To tweet or not to tweet?

Here at GARNet, we’re pretty big fans of social media, and Twitter in particular. You can find me, for example @GARNetweets, Charis is @weedinggems, and Ruth has the enviable Twitter handle @plantscience. We regularly post links to news, journal papers, job posts etc., tweet from conferences, and encourage live-tweeting at our own events too.

Left behind at GARNet Towers while my colleagues attended the Plant & Animal Genome conference in San Diego last week, I followed events virtually, via the Twitter hashtag #PAGXXIII – thanks to everyone who tweeted for keeping me up to speed!

Though once upon a time it would have been considered rude to sit tapping away at your phone during a plenary lecture, in today’s WiFi-enabled world, more and more people are using social media during conferences. As John Innes Centre (@JohnInnesCentre) student Amelia Frizell (@AmeliaFrizell) points out in this blog post, there are many advantages to live-tweeting: it’s a great way to make notes, stay engaged with the speaker, increase your Twitter follower numbers and network with peers.

But there’s an ongoing debate, known as “Twittergate”, about whether it’s appropriate to tweet during a conference, what should and should not be tweeted, and what, exactly, the “twetiquette” is when engaging with social media during live events.

A Twitter account I follow recently retweeted a link to quite an old blog post on The Guardian website, which reminds us that there is a certain level of responsibility involved in live-tweeting. At academic conferences in particular, there are unwritten rules that should be followed. I recommend reading the article as there are some very useful tips and things to bear in mind.

You see, although many of us are fully subscribed to the idea of Twitter as a way to quickly give and receive snippets of news and information, not everyone feels the same way. Not everyone is aware of what Twitter is, how it works, or just how public a channel it is. Many distrust it and are sceptical. Some academics, for example, are comfortable with presenting unpublished work to an audience of peers in the room, but less happy to have it instagrammed and summarised in 140 characters or less and whizzed around the Twitterverse for anyone to read.

Having been lucky enough to attend quite a few conferences last year, it was interesting to note the uptake, or not, of Twitter in different places. At UKPSF (@UKPSF) Plant Sci 2014 and ASPB’s (@ASPB) Plant Biology 2014, for example, tweeting was encouraged and I was among a handful or two of other delegates all using the official conference hashtags. At ICAR 2014 (@ICAR2014) however, Charis, Ruth and I were practically the only ones online.

At SEB (@SEBiology) 2014 in Manchester there were noticeably more ‘tweeps’ in the plant science sessions than there were in the animal or cell biology talks, while at SpotOn London (@SpotOnLondon), a science communication conference I attended at the end of 2013, there were so many people tweeting and using electronic devices that it was a scrum to find available plug sockets to recharge during the lunch break!

Like Amelia, I think – when used responsibly – Twitter is brilliant for conference and workshop communication, and as Anne Osterrieder (@anneosterrieder) and others testify, social media is a great science outreach tool, too. Like it or not, Twitter is a ‘thing’ now. And it’s not just a frivolous plaything for younger students or early career researchers, it’s a bona fide tool for communicating and sharing news and joining in online conversations.

Speakers: don’t be offended if people spend more time looking down at their iPads than up at your slides. If they’re tweeting or live-blogging about your work, they are helping you to communicate your science to far more people than just those in the room. If you’re presenting something you’d rather not have published on the internet, or don’t want your photo taken, just say so during your talk – the twitterati will respect your wishes.

Embrace Twitter. Why not set up your own Twitter account and start posting links to your papers or research websites? Follow people you’re interested in (like us?!) and retweet what they have to say. Tweet about what you get up to in your lab. Put your Twitter handle on your conference presentations so people can @mention you in their tweets, or even start your own catchy hashtag? Who knows, you could end up trending!

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: January 14, 2015

Back after our Christmas/New Year break, here’s a catch-up of the some of the new Arabidopsis papers to be published before Christmas. Today’s round-up features new work by scientists from the Universities of York, Leicester, Cambridge, Edinburgh and Leeds, and from the institutes Rothamsted Research and the James Hutton Institute.

