User:Z5018925

From CellBiology

My Student Page

Group Projects
This year's main topic is Blood Cell Biology. Each group should discuss with group members the specific sub-topic that will be covered by their project.

Here is a list of some of the cell types (Structure and Function)

Cell Type (PuMed citations)


Below are the groups to which students have been randomly assigned. You should now on the project discussion page add your own suggestion for a specific topic. Once your group has agreed on the topic, add this as a heading to the project page before Lab 3.


2016 Projects: Group 1 | Group 2 | Group 3 | Group 4 | Group 5 | Group 6 | Group 7

Group 1: User:Z5017493 | User:Z3330991 | User:Z5020043 | User:Z5020175 | User:Z3489355

Group 2: User:Z5018320 | User:Z5015980 | User:Z3376375 | User:Z3461106

Group 3: User:Z5019595 | User:Z5019962 | User:Z5018925 | User:Z3461911

Group 4: User:Z5020356 | User:Z3463895 | User:Z3376502 | User:Z3423497 | User:Z5021149

Group 5: User:Z5015719 | User:Z3462124 | User:Z3463953 | User:Z5017292

Group 6: User:Z5018866 | User:Z3329177 | User:Z3465531 | User:Z5105710

Group 7: User:Z5021060 | User:Z5016365 | User:Z5016784 | User:Z3414546 | User:Z3417773

Group Assessment Criteria

Group Assessment Criteria

  1. The key points relating to the topic that your group allocated are clearly described.
  2. The choice of content, headings and sub-headings, diagrams, tables, graphs show a good understanding of the topic area.
  3. Content is correctly cited and referenced.
  4. 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.
  5. Evidence of significant research relating to basic and applied sciences that goes beyond the formal teaching activities.
  6. Relates the topic and content of the Wiki entry to learning aims of cell biology.
  7. 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.
  8. Evaluates own performance and that of group peers to give a rounded summary of this wiki process in terms of group effort and achievement.
  9. 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.
  10. Develops and edits the wiki entries in accordance with the above guidelines.
Individual Lab Assessments
Lab 8 Assessment
2016 Lab 8 - Lab 8 Assessment (to be completed before Lab 9)
  1. Add your peer assessment to your own student page to the site.
  2. Add your peer assessment to each project discussion page to the site.
Lab 6 Assessment
2016 Lab 6 -
  1. Identify an antibody against your group blood cell protein that is commercially available.
  2. Add a link to the original data sheet page and identify the type of group blood cell protein.
  3. Include the following information: type of antibody (polyclonal, monoclonal), species raised in, species reacts against, types of application uses, and if available any reference using that antibody.
Lab 2 Assessment
2016 Lab 2 - Super resolution microscopy
  1. Find a recent research article (not review) that uses super resolution microscopy technique.
  2. Write a brief summary of the paper (referenced) and what the super resolution microscopy technique showed.
    1. This should not simply be the abstract of the paper.
    2. This can be 2-3 paragraphs no longer.
  3. Include a super resolution microscopy image from the paper.
    1. Therefore the paper must be from a source that you can reuse.
    2. Image uploaded as in Lab 1 (summary box - description/reference/copyright/student image)
    3. Image should appear as a "thumbnail" (thumb) next to your paper summary (with citation legend) See Test page
Lab 1 Assessment
2016 Lab 1 - Lab 1 Assessment (to be completed before Lab 2) The test page I set up in the Lab
  1. Add your own student page to the site.
  2. Add your signature for Lab attendance.
  3. Add a sub-heading.
  4. Add an external Link.
  5. Add an internal Link.
  6. Add an image from PubMed, PloS or BioMed Central journal related to prokaryote cellular component. Make sure it includes both the reference and copyright information, with the file and where it appears on your page.

Attendance

Z5018925 (talk) 11:55, 10 March 2016 (AEDT)

Z5018925 (talk) 11:11, 7 April 2016 (AEST)

Z5018925 (talk) 11:03, 14 April 2016 (AEST)

Z5018925 (talk) 11:11, 21 April 2016 (AEST)

Z5018925 (talk) 11:11, 28 April 2016 (AEST)

Z5018925 (talk) 11:06, 5 May 2016 (AEST)

Z5018925 (talk) 12:31, 19 May 2016 (AEST)

Z5018925 (talk) 10:58, 26 May 2016 (AEST)


Individual Assessments

Lab 1- practise

Search PubMed

prokaryote cytoskeleton

eukaryote cytoskeleton

PMID 26756351 Katherine Ann Hurley, Thiago M A Santos, Gabriella M Nepomuceno, Valerie Huynh, Jared T Shaw, Douglas B Weibel Targeting the bacterial division protein FtsZ. J. Med. Chem.: 2016; PubMed 26756351


Links

Carnegie stage table

Lecture 1

What I've learned so far

I have learned how to use the various codes to produce headings, titled links, and references in my wiki page. This formatting will help with the group project. I am still a little confused by some of the codes, but with a reference page I should be able to reproduce what we have done today.

