- 1 Personal Page
- 2 Individual Assessments
- 2.1 Lab 1
- 2.2 Lab 2
- 2.3 Lab 3
- 2.3.1 Paraformaldehyde
- 2.3.2 Role of Integrins in Disease: Case Study
- 18.104.22.168 Integrins and cancer: regulators of cancer stemness, metastasis, and drug resistance (Review) 
- 22.214.171.124 Variety in the tumor microenvironment: integrin splicing regulates stemness 
- 126.96.36.199 Tissue mechanics modulate microRNA-dependent PTEN expression to regulate malignant progression. 
- 188.8.131.52 Integrin activation controls metastasis in human breast cancer. 
- 2.4 Lab 5
- 2.5 Lab 6
- 2.6 Lab 9
- 2.7 Lab 11
- 3 References
Porphyromonas gingivalis and macrophages 
In the past, light microscopy was the tool that biologists relied on to study living things. However, with the arrival of the 21st century super resolution technology was developed in stages with the assistance of new discoveries. Super resolution had overcome some of the limits presented by light microscopy, such as the degree of magnification by making a small aperture to prevent light from diffracting near the sample and reducing the quality of the image. With these new technological advanced, biologists can study cells and their organelles with more molecular accuracy, and these details have been enhanced by new techniques such as fluorescent tagging of molecules.
Although this has been a large step of achievement for microscopy and therefore the techniques of study in science, it has disadvantages as the technology isn’t perfect. Factors such as the type of fluorescent dye used and the artifacts present in the imaging need to be considered, and as a result there are strict guidelines for the processing of super resolution images. By standardising this process, the guidelines for analysing data also becomes simpler. Despite these considerations, super resolution microscopy has provided more unknown domains for sciences to explore and clarify questions that have been asked for decades.
Putting super-resolution fluorescence microscopy to work 
Role of Integrins in Disease: Case Study
Integrins and cancer: regulators of cancer stemness, metastasis, and drug resistance (Review) 
This article shows the interactions between the integrins on cell surfaces with the environment - the extracellular matrix and their role in cancer and their metastasis. Integrins have multiple types of receptors derived from various combinations of their alpha and beta units, and tumour initiating cells present integrins like alpha 6, beta 1 and 3 on their cells, which are usually only present on stem cells. This means that they can self regulate proliferation and even differentiation. However different integrins being expressed on the cancer cells also allow them to survive in areas which are usually out of bounds, i.e. outside of the ECM, and this provides some understanding as to how cancer cells survive and proliferate during dissemination in the blood and metastasis. Integrins assist in tumour progression and drug resistance through their interaction with the ECM, where the ECM can regulate cell sensitivity to therapies.
Variety in the tumor microenvironment: integrin splicing regulates stemness 
This article focuses on the findings of expression in integrin subunits α6B and α6A and its relationship with the development of triple negative breast cancer. It is implied that ESRP1 (epithelial splicing regulatory protein) levels affect the expression of integrin α6B, which possibly promotes anchorage independent growth of tumours, resulting in metastases. The important of integrin expression is reinforced in this article, and current research targets the genes that make TICs or the general population express TIC like features.
Tissue mechanics modulate microRNA-dependent PTEN expression to regulate malignant progression. 
MiRNA affects integrin dependent adhesion, and the stiffness of the ECM subsequently affects the levels of mature MiRNA in a cell. In particular, it is discussed the MiRNAs play an essential role in tumour mechanics, where integrins are the facilitators of change in expression. Specifically in mouse breast cancer, we see that miR-18a regulates the maligancy of breast cancer by targetting the tumour suppressor PTEN. The effect of the ECM in regards to the metastatic potential of a tumour can be seen to interact with the actions of integrins on cancer cells.
Integrin activation controls metastasis in human breast cancer. 
