Abiotic Stress

Environmental (abiotic) stress is the most important limiting factor in crop productivity. This master course aims to broaden the student’s horizon in abiotic-stress biology and to gain the latest insights into the molecular mechanisms by which plants perceive such stress signals, how they are transduced, and how stress signals are eventually converted into intracellular responses that allow the plant to react appropriately so that it will survive and resume growth (acclimation).

A second aim of this course is to learn to write a successful grant application/research proposal. Students will be guided through the essential stages of proposal development, how to formulate specific project goals, how to collect and present supportive background data (written and verbally), to determine the level of stakeholder engagement, to measure and evaluate the outcomes, to plan project activities, and to budget appropriate project costs.

The course will start with lectures about various forms of abiotic stresses that plants encounter. These include, osmotic stress (salinity, drought), temperature stress (heat, cold), and heavy metals. The emphasis will be on how plants sense these stresses and how these signals are converted into responses at the molecular and physiological levels that allow plants to cope with the stress. Potential applications for crop improvement will also be discussed. The second part of the course involves the construction of a research proposal, including writing, presenting and data mining. At the end of the course, students are expected to successfully present and defend their own proposal.

Program/Minor

Learning Outcomes

Describe how plants respond to abiotic stress at the physiological, genetic, biochemical, molecular and cellular level; Interpret, analyze and evaluate contemporary research articles in the field of experimental plant sciences; Write and defend your own research grant application; The student can propose molecular tools, techniques and (genetic) screens to identify and unravel molecular mechanisms in stress tolerance.

Prerequisites

Advanced (BSc) knowledge in Plant Molecular & Cellular Biology is required (e.g: Molecular Cell Biology, Cellular Responses, Cell biology, Biochemistry).

Details

Institution: UvA

Period: Period 2

Level: Master

EC: 6 ec

Advanced Bioinformatics (UU)

In de cursus wordt aandacht besteed aan het begrijpen van en werken met grote hoeveelheden gegevens zoals de laatste jaren in veel genetisch en moleculair onderzoek worden verkregen. Deze technologische ontwikkelingen vereisen nieuwe vaardigheden en concepten om life science onderzoek te kunnen begrijpen en uitvoeren. In het eerste deel van de cursus wordt een veel gebruikte programmeertaal (Python) geleerd. In de drie volgende delen wordt achtereenvolgens gewerkt aan het voorspellen van gen-functie, het bepalen van mutaties op grond van sequencing data, en het ontrafelen van het regulatienetwerk.

Program/Minor

Learning Outcomes

Toepassen van de programmeertaal Python voor bioinformatische analyses; Begrijpen en interpreteren van primaire genomics-literatuur, met focus op methodologische 'pipelines'; Zelf eenvoudige bioinformatische pipelines programmeren van sequencing data tot biologische interpretatie; Analyseren van transcriptomic datasets (zoals digital gene expression en differential expression) om transcriptieregulatienetwerken en hun verstoringen in kaart te brengen; Detecteren van DNA-variaties en chromosoomafwijkingen in bijvoorbeeld tumorgenomen; Identificeren van orthologen tussen menselijke (ziekte)eiwitten en hun tegenhangers in modelorganismen; Interpreteren van mutaties in menselijke eiwitten in hun evolutionaire context; Integreren en vergelijken van nieuwe data met bestaande databases zoals Ensembl, UniProt en Cancer Genome Atlas; Begrijpen van de basisprincipes van data-integratie binnen bioinformatica; Toepassen van bioinformatische inzichten voor het duiden van biologische mechanismen in gezondheid en ziekte.

Prerequisites

Het blok sluit aan op eerdere onderdelen van het eerste en tweede jaar Biomedische Wetenschappen (‘Genoom’, ‘Moleculaire Biologie van de Cel’, ‘Genes and Genomes’) en Biologie ('Genomica', ‘Moleculaire biologie’, ‘de Cel’, ‘Cellen en weefsels’, 'Moleculaire en genetische onderzoekstechnieken', 'Voortgezette statistiek en R', en ‘Genoombiologie’). In de genoemde cursussen is aan de orde geweest: transcriptie, transcriptiefactoren, histonmodificaties, translatie, splicing, typen mutaties (SNP's, structural variation), eiwitstructuur, genduplicaties. Bij niet voldoen aan de ingangseisen kan door de examinator stof worden opgegeven, die voorafgaand aan de cursus bestudeerd dient te worden. Voor BMW-studenten geldt dat ze ‘Genoom’ succesvol moeten hebben afgerond om te kunnen deelnemen aan de cursus. Voor Biologiestudenten geldt dat ze ‘de Cel’ succesvol moeten hebben afgerond om te kunnen deelnemen aan de cursus. Voor MBLS studenten geldt dat ze ‘genomes, cells and tissues’ succesvol afgerond moeten hebben.

