Devin O’Connor talks to GARNet

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Published on: November 30, 2017

Devin O’Connor discusses auxin, PINs and protein instrinic qualities during our discussion of his recent eLife paper entitled ‘Cross-species functional diversity within the PIN auxin efflux protein family’.

Arabidopsis Research Roundup: Nov 24th

The week’s UK Arabidopsis research roundup includes seven papers from groups who work on a range of topics.

Firstly Antony Dodd (Bristol) investigates the role of sugar signaling during hypocotyl elongation and provides an audio description of this groups work. Secondly Mike Holdsworth (Nottingham) leads a paper that demonstrates the importance of the N-rule pathway in the response to abiotic stresses. Thirdly are a set of papers that have developed models on three different topics. Mike Blatt’s group at Glasgow University has a cross-scale model that is applied to stomatal opening whilst Stan Maree and Veronica Griensien (JIC) use modeling to predict how the topology of pavement cells is determined. Finally Arabidopsis is used as an example that fits a model that investigates how critical mutation rate (CMR) changes with population size. In the sixth paper Lorraine Williams and colleagues (University of Southampton) investigate the function of a rice transport protein involved in manganese tolerance by expressing it in Arabidopsis. The final paper from Jerzy Paszkowski (SLCU) outlines a novel screening strategy for retrotransposons and the identification of an ecotype specific element.

Simon NM, Kusakina J, Fernández-López Á, Chembath A, Belbin FE, Dodd AN (2017) The energy-signalling hub SnRK1 is important for sucrose-induced hypocotyl elongation. Plant Physiol. doi: 10.1104/pp.17.01395

Open Access

This UK-wide collaboration is led by Anthony Dodd at the University of Bristol and has looked at the factors that control hypocotyl elongation in response to sugar signalling. This response is integrated through the sugar-signalling hub, SnRK1 and is regulated by trehalose-6-phosphate (Tre6P). They also integrate hormone signalling and the influence of diurnal rhythms into the control of this process, importantly showing that the ubiquitous sugar regulator hexokinase is not involved in this process.

Antony kindly provides an audio description of this research that can be found on YouTube or on the GARNet iTunes channel. Please subscribe!

Vicente J, Mendiondo GM, Movahedi M, Peirats-Llobet M, Juan YT, Shen YY, Dambire C, Smart K, Rodriguez PL, Charng YY, Gray JE, Holdsworth MJ (2017) The Cys-Arg/N-End Rule Pathway Is a General Sensor of Abiotic Stress in Flowering Plants. Current Biology doi: 10.1016/j.cub.2017.09.006

Open Access

Mike Holdsworth (University of Nottingham) is the corresponding author of this collaboration with colleagues from Sheffield, Spain and Taiwan that investigates how the N-rule degradation pathway acts a sensor of general abiotic stress in both Arabidopsis and Barley. These responses are integrated through degradation of the group VII Ethylene Response Factor transcription factors (ERFVIIs) family via direct and indirect pathways. In addition they link ERFVII activity with chromatin-remodeling ATPase BRAHMA providing evidence for a single mechanism that links the responses to a number of environmental signals.

Wang Y, Hills A, Vialet-Chabrand SR, Papanatsiou M, Griffiths H, Rogers S, Lawson T, Lew V, Blatt MR (2017) Unexpected Connections between Humidity and Ion Transport Discovered using a Model to Bridge Guard Cell-to-Leaf Scales. Plant Cell. doi: 10.1105/tpc.17.00694

Open Access

Mike Blatt (University of Glasgow) leads this collaboration with researchers at the Universities of Cambridge and Essex. They have developed the OnGuard2 quantitative systems platform that integrates numerous parameters that control guard cell dynamics across many scales including at molecular, cellular, tissue and canopy levels. They experimentally demonstrate that OnGuard2 faithfully reproduces the kinetics of real stomatal movement and therefore that this modeling is able to bridge the micro-macro divide.

