Naresh Loudya discusses nucleus-chloroplast signaling

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Published on: May 20, 2020

Naresh Loudya from Royal Holloway University of London discusses a recent paper published in the Philosophical Transactions of the Royal Society B entitled ‘Retrograde signalling in a virescent mutant triggers an anterograde delay of chloroplast biogenesis that requires GUN1 and is essential for survival‘. Apologies for the high background noise early in the recording.

GARNet Research Roundup: May 7th 2020

This edition of GARNet Research Roundup begins with two studies from the John Innes Centre. The first takes a detailed look at meiosis in Arabidopsis arenosa and the second introduces a novel mode of auxin perception.

The third paper from the Grierson lab in Bristol uses innovative methods to assess root-soil cohesion through study of root hairs. The fourth paper is also from Bristol and looks at the evolution of stomata.

The fifth and sixth papers are from Scotland. Firstly researchers at Edinburgh have developed a deep learning approach for plant phenotyping whilst in the second research from Glasgow looks at the role of UVR8 in the UV response of UV-B adapted plants.

The seventh paper is from The Sainsbury lab, Norwich and reveals a new role for phosphorylation in the formation of the RRS1-R/RPS4 immune receptor complex.

The final paper includes co-authors from Cambridge and looks at the role of epigenetic changes in the reponse to an experimentally evolved plant virus.


Morgan C, Zhang H, Henry CE, Franklin FCH, Bomblies K (2020) Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1919459117 Open Access

Chris Morgan works at the John Innes Centre and leads this research that looks at meiosis in Arabidopsis arenosa. They use super resolution microscopy to look in great detail at the intertaction of the ASY1 and ASY3 loci. Chris discussed this work on the GARNet community podcast.


Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L (2020) Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. Elife doi: 10.7554/eLife.51787 Open Access

Andre Kuhn works with Lars Ostergaard at the John Innes Centre and leads this research that has identified a novel mode of auxin perception in which the ETTIN transcription factor directly interacts with auxin. This allows a rapid response that does not rely on the canonical mode of auxin perception via protein degradation. Andre discussed this work on the GARNet community podcast.


De Baets S, Denbigh TDG, Smyth KM, Eldridge BM, Weldon L, Higgins B, Matyjaszkiewicz A, Meersmans J, Larson ER, Chenchiah IV, Liverpool TB, Quine TA, Grierson CS (2020) Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion. Commun Biol. doi: 10.1038/s42003-020-0886-4 Open Access

This work from the University of Bristol is led by Sarah De Baets S, Tom Denbigh, Kevin Smyth, Beth Eldridge. They have developed a series o fthree innovative assays to investigate the role of root hairs in the cohesion of the roots-soil interaction. This research shows that root hairs play a significant role in this process. Tom and Beth discussed this work on the GARNet community podcast.


Harris BJ, Harrison CJ, Hetherington AM, Williams TA (2020) Phylogenomic Evidence for the Monophyly of Bryophytes and the Reductive Evolution of Stomata. Curr Biol. doi: 10.1016/j.cub.2020.03.048 Open Access

This paper from the University of Bristol is led by Brogan Harris and investigates the evolutionary origins of genes that specify stomatal development and function in bryophytes. They show that important stomatal lineage genes are present in bryophytes, indicating that their stomata have undergone reductive evolution.


Dobrescu A, Giuffrida MV, Tsaftaris SA (2020) Doing More With Less: A Multitask Deep Learning Approach in Plant Phenotyping. Front Plant Sci. 2020 Feb 28;11:141. doi: 10.3389/fpls.2020.00141 Open Access

Andrei Dobrescu leads this methods paper from the University of Edinburgh that uses multitask deep learning to develop software for plant phenotying. They test their method on the analysis of Arabidopsis rosettes.

https://www.frontiersin.org/articles/10.3389/fpls.2020.00141/full

Liao X, Liu W, Yang HQ, Jenkins GI (2020) A dynamic model of UVR8 photoreceptor signaling in UV-B-acclimated Arabidopsis. New Phytol. doi: 10.1111/nph.16581 Open Access

