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--[[User:Z3459282|Z3459282]] ([[User talk:Z3459282|talk]]) 16:07, 28 May 2015 (EST)
 
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--[[User:Z3459282|Z3459282]] ([[User talk:Z3459282|talk]]) 16:09, 4 June 2015 (EST)
  
 
===Lab 1===
 
===Lab 1===

Latest revision as of 16:09, 4 June 2015

Individual Assessments

Lab 1

Distribution of microtubules and microfilaments in rat basophilic leukemia cell lines.jpeg


Distribution of cytoskeletal structures in rat basophilic leukemia cell lines

The image displays the distribution of the microtubules (α-tubulin) in these eukaryotic cells (A), the distribution of microfilaments (F-actin) in these same cells (B), as well as the superimposition of these two cytoskeletal structures (C).

Reference

Pavel Dráber, Vadym Sulimenko, Eduarda Dráberová Cytoskeleton in mast cell signaling. Front Immunol: 2012, 3();130 PMID:22654883

Copyright

© 2012 Dráber, Sulimenko and Dráberová. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.


Lab 2

Journal article summary - super resolution microscopy in determining HSV-1 protein interactions

The outer protective layer and envelope of herpes simplex virus type-1 (HSV-1) was observed by Laine et al. (2015) [1] through the implementation of various techniques, one specifically being super-resolution microscopy. In particular, they utilised super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM). This type of super resolution microscopy uses the positioning of separate fluorescent molecules and their ability to fluoresce at different times, in order to construct a super resolution image. As a result, the diffraction barrier is surpassed and our knowledge of biological forms, such as viruses, is further enhanced.

Prior to this study, the structure and size of HSV-1 was fairly well understood through the use of electron microscopy and electron tomography. However, specific arrangements of proteins in certain structures, such as the capsid, were unable to be determined with the available techniques. It was through super-resolution microscopy that further insight on these layouts was attained. More specifically, the study was successful in identifying the locations of various proteins within both the envelope and outer layer of the viruses and their interactions with one another. For example, they were able to determine that the protein VPI6 interacts with another protein known as VP1/2. Subsequently, Laine et al. (2015) concluded the significance of using dSTORM for future research regarding virion structure and interactions during the different stages of its cell cycle, specifically that of replication.

References

  1. <pubmed> 25609143</pubmed>


--Z3459282 (talk) 23:41, 25 March 2015 (EST)


Lab 3

Article #1: Influence of fibronectin in cardiac development

The transcriptional repressor gene snail1 assists in the migration of cardiac precursors by influencing the assembly of fibronectin in the embryo. Abnormalities in fibronectin function result in cardiac defects, highlighting the significance of fibronectin during embryonic development. In particular, the ordered deposition of fibronectin in control embryos contrasts to the reduced and disorganised arrangement in modified embryos with inactivated snai1b. Hence, snai1b is needed for effective fibronectin assembly, which enables cardiac precursors to migrate where they are needed for successful cardiac development. Moreover, integrins are crucial for effective fibronectin function. In cases were snai1b is inactivated, addition of integrins salvages fibronectin assembly and minimises cardiac defects. Thus, the study can be concluded as having shown that snai1b modulates the expression of a5 integrin, which ultimately modulates fibronectin assembly essential for cardiac development.[1]

Reference
  1. <pubmed>24667151</pubmed>


Article #2: Role of fibronectin in fetal development

Fibronectin is seen to play a role in the maturation of the ovarian follicle. During the first and second trimesters of gestation, the mesenchymal compartment cells of the ovarian cortex and the tunica albuginea express fibronectin. This fibronectin is observed throughout the basement membrane of the developing blood vessels. Hence, fibronectin is seen to play a role in the assembly of the primordial follicles, as well as assisting in the embedding of blood vessels. More specifically, the results from this study suggest that fibronectin influences the defining of the mesenchymal compartment during fetal development.[1]

Reference
  1. <pubmed>25605128</pubmed>


Article #3: Fibronectin in differentiation of human embryonic stem cells

Fibronectin is one specific extracellular matrix protein that most effectively enables differentiation of human embryonic stem cells to definitive endoderm. Subsequently, it can be identified as having a significant role in early embryogenesis. This differentiation of cells is facilitated by integrin receptors. In particular, a5 integrin is required for human embryonic stem cells to bind to fibronectin. The study showed that as this differentiation is occurring, the expression of integrin subunits is increased. Moreover, the cells that are exposed to fibronectin, and other extracellular proteins, begin to secrete extracellular proteins, encouraging further differentiation.[1]

Reference
  1. <pubmed>23154389</pubmed>


Article #4: The influence of fibronectin on neural crest formation

It is suggested that fibronectin plays a role in cranial neural crest cell migration, as well as neural fold and neural crest formation. This is proposed through the study as a5 integrin was observed in the anterior neural ridge, the cranial neural fold, and in the neural crest cells. Moreover, fibronectin was identified as increasing the activity of a specific protein-coding gene known as BMP5. This gene is associated with chicken cranial neural crest formation. Subsequently, fibronectin is noted as influencing the expression of a growth factor.[1]

