User:Z3463953

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My student page

homework from coordinator

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.

week 10- critique of project pages

I have found this process to be enlightening and beneficial. The standard of the pages is very good in general. The pages use very good evidence and are quite readable. Much of what i have learnt has also been useful to other subjects!


  • Z8600021 These are good peer feedback assessments, group 2 was a little brief. (16/20)


group 1: Megakaryocytes (MK)

The page is good, but the main problem is a consistent misuse or no use of proper referencing. Here are my observations:

  • Unreferenced statements thrombopoetin section
  • ET references box is not technically referred to so it’s a bibliography not a reference
  • Glossary is unfinished
  • History is fully unreferenced
  • “Megakaryocytes have been shown to maintain HSC quiescence during homeostasis “ i think this would read better if it was written "in homeostatic conditions"
  • I like the figures but they have very little text information. Figure 4 could discuss in more detail the 4 branches of the mind map of MK functions.
  • Good job inserting the essential thrombocytosis video but I would put it under the Essential thrombocyte title not the “pathology” title seeing as it’s specific to one pathology.
  • For consistency I would ensure that all acronyms are uppercase (in CAMT subsection of pathology some acronyms aren’t in uppercase. Also you use the acronym TPO several times and describe it several times. You could reduce the wordiness by just doing this once.
  • Needs a reread through for minor spelling checks as well.

group 2: Red Blood Cells

great history and function sections. a couple of issues however in the whole page:

  • Under the structure section, the first sentenced is referenced with “Dinkla et al.”. This should be made a footnote and have date attached. Remember it doesn’t have to be a pubmed affiliated article to be made a footnote just put in “[1]
  • Under membrane composition, it seems you’ve tried to encorporate a subsection “defgormity /fluidity. This looks tacky with just a dash. I suggest making it bold. Just add 3 apotrophes before and after.
        	i.e. if I want the word “bold” to be bold, I would write ‘’’ bold ’’’. 
  • I would have wanted to read much more about ABO blood grouping, there isn’t much there, you should also incorporate pictures here. This could be a whole section!
  • Another seriously important factor of RBCs is that they have a Fc receptor and can carry immune complexes to spleen or liver. The immune function of RBCs is not really touched on, and that’s a major issue.

group 3: B cell lymphocytes

A lot of good quality information but a very bland page. Here are some notes:

  • History is not very extensive
  • B-cell development and B cell subset image is very small! I would make it twice as large (800px). And maybe describe it in text more
  • Section: development, 3rd paragraph: spelling error
  • Instead of using in text referencing, you should use footnotes (easier for the reader to find the references). Remember it doesn’t have to be a pubmed affiliated article to be made a footnote, just put in “[2]
  • Section: development. You introduce the term L chains with no description, the reader may have no idea what that is. Make sure you describe newly introduced terms!
  • There is an underwhelming amount of images used. Images should be used for:

o B cell activation o Mind map of different B cells o Different antibodies

  • Tables are bland as well, try adding some colour!
  • Evidently you must finish the immunodeficiency/ and b cell cancer sections!
  • Also go into more depth about the biotechnology applications of B cells and don’t forget references!

group 4 Natural Killer Cells

Looks pretty good, but many sections unfinished, here are soem notes:

  • History is not extensive
  • Receptor image must be made larger
  • Receptor section is unfinished
  • In structure section, the 3 ways that NK identification can be grouped could be bolded. This would make it more distinct.
  • Some claims are not referenced, i.e.: Recent studies speculate that NK cells also play a role in regulation of dendritic cells, macrophages, T cells and endothelial cells

o You cannot tell the reader what recent studies speculate then not reference which you are referring to.

  • Rheumatoid section is 90% unreferenced. A footnote is meant to be used at the end of each piece of information that was used from that source. Theres only one footnote used in the 8 paragraphs.
  • Diabetes and lupus sections are unfinished.
  • The current research section has good content, but doesn’t flow well. And needs to be reread for several small errors, (i.e. there is a random “-“ symbol half way through 2nd paragraph and some of the sentences could be restructured to read better.
  • No glossary


Group 6 T cell

Very extensive, Very colourful, Very informative. The main theme of criticism is in the language used, but the content is great.

Many sentences have good information but need to be reread and rewritten to make sense. A classic example is : A plethora of subtypes and difficulties to find adequate markers have provided difficulty to clearly establish what Treg distinguishes from T effector cells

Technically it makes sense but it may be rewritten to have more flow to example:

There are a plethora of difficulties in finding adequate markers to clearly distinguish Tregs from T effector cells.