Carter R, Sánchez-Corrales YE, Hartley M, Grieneisen VA, Marée AFM (2017) Pavement cells and the topology puzzle. Development. doi: 10.1242/dev.157073

Stan Maree and Veronica Griensien (John Innes Centre) lead this study that has looked at the patterning of 50000 Arabidopsis pavement cells to understand the topological signatures that exist in this population. They have developed a heuristic cellular division rule to produce a model that can reproduce their observations by predicting how these cells divide. They confirmed their model by tracking 800 mitotic events, allowing them to conclude that distinct topology is not a direct consequence of the jigsaw-like shape of the cells, but rather owes itself to life-history-driven process, with limited impact from cell surface mechanics.

Aston E, Channon A, Belavkin RV, Gifford DR, Krašovec R, Knight CG (2017) Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover. Sci Rep. doi: 10.1038/s41598-017-14628-x

Open Access

In this study a team of computational biologists from Keele, Middlesex and Manchester have used Arabidopsis as an exemplar to understand how critical mutation rate (CMR) provides insights into the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness. They have produced a simulation for these parameters that predicts outcomes for a range of biological organisms, showing that CMR decreases with reduced population size. They suggest that the model can be used to understand the conservation strategies exhibited in populations that are approaching extinction.

Farthing EC, Menguer PK, Fett JP, Williams LE (2017) OsMTP11 is localised at the Golgi and contributes to Mn tolerance. Sci Rep. doi: 10.1038/s41598-017-15324-6
Lorraine Williams (University of Southampton) and her colleagues have identified a transporter protein from rice, OsMTP11 that is involved in mangenase tolerance. They show that heterologous expression of this protein is able to rescue the manganese sensitive phenotype of Arabidopsis mtp11-3 knockouts. They show that OsMTP11 localises to the Golgi and have also conducted site directed mutagenesis to identify key residues that are important for the function of this protein.

Griffiths J, Catoni M, Iwasaki M, Paszkowski J (2017) Sequence-independent identification of active LTR retrotransposons in Arabidopsis. Mol Plant. doi: 10.1016/j.molp.2017.10.012

Open Access

Jerzy Paszkowski (SLCU) leads this single-figure short manuscript that has characterised the population of retrotransposons in Arabidopsis. They develop a novel cost-effective screening strategy that allows them to identify sequences found on extrachromosomal DNA (ecDNA), which includes a retroelement found in Lansberg erecta but not in the reference genome ecotype Col-0.

Anthony Dodd talks to GARNet

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Published on: November 24, 2017

Anthony Dodd (Universit of Bristol) talks to GARNet about a recent paper published in Plant Physiology entitled ‘The energy-signalling hub SnRK1 is important for sucrose-induced hypocotyl elongation‘.

iGEM 2017

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Published on: November 17, 2017

The giant jamboree that marks the end of the 2017 International Genetically Engineered Machine (iGEM) competition was again held in Boston, USA in mid November. This unique event brings together up to 3000 students who present, demonstrate and discuss the novel research projects that they have worked on for the past year. These synthetic biology projects can be on any conceivable (safe) topic and are usually supported by academic institutions who, along with a range of sponsors, supply teams with up to £50K to fund the research, registration costs and transport.
The overall number of iGEM teams continues to rise with 295 having their entries finally accepted in 2017. Perhaps notably, 2017 is the first in which the number of Chinese teams was greater than those from the host nation. The number of UK teams has remained static over the past three years, with the identity of competing institutes often changing, no doubt caused by the high financial cost and time commitment needed to support projects and to send a group of students to Boston. Only Edinburgh, Exeter, Glasgow, Kent, Oxford, Sheffield, UCL and Warwick have supported teams in each of the past 4 years since the final jamboree moved to Boston.

