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  • geraintparry
  • GARNet Coordinator @ Cardiff University. Past lecturer in Plant Science and genetics. Researcher into plant nuclear transport and regulation of auxin signalling.
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BRIGIT looking out for Xylella

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Published on: January 14, 2020

Taken from the John Innes Centre

Dame Helen Mirren has helped renew efforts to keep plant disease Xylella fastidiosa out of the UK in 2020 – the UN’s International Year of Plant Health – narrating a new animation that warns of the devastation it causes, including the death of millions of olive trees in Europe.

This video has been put together by the BRIGIT project that is lead from the John Innes Centre

Advice to help prevent the introduction of Xylella includes:

  1. Source new plants carefully, where possible purchase plants grown in the UK
  2. Propagate your own plants from seeds or cuttings
  3. Check plants for signs of disease before purchase and monitor the health of new plants
  4. Never bring plants back with you from abroad

For more information check out the BRIGIT Webpage.

UK Early Career Rice Researchers Meeting

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Published on: January 13, 2020

On 27th/28th February we will be holding the inaugural UK Rice Consortium meeting for Early Career Researchers. This short meeting will be focussed on providing a forum for all postdocs and PhD students involved in rice research projects to come together and exchange ideas and experience on working with rice in the UK.

Download Meeting Schedule


The meeting will be very much led by the researchers themselves, providing them the opportunity to both network (find out about the range of rice research being performed across the country) but with a focus on the nuts-and-bolts of rice research in the lab and field.

The aim is to generate and share knowledge on fundamental yet essential topics for those working at the coal-face of rice research, such as: how to grow and maintain rice; obtaining rice lines and transgenics; genomic resources available and how to access them; the challenges (and opportunities) of working with overseas collaborators, plus other topics raised by the participants themselves. By coming together and sharing best practice and experience, we hope to instigate a network of early career researchers who can help each other to advance rice research in the UK, ensuring that we can contribute most effectively to the global research efforts on this vital crop.

The meeting will consist primarily of short talks by participants plus wide-ranging discussion and networking opportunities, setting the agenda for early career researchers and their contribution to the UK rice research consortium.


We realise the timescale is tight, so if you could actively promote this meeting to all postdocs and PhD students working on rice projects in your group/institute, that would be greatly appreciated. We are, of course, very happy to have more senior researchers attend and chip in with their ideas/suggestions (and the sessions will be moderated by academics at Sheffield), but the meeting is very much focussed on early career researchers and giving them a voice.

For registration, go to:

https://onlineshop.shef.ac.uk/conferences-and-events/faculty-of-science/animal-and-plant-sciences/uk-rice-research-network-february-2020

Registration costs are £150 (including overnight accommodation and evening meal), or £50 for day rate.

Contact for meeting enquiries: J.beasley@sheffield.ac.uk

GARNet Research Roundup: December 23rd 2019

The final GARNet Research Roundup of 2019 begins with three studies from the John Innes Centre. Firstly Steve Penfield’s group conducts a field-experiment that monitors FLC levels in winter oilseed rape. Second is a study from the Zilberman lab looking at the relationship between Histone H1 and DNA methylation.

Third is work from the Yant lab in JIC/Nottingham that investigates adaptive gene flow between Arabidopsis arenosa and Arabidopsis lyrata.

The next two papers are led from the Etchells lab in Durham, the first has developed a vascular-localised transcriptional network and the second is a methods paper for image analysis.

The sixth paper includes co-authors from Southampton and investigates nuclear-chloroplast signaling in Arabidopsis mediated by the GUN1 protein.

The next two papers include members of the current GARNet advisory committee. Yoselin Benitez-Alfonso from the University of Leeds is an author on a paper that models plasmodesma geometry whilst members of the Kaiserli lab in Glasgow are involved in a study that investigates the factors involved in auxin-dependent thermomorphogenesis.

The Dupree lab in Cambridge leads the next research paper that looks at the detailed composition of the cell wall in the softwood Spruce.

The next two papers are from the Sainsbury lab, Norwich. Firstly the Kamoun lab looks at the molecular code of a plant NLR immune receptors whilst in the second paper members of the Zipfel lab are co-authors on a study that looks at defence-related protease activity from a fungal pathogen of strawberry.

The twelfth paper is from Ian Graham’s lab at the University of York and looks at the role of light signaling during seed development.

