and AZI1 paralogs occurs through a mechanism that may enable/facilitate their roles in signal mobilization.


Via Suayib Üstün
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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild | Plant-Microbe Interaction | Scoop.it

Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.


Via Francis Martin
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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays | Plant-Microbe Interaction | Scoop.it
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.

Via Jean-Michel Ané, Francis Martin
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals | Plant-Microbe Interaction | Scoop.it

Trees and their associated rhizosphere organisms play a major role in mineral weathering driving calcium fluxes from the continents to the oceans that ultimately control long-term atmospheric CO2 and climate through the geochemical carbon cycle. Photosynthate allocation to tree roots and their mycorrhizal fungi is hypothesized to fuel the active secretion of protons and organic chelators that enhance calcium dissolution at fungal-mineral interfaces. This was tested using 14CO2 supplied to shoots of Pinus sylvestris ectomycorrhizal with the widespread fungus Paxillus involutus in monoxenic microcosms, revealing preferential allocation by the fungus of plant photoassimilate to weather grains of limestone and silicates each with a combined calcium and magnesium content of over 10 wt.%. Hyphae had acidic surfaces and linear accumulation of weathered calcium with secreted oxalate, increasing significantly in sequence: quartz, granite < basalt, olivine, limestone < gabbro. These findings confirmed the role of mineral-specific oxalate exudation in ectomycorrhizal weathering to dissolve calcium bearing minerals, thus contributing to the geochemical carbon cycle.


Via Francis Martin, Jean-Michel Ané
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Rescooped by Guogen Yang from Rice Blast
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Protein kinase C is essential for viability of the rice blast fungus Magnaporthe oryzae

Protein kinase C is essential for viability of the rice blast fungus Magnaporthe oryzae | Plant-Microbe Interaction | Scoop.it
Protein kinase C constitutes a family of serine-threonine kinases found in all eukaryotes and implicated in a wide range of cellular functions, including regulation of cell growth, cellular differentiation, and immunity. Here, we present three independent lines of evidence which indicate that protein kinase C is essential for viability of Magnaporthe oryzae. First, all attempts to generate a target deletion of PKC1, the single copy protein kinase C-encoding gene, proved unsuccessful. Secondly, conditional gene silencing of PKC1 by RNA interference led to severely reduced growth of the fungus, which was reversed by targeted deletion of the Dicer2-encoding gene, MDL2. Finally, selective kinase inhibition of protein kinase C by targeted allelic replacementwith an analogue-sensitive PKC1ASallele led to specific loss of fungal viability in the presence of the PP1 inhibitor. Global transcriptional profiling following selective PKC inhibition identified significant changes in gene expressionassociated with cell wall re-modelling, autophagy, signal transduction and secondary metabolism.When considered together, these results suggest protein kinase C is essential for growth and development of M. oryzaewith extensive downstream targets in addition to the cell integrity pathway. Targeting protein kinase C signalling may therefore prove an effective means of controlling rice blast disease.

Via Elsa Ballini
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An Arabidopsis Plasma Membrane Proton ATPase Modulates JA Signaling and Is Exploited by the Pseudomonas syringae Effector Protein AvrB for Stomatal Invasion

An Arabidopsis Plasma Membrane Proton ATPase Modulates JA Signaling and Is Exploited by the Pseudomonas syringae Effector Protein AvrB for Stomatal Invasion | Plant-Microbe Interaction | Scoop.it
Stomata are natural openings through which many pathogenic bacteria enter plants. Successful bacterial pathogens have evolved various virulence factors to promote stomatal opening. Here, we show that the Pseudomonas syringae type III effector protein AvrB induces stomatal opening and enhances bacterial virulence in a manner dependent on RPM1-INTERACTING4 (RIN4), which promotes stomatal opening by positively regulating the Arabidopsis plasma membrane H+-ATPase (AHA1), which is presumed to directly regulate guard cell turgor pressure. In support of a role of AHA1 in AvrB-induced stomatal opening, AvrB enhances ATPase activity in plants. Unexpectedly, AHA1 promotes the interaction between the jasmonate (JA) receptor CORONATINE INSENSITIVE1 (COI1) and JASMONATE ZIM-DOMAIN (JAZ) proteins and enhances JA signaling. JA signaling is required for optimum stomatal infection in AHA1-active plants. Similarly, AvrB also induces the COI1-JAZ9 interaction and the degradation of multiple JAZ proteins. AvrB-induced stomatal opening and virulence require the canonical JA signaling pathway, which involves the COI1 and NAC transcription factors. The findings thus point to a previously unknown pathway exploited by P. syringae that acts upstream of COI1 to regulate JA signaling and stomatal opening.