Reference
  1. <pubmed>23587661</pubmed>


Fibronectin and integrin subunits present in a blastocyst.jpg


Fibronectin and integrin subunits present in a blastocyst.[1]

(A) Double immunofluorescent staining for ITGA3 (A, FITC), FN1 (A', Cy5) and merged signals (A"). ITGA3 was mainly expressed at the cell membranes of the TE cells. FN1 and ITGA3 were expressed adjacent to each other but no co-localisation was found (A"'). (B) Double immunofluorescent staining for ITGA5 (B, FITC) and FN1 (B', Cy5) and merged signals (B"). (C) Double immunofluorescent staining for ITGAV (C, FITC) and FN1 (C', Cy5) and merged signals (C"). ITGA5 and ITGAV were mainly expressed in the ICM. Partial co-localisation with FN1 was observed for ITGA5 (B"') as well as ITGAV (C"') by the appearance of yellow areas when signals were merged (indicated by arrows) (Original Magnification ×400).

Reference
  1. <pubmed> 19126199</pubmed>
Copyright

Copyright © 2009 Goossens et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


--Z3459282 (talk) 23:48, 15 April 2015 (EST)


Lab 5

Phenotypes present in control and treated B35 cells.png

--Z3459282 (talk) 17:56, 16 April 2015 (EST)


The graph indicates that cells overexpressing Tm4 displayed phenotypes “pronged” and “stringed” more so than the control cells. Furthermore, the control cells displayed a greater number of “fan”, “broken-fan” and “stumped” phenotypes. Hence, it can be concluded that Tm4 plays a role in the growth of the neurites of these cells. More specifically, Curthoys et al. (2014) depicted that overexpression of Tm4 results in the upregulation of the actin filament bundling protein fascin. Thus, it was suggested through this study that the co-localisation of these two proteins influences the assembly of the actin cytoskeleton in the neurites, ultimately resulting in their growth.[1]

Reference

  1. <pubmed>24211701</pubmed>

--Z3459282 (talk) 23:42, 22 April 2015 (EST)


BioMed Central

http://www.biomedcentral.com/search/results?terms=fibronectin

Lab 6

The identified antibody is Volociximab. It is a monoclonal antibody that acts on a5 beta 1 integrins, preventing the binding of fibronectin. It is sourced from humans, mimicking the actions of the IIA1 antibody derived from mice. The working concentration of Volociximab is 10mg/kg. A secondary antibody that can be used in conjunction with it is goat anti-human IgG Fc-HRP. The paper that has used both these antibodies is Bhaskar et al. (2008). [1]

Reference

  1. <pubmed>17786386</pubmed>

--Z3459282 (talk) 20:16, 29 April 2015 (EST)

Lab 9

Group 1:

Overall I think that this wiki page is coming along really well! The images implemented really contribute to the aesthetics of the wiki page. In particular, I think that it is very clever to have the image of a proteoglycan as the first thing the reader sees when clicking on the page. Also, the images that you guys intend to add to accompany the text on abnormalities is a good idea! However, a particular area where I believe an image or animation will benefit the project is in the synthesis section, as I found it difficult to understand what was being said. Similarly, with the images, I think that the positioning of some makes the page look unbalanced. In particular, I feel as though the table corresponding to structure needs to be closer to the text. The implementation of more sub-headings can also improve the readability of the page. For example, the information in the function section contains great information that can be broken up further into sub-headings, making it easier for readers to sift through the information. Also, in regards to history, I think it would be a good idea to use bullet points or a table.

A lot of the information that you guys have included is very informative, which is great! I think there is a great amount of content on the page, especially in the abnormalities section. However, as is, sentence structure seems to lessen the effectiveness of this information, particularly seen in the structure section. Similarly, the introduction is great and concise, ultimately providing the reader with a clear idea of what the wiki page is discussing, with only minor grammatical changes required. Whilst the glossary is helpful, some information needs to be added in the sections that have been left blank. Lastly, be careful with the references because there are a lot of random references throughout the page and blanks where “citation is needed”.

Group 2:

You guys are doing a really great job with your project! The layout looks really good. There is a great amount of information as well as several images to accompany this text. In particular, the animation really adds to the page and assists in the reader's understanding of the concepts covered. With this being said, there are still sub-headings that require information to be added to them. Also, there are minor grammatical errors that need to be corrected.

It’s great to see that you guys have also implemented your own illustration. However, I suggest maybe adjusting the contrast to increase the quality of the image. Also, you guys have made a good start to the history section but there are still sub-headings that need to be added to it. Similarly, there are sections in the reference list that are blank, and while the glossary is looking good, there are still terms that require defining. Lastly, ensure you guys do not forget to remove all your notes and reminders to each other from the project page before submission. Also, don’t forget to address the issues that Mark has raised on the page.

