I am currently studying experimental analytical assays such as:

1. deletion analysis + reporter assay
2. linker scanning mutation assay
3. DNase I foot-printing assay
4. Electrophoretic mobility shift assay
5. ChIp-Seq

And I would like to look further into the applications of these methods. I am particularly comfortable with (1), (3), and (4) so any suggestions on an experiment I could test would be much appreciated. Not looking to do anything too complex but just something interesting and simple. I know that this isn't the typical homework question, but we do have to write about a paper about such an experiment that uses one of these methods.

Why are parasitic nematodes generally ubiquitous and difficult to control?

Illustrate the evidence provided by Mendel’s experiments in disproving the blending theory of inheritance.

How has the bacterium Y. pestis evolved to become virulent (based on your assigned literature and other literature)? [15 points]

Hermione is using a combination of glyburide and pioglitazone for the treatment of type II diabetes. Her condition is stable as she remains relatively compliant with her treatment. At her bachelorette party, she drinks a more than what she is used to, and faints soon after thereafter. Before fainting she experienced an elevated heart rate and confusion. She is rushed to the hospital, where they administer IV glucose and dextrose. Regarding the presentation, i) explain the underlying reasons leading to her fainting, and ii) why she received glucose as emergency treatment.

Write 75- to 100-word paragraph that summarizes the symptoms and pathology of the disease Werner Syndrome? (premature aging). Your paragraph should include the information listed below, as well as other interesting, relevant information.

Information should include:

o What are the characteristic manifestations and complications of the disease?

o What is the mode of inheritance? What is its penetrance and expressivity?

o What is the main type (responsible for the majority of cases) of mutation involved? What gene is mutated?

o By what molecular/cellular mechanisms does this mutation cause the disease? o   Why is your topic important and/or interesting?

Why do the pole cells (the primordial germ cells which give rise to the gametes) form so early in Drosophila melanogaster development?

Epstein-Barr virus (EBV) has been implicated as an environmental trigger to induce autoimmune diseases, including systemic lupus erythematosus (SLE), multiple sclerosis (MS), and rheumatoid arthritis (RA). Outline 3 possible immunological mechanisms to explain the association of this viral infection with those autoimmune diseases.

Geoffrey, a 40-year old sedentary, heavy-smoking white male, suffers from chronic hypertension (on average >140/95 mmHg). He is currently taking antihypertensive monotherapy and aspirin, and frequently complains of a drug-induced dry cough and taste disturbance. His daughter has brought him to the emergency room as he presented with shortness of breath, fatigue, and muscle weakness. After testing, the medical team diagnoses him with heart failure, and start emergency treatment following a standardised pharmacotherapy algorithm, though maintains the use of his antihypertensive treatment. Based on his clinical presentation, i) describe the drug classes (including a relevant example from each) he will be taking for heart failure, and iii) explain how each would physiologically treat his heart failure.

Cladistics & Homology

• What does it mean when we say a cladogram depicts a “hypothesis of genealogical relationships between taxa”?

• What part of the “anatomy” of a cladogram represents a historical speciation event?

• Define synapomorphy and plesiomorphy. How can one character be both?

• What kind of characters are useful in building a cladogram?

• Why are characters found in only one taxon not informative in phylogeny reconstruction?

• What is the difference between a monophyletic, polyphyletic and paraphyletic group?

Which of these ps is/are “accepted” in cladistics?

• Define homology

• Why is homology considered the central concept of comparative biology?

• What is the relationship between synapomorphy, homology, and monophyly?

• What is one similarity and one difference between traditional homology and serial homology?

• What is the term for similarity due to convergent evolution?

• If presented with two taxa that have a similar structure, what evidence would you look for to determine if those structures were homologous?

• Given a cladogram, could you determine which taxa were more closely related?

• Given multiple cladograms, could you determine which depicted equivalent hypotheses of relationships?

• What is the principle of maximum parsimony, and how would you determine which of two cladograms was more parsimonious?

• Why is it incorrect to refer to any living taxon as being primitive? What does “basal” mean in terms of phylogenies?

Discuss the following different types of transmembrane transport: passive diffusion, facilitate diffusion, and active transport. Compare and contrast their respective advantages and disadvantages and provide an example of each.  

5.Consider again the picture you selected in question #3. What’s attached to the 5’ end of this molecule? (BOLD the correct answer)

   A phosphate group    OR    An OH group (which is attached to the ribose sugar)

6.Consider again the picture you selected in question #3. The way it’s drawn on this page, the bottom end of this molecule is considered to be the…(BOLD the correct answer)

            3’ end      OR      5’ end

Dopaminergic neurons are found in the nucleus accumbens (IB word). Why do we need a nucleus accumbens? [1]

What is the ‘secondary messenger’ concept? [1]

Slow receptors can modulate Fast receptors. How? [2]

Opioids bind to opioid receptors on widely distributed pain pathways. Since they themselves are GPCRs they can act at a distance far from the opioid receptor.   What effect do opioids have on the pre- and post-synaptic membranes of neurons in the pain pathways? [4]