From CellBiology

Lab Attendance

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--z3347321 10:44, 07 April 2011 (EST) **Note: I added this attendance record on 14/4, because I didn't remember to note my attendance on the day of the lab last week

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--Mark Hill 10:03, 18 March 2011 (EST) Note that you have now changed your preferences to identify who you are, any work that you contribute to the group discussion will also be signed by your name.

Individual Assessments

Lab 1

  • What are the key cell biology journals?
    • The Journal of Cell Biology (JCB)
    • BMC Cell Biology
    • Cell
    • Journal of Cell Science
    • Public Library of Science

  • Which journals allow reuse of their published content?
    • Public Library of Science
    • The Journal of Cell Biology
    • BMC Cell Biology

--Mark Hill 10:01, 18 March 2011 (EST) The numbered list formatting, you have tried above, will only work if the list is directly in sequence. See below, then use edit view to see how this is achieved.

Thanks professor, I think I fixed it - 23/3

  1. first point
  2. next point
  3. third point

The bullet listing has similar rules.

  • This is a major bullet
    • This is a sub-section bullet
  • This is the next major bullet

Lab 2

  • Which chromosomes contribute to the nucleolus?

Chromosomes 13, 14, 15, 21, and 22 contain clusters of rRNA genes that contribute to the nucleolus.

  • Identify and add a link to your page of a recent cell biology article using confocal microscopy from the Pubmed database.

Pubmed, March 2011: Nipkow confocal imaging from deep brain tissues


Lab 3

Test reference: Here's an article on neuromuscular junctions: [1]

  1. Stephanie L Courchesne, Maria F Pazyra-Murphy, Daniel J Lee, Rosalind A Segal Neuromuscular junction defects in mice with mutation of dynein heavy chain 1. PLoS ONE: 2011, 6(2);e16753 PubMed 21346813

Chloroform Hazards

Hazards of Chloroform:

  • Chloroform is harmful if you breathe it in. At high concentrations inhalation may be fatal.
  • Chloroform is toxic if swallowed.
  • Small chlorinated hydrocarbons, such as chloroform, are suspected of causing cancer. A brief, mild exposure to this material is extremely unlikely to lead to cancer, but prolonged or repeated exposure may be harmful, so you should ensure that you do not breathe chloroform fumes for long periods.
  • Chloroform, like many chlorinated hydrocarbons, dissolves fat and grease very readily, so if you get it on your skin it may harm the skin. Repeated skin contact might lead to dermatitis.
  • Repeated exposure to chloroform may cause reproductive harm.
  • Chloroform is very harmful in the environment, and interferes with the biological processes widely used in sewage treatment plants, so must not be flushed down a sink.

(test image upload) Mouse Embryonic Stem Cells

Lab 4

  1. RSR Ltd is a commercial supplier of a variety of antibodies and antigens, some of which are relevant to neuroumuscular synaptic experiments RSR Limited Products
  2. Cytochrome C is encoded by the CYCS gene in human mitochondria. Apop-1 has high affinity for Cytochrome C, preventing it from leaving the mitochondria. Part 2: Factors Involved in the Intrinsic Pathway of Apoptosis

Lab 5

Cell Knockout methods lecture and exercise

Lab 6


This is an analysis of the morphological phenotypes in Tropomyosin 4 over-expressing B35 neuro-epithelial cells. Here is a graph of the percentage counts of the various cell phenotypes.

A=Fan, B=Broken Fan, C=Stumped, D=Pronged, E=Stringed, F=Pygnotic

Some phenotypes were more common than others. The majority were phenotype B, C, D, or E, with very few Phenotype A and even fewer Phenotype F (dying cells).

Lizzy graph.JPG

Q1: What are the phenotypic differences between the Group A and Group B cells? How does Tropomyosin-4 lead to phenotypic changes in cells? What is the molecular mechanism at work?

Fan(A) and Pygnotic(F) phenotypes were quite uncommon in both groups. There was a considerable higher proportion of the other four phenotypes. most notably, there seemed to be many more stringed cells in group A than group B, and almost twice as many broken fan cells in group B than in Group C.

Q2: What phenotypic differences are there between the genotype A and the genotype B cells in the second part of the lab?

Almost all cells in both groups appear to be of the "stringed" phenotype (Phenotype E). However, genotype A cells appear greener than the genotype B cells, which have a more reddish appearance. I would hypothesize that this is because they are overepxressing tropomyosin 4. The reddish appearance in the genotype B cells may be due to actin, which is more visible because not as much as much tropomyosin present. Nuclei in both genotypes are consistently uniform and round, with extensive and sometimes numerous neurite processes.

Q3: How does Tm4 mediate these changes?

