GARNet Research Roundup: April 11th 2018

This weeks GARNet research roundup begins with a microscopy-based study led by Lorenzo Frigerio from the University of Warwick that investigates the origin of Protein Storage Vacuoles. The second paper from John Doonan at Aberystwyth University looks at how differential splicing of cyclin-dependent Kinase G1 effects the thermosensory response. Reiner van de Hoorn from Oxford leads the next paper that characterises the use of activity-based protein profiling (ABPP) to identify novel α-glycosidases in model and non-model plants. Simon McQueen-Mason from York is corresponding author of the next paper that identified a new QTL from Brachypodium that is involved in cell wall formation. The fifth paper is led by Anthony Dodd from Bristol and characterises the role of the SnRK1 complex in hypocotyl elongation whilst the penultimate manuscript from Julia Davies’s lab in Cambridge performs patch clamp analysis of dorn1 mutant plants. The final paper from Brendan Davies at the University of Leeds characterises the SMG kinase, a gene that is lacking from the Arabidopsis genome, in Physcomitrella patens.


http://www.plantphysiol.org/content/early/2018/03/19/pp.18.00010.long

Feeney M, Kittelmann M, Menassa R, Hawes C, Frigerio L. Protein storage vacuoles originate from remodelled pre-existing vacuoles in Arabidopsis thaliana (2018) Plant Physiol. 2018 Mar 19. pii: pp.00010.2018. doi: 10.1104/pp.18.00010 Open Access

This collaboration between the Universities of Warwick and Oxford Brookes is led by Lorenzo Frigerio and Chris Hawes. They have investigated the origin of seed Protein Storage Vacuoles (PSV) using a two-pronged approach using confocal and immunoelectron microscopy. They looked at embryo development as well as in leaf cells that have been reprogrammed for embryonic cell fate by overexpression of the LEAFY COTYLEDON2 TF. These studies indicate that PSVs are formed following the reprogramming of pre-existing embryonic vacuole (EV) rather than from de novo assembly.


https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13914

Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH. The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A (2018) Plant J. doi: 10.1111/tpj.13914 Open Access

John Doonan (Aberystwyth University) is the corresponding author on this UK-Austrian collaboration that presents the role of the cyclin-dependent Kinase G1 (CDKG1) in thermosensing in Arabidopsis. Ambient temperature change causes altered gene expression of the spliceosome component, ATU2AF65A. Interestingly the CDKG1 gene is differentially spliced and to produces two protein isoforms that are both needed to complement the expression of ATU2AF65A across a temperature range. This alternative splicing is dependent on CDKG2 and CYCLIN L1 and is a novel control mechanism in the temperature control response.


Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS, van der Hoorn RAL (2018) Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants. Plant Physiol. pii: pp.00250.2018. doi: 10.1104/pp.18.00250 Open Access

Renier Van de Hoorn (University of Oxford) leads this pan-european study that uses novel cyclophellitol aziridine probes that label α-glycosidase enzymes. They identified two novel α-glycosidases in Arabidopsis as well as using the technique in non-model saffron crocus. Finally they showed that this multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases can be used to identify changes in hydrolase activity in response to pathogen infection.


Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen-Mason SJ (2018) A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. New Phytol. doi: 10.1111/nph.15089 Open Access

Simon McQueen-Mason (University of York) leads this study that use QTL mapping to identify a gene in Bracypodium that is involved in cell wall architecture, which might then be a target to develop plants with improved cellulose digestibility. This glycosyl transferase family (GT) 43 protein is an orthologue of Arabidopsis IRX14, which is involved in xylan biosynthesis. When RNAi was used to reduce expression of this gene the resulting plants showed increased digestibility, indicating that this BdGT43A will be a good target for future breeding plans.


Wang L, Wilkins KA, Davies JM (2018) Arabidopsis DORN1 extracellular ATP receptor; activation of plasma membrane K(+) -and Ca(2+) -permeable conductances New Phytol. 2018 Mar 25. doi: 10.1111/nph.15111. Open Access

This letter to New Phytologist from the lab of Julia Davis (University of Cambridge) outlines some experiments to determine whether the DORN1 plasma membrane receptor is responsible for transmitting a signal from extracellular ATP (eATP). They performed patch clamp analysis on isolated protoplasts and showed that DORN1 is involved in the activation of Ca+ and K+ pumps by eATP as, in contrast to wildtype, dorn1 mutant protoplast showed no voltage changes after incubation with eATP.


Simon NML, Sawkins E, Dodd AN. Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation (2018) Plant Signal Behav. 27:1-9. doi: 10.1080/15592324.2018.1457913.

Anthony Dodd (University of Bristol) is the corresponding author of this follow-on study from one that previously featured on the GARNet YouTube channel. This study measures sucrose-induced hypocotyl elongation in two T-DNA mutants of the SnRK1 subunit KIN10 gene. These mutants had altered responses to sucrose leading to the hypothesis that the SnRK1 complex suppresses hypocotyl elongation in the presence of external sugar.


Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B (2018) The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res. doi: 10.1093/nar/gky225 Open Access

Brendan Davis (University of Leeds) is the corresponding author on research that investigates the role of the SMG1 kinase during nonsense-mediated mRNA decay (NMD) in the moss Physcomitrella patens. This kinase plays a critical role in animals but as it is not present in Arabidopsis, its function is not well studied in plants. However moss smg mutants show expression changes in genes involved in a variety of processes indicating that NMD is a common control mechanism in moss. In addition these plants have increased susceptibility to DNA damage, which suggests that the SMG1 kinase is a key player in quality control mechanisms in plants.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky225/4955258

GARNet Research Roundup: March 29th

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Published on: March 29, 2018

This edition of the GARNet research roundup begins with an analysis of the CELLULOSE SYNTHASE COMPLEX led by Simon Turner in Manchester. Next are two papers from Ian Henderson at Cambridge who, in collaboration with Rob Martienssen in the USA, has investigated the epigenetic factors that control meiotic recombination. Next are two papers led by Hugh Nimmo (Glasgow) who is researching alternative splicing of the LATE ELONGATED HYPOCOTYL transcript. Marc Vendrell and Karl Oparka at the University of Edinburgh are co-authors in the next paper that investigates the binding specificity of the AtSUC2 protein. The seventh paper includes David Salt (Nottingham) as a co-author in an investigation in the plants response to zinc. The final three papers are methods papers on gravitropism, ChIP-Seq and calcium sensing from Nottingham University, SLCU and the John Innes Centre respectively.


