Alexander Pozhitkovi külalisseminar 10.09.13

Dr Alexander Pozhitkov (University of Washington, Seattle, USA) peab 10.09.2013 kl 14.00 TÜ Molekulaar- ja rakubioloogia instituudis Riia 23 auditooriumis 217 külalisseminari teemal: 

"Beyond Death: Postmortem Transcriptome and Microbiome of Zebrafish and Mice Assessed by 454 Sequencing and Directly Calibrated Microarrays"

Kokkuvõte:

Cells in a recently deceased organism do not cease activity immediately due to a certain amount of reserved nutrients and energy. The gradual shutdown process should be possible to map and understand in terms of known metabolic pathways if they are accurate. Microorganisms sense changes in the host defense and react appropriately. Understanding of the postmortem gene expression and microbiome dynamics (i.e., 'Thantome') has critical implication in forensics as well as systems biology. Forensics may benefit from the thantome for determining the time and cause of death, while systems biology may be challenged with regard to accuracy of current understanding of the metabolism and regulation.

Experiment. Euthanized animals were kept in their native conditions, i.e., 20degrees for zebrafish and room temperature for mice. A time series of gene expression and microbiological samples from zebrafish (Danio rerio) and mice (Mus musculus) was investigated at regular intervals up to 96h postmortem.  Samples were analyzed by calibrated microarrays and 454 next generation sequencing of the 16S rRNA genes.

Results. A novel microarray calibration approach was developed to directly calibrate microarray probes thereby making each individual probe's response and sensitivity known (i.e., probe response function).  Each probe response function was used as a calibration curve allowing direct conversion of signal intensity into relative mRNA concentration without

any normalization procedures and pertinent assumptions.   Zebrafish

postmortem Transcriptome activity showed much more transitory upregulated genes compared to mice.  In both species, immune response was detected.

Interestingly, for zebrafish the immune response peaked at 24h postmortem and coincided with an 'explosion' of innate microbiome diversity.  Many other known and unknown genes showed transitory upregulation at various postmortem time points.  Analysis gene ontology terms for the upregulated genes is in progress

Lisainfo: prof. Maido Remm (maido.remm@ut.ee)