Difference between revisions of "User:Z3463637"
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--[[User:Z3463637|Z3463637]] ([[User talk:Z3463637|talk]]) 16:11, 28 May 2015 (EST)
--[[User:Z3463637|Z3463637]] ([[User talk:Z3463637|talk]]) 16:11, 28 May 2015 (EST)
Revision as of 16:13, 4 June 2015
- 1 Lab Attendance
- 2 Peer Review
- 3 Individual Assessment
- 4 Lab Work
GROUP 1 PEER REVIEW
The synthesis section needs to be expanded on and is lacking in detail. It doesn’t make sense to me as a reader. The structure section also needs to be worked on; it doesn’t make sense to me either in some areas due to poor expression. I read “It is accepted the LRRS sequence is LXX-LXLXXNXL…” several times before I understood it.The function section is well written and detailed. Perhaps add subheadings for the small leucine rich proteoglycans (SLRP) or bold the names of the SLRPs. This will make it easier to read and better presented for the audience.
It is clear (although incomplete) that the SLRPs will be talked about separately in different sections. I can see that a “function” heading is written under each. However, there is already information written in the function section about each SLRP. This would be repetitive and your group should reconsider organising how the information about function should be presented. Perhaps have a more general and broad definition of the functions of SLRPs in the function section and then go into details about the function of the different SLRPs in their separate sections.
The disease section is extensively researched but I feel as though there is too much information that can be summarised better so that it will be easier to read. Some unnecessary information such as this sentence “Being a congenital disorder, there has been extensive research into the genetic abnormalities that cause this disease. There is ample evidence from gene sequencing studies which highlights the large role that decorin plays in the pathology of the disease…” can be removed.
The header is great and definitely captures my attention. Good inclusion of relevant diagrams images and tables. However, I feel some images are too big and some are too small to see details.
Although the detail is there, there are some areas where grammar, spelling and expression need to be fixed. This should be easily done with proofreading. I understand that the page is still a work in progress. Your wikipedia page is coming together very nicely with the headings well thought out and it is evident that substantial research has been done.
GROUP 2 PEER REVIEW
The organisation of the page is well thought out and there is very good use of subheadings to break up information which makes it much easier to read. The introduction and function sections have been written concisely and organised well. For the history section try to separate different events into dates as a timeline, rather than having a large paragraph. Structure is also well written despite being incomplete. Good use of subheadings but it lacks referencing in this section. The disease section is extremely detailed with large blocks of information. Try to be more concise and break the information up into different paragraphs.
Good inclusion of a video about the interaction of integrins with the extracellular matrix in the function section. There are few relevant images of integrins and interactions with the extracellular matrix. The diagrams, videos and images help in the understanding of the information.
There appears to be some problems with the referencing. References 19-21 do not appear, which is due to some coding error. Otherwise, the other sources appear correctly referenced. Although the page is still a work in progress, the page is really well set out. The function section has been really well done and I believe the layout for this section should be used as an example for other sections.
GROUP 4 PEER REVIEW
The information on your page so far is well written and concise. The function and abnormalities section go into great detail but it is great that it has been divided into many subheadings to break up information. The introduction is too long and fibronectins can be defined better in fewer words. It should be a very short engaging paragraph that gives a quick summary for the audience. The introduction goes into great detail about the relationship between fibronectin and the extracellular matrix, but some of this information can be removed and appear in other sections later. Perhaps, you can define fibronectin in a few sentences and then have the subheading “the relationship between fibronectin and the extracellular matrix,” to include more information.
The structure section can be improved with headings (“secondary structure”, “isoforms” etc.) to break up the information. Good use of dot points to summarise important information about FnI, FnII and FnIII. This information can be tabulated for better presentation. Information about assembly is very brief and should be expanded on. You can list out the steps of assembly or better organise the information to highlight the process of assembly.
The page is currently lacking in pictures. More pictures will help to break up large blocks of information. Good use of subheadings especially in the function and abnormalities section and these sections should set an example for the other sections. Diagrams can be included in the assembly section, which will help to explain the process. Tables can be included for the history section to show a timeline of the historical developments.
References 16-17 and 40 don’t appear on the page, which is most likely due to a coding error that can be easily fixed. There are some spelling errors but this can be corrected with proofreading.