Kumar M, Mishra L, Carr P, Pilling M, Gardner P, Mansfield SD, Turner SR (2018) Exploiting CELLULOSE SYNTHASE (CESA) class-specificity to probe cellulose microfibril biosynthesis. Plant Physiol. doi: 10.1104/pp.18.00263 Open Access

Simon Turner (University of Manchester) leads this study that investigates the subunit specificity of the CELLULOSE SYNTHASE COMPLEX, which is composed of many CESA components. Mutant cesa plants were used to probe the specificity of these subunits. Overall the authors found that CESA classes have similar roles in determining cellulose microfibril structure but that the rates of cellulose synthesis might be altered in a subunit-specific manner.


Choi K,, Zhao X, Tock AJ, Lambing C, Underwood CJ,, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR (2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res. doi: 10.1101/gr.225599.117
The research groups of Ian Henderson (University of Cambridge) and Rob Martienssen (CSHL) co-lead back-to-back papers that investigate the factors that influence meiotic recombination frequencies. The Henderson led-paper focuses on the position of the SPO11 topoisomerase and the epigenetic factors, such as H3K4me3 and DNA methylation that reside in those areas. They discovered some surprising relationships between SPO11 binding and different transposon classes.


Underwood CJ, Choi K, Lambing C, Zhao X, Serra H, Borges F, Simorowski J, Ernst E, Jacob Y, Henderson IR, Martienssen RA (2018) Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res. doi: 10.1101/gr.227116.117

Open Access

The Martienssen–led paper focuses on epigenetic marks, such as H3K9me2 and non-CG DNA methylation that reside at pericentromeric regions. By altering the distribution of these marks, the amount of pericentrometric recombination can be changed and that the number of double stranded breaks increase in H3K9me2/non-CG mutants.


James AB, Sullivan S, Nimmo HG (2018) Global spatial analysis of Arabidopsis natural variants implicates 5’UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature. Plant Cell Environment. doi: 10.1111/pce.13188

James AB, Calixto CPG, Tzioutziou NA, Guo W, Zhang R, Simpson CG, Jiang W, Nimmo GA, Brown JWS, Nimmo HG (2018) How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY). Plant Cell Environ. doi: 10.1111/pce.13193

The first of these back-to-back papers is led by Hugh Nimmo (Glasgow) in a study that characterises a set of 5’UTRs in the LATE ELONGATED HYPOCOTYL (LHY) gene and how they change in response to temperature. This is linked to a correlation of how these LHY haplotypes are global distributed.

The second paper is an extension of this study and includes Hugh Nimmo (Glasgow) and John Brown (JHI, Dundee) as co-corresponding authors. They that show RNA-binding splicing factors (SFs) are necessary for temperature-induced changes in the LHY transcript. LHY might be considered a molecular thermostat whose splicing can response to changes as little as 2°C.


De Moliner F, Knox K, Reinders A, Ward J, McLaughlin P, Oparka K, Vendrell M (2018) Probing binding specificity of the sucrose transporter AtSUC2 with fluorescent coumarin glucosides. J Exp Bot. doi: 10.1093/jxb/ery075 Open Access

Marc Vendrell and Karl Oparka (University of Edinburgh) are the corresponding authors on this bioimaging study that probes the specificity of the AtSUC2 phloem sucrose transporter. They use structural varieties in coumarin glucosides to precisely define the binding characteristics of AtSUC2.


Chen ZR, Kuang L, Gao YQ, Wang YL, Salt DE, Chao DY (2018) AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana. Front Plant Sci. doi: 10.3389/fpls.2018.00270

Open Access

David Salt (University of Nottingham) is a co-author on this Chinese study that characterises the role of the Heavy Metal-ATPase 4 (HMA4) in the respond to zinc.


Muller L, Bennett MJ, French A, Wells DM, Swarup R (2018) Root Gravitropism: Quantification, Challenges, and Solutions. Methods Mol Biol. doi: 10.1007/978-1-4939-7747-5_8

Ranjan Swarup (University of Nottingham) leads this methods paper that describes techniques for the automated measurement of root gravitropic responses.


Cortijo S, Charoensawan V, Roudier F, Wigge PA (2018) Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis. Methods Mol Biol. doi: 10.1007/978-1-4939-7747-5_18

Phillip Wigge (SLCU) leads this methods paper that outlines the technical details for the now common and important technique of ChIP-Seq from Arabidopsis roots.


Kelner A, Leitão N, Chabaud M, Charpentier M, de Carvalho-Niebel F (2018) Dual Color Sensors for Simultaneous Analysis of Calcium Signal Dynamics in the Nuclear and Cytoplasmic Compartments of Plant Cells. Front Plant Sci. doi: 10.3389/fpls.2018.00245 Open Access

Miriam Charpentier (John Innes Centre) is a co-author on this work that uses fluorescent protein-based Ca2+ sensors, the GECOs, to successfully monitor the calcium response to a range of biotic and abiotic elicitors. These GECO-based sensors represent an exciting new tool for the study of calcium dynamics.

Arabidopsis Research Roundup: March 9th

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Published on: March 9, 2018

This Arabidopsis Research Roundup has five papers that includes two from the John Innes Centre and two from the University of Edinburgh. Firstly Kristen Bomblies’s group at the JIC have investigated the relationship between temperature and meiotic recombination rates. Secondly Veronica Grieneisen and Stan Maree have developed a mathematical model to characterise cell morphologies taken from a 2D image. Andrew Miller from Edinburgh is a co-corresponding author on a study that shows how the Arabidopsis proteome changes in different photoperiods. In the fourth paper Peter Doerner is a co-author on work that looks at the phosphate starvation response. Finally researchers from Bristol and Nottingham contribute to an investigation into a novel genetic component that controls auxin-induced root hair development.


