PhenomUK can fund small (£5-25k) preliminary and feasibility studies, following a light internal review process. This funding is intended to allow recipients to assess emerging technologies against phenotyping tasks and perform initial investigations of promising technology combinations. With the emergence of powerful machine learning approaches, annotated data sets are becoming an increasingly important resource, and it is anticipated that some projects will generate such data sets.
Note that the terms of the Technology Touching Life grant require PhenomUK to fund projects at 80% FEC, and that all grant recipients are required to produce a short description of their project and results to be disseminated to members via the PhenomUK website.
potential to advance the capabilities and/or range of application of phenotyping technologies
potential to create new partnerships between the engineering and physical science and plant and crop science communities
Applications will be particularly encouraged from early career researchers, including postdoctoral fellows.
All applications should demonstrate that the funds are sought for a clearly defined, discrete piece of research, which will have an identifiable outcome on completion. Payment of the grant will be made in two tranches, the second, mid -term payment being subject to a review of satisfactory progress.
Applicants are required to nominate two referees and ensure that the supporting statement from their chosen referees is submitted to enquiries@phenomuk.net by the deadline for submission of application.
We are unable to provide feedback on unsuccessful applications.
Eligibility
The following are NOT eligible for funding: attendance to conferences organised by a third party or international organisations; funding for replacement teaching or administrative costs; funding of the PI’s time.
Funding is available to PhenomUK members only. All applicants must be members of the network. Membership is free and membership is obtained by registering here.
https://www.phenomuk.net/membership-join/membership-registration/
To apply for funding please download, complete and email the application form to enquiries@phenomuk.net
THE COMMUNITY RESOURCE FOR WHEAT AND RICE TRANSFORMATION is a resource for UK plant scientists to apply for their genes to be transformed into wheat or rice free of charge, funded by the BBSRC’s Biological and Bioinformatic Resources fund (BBR).
THE 2ND ROUND OF THE APPLICATION PROCESS IS OPEN UNTIL 31ST MARCH 2020 for transformation slots in the summer. There further details and an online application form available via the following link:
One hundred novel genes will be tested during the course of this five year project, selected by an external project advisory group comprised of researchers, industry members and stakeholders. We anticipate that half of the project capacity will be used by scientists working with model species such as _Arabidopsis thaliana_ or _Brachypodium distachyon, in order to find new sources of genes and to encourage and support the scientists to test them in wheat and rice.
The project also provides capacity to characterise 50 regulatory elements in wheat and rice. Promoter and terminator sequences will be included for their expression in a wide range of tissue types.
RESEARCHERS CAN EITHER NOMINATE PROMOTERS TO BE INCLUDED IN THIS PROJECTFOR TESTING IN WHEAT AND RICE.
This weeks GARNet Research Roundup begins with two studies that characterize the role of proteins that are involved in the control of meiotic recombination. The first study is from the Henderson lab at the University of Cambridge and investigates the role of the REC8 protein whilst the second is from John Doonan’s group at Aberystwyth University and investigates the role of the cyclin-dependent kinase CDKG.
The third paper is from the same
research group in Aberystwyth and investigates how alternative splicing
can impact the function of the FLOWERING LOCUS M gene.
The next papers is a cross-UK collaboration led from Rothamsted
Research and the John Innes Centre that identifies an important QTL
associated with the generation of high-fibre wheat. The fifth paper is
from the JIC and reveals how the immune resistance gene MLO plays a role
in a plants association with beneficial microbial symbiotes.
The sixth paper is from the Gibbs lab at the University of
Birmingham and further characterizes the function of the VRN2 component
of the polycomb repressive complex 2.
Nick Harberd from Oxford is a corresponding author of the next
paper, which identifies a new gene that could be used to improve
nitrogen-use efficiency in rice.
The eighth paper is a
proteomic-based study from the University of Cambridge that identifies
novel stress-induced components of the Arabidopsis spliceosome.