Lab 1 Individual

  • Z8600021 I have had to delete your uploaded image (File:Electron Chrytomography of Bacteria.jpg), Nature Reviews requires you to apply for reuse permission through the copyright clearance centre (as I explained in the class tutorial), it is generally free and only required you to register (free) and they either approve or show cost online. If you had done this, there should have been that information pasted in the file summary window. If you had applied please send me a copy of the approval and I will replace the image. (0/5)

500px

Electron Chrytomography of intact Bdellovibrio bacteriovorus cell

Oikonomou, Catherine M., and Grant J. Jensen. "A new view into prokaryotic cell biology from electron cryotomography." Nature Reviews Microbiology (2016).[1]

Reprinted by permission from Macmillan Publishers Ltd: Nature Reviews Microbiology, advance online publication, 17/03/2016 (doi: 10.1038/sj.nrmicro.XXXXX)

Lab 2- Microscopy

  • Z8600021 Your second uploaded image is OK to use, and includes all the required information. I prefer the reference in the summary window (PMID 26605213) to be linked and formatted to Pubmed as shown in my addition to the file. You do not need the copyright information on your student page. Your super-resolution microscopy paper summary is fine. (5/5)


Exercise 1- Nucleus Image

Binary Image Nucleus.jpg

(a) Binary image of the connected nuclei, (b) green band of the connected nuclei, (c) edges of the connected nuclei using Sobel method, and (d) superimposed edges on the binary image of the connected nuclei

Sarrafzadeh, Omid, and Alireza Mehri Dehnavi. "Nucleus and cytoplasm segmentation in microscopic images using K-means clustering and region growing." Advanced biomedical research 4 (2015)[2].

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.

Exercise 2- Research article using super-electron microscopy

Normal microscopy is limited by the refractive index of light, otherwise known as the Abbe/Raleigh limit. Super-resolution microscopy was used by these researchers to investigate the ultrastructure of centromere chromatin beyond this diffraction barrier. As learned in the laboratory, super-resolution microscopy enables more crisp optical sections to be obtained and converted into 3D images. This advantage was used in this experiment to represent the changes in organisation of the centromere chromatin. The researchers found that chromatin ring-structures formed at the centromeres. Super-resolution microscopy allowed differences in chromatin structure to be modeled throughout the various phases of mitosis in real time, collated in a series of videos- for example, during somatic metaphase the ring-structure was replaced with a highly condensed, globular structure. With such high resolution available, the researchers were also able to model the co-operative role of spindle fibers.

Reference

Schubert, Veit, Alevtina Ruban, and Andreas Houben. “Chromatin Ring Formation at Plant Centromeres.” Frontiers in Plant Science 7 (2016): 28. PMC. Web. 23 Mar. 2016.[3]

  • Z8600021 your citation link is not formatted correctly, see your own reference list.

Copyright

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Note - This image was originally uploaded as part of a student project and may contain inaccuracies in either description or acknowledgements. Please contact the site coordinator if the uploaded content does not meet the original copyright permission or requirements, for immediate removal.

B-Lymphocytes Structure- 4 research articles

  • Z8600021 The upload file, I am not sure the current use is listed on the options for the approval you have received. This image may need to be deleted. Your reviews are very brief, but you have used the PubMed extension correctly. (4/5)


Article 1

Cone, Robert E., et al. "Molecular identification of a surface structure on B cells(Lyb-3) and its relationship to B cell triggering." The Journal of Immunology 120.5 (1978): 1733-1740.[4]

This study utilized immunoprecipitation techniques to detect Lyb-3 (a 68 000 d polypeptide) in the membrane of specific subpopulations of B-cells. The results demonstrated that Lyb-3 is distinct from IgD and IgM surface components. Overall, the results suggested that Lyb-3 is involved in the triggering of B-lymphocytes by antigen, and indicate that Lyb-3 may act as a receptor for a T-cell dependent signal.

