Welcome to the MLS Master Academic matters: Christian Fankhauser, CIG Bâtiment Génopode 4008 [email protected] 021 692 3941 Administrative matters: Almudena Vazquez École de Biologie, Bâtiment Amphipôle, bureau 312 [email protected] 021 692 4010

Master MLS

Thank you

Corinne Dentan, CIG Bâtiment Génopode 4006 [email protected] 021 692 3930 Master MLS

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Looking for information? Check the webpage: http://www.unil.ch/eb-mls/home.html -  -  -  -  -  - 

Specializations (mentions) Study program Research projects (how to apply) Host laboratories (some of them) Contact And much more…

Master MLS

Today’’s menu •  A few introductory words about the master •  Some organizational points about the retreat •  Departure for the retreat (9 30)

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Master in Molecular Life Sciences

Genomics

Research

Master MLS

Next generation sequencing to study a broad range of biological questions Model systems

Clinical Research

Plant, microbial and animal genetics

GTF platform Master MLS

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Mentions/specialization Bioinformatique

Integrative Biology

Microbiology

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Specialization (mention)

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A broad range of research areas to chose from: different types of organisms

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…different levels of organisation

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…different analysis methods

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…more applied research

« Red » biology/bio-medical: Nicolas Mermod (IBT) Plant biology: Yves Poirier (DBMV) Microbiology: Jan Roelof van der Meer (DMF) Master MLS

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Bioinformatics in the MLS master: for all and for those who want to specialize •  Bioinformatics: use informatics to analyze biological data •  Basic knowledge in informatics, statistics and data analysis are becoming increasingly more important in biology. •  Mention Bioinformatique: learn how to program •  Bioinformatics is covered at different levels during the MLS master: –  –  –  –  – 

Common classes during the 1st and 2nd semester (sequence a genome) Optional courses in the 1st semester (blue label) Optional courses semester 2 (blue label) 1st step master project (sem 1) and master project (sem 2 & 3) Course to catch up with statistics: Introduction to R

•  More information will follow during the retreat from Ana Claudia Marques

Master MLS

The program

Common activities (semester 1) • Retreat • BIG seminars • Sequence a genome part I • Write a review (part I)

Selected activities (semester 1) • Pick 6 courses (choice of 13) or 3 specific bioinformatics classes (mention bioinformatique) • Choose a first step project Master MLS

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The retreat •  Aim Introduce the program Help you selecting optional courses Starting “Write a review” class Getting to know each other

Master MLS

The retreat (September 20) •  Arrival & Lunch at Le Vieux Chalet, Château d’Oex •  14 00

Introduction about the master program (C. Fankhauser)

•  15 00

2nd year master students meet the new students

•  16 00

Coffee break

•  16 30

Presentation Pharmalp (Dr Philippe Meuwly)

•  17 30

« Write a review»:Overall course presentation (15 min.); 1st presentation of the topics (30 min.); scientific writing (45 min.).

•  19 20

Presentation Bioinformatique: A. Marques

•  19 30

Dinner

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The retreat (September 21) •  08 30

“Write a review”: selection of the topics (M. Sohrmann and C. Fankhauser)

•  09 10

Presentation DMF: S. Mitri

•  09 30

Presentation CIG: R. Benton

•  09 50

Presentation IMUL: A. Ciuffi

•  10 10

Coffee break

•  10 40

“Write a review”: guidelines (M. Sohrmann and C. Fankhauser)

•  11 20

Presentation of DBMV: Y. Poirier

•  11 40

Presentation IBT: A. Berger

•  12 00

General discussion

•  12 15

Departure for a little hike.