The number of projects entered in the ‘Environment Track’ again increased this year and it was notable at this jamboree that there was an increased focus on ideas that involve plant science. Although this hasn’t translated into a significant increase in the number of projects that are actually working WITH a plant synbio chassis, there is certainly an increased focus on finding solutions to global and local challenges that use plant-derived solutions. An example of this is from WashU St Louis whose project’s ultimate goal was to improve plant resistance to damaging UV-B radiation. Although they discussed a possible collaboration with the Cardiff_Wales team who were using transient tobacco expression system as their experimental chassis, their work did not progress further than characterizing their gene circuit in E.coli, which provided resistance to UV-B in that system. This type of project was more common than ever before, where bacterial synthetic biology was used as a starting point to tackle global problems that might ultimately involve plant science.

However it was again pleasing to learn about some outstanding plant synbio projects. The plant synthetic biology lab in Valencia led by Diego Orzaez again excelled in this area, building hardware to monitor changes in plant growth in response to stress, a PlantLabCo software tool and also developing a root-expressed red-light sensor. Information about each of the Valencia projects from the past 4 years can be found here.

Arguably the most impressive plant project, and eventually winner of the Plant Synthetic Biology track, was from the UESTC-China team who had generated stably transformed tobacco plants expressing three biosynthetic enzymes. This Phytoremediation-based project was designed to remove the industrial atmospheric pollutant TCP. Lab experiments showed that transgenic leaf extracts were able to convert TCP to glycerol, demonstrating clear proof of concept. However during questioning the challenge of this (and many other) iGEM project was clear; the issue of scalability. How many tobacco plants would be needed to effectively reduce pollutants and where would these plants be grown? These questions were beyond the scope of this project and yet due to the required extra investment and future research time needed to provide satisfactory solutions they might remain forever unanswered.
Elsewhere it was great to learn about the project from SECA-NZ who had managed to stably transform Arabidopsis plants with a frost-responsive gene from an Arctic plant, not an insubstantial task for a 6-month project!!

iGEM is a fantastic breeding group for innovative, with the competition allowing students to gain research and project management skills that set them on the path to careers in research or entrepreneurship. Synbiobeta is a partner sponsor of the event and during his final address iGEM president Randy Rettberg encouraged iGEMers to go out and ‘find the money’. iGEM also very strongly encourage responsible innovation so hopefully these messages can be successfully interwoven in future projects that the iGEM students will develop.

With UK synthetic biology heavyweights Imperial College (the 2016 overall winners) and Cambridge University absent from the 2017 competition, the UK community looked to others to pick up their slack….and they did so with some significant success! University teams from Exeter (overgrad Environment, Applied Design), Glasgow (undergrad, Food and Nutrition), Oxford (undergraduate Diagnostics), Edinburgh (overgrad Therapeutics) and Kent (undergrad Poster) all won ‘Track awards’ whilst Newcastle OG, Edinburgh UG, Manchester OG and Cardiff UG were also nominated for awards. This strong showing is only possible due to the matched funding that many teams receive from the BBSRC, SEB, Welcome Trust and Society of Microbiology.

iGEM is what it is, a tremendous international melting pot of ideas that is a fantastic experience to all those who participate. The competitive element can be challenging to assess with all teams judged equally with no consideration as to the level of institutional support, available financial resources, team size or length of project. Winning a medal or prize is ultimately a test of those parameters that might sit outside the actual research project so each team should take pride in what they have achieved within the limits of their ambition.


The experiences gained by being involved in a nine-month (or more) multi faceted research project that culminates in a global conference are not found easily elsewhere!

Andrew Fleming talks to GARNet

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Published on: November 2, 2017

Andrew Fleming (University of Sheffield) talks to GARNet about a recent paper published in Current Biology entitled ‘Stomatal Opening Involves Polar, Not Radial, Stiffening Of Guard Cells’.

Andrew also talked to GARNet last year about a paper about stomatal evolution:

Andrew mentioned the excellent Plant Probes resource during the talk.

Arabidopsis Research Roundup: November 1st.

