Course list Biomedical Sciences

Content:

The course focuses on understanding and working with large amounts of data as obtained in recent years in much genetic and molecular research. These technological developments require new skills and concepts to understand and conduct life science research. In the first part of the course, a widely used programming language (Python) is taught. In the three following parts, we successively work on predicting gene function, determining mutations based on sequencing data, and unravelling the regulatory network.
Key words: (cancer) genomics, regulome, transcriptome, proteome, genome and protein evolution, Python scripting, SNP/CNV calling.

Required knowledge:

The block connects to earlier parts of the first and second year Biomedical Sciences ('Genome', 'Molecular Biology of the Cell', 'Genes and Genomes') and Biology ('Systems Biology', 'Molecular Biology', 'The Cell', 'Cells and Tissues', 'Molecular and Genetic Research Techniques', 'Advanced Statistics and R', and 'Genome Biology'). In the courses mentioned: transcription, transcription factors, histone modifications, translation, splicing, types of mutations (SNPs, structural variation), protein structure, gene duplications. If the entrance requirements are not met, the examiner may specify material to be studied prior to the course.
 

Learning outcomes:

Knowledge and insight

At the end of the course, the student is able to:

• To understand and explain the bioinformatic steps (the 'pipeline') of analysis that lie between sequencing data generation and biological interpretation, as this occurs in many primary articles within the Life Sciences.

Skills

At the end of the course, the student is able to:

• Apply the Python programming language;
• Understanding primary genomics literature and especially the 'pipelines' described in so-called 'supplementary methods' of articles;
• Programming simple pipelines themselves to get from sequencing data to biological interpretation;
• Apply the above bioinformatics skill to map transcriptional networks and their perturbations through the analysis of transcriptomic datasets such as digital gene expression profiling and differential gene expression;
• Using this bioinformatic skill to detect DNA variations, such as mutations and chromosomal variations, as they occur in the genome of tumours;
• Integrate newly acquired data and compare it with existing information from different sources like Ensembl, UniProt, Cancer Genome Atlas;
• Using this bioinformatic skill to interpret mutations in human proteins in their evolutionary context.

Learning activities and contact time:

The teaching methods consist of lectures and computer supported eductation (COO) (partly unaccompanied and partly accompanied). The block has 60% contact time. Self-study consists of making the COOs and studying primary literature independently.

Assessment:

The course has two tests and a practical test. The final grade for the course is determined by the weighted average of the three tests. For each subtest a minimum of 4.0 must be obtained to be able to compensate and the average final grade of the course must be 5.5. Participation in computer labs as well as the first contact moment is mandatory.

Required material:

• Use of your own laptop.

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Content

This course focuses on working as a biomedical scientist in business, (semi-)public institutions or start-ups. The process from discovery to (large) company, but also the social role and responsibility of companies is examined.
The course has three main components. First of all, the student gets an idea of the business side of a lab. This part of the course focuses on patenting discoveries in the lab. Subsequently, the development of a business case and the starting of a company within Life Sciences is discussed, on the basis of the interests of stakeholders and the Business Model Canvas. The components that make up a company are also discussed, for both start-ups and established companies. Finally, students get a glimpse of the various work areas in which many graduates end up (such as the pharmaceutical industry, spin-off companies from academic research institutions, NGOs, the biotech industry and start-ups).
Through assignments, the student gains insight into the patent database, learns about company structures and develops entrepreneurial skills, such as giving a pitch and using effectual techniques, which will continue to be useful after the programme. At the end of the course, students will have a better idea of the opportunities that Life Sciences graduates have in the business world and will have answered the question of whether and how a career in the business world suits them.
The course serves as an introduction to the Life Sciences business sector, focusing on those business aspects that Biomedical Sciences students are most likely to encounter. Students who wish to gain more general business knowledge can take a course elsewhere or, for example, move on to the Science and Business Management master's programme.

Learning outcomes

Knowledge and insight

At the end of the course the student will be able to:

• Indicate when to file a patent, what it should comply with and what elements make up a good patent;
• Using the Business Model Canvas, show how each part of a company contributes to the functioning of a company as a whole;
• Explain in their own words the stages to be gone through when marketing a product within start-ups and large companies;
• To critically evaluate what a company's social mission is and whether it is being fulfilled.
• To reflect on what role, within or adjacent to biomedical business, suits one's own talents and interests.

Skills

At the end of the course the student will be able to:

• Testing whether a discovery has already been patented in the patent database;
• Translating and selling an idea to a broad audience through a pitch;
• Apply elements from the Repko methodology to effectively collaborate interdisciplinarily.

Teaching forms and contact time:

Lectures, guest lectures, (group) assignments, giving a pitch and peer feedback on it, writing a reflective essay. ±6 (max. 10) contact hours per week. In addition to the contact hours, there are self-study assignments. The course requires a different way of thinking and collaborating than Life Sciences students are used to. The scheduled time for assignments has been adjusted accordingly.

Assessment:

The final grade is composed of partial grades of both group and individual assignments:

• Patent assignment: 30%
• Business Model Canvas: 35
• Pitch (including peer review): 10%
• Reflection assignment: 25%
• Preparation expert: satisfactory/unsatisfactory

All assignments must be completed with a satisfactory score in order to pass the course.

Required material:

Primary literature, available from library.

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Content:

Within this course the bacterium has a central role. The students will gain thorough knowledge on the molecular build-up of several different types of bacteria and the ways this make-up enables these bacteria to cause infections. Plenary lectures will be given by experts active in diverse fields of microbiological research. Furthermore, the focus will be on giving an overview on experimental techniques in molecular microbiology. 

A large part (~50%) of this course consists of practical work in which the students will perform their own research in a fundamental research setting. Students will be divided into small groups (2-3 students) and will work on different topics. Part of the students will select a set of potential immune evasive bacterial genes and subsequently produce the corresponding proteins (subgroup 1). The other students will integrate fluorescent markers into bacteria that contain or lack the selected genes of interest (subgroup 2). By employing molecular techniques (e.g. flow cytometry and fluorescence microscopy) the corresponding functions will be investigated. Students will furthermore be trained in data analysis, interpretation of obtained results, and critical discussion thereof. Both subgroups will present their work to each other. Besides practical work, students will also have the opportunity to discuss their experiments with several people with different positions (e.g. professor, associate professor, post-doc, PhD student, Master’s student) within the research environment.

This is a challenging course integrating knowledge and practical techniques, thereby forming a bridge between the Bachelor’s programme and research Master’s programme.

Required knowledge:

General knowledge on molecular cell biology is required (“Cellen” and “Weefsels”). Participation in “Infectie & Immuniteit” or a similar course is advised, however not mandatory. Students from outside the Biomedical Sciences programme should contact the course coordinators to determine if their foreknowledge is sufficient for participation. 

Learning outcomes:

Knowledge and insight

After completion of this course the student can:

• describe the molecular and structural features of bacteria (including cell wall, genome, secretion systems);
• explain the diversity within bacterial species based on the above characteristics;
• describe the process of a bacterial infection, from entry, colonization/infection to pathogenesis;
• elaborate on bacterial virulence and survival strategies of bacteria;
• explain the molecular principles of immune evasion strategies employed by bacteria;
• explain the molecular action of bacterial toxins;
• explain the acquisition and molecular basis of antibiotic resistance and describe alternative treatment options (such as antibody therapies);
• be familiar with, know when to use, and how to interpret the most important modern techniques within the field of microbiology (CRISPR-Cas, Flow Cytometry, Imaging, Next Generation Sequencing, Protein Structure and Proteomics).

Skills

After completion of this course the student is able to:

• formulate a research question and translate this into experiments, choosing the right technique;
• perform basic laboratory and microbiological techniques within a research setting;
• perform cloning and expression of foreign proteins in bacteria;
• submit a report of experimental data in the form of a laboratory journal;
• formulate a concise scientific abstract summarizing the main experimental procedures and findings;
• give an oral presentation in English on performed experiments and collected data;
• give a critical analysis (journal club) on literature within the field of molecular microbiology.

Attitudes

After completion of this course the student has:

• the ability to work well in a team;
• developed a critical attitude towards obtained results and scientific literature, but also towards themselves and other students.

Learning activities and contact hours:

Teaching consists of plenary lectures, work groups, and literature assignments (approximately 1/3 of the course), practical work (approximately 2/3 of the course), student presentations, speed dates with researchers, meet the expert, and a written examination. Due to the high amount of practical work the average contact hours are approximately 12 hours per week. The remaining time is reserved for self-study.