Master MLS

The excursion

Pont Turrian (1883) Master MLS

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Let’s go

Master GBE

Life as a master student Important transition -  Less « ex cathedra » classes -  You have to participate more actively -  More independence, handling different tasks at the same time. -  Transition towards a scientific career (lab work, critical analysis, scientific writing) -  More work during the semester, less for exam preparation Master MLS

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Your master program on one slide Semester 1

Module 1

Compulsory and optional courses (16 credits ECTS)

Module 2

First step project (14 credits ECTS)

Exams Semester 2

Module 3

Compulsory and optional courses (15 credits ECTS)

Module 4 Master Project : A personal research project (45 credits ECTS)

Exams Semester 3

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Defense of the Master project

The program 1st semester

Common activities • Retreat • BIG seminars • Sequence a genome part I (3 ECTS) • Write a review (part I) (4 ECTS) • Security course (Thursday 22/9 at 13 15 MAX415). Intro about the school of biology (earlier today)

Selected activities • Pick 6 courses (choice of 13) or 3 specific courses for those who do « bioinformatics » (9 ECTS) • Choose a first step project (14 ECTS) Master MLS

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The program 2nd semester

Common activities • Sequence a genome part II (3 ECTS) • Write a fellowship request (part II) (3 ECTS)

Selected activities • Pick optional courses (9 ECTS) • Supplement Sequence a genome (1.5 ECTS) • Master Project part I (15 ECTS) Master MLS

The program 3rd semester

Finish your master project (30 ECTS)

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Semester 1: organization •  First 2 weeks are special •  Mondays optional classes •  Tuesdays common activities •  When you are not following classes you are expected to work on your 1st step project. You do have ½ a day free per week to prepare various classes (critical readings of scientific literature). •  Last week no more classwork. Your 1st step projects will be presented on Wednesday and Thursday December 21&22. I will organize a schedule Master MLS

First 2 weeks •  Select your optional courses. These courses start next Monday (September 26). •  Start working on the Write a review course •  Start “sequence a genome”. •  Select a 1st step project •  Information from the School of Biology (EB), Biological Security

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Evaluation of the 1st semester •  Theoretical final mark = module 1 Weighted mean of marks of compulsory courses and optional courses (coefficients correspond to ECTS credits)

•  Practical final mark = module 2 Arithmetical mean of three marks on the first step project : written report /oral defense (December 21 and 22)/ practical work.

•  Success conditions Theoretical and practical final marks ≥ 4.0

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Information about courses, your 1st step project & master project •  Common courses •  1st step and master project •  Optional courses

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Sequence a genome This class is evaluated based on your participation 50% and an oral exam 50% (3 credits) •  Objec&ves: -  Learn how to work with latest genome sequencing technologies -  Perform a group experiment studying compara=ve bacterial genomics •  Plan: -  (1st semester): Genome assembly (from Illumina) and annota=on of 15 isolates of Lactobacillus sp. from bumblebees -  (2nd semester): analysis projects by pairs, interpreta=on, wri=ng a manuscript •  Course Organisers: Philipp Engel, Kirsten Ellegaard, Marc Robinson-Rechavi & Jan Roelof van der Meer

Master MLS

Write a review

Informa=on will follow at 17 30 and later during the retreat

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Select 1st step and master projects •  You have a large number of projects to select from •  You have to change labs between the 1st step project and the master project •  The projects are deposited on line. You should select your project by Sunday October 2 at the latest •  Meet the PIs and talk to them before signing up. •  You will be evaluated as follows. 1/3 evaluation of your lab performance (PI + assistant), 1/3 oral presentation (PIs), 1/3 your report (PI + assistant + 1 expert)

Master MLS

Selecting 1st step projects (weeks 1 & 2) •  Check the website for project selection. The schoold of biology informed you this morning about how to proceed. I will provide a little reminder in a few minutes. •  Check the labs on line: lab webpages & new MLS webpage under “Host laboratories” •  Visit labs you found interesting (more than 1!) •  Discuss this amongst yourselves •  Decisions on acceptance are not taken immediately (the PI may have more than one student visiting for a project). Mutual agreement is needed.

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How to select your 1st step project Webpage : www.unil.ch/ecoledebiologie Ø  for students Ø  Master Research project Ø  Project selection & registration (for students) Or https://www.unil.ch/eb-mls/en/home.html Ø  Research project Ø  Project selection & registration (for students)

Master MLS

Signing up: important dates Courses and exam : •  September 20 to October 16, 2016

Please do it ASAP

First-step project : •  September 20 to October 2, 2016 Master project : •  November 1 to 15, 2016 Master project outside of UNIL: •  by November 1, 2016

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Master project (i) 

2nd semester

Check the list and discuss projects with the people from the labs. You may also directly contact a lab which didn’t write an offer.

