Talk:2015 Group 1 Project
Group Assessment Criteria
- The key points relating to the topic that your group allocated are clearly described.
- The choice of content, headings and sub-headings, diagrams, tables, graphs show a good understanding of the topic area.
- Content is correctly cited and referenced.
- The wiki has an element of teaching at a peer level using the student's own innovative diagrams, tables or figures and/or using interesting examples or explanations.
- Evidence of significant research relating to basic and applied sciences that goes beyond the formal teaching activities.
- Relates the topic and content of the Wiki entry to learning aims of cell biology.
- Clearly reflects on editing/feedback from group peers and articulates how the Wiki could be improved (or not) based on peer comments/feedback. Demonstrates an ability to review own work when criticised in an open edited wiki format. Reflects on what was learned from the process of editing a peer's wiki.
- Evaluates own performance and that of group peers to give a rounded summary of this wiki process in terms of group effort and achievement.
- The content of the wiki should demonstrate to the reader that your group has researched adequately on this topic and covered the key areas necessary to inform your peers in their learning.
- Develops and edits the wiki entries in accordance with the above guidelines.
--Z3459996 (talk) 20:02, 23 March 2015 (EST): I don't know if any of you will have seen this yet, but if you do: any ideas for a subtopic? I'm going to do a quick exploration of the extracellular matrix as a field, but do you guys have any particular preference/s? --Z3459996 (talk) 19:24, 24 March 2015 (EST): I was thinking maybe something about regulation of molecular interaction in the ECM (like, how do you regulate which enzymes act on their substrate and when), but this might be a little too molecular for a Cell Biology course. Thoughts?
--Z5030452 (talk) 11:52, 25 March 2015 (EST)Hi, sorry only just seen this because couldn't figure out how to get on it. I don't mind doing that, the only thing is I think it may be a bit vast, I was thinking maybe focus on one component so we can have a more focused page and go into detail on it maybe like proteoglycans or laminins, what do you think ?
--Z3459996 (talk) 22:20, 25 March 2015 (EST) We have until the end of the lab to finalise it, and Dr Hill said he can give suggestions in the lab. It might be good to run our thoughts past him because I agree that my suggestion might be too vast. Proteoglycans or laminins both sound like much better options to me, but we can discuss it with the full group in person tomorrow.
--Z5030452 (talk) 15:25, 12 April 2015 (EST) Just pasting my 4 papers and their summaries for the lab 3 assessment. Also - I did the disease/abnormalities section and I didn't find info on that many specific diseases, just lots on their role in ocular disease and kidney disease and then some skin disorders so I think potentially for this section to focus on maybe their general role in the eye and kidney and then go into detail on some specific ocular & kidney diseases? What do you guys think? It's still early days anyway :)
--Z3459996 (talk) 18:16, 12 April 2015 (EST) Awesome. Is anyone else having difficulty finding articles? Finding stuff about the history is exceedingly difficult. The best I can do is an article from 1990 which links to some articles as far back as the mid 19th century. This is probably basically what you'd expect when you're doing a history section but if everyone's struggling to find info, maybe we should consider a topic switch?
--Z3415779 (talk) 12:26, 16 April 2015 (EST) Yeah I've been busy trying to sort through papers trying to find whats relevent. if youre havinf troubles with the history, maybe try looking through some review papers. Theymight be able to explain it better than individual primary papers can.
--Z3415779 (talk) 12:34, 16 April 2015 (EST) These articles are not really all about my topic, you might be able to find something you can use in them... <pubmed>24324885</pubmed> <pubmed>22358337</pubmed> I'll upload any more useful papers i find
--Z3415779 (talk) 16:54, 26 April 2015 (EST) Hey guys, i thought id write some notes i took after mark went through our page sat thursday. this way we are all up to date about some of the changes he would like to see. I think compared to the other groups we have actually done really well so far...
- clearly define parameters of our topic in the intro and mention what we are not including
- add a visual to the top of the page to make the page more interesting/engaging (done :D)
- try not to reference review papers (if you do maybe say something like "as reviewed in" to make it clear its from a secondary source)
- make the history concise and interesting
- consider a visual representation of the no. of research papers published on the topic over the years (done :D)
- include info on the legends of pictures/images without needing to mention it again on the page
--Z3459996 (talk) 13:53, 30 April 2015 (EST) Also decided that it's probably a good idea to implement a to do list so we can all keep track of what needs to be done in general, and where we're all it in terms of progess! You don't have to use it if you don't want to, of course; I just thought it would be handy for us to divide our goals up a little bit (yay psychology :D).