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Published on: November 1, 2017

This weeks Research Roundup includes three research and two methods papers. Firstly is work from the O’Connor and Leyser groups at SLCU that investigates the diversity of function in PIN auxin transporters between monocots and dicots. Secondly research from the Kover lab at the University of Bath has characterised the photosynthetic contribution of the inflorescence stem whilst the third paper is from the Bill Finch-Savage at the University of Warwick and looks at the effect of temperature on seed dormancy. Finally are two methods paper from the University of Warwick and Leeds that introduce protocols for the imaging of either the endoplasmic reticulum or the ultrastructure of pollen tubes.

O’Connor DL, Elton S, Ticchiarelli F, Hsia MM, Vogel JP, Leyser O (2017) Cross-species functional diversity within the PIN auxin efflux protein family. Elife. doi: 10.7554/eLife.31804

Open Access

Devin O’Connor and Ottoline Leyser (SLCU) lead this research that bridges the divide between a model dicot (Arabidopsis) and a model monocot (Brachypodium)as they investigate mechanisms of auxin transport, focussed on the PIN protein family. Arabidopsis lacks a clade of PIN proteins (termed Sister-of-PIN1 (SoPIN1) that are found in other plant species. They show that Brachypodium sopin1 mutants have inflorescence defects similar to Arabidopsis pin1 mutants, a similarity of function that is confirmed by the ability of soPIN1 to rescue the phenotype of null Atpin1 plants. However Brachy PIN1 is only able to rescue a less severe Atpin1 mutant. Overall they demonstrate that PIN1 functional specificity is determined by membrane and tissue-level accumulation and transport activity. As this paper is published in Elife, the journal provides reviewer comments and in this case they show that this manuscript was initially rejected. However the authors persisted and provided a reworked manuscript that convincing the reviewers that this study was appropriate for publication in Elife. An excellent lesson in persistence!

Gnan S, Marsh T, Kover PX (2017) Inflorescence photosynthetic contribution to fitness releases Arabidopsis thaliana plants from trade-off constraints on early flowering PLoS One doi: 10.1371/journal.pone.0185835

Open Access

In this study from Paula Kover’s lab at the University of Bath they investigate how the photosynthetic capacity of the Arabidopsis influoresence influences the time of flowering in a range of accessions. Interestingly after plants had flowering the authors removed rosette leaves to assess the ability of the influoresence to support future plant growth. Surprisingly there was a wide variation in general fitness following leaf removal, ranging from a growth reduction of 65% to no observed loss in fitness. These changes are due to both the differencies in the flowering time and in the number of lateral branches. This can explain how early flowering accessions can maintain fitness despite reduced vegetative growth.

Huang Z, Footitt S, Tang A, Finch-Savage WE (2017) Predicted global warming scenarios impact on the mother plant to alter seed dormancy and germination behavior in Arabidopsis Plant Cell Environ. doi: 10.1111/pce.13082

William Finch-Savage (University of Warwick) leads this investigation into the effect of temperature on seed development and dormancy. They used specially designed polyethylene tunnels that allowed in vivo variations in temperature and light conditions. Perhaps unsurprisingly they showed that temperature plays a significant role in future seed development with lower temperatures promoting dormancy but higher temperatures reduced dormancy that subsequently alters the timing of future life cycles, which has consequences for the species fitness.

Dzimitrowicz N, Breeze E, Frigerio L (2018) Long-Term Imaging of Endoplasmic Reticulum Morphology in Embryos During Seed Germination. Methods Mol Biol. doi: 10.1007/978-1-4939-7389-7_6

Lorenzo Frigerio (University of Warwick) leads this methods paper that describes the imaging of the endoplasmic reticulum over long periods during seed germination.

Ndinyanka Fabrice T, Kaech A, Barmettler G, Eichenberger C, Knox JP, Grossniklaus U, Ringli C (2017) Efficient preparation of Arabidopsis pollen tubes for ultrastructural analysis using chemical and cryo-fixation. BMC Plant Biol. doi: 10.1186/s12870-017-1136-x

Paul Knox (University of Leeds) is a co-author on this methods paper that outlines the necessary steps for efficient preparation of pollen tubes for subsequent ultrastructural analysis.

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