  • It doesn’t read well to day: as reviewed in (footnote). I would recommend using the normal authors names then foot note that. I.e. as reviewed in Robertson et al. (2000)(footnote)
  • Also, you refer to the same review in two continuous sentences. Perhaps you can make the paragraph flow better by using linking language. i.e. this previously mentioned review by Robertson et al also discussed…
  • I like the video
  • There are some spelling errors which imply a reread is necessary. i.e. subsection function you say “makers” not “markers*” etc. Also the next sentence doesn’t read well “ To gives a mobility the physical structure of the T cell has to continuously remodeling. “ rewrite so it says “to give mobility*” Some sentences have poor grammar i.e. don’t start with a capital letter etc.
  • Great job explaining VDJ recombination, I would give the images titles though. This would make it easier for the reader to have a text title to refer to. You can do this by just making the the title of the images in bold
  • History isn’t very extensive compared to the standard of the rest of the report
  • The sub sub table “autoimmune diseases” needs to be addressed. It’s telling the reader to go look up information! And the following HIV section only has a photo that’s much to small to read from! There are several areas that require addressing
  • Interesting that Tregs are relatively non motile, did you know after appendicitis there’s a massive release of Tregs from the appendix that spread through the colon (with relatively high motility) maybe that would be an interesting add-on
  • Great job on the summarising of Tregs in cancer involvement
  • I love the Research at UNSW section, great original thinking.
  • No glossary’
  • Also when discussing the TCR it says the TCR is "simple" then proceeds to explain the paragraph that is pretty complex. Even if it's simple to the writer, when you use language like that you risk insulting the reader.


group 7 Eosinophils

colourful with short punchy paragraphs that are informative! here are some notes:'

  • History is great, but only goes until 1879! Did nothing happen between then and now!
  • In terms of the paragraph structure of the Birth, Life and Death in the Body section, there is the number 3 (perhaps a footnote) in the 3rd paragraph that needs to be removed or converted to a footnote. There’s also some other spelling mistakes like in MBP section you’ve spelt asthema instead of asthma. Perhaps it’s worth just rereading over the whole thing to correct the little errors.
  • Add some text for the images, and I would recommend having the image title in bold.
  • Video did not play in Wikipedia, but it was spectacular to watch in youtube!
  • I would be interested in knowing if anytreatments are being developed specifically targetging eosinophils in eczema
  • The schematic representation of eosinophil trafficking image should be enlarged. Also to add a text box below the image refer to our first lab class. This should be done with all your images

Week 4 - Super-resolution microscopy

  • Z8600021 Image ([File:Super-resolution_single_molecular_localisation_microscopy_use_in_T-cells.jpeg) the problem here is that you are not the "author" so the conditions you had listed with the file do not apply. I have had to delete the image. You should also include the reference with your summary, which is fine. (3/5)

PMID 25378594


SUMMARY: T-cells are highly mobile and have to travel relatively long distances within and outside the circulatory system whilst forming thousands of transient reactions with antigen presenting cells. Actin rearrangement is significant in the motility and extravasation of T cells. When T-cells bind to MHC to form an immunological synapse the spatio-temporal behaviour of the proteins change. For example, in the formation of micro and nano clusters.

Micro and nano clusters of proteins allow for dynamic control centers in the cell membrane. An example of these are the T cell receptors. However until now most of the information we have about these micro clusters have come from biochemical techniques but now with the advancements in super resolution microscopy, we can "see" beyond the previous diffraction limit to a resolution of 200nm.

The use of the super-resolution microscopy, in particular the single molecular localization microscope techniques, allowed researchers to get high quality data and to elucidate the 3 dimensional structures and even functions of the nano clusters, such as the TCRs and observe their behaviours temporally.

Week 5 - 4 mast cell related studies summarised with pictures

  • Z8600021 Image ([File:Histology of intestine, staining for mast cells.jpg) is not allowed to be reused here I have had to delete the image and you have not included all the information required in the summary box. You were only asked to upload a single image, so (File:Data of PD15 (15% dec in FEV(1)) after 3 weeks of dietary Omega 3 PUFA.png) is OK but the file name is too long and complicated, please use simpler naming structure. Your paper summaries are brief but OK. (3/5)


Matthew J Hamilton, Jason L Hornick, Cem Akin, Mariana C Castells, Norton J Greenberger Mast cell activation syndrome: a newly recognized disorder with systemic clinical manifestations. J. Allergy Clin. Immunol.: 2011, 128(1);147-152.e2 PubMed 21621255

