Biodiversity loss, climate change and the alteration of ecosystem functioning represent major challenges for society and policy makers. The aim of this course is to provide the theoretical and methodological basics essential to understand the causes and consequences of the challenges imposed by global change. The concepts and examples presented during the course will illustrate the complex relationships between biodiversity, ecological processes and human societies, and the need to adopt an interdisciplinary approach (mathematical modelling of a population, physico-chemical properties of soils and vegetation dynamics, human health and air quality, etc.) to address current environmental challenges.

Bio_52991_EP (BIO591) - Biology and Ecology

The Research internship opens fundamental, biomedical, or applied research laboratories (pharmaceutical industry, biotechnology) to students tempted by an in-depth study in Life Sciences, whether in microbiology, virology, immunology, neurobiology, embryology , in structural biology, in molecular biology, in cellular biology, in bioinformatics, in ecology...

Internship topics from previous years are available in a secure sharing space on the Ecole Polytechnique website:
-Subjects of research internships from previous years: (history of X04 to X12) 
https://gargantua.polytechnique.fr/siatel-web/app/auth/login?auth=1/
Folders My documents/Reports/General content Reports/SOI/X2004.....X2012

The student will be able, with the advice of the coordinator and the teaching team, to draw the thematic outlines of their internship, then actively participate, thanks to laboratory visits, in the ultimate definition of their Research internship subject.
The scientific research internship in Biology consists of a minimum of 16 weeks of work in the laboratory. This internship can take place in an academic laboratory or in a company laboratory. Internships take place in the Province, in Paris or in the Paris region (CNRS, INSERM, Institut Pasteur, Institut Curie, INRA, CEA, Universities, etc.) and abroad (United States, Germany, Canada, Italy, Spain, Japan, Portugal etc...)

Final Report: 
We will need an electronic version (in PDF format only) of your microthesis (twenty pages maximum all inclusive) to send by email. 
Reports can be delivered in French or English, as you prefer. 
You will ensure that these documents reach Catherine MORAIS catherine.morais@polytechnique.edu, the members of the jury, the referring teacher of your internship IMPERATIVELY five days minimum excluding weekends before your defense.
This poses no problem if one or other of the documents sent to X is written in English (final report and evaluation sheet sent by your internship director). 
Apart from the limit of 20 pages, annexes included, we have no particular requirements. This is a classic scientific report, and your host laboratory will provide you with useful advice on this subject. In short, the report must introduce first and last name, promotion, the subject by placing it in its context, cover page of the report written according to the model attached in the appendix. A MANDATORY summary in French and English of half a page maximum, all on the same page, then develop the results obtained, and finally discuss them.

Bibliographic references must also be indicated according to current standards for research articles.
The materials and methods used must also be described.
We remind you that compliance with deadlines will be taken into account in the rating. 
NO PAPER VERSION REQUESTED

- Defense: The oral defense must be carried out in person at the École Polytechnique (defense in French or English). 
The organization of the defense is managed by the department (duration, jury, public, etc.) is managed by the department.

- Internship director invitation: 
Your internship director will be invited to participate in the defense. However, his presence at the defense is not obligatory.  Your internship director must IMPERATIVELY send us his/her assessment of the work carried out and the way in which it was carried out, by completing the evaluation form sent by the Department.  This assessment must be sent IMPERATIVELY three days before the defense, by e-mail to: Catherine MORAIS catherine.morais@polytechnique.edu, to the members of the jury, to the teacher responsible for your internship.

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Joint internships:
For students entering a double degree engineering course in the fourth year, the subject, the location of the internship, the terms of the intermediate follow-up and the defense jury are, in certain cases, defined jointly by those responsible for the internship. research of l’X and by teachers of additional diploma training.

Joint internships allow the student to implement, in a real setting, an experimental or theoretical scientific approach, while discovering one of the sectors covered by the additional training.