Xinyang Liao leads this work from the University of Glasgow that continues the Jenkins’ lab research on the UVR8 photoreceptor. In this paper they analysed the role of UVR8 in UV-B-acclimated plants in which the switch between between monomeric and dimeric states can response to high UV-B without the need for new translation. This response is also alters the interaction of UVR8 with the COP1 and RUP2 proteins.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16581

Guo H, Ahn HK, Sklenar J, Huang J, Ma Y, Ding P, Menke FLH, Jones JDG (2020) Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms. Cell Host Microbe. doi: 10.1016/j.chom.2020.03.008

Hailong Guo and Hee-Kyung Ahn work with Jonathan Jones at the Sainsbury lab, Norwich and lead this work that investigates the role of phosphorylation in the formation of the RRS1-R/RPS4 Immune Receptor Complex. This response is different to the effector-triggered conformational changes of RRS1 and represents a distinct novel route for immune signalling.

https://www.sciencedirect.com/science/article/abs/pii/S1931312820301724?via%3Dihub

Corrêa RL, Sanz-Carbonell A, Kogej Z, Müller SY, Ambrós S, López-Gomollón S, Gómez G, Baulcombe DC, Elena SF (2020) Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprogramming of Defense Responses in Plants. Mol Biol Evol. doi: 10.1093/molbev/msaa091

This Spanish led study includes Regis Corrêa as lead author and includes David Baulcombe from Cambridge as a co-author. They infected Arabidopsis with an ancestral and experimentally-evolved isolates of turnip mosaic potyvirus (TuMV). The evolved version was more virulent and triggered a greater transcriptomic response in the plant as well inducing other epigenetic changes.

Andre Kuhn discusses a new auxin receptor with GARNet

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Published on: May 6, 2020

Andre Kuhn works with Lars Ostergaard at the John Innes Centre and discusses a recent Elife paper entitled ‘Direct ETTIN-auxin interaction controls chromatin states in gynoecium development‘. We discuss a new paradigm for auxin perception in the control gene expression.

GARNet talks root hairs with Beth Eldridge and Tom Denbigh

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Published on: April 29, 2020

Bethany Eldridge and Tom Denbigh are co-first authors on a recent paper in Communications Biology entitled ‘Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion‘. We discuss the innovative experimental procedures that they designed to measure the interaction of root hairs with their environment!

GARNet-Presents Webinar Series

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Published on: April 27, 2020

GARNet conducted a short survey to assess community-interest in an UK-focused webinar series that will highlights the excellence in UK plant science. Approximately 100 respondants were supportive of the idea so we are kicking off the GARNet-Presents Webinar series on May 5th 2020.


This series owes a huge debt of thanks to the widely popular Plantae Presents series that has shown that there is a community-need for events of this type.

We will run this series through the GoToWebinar software, which allows simple presentation with the ability for virtual attendees to ask questions in a chat box. These questions will be moderated by the webinar chairperson and some will be asked to the speakers. Each week two speakers will present their research over 30minute sessions.

Please visit the GARNet-Presents home page. Webinars will be freely available on the home page soon after the event. Although closed captioning/subtitles are not available for live webinars after the event a transcription will be available with the recording.


The inaugural event on Tuesday May 5th 2020 at 3pm BST features Professor Jonathan Jones from the Sainsbury Lab, Norwich and Dr Yoselin Benitez-Alfonso from the University of Leeds.

Sign up here ->

https://attendee.gotowebinar.com/register/7873299707710492176


The second event on Tuesday May 19th 2020 at 3pm BST features Dr Daniel Gibbs from the University of Birmingham and Dr Emily Breeze from the University of Warwick

Sign up here ->

https://attendee.gotowebinar.com/register/5162167916512293134


We are looking for Webinar speakers later in the GARNet-Presents series. These will take place on Tuesday 3pm BST every two weeks until July 14th 2020 and then start up again on September 1st 2020.

These are 20minute talks with 5-10 minutes for questions. We run GARNet-Presents through GoToWebinar and will require a decent Wifi connection and a webcam. You’d share your screen for everyone to view as you talk. If you’d be willing to then I’d also like to share the slides you will present with all attendees. Of course this would be minus anything unpublished that you don’t want to share.

