Course Catalogue

This page contains a list of all courses that are offered by the PSC.

Courses of the PhD program Science and Policy are listed separately.

PSC training provides an introduction to conceptual and technical approaches in research and also up-to-date methodological knowledge from research frontiers in plant sciences. Our workshops aim to enhance your interdisciplinary research competence in the field of plant sciences and we offer training in the development of transferable skills.

Be aware that some courses are offered once a year or less frequent

 

Registration for currently available courses: https://www.ethz.ch/services/en/service/courses-continuing-education.html

Choose ► Plant Sciences 

MANDATORY COURSES

Colloquium "Challenges in Plant Sciences"

The colloquium “Challenges in Plant Sciences” is a core event of the Plant Science Center's PhD program and the MSc module. The colloquium introduces participants to the broad spectrum of disciplines in plant sciences. The topics offer integrated knowledge about plant sciences, from the molecular level to the ecosystem level, and from basic to applied science while making use of the synergies between the different research groups of the PSC.

The course offers a unique chance to approach interdisciplinary topics as challenges in the field of plant sciences. During the kick-off meeting, lecturers give talks on various topics as a general introduction to their research fields. Subsequently, each student group prepares a presentation chosen from a variety of topics and based on literature provided by the lecturers. Students gain knowledge and practice discussing and presenting research results.

Individual Performance and Assessment: 14 hours face-to-face meeting and group work phase in between (46 hours). Student groups prepare a presentation to be individually assessed on the second face-to-face day of the seminar.

2 ECTS (60 learning hours)
Annually (fall semester)
PSC professors and group leaders

Scientific Integrity – An Introductory Course

All students who started their PhD after February 2016 have to participate in the LSZGS introduction event Scientific Integrity - An Introductory Course (2 hours, no ECTS).

Please, register via Life Science Zurich Graduate School LSZGS

During this event students sign the declaration of “Good scientific practice” that becomes part of your DissGo documents. All PhD students that have or will participate in a course on “Research Integrity” or “Ethics” in their PhD program don’t need to visit the introduction class. For all accredited training courses check the scientific integrity training course catalogue.

 

 

TECHNICAL SKILLS

Advanced course – 3D plant microscopy and image processing

Resolving the subcellular localization of a fluorescent compound in intact plant tissues or whole organs is a challenging task. Specific problems are posed by the high refractive nature of fresh tissues, sample thickness and stress-induced autofluorescence in dissected tissues. Together with classical problems of photobleaching and phototoxicity, these plants-specific issues make high-resolution and time-lapse imaging of fluorescent reporter proteins (or counterstaining) dye very challenging. The aim of this course is to obtain both an overview and a specific practice. First, this course will give an overview of available microscopy imaging solutions depending on applications. We will specifically practice confocal laser scanning microscopy imaging of Arabidopsis tissues using different mounting and clearing agents; the aim is to learn customizing the acquisition parameters towards maximum possible resolution within specific constraints of speed, viability, bleaching and signal diffraction levels in fresh vs. fixed tissues. The course also offers a brief introduction to high-resolution two-photon microscopy for deep tissue imaging. Second, we will learn exploiting the benefits of 3D imaging at the qualitative and quantitative level. We will practice 3D volume rendering, preparation of attractive image material for publication, image segmentation and extraction of quantitative information for statistical analyses.

Individual Performance and Assessment: In order to complete the course and gain their credit point, students will be required to attend the whole course and participate actively.

 

1 ECTS (30 learning hours)
Biannually (last: 2018)

Lecturer: Dr. Célia Baroux and Prof. Joop Vermeer, University of Zurich; Dr. Alexis Maizel, Center for Organism Science, University of Heidelberg

Alpine Plant Ecology – International Summer School

It’s a comprehensive graduate course on alpine plant life in the Swiss central Alps, jointly organized by the University of Basel and ETH, and the Zurich-Basel Plant Science Center (PSC) for graduate students with basic plant science training. The course covers microclimatology, vegetation ecology, reproduction biology, aspects of biodiversity, soil science, ecophysiology and ecosystem ecology. Morning and evening lectures, field excursions and team-work on small projects will make this week, in a truly alpine environment, a life time experience. The ALPFOR research station is surrounded by a great variety of typical alpine vegetation, including glacier forfields.

Individual performance and assessment: Credits will be given on a pass/fail basis (active participation, design and presentation of mini-poster).

 

3 ECTS (90 learning hours)
Annually (Spring semester)
Lecturer: Dr. Erika Hiltbrunner, Prof. Christian Körner, University of Basel, et al.

Basic Plant Disease Diagnostics

Identification based on host, symptoms and micro-morphology, completed with life cycles and related control measures of the most important fungal diseases and their causal pathogens of selected annual and perennial crops. A half-day excursion will be integrated to allow applied training of symptom recognition on the field level. The students will learn and train preparation skills for microscopy, acquire basic knowledge of selected diseases (Identification, Biology of pathogen, Epidemiology) and understand the corresponding integrated control measures practiced in Swiss agriculture.

Individual Performance and Assessment: Active participation in the exercises is required. In a final test individual skills of microscopical preparation and recognition of structures important for diagnosis are assessed.

1 ECTS (30 learning hours)
Biannually (last 20218)
Lecturer: Dr. Ueli Merz and Dr. Monika Maurhofer, ETH Zurich

Chlorophyll Fluorescence - Practical Applications and Analysis

The overall aim of the course is to get an insight into the practical applications of non-invasive photosynthesis analyses in basic and applied plant biology as well as into the underlying theory of the analysis techniques. At the end of the course, the students can identify scientific questions in which the analysis of photosynthesis will give a surplus in knowledge gain. Furthermore, the students will be able to develop and use appropriate chlorophyll fluorescence analyses in order to elucidate such scientific questions. Finally, they can interpret data generated by chlorophyll fluorescence analysis and draw the correct conclusions. This course wants to give an introduction into wide-spread methods of photosynthesis research that are useful for many (applied) plant scientists; out of scope are techniques that are reserved for experts in basic photosynthesis research.

Individual Performance and Assessment: Active participation in the exercise and discussion. You will need to prepare some literature before the block course. During the course students will handle the instrumentation on their own. They have to solve problems as well as to recognize pitfalls with their own samples and other sample material provided.

1 ECTS (30 learning hours)
Biannually (last 2017)
Lecturer: PD Dr Jörg Leipner and Dr. Eduardo Pérez Torres, ETH Zurich

Concepts in Evolutionary Biology (BIO 395)

In collaboration with URPP

Concepts in evolutionary biology are often used ambiguously, partly because the same terms may have different usage in other fields in biology. The course is designed for graduate students with interdisciplinary projects encompassing evolutionary biology and other disciplines, and provides lectures and simple calculation exercises in population and quantitative genetics.

1 ECTS (30 learning hours)

Annually (Spring semester)
Lecturer: Prof. Barbara König, Prof. Lukas Keller, Prof. Michael Krützen, Prof. Marcelo Sanchez, Prof. Kentaro Shimizu, Prof. Anne Roulin, Dr. Anna K. Lindholm Krützen, University of Zurich

 

Conservation Field Course in Scotland

The course offers an opportunity to Swiss-based students to apply their knowledge and challenge their preconceptions to novel socio-environmental situations. The course specifically encourages students to explore and evaluate alternative management approaches that seek to integrate local economic needs with conservation priorities. An understanding of changing human perspectives to conservation (and associated land management approaches) will be gained. Using this understanding students will consider future challenges to conservation and land management, and develop solutions to resolve them.