Sue Armstrong from Birmingham is a co-author on the next paper in which researchers present a genetic map of the field cress Lepidium campestre.

The final two papers include researchers from Royal Holloway University of London and look at the role of different transcription factors during embryo or root meristem development.


O’Neill CM, Lu X, Calderwood A, Tudor EH, Robinson P, Wells R, Morris R, Penfield S (2019) Vernalization and Floral Transition in Autumn Drive Winter Annual Life History in Oilseed Rape. Curr Biol. doi: 10.1016/j.cub.2019.10.051
Open Access

Carmel O’Neill is first author on the research from the Morris and Penfield labs at the John Innes Centre. This paper describes experiments that monitored FLC levels in field-growth winter oilseed rape. Surprisingly they shows that decline of FLC during October in relatively mild-temperatures of 10-15C reduce FLC levels, leading to floral transition prior to the colder winter temperatures. This work shows the importance of field experiments to understand real-world mechanisms that control crop development.


Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D (2019) DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell. doi: 10.1016/j.molcel.2019.10.011
This research from the Zilberman lab at the John Innes Centre is led by Jaemyoung Choi and looks at the relationship between histone H1 and the DNA methylation machinery during the maintenance of transcriptional homeostasis.

https://www.sciencedirect.com/science/article/abs/pii/S1097276519307890?via%3Dihub

Marburger S, Monnahan P, Seear PJ, Martin SH, Koch J, Paajanen P, Bohutínská M, Higgins JD, Schmickl R, Yant L (2019) Interspecific introgression mediates adaptation to whole genome duplication. Nat Commun. doi: 10.1038/s41467-019-13159-5
Open Access

Sarah Marburger from Levi Yant’s lab at the John Innes Centre/University of Nottingham leads this research that includes co-authors from Leicester, Edinburgh and the Czech Republic. They look at the effect of whole-genome duplication on gene flow between Arabidopsis arenosa and Arabidopsis lyrata.


Smit M, McGregor S, Sun H, Gough C, Bågman AM, Soyars CL, Kroon JTM, Gaudinier A, Williams CJ, Yang X, Nimchuk ZL, Weijers D, Turner SR, Brady SM, Etchells P (2019) A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00562
Open Access

This large-scale systems-biology paper is a UK-US-China-Dutch collaboration led by Margot Smit at Wageningen, Shauni McGregor and Peter Etchells at Durham University. They have developed a detailed transcriptional network based on the vascular-localised PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase.

http://www.plantcell.org/content/early/2019/12/05/tpc.19.00562.long

Bagdassarian KS, Connor KA, Jermyn IH, Etchells JP (2019) Versatile method for quantifying and analyzing morphological differences in experimentally obtained images. Plant Signal Behav. doi: 10.1080/15592324.2019.1693092
This paper from Peter Etchells lab in Durham is led by Kristine Bagdassarian and introduces a bespoke method for inspecting the differences between the morphologies of several plant mutants at the cellular level.


Shimizu T, Kacprzak SM, Mochizuki N, Nagatani A, Watanabe S, Shimada T, Tanaka K, Hayashi Y, Arai M, Leister D, Okamoto H, Terry MJ, Masuda T (2019) The retrograde signaling protein GUN1 regulates tetrapyrrole biosynthesis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1911251116

Open Access

Sylwia M. Kacprzak and Matthew Terry from the University of Southampton are co-authors on this Japanese-led study that looks at the interaction between nuclear and chloroplast genomes as controlled by role that the GUN1 protein plays in control of tetrapyrrole metabolism.

https://www.sciencedirect.com/science/article/abs/pii/S1097276519307890?via%3Dihub

Deinum EE, Mulder BM, Benitez-Alfonso Y (2019) From plasmodesma geometry to effective symplasmic permeability through biophysical modelling. Elife. doi: 10.7554/eLife.49000
Open Access

Eva Deinum is lead author of this study that includes GARNet Committee member Yoselin Benitez-Alfonso as co-author. They have applied biophysical modeling to calculate effective symplasmic permeability for the transport of molecules through plasmodesmata. The resulting open-source model has been refined through experimental observations.