 

  • Delker C, Sonntag L, James GV, et al. The DET1-COP1-HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis. Cell Reports, 18 December 2014. DOI: 10.1016/j.celrep.2014.11.043. [Open Access]

Though it has been known for some time that the transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4) regulates the growth response of Arabidopsis thaliana to elevated ambient temperature by activating hormonal modules, it is not known how, exactly, temperature regulates PIF4 activity. Using a forward genetic approach, this group of German researchers – with the help of Seth J. Davis from the University of York – provide evidence to suggest that seedling growth in response to elevated temperature is transcriptionally regulated by the DE-ETIOLATED 1 (DET1)-CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)-ELONGATED HYPOCOTYL 5 (HY5)-dependent photomorphogensis pathway.

 

  • Park GT, Frost JM, Park J-S, Kim TH, Lee JS, Oh SA, Twell D, Brooks JS, Fischer RL and Choi Y. Nucleoporin MOS7/Nup88 is required for mitosis in gametogenesis and seed development in Arabidopsis. Proceedings of the National Academy of Sciences of the USA, 8 December 2014. DOI: 10.1073/pnas.1421911112. [Open Access]

Working with Korean and American colleagues, David Twell from the University of Leicester was involved in this fascinating study of the mos7-5 mutant line of Arabidopsis thaliana. mos7-5  mutants experience ovule and pollen abortion in MOS7/mos7-5 heterozygous plants, and preglobular statge lethality in homozygous mos7-5 seeds. This study shoes that MOS7 is localized to the nuclear membrane but associated with the spindle apparatus during postmeiotic mitosis; in MOS7/mos7-5 heterozygotes, abortion is accompanied by a failure of spindle formation, cell fate specification and phragmoplast activity. These findings provide an important advance on current knowledge for plant scientists, but because the regulation of mitosis is highly conserved between plants and animals, it could be significant for animal researchers too.

 

  • Landrein B, Refahi Y, Besnard F, Hervieux N, Mirabet V, Boudaoud A, Vernoux T and Hamant O. Meristem size contributes to the robustness of phyllotaxis in Arabidopsis. Journal of Experimental Botany, 11 December 2014. DOI: 10.1093/jxb/eru482. [Open Access]

Led by a French team, this J Ex Bot paper included work by Yassin Refahi of the Sainsbury Laboratory at Cambridge. Using Arabidopsis, the group studied the relationship between day length, the size of the shoot apical meristem, and the robustness of phyllotactic patterns. Among several patterns identified was the overall finding that robustness of the phyllotactic pattern is not optimal in the wild type plant, suggesting that it is regulated by day length; a new example of the link between plant patterning and its environment.

 

  • Bielecka M, Watanabe M, Morcuende R, Scheible WR, Hawkesford MJ, Hesse H and Hoefgen R. Transcription and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis. Frontiers in Plant Science, 22 December 2014. DOI: 10.3389/fpls.2014.00805. [Open Access]

This Frontiers in Plant Science paper advances our basic understanding of the transcriptional effects of short-term sulphur starvation and re-supply in Arabidopsis thaliana; in turn this could have significance down the line for crop improvement. An international collaboration including Malcolm Hawkesford from Rothamsted Researchused a combination of transcriptomics and metabolomics analysis to not only identify the differential expression of 21 transcription factors in response to sulphur levels, but also to predict their downstream gene targets.

 

  • Hu X, Kong X, Wang C, et al. Proteasome-mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization. The Plant Cell, 23 December 2014. DOI: 10.1105/tpc.114.132738.

Gary Loake from the University of Edinburgh was involved in this Plant Cell paper, in which the mostly Chinese team identify that FRIGIDA – a scaffold protein involved in the recruitment of chromatin modifiers that cause epigenetic changes to regulate flowering genes – is degraded in a proteasome-mediated mechanism. The proteolysis mechanism is induced by WRKY34 and is dependent upon CULLIN3A.

