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Lab Attendance:

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Lab 1: Internal and External Links

PubMed


Lecture 2


Group Page

Test page

PMID 25513760

<pubmed>25513760</pubmed>

Cellular interaction network [1]


[2]

Lab 2: Image Referencing

Mitochondria- Cell death and protection .jpg

File:Mitochondria- Cell death and protection [3]


Super-resolution Imaging of the Natural Killer Cell Immunological Synapse on a Glass-supported Planar Lipid Bilayer.[4]

The glass-supported planar lipid bilayer (SLB) system allows the surface of a target cell to be simulated, replicating the mobility and orientation of ligands. This feature makes the technique very useful in the study of immunological synapse (IS) formation. This is because it is a fluid mosaic allowing the surface proteins to move freely in a 2D surface. The only limitation of this SLB system is the imaging techniques. Recent advances in super-resolution microscopy such as the development of techniques like the Stimulated emission depletion microscopy or STED have remedied this limit. These new advances in Super-resolution imaging allow the fine details of synapse structures to be seen. This study combines these two techniques to study the NK cell synapse and examine the application and feasibility of the combination.

The study outlines a protocol detailing how to visualize NK cell synapse formation. First the raw synthetic liposomes must be prepared and undergo dialysis to be utilized in the synthesis of the bilayer. The next step is the determination of antibody density on the lipid bilayer’s attachment sites. The human NK cells must then be isolated and cultured. The glass-supported planar lipid bilayer containing antibodies against CD16 (NK cell activating receptor) must be assembled. The final step involves the imaging of the NK synapse on lipid bilayer using STED. The imaging focuses on the distribution of perforin positive lytic granules and actin at the synapse.

In conclusion the study combined the STED technique with the glass-supported planar lipid bilayer system, demonstrating the applications of such a combination and illustrated the fine details of intracellular structures at NK immunological synapse.


Lab 3: Reference Searching

http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=AU&language=en&productNumber=P6148&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsial%2Fp6148%3Flang%3Den


Search term: Laminin


<pubmed limit=5>Laminin</pubmed>


BioMed Central

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

Laminin 332 expression in breast carcinoma: [5]

Laminin 332 or LN332 is a basally expressed extracellular matrix protein that is part of a group of laminin isoforms that demonstrates tumor-promoting properties. In normal tissue Laminin 332’s main role is to maintain epithelial-mesenchyme cohesion when the tissue is exposed to external disruptive forces. It also stimulates cells including carcinoma cells to migrate allowing for metastasis and has thus been associated with the progression of a tumor. Past research has found a direct correlation between LN331 and both Tumor invasiveness and a poor patient prognosis. The role of Laminin 332 in breast carcinomas is however unclear. This study aims to examine the relationship between Laminin 332 and breast carcinomas. The researchers tested the expression of LN332 in surgically excised breast carcinomas using immunohistochemistry (IHC) and western blot. The primary objective of the study was to examine patterns of expression in varying molecular classes of breast carcinomas. The basal-like phenotypic subgroup has a worse prognosis observed, and thus was of particular interest. The genetic profiling method that defines the basal phenotype was not widely available, so a surrogate was used, namely Triple negative (TN) breast cancer. Triple negative is a sub group of breast carcinomas that lack progesterone receptors, estrogen receptors and HER2 positivity. Results revealed 70% of TN carcinomas stained for LN332 and 14.7% of non-TN carcinomas indicating its expression with a basal phenotype. The combination of LN332 and CK 5/6 or EGFR identified 92% of triple negative breast carcinoma. Expression of the basal marker LN332 and CK 5/6 or EGFR may help in the identification of breast carcinomas with the basal phenotype. Furthermore the expression of LN332 a pro-invasive protein in TN breast carcinomas suggests another mechanism by which the TN phenotype could be aggressive. Further study will need to be performed in order to determine weather LN332 has an effect on the invasive or migratory phenotype.