Assessment:

• Written exam (50%);
• Practical assessment (50%); divided between presentations (20%), a written report in the form of a laboratory journal and abstract (20%), and participation (10%);
• The minimum grades for both the exam and the practical assessment required to pass the course is 5.5.

Necessary material:

• An online course manual is available on the Lifelong Learning Platform;
• Prescott’s Microbiology, Willey et al., Tenth Edition, 2017 McGrawHill (recommended);
• Research articles and other material will be published on the Lifelong Learning Platform.

Content

The human genome is extremely complex. It encodes numerous RNAs and proteins as well as regulatory elements which play a role in gene expression. Medical genetics translates this fundamental knowledge into clinically relevant genetic tests and genome diagnostic tools. Until recently, only  monogenetic disorders were tested and screened for in the clinic. In the near future, however, whole genome sequencing will be technically and financially attainable. But can someone’s genome sequence tell us more about the chances they have of suffering from complex and multifactorial  disorders ? Which statistical correlations will be found and what does such a correlation tell us about what is actually happening in this person’s body? In this course the student will explore the edge of fundamental gene research as well as the contemporary practices in a clinical setting. The aim is to ascertain what remains unknown and what information is currently missing, allowing us to form a plan for the future of genetic testing and genome screening.

A lot of attention will also be paid to the ethical choices that arise with these new developments. These are personal choices such as “Do I want to know it if they find something unexpected?” but also societal choices such as “Should we offer everyone genetic screening as a preventive measure, also when there are no medical indications to do so?”

During this course, the student will explore the possibilities and the desirability of genetic testing and screening from a fundamental scientific point of view, taking into account that the nature of genetic information can be complex and uncertain.

Required background knowledge

The student must have knowledge of complex relations between genetic information and the (dys)functioning of the body. The basis of the background knowledge is the molecular processes surrounding gene expression and gene regulation, as studied in cells and genome courses. Students will be able to review knowledge or gain missing knowledge in the first phase of the course through independent study.

Learning outcomes

Knowledge and insight

At the end of the course the student will be able to:

• analyze the recent scientific, technological and clinical developments in human genetics and relate these to one another;
• explain how the terms complex and uncertain are applicable to genetic information;
• relate the terms complex and unsure to the (im)possibilities and (un)desirabilities of genetic testing and screening.

Skills

At the end of the course the student will be able to:

• Writing, in groups, a dossier on a disease-related topic in clinical genetics viewed from different perspectives (clinic, (big)data, society, research).
• Based on the dossier, an advice for a stakeholder is formulated;
• Based on the theme dossier, provide an individual workshop for fellow students that brings together the professional, social and ethical aspects of medical genetics;
• Express insight into personal consequences and dilemmas arising from genetic testing in a written test result and a personal outcome discussion with the patient.

Attitudes

At the end of the course:

• the student recognizes the importance of knowledge and values as a basis for personal and societal decision-making on genetic testing;
• the student is able to understand and discuss important issues surrounding genetic testing from the points-of-view of the different stakeholders involved  in genetic testing and is able to keep in mind which considerations play a role in their decision-making.

Teaching forms and contact time:

In the first six weeks, the focus is on the subject matter of medical genetics. Groups of six students work intensively together on a dossier on, for example, the genetics of heart failure, immunological, neuromuscular or neurological disorders. Besides the group work, there are interactive lectures, practical assignments and tour. In the last four weeks, the focus is on the social and personal implications of developments in medical genetics. There are workshops and discussion moments with patients and guest speakers. All participants also conduct their own workshop for three fellow students and a lecturer. Finally, all participants will undertake a genome analysis for the presence of genetic risk factors; the clinical implications of this will be described individually in a result letter and discussed as a group in a result discussion.

Assessment:

Assessment of the topic dossier, workshop, outcome letter and outcome interview and participation. All components in the assessment must be satisfactory. The course has no written examination.

Required material:

During the course, recent (review) literature will be used. There is no course textbook.

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Content:

In small groups (3-5 students) you will get to work on a biomedical research project, based on real, ongoing, yet unpublished research from one of the biomedical research labs from the UMC Utrecht and/or Utrecht University.  For this UMC and/or UU researchers from different disciplines will provide a brief description of their projects, as a starting point for your own project. With this information you will formulate your own research question and aim to design a strategy to answer it. You will be supervised one of UMC’s or UU’s researchers. After a round of (peer)feedback and approval of your research proposal and experimental design you will be provided with raw data derived from experiments resembling your own experimental design. Next you will select and process this data to produce clear tables and figures. You will interpret your own results, draw conclusions, and ultimately answer your own research question. Your research will be reported to peers in a scientific article. Additionally, your supervisor will share his or her findings and interpretations of the data and results. You have the opportunity to provide your supervisor with feedback on the study design, data analysis and interpretations and future research. Throughout the course you will be introduced to different concepts of Open Science. As it important to convey the conclusions of your research to a wider audience, in your last assignment you will inform the public about your research. In summary, throughout the course you will progress through most stages of the research cycle with special attention to designing your own research and analyzing and interpreting research data and results. You have a unique opportunity to develop you research and academic writing skills and train your critical attitude towards your own work and the work of others.

Every course we offer different project to work on. They range from fundamental and descriptive studies to applied translational studies. You can choose a research topic from different major biomedical research disciplines from UMC Utrecht and/or Utrecht University.

Requirements for admission:

You must have knowledge of cell biology, cell cycle, genetics, transcription, translation, basic immunology, biochemistry, anatomy and statistics.

Learning outcomes:

Knowledge & Insight:

After the course you can:

• explain the importance and the relevance of their own research;
• explain the most recent research developments within their own research to peers and the general public;
• make out the strengths and limitations of different (project specific) techniques;
• name the benefits and the drawbacks of open science as well as the ambitions of the university with respect to open science.

Skills:         

After the course you are able to:

• design detailed experiments which answer their self-formulated research question;
• select, interpret and process raw data (including the correct statistical analyses) to answer the research question and to formulate new insights and hypotheses;
• process data using spreadsheet programs and to present them in clear tables and graphs;
• report the results and conclusions to peers and the general public;
• critically analyze the work (research design, results and manuscript) of peers and provide it with feedback;
• receive and process feedback to produce an improved piece of work.

Attitude:

After the course you will have:

• a critical attitude towards their own and their peers’ work;
• a critical and honorable attitude towards raw data and analyses;
• knowledge of the ethical aspects of their project specific research subject.

Teaching forms and contact time:

To work on your project, you will collaborate in small groups, and you will be supervised by one researcher. You will meet once a week (avg 2 hours a week) to discuss your project and your progression and to receive feedback. Additionally, you present your work to your fellow students in a weekly meeting (avg. 2 hours a week). We created an online environment with different individual and/or group assignment, discussion for and opportunities for (peer)feedback (self-study). These will support you step-by-step while you transcend through the research cycle and shape your research.

Assessment:

Scientific article (40%):
The scientific article is a group product and will be assessed using a rubric.

Feedback (20%):
You will provide each other’s paper with feedback (individual product) and you will also provide your supervisors work with feedback (group product). The average grade of these two assessments will form the feedback grade. The quality of the feedback will be assessed using a rubric.

Presentation (20%):
In most meetings you will present your progression and your work. Your presentation of the results (week 5 – 8) will be assessed (individual grading). At the end of the course, you will convey your results and conclusions to a wider audience in an open and creative (group product). The oral presentation accounts for 2/3 and the poster presentation account for 1/3 of te presentation grade. Both the presentation and the poster will be assessed using a rubric.

Participation (20%):
Your participation and collaboration during all meetings and in the online environment are graded separately. For this we will use a grading form. The average of both grades accounts for 20% of your final grade. Active and meaningful participation in online forum discussions is mandatory. 

In order to pass the course, the student must score at least a 5.5 in each assessment. Grades from group products are personalized based on peer assessment.

Required material:

None.

Please inform the International Office if you want to do a Research Project (Plus). They will be able to help you further.

Content:

1. The final product is an essay written in English, possibly in the form of a scientific article, with a theoretical introduction that reflects the current literature in the relevant field.
2. Going through a research cycle: reviewing literature, formulating a hypothesis, designing and conducting an experiment, analysing the results, drawing conclusions and writing down the result.