Dr Deinum will be leading a GARNet-supported workshop on this multilevel model during the July 2020 EMBO workshop on ‘Intercellular communication and plasmodesmata in plant development and disease’.


van der Woude LC, Perrella G, Snoek BL, van Hoogdalem M, Novák O, van Verk MC, van Kooten HN, Zorn LE, Tonckens R, Dongus JA, Praat M, Stouten EA, Proveniers MCG, Vellutini E, Patitaki E, Shapulatov U, Kohlen W, Balasubramanian S, Ljung K, van der Krol AR, Smeekens S, Kaiserli E, van Zanten M (2019) HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1911694116

This wide collaboration is led by Lennard van der Woude at Utrecht University and includes Giorgio Perrella and Eirini Kaiserli from Glasgow as co-authors. This research looks at the complex relationship between thermomorphogenesis, auxin and light signaling, histone deacylation and the regulation of histone variant H2A.Z.


Terrett OM, Lyczakowski JJ, Yu L, Iuga D, Franks WT, Brown SP, Dupree R, Dupree P (2019) Molecular architecture of softwood revealed by solid-state NMR. Nat Commun. doi: 10.1038/s41467-019-12979-9

Open Access

This research from the Dupree lab in Cambridge is led by Olivier Terrett and uses solid-state NMR to analyse the cell wall composition of the softwood spruce, in part through comparison with Arabidopsis cell walls. This information is an essential requirement to build experimental strategies for the biorefining of particular wood-types.


Adachi H, Contreras M, Harant A, Wu CH, Derevnina L, Sakai T, Duggan C, Moratto E, Bozkurt TO, Maqbool A, Win J, Kamoun S (2019) An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. Elife. doi: 10.7554/eLife.49956

Open Access

Hiroaki Adachi leads this study from lab of Sophien Kamoun at the Sainsbury lab, Norwich. In this research they interrogate the molecular code of a plant NLR immune receptor to identify the minimal functional motifs that are required to induce hypersensitive cell death in response to a plant pathogen.

https://elifesciences.org/articles/49956

Caro MDP, Holton N, Conti G, Venturuzzi AL, Martínez-Zamora MG, Zipfel C, Asurmendi S, Díaz-Ricci JC (2019) The fungal subtilase AsES elicits a PTI-like defence response in Arabidopsis thaliana plants independently of its enzymatic activity. Mol Plant Pathol. doi: 10.1111/mpp.12881
Open Access

Nicolas Holton and Cyril Zipfel from the Sainsbury Lab in Norwich are co-authors on this Argentinian-led study with María del Pilar Caro as both first and corresponding author. They characterize the proteolytic role of the elicitor subtilisin (AsES) from strawberry fungal pathogen Acremonium strictum during an immune response.


Barros-Galvão T, Dave A, Gilday AD, Harvey D, Vaistij FE, Graham IA (2019) ABA INSENSITIVE4 promotes rather than represses PHYA-dependent seed germination in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.16363
Open Access

Thiago Barros-Galvão and Ian Graham at the University of Leeds lead this research that investigates the role of phytochrome A (PHYA) and PHYB signaling during seed development in Arabidopsis.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16363

Desta ZA, Kolano B, Shamim Z, Armstrong SJ, Rewers M, Sliwinska E, Kushwaha SK, Parkin IAP, Ortiz R, de Koning DJ (2019) Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes. Sci Rep. doi: 10.1038/s41598-019-53320-0

Open Access

This Swedish led study has Zeratsion Abera Desta as lead author and includes Sue Armstrong from the University of Birmingham as a co-author. They have produced an early genome map of field cress (Lepidium campestre), which is a potential oilseed plant. They show that diploid Lepidium campestre has 16 chromosomes.


Leviczky T, Molnár E, Papdi C, Őszi E, Horváth GV, Vizler C, Nagy V, Pauk J, Bögre L, Magyar Z (2019) E2FA and E2FB transcription factors coordinate cell proliferation with seed maturation. Development. doi: 10.1242/dev.179333
Open Access

Tünde Leviczky is first author on this Hungarian-led study that includes co-authors from Royal Hollaway University of London. This work characterises the role of the E2F transcription factors and the RETINOBLASTOMA-RELATED repressor protein during Arabidopsis embryo development.

