User:Z3217345

From CellBiology

Lab Attendance

--z3217345 10:45, 10 March 2011 (EST)

--z3217345 09:08, 17 March 2011 (EST)

--z3217345 10:43, 31 March 2011 (EST)

--z3217345 08:53, 7 April 2011 (EST)

--z3217345 09:09, 14 April 2011 (EST)

--z3217345 09:10, 5 May 2011 (EST)

--z3217345 10:20, 12 May 2011 (EST)

Individual Assessments

Lab 1

1. What are the key cell biology journals?

2. Which journals allow reuse of their published content?


Lab 2

--Mark Hill 07:49, 24 March 2011 (EST) Homework?

1. Which chromosomes contribute to the nucleolus?

The chromosomes that contribute to the make up of the nucleolus are 13, 14, 15, 21, and 22.

The Cell: A Molecular Approach. 2nd edition.

2. Identify and add a link to your page of a recent biology article using confocal microscopy.

Nature Cell Biology Article: Reducing background fluorescence reveals adhesions in 3D matrices


Lab 3

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

University Of New South Wales: Safety Data Sheet for Trichloromethane (Chloroform)

Australian National Pollutant Inventory: Safety Data Sheet for Trichloromethane (Chloroform)


Potential hazards from contact with Trichloromethane (Chloroform) include:


Inhalation - Respiratory tract irritation, dizziness, fatigue, nausea, headaches, vomiting and confusion.

Contact with skin - Skin irritation - dermatitis, rash and burning sensation.

Contact with eyes - Eye irritation - burns.

Ingestion - Harm to central nervous system - depression and irritability, blood, liver damage - hepatitis and jaundice, cardiovascular system, kidneys. In the case of higher doses, death.

NB: Possible carcinogen.

For further information on the hazards refer to the two Safety Data Sheet links above.


2. Upload an image and add it to your page, with the reference and copyright information with the image.

Model for how Perp-deficiency can promote tumorigenesis.jpg Model for how Perp-deficiency can promote tumorigenesis.[1]

Perp loss, combined with chronic UVB exposure, can promote cancer through three mechanisms. A) Compromised apoptosis in the epidermis of Perp-deficient mice in response to UVB light can lead to inappropriate survival of cells sustaining DNA damage and expansion of pre-malignant cells. B) Impaired desmosomal adhesion in Perp-deficient mice, depicted by downregulation of a desmosomal cadherin, can facilitate the complete disruption of desmosomes that stimulates tumorigenesis. The exact placement of Perp, a tetraspan membrane protein, within the desmosome is speculative. C) The recruitment of inflammatory cells to the skin of UVB-treated Perp-deficient mice can promote cancer through mechanisms such as enhancing remodeling of the tumor microenvironment or stimulating angiogenesis.

Image Reference

  1. <pubmed>20975948</pubmed>| PMC2958815 | PLoS Genetics


Lab 4

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

ABD Serotec is a supplier of antibodies for research. They have a number of antibodies that target specific antigens on the desmosome.[1] One of them is Catenin Gamma, which interacts with Plakoglobin.[2] The gene JUP, that encodes Plakoglobin, has much clinical significance and hence research importance since mutations of this gene can cause arrhythmogenic right ventricular dysplasia, commonly known as cardiomyopathy.[3]


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

The gene CYCS (cytochrome c somatic) encodes the protein Cytochrome C in the cytosol, and is located at 7p15.3 (base pair 25,158,269 to base pair 25,164,979 on chromosome 7). Cytochrome C is not properly folded until it enters the mitochondria and the heme, Lygon is added. Once it is folded, Cytochrome C is unable to exit mitochondria as it is then a water soluble molecule and not able to pass the outer membrane of the mitochondria.


Lab 6

1. What are the changes in phenotype that you observe between Group A and Group B? (refer to table 1)


Group 2AnalysisOfMorphologicalPhenotypesInTm4Over-expressingB35NeuroepithelialCells.PNG


Refer to Lab 6 for information on each phenotype.