Article 2

Vogel, L., and D. Haustein. "Immunoglobulin subunits of murine B lymphocytes: structure and associations with other membrane proteins." Immunology 67.2 (1989): 251.[5]

This study investigated possible mechanisms and candidate proteins involved in transmitting the signal from Ig-crosslinking with the antigen or anti-Ig antibody to eventually elevate expression of MHC Class II molecules within B-cells. Utilising radiolabelling procedures, the researchers tested how the Ig proteins (from spleen cells) interact with the plasma membrane. The study discovered proteins that are disulphide-linked to IgM, one of which traverses the plasma membrane and therefore might be involved in transmitting the signal to the interior of B-cells.

Article 3

Greicius, Gediminas, et al. "Microvilli structures on B lymphocytes: inducible functional domains?." International immunology 16.2 (2004): 353-364. [6]

It is well know that interactive contact between B and T lymphocytes occurs during the immune response. Mutual adhesion and clustering of membrane receptors are key elements in co‐activation of B and T lymphocytes. Formations of surface domains such as microvilli all offer an increased functionality in cellular motility, adhesion and signal transduction. Utilising immunoelectron microscopy, this study explored the mechanisms that regulate microvilli expression on lymphocyte surfaces. The study found that microvilli represent a membrane domain rich in ICAM‐1, MHC class II and B7‐2 (CD86), suggesting that they are involved in the regulation of adhesion and/or antigen presentation. Moreover, the researchers found that lipid rafts are concentrated in microvilli‐rich regions.

Image

Cell‐surface morphology and cell–cell interactions in aggregates of mouse B lymphocytes cultured in the presence of LPS (A) or LPS plus IL‐4 (B and C). In LPS‐treated cultures (A), the cells had a relatively smooth contour and only few, short processes extended from the cell surface (arrowheads). In cultures treated with LPS plus IL‐4 (B and C), an intricate system of microvilli‐like processes was found on the cell surface. Via these processes, the individual cells established contact with one or more adjacent cells (arrows). M, mitochondria; N, nuclei. Bars = 1.0 µm.\

  • Z8600021 I have removed the file link until I can clarify reuse conditions are allowed here.

File:B-lymphocyte surface morphology.jpg

Reference

Greicius, Gediminas, et al. "Microvilli structures on B lymphocytes: inducible functional domains?." International immunology 16.2 (2004): 353-364.[7]

Copyright

Permission for reuse or republication of Oxford Journals figures, abstracts, or articles, can be granted for a range of re-uses, including: Republication in a book/ journal; eBook; PowerPoint presentation; Academic course packs; Thesis

The fastest and most efficient way to obtain permission to reuse Oxford Journals content is by using our Rightslink automated permissions system.

This is a License Agreement between George Mallat ("You") and Oxford University Press ("Oxford University Press"). The license consists of your order details, the terms and conditions provided by Oxford University Press, and the payment terms and conditions.

Article 4

Friedrich, R. Joachim, Kerry S. Campbell, and John C. Cambier. "The gamma subunit of the B cell antigen-receptor complex is a C-terminally truncated product of the B29 gene." The Journal of Immunology 150.7 (1993): 2814-2822.[8]

The product of the B29 gene is expressed exclusively in B-lymphocytes. The protein product forms a heterodimer with MB-1/B29, which is phosphorylated following B-cell stimulation. This study conducted N-terminal sequence analysis to determine the protein products of the B29 gene. Immunoblotting confirmed that the B29 gene encodes two 37-kDa and 34-kDa proteins (which are associated with IgM). Using phosphorus labelling of splenocytes, the researchers also measured the distribution of B29 gene products. They determined that B29 gene products associated with the B-cell Ag receptor can exist in 3 forms and are not present in all B-lymphocytes.

Lab 5- Over-expressed Tm4 vs. Wild Type B35 cells

Percentage of Phenotypes in over-expressed Tm4 B35 Vs wildtype B35.PNG

Lab 6- Immunochemistry

Name: Anti-human B-cell specific activator protein

Supplier: http://www.dako.com/au/download.pdf?objectid=119083001

Details

Monoclonal; IgG1 kappa; anti human BSAP (BSAP is a transcription factor that plays a key role in B-lymphocyte development)=== Raised in: mouse Reacts against: humans

Uses

Used in immuno-histochemistry. Antibodies to B-cell-specific activator protein (BSAP) may be useful for the identification of pro-, pre-, and mature B cells and in the classification of lymphomas (1-4). Together with a panel of antibodies it is particularly useful in the differential identification of classic Hodgkin’s disease versus anaplastic large cell lymphoma of T- and null-cell type (1, 3). The clinical interpretation of any staining or its absence should be complemented by morphological studies using proper controls and should be evaluated within the context of the patient's clinical history and other diagnostic tests by a qualified pathologist.

