Ecole doctorale Biologie-Médecine

Programme 2017-2018

Module on metabolism for PhD studentsOrganizers: Mirko Trajkovski and Pierre Maechler

• The module will have five sessions and will include lectures given by the PIs (Mirko Trajkovski (MT), Pierre Maechler (PM), Valérie Schwitzgebel (VS), Michelangelo Foti (MF), Roberto Coppari (RC) and Thierry Brun (TB)) and their assistants; practical (hands on) work by the students; overview on the most important literature in this area; and overview on the clinical aspects in diagnosis and treatment of several metabolic diseases. The main goal is to familiarise the students with the basic principles governing the regulation of the energy homeostasis and metabolism in health and disease, and will be accomplished by addressing the following specific

• subjects:

• • Human and mouse anatomy in context of metabolism; emphasis on the main

• metabolic organs;

• • Importance of gut microbiota in regulation of energy homeostasis;

• • Fat metabolism – different shades of fat, characteristics and importance;

• • Function of the pancreas with emphasis on the insulin secretion;

• • Importance of liver and muscle in the overall glucose homeostasis;

• • Importance of the brain in regulating the energy homeostasis;

• • Clinical overview on the metabolic diseases

• Schedule

• Session 1 Human and mouse anatomy in context of metabolism (~4 hrs) (Tuesday

• 03.10.2017 – 9.30am) – MT (B04.1520)

• a) Lecture by Mirko Trajkovski (45 min)

• b) Dissection of surplus mice. (2h) Two students will work on one mouse. The goal of this is to familiarise the students to the location and morphology of the main metabolic organs. Students will be asked to dissect the animals and to collect and measure most of the organs, with a particular emphasis to the following:

• - Adipose tissue: various types - ingSAT, pgVAT, iBAT (isolation and weight)

• - Liver (number of lobes, weight)

• - Muscle - quadriceps, gastrochemius and soleus

• - Stomach and intestine – weight and morphology of the stomach, weight and

• length of the small and large intestine, cecum

• - Brain (collecting the brain, recognising the regions)

• - Location of the pancreas

• c) Microbiota importance in metabolism – Lecture by Mirko Trajkovski (45 min -1h)

• Session 2 Fat metabolism (~3,5 hrs) (Friday 06.10 – 9.30am) – MT (B04.1520)

• a) Lecture by Mirko Trajkovski – “Three colours beige” (45 min)

• b) Discussion on a landmark paper provided to the students before hand (45 min)

• c) Histological analysis of white, brown and beige fat – H/E stained slides will be provided. Students will be asked to look at them and identify from which depot they originate from. Their characteristics will be drawn by the students and commented on. (2h)

• Session 3 Liver and muscle (2h) (Monday 09.10 – 4pm) – MF (B04.1520)

• a) Lecture by Michelangelo Foti (liver and muscle) (45 min)

• b) Discussion on a landmark paper provided to the students before hand (45 min)

• Session 4 The endocrine pancreas (3 hrs) (Thursday 12.10 – 9.30am) – PM (A04.3016)

• a) Lecture by Pierre Maechler (1h 15min), followed by discussion/pause (30 min)

• - The islet of Langerhans and tools to study its cellular functions

• - Beta-cell function and the regulation of insulin secretion

• - Beta-cell development and maturation 2)

• - metabolism adaptation

• - Alpha-cell function and the regulation of glucagon secretion

• - Glucose homeostasis

• - Glucolipotoxicity, obesity, and type 2 diabetes

• - Beta-cell dysfunction and diabetes

• - Drugs targeting beta-cell function

• - Stem cell approaches for diabetes treatment.

• b) Discussion on landmark paper provided to the students before hand – Thierry Brun (1h

• 15min)

• Session 5 Clinical overview on the metabolic diseases (Monday 16.10 – 9.30am) – VS

• (A04.3016)

• a) Lecture by Valérie Schwitzgebel – Metabolic disorders at the clinical level (45 min)

• b) Overview on the experimental metabolic facilities at the CMU (1.5-2h)

• Session 6 Brain (2hrs) (Wednesday 18.10 – 9.30pm) – RC (B04.1520)

• c) Lecture by Roberto Coppari (Brain) (45 min)

• d) Discussion on landmark paper provided to the students before hand (45 min)

• Exam/Discussion: Thursday 19.10 – 9.30pm – MT&PM (B04.1520)

• Oral exam/discussion with Mirko Trajkovski and Pierre Maechler

IMMUNITY. November - December 2017The aim of the course will be to present key areas of basic and applied immunology over 4 themedsessions. The interdependence of innate and adaptive immune interactions will be stressed, and aselection of protective and pathologic immune processes will be discussed. Students are expected toattend all sessions and to actively participate. Assessment will be made both during the courses (somereading will be required beforehand) and in a final exam.

