User:Z5021149

From CellBiology
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.

My Student Page

Attendance

Z5021149 (talk) 11:53, 10 March 2016 (AEDT) Z5021149 (talk) 11:06, 17 March 2016 (AEDT) Z5021149 (talk) 11:11, 7 April 2016 (AEST) Z5021149 (talk) 11:12, 14 April 2016 (AEST) Z5021149 (talk) 11:05, 21 April 2016 (AEST) Z5021149 (talk) 12:13, 28 April 2016 (AEST) Z5021149 (talk) 11:06, 5 May 2016 (AEST) Z5021149 (talk) 11:01, 19 May 2016 (AEST) Z5021149 (talk) 10:57, 26 May 2016 (AEST)


  • Z8600021 Attended 9 practical classes. A space between each would make it clearer on your page.


Lab 1 Assessment

Search Pubmed

prokaryotic cytoskeleton

eukayotic 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


How to make an in-text citation

Bacterial Division protein FtsZ.[1]

Links

Carnegie stage table

Lecture 1

Sydney Page

BioMed Cental

Testz8600021

What I've Learned So Far

In the first lab I learned the basics of creating and editing a wiki page. I had no prior knowledge on any of this, so everything I did on this page was learned today. I learned how to properly upload a picture which I demonstrated by going home and doing it on my own. Some key points on proper referencing and plagiarism were discussed, some of which were review and some were new to me

Stephen Verespy Iii, Akul Y Mehta, Daniel Afosah, Rami A Al-Horani, Umesh R Desai Allosteric Partial Inhibition of Monomeric Proteases. Sulfated Coumarins Induce Regulation, not just Inhibition, of Thrombin. Sci Rep: 2016, 6;24043 PubMed 27053426


Individual Assessments

lab 1

  • Z8600021 Image reference, copyright and student template with the file you have uploaded. (5/5)


Topology of YuaG.png

Topology of YuaG

Bach JN, Bramkamp M (2015) Dissecting the Molecular Properties of Prokaryotic Flotillins. PLoS ONE 10(1): e0116750. doi:10.1371/journal.pone.0116750

© 2015 Bach, Bramkamp. 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

  • Z8600021 Paper summary is good. Image reference, copyright and student template with the file you have uploaded. (5/5)


Single rAAV molecule passing through the nuclear envelope via a nuclear pore complex[2]

Gene therapy is becoming more sophisticated and starting to look like a real treatment option for patients with a genetic disorder. Gene therapy involves a 'healthy' copy of a gene being incorporated into a hosts genome. This is done through an artificial virus such as the recombinant Adeno-associated virus (rAAV). rAAV must have a way of entering the nucleus in order to deliver its viral genetic material. Virus can enter the nucleus vie Nuclear Envelope (NE) budding or through a nuclear pore complex (NPC). Some viruses are small enough to pass through an NPC in tact, while some need to disassemble and then enter the NPC through to the nucleus. The way a virus enters a host nucleus, as well as the time it takes to do this are important to discover as it may effect the efficiency of a treatment. Kelich et al. investigate these properties.

In the experiment, the NE was labeled with GFP while the rAAV molecules were tagged with Alexa Flour 647 which fluoresces red. 10,000 labelled rAAV molecules per HeLa cell were introduced and could be seen aggregating around the NE after about 1 hour. some rAAV particles were already seen inside the NE at this point. Single rAAV particles were examined as the passed through the NE. About 17% of rAAV particles made it through the NE after interacting with it. Single NPCs were then tagged to see the interaction of a single rAAV particle. As seen in the image, the rAAV particles passes right through the NPC, indicating that it does not enter the nucleus through membrane budding. Further, this process took milliseconds to occur, where membrane budding takes seconds to minutes. In the image, the single rAAV particle can be seen throughout the entire process. At no point does it break off into smaller red dots or loose any of its fluorescence. This indicates that the rAAV molecule is able to pass through the NPC without disassembling.

SPEED microscopy was used in the imaging of the rAAV particles and nuclear envelope. SPEED microscopy allows researchers to look at single point illuminated by a laser at a set wavelength. This was very useful in this experiment when trying to observe a single rAAV molecule passing through a NPC.