- Coordinator - Responsible:
Yves MECHULAM - Tel: 4885 - yves.mechulam@polytechnique.edu
- Department assistant:
Catherine Morais - Tel: 4025 - catherine.morais@polytechnique.edu

- Teachers: all members of the department

Course language: French

ECTS credits: 20

Course description:

Molecular biogeochemistry explores the interplay between the molecular constituents of living organisms and the biogeochemical processes occurring in the environment. This class will provide an overview of the essential concepts in biogeochemistry with an emphasis of processes occurring at the molecular level.  In addition, it will cover how natural and anthropogenic activities impact the molecular transformations of elements like carbon, nitrogen, and sulfur in various environmental domains, such as soil, water, and air, integrating principles from biology, chemistry, and geology to unravel the intricate connections between the molecular biology of organisms and the broader biogeochemical cycles in Earth's ecosystems. We will examine, by delving into scientific literature found in peer-reviewed journals, the molecular aspects of production and degradation of natural organic matter in the biogeosphere, and the linkage of biological molecules with corresponding molecular constituents (chemofossils or biomarkers) that are extracted from sedimentary archives for paleo-reconstructions.

Course goals:

Apart from acquiring the basics of molecular and analytical biogeochemistry, this course aims to achieve the following objectives:

• Develop the ability to critically analyze scientific literature
• Engage in discussions with peers, lead by a subject matter expert, on scientific papers and their impacts
• Cultivate research and presentation skills with classmates and receive direct feedback

Texts and readings:

Reading assignments:

Class 2 (Feb. 28^th) – Ward et al., 2017.  Where carbon goes when water flows: carbon cycling across the aquatic continuum. Frontiers in Marine Science. 4:7. doi: 10.3389/fmars.2017.00007

Class 4 (March. 4^th) – Brown et al., 2014. Source identification of the Antarctic sea ice proxy IP25. Nature. Communications. doi: 10.1038/ncomms5197

Class 6 (March. 11^th) – Solomon et al., 2016. Emergence of healing in the Antarctic ozone layer. Science. 353(6296): 269-274

Class 6 (March. 11^th) - Bergauer et al., 2018. Organic Matter Processing by Microbial Communities throughout the Atlantic Water Column as Revealed by Metaproteomics. Proceedings of the National Academy of Sciences 115 (3) E400-E408.  Particular attention will be paid to the material and method section concerning the proteomic study (see supplementary data). This work will be discuss in small groups in class.

Class 8 (March. 13th^th) – Rabalais et al., 2019. Gulf of Mexico Hypoxia: past, present and future. Limnology and Oceanography Bulletin. 

Paper discussions:

There are 4 sessions of 45 minutes dedicated to reading peer-reviewed papers, each student will be paired (4 groups of 2 students) and assigned a discussion to lead with a classmate based on the paper to read. Each pair will create powerpoint presentation slides and present the paper to the entire class. I will virtually meet with each group a week prior to their scheduled class leadership to address any queries

Participation:

Students are expected to arrive at class ready to engage in discussions about the assigned readings for the day. Full participation points are awarded for both attendance and active involvement in the day's discussion, which may include responding to polls, making verbal comments, contributing to the chat, and more. Mere attendance without active participation is insufficient for earning full credit. My goal, is that you will get out of the class what you put into it.

 Cell Biology (BIO 201) introduces students to the mechanisms that cells use to regulate the physical properties of their dynamic architecture, to produce force and move, to compartmentalize and transport proteins, to regulate growth and death, and to communicate with their environment. The course focuses on human cells, and emphasis is placed on human diseases where appropriate. Upon course completion, students have a comprehensive understanding of the function and architecture of cells.

Because experimentation is at the heart of progress in cell biology, 50% of classes contain practical work, completed over the course of the semester. The intention is to allow students to develop their knowledge in the subject area, to acquire sound scientific reasoning, and to become familiar with the main techniques of modern cell biology, like quantitative microscopy imaging and computer-assisted data analysis.

