Daniel Pass talks to GARNet

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Published on: October 16, 2017

Daniel Pass (Cardiff University) discusses his recent paper published in PLoS Genetics entitled ‘Genome-wide chromatin mapping with size resolution reveals a dynamic sub- nucleosomal landscape in Arabidopsis’. Dan highlights his Github page where the code for the novel graphics in this paper are held.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006988

https://github.com/ChromatinCardiff/DanielPassProcessingPipelines

Miriam Gifford talks to GARNet

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Published on: October 9, 2017

Miriam Gifford talks to GARNet about a recent Large Scale Biology paper in The Plant Cell entitled ‘Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time’.
http://www.plantcell.org/content/early/2017/09/11/tpc.16.00961
More on the eFP browser here: http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi

SEB/GARNet meeting on Post Translational Modifications.

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Published on: October 5, 2017

GARNet are co-organising this exciting symposium and workshop on plant signalling with post-translational modifications held in Edinburgh 11-13 December 2017.
Abstract deadline: 20 October 2017

Early-bird registration deadline: 3 November 2017

http://www.sebiology.org/events/event/from-proteome-to-phenotype

KEYNOTE SPEAKERS

Matthias Mann (Max Planck Institute of Biochemistry

Ron Hay (University of Dundee)

DYNAMIC PHOSPHORYLATION

Cyril Zipfel (The Sainsbury Laboratory)

Gitta Coaker (UC Davis)

John Christie (University of Glasgow)

PROTEIN SUMOYLATION

Ari Sadanandom (Durham University)

Andreas Bachmair (University of Vienna)

Maria Lois (CRAG Spain)

EMERGING PTMS

Piers Hemsley (University of Dundee)

Markus Wirtz (University of Heidelberg)

Stéphane Ravanel (INRA/CNRS)

UBIQUITIN-MEDIATED PROTEASOME

Steven Spoel (University of Edinburgh)

Luz Irina Calderon-Villalobos (IPB Leipniz)

Emmanuelle Graciet (Maynooth University)

REDOX-BASED PTMS

Gary Loake (University of Edinburgh)

Frank van Breusegem (VIB Ghent)

Daniel Gibbs (University of Birmingham)

TECHNOLOGICAL ADVANCES

Alex Jones (University of Warwick, UK)

Frank Menke (The Sainsbury Laboratory, UK)

Katja Baerenfaller (ETH Zurich, Switzerland)

 

GARNET WORKSHOP ON PLANT PROTEOMICS (13 Dec 2017)

Learn about new technologies and available software for analysis of

proteome samples in a workshop led by Dr. Alex Jones (University of

Warwick). FREE for attendees of the symposium but only 30 spaces

available!!

 

Organising committee: Steven Spoel (University of Edinburgh & GARNet),

Geraint Parry (GARNet), Cyril Zipfel (The Sainsbury Laboratory).

GARNet talks to Emily Larson

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Published on: September 11, 2017

Emily Larson from the University of Glasgow talks clathrin, balloons and the publication process as part in our discussion about her recent Plant Physiology paper entitled ‘Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement‘.

Arabidopsis Research Roundup: September 6th

This largest ever Arabidopsis Research Roundup (ARR) includes 6 papers from Norwich Research Park (NRP), including three featuring Cyril Zipfel (TSL) as a co-author on papers that investigate different aspects of plant immune signaling. Elsewhere on the NRP site Veronica Grieneisen (JIC) is a co-author on a study that defines the root auxin maximum whilst Dale Sanders and Saskia Hogenhout lead a paper that defines a method for the analysis of calcium signaling. Finally Robert Sablowski’s group at the JIC investigates the role of the DELLA proteins during meristem development.

Elsewhere investigators from Kew Gardens and Bangor University have used nanopore sequencing for the facile characterisation of field populations of Arabidopsis. Similarly Seth Davies (University of York) is part of a collaboration that looks how alterations in the circadian clock might affect plant fitness.

Verena Kriechbaumer (Oxford Brookes) leads a phylogenetic study into the conservation of auxin biosynthesis genes whilst Hilary Rodgers (Cardiff University) is a co-author on a Chinese-led study that looks into role of cadmium on the Arabidopsis cell cycle.

This ARR is full of examples of UK researchers involved in global collaborations. This includes Cambridge researchers involved in a proteomic analysis of microsomes, Justin Goodrich from the University of Edinburgh as part of a US-led study that defines the regulation of the PRC2 complex and Katherine Denby (University of York) as a member of a consortium that has performed a network analysis of jasmonic acid signaling.

