Online resources for sharing and viewing data

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Published on: August 15, 2012

—-  This page was updated on 17 and 21 August 2012 with recommendations from @BMC_series and others. I will make further changes if necessary so please contact me if you have any suggestions  —-

When reviewing the recent GARNet workshop Making Data Accessible to All, we thought it was a good idea to collate the important bioscience databases on the web. I set to work and came up with the table below.

GARNet are keen to get an impression of how the plant science community actually use online databases, so please use the form at the end of this post to let us know how you use these types of resources. Do you deposit data in them, use them to guide practical work, or build whole research projects around them?

You’ll notice there are some blank spaces – if you know a resource that can fill it, please let me know. Likewise if you think I’ve got something wrong (I have personally worked with only a handful of these resources!) or missed off your favourite database, please leave a comment, tweet me or use the form below to tell me about it. (more…)

Synthetic enzyme reduces lignin content

Public domain image. Source: Glazer, A. W., and Nikaido, H. (1995). Microbial Biotechnology: fundamentals of applied microbiology. San Francisco: W. H. Freeman, p. 340. ISBN 0-71672608-4

Highlighted article: Kewwi Zhang, Mohammad-Wadud Bhuiya, Jorge Rencoret Pazo, Yuchen Miao, Hoon Kim, John Ralph, and Chang-Jun Liu (2012) An Engineered Monolignol 4-O-Methyltransferase Depresses Lignin Biosynthesis and Confers Novel Metabolic Capability in Arabidopsis. Plant Cell Preview.

Zhang et al. reduce lignin content by introducing an artificial enzyme to the cell wall biosynthesis pathway. This is the first time synthetic biology has been used to change cell wall structure, which is usually modified by changing the expression of endogenous enzymes or introducing a protein from another organism. In fact at the moment, synthetic biology is not a common method of manipulating any plant pathway.

Relevant background

public domain image, courtesy of Chino

Lignin is one of three components of secondary cell walls. It is the part which makes extracting sugar from the cell wall, for example for second generation biofuel production, difficult.

Lignin is made up of three monolignols: coniferyl, sinapyl, and p-coumaryl.

They are synthesised in the cytosol and transported to the cell wall. At the cell wall, the monolignols are oxidised, causing their phenol group to become radicalised. The phenoxy radicals polymerise to form the lignin macromolecule.

The Liu lab had the idea of preventing monolignol oxidation by methylation of the phenol group so that the phenoxy radicals were prevented from forming. Their first attempt was to synthesise a selection of monolignol 4-O-methyltransferases (MOMTs). The artificial MOMTS were fusions of two naturally occurring enzymes: lignin biosynthesis pathway methyltransferase COMT, which does not have any 4-O-methyltransferase activity; and fairy fan enzyme isoeugenol O-methyltransferase, which catalyzes 4-O-methylation of isoeugenol and eugenol, but doesn’t affect monolignols. Although several of these artificial enzymes were able to 4-O-methylate monolignols as expected in vitro, they had no activity in vivo.


Zhang et al. used MOMT3, a promising enzyme from their earlier work, as a starting point. (more…)

FESPB-EPSO Plant Congress 2012

Ruth Bastow has put together an excellent Storify on the recent Plant Biology Congress in Freiburg. Here are just a few snippets from the first two days – go to the Storify for the complete story, including insights from diverse speakers like Professor Richard Dixon, farmer Helmut Bonn, and Joachim Schneider from Bayer.


Transcription factor-like effectors (TALEs)

Ubud, Bali by Mee Lin Woon; DNA Sequence by schulergd. Via stock.chng


Xanthomonas spp. are plant pathogens that modulate their host’s gene expression in order to facilitate infection. They do this using transcription activator-like effectors (TALEs). Two domains are conserved in TALEs: an N-terminus, required for type III secretion into the plant cells; and a C-terminus with transcription factor activity. In the middle is a set of tandem repeats of amino acids, which mediates binding to host DNA.

As the binding and effector domains of TALEs can be customised, the possibility of using them for molecular and synthetic biology has been explored for some time. They have been used to change gene expression in plants, yeast, and even human cells.

TALEs have been adapted by researchers to make TALE nucleases (TALENs) – TALEs attached to a FOK1 nuclease domain. TALENs work in pairs that flank either side of the target site so that the nuclease domains meet at the point of cleavage. The nucleases cause a double-stranded DNA break, which is fixed imperfectly, causing an insertion or deletions.