- clearly state why we are focusing on SLRPs and not proteoglycans
- use of human body diagram for abnormalities section
- the use of a glossary for abbreviations or key words (I'll add a heading for glossary at the end of the page that we can each add to as we go along)
- look for potential videos that are relevant
- look for crystal structures of the 4 main SLRPs
--Z5030452 (talk) 13:44, 9 May 2015 (EST) Is anyone else finding it pretty hard to find images? (that allow use?) I am spending so much time trying to find images of these diseases on all the open access articles and there's like nothingggg, nearer the time I might need your guys help to find some
--Z3415779 (talk) 05:13, 14 May 2015 (EST) Also, I think its probs most appropriate for the distribution of the proteoglycans to be apart of the function section because sometimes its related. If anyone has a better spot to put it, let me know.
- Research and write up initial information about Fibromodulin and Lumican
- Separate information into structure and function
- Focus on function of all four proteoglycans
- Image search
- Complete the introductory section.
- Introduce the concept of a proteoglycan
- What is an SLRP? What is special about an SLRP?
- What this article will/will not cover.
- Insert proper references.
- ...in the intro.
- ...in History.
- Amazing coincidence with those student numbers; wow.
- Split it into subheadings & start inserting the relevant info/pictures for each section
- musculoskeletal disease - kidney disease - ocular disease
- Maybe get an illustration of the human body to describe where SLRPs have implications
- Keep everything relatively visually consistent
- Ensure layout remains clean and pleasant - a good balance between text, visuals and whitespace.
- Maybe find a video to put on the page (though this is such a poorly-researched topic that this may be a struggle)?
Articles (Week 4 Lab Assessment)
Posterior amorphous corneal dystrophy (PACD) is a rare genetic disease with pathological features including thin cornea, reduced corneal curvature and often complete loss of corneal transparency. The small leucine-rich family of proteoglycans (SLRP) have an important structural role within the cornea, thus play an important role in the physiology of this disease. SLRPs bind to glycosaminoglycans within the cornea and form fibrils in a lamellar arrangement which has consequential effects on the development, structure and the transparency of the cornea. Previous research has found that mutations of this family of proteoglycans have affected the curvature and clarity of the cornea which tend to be common features seen in this disease. This study found that PACD shows a strong link to the deletion of the genes coding for keratocan, lumican, decorin and epiphycan on chromosome 12. 
Disruption to the structure and arrangement of collagen fibres often has detrimental effects to the meniscus and cartilage thus is often a key pathological feature of musculoskeletal disorders including osteoarthritis. SLRPs have highly important roles in the maintenance and integrity of collagen fibres including organisation and adhesion of the matrix and protect collagen against proteolysis which ultimately permits joint movement and contributes to the stability of the bones. This study showed that the fragmentation of SLRPs has pathological consequences for the cartilage and meniscus, specifically decorin and fibromodulin fragments in higher numbers in diseased tissue. 
Congenital stromal corneal dystrophy (CSCD) is a genetic ocular disease which is characterised by the development of corneal opacification which appears after birth. Research completed prior to this study elucidated that the pathophysiological features are a result of a frameshift mutation of the SLRP decorin which subsequently causes the shortening of the c-terminal containing a repeat which is specific for SLRPs. Thus, considering decorins important role in controlling the development of fibrils and of collagen fibril organisation it is not surprising that this mutation causes the interference of matrix formation and atypical expression of other SLRPs. In this study a transgenic mouse model of the truncated decorin mutation was generated which highlighted that this mutation is the key pathophysiological feature in this genetic disease. 
Renal ischaemia-reperfusion injury (IRI) is a leading cause of acute kidney failure. Following a period of ischaemia or restricted blood flow to the kidneys, the subsequent reperfusion of blood results in an inflammatory cascade of events which have detrimental effects on renal structure and function. Prior research has shown that during injury, biglycan exits the extracellular matrix and acts as a ‘danger signal’ to cause the activation and migration of pro-inflammatory cells e.g. cytokines, macrophages, neutrophils via TLR-2 and TLR-4 receptors which exacerbates the deterioration of renal function. This study used a rat model to investigate the role of biglycan, an SLRP in IRI. The main findings include: biglycan is an agonist of TLR2 and TLR4, biglycan plasma levels increase in IRI and that in knock out TLR2 and TLR4 IRI mice, biglycan’s effects are attenuated. Thus this study highlights the paramount role that biglycan has in the pathology of IRI. 
