SLiMSuite & SeqSuite: New downloads and fixed webpages

SLiMSuite & SeqSuite: open-source bioinformatics in Python: New downloads and fixed webpages: New releases of SeqSuite and SLiMSuite are now available. The webpages have now hopefully been fixed too, including the broken Manual link...

Postdoc opportunity in Short Linear Motif discovery!

As part of the move to UNSW, a 10 month computational postdoc position is available in the lab. The position is not attached to a specific grant and thus the research focus of the position is flexible and open for negotiation. It will, however, be something related to the lab’s primary research focus of computational Short Linear Motif (SLiM) discovery.

Possible projects include (but are not limited to): molecular mimicry by viral or bacterial pathogens; the role of SLiMs in cancer; interrogating protein-protein interaction networks to predict SLiM function; SLiM prediction database/visualisation development. For more on the research of the lab, please visit my old University of Southampton and/or new UNSW pages or email for more information.

Short-listing will (probably!) begin on 1/12/13 but applications are welcome until the position is filled. To apply, or find out more, please email a copy of your CV and your research interests. Candidate should have good computational skills. Start date is flexible but likely to be around January 2014.

SLiM Pickings: mining structural and sequence data for the prediction of short linear protein interaction motifs

Less than a week after starting at UNSW, I was lucky enough to present the work of the lab on Short Linear Motif (SLiM) discovery at the third annual Sydney Bioinformatics Research Symposium, which was held on Friday 8th November at the Garvan Institute. It was a great day, organised by the Australian Bioinformatics Network (ABN) for bioinformaticians and bioscientists in the Sydney region, and I was pleased to see so much exciting stuff going on in the Sydney area and beyond.

Now at the University of New South Wales!

As of Monday 4th November 2013, Rich is a Senior Lecturer in Bioinformatics in the School of Biotechnology and Biomolecular Sciences (BABS) at the University of New South Wales (UNSW) in Sydney, Australia.

The new primary contact details for the lab are:

Room 263B Level 2 Biological Sciences Building
The University of New South Wales
SYDNEY NSW 2052
Australia
email: richard.edwards@unsw.edu.au
web: http://www.babs.unsw.edu.au/staff_academic/dr-richard-edwards

Due to grant restrictions and collaborations, the rest of the lab are staying in Southampton. For now..!

iOES Poster: Using metagenomics to assess soil microbial diversity under future climate scenarios

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster CE-3.

Abstract:

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.

iOES Poster: Using Next Generation Sequencing to Understand Plant Acclimation and Adaptation to the Changing Environment

Alex Watson-Lazowski, Yunan Lin, Jennifer DeWoody, Richard Edwards and Gail Taylor.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster EcO-15.

Abstract:

Plant adaptation to elevated atmospheric carbon dioxide (CO2) is of great interest, as the concentration of this gas in the atmosphere has risen by more than 30% to 388 μmol mol-1 since the industrial revolution. On average there has been a rise of 3 ppm per year. Plant fossil samples suggest that atmospheric CO2 may be acting as a selective agent driving evolution, but limited evidence is available to support this idea for plants subjected to future predicted concentrations. Studying evolutionary responses to this aspect of environmental change is difficult, but here we use a CO2 spring site where plants have been exposed for multiple generations to concentrations of CO2 predicted for 2050. From this, detailed phenotyping data was collected, including data for stomatal patterning. Considerable evidence exists to show that stomatal numbers have declined across geological time and that this is linked to CO2 concentration, but few CO2-sensitive stomatal patterning genes have ever been identified. When grown under elevated CO2 concentrations P. lanceolata (the narrow leaf plantain), seeds collected from the spring site showed a counter-intuitive change in stomatal index and density. Here, in this non- model plant we have investigated the gene expression changes underlying this stomatal patterning response to elevated CO2.

RNA-Seq allows for in depth analysis of plant species with no previous information required, enabling rapid evaluation of any of novel plant acclimations and adaptions. Using this approach we have identified a set of novel genes for stomatal patterning in high CO2 and confirmed previously observed acclimation responses.

RNA-Seq refers to the use of high-throughput deep-sequencing technologies to sequence cDNA in order to get information about the transcriptome of a given biological sample.

1st International Environmental Omics Synthesis (iEOS) Conference

The lab has a couple of posters at the 1st International Environmental Omics Synthesis (iEOS) Conference conference in Cardiff this week (Sept 11-13), so come and say hello to Joe and/or Alex if you are in Cardiff.

