Insights in Life Sciences Micro-module Proposal Form

Transcription

1 Name: Richard Dorrell Lab: Bowler Insights in Life Sciences Micro-module title: Eukaryotic evolution: origins and functions of the other 99% 3 x 1h lecture + 1h exam Exam/evaluation format: 1 hour timed essay, with a relatively open topic. Outline of lectures (approximately one paragraph): Animals, plants and fungi only represent a small fraction of the tree of eukaryotes, with a vast diversity of algal and protist lineages known. Recent genome sequencing projects for eukaryotes have provided valuable insights into the origins and presentday biology of many environmentally and economically important organisms. This module will explore the full diversity of eukaryotes, with a particular focus on photosynthesis. First, we will explore the eukaryotic tree of life in detail. Next, we will discuss how genome sequencing has transformed our understanding of eukaryotic evolution. Finally, we will look at the fundamental processes that underpin the gain, loss, and endosymbiotic replacement of chloroplasts. The students will gain a thorough understanding of eukaryotic diversity, and insights into some of the major questions about how eukaryotes operate at a cellular level.!

2 Name: Patrick Torbey Lab: Charnay Insights in Life Sciences Micro-module title: Genome editing: How to create your dragon. 3*1h The advancements made in the genetic engineering field these last 10 years are simply astonishing, both to the general public and to researchers alike, culminating 3 years ago with the rise of the CRISPR/Cas9 system. This truly revolutionary tool has completely changed the way we approach genome editing, and is pushing the limit of what we think is achievable in biology. During this course we will look at the different tools used to edit the genome and their applications in gene therapy, disease modeling, stem cells, plants and others. We will also explore what this tool could allow us to do in the near future, like adding or deleting traits in organisms, bringing extinct species back to life, and maybe even creating new ones.

3 Insights in Life Sciences Name: Victoire BAILLET Lab: Arabidopsis Epigenetics and Epigenomics (A2E) - IBENS baillet@biologie.ens.fr Micro-module title: Mutation and epimutation 3 x 1h lecture + 1h exam Exam/evaluation format: short answer- & multiple choice questions (ca. 30Min) Being the only process that can create genomic novelty, mutation is the ultimate source of organismal variation and thus a sine qua non of evolution. Combining literature review with ongoing work in the lab, this course bridges molecular biology and population genetics to give an overview of the study of the mutational process. It will also introduce the notion of epimutation (heritable change in gene activity in the absence of changes in the DNA sequence). Lecture1: Introduction (types of mutations, key definitions). Methods used to estimate mutation rates & current pitfalls. Phenotypic effects of new mutations. Phylogenetic variation and evolution of mutation rate. Lecture 2: Genomic and epigenomic influences on mutation. Lecture 3: Epimutation: definition, rate, stability, phenotypic effects.

4 Insights in Life Sciences Name: Juan José Pierella Karlusich Lab: Génomique des Plantes et Diatomées (Chris Bowler) Micro-module title: Microbial metagenomics: beyond the genome 3 x 1h lecture Exam/evaluation format: Practical exercises to resolve at home. The majority of microbes in many environments are considered as yet uncultured and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed researchers to access and study these microbes in a culture-independent manner through DNA sequencing of environmental samples. This micro-module describes the principles of metagenomics, their analytical tools and the main metagenomic projects that are currently carried out.

5 Insights in Life Sciences Name: Francesco De Carli and Vinko Besic Lab: Olivier Hyrien and Alice Lebreton Micro-module title: The central dogma by the numbers 3 x 1h lecture I have deeply regretted that I did not proceed far enough at least to understand something of the great leading principles of mathematics; for men thus endowed seem to have an extra sense. Charles Darwin Most biologists will be familiar with the ever-evolving central dogma of molecular biology. However, not all are familiar with the physical properties of the molecules and processes involved. This primer lecture series will give biological numbers that will lead to an intuitive understanding of the sizes, concentrations, energies and rates involved in DNA replication, transcription and protein translation.