Tm4 is an actin-binding protein. It plays a large role in the remodelling and regeneration of muscle by providing stability and controlling access to actin (e.g., the binding of myosin heads and cycling in muscle cells). Overexpression of Tm4 appears to cause excess growth of the cell cytoskeleton, resulting in the visible excess neurite processes and greener appearance of cells in this form of imaging (less visible red, which is actin).

Lab 9

  1. Identify from one of the cell line repositories: a neural cell line and a muscle cell line.

Neural Cell Line: CRL-10442

Muscle Cell Line: CRL-1772

2. Identify the species and growth conditions for these cell lines.


Organism: Homo sapiens (human) Growth Conditions: The base medium for this cell line is ATCC-formulated Dulbecco's Modified Eagle's Medium, Catalog No. 30-2002. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%. Temperature: 37.0°C

The growth medium must be adjusted to pH 7.35 prior to filtration. [1]


Organism: Mus musculus (mouse) Growth Conditions: ATCC complete growth medium: The base medium for this cell line is ATCC-formulated Dulbecco's Modified Eagle's Medium, Catalog No. 30-2002. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%. Temperature: 37.0°C [2]

Lab 10 - Peer Assessment of Group Projects

Group 5: Adherens junctions

This project was well organized. The layout is clear and well formatted, beginning with history and covering structure, function, regulation, disease, and current research. As for content, one of my favorite ideas is the table describing other kinds of gap junctions, including links to the other group projects.  

The images are eye-catching and relevant but it might look nice to make a couple of them bigger. The hand-drawn image is a great visual for adherens junctions and I think typing up and pasting the handwritten labels would be the cherry on the cake.

The citations are thorough and properly formatted.

The history seems a little thin - it would be nice to read a little more on the relevance of the discoveries and maybe add a few more points. Also, since the history stops at year 2000 but the current research section starts covering at year 2010, it could be good to add information in either of those sections to cover research in the last decade.

Group 4: Desmosomes

Right off the bat, it would be nice to have the title “Desmosomes” bold and legible up at the top to make clear what the project is about. There also seem to be two introductions - one above the history and one below, so maybe combine the two. A highlight for me was the breakdown and etymology of the word “desmosome” in the introduction. I thought that was a clever and interesting bit of information to add.

The history is very thorough. I like how “structure” is described on both a molecular and cellular level, adding clarity to the description. The molecular section might be a little too detailed though. For example, listing all of the cadherin isoforms and the plaque proteins is great information but probably beyond the scope of this class.

Group 3: Tight Junctions

The introduction is very thorough but maybe keep it brief and summarize other kinds of junctions in a separate section.

The history is comprehensive and thorough.

I liked the complete inclusive breakdown of molecular components. The descriptions of components are extensive but perhaps breaking them down a bit could make the information easier to take in (e.g., for “classification of epithelia,” do a section for “leaky” and a separate section for “tight”).

Many diseases are listed, but perhaps under descriptions, explain the tight junction’s role rather than a broad overview of the disease. This could reduce confusion because otherwise it appears as if the main reason for the disease is tight junction malfunction, which is only part of the cause for diseases like breast cancer or cystic fibrosis. As it stands this section looks more like a broad overview and summary of many different diseases.

The glossary lists only six words which I think is a little thin for the amount of information covered in this project.

Group 2: Gap junctions

The history is very thorough. This is great but there are so many points, and it is longer than most of the other sections, so maybe highlighting the more notable contributions so that they pop out to the reader would clarify this section.

Well done on the current research section - the studies are relevant, engaging, and clearly laid out.

The images are lovely and clearly labeled although it would be nice to see more captions to understand how they are relevant to the text.

Just a small note - right at the introduction, perhaps consider listing “gap junctions” rather than “communicating junctions” for clarity. Last but not least, it would be good to see a title at the top of the page.

Group 1 - Synaptic Junctions

The image of stained neurons at the top is great and immediately grabbed my attention. The project is very well laid out, organized, and easy to read. It is written with a peer student audience in mind. The hand drawn images are amazing! They serve as a really, really nice visual. The close-ups make the structure of the synaptic junction much easier to understand, and I like that the text is typed to make it easy to read, and it also clearly identifies the important components of the junction.

Nice use of images and tables. The table on neurotransmitters was a creative and interesting idea, and I liked the varying sizes of images. The images at the bottom of the page are fabulous - especially “dendritic trees” and “synapse.” Consider using these above because they’re beautiful and cool to have a look at!

Maybe add a few specific studies under “current research,” and also run a final spellcheck and edit to catch errors (e.g., I spotted a few in the “neurotransmitters” section). But that's just a brush up and polish. Overall I thought this project was very well done.

Work Area

Here is some bold text

Here is some Italic text.

Link to Lab 1

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