The
penultimate paper is from Jonathan Jones’ lab at the Sainsbury lab,
Norwich in which they characterize a new transgenic line useful for
studying the plant immune response.
The final paper includes Liam Dolan from Oxford as a co-author in a study that characterizes a novel ATPase from the algae Chara australis.
Lambing C, Tock AJ, Topp SD, Choi K, Kuo PC, Zhao X, Osman K, Higgins J, Franklin FCH, Henderson IR (2020) Interacting genomic landscapes of REC8-cohesin, chromatin and meiotic recombination in Arabidopsis thaliana. Plant Cell. doi: 10.1105/tpc.19.00866 Open Access
This study is led by Chris Lambing from
Ian Henderson’s group at the University of Cambridge and includes
collaborators from Leicester and Birmingham. They use ChIP-seq to
identify the genomic regions associated with the REC8 protein, showing
that it interacts with regions with multiple distinct chromatin states.
This interaction plays a key role in controlling the formation of double
strands breaks and is required to organize meiotic chromosome
architecture and interhomolog recombination.
Nibau C, Lloyd AH, Dadarou D, Betekhtin A, Tsilimigka F, Phillips DW, Doonan JH (2020) CDKG1 Is Required for Meiotic and Somatic Recombination Intermediate Processing in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00942 Open Access
Candida Nibau
from Aberystwyth University leads this research that reveals a critical
role for the cyclin-dependent kinase G1 (CDKG) in the control of
recombination, both during meiosis and within somatic cells. The authors
discover that this role occurs early in the process through the
stabilization of recombination intermediates.
Nibau C, Gallemí M, Dadarou D, Doonan JH, Cavallari N (2020) Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. Front Plant Sci. doi: 10.3389/fpls.2019.01680 Open Access
Candida
Nibau is first author on this collaboration between researchers in the
UK (Aberystwyth University) and Vienna, Austria. They assess the factors
that control the contribution of two splicing variants of the FLOWERING
LOCUS M gene on flowering time across a temperature range. They find
that this process is controlled by the activity of the cyclin-dependent
kinase G2 (CDKG2) and its cognate cyclin, CYCLIN L1 (CYCL1).
Lovegrove A, Wingen LU, Plummer A, Wood A, Passmore D, Kosik O, Freeman J, Mitchell RAC, Hassall K, Ulker M, Tremmel-Bede K, Rakszegi M, Bedő Z, Perretant MR, Charmet G, Pont C, Salse J, Waite ML, Orford S, Burridge A, Pellny TK, Shewry PR, Griffiths S (2020) Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour. PLoS One. doi: 10.1371/journal.pone.0227826 Open Access
Alison Lovegrove at Rothamsted Research is the first author on this cross-UK research that has gained significant interest from the main–stream media. Through analysis of a Chinese wheat variety with high dietary fibre due to the high amounts of cell wall polysaccharide arabinoxylan the authors identified a QTL that is responsible for this phenotype. Understanding this QTL will allow use of both marker-assisted breeding and new breeding technologies to aid in the generation of high yield, high fibre varieties.
Jacott CN, Charpentier M, Murray JD, Ridout CJ (2020) Mildew Locus O facilitates colonization by arbuscular mycorrhizal fungi in angiosperms. New Phytol. doi: 10.1111/nph.16465
Catherine Jacott
is first author on this study from the JIC that investigates the role
of the known barley resistance gene Mildew Resistance Locus O (MLO)
during arbuscular mycorrhizal interactions in wheat, barley and
Medicago. They show that MLO is important for this beneficial symbiotic
association and that the role of MLO has been appropriated during
infection with pathogenic powdery mildew.
