UKPPN Root Phenotyping Workshop: April 2016

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Published on: April 15, 2016

The UK Plant Phenotyping Network is a BBSRC sponsored network that has supported meetings and workshops since 2012. A representative from GARNet sits on the UKPPN committee so it was a pleasure to attend the UKPPN Root Phenotyping Meeting that recently took place in the Department of Plant Science at the University of Nottingham.

For someone whose previous research involved growing Arabidopsis plates on agar plates or in controlled growth chambers, this workshop was a real eye-opener as it highlighted the excellent science that is largely aimed at discovering how plant roots interact with their local environment.

This work does mostly not involve Arabdopsis although many of the studies investigate aspects of root growth whose fundamentals have been discovered from lab-studies of the worlds favourite weed. The meeting was hosted by Professor Malcolm Bennett and some of his current Arabidopsis work involves the hydrotropic response which is perfectly aligned to the in-terra studies of how cereal and Brassica roots interact with the available nutrients and water. This work has been facilitated by an amalgamation of research grants that ultimately resulted in the building of the Hounsfield Facility. This purpose built facility contains a generous greenhouse, a human-sized automated robot and three different imagers for CT scanning.

FullSizeRenderThis has allowed a better understanding of how roots interact with soils. However applying more scientific rigour to this process has only been made possible by the analysis software that has been developed at CIPB alongside this imaging technology. During the UKPPN meeting Stefan Mairhofer (CPIB) outlined the development of the Root Phenotyping Pipeline that has allowed researchers to make statistical sense of the CT data that they obtain from the Hounsfield facility. Later in the same session Stefan Gerth (Frauhofer Institute for Integrated Circuits) presented their own technology that they are using for root phenotyping with CT imaging. Finally Erik Esveld (Wageningen) introduces the potential for using XRT imaging to analyse plants grown on drained Rockwool.

Earlier in the day the meeting started with a session on field phenotyping that included an introduction to ‘Shovelomics’ from Tobias Wojciechowski (Julich). He described how they are developing methods for the imaging of whole root systems that have been dug up from the soil. As expected, one difficulty with this work is inconsistency and indeed Tobias showed that the variation between root samples in a plot was greater than that seen between different geographic genotypes isolated from Germany, Norway or Austria. The software that has been developed in house at Julich is able to take 40K images overnight and this data is held in the <a href="http://dirt.iplantcollaborative cialis site officiel.org/welcome” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://dirt.iplantcollaborative.org/welcome’, ‘Digital Imaging of Root Traits’]);” target=”_blank”>Digital Imaging of Root Traits (DIRT) platform,  now being administered through CyVerse. Perhaps there is no greater contrast than the physical digging up plants versus the in silico analysis on CyVerse but perfectly shows the interdiscplinary work occuring in this research area!IMG_9554

The field phenotyping session ended with an enjoyable trip out into the Sutton Bonnington research sites to have demonstrations of Electrical Resistance Tomography by Andrew Binley (this technique allows the measurement of soil water levels) and also Tractor-Mounted Soil Coring from Larry York (which produces soil cores to be used for later root analysis). Pleasingly, the soil water levels predicted by the EMI could be observed in the soil cores.

It might have been unusual for a conference to take people out into the field but it really highlighted the level of challenge that it will take to effectively phenotype a varied field populations of plants!

FullSizeRender_1The second day of the meeting focused on root imaging and modeling, with the audience blown away by the incredible images shown by Jonathan Lynch (Penn State University and University of Nottingham) generated using laser ablation tomography. In this technique root sections are destructively imaged and then digitally reconstituted using 3D software to give fantastic videos that investigate the length of root sections.

Professor Lynch discusses the importance of aerenchyma cells that are found in the cortex of many cereal plants. These essentially empty cells enable a lower overall metabolic cost, therefore clearly benefits the overall energy costs of the plant. Detailed phenotype analysis of aerenchyma has made possible by the RootScan software that has been developed in the PSU Roots lab and is freely available for use.

Later in the session Huw Jones from NIAB described a novel method for the estimation of root biomass. They put together two items that young researchers are told should never mix: soil and PCR. In this technique they perform qPCR on soil samples using primers that are specific for your plant of interest, which allows the approximation of the root biomass within the sample. This technique has also been used to estimate the interactions between plants and weeds across a range of soil depths and struck me as a relatively inexpensive way for this type of analysis, which can provide useful data about the composition of a soil sample.

