Discuss different aspects of disease diagnosis and treatment that can be addressed by the use of genome-wide measurements. (

Question 1 – (25p)

Functional genomics makes use of genome-wide measurements of several different classes of biological molecules (DNA, RNA, proteins, other).

Pick two different classes of molecules. For each of these, give a brief account of current technology for genome-wide measurements and discuss methodological challenges associated with such measurements. (7p)

Functional genomics is expected to contribute widely to improved diagnosis and treatment in future health care.

  1. Discuss different aspects of disease diagnosis and treatment that can be addressed by the use of genome-wide measurements. (5p)
  2. Give examples of opportunities and challenges in functional genomics knowledge management. Discuss how the use of biological background information can improve the value of genome-wide measurements on patient samples. (5p)
  3. How is functional genomics expected to contribute to systems medicine and personalized medicine? Give two examples of proposed applications of personalized medicine. In each example, specify broad type of disease that is addressed and medical strategy proposed. Discuss societal aspects associated with implementation of the given examples of personalized medicine. (8p)

Question 2 (20p)

In your Masters project you are involved in a larger project aiming to identify non-invasive protein biomarkers for early detection of breast cancer. The group has access to modern equipment in protein separation and analysis including several mass spectrometry instruments.

In the first part of the project you aim at identifying whether cells of breast cancer tissue have altered expression of any cell surface transmembrane receptors. You have access to frozen biopsy material from both cancerous and healthy tissues from individual patients and you want to extract proteins from these tissues to identify potential altered expression.

  1. What special consideration would you take into account regarding your extraction buffer to ensure that the surface receptors are present in your protein extracts?
  2. You aim at analyzing the proteins in the two extracts (cancer/healthy) by first performing SDSpolyacrylamide gel electrophoresis and then mass spectrometry. Describe a strategy to undertake this study and explain your choice of methods, including the type of mass spectrometry employed.
  3. Make a schematic drawing and an explanation of the ionization source of the mass spectrometer employed in your method .
  4. The figure below illustrates the MS peaks observed for one peptide ion. Explain why several peaks are seen. What MS ionization method was employed (MALDI or ESI) in this case and what is the charge of the ion? What is the monoisotopic mass of the peptide? Substantiate your answers

 

Question 3 (15p)

The risk of “incidental findings” in genomic research has caused a huge international debate on research ethics.

Give a brief description on what is meant by the term “incidental findings”.

Present important arguments for and against disclosing such findings. Argue why you consider the arguments important.

Question 4 – (15p)

Identification of transcription factor binding sites in promoter regions is an important step in mapping of gene regulatory networks.

Describe briefly how we can identify potential binding sites computationally, using the scanning method, and experimentally, using the ChIP-seq approach. What is the main difference between the two methods with respect to number of sites that will be mapped?

Question 5 – (15p)

Classical forward genetics have successfully been used to unravel many developmental pathways in C. elegans.

  1. Describe how this technique was used to map out and identify genes coupled to elegans vulval development.
  2. What are the problems / challenges associated with classical forward genetics, and how can newly developed technologies be used to find mutated genes?
  3. What are the advantages / disadvantages of using reverse genetics and RNA interference (RNAi) to probe gene function in elegans?

Question 6 (10p)

Great insights have been obtained from fluorescence microscopy. The ultimate goal is the study of subcellular architecture and dynamics.

  1. Name two types of microscopes used for the visualization of fluorescence.
  2. How does these two microscopes differ in respect to light sources.
  3. What type of microscope would you use to monitor fluorescence at the highest possible resolution?
  4. Since the discovery of the Green Fluorescent Protein (GFP) numerous fluorescent proteins have been made using recombinant DNA technology and mutagenesis. How do the different fluorescent proteins differ?
  5. Describe the principle behind Fluorescence Resonance Energy Transfer (FRET).
  6. Give an example on a fluorescent protein FRET-pair.
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