GROUP 5 PEER REVIEW
At first glance, the page is very overwhelming especially having multiple references sections for each heading. The introduction is too long and the dot points underneath the paragraph show that it is still unfinished. The information can be summarised better to give a broad overview of laminins. The history and structure sections are also very extensive, and the information can be organised better under subheadings that will break up the information.
The function section looks like an extensive list of individual laminin types and their functions. Although it is incomplete, the amount of detail written about just one type of laminin should be reduced and summarised better. This can be tabulated and written in dot points to better present the information to make it easier to read because there are so many different types of laminins. For the abnormalities section, the information can be summarised more concisely. Also, the title of the research paper should be removed and the paper should be referred to in the text. The current research section should also be summarised, as there is a large amount of text under each subheading.
The images should have been added to wikipedia correctly and the copyright information should not appear on the main page. References should appear as a single list, and I believe it would be easier to view the page as a whole. The subheading style should remain consistent throughout the whole page. The subheadings under abnormalities and current research have lines under the subtitle and other sections do not have this. Some images are unnecessarily large and more pictures are needed. Tabulating the antibody section would better the presentation of this section. Overall, there is evidence of extensive research, but the group should work together to better organise and present the page. It currently does not look like a unified group project.
GROUP 6 PEER REVIEW
The page has been organised well into the relevant headings. However, information for the introduction and history sections are still missing and the structure and abnormalities sections are incomplete. The information presented in the structure section shows extensive research; however there are some issues with spelling, grammar and expression at times. This can be improved with proof reading. References are also missing in parts of the structure section.
The function section is well written, concise and this is definitely is the strongest section so far. The information under abnormalities can be summarised better and perhaps bold the title of the paper that is referenced in the text. Try to simplify the subheadings under current understanding and areas of research, as they are really long sentences.
The page is lacking in visual stimulus. The antibody section and the glossary can be tabulated for better presentation of the information. Good use of subheadings to break up information in different sections. References 19, 20 and 22 are not referenced properly. Overall, good work in progress and the group is on the right track. However, the large amount of missing information indicates that more research is needed.
GROUP 7 PEER REVIEW
The page looks really well presented and each section appears to be making very good progress. The relevant information has been well written, concise and easy to comprehend. Good introduction to start off the page but I don’t think it is necessary to include this sentence “This page focuses on the structure and function of the BM and how it develops, in addition it also explores historical and current research, along with abnormalities…” because there is already a contents bar that the audience can use to navigate the page.
The formation, plasticity and regeneration section should be presented better using proper dot point formatting or listing of these processes. The functional layer section is lacking in information, as the layers should be described in more detail and also their functions. Structural components still needs significant work. The information in the function section is quite extensive and so subheadings would be useful to break up information. For example describing the functions in areas of the body that they occur (kidney, muscles etc.). The abnormalities section is well set out but the information can be summarised better.
There are many images that really help the presentation of the page and have been positioned and sized nicely. References have been well done. Good use of tables in the history section and good use of subheadings to break up information. However, there are some areas that should have subheadings to break large blocks of information. Overall, the page is coming together very nicely.
Lab 1 Assessment
Figure 5. Microscopic observations of the bacterial cells before and after treatment with the NaOH-SDS solution. 
© Wada 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 Assessment
The study by Izeddin et al. (2011) involves the use of different innovative techniques to study the dynamic nature of cellular structures using superresolution, specifically dendrites. Dendritic spines are about 500nm in diameter and are the site of excitatory neurotransmissions within neurons. F-actin is the cytoskeletal structure that is responsible for the plasticity of dendritic spines during synaptic transmission. However, detailed study of the spine structure, their distribution & their dynamic functional nature within living neurons has been limited by the narrow resolution abilities of conventional fluorescence microscopy. Fluorescence microscopy has diffraction limit of light about 250nm, which has limited detailed observations. With the introduction of nanoscopic imaging techniques of super-resolution microscopy, such as photoactivated localization microscopy (PALM) that uses photoactivatable proteins and photoswitchable flurophobes, we are able to surpass this limitation.