Details

Institution: UU

Period: Period 2

Level: Advanced

EC: 6 ec

Advanced Bioinformatics (WUR)

This course covers the process of bioinformatics data analysis and the interpretation of the results in a biological context. The following topics will be addressed in the course: command line usage, programming/scripting, current bioinformatics data analysis tools, and automated analysis pipelines. The first part of the course will cover command line usage (linux), bioinformatics script programming (python), as well as the theory and tools required to analyse data produced by current sequencing technologies and interpret the results. Topics include genome assembly, sequence annotation, gene expression, biological networks, and comparative genomics. During the second part of the course, students – in teams – will apply their knowledge in a small research project. Given a specific biological question and the required data, the goal is to build a data analysis pipeline and describe the biological interpretation.

Program/Minor

Learning Outcomes

Show proficiency in command line usage; Run existing data analysis tools using the command line; Write computer scripts for data analysis; Design and implement an automated data analysis pipeline connecting multiple tools; Work with large data volumes (big data from NGS technologies); Interpret the results of (NGS) data analysis; Describe a data analysis process; Describe the biological interpretation and implication of the analysis results;

Prerequisites

Introduction to Bioinformatics or Computational Biology and Practical Computing for Biologists or Programming in Python

Details

Institution: WUR

Period: Period 2

Level: Advanced

EC: 7.5 ec

Advanced Biotechnology

Biotechnology is a broad term for all technologies that utilize biological systems, living organisms, or their parts to develop or create different products. This course covers topics ranging from the development of climate-resilient and herbicide-resistant crops using CRISPR/Cas to the development of mRNA therapies and the usage of fungi for removing contaminants from the environment. The course aims to give you an extensive overview of recent developments in biotechnology and the broad array of possibilities within this field. The course will start with an overview of molecular techniques available for biotechnology. Different topics and applications will be discussed, such as metabolic engineering, food production, prevention of infectious diseases, and applications of biotechnology in medicine. In addition, other aspects related to biotechnology, such as intellectual property rights, ethical concerns, and the marketability of a product, are discussed. Throughout the course, guest speakers from different universities, companies and institutes will highlight career prospects within the biotechnology field. Volunteer visits to companies are organized to help students better understand how the knowledge about biology is used in the plant, chemical, and pharmaceutical industries.

Program/Minor

Learning Outcomes

missing

Prerequisites

The student should have followed the level 2 courses Moleculair Genetische Onderzoekstechnieken (MGOT) or Molecular Biology and Biochemical Techniques (MBBT) or courses of similar content. It is not critical if the student has passed these courses by the time the Advanced Biotechnology course starts.

Details

Institution: UU

Period: Period 2

Level: Advanced

EC: 7.5 ec

Advanced Biotechnology (UCU)

This is one of the final courses in a series of three courses in molecular cell biology. In the first introductory course (UCSCIBIO11), you gained a lot of basic knowledge about the major characteristics of life on Earth. In the intermediate UCSCIBIO21 course, we explored the molecular world of the cell in more detail and learned to apply the knowledge to designing, interpreting, and presenting real-world data and scientific literature. This third course, Advanced Biotechnology (UCSCIBIO32), will focus on the implications of this knowledge; the course will cover theoretical and practical aspects of modern biotechnology, its large-scale applications, and its impact on society.

The highlights of UCSCIBIO32 are lectures and discussions with invited speakers from academia or industry in biotechnology. We will also debate on the topic of ethics in biotechnology, and at the end, you will try to develop your business idea to solve societally relevant issues in the second part of the course.

The course is divided into thematic parts devoted to general cloning methods and methods related to plant, animal, microbial, and biomedical biotechnology. Assignments are designed to help understand the practical aspects of the theoretical knowledge learned in lectures. You will get peer or teacher feedback on the first version of some of your assignments; this is meant to deepen your understanding of the lecture materials. In the second part of the course, where you work on the business idea, we will have lectures with invited speakers from industry and research fields related to biotechnology to help you get insight into how innovation works in biotechnology and how one could protect intellectual property.

Program/Minor

Learning Outcomes

give an overview of the different fields of biotechnology; explain the important techniques underlying biotechnology; design an experiment to solve a problem related to a biotechnological process (with emphasis on DNA and protein technologies); discuss ethical and legal problems related to biotechnology; give a well-founded opinion on biotechnological applications; develop a business idea to solve societally relevant issues taking into account financial and ethical aspects.

