This edition of the GARNet Research Roundup begins with research from Durham University that links environmental sensing, SUMOylation and BR signaling. The second paper is from the Baulcombe lab in Cambridge and investigates the epigenetic control of transposons. The third paper is from Aberystwyth University and introduces the DeepPod learning framework for the automated counting of Arabidopsis siliques.
The fourth paper includes co-authors from the University of Nottingham in research that conducts a comprehensive analysis of the Arabidopsis auxin receptor gene family. The next paper from the University of Bristol looks at different statistical methods to measure segregation distortion.
The sixth paper is a structural-biology study of an Arabidopsis histone methyltransferase and includes co-authors from King’s College London and the Crick Institute. The penultimate paper includes Brian Forde from Lancaster University as a co-author and analyses the ZmTMM1 transcription factor from maize. The final paper investigates the role of the WRKY6 transcription factor during seed development and includes Ian Bancroft as a co-author.
Srivastava M, Srivastava AK, Orosa-Puente B, Campanaro A, Zhang C, Sadanandom A (2020) SUMO Conjugation to BZR1 Enables Brassinosteroid Signaling to Integrate Environmental Cues to Shape Plant Growth. Curr Biol. doi: 10.1016/j.cub.2020.01.089 Open Access
Moumita Srivastava
is first author on this study from Durham University that introduces
SUMO regulation of brassinosteroid (BR) signalling through the BZR1
transcription factor. During salt stress Arabidopsis plants arrest
growth by upregulating the SUMO protease ULP1a that in turn deSUMOylates
BZR1 allowing for its destabilizing interaction with the BIN2 kinase.
This study environmental sensing, SUMOylation and the BR response.
Zhengming Wang
and David Baulcombe from the University of Cambridge are authors on
this research that assesses the ordering of the mechanisms through which
transposon-containing chromatin is silenced. They demonstrate that both
RNA-directed DNA methylation (RdDM) and RNA-independent silencing
through chromodomain DNA methyltransferases (CMTs) occurs to provide
long-term control of transposons and concomitant alterations to the
transcriptome.
Hamidinekoo A, Garzón-Martínez GA, Ghahremani M, Corke FMK, Zwiggelaar R, Doonan JH, Lu C (2020) DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis. Gigascience doi: 10.1093/gigascience/giaa012 Open Access
This research from Aberystwyth University includes Azam Hamidinekoo as first author in which they have developed the DeepPod deep learning framework for the automated identification of Arabidopsis siliques from complex images. They used a training set of over 2400 images to develop prediction software that had comparable success with manual expert human counting. The project code is available on GitHub.
Prigge MJ, Platre M, Kadakia N, Zhang Y, Greenham K, Szutu W, Pandey BK, Bhosale RA, Bennett MJ, Busch W, Estelle M (2020) Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals both overlapping and specialized functions. Elife doi: 10.7554/eLife.54740 Open Access
Mike Prigge
from UCSD in California leads this research that includes co-authors
from the University of Nottingham. They analyse the phenotypes of all
mutant combinations of the six-member TIR1/AFB family of auxin
receptors, demonstrating significant functional overlap but that the
presence of a functional TIR1 or AFB2 is needed to maintain growth
throughout the life cycle. Interestingly they find that the mysterious
AFB1 receptor appears to play a specalised role in processes dependent
on more rapid auxin-mediated effects.
Coulton A, Przewieslik-Allen AM, Burridge AJ, Shaw DS, Edwards KJ, Barker GLA (2020) Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods. PLoS One. doi: 10.1371/journal.pone.0228951 Open Access
Alexander Coulton
is the first author on this study from the University of Bristol that
looks at different statistical tests that are used to confirm
segregation distortion in high-density SNP data. In this data they find
that the false discovery rate correction best fits the traditional
p-value threshold of 0.05 and they perform empirical tests using mapping
populations generated between different wheat varieties.
Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau Ø (2020) The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J doi: 10.1111/febs.15256
This Norwegian-led study has Olena Dobrovolska
as first author and co-authors from King’s College London and the Crick
Institute. They have performed a structural analysis using NMR and
molecular dynamics of the Arabidopsis Histone lysine methyltransferase
ASHH2.
