SNEU20002U Experimental design in Neuroscience

Volume 2020/2021
Education

MSc in Neuroscience - compulsory

Not open for credit transfer students or other external students

Content

The course will provide the students with knowledge and understanding of the principles of experimental designs in neuroscience. The students will work with science theory and scientific practice, including experimental design and will be exposed to both theories and data. Students will gain knowledge on how to design research projects and individual experiments with particular focus on translational and clinical neuroscience. The students will conduct data analysis, including statistics and bioinformatics, which will provide the students with skills in analysing, interpreting and critically evaluating scientific results. The students will become familiar with the theory and practice behind important techniques in clinical neuroscience such as imaging (PET, MR), genetics and epidemiology.

The course consists of modules in experimental design, neuroimaging, neurogenetics, bioinformatics and epidemiology. The course will provide the students with translational skills to compare datasets from animal research, human studies and clinical neuroscience. The students will have the opportunity to understand advanced diagnostic methods from the individual level to large biological databases.

There will be lectures, on-line lectures, journal clubs and workshops involving data analysis and statistics. Considerable emphasis will be given to recent advances in the different fields. The students are expected to read, present and discuss original research articles representing different subdisciplines in neuroscience and their methodologies. 

Learning Outcome

After completing the course the student is expected to be able to:

Knowledge

  • Discuss and critically evaluate scientific methods applied within experimental neuroscience
  • Explain the principles, research and clinical applications of magnetic resonance imaging (MRI) and functional MRI
  • Explain the principles, research and clinical applications of positron emission tomography (PET)
  • Evaluate the utility of PET for drug development
  • Discuss the principles of neurogenetics including DNA variation, genotype, haplotype, allele frequencies, Linkage Disequlibrium and heritability.
  • Discuss the basics of genetic mapping including both common and rare variants
  • Principles and methods for downstream analyses of genetic datasets
  • Allen Brain Atlas and other relevant online resources for data analysis in neuroscience
  • Single-cell RNA sequencing data processing and visualization

 

Skills

  • Design and evaluate research studies in the following disciplines: studies using live animals, neuroimaging, neurogenetics, epidemiology
  • Describe and explain the fundamental principles of magnetic resonance imaging including functional MRI
  • Describe and explain the fundamental principles of positron emission transmission imaging
  • Name and describe in general terms what can be measured with PET and MR
  • Describe research and clinical applications of neuroimaging techniques
  • Describe and explain the fundamental principles of neurogenetics
  • Describe principles of genetic mapping and downstream analysis of genetic datasets
  • Perform basic data processing and data visualization in R
  • Describe and explain principles of processing nervous system single cell RNA sequencing data

 

Laboratory Animal Science - Function B

 

Knowledge

  • Describe the concepts of fidelity and discrimination, randomization, blinding and bias and how this is handled in animal studies
  • Recognize causes of biological variability, and and how consistency between animal studies is ensured
  • Identify the experimental unit and recognize issues of non-independence in animal studies.
  • Explain the terms significance and power and identify variables affecting these in animal studies.
  • Describe the principles of a good scientific strategy in animal studies necessary to achieve robust results, including
    • definition of hypotheses
    • determination of the sample size
    • different types of experimental designs
    • experimental measures
    • analysis of results
    • the need for pilot studies
    • the need and methods for proper literature review before the study
    • tools to support proper planning of animal studies, such as PREPARE guidelines and be able to provide examples of the consequences of failing to implement a sound scientific strategy.


Skills

  • Use appropriate statistical methods for the evaluation of an animal study, and explain how and when to access expert help in the design of an animal study and the interpretation of experimental results
  • Explain the importance of rigorous scientific technique in animal studies and the requirements of assured quality standards, such as Good Laboratory Practice (GLP).
  • Explain the importance of dissemination of the study results irrespective of the outcome and describe the key issues to be reported when using live animals in research, such as ARRIVE guidelines 

 

Competencies

  • Design and evaluate experiments using live animals (EU Function B)
  • Design and evaluate experiments in the subdisciplines neuroimaging, neurogenetics, epidemiology
  • Independently and critically assess literature covering neuroimaging, neurogenetics and epidemiology.
  • Independently interpret neuroscientific data and literature
  • Communicate and discuss neuroscientific knowledge and theories
  • After supplementary examination in practical skills relating to EU Function A and D achieve a personal license to independently plan, implement and take responsibility for the design and performance of animal experimentation within the European Union according to the EU Directive 2010/63/EU Article 23.2 and the Danish executive order 12 of 07/01/2016, §56.

