Paige Panter talks to GARNet

Categories: Uncategorized
Tags: No Tags
Comments: No Comments
Published on: October 16, 2019

Dr Paige Panter talks to GARNet about her PhD research conducted at the University of Durham. This paper is published in New Phytologist and is titled ‘MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana‘. Paige is currently working with Antony Dodd in Bristol and some moving to the John Innes Centre! Good work with the move and the new project!

Janneke Balk talks to GARNet

Categories: Uncategorized
Tags: No Tags
Comments: No Comments
Published on: October 9, 2019

Janneke Balk from the John Innes Centre discusses a recent paper from PNAS titled ‘Arabidopsis BRUTUS-LIKE E3 ligases negatively regulate iron uptake by targeting transcription factor FIT for recycling‘. Thanks for discussion and good luck on gaining the follow-on funding for this exciting work! 9/10/19

GARNet Workshop on ‘Advances in Plant Imaging’

Categories: Uncategorized
Tags: No Tags
Comments: No Comments
Published on: October 8, 2019

By Geraint Parry

https://garnetimaging19.weebly.com/

Download the Workshop Abstract Book.

            Over 60 delegates travelled to the University of Warwick for the GARNet workshop on ‘Advances in Plant Imaging’, which received kind support from the Society of Experimantal Biology. This meeting was led by Professor Murray Grant, who is currently a member of the GARNet Advisory Committee.

            The primary aim of this workshop was to introduce early career researchers to the techniques used by researchers who are at the cutting edge of different imaging systems. Throughout the workshop we aimed to engender an atmosphere of discussion and collaboration so to that end we included an early session of short talks so delegates could introduce their work prior to discussions over dinner and drinks. The official Poster session was scheduled after all of the talks had concluded so as to give all the speakers the opportunity to later discuss their work. This timing also allowed attendees to visit posters without the authors in attendance so that they could formulate their own questions to be asked later! Finally we encouraged attendees to use ‘post-its’ to note the techniques and/or initiatives that they would find most useful to aid their future research. These replies were collated and considered at a final wrap-up discussion session.

            These responses could be separated into two main categories; 1, Software and 2, Community; highlighting the need for training in new imaging and imaging analysis techniques and the integration of plant scientists with different communities, such as hardware developers or the experts in computer vision. This feedback was shared with the UKRI-BBSRC representative who attended the meeting and was incorporated into a recent GARNet grant proposal.


            The workshop began with a session on ‘High Resolution Microscopy for Plant Cell Biologythat included talks from Joe McKenna and Martin Goldberg from Oxford Brookes and Durham respectively. They talked about the opportunities available through use of Super Resolution Microscopy and Scanning Electron Microscopy. There was some excitment in the room as Martin supplied ‘old-style’ 3D glasses to view some of his excellent images of the nuclear envelope.

3D images from Martin Golderg, please put on your glasses!

            The bulk of the second day of the workshop was split into two sessions titled Imaging across scales and Imaging with Novel Genetically encoded Reporters. The eight speakers in these sessions had an even gender split and featured two PhD students, two postdocs and four PIs. In particular the PhD students, Anis Meschichi and Emily Morris gave fantastic talks that included some great images. Anis talked about the work from Stefanie Rosa’s lab on single molecule RNA FISH whilst Emily presented amazing whole-root images taken at the Hounsfield microCT facility at the University of Nottingham. Each speaker in these sessions should be credited for excellently presenting their own research as well as providing insights into the opportunities that exist to use different tools and technologies, such as live imaging with light sheet microscopy (Giovanni Sena) or use of novel calcium (Myriam Charpentier) or redox (Phil Mullineaux) responsive reporters.

Emily Morris presenting her research

            A post-workshop survey confirmed that attendees very much enjoyed the talks and the opportunities provided for discussion….. although the catering and arrangements at Warwick weren’t universally enjoyed! Something to learn for next time!

