User:Z3330686

From CellBiology

Attendance

--Z3330686 (talk) 16:34, 12 March 2015 (EST)

--Z3330686 (talk) 16:52, 19 March 2015 (EST)

--Z3330686 (talk) 16:17, 26 March 2015 (EST)

--Z3330686 (talk) 17:56, 2 April 2015 (EST)

--Z3330686 (talk) 16:08, 16 April 2015 (EST)

--Z3330686 (talk) 17:25, 30 April 2015 (EST)

--Z3330686 (talk) 17:06, 7 May 2015 (EST)

--Z3330686 (talk) 16:50, 14 May 2015 (EST)

--Z3330686 (talk) 16:02, 21 May 2015 (EST)

Project Page

2015_Group_6_Project

http://ghr.nlm.nih.gov/search?query=collagenopathy

http://www.omim.org/entry/120140?search=collagen%20type%20ii&highlight=ii%20collagen%20type

http://ghr.nlm.nih.gov/condition/kniest-dysplasia

http://ghr.nlm.nih.gov/gene/COL2A1

http://www.news-medical.net/health/Collagen-Types-and-Linked-Disorders.aspx

Testers

This the Test page http://php.med.unsw.edu.au/cellbiology/index.php?title=Test_page

PubMed

http://php.med.unsw.edu.au/cellbiology/index.php?title=Cells_Eukaryotes_and_Prokaryotes

Cells_Eukaryotes_and_Prokaryotes

PMID 25513760

<pubmed>25513760</pubmed>

<pubmed>25753537</pubmed>

An experimental design.jpg

Lab Assessment 1

Growth curves of Chlamydomonas.png

Growth curves of Chlamydomonas[1]

Reference

  1. <pubmed>25760649</pubmed>

Lab Assessment 2

This article explains the research that is currently undertaken at the presynaptic active zone (AZ) and it introduces us to the organization of proteins and channels, specifically Calcium, that are present and functioning at the AZ. The densely packed proteins located in the AZ had up until recently, only been viewed using diffraction-limited light microscopy and electron microscopy. The sub-cellular compartment that was being viewed with these microscopes was ~200-400 nm in diameter. The development of SRM has allowed the barrier of ~300 nm to be broken, and for sub-cellular structures to be viewed and studied more accurately and clearly.

The first instance where SRM was used to study AZ nanoarchitecture was via the stimulated emission depletion (STED) technique at the Drosophila NMJ. The work conducted in this analysis has given us a clearer idea of the protein structure at the AZ of the Drosophila, and it has also allowed for further studies to be done by alternative SRM methods, to extend this clearer image of the Drosophila AZ.

This article explains the specific contribution that SRM will, and has already made to the research involving AZs, the function of them, the proteins and channels involved and how structure correlates to function in relation to AZ and the protein organization.

<pubmed>25688186</pubmed>

Lab 3 - In Lab Work

Paraformaldehyde

Paraformaldehyde

HAZARD IDENTIFICATION

- Flammable solids (Category 2) - Acute toxicity, Oral (Category 4) - Acute toxicity, Inhalation (Category 4) - Skin irritation (Category 2) - Serious eye damage (Category 1) - Skin sensitisation (Category 1) - Carcinogenicity (Category 2) - Specific target organ toxicity - single exposure (Category 3)

This is used in tissue preservation - they cross link proteins together, therefore it will no longer have it's normal function, and cannot change shape.

Lab 3 Assessment - Collagen Diseases

Search Term: Type 2 Collagen

Article 1

"Premature Arthritis Is a Distinct Type II Collagen Phenotype" This article is produced by the American College of Rheumatism. It's focus is on the type 2 collagen gene, COL2A1, and how mutations in this gene can result in a wide spectrum of phenotypes the affect mainly cartilage and bone. It has an extensive review that places the mutations of COL2A1, as a key marker for those patients whom have isolated degenerative joint disease. This paper gives a great foreground of type 2 collagen.

Article 2

"Autoimmunity to type II collagen an experimental model of arthritis" This paper experiments with Type 2 collagen and it's results show that intradermal injection of native type II collagen, extracted from human, chick or rat cartilage) induces an inflammatory arthritis in approx 40% of rats of several strains. It shows that Type 1 and Type 3 collagen do not have the same effect.

Article 3

"Ophthalmic and molecular genetic findings in Kniest dysplasia" This was a paper that studied the variability of the ophthalmic phenotype in Kniest dysplasia (inherited disorder associated with defects in type II collagen and characterised by short-trunked dwarfism, kyphoscoliosis, and enlarged joints with restricted mobility). It concludes that the ophthalmic features in Kniest dysplasia are very similar to those in other disorders of type II collagen such as Stickler syndrome. It went into great detail explaining the COL2A1 gene which will be very usual for our project.

Article 4

<pubmed>12837047</pubmed> The abstract of this article eludes to the use of a denatured type 2 collagen material, UC-II, and it's success in previous studies in the reduction of joint pain and swelling for patients with Rheumatoid Arthritis and Osteoarthritis. I think this would be a good article for us to look into further. It is inaccessible, due to it not being 'FREE FULL TEXT' but if we would like we could look into it further.

