ECTS credits:

10

 

Course parameters:

Language: English

Level of course: MSc and PhD course

Time of year: Spring 2024

No. of contact hours/hours in total incl. preparation, assignment(s) or the like: 7 contact hours per week on average for 15 weeks. Approximately 270 hours in total, including preparation, contact hours, lab work and exam.

Capacity limits: 24 participants

Course fee: None

 

Objectives of the course:

Conventional biochemical assays and techniques in molecular biology determine average characteristics of populations of cells or molecules. However, population averages can mask a multitude of biological states.  A new paradigm is emerging where analysis of single cells and molecules is crucial for taking biological insight to the next level.

Recent scientific and technical developments in cell-sorting, single-cell RNA sequencing, super-resolution fluorescence microscopy and cryogenic electron microscopy (cryo-EM) offer new and unique experimental opportunities. Together, they now allow coupling cell-specific gene expression data to information on the sub-cellular organization and biological functionality of single molecules to identify the biological state of individual cells. Consequently, structure-function studies at the single cell and molecule levels are becoming increasingly important across research fields from chemistry over molecular biology to medicine.

The study of single cells and molecules relies on an interdisciplinary ensemble of scientific and technical competences originating from chemistry, physics, medicinal chemistry, molecular biology, biochemistry, cell biology, bioinformatics and data science. 

The course will offer insight into how advances in these research fields have made single-cell and single molecule studies possible and continue to drive new developments. In addition to insight from original literature, the current state of the art will be exemplified and explored through experiments and data analysis exercises on isolation of single cells, single-cell transcriptomics, and single-molecule localization and in situ structure determination.

The course is offered as part of the Interdisciplinary Teaching in Natural & Technical Science (ITEASc) course network supported by the Novo Nordisk Foundation and includes a seminar series, facility visits and an interdisciplinary interactions workshop with participation of students from the entire course network.

 

Learning outcomes and competences:

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

• Describe and compare key methods and challenges in single-cell and -molecule analysis
• Describe and perform experiments using state-of-the art single-cell and -molecule approaches
• Explain the theoretical foundation of methods for single-cell and -molecule data analysis
• Analyse data within the selected application areas using high-performance computing clusters, formulate and verify hypotheses by discussing analysis results.
• Evaluate and interpret data obtained using single-cell and -molecule methods
• Discuss original literature within the subjects and reflect on application areas.

 

Compulsory programme:

Participation in at least 80% of lectures, colloquia and lab exercises. Submission and approval of group reports describing the experimental work in modules 1 and 2.

 

Course contents:

Teaching is organized in two 7-week modules. Module 1 is focused on single-cell sequencing methods and analyses. The topic of Module 2 is single-molecule imaging and cellular ultrastructure and in situ structure analysis.

Module 1 - Single cells will include the following components and topics:

• Crash course for students grouped by study, e.g. biology for chemists and vice versa. Aimed at imparting the basic knowledge required to follow the single cell module.
• Harvest, separation and labelling of single cells.
• Single-cell sequencing lab exercise.
• Sequencing and de-multiplexing single cell transcriptomes. Introduction to the scanPy universe of data analyses packages and python in Jupyter notebooks. Dimensionality reduction, cell type identification and pseudotime analysis.
• Spatial analyses using single-cell RNA sequencing, including in situ approaches and methods for spatial reconstruction.
• Differential gene expression and co-expression analysis using single-cell RNA-seq data.
• Single-cell sequencing data analysis from the lab exercise and report writing.

Module 2 – Single molecules will include the following components and topics:

• Crash course for students grouped by study, e.g. biology for chemists and vice versa. Aimed at imparting the basic knowledge required to follow the single molecule module.

• Introduction to single molecule approaches. Single molecules and thermodynamics.
• Imaging single molecules with fluorescence microscopy. Subcellular (co)localization and functional coupling using super-resolution fluorescence microscopy.  Single molecule structure and dynamics.
• Cellular imaging with tomography. Cryogenic electron tomography (CET) – data collection and introduction to pre-processing (motion correction, contrast transfer function estimation) and 3D tomogram reconstruction software using high performance computing clusters.
• Subtomogram averaging for in-situ structural analysis using high performance computing clusters and deep learning algorithms. Docking of experimental or predicted (using eg. AlphaFold2) atomic models of macromolecular structures in nanometer to subnanometer density from 3D tomographic maps.
• Single-molecule lab exercises.
• Single-molecule data analysis and report writing.

 

Prerequisites:

The course is taught at the MSc level for students from molecular biology, molecular medicine, biochemistry, medicinal chemistry, chemistry, nanoscience, bioinformatics, data science, physics, mathematics and related fields. Contingent on available space, the course will also admit PhD students from the abovementioned fields and from medicine.

 

Name of lecturers:

Victoria Birkedal, Thomas Boesen, Mikkel H. Schierup and Stig U. Andersen.

 

Type of course/teaching methods:

Lectures, colloquia and laboratory exercises. Students will work in study groups during laboratory exercises and report writing.

 

Literature:

Laboratory protocols, original scientific literature, and reviews, which will be made available via the course home page.

 

Course homepage:

The University of Aarhus e-learning web site https://brightspace.au.dk

 

Course assessment:

Individual oral exam. Pass/Not pass

Aid: Exam reports

The study groups will submit two reports. Both reports must be approved prior to participating in the exam. The exam is an individual oral exam (30 min) based on both reports. The reports will not count in the final grading, where only the oral performance is assessed.

 

Provider:

Department of Molecular Biology and Genetics, Aarhus University, Denmark

 

Special comments on this course:

Cross-course activities through ITEASc

The course is offered as part of the Interdisciplinary Teaching in Natural & Technical Science (ITEASc) course network supported by the Novo Nordisk Foundation and includes a seminar series, facility visits and a summer camp.

PhD students must contribute to a deeper analysis of single-cell data and write a report at the level of a scientific paper.
 

Time:

Spring 2024

 

Place:

Aarhus University, 8000 Aarhus C

 

Course fee:

None

 

Registration:

Deadline for registration is 15 January 2024. Information regarding admission will be sent out no later than 16 January 2024.

For registration: Please write to Stig U. Andersen (sua@mbg.au.dk).

If you have any questions, please contact Stig U. Andersen e-mail: sua@mbg.au.dk