(ii)  You have to change labs between the 1st step and the master project. (iii)  You have to announce your choice for a master project that isn’t done within the FBM (UNIL) to the EB before November 1st. (acceptance by the EB required) (iv)  Announce your master project choice (done within FBM) to the EB before November 15.

Optional classes during the 2nd semester (i) This is an “à la carte” system. (ii) Organize your menu with input from your master project supervisor. (iii) Check class description which are available on line. (iv) Don’t hesitate to contact people if you want to know more about their classes. (v) I will provide you with some info on those classes later in the semester. Master MLS

Optional classes to select from •  You have to select 6 optional classes from a total of 13 that are proposed. Each class is worth 1.5 credits (9 total) •  All these courses are 14 hours of class. •  The classes are taught in blocks of 4 weeks each. There is one exception (Scientific research in all its forms, taught in French & different schedule) •  Method of evaluation depends on the course •  You have to sign up for all classes. Please hurry up for those starting next Monday. Ask your UNIL colleagues for how to do it. Master MLS

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Molecular Mechanism of Evolution

Niko Geldner (DBMV): “Mechanisms of evolution of plant structure and function” - How do differences in leaf shape arise?

- How is flower morphology changed and selected for? - Adaptations of plants to differences in growth environments - Mechanisms driving speciation

Richard Benton (CIG): “Germline and sex determination in insects and beyond” - How is the “immortal lineage” – the germline – specified during development? - What can study of germ cells tell us about stem cells? - How are male and female sexes differentiated? - What is evolutionarily conserved and divergent between these developmental decisions in different organisms?



Master MLS

Immunology with relevance to infectious diseases 7h. Innate Immunity : Dr. Thierry ROGER (Infec=ous Disease Dpt) Ex cathedra course The objec=ve of the course is to describe the func=ons and the characteris=cs of the innate immune system, focusing on the role played by the external barriers, the complement system, the innate immune cells, the paTern recogni=on receptors and the cytokines. We will also address the involvement of dysregulated inflammatory and innate immune responses in the pathophysiology of sepsis, and how basic and clinical research has led to the iden=fica=on of new therapeu=c op=ons for sep=c pa=ents. 7h. Adap&ve Immunity and Vaccina&on : Dr. Denise NARDELLI (Urology dpt) Lecture , inclass scien8fic paper reading, simula8on-training. •  Brief reminder of adap=ve immune responses to pathogens and immune escape mechanisms. Specific examples on human papillomavirus immunobiology. •  Presenta=on of Vaccina=on approaches and problems. Simula=on training of a Vaccine development.

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Virus-host interaction Pascal Meylan, Stefan Kunz Objective The course will cover fundamental principles of virus-host interaction, cellular, and systemic pathogenesis at an advanced level. Content Basic concepts of cellular and systemic viral pathogenesis (Meylan) Molecular and cellular mechanisms of innate anti-viral immunity (Kunz) Virus infection in the nervous system (Kunz) Medical relevance of viral pathogenesis (Meylan) Format Lectures combined with discussion of key papers in the course Prerequisites Cours virologie générale 5th semester (20 hours) Kunz Recommended accompanying courses Immunology with relevance to infectious disease (Nardelli, Roger, Calandra) 7th semester Master MLS

Plant Functional Genetics Yves Poirier (DBMV) Get an overview of the spectrum of genetic and genomic tools used to isolate and decipher the role of genes involved in various aspects of plant biology Some topics:

- nuclear and plastid transformation - viral vectors - T-DNA and transposon mutagenesis - RNAi

Course is based on lectures (ex cathedra) and will be evaluated by a written exam Master MLS

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Human Molecular Genetics Goals - Provide advanced knowledge on human molecular genetics - Understand the bases of functional analyses of genes via the use of cellular and animal models - Learn how to take advantage the massive amounts of data from in silico databases in everyday laboratory practice Contents - The course will consider hereditary conditions in humans to describe the link between DNA variants and phenotypes - Classes will follow the threads "from observation to the DNA", "from the DNA to the gene" and "from gene to function" to illustrate classical scenarios of genetic investigations - The program will rely heavily on "hands-on" approaches and the direct participation of the students, via individual computers connected to the internet Prerequisites - Knowledge of concepts of genetics and molecular biology Carlo Rivolta (DGM) Master GBE