Decorin is a family of proteoglycans, called small leucine-rich proteoglycans(SLRPs)which is a reptiion of leucine rich repeats which are bordered by cysteine-rich cap regoins. It is important in regulating collagen fibrillogenesis, growth factors and receptor tyrosine kinase. They bind within gap region of the D-period.
Decorin DNA residues of mouse is amplified by PCF form cDNA clone. Proteins were produce in human embryonic kidney in a Dulbecco's modified Eagle Medium at 37C and later frozen. The samples at a concentration of 3mg/ml was thawed and Analysied with Size exclusion Chromatography with Laser Light scattering. Furhter analysed by Differential Scanning Calorimetry, Differential Scanning Fluorimetry, Collagen Fibrillogenesis Assay and Solid-phase binding assay.
Significant results: Mutational disruption of decorin Dimer Interface; The decorin core protein had 4 designed mutations(Y51A/R52A/Q54A0), R151E, Q61N and Y130N that could potentially interrupt dimer interfacing. With the mutations strong yields were still present, Q61N had a higher molecular weight since site 61 is modified by glycans, electrophoretic mobility of Y130N mutation refelcted that of wild-type, (Y51A/R52A/Q54A0)mutation results in two mutant engineered glycosylation sites. Unmodified molecular mass 64.4kDa close to value of calculated dimer mass(72.4kDa). Modified protein gave a molecular mass of 84.6kDa. Difference in stability not significant. Of the four dimer interface mutations only (Y51A,R52A/Q53) delayed fibrillogenesis like wild type. Q61N, Y130N, R151E all were inactive. Additionally Wild and (Y51A,R52A/Q53) mutant showed stronger collagen binding then the other three mutants.
Conclusion: Concave face mutation stopped decorin collagen binding regardless of wether the protein could still create a dimer. There for the concave face is critical in collagen binding and must dissociate form the dimer of bind with collagen
Decorin core protein (decoron) shape complements collagen fibril surface structure and mediates its binding. 
Decorin structure is main small-leucine rich proteoglycan present in the vertebral extracellular matrix. THe Glycosaminoglycuronan chain is key in giving inter-fibrillar organization. Decoron the core binding protein in decorin binding with the d and e bands of type I collagen fibrils.
Previous models suggested that highly curved decoron binds with a single collagen molecule creating strong non-specific binding. It is now apparent the the way collagen aggrates it prevents the one on one binding.
The respective crystal structures of the decoron-fibril complex shape is complementary. One molecule of decoron interacts with 4-6 collagen molecule not one like previous hypothesis. Relying on many hydrogen bonds and elctrostatic interactions
Interaction of the small interstitial proteoglycans biglycan, decorin and fibromodulin with transforming growth factor beta. 
Study looked at the interaction of three short leucine rich proteoglycans interaction with TGF-beta. The proteoglycans were expressed from human DNA and fused with E.coli maltose binding protein. the maltose binding protein displays very limited binding to other growth factors. Intact bovine decorin, biglycan and fibromodulin was able to compete well with fusion proteins for TGF-beta binding sites. the Kd values of the bonding distant her 50-200nM for low affinity bonding sites and 1-20nM for high affinity bonding sites. Fibromodulin and the fusion protein was a more successful at TGF-beta binding then the decorin anf biglycan. In the proteoglycans typical only one in ten of the core proteins displayed a high affinity binding sight and one low affinity binding sight per protein. Removal of chondroitin/dermatan sulphate chains in the decorin and biglycan resulted in a marked increase in binding activity. Displays that binding activity with TGF-beta could be hindered by glycosaminoglycan chains.
Affinity labelling showed in Mv 1 cells TGF-beta binds to betagylcan and type-II receptors, binding to endoglin in endothelial cells was reduced and Type-II binding was unaffected. Showing that different decorin type proteoglycans have slightly altered binding properties to TGF-beta and other potential binding sites. Additionally can regulate TGF-beta activity by sequestering TGF-beta out to the extra cellular matrix
Biglycan is an extracellular MuSK binding protein important for synapse stability  MuSK is a protein crucial is nerve-muscle synapse formation and maintenance. It pre-patterns the endplate zone and is a signal receptor. Though its processes are poorly understood the protein biglycan plays a role in maintaining stability. In the developmental stages there is no significant deviation from biglycan expressing fetus and biglycan null fetus. 5 weeks after birth nerve muscle synapse in biglycan null mice display abnormal perijunctional folding, segmentation and misalignment. THis indicates that presynaptic and postsynaptic regions were vacated. Expression of MuSK phosphorylation proportional to presence of biglycan. Null biglycan results in ACrH clustering to degrade once cluster has reached a certain size.