In May this year, a paper was published demonstrating the huge impact TALEs could have on agriculture. Li et al. prove that transcription activator-like effector nucleases (TALENs) can be used to render rice resistant to the major agricultural pathogen, Xanthomonas oryzae pv. Oryzae (Xoo). (more…)

Programmed Cell Death in action

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Published on: August 7, 2012
Madagascar lace plant. Credit: Jim Yupangco

The lace plant, Aponogeton madagascariensis, is an aquatic plant native to Madagascar. It has characteristic lacey leaves which are formed by programmed cell death (PCD) in the areoles between leaf veins. Wertman et al., from Dalhousie University, used the predictable nature of PCD in lace plants to monitor the process using light, confocal and standing electron microscopy. They were able to discern the precise order of organelle disruption and activity during PCD. They could even video the process using live cell imaging on a light microscope – you can see the cells rupture in front of your eyes in the video below.

Highlighted article: Jaime Wertman, Christina CEN Lord, Adrian N Dauphinee and Arunika HLAN Gunawardena (2012) The pathway of cell dismantling during programmed cell death in lace plant (Aponogeton madagascariensis) leavesBMC Plant Biology 2012, 12:115

The paper is quite straightforward and a nice one to read so I won’t go in to detail here, but I will quickly go over their findings. After initial anthocyanin reduction, which is how the team identified accurately where and when PCD would take place, the first phase of activity included the bundling of actin microfilaments, and transvacuolar strands increased in number. Then the tonoplast membrane began to fold and mitochondrial aggregates and chloroplasts moved randomly. Nuclear DNA, actin microfilaments and the cell wall broke up. The vacuole swelled and its membrane ruptured while the nucleus shrank and the plasma membrane collapsed. The whole process took roughly 48 hours, and it took more than 24 more hours before the cell wall completely disappeared.

Warwick Systems Biology at SEB 2012

It’s time for another guest post today – Katherine Denby writes about the SEB 2012 conference.

Warwick Systems Biology Centre was well represented at the recent SEB conference in Salzburg, with 4 presentations in sessions on Biotic Stress, Environmental Control of Development and Generating New Biological Insights from Complex Data.

Arabidopsis leaf cells, stained to visualise the cell wall and Botrytis cinerea mycelia. Credit: Katherine Denby

First up was Katherine Denby who presented analysis of a gene expression time series from Arabidopsis leaves infected with the fungal pathogen Botrytis cinerea generated in the PRESTA project. Using a variety of network inference algorithms, the group has generated models of the gene regulatory networks underlying the Arabidopsis response to this pathogen. These network models have highlighted specific regulatory interactions, and led to identification of transcription factors with a novel role in defence. Modelling using gene expression time series from other biotic and abiotic stresses has predicted a core regulatory network underlying multiple stress responses with differential flux through the network under different environmental conditions. Katherine also described a novel tool, Wigwams, to identify groups of genes significantly co-expressed across multiple stresses. Integrating this with the network models enables prediction of the upstream regulators of these groups. (more…)

Funding opportunities with deadlines in the next two months

Categories: funding
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Published on: August 1, 2012

Grants with deadlines in August and September

Science outreach from the Biochemical Society: Deadline 27 September. Up to £1000 available for a science outreach project.

BBSRC Policy Placements for BBSRC-funded PhD students: Deadline 14 September. Fully funded three month placement with a science policy team, with a three month extension to your PhD to compensate for your time.

BBSRC Flexible Interchange Programme: Deadline 20 September. £150k for a scheme lasting up to 24 months involving the ‘interchange’ of a person between working environments. The interchange may be between, for example, academia and policy, business, or a different academic discipline.

The Leverhulme Trust International NetworkVisiting Professorships and Research Project Grants. Deadline: 1 September or 1 December. Funding for international collaborations and original research projects.

BBSRC David Phillips Fellowships: Deadline 20 September.Funding for a five year project for an experienced post-doc to become a PI.

COST Open Call: Deadline 28 September. Funding for a research network, not original research. Money can be used for organization of meetings, conferences, workshops etc, and travel and subsistence for them. Initial application is a preliminary report, after which you may be invited to submit a full proposal.

BBSRC Sustainable Energy and Biofuels: Deadline 30 August for intention to submit; 9 October for applications. Funding for a proposed collaborative project between a UK university and an university in India.


Some travel grants which have rolling deadlines

BBSRC International Scientific Exchange Scheme (ISIS): apply 6 weeks before travel. Up to £5000 for travel and subsistence for short term travel intended for meetings, long term travel, and stays of up to one month to work in a lab outside of the UK. Students are not eligible for travel.

EMBO Short-term fellowships: apply at least three months before travel. Funding for early career (PhD students or researchers less than 10 years from the end of their PhD) researchers to work in a lab outside of their own country for up to 3 months. This is for collaborations, not consultancy. Funding covers travel and subsistence.


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