M1 Life Sciences and Health - International Track - Infectiology : Biology of Infectious Diseases - Cambodia

Olivier Lespinet, Université Paris Saclay, olivier.lespinet@universite-paris-saclay.fr Nimol Khim, Institut Pasteur Cambodge, knimol@pasteur-kh.org Dary Chhavvarath, University of Health Sciences, dr_chhavarath@uhs.edu.kh.

- Academic courses and interactive lectures - Case studies and practicals in computer lab.

This bioinformatics course is designed to give students knowledge and skills that will enable them to effectively manage and analyze biological sequences and genomic data.
The followings topics will be covered :
1. From sequences to genomes:
Students will learn
-the basics of genome sequencing and assembly methods
-how to find predicted genes in a genome
-to use similarity search in databases for genes function prediction
-to use comparative genomics approaches for studying differential gene content and for building core and pan genomes
2. In depth sequence analysis:
Students will learn
-how to identify and search for specific sequence patterns
-the basics of pair-wise sequence alignment
-how to perform and extract information from a Multiple sequence alignments.
-how to use phylogenetic trees reconstruction and clustering methods in the scope of genome analysis and taxonomic classification
-how to use alternative sequenced-based methods for taxonomic classification.

- S. Choudhuri (2014) Bioinformatics for beginners (Academic Press) - D. Mount (2004) Bioinformatics: Sequence and Genome Analysis (Cold Spring Harbor Laboratory Press; 2nd edition).

Février.

University of Health Sciences - Phnom Penh (Cambodia)

Sovanthida SUY, sovanthidasuy@uhs.edu.kh Patrice PIOLA, ppiola@pasteur-kh.org Amber KUNKEL, amber.kunkel@pasteur.fr.

- Interactive Lecture - Computer lab practice - Students individual assignments The supported statistical software for this unit are R/RStudio and STATA. Students will be given guidance on how to use these softwares and be expected to conduct their analyses using R/RStudio/STATA for the in-session assessments. Students should also note that the final examination will involve data analysis that contains inline R/STATA code that students need to interpret to answer the exam questions.

This Biostatistics course aim to provide an introduction to the selection of significant topics in biostatistical concepts and reasoning. Specific topics include tools for describing central tendency and variability in data; methods for carrying out inference on population means and proportions via sample data; statistical hypothesis testing and its application to group comparisons; issues of power and sample size in study designs; the analyzing of survival data, and other study types. While there are some formulas and computational elements to the course, the emphasis is on interpretation and concepts.
The proposed course elements are the following:
1.Descriptive statistics
2.Theory of probability
3.Interval estimations
4.Hypothesis testing
5.Linear models
6.Survival analysis.

It is a prerequisite for students to complete Elementary in probability and statistics or Introduction to statistics course in Upgrading course (M0).

Recommended text books: 1. Moore, D.S., McCabe, G. P. and Craig, B.A. (2014) Introduction to the Practice of Statistics, Eighth Edition (W.H. Freeman). 2. Ward, M. D. and Gundlach, E. (2016) Introduction to Probability, W. H. Freeman and Company. 3. Hosmer DW, Lemeshow S and May S (2008). Applied Survival Analysis, John Wiley and Sons, Second Edition.

Online resources: 1. SurfStat at http://surfstat.anu.edu.au/surfstat-home/surfstat.html is a complete introductory statistics course. 2. StatSoft Electronic Textbook at http://www.statsoft.com/textbook/stathome.html is more advanced and material

Janvier - Février.

UHS, Phnom Pen (Cambodia)

- Lectures/Presentations with PPT and visual aid - Brainstorming (Questions and answers) - Skill lab practice for apply technic - Cases studies discussion.

This course is designed to provide to student an advance knowledge of bacteriology applicable in the field of infectious diseases. Students will learn about the important bacteria cause pathogen including their characteristics, epidemiology, mechanisms of transmission, pathogenesis, and preventions.

1. Bacterial structure, physiology of bacterial growth, disinfection and sterilization
1.a. Structure of bacteria, role and function of bacterial structures
1.b. Physiology of bacterial growth, multiplication and division
1.c. Control of bacterial growth
1.d. Basic principles of bacterial metabolism Biofilms and human microbiotes

2.Bacterial pathogenesis, antimicrobial therapy and drug resistance
2.a. Bacterial pathogenesis
2.b.Mode of action of antibiotics against bacteria
2.c.Action of bacteria against antibiotics, Multi-Drug resistance bacteria and its emergence

3.Bacterial Infections
3.a. Central nervous system infections
3.b. Respiratory tract infections
3.c. Gastrointestinal tract infections
3.d. Genitourinary Tract Infections
3.e. Skin and soft-tissue infections
3.f. Systemic infections