The course will allow students to learn about ecology, conservation and management issues in a unique landscape. Daily excursions will focus on specific important issues relating to conservation management in the area. Excursions will be led by local experts representing science, management and policy, each of whom will explore with the students the complexities of the chosen topics. Topics will encompass species, habitats and landscapes from economic, ecological and cultural perspectives across various spatial and temporal scales.

Students will be encouraged to explore selected topics in more detail, examples being (1) trade-offs between deer, that are important to the local economy, and the regeneration of Caledonian pine forests, (2) the implications of changing land use and land-tenure systems, (3) the management of tourism on sensitive upland habitats, (4) securing a balance between renewable energy generation (e.g. wind farms, forestry) and landscape beauty, (5) predicted effects of climate change on plant communities, and (6) the impact of invasive species on natural plant communities.
In the evenings, group presentations and discussions based on the accumulated knowledge will aim to develop feasible solutions to current conservation challenges.

3 ECTS (90 learning hours)
Biannually (last 2017)
Lecturer: Prof. Jaboury Ghazoul, ETH Zurich

Current challenges in Plant Breeding (ETH VVZ 751-3603-00L)

The seminar “Current challenges in plant breeding” aims to bring together national and international experts in plant breeding to discuss current activities, latest achievements and future prospective of a selected topic/area in plant breeding. The topic this year will be: “Potential and limitations of genomic selection in plants”.
The educational objectives for the participants of the PhD Program in Plant Sciences cover both thematic competences and soft skills: Thematic competences: Deepening of scientific knowledge in plant breeding, Critical evaluation of current challenges and new concepts in plant breeding, Promotion of collaboration with practical plant breeders. Soft skills: Independent literature research to get familiar with the selected topic, Critical evaluation and consolidation of the acquired knowledge in an interdisciplinary team, Establishment of a scientific presentation in an interdisciplinary team, Presentation and discussion of the teamwork outcome, Establishing contacts and strengthening the network to national and international plant breeders and scientist.

Individual Performance and Assessment: Enrolled participants will meet with the lecturers as well as four to six tutors, selected according to their expertise in “digital plant breeding”. The tutors and the course participants will be assigned to four to six different groups, to critically evaluate one question/aspect of “digital plant breeding”. Participation on that afternoon will be mandatory (3 hours). The students, guided by tutors, will prepare a presentation of 15 minutes (plus 5 minutes discussion) covering their specific question/aspect for the seminar day (49 hours preparation work). A one-day seminar will be organized. After the students’ presentation in the morning, up to four invited talks from national and international experts in the field will link the selected topics to practical plant breeding. The seminar will be public and serve as annual meeting of the Swiss Society of Agronomy (working group for plant breeding), bringing together national experts in plant breeding.

2 ECTS (60h learning hours)
Annually (Fall semester)
Lecturer: Prof. Bruno Studer and Dr. Andreas Hund, ETH Zurich; PD Dr. Thomas Wicker, University of Zurich

Genetic Diversity: Techniques (ETH VVZ 701-1425-01L)

This course provides training for advanced students (master, doctoral or post-doctoral level) in how to measure and collect genetic diversity data from populations, experiments, field and laboratory. Different DNA/RNA extraction, genotyping and gene expression techniques will be addressed. After an introduction (one afternoon), students will have 3 weeks to work in groups of two through different protocols according to their timetable. At the end the whole group meets for another afternoon to present the techniques/results and to discuss the advantages and disadvantages of the different techniques. Examples are: RNA/DNA extraction, SNP genotyping, pyrosequencing, real-time qPCR.

Individual Performance and Assessment: Two afternoons are hold in the class. The lab work will be done from the students according to their timetable, but has to be finished after 3 weeks. Effort is roughly 1-2 days per week, depending on the skills of the student.

1 ECTS (30 learning hours)
Annually (Fall semester)
Lecturer: Dr. Aria M. Minder, ETH Zurich

Genetic Diversity: Analysis (ETH VVZ 701-1425-00L)

The course provides basic training for advanced students (e.g. master, doctoral or post-doctoral level) in genetic data analysis with special focus on massive-parallel sequencing data (e.g. NGS data). The course is divided into different modules covering the following topics: Introduction into Linux OS and the usage of the command-line interface, Phylogenetics, Reproducible Science, Regular Expressions, R for Biology, Next Generation Sequencing (NGS) data analysis: Quality Control and Filtering/Trimming, Genome and Transcriptome Assembly and Annotation, RNAseq Design and Analysis, Metagenomics / Metatranscriptomics / Amplicon Sequencing, SNP-Calling, RAD Sequencing. Students will work with real data examples or can bring their own data. Exercises are a central part of the course.

Individual Performance and Assessment: Ungraded semester performance.

 

2 ECTS (60 learning hours)
Annually (Spring semester)
Lectuere: Dr. Stefan Zoller, Genetic Diversity Center, ETH Zurich

Introduction to Functional Genomics

The aim of the course is to enable participants to design and interpret functional genomics experiments and critically evaluate available technical options. Demonstrations of available technologies at the FGCZ will be included. In the postgenomic era emphasis of research shifts from merely accumulating sequence data towards the identification of functional significance of gene products. The goal of functional genomics is to understand the relationship between genome sequence and phenotype. An important aspect here is the measurement of molecular activities with the high-throughput ‘omics’ technologies transcriptomics, proteomics and metabolomics. The course comprises a theoretical introduction to mass spectrometry, the key technology for protein and metabolite analyses, and to transcriptional profiling. The diverse set of available technologies and most recent developments will be presented, including bioinformatic approaches to analyse the data and comprehend large amounts of data.

Individual Performance and Assessment: In order to obtain the credit point, active participation during all three courses days is mandatory.

1 ECTS (30 learning hours)
Biannually (last 2017)
Lecturer: Dr. Bernd Roschitzki, Dr. Endre Laczko, Andrea Patrignani, Dr. Lucy Poveda and Dr. Giancarlo Russo (Functional Genomics Center Zurich)

Introduction to Genome-Wide Association Studies (GWAS)

In collaboration with URPP

 

In this course, we will discuss the pre-eminent tool for identifying genes that underlie natural phenotypic variation: genome-wide association studies (GWAS). Originally developed by human geneticists to fine-map genes that underlie human disease, GWAS have the capacity to revolutionize all of the biological sciences. Plant biologists, in particular, have already taken advantage of improvements in sequencing technology in order to characterize genetic variation across the genomes of several species. Doing so has enabled the use of GWAS to fine-map genes that underlie ecologically and agriculturally relevant traits. At the beginning of the course, we will provide an introduction to GWAS. Then, we will discuss the history of gene mapping and the genetic and statistical background on which GWAS are based. The course has a strong practical component, and students will gain experience analyzing real data on the computer. At the end of the course, students will be able to interpret GWAS results and carry out their own analyses. We will also discuss basic concepts (and challenges) in population genetics, genomics, and quantitative genetics. For preparation, the students will have to conduct some literature reading which will be sent out prior to the course.

Individual Performance and Assessment: This 2-day course will be split between lectures and tutorials. Required: attendance, active participation during the exercises (16hours) and handing in of an individual exercise after the course days (14 hours of preparation work).

1 ECTS (30 learning hours)
Biannually (last 2018)
Lecturer: Prof. Matthew Horton (UZH) and Ümit Seren (GMI, Vienna)

Introduction to Light Microscopy and Image Processing

Light microscopy is a frequently used tool in plant sciences. Still, many are not aware of all the factors that are necessary for a good quality, reproducible microscopy images. The aim of the course is to give the students a practice-oriented introduction to the basics of light microscopy, including also a short introduction to image processing. This 3 days course gives a basic introduction into light microscopy. During the mornings lectures will summarize the necessary theory and the afternoon session will concentrate on practical, hand-on exercises. The following subjects will be dealt with transmission microscopy (phase contrast, DIC), fluorescence microscopy (including confocal imaging), basics of image processing.

