Multi-scale biology Archives - Weeding the Gems

Arabidopsis Research Report: May 26th

Categories: Arabidopsis, Audio, Cambridge University, CPIB, Edinburgh University, GARNet, Global, John Innes Centre, Multi-scale biology, University of Oxford

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Published on: May 26, 2016

This weeks Arabidopsis Research Roundup includes six studies across a range of discplines. Firstly Alison Smith provides an excellent audio description of an investigation into the dynamics of night-time starch degradation.

Secondly three UK institutions (Durham, Exeter and Oxford Brookes) participate in a study of VAP27 membrane network proteins. Next a broad collaboration from CPIB in Nottingham then introduce a multi-scale model that helps describe Arabidopsis root development.

We also include two studies that involve collaborations with Korean researchers: Gary Loake is a contributor on a study that introduces plant RALF genes whilst Ian Henderson’s research group participates in a study into the function of the SWR1 complex in miRNA gene expression. Finally we highlight a new Plant Cell teaching tool put together by UK academics from Hull and Bristol.

Feike D, Seung D, Graf A, Bischof S, Ellick T, Coiro M, Soyk S, Eicke S, Mettler-Altmann T, Lu KJ, Trick M, Zeeman SC, Smith AM (2016) The starch granule-associated protein EARLY STARVATION1 (ESV1) is required for the control of starch degradation in Arabidopsis thaliana leaves Plant Cell

http://dx.doi.org/10.1105/tpc.16.00011 Open Access

This UK and Swiss study is led by Alison Smith from the John Innes Centre and investigates starch degradation that occurs during nighttime. They developed a novel screen to identify an uncharacterized mutant called early starvation 1 (esv1) that more rapidly degraded starch so that it is exhausted earlier in the night. They found that ESV1 and the related LESV1 proteins associated with starch granules within the chloroplast stroma. The authors propose that these proteins influence the organisation of the starch granule matrix, facilitating access for starch-degrading enzymes. In addition they also show that this function appears to be conserved throughout all starch-synthesizing organisms.

Professor Smith provides an audio description of this paper:

Wang P, Richardson C, Hawkins TJ, Sparkes I, Hawes C, Hussey PJ (2016) Plant VAP27 proteins: domain characterization, intracellular localization and role in plant development. New Phytol. 210(4):1311-1326 http://dx.doi.org/10.1111/nph.13857

This cell biology-focused study is a collaboration between the Universities of Exeter, Durham and Oxford Brookes and investigates vesicle-associated membrane protein-associated proteins (VAPs), which form part of the network that links the plasma membrane and ER. The Arabidopsis genome contains 10 VAP homologues (VAP27-1 to -10) split into 3 clades. Members of clades I and II localise to both ER as well as to ER/PM contact sites (EPCSs) whilst clade II members are only found at the PM, all discovered through transient expression experiments in tobacco. Interestingly the localisation to the EPCSs is associated with the cytoskeleton but does not require the presence of that underlying structure. These proteins are expressed in most cell types and when their levels are altered, plants show pleiotropic phenotypes. Overall this study shows that VAP27 proteins are required for ER-cytoskeleton interactions that are critical for normal plant development.

Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J (2016) A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol. S0022-5193(16)30070-4 http://dx.doi.org/10.1016/j.jtbi.2016.04.036

From http://dx.doi.org/10.1016/j.jtbi.2016.04.036

This investigation was performed at CPIB in Nottingham in collaboration with the Virtual Plant Project in Montpellier and is led by John King. The authors have developed a multi-scale computational model that allows the study of signalling networks that occurs during Arabidopsis root growth. This model was experimentally tested to investigate how it is affected by hormonal changes during root growth. The model was able to identify two novel mutants that significantly alter root length through perturbations in meristem size. In general this study demonstrates the value of multi-scale modeling as part of the process of evaluating the function of the components that define the formation of the root meristem.

Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW (2016) Comprehensive analysis of plant rapid alkalization factor (RALF) genes Plant Physiol Biochem. 106:82-90

http://dx.doi.org/10.1016/j.plaphy.2016.03.037

This Korean-led study includes a contribution from Gary Loake from the University of Edinburgh and is the first comprehensive investigation of Rapid alkalization factor (RALF) proteins across plant species. These RALF proteins are thought to be important signalling molecules in plant defense and development. This study provides information on gene structure, subcellular locations, conserved motifs, protein structure, protein-ligand interactions and promoter analysis across Arabidopsis, rice, maize and soybean. The RALF genes are phylogenetically divided into 7 clades and their mRNA upregulation following nitrosative and oxidative stresses suggests that they are function in responding to changes in cellular redox status. Overall this manuscript provides a valuable resource to prime future research into the role of RALF genes.

Choi K, Kim J, Müller SY, Oh M, Underwood C, Henderson I, Lee I (2016) Regulation of microRNA-mediated developmental changes by the SWR1 chromatin remodeling complex in Arabidopsis thaliana. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00332

GARNet committee member Ian Henderson (Cambridge) is a contributor on this study that is led by researchers in Seoul, South Korea. In the last ARR, Vinod Kumar described work that looked into the role of the SWR1 chromatin-remodeling complex and this study provides an insight into the role of this same SWR1 complex on microRNA (miRNA)-mediated transcriptional control. In SWR1 complex mutants (arp6, sef, and pie1), deep sequencing revealed that many miRNA types and their target mRNAs are misregulated. This further establishes the role of the SWR1 complex in the control of nucleosome occupancy, likely by mediating the exchange of H2A isoforms, for a range of genes involved in the fine-tuning of numerous developmental processes.

