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Attended Lab--Vishnnu Shanmugam 05:44, 24 March 2010 (UTC), Attended Lab--Vishnnu Shanmugam 05:02, 31 March 2010 (UTC), Attended Lab--Vishnnu Shanmugam 06:34, 14 April 2010 (UTC), Attended Lab--Vishnnu Shanmugam 07:11, 21 April 2010 (UTC), Attended Lab--Vishnnu Shanmugam 06:07, 28 April 2010 (UTC), Attended Lab--Vishnnu Shanmugam 06:10, 5 May 2010 (UTC), Attended Lab--Vishnnu Shanmugam 07:28, 12 May 2010 (UTC), Attended Lab --Vishnnu Shanmugam 14:05, 19 May 2010 (UTC)

Lab 1 - What Cell Biology Journals allow reuse of acknowledged and correctly cited content?

Journal of cell biology allows use of their material as long as it’s referenced fully and after 6 months of publication. BMC Cell Biology has allowed the use of its articles marked “open access”. Molecular Cell biology allows the use of its material so long as it has a full citation and oblige by their “fair use” policy. Public library of science has articles that can be used freely by everyone. Others such as Cell and tissue research, Molecular cell, Nature, Science, CELL require prior permission before use with full and correct citation. --Vishnnu Shanmugam 00:06, 17 March 2010 (UTC)

Lab 2 - What are the "light" regions of DNA within the nucleus called?

The “light” regions are called Euchromatin. It is the portion of the genome that is most active in gene transcription within the animal cell nucleus and it stains lightly with basic dyes. --Vishnnu Shanmugam 06:15, 22 March 2010 (UTC)

Lab 3 - How do we know the hazards associated with research chemicals?

The hazards associated with research chemicals are discovered from a range of toxicity studies on animals. These studies include single dose toxicity tests, repeated dose toxicity tests, irritation studies and sensitisation studies. In each of these tests, a dose response relationship is created which shows the effects of exposure to a chemical at increasing concentrations. As the dose of a toxicant increases, so does the response, either in terms of the proportion of the population responding or in terms of the severity of the graded responses. From this data, a safe level of exposure (NOAEL- no observed adverse effect level) is established and is the recommended exposure concentration found on the MSDS. It is however worth noting that these recommended levels do have an element of inaccuracy and thus can be subject to change at any time. This inaccuracy is a result of the assumptions in toxicity tests such as:

  1. Extrapolation from animal data to humans is valid.
  2. Exposure of experimental animals to high doses for detecting hazards to humans is valid.
  3. Humans are at least as sensitive to the effects of a chemical hazard as those observed in the most sensitive animal species. --Vishnnu Shanmugam 00:53, 30 March 2010 (UTC)

Lab 4 - Identify a commercially available antibody to an adhesion junction protein and add link here.

AF-6, Rabbit Polyclonal Antibody. It is Unconjugated Polyclonal antibody specific to Human AF-6 protein. AF-6 controls integrin-mediated cell adhesion.

Lab 5 - Assessment submitted on paper to Dr. Galina Schevzov.

Lab 6 - Assessment submitted on paper to Dr. Thomas Fath and the same found below.

Graph comparing morphological characteristics of Genotype A (Tm4 expressing) and Genotype B (control B35) blastoma.


a) Comment on any differences that you may see in the phenotpye of tropomyosin 4 (Tm4) overexpressing and control B35 cells.

From the data, it can be observed that cells overexpressing Tm4 had a greater number of neurites than the control group of B35 cells. The B35 cells however display a more complete lamellum. These observations are quantitatively supported from the graph above which shows :

- 47% of group A (Tm4 overexpressing cells) had a “pronged” or “stringed” phenotype while only 14% of group B (control group of B35 cells) had a “pronged” or “stringed” phenotype. This is consistent with the conclusion that the Tm4 overexpressing cells display a greater number of neurites in their phenotype.

- 80% of group B (control group of B35 cells) had a “fan”, “broken fan” or “stumped” phenotype while only 53% of group A (Tm4 overexpressing cells) had a “fan”, “broken fan” or “stumped” phenotype. This is consistent with the conclusion that the control group of B35 cells display a more complete lamellum.

(b) Explain how potential changes in the phenotype may result from the overexpression of tropomyosin 4.

Tropomyosin and actin are linked. Cells overexpressing Tm4 will thus also express more actin and since cytoskeletal structures such as neurites are composed of actin, it can be inferred that the increase in actin has resulted in increased number of stable neurites. Also, from what I understood in Dr. Galina Schevzov’s presentation, it is also possible that the overexpression of tropomyosin can increase the conversion of monomeric actin to filamentous actin found in cytoskeletal structures like neuronal processes. This could explain why the control group of B35 cells had more lamellae (less monomeric actin lamellae are converted to filamentous actin neurites).

Lab 7 - From today's confocal tutorial, identify an advantage to using each of the following objectives: Air, Water or Oil.

Advantage of air objective: Requires minimal preparation and cleaning.

Advantage of water objective: Water provides an ideal medium for visualizing living cells.

Advantage of oil objective: When compared to air and water, oil provides a higher image quality.

Lab 8 - Critically assessed all other group projects (Fluorescent PCR, RNA Interference, Immunohistochemistry, Cell Culture, Electron Microsopy, Confocal Microscopy, Monoclonal Antibodies, Microarray, Somatic Cell Nuclear Transfer). Overall an interesting read that allows you to appreciate the diversity of techniques used in cell biology.

Lab 9 - Microarray Lab: What is the technological bottleneck common to all next generation sequencing (NGS) platforms?

The technological bottleneck common to all NGS platforms is that the current library preparation methods for next-generation sequencing are time-consuming and prone to considerable sample loss. (Adapted from Nature Methods 6,(2009)- Next generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition)