Human gut resistome

EVENT : C3BI Seminars


Main speaker : Amine Ghozlane, from HUB, C3BI, Institut Pasteur Date : 28-02-2019 at 02:00 pm Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


Human gut resistome


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Hands-on microbiome data analysis: tools for understanding microbial communities in health and disease

EVENT : C3BI Training


Main speaker : Gregorio Iraola, from Institut Pasteur de Montevideo Date : 03-12-2018 at 09:00 am Location : Institut Pasteur de Montevideo


This course aims to provide the theoretical and practical concepts for standard bioinformatic analysis in the field of microbiome research. The course will focus on the application of state-of-the-art software tools for the analysis of environmental and host-associated microbiomes, with particular emphasis on understanding how they change or constitute a risk for human health. The course will have expert lectures and theoretical/practical data analysis sessions with real datasets.

 

STUDENT’S PRE-REQUISITES • Directed to post-graduation (M.Sc. or Ph.D.) students. • Basic concepts of high-throughput sequencing technologies. • Basic understanding of metagenomics and microbial ecology. • Basic skills in the Linux terminal.

 

TEACHERS

Institut Pasteur Montevideo

  • Chair: Gregorio Iraola
  • Pablo Fresia
  • Daniela Costa
  • Cecilia Salazar
  • Verónica Antelo
  • Ignacio Ferrés
  • Matias Giménez
Institut Pasteur Paris
  • Marie Lopez
  • Amine Ghozlane
  • Angèle Benard
    • INVITED SPEAKERS
      • Gianfranco Grompone, Discovery Microbiome, Nutrition & Health Science Lead, Lesaffre, France.
      • David Danko, Director of Bioinformatics, MetaSUB International Consortium, Weill Cornell Medicine, US
       

      DEADLINE APPLICATIONS October 19, 2018. Send your CV (one page) and letter of motivation to: antonio.borderia@pasteur.fr

      Flyer_Microbiome_health-course_Montevideo_2018  

Integrated and spatial-temporal multiscale modeling of liver guide in vivo experiments in healthy & chronic disease states: a blue print for systems medicine?

EVENT : C3BI Seminars


Main speaker : Dirk Drasdo, from INRIA / IZBI Joint Research Group Date : 20-09-2018 at 02:00 pm Location : Salle Retrovirus – Bâtiment LWOFF ,Institut Pasteur, Paris


Background and Aims:  Hyperammonemia after drug-induced peri-central liver lobule damage, as from overdosing acetaminophen (paracetamol), and can lead to encephalopathy and dead of the patient. Guided by mathematical models, the consensus set of chemical reactions for detoxification of liver from ammonia has recently been shown to fail in explaining ammonia-detoxification after drug-induced peri-central damage (Schliess et. al., 2014). Our aim is to demonstrate how integrated and spatial-temporal models mimicking detoxification of the blood from ammonia in virtual tissue samples can assist in guiding identification of missing molecular mechanisms, or predicting the impact of micro-architectural alterations due to acute or chronic damage on ammonia detoxification. Our modeling methodology is very general.     Method:The consensus and alternative detoxification mechanisms have been implemented within mathematical integrated and spatial-temporal multi-scale models to test various hypotheses on potentially missing mechanisms in ammonia detoxification during liver regeneration after drug-induced pericentral damage in silicoin a virtual liver lobule (Drasdo et. al., J. Hepat. 2014). The multi-scale model simulates blood flow and molecular transport in the spatial lobule micro-architecture and displays each individual hepatocyte in space and time. Detoxification reactions are executed in each virtual hepatocyte. This makes in silicotesting of hypothesized mechanisms feasible from the molecular up to the tissue scale. The results are directly compared to experiments in mouse. Finally, fibrotic streets have been added to the model to predict the possible impact of architectural distortions and micro-shunts.     Results:We demonstrate how multiscale and multilevel models guided experiments towards identification of a previously unrecognized ammonia detoxification mechanism, that has the potential of improving treatment in hyperammonemia (Ghallab et. al., J. Hepat. 2016). The same model predicts for CCl4-induced fibrosis a reduced detoxification capacity for ammonia. Finally we outline how the whole body scale can be included to arrive at a model spanning molecular up to whole body scale permitting to study the relation of molecular changes and micro-architecture on whole body blood circulation, and briefly summarize results of integration of APAP toxic pathway as HGF signaling.    

Conclusion:Refined multi-scale models increasingly permit realistic prediction of liver function as well as of toxic injury in acute and chronic damage states. Those models can integrate data from various sources, in vitro, different animal models or human data. The direct representation of liver micro-architecture in those models will open up the future perspective to feed these models with patient-specific data, hence generating a virtual twin of a patients’ liver to guide personalized diagnosis and therapy planning.


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Signatures of ecological processes in microbial community time series

EVENT : C3BI Seminars


Main speaker : Karoline Faust, from KU Leuven Date : 04-10-2018 at 02:00 pm Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


Nowadays, a number of densely sampled microbial community time series is available, where the abundance of community members is tracked over several months through sequencing. These data allow exploring community dynamics by investigating signatures of underlying ecological processes that are present in the community time series. In this seminar, I will present our work on the exploitation of time series properties to distinguish between different ecological processes behind the observed dynamics

  http://psbweb05.psb.ugent.be/conet/karoline/

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Computational microbial genomics

EVENT : C3BI Seminars


Main speaker : Zamin Iqbal, from Royal Society/Wellcome Trust Sir Henry Dale Fellow, EMBL-EBI Date : 07-03-2019 at 02:00 pm Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


TBA


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C3BI Courses: Introduction to Molecular Phylogenetics – Hong Kong 2018

General Information:

This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have theoretical morning sessions followed by small groups practice for a few selected students with their own data. Flyer for the course: CLICK ME

Topics:

  • Introduction to phylogeny: General principles for the inference, interpretation of trees, and application to infectious diseases
  • Introduction to the math behind the trees and evolutionary models
  • Distance and parsimony methods
  • Maximum likelihood methods
  • Bayesian methods, phylodynamics
  • Branch supports, bootstrapping
  • How to select the best method and evolutionary model
  • Tree dating, reconstructing and using character evolution
  • Molecular epidemiology

Teachers:

Chair: Olivier Gascuel, C3BI, Institut Pasteur (France)   Anna Zhukova, C3BI, Institut Pasteur (France) Frédéric Lemoine, C3BI, Institut Pasteur (France) Hein Min Tun, School of Public Health, The University of Hong Kong Julien Guglielmini, C3BI, Institut Pasteur (France) Sebastian Duchene, University of Melbourne (Australia) Tim Vaughan, ETH Zürich (Switzerland) Tommy Lam, School of Public Health, The University of Hong Kong Veronika Boskova, ETH Zürich (Switzerland)

Course dates:

Monday, October 22nd to Saturday, October 27th

Pre-requisites:

  • Basic knowledge on how to use sequence databanks
  • Basic knowledge using Blast and multiple alignments software
  • Basic knowledge on statistics (tests, distributions, parameter estimation)

Applications:

Open to postgraduate students, MD, DVM, postdoctoral fellows and young scientists from Hong Kong and overseas. The course fees are 500HK for the theory sessions and 1000HK for the full course. Students coming from the Institut Pasteur International Network will have the fees waived. Please fill in the following application form before August 14th Midnight (HK time). Use the link if you can’t see the embedded form: https://goo.gl/forms/rgYrUNrEz6rqgELP2)

Unit Seminar – Lucas Husquin & Jakob Ruess

 

EVENT : C3BI Unit Seminars


Main speaker : Lucas Husquin, from Human evolutionary genetics unit Date : 15-02-2018 at 02:00 pm Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


Lucas Husquin (Human evolutionary genetics unit) : “Dissecting the impact of population variation in DNA methylation on transcriptional responses to immune activation”

&

Jakob Ruess (InBio : Experimental and computational methods for modeling cellular processes) : “Virtual reality for bacteria”


Unit Seminar – Frédéric Lemoine & Lyam Baudry

 

EVENT : C3BI Unit Seminars


Main speaker : Frederic Lemoine from Bioinformatique evolutive Unit Date : 18-01-2018 at 02:00 pm Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


Frederic Lemoine (Bioinformatique Evolutive) : “Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data”

&

Lyam Baudry (Spatial Regulation of Genomes) : “Metagenome binning using chromosome conformation capture (3C) data”


Seminars – Emergence of de novo protein coding genes from ‘dark genomic matter’ — fact or fiction?

EVENT : C3BI Seminars

Emergence of de novo protein coding genes from ‘dark genomic matter’ — fact or fiction?


Main speaker : Erich Bornberg-Bauer, from The Westfalian Wilhelms University of Muenster, Germany
Date : 09/11/2017 at 02:00 pm
Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


Proteins are the workhorses of the cell and, over billions of years, they have evolved an amazing plethora of extremely diverse and versatile structures with equally diverse functions. Therefore, their evolution echoes the evolution of all forms of life. Evolutionary emergence of new proteins and transitions between existing ones are widely believed to be rare or even impossible.
However, recent advances in comparative genomics have repeatedly called some 10%-30% of all genes without any detectable similarity to existing proteins. Even after careful scrutiny, some of those “orphan” genes contain protein coding reading frames with detectable transcription and translation. Thus some proteins seem to have emerged from previously non-coding ‘dark genomic matter’. These ‘de novo’ proteins tend to be disordered, fast evolving, weakly expressed but also rapidly assuming novel and physiologically important functions. I will review mechanisms by which ‘de novo’ proteins might be created, under which circumstances they may become fixed and why they are elusive. I will present a couple of studies which mostly focus on metazoan genomes.


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Publication – Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov

EVENT : C3BI Publication

Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov


Main speaker : , from Date : 01/09/2017 at Location : ,Institut Pasteur, Paris


The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146(T) = DSM 2975(T) = CCUG 69503(T) = CIP 111191(T)) and Elizabethkingia ursingii sp. nov. (type strain, G4122(T) = DSM 2974(T) = CCUG 69496(T) = CIP 111192(T)), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070(T) = DSM 2976(T) = CCUG 69505(T) = CIP 111193(T)), is proposed.


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