Liu Y, Jia Z, Li X, Wang Z, Chen F, Mi G, Forde B, Takahashi H, Yuan L (2020) Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging. J Exp Bot. doi: 10.1093/jxb/eraa116
Ying Liu leads this Chinese study that includes Brian Forde
from Lancaster as a co-author. They show that the maize ZmTMM1
transcription factor is able to rescue the nitrate foraging defect in
Arabidopsis anr1agl21 double mutants, demonstrating a link between nitrate-induced transcriptional regulation in grasses and dicots.
Song G, Li X, Munir R, Khan AR, Azhar W, Yasin MU, Jiang Q, Bancroft I, Gan Y (2020) The WRKY6 transcription factor affects seed oil accumulation and alters fatty acid compositions in Arabidopsis thaliana. Physiol Plant. doi: 10.1111/ppl.13082
Ian Bancroft
from the University of York is a co-author on this Chinese-led study in
which Ge Song is first author. They discovered a high expression level
of the WRKY6 transcription factor in developing seeds of Arabidopsis and
that wrky6 mutants have larger seeds with altered fatty acid
(FA) content and composition. The authors suggest that WRKY6 could be a
target for the genetic improvement of FA content in the oil-seed crop of
Brassica napus.
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.
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.
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.
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.
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.
This weeks Arabidopsis Research Roundup is lead by two papers that characterise the relationship between cell size and growth in different Arabidopsis tissues. Firstly the lab of GARNet PI Jim Murray look at how the cell cycle influences cell size progression in the SAM whilst George Bassel’s group from Birmingham investigate cell growth within a developing embryo. Thirdly is a paper from the University of Essex that further defines the role of the CP12 protein in control of photosynthesis. Next is a paper from researchers from the University of Warwick who lead a fascinating piece of rocket science that identifies differences in the vernalisation requirement across Brassica species whilst in the fifth paper, researchers from Lancaster identify environmentally defined QTLs that determine the plant response to glutamate. Finally is a paper that highlights a new software tool that has the self-explanatory title of the ‘UEA small RNA Workbench’ and is applicable for use with plant-derived datasets.
R Jones A, Forero-Vargas M, Withers SP, Smith RS, Traas J, Dewitte W, Murray JAH (2017) Cell-size dependent progression of the cell cycle creates homeostasis and flexibility of plant cell size. Nat Commun http://dx.doi.org/10.1038/ncomms15060
Open Access
This study comes from the lab of current GARNet PI Jim Murray at the Cardiff University. Lead author Angharad Jones kindly provides an audio description of the paper for the GARNet YouTube channel. This investigation looks at the factors that control the interaction between cell size and cell growth in a developing shoot meristem. They show that the dynamic regulation of this relationship is linked to the activity of two cyclin dependent kinases (CDKs) and that cell size is key in controlling the transition from G1>S and from G2>M phases of the cell cycle. Importantly this work uses precise imaging to track the progression of individual cell lineages and is therefore able to suggest that cell size is an emergent and not a directly determined property.
Souza NM, Topham AT, Bassel GW (2017) Quantitative analysis of the 3D cell shape changes driving soybean germination. J Exp Bot. http://dx.doi.org/10.1093/jxb/erx048
Open Access
George Bassel (University of Birmingham) leads this paper that uses information gained from the study of patterns of cell expansion in Arabidopsis embryos to investigate a similar process in soybean. Indeed as in Arabidopsis they show that there is preferential early cell expansion closest to the soybean radicle and that starting cell size corresponds to different growth rates. In addition they show that the growing hypocotyl has complex regulation and that differential ansiotrophy growth drives forward the process of germination. Ultimately they show that this occurs equivalently in both model and crop species.
Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C (2017) Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. J Exp Bot http://dx.doi.org/10.1093/jxb/erx084Open Access This study from the photosynthesis group at the University of Essex is led by Tracey Lawson and GARNet committee member Christine Raines. They investigate the role of the CP12 multigene family that has three members in Arabidopsis. These are redox-sensitive proteins that facilitate the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) during the Calvin-Benson cycle. They show that plants with reduced levels of CP12-1 or CP12-2 have lower photosynthetic capacity and subsequently exhibit slower growth. The cell biological explanation for this alteration appears to focus on the PRK protein, which is present at lower levels in plants with reduced CP12-1 or CP12-2. Therefore the authors find that CP12-1 and CP12-2 are the key members of this gene family and they likely show functional redundancy in the tight control of photosynthesis.