Prerequisites

Students must be enrolled for a degree programme of faculty University College Utrecht and have passed Molecular Cell Biology II (UCSCIBIO21), with at least a 1.7

Details

Institution: UU

Period: Period 4

Level: Advanced

EC: 7.5 ec

Advanced Cellular Imaging Techniques

Advanced light microscopy and reporter gene techniques are indispensable for mechanistic studies on the functioning and organization of cells. New microscopy technologies and digital imaging allow us to study dynamic processes at shorter time scales and with higher spatial resolution in living cells. In this practical course the principles and cell biological application of different microscopy techniques will be taught. Topics include microscope construction, (green) fluorescent proteins (GFP), probes for measurement of cellular physiology, widefield and confocal fluorescence microscopy, differential interference contrast microscopy (DIC), fluorescence lifetime imaging microscopy (FLIM), Förster resonance energy transfer (FRET), fluorescence recovery after photobleaching (FRAP), photoconversion, superresolution microscopy, digital image analysis and image noise. These techniques and concepts will be applied to study (sub)cellular physiology; dynamics of membrane organization; (intercellular) protein diffusion; hormonal signalling and intermolecular interactions. An important aspect of the course is data acquisition, reduction, processing and analysis; How can quantitative data be extracted from digital images for comparison with quantitative models of cellular mechanisms?

Program/Minor

Learning Outcomes

Explain principles of light microscopy techniques and reporter methods; Identify the components of advanced light microscopes and summarize the basics of their operation; Operate advanced light microscopes based on knowledge of their design and capabilities; Adapt key microscope parameters under various image distortions (optical / noise); Extract quantitative data from digital images; Adapt a critical attitude towards the presentation of microscopy data in literature papers; Process and analyze data and compare results with provided quantitative models on molecular and cell biological processes; Interpret the cell biological processes that are presented during lectures and practicals in a mechanistic manner; Select appropriate microscopy techniques and reporters for cell biological work; Write a short research paper on a conducted cell biological experiment and present the work orally;

Prerequisites

Assumed: CBI10306 Cell Biology, Basic (cellular) biochemistry (e.g. covered in BIC10306 Practical Biological Chemistry; PCC12303 General Chemistry 1; PCC12803 General Chemistry for the Life Sciences), Fundamentals of algebra and statistics (MAT14903 Mathematics 2, MAT15403 Statistics 2, or equivalent courses). Basic knowledge of optics (lens equation) and electromagnetic waves (wavelength, phase, photons and absorption). Mandatory: ZSS06100 Laboratory Safety

Details

Institution: WUR

Period: Period 2

Level: Advanced

EC: 6 ec

Advanced Crop Physiology

Understanding crop physiology is of utmost importance for adapting agriculture to the challenges associated to climate change and environmental degradation. While molecular biology has made impressive strides in elucidating the regulation of processes in plants, the challenge remains to understand what this means for processes in real crops as this is the level at which farmers act to produce food, forage, fiber, and fuel. Building a deep knowledge on the functioning of crops and their interaction with the environment requires an effective conceptualization of such complex system at different levels through the integration of various disciplines and tools into a framework that is continuously evolving.

This course invites students to develop critical thinking around the discussion on how recent developments in physiology of primary processes, as well as methods such as crop modelling and phenotyping, can provide new and integrative insights on crop physiology. Therefore, the course is based on group and individual assignments accompanied with plenary discussions, for which students will use relevant scientific publications and lectures covering important aspects of crop physiology.

Program/Minor

Learning Outcomes

Identify and describe current gaps in crop physiological knowledge related to crop responses to stress; Integrate in-depth knowledge of crop physiology and formulate specific research hypotheses to inform the design of crop improvement and management strategies; Design a research proposal that addresses the identified knowledge gaps identified; Articulate and communicate scientific ideas clearly and effectively through oral and written communication

Prerequisites

Basic knowledge on plant and/or crop physiology, agronomy and breeding is advised.

Details

Institution: WUR

Period: Period 3

Level: Advanced

EC: 6 ec

Advanced Omics: from Single-Cell to Meta-Omics Approaches

Omics technologies have revolutionized our ways of looking at the relationship between genotype and phenotype of living organisms. Those technologies are nowadays widely applied to many organisms (bacteria, plants, animals, human). Yet for many years researchers have been looking only at average effects by analysing bulk samples. Recently, single-cell analyses have become available for many cell types in different organisms. Today these technologies are mostly employed in the form of single-cell transcriptomics, and can provide information about, for instance, spatiotemporal development of an infection or of an organism or tissue (e.g. plant’s root). However, new methods are currently being implemented for the study of the proteome and metabolome at a single cell resolution.
Single cells can also compose individual organisms (i.e. bacteria) that can live in communities such as the human or animal microbiomes or the rhizosphere of plants. Knowing the composition and quantitative traits of these communities at different levels (genomics, transcriptomics, proteomics, and metabolomics) can tell us about the functions of the system as a whole and help us in designing interventions for the enhancement or removal of specific characteristics.
Therefore, single-cells and meta-omics methods are enabling researcher to investigate challenging questions such as defining tumour or patient heterogeneity. Besides their use can result in the development of applications such as biofertilizers or tools for biopest control.
In this course you as a student will have the chance to discover the new developments in the field of single-cell and multi-organism omics with a focus on exploring the technologies but more deeply the data analysis connected to the complex information produced. Together with your colleagues you will investigate and report on the analysis of such data highlighting the richness of the biological information contained.