 

  • Taylor-Teeples M, Lin L, de Lucas M, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 24 December 2014. DOI: 10.1038/nature14099.

Led by the Brady lab at UC Davis, this Nature paper also involved the work of Cambridge-based theoretical biophysicist, Sebastian Ahnert. The paper presents a novel protein–DNA network model showing the interactions between Arabidopsis thaliana transcription factors and secondary cell wall metabolite genes. This model allowed the group to develop and validate new hypotheses about secondary cell wall gene regulation under abiotic stress.

 

  • Foyer CH, Verrall SR and Hancock RD. Systematic analysis of phloem-feeding insect-induced transcriptional reprogramming in Arabidopsis highlights common features and reveals distinct responses to specialist and generalist insects. Journal of Experimental Botany, 24 December 2014.DOI: 10.1093/jxb/eru491.

In terms of immunity, plants may respond very differently to phloem-feeding insects (PFIs) compared to chewing insects. Here, Christine Foyer from the University of Leeds, and Susan Verrall and Robert Hancock from the James Hutton Institute, provide a comprehensive transcriptomic analysis of Arabidopis thaliana when infested withMyzus persicae, Bemisa tabaci or Brevicoryne brassicae. Though an increase in transcripts associated with WRKY transcription factor genes is a common feature of PFI infestation, there is significant divergeance in secondary metabolism depending on the species of PFI. Nevertheless, this research suggests that plants recognize and respond to perturbations in the cell wall during PFI infestation.

GARNish Issue 22 is Hot off the Press!

Categories: Arabidopsis, GARNet, Global
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Published on: December 12, 2014

 

GARNish cover large

Your December issue of GARNish is now available to download from the GARNet website!

Edition 22 is full of news and views from the UK Arabidopsis and plant science community, including a round-up of some exciting new Arabidopsis projects recently funded by BBSRC. There are also reports from our GARNet 2014 conference in September, and from the second of our sold-out Software Carpentry bootcamps.

In our Plant Science Resources section you can find out more about PlantRegulome.org, and if you weren’t able to be there yourself, you can read all about what happened at the BBSRC Great British Bioscience Festival in London in November.

Finally, we caught up with plant science group leaders at The Genome Analysis Centre and the University of York to find out what’s new.

Enjoy!

 

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: December 10, 2014

Lots of new and interesting papers from the UK Arabidopsis research community this week! New papers have been published by scientists from Rothamsted Research and the Universities of Warwick, Leicester, Aberdeen and Manchester.

 

  • Brewer HC, Hawkins ND and Hammond-Kosack KE. Mutations in the Arabidopsis homoserine kinase gene DMR1 confer enhanced resistance toFusarium culmorum and F. graminearum. BMC Plant Biology, 29 November 2014. DOI: 10.1186/s12870-014-0317-0. [Open Access]

It was already known that mutations to the DMR1 gene affect Arabidopsis’ resistance to the biotrophic pathogens Hyaloperonospora arabidopsidis and Oidium neolycopersici. In this BMC Plant Biology paper, Nelly Brewer, Nathaniel Hawkins and Kim Hammond-Kosack from Rothamsted Research instead investigate the effects of these mutations on resistance to the ascomycete pathogens Fusarium culmorum and F. graminearum.

 

  • Footitt S, Müller K, Kermode AR and Finch-Savage WE. Seed dormancy cycling in Arabidopsis: Chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals. The Plant Journal, 1 December 2014. DOI: 10.1111/tpj.12735.

Working with collaborators in Canada, Bill Finch-Savage and Steven Footitt from the University of Warwick’s Crop Centre present the findings of a study to investigate natural variation in the expression of genes involved in chromatin remodeling in two Arabidopsis ecotypes. Several key observations were made, including changes detected in the histone modifications H3K4me3 and H3K27me3 of the DOG1 gene during dormancy cycling, leading to the proposal that these histone marks serve as a thermal sensing mechanism during dormancy cycling in preparation for light repression of dormancy.