The report or final product is written in English and must contain a literature review of approximately a minimum of 10,000 and a maximum of 16,000 words (excluding the bibliography), using a minimum of 25 primary articles. The literature overview can be seen as a thesis, review or bachelor's thesis, names used in past years. In addition to the literature review, the final product includes coverage of practical work.
The usual form of the final product is in the form of a scientific article, which has been adapted for the purpose of this course: an introduction, introducing the subject of the literature review and stating its importance, then the literature review (including a conclusion/discussion of the findings), contextualising the research done.
The "practical" research conducted and analysed is sometimes incorporated as a separate chapter, sometimes integrated into the literature section and sometimes as an appendix. If it is incorporated in the main text, it is also included in the discussion/conclusion.

Requirements for admission:

Considering the nature of the course, this course should be taken as late as possible during the Bachelor’s programme of a student. 

Learning outcomes:

The student is able to:

• argue at an academic level;
• analyze information, formulate a hypothesis and design a research plan;
• carry out medical-biological techniques, analyze and process research data;
• clearly summarize research results;
• produce a written report in English;
• deal with the gained knowledge in a scientific context.

Teaching forms and contact time:

A computer module (RefWorks) will be offered to students who want to manage their references electronically. Supervision time is approximately 20%. During the practical phase this is 50% for two weeks; during the preparatory and writing phases the contact time will be less.

A few weeks before the start of the course, the student needs to find a supervisor and laboratory.

Week 1: Read necessary literature. Make a working plan, including agreements with your supervisor and a well-defined aim of your literature study;

Weeks 2-3: Practical phase. In consultation with your supervisor, this may be done at a later stage;

Weeks 4: Read and make a plan for the writing phase; write first draft;

Weeks 5-9: Writing phase;

Weeks 9: Supervisor reads and corrects draft;

Week 10: Completion and submission of final version assessed by supervisor and 2nd assessor.

Student and supervisor are allowed to decide on a different time schedule. The aim of the Research Project is that the assignment is executed correctly, rather than that the student writes a long article or reads many scientific articles.

Assessment:

The final product is assessed by both the supervisor and a second assessor appointed by the coordinator. The final grade consists of two sub-grades: 20% of the grade is determined by the practical work, which is assessed by the supervisor only, and 80% by the literature part, which is assessed by both. The final product must be submitted by the student via the Research Project Blackboard site for a check for plagiarism. Rubrics used in the assessment can be found on the above website.

Required material:

None.

Translated with www.DeepL.com/Translator (free version)

Please inform the International Office if you want to do a Research Project (Plus). They will be able to help you further.

The Research Project Plus is identical to the Research Project (BMW30105), except that:

• it entails approximately seven weeks of practical work instead of two;

Requirements for admission:

Considering the nature of the course, this course should be taken as late as possible during the Bachelor’s programme of a student. 

Learning outcomes:

The student is able to:

• argue at an academic level;
• analyze information, formulate a hypothesis and design a research plan;
• carry out medical-biological techniques, analyze and process research data;
• clearly summarize research results;
• produce a written report in English;
• deal with the gained knowledge in a scientific context.

Teaching forms and contact time:

A computer module (RefWorks) will be offered to students who want to manage their references electronically. Supervision time is approximately 20%. During the practical phase this is 50% for two weeks; during the preparatory and writing phases the contact time will be less.
A few weeks before the start of the course, the student needs to find a supervisor and laboratory.
Week 1: Read necessary literature. Make a working plan, including agreements with your supervisor and a well-defined aim of your literature study;
Weeks 2-3: Read and make a plan for the writing phase;
Weeks 4-8: Write first draft;
Weeks 6-8: Writing phase;

Weeks 9-16: Practical phase. In consultation with your supervisor, this may be done at a different stage. Total approximately 7 weeks;
Weeks 17-18: Finish draft version and send it to supervisor.
Week 19: Supervisor reads and corrects draft.
Week 20: Make final version; discuss final version with your supervisor.

Student and supervisor are allowed to decide a different time schedule. The aim of the Research Project is that the assignment is executed correctly, rather than that the student writes a long article or reads a huge amount of scientific articles.

Assessment:

The written report/thesis is assessed by the supervisor and by a 2nd assessor appointed by the coordinator. The final grade consists of two partial grades: 50% of the grade is determined by the practical work and 50% by the writing of an article. The final product must be submitted by the student via the Research Project Blackboard site in Ephorus for a check for plagiarism. Rubrics used in the assessment can be found on the above websites.

Required material:

None.

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Content:

We come into daily contact with potentially toxic substances, ranging from human drugs to environmental pollutants or toxic plants. The toxic effect of a substance is determined not only by the substance itself, but also by the characteristics of the exposed individual. Besides dosage and route of exposure, individual characteristics such as age, gender and nutritional status also play a role. Central to toxicology is the mechanism of action of a potentially toxic substance. Only when this is known can a realistic assessment be made of a possible risk following exposure to the substance, and this risk can be communicated to the general public. Media reports on potential human risks from toxic substances, such as PFAS contamination of soil, fipronil contamination of eggs or in the case of industrial air pollution such as at Tata Steel in IJmuiden, regularly feature reports in which the opinion of a toxicologist is sought.

Requirements for admission:

The student should have basic knowledge of pharmacology, cellular processes (including signal transduction and gene transcription) organs (liver, kidney) and (neuro-, immuno and endocrine) organ systems.

Learning outcomes:

Knowledge and insight

At the end of the course, the students is able to:

• use various principles from toxicology, such as mechanism of action and dose-effect relationships, and apply them in practice;
• describe and explain organ-specific toxic effects by applying pre-existing knowledge of molecular and cellular processes;
• recognise the most common human intoxications and understand them from a mechanistic point of view.

Skills

At the end of the course, the student is able to:

• make an initial risk estimate of a toxic substance using existing literature;
• identify and communicate scientific uncertainties regarding risk assessment to a wider audience;
• when faced with a dilemma, formulate arguments both for and against each of the various options, weigh them up and arrive at one's own viewpoint;
• formulate and present a project proposal based on theoretical knowledge and literature research;
• argue an experimental approach to a research question based on the 3R principles (reduction, refinement, replacement of laboratory animals);
• give honest and constructive feedback on (the work of) another person.

Teaching forms and contact time:

Using lectures and knowledge clips, the basic toxicological principles are explained and a number of toxicologically important organ systems and common classes of toxins are covered. The seminars focus on the application of toxicology to humans and the environment. A variety of topics will be covered through socially relevant case studies, where students will apply their biomedical knowledge to answer societal issues. In addition, during the course, students will work in groups of 3-4 students under the guidance of a lecturer to write a research proposal on a molecular-toxicological topic to deepen his/her knowledge.

Assessment:

Exam (60%): Assessment is by means of one written (closed book) examination with open questions, which must be assessed with at least a 5.5.
Working lecture case study (bonus): There is one tutorial with a case study that will be assessed individually and can earn a bonus of up to 0.5 points for the exam, but only if the exam is completed with a 5.5 or higher.
Research proposal (40%): The project proposal and related presentations will be assessed using rubrics. In addition, collaboration in the group assignment is assessed using an evaluation/reflection paper. The evaluation/reflection form is also used to determine the minimum effort requirement (80%) applicable to the group work.

Required material:

Book: Casarett & Doull's Essentials of Toxicology, 4th edition, edited by Klaassen and Watkins, ISBN 1260452298 OR Casarett and Doull's Toxicology, The Basic Science of Poisons, 8th edition, C.D. Klaassen, McGraw-Hill Education (ISBN 0071769234, available digitally via UU library);
Lecture handouts, knowledge clips, tutorial assignments and supplementary materials are available digitally via Blackboard (uu.blackboard.com);

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Content:

Heart- and coronary diseases are a major cause of death in Western society. The increase in diabetes and obesity will cause a further rise in cardiovascular diseases. This course deals with the pathogenesis and intervention of cardiovascular diseases. This course has a translational character, which means that the results from research will be translated into care for the patient. A lot of knowledge may never, or only in the late future, be of use for the patient. During the course, the subject matter will be dealt with in a way that triggers students to test knowledge for practical applications. The content will therefore not purely focus on cellular and molecular knowledge, but also on knowledge needed to put results of research into practice.

