Difference between revisions of "User:Z3461763"

From CellBiology
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== Assessments ==
 
== Assessments ==
  
=== Lab 1 ===
+
=== Introduction to Lab ===
  
 
'''E. Coli and HeLa Cells'''
 
'''E. Coli and HeLa Cells'''
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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.
 
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 ===
+
=== Microscopy Methods ===
  
 
'''PART 1'''
 
'''PART 1'''
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<ref><pubmed>PMC4278722</pubmed></ref>
 
<ref><pubmed>PMC4278722</pubmed></ref>
  
===Lab 3 ===
+
=== Preparation / Fixation ===
  
 
In Lab:  
 
In Lab:  
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https://proscitech.com/msds/c004.pdf
 
https://proscitech.com/msds/c004.pdf
  
=== Lab 4 ===
+
Article Assessment:
  
 
'''The Heterotrimeric Laminin Coiled – Coil Domain Exerts Anti – Adhesive Effects and Induces a Pro – Invasive Phenotype'''
 
'''The Heterotrimeric Laminin Coiled – Coil Domain Exerts Anti – Adhesive Effects and Induces a Pro – Invasive Phenotype'''
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'''Copyright:''' This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
 
'''Copyright:''' This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
  
=== Lab 5 ===
+
=== Cell Knockout Methods ===
 +
 
 +
In - lab assessment.
 +
 
 +
=== Cytoskeleton Exercise ===
 +
 
 +
In - lab assessment summary:
  
 
'''Tropomyosins induce neuritogenesis and determine neurite branching patterns in B35 neuroblastoma cells'''  
 
'''Tropomyosins induce neuritogenesis and determine neurite branching patterns in B35 neuroblastoma cells'''  
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[[File:Lab_5_Graph.jpg]]
 
[[File:Lab_5_Graph.jpg]]
  
=== Lab 6 ===
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=== Immunochemistry ===
  
 
Laminin antibodies are most predominantly used to highlight basement membranes and blood vessels.
 
Laminin antibodies are most predominantly used to highlight basement membranes and blood vessels.
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http://www.rockland-inc.com/rabbit-secondary-antibodies.aspx
 
http://www.rockland-inc.com/rabbit-secondary-antibodies.aspx
  
=== Lab 9 ===
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=== Project Work ===
 +
 
 +
No assessment.
 +
 
 +
=== Confocal Microscopy ===
 +
 
 +
In - lab assessment.
 +
 
 +
=== Tissue Culture ===
  
 
'''Cell Lines'''
 
'''Cell Lines'''
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I think that the timeline element under the history section is going to work out well.
 
I think that the timeline element under the history section is going to work out well.
 
Formation, plasticity and regeneration appear to be set out like a list. I think it would be better in a paragraph structure. Also when describing the formation, it would be helpful to the reader if you refer to the stages in the diagram, in the text.
 
Formation, plasticity and regeneration appear to be set out like a list. I think it would be better in a paragraph structure. Also when describing the formation, it would be helpful to the reader if you refer to the stages in the diagram, in the text.
 +
 +
=== Stem Cells ===
 +
 +
In - lab assessment.
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===Microarray Visit===
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 +
'''Microarray Paper related to Laminin'''
 +
 +
<pubmed> PMC4409756 </pubmed>
 +
 +
'''Summary of Technique'''
 +
 +
Using 27 normal and 29 cancerous tissue blocks taken from the vaginal portion of cervices, a tissue microarray (TMA) was generated. They were then immunostained for α-smooth muscle actin, laminin - 1, laminin - 5 and fibronectin. Following, they were scanned with a Scan Scope CS2 and analysed by MAN - 0023 Colour Deconvolution Algorithm Positive Pixel Count Analysis software.
  
 
===References===
 
===References===
 
<references/>
 
<references/>

Revision as of 13:20, 9 June 2015


Quick Links Course Timetable | Project | PubMed

Attendance

Lab 1 --Z3461763 (talk) 16:34, 12 March 2015 (EST)

Lab 2 --Z3461763 (talk) 16:38, 19 March 2015 (EST)

Lab 3 --Z3461763 (talk) 16:49, 26 March 2015 (EST)

Lab 4 --Z3461763 (talk) 16:20, 2 April 2015 (EST)

Lab 5 --Z3461763 (talk) 16:21, 16 April 2015 (EST)

Lab 6 --Z3461763 (talk) 17:00, 23 April 2015 (EST)

Lab 7 --Z3461763 (talk) 16:12, 30 April 2015 (EST)

Lab 8 --Z3461763 (talk) 16:34, 7 May 2015 (EST)

Lab 9 --Z3461763 (talk) 16:37, 14 May 2015 (EST)

Lab 10 --Z3461763 (talk) 23:18, 21 May 2015 (EST)

Lab 11 --Z3461763 (talk) 16:43, 28 May 2015 (EST)

Lab 12 --Z3461763 (talk) 12:40, 9 June 2015 (EST) (Was there, forgot to punch in attendance)

Assessments

Introduction to Lab

E. Coli and HeLa Cells


E. Coli and HeLa Cells.jpg [1]

Figure Legend Adhesion of intimin-producing E. coli strains to preinfected HeLa cells carrying the Tir receptor.