Biglycan is an extracellular ligand for MuSK and crucial for prolonged synapse stability
Group 1 Peer Review
This is a good starting point for your Proteoglycan web page. There is evidence of research in each topic of discussion, however, not everything is clearly described. The Early Research and Advances in Technology and Discovery sections display good background information. My tip would be to discuss what GAG's are in structure and function since you have found that there is substantial information on them. Also, adding in SLRP synthesis might be beneficial. When mentioning specific scientific terms that are important to the knowledge of proteoglycans, such as leucine and TFG-B1, give more information. It's better to break down the information so that it is more easily understood by student readers.
I liked the diagrams and photos that you used throughout the webpage. They give the reader a better visual understanding of your topic. Adding in more will only benefit your page. Some paragraphs are choppy and need revision. There are multiple grammatical errors, run-on sentences, and problems with verb tense. Reading aloud will help to pick out mistakes and make changes so that the paragraphs and sentences flow.
The Structure and Function sections need the most work done on them. When discussing secreted proteins in the Structure portion of your web page, I was confused on what that information meant. However, I'm sure you were already planning on expanding on multiple topics that weren't fully described yet. I enjoyed the role of SLRPs in disease section the most. It gave a lot of good information and I appreciated the use of photographs. Grammatical revision will make this section even bette
Group 1 Peer Review I think your page is set up well. You have a brief description outlining what makes up your topic of choice and when you first click on the project page, it doesn’t look boring because of the picture you have included of the proteoglycans. The images used throughout the page make it more interesting and give an appropriate visual representation of your topic. It is also very helpful that you have added a glossary at the end of your page as I did struggle to understand some of the acronyms.
Looking at the contents of your page, it is well set out. You have divided each topic such as history for example into smaller subtypes which makes it more organized and easy to read. It’s also good that in your referencing you have started to differentiate between review articles and clinical trials but this is not yet continued throughout the page.
On the other hand, you do still need to add a lot of information. I get the impression that a lot of it is not finished yet. The disease section is also very extensive and I think it would be more effective if it was a little more simplified. It might also be good to consider drawing your own diagrams instead of using one from an article, will make it look more interesting and also be easier to understand. The table you have included of the various different proteoglycans looks a little awkward on the page, it is not formatted properly or the size might be too big.
Overall, I think you guys are off to a great start and with some finishing touches and editing you page should turn out well.
Group 1 Peer Review
Overall, I think your page is really coming together really well, and I’m looking forward to seeing the final product.
Key points clearly described: I felt that your introductory section was done well. When I was reading though, the first thing I was thinking was ‘what do proteoglycans do’ - this information was at the end of the paragraph, after composition. I think it would work better if you ordered it as function and then composition. The history section I found has just the right amount of information. To further improve, include the full names of those who have historically contributed - not just their first/ last name. In the synthesis section I don’t know what I’m reading. I have no idea how it contributes to the information. My understanding is that it’s describing the formation of sugars and attachment to GAG chain (I think?). I just feel that it needs to be cleared up. It’s difficult to understand and I think it needs to be described/ set out better and possibly supported with an image. Structure section is a work in progress. Function appears to be set out well so far, despite it still being a work in progress. Just an idea, when describing the functions of Decorin, Byglycan, Fibromodulin and Lumican, have a bolded title so readers can quickly flick through and find what they are looking for. However, I don’t understand why you’ve grouped Decorin and Byglycan together? Maybe justify why with a sentence at the beginning of the section just as you did with Fibromodulin and Lumican. I also don’t find the purpose of having a function section and then mini function headings within, very clear. Diseases were completed well! You really explained it in the right depth of information and in a way that’s understandable. As a suggestion, rather then saying ‘below are some images of a range of diseases etc’ have something along the lines of ‘some common examples include (list them)’ and have the images representing them. Same goes for when you say ‘in the following two cases’ – list the cases in SLRP’s and kidney diseases.