•Dr. Paul WALKER, Dept. of Internal Medicine Specialities, Division of Oncology.

•Prof. Carlo CHIZZOLINI, Dept. of Internal Medicine Specialities, Division of Immunology & Allergology.

•Prof. Carol BOURQUIN, Prof. Carole Bourquin, Department of Anaesthesiology, Pharmacology and Intensive Care, Faculty of Medicine & Geneva - Lausanne School of Pharmacy.

•Prof. Monique GANNAGE, Dept. of Pathology and Immunology

• Thursday November 16, 2017 at 2 - 5.30 pm

Paul Walker : Introduction to the Immune system. Innate and adaptive immunity, B cells, antibodies, NK cells.

• Wednesday November 22, 2017 at 2 - 5.30 pm

Carlo Chizzolini : Inflammation

• Thursday November 30, 2017 at 2 – 5.30 pm

Carole Bourquin : Cancer and the Immune System; Immunotherapies including therapeutic antibodies

• Thursday December 7, 2017 at 2 – 5.30 pm

Monique Gannagé : Antigen presentation, cells involved, canonical and non-canonical processing pathways.

• Thursday December 14, 2017 at 2 - 5.30 pm

Examination

The course will take place with a minimum of 6 and a maximum of 16 participants.

Exact times are subject to confirmation.

"Communicating your science: how to make the message stick!”

• Tuesdays 12.12 and 19.12, 9am to 5pm (1 hour lunch break).

• The course will be given by an external guest, Marc Sohrmann, who has been giving this course for the past few years to PhD students from UniL.

• Goals of the course:

• Communicate persuasively your work in an oral presentation

• Create slides that respect fundamental design and principles and present data appropriately

• Experiment strategies to continue improving your presentation skills

• Write a title and a concise abstract that tells your scientific story

• The participants will bring a 5 minute presentation of their research project to the first day of the course.

• Participation is limited to 8 people

REGULATION OF GENE EXPRESSION December 2017- January 2018

• Monitors: Prof. Martine Collart (Department of Microbiology and Molecular Medicine, Prof. Emmanouil Dermitzakis & Prof. Rabih Murr (Department of Genetic Medicine and Development).

• The module comprises four 3,5 hour sessions, including a break. The "philosophy" of the course will be briefly presented at an introductory meeting.

• Before each session: A research problem related to gene expression regulation is proposed to the students, at least one week before each session. The problem is divided into several objectives and each group of students will be assigned to address one objective. To help the students in this process, few articles will be suggested for reading.

• During the session: Each group will be given 20 minutes to present their part of the proposal (in English), which should include: 1) a clear mention of the steps needed to reach the objective, 2) the experimental approach(es) used and the reasons behind choosing these approaches, and 3) expected results. The presentations will be interactively discussed in a critical and detailed manner.

• The aim of this course is not only to provide the students with a general knowledge of the mechanisms underlying the extraordinary diversity in gene expression, but also to give them the opportunity to develop an ability to design and interpret appropriately a project aimed at adressing an issue in the field.

• The introductory meeting will be held on Friday 15 December 2017 from 14h30 to 16h.

• The sessions will take place on Fridays 12, 19, 26 January and 2 February 2018 from 14h30 to 18h.

• ATTENDANCE AT ALL SESSIONS IS MANDATORY

• The course will only take place with a minimum of 8 participants and a maximum of 15

Cardiovascular Physiology & DiseaseJanuary – February 2018

• Dr Christophe MONTESSUIT, Dept of Pathology & Immunology

• Prof. Brenda KWAK, Dept of Pathology & Immunology• Dr Marie-Luce PIALLAT, Dept of Pathology & Immunology

• Dr Georg EHRET, Division of Cardiology• Dr MARC BLONDON, Division of Angiology and Hemostasis

• Wednesday January 10th 2018: Christophe MONTESSUIT / Brenda KWAK• Introduction to cardiac and vascular physiology (lectures)

• Wednesday January 17th 2018: Marc BLONDON• Clinical cardiovascular research (practical course)

• Wednesday January 24th 2018: Georg EHRET• Cardiovascular Genomics (practical course)• Wednesday January 31th 2018: Brenda KWAK • Atherosclerosis research (brief introduction & microscopic pathology)• Wednesday February 7th 2018: Marie-Luce PIALLAT • Cardiovascular pathology illustrated (brief introduction & macroscopic pathology)

• Wednesday February 21th 2018: Christophe MONTESSUIT• Experimental models in cardiac research (brief introduction & Langendorff perfusion)

• Wednesday 7 MARCH 2018 : ORAL EXAM

• The module will take place upon a minimum participation of 5 students from 14 to 17h.