Reference Philipp Oberhettinger, Monika Schütz, Jack C Leo, Nadja Heinz, Jürgen Berger, Ingo B Autenrieth, Dirk Linke Intimin and invasin export their C-terminus to the bacterial cell surface using an inverse mechanism compared to classical autotransport. PLoS ONE: 2012, 7(10);e47069 PMID:23056583

Copyright 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.

Microscopy Methods

PART 1

Nuclear Deformation and Gene Expression.jpg [2]

Nuclear Deformation and Gene Expression

Figure Legend Nuclear deformation and gene expression by modulating cell geometry.

Reference

<pubmed> PMC3532443 </pubmed> Copyright

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.

PART 2

A Microfluidic Platform for Correlative Live – Cell and Super – Resolution Microscopy (Summary)

Introduction Super resolution microscopy (SRM) has allowed us to view subcellular structures. In particular, stochastic reconstruction microscopy (STORM), has allowed “single molecule localization”. This is when photo switchable fluorophores are used to label the structure being investigated. When these are activated, the image separates, allowing localisation and therefore, when repeated, creating a STORM image. However, these methods have only been used on fixed cells and slower dynamic processes because of SRM’s poor temporal resolution. This has prevented us from viewing fast dynamic processes and their relationships to underlying ultrastructures as well as nano scale protein organisations. To overcome this disadvantage, a method that allows the microscopy of live - cells with super – resolution microscopy, described as a correlative and sequential imaging method, was put together. As manual sample preparation techniques are tedious, a simple microfluidic platform was also established, streamlining sample preparation steps between the live cell and super – resolution image. This consisted of a microfluidic chip with mini imaging chambers, coupled with an automated fluid – injection device, made to transfer specific amounts of the reagent to the selected chamber at the set times within the experiment.

Results Bonded to a glass cover slip, a single – layered microfluidic chip, manufactured using polydimethylsiloxane (PDMS) was used. Initial results produced low cell concentrations, didn’t reveal fluorophores and failed to highlight densities. This was found to be a result of the reduction of the size of the tube that the cells flowed through, as density decreases with diameter and also because majority of the sample preparation protocols are designed for materials other than PDMS. To overcome this hurdle, through trial and error, an optimum concentration and imaging buffer was found. Results obtained revealed images with resolutions of up to 23.8 nm. To further highlight the images, a fluid channel containing a fixative solution was added, resulting in images with multiple colours. To improve the reliability of the experiment, the process was demonstrated on mitochondria, 28 times, revealing a 75% success rate. This imaging method enabled the investigation of the relationships between dynamics, size and protein distribution within mitochondria cells. As a bonus, these images were produced using lower laser densities (which is important for cells like mitochondria that are sensitive to photo damage) rapidly and without the need for a buffer or oxygen system.

Conclusion Overall a total of 577 mitochondria were identified. Their dynamics, its relationship with size and interaction with other mitochondria were investigated, reinforcing the success of this experiment in creating an image of high temporal resolution and high spatial resolution quality.

Reference <pubmed>PMC4278722</pubmed> [3]

Preparation / Fixation

In Lab:

Paraformaldehyde: used as a cross - linking agent to preserve cell structures (for short periods of time only). https://proscitech.com/msds/c004.pdf

Article Assessment:

The Heterotrimeric Laminin Coiled – Coil Domain Exerts Anti – Adhesive Effects and Induces a Pro – Invasive Phenotype Laminins are a family of ECM glycoproteins localised in the basement membrane. As well as their structural roles, they also regulate cellular processes. These include cell migration, differentiation and proliferation. Laminins also have multiple binding partners; hence, the study was to determine what would happen to individual truncated Laminin chains in the absence of their normal partners. They did this by selecting a transfectable cell line with low endogenous Laminin chain expression, by first encoding the truncated Laminin α1, β1 and γ1 chains which encode the entire LCC.

