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6th Lausanne CompBio Meeting 15th March 2018

Sarvenaz Choobdar, David Dylus, Sven Bergmann and Christophe Dessimoz

Thursday, March 15, 2018 from 9:30 AM to 1:00 PM (CET)

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Type Remaining End Quantity
General Admission 100 Registrations Mar 14, 2018 Free  

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Event Details

 

About Lausanne CompBio

The goal of this meeting is to bring together various UNIL groups that are active in Computational Biology research. The location of the meeting alternates between the UNIL and the CHUV campus and this 6th event will take place in the Salle A in the Genopode building.




Provisional Schedule

  

9:30 - 9:45: Registration

 

9:45 - 9:50: Opening remarks 

 

9:50 - 10:10: Emanuel Schimd-Siegert (SIB):  Low Number of Fixed Somatic Mutations in a Long-Lived Oak Tree

 

10:10 - 10:30: Noushin Hadadi (EPFL): Translating genome-wide expression and metabolomics reprograming of a soil bacterium in the observed physiology

 

10:30 - 11:00: Coffee break

 

11:00 - 11:20: Daniel Wegmann (University of Fribourg): Statistical challenges in analyzing ancient DNA

 

11:20 - 11:40: Santiago Carmona (UNIL / DCB): Single-cell transcriptomic analysis of tumor infiltrating CD8 T cells

 

11:40 - 11:45: Closing remarks 

 

11:45 - 13:00: Lunch & Coffee

 

 

 



 

Abstract

 

Emanuel Schimd-Siegert (SIB): Low Number of Fixed Somatic Mutations in a Long-Lived Oak Tree

Because plants do not possess a defined germline, deleterious somatic mutations can be passed to gametes and a large number of cell divisions separating zygote from gamete formation in long-lived plants may lead to many mutations. We sequenced the genome of a 234-year-old oak tree to study the number and nature of fixed somatic single-nucleotide variants (SNVs). The highly repetitive 720 Mb genome of Quercus robur was sequenced and assembled with a combination of Illumina short-reads and PacBio long-reads to generate a reference genome. A special focus was set on accurate prediction of coding genes, in order to evaluate the potential effect of SNVs. We then compared the genome from leaves sampled on terminal ramets of one lower and one upper branch of the tree. Unexpectedly, only few fixed somatic SNVs were found, whose sequential appearance in the tree could be traced along nested sectors of younger branches. Our data suggest that stem cells of shoot meristems are robustly protected from accumulation of mutations in trees.

Noushin Hadadi (EPFL): Translating genome-wide expression and metabolomics reprograming of a soil bacterium in the observed physiology

Natural bio-degraders are a class of bacteria with particular metabolic capabilities that enable them to degrade and grow on common pollutants such as aromatic toxic compounds and their activity is constrained by environmental conditions. However, there are lots of ambiguity on how they metabolize pollutants and what are the specific pathways involved in the biodegradation process. A predictive metabolic model of a given natural bio-degrader allows investigating its metabolic exchange with the environment as well as the detailed metabolic response to the environmental changes. This lays the foundation to address more practical questions such as how to improve the bioremediation of these compounds and ultimately the efficiency of the bioaugmentation process. In this study, we investigated the metabolic flexibility and versatility of the natural toluene degrader, P. veronii strain 1YdBTEX2 at the system level through the reconstruction and analysis of its first genome-scale metabolic model (itPvr). Genome-scale metabolic models (GEMs) serve as platforms to integrate context-specific data (i.e., omics data), to predict strain-specific phenotypes, and ultimately allow for better understanding of genotype-phenotype relationships. We performed extensive gene expression-driven and exometabolomics-driven gap-filling analysis, curation, and quality control to reconcile gene expression data obtained under various exposures to environmental stimuli and time-course exometabolomics data (secretome). Through a combined genomic-transcriptomic-metabolomic analysis, we quantitatively assessed, how metabolism is reprogramed under different conditions and what are the metabolic effects of such reprograming on the environment. itPvr provides a holistic overview of the metabolic needs and capacities of P. veronii and can guide experimental strategies to enhance the biodegradation capabilities of this strain to be ultimately used in bioaugmentation of contaminated soils. This model can be further used for a community modeling approach where using GEMs of different soil microbial community members, their metabolic interaction can be analyzed.

Daniel Wegmann (University of Fribourg): TBA

Santiago Carmona (UNIL / DCB): Single-cell transcriptomic analysis of tumor infiltrating CD8 T cells

The response of naïve CD8+ T cells to acute infections results in the generation of defined yet heterogeneous pools of effector and memory cells. In contrast, the complexity of tumor infiltrating CD8+ T cell states is still not fully elucidated. To delineate the landscape of tumor infiltrating CD8+ T cells in an unbiased manner, we collected and analyzed single-cell RNA-Seq data of CD8+ T cells infiltrating mouse and human melanomas. Our unsupervised approach revealed the presence of multiple distinct CD8+ T cell subtypes including exhausted, terminal effector, naive and memory-like CD8 T cells, as well as novel intermediate states. TCR reconstruction and pseudo-time ordering enabled us to follow the differentiation process of single clones and suggested two distinct trajectories towards exhaustion. As a resource for tumor immunologists we are developing a web-based atlas (http://www.TILAtlas.org) for seamless exploration of these high-dimensional and information-rich data, which may guide future investigations of the diversity of tumor infiltrating CD8+ T cells.

 

Have questions about 6th Lausanne CompBio Meeting 15th March 2018? Contact Sarvenaz Choobdar, David Dylus, Sven Bergmann and Christophe Dessimoz

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When & Where


UNIL - Génopode
Génopode
Salle A
1015 Lausanne
Switzerland

Thursday, March 15, 2018 from 9:30 AM to 1:00 PM (CET)


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6th Lausanne CompBio Meeting 15th March 2018
Things to do in Lausanne Networking Science & Tech

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