The keynote talk of the modeling session was Johannes Postma (Julich) who provided an enthusiastic explanation of his attempts to link root phenotypes, soil content and plant biomass. One predicted finding that corresponded with real-life data was that plants with root aerenchyma showed increased biomass in soils with reduced phosphorous. It was excellent to hear this analysis as for much of the meeting the link between root phenotype and yield was not fully made. This is likely to do with the challenges of the imaging technology and the difficulties in fully correlating complex root phenotype with yield.

This meeting demonstrated that the field (pardon the pun) of root phenotyping has great strength especially within the UK, France and Germany. On day one of the meeting Gabriele Pastori (BBSRC) introduced the recently published European Strategy Forum on Research Infrastructures (ESFRI) Roadmap which has “identified the new Research Infrastructures (RI) of pan-European interest corresponding to the long term needs of the European research communities”. Through the work of the UKPPN and others, this document introduces a proposed area of interest in Plant Phenotyping, called EMPHASIS.

EMPHASISThis roadmap is used as an introduction to technologies for which the EU would be interested in developing cross-border infrastructure, by facilitating the legal and financial tools necessary for these type of linkages. At this early stage the EMPHASIS project has no funding associated with it yet the involvement of the BBSRC demonstrates that there is willingness on a national level to discuss future possibilities for funding this area of research. Ultimately any grant funding will come from research bodies within each contributing nation so over the next few years it is encumbent on the UK Plant Phenotyping community to decide how this which occur. Later in the meeting the leader of the French Plant Phenotyping Network (FPPN), Francois Tardieu describes how they have brought together 15 collaborator organisations to tackle phenotyping challenges (see image below)

FPPNThe UK would not look to replicate French or German efforts but rather focus on areas of expertise in which the UK is a world-leader and will provide greatest input toward a pan-European plant phenotyping network. A significant amount of work has already gone into the highlighting of this area for possible European involvement so watch this space to find out how the UKPPN and others can convince UK funders to support this wider initiative.

Overall this was an excellent final meeting of the UKPPN grant and since the first UKPPN gathering the research community has clearly come a long way. It is hoped that the EMPHASIS project and other initiatives will continue to support plant phenotyping across all scales from molecular analysis through to whole field phenotyping and environmental considerations.

Storify of tweets from the meeting put together by the Susie Lydon at CPIB.

Arabidopsis Research Roundup: March 4th

There are six articles in this weeks Arabidopsis Research Roundup that bridge a diverse range of topics. Firstly lead author Deirdre McLachlan provides an audio description of a study that investigates the role of triacylglycerol breakdown in stomatal signaling. Secondly is a study that assesses the role of a Rab GTPase in control of anisotropic cell growth. The third and fourth papers looks into the defence response, focused on either JA or nitric oxide signaling. Finally are two papers that look into the response of Arabidopsis seedlings to growth on either arsenic or cadmium.

McLachlan DH, Lan J, Geilfus CM, Dodd AN, Larson T, Baker A, Hõrak H, Kollist H, He Z, Graham I, Mickelbart MV, Hetherington AM The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening Current Biology http://dx.doi.org/10.1016/j.cub.2016.01.019 Open Access
Slide 1
The control of stomatal opening is a key environmental response to changes in CO2 levels and water availability. This study, led by Alistair Hetherington (Bristol), demonstrates that triacylglycerols (TAGs), contained in lipid droplets (LD), are critical for light-induced stomatal opening. Following illumination, the number of LDs are reduced through the β-oxidation pathway, a response that requires blue-light receptors. The authors postulate that a reduction in ATP-availability due to delayed fatty acid breakdown contributed to the stomatal phenotype. The lack of available ATP was confirmed following analysis of the activity of a plasma membrane H+-ATPase. Overall the authors suggest that the light-induced breakdown of TAG contributes to an evolutionarily conserved signaling pathway that controls stomatal opening therefore playing a key role in environmental adaptation.

The lead author of this study, Deidre McLachlan kindly provides a brief audio description of this paper.

During our discussion Deidre mentioned some related work that links blue-light signaling and starch degradation during stomatal opening that was included in a recent ARR.