Truncated α1 chains were found to be efficiently secreted as a monomer when expressed alone, as opposed to the β1 and γ1, which were poorly secreted. But, when all three were expressed together, they formed a trimer that was secreted into the medium. This confirmed previous findings that a chain subunit expression is necessary for the secretion of the β1 and γ1 chain partners. It also confirmed consistent with previous analysis that the truncated chains can also assemble into the trimetric coiled - coil structure independent of the rest of the molecule.

Through interactions with other ECM molecules and cell surface receptors, Laminins exert multiple biological functions. However, majority of the cell – binding sites map to regions distinct from the coiled – coil domain. This domain is believed to play a key role in chain assembly yet it is considered a functionally silent domain, with a few exceptions. This study first revealed and demonstrated that the Laminin coiled – coil domain inhibits cell adhesion and spreading.

It is also noticed that anti – adhesive properties of ECM proteins are not a common observation. Cell adhesion modulation is often related to cell migration. The actin cytoskeleton plays an important role in the processes of cell movement, with filopodia and lamellipodia formation being crucial. Because decreased actin stress fibre formation and increased membrane ruffle formation are consistent with the promotion of cell migration, it is a tempting speculation that the adhesive property of the Laminin coiled – coil domain is linked to the modulation of cell migration in tissues where the Laminin coiled – coil domain became accessible.

Reference <pubmed>PMC3378518</pubmed> Copyright 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.

The Laminin Response in Inflammatory Bowel Disease: Protection or Malignancy? Laminins are major components of the epithelial basement membrane. They play a crucial role in tissue homeostasis and also an important role in tissue maintenance and cancer progression, which represents an inherent risk of IBD, however this role is poorly understood.

Repetitive tissue destruction, repair and oxidative damage can together trigger mutagenesis and potentially initiate cancer causing events. In wound healing and tissue repair, it is made prevalent that inflammatory responses are commonly associated with the remodelling of the ECM.

Altered ECM expression and ECM binding integrin adhesion receptors have been located in several inflamed tissues. Intestinal basement membranes are specialised ECM networks that functions to separate epithelial cells from underlying connective tissue. They are mainly composed for collagen IV, Laminins, perlecan and nidogens.

The basement membrane functions as a physical and chemical barrier. Several human disorders arise from defects in the BM assembly or composition. Laminin are a family of basement membrane glycoproteins. Each contains an α, β and γ chain, which form characteristic heterotrimers.

Laminin, particularly the α chain that carries the cell binding domains, is important for cell adhesion, migration, proliferation and preventing cell apoptosis. Laminins have also been found in the human intestine.

When there is inflammation in IBD, mucosal ulceration and subsequent tissue repairs occur, promoting the constant remodelling of the basement membrane, hence it is believed that Laminin may play an unknown role in the inflammation response, impacting the bodies response to inflammation. Furthermore, it has also been described that altered immunoreactivity of BM constituents in the IBD, have shown an increase in alpha Laminin, meaning it is likely that Laminin participates in the regeneration of the intestine.

This result was highlighted when an increase in LMα1 and LMα5 expression was present in the colon tissues of IBD patients and in DSS – driven colitis in mice. The inflammation in these cases was accompanied by the nuclear accumulation of p53 as well as changes in the properties of the cell, caused in particular by the presence of the UACL in IBD.

Final results revealed that the LMα1 and LMα5 chains were overexpressed, using human IBD and murine colitis specimens, when inflamed. Furthermore, results also suggested the role that Laminins could play in tissue restitution, as Laminins promoted wound closure in tissue rebuilding when there are disrupted epithelial cell monolayers.

In conclusion, it was found that the forced expression of LMα1 and LMα5 protected against DDS – induced inflammation, yet in carcinogenic conditions, accelerated colitis – associated tumorigenesis.

Reference <pubmed>PMC4210184</pubmed> Copyright 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.

Keratinocyte – Targeted Expression of Human Laminin y2 Rescues Skin Blistering and Early Lethality of Laminin γ2 Deficient Mice Laminin – 332 is heterotrimetric basement membrane component comprised of α3, β3 and γ2 Laminin chains. It is responsible for epithelial cell processes, including adhesion, migration and differentiation and is commonly found in many embryonic and adult tissues. Keratinocytes are responsible for the secretion of Laminin – 332 in the skin, which is identified as a key component of hemidesmosomes that connect the keratinocytes to the underlying dermis.