https://dev.biologists.org/content/146/22/dev179333.long

Lokdarshi A, Papdi C, Pettko-Szandtner A, Dorokhov S, Scheres B, Magyar Z, von Arnim AG, Bogre L, Horváth B (2019) ErbB-3 BINDING PROTEIN 1 Regulates Translation and Counteracts RETINOBLASTOMA RELATED to Maintain the Root Meristem. Plant Physiol. doi: 10.1104/pp.19.0080
This UK-US-Hungary collaboration includes Ansul Lokdarshi and Csaba Papdi as co-first authors and Laszlo Bogre and Beatrix Horvath from Royal Hollaway University of London as corresponding authors. They assessed the role of the ErbB-3 BINDING PROTEIN 1 transcription factor during Arabidopsis root meristem development

GARNet grants for Monogram2020

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Published on: December 19, 2019

GARNet are delighted to be able to support early career researchers to attend the Monogram2020 meeting at the University of Dundee.

https://ics.hutton.ac.uk/monogram20/

We are able to provide £200 to each successful applicant to help with meeting costs. We hope to support attendance of at least 6 applicants.

Please return the application form to geraint@garnetcommunity.org.uk by 5pm on February 7th 2020.

Download the application form here.

Eligibility: At the time of the meeting the applicant must a UK-based early career researcher (student, postdoc or technical staff) who is within 10 years of graduating from their undergraduate degree. The applicant must present a poster or talk at the Monogram meeting. Researchers whose work lies at the intersection between model organisms and crop plants will be given preference. A maximum of two awards will be made to applicants working with the same supervisor.

Successful applicants will be asked to provide a 500-word summary about their experiences at the Monogram meeting for publication in the GARNish newsletter or on the GARNet blog. Applicants will be provided with the bursary once evidence is provided of meeting registration and poster abstract submission.

David Seung talks to GARNet

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Published on: December 4, 2019

David Seung who is a new group leader the John Innes Centre talks to GARNet about a paper in Plant Physiology entitled ‘Natural polymorphisms in Arabidopsis result in wide variation or loss of the amylose component of starch‘. This fascinating paper attempts to begin to answer a key question in plant science: Why do they produce amylose?

GARNet Bursary for EMBO Workshop on ‘Intercellular communication and plasmodesmata in plant development and disease’.

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Published on: November 27, 2019

http://meetings.embo.org/event/20-plant-intercellular-communication

Please return this form to geraint@garnetcommunity.org.uk by 5pm on Wednesday April 1st 2020.

We are able to provide free student/postdoc/technician registration (€330) for five successful applicants who will be selected by members of the organising committee and a representative of GARNet.


Eligibility: At the time of the meeting the applicant must a UK-based researcher who is within 10 years of graduating from their undergraduate degree. The applicant must present a poster or talk at the EMBO Workshop.

Successful applicants will be required to provide a 500-word summary about their experiences at the EMBO Workshop for publication in the GARNish newsletter or on the GARNet blog. GARNet will interact with the organisers at EMBO to ensure that the registration fee is waived for successful applicants. We will let applicants know that they have been successful by Wednesday April 8th 2020.

Download application form here Word or PDF.

Chiara Airoldi talks to GARNet

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Published on: November 27, 2019

Chiara Airoldi talks to GARNet about her recent paper published in Nature Plants entitled ‘TTG1 proteins regulate circadian activity as well as epidermal cell fate and pigmentation’. This work was conducted at the University of Cambridge in the labs of Beverly Glover and Alex Webb and brings together a fascinating evolutionary story of gene family subfunctionalization and the regulation of the circadian clock. Thanks to Chiara for taking the time to chat!

GARNet Research Roundup: November 22nd 2019

This bumper edition of the GARNet Research Roundup begins with three papers that have a focus on the circadian clock. First is from Cambridge and looks at a novel role for TTG1 in control of the clock. The second paper also includes co-authors from Cambridge and looks at the clock Evening Complex. The final clock paper includes co-authors from York and looks at the new roles for EARLY FLOWERING 3 and GIGANTEA.

The next four papers include researchers from the John Innes Centre. Yiling Ding’s lab lead an exciting study into the role of RNA G-quadruplex to define liquid-liquid phase separations. Next David Seung and Alison Baker look at production of amylose starch across Arabidopsis accessions. The third JIC paper is from the Charpentier lab and looks at nuclear calcium signaling in the root. Finally Lars Ostergaard is a co-author on a paper that identifies a novel biostimulant that controls podshatter in Brassica.

The eighth paper is from Glasgow and describes the bioengineering of plants to express a novel antibiotic bacteriocin.