4. Diagnostic of Bacteriology in Laboratory.

1.Medical bacteriology (Azele FERRON 2000) 2.Freney J. « Précis de Bactériologie Clinique », 2ème éd. Paris 3.David G et al. 7th Ed. Medical Microbiology. 2007 4.François Jehl et al Edition Biomérieux. 2012, « De l’antibiogramme à la prescription » 5.Référentiel en microbiologie médicale, Par le groupe Rémic de la Société Française de Microbiologie, 4ème Edition, Rémic 2010. 6.Antibiogramme, coll. sous la direction Patrice Courvalin et al, 2ème édition, ESKA. 7.Atlas of Medical Bacteriology, E-book, June 2016. DOI: 10.13140/RG.2.1.2130.9048.https://www.researchgate.net/publication/303921094

Janvier - Février.

University of Health Sciences - Phnom Penh (Cambodia)

Fabienne Girard-Misguish, fabienne.girard-misguich@uvsq.fr Monidarin Chou, cmonidarin@uhs.edu.kh.

- Lectures/Presentations with PPT and visual aid - Scientific Literature discussions/workshops/TD/group work - Skill lab practice for apply technic: allow student to practice using material and apply technics in the lab.

This course is designed to provide to student advance knowledge in parasite and fungal for application in research to acquire important underlying concepts and current up-to-date knowledge in parasitology/mycology. The course will cover pathogens biological characteristics, epidemiology, and mechanisms of transmission, pathogenesis, treatment and prevention of parasite and fungal responsible for different diseases in human and in animals (zoonoses) responds to a “One Health” concept. Students will also learn about laboratory diagnostic tests for parasites and fungal infectious diseases.

1.Parasitology
a.General of parasitology
b.Helminthology :
c.Cestode
d.Nematodes
e.Trematode
f.Arthropods
g.Insect
h.Acari
i.Protozoology
j.Sarcomastigophora
k.Apicomplexa

2. Mycology
a.Yeasts infectious
b.filamentous fungi
c.Dermatophytes
d.Atypical fungi
e.Apicomplexa

3. Detection and identification of parasites / mycoses.

Viviane Guillaume, Parasitologie Sanguine, fiche pratique, Edition de boeck, 2009. Dominique Chabasse et al, Parasitoses et mycoses des régions tempérées et tropicales, Connaissance et pratique, 2ème Edition, Elsevier Masson, 2010. Basic Malaria microscopy – learning guideline 2010 - ISBN: 9241547820 (available on line http://www.who.int/malaria/areas/diagnosis/rapid-diagnostic-tests/en/) Descriptions of medical fungi, E-Book, 3rd edition, Nov 2017. Laboratory diagnosis of invasive aspergillosis. Lancet Infect Dis 5:609-22 (Available online https://www.cdc.gov/fungal/diseases/other/index

Janvier - Février.

University of Health Sciences - Phnom Penh (Cambodia)

Karim Benihoud, Université Paris Saclay Cécile Lagaudrière-Gesbert, Université Paris Saclay Fabienne Malagnac, Université Paris Saclay Gérald Peyroche, ENS Paris Saclay Laurent Théodore, Université Paris Saclay.

The course is organized over an 8-week period during the first semester. It is based on active learning which includes reverse approaches and problem-based activities. The time spent in class is dedicated to interactive sessions with teachers, conferences from experts in given fields, debates, methodological trainings and tutorials. Students will also be invited to provide working reports on individual or group projects elaborated autonomously before classes. Learning sequences are elaborated over the study of research articles recently published in international peer-reviewed journals. It is a question-based process the goal of which is to highlight unknown theoretical or practical contents, and to acquire what is needed to fully appreciate the information presented in the articles. The expected learning outcomes of the course are profiled in advanced and their completion monitored throughout time.

The course addresses key concepts and challenges in the following basic fields of Life Sciences and Health (LSH): Genetics/Genomics, Cellular Biology, Biochemistry and Cell Signaling. It aims to instill a solid and broad-based background while developing the student’s ability to manage data, integrate/share scientific information, express their ideas and formulate questions/hypothesis whether verbally or in writing with clarity and logic.

Expected outcomes
Students will be able to:
-demonstrate a good understanding of fundamental facts, concepts and challenges in prominent areas of LSH
-master scientific methods and experimental procedures commonly used in LSH
-perform thorough and objective data analyses and formulate hypotheses reflecting the results
-handle informatics tools commonly used to process biological data
-handle diverse information sources and integrate/share scientific information through appropriate means
-show competence in personal and team working skills
-develop transversal skills (autonomy, adaptability, problem solving).