            Throughout the meeting GARNet got the clear message that there is a community-need for a workshop on general Image Analysis and we will look at organising something in this area early in 2020. Watch this space!

Mike Bevan talks to GARNet

Categories: Uncategorized
Tags: No Tags
Comments: No Comments
Published on: October 2, 2019

Mike Bevan from the John Innes Centre talks to GARNet about a paper published in The Plant Cell titled ‘Variation in expression of the HECT E3 ligase UPL3 modulates LEC2 levels, seed size and crop yield in Brassica napus‘. Thanks very much to Mike for the discussion. 2/10/19

Report from 2019 FASEB meeting on Plant Development

Tags: No Tags
Comments: No Comments
Published on: September 30, 2019

By Vicky Spencer, University of Bristol

This past summer I was very fortunate to receive a travel grant from GARNet to attend the highly anticipated FASEB Mechanisms in Plant Development conference. Many prominent scientists regularly join this biennial event; this time held in the quiet town of Olean (New York) at Bonaventure University. Over 150 PIs, post docs and students attended from across the world, making it an exciting and diverse event. It was clear that the regular attendees have a lot of affection for this meeting, and there was a strong sense of support and community that was very welcoming.

I am a newly appointed postdoc at the University of Bristol, researching the genetic mechanisms of shoot branching evolution in vascular plants. This conference gave me a great opportunity to discuss the data that I have already collected and to elaborate my future project plans. I was lucky to present a poster in one of the three evening poster and drink sessions. After three hours of presenting, I had a lot of useful advice and inspiration for future experiments, including technical help for protoplast extraction and transformation.

Many tasks were added to my to-do list when I got back to Bristol!! 


The conference had an exciting and busy schedule of talks from many renowned scientists. This was a great opportunity to learn about the recent advances in the plant development field, and its future directions. Many talks focused on the role of the CLV signalling pathway; including kernel row patterning by Paula McSteen, maize meristem organisation and ROS signalling by Andrea Gallavotti, and filament identity in Physcomitrella patens from our lab member, Zoe Nemec Venza. I thoroughly enjoyed that there was a strong focus on evolution, with many examples of research in Marchantia polymorpha . In particular, I enjoyed talks about the role of CLE peptides in meristem specification by Yuki Hirakawa and ZHOUPI function in cuticle and pegged rhizoid formation by Yen-Ting Lu (also a recipient of a GARNet travel grant: Ed). 

Due to the alarming problems of plastic pollution and energy consumption, it is more critical than ever that biologists take responsibility for their environmental impact in the lab. Such issues were discussed in the Sustainability forum, which was a great way to raise awareness and share eco-friendly ideas between scientists. I think that this kind of event should become commonplace in scientific meetings, to encourage a sustained effort to reduce the environmental damage from our work. A single cell RNA-Seq workshop was also held, which was very timely and useful for the community as many attendees presented novel data from this new and exciting technique.


All meals and coffee breaks were held within the University campus, which was a great way to promote interactions between scientists at different stages of their careers. As well as thought-provoking scientific discussion, it was very useful for me to discuss career development with both new and established PIs and postdocs. I also talked to PhD students about my experiences and hope I have encouraged others to stay in research after graduating and be excited about life after the PhD thesis! 

Between the full schedule of talks and workshops, we went to ‘enjoy’ the local NY wine in the nearby winery, after a fun trip on an iconic yellow school bus.  We also visited a local lake for paddle boarding, which (once stood on the board) was very relaxing after a busy morning. These events were great fun and a lovely way to catch up with old friends and meet new ones. Everybody was so welcoming and friendly, and it was clear that both the people and the quality of science are why researchers come back to this meeting throughout their careers. 

As well as the generous travel funding from GARNet, thanks are due to Dr Jill Harrison and Dr Kenneth Birnbaum for organising such a great conference. I hope I have the opportunity to attend again in the future! 

Fiona Belbin talks to GARNet

Categories: Uncategorized
Tags: No Tags
Comments: 1 Comment
Published on: September 25, 2019

Fiona Belbin from the University of Bristol talks to GARNet about a paper published in Nature Communcations titled ‘Plant circadian rhythms regulate the effectiveness of a glyphosate-based herbicide‘. Good luck to Fiona defending her PhD thesis sometime soon…. 25/9/19

GARNet Research Roundup: September 24th 2019

Due to a significant delay this GARNet Research Roundup is a bumper overview of recent(ish) publications across discovery-led plant science, which have at least one contributor from a UK institution.

These can be (very) loosely separated into the following categories:

Circadian Clock: Greenwood et al, PloS Biology. Belbin et al, Nature Communications.

Environmental responses: Rodríguez-Celma et al, PNAS. Walker and Bennett, Nature Plants. Conn et al, PLoS Comput Biology. de Jong et al,PLoS Genetics. Molina-Contreras et al,The Plant Cell.

Defence signaling: Van de Weyer et al, Cell.Hurst et al, Scientific Reports. Xiao et al, Nature. Wong et al, PNAS.

Cell Biology: Miller et al, The Plant Cell. Coudert et al, Current Biology. Burgess et al,The Plant Cell. Harrington et al, BMC Plant Biology.

Metabolism: Jia et al, J Biol Chem. Perdomo et al, Biochem J. Gurrieri et al, Frontiers in Plant Science. Mucha et al, The Plant Cell. Atkinson et al, JXBot.

Cell Wall Composition: Wightman et al, Micron. Milhinhos et al, PNAS.

Signaling: Hartman et al, Nature Communications. Dittrich et al, Nature Plants. Villaécija-Aguilar et al, PLoS Genetics


Greenwood M, Domijan M, Gould PD, Hall AJW, Locke JCW (2019) Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana. PLoS Biol. 17(8):e3000407. doi: 10.1371/journal.pbio.300040 Open Access

Lead author is Mark Greenwood. UK contribution from The Sainsbury lab University of Cambridge, University of Liverpool and Earlham Institute. Using a mixture of experimental and modeling this paper shows that individual organs have circadian clocks that runs at different speeds.


Belbin FE, Hall GJ, Jackson AB, Schanschieff FE, Archibald G, Formstone C, Dodd AN (2019) Plant circadian rhythms regulate the effectiveness of a glyphosate-based herbicide. Nat Commun. 2019 Aug 16;10(1):3704. doi: 10.1038/s41467-019-11709-5 Open Access

Lead author is Fiona Belbin. UK contribution from University of Bristol and Syngenta Jealott’s Hill. Activity of the circadian clock determines that the plant response to the herbicide glyphosate is lessened at dusk, promoting the idea of agricultural chronotherapy. Fiona discusses this paper on the GARNet Community Podcast.


Rodríguez-Celma J, Connorton JM, Kruse I, Green RT, Franceschetti M, Chen YT, Cui Y, Ling HQ, Yeh KC, Balk J (2019) Arabidopsis BRUTUS-LIKE E3 ligases negatively regulate iron uptake by targeting transcription factor FIT for recycling. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907971116 Open Access

Lead author is Jorge Rodríguez-Celma. UK contribution from John Innes Centre, University of East Anglia.The Arabidopsis E3 ubiquitin ligases, BRUTUS-LIKE1 (BTSL1) and BTSL2 target the FIT transcription factor for degradation, altering the plant response to harmful level of iron.