Scientists produced a photoconvertible probe that reversibly binds to actin with low-affinity and are replenished, which has enabled long term PALM of the cytoskeleton of the spine. It also does not compromise the organisation of the cytoskeletal structure, as it is not directly incorporated into the actin filaments. With the new high resolution PALM imaging of dendrites, the scientists were able to quantify actin distribution in the mature dendrites. It was found that actin densities were greater within the center of the head region of the spine that it was in outer regions. AMPA was utilised to pharmaceutically induce the dendrites to cause morphological changes to the cytoskeleton and to observe adjustment of the shape of the spine. The treatment resulted in the reduction of actin levels and caused shrinkage. Using a combination of PALM imaging and quantum dot tracking techniques, scientists were able to visualise the cytoskeleton and membranes simultaneously at super-resolution. It was concluded that the plasma membrane is dynamic and adapts as the actin cytoskeleton is rearranged. 
Lab 3 Assessment
The study highlights the role of recently identified glycoproteins on or surrounding elastic fibers of tissues and organs. Short fibulins, particularly -3, -4 and -5 have very potent elastogenic activities. The activities of these short fibulins were observed in knockout mice and it was found that they play an integral role in the formation of elastic fibers. This review article is relevant to the formation and structure of elastin.
Before manufacturing biomaterials, the biopolymer materials must be assessed based on their functionality and design parameters. The review article discusses the different biopolymer materials, including elastin, highlighting its structure and functional properties. It is found that a integrated design approach using experimental and computational modeling procedures are required to study these materials.
Elastin is necessary for the elasticity and recoiling properties that are evident in blood vessels. In a study of elastin knockout mice, it was revealed that elastin also plays a role in arterial morphogenesis. This review article is relevant to the sub-topic as it highlights the functions and structure of elastin.
Previous studies have shown that developing arteries and neural crest EGF-like (DANCE) proteins are essential for the formation of elastin. The identification of latent transforming growth factor-β-binding protein 2 (LTBP-2), was found to promote the deposition of DANCE proteins onto fibrillin-1 microfibrils. This ultimately induces the formation of elastin.
Figure 6. Multiphoton images of cross sections of arteries after digestion with static stretch with 56.5, 35.6, 23.7, 15.6, 10.6, 6.8, and 5.6 µg elastin/mg wet tissue (A through G respectively) with the SHG signal (collagen, shown on left) and 2PEF signal (elastin, shown to the right) separated from a single image. There is increased fragmentation of elastic lamellae layers and collagen fibers become more disorganized with elastin removal. Images are 275×275 µm. doi:10.1371/journal.pone.0081951.g006
© 2013 Chow 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 5 Assessment
A greaphical representation of the phenotypic changes of control B35 cells, and overexpressed Tm4 (Tropomyosin 4) B35 cells.
Lab 6 Assessment
1.Identify an antibody that can been used in your group's extracellular matrix project.
Anti-Elastin Antibody [10B8]
2. Identify the species deriving the antibody.
3. Identify the working concentration for the antibody.
100 µg at 1 mg/ml
4. Identify a secondary antibody that could be used with this antibody.
Mouse polyclonal antibody
5. Identify a paper that has used this antibody.
Lab 9 Assessment
Mouse Line: http://www.atcc.org/Products/All/CRL-2446.aspx
Medium: Vascular Cell Basal Medium (Vascular Cell Basal Medium contains essential and non-essential amino acids, vitamins, other organic compounds, trace minerals and inorganic salts)
Medium: RPMI-1640 + 2mM Glutamine + 10% FCS (RPMI 1640 Medium is unique from other media because it contains the reducing agent glutathione and high concentrations of vitamins. RPMI 1640 Medium contains biotin, vitamin B12, and PABA, which are not found in Eagle's Minimal Essential Medium or Dulbecco's Modified Eagle Medium. In addition, the vitamins inositol and choline are present in very high concentrations. RPMI 1640 Medium contains no proteins, lipids, or growth factors. Therefore, RPMI 1640 Medium requires supplementation, commonly with 10% Fetal Bovine Serum (FBS). RPMI 1640 Medium uses a sodium bicarbonate buffer system (2.0 g/L), and therefore requires a 5–10% CO2 environment to maintain physiological pH)
Penicillin: Treat bacterial infections.
Streptomyocin: Used to treat tubercolosis and other infections caused by bacteria and mycobacteria.
- Wada A, Kono M, Kawauchi S, Takagi Y, Morikawa T, et al. (2012) Rapid Discrimination of Gram-Positive and Gram-Negative Bacteria in Liquid Samples by Using NaOH-Sodium Dodecyl Sulfate Solution and Flow Cytometry. PLoS ONE 7(10): e47093. doi:10.1371/journal.pone.0047093