Weeding the Gems - Page 50 of 67 - the GARNet community blog

Plant science – making an impact on scientific publishing

Tags: GARNet, genomics, New Phytologist, Science, TGAC

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Published on: September 5, 2013

This year is proving to be a good year for plant science publications. So far there have been special plant science issues in Science and Genome Biology (and I have it on good authority that there will be plant synthetic biology special issue of another journal coming soon) as well as a landmark birthday for New Phytologist.

Special Issues for Plant Science

The open access journal Genome Biology published their Plant Science Special Issue in June 2013. It was guest edited by Mario Caccamo, acting director and Head of Bioinformatics at The Genome Analysis Centre. He discusses the issue and explains the importance of plant genomics, alongside Dale Sanders and other experts, in this podcast from Biome, BMC’s online magazine. The special issue itself features a whole host of UK researchers, including Cristobal Uauy, Sebastian Schornack, Anna Amtmann and Edgar Huitema.

The Science Special Issue, published just last month, unsurprisingly had a much broader focus – Smarter Pest Control. The featured reports take a global look at issues surrounding crop protection from pests, including RNAi-based pesticides, possible health problems caused by traditional pesticides, and tracking the effects of pesticides in wild animal populations.

New Phytologist Celebration

The Lancaster based journal New Phytologist, founded in 1902, is celebrating 200 volumes in October. By my reckoning, it’s the second oldest plant science journal in the world, after Annals of Botany which began life in 1887 as the Journal of Botanical Science (special mention for strictly botany journal, Flora). There is an incredible celebratory Virtual Special Issue of New Phytologist available here, featuring historic articles from throughout the journal’s lifetime including a 1904 critique of the then fashionable field of plant-based ecology from the great man himself, Sir Arthur Tansley.

Arabidopsis UK research roundup

On a related more local note, our new team member Lisa has been searching the literature each week for publications from UK Arabidopsis or other basic plant science researchers. She’s posting the Arabidopsis Research Round-up to the GARNet News pages, so check it out if you want to keep up with new research from your UK colleagues. If you’ve been published and want to make sure we spot your paper (we’re not perfect!), feel free to email Lisa at lisa@garnetcommunity.org.uk to let her know.

Education and Outreach at Plant Biology 2013

by Charis Cook

Categories: conferences, resource, teaching resources

Tags: Plant Biology 2013

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Published on: August 30, 2013

At Plant Biology 2013, I gave a talk in the Education and Outreach minisymposium, and was in inspiring company.

Vision and Change in Undergraduate Education

Plant science lecturers Nitya Jacob and Thomas Jack gave an overview of the 2011 report Vision and Change in Undergraduate Biology Education (download it here) and PULSE, the initiative set up to address issues raised in the report. They are both US-specific but the principles apply to the UK, and any lecturer from wanting to expand their teaching methods would definitely benefit from looking at the report and PULSE resources.

The report itself looked at the reasons for ‘leaky pipeline’ to a bioscience degree. According to the report, roughly half of students entering college intending to major in biosciences graduate in biosciences – the rest either change courses or drop out of education all together.

ASPB joined with other stakeholders including US biology funders NSF, NIH, and HHMI to set up the PULSE Community to improve undergraduate biology education. Jacob and Jack are both PULSE teaching fellows, a group of university educators who are driving change in undergraduate biosciences education. They are encouraging university departments to commit to the PULSE Vision and Change Rubrix (link to an extremely dry PDF), a set of standards in core concepts, integration of core competencies, assessment, and faculty support.

The Rubrix are designed to be flexible, but meeting them even halfway is impossible with typical courses made up of a lecture-essay-labs-worksheet structure. The Vision and Change toolkit helps lecturers who have committed to the rubrix by suggesting teaching methods including active learning and flipped classes.

Another undergrad teaching tool

Something to consider when teaching undergraduates maths and statistics, and no doubt a valuable tool for US lecturers committed to Vision and Change, are the online MathBench modules, which Christine Fleet presented during the session. The MathBench site is free to use and contains interactive teaching modules on nine broad themes. For example, the Measurement theme includes basic lab techniques, logs and pH, while the Probability and Statistics theme spans bar graphs, standard error and advanced Punnett Squares to understand linked genes and recombination.