 

Kirchhelle C, Chow CM, Foucart C, Neto H, Stierhof YD, Kalde M, Walton C, Fricker M, Smith RS, Jérusalem A, Irani N, Moore I (2016) The Specification of Geometric Edges by a Plant Rab GTPase Is an Essential Cell-Patterning Principle During Organogenesis in Arabidopsis. Developmental Cell 36(4):386-400 http://dx.doi.org/10.1016/j.devcel.2016.01.020 Open Access
Rab5C
Ian Moore (Oxford) is the corresponding author on this UK-German collaboration that investigates the role of a Rab GTPase in pattern formation during organogenesis. It is known that the endomembrane system controls the asymmetric distribution of cargoes to different ‘geometric edges’ of a plant cell, establishing biochemically distinct domains that are important for anisotropic growth. This study identifies a new type of membrane vesicle that accumulates specifically along geometric edges and that contains the RAB-A5c protein which, when inhibited, distorts the geometry of cells in subsequently formed lateral organs (in this case, lateral roots). Interestingly this effect is independent of changes to general endomembrane trafficking. The precise mechanism of RAB-A5c activity is unknown but loss of its activity reduces cell wall stiffness at domain-specific locations, therefore perturbing cell growth in those directions. Therefore this study provides interesting insight into fundamental mechanisms that control the growth of cells in a developing organ.

Thatcher LF, Cevik V, Grant M, Zhai B, Jones JD, Manners JM, Kazan K (2016) Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum J Exp Bot. http://dx.doi.org/10.1093/jxb/erw040 Open Access

Jonathan Jones (TSL) and Murray Grant (Exeter) are collaborators on this research that investigates the role of jasmonic acid signaling in plant resistance to the fungal pathogen Fusarium oxysporum. In this study they show that the JASMONATE ZIM-domain7 (JAZ7) gene is induced by Fusarium oxysporum and that the jaz7-1D mutant has increased suspectibility to infection. This genotype has constitutive JAZ7 expression and also demonstrates sensitivity to a bacterial pathogen. To cause alterations in gene expression, the JAZ7 protein interacts with a range of transcriptional activators and repressors. The authors postulate that in wildtype plants JAZ7 represses the JA-transcriptional network through its interaction with the co-repressor TOPLESS protein and that in the jaz7-1D plants this response network is hyper-activated leading to an inappropriately high response to pathogen attack.

Yun BW, Skelly MJ, Yin M, Yu M, Mun BG, Lee SU, Hussain A, Spoel SH, Loake GJ (2016) Nitric oxide and S-nitrosoglutathione function additively during plant immunity. New Phytol. http://dx.doi.org/10.1111/nph.13903

Gary Loake and GARNet Advisory board member Steven Spoel (Edinburgh) are the leaders of this UK-Korean collaboration that studies the role of Nitric Oxide (NO) in the plant defence response. NO often undergoes S-nitrosylation to produce S-nitrosothiol (SNO), which is important for its bioactivity. This reaction involves the S-nitrosoglutathione reductase 1 (GSNOR1) enzyme, which serves to turnover the NO donor, S-nitrosoglutathione (GSNO). In this study the authors investigate mutant plants that accumulate NO and some a reduction in the basal defence response due to a reduction in salicylic acid (SA) signaling. This response was not rescued by the overexpression of GSNOR1 even though this was able to reduce phenotypes resulting from SNO accumulation. Mutant plants that have increased NO accumulation but lower activity of GSNOR1, so therefore an increased ratio of NO:SNO, were more suspectible to growth of bacterial pathogens. The authors conclude that the relationship between NO and GSNO is critically for plant immunity and development.

Lindsay ER, Maathuis FJ (2016) Arabidopsis thaliana NIP7;1 is Involved in Tissue Arsenic Distribution and Tolerance in Response to Arsenate FEBS Lett. http://dx.doi.org/10.1002/1873-3468.12103

Francois Maathuis (York) is the corresponding author of this study that investigates the role of the Arabidopsis aquaglyceroporin NIP7;1 in the uptake of different chemical forms of arsenic. Mutant nip7;1 plants improved the tolerance of arsenic by reducing uptake of the chemical. This is the first demonstration for the role of a NIP transporter in the response to arsenic and highlights the possibility of focussing on these proteins as a target for breeding or genetically-modifying tolerance to this toxic metal.

