From single molecule to cell ; from fundamental to applications

 
The France Excellence 2018 Summer School "From single molecule to cell ; from fundamental to applications" will take place from July 2nd to 20th 2018 in Université Évry-Val d'Essonne.

Abstract 

The main research and training expertise of the UEVE-Paris-Saclay and Genopole campus concerns modern Genomics and its applications to human and industry. To that end research and training includes all the basic aspects of genomics together with other sciences that are needed for its success i.e. bioinformatics, statistics, big data, physics and chemistry. Furthermore to foster applications, research is developed in close relationship with start-ups and companies that are incubated on the campus. Then, we propose a high level summer school with lectures, conferences, bibliographic projects, and experimental work in the very heart of our laboratories. The school will consider personalized medicine, synthetic and systemic biology, human pluripotent stem cells, biotherapies, structure-function relationships of macromolecular assemblies, biomimetic nanopores for biology and biotechnologies. The school will provide students critical knowledge for their professional project by bringing them an up-to-date view of these thematics.


Facilities

Period: from July 2nd to 20th 2018 (three weeks).

Arrival: The students are expected to arrive at Charles-de-Gaulle airport on June 30th 2018 in the afternoon. The transport from the airport to the city Evry will be organized either by remote guidance or by bus.

Departure: The students are expected to leave on July 22nd, a special event being organized on July 21st.  

Accommodation: Students will live in the students’ dormitories Marguerite Yourcenar

Meals: All meals are included

 

 

Teaching team

Our teaching team encompasses academic researchers with teaching duties employed by the University and full-time researchers originating from research institutions (CNRS , INSERM , CEA ). They are all working in our laboratories, and, collectively have a wide-range expertise, from cell biology, physiology, genomics and post-genomics to synthetic biology, bioinformatics and nanotechnologies.

 

Thematic and localization of the Summer school

The University of Evry-Paris-Saclay is located amidst Genopole which is the biggest French Biocluster, thus providing a unique research and teaching environment. A hundred of research laboratories and biotech companies under the label of University Evry -Paris-Saclay or Genopole enables access to leading-edge biological techniques and research valorization.

 

Academic laboratories are dedicated to (post-) genomics, synthetic biology as well as cellular and molecular biophysics topics. They are: the Institute of Stem Cells for the Treatment and Study of Monogenic Diseases (I-STEM), the Genethon Laboratory founded by the French Myopathy Association (AFM), and the Genomics Institute. The South-Greater Paris Hospital (CHSF), also offers services in functional genomics, gene therapy and medical translational research, working in partnership with the University of Evry-Paris-Saclay. Personalized medicine is one of the goals and highlights of the biological research in Evry. It requires fundamental knowledge in molecular biology, and innovative technologies to be able to develop and lead to biotherapies in the near future.

 

The academic laboratories of the University of Evry-Paris-Saclay are associated to two doctoral schools of the University Paris-Saclay : “Therapeutic innovation, from fundamental to applications” and “Structure and dynamics of living systems”.

 

In summary, the University of Evry-Paris-Saclay possesses an outstanding expertise for organizing a Summer School oriented towards various aspects of the modern cellular and molecular biology, focusing on structural and functional genomics, synthetic biology, biotherapies and bioinformatics.

 

Interaction with other events:

A Pre-Master Summer School will be held at the University in July 2018, in cooperation with the Life Sciences Department of HUST (Huazhong University of Science and Technology, Wuhan, China).

 

Scientific program

Several laboratories are taking part to this Summer School, in order to cover a broad range of approaches and provide scientific opportunities for open-minded students. The Summer-School will be split in several modules (all mandatory) held in each laboratory. These modules will include a theoretical introduction, interactive discussions between students and teachers on state-of-the-art scientific literature of the field and relevant papers issued by the laboratories, and some experimental work. It is expected that this organization will promote discovery of topics, interactions and communication.

 

1. Structure Activity of Normal and Pathological Biomolecules Laboratory (SABNP, UMRS 1204)

Director David PASTRÉ, Professor

david.pastre@univ-evry.fr

 

Thematic: Dynamics and Structure-Function relationships of macromolecular assemblies

 

Based on a multidisciplinary approach, we will explore notably RNA-protein complexes and microtubules. We will especially focus our attention on three major topics.

 

- Translation regulation

Among postgenomic regulation, translation regulation is of critical importance in mammalian cell biology. Indeed dedicated mRNA-binding proteins are involved in spatio-temporal control of a specific set of proteins by direct binding their mRNA. However how RNA-binding proteins specifically process some transcripts in the cytoplasm remains an open question. This issues is notably relevant in neuron diseases since RNA transport is critical for localized translation in specific neuronal compartments but also in cancer as translation of oncogenes is unregulated to sustain invasiveness and proliferation of cancer cells

 

- Alternative splicing

Alternative splicing has an essential contribution to the diversity of protein isoforms that are expressed from a limited number of genes. Furthermore alternative splicing is highly regulated and cell type specific. The following projects aim at characterizing splicing factors with known or putative implications in neuronal cell regulations. We will also consider splicing factors implicated in neurons diseases like amyotrophic lateral sclerosis (ALS).

 

- Microtubules dynamics

The understanding of the dynamics of microtubules and the role of their protein partners that regulate the cytoskeleton remains incomplete. A better knowledge will enlighten fundamental processes of critical importance in biology (cell cycle, neurobiology). Indeed, increasing evidence show that minor alteration of cytoskeleton dynamics is accompanied by major cellular effects, as demonstrated on the cell cycle  and transport in neurons, which opens perspectives in medicine (cancer, neurodegenerative diseases).

 

The methods and technologies developed to explore these three topics will be also presented including Atomic Force Microscopy (AFM), Nuclear Magnetic Resonance (NMR) and florescence microscopy (nanodiamonds).

 

School team : David PASTRÉ, Professor ; Alexandre MAUCUER, Researcher INSERM ; Marie-Odile DAVID, Associated Professor ; R. Charbel MAROUN, Researcher INSERM; Andrea BURGO, Associated Professor ; Ahmed BOUHSS, Researcher CNRS; Ioana DOBRA, PhD.

 

 

2. Laboratory for Analysis and Modelling for Biology and Environment (LAMBE UMR 8587), Team Nanopores

 

Juan PELTA, Professor

juan.pelta@univ-evry.fr

 

Thematic: biomimetic nanopores, fundamental to health, biotechnology, industrial applications

 

- Lectures

We propose to discuss societal challenges of health, biotechnology, biology, industry and to introduce a new powerful method, at single molecule level, in order to try to answer to these challenges. A potential difference is applied between both sides of a lipid or solid-state membrane which separates two compartments filled with an electrolyte buffer. One protein channel inside the bilayer or one nanopore drilled in thin solid state membrane, lead to an ionic current of the empty pore. After the addition of a biomolecule or a nanoparticule, we observe several current blockades (see figure below). The blockades duration and amplitude depend on the shape, conformation, structure, length and size, net charge, sequence, of the molecule or particule passing, on the driving force applied. The dynamics is influenced by the nanopore geometry or net charge and by the interaction between the molecule (or particule) and the nanopore and by the driving force applied. We will focus on the nanopore used, the principle of electric detection of a molecule through a nanopore, data analysis, protein folding, mass and size discrimination by a nanopore, ultra-fast sequencing of biomolecules, biomarkers  and virus detection.

 

 

- Bibliographic projects

Each student will make a short talk form selected articles according these research fields: protein folding, mass and size discrimination by a nanopore, ultra-fast sequencing of biomolecules, biomarkers and virus detection. After the talk an open discussion with be host by the professor.

 

- Practical course in laboratory 

Students will learn to plan and perform experiments in research laboratory about the solid-state nanopore insertion into a microfluidic set-up, electrical measurements and particles detection.

 

- Scientific interaction

Students will participate to all the meetings organized in the laboratory and will be able to discuss with the different groups.

 

School team:

Juan PELTA (Professor, biochemistry and biophysics), Laurent BACRI (Associated Professor, physics and biophysics), Nathalie JARROUX (Associated Professor, chemistry), Jean ROMAN (PhD student).

 

3. Metabolic Genomics (UMR 8030), Laboratoire iSSB (Institute for System and Synthetic Biology)

 

Directeur Marcel SALANOUBAT

salanou@genoscope.cns.fr

 

Thematic : Synthetic Biology

 

- Challenges and consequences of synthetic biology:

Biological processes provide humanity with food, drugs, clothing and some of its energy from its origins. We are now witnessing the ever-increasing spread of the bioeconomy to our medicine, materials, fuels and environmental protection. The reasons for this extension of the bioeconomy are strong and durable: reduction of the carbon footprint, increasing use of renewable resources rather than fossils, replacement of highly polluting chemical processes by biological equivalents that are more respectful of the environment. The spearhead of this extension is the progress of life technologies, or biotechnologies. To date, biotechnologies are far from putting into practice the principles that underlie any mature engineering. They still represent a difficult craft of ad hoc solutions obtained by trials and errors.