Molecular identification of collagen 17a1 as a major genetic modifier of laminin gamma 2 mutation-induced junctional epidermolysis bullosa in mice:[6]

Epidermolysis bullosa (EB) is a disorder resulting in structural weakening of the skin and mucous layer. Junctional EB is caused by a mutation that results in the cleavage of the dermal-epidermal junction. An unexplained phenotypic variability that is present in these mutations promotes the idea of genetic modifier effects. The study in question aims to analyze the effect of genetic modifiers on the strength of dermal-epidermal adhesion and clinical severity of Junctional EB. The results indicated that Col17a1 is a strong genetic modifier of Junctional EB that develops by mutation of Lamc2.jeb Allelic variants in Col17a1 alters the strength of dermal-epidermal adhesion therefore impacting the severity of Junctional EB. Overall the results indicated that normally innocuous allelic variants could cause mutations to have an impact on the strength of dermal-epidermal adhesion and severity of Junctional EB. This may help the genetic prognosis and diagnosis of Epidermolysis bullosa.


Laminin alpha2 deficiency and muscular dystrophy; genotype-phenotype correlation in mutant mice:[7]

Muscular dystrophy is a group of disorders characterized by the weakening of the skeletal muscle. The muscular disorders that can be caused by over 30 mutated genes, many of which encode for molecules involved in maintain structural integrity and cell adhesion. One of the most sever forms of muscular dystrophy involve the mutation of laminin α2 or LAMA2. Mutations on LAMA2 have been reported to range from absence of laminin α2 to the partial deficiency. It is however not clear as to how a laminin α2 mutation may effect protein expression and how these effected proteins cause affect disease. The aim of this study to analyze the genotype and phenotype, determine the mechanism of disease and determine the function of laminin. The study uses animal models to do this. An allelic series of mutations in the mice were used to facilitate genotype-phenotype correlation. The allelic series included mice with absence of laminin α2, reduced levels of laminin α2, truncated protein and reduced levels of truncated protein. Three lines of LAMA2 mutated mice with a complete deficiency in laminin α2 and two lines of transgenic mice with overexpressed laminin α2 were used to analyze protein expression. All the mutated mice lacked laminin α2 in peripheral nerve. The results indicate the muscular dystrophy in truncate protein mice was mild but more severe than that of the laminin α2 absent mice. The mechanisms for expression of laminin α2 in muscle and nerve also appeared different. The results provided evidence that the amount of laminin α2 is critical in the prevention of muscular dystrophy and could thus act as a possible treatment.

Variation in the onset and severity of JEB-nH.jpg

File:Variation in the onset and severity of JEB-nH

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.

Biologically-active laminin-111 fragment that modulates the epithelial-to-mesenchymal transition in embryonic stem cells: [8]

Epithelial-to-mesenchymal transition (EMT) is a process allowing an epithelial cell to assume a mesenchymal phenotype through biochemical changes via its basement membrane and is essential for cell migration and early embryonic development. This process is regulated by signalling pathways and cellular changes involving the expression of E-cadherin, matrix metalloproteinase 2 (MMP2) and matrix metalloproteinase 9 (MMP9). Laminin-111, a trimeric basement membrane glycoprotein is one of the first extracellular matrix (ECM) proteins expressed during the two-cell stage in early embryogenesis and its importance together with other proteins, collagen IV, nidogen and perlecan in the assembly of the basement membrane is known. This study proposes a previously unidentified role of Laminin-111, namely its ability to influence the regulation of EMT. They report the generation of a biologically active Laminin-111 fragment by MMP2 processing and demonstrate that the fragment acts through the α3β1-integrin/extracellular matrix metalloproteinase inducer complex to trigger the down-regulation of MMP2 in human and mouse ECM. Recognizing ECM and MMP2 interactions will increase our understanding of the pluripotent stage of early embryonic development to develop new applications and disease-modeling platforms.

Lab 6: Immunochemistry

1) Identify an antibody that can been used in your group's transport project: Laminin α-1 Antibody (M-20)

2) Identify the species deriving the antibody: Goat polyclonal IgG

3) Identify the working concentration for the antibody: 200 µg/ml

4) Identify a secondary antibody that could be used with this antibody.

