User:Z3459592

From CellBiology

Attendance

Lab 1 --Z3459592 (talk) 16:34, 12 March 2015 (EST)

Lab 2 --Z3459592 (talk) 16:53, 19 March 2015 (EST)

Lab 3 --Z3459592 (talk) 16:08, 26 March 2015 (EST)

Lab 4 --Z3459592 (talk) 16:14, 2 April 2015 (EST)

Lab 5 --Z3459592 (talk) 16:01, 16 April 2015 (EST)

Lab 6 --Z3459592 (talk) 15:58, 23 April 2015 (EST)

Lab 7 --Z3459592 (talk) 16:00, 30 April 2015 (EST)

Lab 8 --Z3459592 (talk) 17:13, 7 May 2015 (EST)

Lab 9 --Z3459592 (talk) 16:07, 14 May 2015 (EST)

Lab 10 --Z3459592 (talk) 16:02, 21 May 2015 (EST)

Lab 11 --Z3459592 (talk) 16:08, 28 May 2015 (EST)

Lab 12 --Z3459592 (talk) 16:04, 4 June 2015 (EST)

Lectures

Lecture 1 Eukaryotes and Prokaryotes

Lecture 2 Cell Membranes and Compartments

Lecture 3 - Cell Nucleus

Lecture 4 - Exocytosis

Individual Assessments

Lab 1

Condensation and fragmentation caused by HAMLET.png

[1]

Condensation and fragmentation caused by HAMLET


Anders P Hakansson, Hazeline Roche-Hakansson, Ann-Kristin Mossberg, Catharina Svanborg Apoptosis-like death in bacteria induced by HAMLET, a human milk lipid-protein complex. PLoS ONE: 2011, 6(3);e17717 PMID:21423701


© 2011 Hakansson et al. 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.

Lab 2

This article tests a sample generator program (TestSTORM) which aims to increase image quality of super-resolution microscopy. Super resolution microscopy methods currently requires system modifications to achieve the best resolution however this takes time and money. Some factors that require adjusting are; dye choice, labeling stratergy, microscope quality, frame rate, image processing, camera exposure time. TestSTORM aims to optimise the parameters to give the best outcome quicker.

From the tests, the program was effective in creating an image of the sample by combining 4 patterns (star, array, vesicles and lines). However, there were some artifacts in the results showing that the program is not perfect.

<pubmed>24688813</pubmed>


Lab 3

Paraformaldehyde MSDS

individual assessment


The Role of integrins in the trabecular meshwork

This paper[2] is about the role of integrins and how they can control the function of the trabecular meshwork. Integrins are known to promote adhesion to the ECM however they are not just adhesion receptors they act as conduits to convey information about the ECM. This signalling regulates many processes of the trabecular meshwork such as growth factor and cell death. There are many different types of integrins in the trabecular meshwork, and this paper found that they are likely to have unique and specialised functions.


Molecular Biology of the Cell. 4th edition.

This book [3] talks in general about what integrins are, structure, signalling and how they interact with the cytoskeleton.


RGD and other recognition sequences for integrins (review)

This review [4] looks at how the discovery RGD by ruoslahti has lead to a large number of pharmaceutical applications explaining how it binds and the importance of cell adhesion.


The emergence of integrins: a personal and historical perspective

This article [5] discusses what lead to the discovery of intergrins. Serveral investigations help lead to its discovery including; the investigation of fibronectin structure, monocolonal antibodies that had been raised against chicken myoblasts. The investigation of the fibronectn lead to a small fragment of fibronectin that promotes cell adhesion which is RGDS. The monocolonal antibodies lead to CSAT and JG22 being discovered which interfered with myoblast adhering to the matrix. From this Hynes deduced that the CSAT and JG22 antigen was the molecule which links the myoblast to the matrix.


http://sciencewatch.com/nobel/predictions/cell-adhesion This article is on the history of integrins. It states that Richard Hynes and his group discovered and named the protein 'intergrin' which connected fibronectin to actin in the cell wall. While Ruoslahti identified RGD peptide (a small fragment containing a sequence of 3 amino acids) which is a vital recognition sequence in the integrin family. Both are accredited for its discovery.


intergrins (review)

This review [6] which provides the basic facts about integrins hence why I dot pointed for future reference when we do the actual page :)

- cell adhesion receptors

- The name integrin was given to indicate the importance of these receptors for maintaining the integrity of the ECM.

- RGDS peptides enabled us to see that functional receptors of intergrins are heterodimers

- composed of alpha and beta subunits which are non-colvalently associated

- grouped based on ligand binding properties

- alpha subunit determines which ligand it binds

- alphaI domain - inserted domain ~200 amino acids

- Beta subunit connects to cytoskeleton

- integrins can exist in a compact bent conformation

- links ECM and cytoskeleton, mostly actin cytoskeleton

- by-directional signaling receptors


Integrin structure.png

[7]

This picture shows the structure of an integrin on both sides




<pubmed limit=5>Cell Signalling in Extracellular Matrix</pubmed>


Lab 5

Genotypepercentage.PNG

lab 5 - how tm4 effects the genotype of a cell


Lab 6

Identify an antibody against an adhesion junction protein that is commercially available.