Next are three papers introduce exciting new research tools. 1. Weibei Yang in the Meyerowitz lab introduces a method for co-labeling of RNAs and protein 2. Researchers in Nottingham introduce RootNav2.0 for the automated measurement of root archtiectures 3. The Haydon Lab has developed a GAL4-GFP luciferase system for tissue-specific gene expression analysis.

Two Photosynthesis-based papers come next with firstly an analysis on the link between metabolism and the light response curve (from Manchester) and secondly a look at the role of aquaporins in control of CO2 conductance (Cambridge and Lancaster).

The fourteenth paper is from Durham and characterises an important protein regulator of the autophagy-dependent degradation pathway whilst the fifteenth is from Cambridge and uses cryo-SEM to analyse cell wall structures.

The penultimate paper is from Birmingham and looks at the role of redox signaling in aphid fecundity and the final paper includes co-authors from RHUL and looks at the interaction between the E2FB and RETINOBLASTOMA-RELATED proteins.


Airoldi CA, Hearn TJ, Brockington SF, Webb AAR, Glover BJ (2019) TTG1 proteins regulate circadian activity as well as epidermal cell fate and pigmentation. Nat Plants. doi: 10.1038/s41477-019-0544-3

This study from the University of Cambridge is led by Chiara Airoldi and introduces a new role for the TRANSPARENT TESTA GLABRA 1 (TTG1) WD-repeat (WDR) subfamily in the regulation of the circadian clock. TTG1 regulates epidermal cell differentiation and pigment production, while LIGHT-REGULATED WD1 and LIGHT-REGULATED WD2A are known to regulate the clock. The triple lwd1 lwd2 ttg1 mutant has no detectable circadian rhythym. This suggests that members of this protein family have undergone subfunctionalization to diverge from their core functions. This paper is of interest to those who research evolution of protein function as well as the to those interested in the control of the circadian clock.

https://www.nature.com/articles/s41477-019-0544-3

Tong M, Lee K, Ezer D, Cortijo S, Jung J, Charoensawan V, Box MS, Jaeger K, Takahashi N, Mas P, Wigge PA, Seo PJ (2019) The Evening Complex establishes repressive chromatin domains via H2A.Z deposition. Plant Physiol. doi: 10.1104/pp.19.00881

This collaboration between the UK and South Korea is led by Meixuezi Tong and investigates how the Evening Complex (EC) component of the circadian clock interacts with chromatin to control gene expression at dusk. This occurs through direct interaction with the SWI2/SNF2-RELATED complex and together they bind to the core clock genes PRR7 and PRR9, causing the deposition of H2A.Z at these loci subsequent to causing their repression at dusk.


Anwer MU, Davis A, Davis SJ, Quint M (2019) Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA. Plant J. doi: 10.1111/tpj.14604

Amanda Davies and Seth Davies from the University of York are co-authors on this German-led study with Muhammad Anwer as both first and corresponding author. They look at the role of important circadian regulators ELF3 and GIGANTEA through generation of previously unanalysed elf3gi double mutants. In these plants the circadian oscillator fails to synchronize to light-dark cycles even under diurnal conditions, demonstrating that these genes act together to convey photoperiod sensing to the central oscillator.


Zhang Y, Yang M, Duncan S, Yang X, Abdelhamid MAS, Huang L, Zhang H, Benfey PN, Waller ZAE, Ding Y (2019) G-quadruplex structures trigger RNA phase separation. Nucleic Acids Res. doi: 10.1093/nar/gkz978
Open Access

Yueying Zhang is the first author of this study conducted in the lab of Yiliang Ding at the John Innes Centre, in collaboration with the Benfey lab in the USA. They reveal an exciting mode of regulating RNA activity through the formation of RNA G-quadruplex (GQ) complexes. They use the SHORTROOT mRNA as the model for this study, showing that GQ-mediated complex formation can bring liquid-liquid phase separation. This study is of fundamental importance as it provides the first evidence that RNA can adopt structural motifs to trigger and/or maintain the specificity of RNA-driven phase separation.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz978/5624975?guestAccessKey=d3913912-fdbb-4f35-aa71-625442722842

Seung D, Echevarría-Poza A, Steuernagel B, Smith AM (2019) Natural polymorphisms in Arabidopsis result in wide variation or loss of the amylose component of starch. Plant Physiol. doi: 10.1104/pp.19.01062
Open Access

David Seung at the John Innes Centre the first and corresponding author of this study that used data from the Arabidopsis 1135 Genome project to investigate the prevelance of amylose production. Plants with amylose-free starch have no detrimental phenotypes so the function of this glucose-polymer, that accounts for up to 30% of all natural starch, is unknown. They looked at the polymorphisms within the GRANULE-BOUND STARCH SYNTHASE (GBSS) enzyme, identifying natural accessions that have no GBSS activity yet are viable within their natural environments. This study is a prelude to future research that will discover the adaptive significance of amylose.


