- 1 Alice Welch
- 1.1 Lab attendance
- 1.2 Laboratory 1
- 1.3 Laboratory 2 - Image referencing
- 1.4 Laboratory 3
- 1.5 Laboratory 9
- 1.6 References
Laboratory 1 Individual assessment
Laboratory 2 - Image referencing
A model for cop system in P. syringae pv. Tomato. Abbreviations: CM cytoplasmic membrane, PS periplasmic space, OM outer membrane. Arrows indicate presumed interactions between proteins.
Laboratory 2 Individual assessment
Cellulose fibrils are the principle component contributing to the formation of the complex cell wall which protects and alters the structure of plant cells. Therefore, the ability to visualise the morphology of plant cell walls in detail allows for more knowledge to be gained on the effect that the fibrils have on cell growth and also the breakdown of the wall which has implications for the biofuel industry. Previous research into this area has been limited as a result of the poor resolution of microscopy techniques (i.e. confocal microscopy), thus there has only been visualisation of larger clusters of cellulose fibrils and their reorganisation during cell elongation, however there is the need to investigate and visualise the smaller microfibrils which is what this paper by Liesche et al 2013 aimed to do. This study used two super resolution microscopy techniques, direct stochastic optical reconstruction microscopy (dSTORM) and total internal reflection fluorescence microscopy (TIRF) in an attempt to visualize cellulose fibrils of the onion bulb scale epidermis which were stained with fluorescent dye Pontamine Fast Scarlet 4BS (PFS). Whilst TIRF allowed visualisation of cellulose fibrils in the cell wall, this technique restricts the visualisation to the cell surface and thus no further information could be obtained about the orientation of fibrils in other layers. dSTORM produced a much higher resolution image than TIRF, however, 3D-SIM, another super-resolution microscopic technique, failed to resolve fibrils in the cell wall due to interference of the PFS. Although it does not have as good of a resolving power than dSTORM and 3d-SIM, image deconvolution was used as an alternative and significant improvements in the quality of the images were produced allowing the observation of deeper layers in the cell wall, fibril orientation, connection architecture and the organisation of cellulose surrounding plasmodesmata. Overall, this study showed that super-resolution microscopy is a useful, valuable technique used in the investigation of cell wall morphology.
Search term: Proteoglycans
Laboratory 3 Individual 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. 
Lumican in ocular disease
Culture medium: Dulbecco's modified Eagle's medium with 4.5 g/L glucose and 10 mcg/ml insulin, 90%; fetal bovine serum, 10%
Dulbecco's Modified Eagle's Medium (DMEM) modified to contain 4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate.
Mode of Action: Penicillin-Streptomycin acts in two ways. Penicillin inhibits bacterial cell wall synthesis. Streptomycin inhibits prokaryote protein synthesis by preventing the transition from initiation complex to chain-elongating ribosome, causing miscoding (Sigma-Aldrich)
Laboratory 9 Individual assessment: Peer reviews
Good use of hand drawn image to show how the integrins interact with the other proteins, however maybe make it a bit bigger so it is clearer and could have been better if there was a bit of colour in it to make it more eye catching. It corresponds with the adjacent text which is also informative and provides a good introduction to the topic. For the history section, you have used text to describe the events but instead it may be better presented as a drawn timeline or as a table so it is clearer and much easier to follow, but it seems as though you guys are in the process of making a timeline with dates anyway which looks good. Also good graph showing the levels of interest in integrins, really good to visualise. Good diagram in the structures section, but maybe give reference to it i.e. figure 1, when talking about the fact there is an a and b subunit in the text, because you’ve referenced it when talking about the different configurational states which is good. Also, really good use of the animation but maybe some reference to it would be good. The diagram of the 3D structure of integrin is good but maybe moved up a bit in the structure section. The section on structure is the most eye catching and has good amounts of diagrams and lots of information which isn’t in block text which is good! For the final section about disease, it appears that there is lots of information there which is good however it is in block text and a few diagrams/images/images should be inserted here or use subheadings to split it up and keep the reader’s attention. Overall, so far the page looks good, just requires touching up and a few more diagrams/images which I’m sure will be put in!
