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)

--z3217345 09:24, 19 May 2011 (EST)

--z3217345 10:26, 26 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. Veronica G Beaudry, Dadi Jiang, Rachel L Dusek, Eunice J Park, Stevan Knezevich, Katie Ridd, Hannes Vogel, Boris C Bastian, Laura D Attardi Loss of the p53/p63 regulated desmosomal protein Perp promotes tumorigenesis. PLoS Genet.: 2010, 6(10);e1001168 PubMed 20975948 | 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

Introduction: Commas are used too frequently. Instead some sentences could be broken into two for an easier, more fluid read. Examples include, 'Neurons are a specialised cell which form the network of nerves, spinal cord and brain and will be explained in detail, how they play a key role in electrical signalling, later on.' and, 'Without Synaptic junctions, information and signals cannot be transmitted to areas of the body, its structure, mechanics dysfunctions and current related topics will now be explored in detail.' However, the general information and outline of what is to be be discussed is very clear.

History: A few entries about more recent research/discoveries may be able to give the reader a brief idea of where the field is progressing to.

What is: It would be helpful for the reader if a short explanation or a link to the glossary is given for each of the components listed for reference to the sketch.

Types: This section is clear both in terms of the layout of information (tables, diagrams etc.) and the content given.

Integration and modulation: This section extends on the previous entry very smoothly.

Diseases: The disease headings could be in a larger font so that they can be more quickly identified.

Gallery: The information about adding and sharing pictures could be placed on the discussion page as a reminder, as it detracts from the professionalism of the page.


Group 2: Gap Junctions

Introduction: The introduction is very clear and explains both the topic and what your article details.

History: The pictures below the history, could adjoin a specific entry so that the reader can see how they directly relate to the history. Whilst the pictures themselves are good, at the moment it is a little unclear how the pictures extend on what is being said in the history section. However the written content of the history is informative, covering both discovery up till very recent times. This overview is well done.

Structure: A brief structure, or explanation of the difference between the various connexins mentioned in the next two sections would be helpful.

Location And Comparison with Other Junctions: These are both helpful sections, that add more accessibility to the page by giving the reader more information about gap junctions and their context.

Glossary: The glossary could be alphabetised for ease of use.

Note: Uploading some of your own drawings would be helpful.


Group 3: Tight Junctions

Introduction And History: The introduction is good due to its concise nature. Also, the history adds to this overview with a good description of how the research into tight junctions has evolved.

Structure: The detailed description of the molecules is helpful, although more about their interaction and placement would be useful.

Classification: Sub-headings in this section, between the types described - tight and leaky - would help to make the section more clear. This was done well in the function section.

Diseases: This is a really clear table showing the diseases, however maybe an extra column with the disease pictures would be more helpful. It would make the relationship between the specific diseases and the adjoining pictures clearer. The introduction to the disease table gives a nice overview and at the same time is very informative.

Glossary: The glossary could be more extensive to assist the reader with quick reference to more of the technical terms.


Group 5: Adherens Junctions

Introduction: The introduction's sentence structure is a bit difficult to understand. Whilst much of the content is there, it could be written a bit clearer. Also a bit of an overview on what will be discussed would be helpful for the reader.

History: The history has too few enteries, however the layout makes it easy to read and understand.

Structure: The structure is informative and the adjoining pictures are good, giving the reader an idea of their form on a molecular and what they actually look like through a microscope.

Function: Whilst the section is clearer, it could be made even more accessible by the addition of subheadings for the main functions.

Importance And Regulation: The link to the picture at the beginning of this section does look very detailed and important to your subject, however it may be better to either explain the link or upload the actual picture to the page. Also the extracellular regulator sentence would be more informative and professional if you finished listing the regulators. In addition, the grammar in the last sentence of the section does not seem to flow. Is it meant to say, "if quite"?

Abnormalities: This topic on adherens junctions is very well explained.

Research: It looks as though you have current research areas with good links, although the actual content is sometimes not easily understood. An example of this is, "They were able to characterise. The proteins function, expression and localisation whist also labelling the junctions regions within cultured kidney cells. Specifically they established that definitively establishes that PLEKHA7 is localized at the adherens junctions in colonic epithelial cells."

Other Types Of Cell Junctions: Good formatting and pictures.

Glossary: The headings of the letters may be a simple touch, but is enough to make this an easier read.


Group 6: Neuromuscular Junctions

Introduction: The placement of the opening picture adjacent to the contents really engages the reader. Also, the actual introduction gives a good overview of what is to come.

History: This section is concise, however some of the entries could be cleared up such as, "At the Paris conference..." The conference does not seem to have been mentioned prior, so just some rewording or clarification would be helpful.

Mechanism Of Action: The dot points are good. Maybe to make the steps clearer, you could number them.

Structure: Breaking down the structural components in a table format really makes the information accessible.

Glossary: Potentially to make it an easier read, you could put the letters above their respective entries such as 'A' above the entries beginning with 'A'.

Note: The project format and content are very good. Just make sure to look over any spelling mistakes such as in the embryonic development section, 'The growing end of motor neuron axons secret...' when i think it should be 'secrete'.

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