Individual Performance and Assessment: Active participation during the course and in the hands-on training is necessary.

1 ECTS (30 learning hours)
Biannually (last 2017)
Lecturer: Dr. Gábor Csúc, ETH Zurich

Introduction to UNIX/Linux and Bash Scripting (BIO609, introductory course for BIO 610)

In collaboration with URPP

The aim of this course is to introduce students to the Linux/Unix command line and shell scripting by taking a hands-on approach. Short lectures will present an overview of the Linux/Unix command line focusing on commands for working with files/directories and text files. Students will also practice how to install and run software. Students will teach how to write simple shell scripts as they are often used to automate repetitive tasks and to build software pipelines. They will also discuss recommendations for reproducible research such as good coding practices. The course is composed of lectures and guided computer exercises. Students will spend most of the time solving computer exercises.

Individual Performance and Assessment: Attendance at lectures and active participation in the hands-on exercises are required.

0 ECTS (8 learning hours)
Annually (Spring semester)
Lecturer: Dr. Heidi Lischer, UZH

 

Next-Generation Sequencing 1: Introductory Course - Assembly, annotation and transcriptomes (BIO 610)

In collaboration with URPP

Handling of the huge data produced by next generation sequencers (NGS) requires us experimental knowledge and computational skills. The aim of this course is to familiarize the participants with experimental methods and data analysis about NGS. Topics will include: fundamental analysis of the sequence data, UNIX tools, and RNA-seq analysis. Learning outcomes are: - Understand concepts of NGS technologies, - Understand basic operation of UNIX operating system, - Design a research experiment and the data analysis involving biologically relevant issues affecting populations of plants or animals, - Map NGS data onto a reference genome and estimate gene expression level, - Understand differential gene expression and polymorphism analysis using NGS data, - Understand algorithms of De novo assembly and alignment of NGS data, and - Understand basic bioinformatics of large datasets for practical use in genetic analyses.

Individual Performance and Assessment: Attendance at lectures and active participation in the hands-on exercises are required.

1 ECTS (30 learning hours)
Annually (Spring semester)
Lecturer: Prof. Kentaro Shimizu, Prof. Jun Sese, Dr. Rie Inatsugi, Dr. Masaomi Hatakeyama, Dr. Tony Kuo, Dr. Jianqiang Sun, Dr. Heidi Lischer

Next-Generation Sequencing 2: Advanced Course - Transcriptomes, Variant Calling and Biological Interpretation (BIO 634)

In collaboration with URPP

Fast advances in Next-Generation Sequencing (NGS) technologies are opening fascinating opportunities in life science research. The analysis of the large amounts of data produced requires knowledge of NGS methods as well as practical skills in computing. The aim of this course is to introduce students to the design and analysis principles of widely used NGS applications at an advanced level, based on the course "Next-Generation Sequencing 1 – Introductory Course: Assembly, Mapping, and Variant Calling". The focus of this advanced course lies in transcriptome analysis and biological interpretation of gene lists. This course also provides hands-on computer training on the Linux/Unix command line and shell scripting.

Individual Performance and Assessment: Attendance at lectures and active participation in the hands-on exercises are required.

1 ECTS (30 learning hours)
Annually (Spring semester)
Lecturer: Dr. Heidi Lischer, Prof. Kentaro Shimizu

 

Pathways and Fluxes: Exploring the Plant Metabolic Network

The fluxes that flow through the plant metabolic network sustain life and are directly linked to the agronomically important parameters of crop yield and composition. Flux is the only direct measure of metabolic activity, and so measurements of metabolic flux allow the definition of metabolic phenotypes that are closely related to biological function. An understanding of these phenotypes and the flux distributions that define them is therefore essential for analysis of the behavior and regulation of the plant metabolic network. This course provides a theoretical and practical introduction to the methods available for measuring, inferring or predicting fluxes and considers how this knowledge informs our understanding of the function of the plant metabolic network. The course will describe the methods used for the prediction and measurement of fluxes in the plant metabolic network. It will provide an assessment of the applicability of these methods and a discussion of the significance of the results that have been obtained. This will include an analysis of the contribution of these methods to our understanding of the network as well as a discussion of the relevance of the methods to plant metabolic engineering. The lectures will be complemented by computing sessions that will introduce some of the modelling software used to analyse fluxes, providing an opportunity to explore the complex (and often counter-intuitive) behavior of metabolic networks.

Individual Performance and Assessment: Participants will be assessed on the basis of their contribution to the practical exercises that are integral to the course.

1 ECTS (24 learning hours)
Biannually (last 2018)
Lecturer: Prof. R. George Ratcliffe, Dr Nicholas J. Kruger, Department of Plant Sciences, University of Oxford, UK

Population Genetics and Genomics of Adaptation

The rapid increase in the amount of phenotypic and genomic information from natural populations, common garden experiments and mapping populations allows to dissect patterns and processes of plant adaptation. This development is matched by new statistical approaches and software tools to analyse genomic and phenotypic data. The course provides a hands-on introduction to the study of plant adaptation with a focus on population genetics concepts and tools. We will cover demographic analysis with coalescent simulations and Approximate Bayesian Computation (ABC), model selection and validation, identification of genomic regions involved in local adaptation using tests of selection or correlations with environmental parameters.

Individual Performance and Assessment: Evaluation will be based on a written and executable report created with RMarkdown that describes the analysis of the given dataset and discusses the result.

1 ECTS (30 learning hours)
Biannually (last 2016)
Lecturer: Prof. Dr. Karl Schmid and Dr. Fabian Freund, University of Hohenheim

Protein-coding Evolution and Detecting Natural Selection

Molecular data provide rich information about the biological forces shaping biodiversity. Molecular phylogenies are now routinely used to test a variety of biological hypotheses, with applications ranging from medicine and epidemiology to agriculture and ecology. Natural selection is one of the major forces shaping the genomic diversity, often responsible for adaptations to new pathogens and environments. This course will provide an introduction to modelling the molecular evolution, phylogeny inference and statistical hypothesis testing in phylogenetics. These techniques became a must in most genomic analyses. Models of sequence substitution, Inferring phylogenies in a nutshell, Detecting positive selection at the protein coding level.

Individual Performance and Assessment: Project-based individual assignment, which should be submitted within 1 week after the course.

1 ECTS (30 learning hours)
Triannually (last 2016)
Lecturer:
Dr. Maria Anisimova, ZHAW

QTL Analysis in Arabidopsis

This course is an introduction to current methods used in the study of polygenetic variation in plants. In particular, we’ll explore the use of quantitative genetic experiments, quantitative trait locus (QTL) analyses, and linkage disequilibrium (LD) mapping as tools for dissecting the genetic details of continuous variation. The course will concentrate on providing students with the basic statistical and conceptual foundation for understanding continuous variation as well as an introduction to various mapping methods and current challenges in QTL cloning. Finally, we will collect phenotypic data on an Arabidopsis thaliana experimental population and conduct basic mapping analyses in a hands-on lab setting.

Individual Performance and Assessment: In order to obtain the ECTS, each participant is required to actively participate in classroom discussions and computer based analyses.

