Weeding the Gems - Page 61 of 67 - the GARNet community blog

From systems biology to digital organism

Categories: synthetic biology, systems biology

Tags: BBSRC, Friday film, GARNet, survey, synthetic biology, systems biology, teaching resources

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Published on: October 19, 2012

GARNet needs your help to assess the uptake, influence and future of systems biology in the plant science community. This is the second time GARNet has conducted a survey about systems biology, as in 2006 the BBSRC commissioned GARNet to produce a report on how systems biology could best be approached in UK Arabidopsis research. We believe that report and the various activities that accompanied it helped the Arabidopsis community get its foot on the ‘System Biology Ladder’ – and to win some of the associated grants.

Now, six years later, systems biology is supporting systems biology and the digital organism efforts. We feel it is time to write a follow up report to the 2006 Systems Biology report in order to advise the BBSRC and other funders on the community’s capabilities, current needs, and readiness for future initiatives that build on Systems Biology.

Please help us collect data and information for this report by filling in a questionnaire, which will take about 20 minutes of your time. Please click here to go to the questionnaire. Please contribute your ideas before the 5th November.

Video credit: Pacific Biosciences.

Making Data Accessible to All

by Charis Cook

Categories: Workshops

Tags: data sharing, GARNet, GARNet workshop

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Published on: October 18, 2012

In July 2012, GARNet held a workshop entitled ‘Making Data Accessible to All’. Speakers included Mark Hahnel, founder of Figshare, TGAC Genome Analysis team leader David Swarbreck, senior editors and publishers from publishing groups, and a number of academics with experience in data dissemination. Together, workshop speakers and delegates discussed the current challenges in data storage, which data are ‘valuable’ and which may reasonably be left behind, and who should have the responsibility of sharing, storing, and curating data.

The report containing the summary of this workshop concludes that incentive, policing measures, and shifts in culture are needed in order for data sharing to take hold and bear fruit within biology as a whole. Funding bodies, universities, and publishers and journals can provide important ‘sticks and carrots’ by shifting priorities and attitudes to support the practice of data sharing, with all its demands. At the same time, researchers need to seriously commit to data sharing by making it part of their principal aims and outputs. In most cases, community involvement matters much more than the availability of technology. Recent initiatives to encourage data publication, such as data only journals, and data sharing, principally Dryad and Figshare, are acknowledged as important drivers of the shift toward an ethos of data sharing.

To see the resources and repositories GARNet recommends for sharing different types of data, including plant-specific ones, see this post.

Full list of speakers at the workshop: Sabina Leonelli, Andrew Millar, Nick Smirnoff, Jay Moore, Jacob Newman, Mary Traynor, Giles Jonker, Ruth Wilson, Mark Hahnel, Claire Bird, Sean May, David Swarbreck, Alan Pottage, and Paul Burlinson. Their affiliations and their presentation slides can be found on the UKPSF website.

Thinking about phytoplankton

by Charis Cook

Categories: Summary for non-specialists

Tags: algae, summary for non-specialists

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Published on: October 16, 2012

H. akashiwo on the right, with predator Favella sp.

I’m aware phytoplankton are not usual subjects for plant science research, but these small algae are quite plant-like, in general – although they don’t have organs to complicate things. Like plants, they photosynthesize and are able to respond to their environment. Importantly, unlike plants, phytoplankton are mobile, hence the name which in Greek means ‘drifting plants’. Being extremely tiny ‘plants’, phytoplankton present an excellent opportunity for plant scientists to consider synthetic biology, which seems more feasible on a cell-scale rather than an entire plant. The super-theme of the FP7 2013 funding call was ‘The Oceans of Tomorrow,’ and while that call closes in a few short months, synthetic biology, water security and bio-sensors are important research themes which are here to stay.

Highlighted article: Elizabeth L. Harvey and Susanne Menden-Deuer (2012) Predator-Induced Fleeing Behaviors in Phytoplankton: A New Mechanism for Harmful Algal Bloom Formation? PLoS ONE 7(9): e46438. doi:10.1371/journal.pone.0046438

This research focuses on toxic phytoplankton Heterosigma akashiwo, a known cause of harmful algal blooms (HABs; for a fairly recent review of HABs and their effects on human health, see Backer and McGillicuddy Jr., 2006). (more…)

Friday Film: Powerful Plants

by Charis Cook

Categories: teaching resources

Tags: Friday film, teaching resources

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Published on: October 12, 2012

If you thought that plants were stationary, lazy beings, think again. Bladderworts are water-dwelling carnivorous plants that trap prey by storing elastic energy in the trap body and releasing it by very fast opening and closing of a water-tight trap door. This video was made by Phillippe Marmottant and his research group from Grenoble, who published the mechanism of bladderwort action in their 2011 paper.

Another super fast plant is the dogwood species, Cornus canadensis, whose flowers explode faster than a rifle shot as they disperse their pollen.

While exploding plants and super-suction make for exciting viewing, they happen too fast for the human eye to see without the benefit of slow motion footage. It is possible to show slightly slower plant reflexes to students in schools, though – SAPS have a carnivorous plants information page and worksheets.

Pollen epigenetics

by Charis Cook

Categories: epigenetics, Summary for non-specialists

Tags: Arabidopsis, epigenetics, summary for non-specialists

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Published on: October 11, 2012

Biology learned in school and as a first year undergraduate is easily forgotten if it is not relevant to your current research. Today’s highlighted article required me to refresh my memory of plant germ line development, so I included my basic research here.

