Aktiviteter 2007

Abstract:

Human embryonic stem cells (hESCs) are pluripotent and can differentiate into a variety of functional cell types. Thus, they provide a model system for embryonic development with the possibility to investigate the molecular processes of cell differentiation and lineage commitment. In hESC differentiation cultures, the development of the cardiac lineage is easily detected among other differentiated cell types by the appearance of spontaneously contracting areas of cells. However, our understanding of the regulatory mechanisms during early differentiation of the cardiac lineages is limited.
In the present study, we performed gene expression profiling of undifferentiated and differentiating hESCs and monitored approximately 500 genes expressed during cardiac development and/or in cardiac tissue. Their transcription during early differentiation of hESCs through embryoid bodies (EBs), was investigated and compared with spontaneously differentiating hESCs maintained on feeders in culture without passaging (high density (HD) protocol). We examined their expression profiles during differentiation hESCs through embryoid bodies (EBs), a culture condition known to generate contracting cardiomyocytes. Focusing on the ~500 cardiac related genes, we clustered their expression profiles and observed that there was a larger variation in gene expression between cells from a single cell line that were differentiated using different protocols, than in cells from different cell lines that were cultured according to the same protocol. The result indicates that some of the genes potentially share common regulatory mechanisms and prompted us to search for common motifs among the promoter sequences of the genes in each cluster. All together 27 motifs were identified within the promoter regions of the 161 genes from five selected clusters. Our results provide new information about gene regulation during early differentiation of hESCs with emphasis on the cardiomyogenic program. In addition, we also identified potentially important regulating elements that may prove critical for the development of the cardiomyocyte lineage.

Abstract:

Many organisms in nature are very host-specific and specialized on specific host-species. I am working on a theory saying neural constraints in exploiter guilds can promote specialized exploiters. By modeling exploiters' discrimination mechanisms, using artificial neural networks with simulations running over ecological and evolutionary time scales, I study possible effects of specialization from a fundamental genetic level, through the ecological level and ultimately on evolutionary strategies. The first parts of my research were aimed at understanding the coevolutionary interactions between haploid exploiters and their host-species. The second part of my research is aimed at understanding the speciation process of diploid exploiters where behavior may isolate populations and create species, a process referred to as sympatric speciation. My half-time presentation will cover the research I have conducted up till today.

Abstract:

Analysis of gene expression data (e.g. chip intensity value filtering, differential expression, clustering) basically leads to a list of "interesting" genes as the end result. It is often desirable to go beyond that and investigate the relationships between the genes. We will demonstrate PathOptimizer, a research application which attempts to create models of cause and effect relations among a set of genes, given only steady-state data of gene expression levels. Based on our evaluation results on simulated data sets we will briefly discuss the implications on performing this type of analysis on realistic data sets.

Existing basic level courses:

Presenter: Dan Lundh

Systems biology – medical applications, basic A, flexible, 7.5 högskolepoäng/ECTS

Presenter: Zelmina Lubovac

Systems biology – introduction, basic A, flexible, 7.5 högskolepoäng/ECTS

Courses under development:

Presenter: Erik Gustafsson

Course package on advanced level with flexible start

Discussion about developing new PhD courses

Presenter: Annie Jonsson

• Systembiologisk forskning och kritiskt läsande, Avancerad nivå, Research in systems biology and critical reading, Advance level, 3 högskolepoäng/ECTS
• Systembiologisk forskning och muntlig presentation, Avancerad nivå, Research in systems biology and oral presentation, Advance level, 3 högskolepoäng/ECTS
• Systembiologisk forskning och posterpresentation, Avancerad nivå, Research in systems biology and poster presentation, Advance level, 3 högskolepoäng/ECTS
• Systembiologisk forskning och vetenskapligt skrivande, Avancerad nivå, Research in systems biology and scientific writing, Advance level, 3 högskolepoäng/ECTS
• Systembiologisk forskning och populärvetenskaplig presentation, Avancerad nivå, Research in systems biology and popular science communication, Advance level, 3 högskolepoäng/ECTS

Abstract (Swedish):

Mul- och klövsjuka är en väldigt smittsam djursjukdom som kan spridas via alla sorters kontakter mellan gårdar. Dessa kontakter tillsammans med gårdarna kan ses som ett nätverk där smitta kan spridas via kontakterna. Kontaktnätverkens utseende varierar beroende på skillnader i gårdsplacering, antal kontakter, djurslag, tid/säsong mm. För att mäta dessa skillnader använder vi olika nätverksmått samt simulerar smittspridning mellan gårdarna.