Something for teachers and science outreach activists

Miranda Haus presented the education and outreach resources she and her fellow University of Illinois PhD students have developed. The Plants iView team take interactive plant science to after school clubs, and Haus admitted her own surprise at how popular the program had proved – the students in the after school club could chose from a lot of activities including different sports, arts and watching films, but the Plants iView sessions were always full (group size is limited) and students stayed for the duration, and often returned on another day. Some of the activities the PhD students run can be downloaded on the Lessons page.

Technical writers and Pathways to Impact

by Charis Cook

Categories: funding, resource

Tags: BBSRC, funding, Pathways to Impact

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Published on: August 20, 2013

Last week I attended a workshop for e-Infrastructure trainers hosted by the Software Sustainability Institute. As you may know, I am no e-Infrastructure trainer, but training in computing, software, and data analysis definitely affects plant scientists, so there I was. I learned a lot and found some resources to share with the GARNet network in the next few weeks as they become available. However, I also learned something about RCUK funding that is totally non-related to e-Infrastructure training: Technical writers are a suggested expenditure in your Pathways to Impact in RCUK grant proposals.

The Checklist for Completing the Impact Summary and Pathways to Impact (see also this RCUK webpage) lists this as an option:

And the Impact Requirements FAQ state that:

Science outreach, informing public policy or legislation, and skills transfer are all allowed in Pathways to Impact – so long as they are directly related to the proposed research and beyond expected academic output, like publishing papers and going to conferences (see the links above for more details). So plant scientists might use technical writers for:

Writing a user interface and training materials for an online resource to be developed during the project
Writing a manual for an expected new lab protocol that will come out of the project
Writing outreach material designed around your research, for example a website pitched at non-experts or a teaching resource
Knowledge transfer to user communities, for example writing a policy briefing or an article for a specialist publication

Have you ever worked with a technical writer on a BBSRC-funded project? Would you consider writing one into your next grant?

The Plant Science Panel

by Charis Cook

Categories: something fun, teaching resources

Tags: Science Outreach

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Published on: August 15, 2013

Have you heard about the Plant Science Panel? It is a panel of plant scientists, including GARNet committee member Smita Kurup, and previous guest bloggers Anne Osterrieder and Alan Jones, ready and waiting to answer questions from the public about plant biotechnology and plant science.

There are regular live Q&A sessions online, during which people can ask questions via email or on the #plantsci Twitter hashtag. The first few of these sessions, which took place over summer 2012, tackled the Big Question surrounding plant science, agri-technology and the public – genetically modified foods. You can see the topics and the questions and answers on the Plant Science Panel webpage.

Now though, the Plant Science Panel is bigger than the classic GMO debate, covering the many areas of every day life that feature plant science affects. There have been Q&As about ash dieback, bee colony collapse, and organic farming. The questions submitted and answered outside of the allocated Q&A times are broader still, including the subtle differences in herbs like lemon and orange thyme, nutrient uptake by roots, and why nutrient burn causes leaf tips to brown and curl.

Postcards advertising the plant science panel are now available from Sense About Science. Frances Downey, who runs the Plant Science Panel, says, “If you are doing some outreach, giving a talk or just want to give them out to your friends and family contact plantsci@senseaboutscience.org. Help us ensure as many people know about it as possible – request some postcards and give them out to anyone you think might want to send a question in.”

Reports from ICAR 2013 – Sarah Harvey

by Guest Blogger

Categories: Arabidopsis, conferences, guest blogger, plant pathogens

Tags: ICAR

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Published on: August 12, 2013

Sarah Harvey, from the Beynon Group at the University of Warwick, brings us our final report from ICAR 2013.

I am a final year PhD student working in Professor Jim Beynon’s group at the University of Warwick. Our group focuses on the interactions of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis, a natural model system used for the molecular study of host-pathogen interactions. My project focuses on one effector protein identified from this pathogen and it’s molecular function within the host plant, including direct protein interactions and biochemical function, as well as transcriptional impacts on the host plant.

I was lucky enough to receive funding from the Gatsby Charitable Foundation through GARNet, and also from SEB and the Company of Biologists, which allowed me to attend The 24th International Conference on Arabidopsis Research (ICAR) in Sydney, June 2013. The conference is the world’s leading conference on Arabidopsis research and attracts many prominent researchers in the field as well as covering many areas of Arabidopsis research, for example biotic and abiotic stresses, epigenetics and hormones which were particularly interesting to me. (more…)

Reports from ICAR 2013 – Nur Izzati Mohd Noh

by Guest Blogger

Categories: Arabidopsis, conferences, guest blogger

Tags: ICAR

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Published on: August 7, 2013

The second of our posts from ICAR 2013 travel bursary awardees is from Nur Izzati Mohammed Noh, a PhD student in the Signal Transduction Group at the University of Cambridge.