The following secondary antibodies are recommended:

1. Western Blotting: donkey anti-goat IgG-HRP: sc-2020 (dilution range: 1:2000-1:100,000) or Cruz Marker™ compatible donkey anti-goat IgG-HRP: sc-2033 (dilution range: 1:2000-1:5000), Cruz Marker™ Molecular Weight Standards: sc-2035, TBS Blotto A Blocking Reagent: sc-2333 and Western Blotting Luminal Reagent: sc-2048.

2. Immunofluorescence: donkey anti-goat IgG-FITC: sc-2024 (dilution range: 1:100- 1:400) or donkey anti-goat IgG-TR: sc-2783 (dilution range: 1:100-1:400) with UltraCruz™ Mounting Medium: sc-24941.

5) Identify a paper that has used this antibody.

<pubmed>17364662</pubmed>

Lab 9: Tissue Culture

Mouse cell line:

NMuMG

Complete Growth 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


Human cell line:

143B

Complete Growth Medium: Minimum essential medium (Eagle) in Earle's BSS with 0.015 mg/ml 5-bromo-2'-deoxyuridine, 90%; fetal bovine serum, 10%

Minimum essential medium (Eagle)


Lab 10: Peer Review

Group 1:

The introduction was done quite well. The students have given a brief introduction explaining what Small Leucine-Rich Proteoglycans are. The picture used is also very helpful in giving the reader a basic introduction to the page. Furthermore they have summarised what the wiki page describes. The history section was done quite well with the headings making it easier to read and the graph a good visual backing up the writing. While the majority of this section was done well, there are some sections that could be fixed. In the history section a lot of last names are stated. ‘Jorpes and Gardell worked on heparan sulfate, and Hascall and Sadjera explored cartilage proteoglycans.[4] Alongside this, Dorfman, Silbert and Lindahl performed studies on glycosaminoglycan biosynthesis.’ When describing the work of scientist, try and use full names and state briefly who they are. For example ‘Erik Jorpes a Swedish biochemist.’ Furthermore the sub heading ‘future avenues of research’ does not directly fit under the heading history. Your group should consider altering its position, perhaps making it its own section. Overall the history section was done well. The synthesis section does not make much sense. It is evidently unfinished. More information and one or more subheadings will improve this section drastically. Similarly the section ‘structure’ needs more work and the layout should be revised. The tables of pictures are very informative and show an adequate amount of research. The section on function has been done very well. The information is detailed going beyond basic science while relating back to the cell biology aims. Consider including a picture to aid the teaching element.

The sections on Fibromodulin and lumican and decorin and biglycan appear to be unfinished. However what is there seems to be informative. The Content is correctly cited with in text citation used throughout the wiki page. The references under the subhead Fibromodulin and lumican as well as structure should be placed at the bottom.

The section on diseases has also been done quite well. The student has used subheadings that aid the reader. The content indicates an extensive amount of research and appears to be very informative. There is also an extensive use of images in this section, which back up the content.

Overall this group project was done very well. The choices of headings used are quite good, covering the key areas necessary to inform learning and indicating a good understanding of the topic. Some of the subheadings however need revising. The content effectively demonstrates an adequate amount of research on this topic and is very informative. Furthermore the information is quite detailed going beyond basic science while relating back to the cell biology aims. Overall a wide variety of pictures have been used adding an element of teaching. The Content is correctly cited with in text citation used throughout the wiki page. The references are also done correctly except for a few references not at the bottom. A lot of work still needs to be done but the basis of this report is very good.


Group 2:

The Integrin introduction appears to be unfinished, however the subheadings and text indicates an adequate amount of research on this topic. The timeline is a good teaching skill which sets out the history is an effective manner. The picture used is a little dark. Consider using pen or color in pictures. In section of structure the information is detailed going beyond basic science while relating back to the cell biology aims. More work needs to be done under the headings specialty, function structure and synthesis and regulation. The section on function has been done very well. The content effectively demonstrates an adequate amount of research on this topic and is very informative. The subheadings, diagrams and videos are very effective in aiding teaching and add to the section as a whole. The section on disease has also been done very well. The information is detailed going beyond basic science while relating back to the cell biology aims. Consider including a picture to aid the teaching element. The glossary at the bottom of the page is a very effective tool to aid the reader and the color makes the page more interesting.