Wang H, He L, Song J, Cui W, Zhang Y, Jia C, Francis D, Rogers HJ, Sun L, Tai P, Hui X, Yang Y, Liu W (2016) Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress Chemosphere 150:258-265 http://dx.doi.org/10.1016/j.chemosphere.2016.02.042

Hilary Rodgers (Cardiff) is the sole UK representative on this Chinese study that has developed screening parameters to evaluate the growth of plants on cadmium. The study uses microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) to define a range of genomic alterations that occurred after growth of Arabidopsis plants across a range of concentrations of cadmium. They conclude that analysis of genomic methylation polymorphisms were the most sensitive biomarkers to diagnosis early cadmium stress in these plants and provide important insights for future biomonitoring strategies.

Arabidopsis Research Roundup: July 20th

There is a bumper crop of publications in high quality journals in this weeks UK Arabidopsis Research Roundup, including manuscripts in PNAS, Nature Communications, PLoS Genetics , PloS One and Plant Physiology. Malcolm Bennett, Alex Webb and Anthony Hall lead a major collaborative effort that links the circadian clock with lateral root formation whilst Ottoline Leyser (SLCU) and Mike Bevan (JIC) participate in a similarly broad consortium in a study linking organ size and MAPK signaling. Liam Dolan’s group from Oxford looks at mechanisms of tip-growth across the plant kingdoms whilst elsewhere three members of faculty at the University of Birmingham are involved in two papers looking at the regulation of meiosis. Finally there are two US-led studies that include significant contributions from UK-based researchers, including Matthew Jones from the University of Essex.

 

Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, Wells DM, Péret B, Goh T, Fukaki H, Hodgman TC, Laplaze L, Halliday KJ, Ljung K, Murphy AS, Hall AJ, Webb AA, Bennett MJ (2015) The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana Nature Communication 6:7641. http://dx.doi.org/10.1038/ncomms8641

Once again Malcolm Bennett (CPIB) leads a multi-Institute collaboration that includes Alex Webb (Cambridge) and current GARNet board member Anthony Hall (Liverpool). This is also an extremely international effect with groups from the UK, USA, Sweden, Japan, Spain and France. The science looks at lateral root stems cells and how the circadian clock is rephased during LR emergence. They show that the clock controls auxin levels and auxin-related genes. The conclusion is that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence and adds to a growing portfolio of evidence that suggest the circadian clock might act in a cell autonomous manner. Anthony Hall, James Locke and Peter Gould currently have a grant that is looking at this phenomenon in Arabidopsis root cells.

 

Johnson KL, Ramm S, Kappel C, Ward S, Leyser O, Sakamoto T, Kurata T, Bevan MW, Lenhard M (2015) The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis PLoS One.10(7):e0131103. http://dx.doi.org/10.1371/journal.pone.0131103

Ottoline Leyser, Sally Ward (Sainsbury lab, Cambridge) and Mike Bevan (JIC) are the UK contributors to this joint UK-German-Japanese-Australian collaboration. This study follows a screen for plants with reduced organ size and introduces a novel allele of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5), named Tinkerbell (tink). This mutation reveals that IBR5 is a novel regulator of organ size by changing the growth rate in petals and leaves although this occurs independent of the previously characterised KLU pathway. The authors use microarray data to suggest an additional role for TINK/IBR5 during male gametophyte development. Ultimately they conclude that IBR5 might influence organ size through auxin and TCP growth regulatory pathways.

 

Tam TH, Catarino B, Dolan L (2015) Conserved regulatory mechanism controls the development of cells with rooting functions in land plants Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1416324112

Liam Dolan’s lab at the University of Oxford is a world leader in the study of root hair development. Previously it has been shown the group XI basic helix-loop-helix (bHLH) transcription factor (LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) regulates root hair growth in Arabidopsis, Lotus or rice. This study investigates the equivalent proteins in the moss Phycomitrella patens and show that they are involved in an auxin signaling pathway that promotes cell outgrowth albeit via a different set of signaling intermediates. Overall the authors show that a core auxin network that supports cellular ‘tip-growth’ exists throughout land plant lineages even though the specificity of this signaling has diverged over the course of the ~420million years that separates angiosperms and mosses.