Labandera AM, Tedds HM, Bailey M, Sprigg C, Etherington RD, Akintewe O, Kalleechurn G, Holdsworth MJ, Gibbs DJ (2020) The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. New Phytol. doi: 10.1111/nph.16477
Anne-Marie Labandera
is first author on this work from Dan Gibbs’ lab in Birmingham. They
show that ubiquitin-mediated proteolysis of the VERNALIZATION2 (VRN2)
protein via the oxygen-dependent PRT6 N-degron pathway is important for
many areas of plant development. This regulation of VRN2 has different
developmental outcomes depending on whether it occurs in or out of
meristematic tissues.
Wu K, Wang S, Song W, Zhang J, Wang Y, Liu
Q, Yu J, Ye Y, Li S, Chen J, Zhao Y, Wang J, Wu X, Wang M, Zhang Y, Liu
B, Wu Y, Harberd NP, Fu X (2020) Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice. Science. doi: 10.1126/science.aaz2046
Kun Wu is first author on this Chinese-led investigation that also includes Nick Harberd from
Oxford University as a corresponding author. Working in rice they link
genomic-wide chromatin changes with expression of the NGR5
(NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) transcription factor during
nitrogen-induced growth. Overexpression of NGR5 can uncouple
nitrogen-sensing from tiller production and therefore provide a novel
tool to possibly enhance agricultural production in low nitrogen
conditions.
Marondedze C, Thomas L, Lilley KS, Gehring C (2020) Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. Front Mol Biosci. doi: 10.3389/fmolb.2019.00163 Open Access
Claudius Marondedze
is the first author on this collaboration between the University of
Cambridge and KAUST in Saudi Arabia. They perform label-free mRNA
interactome-capture to identify RNA interacting proteins that are
induced after drought stress. This reveals over 40 novel
spliceosome-interacting proteins but also 32 proteins that associate
with stress granules, which are indicative of transcriptional arrest.
This provides new insights into how plant stress responses might be
altered by the activity of spliceosome components.
Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG (2020) Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. J Exp Bot. doi: 10.1093/jxb/erz571
This research from Jonathan Jones’ group
at the Sainsbury Lab, Norwich is led by Bruno Pok Man Ngou. They have
developed a transgenic line that enables the transient in planta
expression of AvrRps4, which is a potent bacterial immune effector. This
stimulates the RRS1/RPS4-dependent immune response and provides
insights into certain mechanisms of this pathway without exposing the
plants to pathogens.
Zhang S, Habets M, Breuninger H, Dolan L, Offringa R, van Duijn B (2020) Evolutionary and Functional Analysis of a Chara Plasma Membrane H(+)-ATPase. Front Plant Sci. doi: 10.3389/fpls.2019.01707 Open Access
Liam Dolan
from the University of Oxford is a co-author on this Dutch-led research
that includes Sutun Zhang as first author. They characterize a plasma
membrane localised ATPase from the algae Chara australis and perform
complementation studies in both yeast and Arabidopsis. These studies
allow the authors to propose that the mode of regulation of this algal
ATPase is likely different from that of known yeast and land plant PM
H+-ATPases.
This workshop brings together established
group leaders and early career researchers to discuss the latest developments
in research that is linked to the ubiquitous phytohormone auxin.
The workshop takes place at the Hotel
Croatia, Cavtat for which delegates will have preferential booking rates. This
location is just 10minutes from Dubrovnik airport.
The PhenomUK network is into its second year of operating supported by the UKRI Technology Touching Life scheme. PhenomUK focuses on how technological developments in plant phenotyping can impact agricultural productivity for the benefit of UK and global food production.
Despite being early in its four-year funding cycle PhenomUK has a growing mailing list, social media following and welcomed around 60 attendees to this annual meeting at the National Physical Laboratory (NPL). For those not familiar; the NPL is situated in west London and employs 600 people who research and support the science of measurement, Metrology. Around 50% of NPL funding comes direct from UK government with the remainder from competitive grants and private partnerships. The core activities of the NPL are in calibration services that are linked to the maintenance of SI base units such as the kilogram, second, ampere or metre. However as part of their data science program, researchers at NPL are applying their technical expertise to agricultural challenges.