Leitão N, Dangeville P, Carter R, Charpentier M (2019) Nuclear calcium signatures are associated with root development. Nat Commun. doi: 10.1038/s41467-019-12845-8
Open Access

Nuno Leitao is first author on this research from the Charpentier lab at the John Innes Centre. They looked at the role of nuclear Ca2+ signalling on primary root meristem development and auxin homeostasis through activity of the nuclear membrane localised ion channel DOES NOT MAKE INFECTIONS 1 (DMI1). This study discovers a previously unappreciated role for intracellular Ca2+ signalling during plant development.


Łangowski Ł, Goñi O, Quille P, Stephenson P, Carmody N, Feeney E, Barton D, Østergaard L, O’Connell S (2019 A plant biostimulant from the seaweed Ascophyllum nodosum (Sealicit) reduces podshatter and yield loss in oilseed rape through modulation of IND expression. Sci Rep. doi: 10.1038/s41598-019-52958-0
Open Access

Lars Ostergaard is a co-author on this Irish-study led by Lukasz Łangowski that investigates the factors that control pod shatter in oil seed rape. They show that the seaweed Ascophyllum nodosum-based biostimulant (Sealicit) is able to reduce podshatter by effecting the expression of the major regulator of pod shattering, INDEHISCENT. This has implications for the use of this compound by farmers wanting to reduce the amount of seed loss due to premature pod shatter.


Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC, Milner JJ (2019) Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae. Plant Biotechnol J. doi: 10.1111/pbi.13294
Open Access

William Rooney at the University of Glasgow is lead author on this study that attempts to combat Pseudomonas syringae infections through expression of a novel protein antibiotic bacteriocin, putidacin. They show that transgenic expression of this bacterial protein provides effective protection against Pseudomonas. This proof of concept opens the possibility for more widespread use of bacteriocins as an effective plant protection strategy.

https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.13294

Yang W, Schuster C, Prunet N, Dong Q, Landrein B, Wightman R, Meyerowitz EM (2019) Visualization of Protein Coding, Long Non-coding and Nuclear RNAs by FISH in Sections of Shoot Apical Meristems and Developing Flowers. Plant Physiol. doi: 10.1104/pp.19.00980
This extended methods paper is led by Weibing Yang at the Sainsbury lab in Cambridge. They have adapted RNA fluorescence in situ hybridization (rnaFISH) to explore RNA localization in the shoot apical meristem of Arabidopsis. They are able to label mRNA as well as long ncRNAs and have developed double labeling to assay two separate RNAs in the same cell and to assess nucleo-cytoplasmic separation of RNA species. Finally they link rnaFISH with fluorescence immunocytochemistry for the simultaneous localization of a single genes mRNA and protein.

https://www.frontiersin.org/articles/10.3389/fpls.2019.01398/full

Yasrab R, Atkinson JA, Wells DM, French AP, Pridmore TP, Pound MP (2019) RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures. Gigascience. doi: 10.1093/gigascience/giz123
Open Access

Robail Yasrab is lead author on this work from the University of Nottingham that introduces the RootNav2.0 software tool. This was developed by modern deep-learning approaches and allows the fully automated measurement of vertically growth root systems. RootNav2.0 was favourably compared with its semi-automated predecessor RootNav1.0 and can be used for measurement of root architectures from a range of different plant species.


Román Á, Golz JF, Webb AA, Graham IA, Haydon MJ (2019) Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. Plant J. doi: 10.1111/tpj.14603

This technical advance is led by Angela Roman, was in the Haydon lab during its time at the University of York. They have used the GAL4-GFP enhancer trap system, to develop a tissue-specific split luciferase assay for non-invasive detection of spatiotemporal gene expression in Arabidopsis. In this example they use the study to measure dynamics of circadian gene expression but is clearly applicable to answer many other experimental questions.