Blood clot formation because of arteriosclerosis is the pathological substrate of a coronary attack. It is of major importance to understand which plaques are the cause for blood clotting (unstable plaques). A lot of research is being conducted to investigate this, at molecular and cellular level, laboratory animals and humans. It is known that increased enzymatic degradation of collagen by proteases from inflammatory cells and the innate immune system plays an important role in destabilizing atherosclerotic plaques. After a coronary attack, the heart will undergo a lot of structural differences. Locally, inflammatory cells will try to remove necrotic tissue and collagen will be set down to close the wound. The contractile capacity of the heart will decrease because cardiomyocytes will have died. Insight in the molecular processes which are the basis of repair of the myocard is essential to develop new techniques for intervention. Several therapies are being developed to treat heart- and coronary diseases: mechanical (surgery), cellular (stem cells), and molecular (RNA interference). This course will discuss these therapeutic interventions and their molecular mechanisms.

Required knowledge:

Basic knowledge of physiology and immunology is required.

Learning outcomes:

Knowledge and insight

At the end of the course, the student is able to:

• describe the biological aspects of cardiovascular diseases, including therapeutic interventions;
• clarify the role of molecular and cellular processes in the development of vessel constriction and oxygen deprival of the organ;
• explain the development of cardiovascular diseases from preclinical and clinical disciplines;
• describe possible therapeutic interventions.

Skills

At the end of the course, the student is able to:

• formulate a research proposal to solve a scientific cardiovascular problem;
• analyse and present a scientific problem, together with other students in a team;
• critically assess research proposals and research methods for their use in science and marketing.

Attitudes

At the end of this course, the student is able to:

• show a critical and inquisitive attitude towards the developments in research to cardiovascular diseases.

Learning activities and contact time:

The course consists of lectures, e-tutorials, group meetings and private study. To understand the pathogenesis of a syndrome, the student will formulate a hypothesis form a clinical problem and make plan for research experiments. The practical part consists of demonstrations of experiments with laboratory animals, e.g. open-heart surgery and catheter interventions. Contact time is approximately 30%.

Assessment:

There will be an individual, written examination with open questions. The final grade is a combination of the grade obtained for the written examination (60%), discussion of an article (10%) and active participation during tutorials (30%). The tutorials will partly be web based.

Required material:

• Course manual

Content:

The main topic of this course is  “Plasticity”, and during this course neurochemical, neurophysiological, and molecular biological concepts and methods that play a role in the (patho)physiology of the nervous system will be addressed. The focus will be on the multidisciplinary character of neuroscience research, on designing and conducting experiments independently, and on gaining experimental skills in neurobiological and neuropharmalogical research.

Requirements for admission:

Students need to have completed for 15 ECTS in neurosciences courses (level 2). Basic knowledge of anatomy, physiology and pharmacology of the nervous system is required.

Learning outcomes:

At the end of this course, the student is able to:

• describe the main neurochemical, neurophysiological and molecular biological processes in the nervous system;
• explain the pathophysiological consequences of disturbances of these neurochemical, neurophysiological and molecular biological processes in relation to psychiatric and neurological syndromes such as epilepsy, schizophrenia, obesity/anorexia and Alzheimer's disease.
• devise and conduct a meaningful experiment to answer a question within the neuroscience field.

Teaching forms and contact time:

This course will consist of lectures (40 hours) and practical training sessions (120 hours), with a contact time of 60%. 

Assessment:

Assessment is based on the final examination (50% of the final grade) and the written and oral report of the practicals and assignments (50% of the final grade), whereby the practicals have been followed. For each partial mark, 4.0 must be obtained to complete the course with a pass mark. The final mark must be 5.5.

Required material:

• Recommended: Neuroscience, Purves et al., Oxford University Press, 2017. ISBN 97816053538413.

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Content:

This course is offered from the 'Circulatory Health' spearhead and the topics of this spearhead are the focus of this course. In the course, we focus specifically on current research developments in various cardiac diseases (including heart failure, cardiomyopathy and arrhythmias). The molecular basis, prevention, diagnosis and treatment of these diseases will be highlighted from the following perspectives:

• risk groups and factors;
• genetic basis;
• molecular & cellular biology;
• imaging techniques;
• clinical interventions and therapeutic innovations;
• prevention & health;
• regenerative medicine.

The first four weeks of the course consist of lectures on the topics described above. Interpreting the scientific literature covered in the lectures is tested in writing.
Besides knowledge of (the study of) cardiac pathophysiology, this course focuses on communicating scientific results, both in a presentation format and in written form.

Requirements for admission:

Basic knowledge of the construction and function of the heart, vessels, lungs and kidneys, and their physiological, physical, and chemical principles, is required.

Learning outcomes:

At the end of the course the student is able to:

• in the context of heart disease, understand and explain the latest research developments in terms of molecular basis, prevention, diagnosis and treatment.
• present a clear and good message to the public (both orally and in writing);
• read and interpret primary literature together with fellow students;
• present results from primary literature in an oral or written way (presentation and essay);
• comment on and assess fellow students' presentations and essays.

Teaching forms and contact time:

The course includes lectures, journal clubs, and workshops. In addition, students work independently on a pitch, a presentation and an essay. The course consists of approximately 25% contact time and 75% self-study.

Assessment:

The final grade is determined as follows: Test 20% - (group) presentation 30% - essay 50%. A minimum grade of 5.5 must be obtained for both the test and presentation and the essay in order to pass the course. Students also assess each other's presentation and essay (peer-review).

Required material:

Will be handed out during the course.

Translated with www.DeepL.com/Translator (free version)

Content:

The central nervous system (CNS) is probably the most complex structure in nature. It integrates and stores sensory information from our body and the world around us, determines the relevance of our environment, and lets us behave accordingly. We are only beginning to understand the biological systems that play a role in judging our environment, the intentions of others, our emotions and behavior. Usually, we are hardly aware of all these processes taking place, but whenever they become disrupted, severe suffering or dysfunction may result. Psychiatric and neurological disorders have serious consequences for the patient, the people around him or her, and for society.
 
The biomedical course 'Central nervous system disorders’ is built around neurological and psychiatric disorders. Each week a neurological or psychiatric disorder will be covered in detail. You will learn about the clinical presentation, the underlying biological systems and prominent research methods used for investigating the disorder. Studying the literature will provide you with the necessary background knowledge. Lectures will cover part of the theory and will illustrate certain clinical aspects of the disorders, when possible by patient demonstrations or video recordings, and highlight relevant biological systems. Prominent researchers will show their research into the specific disorder. In small groups you will focus on a specific neurological or psychiatric disorder. The aim is to write a topical review, using all available information from the literature, the presented research methods in other disorders, and your imagination. At the end of the course, topical reviews will be demonstrated to each other during a mini symposium with peers.

Requirements for admission:

Knowledge of functional neuroanatomy and neurotransmission, as acquired in the BMW course Neuroscience or a similar course.

Learning outcomes:

Knowledge & Insight

At the end of the course, the student is able to:

• is able to describe the clinical presentation of the CNS dysfunction;
• can explain how the CNS dysfunction affects the life of the patient;
• is capable of explaining the known underlying neurobiological systems;
• can summarize and explain published research and describe research methods used to investigate CNS dysfunction.

Skills

At the end of the course, the student is able to:

• discuss scientific articles about the discussed CNS dysfunction;
• write and present a topical review;
• provide feedback on another group's proposal/topical review.

Teaching forms and contact time:

This course will consist of independent study, seminars, tutorials and a practical assignment (topical review). Max 50% of the course will consist of contact time. 

Assessment:

The course grade is composed of the grade for the first test (30%), the grade for the second test (30%), the grade for the topical review (25%) and the grade for the PeerWise assignment (15%). To complete the course with satisfactory results, the student must obtain a final grade higher or equal to 5.5. A student must obtain at least a 5.0 for each partial grade.

Required material:

• Purves, D. et al.: Neuroscience, 5th or 6th edition, Sinnauer Associates Inc.;
• Additional literature can be downloaded via weblinks on BlackBoard.

Translated with www.DeepL.com/Translator (free version)

Content:

The failure or hyperactivity of the immune system leads to a kaleidoscope of disorders that are genetically set or induced by infections or cancer therapies.
During the first 4 weeks of the course, four important topics of clinical immunology will be adressed during lectures and tutorials:

• Immune deficiencies
• Transplantation of organs & bone marrow
• Tumor immunology / immunotherapy
• Autoimmune diseases + allergies

Furthermore, the programme will mainly consist of an in-depth project. Each group will write a research proposal on a certain subject. Another group will review this proposal in a formal way. A third group will study the proposal and the review and give an integrated presentation. Each group will gain experience in gaining primary data, commenting and presenting whilst working on three different subjects. Special attention will be given to the group process and giving feedback within the group.