1 ECTS (24 learning hours)
Biannually (last 2017)
Lecturer:
Prof Ueli Grossniklaus, University of Zurich, Prof. Tom Juenger, University of Texas at Austin

RNA Sequencing – A Practical Course for Plant Scientists

Next-generation sequencing (NGS) technologies have revolutionized many fields in biology. The Functional Genomics Center Zurich (FGCZ) offers a four-day course with hands-on practicals. The aim is to help scientists interested in NGS technologies, particularly applied to RNA sequencing, to gain a better understanding of the techniques available and their applications. The practical consists of a library preparation starting from polyA enriched RNA, followed by a sequencing run on a bench top sequencer. An introduction to the analyses of the resulting data and some exercises will be offered too. The lectures cover existing and upcoming NGS technologies, their applications and the principles of downstream data analysis. By the end of the course participants should be able to make informed decisions about which technology and workflow to apply to solve specific research questions.
Course Program
Library Prep: PolyA RNA-seq library generation: principles and types
Sequencing: Detailed description of available sequencing technologies platforms, Hands-on laboratory work: preparing and performing sequencing runs
Data analysis: Run QC: Criteria for run performance and quality of data, Preprocessing of the raw data, Mapping the data to a reference, Mapping quality control for RNA-seq data, Transcripts expression quantification and tests for differential expression, Set-based analysis (e.g., pathways, GO-categories) IT and awareness of the data storage and its size

Individual Performance and Assessment: Attendance and active participation during all four days of the course (32 hours) plus completing an individual assignment of around 6 hours.

1 ECTS (38 learning hours)
Biannually (last 2018)
Lecturer: Dr. Lucy Poveda, Dr. Weihong Qi and others, Functional Genomics Center Zurich

Scientific Integrity: How to publish reproducible results

This course aims to focus on a key step in the scientific process: the rendering of scientific data in a form that can be shared with colleagues – usually in the form of a published research paper, a preprint or a scientific talk. This step is critical as it is all too easy to misrepresent research findings in the rush to publish and given the pressures to publish ‘high impact’ research papers. The course aims to complement other training at the PSC PhD program and therefore focuses on image based data and digital processing of such data for publication.
Topics covered will include:
1)    Best practice and responsible conduct when acquiring and processing image based data. How to assemble a compelling paper that nevertheless represents the scientific findings in an accurate, unbiased manner.
2)    Reproducibility: critical evaluation of the ‘reproducibility crisis’ and how to render papers more reproducible. New policies and mechanisms that enhance reproducibility.
3)    The most frequent digital image aberrations observed in the literature and how to prevent them.
4)    What to do if you find image aberrations in unpublished work and published work (including your own data, data from your lab and other labs).
5)    How to peer review image based data and screening mechanisms at journals for digital image aberrations.
How journals deal with image aberrations – emerging best practice.

Individual Performance and Assessment: In order to obtain the ECTS points, participants are required to actively participate in the course with questions and comments; to complete the course exercises successfully.

1 ECTS (30 learning hours)
Biannually (last: 2016)

Lecturer:
Dr. Bernd Pulverer, European Molecular Biology Organization (EMBO)

 

Sustainable Plant Systems (ETH VVZ 551-0209-00)

Future demand in agricultural output is supposed to match the needs of 9-billion people with less input of resources. We will discuss current plant science research in the context of sustainability on the production side. A special focus will be on research on agro-ecological systems and farming system research. Can we transform our agricultural practices and move behind existing paradigms to develop innovative and sustainable agriculture production systems? Where does current research indicate on directions for transformation of current practice and how can we assess and analyze them though research? The seminar is set up as a blended-learning seminar, i.e. a combination of face-to-face meetings and self-organized learning with provided online learning material. The seminar comprises two workshop afternoons and an intensive, well-structured self-study/ group work phase in between the workshops. Students can earn 2 ECTS for successful completion of the seminar. Key objectives for the seminar are that (1) participants will be able to discuss issues of sustainability in the context of current plant science research topics (2) participants will be able to phrase their own visions for sustainability in plant sciences, their group work topic and their own MSc or PhD project.

Individual Performance and Assessment: ungraded semester performance. Students will actively participate during the two afternoons with presentations on the second afternoon (8 hours). In between the will independently work in the online course with assignments to be handed in and they will in groups prepare a presentation and essay on a sustainability topic (52 hours).

2 ECTS (60 learning hours)
Annually (Fall semester)
Lecturer:
Dr. G. Singh Bhullar, FIBL; Prof. Marcel van der Heijden UZH; Dr. Frank Liebisch and Dr. Melanie Paschke, ETH Zurich

Transdisciplinary Seminar on Research for Sustainable Development (ETH VVZ 701-0015-00L)

The participants understand the specific challenges of inter- and transdisciplinary research in general and in the context of sustainable development in particular. They know methods and concepts to address these challenges and apply them to their research projects. The seminar covers the following topics: Theories and concepts of inter- and transdisciplinary research, The specific challenges of inter- and transdisciplinary research, Involving stakeholders, Collaborating disciplines, Exploration of tools and methods, Analysing participants' projects to improve inter- and transdisciplinary elements.

Individual Performance and Assessment: Ungraded semester performance. Active participation during the course days: 24 hours and preparation work for paper presentation in between (36 hours).

2 ECTS (60 learning hours)
Annually (Fall semester)
Lecturer:
C. E. Pohl, M. Stauffacher, B. Truffer, ETH.

 

for PhD students at ETH: register via MyStudies.

for PhD students at Uni Basel: you have to register as Special student "University of Basel (UBa)" at ETHZ first.

for PhD students at UZH: you have to register as Special student "University of Zurich (UZH)" at ETHZ first.

Visual analytics of large-scale biological data

In this course, we will focus on omics data (mainly genomics and transcriptomics data) and combined data such as GWAS and eQTL. The course is a mixture of theoretical lectures and interactive, practical sessions. The hands-on training will introduce the most commonly applied tools in the field as well as some maybe less commonly but nonetheless very useful ones. Dependent on the participants’ programming abilities we will use GUI-based tools as well as R/Bioconductor and other scripting languages. Learning Outcomes: Understand the process of visual analytics, Know the basics and do’s and don’ts of visualization, Learn how to visualize large-scale genome data, Learn how to visualize transcriptional regulation and abundance, Understand the challenge of GWAS and eQTL data visualization and learn new approaches to address these challenges.

Individual Performance and Assessment: Active participation is expected on all course days (24 hours). Participants will be given practical tasks, their performance will be assessed by their degree of commitment, ability to apply the theoretical concepts to the task in question and creativity. A summary of the completed task and a course diary will have to be handed in after the course (approx. 6 hours effort)

1 ECTS (30 learning hours)
Biannually (last 2017)
Lecturer:
PD Dr. Kay Nieselt, Center for Bioinformatics Tübingen, Integrative Transcriptomics, University of Tübingen

STATISTICAL SKILLS

Advanced Data Management and Manipulation using R

The analysis of large data sets (“big data”) is becoming increasingly important in science and elsewhere. In this course, you will learn how to use R to manage and manipulate large data sets, i.e. to sort, merge, subset, aggregate and reshape data, including outlier detection and gap filling algorithms. For advanced data manipulation, we are going to use novel developments such as plyr/dplyr (“A Grammar of Data Manipulation”), the pipe operator (%>%) for simpler R-coding and data.table for the fast aggregation of large data sets. Furthermore, we will have a closer look at R-data base connections, MySQL queries and the creation of new data bases from R. Depending on the course progress, there will be scope for individuals to work on small projects and / or their own data sets.

Individual Performance and Assessment: In order to obtain the credit points, participants are required to hand in an assignment to be carried out at home. The details will be explained during the course. The assignment is due no later than one week after the course has ended.