Group 3:

As a whole, this page is very informative and contains great images and an illustration. However, I think it may be a good idea to make some changes to the layout of the page, such as the positioning of images, so as to make the page more aesthetically pleasing. While the introduction is brief, it gives the reader a good understanding of what the page is about. However, note that there are minor grammatical mistakes present in this section, as well as others, which need to be addressed. In particular, there are different spellings of fibre utilised throughout the project.

Furthermore, more images can be implemented to accompany the text. Specifically in the case of clinical manifestations, it would be good for the reader to have a visual representation of what these abnormalities are. Also, I think it would be a good idea to add a history section as it provides the reader with the background context of elastic fibres, and a glossary to clarify terms for the reader. Lastly, make sure that you guys proof-read through the reference list as there are some that are blank.

Group 5:

This project page is coming along pretty well, just make sure that you guys watch out for grammatical errors. There is great information present in the history section but I think it would be good if you guys explicitly stated the years that these advances were made. Also, there is a lot of text in the structure section, which is good, but I think that it would be more appealing for the reader if you guys had images separating the different paragraphs so it doesn’t look too overwhelming. This is the same for the current research section. In addition, I think it's great that you guys are writing the function for so many different types of laminins but a lot are still blank so maybe it would be better if you guys did a general overall function for laminins and then include specific examples?

Moreover, I suggest the “image” heading is changed to describe specifically what the image is, and I think it would be good to get images to accompany all the abnormalities as well. Also, I don’t think the copyright information is required to be present on the project page so you may want to double check that. Furthermore, it may be worth adding a glossary at the end of the page, and to make changes to the antibodies section because as it is currently, I am unsure of what is specifically being said here and hence the purpose of its inclusion. Lastly, don’t forget to compile all the references throughout the page in a final list at the end of the page.

Group 6:

Overall a good effort has been made in regards to the content of this page, but there are still sections that need to be added to or tidied up. Similarly, some sentences can be constructed differently so that what is being said is clearer to the readers. Additionally, I think an introduction is critical and including historical findings will help the readers put everything into context and have a good understanding of the topic. They don’t need to be extensive but I think they should be present. Also, I think it may be worth adding a small introduction to the antibody section before listing all the antibodies because right now the inclusion of this section is not very clear. Lastly, the 5 most recent PubMed articles at the bottom of the page currently seems slightly out of place so it may be worth putting it under its own sub-heading for current research.

Furthermore, the structure of the abnormalities section needs to be tidied up, and I think it would be worth seeing if you guys can find images to accompany the different abnormalities so that the readers attain a visual representation of these issues. Possibly an animation can be included somewhere in the project. The glossary is good, however I suggest constructing it in a table to add some variation to the layout of the page. Also, make sure that all terms have a definition.

Group 7:

As the page currently stands, it appears to be very aesthetically pleasing with a good amount of images accompanying the included information. However, there are a few punctuation mistakes that need to be addressed, such as double full stops and missing spaces between words. The layout of the history section is good, however more information needs to be added here. Also, additional information needs to be added to the current research section. There is great information present in the function section but I think another image or even an animation would increase its appeal to the reader, ultimately making all the information easier to digest.

Additionally, the references that are amongst the text need to be moved to the reference list at the bottom of the page. Nonetheless, it is great to see that your references appear to be sited correctly! Lastly, I think that the links to the glomerulus info and the rare abnormalities is a very cool idea but currently it directs you back to the same page, so just double check those links. Overall, its looking good so far!

--Z3459282 (talk) 07:55, 21 May 2015 (EST)


Test page

In-class Activities

Lab Attendance

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--Z3459282 (talk) 16:09, 4 June 2015 (EST)

Lab 1

PubMed


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


Apples and Oranges


PMID 25513760

<pubmed>25513760</pubmed>

PMID 25744690


<pubmed>25744690</pubmed>

Cellular interaction network 01.jpg

Lab 2

Distribution of microtubules and microfilaments in rat basophilic leukemia cell lines.jpeg

Distribution of cytoskeletal structures in rat basophilic leukemia cell lines[1]

References

  1. <pubmed>22654883</pubmed>

Lab 3

Paraformaldehyde MSDS


Reference searching

Search term: Fibronectin


Recent PubMed articles:

<pubmed limit=5>Fibronectin</pubmed>


Lab 9

ATCC: Mouse cell line

Dulbecco's Modified Eagle's medium, Catalog No. 30-2002. To make the complete growth medium, add the following components to the base medium: heat-inactivated fetal bovine serum to a final concentration of 15%. Media Contents of media

ATCC: Human cell line Media Contents of media

ECACC: Human cell line

ECACC: Mouse cell line


Penicillin-Streptomycin