 

Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M (2015) Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant. PLoS Genet.11(7): e1005301. http://dx.doi.org/10.1371/journal.pgen.1005301

The work led by Monica Pradillo at the University of Madrid includes a contribution from Eugenio Sanchez-Moran from the University of Birmingham. This work focuses on the hetero-trimeric Chromatin Assembly Factor 1 (CAF-1), which is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA. In Arabidopsis the CAF1 complex is composed of the FAS1, FAS2 and MSI1 proteins. Atfas1 mutant plants are less fertility, have a higher number of double stranded breaks (DSB) and show a higher gene conversion frequency. The authors investigate how DSBs can influence meiotic recombination and synaptonemal complex (SC) formation by genetic analysis of Atfas1-containing double mutants. Ultimately their experiments provide new insights into the relationships between different recombinase proteins in Arabidopsis. Overall an increase in the number of DSBs does not translate to an increase in the number of crossovers (COs) but instead in a higher GC frequency. The authors provide different theories to explain this mechanism, including the possible existence of CO homeostasis in plants.

 

Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372 http://dx.doi.org/10.1371/journal.pgen.1005372

The University of Birmingham is the lead Instiution in this study that also investigates regulation of meiosis. The groups of Chris Franklin and Sue Armstrong collaborate with US and Austrian partners to study the organization of meiotic chromosomes during prophase I. Using structured illumination microscopy (SIM) they show that dynamic changes in chromosome axis is coincident with synaptonemal complex (SC) formation and depletion of the ASY1 protein, which requires the function of the PCH2 ATPase. Using a pch2 mutant the authors are able to tease apart different aspects of ‘crossover’ (CO) biology and that the pch2 defect occurs precisely during CO maturation, not during designation. In addition, CO distribution is also affected in some chromosome regions showing that failure to deplete ASY1 can result in downstream events that include disruption of CO patterning.

 

Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer S (2015) A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light Plant Physiology. http://dx.doi.org/pp.00782.2015

Matthew Jones (University of Essex) is the primary author of this work that comes from a collaboration from his time in the lab of Stacey Harmer in UC Davis. Since 2012 Matthew has been a lecturer at the University of Essex where he continues with work of this nature. In this study they introduce a constitutively active allele of the PHYB photoreceptor that is able to phenoopy red-light input into the circadian clock. In these mutants the pace of the clock is insensitive to light-intensity and this response is dependant on its PHYB nuclear localisation. Finally they show that fine tuning of PHYB signalling requires PHYC and overall they conclude that nuclear phytocrome signalling is necessary for sustaining clock function under red light.

 

Chakravorty D, Gookin TE, Milner M, Yu Y, Assmann SM (2015) Extra-Large G proteins (XLGs) expand the repertoire of subunits in Arabidopsis heterotrimeric G protein signalling Plant Physiol. http://dx.doi.org/10.1104/pp.15.00251

Sally Assman from Penn State University leads this study that includes a contribution from Matthew Milner who now works at NIAB. The number of proposed G protein subunits is greatly reduced in diploid plant genomes yet this study shows that a family of Arabidopsis GPA-related proteins (XLG1-3) can increase the repertoire of potential G proteins interactions by interacting with beta and gamma subunits. The authors propose they have uncovered a new plant-specific paradigm in cell signaling.

COPO 2015 Meeting

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Published on: June 25, 2015

COPO has big plans…. and if it is to be truly successful and benefit the plant community there needs to be a cultural change! That’s the simple if revolutionary message that came out of the recent COPO meeting held at TGAC on June 23rd-24th.

So the uninitiated will be asking: ‘What is COPO?‘ The answer is the Collaborative Open Plant Omics group which was funded by a BBSRC BBR grant in 2014. This is a >£1m collaboration between The Genome Analysis Centre (TGAC), University of Oxford, the European Bioinformatics Institute (EMBL) and the University of Warwick.

This workshop was to introduce the aims of COPO to a range of stakeholders, from curators of available data repositories to experimentalists who are generating large datasets. By the end of the 2-day session it was hoped that everyone would gain an understanding of what COPO can offer the community with regard facilitating the sharing of large datasets.

White Board Discussions

The workshop was led by Rob Davey (TGAC) and Ruth Bastow (GPC, GARNet, Warwick). Rob kicked off the meeting by describing the aims of COPO which included asking ‘What are the barriers for you and your data and how can COPO facilitate access to the workflows used to analyse data’.