Requirements for admission:

Students have to have succesfully completed equivalent courses of 15 ects covering basic immunology (level 2).
If students do not fulfill these requirements, the course coordinator can decide to assign additional study material.

Learning outcomes:

Knowledge & Insight

At the conclusion of this course, the student has the ability:

• to relate immunological principles, clinical consequences, therapies, & new developments of some disorders: Primary immune deficiëncies & AIDS, Allergies & Autoimmune diseases (AID), Transplantations & Tumor immunology
• to render examples and principles of new therapies in rheumatic disorders & animal models applied to rheumatological research
• to describe the role of T cell subsets in allergies and autoimmune diseases, to explain the mechanisms of (some types of) chronic inflammatory reactions, to coherently describe the relationship between tumor and immune system of the host.

Skills

At the conclusion of this course, the student must be able (at the level of a (fledgeling) scientist):

• to come up with a sound research question and write a scientific grant application about it including among other things, a state-of-the-art literature survey, study design, methods and timetable
• to review a scientific grant application & to write an according comment incl. suggestions for improvement.
• to present, at the level of a (fledgeling) scientist a coherent, clearly structured, critical survey of one or more scientific articles, which discusses strong and weak points, and pro’s and con’s, of a methodological approach and/or a presented concept.

Attitudes

At the conclusion of this course, the student must be able to exhibit:

• a critical and inquisitive attitude towards claims concerning animal models and immunopathogenic concepts.
• a respectful and cooperative attitude towards those with whom the student prepares presentations and conducts discussions.

Teaching forms and contact time:

This course consists of lectures, tutorials, including presentations by students, and a project with a symposium. There will be an average of 7 contact hours each week.
The successful outcome of the project depends on the active participation of all students. The students will be monitored for their active participation by the course coordinator.

Assessment:

Active participation in tutorials with presentations (10%); Midterm examination (20%); Assessment of the project by students and teachers (40%); Final examination (30%).
The student has to get an average grade of 5.5 for the midterm and final examination. Not until this requirement is fulfilled, the assessment of the project and the tutorials are taken into account.

Required material:

Kindt et al.: Kuby – Immunology, 7th edition 2013, ISBN: 1-4641-3784-6

Content:

This course addresses the normal development as well as disorders of development of the animal organism, and pays specific attention to the genetic, hormonal, and environmental variables that influence the proliferation and differentiation of cells.
Key words are: conception, cleavages, gastrulation, neurulation, formation of axes, Hox-genes, cell differentiation, sex determination and differentiation, reproduction, organogenesis, evolution and development, recombinant/knock-out/transgene animals, teratology.

Requirements for admission:

Basic knowledge of transcription, translation, cell-cell-interaction, signal transduction, cell cycle control, embryogenesis is required. If a student does not fulfill the requirements for admission, the course coordinator can impose additional study material, which has to be completed before the course starts.

Learning outcomes:

At the end of the course, the student is capable of:

• understanding embryonic development of the model systems used in developmental biology: mouse, zebrafish, Xenopus, Drosophila, and C. elegans;
• understanding how molecular and genetic information of DNA is translated into the developmental plan of an embryo, cell differentiation, formation of organs, growth of an embryo to a mature individual, and the relationship between developmental biology and evolution;
• explaining how disturbances of these processes can lead to a deregulation in cell growth or cell differentiation and to impairments of development;
• producing an essay based on three recent scientific papers on developmental biology.

Teaching forms and contact time:

Lectures (28 hours), discussions (7), practical trainings (22) and computer-assisted instruction (7). The course will have a contact time of about 40%.

Assessment:

There will be three examinations spread throughout the course. The final assessment will be the result of the three examinations (80%) and an essay (20%). All students, also those who have done the course earlier, are obliged to attend the first lecture, practicals, and computer-assisted instructions.

Required material:

• Wolpert L, Principles of Development. 4th ed., Current Biology/Oxford University Press, 2011; (± €60);
• Course manual (± €20);
• Surgical knives;
• Lab coat;
• Coloured pencils.

Lecturers

Dr. Cora Nijboer (NIDOD), Dr. Caroline de Theije (NIDOD), Dr. Jeroen Dudink (Neonatology), Dr. Marijke Achterberg (Veterinarian Medicine), Dr. Heidi Lesscher (Veterinarian Medicine), Dr. Agnes van den Hoogen (Clinical health sciences), Dr. Titia Lely (Gyneacology), Dr. Peter Nikkels (Pathology), Dr. Lotte van der Meeren (Pathology), Dr. Tanja Nijboer (Cognitive neuropsychology), Dr. Olaf Verschuren (Rehabilitation center de Hoogstraat), Dr. Helen Torrance (Fertility), Dr. Casper Schoemaker (Pediatric immunology)

Technical support

Karima Amarouchi, Rebecca Kleisen.

Content:

1. This course adheres to the general theme ‘the first 1001 days’ of Utrecht University and focusses on the diagnostics, treatment and biomedical research of the division ‘Woman & Baby’ of the University Medical Center Utrecht. During the course ‘Early Life Events: Diagnostics and Treatment’ students will be trained by lecturers from the departments of Fertility, Gynecology, Obstetrics, Neonatology and the Department for Translational Research. Students will be provided with a broad overview of the options that bio-medically trained experts have to work in these multidisciplinary research teams. The lecturers have a diverse background (medicine, biomedical sciences, psychology, pathology, biology and bioelectronics), which ensures that the students will gain insights from all relevant points of view.    

    

   The main topics of this course are the causes, consequences and (experimental) treatment options for children born pre-term or for a-term born children with pathology, which are known as ‘early life events’. This course particularly emphasizes the multidisciplinary character of diagnostics and pre-clinical research. In a series of lectures, active seminars and practicals the students will be provided with insights in the biomedical and clinical topics relevant to improve fertility, intra-uterine growth and neonatal care. The students will work in small groups as a research team and jointly gain knowledge on how translational experiments work. Upon completion of the course, the students will be able to answer the following questions: what are the most common causes of extreme prematurity? What translational models are relevant for improving fertility, gynecology, obstetrics and neonatology? What diagnostic tools are used to monitor the children? What technological advancements are currently implemented in the clinic? What are the sensorimotor and cognitive consequences of extreme prematurity and fetal growth restriction for children later in life? What biological processes provide options to improve the rehabilitation process?

   This course contains introductory lectures by biomedical investigators and physicians providing a (limited) review of background knowledge to support the students in gaining expert knowledge from reviewing case reports. Additionally the students will be given the opportunity for guided tours at the neonatal intensive care unit of the Wilhelmina Children’s Hospital and the rehabilitation center ‘De Hoogstraat’. In a series of pro-active seminars the students will learn which aspects of pathology and radiology diagnostics are currently being developed using biomedical research. The students will also be trained in what aspects of rodent behavior are relevant for therapeutic innovations and how computer simulations can be used to support rehabilitation processes.

   A substantial part (5 weeks) of this course is reserved for a practical, for which the students will operate in teams of maximum 6 and set up a neuronal cell culture, induce the differentiation of these cells and evaluate the viability and specificity of the cells using immunofluorescent stainings and microscopy. This practical will provide in depth knowledge on how biomedical research develops stem cell treatment to improve cures for the children with perinatal asphyxia and brain damage. During the practical the students will be requested to generate a novel research protocol, a lab journal and a written report (journal paper style). Finally the group should also present their findings.

Requirements for admission:

Previous knowledge of anatomy, physiology and cell biology is required, as provided by the Biomedical Sciences courses ‘Developmental Biology’ (period 1 BC or period 4 AD) and/or ‘Neuroscience’ (period 3 BC).  

Learning outcomes:

Knowledge and insight:

After completion of this course, the student is able to:

• explain what the most common causes are of ‘early life events’;
• determine what complications are likely to occur prior to and during premature birth;
• list which biological processes are monitored at neonatal intensive care units;
• argue what the most common consequences of birth defects are and how they are caused;
• describe the essential components of translational experiments that are used to evaluate the role of social play in the rehabilitation process after ‘early life events’;
• provide an overview of experimental treatment options for children born with brain damage;
• explain how patient participation is optimally utilized to guide future biomedical research on early life events.