Lab 3

  • Z8600021 These papers relate to the group project and summaries are concise. Image reference, copyright and student template with the file you have uploaded. (5/5)


NF-kB inhibitor blocks B cell development at two checkpoints[3]

During development, B cells start in bone marrow and then move through different stages until they finally mature in the spleen. Various checkpoints, transcription factors and regulatory factors are utilized during this process to ensure only healthy b cells continue down the path of development. NF-kB is an example of a protein complex transcription factor that plays a role in b cell development. In order to identify when NF-kB was acting during development, Feng et al introduced an NF-kB inhibitor (IkBα) via a viral vector. What they found was that in subjects that received the viral IkBα, the reconstitution levels of b cells was much less in bone marrow and spleen compared to the subjects who did not receive the inhibitor. This lead to the conclusion that NF-kB plays a role in the development od B cells in the bone marrow, as well as maturation and survival in the spleen

The immunosenescence-related gene Zizimin2 is associated with early bone marrow B cell development and marginal zone B cell formation[4]

The Zizimin2 gene has previously been identified to be related to immuno-senescence and filopodia formation in immune tissues. Expression of the gene has been observed in aging mice. There has been little research into how the Zizimin2 gene actually effects the immune response and how the decline in expression of the gene leads to immuno-senescence. Matsuda et al generated Ziz2 knock out (KO) mice to examine what effects removing this gene would have on the immune response. when thy compared the KO mice to wild type, they found that the KO mice had a higher percentage of early bone marrow B cells, but a reduced number of mature marginal zone B cells. The Ziz2 gene clearly has en effect on marginal zone B cell maturation, but had little effect on the folical B cells. Marginal zone B cells play a role in fighting infectious disease by reducing the time that it takes the body to mount a response against the infectious substance. A decrease in the expression of Ziz2 with age may effect the hosts ability to fight off infectious disease by decreasing the fraction of marginal zone B cells.

Effects of lasofoxifene and bazedoxifene on B cell development and function.[5]

Initially, estrogen was seen as an effective treatment for menopausal women with osteoporosis. Estrogen does increase the bone mineral density in women with osteoporosis, however estrogen treatment has been linked with increased risk of endometrial and breast cancer. SERMs are a class of estrogen receptor agonist/antagonists, which act differently depending on the tissue type. Second generation SERMs such as raloxifene have been observed to increase BMD but not increase the weight of the uterus in mice. Estrogen has effects not only on BMD and uterine weight, but also on the immune system. Bernardi et al set out to investigate what effects third generation SERMs such as lasofoxifene (las) and bazedoxifene (bza) have on the immune system compared to traditional estrogen treatments. It was observed that while estrogen treatment lead to a decrease in B cell numbers across all of the developmental stages, while las and bza only effected b cells in the late stages of bone marrow b cell development and splenic transitional 1 b cells.Estrogen treated subjects also had an increase in antibody producing cells while those treated with las or bza did not.

Zinc transporter SLC39A10/ZIP10 facilitates antiapoptotic signaling during early B-cell development[6]

As B cells move through the different stages of development, various requirements must be met in order to for the cell to move down the path of differentiation. Zinc has long been know to be related to immune function as people with Zinc deficiency present with low immune function. While the link has been clearly established, the mechanism behind the lack in immune function has not been demonstrated. Miyai et all set out to find a mechanism behind zinc deficiency by examining the role of the ZIP10 zinc transporter. By down regulating the ZIP10 transporter, decreased levels of Zn were seen in the cell. This activated caspase activity and lead to the cell undergoing apotosis. Overall, the down regulation of ZIP10 lead to a decrease in the population of B cells. This ZIP10-mediated Zn homeostasis is vital for the survival of early B cells which go on to become functional immune cells.

Immune responses in KO and wild type mice.gif

Lab 5

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

lab 6

  • Z8600021 All antibody information is here. (5/5)


Name: Anti-human B-cell specific activator protein

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

Features: Monoclonal; IgG1 kappa; anti human BSAP

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.

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.

Reference that has used this antibody: [7]

Project Peer Reviews

  • Z8600021 You have made some useful comments in your peer assessments, including specific details. (18/20)


Group 1

Really good introduction. Provided a very good overview about what the project will be about, and got me thinking about the important topics related to megakaryocytes.

The history was a bit too long. The history should provide a timeline of the major breakthroughs in understanding of human megakaryocytes. For example I would exclude the 1964 point, it doesn’t seem super integral to the understanding of megakaryocytes.

Structure had a very good flow, it was easy to follow the progression of the different zones.

A few terms need to be explained, polypoid, endomitosis and platelet granules being the main ones.

It is important to define new terms at they come up on the wiki. Alpha granules are mentioned under the Outer Zone heading, but not explained until the second paragraph under the platelets heading. I would like to see the explanation right after the first time the new term is used.

When moving to the HSC to CMP sections under the development heading, I liked that the last sentence under HSCs talked about CMPS. And then the first sentence under CMPs mentions CMPs. This created a really nice flow that made it really easy to follow. I would like to see the continued through development, so for example, mention MEPs in the last sentence under CMP and the mentions MEPs again in the first sentence under MEP. When this is done throughout the whole development section, it will make it really easy for the reader to follow along through the stages of megakaryocyte development.

The Hematopoiesis factors section was really well done. This was not something that I expected to see but it was interesting to hear about the different factors. I really liked how you related the effects of the factors back to stuff that was previously mentioned such as RhoA's role in blocking contractile ring formation.