Phenotype observations (as a percentage of the total cells) between Tm4 Group and Control Group:

- No fan cells in Tm4 Group

- More broken fans, stumped and pygnotic cells in Tm4 Group

- More pronged and stringed cells in Control Group

- Stringed cells are the most prominent phenotype in the Tm4 Group

- Stumped and almost equally pronged are the most prominent phenotypes in the Control Group


2. How does Tm4 mediate these changes? (refer to table 2)


As observed in the Tm4 Group vs the Control Group, Tm4 does mediates some morphological changes in B35 neurons. Tm4 drives the growth of at 'least one neurite is a length exceeding that of 3x the diameter of the nucleus at its widest part' which is the defining morphology of a stringed cell as explained in Lab 6. It also may inhibit extension of an unbroken lamellum around the cell soma, as no complete fans were observed in the Tm4 Group.


Lab 9

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

One of the neural cell line products from ATCC is CRL-2768 and one of their muscle cell lines is CCL-197.


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

CRL-2768

Species: Rattus norvegicus (rat)

Growth Conditions:

For the complete growth medium: Add fetal bovine serum to a concentration of 10% (ATCC-formulated Dulbecco's Modified Eagle's Medium)

Atmosphere: air, 95%; carbon dioxide (CO2), 5%

Temperature: 37.0°C


CCL-197

Species: Mus musculus (mouse)

Growth Conditions:

For the complete growth medium: Add fetal bovine serum to a concentration of 20% (ATCC-formulated Dulbecco's Modified Eagle's Medium)

Temperature: 37.0°C

Atmosphere: air, 95%; carbon dioxide (CO2), 5%


Lab 10

Peer Assessment

General Criteria:

   * The key points relating to the topic that your group was allocated are clearly described.
   * The choice of content, headings and sub-headings, diagrams, tables, graphs show a good understanding of the topic area.
   * Content is correctly cited and referenced.
   * The wiki has an element of teaching at a peer level using the student’s own innovative diagrams, tables or figures and/or using interesting examples or explanations.
   * Evidence of significant research relating to basic and applied sciences that goes beyond the formal teaching activities.
   * Relates the topics and content of the Wiki entry to learning aims of cell biology.
   * Clearly reflects on editing/feedback from group peers and articulates how the Wiki could be improved (or not) based on peer comments/feedback. Demonstrates an ability to review own work when criticised in an open edited wiki format. Reflects on what was learned from the process of editing a peer’s wiki.
   * Evaluates own performance and that of group peers to give a rounded summary of this wiki process in terms of group effort and achievement.
   * The content of the wiki should demonstrate to the reader that your group has researched adequately on this topic and covered the key areas necessary to inform your peers in their learning.
   * Develops and edits the wiki entries in accordance with this sites wiki guidelines.

Group 1: Synaptic Junctions


Group 2: Gap Junctions


Group 3: Tight Junctions


Group 5: Adherens Junctions


Group 6: Neuromuscular Junctions

Work Area

Lab 1

Here is some bold text.

Here is some italic text.

2011_Lab_1

[4]

Lab 2

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

PubMed


Lab Notes

Knock-out:

- Pluripotent embryonic stem cells are required

- Construction of Knock-out vector using standard cloning techniques

- Electroporation is used to insert the Knock-out vector into the embryonic stem cells

- In vitro cultivation

- The knock-out vector contains both a positive (neomycin phosphorotransferase) and negative (thymidine kinase) selectable marker, so that random recombination and homologous recombination are more easily identified and selected.

- Selection by treating with neomycin (positive selection) and then with gancilovir (negative selection), allows one to identify the mice where homologous recombination has taken place

- Screening of the embryonic stem cells by DNA isolation, cutting with restriction enzymes, running on a gel and hybridizing with radioactively labelled DNA probes is performed. This is to test for organisation of target gene, and also allows one to double check that a homologous recombination has occurred and that the selectors haven't let any other cells through.

- Inject Knock-out cells into a blastocyst


Transgenic:

- DNA microinjection into the pronucleus of the fertilized oocyte

- Inject embryos into pseudopregnant mother mouse

- DNA is randomly integrated

- study overexpession of a gene


Lipid based transfection:

- Introduce nucleic acids into cells

- Opening transient pores in cell membrane to allow for uptake of nucleic acid

- Culture cells for many generations - generate a stable clone - to have all cells deriving from same genome

- Analyse morphological changes, that the specific protein has influenced