Note: A lot of information was available regarding the use of denatured type 2 collagen when discussing diseases and ways to treat them. This may be a branch that my group might consider including when completing our 'Type 2 Collagen - Disease' section.

X-ray, coronal and sagittal micro-CT images1.jpg

X-ray, coronal and sagittal micro-CT images1 [1]

Reference

Lab Assessment 5

Phenotypes found in cells with over-expression of Tm4 and wildtype cells.PNG


Lab Assessment 6

Collagen II Antibody = 2B1.5 (MA5-12789)

Species deriving Antibody = Mouse

Concentration = 0.2mg/ml

Secondary Antibody = Mouse anti-Human IgA (Alpha heavy chain) GA01

Paper = <pubmed>18980201</pubmed>


Lab 9 Assessment

"Human Cell Line" Medium = Eagle's Minimum Essential Medium EMEM in Earle's BSS with 0.015 mg/ml 5-bromo-2'-deoxyuridine, 90%; fetal bovine serum, 10%

"Mouse Cell Line"

What is Penicillin Streptomycin (Pen Strep)? Pen Strep The antibiotics penicillin and streptomycin are used to prevent bacterial contamination of cell cultures due to their effective combined action against gram-positive and gram-negative bacteria. Penicillin was originally purified from the fungi Penicillium and acts by interfering directly with the turnover of the bacterial cell wall and indirectly by triggering the release of enzymes that further alter the cell wall. Streptomycin was originally purified from Streptomyces griseus. It acts by binding to the 30S subunit of the bacterial ribosome, leading to inhibition of protein synthesis and death in susceptible bacteria.


Peer Reviews

'''Group 1 Peer Review'''

The image heading is a great idea, very eye-catching. You have a strong introductory paragraph with good linkage back to the ECM. I like that you included the main function of Proteoglycans and GAGs in the introduction, as well as some composition components – gives a good insight as to what this page, and Proteoglycans, are essentially about. The heading that currently says ‘Small Leucine-Rich Proteoglycans,’ I think, should say ‘Proteoglycans,’ and then somehow integrate the heading ‘Small Leucine-Rich Proteoglycans,’ further down the section maybe?

I think the history section is too lengthy and some of the information is unnecessary. Consider making this section significantly shorter so that your readers don’t get caught up on less important information before they get into reading the crux of your topic.

The breakdown of the structure is good, however I feel that more information could be added here, considering it is a major aspect of this project. I think in this section you could also include some information on the developmental stages of SLRPs (from the embryo and compare it to the final stage of the molecule in an adult?)

The disease section, again, is too lengthy and at this stage, your project seems to focus on this due to the shear amount of information that is here. Focus each of the four diseases on 4-5 main points and it will allow for your information to be more specific and easier for readers to comprehend.

Some images are great, (heading, disease affects) – size and placement are relevant to what is being said in the paragraphs near them. The other images are somewhat unnecessary eg. the table showing the difference in Glycosaminoglycan chains.

Overall, I can see that you have done a lot of research into your topic and I think that it is well developed. Sometimes, less is more, so keep that in mind when explaining difficult concepts and functions. There are some grammatical errors so be sure to go back and fix them up.


""Group 2 Peer Review""

The integrins introduction is very well done. The key points are clear, it’s very straight forward and comprehensive. The association with the ECM here is a good start to your page.

The hand drawn image of integrin interaction with cytoskeleton is well drawn – however, I think you should scan the image for a better quality finish and also place this image in your structure/function section where it can be referred to there. Being in your introduction section with little to no reference to it, makes it appear less essential to your project.

The History section has enough information to give us an insight to the years of research that went into integrin discovery. Once the Future Research section is complete I think this section of your wiki will be very informative.

Good start to the structure component of your wiki – the image ‘Integrin Structure and Function schematic’ is well referred to in the paragraph to its left. Consider labeling the image or drawing your own or attaching a legend to the image because at this stage there’s no telling what is what in the image, eg. MIDAS, ligands, etc.

The images that are for structure should be in your structure section, not with the functional paragraphs. The video is a great addition to the wiki and also the linkage between ECM and integrins.

The disease section is very extensive and it’s clear that you have done a lot of research in this area. It could be further aided by the addition of a few images.

Your sub-headings show you have a good understanding of what your topic is about, and what your wiki needs in order to inform your readers about topic. There are some grammatical errors so be sure to go back and fix them up as well as the links that are just ‘lying around!’


""Group 3 Peer Review""

Wow, your page is really well developed. The introduction is clear and I feel as though the key points that are addressed in the remainder of the wiki are briefly mentioned here. A good start.

Headings are good and I think the ‘Assembly of Elastic Fibre’ heading/paragraph, is a great addition between the ‘Structure’ and ‘Function’ headings and to your wiki page in general. I’m being picky, but your heading ‘Tropoelastin and Elastin’ should read ‘Elastin and Tropoelastin’ because your information below begins with information on Elastin first.