Finally are two studies in which the research takes place within a single institution. Malcolm Hawksford (Rothamsted Research) looks at the effect of wheat transcription factors in the response to the heavy metal zinc whilst Emily Larson and Mike Blatt (University of Glasgow) investigate the role of clathrin on plant vesicular transport.


D’Ambrosio JM, Couto D, Fabro G, Scuffi D, Lamattina L, Munnik T, Andersson MX, Alvarez ME, Zipfel C, Laxalt AM (2017) PLC2 Regulates MAMP-Triggered Immunity by Modulating ROS Production in Arabidopsis. Plant Physiol 10.1104/pp.17.00173

This Argentinian-led study includes Cyril Zipfel (TSL) as a co-author on this work that uses miRNA-mediated gene silencing to assess the role of the phosphoinositide-specific phospholipase C (PI-PLC) in plant immune signaling.


Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, vanDongen WM, Stahl M, Zipfel C, Goshe MB, Clouse S, de Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1. Plant Cell. 10.1105/tpc.17.00376

Cyril Zipfel (TSL) is a co-author on this global collaboration that further defines the role of the BAK1 receptor in hormone and immune signaling through its interaction with two LRR-RK proteins (BIR2 and BIR3).


Singh V, Perraki A, Kim SY, Shrivastava S, Lee JH, Zhao Y, Schwessinger B, Oh MH, Marshall-Colon A, Zipfel C, Huber SC (2017) Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front Plant Sci. 10.3389/fpls.2017.01273

Cyril Zipfel (TSL) is a co-author on this US-led manuscript that again looks into the role of the BRI1-ASSOCIATED KINASE1 (BAK1) on plant immune signaling. Importantly they show that the phosphorylation of tyrosine-610 is actually not necessary for this proteins role in brassinosteroid or immune signaling


Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

Veronica Grieneisen (JIC) is a co-corresponding author on this work with Sabrina Sabatini from the University of Rome. They define the auxin minimum, a newly characterised determinat of root patterning that delineates the separation of root division and the differentiation zones. This is defined by the interaction between cytokinin and auxin signaling cascades.

Veronica discusses this paper on the GARNet YouTube channel: https://www.youtube.com/watch?v=gYdL6eddOcA


Vincent TR, Canham J, Toyota M, Avramova M, Mugford ST, Gilroy S, Miller AJ, Hogenhout S, Sanders D (2017) Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor. J Vis Exp. 10.3791/56142

Dale Sanders and GARNet committee member Saskia Hogenhout (JIC) lead this study that describes an imaging technique that allows for the real time assessment of calcium dynamics using a fluorescently tagged sensor.


Serrano-Mislata A, Bencivenga S, Bush M, Schiessl K, Boden S, Sablowski R (2017) DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants. 10.1038/s41477-017-0003-y

Robert Sablowski (JIC) leads this paper that investigates the role of DELLA proteins in the control of cell cycle regulators and how this impacts meristem size in both barley and Arabidopsis. Read more about it on the John Innes Centre website.


Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST (2017) Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep. 10.1038/s41598-017-08461-5 Open Access

This investigation led by researchers at Kew Gardens and at the Bangor University use Real Time Nanopore Sequencing (RTnS) that allows for rapid species identification in the field and that combining RTnS and laboratory-based high-throughput sequencing leads to a significant improvement in genome assembly.


Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN7, Davis SJ, Weinig C (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol. 10.1111/mec.14287 Open Access

Seth Davies (University of York) is a co-author on this US-led work that conducts a study of field-growth Arabidopsis to evaluate the contribution of the circadian clock toward survival and fecundity. They show that variation in clock function correlates with growth performance in a natural environment.


Poulet A, Kriechbaumer V (2017) Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. Int J Mol Sci. 10.3390/ijms18081791 Open Access

The paper from Oxford Brookes University provides a phylogenetic analysis of TAA/TAR (tryptophan aminotransferase related) and YUCCA proteins that are involved in auxin biosynthesis. In addition they provide tissue and cell-specific information about the function of these proteins and that their function is conserved in lower plant species.


Cui W, Wang H, Song J, Cao X, Rogers HJ, Francis D, Jia C, Sun L, Hou M, Yang Y, Tai P, Liu W (2017) Cell cycle arrest mediated by Cd-induced DNA damage in Arabidopsis root tips. Ecotoxicol Environ Saf. 10.1016/j.ecoenv.2017.07.074 Open Access

Hilary Rodgers (Cardiff University) is a co-author on this Chinese-led study that looks into the effect of cadmium treatment on the regulation of the cell cycle and DNA damage repair. They show that different cadmium concentrations effect different phases of the cell cycle.


