Difference between revisions of "User:Z3375627"

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*Lab 10 --[[User:Z3375627|Z3375627]] ([[User talk:Z3375627|talk]]) 16:23, 21 May 2015 (EST)
*Lab 10 --[[User:Z3375627|Z3375627]] ([[User talk:Z3375627|talk]]) 16:23, 21 May 2015 (EST)
*Lab 11 --[[User:Z3375627|Z3375627]] ([[User talk:Z3375627|talk]]) 16:15, 28 May 2015 (EST)
*Lab 11 --[[User:Z3375627|Z3375627]] ([[User talk:Z3375627|talk]]) 16:15, 28 May 2015 (EST)
*Lab 12
*Lab 12 --[[User:Z3375627|Z3375627]] ([[User talk:Z3375627|talk]]) 16:07, 4 June 2015 (EST)
==Individual Assessment== <!-- Be Gentle -->
==Individual Assessment== <!-- Be Gentle -->

Revision as of 16:07, 4 June 2015


Lab Attendance

Individual Assessment

Lab 1


Cells Eukaryotes and Prokaryotes

PMID 25513760


Localization of prokaryotic protein expression.jpg

Localization of prokaryotic protein expression [1]

Lab 2

In 2014, Kevin Takasaki and Bernardo L. Sabatini, conducted a study on whether the time-course of a passive diffusional equilibrium across the spine neck of a dendritic spine neck was determined by its structure. Previous optical technique, 2-photon laser scanning microscopy (400nm), was limiting image resolution of dendrite spine necks, having a a diameter of around 100nm. using stimulated emission depletion (STED), fluorescence imaging of neurons was allwed to a resolution of around 50nm within brain tissue, making it viable to distinguish the fine morphology that could predict the synaptic signalling of the spine

Brain tissue sliced from the hippocampus of mice was prepared and dye filled and then photobleached. Using this combination of 2PLSM and STED, the STED-2P microscope was able to make a morphological analysis and observe diffusional transfer across the spine neck. Although the study demonstrated that more complex geometric models may be required in the instance of those particular dendrites, the use of STED-2P in nanoscale visualisation of other biological systems could be of huge potential [2]


Lab 3

Paraformaldehyde msds


Fibronectin wound healing.jpg

Fibronectin Wound healing [3]

Reference Searching


Plasma Fibronectin (pFN) can be found to be upregulated in tumour cells, supporting tumor retention. Tumor cell adhesion to and invasion in fibrin when paired with fibronectin (fibFN) is mediated mainly by integrin avB3 and activated by the former. fibFN however had no effect on the cell tumor growth. pFN in accociation with fibrin is shown to assist in the cell adhesion of clotted plasma. pFN does not assist in the initial tumor cell arrest.[4]

<pubmed>23356939</pubmed> Sheep Carotid ateries were used to test the coating of proteins on Extracorporeal membrane oxygentators to overcome it's limitations with hemocompatibility, the activation of the coagulation and complement system as well as plasma leakage and protein deposition. Fibronectin increased cell attachment compared to other methods (including uncoated) on ECMO oxygenator membrane. 93% FN cells seeded adhered on treated surfaces after 24hrs compared to 73% on control. adherance occured for 4 days which leads to the discussion of endothelialisation of ECMO membranes to make them more suitable for long term use. [5]


Plasma fibronectin is found to deposit in vessal injury sites (independant of fibrinogen, von Willebrand factor, β3 integrin, and platelets) before before acummulation of platelets which was previously understood to be the first wave of hemostasis. Promotes platetlet aggregation when in conjunction of fibrin, but acts conversely when fibrin is absent. Working off the fibrin gradient, fibronectin is a regulator of thrombosis[6]

<pubmed>22514136</pubmed> A high fat diet was experiment in mice was conducted in order to cultivate atherosclerotic lesion and the effect the lack of plasma fibronectin would have on the formation of these lesions. Mx-Cre-mediated deletion of the the FN gene was found to reduce atherosclerosis formation.

