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From CellBiology

Lab Attendance

--Robert Dikeman 10:55, 10 March 2011 (EST)

--Robert Dikeman 09:05, 17 March 2011 (EST)

--Robert Dikeman 09:09, 24 March 2011 (EST)

--Robert Dikeman 09:05, 31 March 2011 (EST)

--Robert Dikeman 09:07, 7 April 2011 (EST)

--Robert Dikeman 09:03, 14 April 2011 (EST)

--Robert Dikeman 09:00, 21 April 2011 (EST)

--Robert Dikeman 09:18, 5 May 2011 (EST)

--Robert Dikeman 10:07, 12 May 2011 (EST)

--Robert Dikeman 09:01, 19 May 2011 (EST)

Forgot to sign in on May 26th, but turned in my lab assessment which proves my attendance.

--Robert Dikeman 08:59, 2 June 2011 (EST)

Individual Assessments

Lab 1

1. What are the key cell biology journals?

The key cell biology journals include The Journal of Cell Biology, BMC Cell Biology, Public Library of Sciences Journals, Nature Journals, Trends in Cell Biology, Current Opinion in Cell Biology, Cell, Journal of Cell Science, Molecular Biology of the Cell, and Proceedings of the National Academy of Sciences Journals.

2. Which journal allows reuse of their published content?

BMC Cell Biology, The Public Library of Science Journals, and The Journal of Cell Biology allow reuse of their published content.

Lab 2

1.) Which chromosomes contribute to the nucleolus?

Chromosomes 13, 14, 15, 21, and 22 contribute to the nucleolus.

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

PubMed Confocal Microscopy Article

Group Project Topic Ideas

  • Mitochondria replication
  • Protein folding process
  • Regulation of gene expression

PubMed

Bold text

Italic text

new link title

outside link

Lab 3

1. Find the SDS information for chloroform and identify the hazards associated with this chemical.

SDS for chloroform

The hazards associated with this chemical are as follows:

  • HARMFUL IF SWALLOWED.
  • CAUSES SKIN IRRITATION.
  • CAUSES EYE IRRITATION.
  • SUSPECTED OF CAUSING CANCER.
  • SUSPECTED OF DAMAGING THE UNBORN CHILD.
  • MAY CAUSE DROWSINESS OR DIZZINESS.
  • MAY CAUSE DAMAGE TO LIVER AND KIDNEYS THROUGH PROLONGED OR REPEATED EXPOSURE.

2. You will need to upload an image and add it to your page, with the reference and copyright information with the image.

Practice Uploaded Image

Bio image.jpg

Figure 6

The embryonic cold SJ phenotypes are cell autonomous. (A) Projection of a confocal stack showing a stage 16 coldf05607 homozygous embryo stained for FasIII (magenta) and expressing FLAG-Cold and Actin-GFP (green) proteins under the control of btlGAL4. (A′,A″) Single confocal sections at a higher magnification of the trachea dorsal trunk (A′) and the salivary gland (A″) of the same embryo, showing the distribution of the SJ marker FasIII. Notice the delocalisation of this marker in the salivary gland (arrowhead) and its normal distribution in the trachea (arrowhead). (B–C′) Distribution of FasIII (shown in magenta in B,C and in greyscale in B′,C′) in the hindgut of stage 16 embryos expressing FLAG-Cold in the engrailedGAL4 territory, marked by GFP (green). In wild type embryos, expression of FLAG-Cold in the en cells (green) did not affect the localisation of the FasIII marker in the apical portion of the lateral membrane (arrowheads) (B,B′). In coldf05607 homozygous embryos normal apical accumulation of FasIII was only observed in the en cells (green, arrowheads.[1]

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Image Reference

  1. Assia Hijazi, Marc Haenlin, Lucas Waltzer, Fernando Roch The Ly6 protein coiled is required for septate junction and blood brain barrier organisation in Drosophila. PLoS ONE: 2011, 6(3);e17763 PubMed 21423573
Note - This image was originally uploaded as part of a student project and may contain inaccuracies in either description or acknowledgements. Please contact the site coordinator if the uploaded content does not meet the original copyright permission or requirements, for immediate removal.

Lab 4

1.) Identify a commercial supplier of an antibody that relates to your group project topic.

BioLegend

Description of particular antibody given on BioLegend website: Cell adhesion molecules are necessary for many different cellular functions including cell to cell signaling, cell migration, cell rolling, activation, cell killing, apoptosis, maturation, formation of tight junctions, as well as other functions. Understanding cell adhesion is important in fully elucidating immune cell functions. Biolegend provides an array of antibodies against adhesion molecules for the study of cell adhesion, including applications such functional assays, western blotting, immunoprecipitation, immunohistochemistry, and flow cytometry.

2.) In mitochondria, where is the gene located that encode Cytochrome C and what keeps this protein trapped within the mitochondria?

The gene that encodes Cytochrome C is found in the nucleus on chromosome 7. Oxidative damage to cardiolipin which anchors Cytochrome C to the inner mitochondrial membrane releases Cytochrome C into the cytosol.

Reference: [1] --Robert Dikeman 22:39, 6 April 2011 (EST)

Lab 5

Assessment turned in during class.

Lab 6

Group 3 graph.JPG

Part A

1.) What are the changes in phenotypes that you observe between group A and group B?

In group A, in which Tropomyosin 4 was over-expressed, the "stringed" phenotype was the most common among the cells observed. In the control group (group B) the "pronged" phenotype was the most common.

2.) How does Tm4 mediate these changes?

