During 2011, my research has been aimed towards microbial communities, and how these c0mmunitites cope with various selection pressures, primarily those posed by toxicants in the environment. The year has seen the finishing of one project that has been ongoing since 2008, relating to the distribution and diversity of detoxification systems in the global ocean environment, based on Global Ocean Sampling data. This manuscript is now ready for publication and will be submitted any day. I have also been deeply involved in a project working with marine biofilms – periphyton – and the genomic content hosted by them. As part of this project, I have been involved in the development of one published bioinformatics tool – Metaxa – and one tool that is soon to be publicly unveiled.
In my main project, started in April this year, I am studying microbial communities under varying selection pressure from antibiotics, in a variety of environments. We are still awaiting sequencing data from these samples, and have several more interesting experiments planned, so I am sure 2012 will be an exciting year for large scale data analysis of microbial communities. This project is supervised by Joakim Larsson and Erik Kristiansson, who I will be working with for the next four years.
In publications, there is a lot in the pipeline, but the only thing I managed to squeeze out before the new year was the paper on the bioinformatics tool Metaxa, designed to find SSU (12S/16S/18S) sequences in environmental sequencing data, and classify them according to taxonomic origin. There is a paper on marine detoxification systems, and one on another bioinformatics tool ready to be submitted, so it looks like 2012 will be a more productive-looking year than 2011 for me. In addition to the Metaxa paper, I have also finished a masters thesis, and produced a Metaxa poster, presented at two occasions.
The year ended with a Christmas celebration in South Africa with my family, which was great, but now it actually feels pretty good to be back at work, ready for another exciting year!
- Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa: A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek Journal of Microbiology, 2011, doi:10.1007/s10482-011-9598-6.
- Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH: Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts. SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
(This poster was also presented at the 11th Swedish Bioinformatics Workshop in Lund.)
- Bengtsson J: Metagenomic Analysis of Marine Periphyton Communities. Degree project for Master of Science in Systems Biology, Department of Cell and Molecular Biology and Department of Plant and Environmental Sciences, University of Gothenburg, 2011.
Conferences and workshops
- SocBin Bioinformatics Conference 2011
in Helsinki, Finland
- Open Day in Life Science (2011-05-02)
organized by the Faculty of Science, University of Gothenburg
- Molecular Frontiers Symposium 2011: Origin of Life and Molecular Evolution
at the Royal Swedish Academy of Science, Stockholm, Sweden
- 11th Swedish Bioinformatics Workshop (SBW2011)
in Lund, Sweden
- Chalmers e-science Initiative Seminar
at Chalmers University of Technology, Gothenburg, Sweden
- Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts.
SocBiN Bioinformatics Conference 2011, Helsinki, Finland, 2011-05-12.
- Identification of detoxification systems in marine environments using sequence collections from global ocean sampling.
Open Day in Life Sciences, University of Gothenburg, 2011-05-02.
Research platforms and projects
A MISTRA-funded project to assess risks of human pharmaceuticals in the environment
- Ecotoxicology from Gene to Ocean (EGO)
at the Faculty of Science, University of Gothenburg
Other committees etc.
- Member of the Biology Programme Committee, University of Gothenburg, 2 meetings
- Member of the Systems Biology Programme Committee, University of Gothenburg, 2 meetings
- Reviewed manuscripts for Molecular Biology and Evolution, Statistical Applications in Genetics and Molecular Biology, BMC Bioinformatics, PLoS ONE, Water Research, Science of the Total Environment