The images are all placed in appropriate spots and the information that refers to them is very well done. The hand drawn image, ‘Process of Elastic Fibre Assembly’ is superb and aids in my comprehension and understanding of the concept your were trying to explain.

I think your wiki could include some information on the developmental stages of elastic fibres (from the embryo and compare it to the final stage of the fibre in an adult?)

The comparison of elastin fibres to a rubber band was genius, and allowed me to further understand and get an idea of just how essential elastin fibres are! This was a good way of showing that you can teach at a peer level. I like how you related the function of elastin with heart, lungs and the skin – a great idea.

More information and research needs to be added under the ‘Skin’ heading. I think you are going to do this anyway, but add some information on the five layers of skin and maybe include an image (it would be useful and also because ‘Heart’ and ‘Lung’ also has one!)

Images and/or a table could be used in the disease section. There’s a lot of information to get through and this may be useful.

Fix up the spelling mistakes before submission and also be consistent with your spelling – fibres vs fibers.

""Group 4 Peer Review""

Immediately, there’s a link to the ECM – good job. The rest of the introduction however has too much information and too much structural information here. Move this further down your page to where it is more appropriate.

The information in each section is actually quite detailed and would benefit with some images so that it was easier to visualize and help aid your explanations and concepts. The structure section I think needs to be reviewed as it jumps around too much in trying to describe each component of fibronectin. The dot points used to describe Fn1, Fn2 and Fn3, were a great idea and the information is clear and concise.

I can’t currently see how the image ‘The complex of ROBO1…’ fits into your wiki because there’s no information relating to it (other than a few sentences in the disease section). As well as the other images, make sure you further explain the image, to give readers more information, in the actual image file.

Your embryogenesis section is a great addition to your wiki and is well done. An image here would be useful though. Add some images to your disease section for better visualization on what you are describing. I’m not sure if you’re leaving the ‘Current Research’ section as it is, but it would benefit from a sentence or two, explaining each article and why you think it’s relevant/important.

Your sub-headings show you have a good understanding of what your topic is about, and what your wiki needs in order to inform your readers about topic. Your text referencing is extensive and well documented so far, good job. Image referencing needs some fixing up before submission though. There are some grammatical errors so be sure to go back and fix them up.

""Group 5 Peer Review""

The laminin introduction is well done and different to the other wikis. There’s an immediate link to ECM – good job. There may be too much information here, as you seem to overlap it in the structure section again – consider reviewing this. History section would be better as a timeline or overall, with less information and just the key points.

There needs to be a lot more referencing in the structure section. The images however are very well done and further information about the image is provided in the image file which is good. Be sure to add an image produced by a student, I’m not sure if a student did the image ‘Laminin Structure’ though… If yes, make this clear in the referencing of the image.

Function section needs a lot of work. Chose only a few laminin to present in your wiki as there is way too much information for us to read if you include all of the ones you currently have listed.

More images in disease section and shorten the information. Your wiki has so much disease information that it looks like this is the focus! – review this. Consider putting this information in a table as you don’t have one in your wiki yet. Also shorten the anitbodies section and focus on one or two.

Your referencing is also different to the other wikis, I’m assuming you’re leaving it like this for now and changing it later? It’s a little too messy and unprofessional like this. Fix up the current in text referencing you have and make sure you’re not breaching plagiarism by just putting slabs of information in. There are some grammatical errors so be sure to go back and fix them up.

Would an embryogenesis section prove useful and add to your page?

I don’t think this is as unorganized as everyone thinks – you have good headings and sub-headings (minus the function section which needs to be shortened with a few laminins) and I think you can see how your project will look in the end and what you need to include to inform your readers about your topic. Keep at it and take on board what everyone is saying. Heads up. Haterz gon hate. Lol

""Group 7 Peer Review""

Finally an introduction that is spot on! I really think it’s great. Immediate link to ECM – good job. Good start to the history section with the table but more information needs to go here. I’m not sure if you’re leaving the ‘Current Research’ section as it is, but it would benefit from a sentence or two, explaining each article and why you think it’s relevant/important.

The ‘Function Layers’ section/heading is an appropriate addition to your wiki and headings as it is a combination between structure and function and wouldn’t have fit perfectly into either of these – good job.

The structure section needs some more information and it would be good to include a hand drawn or student produced image here. Great use of images throughout the page. Function and abnormalities sections I find I hard to fault – again, good job.

The ‘additional info glomerulus’ pop up is a great addition – aids in that section of your project. The hand drawn image here is good and the use of color to differentiate the structure is effective.

I think you could come up with an analogy that would contribute to your peer teaching skills and contribute to your wiki! Would an embryogenesis section prove useful and add to your page? Your sub-headings show you have a good understanding of what your topic is about, and what your wiki needs in order to inform your readers about topic. Fix up your referencing by using the wiki editing basics that Mark gave us! Some of your image referencing and image file information however, is good, and I think gives readers that extra bit of information that they needed – fix the other images up though (‘basement membrane layer interactions’).