Lloyd A, Morgan C, Franklin C, Bomblies K (2018) Plasticity of Meiotic Recombination Rates in Response to Temperature in Arabidopsis. Genetics. doi: 10.1534/genetics.117.300588

Open Access

Kristen Bomblies (John Innes Centre) leads this study that investigates the influence of temperature on meiotic recombination rate. They show that in Arabidopsis the number of crossovers positively correlates with increasing temperature. However the mechanistic explanation for the increase at higher temperatures remains opaque as, in contrast to findings from other plants, synaptonemal complex length negatively correlates with temperature.


Sánchez-Corrales YE, Hartley M, van Rooij J, Marée AFM, Grieneisen VA (2018) Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA). Development. doi: 10.1242/dev.15677

http://dev.biologists.org/content/early/2018/02/08/dev.156778.long

Open Access

Veronica Grieneisen and Stan Maree (John Innes Centre) lead this study that has developed the Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA) method. This generates meaningful descriptors from a 2D image of cells that can then be linked to morphological features. This tool allows for the efficient phenotyping of cell morphologies that they demonstrate by analysing images of Arabidopsis leaf pavement cells. They extend this analysis to larger populations where they used LOCO-EFA to predict how cell shapes change when they move into a more crowded space.


Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access

http://onlinelibrary.wiley.com/doi/10.15252/msb.20177962/abstract

Andrew Miller (University of Edinburgh) is the corresponding author on this collaboration with German and Swiss colleagues that compares the Arabidopsis proteome across four photoperiods. They shows coordinated changes across the proteome, most notably at longer photoperiods in the abundance of proteins involved in photosynthesis and metabolism. They show higher translation rates during the day that correspond with the increased RNA abundance that is a characteristic of circadian rhythms. This ‘translational coincidence’ describes the alignment of higher translation rates with high transcript levels and they assigned a mathematical model in an attempt to explain this phenomenon.


Hanchi M, Thibaud MC, Légeret B, Kuwata K, Pochon N, Beisson F, Cao A, Cuyas L, David P, Doerner P, Ferjani A, Lai F, Li-Beisson Y, Mutterer J, Philibert M, Raghothama KG, Rivasseau C, Secco D, Whelan J, Nussaume L, Javot H (2018) The phosphate fast-responsive genes PECP1 and PPsPase1 affect phosphocholine and phosphoethanolamine content. Plant Physiol. doi: 10.1104/pp.17.01246 Open Access

Peter Doerner (University of Edinburgh) is a co-author on this global study that characterises the phosphate starvation-mediated induction of the HAD-type phosphatases PPsPase1 (AT1G73010) and PECP1 (AT1G17710). They show that expression of these genes closely follows phosphate status but that their activity does not alter phospate content. The role of these proteins is to control phosphocholine and phosphoethanolamine content, which is a output of changing phosphate conditions. The authors conclude that expression of these genes can be an excellent molecular marker for the phosphate starvation response.


www.cell.com/current-biology/fulltext/S0960-9822(18)30083-6

Schoenaers S, Balcerowicz D, Breen G, Hill K, Zdanio M, Mouille G, Holman TJ, Oh J, Wilson MH, Nikonorova N, Vu LD, De Smet I, Swarup R, De Vos WH, Pintelon I, Adriaensen D, Grierson C, Bennett MJ, Vissenberg K (2018) The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Current Biology doi: 10.1016/j.cub.2018.01.050

This Belgian-led study includes contributions from Claire Greirson’s and Malcolm Bennett’s labs in Bristol and Nottingham respectively. They investigate the role of the ERULUS (ERU) protein, an auxin-induced receptor-like kinase, during the development of root hairs. ERU localises to the apical root hair plasma membrane and regulates cell wall composition by altering pectin dynamic. The authors conclude that ERU is a key regulator of auxin-mediated control of root hair development.

Arabidopsis Research Roundup: March 2nd.

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Published on: March 2, 2018

The first two papers in this weeks Arabidopsis Research Roundup investigate different aspects of the plants response to temperature fluctuations. Firstly Lars Ostergaard (JIC) looks at the influence of temperature in the control of fruit dehiscence whilst Phil Wigge (SLCU) investigates crosstalk between chloroplast and nuclear signaling.

The third paper from Ian Henderson (University of Cambridge) studies the genetic elements that control rates of meiotic recombination. The next paper from the University of Leeds looks at the potential of using MET1 in the induction of novel epi-alleles whilst the penultimate paper includes the GARNet PI Jim Murray (Cardiff University) as a co-author and defines the role of CYCD7;1 in guard cell formation.

The final paper focusses on an enzyme involved in chlorophyll biosynthesis and includes Guy Hanke (QMUL) as a co-author.


https://linkinghub.elsevier.com/retrieve/pii/S1674-2052(18)30023-6

Li XR, Deb J, Kumar SV, Østergaard L (2018) Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae. Molecular Plant doi: 10.1016/j.molp.2018.01.003 Open Access

Lars Ostergaard (John Innes Centre) is the corresponding author that continues his groups work on the function of the INDEHISCENT protein, on this occasion looking at its involvement in the link between temperature and fruit dehiscence. They show that fruit valve margin development is accelerated at higher temperatures, facilitated by the activity of IND. This activity is associated with the changes in the induction dynamics of the known thermosensory histone H2A.Z and demonstrate a molecular framework for the response to changing temperature during fruit ripening.


http://www.cell.com/cell-reports/references/S2211-1247(18)30103-7

Dickinson PJ, Kumar M, Martinho C, Yoo SJ, Lan H, Artavanis G, Charoensawan V, Schöttler MA, Bock R, Jaeger KE, Wigge PA (2018) Chloroplast Signaling Gates Thermotolerance in Arabidopsis. Cell Rep. doi: 10.1016/j.celrep.2018.01.054 Open Access

Phil Wigge (SLCU) is the corresponding author on this study of the link between light-induced chloroplast signaling and thermotolerance. A forward genetic screen allowed the authors to identify two genes that demonstrated a key role for chloroplast signaling in controlling the activity of heat shock factors (HSFs), which enable the plant to cope with temperature variations. Subsequently they show that altering the binding activities of the HSFA1a protein can mimic heat shock response independent of any changes in temperature.