Skills:

The student is able to:

• design a histological staining experiment to analyze placenta pathology;
• develop a protocol for neuronal cell culture;
• culture, stain and image neuronal stem cells and name which type of neuron has been cultured;
• systematically analyze and report about the resulting data in a group.

Teaching forms and contact time:

Prior to the lectures the students are expected to gain background knowledge from reading scientific literature and text book chapters. In class, the lectures and discussions will deal with case reports to further develop the understanding of the underlying biomedical processes. The students are expected to actively participate in seminars and provide ideas for novel research lines and experiments. To support a successful neural stem cell experiment, the students will be provided with a limited introductory session to working with biomaterial in flow cabinets and general lab rules.

This course will be in Dutch, unless an exchange student is enrolled. In this case the course will be taught in English. The total contact time is approximately 50%.

Assessment:

The students will be assessed based on their individual performance (written exam) and on their participation and performance when working in a group (oral presentation and written report stem cell culture experiment). To provide the students with individual feedback on their work in a group anonymous evaluation forms will be used. The final grade is weighted from the written exam (40%) in which knowledge and insight are tested (partially using case report questions), the level of participation and quality of the presentation (15%), the quality of the novel research protocol generated by the group (15%), the group presentation (15%) and the individually written report (journal paper style) of the neuronal cell culture experiment (15%). 

Required material:

A reader will be provided containing the course material.

Content:

The student will learn the concepts of kinetics (what the body does to the drug) and the dynamics (what the drug does to the body) of pharmacology. In addition, the student will learn the basic principles of the neuro/psychopharmacology.
The course encompasses the following topics:

1. the basic principles of pharmacokinetics: pharmacology, transport of drugs over biological membranes, ways of administration, resorption, distribution, and elimination of drugs, pharmacokinetics (concentration-time relations), and variability in the reactions to drugs;
2. the basic principles of pharmacodynamics: signal-transduction, receptor-ligand (pharmacon) interactions, quantitative aspects of pharmacon-receptor interactions, dose-response curves, agonists, antagonists;
3. the basic principles of neuropharmacology: the effect of drugs on the peripheral and central nervous system, neurotransmitters in the peripheral and central nervous system.

Requirements for admission:

Knowledge of mathematics is required at the level of pre-university education (V.W.O.). Basic knowledge of anatomy, cell biology, physiology and biochemistry, in particular knowledge of receptors and signal transduction mechanisms, is essential.

Learning outcomes:

At the end of this course, the student is able to:

• describe the absorption, distribution, metabolism and elimination (ADME) of drugs;
• translate the ADME processes in a mathematical way to plasma concentrations of the pharmacon;
• describe the relation between the concentration and the effects of a pharmacon in a qualitative and quantitative manner;
• describe the properties of agonists, antagonists, partial agonists and inverse agonists in a qualitative and quantitative manner;
• describe and explain the functioning of the autonomous nerve system and the effects of drugs on the autonomous nerve system;
• understand the role of the central neurotransmitter systems with normal physiological function and behaviour;
• understand the working mechanisms and co-effects of relevant neuro- and psychopharmaca for several psychological and neurological diseases.

Teaching forms and contact time:

The student will need to create a mental view on complex pharmacokinetic and pharmacodynamic principles and their mathematical foundations.
Tutorials, lectures, computer simulations and practical trainings will be used frequently. The course will have a maximum of 30% contact time.

Assessment:

The knowledge of pharmacology and the basic principles of neuro- and psychopharmacology will be assessed individually by interim examinations.

Required material:

Rang, Dale, Ritter & Moore - Pharmacology; (7th edition, 2012).

Content:

This course deals with the integrative regulation of processes by hormones, in particular the regulation of energy, growth, stress, and reproduction. This course builds on the course “Organ systems” and is a good preparation for the course “Metabolism”. These three courses together cover the endocrine and metabolic processes and their regulation. Basic principles will be discussed first, such as homeostasis, hormonal axes, feedback mechanisms, biochemical structure of hormones, and structure and function of their receptors. Then the functional anatomy and histology of the endocrine organs are discussed, followed by the discussion of hormones that play a role in metabolism (including gut hormones and adipocytokines) and during growth, stress and reproduction. During this course, specific attention will be given to academic skills such as analysing a scientific research paper and writing a scientific paper.

Requirements for admission:

This course is open for students in Biomedical Sciences or Biology who have knowledge of molecular biology, cell biology and the structure and function of DNA, RNA and proteins. Students from other programs need to demonstrate that they meet the requirements for admission in an individual interview.

Learning outcomes:

Knowledge & Insight

At the end of this course, the student is able to:

• understand and demonstrate the concept of hormonal regulation of processes on the level of the organism;
• recognize (by anatomy and histology) the organs that are involved in the production of hormones and describe their function and their reaction to several stimuli;
• describe the endocrine regulation of physiological processes of the organism on a conceptual and molecular level;
• understand and describe the integrative regulation of homeostasis of energy, growth, reproduction and stress;
• understand how selected diseases connect with abnormalities in the development and endocrine regulation of the organism.

Skills

At the end of this course, the student is able to:

• generate and interpret endocrinological data (perform ELISA for growth hormone);
• write a report following the format of a scientific paper, using data obtained experimentally;
• critically read, analyse and discuss a scientific article.

Teaching forms and contact time:

• (Interactive) lectures, assignments for private study, tutorials, computer-assisted instruction, microscopy training, practical lab training, critical reading and interpreting;
• An assignment to write a report on the practical training.

The course will have approximately 40% contact time.

Assessment:

• Two exams (multiple choice and open questions): 40% each;
• Scientific report of practical work: 20%.

Required material:

• Human Physiology, an Integrated Approach, by D.U. Silverthorn et al. (8th edition);
• Review articles on selected subjects;
• Selected research papers.

Content:

This course treats how genetic factors that influence human traits are identified. The traits we are focusing on will be human diseases, but the techniques can be applied to a wide field of subjects. We will teach the background knowledge necessary to understand and apply the different methods, the molecular laboratory techniques (theoretically) and the approaches to finding causal variants for human heritable diseases. Also, we will practice with using the vast number of databases containing human genetic information. The subjects can roughly be divided into two main groups:

Organisation and evolution of genomes and genes

General organisation of the genome of higher eukaryotes

• Comparative genomics and genome annotation. Special attention for gene structure, gene duplication, molecular phylogeny, genome analysis, species comparisons and useful software and databases.
• Functional genomics, including functional annotation of genes, gene expression, proteomics.
• We pay attention to how knowledge is obtained, and how information can be extracted from existing sources.

Identification of mutations that influence human diseases

• Linkage analysis in families with a monogenic disease to localise the causal variant up to a region of ca 15 cM/
• Laboratory aspects of DNA research: the techniques, their interpretation and the causes of artefacts
• Positional cloning/Prioritising genes within a defined region. Mutation analysis; the role of new technology.
• Molecular pathology: how mutations change phenotypes, and how to prove it.

Requirements for admission:

We require the students to have knowledge of the structure and organisation of DNA; the processes of meiosis and mitosis, including recombination; transcription and translation; gene expression. In addition we ask for some basic knowledge of laboratory techniques such as PCR, restriction enzymes and DNA-hybridisation. In case of deficiencies, contact the coordinator for background reading to be done before the start of the course.

Learning outcomes:

Knowledge & Insight

After completing this course, the student will be able to:

• Reproduce the organisation of the human genome in approximate numbers;
• Explain how genome projects have contributed to our current knowledge of the influence of genes on traits;
• Describe the steps with which genomes are characterized;
• Describe approaches that help us understand the function of genes;
• Understand the value and drawbacks of species comparisons in genetic studies;
• Explain the principles of linkage analysis, and use this method for simple cases;
• Choose appropriate molecular techniques for different purposes;
• Interpret the link between mutation and disease.

Skills

After completing this course, the student will be able to:

• Use genome data, gene data and functional data from existing sources to interpret new data in the process of identifying a mutation that might be causing a disease;
• Apply comparative genomics with the appropriate software;
• Apply and understand the law of Hardy-Weinberg.

Academic skills

• Read academic articles with a critical mind.
• Combine information from different sources.
• Write a report according to academic standards.
• Orally present your work, and formulate questions about other people’s oral presentations.
• Collaborate in such a way that the best possible group effort is achieved.

