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The Committee for Scientific and Technical Cooperation with Vietnam (CCSTVN), and the Orsay Scientific Center of the Paris-Sud University have organized five remote lectures in 2009-2010.

These lectures were addressed to students of the Master level, they were given in English and transmitted to the University of Ho Chi Minh City : Linh Trung campus, Linh Trung ward, Thu Duc District, HCMC.

Lecture on 14 May 2010

Pierre CAPY

Laboratoire Evolution, Génomes et Spéciation, CNRS - 91198 Gif sur Yvette - France

Evolution : from Lamarck and Darwin to nowadays

The biodiversity observed today is the result of 3,5 billion years of evolution. The concept of evolution of living organisms is quite recent (19th century) and is now accepted by the major part of the scientific community whereas some opponents keep denying it for many reasons.

Several mechanisms have been proposed to explain the modification of the genetic characteristics of natural populations along the successive generations. Some of them have been rejected like the inheritance of acquired characters proposed by Lamarck while others have been proved to be more relevant. The latter include natural selection as suggested by Darwin from his observation of the result of artificial selection applied by all breeders and from his trip around the world on the Beagle. Genetic drift is also an important component of evolution. This mechanism was evoked by Kimura in 1968 in the neutral theory of evolution. This is also a key evolutionary force, relevant in small populations and it is assumed that the modification of several traits observed from one generation to the next is only due to the sampling variability among the gametes. During this conference, a short history of the idea in this domain – evolution and its the mechanisms - will be presented, along with the idea that evolution is not only an academic science but can also be very useful in domains such as health and agriculture.

The presentation slides are available here.


Lecture on 12 March 2010


Université Paris Sud XI, Institut de Génétique et Microbiologie, 91405 Orsay - France

The antibiotics

1. A brief history of the fight against pathogenic microorganisms.

- Germ theory of disease: microorganisms are the cause of many infectious diseases (Koch, Lister, Pasteur)

- How to combat pathogenic microorganisms?

Natural products
Early observations of antagonism between microorganisms: antibiosis
Search for natural products responsible for this antagonism
Duchesne, Fleming, Florey, Chain, Dubos, Waksman

Chemical products
Search for chemicals with a selective inhibitory effect
Erlich, Domagk

- Definition(s) of antibiotics

restricted to natural products Waksman 1947

larger definition, encompassing natural products, natural products modified by hemisynthesis and chemically synthesized products

- The golden age of antibiotic discovery

- The current problems with antibiotic resistant pathogenic bacteria

2. The antibiotics

- Classifications bacteriostatic, bactericidal
according to chemical structure
according to targets

- Modes of action inhibitors of protein synthesis inhibitors of cell wall synthesis inhibitors of nucleic acid metabolism

- Resistance to antibiotics intrinsic resistance acquired resistance (mutation, gene acquisition) Resistance mechanisms

Permeability barrier and efflux
Inactivation of the antibiotic
Target modification or substitution

3. The biosynthesis of antibiotics

-Streptomyces, the antibiotic makers Streptomyces filamentous sporulating soil and marine bacteria, responsible for the synthesis of about two thirds of the antibiotics used in human medicine.
development cycle, structure of their genome, synthesis of various secondary metabolites

-Primary and secondary metabolism

-The genetics of antibiotic biosynthesis
genetic studies of secondary metabolism
clustering of the genes involved in the synthesis of an antibiotic
regulation of antibiotic biosynthesis

-The biosynthesis of polyketides and nonribosomal peptides polyketides assembled from carboxylic acid derivatives by successive condensation steps peptides assembled from amino acids by a nonribosomal process

4. Where will new antibiotics come from?

- Chemistry? Natural products?

- Combinatorial biosynthesis

- The unexplored genetic potential in bacterial genomes

- Metagenomic approaches…


The presentation slides are available here.