1 ECTS (24 learning hours)
Annually (Spring semester)
Lecturer:
Dr. Jan Wunder

Get going with statistics in functional genomics

This course trains how to handle larger amounts of data efficiently, securely, and reproducibly. For this reason, the main objective of this course is to provide students the most basic and most crucial sets of skills to work with genomic datasets. The students will not just learn to manage data and run analysis but also to document their workflow in an easy but reproducible way. The course will also cover different aspects of basic statistical analysis for genomics.

Individual Performance and Assessment: The course will be a mix between lectures and hands-on exercise. Required: attendance, active participation during the lectures and especially the exercises. There is an assignment for each topic that needs to be handed in by the end of the course.

1 ECTS (30 learning hours)
Biannually (last 2019)
Lecturer: Prof. Dr. Anne Roulin (UZH)

Introduction to Data Analysis using R

This course provides an introduction to statistics ideal for MSc and PhD students in ecology or related fields. Of course, molecular biologists with an interest in statistics are welcome to join as well. Topics treated in this course include: important probability distributions, classical statistical tests (t-test, chi-square-test, U-test), the theory of hypothesis testing (examples: randomisation test and t-test, analysis of variance ANOVA, linear regression (simple and multiple), analysis of covariance ANCOVA, outlook, e.g. GLMs, MEMs. The course will consist of both lectures and computer practicals using the free software package R for statistics and graphics. Participants can bring their own PC or Mac laptops with the latest version of R downloaded from http://stat.ethz.ch/CRAN/ (a small number of computers will be available for those without laptops). The course will be limited to 20 people to allow one-to-one supervision during the computer practical exercises. Prerequisites: Knowledge of the R (or S-Plus) language would be ideal, but is not essential.

Individual Performance and Assessment: Attendance and active participation in the course (16 hours). In order to obtain the credit points, participants are required to hand in an assignment to be carried out at home. The details will be explained during the course. The assignment is due no later than one week after the course has ended. Preparation work for the assignment is 14 hours.

1 ECTS (30 learning hours)
Biannually (last 2018)
Lecturer: 
Dr. Stefanie von Felten, oikostat GmbH

Introduction to R

This basic introduction to R focuses on the technical aspects of data organisation, handling, analysis and presentation using the wide-spread command line program R. This course is not an introduction to statistics, but lays the foundation to efficiently use statistical applications of R, which are introduced in other courses. No previous experience with programming languages is required. The course addresses students who would like to become familiar with a powerful, single and freely available alternative to spreadsheet programmes (excel), other, less flexible commercial statistical packages (SPSS, Jump, Minitab etc.) and graphics software for presenting data (excel, Sigmaplot etc.). Topics covered include the proper organisation of the workspace, reading and writing data files, using R as a calculator, using logic operators, manipulating data frames, summarising and aggregating data, programming ‘ifelse’ statements, loops, short routines, handling time fields in data frames, drawing and customising graphs. Depending on the course progress, there will be scope for individuals to work on small projects and / or their own data sets.

Individual Performance and Assessment:  Attendance and active participation during the course days (16 hours). In order to obtain the credit points, participants are required to hand in an assignment to be carried out at home (preparation work of 14 hours). The details will be explained during the course. The assignment is due no later than one week after the course has ended.

1 ECTS (30 learning hours)
Annually (Fall Semester)
Lecturer: 
Dr. Jan Wunder

Scientific Visualisation Using R

Visualisations can decide about the success of scientific lectures, poster presentations or journal articles. In this course you will get a very brief introduction into general design principles and guidelines for data visualisations. Based on this theoretical framework we will spend most of the course time to learn how to use R as a powerful graphical software to create a wide range of customised graphics that include - but are not limited to - traditional scatter plots, bar plots, mosaic plots, box plots, density plots, violin plots, and interactive graphics as well as grid-based geographic maps and state-of-the-art multipanel conditioning plots (and many more). You will learn about the two pillars of the R graphics systems, i.e. Traditional and Grid graphics. The course focuses on the latter system and more recent developments such as ggplot2 and other advanced libraries based on the “The grammar of graphics”-concept. Depending on the course progress, there will be scope for students to work on small projects and / or their own data sets.

Individual Performance and Assessment: Attendance and active participation during the course days (16 hours). In order to obtain the credit points, participants are required to hand in an assignment to be carried out at home (preparation work of 14 hours). The details will be explained during the course. The assignment is due no later than one week after the course has ended.

1 ECTS (30 learning hours)
Annually (Fall Semester)
Lecturer: 
Dr. Jan Wunder

Statistics for Ecologists (ETH VVZ 701-1419-00L - Analysis of Ecological Data)

This class provides students with an overview of techniques for data analysis used in modern ecological research, as well as practical experience in running these analyses with R and interpreting the results. Topics include linear models, generalized linear models, mixed models, model selection and randomization methods. Students will be able to: - describe the aims and principles of important techniques for the analysis of ecological data; - choose appropriate techniques for given problems and types of data; - evaluate assumptions and limitations
- implement the analyses in R; - represent the relevant results in graphs, tables and text;  and to interpret and evaluate the results in ecological terms. Course Contents will address: - Linear models for experimental and observational studies; - Model selection; - Introduction to likelihood inference and Bayesian statistics; - Analysis of counts and proportions (generalised linear models); - Models for non-linear relationships; - Grouping and correlation structures (mixed models); and Randomisation methods.

Individual Performance and Assessment: Graded semester performance.

1 ECTS (30 learning hours)
Annually (Fall Semester)
Lecturer: 
Dr. Sabine Güsewell

Introduction to Meta-analysis and Research Synthesis in Ecology

In collaboration with URPP

This course aims to promote and facilitate the thoughtful and critical use of meta-analysis for research synthesis in ecology by: 1) Explaining the principles and advantages of meta-analysis for research synthesis, 2) Demonstrating the range of applications of meta-analysis in ecology, 3) Promoting understanding of the assumptions and limitations of meta-analysis, 4) Providing first-hand experience in question formulation, data extraction, database design, use of software for meta-analysis and report preparation. The course program includes: Lectures on the history of meta-analysis, types of quantitative research synthesis, conversion of ecological data to effect sizes, and question formulation; combining effect sizes across studies and testing for moderators in meta-analysis (meta-regression), practical on conducting meta-analysis using OpenMEE software; publication bias, dealing with varying research quality and non-independence of observations; format of meta-analysis report, review of case studies of meta-analysis in ecology, and critique of meta-analysis. Practical exercises on data extraction and inclusion criteria and metrics of effect size for their own meta-analysis, testing for moderators; testing for publication bias in own dataset, and considering sources of non-independence.

1 ECTS (30 learning hours)
Biannually (last 2018)
Lecturer: Prof. Dr. Julia Koricheva, UK

TRANSFERRABLE SKILLS

Dealing with the Publication Process

In this 2-day workshop PhD students will learn specifically to deal with the whole publication process: from choosing journals strategically, to submission, to publication. The course can be visited in parallel or after Scientific Writing I, Scientific Writing II. Objectives: Understand the publishing process and develop individual publishing strategies.

Individual Performance and Assessment: In order to obtain the ECTS point, each participant is required to actively participate in the case-study work, discussions, and presentations during the course days. Participants are expected to provide a short abstract of their research project prior to the course. In addition, participants are expected to: 1. Select six journals appropriate for publishing their research. Participants study the journal websites and bring information to the workshop about: (1) aims and scopes, (2) editors and editorial staff, (3) journal reputation (4) access to the journals: is it free, or is a licence required? (5) publishing contract, author’s rights: which rights remain with the authors? 2. bring a research article to the workshop. They choose an article which is important for their research, and which they know very well. They should not be involved in the preparation of this article. The assessment of the first day is based on: a short presentation about journal selection, a cover letter drafted in the workshop, a review report drafted in the workshop.

