Search result: Catalogue data in Autumn Semester 2022
Biology Master  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 Elective Major Subject Areas | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Elective Major: Ecology and Evolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Compulsory Concept Courses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 701-2413-00L | Evolutionary Genetics | O | 6 credits | 4V | T. Städler, A. Widmer, S. Fior, M. Fischer, J. Stapley | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The concept course 'Evolutionary Genetics' consists of two lectures that jointly provide an introduction to the fields of population and quantitative genetics (emphasis on basic concepts) and ecological genetics (more emphasis on evolutionary and ecological processes of adaptation and speciation). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The aim of the course is to provide students with a solid introduction to the fields of population genetics, quantitative genetics, and ecological genetics. The concepts and research methods developed in these fields have undergone profound transformations; they are of fundamental importance in our understanding of evolutionary processes, both past and present. Students should gain an appreciation for the concepts, methods and explanatory power of evolutionary genetics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Population genetics - Types and sources of genetic variation; randomly mating populations and the Hardy-Weinberg equilibrium; effects of inbreeding; natural selection; random genetic drift and effective population size; gene flow and hierarchical population structure; molecular population genetics: neutral theory of molecular evolution and basics of coalescent theory. Quantitative genetics - Continuous variation; measurement of quant. characters; genes, environments and their interactions; measuring their influence; response to selection; inbreeding and crossbreeding, effects on fitness; Fisher's fundamental theorem. Ecological Genetics - Concepts and methods for the study of genetic variation and its role in adaptation, reproductive isolation, hybridization and speciation | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Handouts | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Hamilton, M.B. 2009. Population Genetics. Wiley-Blackwell, Chichester, U.K. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Elective Compulsory Master Courses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 701-1409-00L | Research Seminar: Ecological Genetics Minimum number of participants is 5. | W | 2 credits | 1S | S. Fior | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | In this research seminar we will critically discuss recent publications on current topics in Ecological Genetics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | It is our aim that participants gain insight into current research topics and approaches in Ecological Genetics and learn to critically assess and appreciate scientific publications in this field. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | none | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | will be distributed | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Active and regular participation in the discussions, together with the presentation of a scientific paper are required to successfully pass this course. It is strongly recommended that participants have in advance successfully participated in the course Evolutionary Genetics (701-2413-00) or Ecological Genetics (701-1413-01). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 751-5121-00L | Insect Ecology  | W | 2 credits | 2V | C. De Moraes, N. Stanczyk | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This is an introductory class on insect ecology. During the course you will learn about insect interactions with, and adaptations to, their environment and other organisms, and the importance of insect roles in our ecosystems. This course includes lectures, small group discussions and outside readings. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The aim of the course is to gain an understanding of how insects have specialised and adapted to occupy diverse environmental niches and become vital to ecosystem processes. Important topics include: insect-plant interactions, chemical ecology, predator-prey interactions, vectors of disease, social insects, mutual and parasitic interactions and examining insect ecology in an evolutionary context. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Provided to students through Moodle | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Selected required readings (peer reviewed literature). Optional recommended readings with additional information. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 401-0625-01L | Applied Analysis of Variance and Experimental Design | W | 5 credits | 2V + 1U | L. Meier | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Principles of experimental design, one-way analysis of variance, contrasts and multiple comparisons, multi-factor designs and analysis of variance, complete block designs, Latin square designs, random effects and mixed effects models, split-plot designs, incomplete block designs, two-series factorials and fractional designs, power. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Participants will be able to plan and analyze efficient experiments in the fields of natural sciences. They will gain practical experience by using the software R. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Principles of experimental design, one-way analysis of variance, contrasts and multiple comparisons, multi-factor designs and analysis of variance, complete block designs, Latin square designs, random effects and mixed effects models, split-plot designs, incomplete block designs, two-series factorials and fractional designs, power. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | G. Oehlert: A First Course in Design and Analysis of Experiments, W.H. Freeman and Company, New York, 2000. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The exercises, but also the classes will be based on procedures from the freely available, open-source statistical software R, for which an introduction will be held. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 401-0649-00L | Applied Statistical Regression | W | 5 credits | 2V + 1U | M. Dettling | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course offers a practically oriented introduction into regression modeling methods. The basic concepts and some mathematical background are included, with the emphasis lying in learning "good practice" that can be applied in every student's own projects and daily work life. A special focus will be laid in the use of the statistical software package R for regression analysis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students acquire advanced practical skills in linear regression analysis and are also familiar with its extensions to generalized linear modeling. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course starts with the basics of linear modeling, and then proceeds to parameter estimation, tests, confidence intervals, residual analysis, model choice, and prediction. More rarely touched but practically relevant topics that will be covered include variable transformations, multicollinearity problems and model interpretation, as well as general modeling strategies. The last third of the course is dedicated to an introduction to generalized linear models: this includes the generalized additive model, logistic regression for binary response variables, binomial regression for grouped data and poisson regression for count data. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | A script will be available. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Faraway (2005): Linear Models with R Faraway (2006): Extending the Linear Model with R Draper & Smith (1998): Applied Regression Analysis Fox (2008): Applied Regression Analysis and GLMs Montgomery et al. (2006): Introduction to Linear Regression Analysis | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The exercises, but also the classes will be based on procedures from the freely available, open-source statistical software package R, for which an introduction will be held. In the Mathematics Bachelor and Master programmes, the two course units 401-0649-00L "Applied Statistical Regression" and 401-3622-00L "Statistical Modelling" are mutually exclusive. Registration for the examination of one of these two course units is only allowed if you have not registered for the examination of the other course unit. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 701-0301-00L | Applied Systems Ecology Number of participants limited to 35. Waiting list will be deleted 02.10.2022. | W | 3 credits | 2V | A. Gessler | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course provides the ecological systems` knowledge needed to question applied solutions to current environmental issues. Our central aim is to balance participants' respect for complexity with a sense of possibility by providing examples from the vast solution space offered by ecological systems, such as e.g. green infrastructure to manage water. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | At the end of the course... ...you know how to structure your inquiry and how to proceed the analysis when faced with a complex environmental issue. You can formulate the relevant questions, find answers (supported by discussions, input from the lecturers and the literature), and you are able to present your conclusions clearly and cautiously. ...you understand the complexity of interactions and structures in ecosystems. You know how ecosystem processes, functions and services interact and feed back across multiple spatio-temporal scales (in general, plus in depth case examples). ...you understand that biodiversity and the interaction between organisms are an integral part of ecosystems. You are aware that the link between biodiversity and process/function/service is rarely fully understood. You know how to honestly deal with this lack of understanding and can nevertheless find, critically analyse and communicate solutions. ...you understand the importance of ecosystem services for society. ...you have an overview of the methods of ecosystem research and have a deeper insight into some of them, e.g. ecosystem observation, manipulation and modelling. ...you have reflected on ecology as a young discipline at the heart of significant applied questions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | This course provides the ecological systems' knowledge needed to question applied sustainability solutions. We will critically assess the complexity of current environmental issues, illustrating basic ecological concepts and principles. Our central aim is to balance participants' respect for complexity with a sense of possibility by providing examples from the vast solution space offered by ecological systems, such as e.g. green infrastructure to manage water. The course is structured around four larger topical areas: (1) Integrated Water Management -- Green infrastructure (land management options) as an alternative to engineered solutions (e.g. large reservoirs) in flood and drought management; (2) Fire dynamics, the water cycle and biodiversity -- The surprising dynamics of species life cycles and populations in arid landscapes; (3) Rewilding, e.g. re-introducing apex predators (e.g. wolves), or large ungulates (e.g. bisons) in protected areas -- A nature conservation trend with counterintuitive effects; (4) Coupling of aquatic and terrestrial systems: carbon, nitrogen and phosphorus transfers of global importance on landscape scale. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Case descriptions, commented glossary and a list of literature and further resources per case. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | It is not essential to borrow/buy the following books. We will continuously provide excerpts and other literature during the course. Agren GI and Andersson FO (2012) Principles of Terrestrial Ecosystem Ecology, Cambridge University Press. Chapin et al. (2011), Principles of Terrestrial Ecosystem Ecology, Springer. Schulze et al. (2005) Plant Ecology; Springer. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The course combines elements of a classic lecture, group discussions and problem based learning. It is helpful, but not essential to be familiar with the "seven stages" method (see e.g. course 701-0352-00L "Analysis and Assessment of Environmental Sustainability" by Christian Pohl et al.). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 401-6215-00L | Using R for Data Analysis and Graphics (Part I) | W | 1.5 credits | 1G | M. Mächler | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The course provides the first part an introduction to the statistical/graphical/data science software R (https://www.r-project.org/) for scientists. Topics covered are data generation and selection, graphical and basic statistical functions, creating simple functions, basic types of objects. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students will be able to use the software R for simple data analysis and graphics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course provides the first part of an introduction to the statistical software R for scientists. R is free software that contains a huge collection of functions with focus on statistics and graphics. If one wants to use R one has to learn the programming language R - on very rudimentary level. The course aims to facilitate this by providing a basic introduction to R. Part I of the course covers the following topics: - What is R? - R Basics: reading and writing data from/to files, creating vectors & matrices, selecting elements of dataframes, vectors and matrices, arithmetics; - Types of data: numeric, character, logical and categorical data, missing values; - Simple (statistical) functions: summary, mean, var, etc., simple statistical tests; - Writing simple functions; - Introduction to graphics: scatter-, boxplots and other high-level plotting functions, embellishing plots by title, axis labels, etc., adding elements (lines, points) to existing plots. The course focuses on practical work at the computer with R. We will make use of the graphical user interface RStudio: www.rstudio.org Note: Part I of UsingR is complemented and extended by Part II, which is offered during the second part of the semester and which can be taken independently from Part I. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | An Introduction to R. http://stat.ethz.ch/CRAN/doc/contrib/Lam-IntroductionToR_LHL.pdf | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The course resources will be provided via the Moodle web learning platform. Subscribing via Mystudies *automatically* makes you a student participant of the Moodle course of this lecture, which is at https://moodle-app2.let.ethz.ch/course/view.php?id=18279 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 401-6217-00L | Using R for Data Analysis and Graphics (Part II) | W | 1.5 credits | 1G | M. Mächler | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The course provides the second part an introduction to the statistical software R for scientists. Topics are data generation and selection, graphical functions, important statistical functions, types of objects, models, programming and writing functions. Note: This part builds on "Using R... (Part I)", but can be taken independently if the basics of R are already known. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The students will be able to use the software R efficiently for data analysis, graphics and simple programming | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course provides the second part of an introduction to the statistical software R (https://www.r-project.org/) for scientists. R is free software that contains a huge collection of functions with focus on statistics and graphics. If one wants to use R one has to learn the programming language R - on very rudimentary level. The course aims to facilitate this by providing a basic introduction to R. Part II of the course builds on part I and covers the following additional topics: - Elements of the R language: control structures (if, else, loops), lists, overview of R objects, attributes of R objects; - More on R functions; - Applying functions to elements of vectors, matrices and lists; - Object oriented programming with R: classes and methods; - Tayloring R: options - Extending basic R: packages The course focuses on practical work at the computer. We will make use of the graphical user interface RStudio: www.rstudio.org | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | An Introduction to R. http://stat.ethz.ch/CRAN/doc/contrib/Lam-IntroductionToR_LHL.pdf | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Basic knowledge of R equivalent to "Using R .. (part 1)" ( = 401-6215-00L ) is a prerequisite for this course. The course resources will be provided via the Moodle web learning platform. As from FS 2019, subscribing via Mystudies should *automatically* make you a student participant of the Moodle course of this lecture, which is at https://moodle-app2.let.ethz.ch/course/view.php?id=15522 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 751-4504-00L | Plant Pathology I | W | 2 credits | 2G | B. McDonald | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Plant Pathology I will focus on pathogen-plant interactions, epidemiology, disease assessment, and disease development in agroecosystems. Themes will include: 1) how pathogens attack plants and; 2) how plants defend themselves against pathogens; 3) factors driving the development of epidemics in agroecosystems. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Students will understand: 1) how pathogens attack plants and; 2) how plants defend themselves against pathogens; 3) factors driving the development of epidemics in agroecosystems as a basis for implementing disease management strategies in agroecosystems. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Course description: Plant Pathology I will focus on pathogen-plant interactions, epidemiology, disease assessment, and disease development in agroecosystems. Themes will include: 1) how pathogens attack plants and; 2) how plants defend themselves against pathogens; 3) factors driving the development of epidemics in agroecosystems. Topics under the first theme will include pathogen life cycles, disease cycles, and an overview of plant pathogenic nematodes, viruses, bacteria, and fungi. Topics under the second theme will include plant defense strategies, host range, passive and active defenses, and chemical and structural defenses. Topics under the third theme will include the disease triangle and cultural control strategies. Lecture Topics and Tentative Schedule Week 1 The nature of plant diseases, symbiosis, parasites, mutualism, biotrophs and necrotrophs, disease cycles and pathogen life cycles. Week 2 Nematode attack strategies and types of damage. Viral pathogens, classification, reproduction and transmission, attack strategies and types of damage. Examples TMV, BYDV. Bacterial pathogens and phytoplasmas, classification, reproduction and transmission. Week 3 Bacterial attack strategies and symptoms. Example bacterial diseases: fire blight, Agrobacterium crown gall, soft rots. Fungal and oomycete pathogens, classification, growth and reproduction, sexual and asexual spores, transmission. Week 4 Fungal and oomycete life cycles, disease cycles, infection processes, colonization, phytotoxins and mycotoxins. Attack strategies of fungal necrotrophs and biotrophs. Symptoms and signs of fungal infection. Example fungal diseases: potato late blight. Week 5 Example fungal diseases: wheat stem rust, grape powdery mildew, wheat septoria tritici blotch. Plant defense mechanisms, host range and non-host resistance. Passive structural and chemical defenses, preformed chemical defenses. Active structural defense, histological and cellular (papillae). Week 6 Active chemical defense, hypersensitive response, pathogenesis-related (PR) proteins, phytoalexins and disease resistance. Pisatin and pisatin demethylase. Local and systemic acquired resistance (LAR, SAR), induced systemic resistance (ISR), signal molecules, defense activators (Bion). Pathogen effects on food quality. Positive and negative transformations. Week 7 Negative pathogen impacts on crop yield and quality. Pathogen effects on food safety. Mycotoxins in the food chain. Aflatoxin, patulin safety assessment and action thresholds. Epidemiology: historical epidemics. Week 8 Epidemiology: Disease pyramid, environmental effects on epidemic development, plant effects on development of epidemics, including resistance, physiology, density, uniformity. Week 9 Disease assessment: incidence and severity measures, keys, diagrams, scales, measurement errors. Correlations between incidence and severity. Molecular detection and diagnosis of pathogens. Host indexing, serology, monoclonal and polyclonal antibodies, ELISA. Week 10 Molecular detection and diagnosis of pathogens: PCR, rDNA and loop-mediated isothermal amplification. Strategies for minimizing disease risks: calculating disease thresholds, disease forecasting systems. Week 11 Strategies for minimizing disease risks: lowering epidemic risk, ecological risk assessment, natural and synthetic pesticides. Disease control strategies: economic thresholds, overview of control strategies. Week 12 Physical control methods. Cultural control methods: avoidance, tillage practices, crop sanitation. Week 13 Cultural control methods: fertilizers, crop rotations. Week 14 Open lecture. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Detailed lecture notes (~160 pages) will be available for purchase at the cost of reproduction at the start of the semester. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 636-0017-00L | Computational Biology | W | 6 credits | 3G + 2A | T. Vaughan, C. Magnus, T. Stadler | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The aim of the course is to provide up-to-date knowledge on how we can study biological processes using genetic sequencing data. Computational algorithms extracting biological information from genetic sequence data are discussed, and statistical tools to understand this information in detail are introduced. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Attendees will learn which information is contained in genetic sequencing data and how to extract information from this data using computational tools. The main concepts introduced are: * stochastic models in molecular evolution * phylogenetic & phylodynamic inference * maximum likelihood and Bayesian statistics Attendees will apply these concepts to a number of applications yielding biological insight into: * epidemiology * pathogen evolution * macroevolution of species | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course consists of four parts. We first introduce modern genetic sequencing technology, and algorithms to obtain sequence alignments from the output of the sequencers. We then present methods for direct alignment analysis using approaches such as BLAST and GWAS. Second, we introduce mechanisms and concepts of molecular evolution, i.e. we discuss how genetic sequences change over time. Third, we employ evolutionary concepts to infer ancestral relationships between organisms based on their genetic sequences, i.e. we discuss methods to infer genealogies and phylogenies. Lastly, we introduce the field of phylodynamics, the aim of which is to understand and quantify population dynamic processes (such as transmission in epidemiology or speciation & extinction in macroevolution) based on a phylogeny. Throughout the class, the models and methods are illustrated on different datasets giving insight into the epidemiology and evolution of a range of infectious diseases (e.g. HIV, HCV, influenza, Ebola). Applications of the methods to the field of macroevolution provide insight into the evolution and ecology of different species clades. Students will be trained in the algorithms and their application both on paper and in silico as part of the exercises. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Lecture slides will be available on moodle. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | The course is not based on any of the textbooks below, but they are excellent choices as accompanying material: * Yang, Z. 2006. Computational Molecular Evolution. * Felsenstein, J. 2004. Inferring Phylogenies. * Semple, C. & Steel, M. 2003. Phylogenetics. * Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Basic knowledge in linear algebra, analysis, and statistics will be helpful. Programming in R will be required for the project work (compulsory continuous performance assessments). In case you do not have any previous experience with R, we strongly recommend to get familiar with R prior to the semester start. For the D-BSSE students, we highly recommend the voluntary course „Introduction to Programming“, which takes place in Basel before the start of the semester. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 701-1471-00L | Ecological Parasitology Number of participants limited to 20. A minimum of 6 students is required that the course will take place. Waiting list will be deleted on 30.09.2022. | W | 3 credits | 1V + 1P | F. Feijen, J. Jokela, C. Vorburger | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Course focuses on the ecology and evolution of macroparasites and their hosts. Through lectures and practical work, students learn about diversity and natural history of parasites, adaptations of parasites, ecology of host-parasite interactions, applied parasitology, and human macroparasites in the modern world. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | 1. Identify common macroparasites in invertebrates. 2. Understand ecological and evolutionary processes in host-parasite interactions. 3. Conduct parasitological research | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Lectures: 1. Diversity and natural history of parasites (i.e. systematic groups and life-cycles). 2. Adaptations of parasites (e.g. evolution of life-cycles, host manipulation). 3. Ecology of host-parasite interactions (e.g. parasite communities, effects of environmental changes). 4. Ecology and evolution of parasitoids and their applications in biocontrol 5. Human macroparasites (schistosomiasis, malaria). Practical exercises: 1. Examination of parasites in molluscs (identification and examination of host exploitation strategies). 2. Examination of parasites in amphipods (identification and examination of effects on hosts). 3. Examination of parasitoids of aphids. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The three practicals will take place at the 04.10.2022, the 18.10.2022 and the 08.11.2022 at Eawag Dübendorf from 08:15 - 12:00. Note that each practical takes 2 hours longer than the weekly lecture. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 701-1703-00L | Evolutionary Medicine for Infectious Diseases Number of participants limited to 35. Waiting list will be deleted 02.10.2022. | W | 3 credits | 2G | A. Hall | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course explores infectious disease from both the host and pathogen perspective. Through short lectures, reading and active discussion, students will identify areas where evolutionary thinking can improve our understanding of infectious diseases and, ultimately, our ability to treat them effectively. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Students will learn to (i) identify evolutionary explanations for the origins and characteristics of infectious diseases in a range of organisms and (ii) evaluate ways of integrating evolutionary thinking into improved strategies for treating infections of humans and animals. This will incorporate principles that apply across any host-pathogen interaction, as well as system-specific mechanistic information, with particular emphasis on bacteria and viruses. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | We will cover several topics where evolutionary thinking is relevant to understanding or treating infectious diseases. This includes: (i) determinants of pathogen host range and virulence, (ii) dynamics of host-parasite coevolution, (iii) pathogen adaptation to evade or suppress immune responses, (iv) antimicrobial resistance, (v) evolution-proof medicine. For each topic there will be a short (< 20 minutes) introductory lecture, before students independently research the primary literature and develop discussion points and questions, followed by interactive discussion in class. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | The focus is on primary literature, but for some parts the following text books provide good background information: Schmid Hempel 2011 Evolutionary Parasitology Stearns & Medzhitov 2016 Evolutionary Medicine | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | A basic understanding of evolutionary biology, microbiology or parasitology will be advantageous but is not essential. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 636-0009-00L | Evolutionary Dynamics | W | 6 credits | 2V + 1U + 2A | N. Beerenwinkel | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Evolutionary dynamics is concerned with the mathematical principles according to which life has evolved. This course offers an introduction to mathematical modeling of evolution, including deterministic and stochastic models, with an emphasis on tumor evolution. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The goal of this course is to understand and to appreciate mathematical models and computational methods that provide insight into the evolutionary process in general and tumor evolution in particular. Students should analyze and evaluate models and their application critically and be able to design new models. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Evolution is the one theory that encompasses all of biology. It provides a single, unifying concept to understand the living systems that we observe today. We will introduce several types of mathematical models of evolution to describe gene frequency changes over time in the context of different biological systems, focusing on asexual populations. Viruses and cancer cells provide the most prominent examples of such systems and they are at the same time of great biomedical interest. The course will cover some classical mathematical population genetics and population dynamics, and also introduce several new approaches. This is reflected in a diverse set of mathematical concepts which make their appearance throughout the course, all of which are introduced from scratch. Topics covered include the quasispecies equation, evolution of HIV, evolutionary game theory, evolutionary stability, evolutionary graph theory, tumor evolution, stochastic tunneling, genetic progression of cancer, diffusion theory, fitness landscapes, branching processes, and evolutionary escape. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | No. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | - Evolutionary Dynamics. Martin A. Nowak. The Belknap Press of Harvard University Press, 2006. - Evolutionary Theory: Mathematical and Conceptual Foundations. Sean H. Rice. Sinauer Associates, Inc., 2004. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Prerequisites: Basic mathematics (linear algebra, calculus, probability) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 701-0328-00L | Advanced Ecological Processes For students of the following study programmes only: Biology Master Teaching certificate Biology Environmental Sciences Master UZH MNF Biology UZH MNF Geography /Earth Sciences | W | 4 credits | 2V | J. Hille Ris Lambers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course presents theoretical and empirical approaches to understanding the ecological processes structuring populations and communities. Central problems covered include species interactions, spatial structure, resource dynamics, and ecological responses to environmental change. These and other topics will be explored from basic and applied perspectives. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Students will understand how ecological processes operate in natural communities. They will appreciate how mathematical theory, field experimentation, and observational studies combine to generate a predictive science of ecological processes, and how this predictive science informs conservation and management decisions. Upon completing the course, students will be able to: Understand the factors determining the outcome of species interactions in communities, and how this information informs management. Apply theoretical knowledge on species interactions to predict the potential outcomes of novel species introductions. Understanding the role of spatial structure in mediating population dynamics and persistence, species interactions, and patterns of species diversity. Use population and community models to predict the stability of interactions between predators and prey and between different competitors. Understand the conceptual basis of predictions concerning how ecological communities will respond to global change. Discuss the types of conceptual advances ecology as a science can realistically achieve, and how these relate to the applications of the discipline. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Lectures supplemented with readings from the primary literature and occasional computer exercises will focus on understanding central processes in community ecology. Topics will include demographic and spatial structure, consumer resource interactions, food webs, competition, mutualism, invasion, the maintenance of species diversity, and species effects on ecosystem processes. Each of these more conceptual topics will be discussed in concert with their applications to the conservation and management of species and communities in a changing world. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| Elective Concept Courses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0313-00L | Microbiology (Part I) | W | 3 credits | 2V | W.‑D. Hardt, L. Eberl, B. Nguyen, J. Piel, M. Pilhofer, A. Vagstad | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Advanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | This concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Advanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Updated handouts will be provided during the class. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Current literature references will be provided during the lectures. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | English The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0309-00L | Concepts in Modern Genetics Information for UZH students: Enrolment to this course unit only possible at ETH. No enrolment to module BIO348 at UZH. Please mind the ETH enrolment deadlines for UZH students: Link | W | 6 credits | 4V | Y. Barral, D. Bopp, A. Hajnal, O. Voinnet | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Concepts of modern genetics and genomics, including principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | This course focuses on the concepts of classical and modern genetics and genomics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The topics include principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Scripts and additional material will be provided during the semester. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-1299-00L | Bioinformatics | W | 6 credits | 4G | S. Sunagawa, P. Beltrao, A. Blasimme, V. Boeva, A. Kahles, C. von Mering, N. Zamboni | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Students will study bioinformatic concepts in the areas of genomics, metagenomics, proteomics, biological networks, biostatistics and bioethics. Through integrated lectures, practical hands-on sessions and homework assignments, students will also be trained in analytical and programming skills to meet the emerging increase in data-driven knowledge generation in biology in the 21st century. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Students will have an advanced understanding of the underlying concepts behind modern bioinformatic analyses at genome, metagenome and proteome-wide scales. They will be familiar with the most common data types, where to access them, and how to analytically work with them to address contemporary questions in the field of biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Course participants have already acquired basic programming skills in UNIX, Python and R. Students bring their own computer with keyboard, internet access (browser) and software to connect to the ETH network via VPN. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| Elective Major: Microbiology and Immunology | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Compulsory Concept Courses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0313-00L | Microbiology (Part I) | O | 3 credits | 2V | W.‑D. Hardt, L. Eberl, B. Nguyen, J. Piel, M. Pilhofer, A. Vagstad | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Advanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | This concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Advanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Updated handouts will be provided during the class. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Current literature references will be provided during the lectures. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | English The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0317-00L | Immunology I | O | 3 credits | 2V | M. Kopf, A. Oxenius | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Introduction into structural and functional aspects of the immune system. Basic knowledge of the mechanisms and the regulation of an immune response. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Introduction into structural and functional aspects of the immune system. Basic knowledge of the mechanisms and the regulation of an immune response. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | - Introduction and historical background - Innate and adaptive immunity, Cells and organs of the immune system - B cells and antibodies - Generation of diversity - Antigen presentation and Major Histoincompatibility (MHC) antigens - Thymus and T cell selection - Autoimmunity - Cytotoxic T cells and NK cells - Th1 and Th2 cells, regulatory T cells - Allergies - Hypersensitivities - Vaccines, immune-therapeutic interventions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Electronic access to the documentation will be provided. The link can be found at "Lernmaterialien" | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | - Kuby, Immunology, 9th edition, Freemen + Co., New York, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | For D-BIOL students Immunology I (WS) and Immunology II (SS) will be examined as one learning entity in a "Sessionsprüfung". All other students write separate exams for Immunology I and Immunology II. All exams (combined exam Immunology I and II, individual exams) are offered in each exam session. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| Elective Compulsory Master Courses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 551-0223-00L | Immunology III | W | 4 credits | 2V | M. Kopf, S. B. Freigang, S. R. Leibundgut, F. Mair, A. Oxenius, C. Schneider, E. Slack, R. Spörri, L. Tortola | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course provides a detailed understanding of - development of T and B cells - the dynamics of a immune response during acute and chronic infection - mechanisms of immunopathology - modern vaccination strategies Key experimental results will be shown to help understanding how immunological text book knowledge has evolved. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Obtain a detailed understanding of - the development, activation, and differentiation of different types of T cells and their effectormechanisms during immune responses, - Recognition of pathogenic microorganisms by the host cells and molecular events thereafter, - events and signals for maturation of naive B cells to antibody producing plasma cells and memory B cells. - Optimization of B cell responses by intelligent design of new vaccines | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | o Development and selection of CD4 and CD8 T cells, natural killer T cells (NKT), and regulatory T cells (Treg) o NK T cells and responses to lipid antigens o Differentiation, characterization, and function of CD4 T cell subsets such as Th1, Th2, and Th17 o Overview of cytokines and their effector function o Co-stimulation (signals 1-3) o Dendritic cells o Evolution of the "Danger" concept o Cells expressing Pattern Recognition Receptors and their downstream signals o T cell function and dysfunction in acute and chronic viral infections | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Documents of the lectures are available for download at: https://moodle-app2.let.ethz.ch/course/view.php?id=2581¬ifyeditingon=1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Immunology I and II recommended but not compulsory | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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