Herrmann HA, Schwartz JM, Johnson GN (2019) From empirical to theoretical models of light response curves – linking photosynthetic and metabolic acclimation. Photosynth Res. doi: 10.1007/s11120-019-00681-2
Open Access

Helena Herrmann is lead author on this work fro the University of Manchester. In this study they developed and then empirically tested a series of simple kinetic models that explains the metabolic changes that are required to alter light response curves (LRCs) across a range of temperatures. This allowed them to show how changes in NADPH and CO2 utilization respond to environmental changes. This provides useful information as to how a plant adapts its metabolic response to light depending on the growth temperature.

Helena explaining her research

Kromdijk J, Głowacka K, Long SP (2019) Photosynthetic efficiency and mesophyll conductance are unaffected in Arabidopsis thaliana aquaporin knock-out lines. J Exp Bot. doi: 10.1093/jxb/erz442

Open Access
Wanne Kromdijk leads this US-led research that includes contributions from the Universities of Cambridge and Lancaster. They looked at the potential role of membrane-bound aquaporins in the control of diffusion conductance for CO2 transfer from substomatal cavity to chloroplast stroma (gm). They tested three aquaporin mutants across a range of light and CO2 concentrations and surprisingly found that they appear to play no significant contribution to the control of gm. The reporting of this type of ‘negative’ result will prevent unnecessary replication of experiments and help to streamline the research process.


Wang P, Pleskot R, Zang J, Winkler J, Wang J, Yperman K, Zhang T, Wang K, Gong J, Guan Y, Richardson C, Duckney P, Vandorpe M, Mylle E, Fiserova J, Van Damme D, Hussey PJ (2019) Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat Commun. doi: 10.1038/s41467-019-12782-6
Open Access

Pengwei Wang is first author in this research led from Durham University that incudes Chinese and Belgian collaborators. They show that the AtEH/Pan1 protein is involved with actin cytoskeleton regulated autophagy and recruits multiple other components to autophagosomes during this process. In addition they show vesicle bound-AtEH/Pan1 interact with VAP27-1 at the ER-PM. This demonstrates that AtEH/Pan1 is a key component of the autophagy-dependent degradation pathway.


Lyczakowski JJ, Bourdon M, Terrett OM, Helariutta Y, Wightman R, Dupree P (2019) Structural Imaging of Native Cryo-Preserved Secondary Cell Walls Reveals the Presence of Macrofibrils and Their Formation Requires Normal Cellulose, Lignin and Xylan Biosynthesis. Front Plant Sci. doi: 10.3389/fpls.2019.01398
Open Access

Jan Lyczakowski from the Dupree lab at the University of Cambridge is first author on this study that has adapted low temperature scanning electron microscopy (cryo-SEM) to visualize the cell walls of both angiosperm and gymnosperms. They have used Arabidopsis mutants to reveal that cell wall macrofibrils at composed of cellulose, xylan, and lignin. They demonstrate that cryo-SEM is a useful tool for native nanoscale cell wall architectures.


Rasool B, Karpinska B, Pascual J, Kangasjärvi S, Foyer CH (2019) Catalase, glutathione and protein phosphatase 2A-dependent organellar redox signalling regulate aphid fecundity under moderate and high irradiance. Plant Cell Environ. doi: 10.1111/pce.13669
Brwa Rasool is first author on this collaboration between the Universities of Birmingham and Helsinki that looks at how aphids respond to redox changes in Arabidopsis thaliana grown under different light conditions. They also identified defence-related transcription factors differentially upregulated by aphid predation in different light conditions. Overall they show aphid fecundity is in part determined by the plants cellular redox signaling.


Őszi E, Papdi C, Mohammed B, Pettkó-Szandtner A, Vaskó-Leviczky T, Molnár E, Ampudia CG, Khan S, Lopez-Juez E, Horváth B, Bögre L, Magyar Z (2019) E2FB interacts with RETINOBLASTOMA RELATED and regulates cell proliferation during leaf development. Plant Physiol. doi: 10.1104/pp.19.00212
Erika Oszi is first author of this Hungarian-led research that includes co-authors from Royal Holloway University of London. This research looks at the interaction between the transcription factors E2FB and RETINOBLASTOMA-RELATED (RBR) and how this contributes to cell proliferation during organ development in Arabidopsis leaves. The relationship between these proteins changes throughout the stages of leaf development and is critical to determine final leaf cell number.

http://www.plantphysiol.org/content/early/2019/11/06/pp.19.00212.long
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