Hubbard, K, Dodd, A. (2016). Rhythms of Life: The Plant Circadian Clock. Teaching Tools in Plant Biology: Lecture Notes. http://dx.doi.org/10.1105/tpc.116.tt0416

Katherine Hubbard and Anthony Dodd have produced a teaching resource focused on the Circadian Clock as part of the increasingly comprehensive Plant Cell Teaching Tools. Most academics are looking to save time and this resource will allow them to do this and provides excellent coverage of the topic.

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Multi-scale Biology Meeting.

by Geraint

Categories: Arabidopsis, bioinformatics, Celebrating Basic Plant Science, conferences, John Innes Centre, Multi-scale biology

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Published on: June 2, 2015

What is Multi-scale Biology?

That was the overriding question that occupied attendees of the inaugural meeting of the Multi-scale Biology Network, held at the University of Nottingham on June 1^st 2015. This newly funded BBSRC network brought together biologists, physicists, engineers, and the funding bodies (amongst others) for this meeting that aimed to set the agenda for this area of future collaboration. Storify of the meeting.

Those who had also been involved in the genesis of synthetic biology policy might have felt a touch of deja-vu over the questions being asked at this meeting. However whereas the term ‘synthetic biology’ might have remained opaque after those early meetings, the feeling at the end of this day was that good progress had been made into an understanding of what this network might achieve.

Although there were <a href="http://www.multiscalebiology.org.uk/events/event/springboard/" onclick="_gaq.push(['_trackEvent', 'outbound-article', 'http://www cialis 20mg en france.multiscalebiology.org.uk/events/event/springboard/’, ‘speakers from a range of biological disciplines’]);” target=”_blank”>speakers from a range of biological disciplines there was no requirement for forced interactions between different research areas. Instead there was a sense of ‘wondering what can be learnt‘ when for example, plant scientists talked to neurobiologists…

The meeting was kicked off by Professor Markus Owen from the Nottingham Maths department and the agenda had been clearly designed to encourage significant amounts of discussion, be it during the lecture period or over an extended lunch in which attendees split into small groups to discuss challenges in MSB.

Many of the attendees were involved in some form of systems biology so the sense was that MSB comes as the natural extension of that area of research. Instead of looking at a single network, how should researchers extend their thinking to include how these networks interact at different scales…..without losing the quality of analytic data?

Professor Alfonso Martinez-Arias (Cambridge) led the first discussion and made the important point that even though we now have enormous amounts of data, what is it we actually want to learn?….and is focusing on that type of question compatible with current necessity for publication in high quality journals?

Immediately after lunch Professor Carole Goble introduced a new ERASysApp network (FAIRdom) in which she is involved that aims to ensure that systems biology projects make their data, operating procedures and models, Findable, Accessible, Interoperable and Reusable (FAIR). This was a timely reminder that it is very important to produce data that is reusable by the community so that people aren’t reinventing the wheel in each experiment. In 2016 GARNet will be hosting a meeting with the Exeter Centre for the Study of Life Sciences that will address issues surrounding data reuse. Details to follow later in 2015!

Toward the end of the day Professor Martin Howard from the John Innes Centre led the final discussion that attempted to coalesce the thoughts of attendees. One suggestion was for biologists to act ‘like engineers’ and to use ‘dirty tricks’ as to get tasks completed. Understanding the details can come later…. getting the job done is most important….. whatever the job is that needs to be done! It was also discussed that coming to any ‘effective theory’ of biology is almost impossible given the unpredictable nature of the field.

The results of group discussions!

Overall it seems that making any decisions about how multi-scale biology projects can be implemented will depend on the funding environment. To that end Michael Ward from the EPSRC stressed that mathematical biology is important for mathematical science funding and urged attendees not to be put off from looking in their direction. Ceri Lyn-Adams from the BBSRC informed the group that although there wasn’t any money specifically ring-fenced for MSB, they welcome applications in this area under existing mechanisms. What was clear is that MSB and systems biology remain in the forefront of BBSRC funding strategy!

By it’s very nature MSB will require large projects that might bring together a few responsive mode-size projects under a single umbrella. Hopefully new researchers will be able to be involved in this type of project and the money doesn’t all go to large established groups.

Plant Scientists were well represented at the meeting most notably by Martin Howard, Malcolm Bennett and Leah Band, who gave the final talk of the day. The multi-scale nature of plant biology was highlighted in this more than any other talk, as Leah discussed biology at the organismal, tissue, network, cellular and enzyme level. Her work builds the prior knowledge of GA transport and biosynthesis to make mathematical models to predict tissue expansion.

Importantly for the GARNet community, the take home message from the meeting was that plant scientists will play a major role in the future of multi-scale biology so once the funding opportunities are revealed they should not be reticent in submitting bids.

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