The main topics covered will be

• the internal organization of the cell (membranes, compartmentalization, traffic)
• integration of the cell into its environment
• cell multiplication and death
• the construction of a complex multicellular organism (appearance of different cell types, stem cells, the establishment of axes of symmetry and regionalization, morphogenesis).

BIO451 provides a strong foundation and is recommended for other second and third year biology courses. It is complementary to BIO452. Some concepts seen in BIO452 are used. However, they will be reviewed at the beginning of the course, and taking BIO451 without having taken BIO452 is not a problem.

Optional Year 3 project for both periods.

Alone or in pairs projects will be the subject of discussions between students and teachers and will be assiociate to one of the followed units.

The proposed projects by the Biology Department will be available in the BioInformatics PA.

The project ca be carried out according to one of the three following options with the teachers during the starting PA lecture hall: P1 or P1 and P2

- BIO511

Research project: the first option involves a research activity in laboratory. In most projects of this option, a part of data production will be followed by an analysis and modeling part.

It is a first introduction and a personal initial contact with the research world.

- Bibliographic project: This option involves developing a bibliographic in-depth research on a specific subject related with one of the year 3 course.

The purpose is to be capable of presenting this topics in a concise, understandable and instructive way in the form of a course presentation with a written document.

- Project development: This option involves developing a funding request for a research project. The purpose will be to define a scientific project innovative and ambitious on one of the topics proposed in year 3, to write and present it orally.

For all this options, exchanges between teachers in the department and between departments are highly encouraged. All these topics can also be developed in engineering perspective, incuding the developement of methods, tools, software, databases and genetically modified organisms.

The purpose of the year 3 project is to start a personal project on a biology research topic by combining reflection, bibliographic analysis and/or experiments and data analases. The project is to be realized alone or in pairs (possibly more but a clear division of tasks will be required). It will be attached to one of the year 3 teachers that you have chosen so you can discuss your progress and interogations regurarly with your teachers. In order that your projects are succesful, a real engagement is required, both in terms of working time you will devote to it in the first weeks and in terms of openness and maturity you must demonstrate, to collect sources of information from your teachers but also from teachers in other departments or regional researchers. You will learn the most by keeping the project alive.

Schedule:

A list of projects and subjects will be presented at the lecture hall 0 in September.

At the end of the day, each student must have defined a project, a subject and/or chosen a referent teacher. The projects and subjects presented remain open and are intended to give you a starting point and to show you the different fields of expertise of the biology department's teachers. Feel free to develop these projects or to discuss with the teachers to bring out new ones that are important to you, our only goal is to make sure that these projects are coherent and realizable, so you can develop your full potential. You can also choose an article analysis with a unit of P1, especially BIO571.

Evaluation modality:

• September to end of February: project development, a half-day each week with your tutor.
• Mid-December: intermediate defense organized at the end of the first period.
• Mid-March/end of March: redaction of a short report and oral defense.

A 10 minutes oral presentation (15 minutes for a duo) will be followed by a 15 minutes discussion with coordinators and project tutors. We do not ask for a written report but we encourage you to deliver a report to your renferent so they can keep a record of your work. Check with them for the expected form.

Course language: French

Quantitative study of size homoeostasis in the fission yeast S. pombe

Interdisciplinarity is key in today's life sciences. On top of the experimental techniques of biology and biochemistry, applied mathematics, computer science or physics are increasingly mandatory for the quantitative study of a biological question. In particular, imaging through fluorescence microscopy and the automated analysis of the resulting acquired images play a crucial role in the study of dynamical phenomenon in vivo. Following that spirit, we will look at cell growth and size homoeostasis in the fission yeast S. pombe, using classical experimental biology techniques to build genetically modified strains, video-microscopy to observe them in vivo and image analysis to obtain quantitative data, which will be confronted to simple models and simulations.

Note: This module contains a practical experimental biology part as well as a computational part in Python.
Course language: French
ECTS credits: 4