Teaching forms and contact time:

Knowledge and skills are mainly taught in three different forms: in lectures, during exercises and in the textbook. These three forms overlap only partially: information is often only presented in one form. During the first eight weeks, each week a new topic is introduced by a specialised teacher. In the fifth week, students start working in groups on an essay, which will be handed in on paper, as well presented orally. During the last two weeks, the students can devote all their time to this essay. The work on this essay will help processing and integrating the material presented during the course. It will also serve to practice academic skills.
On average, about six hours of contact time per week.

Assessment:

The final grade is composed of the results of two tests, a database assignment, the essay and the oral presentation of the essay. Passing the course requires: 5,5 as final grade, but also 5,5 as weighted average of the two tests.

Required material:

• Textbook: Human Molecular Genetics, T. Strachan and A. P. Read 4th edition, Garland Science, 2010, ISBN 0815341490;
• Access to Blackboard

Content:

During this course, the student will get acquainted with the latest developments in the (diagnostic) molecular pathology (both in theory and in practice) and will gain insight in the molecular biological concepts of diseases. Specific themes will be used to describe the entire process from obtaining tissues until diagnosis. Histological and immunohistochemical techniques will be discussed, but the focus will be on molecular pathological approaches/techniques ((next generation) sequence analysis, proteomics, laser microdissection, tissue-arrays, etc.). The execution of these techniques by the students will be an important aspect of this course, as well as writing a scientific report. The course will start with a general introduction in the molecular pathology and accompanying genetic aspects, followed by specific themes on (1) Cardiovascular and transplantation pathology; (2) Laboratory animal models in molecular pathology; (3) Genetic and (4) Epigenetic aspects of tumor genesis.

Requirements for admission:

Students are recommended to have basic knowledge of cell biology, immunology, molecular biology and pathology.

Learning outcomes:

Knowledge & Insight

At the conclusion of this course, the student is able to:

• describe the most important principles of molecular pathology;
• describe the role of molecular pathology in modern (tumor) diagnostics (personalized medicine);
• recognize and justify the use of experimental models for molecular pathological analysis.

Skills

The students is able to:

• choose the correct approach for the molecular analysis of specific diseases from a range of molecular biological techniques, and conduct these experiments independently;
• describe the experimental results in a scientific paper.

Attitudes

At the conclusion of this course, the student must be conscious of the ethical aspects and problems that are connected to the generation of molecular pathological data and the possible (prognostic) consequences for the patient.

Teaching forms and contact time:

There will be 6 introductory lectures, 2 practical trainings including demonstrations (3-4 hours), and a seminar (2 hours) every two weeks. During the seminars, the students will present a number of diseases by discussing a case or an article, during which the experimental approach for the molecular pathological analysis will be most important.
Total contact time is approximately 35-40%.

Assessment:

The presentations during the seminars and the participation during the discussion will be assessed by the group leaders. The reports of several practical trainings/demonstrations will also be assessed (20%). The results of two practical trainings must be described in a scientific article, which is an important part of the course (40%). There will be a final assessment (theoretical exam, 40%) which consists of 15 multiple choice questions and 6 essay questions of which 5 need to be answered.
The student has to get a grade of at least 5.0 for each of the assessments.

Required material:

There is no book required. Most of the background literature will be handed out during the course, but recommended is: In Dutch: Moleculaire Diagnostiek (2nd edition), edited by E. van Pelt-Verkuil en W.B. van Leeuwen (ISBN 978-90-77423-95-0). In English: Diagnostic Molecular Pathology in Practice, edited by I. Schrijver (ISBN 978-3-642-19676-8)
Recommended reference book for basic knowledge in pathology:
Robbins and Cotran "Pathologic Basis of Disease" by Kumar, Abbas and Fausto, 7th edition (ISBN: 0-7216-0187.1)

Content:

Topics covered by oral teaching by experts in the research field:

• Regulation of oogenesis & follicogenesis and processes involved in follicle development;
• The female hormonal cycle, regulation of ovulation, pathologies in the female cycle and intervention possibilities for the human species.
• The process of spermatogenesis, the functional concept of sperm cell, the importance of sperm maturation, transport, and activation (capacitation) for the fertilization;
• Recognition and mating behavior at estrus of animals;
• The physiology of copulation;
• Artificial Reproductive Techniques (ART);
• The development of zygote to blastocyst;
• Maternal recognition of the conception;
• Regulation of birth;
• Embryo and primary stem cells;
• Cloning and preparation of embryonal stem cells and the application of these techniques for production of organs and organisms;
• Reproductive ageing and degeneration of gonocytes;
• Ethical considerations in ART
• FISH and prenatal diagnosis of chromosomal aberrations;
• Principles of advanced detection techniques (flow cytometry, confocal microscopy) for detection of processes in living gametes and embryo’s (live imaging).

Requirements for admission:

The Biomedical Sciences curriculum or equivalent level.

Learning outcomes:

Knowledge & Insight

At the end of this course, the student is able to:

• Describe processes that are involved in the generation of gametes;
• Name the way how fertilization takes place in mammals;
• Explain which ART are used in a modern IVF clinic to enhance the fertilization rate in in/sub-ferile couples;
• Describe the early embryogenesis and nestling of the embryo in the endometrium and how this results in off-spring;
• Explain how and why embryo materials can be used for genetic cloning;
• Work with, and describe analytical methods to study the process of fertilization;
• Describe the evolutionary diversity in reproductive strategies in the animal kingdom with special attention to mammals;
• Explain the evolutionary profit of sexual reproduction.

Technical skills

At the end of this course, the student is able to:

• Use the techniques FISH, ART, Live imaging in this type of research.

Teaching forms and contact time:

The education will be given in the form of oral communications given by docents (30 hrs) interactive communications between students and docents (25 hrs) and practicum (8 half day sessions) Total contact time is approx. 87 hours (45%).

Assessment:

• Presentation of a specific research topic (both oral and with a written thesis) (40%);
• Written examination (60%).

The course is successfully finished when the final grade is > 5.50.

Required material:

• MH Johnson & BJ Everitt, Essential Reproduction (6th edition), Blackwell Science, Oxford, UK (2007); ca. € 50;
• Reader and hand outs will be provided during the course (free of charge).

Please inform the International Office if you want to do a Research Project (Plus). They will be able to help you further.

Content:

1. The final product is an essay written in English, possibly in the form of a scientific article, with a theoretical introduction that reflects the current literature in the relevant field.
2. Going through a research cycle: reviewing literature, formulating a hypothesis, designing and conducting an experiment, analysing the results, drawing conclusions and writing down the result.

The report or final product is written in English and must contain a literature review of approximately a minimum of 10,000 and a maximum of 16,000 words (excluding the bibliography), using a minimum of 25 primary articles. The literature overview can be seen as a thesis, review or bachelor's thesis, names used in past years. In addition to the literature review, the final product includes coverage of practical work.
The usual form of the final product is in the form of a scientific article, which has been adapted for the purpose of this course: an introduction, introducing the subject of the literature review and stating its importance, then the literature review (including a conclusion/discussion of the findings), contextualising the research done.
The "practical" research conducted and analysed is sometimes incorporated as a separate chapter, sometimes integrated into the literature section and sometimes as an appendix. If it is incorporated in the main text, it is also included in the discussion/conclusion.

Requirements for admission:

Considering the nature of the course, this course should be taken as late as possible during the Bachelor’s programme of a student. 

Learning outcomes:

The student is able to:

• argue at an academic level;
• analyze information, formulate a hypothesis and design a research plan;
• carry out medical-biological techniques, analyze and process research data;
• clearly summarize research results;
• produce a written report in English;
• deal with the gained knowledge in a scientific context.

Teaching forms and contact time:

A computer module (RefWorks) will be offered to students who want to manage their references electronically. Supervision time is approximately 20%. During the practical phase this is 50% for two weeks; during the preparatory and writing phases the contact time will be less.

A few weeks before the start of the course, the student needs to find a supervisor and laboratory.

Week 1: Read necessary literature. Make a working plan, including agreements with your supervisor and a well-defined aim of your literature study;

Weeks 2-3: Practical phase. In consultation with your supervisor, this may be done at a later stage;

Weeks 4: Read and make a plan for the writing phase; write first draft;

Weeks 5-9: Writing phase;

Weeks 9: Supervisor reads and corrects draft;

Week 10: Completion and submission of final version assessed by supervisor and 2nd assessor.