From the 24th until 28th of June I was in Sydney, Australia, for ICAR 2013, and I had a chance to present a poster of my work. That was my first experience attending an international conference and I met a lot of great scientists who have done amazing studies on Arabidopsis. Here are some of the interesting topics that were presented in the conference:

Ian Small (Western University of Australia) described his group’s studies on PRR (pentatricopeptide repeat) proteins, which are important for plant development. PRRs can recognise a specific sequence present in RNA to control gene expression. Ian’s group has also identified two arginine methylation genes, PRMT10 and PRMT5, involved in autonomous pathway and flowering time regulation. PRMT10 is a plant specific protein, whereas PRMT5 has a close homolog of human PRMT5. Together, PRMTs control plant development by regulating RNA splicing.
Gonzalo Estavillo (Australian National University) gave a talk on retrograde signalling and drought. It is known that organelles can act as sensors in order to tolerate environmental stress. However, how organelles are involved in this process is a big question to be answered. Estavillo’s group propose that plants can tolerate drought stress via SAL1 and PAP interaction. (more…)

From Plant Biology 2013

by Charis Cook

Categories: conferences, resource

Tags: Plant Biology 2013, resources

Comments: 1 Comment

Published on: August 1, 2013

Last week I was at ASPB’s annual conference, Plant Biology 2013. It was a great week and I learned a lot of new science and discovered a lot of new resources to share with UK plant scientists – some brand new, and some golden oldies that get better with time.

First of all through, some shameless self-promotion – I wrote a report for New Phytologist on the UK’s own Plant Science conference, PlantSci 2013, with Ruth and Mimi. It’s now published (open access) here.

For the last three years, ASPB have been working on a decadal vision for plant science in the US. The final report was released in July, and will be rolled out to Congress in the autumn with the aim of raising awareness of the importance of plant science and getting extra funding. You can download the report, entitled Unleashing a Decade of Innovation in Plant Science, here. The Plant Science Research Summit website also explains how the report was written and includes the preliminary report from 2011.

Kate Dreher gave an excellent talk in the Genomic Tools minisymposium on the ever expanding output from the Plant Metabolomic Network, the free online tool which enables users to find and predict genes or proteins, other metabolites, reactions, and pathways. In June this year seven new databases were released, including BarleyCyc and OryzaCyc. In July, many existing databases were updated – AraCyc 11.5 now contains data on 597 pathways, 9041 enzymes, 3490 interactions, and 2613 compounds. For tutorials, see this page. (more…)

Reports from ICAR 2013 – Emily Breeze

by Guest Blogger

Categories: Arabidopsis, conferences, guest blogger

Tags: conference, Gatsby, ICAR

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Published on: July 25, 2013

This year GARNet was able to contribute to the travel costs of four students attending ICAR 2013, thanks to a kind donation from the Gatsby Charitable Foundation. They will each write an article about their experience – here is the first, by University of Warwick student Emily Breeze.

Emily with her poster; and the inflatable plant cell BioBounce.

Global food security is one of the prominent challenges facing mankind with environmental stresses such as drought and pathogen attack causing significant crop losses worldwide. I am in the final year of my PhD at the University of Warwick researching the role played by the NF-Y transcription factor family in regulating the plant’s response to environmental stress, using the plant model organism, Arabidopsis thaliana.

I was fortunate to receive a travel bursary from GARNet funded by the Gatsby Charitable Foundation, to enable me to attend the International Conference on Arabidopsis Research (ICAR) in Sydney, Australia. ICAR is the primary international scientific conference for the Arabidopsis research community and around 700 delegates from all over the world attended over the five days, including a number of eminent scientists within my field of study. The conference was made up of a mixture of lectures from keynote speakers and concurrent symposium sessions on a wide variety of biological themes including development, epigenetics, proteomics, biotic interactions, systems biology, signalling, phenomics and translational biology. Although some of the topics were not directly related to my own research interests, they introduced me to novel techniques and approaches that I can potentially apply to my own research and/or in the future, as well as broadening my wider understanding of plant biology.

The thirteen keynote lectures given by internationally renowned plant scientists were all captivating. (more…)

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