Synthetic biology is a multidisciplinary area aiming to introduce engineering principles in biotechnology. Let's mention the standardization, the coupling between design (mathematical computing, modeling) and manufacturing (molecular biology). It will thus promote the emergence of a true rational bioeconomy based on knowledge.

For the record, direct and indirect markets of global nanotechnology and synthetic biology are estimated at $ 3 trillion and $ 10 trillion, respectively, by 2025. The 2012 Davos World Economic Forum ranked Synthetic Biology second of the "top 10 emerging technologies".

 

 

 

- iSSB:

In France, the campus of Evry (Genopole®, University of Evry-Paris-Saclay) represents one of the largest clusters of laboratories and companies dedicated to synthetic biology, and the iSSB laboratory is the most important academic group of synthetic biology. Its motivation is two-fold: a better understanding of the logics and the mechanisms underpinning living organisms, eventually including the discovery of novel ones, and the development of Systems & Synthetic Biology tools and techniques to be utilized by the biotechnology community.

These summer courses will cover some of the thematics developed at iSSB: engineering of regulatory genetic devices, computer assisted metabolic engineering, engineering of synthetic chromosomes, development of biotherapies based on synthetic biology approaches.

 

- Courses:

- Introduction to synthetic biology (Dominique ZELISZEWSKI, Researcher CNRS, PhD)

- Engineering of synthetic genomes (Alfonso JARAMILLO, Research Director CNRS; Prof at the University Warwick, Synthetic Biology)

- Computer assisted metabolic engineering (Ioana POPESCU, Associated Professor, Biochemistry and Synthetic Biology)

- Application of synthetic biology to biotherapies (Bruno COLOMBO, Professor, Synthetic Biology)

- The plateform abSYNTH (Joan HERISSON, Research engineer, Informatics; Dominique ZELISZEWSKI), facility allowing to develop synthetic biology projects, from their design until their achievement in an unified and modular pipeline (design - build - test).

 

 

4. Institute of Stem Cells for the Treatment and Study of Monogenic Diseases (I-STEM, UMRS 861)

 

Director Cécile Martinat,

cmartinat@istem.fr

 

Thematic: Human pluripotent stem cells and diseases

 

The I-Stem laboratory is an institution dedicated to the exploration of potential therapeutic applications of human ES and iPS cells and therefore, is rather a scientific center focusing on Research and Development. The therapeutic target goal is a constant preoccupation which translates into the organization of teams focused on specific aims and time lines. Such an organization has enabled us to easily test the feasibility of the scientific process since each calendar displays benchmarks, with specific objectives in specified periods.

The primary focus of the research teams has been targeting several monogenic diseases (muscular, moto-neuronal, neuronal, retinal, skin…). These diseases were chosen primarily as scientific opportunities and their number will be expanded as the I-STEM Institute increases in size.

 

The ambition of I-STEM is to develop a research technology capable of covering all aspects of discovery and development of therapeutic molecules as well as cell therapy for pre-clinical trials as defined by clinical and epidemiological studies of monogenic diseases, until a candidate molecule or a cell therapy product is identified for clinical trials.

 

For research as well as technological development teams, many industrial and academic partnerships have already been established.

 

For more information see the web site: www.istem.eu

 

- Lectures

1.    Application of Human Pluripotent stem cells for eye cell therapy  (C. MONVILLE, Professor)

2.    Disease modeling and drug screening using human pluripotent stem cells (X. NISSAN, Associated researcher, PhD)

 

- Bibliographic projects

1.    Disease modeling using organoid technology

Bibliographic project to evaluate the possibility to use organoids for disease modeling and drug screening (G. MAHE, Engineer)

 

2.    Human pluripotent stem cells for cell therapy application

From the literature, summarize the place of human pluripotent stem cells for cell therapy application as well as their limitations. Discuss about the next challenges in this field (G. LEMAITRE, Research engineer, PhD, HDR).

 

3.    Culture automatization, dreams and facts

What is the role of standardization for pluripotent stem cell culture technics? Laboratory tour to visualize culture cell robots in action (L. MORIZUR, Research engineer, PhD)

 

- Scientific interaction

Students will participate to all the meetings organized in the Institute and will be able to discuss with the different groups.

