Frédéric Allain: Catalogue data in Autumn Semester 2023 |
| Name | Prof. Dr. Frédéric Allain |
| Field | Biomolecular NMR |
| Address | Institut für Biochemie ETH Zürich, HPP L 14.1 Hönggerbergring 64 8093 Zürich SWITZERLAND |
| Telephone | +41 44 633 39 40 |
| Fax | +41 44 633 12 94 |
| allain@bc.biol.ethz.ch | |
| Department | Biology |
| Relationship | Full Professor |
| Number | Title | ECTS | Hours | Lecturers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 551-0033-00L | Molecular Genetics and Cell Biology  | 5 credits | 5G | J. Corn, F. Allain, K. Köhler | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course teaches the basic principles of evolution, cell biology, molecular biology, genetics and developmental biology using the example of humans. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | 1) Students can explain the importance of evolution for the development of humans and diseases. 2) The students know the cell as the smallest unit of the body. They can explain how the functions of the cell are disturbed in certain diseases and where therapies intervene. They can describe the multiplication of cells in the body and show how errors in this multiplication can lead to diseases. 3) The students know DNA as the basis of life. They can explain how the DNA information is stored and how this information can be reproduced and protected from damage. They can describe how the information is read and translated into proteins. They can explain which mechanisms at the level of DNA, RNA and proteins can cause diseases. 4) Students can explain which technologies can be used to diagnose and treat diseases. 5) Students can explain how people differ genetically and know the molecular basis of these differences. They can explain how these differences can lead to diseases and why some of these differences do not affect diseases. 6) The students know the molecular causes of the most common hereditary diseases and can determine the probability of occurrence and transmission to offspring. 7) Students can explain the biochemical and molecular basis of human reproduction and know the basic principles of human embryonic development. The students can explain which mechanisms can be disturbed by a faulty development. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Competencies |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0319-00L | Cellular Biochemistry (Part I) | 3 credits | 2V | U. Kutay, F. Allain, T. Kleele, I. Zemp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Concepts and molecular mechanisms underlying the biochemistry of the cell, providing advanced insights into structure, function and regulation of individual cell components. Particular emphasis will be put on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes such as intracellular transport, cell division & growth, and cell migration. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterisation of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry. The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain the integration of different molecules and signaling pathways into complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, cell division and cell growth. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Structural and functional details of individual cell components, regulation of their interactions, and various aspects of the regulation and compartmentalisation of biochemical processes. Topics include: biophysical and electrical properties of membranes; viral membranes; structural and functional insights into intracellular transport and targeting; vesicular trafficking and phagocytosis; post-transcriptional regulation of gene expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Scripts and additional material will be provided during the semester. Please contact Dr. Alicia Smith for assistance with the learning materials. (alicia.smith@bc.biol.ethz.ch) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Recommended supplementary literature (review articles and selected primary literature) will be provided during the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | To attend this course the students must have a solid basic knowledge in chemistry, biochemistry and general biology. The course will be taught in English. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0357-00L | Cellular Matters: Properties, Functions and Applications of Biomolecular Condensates The number of participants is limited to 30 and will only take place with a minimum of 6 participants. The first lecture will serve to form groups of students and assign papers. | 4 credits | 2S | T. Michaels, F. Allain, P. Arosio, Y. Barral, D. Hilvert, M. Jagannathan, R. Mezzenga, G. Neurohr, R. Riek, A. E. Smith, K. Weis, H. Wennemers, further lecturers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This Master level course delves into the emerging field of biomolecular condensates - membrane-less organelles in cells. Using interdisciplinary concepts from biology, chemistry, biophysics, and soft matter, we will explore the biological properties of these condensates, their functions in health and disease, and their potentiol as new biomimetic materials for various applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | In the last decade, a novel type of cell compartments called biomolecular condensates have been discovered. This discovery is radically changing our understanding of the cell, its organization, and dynamics. The emerging picture is that the cytoplasm and nucleoplasm are highly complex fluids that can (meta)stably segregate into membrane-less compartments, similary to emulsions. This interdisciplinary course encompasses milestone works and cutting-edge research questions in the young field of biomolecular condensates, including their properties, functions, and applications. The course begins with a lecture series that introduces the topic of condensates to an interdisciplinary audience and provides a theoretical foundation for understanding current research questions in the field. the lecturesprovide a base for student presentations of recent publications in the field, and for research seminars given by course lecturers, who are all active researchers with diverse expertise. Through this exciting interdisciplinary understanding of biomolecular condensates, bridging biology, chemistry, biophysics, and soft matter. Students will not only learn how to critically read and evaluate scientific literature but will also gain valuable experience in giving scientific presentations to an interdisciplinary audience. Each presentation will require an introduction, critical analysis of the results, and a discussion of their significance, allowing student to substantiate their statements with a critical mindset that considers the pros and cons of chosen approaches and methods, as well as any limitations or possible follow-up experiments. This process will enable student to ask relevant querions and actively participate in class discussions, further enhancing their scientific skills. In preparing the presentations, the students will have the unique opportunity to interact closely with each other and with the lecturers, who are all internationally well-established experts, and receive guidance in selectin a topic for the final presentaton and supporting literature. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The topic of biomolecular condensates goes beyond the boundaries of traditional disciplines and requires a multi-disciplinary approach that leverages and cross-fertilizes biology, physical chemistry, biophysics, and soft matter. This course will explore the properties, functions and potentioal applicatons of biomolecular condensates, including their role in neurodegenerative diseases such as Alzheimer's and Parkinson's, as well as their use as smart biomimetic materials. This course is divided into two parts. The fist part will introduce the basic concepts essentialto the study of biomolecular condensates and phase separation. Topics include: fundamental units and scales in soft matter, phase transitions in biology, biopolymers and molecular self-assembly, introduction to active matter. This will establish a foundation for the second part, which will explore milestone works and current research in the field of biomolecular condensates. Each lecture of this second part will consist of: 1) a short literature seminar, where student groups will present and discuss a milestone paper assigned in advance and 2) a research seminar, where one of the course lecturers will present their own state-of-the art research in the field, building upon the milestone literature. At the beginning of the course, student groups will be formed and assigned the milestone papers. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Lecture slides and some scripts will be provided. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | No compulsory textbooks. Literature will be provided during the course | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-1005-00L | Bioanalytics | 4 credits | 4G | P. Picotti, F. Allain, V. Korkhov, M. Pilhofer, R. Schlapbach, K. Weis, K. Wüthrich, further lecturers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The course will introduce students to a selected set of laboratory techniques that are foundational to modern biological research. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | For each of the techniques covered in the course, the students will be able to explain: a) the physical, chemical and biological principles underlying the technique, b) the requirements for the sample, c) the type of raw data collected by the technique, d) the assumptions and auxiliarry information used in the interpretation of the data and e) how these data can be used to answer a given biological question. By the end of the course the students will be able to select the appropriate experimental technique to answer a given biological problem and will be able to discuss the advantages and limitations of individual techniques as well as how different techniques can be combined to gain a more complete understanding of a given biological questions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course will be based on a combination of lectures, selfstudy elements and exercises. The focus will be on the following experimental techniques: - DNA sequencing - chromatography - mass-spectrometry - UV/Vis and fluorescence spectrometry - light microscopy - electron microscopy - X-ray crystallography - NMR spectroscopy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | The course is supported by a Moodle page that gives access to all supporting materials necessary for the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-1309-00L | RNA-Biology Number of participants limited to 17. The enrolment is done by the D-BIOL study administration. | 6 credits | 7P | F. Allain, J. Corn, J. Hall, M. Jinek, S. Jonas, B. Mateescu, R. Santoro, O. Voinnet | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Introduction to the diversity of current RNA-research at all levels from structural biology to systems biology using mainly model systems like S. cerevisiae (yeast), mammalian cells. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students will obtain an overview about the diversity of current RNA-research. They will learn to design experiments and use techniques necessary to analyze different aspects of RNA biology. Through lectures and literature seminars, they will learn about the burning questions of RNA research and discuss approaches to address these questions experimentally. In practical lab projects the students will work in one of the participating laboratories. Finally, they will learn how to present and discuss their data in an appropriate manner. Student assessment is a graded semester performance based on individual performance in the laboratory, the written exam and the poster presentation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Documentation and recommended literature will be provided at the beginning and during the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The course will be taught in English. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-1407-00L | RNA Biology Lecture Series I: Transcription & Processing & Translation Does not take place this semester. | 4 credits | 2V | F. Allain, N. Ban, S. Jonas, U. Kutay, further lecturers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course covers aspects of RNA biology related to gene expression at the posttranscriptional level. These include RNA transcription, processing, alternative splicing, editing, export and translation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students should obtain an understanding of these processes, which are at work during gene expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Transcription & 3'end formation ; splicing, alternative splicing, RNA editing; the ribosome & translation, translation regulation, RNP biogenesis & nuclear export, mRNA surveillance & mRNA turnover; signal transduction & RNA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Basic knowledge of cell and molecular biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||