It is seen in breast cancer cells that integrins can bind to platelets in the bloodstream, therefore alluding to the possibility of metastasis. The activated αvβ3 integrin allows for breast cancer cells to do so, and therefore the expression of this integrin on cancer cells indicate the potential for metastasis. It is not however a definitive factor for metastasis, but has an essential role in cancer cells metastasising through blood dissemination.
LM609 is a specific antibody that marks αVβ3 integrins, which is a key integrin involved in the process of cancer metastases. It is a murine derived antibody that is used usually at 10-25ug/ml. The secondary antibody that was used in the following paper for LM609 is AlexFluo 555-labelled secondary antibody.
Roles for GP IIb/IIIa and αvβ3 integrins in MDA-MB-231 cell invasion and shear flow-induced cancer cell mechanotransduction 
Antibody: NCH-38 is a monoclonal mouse antibody that works against human and rat antigens. It binds to cadherins which are usually in adherens junctions. It is mainly used in immunohistochemistry, like in the following article.
E-cadherin downregulation at the infiltrating tumour front is associated with histological grade and stage in colorectal carcinoma of Malaysians. 
Keratinocyte-Serum Free medium (GIBCO-BRL 17005-042) with 5 ng/ml human recombinant EGF, 0.05 mg/ml bovine pituitary extract, 0.005 mg/ml insulin and 500 ng/ml hydrocortisone.
Keratinocyte Serum Free Medium Contains: Keratinocyte-SFM Keratinocytes Supplements Bovine Pituitary Extract (BPE) EGF, Human Recombinant
Dulbecco's modified Eagle's medium with 4.5 g/L glucose and 10 mcg/ml insulin, 90%; fetal bovine serum, 10%
Streptomycin and Penicillin are used in combination to destroy all gram negative and gram positive bacteria in cell cultures.
Group 1 is doing their project page on small leucine rich proteoglycans. Upon first glance of the page, it looks like most of the sections are well planned out, as well as the content in the sections being relatively comprehensive and gives a good idea of what topic they are under. They also seem to have covered a lot of ground for the stage that the page should be in. The hand drawn illustrations were also a really good way to summarise the information that was presented in text, but I kind of wonder why I need to know all of that information in detail. I also think that the disease sections should really emphasise the relation of proteoglycans with the extracellular matrix. In the introduction of the function section, there are paragraphs on the specific molecules that were researched, and it is probably better off if you put that in the section under the title. The only consistent problem that was present in the sections is small spelling and grammar mistakes, and that would just be fixed by looking over the page in the last stages to make sure that all it correct and easiest to understand. Perhaps another change that can be made is in the disease section where you can really add more information about each disease that is mentioned, through text or through pictures, but it is also questionable as to whether or not that is necessary. There are some sections that haven't been filled in, and hopefully that can be done soon, not really too much of a problem.
All in all, this was actually a really good page, and there is a lot of stimulation for the reader, whether it be by text or by images. Well done and keep it up!
Group 2 is doing their project page on Elastic Fibres. The first thing that needs to be developed is the introduction, but it is understandable that you need the rest of the information to be finished before you can summarise it simply in the introduction. There is good use of illustrations and pictures to summarise the information accompanying it, but as I scrolled down I got confused when the information transitioned suddenly to examples in the heart, lung and skin. It would be good if there is a separate heading to clearly mark out the examples regarding how elastic fibres function in common tissues where they exist. The images in that section also need to be referenced, may have to ask Mark how to do it if you got it from virtual slides (it looks like those images). There are some uncompleted parts here but thats fine as well, as long as they are finished soon. In the diseases section, are there any pathways related in the diseases that involve other molecules that interact with the elastin? Do these diseases illustrate the role of these elastin fibres in the extracellular matrix? You may want to make sure that references section is actually a new section, I have a feeling that the coding is wrong.
Overall I think this is a project in development, but the elements are all there, just need to be developed a little :D good job!