Program/Minor

Learning Outcomes

Define the meta- and single-cell omics approaches currently available; Illustrate the questions answered by meta- and single-cell omics approaches; Execute basic and advanced analysis of meta- and single-cell omics data; Develop a professional notebook containing data, code and descriptions to report on project’s results considering FAIR principles; Assess limitation and applicability of meta- and single-cell omics approaches;

Prerequisites

Molecular Systems Biology (SSB30306) and Advanced Bioinformatics (BIF30806)

Details

Institution: WUR

Period: Period 6

Level: Advanced

EC: 6 ec

Adviseren gewasbescherming, akkerbouwadviseur 2030, bodem en bemesting, telen met licht

Life-long learning: Heavily geared towards people who work in the arable/horticulture sector themselves or provide advice. South of the Netherlands

Details

Institution: HAS Green Academy

EC: LLO ec

Agroecology

The course focuses on agroecological principles to analyse and design sustainable and productive farming systems. Agroecological principles include: Recycling and efficiency; Living Soils; Biodiversity; Ecosystem services and multi-functionality; Resilience; Fair Markets; Culture & spirituality; Youth & Women; Adequate Policies & governance; Knowledge co-creation and collaboration. Students will explore how agroecological farming systems are developed across the world, and how principles can be applied and translated into adaptive farming practices and management. There will be a strong focus on methods, approaches and indicators used to assess mechanisms that regulate the ecological functioning of farming systems. In addition, students will learn methodologies to involve farmers and promote the dialogue between scientific and practical knowledge for the design of agroecological farming systems.

Program/Minor

Learning Outcomes

Identify and understand agroecological principles and how they can be translated into farming practices. Select and use indicators to assess the ecological functioning and sustainability of farming systems. Understand how participatory approaches can enhance the transition to sustainable farming systems. Re-design farming systems based on agroecological principles and practices.

Details

Institution: UU

Period: Period 1

Level: Intermediate

EC: 7.5 ec

Agroecology and Agronomy 1

The course focuses on the mutual relation between crop production and environment and consists of two pillars: a. basic principles of crop production ecology, b. sustainability of crop production. The first pillar consists of basic knowledge on how a-biotic (e.g. radiation, temperature, nutrients) and biotic (e.g. pests, diseases and weed) factors influence the productivity of crops. Here, the distinction in potential, water- and nutrient limited and actual production level is presented and used as a thread. Within the actual production level, the ecology and biology of arable weeds is handled, including crop-weed competition. In the second pillar, sustainability issues of crop production are discussed. A comparison is made between the environmental impact of crop production in conventional and organic farming systems. In addition, the potential of crop diversification, specifically through crop rotation and intercropping, as a means to increase the sustainability of cropping systems, is discussed.

Within the course, a MOOC (massive open on-line course) will be used to teach the principles of crop production ecology. Exercises and practicals will be used to improve insight regarding the consequences of agroecological practices on crop production and the environment. These exercises will be quantitative in nature. In addition, we introduce the basic principles of modelling. Crop modelling will then be used as a tool to integrate the influence of various environmental factors on crop production.

Throughout the course, theoretical concepts and methodological issues are linked and applied in exercises, practicals and case studies. In the final week, a visit is made to an organic farm where we discuss, among others, the importance of crop rotation.

Program/Minor

Learning Outcomes

Explain how radiation, temperature and crop characteristics determine the potential growth, development and production of crops in agro-ecosystems; Explain how a-biotic (water and nutrients) and biotic (pest, diseases and weeds) production constraints interfere with crop production; Understand the ecology and biology of arable weeds and their effect on yield; Identify the sustainability issues of a cropping system; Explain how the environmental impact of a cropping system can be evaluated; Understand how crop diversification (crop rotation, intercropping) can be used to improve sustainability of cropping systems; Master elementary facets of systems analysis and simulation; Understand the difference between descriptive and mechanistic models

Prerequisites

ZSS06200 Fieldwork Safety

Details

Institution: WUR

Period: Period 5

Level: Introductory

EC: 6 ec

AI bootcamp voor leidinggevenden, AI geletterdheid

Life-long learning: Short data and AI courses

Details

Institution: Aeres Training Centre

EC: LLO ec