Fungal virulence and pathogenicity • 

Dominique Sanglard (IMUL)

• 

Characteristics of major fungal pathogens (Candida, Cryptococcus, Aspergillus) and genome structures

• 

Key steps in the pathogenesis of fungal pathogens

• 

Virulence factors and resistance to host defense mechanisms

• 

Fungal- host interactions with emphasis to fungal cell walls

• 

Pathogenesis of dermatophytes: importance of secreted enzymes (M. Monod)

- other teachers (Philippe Hauser (IMUL) Michel Monod (CHUV)

Candida yeast and hyphae

Arthroderma benhamiae Infecting animal skin

• 

Epidemiology and pathogenesis of dimorphic fungi and

• 

Paper presentations and discussion

• 

Visit of a hospital laboratory and initiation to fungal diagnostics

Pneumocystis spp. (P. Hauser) Pneumocystis in human samples

D. Sanglard

M. Monod

P. Hauser

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Plant interactions with microbes and insects: Friends and foes

… lectures and a student excercise for designing research … Ted Farmer (DBMV)

Molecular study of plant - insect interac&ons -  Transcrip=onal control of plant defense responses -  Suppression of defenses by insects -  Insects as friends of the plant

Christoph Keel (DMF)

Molecular basis of host specificity in phytopthogenic bacteria - Virulence and avirulence -  Injec=on devices and effectors for subver=ng plant defense -  Conserved virulence machinery in human pathogenic bacteria

Master MLS

Development of the nervous system Olivier Braissant Course: 14h, including 12 h « ex cathedra », and 2h paper presentation and discussion by students. Molecular and cellular mechanisms of brain development in vertebrates, including the main pathologies affecting CNS development. Important accent on the various experimental models to be used to analyze vertebrate CNS development, both in vivo and in vitro. Master MLS

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Protein homeostasy and adaptation of organisms to stress!

Pierre Goloubinoff (DBMV) ! - Principles of protein native folding, alternative folding, unfolding misfolding and aggregation" -  Mechanisms of disaggregating and unfolding chaperones and proteases" -  The heat-shock response in animal and plants" -  Mechanisms of acquired thermotolerance" - Teaching style: combination of frontal lectures and paper discussions" Master MLS

Advanced microbial genetics Basic idea:

Course objectives

Justine Collier, Serge Pelet, DMF

Learn how to design genetic screens to understand molecular mechanisms in microbes?

- Appreciate the history and founding principles of microbial genetics. - Think logically about experimental approaches. - Illustrate how cleverly designed genetic experiments can provide answers to fundamental problems. - Learn about new technology developments in genome-wide screens. - Read the scientific literature critically.

How? Courses on bacterial and yeast genetics; literature reading and discussion during class Master MLS

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Bacterial Genomes and Genome evolution

Jan Roelof van der Meer, DMF

Basic idea: More than 1000 bacterial genomes have been sequenced! Course objectives

What can you do with this information?

1. Being able to interrogate and interpret genomic databases for metabolic information (pathways, genes and enzymes, compounds) 2. Understand basic principles of metabolic maps and metabolic modelling 3. Understand specific metabolic adaptations to the environment or host 4. Being able to compare genomic information across different bacterial species 5. Learning to read and comprehend (bacterial) genomic literature

How? Some classical teaching (by me), database exercises (by all), literature reading and discussion during class Master MLS

Biotechnology •  Yves Poirier (DBMV) and Nicolas Mermod (IBT)

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La recherche dans tous ses états Regards croisés de scientifiques de tous bords sur une même thématique à points de vue des biologistes, sociologues, politologues, historiens, économistes, etc.

Organisé par Delphine Preissmann (DEE) La tragédie des communs Comment exploiter de manière durable une ressource à la fois limitée et mise à disposition de tout un chacun?

Bioinformatics classes (semester 1) •  Advanced Data Analysis in Biology I-II (F. Schütz) •  Those who did not follow the UNIL Bachelor are strongly encouraged to follow Introduction to R (F. Schütz) •  Case studies in Bioinformatics (S. Bergmann + others) •  Programming for Bioinformatics (N. Salamin)

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