Lecture on 15 May 2009 at 2 PM

Sylvain BRISSE

Institut Pasteur, Paris

Biodiversity of species and strains of bacterial pathogens: latest approaches and applications to Salmonella and Listeria

Characterization of microbial pathogens at the phylogenetic levels of species and strains is fundamental for understanding their evolution and for a better control of infectious diseases. The study of genetic diversity, evolution and epidemiological tracking of microbial pathogens is currently undergoing a revolution, with rapid advances in both methodological and conceptual approaches. Recent developments of microbial species definition and population genetics and strain genotyping based on multiple gene sequencing (MLSA and MLST approaches) will be presented. Emphasis will be given on genotyping methods that are standardized and applicable to a wide range of pathogens (parasites, bacteria, fungi). Applications of genotyping data and of new phylogenetic analysis methods to the diversity and evolution of important pathogens such as Salmonella enterica and Listeria monocytogenes will be presented. The advantages and limitations of gene sequencing methods in the face of genome-wide high throughput sequencing will be discussed.


A new perspective on Listeria monocytogenes evolution.

Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization.


The lecture slides are available here.

Click here to watch the whole recorded lecture: high-speed connexion or mp4, 129 Mo


Lecture on 9 April 2009 at 2 PM

Jean-Marc SENG

Université Paris Sud XI, Institut de Biotechnologie des Plantes, laboratoire de Phytopathologie moléculaire, 91405 Orsay - France

Study of the Life Cycle of Phytopatogenic fungi

Fungi are responsible  of the most economically important plant diseases, compared to viruses and bacteria. For this reason, they focus most of our attention, both in tropical as well as temperate countries.

The life cycle of a phytopathogenic fungus can be described as follows:

1. A first step consists of infecting the host: wind as well splashing rain and even insects can help spores to be transported at the surface of the plant. When conditions are favourable (generally high moisture level), spores germinate and build a first filament (germ tube).
2. The penetration takes place when the spore germs at the plant surface and penetrate via stomata (plant natural organs) as well as directly by breaking the cuticle (enzymatically).
3. The incubation phase corresponds to the period during which the fungus is taking nutrients from the host. During that phase, symptoms are not visible at the surface of the plant, although yield can be strongly affected in the crop. The length of the incubation period is strongly dependent on the pathogen species. For example, Pyrenophora teres has a very short incubation period in barley leaves i.e. 2-3 days!. While Septoria diseases take 2-3 weeks to complete their incubation period in wheat tissues. Downy and powdery mildews which are responsible of very important diseases all over the world have generally a one week incubation period, if the weather conditions are favourable.
4. At last, the pathogen is expressing symptoms, when the nutrient flow is too low in plant tissues. Symptoms are characteristics of the pathogen biology: they are vey diverse: wilt, leaf spot, necrotic tissues, soft rot, etc.
5. The sporulation does occur in the symptoms, allowing the fungus to infect new healthy plants. Spores are usually very small structures (a few microns length) and are easily transported on new plants, thus continuing the epidemics.
From a theoretical point of view, epidemics should only stop when no more healthy plant material is available! This is fortunately rarely the case…!

A tremendous amount of work has been done in the last 30 years to forecast epidemics. Mathematical models have been developed to integrate climatic conditions as well as inoculum presence in the field. So far, models are not fully operational: the problem of the quantification of fungal inoculum in the field reamains to be solved. Even if laboratory methods exist such as Quantitative PCR (Q-PCR), difficulties are met in the number of samples to be analyzed statistically. The sampling should be actually representative of the epidemics at the field level which is still not the case nowadays.


The presentation slides are available here.

Lecture on 23 February 2009 at 4 PM

Danielle BLONDEL

Laboratoire de Virologie Moléculaire et Structurale, UMR CNRS 2472-INRA 1157 - CNRS - 91198 Gif sur Yvette - France

RNA viruses

I - Introduction to viruses

1. Definition

2. Diversity : nature and structure

3. Classification

II - RNA viruses replication strategies

1. Plus-stranded RNA viruses (Ex : Poliovirus)

2. Negative-stranded RNA viruses

2a) Non –segmented (Ex : Rabies virus)
2b) Segmented (Ex : Influenza virus)

3. Double-stranded RNA viruses (Ex : Rotavirus)

4. Retroviruses

5. Variability of viral genomes

The presentation slides are available here.