FROM SINGLE MOLECULE TO CELL; FUNDAMENTAL AND APPLIED ASPECTS

 
The summer school from signe molecul to cell; fundamental and applied aspect will take place in Paris from June 29th to July 21st

 HEALTH – BIOTECHNOLOGIES - NANOSCIENCES 

Date d’accueil à Paris, date de début des cours : June 29th 2019, July 1st 2019

The main research and training expertise of the University Evry-Paris-Saclay and the Biocluster Genopole 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 in Genepole. 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.

1 - FACILITIES

ARRIVAL IN FRANCE

Participants will be welcomed at Charles-de-Gaulle airport in Paris on Saturday June 29th 2019 in the afternoon.

Courses will start on Monday July 1st 2019.

At their arrival in France, participants will be welcomed at Charles-de-Gaulle airport by members of the International Relations Office as well as by students of the University Evry-Paris-Saclay. They will be conducted to their accommodation by bus.

ACCOMODATION

The school will provide accommodation for all the participants in the Montempo hotel offering single studios with private bathroom. The hotel is located ten minutes afoot away from the campus.

MEALS

All meals are included in the program (breakfast, lunches and dinners) and will take place in university restaurants and restaurants outside.

TRANSPORTATION

Participants will be transported by bus to the different places of interest.

RETURN TO CHINA

Participants will be transported to Charles-de-Gaulle airport on Sunday July 21st 2019 in the afternoon.


2 - SCIENTIFIC SYLLABUS

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 experimental work. It is expected that this organization will promote discovery of topics, interactions and communication.

a. STRUCTURE ACTIVITY OF NORMAL AND PATHOLOGICAL BIOMOLECULES LABORATORY (SABNP)

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 (2h)

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 (2h)

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 (2h)

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 presented including Atomic Force Microscopy (AFM), Nuclear Magnetic Resonance (NMR) and Florescence Microscopy (nanodiamonds) (2h).

 

b. LABORATORY FOR ANALYSIS AND MODELLING FOR BIOLOGY AND ENVIRONMENT (LAMBE), TEAM NANOPORES

 

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

 

LECTURES (4h)

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 (3h)

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 (3h)

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.

 

c. METABOLIC GENOMICS, INSTITUTE FOR SYSTEM AND SYNTHETIC BIOLOGY (ISSB)

 

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 bio-economy 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.

 

LECTURES (6h)

Introduction to synthetic biology

Computer assisted metabolic engineering

Application of synthetic biology to biotherapies

The platform abSYNTH: facility allowing to develop synthetic biology projects, from their design until their achievement in an unified and modular pipeline (design - build - test).

 

 

 

d. INSTITUTE OF STEM CELLS FOR THE TREATMENT AND STUDY OF MONOGENIC DISEASES (I-STEM)

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 (9h)

Stem cells introduction and state of art

Pathological modeling and pharmacological screening

New tools for stem cells

Pluripotent stem cells and cell therapy

Pluripotent stem cells applications: the skin

 

e. SUP’BIOTECH SCHOOL FOR BIOENGINEERING

(ENGINEERING SCHOOL SPECIALIZED IN BIOTECHNOLOGY)

 

PRACTICAL LAB WORK: CURRENT PROTOCOLS IN PLURIPOTENT STEM CELL BIOLOGY

 

Sup’Biotech will provide access to its Cell Culture Practical Laboratory for up to 15 students.

(60 m2 lab space, two sterile hoods, imaging facility, cell culture material)

 

During two days (12h), students will benefit from an initiation to culturing stem cells followed by a hands-on experience in induced pluripotent (IPS) stem cell culture and differentiation. Reagents and Materials will be provided to the students. Every student will observe, manipulate, culture and differentiate human induced pluripotent stem cells. 

 

The practical approach to stem cells will be complementary to the courses given at the I-STEM institute, which addresses the therapeutically applications and challenges of stem cell technologies.

 

f. COMPUTER SCIENCE, INTEGRATIVE BIOLOGY AND COMPLEX SYSTEMS (IBISC), DEPARTMENT OF COMPUTER SCIENCE

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 presentation is  divided in three parts:

INTRODUCTION TO BIOINFORMATICS (3h)

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 (3h)

 

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 (3h)

 

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.

 

g. 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 Small and Medium Enterprises (SME) and big pharma to find their places within the Biocluster.

The following presentations will take place:

THE ENTREPRENEURSHIP (3h)

Part 1: Genopole as a Lead BioCluster

Part 2: Are you entrepreneurial?

THE FRENCH LEADING BIOCLUSTER GENOPOLE (3h)

Presentation of Genopole-Enterprises, of the Incubator Shaker and of the accelerator Booster

Visit of the Campus

Visit of the Incubator

 

3- CULTURAL SYLLABUS

FRENCH AS A FOREIGN LANGUAGE

15 hours of French lessons learning basics of French grammar and communication. Through games and a lot of oral presentation, the students learn to present themselves and interact in easy situations like shopping and meeting someone.

FRENCH HISTORY AND CULTURE

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: Sightseeing Tour

Versailles Palace, gardens, parc, Trianon

The river Seine (Cruise)

Fontainebleau Palace, hiking in the forest

Etretat (on the Channel)

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

 Achievement delivered by the President of the University Evry-Paris-Saclay.

 

4- RESUME

NAME OF THE SCHOOL: FROM SINGLE MOLECULE TO CELL; FUNDAMENTAL AND APPLIED ASPECTS, HEALTH – BIOTECHNOLOGIES - NANOSCIENCES

Welcome date: June 29th 2019 in the afternoon

From June 29th 2019 to July 21st 2019 in Université Evry-Paris-Saclay

The number of places is limited to 15.

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

Accommodation, meals and local transportation are all included

The summer school is open to MASTER students.