Serra H, Lambing C, Griffin CH, Topp SD, Nageswaran DC, Underwood CJ, Ziolkowski PA, Séguéla-Arnaud M, Fernandes JB,, Mercier R, Henderson IR (2018) Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis. PNAS doi: 10.1073/pnas.1713071115

Ian Henderson (University of Cambridge) is the corresponding author on this collaboration with French colleagues in a study that investigates the factors that control recombination frequency in meiosis. During normal meiotic recombination the majority of double stranded breaks will not form crossovers (over 90%) so to increase this frequency they altered the active dosage of genetic elements that are either pro-crossover or anti-crossover control. This strategy results in a massive increase in crossovers and provides a genetic framework for increasing recombination, a strategy that can be critically important for increasing variation during crop breeding.


Brocklehurst S, Watson M, Carr IM, Out S, Heidmann I, Meyer P (2018) Induction of epigenetic variation in Arabidopsis by over-expression of DNA METHYLTRANSFERASE1 (MET1). PLoS One. doi: 10.1371/journal.pone.0192170 Open Access

This study from the University of Leeds is led by Peter Meyer and investigates how overexpression of the METHYLTRANSFERASE1 (MET1) gene might generate novel epi-alleles that result in altered gene expression. This strategy indeed generated novel epi-alleles that increased expression at loci encoding TEs, non-coding RNAs and protein coding genes. Importantly any altered expression can be transmitted to the next generation, independent of the presence of a MET1 expressing transgene. However the long term stability of these epi-alleles differs in an loci-specific manner.


Weimer AK, Matos JL, Sharma N, Patell F, Murray JAH, Dewitte W, Bergmann DC (2018) Lineage and stage-specific expressed CYCD7;1 coordinates the single symmetric division that creates stomatal guard cells. Development. doi: 10.1242/dev.160671

GARNet PI Jim Murray and Walter DeWitte (Cardiff University) are co-authors on this US-led study that adds complexity to our understanding of the molecular players that control guard cell specification. The authors show that the D-type cyclin CYCD7;1 is expressed during a short time window prior to the symmetry division that forms two guard cells. This activity is controlled by cell-type specific transcription factors acting in the appropriate time period.

http://dev.biologists.org/content/early/2018/02/14/dev.160671.long

Herbst J, Girke A, Hajirezaei MR, Hanke G, Grimm B (2018) Potential Roles of YCF54 and Ferredoxin-NADPH Reductase for Magnesium Protoporphyrin Monomethylester Cyclase. Plant J. doi: 10.1111/tpj.13869

Guy Hanke (QMUL) is a co-author on this German-led study that investigates an enzyme reactions that occur during chlorophyll biosynthesis. Specifically they showed that plants lacking the LCAA/YCF54 subunit of the enzyme MgProto monomethylester (MgProtoME) cyclase causes accumulation of MgProtoME and destabilization of the entire cyclase enzyme. This disrupts chlorophyll synthesis and negatively effects photosynthetic activity.

Arabidopsis Research Roundup: February 22nd 2018

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Published on: February 22, 2018

This edition of the Arabidopsis Research roundup beings with a study from SLCU that provides a molecular context to the changes that occur at graft junctions. Second is a study from Edinburgh that reports on the findings of a citizen science plant phenotyping project. Third are two studies from the John Innes Centre that follow-on from previous studies. These characterise the molecular response to seasonal transitions and the factors that control floral development.

The fifth paper is led by Chris Hawes at Oxford Brookes and characterises a novel sub-group of ER localized reticulon proteins. The next paper from the University of Sheffield looks at the whole plant response to changing global carbon dioxide concentrations. The seventh paper from Bristol and York also broadly looks at CO2 but this time at the molecular factors that control stomatal closure in response to both ABA and CO2 signals. Christine Foyer (Leeds) is a co-author on the penultimate paper that characterises the role of ascorbic acid in hormone signaling whilst the final paper from Julian Hibberd at the University of Cambridge analyses a regulatory element that contributes to the evolutionary transition to C4 photosynthesis.


Melnyk CW, Gabel A, Hardcastle TJ, Robinson S, Miyashima S, Grosse I, Meyerowitz EM (2018) Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1718263115 Open Access
This research was led by Charles Melynk during this time working with Elliot Meyerowitz at SLCU. Grafting is an important classic and contemporary technique in plant biology and this study investigates the gene expression changes that occur on either side of a graft junction. They show asymmetry changes in gene expression on either side of a graft that include an increase in vascular initiation but only in grafted tissues and not in those that are cut and then separated. This study provides an exciting insight into the molecular changes that occur during tissue grafting.


Giuffrida MV, Chen F, Scharr H, Tsaftaris SA (2018) Citizen crowds and experts: observer variability in image-based plant phenotyping. Plant Methods. doi: 10.1186/s13007-018-0278-7 Open Access

This UK, German and Italian study is led by Sotirios Tsaftaris at the University of Edinburgh and reports on a fascinating citizen science study that evaluated the ability of experts and non-experts to use plant phenotyping software. They demonstrate that non-experts can be effectively involved in plant phenotyping annotation tasks given enough statistical power and if the study is suitably designed.


Hepworth J, Antoniou-Kourounioti RL, Bloomer RH, Selga C, Berggren K, Cox D, Collier Harris BR, Irwin JA, Holm S, Säll T,Howard M, Dean C (2018) Absence of warmth permits epigenetic memory of winter in Arabidopsis. Nat Commun. doi: 10.1038/s41467-018-03065-7 Open Access

Caroline Dean and Martin Howard (John Innes Centre) lead this study that further characterise the relationship between the VERNALIZATION INSENSITIVE3 (VIN3) an FLOWERING LOCUS C (FLC) genes in two separate thermosensory processes that monitor long term temperature changes. They suggest that the regulatory strategies currently employed by plants might become less effective as the climate becomes more variable and will have a knock-on effect on plant growth and productivity.