In mice, when any of the three Laminin – 332 chains are not expressed, impaired anchorage and detachment of the epidermis occurs. This is similarly seen in human Junctional Epidermolysis Bullosa. As a result of this condition, death occurs a few days after birth. A dox – controllable human Laminin γ2 transgene was expressed, under a keratinocyte – specific promoter on the Laminin γ2 knockout background. The mice, as a result appeared similar to their wild – type littermates, didn’t develop skin blisters, were fertile and survived for more than 1.5 years.

Skin is a protective barrier, composed of two primary layers, known as the epidermis and dermis. These two layers are separated a sheet of specialised extracellular matrix known at the basement membrane zone (BMZ). The BMZ functions as a border, for structural support, influences cell attachment, proliferation, differentiation and migration. Should a defect occur in the structure or in one of the components of the BMZ, tissue separation and blister formation may result.

Junctional Epidermolysis Bullosa (JEB) is a genetic skin blistering disease, which results in, in the most severe cases, the death of infants within their first year of life. JEB is mostly caused by the absence of Laminin – 332, due to mutations arising within the chains. Lm -332 is secreted by skin keratinocytes and forms a critical component of the BMZ, functioning as an adhesion molecule between the epidermis and dermis.

Lm – 332 is present in the basement membranes of the brain, gastrointestinal tract, heart, kidney, liver, lung, trachea, skin, spleen, thymus, salivary gland, mammary gland, ovary, prostate and testis. Hence, those who experience the skin blistering also experience blistering of the mucous membranes of the mouth and gastrointestinal tract, in turn affecting nutrition.

The experiment involved the expression of the human Laminin γ2 in the mice, to test whether or not it helped prevent their early lethality. Newborn offspring that carried neither of one of the transgenes had blistered skin, smaller milk pouches and died a few days after birth. However, the mice that were carrying the human gene looked the same as the others at birth, survived for more than a year and had similar weights and lengths as the normal mice.

When examining the affects of the human gene expression in the mice, the Laminin γ2 was detected in the mouth of the mice. It was also found that the newborn mice, which lacked the transgene, had a separated epidermal layer, while those who had the human Laminin showed a more attached structure.

Reference <pubmed>PMC3445496</pubmed> Copyright 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.

Laminin – 511 A multi – functional adhesion protein regulating cell migration, tumor invasion and metastasis Laminins are major constituents of basement membranes. Recent studies indicate that Laminin – 511 contributes to tumor dissemination and metastasis in advanced breast carcinomas as well as other tumor types. Furthermore, experimental evidence has suggested that there is a prognostic significance with a higher expression of Laminin – 511 and that by targeting tumor – Laminin – 511 interactions, there may be a therapeutic potential in advanced cancer patients.

Laminins are abundant extracellular matric proteins, present predominately in basement membranes. There are approximately 16 isoforms, named according to their specific combination of the α, β and γ chains. A combination of technological advances and experiments has contributed to the belief that LM – 511 and its receptors regulate cancer progression.

The LM – 511 expression patterns vary between different tumor types whether it be basement membrane localisation to diffuse stromal or tumor cell expression. It’s level in tumor cells or surrounding vasculature varies based on the stage of tumor progression. Many studies show that LM – 511 expressions in advanced tumors is maintained or even increased. It’s also observed that in advanced human breast cancers and bone metastases, there is high tumor cell expression of LM – 511. Discussions are about whether future studies should look at LM – 511 expression in tumors and whether it has a particular clinical relevance with a propensity to metastasize to bone. Whether or not LM – 511 expression has any contribution to breast tumors, has not yet been fully confirmed.

As has been found from previous studies, many tumor lines synthesize, secrete and adhere to LM-511, potentially indicating that LM – 511 is able to produce it’s effect on tumors via autocrine stimulation in part. Receptor studies are the reason for the many believed functions of LM’s in breast cancer progression and metastasis and it is possibly inferred, from several observations that LM – binding integrins in metastatic breast tumors are mediated through attachment to LM – 511.

Laboratory results are consistent with this theory, specifically observing that metastatic breast tumor lines adhere and migrate more efficiently on LM – 511, as opposed to on metastatic lines. If the believed and found observations are correct then metastatic potential can be impacted by blocking the production of LM – 511 and or the function and expression of its receptors.

Increasing experimental evidence is supporting the link of LM – 511 to cancer progression and reinforcing the belief that LM – 511 has a broad role in tumor invasion and metastasis. However, questions in regards to its prognostic significance, precise mechanism of action and potential as a therapeutic target still need to be addressed and answered.