BACTERIOLOGY(from classical bacterial genetics

to modern medicine)FEBRUARY 2018

• Profs. Patrick LINDER & Patrick Viollier, Dept of Microbiology & Molecular Medicine

• Teachers are : Patrick VIOLLIER(PV), Thilo KOEHLER(TK), William KELLEY(WK), Patrick LINDER(PL), Adriana Renzoni (AR) and proposed subjects are (subjects may change, according to speakers we will be able to attract for the seminars) :

• CRISPR/Cas in biotecnology(AR)• Secretion (WK, PL)• Cell division cycle (PV)• Quorum sensing/ antibiotic reisistance (TK)

• The course will be held on Monday 29 January 2018, 05 February 2018, 12 February 2018, 19 February 2018, from 14h to 16h. Room A09.2525

• 26 February 2018, from 14h to 17h / EXAM / Room E07.3347 .

• Discussion of a recent paper and a review on the topic

• The 4 courses may be combined with a Monday seminar from 11:30-12:30 that should be attended

• Prof. E. Zdobnov Département de Médecine Génétique et Développement

• Le Prof. E. Zdobnov vous invite à une première réunion le mardi 27 février 2018, de 14h. à16h., dans la salle E09.2753.A (ex 9078), 9e étage (CMU).

• La classe se réunira de 14h. à 16h., salle E09.2753.A, 9e étage, aux dates suivantes :

• mardi 27 février 2018: Introduction par le Prof. E. Zdobnov

• jeudi 1er mars 2018 : Genetic Variation par le Prof. E. Dermitzakis

• lundi 5 mars 2018 : Mendelian Disorders par le Prof. S.E. Antonarakis

• jeudi 8 mars 2018 : Cytogenetics par la Dre F. Bena

• lundi 12 mars 2018 : Technology par la Dre E. Kriventseva

• mardi 13 mars 2018 : Comparative Genomics par le Prof. E. Zdobnov

• lundi 19 mars 2018 : Complex Disorders /Traits par le Prof. E. Dermitzakis

• mardi 20 mars 2018 : Epigenetics Prof. R. Murr

• mardi 27 mars 2018 : Exam Prof. E. Zdobnov

Génétique Médicalefévrier-mars 2018

CELL INTERACTION March – April 2018

• Dr. B. WEHRLE-HALLER, Dépt. Physiologie Cellulaire & Métabolisme /

• contact: bernhard.wehrle-haller@unige.ch• Dr. S. Garrido-Urbani, Dépt .de Pathologie et Immunologie; Dr. L. Fontao, Dépt. de Neurosciences

Clinique & Dermatologie; Dr. P. Soulie, Dépt. Physiologie Cellulaire et Métabolisme ; Prof. Marc Chanson, Dépt. Physiologie Cellulaire et Métabolisme; Prof. W. Kelley, Dépt. de Microbiologie.

• The course aims to introduce students to the biology of cell interaction, from pathogen-host to cell-cellcommunication, and from molecular and genetic factors to tissue function and disease. The course involves attending 6 sessions held in a three –week period, guided by experts in their respective fields.

• Each session lasts no more than 2 hours and is focused on discussing current knowledge and techniques used in studying cell interactions, using as reference pre-assigned research articles relevant to the chosen topics (see below). It is essential for students to read the material before class and to actively engage in the discussions. Student evaluation is achieved through a 30 minutes oral examination and the format will be explained during the first session.

• « Adhesion, Integrins and Signaling », Dr. B. Wehrle-Haller• « Tight Junctions : a Dynamic Fence », Dr. S. Garrido-Urbani• « Epithelium-Substrate Adhesion », Dr. Lionel Fontao• « Direct Communication : Gap Junctions », Prof. M. Chanson• « From Cells to Tissues », Dr. P. Soulie• « Bacterial Interactions », Prof. W. Kelley

• SCHEDULED DATES: Friday, March 9th, Wednesday, March 14th Friday, March 16th, Wednesday, March 21st Friday, March 23rd, Wednesday, March 28th from 14pm to 16pm

• (CMU/Room 5000)• ORAL EXAM : Tuesday and Wednesday, April the 9th and 10th

Statistics course March-May 2018

• PD Christophe COMBESCURE, Service d’épidémiologie clinique, Direction médicale et qualité, HUG• Prof. Thomas V. PERNEGER, Service d’épidémiologie clinique, Direction médicale et qualité, HUG

• The aim of this course is to provide to the students a general knowledge of statistical inference, methods to describe data, to test hypotheses and to characterize associations between two variables. In addition to the theory, students will put into practice statistical methods with a statistical software and will conduct a critical appraisal of the statistical methodology in a selection of published articles.