A reference that has used this antibody is: Krenacs, Laszlo, et al. "Transcription factor B-cell–specific activator protein (BSAP) is differentially expressed in B cells and in subsets of B-cell lymphomas." Blood 92.4 (1998): 1308-1316.[9]

Using Western Blotting, found that SAP expression is largely restricted to lymphomas of B-cell lineage and that BSAP expression varies in B-cell subsets and subtypes of B-cell NHL.

Peer review

  • Z8600021 Very good. You have kept this brief and provide useful neutral-toned feedback. (18/20)


Group 1- Megakaryocytes

The introduction was a very clear overview of megakaryocyte function, location and structure, providing a good basis for the more detailed information to come. The history section was had two problems. First, you don’t reference the key findings. It is also a little to long; I think it would be better to reduce this section to only the most important findings because you can bring in the more specific research later on in the page. For example, the structure section would benefit from some references to important research articles that have found interesting things about the megakaryocyte cell composition- e.g. analysis of unique proteins. Also, in the development and maturation section you explain different stages of the megakaryocyte lineage. The structure section would be a good time to explain how components of the megakaryocyte vary as the cell matures. I thought the information on function was very well explained. The disease section explains the disease well, but you only state the possible treatments. You should explain how they work (for example, what is the mechanism of action of anagrelide in treating essential thrombocytosis and what does it do to the cell’s function)- this can reveal important things about the cell itself. Overall, I thought your project was very easy to understand, but the details were a little too simple at times- a normal wikipedia page on megakaryoctes has most of the information you have. If you expand your information with recent research in the early sections (e.g. structure) you will have a really good balance of clarity and complexity- I think the sections on ‘Function and Role’ and ‘Essential thrombocytosis’ achieve this so you could model off these.

Group 2- Red Blood Cells

I like the way you break up the structure section- it works well to move from the general features of erythrocytes into more specific details about its membrane and cytoskeleton. However, you have limited research articles in this section. While you reference a review article, it would be useful to look at some specific experiments undertaken that have revealed unique/interesting features- for example: how do the major proteins interact with each other, or with the cytoskeleton? You do this better in the cytoskeleton section. The subsection on deformability/fluidity was a little confusing- I don’t understand why you start talking about antibiotics here. The function section is too brief. I think this should be the focus of the project, as it links together a lot of other sections- e.g. how does structure contribute to function, how do structure and function change as the RBC matures. Again, there was a lack of specific research articles in this section that might help elaborate your information. The best section was the disease section. Each disease goes into an appropriate depth of detail and incorporates relevant research- e.g. the specific mutations that have been found in hereditary diseases of RBCs, and the pathogenesis of polycythaemia draw on some interesting research findings. The current research section is good, but I think it would be better if you try and find research pertaining to each section and include it within/at the end of the section. Your figures are clear you should refer to them in the information- otherwise it is hard to see exactly what they are showing.

Group 4- Natural Killer Cells

In your structure section you talk about differentiation. It would be better to have your section on development and differentiation before this, and then explain in ‘structure’ how the composition of the cell changes (including the clusters of differentiation you talk about). Overall your information in this section is lacking a lot of detail and it is not coherent. You jump from talking about ‘functionally natural killer cells can be differentiated into…’ (this should be in function section) to ‘structurally natural killer cells can be differentiated into …’ without going into any specific research. Also simple things like spelling and capitals are missing which makes it look non-academic. The function section has better detail, and is better explained- e.g. you explain specific chemical signaling that enables NKs to distinguish self and non-self. However, you should go to a few specific research papers (e.g. the ones you reference in ‘History’) and then try interpret the key findings yourself. This will add complexity to the information you already have and make it a more useful academic resource (since it is targeted at university students). A good example of this is your section on rheumatoid arthritis- you explain the disease, its pathogenesis and incorporate some interesting research on the role of NKp44+NK cells and the proinflammatory cytokine IL-22. The earlier sections should aim to match this level of detail. The current research section is also good. Overall, there is a lot of missing detail and at times it is difficult to understand the relevance of the information. Drawing on relevant research and making sure each section sticks to its subject will improve your project.