 

  • Hoedemaekers K, Derksen J, Hoogstrate SW, Wolters-Arts M, Oh S-A, Twell D, Mariani C and Rieu I. BURSTING POLLEN is required to organize the pollen germination plaque and pollen tube tip in Arabidopsis thaliana. New Phytologist, 1 December 2014. DOI: 10.1111/nph.13200.

David Twell from the University of Leicester was involved in this study with Dutch colleagues from Radboud University Nijmegen. The group explored the processes taking place during pollen hydration in Arabidopsis; the step in pollination before emergence of the pollen tube. Expression of the gene BURSTING POLLEN (BUP) was found to be essential for the correct organisation of a ‘germination plaque’ – an intine-like structure consisting of cellulose, callose and party de-esterified pectin – which provides passage for the emerging pollen tube.

 

  • Chao D-Y, Chen Y, Chen J, Shi S, Chen Z, Wang C, Danku JM, Zhao F-J and Salt DE. Genome-wide association mapping identified a new arsenate reductase enzyme critical for limiting arsenic accumulation in plants. PLOS Biology, 2 December 2014. DOI: 10.1371/journal.pbio.1002009. [Open Access]

In a collaboration with scientists based in China, Fang-Jie Zhao and Yi Chen (Rothamsted Research), and new GARNet Chair David Salt (University of Aberdeen) carried out genome-wide association mapping in Arabidopsis in order to learn more about natural variation in the genetic control of the reduction of arsenate to arsenite. Understanding the control of this chemical reaction, and the extent to which inorganic arsenic accumulates in crops such as rice, is key to reducing the carcinogenic risk to human health. Analysis revealed a new arsenate reductase enzyme, High Arsenic Content 1 (HAC1).

 

  • Dyson BC, Allwood JW, Feil R, Xu Y, Miller M, Bowsher CG, Goodacre R, Lunn JE and Johnson GN. Acclimation of metabolism to light in Arabidopsis thaliana – the glucose 6-phosphate/phosphate translocator GPT2 directs metabolic acclimation. Plant, Cell & Environment, 4 December 2014. DOI: 10.1111/pce.12495.

When transferred from low light conditions to high light conditions, mature plant leaves typically increase their photosynthetic capacity via expression of GPT2. In this study, researchers from Germany and the University of Manchester used wild type and GPT2 knockout plants to try and work out how and why this happens.

First Arabidopsis Information Portal developer workshop a success

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Published on: December 4, 2014

The Arabidopsis Information Portal (AIP) was funded in 2013 by NSF, and co-funded this year by BBSRC. The UK team is led by Gos Micklem at the University of Cambridge. AIP provides the Arabidopsis thaliana Col-0 reference genome sequence with associated annotation, including gene structure, gene expression, protein function, and interaction networks. It is much more than this however: an open-access online community resource for Arabidopsis research. AIP is intended to be full of resources and tools to navigating the genome, all built by community developers as part of their own research and shared with the rest of the community via AIP. 

Here Makeda Easter blogs about the first AIP developer workshop, which was hosted by TACC, JCVI, and the University of Cambridge. This post was originally published on the news pages at the Texas Advanced Computing Centre

 

AIP dev workshop 1000

Last month, a group of 20 plant scientists from the U.S. and Europe convened at the Texas Advanced Computing Center (TACC) in Austin to participate in the Arabidopsis Information Portal (AIP) Developer Workshop.

“Our key goal with this workshop was to onboard a group of developers with varying degrees of experience with web technologies to contribute web apps and APIs to our platform,” said TACC Life Sciences Computing Director Matthew Vaughn, co-PI of the project. “With the growing number and diversity of data types available for Arabidopsis, effective developer engagement is crucial to making it all available in a single place. No one group can do it all.