The signaling section was a good idea but if it is going to be kept as part of the wiki, more explanation needs to happen. There are many terms used that aren't explained, and generally the whole signaling process needs to be elaborated on. JAK/STAT signaling was particularly confusing and requires a bit more information. I would like to see some possible explanations as to why megakaryocyte function relates to bone disorders like osteoporosis

Under the section Platelet production, there is no mention of endomitosis or how platelets are formed inside the megakaryocyte. This is where I would expect to see a detailed account of how platelets are formed inside the megakaryocyte.

The references under Essential Thrombocytosis needs to be in the same format as the rest of the wiki.

The Osteoporosis section needs to be expanded if kept part of the wiki. I would make a clear connection between megakaryocytes and osteoporosis or just leave that part out.

The future of megakaryocytes section was very well done. It introduced a few current areas of research while not going into to too much detail about them.

Group 2

Great introduction, really provided a basic yet rounded view of what RBCs are and what is going to be included in the Wiki.

The History of RBCs is a bit long. I would take out anything that isnt specific to RBcs such as the point made about 1590.

Under Structure there is mention of endovesicles but its never explained actually what they do, I would include a bit about why they are significant. Vesiculation also needs to be explained and why vesiculation is apparent in inflammation-associated diseases should also be addressed.

The Doermability/fluidity sections needs some work to make it more coherent. Im not sure how antibiotics are part of the membrane composition. How does low levels of ATP actually lead to loss of structure? How does structure relate to RBCs being sequestered and removed from circulation by the spleen?

The cytoskeleton section was well done, really good in terms of related structure to function. The study cited sounds interesting, it might be worth uploading some of the images of mice RBCs that are mentioned.

Function section also well done. Very concise but was easily understood. Im not sure what the Band 3 protein part is about. If it is part of the plasma membrane it should be under membrane composition.

Disease section is very large but it was extremely well done. Each disease mentioned was directly related to content previously mentioned in the wiki. The disease section really enhanced understanding of the material by discussing it in a different context.

Even the current research section was related back to the content that was discussed in the wiki

Really good project. Topics were discussed at a depth that was very appropriate for this level. Biggest thing would be to include more information about the intracellular aspects of RBCs.

Group 4

The history of NK cells was good, not too long but highlighted the major discoveries related to NK cells.

There is a line saying "do hand drawing showing this" under structure. Make sure this is taken out and replaced with an actual picture .

Granules seen in the cytoplasm give NK cells their name but I'm not sure what this means?

I would elaborate on CD65 bright/dim. What is actually measured to determine which type an NK cell is? This is discussed further on in the wiki but I was left confused for a while until I reached the answer. A student may not read the entire wiki when looking for information.

What is NKp46? What role does this play in NK cells function?

Under Structure, there is a paragraph that talks about the immune synapse and granules of NK cells. The paragraph is on the right track with relating the structure of NK cells to their function, but the whole paragraph needs to be elaborated. Explain what an IS is.

The function in innate immune response needs some organizing. All the relevant information is there but not in a way that is easy to understand. Try talking about activation first, then move into what happens once an NK cell is activated. The distress signals that NK cells respond to should ne explain ie where do they come from and what do they mean.

The RA section is well written. It may be a bit too long, it seems like there is a lot of information in there and not all of it specifically related to NK cells. The purpose of discussing RA is not to provide a bunch of information about RA, but to provide information about NK cells role in RA.

Under cancer, when a study is specifically mentioned I would at least mention the author's name, not just put a reference number at the end of 3 paragraphs. The section was well done with an easy to understand flow.

Without a clear role in Asthma, I would leave this section out. A small part could be added in current research, describing that there is a possible link between NK cells and Asthma.

Define what IST is under the SAA section.

Under Current research, the section on MM was well done. The paragraphs prior to this seem to be giving a conclusion about NK cells. This should not appear under current research but I found the information to be helpful. Think about incorporating this information into other parts of the wiki or create a conclusion section.

The major areas of improvement for this wiki all revolve around expanding and clarifying the information that is there. The content on the wiki currently is good but more needs to be added. Focus a bit more on the structure of NK cells and what their structure has to do with their function.

Group 5

The introduction is good but I would rearrange some of the information. Talk about its major roles first and then talk about how recently it has been discovered that they play another role.

The history section was good. I like that you made it a different colour to stand out.

Define anaphylactic.

Function and morphology sections are really well done. The information flowed really well, was easy to understand and went into an appropriate amount of detail I.e not too much or too little.

This wiki was extremely well done. Most of the time while reading it, I felt as though I was reading the actual wikipedia page on mast cells. It was written in such a way that it was easy to understand, yet still provided a lot of information. The tables used were really helpful. There isn't much I would say about changing or adding to this wiki! Well done.