A bachelor’s degree corresponding to a “Licence” in France (L-M-D European system, 180 ECTS, 3-year program) or equivalent academic qualification in Science (with a Biology content) from an internationally-recognized University is required.

A specific bibliography will be provided during the course.

Octobre - Novembre - Décembre.

University of Health Sciences - Phnom Penh (Cambodia)

Lagaudriere-Gesbert Cécile Sola Christophe Duru Valentine.

Students will be group in pairs. Each group will work under the guidance of a faculty member with expertise in the field and who will dialogue with them on a regular basis.

This course aims to provide the students with a comprehensive view of the wide variety of approaches that can be applied to identify and study genetic factors linked to infection succeptibility or disease outcome.
Faculty member involved in the course will select scientific articles that will be assigned to students.
Based on the scientific articles, the student will have to carry out an exhaustive bibliographic research to :
- review previous articles on the subject,
- search for the follow-up given to this article in the literature,
- propose future experiments to conduct in order to get further insight on the topic.

The selected themes will focus on case studies related to the genetics of host-pathogen interactions in the field of virology, bacteriology and parasitology, allowing students to integrate the different themes covered in the core courses.

Strong knowledge in genetics and, molecular and cellular biology.

Mars - Avril.

University of Health Sciences - Phnom Penh (Cambodia)

Tineke Cantaert Polidy Pean Géraldine Schlecht-Louf Daniel Scott-Algara.

The following methods will be used for teaching: -lectures and seminars: 17.5h -MOOC innate immunity: 12.5h -Tutorial classes (TD): 10h -literature study, discussion and interpretation: 10h Continuous assessment (CA) will include oral presentations of data published in the literature as well as written reports on data analyses done in the course of TDs. The written exam (WE) will consist in multiple choice and/or short written questions.

The course aims to provide the postgraduate students a training in basic immunology first, with focus on the interaction of immune system and infectious agents.
The contents of the course will cover:
1.Introduction to the human immune system
Components of the immune system, their origin and function
2.Pathogen recognition by innate immune cells
The induced response of innate immunity: Pattern recognition receptors
PRR-associated signaling
3.Antigen recognition by B cells and T cells
Antigen recognition, BCR and TCR
Selection and clonality of B and T cells
Antigen presentation
BCR and TCR signaling
4.Immune responses to infectious diseases
Innate immune response to infection
Adaptive immune response to infection
Immunological memory
5.Immune regulation
Regulatory mechanisms in the immune system
6.Basic techniques in Immunology
Immunologist’s Toolbox.

Profound knowledge of cell biology, biochemistry and molecular biology are compulsory. This TU will provide insight into how the immune system responds to infectious agents in order to mount a protective host response, as well as how failure in the regulation of this host response can lead to pathology.

Janeway’s ImmunoBiology (8th edition) Cellular and Molecular Immunology, Abbas & coll (8th Edition) Kuby Immunology, (8th edition, 2018), written by Punt, Stranford, Jones and Owen (MacMillan Education), The Immune System (4th edition, 2015), written by Peter Parham (Garland Science). Roitt’s Essential Immunology (13th edition, 2017), written by Delves, Martin, Burton and Roitt (Wiley-Blackwell). Additional literature will be provided during the lectures.

Mars - Avril.

University of Health Sciences - Phnom Penh (Cambodia)

Didier Fontenille, didier.fontenille@ird.fr Tamara Basta le Berre, tamara.basta@i2bc.paris-saclay.fr.

The following methods will be used for teaching: - Academic courses and lectures face-to-face - Academic courses and lectures by visioconferences - Questions and Answers - Individual student article analysis and presentation of scientific articles distributed at the beginning of the module.

This course is designed to give students knowledge and skills that will enable them to understand diversity and evolution of pathogens and infectious diseases. Through examples, the student will learn how pathogens emerge, spread, evolve and adapt to human.
The contents of the course will cover the following topics:
-history of human infectious diseases
-History of evolutionary thought; modern classification of microorganisms by phylogenetic approaches and discovery of the Archaeas
-Last Universal Common Ancestor (LUCA) and origin of viruses
-Origin and evolution of HIV
-Origin and evolution of Malaria
-Origin and evolution of Tuberculosis
-Origin and evolution of Dengue, yellow fever, chikungunya and Zika viruses
-Origin and evolution of Rabies
-Host Manipulation by Parasites.

Students must have knowledge on infectious diseases and pathogens. They must have notions of genetics and phylogeny.