1 ECTS (30 learning hours)
Annually (Fall semester)
Lecturer:  Dr. Philipp Mayer (science-textflow, http://www.science-textflow.ch/), Prof. Dr. Christian Fuhrer and Dr. Melanie Paschke, UZH

Scientific Communication Practice (also part of Science & Policy)

Scientists are under pressure to communicate with the public about their research. This pressure comes from funding bodies such as the EU, the SNF, the taxpayers, recruiting agencies and policy makers. Improved public and media communication is essential if the public is to better understand who scientists are and what they do. Also, communicating is a source of personal satisfaction. For scientists, it's worth learning the basics of communication early in their careers. This course provides a guide to effective science communication, in theory and practice.

Individual Performance and Assessment: Attendance and active participation during the two course days (16 hours). In the weeks between the two workshop days you should plan for available time for group work and individual work of min. 30-40 hours.

2 ECTS (60 learning hours)
Biannually (last 2018)
Lecturer:  Dr. Jacopo Pasotti

Scientific Presentation Practice

Effective oral communication is an important skill in scientific and academic endeavors. In fact, success in both the academic and the professional arenas may well depend upon your ability to communicate orally with a variety of audiences. It goes without saying that you need to create presentations that are well constructed, logical and interesting, but achieving this goal can take a fair amount of preparation and practice, especially when you are working in a second language. This course will provide you with the opportunity to prepare a presentation and practice your presenting skills in English. Particular attention will be paid to the following points: Identifying your MAP (Message, Audience and Purpose), Creating rapport with your audience, Achieving logical structure, Using appropriate visuals, Improving your delivery in English. The skills that you practice during this course should prove helpful when you are faced with tasks such as making public presentations, presenting lab reports, giving technical briefings or training sessions, presenting at conferences, attending job interviews, and speaking at seminars.

Individual Performance and Assessment: Each participant is required to actively participate in the discussions, and presentations during the course days. The assignment must be completed.

1 ECTS (30 learning hours)
Annually (Spring term)
Lecturer:  Dr. Barbara Hellermann

Scientific Writing 1

This course is a foundation course in scientific writing skills. It offers writers practice in expressing themselves precisely, concisely and, above all, clearly when writing English for scientific purposes. Particular attention is paid to Organisation, Flow and Style. Participants will receive feedback on their writing and will have the opportunity to edit and improve texts written in English. The course serves as preparation for a second course, “Scientific Writing Practice 2: Writing Up Research in English”, which accompanies scientific writers as they produce the individual chapters of a research article in English.

Individual Performance and Assessment: Attendance and active participation during day 1 and day 2 (16 hours). In order to complete the course and gain their credit point, students will be required to complete a writing task between Day 1 and Day 2 of the course and submit it to the course instructor for evaluation (preparation work of 14 hours).

1 ECTS (30 learning hours)
Annually (Fall semester)
Lecturer:  Dr. Patrick Turko, USZ

Scientific Writing 2

This course is tailored for PhD students working in life sciences, who wish to improve their writing skills in English. The course emphasizes the importance of simplicity, clarity, and brevity to communicate science in an effective manner. During the course, participants will develop a critical approach towards the recognition of elements that make written communication weaker or stronger. Participants will improve their self-confidence towards the writing of scientific manuscripts and the communication of science as a whole.

The course covers the following topics: 1) Grammar and syntax. Where to position different types of words (nouns, adverbs, etc.) within a sentence. The importance of punctuation, and its use in scientific writing to avoid ambiguity. Breaking up long sentences. The use of active and passive voices. Removing redundancy. How to connect sentences. 2) Avoid ambiguity and vagueness. The use of “which, who, that”. The use of “a, one, the”. Latin words and numbers.; 3) The structure of a paragraph. Where to put new and old information. Breaking up long paragraphs. Readability tests and the use of spell checkers.; 4) Sections of a scientific manuscript. The importance of figures to draw a story-line. The title. The abstract. How Hollywood movie industry can help scientists writing better abstracts. How to structure the introduction, methods, results, and discussion. Hedging and criticism.

Individual Performance and Assessment: Practical activities will be carried out during the course. Students will be requested to complete the assigned homework. Homework include grammar exercises, the writing of a short essay (e.g. in the style of a Nature commentary on a recent scientific discovery, or the Working Life column of Science), and the writing of a mini-paper. Successful achievement of the credit point is based on course attendance and completion of assigned work.

1 ECTS (30 learning hours)
Annually (Spring semester)
Lecturer: 
Dr. Jacopo Marino, Paul Scherrer Institute (PSI)

Responsible Conduct in Research (ETH VVZ 751-1040-00L)

When studying at a University, Master’s and PhD students are joining the scientific community and, therefore, have to learn the codes of professional and responsible conduct in research. In this course, we provide information about specific rules, regulations and guidelines for research integrity and responsible conduct as well as a tool kit for moral reasoning. The course will rise awareness for potential conflicts of interest and will discuss real life examples, e.g., about questions of authorship and giving credits, data treatment and interpretation, communication and responsibility in the public. Students will discuss case studies with a typical conflict potential or a dilemma. They will work together in teams, discuss the codes of conduct and values established in science, and apply them to their case studies. The teams have to agree on actions to be taken for each case and present a consensus view.

1 ECTS (30 learning hours)
Annually (Spring semester)
Lecturer: 
Prof. Nina Buchmann, ETH Zurich, Dr. Melanie Paschke, Zurich-Basel Plant Science Center

Research with biological material from abroad – International regulations and good research practice (CBD ABS, IT FAO & CITES)

Utilization of non-human biological material that comes from abroad is more than just a matter of competence in research techniques and methods. Scientists must be aware of legal and procedural requirements in order to correctly access biological material and to respect existing international and national  regulations on plant genetic resources. Researchers need to be familiar with the Nagoya Protocol and terms such as Prior Informed Consent,  Mutually Agreed Terms, Benefit-Sharing and Due Diligence in research. The overall goal of this course is to inform young scientists about the relevant international treaties and existing international and Swiss regulations that affect research projects with genetic resources and to illustrate which steps to undertake.

Training will focus on the a) Nagoya Protocol on Access to Genetic Resources and Benefit Sharing (ABS) and the Convention on Biological Diversity (CBD), b)   International Treaty on Plant Genetic Resources for Food and Agriculture (IT FAO), and c) Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The course will provide solid knowledge on a) Correct and legitimate access to genetic resources and benefit-sharing for academic research,b) The Multilateral System of the plant treaty (ITPGRFA), c) Requirements for importing material under CITES in general, and specifically for plant genetic resources, and d)   Swiss regulations, and available support and counseling services for scientists in Switzerland.

1 ECTS (30 learning hours)
Biannually (last 2017)
Lecturer: 
Dr. Susette Biber-Klemm, SCNAT & University of Basel; Sylvia Martínez M.Sc., Univ. of Basel & Zurich-Basel Plant Science Center

Project Management for Research

Every project has high scientific and organisational demands. Not only your project work but also other activities, such as organising workshops and meetings, require good planning and management and are the focus of this course. With the help of internationally standardised project management and its tools, the project internal communication as well as the monitoring of results can be simplified. And the experience has shown: project management boosts the performance of researchers and is at the same time a promising basis for the successful collaboration between industry and academia. This course should motivate researchers to develop further their personal leadership qualities and to initiate and coordinate in the near future their own projects.