Group 4 is doing their project page on fibronectin. When reading the introduction, I felt that it included too much information from the structure - I would really expect to see some words like "disulfide" in the actual description of the structure in detail in the appropriate section, so maybe it would be an idea to review that section. The history section seems to be a little small, but it would be a good idea to put it in a hand drawn timeline or something, rather than just seeing a few dot points. I also feel like there are a lot of subsections to each category of information, but there's not a lot of detail regarding each one, perhaps it would be easier to either put them in more general categories, or elaborate on each of them more if there is time. I'm hoping that the current research section will give me more insight regarding the relation of fibronectin with disease, and integrating its function with its relationship with the extracellular matrix as well. There are some replicates in the reference section, that can be fixed as well. I feel like more images can be used to better represent the information that is being discussed, and it might even provide a good explanation for parts of material that you can't actually cover in the text, but can talk about the mechanics in the picture instead.
Overall this project is pretty good, but there are some things can be worked on in terms of structuring the page, and making it easier to navigate.
Group 5 is doing their project on Laminins. Upon the first look of their project page, it looks like it is HIGHLY disorganised. The references are separated for each section, and when I try to organise the information I'm reading, I feel like the categorising is just hard to understand. Also, the function section is just filled with a huge list of laminins, which makes me wonder if such a long list is needed, or if all of them are just as important and needed to be covered. To be honest, it is probably a better idea to take a few significant laminins and concentrate the research and article around them. Quality information is better than quantity, and maybe if you really must cover all of them, a table will help illustrate a summary of the information. Also try to break up some blocks of text into smaller paragraphs or under subheadings because it makes it easier to read, but thats just an opinion. For the diseases section, it seems like the information is categorised by papers regarding the disease. A suggestion would be to try and integrate some of the information and generalise it, because you run the risk of repeating the same information in the different papers that you cover. Some more images can be used to break up the text.
Apart from all of that, it was really interesting reading about laminins. The organisation of the page could be better, but if these changes are considered their page will be much more welcoming and easier to the eye :) Good job!
Group 6 is doing their project on Type II Collagen. The group page at first sight looks really organised, and the most important information is present on the page. I also think that the images included are relevant and good as a summary for the information, but perhaps more pictures can break up the text. There are some issues with spelling and grammar, however that just needs to be edited in the final stages of the assessment. Again its not necessary, but perhaps the information in the "Current understanding and Research" section can be integrated rather than put into categories of papers. However, regarding that last point, it is really good that it was made clear what part of research was being addressed in the information and gave the reader a good idea of what was going to be addressed. I'm not sure what you plan to do with the list of antibodies, but perhaps it is better to put it in a table to condense the information and make it easier to refer to.
All in all a good assessment, just needs to be wrapped up at the ends, especially the introduction and history :) Good job!
Group 7 is doing their project on the basement membrane. When examining the layout of the page, it is confusing to see that current research is actually put at the top. If you consider reading it chronologically, it wouldn't make sense because the reader has no idea what the basement membrane is or its function, and already you put the current research before them. Another idea would be to keep the references in one place, though hopefully the ones in the current research section are for frequent use. In the formation section, it really needs to have moved on from dot point form, and it is the same for the functional section. It seems really lacking in the sense that theres not much text, or explanation in that section and I think there should be more elaboration of information to go with the image provided. The structural components of the basement seem simple enough to understand but again, the information isn't presented in a way that seems educational, but its clearly a work in progress. The sections regarding abnormalities and function of the basement membrane is really comprehensive and clearly organised, and is a good model to base the rest of the page on.
This assignment page needs a lot of work, both to make the information more interesting but also to actually add information, but so far they have the right idea. Keep at it!
Correlation between the expression of integrins in prostate cancer and clinical outcome in 1284 patients 
The microarray technique was applied in this paper. Microarrays are essentially a piece of glass where sections of desired DNA are attached, and this allows scientists to use different samples of DNA from different patients to test the gene expression of that in study, in this case, integrins.
- <pubmed> 3658619 </pubmed>
- <pubmed>25305804 </pubed>