Good, short and concise introduction to the topic. You briefly touch on a bit of the history of elastin in the tropoelastin and elastin section (about the study of it being hindered), potentially this could be moved so its after the intro section, with a bit more detail on the history of it? Alongside the text describing the structure it may be useful to have some diagrams of it so people can visualise it next to the description. Really like the way you’ve put the key words in bold, really makes them stand out! The section about the assembly of elastic fibre is really good, really good hand drawn image and other diagram obtained is clear and informative. Good use of number bullet points to split up the text and explain the process. I don’t think much would need changing in this section, except some of the words i.e. Lysyl Oxidases have already been abbreviated (LOX) in the previous section, so don’t think it’s necessary to do it again. The function section seems a bit disorganised because a brief intro to the function is given which refers to a diagram further down the page and then following this is a random bit on tropoelastin, so I think this section should be moved to somewhere more appropriate or use a different heading. Also, instead of using the paper titles as the subheadings I think these should be summarised into a shorter title. Good use of diagrams in this section, maybe if they were made square to the text it’d look a bit neater. The clinical significance section is very informative, lots of information which is good and I like that a range of conditions have been used – nice and topical using ebola virus. The only thing for this section to improve on would be the addition of videos/images to split up the text.
Really like the organisation of this project, the order of the subheadings flows well as you first introduce it with the history & structure and the function and then how this can go wrong. Good amount of text for the introduction, the only thing I would suggest is to get an image to go alongside the text – maybe showing where it’s highly expressed in the body i.e. lymphatic tissues/muscle fibres etc. Good use of bullet points to explain the history, kept really concise and clear. Lots of information on the structure section but again it’d be good if an image/animation (if you can find one) should be put in here just to split up the text a bit. Good idea to split up the 3 different types and use bullet points, maybe put images to the right hand side of this where there is the blank space. Also, good image below but this may look better if it was alongside text and also with a caption and reference in the text explaining what it is a bit more. Really good range of information on the function section, clearly explaining each subheading with a good amount of text! Would say similar for the abnormalities section, but for this I think photos maybe showing the phenotypes of some of the conditions mentioned would be good so people can visualise these abnormalities. Also a glossary may be quite useful! Overall, this page looks neat and organised, most of the information appears to be there which is good, I just think a bit more colour (diagrams/images) is needed to make the page a bit more eye-catching!
Informative, well referenced introduction – concise and gives a good overview into laminins. I don’t think it’s necessary to list the defects and current research here when there are sections dedicated to this near the end of the page. For the history section, it may be more eye catching if this text was split up into a timeline or flow diagram of some sort, but either way the text gives a thorough overview of the history which is good! Really good image created to highlight the structure, it’s simple and clearly explains the structure – but maybe would be good to refer to it when discussing it in the text. For this section, there is a bit too much text so maybe summarise it a bit, or maybe making both diagrams a bit smaller and wrapped around the text it’ll be sufficient to split up the big blocks of text! There are clearly lots of different laminins with different functions, therefore for this section it may be better to use a table to summarise their different functions in a concise manner, and maybe then go into detail on a few? Just below the abnormalities subheading I think it’d be good if you gave a really brief overview into the abnormalities. Well referenced information, I think it may be better if you could find some images to go with the text i.e. an image of someone with muscular dystrophy to go with the section? Some of the sections have their own reference list at the end but this would look less messy if there was just a large reference list right at the end of the project, but this is probably something you guys were planning on doing anyway! Overall, seems like you’ve got the written content sorted which is good and just need to make it a bit neater and cut down some of the large chunks of text.
Information needs to be put in the introduction and history section because just empty subheadings. The structure section has lots of written information which is good, with a few empty subheadings which need to be finished, but overall very informative and I like the use of the diagram it’s a good visual aid and splits up the text. I’m not sure how the section on developmental stage is relevant to the structure though. Function section looks good with the diagram, clearly labelled and corresponds well to what is written in the adjacent text. I would say a few more functions should be given in this section but that’s all that would need improving in my opinion! The abnormalities section appears unfinished too but I like the introduction to the section outlining what will be in the section. For the current research section I think it’d be good if the different areas that new research is focussing on is summarised and then a brief overview into the studies because it’s quite hard to follow with the paper titles as the subheadings i.e. ‘Type 1 regulatory T cells specific for collagen type II as an efficient cell-based therapy in arthritis’ could be changed into cell-based therapy for arthritis ? Good use of the glossary at the end! The structure of this page is good it just needs a bit more work finishing the content!
Really good concise introduction, I like the way at the end you outline what will be included in the page, also a good eye catching diagram is used alongside the text which immediately gets the reader’s attention. Even though it’s incomplete, the use of a table is very good to explain the history. Good use of the diagram alongside the text for the sections, but maybe some reference to them in the text would be useful.
Abnormalities section is really good, good introduction to the section and also the use of the collapsible table is really useful but I think you should maybe refer to it in the text and state that to click there for more a bit more background information. I like the way it focuses on renal abnormalities then goes into details into individual diseases and has images alongside. Overall, even though some bits are unfinished this page looks really good as there are lots of diagrams/images and you’ve split up the text well using subheadings and bullet points.