Walker CH, Bennett T (2019) A distributive ‘50% rule’ determines floral initiation rates in the Brassicaceae. Nat Plants. doi: 10.1038/s41477-019-0503-z
Lead author Catriona Walker. UK contribution from the University of Leeds. The authors introduce the 50%-rule that defines the relationshop between the total number of flowers the number of secondary inflorescences


Conn A, Chandrasekhar A, Rongen MV, Leyser O, Chory J, Navlakha S (2019) Network trade-offs and homeostasis in Arabidopsis shoot architectures. PLoS Comput Biol. doi: 10.1371/journal.pcbi.100732 Open Access

Lead author is Adam Conn. UK contribution from Sainsbury Laboratory, University of Cambridge. This study performed 3D scanning of 152 Arabidopsis shoot architectures to investigate how plants make trade-offs between competing objectives.


de Jong M, Tavares H, Pasam RK, Butler R, Ward S, George G, Melnyk CW, Challis R, Kover PX, Leyser O (2019) Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness. PLoS Genet. doi: 10.1371/journal.pgen.1008366 Open Access

Lead author is Maaike de Jong. UK contribution from the Sainsbury Laboratory, University of Cambridge, the University of York and the University of Bath. This study looks at phenotypic plasticity of shoot branching in Arabidopsis diversity panels grown until different nitrate concentrations.


Molina-Contreras MJ, Paulišić S, Then C, Moreno-Romero J, Pastor-Andreu P, Morelli L, Roig-Villanova I, Jenkins H, Hallab A, Gan X, Gómez-Cadenas A, Tsiantis M, Rodriguez-Concepcion M, Martinez-Garcia JF (2019) Photoreceptor Activity Contributes to Contrasting Responses to Shade in Cardamine and Arabidopsis Seedlings. Plant Cell. doi: 10.1105/tpc.19.00275 Open Access

Lead author is Maria Jose Molina-Contreras. UK contribution from the University of Oxford. The authors looks at the response to different light conditions and how they contribute to phenotypic determination in Cardamine and Arabidopsis seedlings.


Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F (2019) A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell. doi: 10.1016/j.cell.2019.07.038 Open Access

Lead author is Anna-Lena Van de Weyer. UK contribution from The Sainsbury Laboratory, Norwich. Using sequence enrichment and long-read sequencing the authors present the pan-NLRome constructed from 40 Arabidopsis accessions.


Hurst CH, Wright KM, Turnbull D, Leslie K, Jones S, Hemsley PA (2019) Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function. Sci Rep. doi: 10.1038/s41598-019-49302-x Open Access

Lead author is Charlotte Hurst. UK contribution from the James Hutton Institute and the University of Dundee. They look at the functional role of post-translational modification S-acylation with a focus on the plant pathogen perceiving receptor-like kinase FLS2.


Xiao Y, Stegmann M, Han Z, DeFalco TA, Parys K, Xu L, Belkhadir Y, Zipfel C, Chai J (2019) Mechanisms of RALF peptide perception by a heterotypic receptor complex. Nature. doi: 10.1038/s41586-019-1409-7
Lead author is Yu Xiao. UK contribution from The Sainsbury Laboratory, Norwich. This study investigates how RAPID ALKALINIZATION FACTOR (RALF) peptides induce receptor complex formation to regulate immune signaling.


Wong JEMM, Nadzieja M, Madsen LH, Bücherl CA, Dam S, Sandal NN, Couto D, Derbyshire P, Uldum-Berentsen M, Schroeder S, Schwämmle V, Nogueira FCS, Asmussen MH, Thirup S, Radutoiu S, Blaise M, Andersen KR, Menke FLH, Zipfel C, Stougaard J (2019). A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1815425116
Open Access

Lead author is Jaslyn Wong. UK contribution from The Sainsbury Laboratory, University of East Anglia. This work was conducted in the legume Lotus and after a proteomic screen, the authors identified NFR5-interacting cytoplasmic kinase 4 that is involved in control of Nod factor perception.


Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW (2019) Variation in expression of the HECT E3 ligase UPL3 modulates LEC2 levels, seed size and crop yield in Brassica napus. Plant Cell. doi: 10.1105/tpc.18.00577
Open Access

Lead author in Charlotte Miller. UK contribution from the John Innes Centre. Activity of the Brassica napus HECT E3 ligase gene BnaUPL3 controls seed weight per pod through degradation of LEC2, a master transcriptional regulator of seed maturation and reveals a potential target for crop improvement


Coudert Y, Novák O, Harrison CJ (2019) A KNOX-Cytokinin Regulatory Module Predates the Origin of Indeterminate Vascular Plants. Curr Biol. 2019 Aug 19;29(16):2743-2750.e5. doi: 10.1016/j.cub.2019.06.083

Lead author is Yoan Coudert. UK contribution from the University of Cambridge and University of Bristol. Class I KNOX gene activity is shown to be necessary for axis extension from an intercalary region of determinate moss shoots, in part through promotion of cytokinin biosynthesis.


Burgess SJ, Reyna-Llorens I, Stevenson SR, Singh P, Jaeger K, Hibberd JM (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses Plant Cell.  doi: 10.1105/tpc.19.00078 Open Access

Lead author is Steven Burgess. UK contribution from University of Cambridge, The Sainsbury lab University of Cambridge, University of Leeds The authors use DNaseI-SEQ to assess the similarities and differences in transcription factor binding sites in the leaves across a set of four C3 and C4 grasses.


Harrington SA, Overend LE, Cobo N, Borrill P, Uauy C (2019) Conserved residues in the wheat (Triticum aestivum) NAM-A1 NAC domain are required for protein binding and when mutated lead to delayed peduncle and flag leaf senescence. BMC Plant Biol. doi: 10.1186/s12870-019-2022-
Lead author is Sophie Harrington. UK contributions from the John Innes Centre and University of Birmingham. The authors used a wheat TILLING resource to investigate mutrant allele with the NAC domain of the NAM-A1 transcription factor and their contribution to phenotypes in lab and field.


Jia Y, Burbidge CA, Sweetman C, Schutz E, Soole K, Jenkins C, Hancock RD, Bruning JB, Ford CM (2019) An aldo-keto reductase with 2-keto- L-gulonate reductase activity functions in L-tartaric acid biosynthesis from vitamin C in Vitis vinifera. J Biol Chem. doi: 10.1074/jbc.RA119.010196 Open Access

Lead author Yong Jia. UK contribution from the James Hutton Institute. This work conducted in grape reveals the mechanism by which an aldo-keto reductase functions in tartaric acid biosynthesis.


Perdomo JA, Degen GE, Worrall D, Carmo-Silva E (2019) Rubisco activation by wheat Rubisco activase isoform 2β is insensitive to inhibition by ADP. Biochem J. doi: 10.1042/BCJ2019011 Open Access

Lead author is Juan Alejandro Perdomo. UK contribution from Lancaster University. They show through analysis of site-directed mutations across three isoforms of wheat Rubisco activase that these isoforms have different sensitivities to ADP.


Gurrieri L, Distefano L, Pirone C, Horrer D, Seung D, Zaffagnini M, Rouhier N, Trost P, Santelia D, Sparla F (2019) The Thioredoxin-Regulated α-Amylase 3 of Arabidopsis thaliana Is a Target of S-Glutathionylation. Front Plant Sci. doi: 10.3389/fpls.2019.00993 Open Access

Lead author is Libero Gurrieri. UK contribution from John Innes Centre. The chloroplastic α-Amylases, AtAMY3 is post-translationally modified by S-glutathionylation in response to oxidative stress.


Mucha S, Heinzlmeir S, Kriechbaumer V, Strickland B, Kirchhelle C, Choudhary M, Kowalski N, Eichmann R, Hueckelhoven R, Grill E, Kuster B, Glawischnig E (2019) The formation of a camalexin-biosynthetic metabolon. Plant Cell. doi: 10.1105/tpc.19.00403 Open Access

Lead author is Stefanie Mucha. UK contribution from Oxford Brookes University and University of Warwick. The authors performed two independent untargeted co-immunoprecipitations to identify components involved in biosynthesis of the antifungal phytoalexin camalexin.