Highlighted article: Joseph P. Calarco, Filipe Borges, Mark T.A. Donoghue, Frédéric Van Ex, Pauline E. Jullien, Telma Lopes, Rui Gardner, Frédéric Berger, José A. Feijó, Jörg D. Becker and Robert A. Martienssen (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell 151:194-205.

Germline biosynthesis: A pollen mother cell undergoes meiosis to make haploid microspores, which unevenly split into a larger vegetative cell and a small generative cell. The generative cell splits symmetrically into two – these are the plant ‘sperm’ cells. Each pollen grain contains two sperm cells, which are surrounded by a vegetative cell. The vegetative nucleus contains completely decondensed heterochromatin, but DNA in generative nuclei is tightly condensed.

The female gametophyte develops from a megaspore mother cell. Both the megaspore mother cell and pollen mother cell are specified from somatic cells in developing flowers.

GFP staining in the two sperm nuclei and vegetative nucleus in the vegetative cell.

Bisulphite sequencing is a DNA sequencing method which determines methylation pattern by treating DNA with sodium bisulphite before sequencing it using a conventional DNA sequencing method. Bisulphite induces the conversion of unmethylated cytosines to uracil, but this is not a perfect technique so unmethylated DNA may be recorded as methylated. Additionally, bisulphite treatment can cause DNA degradation. Sequencing the DNA of interest multiple times, in the case of Calarco et al., anywhere from 7 to 17 times, improves reliability of the method. There is a brief overview of DNA methylation in this post. (more…)

Crop Plant Trait Ontology Workshop, Oregon State University

by Charis Cook

Categories: guest blogger, Workshops

Tags: crop science, GARNet workshop, ontology

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Published on: October 9, 2012

For the last few months, Ruth has been involved in organising a Crop Plant Trait Ontology Workshop which happened at Oregon State University on 13-15 September. Laura Cooper and the Crop Ontology Workshop Planning Committee put together a news piece about the event.

Plant breeders, biologists and bioinformatics specialists from ten countries and two plant agribusinesses gathered in Corvallis, Oregon for the Crop Plant Trait Ontology Workshop. The workshop was hosted by the Plant Ontology and the Trait Ontology consortiums, and co-organised by TransPlant, European Bioinformatics Institute, GARNet, Generation Challenge Program, Sol Genomics Network, and SoyBase.

The goal of the workshop was to engage researchers associated with major cultivated crops worldwide, in order to widen their awareness about ontologies and showcase the latest developments in ontologies for plants. In addition to hearing presentations, participants learned to use the ontology editor OBO-Edit and worked in small groups to classify plant trait terms which had been submitted in advance.

The main conclusion of the workshop was that there is a need for a broad, co-ordinated effort to create a semantic framework for meaningful cross-species queries using a Common Reference Ontology for Plants. This Reference Ontology will encompass all green plants and will facilitate queries for related gene expression and phenotype data from plant genomics, genetics experiments from the various species- and clade-specific databases, and describe accessions in the various international crop germplasm collections.

The hope is that in creating a Common Reference Trait Ontology for Plants, we will facilitate plant genetic and phenotypic data discovery and exchange.

For further information including a list of participants and sponsors, and links to presentations, visit the workshop wiki page at http://tinyurl.com/Trait-Ontology.

Other links:

Plant Ontology http://www.plantontology.org

Trait Ontology: http://www.gramene.org/plant_ontology/ontology_browse.html#to

TransPlant: http://transplantdb.eu/

European Bioinformatics Institute: http://www.ebi.ac.uk

GARNet: http://www.garnetcommunity.org.uk

Generation Challenge Program: http://www.generationcp.org

Sol Genomics Network: http://solgenomics.net/

SoyBase: http://soybase.org/

OBO-Edit; http://oboedit.org/

Friday Film: Automatic cell counting with ImageJ

by Charis Cook

Categories: methods, resource

Tags: Friday film, methods, resource

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Published on: October 5, 2012

This is a video tutorial on quantifying cells using ImageJ. ImageJ is a free tool for image processing and analysis in Java. I chose to highlight this tutorial as it is clearly explained and may be of use to many plant scientists, but YouTube is a goldmine of other less professional tutorials on using ImageJ for any number of applications. I was particularly interested in this one on quantifying stained liver tissue, as I used to work on secondary cell walls and it would have been a handy tool for qualitative analysis of my many images of phloroglucinol stained tobacco stem cross-sections.

Created by Keene State College’s Center for Engagement, Learning, and Teaching.

NASC

by Charis Cook

Categories: resource

Tags: resource

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Published on: October 4, 2012

Many European Arabidopsis researchers use transgenic Arabidopsis lines from NASC, which has a large catalogue of germplasm kept up-to-date by donations from plant scientists and industry from all over the world. The catalogue is searchable by keyword, collection, or ontology and there is a help page containing a number of useful tips on searching, ordering and referencing the collection. Also available are photos of each line and tips on working with Arabidopsis.

NASC run an Affymetrix Service. The current lowest all inclusive price is £250 for RNA onto any plate based chip. NASC are happy to process any private consortium chip or a chip from another species, as well as any commercially available Affymetrix Chip.

Microarray data is available from NASC free of charge, and users can donate their own microarray data. Again, there is a help page for this service containing tips on data analysis, and elsewhere there is advice for new users of microarrays including advice on sample preparation and NASC’s requirements.

You can follow NASC on Twitter on @NASCArabidopsis for updates on new array experiments and germlines.

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