Subsequently a range of stakeholders introduced the fantastic tools that are out there for repositing data of many different types. These included David Salt (University of Aberdeen, Ionomics), Elizabeth Arnaud (Montpellier, CropOntology), David Marshall (James Hutton Institute, Germinate: Plant Genetic Resources), Esther Kabore (INRA, Wheat Data Repository) Reza Salek (EMBL, Metabolights), and finally Tomasz Zielinski (Edinburgh, BioDare) who made the telling observation that ‘data Management is a user interface/user experience problem NOT a software engineering/ data modelling problem’. Many researchers are often reluctant to take the time and effort required to submit their data to an appropriate repository in a reasonable manner, for any number of opaque reasons. However the take-home message from the early talks was very positive as there are a large number of data platforms available for people to use and benefit from. One of the challenges for COPO is to not only to help convince people to use these resources but encourage them to share data in a standardised manner.

Following a useful coffee break it was time for researchers to explain the data they are producing and the challenges for their analysis. Miriam Gifford (Warwick) discussed her generation of transcriptomic data, Christine Sambles (Exeter) talked about developing a workflow for metabolomics data and TGAC group leader Ksenia Krasileva introduced her work on wheat functional genomics. Ksenia also highlighted a new portal for communication between data generators and data users called Grassroot Genomics.

The final three talks of the day highlighted the amount of data that can be produced in different sets of biological experiments. Ji Zhou (TGAC) and Chris Rawlings (Rothamstead) introduced cutting-edge field phenotyping technologies that use large imagers to capture visible and spectral aspects of plant growth. Workshop attendee Professor Peter Murray-Rust summed it up with a tweet: ‘Blown away by the crop monitoring equipment at Rothamstead’. On an opposite end of the spectrum Jim Murray (Cardiff) showed a single fluorescent image of a zebrafish taken on a light-sheet microscope that weighed in at an impressive 23Tb of data. Overall these talks served to highlight the vast amounts of data that can be produced and provided the second take-home message of the day that ‘Getting data is NOT the issue, making any sense of it IS the challenge’……

 

The task of second day discussions was to make sense of what had been presented the previous day and identify the best opportunities for COPO to impact on the process of data sharing. A lively first hour of debate included Dr Philippe Rocca-Serra (COPO Co-PI from Oxford) presenting a somewhat sobering eight slides of ‘Pain Points’ that he had taken out of the previous days presentations! However it was refreshing to observe that the challenge of the task was not underestimated and being tackled with realistic planning.

Pain Points!

Later in the morning discussions turned more specific with a white-board brainstorming session that was divided into ‘Data Collection’.Data Storage’ and ‘Data Analysis’ sections. Most progress was made in the first two sections with a long list of storage repositories identified that bridged the breath of biological data and with which COPO could potentially interact.

It was felt that successful interactions would be predicated on some level of data standardisation so perhaps the most effective initial use of the COPO resources would be to develop a workflow for standard data collection. This would hopefully make experimentalists think about the format of their data submission as they are planning and generating the data. The consensus was that attaching these standards to legacy-data might be a difficult task but that for future data generation, COPO could influence data sharing at this level.

IMG_8241

Ultimately it is clear that plant science has the same generic problems as many other disciplines and the greatest challenge is to change the ‘culture’ of sharing data. The most obvious and direct way to promote this change will be via the funders and publishers. Some progress has been made in this arena with a recent shift towards open access publication in the REF process, and it would only take another small additional step to make it a requirement to share data in any REF-returnable publications. So I hope that those with greater power and influence than me, are reading the GARNet blog!

Regardless of the pace of cultural change, the feeling in the meeting was that the COPO mandate is to encourage data sharing whilst moving to a position to effectively interact with the data that is shared. There is plenty of work to do but at the end of this exploratory workshop the COPO organisers had plenty to think about regarding the direction of the project. Watch their space!

Storify of tweets from the meeting

Great British Success in ERA-CAPS

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:
logo-era-caps
Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

A few funding opportunities for UK plant scientists

Here are the details of a few funding opportunities we have recently came across for early career and more established researchers – some of the deadlines are quite soon so if you’re interested, be quick!