 

5. Computer Science, Integrative Biology and Complex Systems (IBISC)

Department of Computer Science

 

Franck DELAPLACE, Director of IBISC

Professor in Computational Biology and Computer Science,

franck.delaplace@ibisc.univ-evry.fr 

 

Thematic: Data analysis, modeling and prediction applied to (epi-) genomic medicine.

During the last decade, the major advances in high-throughput genomic data acquisition open avenues to new societal challenges in precision medicine. Precision medicine aims at developing a genomic data based analysis to assess the health or disease state of patients for diagnosis, prognosis and predictive therapies. The issue is to determine the molecular causes of the disease as well as predicting and personalizing treatments.

In this undertaking, computer science and mathematics play crucial roles. The precision medicine challenge in bioinformatics is structured in a twofold approach: analyzing genomic data using methods derived from statistics and machine learning (clustering, prediction ...), and modeling biological networks and their dynamics (network medicine). The course will present the main methods used in these approaches. The présentation is  divided in three parts:

 

- Introduction to bioinformatics: After a background review of bioinformatics examining the contribution of informatics to modern biology, and the main major challenges in bioinformatics including precision medicine, we will introduce the basic methods in structural modeling and prediction of non-coding RNAs.

 

- Introduction to data analysis: we first introduce the theoretical and practical bases of data analysis. Then, we focus on descriptive methods (descriptive statistics, principal component analysis, clustering ...) and predictive methods (supervised learning). The studied notions will be illustrated by concrete example in precision medicine.

 

- Network based model: After introducing the theoretical foundations of graphs and network dynamics using discrete models, we examine concrete applications of these methods for diagnosis and prediction of therapeutic targets.

 

School team: Franck DELAPLACE, Professor; Fariza TAHI, Blaise HANCZAR

5. Genopole

 

Genopole will present its expertise in the building of a dynamic Biocluster which makes the link between research (fundamental and applied) and its valorization. This includes the earliest steps (pre-incubation) to the accompaniment of start-ups to find financement support and market partners, together with an active policy for SMEs  and big pharma to find their places within the Biocluster.

 

The following presentations will take place:

 

- The Entrepreneurship 

 Denis GAUVREAU, Director of International Affairs 

denis.gauvreau@genopole.fr

 

- The French leading Biocluster Genopole: Incubator Building, Companies: Global Bioenergies, Ynsect, Watchfrog….

Hélène VIRASITH, Project Manager at Genopole Entreprises

helene.virasith@genopole.fr

 

- Algobiotech:

Research and valorization of microalgae for cosmetic, nutraceutical and therapeutic applications 

Vikramsingh RAI, Project Manager at Genopole Entreprises

vignesh.janakiraman@algobiotech.com

 

Cultural Program

 

It is organized in collaboration with the Association “Science Accueil”.

 

- French as a foreign language

 

Solène ZOZIME, French language assistant, DELF examiner

solene.zozime@gmail.com

 

The teaching comprises 12 hours of “French as a foreign language”.

 

- French History and Culture (course)

 

Marjorie-Alexandra BELLINI, History professor, touristic guide, cultural mediator at Science Accueil

marjoriealexandrabellini@gmail.com

 

The teaching comprises 15 hours of “Introduction to French History and Culture”.

 

- Visits of sites

 

The visits of the sites are guided by the History professor and Cultural mediator. These visits will take place the week-ends.

 

The following sites have been chosen:

 

- Paris, Sightseing Tour, Cruise on the river Seine

- Paris by night

- Etretat, including a cruise on the river Seine to the Monet Museum at Giverny (the whole week-end)

- Fontainebleau’s castle and forest

- Loire’s castles (the whole week-end)

- Vaux-le-Vicomte’s castle and “diner aux chandelles”, closing night

Award the Certificates of Achievement delivered by Patrick CURMI, President of the University Evry-Paris-Saclay.

 

 

REGISTRATION


From single molecule to cell ; from fundamental to applications

From July 2nd to 27th,  2018 in Université Évry-Val d'Essonne

The total number of places is limited to 20. 

 The price does not include the trip from China to Paris.

Accommodation, meals and local transportation are all included.

The summer school will deliver ECTS (to be confirmed)

The summer school is reserved to Chinese master students.

To apply, please follow the application procedure described on the main page.

Price: 25.000 CNY

 

The French Embassy reserves a limited number of grants to students with an exceptional academic background. Grants cover the tuition fees but do not cover the trip from China to Paris.