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’.

http://www.cell.com/current-biology/references/S0960-9822(17)3101

Andrew also talked to GARNet last year about a paper about stomatal evolution: https://www.youtube.com/watch?v=NvRfzJwKEqo&t=68s

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.

Arabidopsis Research Roundup: October 23rd

Different aspects of plant cell wall biology dominant the first few papers of this weeks Arabidopsis Research Roundup. Firstly Andrew Fleming (University of Sheffield) and colleagues identify that a specific type of cell wall stiffening is important in control of stomatal opening. Secondly are two papers from the lab of Paul Dupree (University of Cambridge) that investigate the role that xylan modifications play in the formation of the cell wall. Finally in this broad area John Runions (Oxford Brookes) and colleagues show that attachment to the cell wall is critical for correct function of the dynamic actin filament network. Elsewhere Jerry Roberts (CPIB) leads a study that looks at proteins that control floral development. Next the group of Alexander Jones  at SLCU has developed an exciting new tool that allows for in vivo visualization of the plant hormone GA. Finally the lab of Phil Wigge (also at SLCU) further expands their work that dissects the signaling pathways that controlling the response to temperature.


Carter R, Woolfenden H, Baillie A, Amsbury S, Carroll S, Healicon E, Sovatzoglou S, Braybrook S, Gray JE, Hobbs J, Morris RJ, Fleming AJ (2017) Stomatal Opening Involves Polar, Not Radial, Stiffening Of Guard Cells. Curr Biol. doi: 10.1016/j.cub.2017.08.006 Open Access

This broad UK collaboration is led by Andrew Fleming at the University of Sheffield and looks into the factors that control stiffening of cell walls in stomatal guard cells. They use Atomic Force Microscopy to show that stiffening of the polar regions of guard cell walls pins down these ends of cells during stomatal opening. This study provides exciting new insights into the importance of cell wall dynamics on stomatal opening and likely has significant agronomic importance.


Grantham NJ, Wurman-Rodrich J, Terrett OM, Lyczakowski JJ, Stott K, Iuga D, Simmons TJ, Durand-Tardif M, Brown SP, Dupree R, Busse-Wicher M, Dupree P (2017) An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls. Nat Plants doi: 10.1038/s41477-017-0030-8

Lyczakowski JJ,,, Wicher KB,, Terrett OM, Faria-Blanc N, Yu X, Brown D,, Krogh KBRM, Dupree P,,, Busse-Wicher M (2017) Removal of glucuronic acid from xylan is a strategy to improve the conversion of plant biomass to sugars for bioenergy. Biotechnol Biofuels. doi: 10.1186/s13068-017-0902-1

Open Access

Paul Dupree (University of Cambridge) is involved in two papers that investigate the chemical decorations that adorn components of the plant cell wall. In the first paper they demonstrate that the incorrect addition of acetyl esters onto xylan prevents the formation of the secondary cell wall due to a reduced interaction between xylan and cellulose microfibrils. They undertake a genetic study to show that the ESKIMO1/XOAT1/TBL29, a xylan-specific O-acetyltransferase is responsive for correct attachment of acetyl esters to xylan.

In the second paper they show that a reduction in the attachment of the acetyl ester glucuronic acid to xylan allows increased isolation of ethanol following saccharification. This has enormous potential significance in ongoing attempts to generate lignocellulose biomass that is more amenable to conversion into potential biofuels.


Tolmie F, Poulet A, McKenna J, Sassmann S, Graumann K, Deeks M, Runions J (2017) The cell wall of Arabidopsis thaliana influences actin network dynamics. J Exp Bot. doi: 10.1093/jxb/erx269.
This collaboration between Oxford Brookes and Exeter Universities looks in details at the Arabidopsis actin filament network using a set of novel imaging tools. In addition they show that the network is distributed when the link to the cell wall is disrupted. As might be expected this also effects the function of the network as evidenced by changes in Golgi body motility.


González-Carranza ZH, Zhang X, Peters JL, Boltz V, Szecsi J, Bendahmane M, Roberts JA (2017) HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS One.

doi: 10.1371/journal.pone.0185106 Open Access

Jerry Roberts (CPIB, Nottingham) leads a collaboration with Dutch and French colleagues to investigate the role of the F-box gene HAWAIIAN SKIRT in control of flower development. This protein acts by interacting with the CUC-SHAPED COTYLEDON 1 (CUC1) and CUC2 transcription factors to restrict petal size by altering cell proliferation and mitotic growth.


Rizza A, Walia A, Lanquar V, Frommer WB, Jones AM (2017) In vivo gibberellin gradients visualized in rapidly elongating tissues. Nat Plants. doi: 10.1038/s41477-017-0021-9

Free with the link: rdcu.be/wnOh

Alexander Jones (SLCU) collaborates with Wolf Frommers’ lab in Stanford to develop a novel tool to analyse the plant hormone gibberellin in planta. This optogenetic biosensor protein allowed them to show that GA levels correlate with cell length in hypocotyl and root tissues. GA levels are dependent on PIF signalling in a relationship that controls rapid tissue elongation in reponse to favourable environmental conditions. We’re pleased to announce that Alexander will be speaking at next September’s GARNet2018: A Plant Science Showcase at the University of York.


Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA (2017) Transcriptional regulation of the ambient temperature response by H2A.Z-nucleosomes and HSF1 transcription factors in Arabidopsis. Molecular Plant doi: 10.1016/j.molp.2017.08.014

Open Access

Phil Wigge (SLCU) leads this work that investigates how the temperature responsive histone variant H2A.Z interacts with heat shock transcription factors (HSFs). They find that the activity of HSFs is able to evict H2A.Z histones yet at non-inducible temperatures these heat responsive genes show an over-representation of H2A.Z-nucleosomes. They demonstrate that this relationship allows plants to be primed to rapidly response to temperature change whilst preventing leaky transcription in times of low temperature.

Daniel Pass talks to GARNet

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Published on: October 16, 2017

Daniel Pass (Cardiff University) discusses his recent paper published in PLoS Genetics entitled ‘Genome-wide chromatin mapping with size resolution reveals a dynamic sub- nucleosomal landscape in Arabidopsis’. Dan highlights his Github page where the code for the novel graphics in this paper are held.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006988

https://github.com/ChromatinCardiff/DanielPassProcessingPipelines

Miriam Gifford talks to GARNet

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Published on: October 9, 2017

Miriam Gifford talks to GARNet about a recent Large Scale Biology paper in The Plant Cell entitled ‘Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time’.
http://www.plantcell.org/content/early/2017/09/11/tpc.16.00961
More on the eFP browser here: http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi

Arabidopsis Research Roundup: October 5th

After a brief hiatus the UK Arabidopsis Research Roundup returns with eight papers that focus on different aspects of Arabidopsis cell biology.

Firstly GARNet PI Jim Murray leads a study that performs a genome-wide analysis of sub-nucleosomal particles whilst Phil Wigge’s lab at SLCU conducts a more focused study on G-box regulatory sequences.

Thirdly Veronica Grieneisen (JIC) and co-workers have modelled the process of boron transport in the root, revealing exciting insights into how traffic jams might form.

Fourthly is a large scale biology paper led by Miriam Gifford (University of Warwick) that looks at the temporal and spatial expression patterns that control lateral root development.

Next Alexander Ruban (QMUL) investigates how low-light acclimated plants respond to high light.

The sixth and seventh studies are led by Alison Baker (Leeds) or Bill Davies (Lancaster) and look at phosphate or hormone signaling respectively.

Finally Gareth Jenkins (University of Glasgow) compares the UV-B signaling module in lower plants with that in Arabidopsis.


Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH (2017) Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1006988

Open Access

GARNet PI Jim Murray is the corresponding author on this study that performs a whole-genome scan of sub-nucleosomal particles (subNSPs) that have been identified using differential micrococcal nuclease (MNase) digestion. They link the position of subNSPs with RNAseq data taken from plants grown in different light conditions. They show that this new technique is able to discriminate regulatory regions that have been obscured by previous experimental procedures and therefore represents a very useful experimental method.


Ezer D, Shepherd SJ, Brestovitsky A, Dickinson P, Cortijo S, Charoensawan V, Box MS, Biswas S, Jaeger K, Wigge PA (2017) The G-box transcriptional regulatory code in Arabidopsis. Plant Physiol. 10.1104/pp.17.01086

Open Access

Phil Wigge (SLCU) is the corresponding author of this study that investigates the sequence elements that are linked to the conserved G-box regulatory motifs. They identify a set of bZIP and bHLH transcription factors that predict the expression of genes downstream of perfect G-boxes. In addition they have developed a website that provide visualisations of the G-box regulatory network (araboxcis.org).


Sotta N, Duncan S, Tanaka M, Takafumi S, Marée AF, Fujiwara T, Grieneisen VA (2017) Rapid transporter regulation prevents substrate flow traffic jams in boron transport. Elife. doi: 10.7554/eLife.27038

Open Access

Veronica Grieneisen (JIC) is the lead author on this detailed analysis of the regulatory circuits that are established during boron uptake in Arabidopsis roots. They used mathematical modelling to show that during boron uptake, swift regulation of transport activity is needed to prevent toxic accumulation of the metal. This system has analogy to the way in which traffic jams of nutrient flow might form and has relevance for regulatory systems outside of plant science. https://www.sciencedaily.com/releases/2017/09/170905104358.htm


Walker L, Boddington C, Jenkins D, Wang Y, Grønlund JT, Hulsmans J, Kumar S, Patel D, Moore JD, Carter A, Samavedam S, Bomono G, Hersh DS, Coruzzi GM, Burroughs NJ, Gifford ML (2017) Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time. Plant Cell. doi: 10.1105/tpc.16.00961

Open Access

Miriam Gifford (University of Warwick) leads this broad consortium that has taken a systems biology approach to better define the environmental factors that control dynamic root architecture. They track transcriptional responses during lateral root development in remarkable detail, looking at individual transcripts. They confirm the idea that the activity of a gene is not simply a function of its amino acid sequence but rather the temporal and spatial regulation of its expression.