- The β1 integrin (clone P5D2) antibody


Add a link to the original data sheet page and identify the type of adhesion junction.

http://www.emdmillipore.com/Web-US-Site/en_CA/-/USD/ShowDocument-File?ProductSKU=MM_NF-MAB1959&DocumentId=201306.7177.ProNet&DocumentType=DS&Language=EN&Country=NF


Include the following information: type of antibody (polyclonal, monoclonal), species raised in, species reacts against, types of application uses, and if available any reference using that antibody.

type: monoclonal

raised in: mouse

species reacts against: Humans

Applications: immunoprecipitation, functional blocking, FACS anaylsis, immunohistochemistry

Article which uses this antibody:

Mesothelial cells promote early ovarian cancer metastasis through fibronectin secretion. [8]


http://www.jci.org/articles/view/74778


Lab 9

http://www.atcc.org/Products/Cells_and_Microorganisms/Cell_Lines/Human/Alphanumeric/CRL-11515.aspx

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

http://www.atcc.org/Products/Cells_and_Microorganisms/Cell_Lines/Animal/Mouse/CRL-1636.aspx

Dulbecco's modified Eagle's medium with 4.5 g/L glucose and 10 mcg/ml insulin, 90%; fetal bovine serum, 10%

http://www.sigmaaldrich.com/life-science/cell-culture/classical-media-salts/dmem.html

Streptomycin and Penicillin are used in combination to destroy all gram negative and gram positive bacteria in cell cultures.


Peer Reviews

G7

The introduction was written very well and provides an idea of what the overall page is about. I think that it was a good idea to include this, as it will save the viewer time if they were looking for something specific on the basement membranes. The history is obviously still a working progress but so far it is looking good by displaying it as a table and giving your page a balance of visual and written media to keep the viewer interested.

The current research subheading seems like a waste of time to me at the moment. I’m not sure if it is finished, but having 5 papers listed does not tell the reader anything. I think you need to go into detail about what each of these papers mean and explain what this could lead to.

I’m not a total fan of the use of dot points but I guess it does show the information in a simple and concise form. Preferably put a space between the bullet point and the text, as it just doesn’t look right.

The structure component is still a working progress. However, if you are going to use abbreviations make sure to mention the full name atleast once before it or have a glossary that the viewer can refer to (which you have done for most but what is GAG?).

The function and abnormality section is well done. It provides the viewer with easy to understand information with a mixture of visual and written media. From first glance it looks like you have referenced well but you have multiple copies of the same reference in the reference list which is easily fixed. All the images seem to be referenced correctly from what I can tell.

Overall this project is on the right track however you will definitely need more on structure and maybe a hand drawn sketch of the structure. Adding a video may also help the viewer gain more from this page.


G6

This project is still incomplete having nothing written for the introduction and history section. The structure has some information however this is also missing parts. From what I have read so far there are a few grammatical and spelling errors. Maybe have someone else go over it, which is what I normally do because I know I’m not the best at english. You have used some images to keep the viewer engaged however, they are not referenced properly as they do not contain the copyright information.

The function section seems to contain a lot about the structure of cartilage. Maybe move this into the structure subheading and focus more solely on the function of cartilage and type II collagen. Recent findings are also under function which I personally don’t think belongs there unless these a findings about the function of type II collagen. Captions should also be underneath the photos.

When using abbreviations make sure to put what the whole thing is atleast once before it or in a glossary so that the reader can refer to it. What is COL2A1? Im guessing its collagen type 2 gene? But what is A1? If it is maybe put it in brackets to make it more obvious rather than commas. I don’t like how you have incorporated the references in the text because it just makes it so much harder to read fluently. Also when amounts are involved in text, write it out instead of putting the number, for example two instead of 2.

Overall, the project is good as it has got good structure and is on the way however it is missing quite a bit of content across all the areas. Make sure to add a hand drawn image and to fix the image references as from what I can tell that is what Mark loves to take marks off for. Also there are a lot of repeats in your reference list, which can be easily fixed in the editting process. good job so far :)


G5

Peer Review


The introduction is provides a good idea what the page is about, speaking generally about each topic. However, I don’t think the lists at the end of the introduction are in the right subheading. I’m assuming all the references are going to be compiled at the end of the page in the final editing process. I personally don’t see the point of doing it this way since it just makes it look messy and then you are going to have to fix up all the repeating references since its harder to tell what the other people have used.

The history section has been well done in my opinion, maybe add a timeline to quickly summaries the history and give a balance between visual and written media?

The structure section is very detailed and informative however it just seems like a slab of text which makes it very boring to read. I think you guys need to add more visual media such as pictures or videos to make it more engaging.

I do not like how you have set out the function section at all (no offense). I think you need to condense the subheadings into a more general one because it just looks silly listing all the different types and will become just a wall of text, which would not be enjoyable to read at all. If it were me I’d focus on the general function of laminins then go into a few of the main types.