6 Name: Olivier GEMIN Lab: Triller Insights in Life Sciences Micro-module title: The wondrous little world of electron microscopy : all you want to know about the Nobel Prize 2017 in Chemistry 3 x 1h lecture Exam/evaluation format: Written exam /French, depending on the students Electron Microscopy (EM) is the most resolutive imaging technique available in biology, yielding exquisitely detailed images of cellular ultrastructure. Recent technical developments have enabled electron microscopists to record protein structures with near-atomic resolution, to reconstruct entire neuronal architectures with nanometric resolution, and even to make peace with light microscopists. In this micro-module, I will present the basic principles of EM, comment on the diversity of technologies it gets involved in, and dwell on a few fabulous applications in life sciences.

7 Name: Nora Assendorp Lab: Triller Lab (biologie de la synapse) Insights in Life Sciences Micro-module title: The Making of the Human brain 3 x 1h lecture + 1h exam Exam/evaluation format: written exam. Multiple choice and open questions What makes us human? How did Homo sapiens end up being the dominant species on earth? Are we special in comparison to other animals? Central to answering these questions stands the evolution of the human brain. During this micro-module I will show you what we have learned about the evolution of our own brain and which aspects still remain to be unraveled. We will discuss the different approaches and touch upon the evolution of language and other closely related topics. By the end of this module you will have insight into our current understanding of human brain evolution and which knowledge gaps still remain to be filled to answer the centuries-old questions above.

8 Name: Menezes Nikita Lab: Olivier Hyrien / Auguste Genovesio menezes@biologie.ens.fr Insights in Life Sciences Micro-module Proposal Form Micro-module title: Once upon a time the dark side of Bioinformatics : Bioimaging. Micro-module format: 3 x 1h lecture + 1h exam Exam/evaluation format (preferentially, NOT a paper presentation): QCM-QROC, Presentation on specified topics related to bioimaging (no paper) or small project Preferred weeks/months/semester and times (lunch time or at 6-7 pm) : 2nd semester (not on thursday) lunch time or 6-7 pm Additional resources required (ie. Computer, lab): Computers Maximum number of students (if applicable): Minimum number of students you are willing to give the course to: 2-3 Open this course to all IBENS personnel: Yes (depending on the number of students) Language of Instruction: English (or French) Outline of lectures (one paragraph): Bio-imaging is not as widely spread as genomics and could be considered as the dark side of bio-informatics. During this module, you will have an overview on what an image. You will also understand how some of the common filters that are used in Instagram, Prisma, Snapchat are being used in biological image analysis and their purpose. And by the end, bioimaging is not as bad as it seem since it comes to the rescue of biology and you will see how. Pre-requisite : python coding (basics) Exam : QCM, presentation or small project (coding)

9 Insights in Life Sciences Name: Guillaume LOUVEL Lab: DYOGEN (Hugues Roest Crollius), Section Génomique Fonctionnelle Micro-module title: Untwist the branches: how to test correlations on a phylogeny? 3 x 1h lecture + 1h exam Exam/evaluation format: exercises on paper and computer /French In regular statistical testing, data points are often treated as independent. Unfortunately in (evolutionary) biology, due to common ancestry, a group of related organisms can rarely be considered as all independent. Some share a longer common history than others (scoop). In that case it can be difficult to disentangle between the correlation of interest, or just an effect of phylogenetic inertia. For example, one might ask whether primate brain size is rather caused by diet, or by sociality. Taking data from all primate species independently would lead to overestimate the number of degrees of freedom, and finding significant relationship where there is only an effect of relatedness. This course aims at progressively introducing basic to more elaborate methods of phylogenetic testing: sister-clade method, a derived fisher exact test for testing the correlation between two discrete traits, methods that account for branch lengths, phylogenetic independent contrasts, phylogenetic regression, parametric methods modeling the underlying trait evolution, methods comparing a trait with diversification dynamics, etc. Existing bioinformatics tools (for example in R) will be presented.