Individual Performance and Assessment: The students are expected to attend both course days and participate actively during the workshop. Additionally, they are expected to submit the planning of a fictional or real project containing the main models discussed in class.

1 ECTS (30 learning hours)
Biannually (last 2019)
Lecturer: 
Dr. Andrea Degen, eurelations AG

Writing a Post-doctoral Grant

To train involved PhD-students/future Post-docs to write grant/fellowship applications to proceed in their scientific careers and get informed and updated about most common research funding organisations (national & international, public & private). Prior Knowledge: Ideally, you plan a grant application in due term (not later than one year after this course) or you are already involved in grant writing. We expect that you have already good to excellent knowledge in scientific writing and project management for research (e.g. by visiting the specific courses in our PhD Program in Plant Sciences). Content: Funding opportunities for PhD-students/future Post-docs to plan their further career, Know more about the mission of funding organisations and align the application, Plan and structure a grant application, Learn about some basic techniques of grant writing (not identical to scientific writing), Learn how to calculate the finances of a grant application, Learn about basics of IPR (intellectual property rights) and international scientific networking. Methods: Theoretical introduction and practical exercises in groups, Database research on the internet
Feedback on technical aspects of the grants you are currently working on.

Individual Performance and Assessment: ungraded semester performance. Course attendance and active participation: 16 hours. Preparation work and home work: 14 hours.

1 ECTS (30 learning hours)
Annually (Fall semester)
Lecturer:  Dr. Andrea Degen, eurelations AG, Dr. Melanie Paschke

Patenting in the Life Sciences

What is a patent? How is it obtained? What are the implications of Life Science patents for – my career perspectives? – academic research? – society?

1 ECTS (30 learning hours)
Biannually (last 2018)
Lecturer: 
Prof. H. Müller, University of Basel et al. (organized by Life Science Zurich Graduate School.

NOTE: Please register through Life Science Zurich Graduate School: http://www.lifescience-graduateschool.uzh.ch/en/courses/tsc.html

CAREER DEVELOPMENT

Please register through Life Science Zurich Graduate School

Such as

Career Cornerstones - Active Career Building in Academia and Business (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).


Self-marketing Skills – Improve your International Presence (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).


• Competency Awareness – the Foundation of a Confident Self-Presentation (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).

 

• The Successful Start of a Business Career (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).

PSC PHD SYMPOSIUM

3 ECTS (90 working hours)
Note: organized every two years – next time 2020
Target group: PSC PhD Students

Together with a group of 5-6 PSC PhD students, you will be responsible for the organisation of an international and interdisciplinary science conference. As a member of the scientific and organisation committee (OK), you will cover the following tasks:
•    Development of a symposium topic
•    Invitation of speakers from around the world to contribute to a high-quality scientific program
•    Organization of symposium logistics
•    Fundraising and finances.

Have a look at past PSC Symposia

If interested to join the OK of the next one organised by PhD students, please contact the PhD Program coordinator

SCIENCE AND POLICY COURSES (TRANSFERRABLE SKILL COURSES)

Students can also attend courses from our specialized PSC PhD Program in Science and Policy. Details on these courses may be found at:

Workshop and course titles:

  • Evidence-based Policy-making (2 ECTS)
  • Stakeholder Engagement (2 ECTS)
  • Communicating Science (2 ECTS)
  • Building Political Support (2 ECTS)
  • Analysis and Communication of Risks and Uncertainties (2 ECTS)
  • Understanding Policy Evaluation (2 ECTS)
  • Introduction to Political Sciences (1 ECTS)

PREVIOUS COURSES (NOT OFFERED ANYMORE)

Computational Biology

 

(1 ECTS), Christian von Mering, Andreas Wagner, Kentaro Shimizu, UZH

In this course, the theoretical and practical aspects of sequence alignment, phylogeny reconstruction, genome-wide association of phenotypes and genotypes, and more was studies. In doing so, students learned how to generally manipulate data and launch software from the command line, including.

Innate Immunity in Plants

 

(1 ECTS), Prof. Thomas Boller, University of Basel

The aim of this course is to present an introduction to and overview of theory and experimental approaches to investigate "innate immunity" in plants. Recent work has shown that innate immunity in plants and animals are based on similar basic principles. In particular, both plants and animals recognize so-called "pathogen-associated molecular patterns" (PAMPs). These PAMPs elicit a defense response including formation of reactive oxygen species and induction of a multitude of genes.

Radio-Isotopes in Plant Nutrition

 

(3 ECTS), Prof. Emmanuel Frossard, ETH Zurich

Radio-isotopes are extensively used at the soil/plant or ecosystem level to quantify the fluxes of elements (phosphorus (P), heavy metals, radionuclides) within a given system and to assess the importance of processes controlling these fluxes (e.g. exchange reactions between the soil solution and the soil solid phase, element turnover through the microbial biomass, organic matter mineralization etc.).

The course will first present the principles, the basic assumptions and the theoretical framework that underlay the work with radioisotopes. It will present how the introduction of an isotope into a system can be done so as to get information on the structure of the system (e.g. number and size of compartments). Secondly, case studies on isotopic dilution and tracer work will be presented for instance on the isotopic exchange kinetics method to determine nutrients or pollutants availability. The case studies will be adapted to the ongoing research of the group of plant nutrition and will thus give an insight into our current research. In addition, published studies will be analyzed and presented by the students. Finally, the advantages and disadvantages of work with radioisotopes will be analyzed and discussed critically.

Transport Processes in Plants

 

(1 ECTS), Prof. Enrico Martinoia, University of Zurich

Life exists due to barriers established between the environment and the cell. Biological membranes establish these barriers. The lipid bilayer does not allow hydrophilic molecules such as ions and sugars to cross the membrane. On the other side, proteins embedded in the lipid bilayer are responsible for the selective uptake of constituents into the cell. Within eukaryotic cells compartmentation allows that different processes can occur at the same time in a cell.  In this course we will show some techniques, how fluxes between the outside and within the cell can be measured. We will perform classical flux analysis using radiolabelled compounds with yeasts and protoplast and use the patch clamp technique to demonstrate ion currents across the vacuolar membrane.

Stable Isotope Ecology of Terrestrial Ecosystems

 

(2 ECTS) Prof. Nina Buchmann, Dr. Rolf Siegwolf, ETHZ

This course provides an overview about the applicability of stable isotopes (carbon 13C, nitrogen 15N, oxygen 18O and water 2H) to process-oriented ecological research. Topics focus on stable isotopes as indicators for the origin of pools and fluxes, partitioning of composite fluxes as well as to trace and integrate processes. In addition, students carry out a small project during lab sessions. Learning Objective: Students will be familiar with be familiar with basic and advanced applications of stable isotopes in studies on plants, soils, water and trace gases, know the relevant approaches, concepts and recent results in stable isotope ecology, know how to combine classical and modern techniques to solve ecophysiological or ecological problems, learn to design, carry out and interpret a small IsoProject, practice to search and analyze literature as well as to give an oral presentation. Content: The analyses of stable isotopes often provide insights into ecophysiological and ecological processes that otherwise would not be available with classical methods only. Stable isotopes proved useful to determine origin of pools and fluxes in ecosystems, to partition composite fluxes and to integrate processes spatially and temporally.                                                                       

Online Publishing, Communicating and Creating a Web Presence: How to Make your Research Visible

 

(1 ECTS), Dr. Melanie Paschke, PSC

Online publishing and communicating has become an important channel for scientist to make their research visible, connect with other scientists, and open science to the interested public. Several technologies have popped up in recent years that can support scientists in their publication, communication and self-marketing purposes: open-access journals, research blogs and portfolios, research wikis and professional online networks.