Again the abnormality section is detailed but it just seems like slabs of text. Maybe move the pictures to the right to make it more interesting instead of slab of text then a picture.

Overall, the page is well on its way with a lot of content which is good because now you can cut back and make it more appealing. You definitely need to add more images to make your page more engaging because at the moment it is very boring to read. Lastly make sure all your images are reference correctly and containing the copyright information!. The copyright information for one picture is on the page for some reason when it should be in the pictures page. Other than that good job! :)


G4

The introduction is well done giving the reader a general idea of what fibronectin is. However, the page only contains two images, one of which does not have a caption. At the moment it just feels like slabs of text making it very dull and boring to read. You definitely need to add more visual media throughout the entire page such as pictures and videos. I like how you have done the history section. By using dot points it has keep it simple and easy for the reader to comprehend. Maybe convert it into a table to brighten up the page and make it visually appealing since it is just slabs at the moment.

The structure section contains good content and explains the structure of fibronectin well. I like how you have given three examples and briefly outlined the difference between them. Again images are needed, maybe put the image to the side so it isn’t just slab of information then text. You definitely need to add a caption to the picture to explain what it is, otherwise it is just pointless having there. I like how the function section is broken up into its various individual functions. However, I think you need to speak generally first before you jump into each individual function.

The abnormality section is good but I think it is missing important information at the current moment which is expected as it is still a working progress. I think you need to explain what each of the abnormalities are such as ehlers-danlos syndrome instead of just saying what causes it. You say they have ‘diminished fibrillar network’ but what does that mean for the patient?

Overall, the content and structure of the page is good. However, you really need to add more visual media to keep the reader engaged. Also make sure to fix your reference list as there are a few repeats.


G3

The introduction is well written as it is accurate and concise. You have briefly mentioned the discovery/history of elastin in the structure and components subheading. You may want to create a section devoted to history as it is always nice to know how we know the things we do today. Mark also seems to love history :).

The structure section is well done, I especially like how you talked about the synthesis of an elastic fibre. The hand drawn diagram is also very good as it is colourful which captures the viewers eye but is also very informative (it makes my drawing look bad)

The function section has been done really well, providing the reader with easy to understand information. However the two images in this section have no caption. How is the viewer suppose to draw information from this if they don’t know what it is? On a whole, I think the page needs more visual material such as pictures or videos such as something to support the rubber band analogy. Have a video showing an elastic band stretching and returning to its original size? That’s just a suggestion it is already pretty well explained.

From the looks of things the referencing has been done correctly, there are no duplicates in the reference list from what I can see. However, there are a few empty slots which Im guessing they are not pubmed articles. You need to manually put them in which is a pain but easily fixed :). The images look correctly referenced from what I can tell, containing the appropriate copyright information.

Overall, I think this page is coming together really well. There is still more research that needs to be done and you need to make sure you try keep a balance of visual and written media to keep the viewer engaged.

G1

Firstly, I personally really like the banner at the top as it captures the viewers attention even if it doesn’t give any information on the topic. The introduction is done really well as it speaks generally about proteoglycans and then zooms in on the small Leucine-rich proteoglycans. My only complaint is “but first, some history..”. Is that really necessary to have? Just seems a bit casual.

The history section gives a good background to the discovery of proteoglycans. You could possibly improve this section by creating a timeline to simply the information and make it more visually pleasing?. The synthesis section is not very clear, maybe add a diagram or a video on how it is synthesized to reinforce the text.

The structure section was rather confusing and took me a couple of time to comprehend what it was saying. I think you may need a diagram of the general structure or something to make it clearer. The function of proteoglycans was covered well. However, it just seems like a slab of text at the moment and was rather boring to read. You also might want to explain what fibrillogenesis is.

The role of SLRPs in disease is definitely the strongest section at the moment as it contains good content and a good balance of visual and written media. I also like how a glossary is at the end which can be referred to by the viewer if they forget what an abbreviation stands for.

Overall, this is probably the best project I’ve seen (I started from group 7 for some reason). This page is well on its way to being complete, however you may want to add more images to engage the reader more. Make sure to add a caption to the table and the first image in the introduction. Other than that, I struggled to fault this page even the referencing is correct from what I can tell.


Lab 12

<pubmed>26051997</pubmed>

Microarrays are used to measure the expression of a large number of genes at the same time. In this paper they used microarray to compare and find dysregulated genes and miRNA unique to pRCC1.

External Links

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959829/

PubMed


Reference

  1. <pubmed>21423701</pubmed>
  2. <pubmed>3991962</pubmed>
  3. <pubmed>Alberts B, Johnson A, Lewis J, et al. New York: Garland Science; 2002.</pubmed>
  4. <pubmed>8970741</pubmed>
  5. <pubmed>3493146</pubmed>
  6. <pubmed>2784866</pubmed>
  7. <pubmed>3561355</pubmed>
  8. <pubmed>25202979</pubmed>