Simonini S, Stephenson P, Østergaard L (2018) A molecular framework controlling style morphology in Brassicaceae. Development. doi: 10.1242/dev.158105 Open Access
Lars Ostergaard (John Innes Centre) leads this study that characterises how the activity of five transcription factors (TF) integrate with auxin signaling in the control of gynoecium development. The auxin response factor ETTIN is a central controller of this relationship across members of the Brassicaceae and that variation in an ETTIN sub-domain effects TF affinities, interaction strength and gynoecium morphology


Kriechbaumer V, Maneta-Peyret L, Fouillen L, Botchway SW, Upson J, Hughes L, Richardson J, Kittelmann M, Moreau P, Hawes C

The odd one out: Arabidopsis reticulon 20 does not bend ER membranes but has a role in lipid regulation. Sci Rep. doi: 10.1038/s41598-018-20840-0

This study is led by Chris Hawes (Oxford Brookes) and continues his labs work on the plant ER. They are working on a subgroup of reticulons, which are ER membrane proteins, that have an extended N-terminal domain. Three members of this subgroup show different localisation patterns that indicates that along their sequences are similar they might play different cellular roles.


Williams A, Pétriacq P, Schwarzenbacher RE, Beerling DJ, Ton J (2018) Mechanisms of glacial-to-future atmospheric CO2 effects on plant immunity. New Phytol. doi: 10.1111/nph.15018 Open Access
This article from the University of Sheffield uses Arabidopsis to investigate the impact that changing climatic CO2 concentrations might have on plant immunity. The authors performed a global analysis on the response to sub-ambient and elevated CO2 and found that both changes causes alterations to salicyclic acid or jasmonic acid response pathways. However these responses are not always opposite, revealing new insights in the response to changing CO2 concentrations.


 

Isner JC, Begum A, Nuehse T, Hetherington AM, Maathuis FJM (2018) KIN7 Kinase Regulates the Vacuolar TPK1 K+ Channel during Stomatal Closure. Curr Biol. doi: 10.1016/j.cub.2017.12.046.

This is collaborative work between the Universities of York and Bristol and analyses factors that control stomatal closure. They show the TPK1 vacuolar K+ channel is important for ABA and CO2 mediated closure and that the function of this protein is regulated by the KIN7 receptor-like kinase. These activities result in potassium release from the vacuole leading to osmotic changes that contribute to stomatal closure.


Caviglia M, Mazorra Morales LM, Concellón A, Gergoff Grozeff GE, Wilson M, Foyer CH, Bartoli CG (2018) Ethylene signaling triggered by low concentrations of ascorbic acid regulates biomass accumulation in Arabidopsis thaliana. Free Radic Biol Med. doi: 10.1016/j.freeradbiomed.2018.01.032

Christine Foyer (University of Leeds) is a co-author on this research showing that a defect in ascorbic acid production leads to elevated levels of the hormone ethylene as well as having a wider impact on the control of growth-mediating hormone signalling. This result indicates that the cellular redox buffer AA is a significant contributor to hormone signalling pathways.


Reyna-Llorens I, Burgess SJ, Reeves G, Singh P, Stevenson SR, Williams BP, Stanley S, Hibberd JM (2018) Ancient duons may underpin spatial patterning of gene expression in C4 leaves.Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1720576115

Julian Hibberd (University of Cambridge) is the corresponding author on this study that is part of his labs overarching aim of discovering what is necessary to transfer C4 photosynthesis into C3 plants. As part of this work they are searching for master regulator sequences that have allowed for the multiple independent evolution of C4 photosynthesis. They have identified a regulatory duon that is a pair of cis-elements located in coding sequences of genes preferentially expressed in bundle sheath cells of C4 leaves and are also present in C3 plants and algae. Therefore they discuss how C4 plants have co-opted these regulatory elements and how it might be exploited in future molecular engineering projects.

Arabidopsis Research Roundup: February 12th

This weeks Arabidopsis Research Roundup begins with a study from SLCU that investigates the interaction between nitrate and cytokinin signaling in the shoot meristem. Next is research from Sheffield that studies changes to the macromolecular composition of the photosynthetic apparatus following the transition from dark to light. Third are three papers that include University of Edinburgh faculty members as co-authors; Gary Loake is involved in a global study on NO signaling, Karen Halliday is included on a study into the relationship between clock components and the PIF-mediated hypocotyl elongation and Naomi Nakayama contributes to the development of a model that explains PIN protein localisation. Cyril Zipfel (TSL) is a co-author on the fifth paper, which introduces a new signaling component in the defence response and whilst the penultimate paper includes Denis Murphy (University of South Wales) and investigates the effect of dioxins on seed development. The final paper documents research from Manchester and Nottingham that uses a cress endosperm as a model to test the elastic properties of thin biological membranes.


Landrein B, Formosa-Jordan P, Malivert A,, Schuster C, Melnyk CW,, Yang W, Turnbull C, Meyerowitz EM, Locke JCW,, Jönsson H (2018) Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins. PNAS doi: 10.1073/pnas.1718670115.

Open Access

http://www.pnas.org/content/early/2018/01/22/1718670115

Henrik Jonsson and James Locke (SLCU) are corresponding authors on this investigation into the relationship between nitrate and cytokinin signalling in the Arabidopsis shoot meristem (SAM). They show that nitrate availability determines the size of the SAM, which is controlled by the transport of cytokinin precursors from the root to the shoot. A discussion about this paper with lead author Benoit Landrien and Professor Jonsson is available on the GARNet YouTube and iTunes channels.


Wood WHJ, MacGregor-Chatwin C, Barnett SFH, Mayneord GE, Huang X, Hobbs JK, Hunter CN, Johnson MP (2018) Dynamic thylakoid stacking regulates the balance between linear and cyclic photosynthetic electron transfer. Nature Plants. doi: 10.1038/s41477-017-0092-7

Open with this link

This research in this manuscript has come from the University of Sheffield with Matthew Johnson as the corresponding author. They have used atomic force microscopy (AFM) to investigate how the transition from dark to light affects the macromolecular architecture of the photosynthetic apparatus within the thylakoid membrane. This transition does not alter the antenna size of either photosystem yet increases the number of thylakoid grana. Overall these changes serve to regulate the balance between light harvesting, CO2 fixation and enabling the protection of PSII activity from the destructive effects of non-photochemical quenching.


