3578.17 - Molecular Laboratory Methods

3578.17

Molecular Laboratory Methods

7.5

A) Admitted to the bachelor programme in biology at the University of the Faroe Islands, and following the normal study progression or B) Students following single courses need to have sufficient background in molecular courses, like 3514 Biochemistry, 3518 Cell and molecular biology I, 3516 Genetics, 3576 Cell and molecular biology II, 3577 Bioinformatics in Practice.

To provide the students with hands-on experience and knowledge of common molecular laboratory methods concerning small molecules, nucleic acids and proteins.

The exact content may vary from time to time, but includes a variety of molecular methods concerning small molecules (for example metabolites or environmental pollutants), proteins and nucleic acids. This description is based on the methods included in the 2017 course. Examples of small molecule methods include: Work-up of biological (blood, liver or other organs/tissues from fish, birds or mammals, etc.) or environmental (water, sediments, soil) samples for subsequent analysis of pollutants; mass spectrometry. Examples of protein methods include: SDS-PAGE; silver staining of gels; Western blotting; immunoprecipitation; mass spectrometry; flow cytometry; histochemistry. Examples of nucleic acid methods: Purification of DNA or RNA from a variety of samples; different kinds of nucleic acid analyses, like quantitative PCR, large-scale sequencing (16S metagenomics, bacterial or eukaryotic genome sequencing); ChIP Seq. If possible (cannot be guaranteed), parts of the course will include participation in on-going research projects and/or trial of new methods. Lectures will provide some theoretical and practical background for methods included in the course, and will also introduce some common laboratory methods/techniques/instruments that are not necessarily available in the Faroe Islands.

Lectures. Laboratory demonstrations and exercises. Discussions and presentations with focus on methods and techniques. The students are given manuals and procedures as they will meet them in practical life. The students must themselves to able to perform the needed calculations, the making of necessary buffers and solutions, etc. Long days (10 h or more) should be expected during some of the exercises. Different (groups of) students may perform different tasks in parallel. All parts of the course are obligatory.

On completion of the course, the successful student should be able to: 1. Perform the analysis of a protein sample by SDS-PAGE and silver staining of the gels. 2. Manage and execute Western blotting experiments and analyze the presence of a specific protein, and explain the limitations and strengths of Western blotting. 3. Plan and perform immunoprecipitation and combine this with SDS-PAGE and Western blotting; and explain the limitations and strengths of immunoprecipitation. 4. Explain the principles of flow cytometry and its strengths and limitations. 5. Explain the principles of histochemistry and perform histochemical analyses of tissue samples (histological slides). 6. Describe how antibodies can be used as molecular tools in diverse settings, and the strengths and limitations of such approaches. 7. Describe the principles of mass spectrometry and give some basal interpretation of mass spectra of intact ions and of fragment spectra (MS/MS), whether the spectra originate from peptides/proteins or small molecules. 8. Explain the principles of targeted mass spectrometry and mass spectrometrical quantitation. 9. Explain and contrast a few common sample preparation techniques (solvent extraction; solid phase extraction; QuEChERS). 10. Explain, perform and analyze quantitative PCR. 11. Explain and perform all laboratory steps of large-scale (NGS) 16S metagenomic sequencing. 12. Explain library preparation methods for genomic large scale sequencing. 13. Explain and discuss some techniques that only introduced by lectures, like NMR, electron microscopy, siRNA, etc. 14. To analyze the problem in question, find experimental approaches that can give answers or in other ways shed light onto the problem, and perform these experiments.

Combination of 1) active presence during the course, 2) acceptance of written report (focusing on methods), and 3) obligatory student presentations (focusing on methods).

Internal

P-

The lectures, handouts and experimental methods define the curriculum.

Svein-Ole Mikalsen