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Microbial Forensics

Microbial Forensics is an emerging scientific field that got its breakthrough after the anthrax letters in USA 2001. Knowing the evolution patterns and history of pathogen is important for tracking outbreaks and differentiate natural from deliberate outbreaks. The new sequencing technologies have open new possibilities to accomplish this task by sequencing different pathogen isolates to understand the difference between clinical and environmental clones.

The aim with this work has been to use next-generation sequencing to achieve higher resolution compared to former used molecular methods and to increase the understanding in bacterial evolution and genetics. During the last years bacterial genomes has been sequenced using 454 and Illumina technology. The sequenced genomes are both human pathogen and environmental isolates. The reason for studying environmental samples is to be able to understand the natural background of close relatives of human pathogens. Knowing what kind of close relatives and how fast genomes evolve will help in distinguee natural outbreaks from potential terrorist attacks. The outcome from this project is to understand difference of bacterial evolution in laboratory and under natural environments plus how the new sequencing technologies can help us to achieve it.

PopGenIE

The first release of Popgenie contained basic information about the Populus genome [1]. An immediate positive response from the community was asking for more extensive development to support their research. The work of Popgenie2 started in 2009 after the Popgenie article got published. The new version is a major extension compared to the initial release. The database has been totally rewritten and is now hosted by a Drupal installation. New additions include for example gene pages, next-generation data support and additional easy accessible bioinformatic tools.

Populus transcriptomics - from noise to biology

The project was separated in two parts, method development for transcriptomics and biological conclusions about free-growing aspens trees based on transcriptomics. I was also involved in several inhouse and international collaborations in addition to my own biological research. The involvement in other projects has mainly been implementing new tools and algorithms to streamline the analysis pipeline of microarray data.

Method development

The method development was focused on streamlining the analysis pipeline and to provide tools for the biology researchers. It can be summarized in three main points.

  • Improved image analysis and quality control[2][3]
  • Novel normalisation of microarray data[4]
  • Database resource for Populus microarrays (UPSC-BASE)[5]

In addition to these publications several minor tools for various uses were implemented as Python, Perl, R or web applications. Future interest involves further development and cross integration of available omics-technologies.

Biological achievements

The main part was to use transcriptomic tools on free-growing trees all over the season to find important phases describing the process from bud burst to senescence. The work is published in two main articles, spring and summer data [6], and the senescence process [7]. The collaboration with other research groups was valuable for gathering transcriptional information about different stress conditions for Populus. The complete data set stored in UPSC-BASE was then used to screen for individual genes and gene regulon networks important for wood and leaf development and stress responses.

References

  1. Sjödin A, Street NR, Sandberg G, Gustafsson P, Jansson S. The New phytologist. 2009;182(4).
  2. Bylesjö M, Eriksson D, Sjödin A, Sjöström M, Jansson S, Antti H, Trygg J. BMC bioinformatics. 2005;6.
  3. Bylesjö M, Sjödin A, Eriksson D, Antti H, Moritz T, Jansson S, Trygg J. Bioinformatics (Oxford, England). 2006;22(20).
  4. Bylesjö M, Eriksson D, Sjödin A, Jansson S, Moritz T, Trygg J. BMC bioinformatics. 2007;8.
  5. Sjödin A, Bylesjö M, Skogström O, Eriksson D, Nilsson P, Rydén P, Jansson S, Karlsson J. The Plant journal : for cell and molecular biology. 2006;48(5).
  6. Sjödin A, Wissel K, Bylesjö M, Trygg J, Jansson S. BMC plant biology. 2008;8.
  7. Andersson A, Keskitalo J, Sjödin A, Bhalerao R, Sterky F, Wissel K, Tandre K, Aspeborg H, Moyle R, Ohmiya Y. Genome biology. 2004;5(4).