Imran QM, Hussain A, Lee SU, Mun BG, Falak N, Loake GJ, Yun BW (2018) Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes. Sci Rep. doi: 10.1038/s41598-017-18850-5.

https://www.nature.com/articles/s41598-017-18850-5

Open Access

Gary Loake (University of Edinburgh) is a contributor to this Korean-led manuscript that has performed expression analysis on plants treated with S-nitrosocysteine (CySNO). They have identified many novel NO-responsive transcription factors and were able to confirm the role of three random TFs in this response following analysis of loss of function mutants. This paper provides new insights into the molecular components that contribute to NO signalling during plant defence and immunity.


Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P, Monte E Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2017.12.021

Karen Halliday (University of Ediburgh) is a co-author on this Spanish-led study that investigates how the expression of PHYTOCHROME-INTERACTING FACTORS (PIFs) genes is controlled. The activity of PIFs are responsible for determining the rate of hypocotyl elongation in different light conditions and this paper demonstrates that PSEUDO-RESPONSE REGULATORS PRR9/7/5 proteins act antagonistically to the PIFs by interacting at the promotor of the CDF5 transcription factor. This provides a mechanism to explain the circadian-controlled regulation of hypocotyl cell elongation.


Hernandez V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal Lujan C (2018) A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol. doi: 10.1088/1478-3975/aaac99

Naomi Nakayama (University of Edinburgh) is a co-author on this Mexican-led study that proposes a physico-genetic model that explains the localization of PIN auxin transporter proteins to the Arabidopsis plasma membrane. This model confirms experimental observations and allows the prediction that mechanical forces can predominate over molecular components.


www.cell.com/molecular-cell/fulltext/S1097-2765(17)30983-8

Wang J, Grubb LE, Wang J, Liang X, Li L, Gao C, Ma M, Feng F, Li M, Li L, Zhang X, Yu F, Xie Q, Chen S, Zipfel C, Monaghan J, Zhou JM (2018) A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase. Mol Cell. doi: 10.1016/j.molcel.2017.12.026

This Chinese-led paper includes Cyril Zipfel (TSL) as a co-author and identifies the U-box proteins PUB25 and PUB26 as E3 ligases for the cytoplasmic kinase BIK1, which is a key rate limiting component of the plant defence response. This multi-protein regulatory module provides another level of complexity to our understanding of the molecular factors involved in plant immunity.


Hanano A, Almousally I, Shaban M, Murphy DJ (2018) Exposure of Arabidopsis Plants to Dioxin Results in a Wrinkled Seed Phenotype that is likely due to 20S Proteasomal Degradation of WRI1. J Exp Bot. doi: 10.1093/jxb/ery027

Denis Murphy (University of South Wales) is a co-author on this Syrian-led study that uses Arabidopsis seeds to test the negative effects of dioxins. Seeds treated with dioxins have a wrinked phenotype that corresponds to changes in the expression of genes related to lipid and carbohydrate metabolism. Overall this study reveals a novel set of genetic changes effects caused by dioxins that explain the profound effects on seed development.


S. P. Pearce, J. R. King, T. Steinbrecher, G. Leubner-Metzger, N. M. Everitt, M. J. Holdsworth (2018) Finite indentation of highly curved elastic shells Proceedings of the Royal Society A doi: 10.1098/rspa.2017.0482

Open Access

Plant scientist Mike Holdsworth (University of Nottingham) is a co-author on this paper that has used the endosperm from garden cress (Lepidium sativum) as the experimental model to define the elastic properties of a thin biological surface. Indentation experiments have been classically used to measure these properties and then develop mathematically models that explain their characteristics. These models rely on an assumed flat surface whereas in reality any surface will often be curved. By obtaining measurements from identations studies on the cress endosperm they are able to better refine the models that explain the properties of the membrane in this context.

Arabidopsis Research Roundup: January 23rd.

This weeks Arabidopsis Research Roundup begins with two papers from Royal Hollaway University of London that investigate the factors that control leaf development in the dark and the control of PIN1 phosphorylation. Third is a paper from Bristol that demonstrates the translation of research from Arabidopsis into coriander with regard the control of the response to UV light. Next is research from the John Innes Centre that characterises the role of DNA methylation during meiosis in the male lineage.

Christine Foyer (Leeds) leads the next paper that defines the relationship between cold treatment and strigolactone signalling. The penultimate paper is led by Richard Napier from the University of Warwick and determines the parameters that define the substrates of the AUX1 protein whilst the final paper includes Cyril Zipfel (TSL) as a co-author and uses systems biology approaches to characterise the interactions between leucine-rich repeat receptor kinases (LRR-RKs).


Mohammed B, Farahi Bilooei S, Doczi R, Grove E, Railo S, Palme K, Ditengou FA, Bögre L, Lopez-Juez E (2017) Converging energy and hormonal signalling control meristem activity, leaf initiation and growth Plant Phys doi: 10.1104/pp.17.01730

http://www.plantphysiol.org/content/early/2017/12/28/pp.17.01730.long

Open Access

Enrique Lopez-Juez (RHUL) leads this collaboration with German and Hungarian colleagues that investigates the fundamental question; ‘Why don’t leaves grow in the dark’. They show that this response is influenced by both auxin transport and the plants energy sensing mechanisms. Interestingly when energy is provided via external sucrose, leaves develop differently in the dark than they do in the light indicating that multiple signaling pathways differentially influence this phenotype.

Enrique discusses this paper on the GARNet YouTube page.