The Arabidopsis Information Portal is an open-access, community extensible, online resource for Arabidopsis research. AIP is an international effort from collaborators TACC, J. Craig Venter Institute (JCVI), and Cambridge University and is powered by cutting edge technologies such as InterMine, Jbrowse, Drupal, and the iPlant Agave API.

The portal not only provides users access to genomic information, but it also allows researchers to contribute their own data through developing scientific applications.

(more…)

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: December 3, 2014

It’s all about the Institutes in today’s UK Arabidopsis Research Round-up! New work this week comes from the John Innes Centre, the Sainsbury Laboratory, Rothamsted Research – and theEuropean Bioinformatics Institute, part of the European Molecular Biology Laboratory (EMBL-EBI) based in Cambridge, makes an appearance too.

  • Wirthmueller L, Roth C, Fabro G, et al. Probing formation of cargo/importin-a transport complexes in plant cells using a pathogen effector. The Plant Journal, 17 November 2014. DOI: 10.1111/tpj.12691.

With collaborators in Germany, researchers from the John Innes Centre and the Sainsbury Laboratory in Norwich deduce that complexes between the adapter proteins importin-a, and the cargo proteins they recruit for active nuclear transport, are formed dependent upon cargo specificity, variation at the importin-a nuclear localisation sequence-binding sites, and tissue-specific expression levels of importin-a.

  • Hsiao A-S, Haslam RP, Michaelson LV, Liao P, Chen Q-F, Sooriyaarachchi S, Mowbray SL, Napier JA, Tanner JA and Chye M-L. Arabidopsis cytosolic acyl-CoA-binding proteins ACBP4, ACBP5 and ACBP6 have overlapping but distinct roles in seed development. Bioscience Reports, 21 November 2014. DOI: 10.1042/BSR20140139.

This Bioscience Report included a number of researchers from Rothamsted Research, and explores the previously poorly understood roles of three cytosolic acyl-CoA-bding proteins (ACBPs). Microarray data revealed that all three are expressed in seeds, but further analysis in transgenic Arabidopsis revealed overlapping, but differing physiological effects on seeds.

  • Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I and Loudet O. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. The Plant Cell, 26 November 2014. DOI: 10.1105/tpc.114.130310.

Led by a French team, this study also involved Oliver Stegle from EMBL-EBI in Cambridge. Using drought stress as an example of environmental variation, the aim here was to produce a detailed map of the ways in which cis- and trans-acting factors affect gene expression and responses to environmental conditions in Arabidopsis thaliana.

Guest post: Software Carpentry for Plant Scientists bootcamp

Categories: guest blogger, Workshops
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Published on: December 2, 2014
Software Carpentry Liverpool
Photos from the Bootcamp. Instructors and helpers shown in the bottom photo: Bert Overduin, Marios Isaakidis, Kwasi Kwakwa, Fatima Silva.

Thanks to Robyn Drinkwater from the Royal Botanic Garden Edinburgh for this guest post about the Software Carpentry Bootcamp we ran with CGR Liverpool a couple of weeks ago. This piece was first published on Botanics Stories, the RBGE blog. 

Programming is becoming an increasingly useful skill as it can aid in the execution of large, repetitive tasks, and in running analyses of large data sets. Four staff from RBGE recently attended a workshop set up by GARNet and the University of Liverpool’s Centre for Genomic Research along with Software Carpentry, to help them learn and improve their use of some simple tools and programming.

During the workshop they explored the principles of good programming, which can be applied to any programming language, the use of the Command Line, version control using Git and GitHub, and Python, a widely used programming language, which can be used for data manipulation, as well as other programming tasks.

The workshop led us from first principles through each tool, building our understanding of how it works, and showing us examples of how it could be used. During the workshop we started to explore how we could use these tools to look at our own data, and for some of us, we were still seeing what we could do on the train home!

The next step for all of us is to keep practicing and looking at how we can use Python, Git and the Command Line in our work and keep building on the good foundation the bootcamp gave us.