Genetics and evolution of infectious diseases, 2017 (ed Michel Tibayrenc, 2nd ed) Infectious diseases and host pathogen evolution 2010 (ed Krishna Dronamraju) Evolutionary Medicine, 2015, by Stephen C. Stearns and Ruslan Medzhitov. Oxford University press Les maladies infectieuses 2015, Santé Médecine et sciences de l’évolution. De boeck solal (ed Vittecoq et al. in french) Principles of Microbial Diversity, 2015, James W. Brown. 416 p. Garland Science.

Mars - Avril.

University of Health Sciences - Phnom Penh (Cambodia)

Uriel HAZAN Veasna DUONG.

- Lectures with visual support - Brainstorming (Questions and answers).

This course is designed to provide general and basic knowledge of eukaryotic virology necessary to understand host-virus relationship. Important viral families will also be addressed. These first lectures will then allow students to approach important issues in virology as exemplified by viral oncogenesis, viral zoonose and emergence, antiviral strategies and preventions. The objective is to attain sufficient knowledge in eukaryotic virology to know how to identify, detect, eventually treat and prevent global and regional important viral risks: arbovirosis, avian flu, etc.
I. General Virology
1.Introduction to Virology/ Viral structure and classification
2.Viral cycle 1: entry and expression of viral genomes
3.Viral cycle 2: genome replication, assembly and egress/budding
4.Genetic variability of viruses
II. Monographs of important viral families
5.Retroviridae
6.Picornaviridae
7.Flaviviridae
8.Papillomaviridae and Polyomaviridae
III. Host-pathogen interactions
9.Restriction factors
10.Viral oncogenesis
11.Latency & persistence
12.Viral emergence 1
13.Viral emergence 2
14.Antiviral strategies: Antiviral molecules/antiviral Vaccines
15.Viral vectors as genetic tools in gene therapy and vaccination.

Strong knowledge in molecular and cellular biology.

DIMMOCK, Introduction to modern virology (Ed. Blackwell Publ., 2001). FAUQUET / … Virus taxonomy: Classification and Nomenclature of Viruses : Eight report of the International Committee on Taxonomy of Viruses (Ed. Elsevier, 2005) FENNER / GIBBS / MURPHY / ROTT, Veterinary Virology (Ed. Academic Press, 1993) FLINT, Principles of virology (3e éd.) vol 2: pathogenesis and control (Ed. ASM press, 2009) FLINT, Principles of virology (3e éd.) vol 1: molecular biology (Ed. ASM press, 2009) KNIPE / HOWLEY, Fieds Virology: tome 1 & tome 2 (5e éd.) (Ed. Lippincott Williams & Wilkins, 2006) MAHY, A

Avril.

University of Health Sciences - Phnom Penh (Cambodia)

During the first semester, the students have to find a host laboratory. To this end they must write a CV, consult the internship offers and contact research teams of their choice for an interview. The internship is tied up to the “Scientific project” teaching unit, during which the scientific context and the experimental approaches suitable to address the biological questions will be defined. The internship spans 8-weeks in an academic laboratory or in a R&D department within a company, in France or abroad. At the end of the internship, the students complete a research report and an oral presentation, to highlight the biological questions raised, the experimental designs and to present and discuss their results.

The internship allows students to get familiar with various experimental approaches as well as the daily activities of a research team.
During the internship, the students participate in an ongoing research project under the guidance of laboratory staff scientists or engineers. They attend lab meetings and conferences. They are introduced to the hygiene and safety rules. They acquire and analyze experimental data. They have to synthetize their results in the form of a written report and an oral defense.
At the end of this teaching unit, the student will be able to:
- apply to research teams
- integrate a research team and participate in its activities
- follow Health and Safety rules
- to carry out a scientific experiment and integrate the controls required for its interpretation.
- write a laboratory notebook
- analyze critically the results obtained
- synthesize and present a scientific research process and the results obtained in oral and written form.

Mai - Juin - Juillet.

University of Health Sciences - Phnom Penh (Cambodia)

The Scientific Project is organized over a period of 8 weeks at a rate of one day per week spent in the host laboratory. This period is devoted to discussions between the student and his supervisor, the reflection and a bibliographic work to define the internship project. The student will present a bibliographic synthesis of the topic and the problematic of his internship project in a written report.

The Scientific Project is a groundwork for the laboratory internship. It consists of a thoughtful work based on bibliographic researches and on discussions with the internship’s supervisor.
It aims at clarifying the general scientific context and the state of knowledge. It allows highlighting the scientific questions that will be addressed during the internship, the experimental models chosen and the workflow of experiences that will be conducted. The whole is synthesized in a written report.
At the end of this training, the student will be able to:
- define a biological problem
- acquire, analyze and synthesize data from the literature
- formulate scientific hypotheses
- build a coherent scientific approach
- write a research project.

Mars - Avril.

France, Abroad