Alqurashi M, Thomas L, Gehring C, Marondedze C (2017) A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses. Proteomes. 10.3390/proteomes5030022 Open Access

This international collaboration includes members of the Cambridge Centre for Proteomics and conducts a quantitative analysis of the Arabidopsis microsomal proteome following treatment with hydrogen peroxide or ABA. Perhaps unsurprisingly a high number of proteins characterized as ‘responsing to stress’ were found upregulated following treatment with H2O2 or ABA.


Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS,, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genet 10.1038/ng.3937

Justin Goodrich (University of Edinburgh) is a co-author on this US-led study that looks into the role of Polycomb response element (PREs) in directing the placement of the Polycomb repressive complex 2 (PRC2) via their interaction with a newly identified transcription factors. Justin has recently discussed a paper on a similar topic on the GARNet YouTube channel.


Hickman R, van Verk MC, Van Dijken AJH, Pereira Mendes M, Vroegop-Vos IA, Caarls L, Steenbergen M, Van Der Nagel I, Wesselink GJ, Jironkin A, Talbot A, Rhodes J, de Vries M, Schuurink RC, Denby K, Pieterse CMJ, Van Wees SCM (2017) Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. The Plant Cell 10.1105/tpc.16.00958 Open Access

GARNet committee member Katherine Denby (University of York) is a member of this large consortium of researchers who have performed a network analysis on the dynamics of jasmonic acid signaling


Evens NP, Buchner P, Williams LE, Hawkesford MJ (2017) The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum) Plant J. 10.1111/tpj.13655 Open Access

Malcolm Hawkesford (Rothamsted Research) leads this study that investigate a set of wheat bZIP transcription factors and ZIP transporters that are involved in the uptake and transport of zinc. As part of this work they use Arabidopsis to test the conserved function of these wheat proteins.


Larson ER, Van Zelm E, Roux C, Marion-Poll A, Blatt MR (2017) Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement. Plant Physiol. 10.1104/pp.17.00970 Open Access

Mike Blatt and Emily Larson (University of Glasgow) are the co-corresponding authors on this study that looks into the role of clathrin heavy chain on vesicular transport in Arabidopsis. They looked at clathrin mutants to show that the protein plays an unsurprisingly important role in both endo- and exocytosis.

Veronica Grieneisen talks to GARNet!

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Published on: September 5, 2017

Veronica Grieneisen (John Innes Centre) shows much excitement for her science as we discuss a recent PNAS paper entitled ‘Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root’
http://www.pnas.org/content/early/2017/08/17/1705833114.abstract
https://www.jic.ac.uk/directory/veronica-grieneisen/

Lars Ostergaard talks to GARNet

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Published on: August 31, 2017

Lars Ostergaard has an enthusuastic discussion with GARNet about his groups recent paper published in The Plant Cell entitled: Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis’.
http://www.plantcell.org/content/early/2017/08/13/tpc.17.00389
https://www.jic.ac.uk/directory/lars-ostergaard/

Find his discussion about a previous paper here: https://www.youtube.com/watch?v=POWspYw6aXs

SEB-GARNet Meeting on PTMs

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Published on: August 29, 2017

The SEB and GARNet are organising an exciting conference entitled ‘From Proteome to Phenotype: role of post-translational modifications‘ at the University of Edinburgh in December this year.

The registration for this meeting is now open and the full programme is below.

In addition GARNet are hosting an extra workshop that is led by Dr Alex Jones (University of Warwick). This workshop is open to just 30 delegates who will be selected from interested delegates who have registered for the main meeting. There is the opportunity to apply to attend the workshop on the main registration page.

The workshop is intended to help early career researchers get started using proteomics. We will introduce sample preparation methods for common research goals such as “total” soluble protein extraction, enrichment of phosphopeptides and affinity enrichment of fusion proteins. We’ll discuss how best to approach proteomic service providers and the type of information and quality controls that can help to ensure your experiments succeed. After this introductory session we will have short talks from Hirofumi Nakagami (MPIPZ) on phosphoproteomics, Kathryn Lilley (Cambridge) on organelle proteomics and Piers Hemsley (James Hutton Institute) on SLIAC quantification and S-acylation. These talks will be interspersed with data analysis sessions and discussions regarding the troubleshooting of common errors. We will then consider how to evaluate and critically access mass spectrometric data. Our objective is to have a very open discussion throughout and delegates will be required requested to bring a laptop to work through provided examples and fully participate in discussions throughout the day.


In addition GARNet will provide up to ten £200 travel grants for early career researchers who have registered for the workshop before November 3rd.

Information about these grants can be found on the SEB website.


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