File:Histology of intestine, staining for mast cells.jpg
File:Histology of intestine, staining for mast cells.jpg[3]

Summary: People who suffer from systemic mastocytosis have clinical manifestations that are characteristic of mast cell mediator release. A similar disorder called monoclonal mast cell activation sydrome (MCAS) has an unclarified clinical manifestation. Unlike mastocytosis the patient doesn’t have abnormally high levels of mast cells (MCs), rather, the MCs they have express chemical mediators excessively. The aim of the study was to determine the clinical manifestations of MCAS and to compare it against the recently proposed diagnostic criteria. The authors of the paper ruled out clonal MC disease and found lab data indicative of MC activation. Further, the patients responded to anti-MC therapy. This was part of the classification used in this experiment to include patients as MCAS sufferers (this criteria was pre-established by previous research). The clinical manifestations and diagnostic criteria were consistent with one another. Almost all patients had abdominal pain, dermatographism or flushing. The research suggested that MCAS should have a more significant clinical profile due to its excellent response to anti-MC mediators. There were, however, some limitations such as: it was a nonblind study and there is no consensus as to a reference standard for number of mucosal mast cells in GIT.



John D Brannan, Johan Bood, Ahmad Alkhabaz, David Balgoma, Joceline Otis, Ingrid Delin, Barbro Dahlén, Craig E Wheelock, Parameswaran Nair, Sven-Erik Dahlén, Paul M O'Byrne The effect of omega-3 fatty acids on bronchial hyperresponsiveness, sputum eosinophilia, and mast cell mediators in asthma. Chest: 2015, 147(2);397-405 PubMed 25321659

File:Data of PD15 (15% dec in FEV(1)) after 3 weeks of dietary Omega 3 PUFA.png[4]

Summary: Poly-unsaturated fatty acids, such as some mast cell mediators, are involved in inflammation. Bronchial hyper-responsiveness (BHR) is a state of heightened sensitivity to bronchospasm that can occur as a result of mast cell mediator release in asthma and COPD. This study aimed to investigate whether dietary omega-3 PUFAs could inhibit mannitol-induced BHR. Mannitol induction of BHR mimics mast cell activation. The study was a randomize, double-blind, placebo controlled and crossover trial design. Patients suffered from asthma, did not smoke, and took omega-3s for 3 weeks. The omega 3 supplementation did not change the levels of mast cell pro-inflammatory mediator release. It is likely that it is more difficult to change the metabolic profile of mast cells than just by dietary intervention as the mast cell probably still has a significant reserve of pro-inflammatory lipids.


Daniel Smrz, Glenn Cruse, Michael A Beaven, Arnold Kirshenbaum, Dean D Metcalfe, Alasdair M Gilfillan Rictor negatively regulates high-affinity receptors for IgE-induced mast cell degranulation. J. Immunol.: 2014, 193(12);5924-32 PubMed 25378594

File:MTOR and RICTOR in LAD2 cells in different environments.gif
File:MTOR and RICTOR in LAD2 cells in different environments.gif[5]

Summary:

'Rapamycin-insensitive companion of mammalian target of rapamycin' (RICTOR) is a protein that regulates cell growth as a result of the presence nutrients and growth factors. This study showed that RICTOR can function as a negative regulator in igE induced mast cell degranulation, independent of other regulatory proteins like mTOR or mTOR2. They further showed at what stages in the molecular pathways the regulation took place. By analysing Ca2+ mobilisation and cytoskeletal rearrangement with confocal microscopy they were able to hypothesise that there was phosphorylation of certain proteins (LAT and PLCy1). They compared their results with a RICTOR knock-down model and found a decrease in igE induced degranulation



Zhuo Zhao, Hao Wang, Marina Lin, Leanne Groban GPR30 decreases cardiac chymase/angiotensin II by inhibiting local mast cell number. Biochem. Biophys. Res. Commun.: 2015, 459(1);131-6 PubMed 25712524

File:Cardiac angiotensin (Ang) II levels in the left ventricles of sham-operated and ovariectomized (OVX) female rats.jpg
File:Cardiac angiotensin (Ang) II levels in the left ventricles of sham-operated and ovariectomized (OVX) female rats.jpg[6]