Tian Y, Sacharz J, Ware MA, Zhang H, Ruban AV (2017) Effects of periodic photoinhibitory light exposure on physiology and productivity of Arabidopsis plants grown under low light. J Exp Bot. doi: 10.1093/jxb/erx213. Open Access

Alexander Ruban (QMUL) is the corresponding author on this collaboration with Chinese colleagues that examined the effect of high-light stress on low-light acclimated Arabidopsis plants. Initially these plants showed significant photo-inhibition but that they recovered rapidly and after 2 weeks of treatment there was no change in photosynthetic yield. In addition high light acclimated plants showed accelerated reproductive phase change that coincided with higher seed yield.


Qi W, Manfield IW, Muench SP, Baker A (2017) AtSPX1 affects the AtPHR1 -DNA binding equilibrium by binding monomeric AtPHR1 in solution. Biochem J. doi: 10.1042/BCJ20170522 Open Access

Alison Baker (University of Leeds) leads this research that focusses on the binding of the Phosphate Starvation Response 1 (PHR1) transcription factor to regulatory P1BS DNA sequences. They show a tandem P1BS sequence is bound more strongly than a single P1BS site. Ultimately they demonstrate tight regulation of phosphate signaling both by the concentration of phosphate as well as the activity of the interacting SPX protein.


Li X, Chen L, Forde BG, Davies WJ (2017) The Biphasic Root Growth Response to Abscisic Acid in Arabidopsis Involves Interaction with Ethylene and Auxin Signalling Pathways. Front Plant Sci. doi: 10.3389/fpls.2017.01493 Open Access

Bill Davies and Brian Forde (Lancaster University) lead this work that investigates the effect on ethylene and auxin on the biphasic response to ABA during root elongation. They used a range of hormone signalling mutants to show that the response to high ABA is via both ethylene and auzin signalling. In contrast the response to low ABA does not require ethylene signalling.


Soriano G, Cloix C, Heilmann M, Núñez-Olivera E, Martínez-Abaigar J, Jenkins GI (2017) Evolutionary conservation of structure and function of the UVR8 photoreceptor from the liverwort Marchantia polymorpha and the moss Physcomitrella patens. New Phytol. doi: 10.1111/nph.14767

Gareth Jenkins (University of Glasgow) is the corresponding author of this work that looks at the role of the UVR8 UV-B receptor in lower plants. They expressed the versions of UVR8 from a moss or a liverwort in Arabidopsis and showed that although there appears to be differences in the regulation of this protein, the mechanism of UV-B signaling is evolutionarily conserved

SEB/GARNet meeting on Post Translational Modifications.

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Published on: October 5, 2017

GARNet are co-organising this exciting symposium and workshop on plant signalling with post-translational modifications held in Edinburgh 11-13 December 2017.
Abstract deadline: 20 October 2017

Early-bird registration deadline: 3 November 2017

http://www.sebiology.org/events/event/from-proteome-to-phenotype

KEYNOTE SPEAKERS

Matthias Mann (Max Planck Institute of Biochemistry

Ron Hay (University of Dundee)

DYNAMIC PHOSPHORYLATION

Cyril Zipfel (The Sainsbury Laboratory)

Gitta Coaker (UC Davis)

John Christie (University of Glasgow)

PROTEIN SUMOYLATION

Ari Sadanandom (Durham University)

Andreas Bachmair (University of Vienna)

Maria Lois (CRAG Spain)

EMERGING PTMS

Piers Hemsley (University of Dundee)

Markus Wirtz (University of Heidelberg)

Stéphane Ravanel (INRA/CNRS)

UBIQUITIN-MEDIATED PROTEASOME

Steven Spoel (University of Edinburgh)

Luz Irina Calderon-Villalobos (IPB Leipniz)

Emmanuelle Graciet (Maynooth University)

REDOX-BASED PTMS

Gary Loake (University of Edinburgh)

Frank van Breusegem (VIB Ghent)

Daniel Gibbs (University of Birmingham)

TECHNOLOGICAL ADVANCES

Alex Jones (University of Warwick, UK)

Frank Menke (The Sainsbury Laboratory, UK)

Katja Baerenfaller (ETH Zurich, Switzerland)

 

GARNET WORKSHOP ON PLANT PROTEOMICS (13 Dec 2017)

Learn about new technologies and available software for analysis of

proteome samples in a workshop led by Dr. Alex Jones (University of

Warwick). FREE for attendees of the symposium but only 30 spaces

available!!

 

Organising committee: Steven Spoel (University of Edinburgh & GARNet),

Geraint Parry (GARNet), Cyril Zipfel (The Sainsbury Laboratory).

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