Royal Society Research Grants

The Royal Society invites applications for its research grants. These provide seed-corn funding for early-career UK scientists for research within the society’s remit in the natural sciences, including the history of science. The aim is to increase the availability of specialised equipment and consumables for high quality research, and to enable scientists to further develop their new projects by obtaining funding from other sources.

Applicants should have a PhD or equivalent status, be working as independent researchers within five years of their first academic position and be resident in the UK. Non-tenured researchers and retired scientists may apply if the application is related to the history of science and the applicant works in association with an eligible institution. Eligible organisations are UK universities and non-profit research organisations, including institutes funded by the UK Research Councils.

Two types of grants are available for a maximum period of 12 months: grants of up to £15,000 for specialised equipment, essential consumable materials and services, and travel and subsistence for essential field research; and grants of up to £5,000 for the publication of scholarly works on the history of science.

Deadline: 26th May 2015

 

BBSRC Future Leader Fellowship

The Biotechnology and Biological Sciences Research Council and the Food Standards Agency invite applications for their future leader fellowship. This enables early-career researchers to undertake independent research on any area within biotechnology and biological sciences, and to gain leadership skills.

Applications that align with the following strategic priorities are particularly welcome:

  • animal health;
  • bioenergy – generating new replacement fuels for a greener, sustainable future;
  • combating antimicrobial resistance;
  • data driven biology;
  • food, nutrition and health;
  • healthy ageing across the lifecourse;
  • new strategic approaches to industrial biotechnology;
  • reducing waste in the food chain;
  • replacement, refinement and reduction in research using animals;
  • sustainably enhancing agricultural production;
  • synthetic biology;
  • systems approaches to the biosciences;
  • technology development for the biosciences;
  • welfare of managed animals.

In addition, the FSA will co-fund proposals that have the potential to impact on issues highlighted in its emerging strategy 2015–2020 and underpinning science, evidence and information strategy. A particular interest is for proposals that aim to realise the potential of utilising big data approaches to address complex issues that will ultimately lead to benefits for consumers. Fellows whose proposals are co-funded by the FSA may undertake a short term placement with the agency.

Applicants should have a PhD, or be expecting to have passed their viva prior to 30 November 2015. They should have no more than five years’ postdoctoral research employment by this point.

Approximately 12 fellowships are available. Each fellowship is worth up to £250,000 over a period of three years. Awards include personal salary as well as support for travel and subsistence, training activities and research consumables.

Deadline: 4th June 2015

 

Rank Prize Nutrition Fund New Lecturer Award

The Rank Prize Funds’ nutrition committee invites applications for its new lecturer awards. These support scientists who are conducting research in an area of human nutrition or crop science in order to further their careers.

Newly-appointed lecturers, researchers of equivalent status who are based in research institutes, or fellows with their own independent support who are working in a UK institution, may apply. The post must have been started at the earliest in 2013, and applicants should normally be three to nine years from their PhD. Postdoctoral scientists supported on a senior investigator’s funding are not eligible.

Awards are worth up to £20,000 each for a period of up to two years. Funding may be used for consumables, equipment or a contribution towards a salary or student support.

Deadline: 28 August 2015

iPlant is coming to the UK

Back in 2013, the GARNet team brought the iPlant Collaborative over to the UK to run a four-day workshop. Now, we’ve secured funding to bring iPlant to the UK again – but this time, it’s here to stay!

During 2014, the GARNet team and committee – together with iPlant collaborators in the US – were busy preparing a grant application for an invited BBSRC capital funding call. Our proposal was to work with iPlant to develop a ‘node’ of iPlant here in the UK. Our application was sucessful and the award was announced at the end of January at the AAAS 2015 meeting.

What is iPlant?

Funded by the US National Science Foundation (NSF) the iPlant Collaborative provides free and open access to ‘cyberinfrastructure’, originally just for plant scientists, but now for all the life sciences. Here’s a short video clip to explain more:

Harnessing the power of some of the world’s most powerful supercomputers, iPlant users can access the cloud-based Data Store, which provides very large amounts of space for researchers to store, and quickly transfer and share ‘big data’ files.

iPlant users also have access to the Discovery Environment – a web-based, graphical interface that provides access to an ever-expanding suite of modular, integrated ‘apps’ for data analysis. Apps can be built either by the iPlant team or by more experienced users, and cover a wide range of analysis needs. They are user-friendly and very intuitive, meaning that even researchers with little or no knowledge of command line computer programming can easily run an app, or create a pipeline of apps, to analyse large and complex data files.