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Front. Plant Sci.: The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid (2015)

Front. Plant Sci.: The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid (2015) | Plant-Microbe Interaction | Scoop.it

XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) – dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) –like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.

 

Üstün S, Bartetzko V and Börnke F

 

 


Via Nicolas Denancé, Suayib Üstün
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The Plant Genome Integrative Explorer Resource: PlantGenIE.org - Sundell - 2015 - New Phytologist - Wiley Online Library

The Plant Genome Integrative Explorer Resource: PlantGenIE.org - Sundell - 2015 - New Phytologist - Wiley Online Library | Plant-Microbe Interaction | Scoop.it
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training.
We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo.
We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated.
The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

Via Francis Martin
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Elsa Ballini's curator insight, July 22, 2:00 AM

Waiting for rice !

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Clonal reproduction in fungi

Clonal reproduction in fungi | Plant-Microbe Interaction | Scoop.it

Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.


Via Steve Marek, Niklaus Grunwald
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Steve Marek's curator insight, July 21, 4:43 PM

Great review!

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The dangers of default parameters in bioinformatics: lessons from Bowtie and TopHat

The dangers of default parameters in bioinformatics: lessons from Bowtie and TopHat | Plant-Microbe Interaction | Scoop.it

Most bioinformatics tools are equipped with a vast array of command-line options which let the user configure the inputs, outputs, and performance of the software. You may not wish to explore every possible option when using a particular piece of software, but you should always try to have a look at the manual. 


Via Pablo Vicente Munuera, Niklaus Grunwald
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Rescooped by Guogen Yang from Effectors and Plant Immunity
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Science: Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa (2015)

Immune systems distinguish “self” from “non-self” to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, non-pathogenic microbes. Plant roots grow within extremely diverse soil microbial communities, but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.

 

Sarah L. Lebeis, Sur Herrera Paredes, Derek S. Lundberg, Natalie Breakfield, Jase Gehring, Meredith McDonald, Stephanie Malfatti, Tijana Glavina del Rio, Corbin D. Jones, Susannah G. Tringe, Jeffery L. Dangl


Via Nicolas Denancé
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Conserved nematode signalling molecules elicit plant defenses and pathogen resistance

Conserved nematode signalling molecules elicit plant defenses and pathogen resistance | Plant-Microbe Interaction | Scoop.it
Article
Plants are able to induce defense responses following recognition of certain pathogen derived molecules at the cell surface. Here, Manosalva et al .

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Pseudomonas syringae effector AvrE localizes to the host plasma membrane and down-regulates the expression of the NDR/HIN1-like 13 gene required for antibacterial immunity in Arabidopsis