Group 5- Mast cell

The introduction drew together all of the major points really well- I liked each point followed logically from the previous (e.g. “the major role of mast cells in pathogen recognition is supported by their location…”). Compared with the other projects I read, the history section was well selected- each discovery was significant and it was well balanced from early times to recently. The morphology and function sections were very clear. However, they were far too brief- I think these two sections should be the most in depth (since the course stresses structure and function). What you have is a good overview, but within each point should then go into some of the more complex findings- using research papers. Just to use one point as an example, you say “Mast cells have the ability to release selective mediators without degranulation, which means an anaphylactic reaction will not occur.” Just looking at the abstract of the source you used, there is a lot of complexity in this single process which you should elaborate on: e.g. the researchers found that “the process appears to involve de novo synthesis of mediators, such as IL-6 and vascular endothelial growth factor”. This will give a more in depth understanding of the processes involved in certain functions, which I think is required in this project. The rest of the project was very clear. The images, including your hand drawn one, were well selected and well explained in the caption but you should refer to them within the text to explain their relevance. The pathology section went into a lot of detail, but like I mentioned it was disproportionate when compared to function and structure. I thought it enhanced the rest of the project because it was linked specifically with how normal mast cell function can become pathogenic in certain conditions. Overall the project was the most well explained I read but lacked in the two most important sections, as well lacking in depth reference to research articles.

Group 6-T-lymphocytes

The introduction was succinct and a good overview. As a side not there are a few grammatical errors that you should fix: For example, the second sentence of ‘Function’ is filled with mistakes: “especially dendrite cell takes huge part of T-cell activation” does not make sense, and “phagocyte” is not a verb, you say “this naïve T-cell with antigen never with antigen thus never activated”. The accumulation of all these errors made it very difficult to understand what you were saying and makes it seem non-academic. The ‘Function’ section really needs to be refined- there is good information, and you have references to recent research, but it is too hard to follow. It should also be expanded- particularly expand on recent research and how it has changed our understanding of function. The structure section is far better. I like that you focused on T-cell receptors and co-receptors because most of the T-cell functions are based around recognition at the cell-surface. It is good that you compare with B-cells because the two interact. Again it will make it more clear if you refine the grammar. The development section goes into good depth and draws on . It also follows a logical progression- perhaps think about linking this with some of the structure aspects you talk about because from what I know T-cell surface receptors change at different stages of its development. Also, whole project would make more sense if you move some of the information around: I would move “types” to the top and then under each type talk about its specific structure and function, rather than having separate sections on structure and function and then going on to talk about each sub-type individually. The Current Research and Future Directions part was very interesting. I also like that you finish with “final thoughts” as it gives some perspective to all the information you have discussed, answering the important question of why T-cells are so important in research.

Group 7-Eosinphils

I think you need to include an introduction that summarises the eosinophil and points to the major aspects that you will discuss. The history section goes into too much depth- it should just state the key finding- and also does not include any dates after 1879 which is a long gap between then and now. The birth, life and death section is very clear and I like that it follows the lifetime of the eosinophil. The morphology diagram makes is very useful when orienting the reader to interpret the electron microscope image. It is well laid out- I like how you move from structure to components to mechanisms of release etc. However, each section needs to be more detailed. You should go into specific research here-. E. g. you only have one sentence on “classic exocytosis”- you should expand by trying to find research articles that have investigated this mechanism of release: how is it regulated? What proteins does it involve? The role in allergy and disease section is well described but again lacks detail in important parts: one to two sentences explaining its role in bacterial infection is insufficient. Go into more precise detail explaining how they eliminate the bacteria (or virus etc.).

References

  1. pubmed> 4753331</pubmed>
  2. R E Cone, B Huber, H Cantor, R K Gershon Molecular identification of a surface structure on B cells (Lyb-3) and its relationship to B cell triggering. J. Immunol.: 1978, 120(5);1733-40 PubMed 307021
  3. A R Templeton, K A Crandall, C F Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics: 1992, 132(2);619-33 PubMed 1385266
  4. Gediminas Greicius, Lisa Westerberg, Edward J Davey, Eva Buentke, Annika Scheynius, Johan Thyberg, Eva Severinson Microvilli structures on B lymphocytes: inducible functional domains? Int. Immunol.: 2004, 16(2);353-64 PubMed 14734621
  5. Gediminas Greicius, Lisa Westerberg, Edward J Davey, Eva Buentke, Annika Scheynius, Johan Thyberg, Eva Severinson Microvilli structures on B lymphocytes: inducible functional domains? Int. Immunol.: 2004, 16(2);353-64 PubMed 14734621
  6. R J Friedrich, K S Campbell, J C Cambier The gamma subunit of the B cell antigen-receptor complex is a C-terminally truncated product of the B29 gene. J. Immunol.: 1993, 150(7);2814-22 PubMed 8454858
  7. L Krenacs, A W Himmelmann, L Quintanilla-Martinez, T Fest, A Riva, A Wellmann, E Bagdi, J H Kehrl, E S Jaffe, M Raffeld Transcription factor B-cell-specific activator protein (BSAP) is differentially expressed in B cells and in subsets of B-cell lymphomas. Blood: 1998, 92(4);1308-16 PubMed 9694719