Taylor JL, Massiah A, Kennedy S, Hong Y, Jackson SD (2017) FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected. J Plant Physiol.
http://dx.doi.org/10.1016/j.jplph.2017.03.015 Open Access
a
Steve Jackson (University of Warwick) leads this work that also features Chinese collaborators and investigates the role of FLOWERING LOCUS C (FLC) in the popular peppery salad plant Rocket (Diplotaxis tenuifolia) that, as a Brassica, is a somewhat closely related to Arabdopsis. The authors studied the vernalisation requirement in this plant so isolated its version of FLC, which was shown to functional compliment an Arabidopsis flc null mutant. However they showed that even though cold treatment reduced levels of DtFLC this did not alter the bolting time of the plant. This somewhat surprising result demonstrates that the link between FLC and flowering time is uncoupled in this species and that other mechanisms may take precedence, a situation different to that observed in Arabidopsis and other Brassicas.
Walch-Liu P, Meyer RC, Altmann T, Forde BG (2017) QTL analysis of the developmental response to L-glutamate in Arabidopsis roots and its genotype-by-environment interactions. J Exp Bot.
http://dx.doi.org/10.1093/jxb/erx132 Open AccessResearchers from the groups of Brian Forde (Lancaster University) and Thomas Altmann (Leibniz Institute) collaborate in this research that identifies three novel QTLs (GluS1-3) that are involved in the response of Arabdopsis roots to external L-glutamate. When this experiment was extended they discovered that different environmental factors play a significant role in the control of this trait. The GluS1 locus is located on Chr3 yet is epistatically controlled by loci on Chr1 and Chr5 in response to temperatures. Overall this study demonstrates that the response to glutamate is controlled by multiple environmentally sensitive loci that vary between Arabidopsis ecotypes
Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V (2017) The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis. Methods Mol Biol.
This manuscript from the University of East Anglia describes a set of software tools for the analysis of small RNAs. They used an Arabidopsis dataset to demonstrate the utility of the UEA small RNA Workbench, which can be found here: http://srna-workbench.cmp.uea.ac.uk/
Over the past thirty years the Multinational Arabidopsis Steering Committee (MASC) has represented the global Arabidopsis community through its collaborative oversight of the annual International Conference on Arabidopsis Research (ICAR), production of a MASC annual report and preparation of the series of decadal Roadmaps that have helped coordinate the future activities of the community. In[…]
https://meetings.embo.org/event/20-plant-systems This EMBO Workshop on international Plant Systems Biology (iPSB) is the central gathering of plant systems biology researchers from across the world. Climate change poses unique challenges for how to feed and power humanity without further degrading the environment. Plant science therefore is a key discipline in meeting the challenge of adapting food and[…]
The spring season of #UKPlantSciPresents begins on January 12th and we have a strong schedule set until the end of April! Each webinar is at Tuesday afternoon at 3pm GMT (or BST)! Registration is free and webinars will be made freely available soon after the event. Although closed captioning/subtitles are not available for live webinars,[…]
The previously awesome #GARNetPresents webinar series is morphing into the #UKPlantSciPresents webinar series. This series has the aim of promoting plant science excellence across the UK! UK plant science research uses many different experimental organisms such as Arabidopsis, Wheat, Brassicas, Brachypodium, Marchantia, Physomitrella and many others. This webinar series is supported by both GARNet and[…]
Contents: – Society Updates– Introducing Quantitative Plant Biology– Congratulations to Ottoline Leyser– Conference Updates– Bacterial Plant Diseases Programme– Introducing CHAP– Twenty Years of GARNet– GARNet Research Roundup– MASC Publication Update– Plant RNA Interactome Capture– Update on new BBSRC Projects– Spotlight on University of Nottingham Download here: https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish33_Online_Final_0.pdf
Marcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and[…]
This edition of GARNet Research Roundup begins with a remarkable four papers that include work from Caroline Dean’s lab at the John Innes Centre. The first two papers are collaborations with members of Martin Howard’s lab and look at the molecular mechanisms that control long-term cold sensing or the antisense regulation of FLC respectively. The[…]
Christos Velanis works at the University of Edinburgh and discusses work published in PloS Genetics entitled ‘The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)‘. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/07/Velanis_edit-13072020-09.32.mp3Pumi Perera is co-first author on this work from the Goodrich lab that[…]
This has been a challenging time for both conference organisers and conference venues. Most 2020 plant science conferences have cancelled, postponed or majorly changed their events. Below is a non-exhaustive list of the changes that have been made to different conferences. Up to date as July 6th 2020. (download)
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