GARNet Research Roundup: May 17th

This weeks GARNet research roundup includes six excellent papers investigating many aspects of Arabidopsis cell biology. Firstly Eirini Kaiserli from Glasgow introduces a novel regulator of blue-light signaling. Second is a paper that analyses the circadian clock with single cell resolution and is led by James Locke (SLCU) and Anthony Hall (Earlham Institute). The next two papers investigate different aspects of hormone signaling, with Keith Lindsey’s group at Durham looking at the relationshop between the HYDRA protein and the auxin response whilst Ottoline Leysers group in Cambridge looks at the link between auxin and cytokinin during shoot growth. The fifth paper from Phillip Mullineaux (University of Essex) provides a genome-wide analysis into the role of HEAT SHOCK TRANSCRIPTION FACTORA1b protein. The final paper from the lab of Piers Hemsley (James Hutton Institute, University of Dundee) should be of interest to many plant molecular biologists as they assess the functional significance of different epitope tags.


Perrella G, Davidson MLH, O’Donnell L, Nastase AM, Herzyk P, Breton G, Pruneda-Paz JL, Kay SA, Chory J, Kaiserli E (2018) ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis. Proc Natl Acad Sci U S A.. pii: 201718099. doi: 10.1073/pnas.1718099115

Open Access

Eirini Kaiserli (University of Glasgow) leads this study that identifies the ZINC-FINGER HOMEODOMAIN 10 (ZFHD10) as a novel regulator of light signaling. ZFHD10 physically interacts with TANDEM ZINC-FINGER PLUS3 (TZP) and these proteins coassociate at promotors that are blue-light regulated. These results reveal of novel mechanism of action for the key multiple signal integrator TZP in the light regulated growth of Arabidopsis hypocotyls.

Eirini discusses this paper on the GARNet YouTube channel.


Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ, Locke JC (2018). Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. Elife. 26;7. pii: e31700. doi: 10.7554/eLife.31700 Open Access

https://elifesciences.org/articles/31700

This paper is led by James Locke (SLCU) and Anthony Hall (Earlham) and investigates the circadian clock at single cell resolution. They use Arabidopsis plants grown in constant environmental conditions to show two desynchronised yet robust single cell oscillations that move both up and down the root. Their results indicate that the clock shows cell-to-cell coupling and they they modeled this relationship to recapitulate the observed waves of activity. Overall their results are suggestive of multiple coordination points for the Arabidopsis clock, which is different from the mammalian system of regulation.


http://dev.biologists.org/content/145/10/dev160572

Short E, Leighton M, Imriz G, Liu D, Cope-Selby N, Hetherington F, Smertenko A, Hussey PJ, Topping JF, Lindsey K (2018) Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell autonomous mechanism in Arabidopsis. Development . pii: dev.160572. doi: 10.1242/dev.160572 Open Access

This collaboration between the research groups of Keith Lindsey and Patrick Hussey at the University of Durham investigates the role of the HYDRA1 (HYD1) sterol Δ8-Δ7 isomerase in epidermal patterning. This tissue shows highest HYD1 expression and hyd mutants have major root patterning defects. Tissue-specific expression of HYD1 indicates that it is involved with some type of non-cell autonomous signaling. Analysis of PIN1 and PIN2 protein expression suggests that auxin might be this functional signal


http://www.plantphysiol.org/content/early/2018/05/01/pp.17.01691.long

Waldie T, Leyser O (2018) Cytokinin targets auxin transport to promote shoot branching. Plant Physiol. 2018 May 1. pii: pp.01691.2017. doi: 10.1104/pp.17.01691.Open Access

This study from the lab of Ottoline Leyser (SLCU) investigates the integration between the plant hormones cytokinin and auxin. They investigate the role of cytokinin in shoot branching through analysis of Arabidopsis Response Regulators (ARRs) mutants. They show arr mutant phenotypes correlate with changes in stem auxin transport mediated by the PIN3, PIN4 and PIN7 efflux carriers, the expression of each respond to cytokinin signaling. Overall this study identifies a novel alternative pathway by which cytokinin impacts bud outgrowth through alterations in auxin transport.