Pseudomonas syringae effector AvrE localizes to the host plasma membrane and down-regulates the expression of the NDR/HIN1-like 13 gene required for antibacterial immunity in Arabidopsis | Plant-Microbe Interaction | Scoop.it
Many bacterial pathogens of plants and animals deliver effector proteins into host cells to promote infection. Elucidation of how pathogen effector proteins function not only is critical for understanding bacterial pathogenesis, but also provides a useful tool in discovering the functions of host genes. In this study, we characterized the Pseudomonas syringae pv. tomato DC3000 effector protein AvrE, the founding member of a widely distributed, yet functionally enigmatic, bacterial effector family. We show that AvrE is localized in the plasma membrane (PM) and PM-associated vesicle-like structures in the plant cell. AvrE contains two physically interacting domains, and the N-terminal portion contains a PM-localization signal. Genome-wide microarray analysis indicates that AvrE, as well as a functionally-redundant effector HopM1, down-regulates the expression of the NDR1/HIN1-Like 13 gene in Arabidopsis. Mutational analysis shows that NHL13 is required for plant immunity, as the nhl13 mutant plant displayed enhanced disease susceptibility. Our results defined the action site of one of the most important bacterial virulence proteins in plants and the anti-bacterial immunity function of the NHL13 gene.

Via Suayib Üstün
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Rescooped by Guogen Yang from Virology and Bioinformatics from Virology.ca
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Comprehensive serological profiling of human populations using a synthetic human virome

Comprehensive serological profiling of human populations using a synthetic human virome | Plant-Microbe Interaction | Scoop.it

ABSTRACT

The human virome plays important roles in health and immunity. However, current methods for detecting viral infections and antiviral responses have limited throughput and coverage. Here, we present VirScan, a high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. We assayed over 108 antibody-peptide interactions in 569 humans across four continents, nearly doubling the number of previously established viral epitopes. We detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strongly conserved “public epitopes” for each virus, suggesting that they may elicit highly similar antibodies. VirScan is a powerful approach for studying interactions between the virome and the immune system.


Via Krishan Maggon , Kathleen McLeod
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Krishan Maggon 's curator insight, June 5, 3:23 PM
Science 5 June 2015: 
Vol. 348 no. 6239 
DOI: 10.1126/science.aaa0698RESEARCH ARTICLEComprehensive serological profiling of human populations using a synthetic human viromeGeorge J. Xu1,2,3,4,*, Tomasz Kula3,4,5,*, Qikai Xu3,4, Mamie Z. Li3,4, Suzanne D. Vernon6, Thumbi Ndung’u7,8,9,10,Kiat Ruxrungtham11, Jorge Sanchez12, Christian Brander13, Raymond T. Chung14, Kevin C. O’Connor15,Bruce Walker8,9, H. Benjamin Larman16, Stephen J. Elledge3,4,6,†

+Author Affiliations

1Program in Biophysics, Harvard University, Cambridge, MA 02115, USA.2Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA.3Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.4Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.5Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA.6Solve ME/CFS Initiative, Los Angeles, CA 90036, USA.7KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.8HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, Durban, South Africa.9Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, MA 02139, USA.10Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany.11Vaccine and Cellular Immunology Laboratory, Department of Medicine, Faculty of Medicine; and Chula-Vaccine Research Center, Chulalongkorn University, Bangkok, Thailand.12Asociación Civil IMPACTA Salud y Educación, Lima, Peru.13AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.14Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.15Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA.16Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.↵†Corresponding author. E-mail: selledge@genetics.med.harvard.edu
Krishan Maggon 's curator insight, June 5, 3:24 PM
Science 5 June 2015: 
Vol. 348 no. 6239 
DOI: 10.1126/science.aaa0698RESEARCH ARTICLEComprehensive serological profiling of human populations using a synthetic human viromeGeorge J. Xu1,2,3,4,*, Tomasz Kula3,4,5,*, Qikai Xu3,4, Mamie Z. Li3,4, Suzanne D. Vernon6, Thumbi Ndung’u7,8,9,10,Kiat Ruxrungtham11, Jorge Sanchez12, Christian Brander13, Raymond T. Chung14, Kevin C. O’Connor15,Bruce Walker8,9, H. Benjamin Larman16, Stephen J. Elledge3,4,6,†

+Author Affiliations

1Program in Biophysics, Harvard University, Cambridge, MA 02115, USA.2Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA.3Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.4Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.5Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA.6Solve ME/CFS Initiative, Los Angeles, CA 90036, USA.7KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.8HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, Durban, South Africa.9Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, MA 02139, USA.10Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany.11Vaccine and Cellular Immunology Laboratory, Department of Medicine, Faculty of Medicine; and Chula-Vaccine Research Center, Chulalongkorn University, Bangkok, Thailand.12Asociación Civil IMPACTA Salud y Educación, Lima, Peru.13AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.14Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.15Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA.16Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.↵†Corresponding author. E-mail: selledge@genetics.med.harvard.edu

 

Systematic viral epitope scanning (VirScan).