Tweets from participants and organisers of the event have all been brought together by the organisers:

http://sfy.co/ppQS

Image credit: Charis Cook

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: November 26, 2014

There are some really interesting new papers for you this week. We have two different protein interaction studies, one on microtubules involving scientists from Durham, and one on meiotic chromosome movement from Oxford Brookes and Birmingham. There’s also a report on ‘FANS’, a new technique used to study Arabidopsis embryos from Nottingham researchers, a US–UK collaborative project to develop Araport – a new online resource for plant scientists, and an exciting new rapid report from theJohn Innes Centre. Enjoy!

 

  • Galva C, Kirik V, Lindeboom JJ, Kaloriti D, Rancour DM, Hussey PJ, Bednarek SY, Ehrhardt DW and Sedbrook JC. The microtubule plus-end tracking proteins SPR1 and EB1b interact to maintain polar cell elongation and directional organ growth in Arabidopsis. The Plant Cell, 18 November 2014.DOI: 10.1105/tpc.114.131482.

Researchers from the University of Durham were collaborators on this paper, which describes efforts to understand the interactions between the microtubule plus-end tracking proteins (+TIPS) EB1b and SPR1. Data suggest that SPR1 and EB1b have complex interactions as they load onto microtubule plus ends and direct polar cell expansion and organ growth in response to directional cues.

 

  • Slane D, Kong J, Berendzen KW, et al. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development, 19 November 2014. DOI: 10.1242/dev.116459.

Ive De Smet from the University of Nottingham worked with a German–Belgian team to put together this ‘Techniques and Resources’ paper in Development journal. Here, the team describes the use of fluorescence-activated nuclear sorting (FANS) to conduct cell type-specific transcriptome analysis in the early Arabidopsis embryo.

 

  • Krishnakumar V, Hanlon MR, Contrino S, et al. Araport: the Arabidopsis Information Portal. Nucleic Acids Research, 20 November 2014. DOI: 10.1093/nar/gku1200.

This paper, involving scientists from the University of Cambridge, describes the Arabidopsis Information Portal (AIP, or Araport), a new online resource for plant biologists. At its core, it is the home for the Arabidopsis thaliana genome sequence and associated annotation, but it does much more than this. Users can access data curated from a variety of sources – including TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe – as well as make use of feature-rich web applications to search, download, data-mine and genome-browse to their hearts content.

Araport also posts news, jobs and information relevant to the global Arabidopsis community – in fact, GARNet regularly posts information, including this Round-Up!https://www.araport.org/community/news.

 

  • Varas J, Graumann K, Osman K, Pradillo M, Evans DE, Santos JL and Armstrong SJ. Absence of SUN1 and SUN2 proteins in Arabidopsis thaliana leads to a delay in meiotic progression and defects in synapsis and recombination. The Plant Journal, 21 November 2014. DOI: 10.1111/tpj.12730.

In eukaryotes, Sad1/UNC-84 (SUN)-domain proteins are part of a complex responsible for forming attachments between the chromosome telomeres and the components of the cytoplasm, which help the chromosomes to move appropriately during meiosis. This paper, involving scientists from Oxford Brookes University and the University of Birmingham, describes the discovery of homologous proteins – AtSUN1 and AtSUN2 – in Arabidopsis thaliana.

 

  • Nützmann H-W and Osbourn A. Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytologist, 21 November 2014. DOI: 10.1111/nph.13189.

This rapid report comes from Hans-Wilhelm Nützmann and Anne Osbourn from the John Innes Centre. Comparing gene expression in chromatin mutants, they find that ARP6 and H2A.Z are involved in the regulatory process required for the normal expression of metabolic gene clusters in Arabidopsis. Specifically, these proteins are implicated in localized chromatin modifications that allow contiguous genes to be expressed in a coordinated way. This is a major finding that could open up new opportunities for the discovery and manipulation of specific metabolic pathways in plants!

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