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

3D-RNA-seq Analysis Tool

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Published on: November 15, 2019

At the end of October GARNet hosted a workshop on the the 3d RNAseq App that has been developed by Wenbin Guo and Runxuan Zhang at the James Hutton Institute. Workshop schedule and attendees can be downloaded here (PDF).

The 3D RNA-Seq Analysis Tool is designed for the comprehensive differential expression, alternative splicing analysis and visualisation of RNASeq Data.

https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

It runs the analysis through a user-friendly graphical interface, that can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures and customerised  analysis reports.


The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to take control of the analysis of their RNA-seq data.

The designers also provide a explanation on how RNAseq FastQ reads can be processed through Salmon or Kallisto using the Galaxy platform.

This entire process allows non-experts to take their raw data through to detailed outputs within a couple of days!


Instructional documents can be downloaded here and please check out the accompanying YouTube video.

  1. Transcript quantification using Galaxy (HTML)
  2. 3D RNAseq Manual (zipped HTML)
  3. 3D Workshop presentation (PPT)

CONNECTED Vector-borne Plant Virus Training Program

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Published on: November 7, 2019

A group of African early career researchers feature in a new short film about vector-borne plant viruses that devastate crops in Sub-Saharan African countries.

The seven-minute film focuses on the ground-breaking Virus-Vector Vice-Versa training course for early career researchers, run by the CONNECTED Network, which took place at The University of Bristol, UK, in summer 2019.


A group of early career researchers from 11 African countries took up fully-funded places at the course. The film features interviews with delegates discussing: 

  • what they learned on the course
  • how they will use their new skills and knowledge, and
  • the value to them of the collaborative CONNECTED network.

There are also clips from interviews with:

  • Prof. Nicola Spence, Defra, UK (Chair of the CONNECTED Management Board)
  • Prof. Gary Foster, University of Bristol (CONNECTED Network Director)
  • Prof. Susan Seal, Natural Resources Institute, University of Greenwich (CONNECTED Management Board member).

In the film Prof. Foster says: “CONNECTED is sowing the seeds of a new generation of collaborators, whose work will transform African agriculture for the next 20 to 30 years.”

You can watch below or on the CONNECTED Vimeo channel.

Waqas Khokhar talks to GARNet

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Published on: November 6, 2019

Waqas Khokhar from Canterbury Christ Church University in Kent talks to GARNet about a new publication in Frontiers in Plant Science on ‘Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana‘. Waqas has produced a really exciting dataset that will be of great use to many other researchers!

GARNet Research Roundup: November 1st 2019

This edition of the GARNet Research Roundup begins with a pan-UK study that has identified a gene involved in starch granule formation in polyploid wheat. Second is a study from Canterbury that identifies Arabidopsis QTLs involved in alternative splicing. Third is research from Cambridge that investigates the role of the nuclear circadian oscillator on sub-cellular calcium fluctuations. The fourth paper describes the development of a computer-vision tool designed for automated measurements of wheat spikes in the field. The fifth paper is a Korean-led study that has identified a transcription factor involved in pollen development and includes co-authors from Leicester. Last is a study from the University of Warwick that has looked into light-regulated gene expression during bulb initiation in onion.


Chia T, Chirico M, King R, Ramirez-Gonzalez R, Saccomanno B, Seung D, Simmonds J, Trick M, Uauy C, Verhoeven T, Trafford K (2019) A carbohydrate-binding protein, B-GRANULE CONTENT 1, influences starch granule size distribution in a dose-dependent manner in polyploid wheat. J Exp Bot. doi: 10.1093/jxb/erz405
Open Access

Tansy Chia is lead author on this study that brings together three of the UKs major plant breeding research centres; NIAB, Rothamsted and the JIC. They take advantage of the new genomic tools and mutant populations available in wheat to characterize the complex role of the BGC1 (B-GRANULE CONTENT 1) gene during formation of B-type starch granules.


Khokhar W, Hassan MA, Reddy ASN, Chaudhary S, Jabre I, Byrne LJ, Syed NH (2019) Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana Front Plant Sci. doi: 10.3389/fpls.2019.01160
Open Access

This work from Canterbury Christ Church University is led by Waqas Khokhar and Naeem Syed. They analysed 666 diverse Arabidopsis ecotypes to look for splicing quantitative trait loci (sQTLs)] that alter rates of alternative splicing. They identified a number of trans-sQTLs hotspots that align with known functional SNPs. This study provides the first sQTL resource across diverse ecotypes that can be used to compliment other available genome and transcriptome datasets.


Martí Ruiz MC, Jung HJ, Webb AAR (2019) Circadian gating of dark-induced increases in chloroplast- and cytosolic-free calcium in Arabidopsis. New Phytol. doi: 10.1111/nph.16280

María Carmen Martí Ruiz is lead author on this research undertaken in Alex Webb’s lab in Cambridge. They have looked at the role of the circadian clock in the control of calcium fluctuations in both cytoplasm and chloroplast stroma. They show the extent these changes are dependent on a nuclear-encoded circadian oscillator, adding a new role in sub-cellular Ca2+ signaling to the circadian machinery.


Sadeghi-Tehran P, Virlet N, Ampe EM, Reyns P, Hawkesford MJ (2019) DeepCount: In-Field Automatic Quantification of Wheat Spikes Using Simple Linear Iterative Clustering and Deep Convolutional Neural Networks. Front Plant Sci. doi: 10.3389/fpls.2019.01176
Open Access

Pouria Sadeghi-Tehran leads this theorectical study from Rothamsted Research that has developed an automated ‘DeepCount’ system for quantifying wheat spikes in the field. They use a deep convolutional neural network to test their program on field images and compare this method to other automated systems based on edge detection techniques and morphological analysis. Overall they show that this method has potential toward development of a portable and smartphone-assisted wheat-ear counting systems, that will have the associated benefits of counting accuracy and reduced labour.

https://www.frontiersin.org/articles/10.3389/fpls.2019.01176/full

Oh SA, Hoai TNT, Park HJ, Zhao M, Twell D, Honys D, Park SK (2019) MYB81, a microspore-specific GAMYB transcription factor, promotes pollen mitosis I and cell lineage formation in Arabidopsis. Plant J. doi: 10.1111/tpj.14564

Mingmin Zhao and David Twell are co-authors on this project led by Sung‐Aeong Oh and Korean colleagues. After screening pollen cell patterning mutants they have identified a role for the GAMYB transcription factor MYB81 during a narrow window prior to pollen mitosis I. They demonstrate that this protein is essential for establishing the male cell lineage in Arabidopsis pollen.


Rashid MHA, Cheng W, Thomas B (2019) Temporal and Spatial Expression of Arabidopsis Gene Homologs Control Daylength Adaptation and Bulb Formation in Onion (Allium cepa L.). Sci Rep. doi: 10.1038/s41598-019-51262-1 Open Access

This collaboration between the University of Warwick and Bangladesh Agricultural University is led by Harun Ar Rashid. They look at genetic regulation of light-dependent onion bulb initiation by growing plants under short and long days and testing the expression of known regulators of flowering time; AcFT, Ac LFY and AcGA3ox1. They also performed tissue-specific analysis to demonstrate differences in expression patterns that begin to suggest how these genes are involved in bulb initiation.

https://www.nature.com/articles/s41598-019-51262-1

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