Atkinson N, Velanis CN, Wunder T, Clarke DJ, Mueller-Cajar O, McCormick AJ (2019) The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis-Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit. J Exp Bot. doi: 10.1093/jxb/erz275
Open Access

Lead author is Nicky Atkinson. UK contribution from the University of Edinburgh. This study uses Arabidopsis-Chlamydomonas to investigate the protein-protein interaction between Rubisco and essential pyrenoid component 1 (EPYC1).


Wightman R, Busse-Wicher M, Dupree P (2019) Correlative FLIM-confocal-Raman mapping applied to plant lignin composition and autofluorescence. Micron. doi: 10.1016/j.micron.2019.102733
Lead author Raymond Wightman. UK contribution from the Sainsbury Laboratory, University of Cambridge and the University of Cambridge. This study uses applies a novelmethod of correlative FLIM-confocal-Raman imaging to analyse lignin composition in Arabidopsis stems.


Milhinhos A, Vera-Sirera F, Blanco-Touriñán N, Mari-Carmona C, Carrió-Seguí À, Forment J, Champion C, Thamm A, Urbez C, Prescott H, Agustí J (2019) SOBIR1/EVR prevents precocious initiation of fiber differentiation during wood development through a mechanism involving BP and ERECTA. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1807863116
Lead author is Ana Milhinho. UK contribution from the University of Oxford. The authors used GWAS in Arabidopsis to identify the SOBIR1/EVR as an important regulator of the control of secondary growth in xylem fibers.


Hartman S, Liu Z, van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, van Dongen N, Bosman F, Bassel GW, Visser EJW, Bailey-Serres J, Theodoulou FL, Hebelstrup KH, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ (2019) Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress. Nat Commun. doi: 10.1038/s41467-019-12045-4 Open Access

Lead author is Sjon Hartman. UK contribution from the University of Nottingham, Rothamsted Research and the University of Birmingham. This multinational collaboration looks into the relationship of how ethylene mediated nitric-oxide signaling responds to environmental signals.


Dittrich M, Mueller HM, Bauer H, Peirats-Llobet M, Rodriguez PL, Geilfus CM, Carpentier SC, Al Rasheid KAS, Kollist H, Merilo E, Herrmann J, Müller T, Ache P, Hetherington AM, Hedrich R (2019) The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. Nat Plants. doi: 10.1038/s41477-019-0490-0
Lead author Marcus Dittrich. UK contribution from the University of Bristol. This work looks at the role of ABA signaling in stomatal responses and that the multiple ABA receptors can be modulated differentially in a stimulus-specific manner.


Villaécija-Aguilar JA, Hamon-Josse M, Carbonnel S, Kretschmar A, Schmid C, Dawid C, Bennett T, Gutjahr C (2019). SMAX1/SMXL2 regulate root and root hair development downstream of KAI2-mediated signalling in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1008327 Open Access

Lead author Jose Antonio Villaécija-Aguilar. UK contribution from the University of Leeds and The Sainsbury lab, University of Cambridge. This demonstrates that KAI2 signalling through SMAX1/SMXL2 , is an important new regulator of root hair and root development in Arabidopsis.

Dana MacGregor talks to GARNet

Categories: Uncategorized
Tags: No Tags
Comments: No Comments
Published on: September 18, 2019

Dana MacGregor from Rothamsted Research talks to GARNet about a paper published in The Plant Journal titled ‘ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development‘. We also discussed the challenges of publishing research that was conducted a long time ago in a previous lab! 18/9/19

«page 1 of 59

Follow Me
TwitterRSS
GARNetweets
October 2019
M T W T F S S
« Sep    
 123456
78910111213
14151617181920
21222324252627
28293031  

Welcome , today is Wednesday, October 16, 2019