Overall this group project was done very well. The choices of headings used are quite good, covering the key areas necessary to inform learning and indicating a good understanding of the topic. The subheadings indicate a good understanding of the topic. The content effectively demonstrates an adequate amount of research on this topic and is very informative. Furthermore the information is quite detailed going beyond basic science while relating back to the cell biology aims. Overall a wide variety of pictures have been used adding an element of teaching. The Content is correctly cited with in text citation used throughout the wiki page. The references are also done correctly except for a few missing references at the bottom (17, 19, 20 and 21). A lot of work still needs to be done but the basis of this report is very good.

Group 3:

The introduction has been done well, providing an intro into the topic of elastin fibers. It however is very short. You should consider expanding the text. You should also consider inserting a general image of an elastin fibre. The structure and component section is quite extensive. The content effectively demonstrates an adequate amount of research on this topic and is very informative. The Content in this section is correctly cited and referenced. The assembly section has also been down well, with the pictures standing out. The colours used and the numbers cited in the text aid in the teaching aspect by making this section more understandable. You should consider indenting the numbers in the text so that they stand out. While the section on function seems to be fairly extensive, some extra work should be done. The subheadings in this section effectively indicate a good understanding of the topic while help the reader follow this section. The images used are very good in visually aiding the reader. You should however provide a description of what is going in in the images and relate it back to a segment of the text. Some random phrases such as ‘Skin is composed of five layers’ should be revised. Further elaboration would be beneficial in this case as the text under skin is quite short. The section on clinical significance has been done very well. The division into diseases makes it easier to read. Not too much is needed to fix this section, however the student should consider adding some images to aid in the teaching aspect and provide a visual representation.

This project as a whole has been done quite well. The choices of headings used are quite good, but you should consider adding a bit of history and current research to indicate a good understanding of the topic. The subheadings used indicate a good understanding of the topic. The content effectively demonstrates an adequate amount of research on this topic and is very informative. Furthermore the information is quite detailed going beyond basic science while relating back to the cell biology aims. Overall a wide variety of pictures have been used including drawing and histological diagrams which add an element of teaching. Some sections do however need additional pictures and descriptions. The Content is correctly cited with in text citation used throughout the wiki page. The references are also done correctly except for a few missing references at the bottom (23, 24 and 25). Overall some extra work in each section will make this a great project.


Group 4:

The introduction has been done well, providing an intro into the topic of fibronectin. You should consider inserting a general image of fibronectin here. Citation throughout this section appears to be quite extensive and done correctly. The timeline is a good teaching skill which sets out the history is an effective manner. The section however appears to be unfinished. Consider adding addition text under this subheading. The structure section appears to be done quite well with a lot of text given. The image used is very good in visually aiding the reader. You should however provide a description of what is going in in the images and relate it back to a segment of the text. The subheadings indicate an adequate amount of research on this topic while making it easy for the reader to follow. You should consider fixing the very short paragraphs that appear out of place.

The assembly has been done well, it however is very short. You should consider expanding the text and elaborate of the assembly process. You should also consider inserting an image of this process. The function section has also been done very well. The picture and subheadings indicate an adequate amount of research on this topic while making it easy for the reader to follow. The text under each subheading is however very short. You should consider expanding on some of the shorter sections such as ‘role in blood.’ Similar to the function section the abnormality section needs extra work. The subheadings indicate an adequate amount of research on this topic while making it easy for the reader to follow. You should consider adding a picture to this section and expand on the text under each subheading. The sections on therapeutics and current research appear to be unfinished. Expanding on these sections will improve the wiki page.

Overall this project is very good, but needs a bit of work. The pictures used are very good however there should be a wider range of pictures to aid in the teaching aspect of the wiki page. The choices of headings used are quite good, covering the key areas necessary to inform learning and indicating a good understanding of the topic. The way in which these headings are edited should be revised. Consider changing the subheadings such as introduction, function etc. to headings so a line divides each section in the text. The content effectively demonstrates an adequate amount of research on this topic and is very informative. Furthermore the information is quite detailed going beyond basic science while relating back to the cell biology aims. The Content is correctly cited with in text citation used throughout the wiki page. The references are also done correctly and appear quite extensive except for a few references missing from the bottom (16 and17). If these errors are fixed this project could be very good.