This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines DNA microarray synthesis and bacteriophage display to create a uniform, synthetic representation of peptide epitopes comprising the human virome. Immunoprecipitation and high-throughput DNA sequencing reveal the peptides recognized by antibodies in the sample. The color of each cell in the heatmap depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns).

Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life | Plant-Microbe Interaction | Scoop.it

Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.


Via Francis Martin
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PUB22 and PUB23 U-BOX E3 ligases directly ubiquitinate RPN6, a 26S proteasome lid subunit, for subsequent degradation in Arabidopsis thaliana

PUB22 and PUB23 U-BOX E3 ligases directly ubiquitinate RPN6, a 26S proteasome lid subunit, for subsequent degradation in Arabidopsis thaliana | Plant-Microbe Interaction | Scoop.it
Drought stress strongly affects plant growth and development, directly connected with crop yields, accordingly. However, related to the function of U-BOX E3 ligases, the underlying molecular mechanisms of desiccation stress response in plants are still largely unknown. Here we report that PUB22 and PUB23, two U-box E3 ligase homologs, tether ubiquitins to 19S proteasome regulatory particle (RP) subunit RPN6, leading to its degradation. RPN6 was identified as an interacting substrate of PUB22 by yeast two-hybrid screening, and in vitro pull-down assay confirmed that RPN6 interacts not only with PUB22, but also with PUB23. Both PUB22 and PUB23 were able to conjugate ubiquitins on RPN6 in vitro. Furthermore, RPN6 showed a shorter protein half-life in PUB22 overexpressing plants than in wild-type, besides RPN6 was significantly stabilized in pub22pub23 double knockout plants. Taken together, these results solidify a notion that PUB22 and PUB23 can alter the activity of 26S proteasome in response to drought stress.

Via Suayib Üstün
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Rescooped by Guogen Yang from Plant Immunity And Microbial Effectors
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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing | Plant-Microbe Interaction | Scoop.it
Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.

Via Francis Martin, IPM Lab
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Rescooped by Guogen Yang from Rice Blast
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Stress-Responsive Expression, Subcellular Localization and Protein–Protein Interactions of the Rice Metacaspase Family

Stress-Responsive Expression, Subcellular Localization and Protein–Protein Interactions of the Rice Metacaspase Family | Plant-Microbe Interaction | Scoop.it
Metacaspases, a class of cysteine-dependent proteases like caspases in animals, are important regulators of programmed cell death (PCD) during development and stress responses in plants. The present study was focused on comprehensive analyses of expression patterns of the rice metacaspase (OsMC) genes in response to abiotic and biotic stresses and stress-related hormones. Results indicate that members of the OsMC family displayed differential expression patterns in response to abiotic (e.g., dro

Via Elsa Ballini
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Rescooped by Guogen Yang from Plant-microbe interaction
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Phosphorylation of the Plant Immune Regulator RPM1-INTERACTING PROTEIN4 Enhances Plant Plasma Membrane H+-ATPase Activity and Inhibits Flagellin-Triggered Immune Responses in Arabidopsis