Understanding? Content, headings, sub – headings, diagrams, tables, graphs? Teaching at peer level? Own innovative diagrams, tables or figures, Interesting examples or explanations?: Overall, I really liked the images used and the flow charts and tables. The header is amazing! I love it! It’s very appealing to the eye! Diagrams were well chosen. In particular, the first diagram is very eye – catchy and detailed. I think it would be beneficial if within the text, there were references to this diagram, e.g. The vast majority of these molecules have GAGS (Figure 1a) etc, where figure one refers to the little bit highlighting the GAGS. Maybe you should include an image of Meyer in the history section? The table in the structure section is really good. It really helps visualise the chains and their components as described in the test. To make the table stand out try adding colour and possibly constructing the schematics on computer to avoid size differences, smudge marks and irregular writing. Increase the size of the images so that they stand out more, and include more in areas lacking images, such as for the diseases (I know you’re still editing) and have the images scattered, rather then clumped together as diseases.
Content correctly cited and referenced: References appear correctly done.
Evidence of significant research / Adequate research: Your page appears to have a good amount of information, however I still feel there needs to be some more research done. In particular, in the sections where you say ‘there is ample evidence’, provide us with the evidence.
Other: In general, your page needs a lot of editing in spelling, punctuation and grammar - but I think you will be doing that anyway. Some sentence structures are a bit wordy as well. Avoid repetition of words in close proximity of each other. Avoid saying ‘see right left/ below’ – refer to them as ‘figure 1, 2 etc’. I love the idea of a glossary. Add some of the scientific terminology that may be difficult to understand if you don’t study science, to the list. The ‘fundamental role in collagen’ – what role? Also, just to note - you have two spellings of byglycan/ biglycan on your page.
Group 1 Peer Review
Group 1, your project seems to be very organized and well explained, regarding each subtopic you guys presented. The fact that you chose four of the SLRP came to vary even more the information given, making the work richer. I see in Lumican there are some missing info but surely you will come up with something; the diseases section is very complete as you contemplated a vast number of topics. The images were well selected as well as the charts. I think the layout of decoryn and byglycan and fibromodulin and lumican can be improved, maybe by heading hyphens or highlighting the function, structure etc in order to look more organized and have a better visual appearance.
Group 1 Peer Review
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 1 Peer Review
Hello, dear classmates!! I really liked your project!! There is a lot of information about the Small Leucine-Rich Proteoglycans, which can lead the reader to a good understanding about this molecule. The history part is very good, it follows a logical and chronological sequence which leads the reader to a very good understanding about how the Small Leucine-Rich Proteoglycans were discovered and how humanity reached today´s knowledge about this molecule. The Function and Structure parts are also clear, logical and easy to understand.
Despite being an excellent project, I think it would be great if you guys improved the introduction part: for me it does not seem very clear what a Proteoglycan, and improving the introduction will certainly lead to a much better understanding about the following topics. Furthermore, the Synthesis part it is not very clear, I could not have a good understanding about how the molecule it is produced. In this part, however, I think you guys should only rewrite the text, because it seems that you have enough information.
The following parts are very clear and the information provided is much more than enough to satisfy a curious reader. Also, I have to say that the page is very good looking, which attracts even more the reader´s attention.
Congratulations for your effort, if you guys correct the very few things that are not very good in your project, it will be undoubtedly an excellent one! Cheers!
Group 1: Pros: The choices of the sub-headings, tables, diagrams and pictures seem to show a good understanding of the topic area thus far. The pictures for the diseases look interesting and they caught my eye. I really like how you guys got creative and included a banner for your project page. The group has utilised their own innovative diagrams.
Cons/improvements: The picture for the proteoglycan molecule is too large and at the very centre of the project page. I feel like you guys might be concentrating on too many diseases? Maybe focus on three interesting ones. You guy have a subheading for decorin and biglycan and then further bold subheadings for them, I feel like this could be better presented.
Group 1 Peer Review
The project begins with an important and well-explained description about proteoglycans, informing that the group will focus on four particular types of proteoglycans due to its vast number. Thus, it is provided a brief history regarding proteoglycans, where you can learn about its discovery, the way it has been used for research overtime and the emerging evidence that some Small leucine-rich proteoglycans (SLRPs) can produce antitumorigenic effect, presenting an exciting new avenue for future researches.
Furthermore, the project covers glycosaminoglycans synthesis and SLRPs structure, supporting it with good evidence and pictures that allows a good understanding and a not boring approach.
Overall, decorin, biglycan, fibromodulin and lumican descriptions about structure, function and distribution are well-organized, though there is still some information missing regarding these proteoglycans in order to provide a better understanding about them. For instance, the function of lumina is not yet informed.
The role of SLRPs in disease: the project presents relevant diseases that are due to alterations in SLRPs, affecting different organs of the body. The explanations are clear, however there are still some images missing. Some editing is necessary in a way that the breaking down of long texts would turn the project even more interesting.