NPL scientist Andrew Thompson
presented some of his groups early data in which they first used 3D imaging to
visualize wheat fields and then applied density calculations to isolate individual
wheat-ears. There will be plenty to come from this research program and they
are happy to discuss collaborations with anyone who wants to tap into their expertise.
Andrew Thompson shows his 3D imaging of wheat
The keynote talks were provided by Hanno Scharr from Forschungszentrum Jülich and Mark Aarts from Wageningen University & Research (WUR). Jülich has an outstanding selection of across-scale technologies to support phenotyping, from automated seed picking through to satellite-enabled field imaging whilst WUR are collaborating with the University of Utrecht to develop the Netherlands Plant Eco-phenotyping Centre (NPEC). Both facilities cost in excess of €20M and highlight the infrastructural support required to develop a national capability. It remains to be seen whether this will be possible across the more fragmented UK plant science community.
UKRI/BBSRC understand the importance of plant phenotyping technologies and are supportive of the community….however a £10M+ investment might be a little way off! It was excellent to hear Professor Aarts provide an perspective of where the NEPC will sit within the European and International phenotyping communities.
Mark Aarts explains where NPEC fits into the International communitty.
On that note the EMPHASIS project is now reaching the end of its exploratory phase and will thereafter hopefully provide a constant presence for plant phenotyping within the European funding landscape. The meeting included a promising discussion that suggested that the EMPHASIS legal entity sits outside of the Horizon program (and its successor) so the UK should be able to remain a full participant. Fingers crossed!
The remainder of the meeting was taken with an update from PhenomUK PI Tony Pridmore who outlined the aims of the network and the available funding schemes:
1. Networking Visit Funding. PhenomUK can fund travel, accommodation and subsistence bursaries to support short fact-finding and networking visits between UK institutions and between UK and international centres. This is an open call yet no-one has taken advantage of this scheme. Please consider applying for it! https://www.phenomuk.net/applications/networking-visit-funding-applications/
2. Pilot Project Funding. This is the main funding instrument through which PhenomUK supports plant-phenotyping applications on behalf of UKRI-BBSRC. Network members can request £25K for these pilot projects and in the first round 4 projects were funded from 13 applications. Professor Pridmore was very clear to emphasise that proposals are only eligible if the project contains a technology-development component. Proposals that ‘simply’ support a scientific experiment will not be considered. The second round of applications will open over the coming weeks. These grants represent significant finance support for a nascent project so please consider how you might take advantage of this opportunity. https://www.phenomuk.net/applications/pilot-project-funding-applications/
Tony Pridmore presents the next pilot project scheme
Representatives from the four successful pilot projects outlined their plans, which are at different levels of complexity and progress. Dr Bo Li from UWE outlined his team’s early attempts to use microwaves to image fruit damage and root development whilst Dr Ji Zhou from NIAB demonstrated their plans for large-scale field phenotyping using drones. The full list of pilot projects can be found here
Ji Zhou presents his lab’s field phenomics research through Designing Future Wheat
The PhenomUK community is characterised by excellent multidisciplinary relationships between plant scientists, computer scientists, data scientists, engineers and imaging technologists. The increasingly complex technical capabilities and development of advanced image processing is moving this field forward at a rapid rate. The major challenge will come in ensuring that there is access to these technologies across a wider set of academics, members of industry and even farmers. Hopefully PhenomUK will facilitate this process
Some work needs to be done with the gender diversity
within this community as this meeting didn’t include any female contributors.
This will hopefully change over the life of the project.
After a 10 year hiatus, the Genetics Society Arabidopsis Meeting is back with a two-day meeting on the 21st and 22nd of April, 2020 at the department of Biosciences at Durham University
On April 20th we have have added a FREE GARNet-supported hands-on workshop on rice transformation.
The lab-based workshop, led by rice transformation expert Dr Cunjin Zhang, will provide hands-on experience of aseptic technique, plant tissue culture, tissue sampling, explant preparation, and the generation of somatic embryogenic callus. Attendees will have the opportunity to practice (1) seed sterilisation (2) callus subculturing and (3) see a demonstration of culture inoculation and proper handling of Agrobacterium .