Phosphorylation of the Plant Immune Regulator RPM1-INTERACTING PROTEIN4 Enhances Plant Plasma Membrane H+-ATPase Activity and Inhibits Flagellin-Triggered Immune Responses in Arabidopsis | Plant-Microbe Interaction | Scoop.it
The Pseudomonas syringae effector AvrB targets multiple host proteins during infection, including the plant immune regulator RPM1-INTERACTING PROTEIN4 (RIN4) and RPM1-INDUCED PROTEIN KINASE (RIPK). In the presence of AvrB, RIPK phosphorylates RIN4 at Thr-21, Ser-160, and Thr-166, leading to activation of the immune receptor RPM1. Here, we investigated the role of RIN4 phosphorylation in susceptible Arabidopsis thaliana genotypes. Using circular dichroism spectroscopy, we show that RIN4 is a disordered protein and phosphorylation affects protein flexibility. RIN4 T21D/S160D/T166D phosphomimetic mutants exhibited enhanced disease susceptibility upon surface inoculation with P. syringae, wider stomatal apertures, and enhanced plasma membrane H+-ATPase activity. The plasma membrane H+-ATPase AHA1 is highly expressed in guard cells, and its activation can induce stomatal opening. The ripk knockout also exhibited a strong defect in pathogen-induced stomatal opening. The basal level of RIN4 Thr-166 phosphorylation decreased in response to immune perception of bacterial flagellin. RIN4 Thr166D lines exhibited reduced flagellin-triggered immune responses. Flagellin perception did not lower RIN4 Thr-166 phosphorylation in the presence of strong ectopic expression of AvrB. Taken together, these results indicate that the AvrB effector targets RIN4 in order to enhance pathogen entry on the leaf surface as well as dampen responses to conserved microbial features.

Via Suayib Üstün
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation

Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation | Plant-Microbe Interaction | Scoop.it

Understanding how developmental and functional complexity of organisms evolves is a longstanding challenge in biology. Genetic mutation has long been thought to be the cause of biological complexity. However, increasing evidence indicates that epigenetic variation provides a parallel path for the evolution of biological complexity. Cytosine DNA methylation, the addition of a chemical mark on DNA, is a conserved and essential gene regulatory mechanism. Recent studies have greatly advanced our understanding of the DNA methylation landscapes and key regulatory components across many species. In this review, I summarize recent advances in understanding DNA methylation from an evolutionary perspective. Using comparative approaches, I highlight the conservation and divergence of DNA methylation patterns and regulatory machinery in plants and other eukaryotic organisms.


Via Francis Martin
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites | Plant-Microbe Interaction | Scoop.it
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.

Via Francis Martin
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes -

Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes - | Plant-Microbe Interaction | Scoop.it
Plants that form root-nodule symbioses are within a monophyletic ‘nitrogen-fixing’ clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca2+), occurring in the root hairs of several legume species in response to the rhizobial Nod factor signal.
In this study we expanded the species analysed for activation of Ca2+ oscillations, including nonleguminous species within the nitrogen-fixing clade.
We showed that Ca2+ oscillations are a common feature of legumes in their association with rhizobia, while Cercis, a non-nodulating legume, does not show Ca2+ oscillations in response to Nod factors from Sinorhizobium fredii NGR234. Parasponia andersonii, a nonlegume that can associate with rhizobia, showed Nod factor-induced calcium oscillations to S. fredii NGR234 Nod factors, but its non-nodulating sister species, Trema tomentosa, did not. Also within the nitrogen-fixing clade are actinorhizal species that associate with Frankia bacteria and we showed that Alnus glutinosa induces Ca2+ oscillations in root hairs in response to exudates from Frankia alni, but not to S. fredii NGR234 Nod factors.
We conclude that the ability to mount Ca2+ oscillations in response to symbiotic bacteria is a common feature of nodulating species within the nitrogen-fixing clade.

Via Christophe Jacquet
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Rescooped by Guogen Yang from TAL effector science
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Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR | Plant-Microbe Interaction | Scoop.it

Boettcher & McManus 2015

The most widely used approach for defining gene function is to reduce or completely disrupt its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to disrupt gene expression in many organisms. However, new biotechnological tools—specifically CRISPR-based technologies—have become available and are squeezing out RNAi dominance in mammalian cell studies. These seemingly competing technologies leave research investigators with the question: “Which technology should I use in my experiment?” This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools.


Via dromius
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