Dory M, Hatzimasoura E, Kállai BM, Nagy SK, Jäger K, Darula Z, Nádai TV, Mészáros T, López-Juez E, Barnabás B, Palme K,,, Bögre L, Ditengou FA,,, Dóczi R (2017) Coevolving MAPK and PID phosphosites indicate an ancient environmental control of PIN auxin transporters in land plants. FEBS Lett. doi: 10.1002/1873-3468.12929

Laszlo Bogre and Enrique Lopez-Juez (RHUL) are co-authors on this Hungarian-led study that has discovered 3 conserved putative MAPK sites within the auxin transport protein PIN1. Phosphorylation of two of these sites causes partial loss of PIN1 membrane localization and therefore opposes the effect of the PINOID kinase, whose activity promotes PIN1 membrane localisation.


https://www.nature.com/articles/s41598-017-18073-8

Fraser DP, Sharma A, Fletcher T, Budge S, Moncrieff C, Dodd AN, Franklin KA (2017) UV-B antagonises shade avoidance and increases levels of the flavonoid quercetin in coriander (Coriandrum sativum). Sci Rep. doi: 10.1038/s41598-017-18073-8 Open Access

Keara Franklin and Anthony Dodd (University of Bristol) lead this collaboration between academic researchers and those in the company Vitacress. They translate research from Arabidopsis into Coriander that looks at the effect of UV-B on stem elongation and the interaction with flavonoid signaling. This work shows that alterations to the UV-B regime during growth of potted herbs might reduce deleterious effects caused by neighbour proximity.


Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X (2017) Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat Genet. doi: 10.1038/s41588-017-0008-5

Xiaoqi Feng (JIC) is the corresponding author on this collaboration with James Higgins from Leicester and they investigate the role of DNA methylation in the control of male meiosis. They demonstrate that RNA-directed DNA methylation (RdDM) in the male lineage regulates gene expression in meiocytes and results in the mis-splicing of the MPS1/PRD2 transcipt, which causes aberrant alterations in spindle formation.


Cooper JW, Hu Y, Beyyoudh L, Yildiz Dasgan H, Kunert K, Beveridge CA, Foyer CH (2018) Strigolactones positively regulate chilling tolerance in pea and in Arabidopsis. Plant Cell Environ. doi: 10.1111/pce.13147

Christine Foyer (Leeds) is the corresponding author on this collaboration with Australian, Turkish and South African colleagues that looks into the role strigolactones play during chilling tolerance in both Arabidopsis and pea plants. Plants that have been chilled during the night have reduced biomass, which was not observed in either pea or Arabidopsis strigolactone mutants. This demonstrates a clear role for this hormone in this response and provides a potential target for the manipulation of plant growth under environmental conditions.


Hoyerova K, Hosek P, Quareshy M, Li J, Klima P, Kubes M,, Yemm AA, Neve P, Tripathi A, Bennett MJ, Napier RM (2017) Auxin molecular field maps define AUX1 selectivity: many auxin herbicides are not substrates. New Phytol. doi: 10.1111/nph.14950

onlinelibrary.wiley.com/doi/10.1111/nph.14950/abstract

Together with Czech co-authors Richard Napier (Warwick University) leads this investigation into the mode of action of the AUX1 auxin influx carrier and its substrate preferences. This work made use of a novel auxin accumulation assay and associated mathematical modeling to describe the parameters that make difference auxins to be good candidates for the AUX1 transport. Interesting they find that many commonly used auxinicide herbicides are poor substrates for AUX1 and the relevance of this finding for herbicide management strategies.


https://www.nature.com/articles/nature25184

Smakowska-Luzan E et al (2018) An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Nature doi: 10.1038/nature25184

Cyril Zipfel (TSL) is a co-author on this US-European study that performs a systems-biology analysis on the possible interactions between extracellular domains of the leucine-rich repeat receptor kinases (LRR-RKs) gene family in Arabidopsis. Analysis of 40K potential interactions allows the generation of a LRR-based cell surface interaction network (CSI-LRR). This was used to discover previously uncharacterized interactions between LRR-RKs and to demonstrate that these interactions allow the translocation of extracellular signals in balanced and tightly regulated patterns.

Arabidopsis Research Roundup: January 10th 2018

This Arabidopsis Research Roundup covers the final papers of 2017 and the first of this new year. The initial paper is led by researchers in Bristol and characterises how the multifaceted BIG protein influences stomatal dynamics in response to altered CO2. Second is a manuscript from SLCU that for the first time in plants demonstrates nuclear sequestration of cell cycle regulated mRNAs.

Next is a paper from Rothamsted that describes a role for the hormone GA during floral development. David Salt (Nottingham) is then a co-author on a manuscript that has determined a role for the CTL protein in ion homeostasis.

Seth Davies from York is the lead author on the next study that investigates a link between metabolism and the circadian clock. The sixth paper looks at genes involved in the control of autophagy and features Patrick Gallois (Manchester) as a co-author.

There are three papers from researchers working on Norwich Research Park with Cyril Zipfel (TSL) involved in a study that looks at vacuolar trafficking of BR signaling components. Janneke Balk leads a study that characterises enzymes involved in biosynthesis of metal co-factors whilst the final NRP-based paper from Nick Pullen and Steven Penfield (John Innes Centre) describes the Leaf-GP open software for automated plant phenotyping.

The penultimate paper uses a set of PlantProbes (developed by Paul Knox at Leeds) to study pollen development whilst the final paper from Keith Lindsey (Durham) describes the application of a Bayesian statistical methodology to model the parameters that control a hormone signaling network.


He J, Zhang RX, Peng K, Tagliavia C, Li S, Xue S, Liu A, Hu H,, Zhang J, Hubbard KE,, Held K, McAinsh MR, Gray JE, Kudla J, Schroeder JI, Liang YK, Hetherington AM (2018) The BIG protein distinguishes the process of CO2 -induced stomatal closure from the inhibition of stomatal opening by CO2. New Phytol. doi: 10.1111/nph.14957 Open Access

Alistair Hetherington (University of Bristol) leads this UK-USA-China collaboration that has characterised a role for the mysterious BIG protein during stomatal closure in response to altered CO2 concentration. Interestingly BIG mutants do not show a defect in stomatal opening in response to altered CO2, allowing the dissection of this complex response through the activity of this protein. It remains to be determined exactly how the BIG protein influences this process.


Yang W, Wightman R, Meyerowitz EM (2017) Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells. Mol Cell. doi: 10.1016/j.molcel.2017.11.008

Elliott Meyerowitz (SLCU) is the corresponding author of this research that provides the first characterisation in plants of nuclear sequestration of mRNAs from developmental important genes. The authors show that Arabidopsis anaphase-promoting complex/cyclosome (APC/C) coactivator genes CDC20 and CCS52B are confined to the nucleus in prophase, preventing translation of the cognate proteins until metaphase, which appears to protect cyclins from degradation at an inappropriate phase of the cell cycle


Plackett ARG, Powers SJ, Phillips AL, Wilson ZA, Hedden P, Thomas SG4 (2017) The early inflorescence of Arabidopsis thaliana demonstrates positional effects in floral organ growth and meristem patterning. Plant Reprod. doi: 10.1007/s00497-017-0320-3

This study is led from Rothamsted Research and includes Zoe Wilson from the University of Nottingham. They perform a systematic analysis of early floral organ initiation across the Arabidopsis inflorescence, discovering that both GA-dependent and independent stages are important for this process, albeit via the activity of presently unknown factors.


Gao YQ, Chen JG, Chen ZR An D, Lv QY, Han ML, Wang YL, Salt DE, Chao DY (2017) A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis. PLoS Biol. doi: 10.1371/journal.pbio.2002978

Open Access

David Salt (University of Nottingham) is a co-author on this Chinese-led investigation into the role of the vesicle trafficking regulator choline transporter (CTL) during the control of ionome homeostasis. Using ctl1 mutants they show that this function is required for the action of certain ion transporters as well as during plasmodesmata (PD) development. This study provides novel insights into the role of vesicular transport in the control of ion homeostasis and how the location of these ions might alter vesicle activity.


Sánchez-Villarreal A, Davis AM, Davis SJ (2017) AKIN10 Activity as a Cellular Link Between Metabolism and Circadian-Clock Entrainment in Arabidopsis thaliana.

Plant Signal Behav. doi: 10.1080/15592324.2017.1411448

Seth Davies (University of York) is the corresponding author on this study demonstrating that overexpression of the AKIN10 subunit of the SnRK1 complex results in increased period length of the circadian clock. The authors postulate about the possible links between metabolic rate and function of the clock, allowing them to present a model of action that features each of the central regulatory elements.


Havé M, Balliau T, Cottyn-Boitte B, Dérond E, Cueff G, Soulay F, Lornac A, Reichman P, Dissmeyer N, Avice JC, Gallois P, Rajjou L, Zivy M, Masclaux-Daubresse C (2017) Increase of proteasome and papain-like cysteine protease activities in autophagy mutants: backup compensatory effect or pro cell-death effect? J Exp Bot. doi: 10.1093/jxb/erx482

Open Access
This study is led by French researchers and includes Patrick Gallois (University of Manchester) as a co-author. The work focuses on the role of the ATG genes during autophagy, the key process that controls nutrient recycling during senescence. In atg5 mutants they show that different sets of proteases are misregulated, suggestive of a complex relationship between the enzymes involved in nutrient remobilization.


Liu Q, Vain T, Viotti C, Doyle SM, Tarkowská D, Novák O, Zipfel C, Sitbon F, Robert S, Hofius D (2017) Vacuole Integrity Maintained by DUF300 Proteins Is Required for Brassinosteroid Signaling Regulation. Mol Plant. doi: 10.1016/j.molp.2017.12.015

Cyril Zipfel (TSL) is a member of this Pan-European consortium that investigates the role of the vacuolar proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1) on the cellular cycling of BR-signaling components. Plants with mutations in laz1 and laz1h1 show increased BAK1 accumulation at the tonoplast as well as enhanced BRI1 trafficking and degradation. These DUF300 proteins appear to play a specific role in BR signalling as other vacuolar-associated proteins are not involved in this process.


Kruse I, Maclean A, Hill L, Balk J (2017) Genetic dissection of cyclic pyranopterin monophosphate biosynthesis in plant mitochondria. Biochem J. doi: 10.1042/BCJ20170559 Open Access

Janneke Balk (John Innes Centre) leads this study that has identified novel alleles in mitochondrial enzymes that are involved in the biosynthesis of metal cofactors. Analysis of these enzyme mutant reveals that they show deficiencies in the synthesis of cyclic pyranopterin monophosphate (cPMP), revealing fresh insights into the metabolic processes involving this key intermediate.


Zhou J, Applegate C, Alonso AD, Reynolds D, Orford S, Mackiewicz M, Griffiths S, Penfield S, Pullen N (2017) Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat. Plant Methods. doi: 10.1186/s13007-017-0266-3

Open Access

Nick Pullen and Steve Penfield (John Innes Centre) introduce this new software tool for the automated measurement of plant phenotypes. This Leaf-GP software is open access and has the sophistication to discriminate between different aspects of both Arabidopsis and greenhouse growth wheat.

This paper is back of a special issue of Plant Methods that is based on the use of Computer Vision in Plant Phenotyping.


Ndinyanka Fabrice T, Vogler H, Draeger C, Munglani G, Gupta S, Herger AG, Knox JP, Grossniklaus U, Ringli C (2017) LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development. Plant Physiol. doi: 10.1104/pp.17.01374

Open Access

This Swiss-led study looks into the role of LRX proteins during cell wall formation and how they affect pollen germination and pollen tube formation. The authors took advantage of the molecular tools produced by Paul Knox (University of Leeds) as part of his Plant Probes project.


Vernon I, Liu J, Goldstein M, Rowe J, Topping J, Lindsey K (2017) Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. BMC Syst Biol. doi: 10.1186/s12918-017-0484-3 Open Access

Keith Lindsey (University of Durham) leads this paper that applies a Bayesian statistical methodology to analyse a model of hormonal crosstalk in the Arabidopsis root. They show that this technique can provide new insight into the behavior of models and enables the identification of new interesting rate parameters.

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