Hence, the following should be looked more into: - For staining archival material, the generation of more robust antibodies. - Clarification of the precise contribution of LM – 511 to the metastatic process. - Contribution (if any) of stromal/ vascular LM – 511 to metastasis (tumor – derived LM – 511 in metastasis is already supported). - Studies in vivo, to provide proof of the therapeutic benefits that targeting LM receptors could have.

As metastasis is responsible for majority of cancer – related deaths and is a clinical challenge, the continuation of research of Laminins has the potential to present several information and solutions to overcoming this disease, as well as assist in the development of alternative strategies to prevent and/ or delay metastatic progression.

Reference <pubmed> PMC3544778 </pubmed> Copyright This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Proposed Model

Proposed model.jpg [4]

Figure Legend: Proposed model of LM-511 expression and function during cancer progression and metastasis.

Reference: <pubmed> 23076212 </pubmed> Copyright: This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Cell Knockout Methods

In - lab assessment.

Cytoskeleton Exercise

In - lab assessment summary:

Tropomyosins induce neuritogenesis and determine neurite branching patterns in B35 neuroblastoma cells [5]

According to previous studies, it has been identified that the actin cytoskeleton plays a major role in the regulation of neurite outgowth, with this experiment confirming that tropomyosin is this key regulator. It was found that tropomyosin, which is a structural protein, promoted neurite outgrowth in B35 neuroblastoma cells and regulated neurite branching. In particular, it was noted that tropomyosin significantly increased the proportion of cells which display the "neurite" phenotype. This finding of the molecular machinery increases the potential for new therapeutic strategies, supporting neurite regeneration following nerve injury.

Reference <pubmed> 24211701</pubmed> In our findings, the "Pronged" phenotype was found to be more prominent in the Tm4 over - expressing cells. In the wild type cells the "Stumped" phenotype was found to be most common. This is consistent with academic findings that tropomyosin promotes neurite outgrowth.

Lab 5 Graph.jpg

Immunochemistry

Laminin antibodies are most predominantly used to highlight basement membranes and blood vessels.

Antibody Laminin Antibody 0.1 ml Basement Membrane Marker (NB300 - 144)

Marker Basement membrane

Alternate names LAMA, LAMA1, Laminin A chain, Laminin subunit alpha - 1, Laminin, alpha 1, Laminin - 1 subunit alpha, Laminin - 3 subunit alpha, S - LAM alpha, S - laminin subunit alpha

Host Rabbit

Species deriving the antibody Human, Mouse, Rat, Rabbit, Sheep

Clonality Polyclonal

Working concentration 1 ug at 1.0 mg/ ml

Secondary antibody Anti - Rabbit IgG (H&L) (Goat) Antibody Peroxidase Conjugated

Antibody paper

<pubmed> PMC3327439 </pubmed> Other references

http://www.novusbio.com/Laminin-Antibody_NB300-144.html#dsTab0

http://www.rockland-inc.com/rabbit-secondary-antibodies.aspx

Project Work

No assessment.

Confocal Microscopy

In - lab assessment.

Tissue Culture

Cell Lines

Human Embryo Kidney

Culture Medium Eagle's Minimum Essential Medium (EMEM (EBSS) + 2mM Glutamine + 1% Non Essential Amino Acids (NEAA) + 10% FCS)

Human Skin Fibroblast

Culture Medium Eagle's Minimum Essential Medium (EMEM (EBSS) + 2mM Glutamine + 1% Non Essential Amino Acids (NEAA) + 15% Foetal Bovine Serum (FBS))

Human Brain Astrocytoma

Culture Medium Dulbecco's Modified Eagle's Medium (DMEM + 2mM Glutamine + 10% Foetal Bovine Serum (FBS))

Composition

Eagle's Minimum Essential Medium (EMEM) Developed by Harry Eagle. Widely used synthetic cell culture media. Contains liquids, salts, amino acids and vitamins.

Dulbecco's Modified Eagle's Medium (DMEM) Is a variation of EMEM. Modification in of the Basal Medium Eagle (BME). Contains four times the concentration of amino acids and vitamins found in EMEM and two to four times the amount of glucose.

Human (Homo sapiens) Cervical Adenocarcinoma

HeLa Cells Named for Henrietta Lacks. She died in 1952 from cervical adenocarcinoma.

Penicillin and Streptomycin

Penicillin Antibiotic that kills infection - causing bacteria; in particular the gram - positive organisms. Originate from Penicillium fungi. Used to: - Counteract bacterial infections, e.g. tonsillitis - Prevent further infection for those who have an existing condition, causing a weakened immune system, e.g. sickle cell disease - Support and boost the immune system of those undergoing treatment where the chances of infection are increased.