Student and supervisor are allowed to decide on a different time schedule. The aim of the Research Project is that the assignment is executed correctly, rather than that the student writes a long article or reads many scientific articles.

Assessment:

The final product is assessed by both the supervisor and a second assessor appointed by the coordinator. The final grade consists of two sub-grades: 20% of the grade is determined by the practical work, which is assessed by the supervisor only, and 80% by the literature part, which is assessed by both. The final product must be submitted by the student via the Research Project Blackboard site for a check for plagiarism. Rubrics used in the assessment can be found on the above website.

Required material:

None.

Translated with www.DeepL.com/Translator (free version)

Please inform the International Office if you want to do a Research Project (Plus). They will be able to help you further.

The Research Project Plus is identical to the Research Project (BMW30105), except that:

• it entails approximately seven weeks of practical work instead of two;

Requirements for admission:

Considering the nature of the course, this course should be taken as late as possible during the Bachelor’s programme of a student. 

Learning outcomes:

The student is able to:

• argue at an academic level;
• analyze information, formulate a hypothesis and design a research plan;
• carry out medical-biological techniques, analyze and process research data;
• clearly summarize research results;
• produce a written report in English;
• deal with the gained knowledge in a scientific context.

Teaching forms and contact time:

A computer module (RefWorks) will be offered to students who want to manage their references electronically. Supervision time is approximately 20%. During the practical phase this is 50% for two weeks; during the preparatory and writing phases the contact time will be less.
A few weeks before the start of the course, the student needs to find a supervisor and laboratory.
Week 1: Read necessary literature. Make a working plan, including agreements with your supervisor and a well-defined aim of your literature study;
Weeks 2-3: Read and make a plan for the writing phase;
Weeks 4-8: Write first draft;
Weeks 6-8: Writing phase;

Weeks 9-16: Practical phase. In consultation with your supervisor, this may be done at a different stage. Total approximately 7 weeks;
Weeks 17-18: Finish draft version and send it to supervisor.
Week 19: Supervisor reads and corrects draft.
Week 20: Make final version; discuss final version with your supervisor.

Student and supervisor are allowed to decide a different time schedule. The aim of the Research Project is that the assignment is executed correctly, rather than that the student writes a long article or reads a huge amount of scientific articles.

Assessment:

The written report/thesis is assessed by the supervisor and by a 2nd assessor appointed by the coordinator. The final grade consists of two partial grades: 50% of the grade is determined by the practical work and 50% by the writing of an article. The final product must be submitted by the student via the Research Project Blackboard site in Ephorus for a check for plagiarism. Rubrics used in the assessment can be found on the above websites.

Required material:

None.

Translated with www.DeepL.com/Translator (free version)

It is a required that all participants have a Hepatitis B vaccination due to practical work with blood!

Content:

This course will elaborate the mechanisms responsible to prevent bleeding after injury (haemostasis) and the role of these mechanisms in the etiology of arterial and venous thrombosis. The biology of coagulation and the interaction between the vascular wall and circulating blood (cells) will be explained. Haemostasis is an essential process in the prevention of blood loss, but on the other hand, hyperactivity of the haemostatic system will increase the risk of thrombotic events. Haemostasis consists of multiple components, including platelets and plasma proteins that together make the coagulation cascade. Furthermore, endothelial cells covering the vascular wall surface release inhibitors that prevent platelet aggregation, express proteins that inhibit the coagulation system and synthesize components that stimulate the degradation of a fibrin clot. A well balanced haemostasis is essential for normal life. Inherited or acquired deficiencies may lead to an increased risk of bleeding or on the other hand to an increased risk of arterial and venous thrombosis.
In addition to basal biochemical sessions, the course will also contain special sessions on treatment, such as oral anticoagulants and thrombosis, state of the art developments and actual business such as the risk of thrombosis during air travel, thrombosis prevention with healthy nutrition and epidemiology of thrombosis for thrombosis prediction. The students will train their knowledge of thrombosis and haemostasis in workshops and students will get the opportunity to perform state of the art experiments in thrombosis and haemostasis research.

Requirements for admission:

Basic knowledge of cell biology and biochemistry.

Learning outcomes:

Knowledge & Insight

At the end of the course, the student will be able to:

• describe the mechanism of haemostasis, including the activation of blood platelets and blood coagulation;
• understand the disorders that lead to increased risk of bleeding or thrombosis and formulate advices for medication and therapy.

Skills

At the end of the course the student will be able to:

• plan and execute scientific experiments and give adequate interpretation of the results in a presentation;
• review the literature about an actual theme in the thrombosis and haemostasis research field and to report it;
• analyse and discuss a scientific report.

Teaching forms and contact time:

The course will consist of lectures (21 hours), practical training (24 hours), tutorials (30 hours) and an exam (2 hours). The practical training consists of experiments that will be executed under supervision of a PhD student or a technician. Novel scientific developments in the thrombosis and haemostasis will be discussed, summarized and reported in the workshops.

Assessment:

The final test is an individual written exam with "open end" and "multiple choice" questions. The final grade will be based on the assessment during practical training (20%), tutorials (20%) and the test (60%).

Required material:

"Handboek Hematologie", dr. B. Lowenberg, dr. G.J. Ossenkoppele, dr. T. de Witte, dr. M.A. Boogaerts, De Tijdstroom uitgeverij, 2008, Utrecht (in Dutch!).

Content:

If we take a critical look at science, many biases are present in research settings. Consequently, we have less knowledge about disease progression in women or pharmacokinetics in different ethnic populations. Also, biomedical researchers might not be aware of the biomedical mechanisms underlying unconscious biases that influence their (research) choices. Being aware of implicit biases in science is therefore important as biomedical innovations affect healthcare.

The first half of the course will focus on biomedical knowledge linked to bias. Students will learn which neurobiological mechanisms are behind implicit bias and what the effect is of these biases on research choices. The difference between the terms sex and gender will be discussed and students will be taught about sex-differences in different diseases such as cardiovascular disease as well as sex- and ethnicity-differences in pharmacology. We will discuss the ethical implications of culture-sensitive subjects and students will learn to present sex- and ethnicity-related data in a sensitive manner.

In the second half of the course, students will learn to recognize biased research and will be trained to design research in which bias is minimized. Throughout the course, students will receive interactive workshops to learn different skills needed in research. Finally, students will perform a project in which they will be challenged to generate innovative strategies for raising awareness about biased science and promote better scientific research.

Knowledge requirements:

Basic knowledge of molecular cell biology and genetics, as well as basic physiology and basic mechanisms in immunology are required (Biomedical Sciences bachelor’s program year 1) as well as the contents of the course Organ Systems as offered in the Biomedical Sciences bachelor’s program.

Learning outcomes:

Knowledge and insight:

At the end of the course the student will be able to:

• explain the molecular, metabolic and physiological differences between men and women in heart disease;
• explain why different groups react differently to pharmacotherapy on a molecular and cellular level;
• clarify why there are metabolic differences between different groups based on their genetic differences;
• explain the neurobiological basis of implicit bias;
• use the proper nomenclature related to gender and sex differences.

Skills:

At the end of the course the student will be able to:

• critically evaluate experimental designs in literature for the possible presence of bias;
• write a research proposal where bias is minimalized;
• communicate effectively with different cultural groups;
• present culture-, sex- and gender-sensitive subjects in a sensitive manner;
• raise awareness of bias and promote diversity in science.

Attitude:

• At the end of the course the student will be able to:
• critically reflect on their own choices in doing research whilst accounting for possible bias;
• reflect on ethical implications of physiological and genetic differences in target groups in scientific research.

Teaching forms and contact hours:

Lectures, interactive workshops, working groups, group discussions and independent study. The contact time for the course is 70%. This includes time to work on assignments and the project.

Assessment:

Assessment will be based on the literature review (30%), project product (30%), the written exam (30%) and active participation (10%).

Students must attain a ³ 5.0 on all assessment components and a ³ 5.5 final grade to pass the course.

Required materials:

Required literature will be provided at the start of and during the course.

Prerequisite knowledge:

Basic knowledge of molecular cell biology and genetics, as well as basic physiology and basic mechanisms in immunology are required (Biomedical Sciences bachelor’s program year 1) as well as the contents of the course Organ Systems as offered in the Biomedical Sciences bachelor’s program.