Poster EcO-15:

UNDERSTANDING PLANT ADAPTATION TO THE CHANGING ENVIRONMENT USING NEXT GENERATION RNA TRANSCRIPTOME SEQUENCING

Alex Watson-Lazowski, Yunan Lin, Jennifer DeWoody, Richard Edwards and Gail Taylor. Centre for Biological Sciences, University of Southampton.

Plant adaptation to elevated atmospheric carbon dioxide (CO2) is of great interest, as the concentration of this gas in the atmosphere has risen by more than 30% to 388 μmol mol-1 since the industrial revolution. On average there has been a rise of 3 ppm per year. Plant fossil samples suggest that atmospheric CO2 may be acting as a selective agent driving evolution, but limited evidence is available to support this idea for plants subjected to future predicted concentrations. Studying evolutionary responses to this aspect of environmental change is difficult, but here we use a CO2 spring site where plants have been exposed for multiple generations to concentrations of CO2 predicted for 2050. From this, detailed phenotyping data was collected, including data for stomatal patterning. Considerable evidence exists to show that stomatal numbers have declined across geological time and that this is linked to CO2 concentration, but few CO2-sensitive stomatal patterning genes have ever been identified. When grown under elevated CO2 concentrations P. lanceolata (the narrow leaf plantain), seeds collected from the spring site showed a counter-intuitive change in stomatal index and density. Here, in this non- model plant we have investigated the gene expression changes underlying this stomatal patterning response to elevated CO2.

RNA-Seq allows for in depth analysis of plant species with no previous information required, enabling rapid evaluation of any of novel plant acclimations and adaptions. Using this approach we have identified a set of novel genes for stomatal patterning in high CO2 and confirmed previously observed acclimation responses.

RNA-Seq refers to the use of high-throughput deep-sequencing technologies to sequence cDNA in order to get information about the transcriptome of a given biological sample.

Poster CE-3:

USING METAGENOMICS TO ASSESS SOIL MICROBIAL DIVERSITY UNDER FUTURE CLIMATE SCENARIOS

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards. University of Southampton, ExpeER, EuroChar.

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.

New website under construction

Welcome to the new Edwards Lab website. The site is currently under construction, so content should appear over the next few weeks. In the meantime, you can visit my old webpage for research and software, or the University of Southampton Centre for Biological Sciences and Computational Modelling Group websites for more on lab members and research projects.

Responses of the Emiliania huxleyi proteome to ocean acidification

Jones BM, Iglesias-Rodriguez MD, Skipp PJS, Edwards RJ, Greaves MJ, Young JR, Elderfield H & O’Connor CD (2013): Responses of the Emiliania huxleyi proteome to ocean acidification. PLoS One 8(4): e61868.

Abstract

Ocean acidification due to rising atmospheric CO2 is expected to affect the physiology of important calcifying marine organisms, but the nature and magnitude of change is yet to be established. In coccolithophores, different species and strains display varying calcification responses to ocean acidification, but the underlying biochemical properties remain unknown. We employed an approach combining tandem mass-spectrometry with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differentially expressed in cells of the marine coccolithophore species Emiliania huxleyi (strain NZEH) between two CO2 conditions: 395 (∼current day) and ∼1340 p.p.m.v. CO2. Cells exposed to the higher CO2 condition contained more cellular particulate inorganic carbon (CaCO3) and particulate organic nitrogen and carbon than those maintained in present-day conditions. These results are linked with the observation that cells grew slower under elevated CO2, indicating cell cycle disruption. Under high CO2 conditions, coccospheres were larger and cells possessed bigger coccoliths that did not show any signs of malformation compared to those from cells grown under present-day CO2 levels. No differences in calcification rate, particulate organic carbon production or cellular organic carbon: nitrogen ratios were observed. Results were not related to nutrient limitation or acclimation status of cells. At least 46 homologous protein groups from a variety of functional processes were quantified in these experiments, of which four (histones H2A, H3, H4 and a chloroplastic 30S ribosomal protein S7) showed down-regulation in all replicates exposed to high CO2, perhaps reflecting the decrease in growth rate. We present evidence of cellular stress responses but proteins associated with many key metabolic processes remained unaltered. Our results therefore suggest that this E. huxleyi strain possesses some acclimation mechanisms to tolerate future CO2 scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans.

PMID: 23593500