Streptomycin Antibiotic that inhibits certain bacterial infections; in particular those caused by gram - negative bacteria. It is also used in the treatment of tuberculosis. Being an aminogylcoside, it kills sensitive bacteria by preventing the production of proteins essential to the bacteria's survival.

Peer Reviews

Group 1 Peer Review SMALL LEUCINE - RICH PROTEOGLYCANS

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 2 Peer Review INTEGRINS

Overall well structured and presented page so far.

Key points clearly described: From what I read on your page, the key points appear to have been clearly described. If I was reading about something, that I was not sure of, I could easily find a description or definition elsewhere on your page.

Understanding? Content, headings, sub – headings, diagrams, tables, graphs? Teaching at peer level? Own innovative diagrams, tables or figures, Interesting examples or explanations?: I like how you’ve set out the page, breaking down the information, and explaining it as you go along in a logical sequence. Content and sub – headings are well chosen, and provide a good background to integrins. The diagram under the ‘Integrins’ heading, ‘A simple diagram of … cytoskeleton to the ECM’, helps the reader visual the process. Possibly though, tidy up the diagram (and scan it (I don’t think it’s a ‘scanned’ image) for better quality) by ensuring that the different parts of the diagram are in correspondence with each other, e.g. the plasma membrane is not uniform in shape and size. Furthermore, to maintain professionalism, maybe the labels should all be in capitals (so that it looks neater) or typed. The graph is well chosen. So are the other images on the page and their corresponding labels. However, why were the integrin structure images next to the ‘Function’ section of the page? I found this to be odd – placed. If it was intended to be for ‘Functional Structure’, you should relocate the images accordingly to avoid the confusion. Alternatively (and possibly for the other images as well), have references to the images, within the text, e.g. under ‘general structure’ you have (iii.) referring to the diagram – include ‘see figure 1’, or something similar to make it clearer. Also, I thought the video was a fantastic idea! It really helps visualise the integrin interaction.

Content correctly cited and referenced:The content appeared to be correctly cited. There are random citations and links here and there - I understand it’s still a work in progress; just don’t forget to fix this up!

Evidence of significant research / Adequate research: There appears to be a good deal of research, as when you read through the page, the different elements tie up well together. However, I don’t feel that this research is necessarily ‘adequate’. I feel you need to read a couple more articles and reference them on your page, rather then referencing the same article 2 – 3 times throughout the text. The more articles you use, the more supported and accurate your page will be, and the concepts will be better worded/ explained.

Other: Knowing that the page is still in progress, make sure you go over and correct and spelling, punctuation and grammatical errors (I noticed quite a few). Some of your sentences are too long and wordy – work on sentence structure. Under ‘general function’, the sentence reads ‘two main cellular functions’ – what are they? List them or point them out. You also need to add paragraphs to this same section (gen. function). It’s too clumped and difficult to read when together. I also think you need a paragraph explaining why you’ve listed ‘integrin trafficking, fibronetin, collagen, laminin etc’ under ‘interaction with the extracellular matrix’. Just a sentence saying what role those components play in interaction should be sufficient, so that the viewer knows why they are reading about all those other components and how they fit in with ‘integrins’. Initiation of metastasis and interaction with ECM components and stiffening of the ECM are two very, very long paragraphs. Ensure the paragraph breaks are more obvious and add pictures. When you read scientific papers/ wikis/ articles, you find yourself distracted when you have to read long lengthy paragraphs. In particular if scientific terminology is used that you’re not familiar with – you dread it! If you separate the text into more obvious paragraphs, it will give the reader a break and help them absorb what they read. Glossary is a fantastic idea. Possibly even list any terminology that those who are not in the scientific field, may not understand.

Group 3 Peer Review ELASTIC FIBRES

Overall, I think your page is coming together really well and on the border of completion!

Key points clearly described: I felt that the key points were clearly described, and didn’t feel that I had any difficulty in understanding any of the components. However, I think your page does need a bit more information. For example, under ‘Skin’, when you mention that the skin is composed of five layers, I think you should address/ list these five layers (however I do see an article there, so I’m assuming this is a work in progress). The same goes for ‘Spatial Distribution and Mechanical Function of Elastin in Resistance Arteries’, where you mention ‘three layers’. They are labelled in the image, but I think you should address them in the text as well. Just a note, I really liked your analogy to the rubber band! I thought it worked well!