• Contact : Christophe COMBESCURE

• The number of course participants is limited to 14.

• Sessions (classroom E.09.2753.A, from 2:15 to 5:15 pm):

• Descriptive statistics and introduction to GraphPad (15.03.2018)

• Statistical inference and confidence intervals (22.03.2018)

• Basic principles of statistical hypothesis testing (29.03.2018)

• Common statistical tests (12.04.2018)

• Statistical power and sample size (19.04.2018)

• Correlation and regression models (26.04.2018)

• Reporting statistical analyses / Exam (03.05.2018)

VIROLOGYMay-June 2018

• Dr. D. Garcin, Dépt de Microbiologie et Médecine Moléculaire

• Virus cycle (entry, replication, budding…)

• RNA viruses : genetic variability, quasi-species, adaptation and evolution..

• Anti-viral innate immunity, detection, interferon system and viral counter measures.

• An introductory course in each topic, articles to read and present, discussions, criticalanalysis (sort of «battle» over the article J).

• 4 sessions of 3 to 4 hours plus one session for the exam.

• The course will be held on:

• Monday April 30 2018 : Introduction virology–introduction viral cycle.

• Monday May 7 2018: Viral cycle (presentation 3 publications) – Introduction quasi-species

• Monday May 14 2018: Quasi-species (presentation 3 publications)– Introduction innate immunity

• Monday May 28 2018 : Innate immunity (presentation 3 publications)

• Monday JUNE 4 2018 :EXAM

• Location : will be specified later

Developmental BiologyMay-June 2018

• Prof. P. Herrera, Dr. F. Thorel (dépt. de médecine génétique & développement CMU).

• M.O. Fazio, Service de Transgénèse (cours pratique sur la production de souris transgéniques).

• Transgenics and mouse molecular genetics

• Sex determination

• Regenerative medicine : ES and IPS cells; cell reprogramming

• Pancreas development and regeneration

• Courses will be held on, in English,

• Every Wednesday of

• May (30.05.18) & June (06/13/20.06.2018); room E09.2753.a, from 2pm to 5pm.

• (4 sessions)

• EXAM DATE TO CONFIRM

• The course will only take place with a minimum of 4 and a maximum of 12 students.

• Attendance at all sessions is mandatory

HISTOLOGYSEPTEMBER-OCTOBER 2018

• NB: this module is not opened to MD-PhD students

• Number of students : 18 max

• Contact: Dre Marie-Luce BOCHATON-PIALLAT Dpt of Pathology and Immunology

• Prof. M. Foti Dpt of Cellular Physiology and Metabolism; Dre P. Soulié Dpt of Cellular Physiologyand Metabolism; Dre J. Perrin-Simonnot Dpt of Cellular Physiology and Metabolism; Dre. S. Clément Dpt of Clinical Pathology; Dr J-C Tille Dpt of Clinical Pathology.

• HISTOLOGY (2 sessions): study of primary tissues(epithelium, connective tissue, muscles, vessels, nervous tissue, lymphoid tissue) and some representive organs.

• HISTOPATHOLOGY (2 sessions): study of the main concepts of general pathology(cell death: necrosis and apoptosis, inflammation, tissue repair, tumor) and some representive organs with typicalpathological alterations.

• HISTOLOGY AND RESEARCH (2 sessions): study of different microscopic approaches (optical, immuno-fluorescence, confocal and electron microscopy) and their applications in research(autoradiography, in situ hybridization, immunohisto/cytochemistry, live imaging).

• ORAL EXAM (2 parts): description of slides at the microscope & discussion on research application

• Dates: from September 10 to October 19, 2018

• NB : PhD students are required to attend all sessions.

CancerNovember 2017

• Prof. Patrick Meraldi, Cell Physiology and Metabolism Department,

• Dr. Intidhar Labidi-Galy, Department of Oncology, HUG

• Goal of the course: learn to read and analyze the biomedical literature in the context of cancer biology

• 3rd, 7th, 10th, 17th of November, 2-5.30pm: in depth analysis of individual cancer biology studies ranging from cellular/molecular biology to clinical studies

• 21st of November, 2-5pm: written exam (composing an abstract)

• 28th of November: 2-6pm Individual 15 mins feedback session on written exam

• The number of course participants is limited to 4-16.