Plasma Fibronectin is found to help and hinder atherosclerosis. It increases the number and size of Atherosclerosis plaques that form with it's deposition within lesions, but also helps in the formation of a protective fibrous cap, helping prevent rupture of said athersclerotic plaque. Also indicated that plasma fibronectin, rather than the hemopoietic cell-driven fibronectin, is deposited at atherosclerosis-prone sites prior to the development of atherosclerotic lesions.[7]

Lab 4

Knockout mice lab worksheet

Lab 5

Tm4 against control.PNG

Lab 6

Identify an antibody that can been used in your group's extracellular matrix project. Anti-Fibronectin antibody [A17] (ab26245) - This antibody inhibits integrin-mediated cell adhesion to the cell binding domain of fibronectin. It can be used to probe fibronectin conformation. Strong reaction is seen in ELISA with thrombospondin directly coated onto the microtiter well.

Identify the species deriving the antibody. Mouse monoclonal [A17] to Fibronectin

Identify the working concentration for the antibody. stored at 100 µg at 1 mg/ml

1/100 for Western Blotting

1/30000 for enzyme-linked immunosorbent assay

IP, IHC-P, IGC-Fr, ICC/IF: Use at an assay dependent concentration.

Identify a secondary antibody that could be used with this antibody. Goat Anti-Mouse IgG H&L (Alexa Fluor® 488) (ab150113)

Identify a paper that has used this antibody. <pubmed>1385458</pubmed>[8]

Lab 7

no individual assessment

Lab 8

Lab 9

Cell line databases


human: Hybridoma Collection: W6/1


Mouse: Hybridoma Collection: OX-80


  • ATCC

Human: 293T/17 [HEK 293T/17] (ATCC® CRL-11268™)


human cell line culture medium: Dulbecco's Modified Eagle's Medium (DMEM) (ATCC® 30-2002™). To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.


medium formulation: http://www.atcc.org/~/media/D7399222FD8B4EF68FD56DD8058804BA.ashx

Mouse: MPRO Cell Line, Clone 2.1 (ATCC® CRL-11422™)


penicillin streptomycin This antibiotic mixture contains penicillin and streptomycin. Penicillin is an anti-bacterial agent produced by Penicillium. It interferes with the final stage of bacterial cell wall synthesis, the cross-linking of different peptidoglycan strands. Streptomycin is an anti-bacterial agent produced by Streptomyces. It binds to the 30S subunit of the bacterial 70S ribosome and blocks the initiation complex of protein synthesis. The antimicrobial spectrum for Penicillin- Streptomycin Solutions includes gram-positive and gram-negative bacteria.

Peer reviews

Group 1 Peer review

The banner is a fantastic opening for the page directing attention to the page as a whole. It livens up the information being presented, good job! Introduction is well laid out but i would do without the section leading to the next segment. it make the page read out as an essay not a informative piece. History (and future) section needs a title rewording, but content is good. need o see more citations in the section. Synthesis needs a bit more to the section. maybe a picture? The table in Structure section was a good addition, but the text needs to be broken up into more paragraphs so as to not look like a column of text. Function info good, needs (a) picture. I'd like to see more in the individual proteoglycan section rather than a link to studies. in a drop down with some text on each would be good (or perhaps this was unintended and will be removed?)Disease section is very good. the rest should like this in terms of information level. Glossary is a nice touch at the end. As a whole, great effort guys!

Group 2 Peer review

Introduction text is good, but doesn't do a very good job in drawing in the reader's attention. Some formatting should fix that up. Discovery (history) section is very informative, but maybe try to add the images that you refer to in that section. Future/Current Research obviously needs to have something added. I would say that the interest in integrins section is redundant and doesn't need to be there. Consider removing or placing that section in a dropdown/link as it doesn't really add anything to the page. make sure to review what you have on the page before submitting work. don't want parts like the NOTES comment or in the intro to Structure. Structure information looks good, but there is very little citations, none, in some areas. make sure to cite everything guys. Some formatting work and in text review is in order, but the page is on the right track.