Programme Monday April 20th: 1.00 – 1.15 pm : Welcome from Prof Ari Sadanandom 1.15 – 2.00 pm : Introduction to transformation by Dr Cunjin Zhang 2.00 – 2.30 pm : Tour of facilities 2.30 – 3.00 pm : Coffee break 3.00 – 4.30 pm : Practical session 4.30 – 5.30 pm : Pizza 5.30 – 6.00 pm : Q&A
The main GenSoc meeting runs from on April 21st-22nd and includes the following Scientific sessions include: – Development – Abiotic Interactions – Teaching Plant Biology – Natural Variation – Biotic Interactions – Computational Biology
Invited Speakers include: Christian Hardtke (University of Lausanne) Veronica Grieneisen (Cardiff University) Steven Spoel (University of Edinburgh) Vardis Ntoukakis (University of Warwick) Mary Williams (ASPB & University of Glasgow) Henrik Jönsson (SLCU, Cambridge) Celia Knight (University of Leeds) Ian Henderson (University of Cambridge) Yoselin Benitez-Alfonso (University of Leeds) Uli Bechtold (University of Essex) Heather Knight (Durham University) Dan Gibbs (University of Birmingham) Sarah Robinson (SLCU, Cambridge).
Over the past thirty years the Multinational Arabidopsis Steering Committee (MASC) has represented the global Arabidopsis community through its collaborative oversight of the annual International Conference on Arabidopsis Research (ICAR), production of a MASC annual report and preparation of the series of decadal Roadmaps that have helped coordinate the future activities of the community. In[…]
https://meetings.embo.org/event/20-plant-systems This EMBO Workshop on international Plant Systems Biology (iPSB) is the central gathering of plant systems biology researchers from across the world. Climate change poses unique challenges for how to feed and power humanity without further degrading the environment. Plant science therefore is a key discipline in meeting the challenge of adapting food and[…]
The spring season of #UKPlantSciPresents begins on January 12th and we have a strong schedule set until the end of April! Each webinar is at Tuesday afternoon at 3pm GMT (or BST)! Registration is free and webinars will be made freely available soon after the event. Although closed captioning/subtitles are not available for live webinars,[…]
The previously awesome #GARNetPresents webinar series is morphing into the #UKPlantSciPresents webinar series. This series has the aim of promoting plant science excellence across the UK! UK plant science research uses many different experimental organisms such as Arabidopsis, Wheat, Brassicas, Brachypodium, Marchantia, Physomitrella and many others. This webinar series is supported by both GARNet and[…]
Contents: – Society Updates– Introducing Quantitative Plant Biology– Congratulations to Ottoline Leyser– Conference Updates– Bacterial Plant Diseases Programme– Introducing CHAP– Twenty Years of GARNet– GARNet Research Roundup– MASC Publication Update– Plant RNA Interactome Capture– Update on new BBSRC Projects– Spotlight on University of Nottingham Download here: https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish33_Online_Final_0.pdf
Marcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and[…]
This edition of GARNet Research Roundup begins with a remarkable four papers that include work from Caroline Dean’s lab at the John Innes Centre. The first two papers are collaborations with members of Martin Howard’s lab and look at the molecular mechanisms that control long-term cold sensing or the antisense regulation of FLC respectively. The[…]
Christos Velanis works at the University of Edinburgh and discusses work published in PloS Genetics entitled ‘The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)‘. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/07/Velanis_edit-13072020-09.32.mp3Pumi Perera is co-first author on this work from the Goodrich lab that[…]
This has been a challenging time for both conference organisers and conference venues. Most 2020 plant science conferences have cancelled, postponed or majorly changed their events. Below is a non-exhaustive list of the changes that have been made to different conferences. Up to date as July 6th 2020. (download)
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