In this two-day workshop, you will learn:

  • about these technologies and how to use them.
  • how to improve your visibility and creating a web presence using e.g. research portfolios or online research networks.

Topics discussed will include:

  • Publication strategies as part of your web presence (online open-access journals vs. traditional journals)
  • Using bibliometric measurements (e.g. impact factor, citation indexes) for online publications
  • Using weblogs and wikis in your daily work
  • Writing for a research blog
  • Creating personal research portfolio (hands-on training)
  • Using professional online research networks.

Role of Agriculture in our society in 2020

 

(1 ECTS), Luc Henry, Syngenta Basel, Switzerland

Currently, there is a remarkable gap between public perception and understanding of world agriculture and its role in our society. This places enormous stress and tension not only on governments and agribusinesses, but also on individuals as consumers. This gap, unfortunately, is widening and future opinion leaders have a major role to play in filling this gap. The objective of this course therefore is to provide students with the opportunity to explore the topic of world agriculture (including production and consumption, the technologies used and being developed, the impact on the environment, the food security challenge, the carbon footprint of agriculture, the biofuels, etc), and to put in place a framework to understand and foresee the potential required changes over the next years. The purpose of the course, by its very nature, is not to provide a single, “correct” perspective about agriculture. Instead, it aims at making students aware of possible scenarios, the consequences of the different scenarios, and help them to shape their own vision of agriculture in 2020.

Molecular Biology and Genomics of Plant-Pathogen Interactions

 

(1 ECTS), Prof. Beat Keller, University of Zurich

Genetic resistance is the most economical and environmentally friendly option for controlling plant diseases in agricultural ecosystems.  Plant breeders have expended considerable effort to incorporate resistance genes into the major crops over the past 100 years.  Pathogens have evolved to overcome many of these resistance genes, leading to a cycle of boom-and-bust with significant economic and societal consequences. This course will explore the molecular basis of disease resistance with an emphasis on agricultural crops. Topics will include: mechanisms of resistance; major gene resistance and quantitative resistance; genetic and biochemical models of gene-for-gene interactions; resistance gene structure and evolution; effector molecules in pathogens, boom-and-bust cycles and durable resistance; resistance gene deployment and management strategies; approaches for genetic engineering of resistance; identification and mapping of major resistance genes and quantitative (QTL) resistance; bioinformatics of plant pathogen genomes (“Pathogenomics”).

Niche Modeling

 

(1 ECTS) Prof. Antoine Guisan (U Lausanne), Prof. Niklaus E. Zimmermann (WSL, ETHZ), Prof. Yvonne Willi (U Basel)

The course will be based on a mix of lectures and practicals. The lectures will cover the preparation of data (species data and environmental predictors) for modelling, an introduction to basic and more advanced SDM fitting (e.g. GLM/GAM, CART, and their bagging/boosting versions) and evaluation methods, and how to derive projections to the same or different study areas, or to different time steps, such as future climates. The use of ensemble of models to assess uncertainty will also be covered. Practicals will allow the students to get trained in all these aspects. Due to the limited number of days (2), only an overview of these different aspects will be given and short practicals conducted. Depending on the course progress, there may be scope for individuals to work on their own data sets, so participants are encouraged to prepare their datasets as [species x sites] and [environment x sites] matrices before the course.

Applications of Stable Isotopes in Plant Sciences

 

(1 ECTS), Prof. Nina Buchmann, Prof. Emmanuel Frossard, Prof. Johan Six, Dr. Roland Werner, Dr. Matthias Barthel, Dr. Charlotte Decock (ETH Zurich) and Prof. Ansgar Kahmen (University of Basel). Scientists at both field sites (DOK trial: Dr. Paul Mäder, Dr. Andreas Fliessbach (FiBl), Juliane Hirte (Agroscope); Hofstetten crane: Ansgar Kahmen)

Lectures: Introduction to stable isotopes, tracer vs. natural abundance applications, instrumentation. Overview lectures on stable carbon, nitrogen, oxygen and hydrogen isotope applications in agricultural and forest ecosystem sciences.  Field visit: Students will get to know stable isotope applications in agricultural (DOK trial) and forest (Hofstetten crane site) ecosystems, interact with those who had carried out different stable isotope studies at the sites. Students know the basics about stable isotope applications to study plant and soil related research questions. Students are able to decide on tracer vs. natural abundance designs for a given research objective. Students understand the main mechanisms and processes imprinting on the stable isotope composition of the material of interest (e.g., plants, soils, gases).

Chlorophyll Fluorescence - Principles and Applications

(1 ECTS), Dr. Diana Santelia, University of Zurich, Dr. Klara Panzarova, Photon Systems Instruments

Chlorophyll fluorescence analysis is one of the most powerful and widely used techniques by plant physiologists and ecophysiologists. Chlorophyll fluorescence is used for rapid non-invasive measurement of photosystem II activity. PSII activity is very sensitive to range of biotic and abiotic factors and therefore chlorophyll fluorescence technique is used as rapid indicator of photosynthetic performance of plants in different developmental stages and/or in response to changing environment. The course will consist of lectures related to the theoretical background of this technique and practicals where different measuring protocols will be used to illustrate the types of information that fluorescence can provide. We will use both imaging and non-imaging tools for analysis of chlorophyll fluorescence kinetics. The analysed samples will be from cyanobacteria, algae and plants.

Metabarcoding and DNA Barcoding

 

(1 ECTS), Prof. Alex Widmer, ETH Institut für Integrative Biologie, Dr. Stefan Zoller and Dr. Jean-Claude Walser, Genetic Diversity Center, ETH Zurich

The goal of DNA barcoding is the identification of species through the analysis of nucleotide variation in short, standardized gene regions. These gene regions are typically amplified by PCR from samples of unknown origin and are then sequenced individually using standard Sanger sequencing technology. DNA metabarcoding is an extension that aims at identifying multiple species from a single, often complex and possibly degraded, environmental sample. A target gene region from all species represented in the sample is then amplified by PCR and sequenced using a high throughput nucleotide sequencing approach. DNA barcoding is widely used by ecologists and conservation biologists to identify species. Examples include the analysis of wood samples from logged trees or the validation of field identifications of vegetative plant parts. DNA metabarcoding is mainly used by ecologists and evolutionary biologists interested in biodiversity assessment, for example from water or soil samples, or the analysis of animal diet, gut bacteria composition and parasite diversity.

OTHER COURSE OFFERS

The PSC PhD Program in Plant Science organizes courses in cooperation with:

Life Science Zurich Graduate School

URPP Evolution in Action (UZH)

 

Additionally, courses of the following organisations can be fully accredited:

 

Transferable Skill Courses, University of Zurich:

for PhD students at Uni Basel: you have to register for  Module Mobility at UZH first.

for PhD  students at ETHZ: you have to register as Special student "University of Zurich (UZH)" at UZH first.

 

Hochschuldidaktik at University of Zurich Didactica

Graduate Campus (GRC, UZH), register for  Module Mobility first!

 

Transferable Skill Courses, ETHZ:

for PhD students at Uni Basel: you have to register as Special student "University of Basel (UBa)" at ETHZ first.

for PhD students at UZH: you have to register as Special student "University of Zurich (UZH)" at ETHZ first.

 

Transferable Skill Courses at University of Basel GRACE

 

Excellent English language skills are a core requirements for the successful completion the PSC PhD Program in Plant Sciences. Additional training can be obtained through University of Zurich and ETH Zurich