Group 3 Peer review The amount of information on this page is excellent, although it looks like it may be missing some citations in areas. With this great amount of text, some more formatting with more pictures added would go a long way. The student drawing looks amazing, whoever made it should do a banner at the top of the page as well! The pictures that are included should have some work done in their formatting to have them more central with the text as currently they are serving to pull attention away from the information present in the text. Missing a history and current/future research section. Not sure if that's intentional, but they both can serve and a good way of orientating the reader into the information and then lead them off to further reading if they are interested in the topic. It's a very good project, but i can't stress enough. Formatting and pictures!

Group 5 Peer review

First of all, the references need to be moved to the end of the page. it is an eyesore and makes the page hard to navigate. Introduction is very consise, perhaps too much so considering the amount of citations used. The reference to defects should be moved down to the abnormalities part of the project. History section needs some more citations and perhaps change the format of this part to less that a block of text. History should read more like a timetable. Dotpoints, dropdowns, tables, anything to make it easier to grab the important information of of this bit quickly. With the amount of text you have, having only 5 pictures, makes it a very tiresome read. adding more pictures to break the tedium is appreciated. the whole sections with only one citation each makes it like like none of the information has been cross referenced and makes me dubious to the validity of what's presented. Some more work needs to go in to making your Contents table more accessible for Navigation. there is just too much there. Perhaps downgrading all of the titles would allow for that. Finally, make sure to review your own page prior to submission to remove or rectify any notes you've placed for yourself. There is lots of information that you've got to work with. Make some effort to make it look good formatting wise and you've got a killer page here. Great work.

Group 6 Peer review

Introduction needs some information. Something that will orientate the reader into the basic concept of Collagen. History section is good for the molecular structure of collagen. Appears to be lacking from Collagen family as there is nothing below text. Information in beginning of Structure section is presented well, however work needs to be done in finishing the work. there is very little ciations in the body of text that needs to be rectified. The Skeletal bone and Fracture healing sections need more information added to the sections as there is a lot to talk about that is missing. Need to add more abnormalities and some more pictures in this section under at least a few of them to provide some variance in the medium. At the moment, the subheading in the abnormalities section is dismally empty. Current research section looks good. maybe add one more closer to submission date and maybe some links. Antibodies section is well laid out. and the formatting of this section is visually appealing. consider the work that has gone into this part and do something for the previous areas. Models and Methods sections need information. Glossary is a nice addition. perhaps place them in a table for a better look. Citations, more information, pictures, and an overhaul on the formatting. It's coming along but needs some work to get it looking good. Keep it up.

Group 7 Peer review

The Contents section is easy to navigate to all areas on the page, good work! Introduction is great in orientation of the reader and a good choice of picture to begin the page with. The formatting of the history section is a nice touch, just make sure to add more events and cite them. Current research could have some handpicked studies with a small note about what is going on in each one rather than a grab from pubmed. Could be a current research (as of 2015). Great formation text and picture, again, really helpful in making it easier for the reader to understand the content. Some formatting on this section to make it like the others would help. With the Functional layers, the information and layout is good, but if you choose to add more information (which couldn't hurt), maybe have the extra information come as a dropdown when clicking each subheading. Structual components section is a little bare. more information and pictures need to be added there. Function section has a lot of information but needs something to break up the wall of text. A table, bullet points, or pictures could remedy this. Abnormality section looks great, keep adding to the list of them. There is lots of information here, just make sure to fix up the citation list at the bottom of the page. Add some pictures and some formatting work. good work so far.

Lab 10

Stem Cell presentations

  • Group 3: Characterization of Human Induced Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Cell Sheets Aiming for Clinical Application

Lab 11

Lab 12


  1. <pubmed>23951183</pubmed>
  2. <pubmed>24847215</pubmed>
  3. <pubmed>21923916</pubmed>
  4. <pubmed>20501851</pubmed>
  5. <pubmed>23356939</pubmed>
  6. <pubmed>25180602</pubmed>
  7. <pubmed>22514136</pubmed>
  8. <pubmed>1385458</pubmed>

Group Assessment