If you are interested in presented then please email Geraint Parry with a statement of interest and a talk title. We are hoping to recruit plant scientists of any career stage or research interest.

Chris Morgan talks to GARNet

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Published on: April 22, 2020

Chris Morgan who works at the John Innes Centre discusses a recent PNAS paper entitled ‘Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa‘. We discuss the technical challenges of this research as well as the difficulties working from home (or not) with a super-resolution microscope!

FutureLearn: Image Analysis Methods for Biologists

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Published on: April 9, 2020

The use of automatic image analysis in the biological sciences has increased significantly in recent years, especially with automated image capture and the rise of phenotyping.

This online course will help improve your understanding of image analysis methods, and improve your practical skills and ability to apply the techniques to your images.

You will explore the process of image acquisition, through to segmenting regions, counting objects and tracking movement. Importantly, we’ll also try to highlight what to watch out for when using different image analysis approaches.


This is led by a team at the University of Nottingham that includes Tony Pridmore, Andrew French, Amy Lowe and Mike Pound. This team has worked a great deal with plant scientists and are global leader in the automated and AI approaches to tackle the challenges of plant phenotyping.


This training course is FREE and begins on May 11th.

More information can be found on this URL:

https://www.futurelearn.com/courses/image-analysis

GARNet Research Roundup: April 9th 2020

This Easter edition of the GARNet Research Roundup begins with research from Aberystwyth University that has developed a system for studying self-incompatability in self-compatible Arabidopsis. Next is an outstanding community-focussed study led from the John Innes Centre that outlines the development of new resources that better enable discovery-led science to be conducted within hexaploid wheat.

Third is a study led by the Dodd group at the JIC that links the circadian clock to water-use efficiency. The fourth paper is from the Edwards group at Bristol investigates the effect of higher temperatures on meiotic recombination in wheat. The fifth paper is from Rothamsted Research and introduces novel molecular tools that will be useful in future studies of the economically important weed Blackgrass.

The next paper includes co-authors from the Sainsbury lab in Norwich and looks at the role of carbonic anhydrases in plant immunity at higher levels of CO2. The seventh paper looks at the integration of light signaling and the circadian clock and includes Paul Devlin from RHUL as a co-author. The penultimate paper includes Gareth Jenkins from Glasgow as a co-author and looks at the perception of different wavelengths of UV light by the photoreceptor UVR8. The final paper includes Marko Hyvönen from Cambridge as a co-author and investigates the organisation of the RALF gene family in strawberry.


Wang L, Triviño M, Lin Z, Carli J, Eaves DJ, Van Damme D, Nowack MK, Franklin-Tong VE, Bosch M (2020) New opportunities and insights into Papaver self-incompatibility by imaging engineered Arabidopsis pollen. J Exp Bot. doi: 10.1093/jxb/eraa092 Open Access

Ludi Wang is first author on this work led from Maurice Bosch’s lab at Aberystwyth University. They have transferred their work on self-incompatability (SI) in Papaver into Arabidopsis, so as to take advantage of its excellent genetic resources. They show that the SI response can be recapitulated in Arabidopsis, even though it is self-compatible. This research has allowed them to discover new roles for clathrin-mediated endocytosis, the actin cytoskeleton and calcium signaling during SI.

Ludi and Maurice discuss this work on the GARNet Community podcast.


Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BB, Uauy C (2020) A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. Elife. doi: 10.7554/eLife.55646 Open Access

This research is led from the Uauy lab at the John Innes Centre by Nikolai Adamski, Phillippa Borrill (now at Birmingham), Jemima Brinton, Sophie Harrington and Clemence Marchal. This team worked with collaborators based around the UK, in Australia, Canada and Mexico and they outline the resources that they have developed that will promote the use of wheat as an experimental organism for discovery-led research.


Simon NM, Graham CA, Comben NE, Hetherington AM, Dodd AN (2020) The circadian clock influences the long-term water use efficiency of Arabidopsis. Plant Physiol. doi: 10.1104/pp.20.00030 Open Access

This research is led by Noriane Simon who worked with Anthony Dodd at the University of Bristol and the John Innes Centre. They showed that misregulation of components that control the circadian oscillator causes alterations in water-use efficiency in Arabidopsis plants. This response is linked to the control of transpiration via circadian control of guard cell physiology.