Summary: Estrogen seems to have protective effect on heart cells. It likely interacts via the receptor GPR30 which is expressed in the heart. Estrogen may even regulate components of hormone systems associated with the heart like the renin-angiotensin pathway. This study aimed to investigate whether the cardioprotective effects observed as a result of estrogen occur via GPR30. GPR30 has important regulatory roles in cardiac mast cell activity and proliferation. This experiment will be looking at the latter. The findings suggested that the effects of estrogen on cardiac mast cells/chymase/Ang II occur specifically through activation of GPR30 to decrease cardiac mast cell number. However, further investigations are needed for the exact mechanisms by which GPR30 affects cardiac mast cell number in vivo. Investigation in the mast cell GPR30/chymase/angII pathway could have therapeutic uses in postmenopausal women at risk of cardiovascular disease


Week 6 homework: cytoskeleton

notes: non-primary neurons used in lab. Use neuroblastoma line that have been immortalized. Primary neurons come directly from neuronal tissue of organism.


File:A Comparason of Neuroblastoma morphologies in Group Tm4 over expression-mice and wild-type.PNG

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Week7/lab6 Homework

1.Anti-Mast cell antibody [MCG35]

2. http://www.abcam.com/mast-cell-antibody-mcg35-ab20217.html

3. i)monoclonal ii) mouse iii)reacts with humans iv)useful for mast cell identification in immunological reactions and hypersensitivity diseases. The antigen is found in granule components of mast cells.

references used: Rimmer EF & Horton MA Origin of human mast cells studied by dual immunofluorescence. Clin Exp Immunol 68:712-8 (1987). Read more (PubMed 3308221) Rimmer EF et al. Human mast cells detected by monoclonal antibodies. J Clin Pathol 37:1249-55 (1984). Read more (PubMed 6389604)


  • Z8600021 You have not included the possible research applications in your summary. I also fixed the PMIDs by removing the colon, that changes them now into a link. (4/5)





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Attendance

Z3463953 (talk) 11:55, 10 March 2016 (AEDT) Z3463953 (talk) 11:07, 17 March 2016 (AEDT) Z3463953 (talk) 11:20, 24 March 2016 (AEDT) Z3463953 (talk) Z3463953 (talk) 11:10, 14 April 2016 (AEST) was present lab on 7 th april as evident by my groups assessible CRISPR work Z3463953 (talk) 11:42, 21 April 2016 (AEST) Z3463953 (talk) 11:11, 28 April 2016 (AEST) Z3463953 (talk) 12:07, 5 May 2016 (AEST) Z3463953 (talk) 11:22, 12 May 2016 (AEST) Z3463953 (talk) 10:59, 26 May 2016 (AEST) i've been present at every lab, but may have forgotten to sign in for a couple? Z3463953 (talk) 11:09, 2 June 2016 (AEST)

Lab one assessment

Search pubmed

prokaryotic cytoskeleton

http://www.ncbi.nlm.nih.gov/pubmed/?term=eukaryotic+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.[7]
  1. ‘type out whole reference’
  2. ‘type out whole reference’
  3. Matthew J Hamilton, Jason L Hornick, Cem Akin, Mariana C Castells, Norton J Greenberger Mast cell activation syndrome: a newly recognized disorder with systemic clinical manifestations. J. Allergy Clin. Immunol.: 2011, 128(1);147-152.e2 PubMed 21621255
  4. John D Brannan, Johan Bood, Ahmad Alkhabaz, David Balgoma, Joceline Otis, Ingrid Delin, Barbro Dahlén, Craig E Wheelock, Parameswaran Nair, Sven-Erik Dahlén, Paul M O'Byrne The effect of omega-3 fatty acids on bronchial hyperresponsiveness, sputum eosinophilia, and mast cell mediators in asthma. Chest: 2015, 147(2);397-405 PubMed 25321659
  5. Daniel Smrz, Glenn Cruse, Michael A Beaven, Arnold Kirshenbaum, Dean D Metcalfe, Alasdair M Gilfillan Rictor negatively regulates high-affinity receptors for IgE-induced mast cell degranulation. J. Immunol.: 2014, 193(12);5924-32 PubMed 25378594
  6. Zhuo Zhao, Hao Wang, Marina Lin, Leanne Groban GPR30 decreases cardiac chymase/angiotensin II by inhibiting local mast cell number. Biochem. Biophys. Res. Commun.: 2015, 459(1);131-6 PubMed 25712524
  7. 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

Addition of prokaryote image

Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome




Lecture 1

smh My little pony

bio med


testz8600021

What have i learnt today? (10/4/16)

This beautiful morning i have spent the past hour enjoying the tasty luxury of learning about the programming involved in the creation of wikipages. It is quite an auspicious opportunity to spend such precious time among such rich company. Attendances, links and even subheadings have been mastered in this lab.