GARNet Research Roundup: June 4th

This weeks GARNet Research Roundup begins with a paper from researchers at the University of Dundee, James Hutton Institute, Durham University and the University of Glasgow that characterises a functional role for alternative splicing during the cold response. Second is a paper from Newcastle University that investigates the role of the OXI1 kinase during aphid predation. Third is a paper that includes University of Bristol co-authors that looks at strigolactone signaling in moss whilst the fourth paper from researchers at Leeds and QMUL studies the role of ascorbate during photosynthesis. The final paper from Warwick and York uses gene expression data from pathogen-infected plants to generate a model for predicting a strategy for synthetic engineering of the defence response.

Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo H, Zhang R, Brown JWS (2018) Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell doi: 10.1105/tpc.18.00177.

Open Access

Cristiane Calixto and Wenbin Guo work with John Brown at University of Dundee and the James Hutton Institute and in this large-scale biology paper they characterise the role of alternative splicing (AS) during a stress response. RNAseq was performed on plants exposed to cold stress and they showed that hundreds of genes undergo AS just a few hours after temperature decrease and that this response is sensitive to small changes. The authors propose that AS is a mechanism to fine-tune changes in thermo-plasticity of gene expression and in addition they investigate the activity of the novel splicing factor U2B”-LIKE.

Christiane will discuss this research at the upcoming GARNet2018 meeting held at the University of York in September 2018.

Shoala T, Edwards MG, Knight MR, Gatehouse AMR. OXI1 kinase plays a key role in resistance of Arabidopsis towards aphids (Myzus persicae) (2018) Transgenic Res. doi: 10.1007/s11248-018-0078-x.

Open Access

This work is led by Tahsin Shoala in the lab of Angharad Gatehouse at Newcastle University and demonstrates a novel role for MAPK cascades in resistance to aphid predation. They investigate mutants in OXI1 kinase, a gene that activates MAPK signaling and demonstrate a reduction in the aphid population build-up. Furthermore they show that the effect of OXI works through a mechanism that involves callose deposition, demonstrated as oxi1 mutants lack the upregulation of a set of β-1,3-glucanase genes following predation.

Lopez-Obando M, de Villiers R, Hoffmann B, Ma L, de Saint Germain A, Kossmann J, Coudert Y, Harrison CJ, Rameau C, Hills P, Bonhomme S (2018) Physcomitrella patens MAX2 characterization suggests an ancient role for this F-box protein in photomorphogenesis rather than strigolactone signalling. New Phytol. doi: 10.1111/nph.15214

GARNet committee member Jill Harrison is a co-author on this paper that is led by Mauricio Lopez‐Obando working at Université Paris-Saclay. In Physcomitrella patens development they investigate the role of the moss ortholog of the Arabidopsis strigolactone signaling mutant MAX2. Previous work had shown that moss does response to SL signaing but they find that although Ppmax2 mutants showed defects in early development and photomorphogenesis they do not show changes in the SL response. Fascinatingly this indicates that the molecular components that control SL signaling have diverged in vascular plants and seemingly co-opted a role for MAX2 that was previously not required in mosses.

Plumb W, Townsend AJ, Rasool B, Alomrani S, Razak N, Karpinska B, Ruban AV, Foyer CH. Ascorbate-mediated regulation of growth, photoprotection and photoinhibition in Arabidopsis thaliana (2018) J Exp Bot. doi: 10.1093/jxb/ery170

William Plumb (Leeds) and Alexandra Townsend (QMUL) are the lead authors on this study that investigates the importance of ascorbate during photosynthesis. In this work they analysed the growth of ascorbate synthesis mutants that are smaller and have less biomass than wildtype plants. However these plants have normal levels of non-photoinhibiton, allowing the authors to conclude that ascorbate is needed for growth but not photoprotection.

Foo M, Gherman I, Zhang P, Bates DG, Denby K (2018) A Framework for Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring. ACS Synth Biol. doi: 10.1021/acssynbio.8b00037
Mathias Foo and Iulia Gherman (University of Warwick) are lead authors on work that analyses gene expression data taken from Botrytis cinerea-infected Arabidopsis. They have identified a network of genes involved in the defence response. They validate their model against previously obtained time series data and then perturb the model in two differences ways, focused on the transcription factor CHE. This analysis demonstrates the potential of combining feedback control theory with synthetic engineering in order to generate plants that are resistant to biotic stress.

Monogram 2018 Report: Ben Sibbett

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Published on: May 29, 2018

Ben Sibbett University of Southampton

Attending Monogram 2018 gave me a fantastic insight into the broad range of high quality research that is being conducted in the small grains community. As a PhD student, working on a specific project, it can become easy to neglect research that is outside of your primary focus. In addition, it is easy to lose sight of how your own research fits into the bigger picture and how important it is to understand how your own research can be applied.

Related to applied research, I particularly enjoyed the talk given by the plenary speaker Professor Scott Haley. Professor Haley described how his group is using genomics and bioinformatics to improve wheat varieties for farmers. He touched upon the challenges of working with farmers that are responsible for thousands of hectares of farmland and the enjoyment he has had developing a relationship between scientists and farmers.

Another aspect of Monogram 2018 that I found interesting was the opportunity to learn about how technology and the tools now available to scientists working with crop species have developed. This includes how the latest wheat genome reference is being used to assist research.

Furthermore, learning about the progress that has been made in gene editing at NIAB in rice, wheat and barley was exciting. In addition to gene editing, it was fascinating to find out how the TILLING populations in wheat are now being used widely by researchers. I have used this technology in my own research so it was interesting to see how other groups have taken advantage of this resource.

Ben gives a Flash talk at Monogram 2018

Of real interest was the talk given by James Simmonds from the Uauy lab. He discussed how the generation of double and triple mutants were allowing their group to test hypotheses. He also briefly discussed the notion of speed breeding to reduce the time taken to generate these mutants which could be helpful for my own research.

Attending Monogram also gave me the opportunity to see how other PhD students were getting along in their own projects. With the support of GARNet, I presented a poster at Monogram 2017 in Bristol. This year enabled me to talk to students I had met in Bristol and discuss the progress that had been made in our respective work. I truly enjoyed the MonoGram 2018 meeting and I am extremely grateful for the support of GARNet that has allowed me to attend.

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

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.

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

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.


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

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

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

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.

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.

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