Albihlal WS, Irabonosi O, Blein T, Persad R, Chernukhin I, Crespi M, Bechtold U, Mullineaux PM (2018) Arabidopsis Heat Shock Transcription FactorA1b regulates multiple developmental genes under benign and stress conditions. J Exp Bot. doi: 10.1093/jxb/ery142 Open Access

Phillip Mullineaux (University of Essex) leads this collaboration with French colleagues in a study that investigates the genome-wide targets of the HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) protein. Under non-stress ad heat-stress conditions they showed that 1000s of genes are differentially expressed with a smaller proportion of genes showing different levels of direct interaction. The indirect targets of HSFA1b are regulated through a network of 27 transcription factors and they also provide evidence for the role of hundreds of natural antisense non-coding RNA in the regulation of HSFA1b targets. Overall they show that HSFA1b is a key regulator of environmental cues to regulate both developmental genes and those involved in stress tolerance.


Hurst CH, Turnbull D, Myles SM, Leslie K, Keinath NF, Hemsley PA (2018) Variable effects of C-terminal tags on FLS2 function – not all epitope tags are created equal. Plant Physiol. doi: 10.1104/pp.17.01700 Open Access

This study from the Hemsley lab (James Hutton Institute, University of Dundee) is a cautionary tale on the use and interpretation of results obtained from experiments with commonly-used epitope tags. They assessed the activity of plants containing transgenic FLS2 proteins, which is a receptor-like kinase (RLKs) involved in the defence response. They show that various FLS2 C-terminal epitope fusions reveal highly variable and unpredictable outputs, indicating that the presence of different tags significantly alters protein function. This finding might require a reassessment of many experiments that rely on interpreting the function of epitope-tagged proteins and has significant for many if not all plant molecular biologists.

Reversing the Decline in Plant Science Applications to the BBSRC: analysis and recommendations from GARNet

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Published on: May 14, 2018

GARNet is a community-facing UK network funded by BBSRC through Responsive Mode that supports the delivery of outstanding plant science research. GARNet’s primary focus is supporting researchers who work on fundamental areas of plant science, particularly around the adoption of new technologies and new ways of working. Recently members of the plant science community have expressed concerns about a perceived lack of opportunities to obtain funding for fundamental plant science.

The primary mechanism for obtaining funding of this type comes through BBSRC Responsive Mode funding predominantly via Research Committee B: Plants, microbes, food and sustainability. As a service to the community, GARNet asked the BBSRC to analyse their data regarding the number of plant science applications, which is not in the public domain. The BBSRC found that the number of total plant science applications is declining in line with the number of funded projects. However the number of applications to study aspects of fundamental plant science is declining at a faster rate (Figure 1).

Therefore GARNet investigated the factors that might have contributed to this worrying trend and our findings allowed us to make a series of recommendations outlined below. The discussion and reasoning that led to these recommendations is included in a longer article that is available for download from the GARNet website.

A- showing number of submitted and successful grants from Responsive Mode that propose to work on any aspect of plant science (2014-2017) B- showing number of submitted and successful grants from Responsive Mode that propose to work on an aspect of fundamental plant science (2014-2017). Data provided by BBSRC.

Recommendations

1. GARNet and other UK plant science stakeholders to spread the message that the BBSRC is ‘open-for-business’ to fund world-class grants based on fundamental plant science, including Arabidopsis-only or other plant model-only research.

2. GARNet and other UK plant science stakeholders to encourage the academic community to review Responsive Mode grants and to apply to join Research Committees. Currently, this is a particularly important action point for fundamental plant scientists.

3. GARNet uncovered considerable confusion over what can be considered ‘Impact’ within Responsive Mode proposals. We recommend that BBSRC circulates updated information to potential applicants and Research Committee panel members to clarify what exactly can be considered as ‘Impact’. The BBSRC is providing a piece on this topic for GARNish issue 29, published in Summer 2018.