Understanding? Content, headings, sub – headings, diagrams, tables, graphs? Teaching at peer level? Own innovative diagrams, tables or figures, Interesting examples or explanations?: The images used were good and relevant to what was being described. I do think that you need to include a lot more images though, particularly in the function and clinical significance section to break up the text. I really liked the ‘Process of Elastic Fibre Assembly’ image that you created. It’s really well done! However, I noticed in the text that you describe the steps in the image from 1 -5. This is not obvious or very clear. Maybe you should either centre the image and have the steps following or include the steps in the image description. Also, under the ‘Spatial Distribution…’ heading, the images you have are really good, but the one on the right I feel needs to either be referred to in the text or described in a text box, because it is not clear what the image is showing. Overall, in terms of images, spread them out so they are not clumped together, or even on the same side of the page consistently.

Content correctly cited and referenced: Everything appears to be referenced well. Don’t forget to remove the reference link under Skin!

Evidence of significant research / Adequate research: It appears you have done a great deal of research, and your concepts are clearly well – covered. Just fill in the little gaps I mentioned (layers of skin and three layers), and find supporting articles for areas where only minimal references have been made. The more articles you look at and derive information from, the better and more credible your page will sound.

Other: There is quite a few grammatical errors. Just fix that up. And on another note, under the ‘Tropoelastin and Elastin’ title, if you talk about elastin first, I think it is more logical that the heading has elastin first.

Group 4 Peer Review FIBRONECTIN

Overall, I think your page is coming together well and is on the border of completion!

Key points clearly described: I found that majority of your key points were clearly described, and the main concepts were addressed. In particular, I found that the concepts under ‘Function’ and ‘Abnormalities’ was summarised really well. However, in the introduction, I think you should define what the extracellular matrix is and what a glycoprotein is, rather than just describing fibronectin as ‘an essential ECM glycoprotein.’ Possibly even have a glossary at the end of the page defining them. In the introduction the information was difficult to read because I felt there was too much information. Keep the structure and function separate from this part. Only have a brief sentence in the intro on each. Under ‘Structure’, I also feel you need to change how you have listed FnI, FnII and FnIII. A table may be more appropriate. Other scientific terms, such as ‘opsonise, angiogenesis and atherosclerosis’, should probably be defined in the text, or in a glossary at the end of the page. Include any terminology used on your page that is not common scientific language. Also, why is current research only a list of references? If that’s how you choose to display the current research, then I feel you should at least summarise the articles/ write an abstract, so the reader knows what the article is about.

Understanding? Content, headings, sub – headings, diagrams, tables, graphs? Teaching at peer level? Own innovative diagrams, tables or figures, Interesting examples or explanations?: Your page needs a lot more images! Add some to the introduction. Because there is a lot of content, pictures will break the text up. In the history section possibly a timeline layout is better and more appealing to the eye. The image in your structure section needs a label and / or a description of what is being shown. Maybe even refer to the image in the text where possible. An image for assembly, highlighting the process described, would be ideal, as it would help the reader understand the concept. Furthermore, I feel that a description is needed under the ‘Wound Healing’ image, so that the process is clearer, or alternatively, referring to parts of the image in the text. From ‘Role in Tumours’ down (especially embryogenesis) the text looks like a lot and is difficult to read through. Break the text up with images or maybe you can even list the different functions and/ or abnormalities in tables? I also noticed that you don’t have your ‘hand – drawn’/ created image. I think you should include one. ☺

Content correctly cited and referenced: Everything text wise, appears to be correctly cited. However, just look over the image references. You’re missing some details such as figure legend and web link.

Evidence of significant research / Adequate research: While there is evidence of significant research on your page, as you do have a lot of information, I’m not sure about the current research section. I feel as if that area is a work in progress.

Other: Avoid long, lengthy paragraphs, e.g. Introduction, Embryogenesis. Make sure the paragraph breaks are evident otherwise it’s too difficult to read. Avoid repetition of words in close proximity, such as ‘fibronectin’ in the first paragraph of structure. Overall, have a look at grammar and punctuation. While your page seems to have been edited for grammatical errors, I still noticed a few. Just a note, it would be better if you had larger/ more evident titles for ‘History, Structure, Function, Abnormalities’, like that of Fibronectin.

Group 6 Peer Review TYPE II COLLAGEN

Overall , I think you’re on the right track with your page, and once you fill in the missing bits, it will be good!