Group 6

Introduction is a bit long. I would condense it down to give a short overview about T cells and what is going to be covered in the wiki. Highlighting the differences between different t cell types and their function could be shortened. A lot of the references used are reviews, some of those references need to be replaces with some research articles.

The section commonalities between t cell: function, contains a lot of information about the different ways t cell subtypes function. This section should only have the common features, not focus on differences. There is a large section relating to structure in this section, this should be moved to the structure section.

Location and morphology sections were well done, they focused generally on t cells and didn’t go into much detail about specific t cell subtypes.

The T cell Receptor and C0-Receptors section needs to be condensed down. There is a lot of information packed in there which makes the whole thing difficult to follow. 'TCRα is related with CD3δε, and TCRβ with CD3γε, and then the ζζ module associated with TCRα' is an example of a part that you could consider taking out. It doesn't make a lot of sense and doesn’t contribute to the understanding of t cell receptors and co receptors.

The history section seems a bit out of place. I would try putting it towards the start of the wiki as a history is like an overview of t cells. It makes sense to put it with the introduction.

I liked the paragraph before the different subtypes, provided some context In which to read about the different subtypes

It was interesting to see a small description of the different subtypes and then have an expandable section for more information. Students may want just a small in. production to the cell subtype and not a really long, detailed explanation. This provides a way to either get a snapshot of the cell or a full description, depending on what the reader is looking for. These sections were well written.

The section on CARS was very well done an extremely interesting. It related a current research project back to the basics of T cells that was discussed in the wiki.

The Crispr section is really small and probably not worth mentioning in the wiki unless it is expanded in greater detail.

Overall, it is clear a lot of work went into this wiki. I would focus on condensing down some of the information, and working on some grammar. The sections on commonalities between t cells specifically needs a lot of editing, there is a massive overuse of commas that should be sorted out! There are a large number of review articles cited, probably too many. Try to replace some of these with research articles.

Group 7

It would be good to start with an introduction to eosinophils. Talk about the basics of the cell, what they are, what they do and where they can be found. Basically summarize what will be covered in the wiki which should be the main points pertaining to eosinophils.

The development section is good but I would add in some information about the steps from hematopoietic progenitor cells to eosinophils. This doesn't have to be long but it would be good to show the intermediate cells.

In terms of flow of information, it would be good to have the roles of the components come after the list of components. I had to go back to remember what an MPB was. Try putting methods of degranulation after the roles of the components.

Include the mechanism of how MBP are toxic to worms.

Explain the surface markers a bit more I.e what role does CD68/CD69 play in eosinophil function.

The video of eosinophils attacking a helminth doesn’t work. Not sure if it's an issue on my computer, but look into this as the video sounded interesting and very relevant!

Expand on eosinophils role in fighting infections organisms especially bacteria.

Expand on how MBP causes eczema, if eosinophils play a role in the disease why does it still occur in the absence of eosinophils?

The wiki overall is a good start to understanding eosinophils. I would work on expanding and going more in depth into topics like their role in disease and structure

The videos and pictures were really good, related to content and enhanced understanding of the material. It made it easier to understand.
  1. 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
  2. Joseph M Kelich, Jiong Ma, Biao Dong, Qizhao Wang, Mario Chin, Connor M Magura, Weidong Xiao, Weidong Yang Super-resolution imaging of nuclear import of adeno-associated virus in live cells. Mol Ther Methods Clin Dev: 2015, 2;15047 PubMed 26665132
  3. Biao Feng, Shuhua Cheng, Warren S Pear, Hsiou-Chi Liou NF-kB inhibitor blocks B cell development at two checkpoints. Med Immunol: 2004, 3(1);1 PubMed 15050028
  4. Takenori Matsuda, Shougo Yanase, Akinori Takaoka, Mitsuo Maruyama The immunosenescence-related gene Zizimin2 is associated with early bone marrow B cell development and marginal zone B cell formation. Immun Ageing: 2015, 12;1 PubMed 25729399
  5. Mohamed-Amin Choukrallah, Shuang Song, Antonius G Rolink, Lukas Burger, Patrick Matthias Enhancer repertoires are reshaped independently of early priming and heterochromatin dynamics during B cell differentiation. Nat Commun: 2015, 6;8324 PubMed 26477271
  6. Tomohiro Miyai, Shintaro Hojyo, Tomokatsu Ikawa, Masami Kawamura, Tarou Irié, Hideki Ogura, Atsushi Hijikata, Bum-Ho Bin, Takuwa Yasuda, Hiroshi Kitamura, Manabu Nakayama, Osamu Ohara, Hisahiro Yoshida, Haruhiko Koseki, Kenji Mishima, Toshiyuki Fukada Zinc transporter SLC39A10/ZIP10 facilitates antiapoptotic signaling during early B-cell development. Proc. Natl. Acad. Sci. U.S.A.: 2014, 111(32);11780-5 PubMed 25074913
  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