Coulton A, Burridge AJ, Edwards KJ (2020) Examining the Effects of Temperature on Recombination in Wheat. Front Plant Sci. doi: 10.3389/fpls.2020.00230 Open Access

Alexander Coulton is lead author on this study from the University of Bristol that has looked at how temperature changes alter the landscape of meiotic recombination in wheat. Despite showing that high temperature induces movement of recombination events toward centromeres, the overall effect is limited due to the tight linkages of many wheat genes.


Mellado-Sánchez M, McDiarmid F, Cardoso V, Kanyuka K, MacGregor DR (2020) Virus-mediated transient expression techniques enable gene function studies in black-grass. Plant Physiol. doi: 10.1104/pp.20.00205 Open Access

This Letter to the editor of Plant Physiology is led by Macarena Mellado-Sánchez, who works with Dana MacGregor at Rothamsted Research. They demonstrate the first usage of Virus-mediated gene silencing (VIGS) and Virus-mediated protein overexpression (VOX) in Blackgrass, which is a significant crop weed. They use these techniques in genetic gain and loss of function studies that result in changes in herbicide resistance in transformed blackgrass. Hopefully this work can be a prelude to future research in this potentially important experimental system for understanding how weeds effect crop yields.

http://www.plantphysiol.org/content/early/2020/04/01/pp.20.00205.long

Zhou Y, Vroegop-Vos IA, Van Dijken AJH, Van der Does D, Zipfel C, Pieterse CMJ, Van Wees SCM (2020) Carbonic anhydrases CA1 and CA4 function in atmospheric CO(2)-modulated disease resistance. Planta. doi: 10.1007/s00425-020-03370-w

Yeling Zhou is first author on this Dutch-led research that includes Dieuwertje Van der Does and Cyril Zipfel from the Sainsbury lab in Norwich. They show that the Carbonic anhydrases CA1 and CA4 play a role in plant immunity under higher levels of atmospheric CO2. This indicates that these genes might be future targets for improving plant disease resistance.


Liu Y, Ma M, Li G, Yuan L, Xie Y, Wei H, Ma X, Li Q, Devlin PF, Xu X, Wang H (2020) Transcription Factors FHY3 and FAR1 Regulate Light-induced CIRCADIAN CLOCK ASSOCIATED1 Gene Expression in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00981

Paul Devlin from RHUL is a co-author on this Chinese-study led by Yang Liu. They show that FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its paralogue FAR-RED IMPAIRED RESPONSE1 (FAR1) are essential for light induction of CCA1, which contracts to the repressive effect of PHYTOCHROME INTERACTING FACTOR 5 (PIF5). They introduce an integrated photosensory signaling pathway that brings together light signalling with control of the circadian clock.


Rai N, O’Hara A, Farkas D, Safronov O, Ratanasopa K, Wang F, Lindfors AV, Jenkins GI, Lehto T, Salojärvi J, Brosché M, Strid Å, Aphalo PJ, Morales LO. (2020) The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes. Plant Cell Environ. doi: 10.1111/pce.13752 Open Access

Neha Rai is first author on this Finnish-led study that includes Gareth Jenkins from the University of Glasgow as a co-author. They investigated the response of the photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) to UV wavelengths included in sunlight. They show that the wavelength of 350 nm is an important cut-off for the perception of UV-B and UV-A by these different photoreceptors.

https://onlinelibrary.wiley.com/doi/full/10.1111/pce.13752

Negrini F, O’Grady K, Hyvönen M, Folta KM, Baraldi E (2020) Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry. PLoS One. doi: 10.1371/journal.pone.0226448 Open Access

Marko Hyvönen working at the University of Cambridge is a co-author on this Italian-US collaboration led by Francesca Negrini. This work describes the genomic organisation of the family of the Rapid Alkalinization Factors (RALFs) in octoploid strawberry. In addition they describe the upregulation of one family member, FanRALF3-1, during fungal infection. This will lead to future research aimed at defining the precise molecular relationship between FanRALF3-1 expression and the immune response in strawberry.

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