Key points clearly described: I felt that your page was structured / set up well, however there is a great deal of information missing (work in progress). Nonetheless, most of the parts that had information were well done. In particular, I felt the clinical application was narrowed down really well and highlights the clinical significance of the research. Just a note, under ‘Function’, when describing the layers of the articular cartilage, you should make obvious the three ‘zones’, i.e. ‘The first zone is the articular surface’, or even number them, such as ‘1. Articular Surface’ and then include all the information following. I just felt that the zones needed to be distinguished better. The abnormalities section was really confusing and complex to understand. The incorporation of the referencing into the text did not work. I think you need to just reference at the end and only use last names and/ or reword that entire section to eliminate having to reference in text. Seeing the references within the text made me lose track of what I was reading. You also need to break the abnormalities paragraph down, and define the different components mentioned, for example, what are exons?

Understanding? Content, headings, sub – headings, diagrams, tables, graphs? Teaching at peer level? Own innovative diagrams, tables or figures, Interesting examples or explanations?: I thought your hand – drawn image was fantastic! Well done! It really outlines the structure of articular cartilage. I also liked the other images you used, but feel you need to add an image description below the ‘Mature Chondrocytes’ image and add a lot more images in general. An image showing the development stages described under ‘Developmental stages’ would be beneficial.

Content correctly cited and referenced: I think you should look over your references. In particular, under some of the images, you are lacking quite a bit of the necessary information, including copyright!

Evidence of significant research / Adequate research: There is a lot of missing information on your page. You obviously need to do a lot more research and you can see that your page is a work in progress. The more articles you use and the more research you do, the more credible your page will be! As for the parts, where research has been completed; while you have done research, maybe look at a couple more articles so you are not only gathering information from one source.

Other: There are quite a few grammatical errors on your page; a few spelling errors, punctuation and problems with sentence structure. This really needs to be looked over, because it takes away from the quality of your work. In particular, look over the structure component. I like the idea of a glossary! Add words to it that may not be understood by a person who is not familiar in the scientific field. As for antibodies, maybe you should list that information in a collapsible box. It seems out of place on the page the way it currently is.

Group 7 Peer Review BASEMENT MEMBRANE

Overall, page is coming together well and appears well thought out.

Key points clearly described: I found that the key points were clearly described. In particular I found the renal abnormalities really well done. I felt as if you need more information under functional layers – describe them a bit more – why are they like that? How does that structure contribute to their function? What about the components of basal lamina (lucida and densa)? When I read that section, I just felt that I needed a bit more information.

Understanding? Content, headings, sub – headings, diagrams, tables, graphs? Teaching at peer level? Own innovative diagrams, tables or figures, Interesting examples or explanations?: Your images were really good and beneficial to the page. Just include more images in areas lacking, such as under renal abnormalities. I also think it may be beneficial if you refer to the images in the text, so readers can look at the image and get a better understanding. Some of the images also, I feel need a better description, such as under the image ‘Loss of basement membrane’ – explain how/ why maybe? Also, the little paragraph at the beginning of ‘Function’ about the image adjacent to it – I found that out of place – maybe that text should accompany the image? I really like the little ‘expand for additional info’ components. They were fantastic! The diagrams were well chosen too! In particular, I really liked your hand drawn image under ‘additional info glomerulus’.

Content correctly cited and referenced: References appear properly done.

Evidence of significant research / Adequate research: There is clearly evidence of significant research. However, in some sections I didn’t find this adequate – but I’m assuming this is so because the pages are still being worked on. For example, under current research – why is it only a list of articles? If you’re going to leave that section like that, maybe format the references in a list? Alternatively, if the articles are going to be incorporated as part of your text (not just a reference), you should provide a brief summary/ abstract of what the reader is expected to read or gain from the article.

Other: Some of your paragraphs lacked evident paragraph spacing, making it difficult to read – introduction and heterogeneity of BM. I think that the timeline element under the history section is going to work out well. Formation, plasticity and regeneration appear to be set out like a list. I think it would be better in a paragraph structure. Also when describing the formation, it would be helpful to the reader if you refer to the stages in the diagram, in the text.

Stem Cells

In - lab assessment.

Microarray Visit

Microarray Paper related to Laminin

<pubmed> PMC4409756 </pubmed>

Summary of Technique

Using 27 normal and 29 cancerous tissue blocks taken from the vaginal portion of cervices, a tissue microarray (TMA) was generated. They were then immunostained for α-smooth muscle actin, laminin - 1, laminin - 5 and fibronectin. Following, they were scanned with a Scan Scope CS2 and analysed by MAN - 0023 Colour Deconvolution Algorithm Positive Pixel Count Analysis software.

References

  1. <pubmed>23056583</pubmed>
  2. <pubmed>23285252</pubmed>
  3. <pubmed>PMC4278722</pubmed>
  4. <pubmed>23076212</pubmed>
  5. <pubmed>24211701<pubmed>