Tm4 mediates these changes due to its effect on actin filaments within the cells. Tropomyosin, of which Tm4 is an isoform, is a protein that binds to actin filaments and promotes their stability. Actin filaments are important structural components of neurites, which are projections of the cell body of the neuron. [2] Due to the overexpression of the tropomyosin isoform in group A the higher percentage of cells with the "stringed" phenotype makes sense. The greater expression of tropomyosin means that there is a higher level of stabilized actin filaments, which would explain the presence of more cells with long neurites than the control group. The lower levels of tropomyosin in the control group means that long, stable actin filaments are not as likely to form which would mean that long neurites would be equally scarce. This explains the prevalence of the "pronged" phenotype in the control group which is characterized by shorter neurites.

Part B

1.) What are the changes in phenotypes that you observe between group A and group B?

Overall, the group A cells are characterized by long thin neurites, with have a lot of branching. The group B cells have shorter, thicker neurites which are mostly unbranched.

2.) How does Tm4 mediate these changes?

The different levels of Tm4 may mediate these changes again by affecting the actin filaments of the cells. As with the first groups of cells, Tm4 over expression in group A leads to the presence of more stable actin filaments which are then able to grow longer than their less stable counterparts in the control group. Thus, the group A cells will be able to put out longer neurites with extended branching because they are supported by these Tm4 stabilized filaments. The group B cells have less Tm4 and, thus, have actin filaments that are less stabilized and less likely to form long branched filaments which allow for longer neurites.

Lab 9

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

Muscle cell line

Neural cell line

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

Muscle cell line

Species

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

Neural cell line

Species

Homo sapiens (human)

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
  • pH: The growth medium must be adjusted to pH 7.35 prior to filtration

Lab 10

Peer review of other five projects. Post on personal page, and on group's discussion page.

Synaptic Junctions:

  • Introduction needs to be gone over to correct minor grammatical errors, and problems with sentence structure.
  • History section need citations!
  • Listing components of synapses in main body and the diagram is redundant.
  • Chemical Synapse diagram not labeled.
  • I was confused by the last sentence of "What is Synaptic Junction?" about fast and slow acting neurotransmitters, try to make this clearer.
  • In "Synaptic Integration and Modulation" the introduction about integration and modulation wasn't clear to me. What exactly are they?
  • Overall, good balance of text, images, and tables. You guys gave a lot of other information which helps put synaptic junctions into context which is good. Mostly the text is easy to understand, but I would recommend reading it over again to see if some parts could be made clearer.

Gap Junctions:

  • Intro is well-written, but too much specific information. You just repeat it all later in the page. Also, I'm not sure if you need to spell out the sections that are on the rest of the page. You can just tell by the headings of the sections.
  • "Structure" and "Function" is concise and well-written. Good images.
  • "Location" is a good section and helps to contextualize gap junction in the body.
  • "Comparison" is a well done section but is it necessary? Also, how are you comparing other junctions with gap junctions like the title says? Maybe you could say how gap junctions are associated with other junctions?
  • "Diseases" nicely formatted section, easy to read, good images.
  • "Current Research" language a little hard to follow sometimes. Maybe try to portray information with less technical language.
  • Overall, nice job. Make sure you go over and correct grammatical errors and typos.

Desmosomes:

  • Intro pretty short and specific and a little awkward; it doesn't ease the reader into the topic. Maybe start off with a broader discussion and then focus in on desmosomes.
  • "Introduction to the Structure of Desmosomes" is describing the function of desmosomes not the structure. I think entomology of the name would also be better suited to the function section.
  • The different cadherin isoforms part is not easy to follow, why do we need to know this?
  • Some awkward sentence structure in "Structure," makes it hard to follow sometimes
  • "The structure of the major plaque proteins" is hard to read. What does it mean? It seems like the info is also more effectively conveyed in the corresponding image.
  • "Investigations into function through knock out gene models" seems like it should be in the diseases section not function.
  • "Current Research" seems a little narrow in scope. More examples?
  • Overall, need to look at paragraph structuring and make sure that the information in the section matches the title.

Adherens Junctions:

  • Poor grammar and sentence structure in intro, very hard to follow.
  • History seems a little scarce. Maybe add more information or expand on the stuff you already have.
  • Structure well written section, good images, like the video
  • "Function" good section, maybe talk more about how AJs are involved in cell contraction, specifically the mechanisms, I was a little confused when you talked about this in the next section.
  • "Importance and Regulation" don't really go together, I think these could be split up.
  • Is the comparison with other cell junctions necessary? Maybe you could discuss how adherens junctions specifically interact with other junctions.
  • Overall, most sections well written and easy to follow. Go over again to correct some grammatical errors and sentence structure to make clearer.

Neuromuscular Junctions:

  • Good intro, eases reader nicely into topic
  • "Motor neuron" bullet points not best way to convey this information maybe. The info in the previous bullet point list is good but doesn't it just repeat what was said in the paragraph? try to consolidate the information.
  • "Acetylcholine" bullet points confusing. what information are you trying to convey? are these the functions of ACh?
  • I'm confused by a lot of the bullet points. Can you spell out what information you're going to say in the list before you list it?
  • The stuff about microscopy, while interesting, seems unrelated to your topic
  • Muscle cell organization seems beyond the scope of your topic, especially the stuff about ATP
  • "Embryonic Development of the neuromuscular junction" good section, very informative.
  • Nice disease table, conveys information really well.
  • Well done current and associated research.
  • Overall, very nice project, it was hard to come up with criticism. You have a lot of information that does not seem to be associated with NMJs. Take out some stuff that is too far away from your topic so that the page is more focused.