4. Plant scientists are encouraged to submit their proposal to Research Committee B, but where more appropriate for the proposed research program they are also invited to submit to any of the other Research Committees. Should BBSRC deem it necessary to transfer proposals between committees, they will provide applicants the choice to withdraw their proposal.

5. BBSRC to advise potential applicants that world-class fundamental research is appropriate to be included in relevant GCRF applications, provided that it includes a clear long-term path toward a demonstrable benefit in an ODA country.

6. Given the success of IPAs, we recommend BBSRC reassesses the criteria for evaluating these grants. BBSRC could look into the possibility of capping the number of successful LINK/IPA proposals to a reasonable proportion of funded applications within a single grant round. Grants of sufficient quality would be encouraged to reapply in subsequent funding rounds if they do not fit under the cap in any one round.

7. Plant scientists are encouraged to engage with BBSRC to suggest areas that are relevant for special grant calls. The BBSRC has some flexibility to use Newton Fund and GCRF calls to respond to novel areas of research interest if there is a demonstrable community need.

INDEPTH Short Term Scientific Missions

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Published on: May 11, 2018

The GARNet Coordinator Geraint Parry also acts as the science communication manager of the EU COST Action entitled ‘Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH).

A major part of this activity includes supporting training opportunities for early career researchers. These can take the form of Short Term Scientific Missions (STSMs) and we are currently accepting applications for the 3rd round of STSMs. This call has a deadline of May 31st.

  • STSMs are exchange visits between researchers (PhD student, postdoc or permanent staff) from a COST member country involved in INDEPTH, allowing scientists from the home institution to visit an host institution from another COST member country;
  • These are aimed at fostering collaboration, sharing new techniques and infrastructure that may not be available in other participants’ institutions;
  • STSMs must be a minimum of 5 calendar days and a maximum of 90 calendar days;
  • The should support the Action in achieving at least one its specific objectives listed below:
  1. Generate standardized protocols in 3D imaging of the nucleus (WG1), nuclear proteomics (WG2), chromatin domains (WG2), phenotyping during development & under stress conditions (WG3);
  2. Collect plant data sets in 3D imaging of the nucleus (WG1), nuclear proteomics (WG2), chromatin domains (WG2), phenotyping during development & under stress conditions (WG3);
  3. Perform analyses using the collected datasets to predict the nuclear protein interactome (WG4);
  4. Create new application tools such as new softwares (WG1, WG4), new bioinformatic pipelines to predict Protein-Protein Interactions (PPI) (WG4) and periodicity and distribution patterns (WG4);
  5. Promote synergies between model and cultivated plant species; foster the transfer of knowledge between model and cultivated species and creation of intellectual property in image analysis

More information about this STSM can be download here and the general STSM rules can be downloaded here.

If you require more information then please contact INDEPTH STSM Coordinator Laszlo KOZMA- BOGNAR. 

 

Eirini Kaiserli talks GARNet

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Published on: May 8, 2018

Eirini Kaiserli talks to GARNet about a recent open access paper in PNAS entitled ‘ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis‘.

GARNet Research Roundup: April 27th

This weeks GARNet research roundup features four papers that include Malcolm Bennett (University of Nottingham) as an author. The first three are linked manuscripts that investigate the role of auxin on root hair development that is controlled by varying phosphate levels. Ranjan Swarup provides an audio summary of two of these papers on the GARNet YouTube and podcast feeds.

The fourth paper from Nottingham is a collaboration with GARNet PI Jim Murray (Cardiff University) that characterises the STM gene network and its influence on meristem development.

The fifth paper from the lab of Paul Dupree in Cambridge characterises the stem transcriptome whilst the next paper from Iain Johnston and George Bassel (University of Birmingham) identifies a bet-hedging network that influences seed germination. The final paper features Seth Davies (University of York) as a co-author and investigates the impact of changes in circadian rhythms on short architecture.


Researchers at the University of Nottingham are involved in three back-to-back papers that add a mechanistic framework to the relationship between phosphate and auxin signaling in root hairs.

Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R (2018) A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun. 9(1):1409. doi: 10.1038/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03851-3

Open Access

The first paper is led by Ranjan Swarup and defines components of auxin biosynthetic, transport and signaling pathways that are involved in the change root hair development in response to different phosphate concentrations in Arabidopsis. Ranjan discusses this paper on YouTube.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ (2018). Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun. 9(1):1408. doi: 10.1038/s41467-018-03850-4

https://www.nature.com/articles/s41467-018-03850-4

Open Access

This paper led by Malcolm Bennett uses a rice model to investigate the relationship between auxin and root hair elongation in response to low concentrations of phosphate. They show rice aux1 mutants have significant changes in root architecture.

Dindas J, Scherzer S, Roelfsema MRG, von Meyer K, Müller HM, Al-Rasheid KAS, Palme K, Dietrich P, Becker D, Bennett MJ, Hedrich R (2018) AUX1-mediated root hair auxin influx governs SCF(TIR1/AFB)-type Ca(2+) signaling. Nat Commun. 9(1):1174. doi: 10.1038/s41467-018-03582-5

Open Access

The third paper includes Malcolm Bennett as a co-author and investigates how the auxin transport and signaling pathways stimulate calcium signaling during root hair elongation.


Scofield S, Murison A, Jones A, Fozard J, Aida M, Band LR, Bennett M, Murray JAH (2018) Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development pii: dev.157081. doi: 10.1242/dev.157081

http://dev.biologists.org/content/early/2018/04/12/dev.157081.long

Open Access
GARNet PI Jim Murray is the corresponding author on this manuscript that is led by Dr Simon Scofield and includes collaborators from the University of Nottingham. They have explored the gene regulatory network that is regulated by the key meristem identity gene SHOOT MERISTEMLESS (STM). This network includes an over-representation of transcription factor families, each of which have distinct roles in meristem development. They use in planta experimentation and in silico modeling to investigate the relationship between STM and CUC1 in more detail. Overall this study confirms that STM is a central regulator of shoot meristem function.


Faria-Blanc N, Mortimer JC, Dupree P (2018) A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis. Front Plant Sci. 9:384. doi: 10.3389/fpls.2018.00384

Open Access

Paul Dupree (University of Cambridge) is the corresponding author of this study that uses a range of Arabidopsis cell wall mutants to investigate the stem transcriptome. In plants with defects in xylan synthesis the authors found surprisingly few transcriptional changes. This indicates that once plants have committed to a terminal secondary cell wall program there is little need for transcriptional changes even after cell wall damage.


Johnston IG, Bassel GW (2018) Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis. J R Soc Interface. 15(141). pii: 20180042. doi: 10.1098/rsif.2018.0042.

Open Access
Iain Johnston (University of Birmingham) leads this study that has identified a bet-hedging network that links hormone signaling during Arabidopsis germination. This type of network allows plants to more easily adapt to varying environmental conditions but can preclude maximum growth. In this system the network is based upon the regulation of ABA synthesis, activity and degradation, which is maintained at a constant mean level even though it exhibits significant noise. They investigate the parameters that might be tweaked to reduce variation in germination rate and therefore might be targets for modification in order to maximise responses under particular environmental conditions.

George Bassel who is a co-author on this paper will be speaking at the GARNet2018 Meeting in York in September.

http://rsif.royalsocietypublishing.org/content/15/141/20180042.long

Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C (2018) Circadian rhythms are associated with shoot architecture in natural settings. New Phytol. doi: 10.1111/nph.15162.

Seth Davies (University of York) is a co-author on this study that assesses the effect of circadian rhythms on aerial phenotypes that lead to fruit production in field grown Arabidopsis. This was assessed over two growing seasons and they show that variation in clock function significantly impacts shoot architecture.

Ranjan Swarup talks to GARNet

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Published on: April 23, 2018

Ranjan Swarup (University of Nottingham) discusses a couple of recent papers published in Nature Communications that describe the relationship between phosphate and auxin signaling in the roots of Arabidopsis and rice plants.

https://www.nature.com/articles/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03850-4

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.

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Welcome , today is Tuesday, May 22, 2018