See Absalon.

Cell biology incl. gene transcription and translation.
There will be lectures, on-line lectures, journal clubs, and workshops involving data analysis and statistics.
  • Category
  • Hours
  • Lectures
  • 29
  • Class Instruction
  • 15
  • Preparation
  • 194
  • Exercises
  • 31
  • E-Learning
  • 3
  • Excursions
  • 3
  • Exam
  • 3
  • Total
  • 278
Collective
Continuous feedback during the course of the semester
Peer feedback (Students give each other feedback)
Credit
2,5 ECTS
Type of assessment
Written examination, 1 hour under invigilation
Short essay questions (half to one page), Multiple Choice and Short Questions.
Exam registration requirements

None

Aid
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
Internal examiners
Criteria for exam assesment

To achieve the grade Passed, the student must adequately be able to:

The candidate must be able to fulfill all learning outcomes as described in the European Union guidelines for training animal researchers for Function B which implies being able to:

Knowledge

  • Describe the concepts of fidelity and discrimination, randomization, blinding and bias and how this is handled in animal studies
  • Recognize causes of biological variability, and and how consistency between animal studies is ensured
  • Identify the experimental unit and recognize issues of non-independence in animal studies.
  • Explain the terms significance and power and identify variables affecting these in animal studies.
  • Describe the principles of a good scientific strategy in animal studies necessary to achieve robust results, including
    • definition of hypotheses
    • determination of the sample size
    • different types of experimental designs
    • experimental measures
    • analysis of results
    • the need for pilot studies
    • the need and methods for proper literature review before the study
    • tools to support proper planning of animal studies, such as PREPARE guidelines and be able to provide examples of the consequences of failing to implement a sound scientific strategy.

 

Skills

  • Use appropriate statistical methods for the evaluation of an animal study, and explain how and when to access expert help in the design of an animal study and the interpretation of experimental results.
  • Explain the importance of rigorous scientific technique in animal studies and the requirements of assured quality standards, such as Good Laboratory Practice (GLP).
  • Explain the importance of dissemination of the study results irrespective of the outcome and describe the key issues to be reported when using live animals in research, such as ARRIVE guidelines.
Credit
7,5 ECTS
Type of assessment
Written examination, 2 hours under invigilation
Essay questions and short true/false questions.
Aid
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Internal examiners
Criteria for exam assesment

To achieve the maximum grade of 12, the student must be able to:

Knowledge

  • Explain scientific methods applied within experimental neuroscience
  • Eplain the basic principles on how to use animals for research
  • Explain principles, research and clinical applications of magnetic resonance imaging (MRI) and functional MRI
  • Explain principles, research and clinical applications of positron emission tomography (PET)
  • Discuss the utility of PET for drug development 
  • Discuss the principles of neurogenetics including DNA variation, genotype, haplotype, allele frequencies, Linkage Disequlibrium and heritability
  • Identify the basics of genetic mapping including both common and rare variants
  • Discuss principles and methods for downstream analyses of genetic datasets
  • Summarize Allen Brain Atlas and other relevant online resources for data analysis in neuroscience
  • Identify single-cell RNA sequencing data processing and visualization
  • Name and describe in general terms what can be measured with PET and MR
  • Describe and explain the fundamental principles of magnetic resonance imaging including functional MRI
  • Describe and explain the fundamental principles of positron emission transmission imaging

 

Skills

  • Critically evaluate scientific methods applied within experimental neuroscience
  • Discuss and evaluate the basic principles on how to use animals for research
  • Discuss, evaluate and argue about the ethical basis for the use of animals for research
  • Design and evaluate research studies in the following disciplines: studies using live animals, neuroimaging, neurogenetics, epidemiology
  • Describe research and clinical applications of neuroimaging techniques
  • Describe and explain the fundamental principles of neurogenetics
  • Describe principles of genetic mapping and downstream analysis of genetic datasets
  • Perform basic data processing and data visualization in R
  • Describe and explain principles of processing nervous system single cell RNA sequencing data