Group 6:

It is not evident whether or not section 1 type 2 collagen is a heading or a section. At the moment it is appearing as a heading. If this is not the case you should consider changing it. The introduction does not appear to be finished. The history text is done quite well but is very short. You should consider expanding the text. The section of structure has a lot of text and a good quality image. The student should consider expanding on the description of the image by explain what the images a, b, c and d are. The student has used subheadings that aid the reader and indicate an extensive amount of research. Information under the empty headings is still needed.

The section on function has been done very well. The student has used subheadings that aid the reader. The content indicates an extensive amount of research and appears to be very informative. Furthermore the information is quite detailed going beyond basic science while relating back to the cell biology aims. The intro and image used in this section effectively back up the content and aid the reader in understanding the function of collagen 2. The red labeling in the image also stands out making this section much better. The synthesis section does not make much sense. It is evidently unfinished. More information and one or more subheadings will improve this section drastically. Current research section has also been done nicely with an image included that aids the reader. The subheadings used indicate a good understanding in the topic and an extensive amount of research. This section does however appear to be a bit messy and disorganized especially under the antibody section.

Overall a good job on this project. The current images and text of this project appear to be of good quality, there is however a lot of work that still needs to be. The choices of headings used are quite good, covering the key areas necessary to inform learning and indicating a good understanding of the topic. The subheadings for sections such as structure and current research indicate a detailed a good understanding, however the there should be more subheadings in each of the other sections to aid learning. The pictures used are very good however there should be a wider range of pictures to aid in the teaching aspect of the wiki page. The text is lacking in a lot of sections and needs more work. The Content is correctly cited with in text citation used throughout the wiki page. The references are also done correctly and appear quite extensive. If these errors are fixed and the extra text is added this project will improve drastically.


Group 7:

The introduction and Formation, Plasticity and Regeneration section are both very good sections. They both have colourful images that aid the text and provided a good amount of informative text. Functional layers current research and history appear to be unfinished and require more text. The timeline in the history section is a good teaching skill, which sets out the history in an effective manner. Furthermore the picture and subheadings in the functional layer sections are very good, with short concise text that makes it easy for the reader to understand. The structural component section provides a good introduction to the section with a variety of subheadings that indicate a good amount of research. The section however appears to be unfinished. The student should consider adding additional information while also tidying up this section. The references should also be placed at the bottom of the page. The sections on function and abnormalities have been done very well. The information is detailed going beyond basic science while relating back to the cell biology aims. The headings and subheadings indicate an extensive amount of research done on the topic, while aiding the reader. The introduction and pictures used in these sections are also very helpful to the reader aiding in the teaching aspect of the wiki page. The editing, citation and references have also been done well making the section look visually good.

Overall this is a great project. The choices of headings used are quite good, covering the key areas necessary to inform learning and indicating a good understanding of the topic. The content and images used are very informative, going beyond basic science while relating back to the cell biology aims. The Content is correctly cited with in text citation used throughout the wiki page with references correctly at the bottom. If these errors are fixed this project could be very good.

[9]


Lab 11: Ramaciotti Centre techniques

PacBio RSII long read sequencing service:

<pubmed>25887218</pubmed>

This study outlines a method that combines oligonucleotide-based DNA target-capture enrichment technologies with PacBio large-insert library preparation. This was done to enable SV studies at specific regions on chromosomal. The study found that this method was cost efficient and suitable for SV studies.

Reference

  1. <pubmed>25734423</pubmed>
  2. <pubmed>11810295</pubmed>
  3. <pubmed>25753421</pubmed>
  4. <pubmed>25741636</pubmed>
  5. <pubmed>22427740</pubmed>
  6. <pubmed>24550734</pubmed>
  7. <pubmed>12609502</pubmed>
  8. <pubmed>24706882</pubmed>
  9. <pubmed>23076210</pubmed>