Why do we need iPlant UK?

iPlant, which is free for anyone around the world to use, is currently distributed across three locations in the US – the Texas Advanced Computing Center, the University of Arizona and Cold Spring Harbor Laboratory. Though the high performance computing power it utilises is currently sufficient, iPlant was designed to be extendable to spread resources between even greater numbers of ‘nodes’. iPlant UK will be the first – hopefully of many – international iPlant hubs to ensure the future sustainability of the resource on a global scale.

As we noted in our recent Journal of Experimental Botany paper, one of the drawbacks of having iPlant located solely in the US, is that technical user support is only currently available during US office hours. When we hosted our workshop at the University of Warwick in September 2013, iPlant’s US-based support engineers kindly agreed to be woken up if we needed them – and we did! Clearly that’s not an ideal solution going forwards, especially as the number of worldwide users grows and grows.

As well as having access to technical support on the GMT timezone, the project’s collaborators at the Universities of Warwick, Liverpool, Nottingham and at The Genome Analysis Centre (TGAC), aim to convert existing BBSRC-funded software tools for the iPlant environment. This will increase community access to these useful resources, and their uptake, giving the plant science community even greater opportunities for efficient, effective, collaborative research.

How will it work?

iPlant UK will run as an independent, UK-hosted iPlant node that will centralise compute power and data storage to a single site at TGAC.

The team at TGAC, managed by Dr Tim Stitt and Dr Rob Davey, will work together to install and maintain new and existing hardware infrastructure at TGAC, and once that phase is complete, they will start work to establish and launch the iPlant UK node.

Meanwhile, teams at the Universities of Warwick, Nottingham and Liverpool will convert software tools they have created from their existing formats to the iPlant environment.

  1. University of Liverpool: Next generation sequencing workflows (led by Professor Anthony Hall). Working with the wheat community, the team at Liverpool will optimise a wheat genetic tool bench for next generation sequencing, and a pipeline for mapping-by-sequencing.
  2. University of Warwick: Gene expression, networks and promoter motif tools and pipelines (led by Professor Jim Beynon). The Warwick team will port tools from the PRESTA project into the iPlant environment. These tools include those for identifying differential gene expressions, clustering and network inference, and promoter analysis.
  3. University of Nottingham: Image-based phenotyping (led by Professor Tony Pridmore, Centre for Plant Integrative Biology). The team at Nottingham will convert a range of popular tools for visualising root phenotypes, so that they can be accessed and used from the iPlant environment.

If you are interested in getting involved with this project, two posts at TGAC are currently being advertised (but hurry, the closing date is tomorrow, 3rd March!)

Opportunities at Warwick and Nottingham will be announced soon so stay tuned for updates!

Funding and networking opportunities from BBSRC plant science NIBBS

Categories: funding
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Published on: December 9, 2014

Early this year, BBSRC announced 13 new Networks in Industrial Biotechnology and Bioenergy (NIBBS). Their aim is to foster collaborations between the academic research base and industry in order to drive new ideas in specific areas of focus. Four NIBBS have plant science themes:

•   A Network of Integrated Technologies: Plants to Products: http://www.nibbp2p.org/

•   High Value Chemicals from Plants Network: https://hvcfp.net/

•   Lignocellulosic Biorefinery Network (LBNet): http://lb-net.net/

•   PHYCONET: unlocking the IB potential of microalgae: http://www.phyconet.org.uk/

Each BBSRC NIBB organises free residential networking events and awards funding in the form of Business Interaction Vouchers and Proof-of-Concept funds. You need to be a member of the NIBB to access any of these resources, but they are all free to join.

Business Interaction Vouchers are worth up to £5000 and are intended to support research done by an academic partner for an industrial partner of the NIBB. Depending on the NIBB, there are deadlines throughout the year or applications are accepted at any time.

Proof-of-concept funds are more flexible in scope and amount awarded, but have stricter deadlines. Each NIBB is dealing with their awards differently: The HvCFP deadline is 19 January 2015; and the LB-Net has organised Challenge Workshops in 2015, which will lead to funding for multi-disciplinary teams formed at the workshops. The other networks do not currently have proof-of-concept calls open.

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