User:Z3461106

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

Z3461106 (talk) 11:54, 10 March 2016 (AEDT)

Z3461106 (talk) 11:06, 17 March 2016 (AEDT)

Z3461106 (talk) 11:04, 24 March 2016 (AEDT)

Z3461106 (talk) 11:05, 7 April 2016 (AEST)

Z3461106 (talk) 11:06, 14 April 2016 (AEST)

Z3461106 (talk) 11:07, 21 April 2016 (AEST)

Z3461106 (talk) 11:11, 28 April 2016 (AEST)

Z3461106 (talk) 11:00, 5 May 2016 (AEST)

Z3461106 (talk) 10:58, 12 May 2016 (AEST)

Z3461106 (talk) 12:37, 19 May 2016 (AEST)

Z3461106 (talk) 11:04, 26 May 2016 (AEST)

Z3461106 (talk) 11:06, 2 June 2016 (AEST)


  • Z8600021 Attended 12 practical classes.

Lab 1 Assessment

Search Pubmed

prokaryotic cytoskeleton

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


BioMed Central

What I've Learned So Far

I have learned how to setup a Wiki page for myself. It has been an interesting experience because it's something that I have not done before. The instructions to get set up are not all that complicated. Just a few minor coding steps.

Lab 2 Assessment

  • Z8600021 Image added and correct Ref/copyright/student template (5/5)

This article outlines how super-resolved structured illumination microscopy (SR-SIM) results can be processed through open-source programs such as ImageJ as opposed to proprietary softwares. Usually, companies which produce SR-SIM only allow image processing through their own proprietary computers. But, with the advent of fairSIM (free analysis and interactive interactive reconstruction for structured illumination microscopy), an open-source SR-SIM imaging software, there is a new solution for if users of SR-SIM require access to processing software. This software aims to be ready to use, easy to operate, free and open-source.

Testing on fairSIM was executed on different samples and microscopes such as DeltaVision|OMX which provided three-beam and two-beam interference illumination data to assess for compatibility with fairSIM. The first specimen was fluorescent Tetraspeck beads that are easily distinguished when applying SR-SIM, but not on widefield. This was apparent on the home-built system and the OMX. The next specimen was a liver sinusoidal endothelial cells sample stained with fluorophore. These were once again imaged on the OMX, with the fairSIM being able to process faster than the SoftWORX software that was built by Deltavision. This was due to fairSIM utilising single-slice mode as opposed to 3D SIM reconstructions. But nevertheless, both were able to project images that were clearly visible.

Some other additional samples used included cytoskeletal protein fibrils and mitochondria which were this time imaged on the Zeiss Elyra S1 and gave similarly clear reconstructions. Therefore, it was discussed that the fairSIM software which uses the Gustafsson approach, although is early in development, will become a highly useful tool for SR-SIM users and will be a cost-effective, fast and customisable solution.


Marcel Müller, Viola Mönkemöller, Simon Hennig, Wolfgang Hübner, Thomas Huser Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ. Nat Commun: 2016, 7;10980 PubMed 26996201


Ncomms10980-f1.jpg

Examples for intermediate SR-SIM results displayed as power spectra in frequency space. [1]


How to make an in-text citation

Bacterial division protein FtsZ.[2]


  1. Marcel Müller, Viola Mönkemöller, Simon Hennig, Wolfgang Hübner, Thomas Huser Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ. Nat Commun: 2016, 7;10980 PubMed 26996201
  2. 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

The Sydney Morning Herald

Student Image

  • Z8600021 Image added and correct Ref/copyright/student template (5/5)


AdFIZZI Effects on Lung Fibrosis.jpeg

AdFIZZI Effects on Lung Fibrosis [1]


You can also make it smaller, e.g. 200px!

AdFIZZI Effects on Lung Fibrosis.jpeg

AdFIZZI Effects on Lung Fibrosis [1]

Or a thumb!

AdFIZZI Effects on Lung Fibrosis.jpeg

AdFIZZI Effects on Lung Fibrosis [1]

Lab 3 Assessment

Paper 1

Ciccoli et al. [2] developed a study in patients with Austism spectrum disorders (ASDs) through measuring shape abnormalities of red blood cells, oxidative damage and B-actin alterations. There were two groups in which these variables were tested for, a positive group that were diagnosed with ASDs and a negative group of healthy patients. It was found that shape abnormalities such as elliptocytes are found in patients with ASDs, which is associated with oxidisation of some of the main cytoskeletal proteins, hence affecting erythrocyte membrane. Through this paper, the structural information of RBCs can be derived such as its discoid shape and that the abnormality of elliptocytes can be attributed to Diseases and Abnormalities if Austism is to be discussed.

Paper 2

Higgins [3] investigated how quantifying red blood cell (RBC) dynamics such as reticulocyte count through hematology analysers would provide further information about diagnosis and clinical action of diseases such as anemia. In addition, the health of a patient’s hematologic system can be evaluated based on the maturation and turnover of RBCs, as there are many changes that occur in its characteristics during its life such as volume decrease, Hb mass decrease and reduction of the RBC’s surface area. This relates to the Diseases and Abnormalities component of our project about RBCs and may provide an insight into the pathogenesis of anemia over the lifespan of red blood cells.

Paper 3

Aragon-Martinez et al.[4] proved that the liquid chromatographic (LC) method in conjunction with diode-array technology allows faster detection times of ATP-related compounds in human erythrocytes. These compounds included ATP, ADP, AMP, cAMP and IMP. It was noted that this method in comparison to traditional methods required only one-sixteenth of the whole blood (125 microlitres) volume. In addition, this method is more efficient as the measurement took only 20 minutes of which 8 compounds were able to be detected. Previously, measurement times took longer and the amount of compounds detected were less. Through this paper, we are able to utilise the results to confirm ATP-compounds in human erythrocytes and derive at a more profound understanding of RBC structure, function and regulation.

Paper 4

Mu et al. [5] confirmed that higher red blood cell saturated fatty acids are associated with inflammation through elevated IL-6 levels and C-reactive protein levels (CRP), after administering doses of palmitic acid and stearic acid respectively over a 2.5 year period. The impact of inflammation is a factor which could lead to the increased risk in chronic diseases such as coronary heart disease and cancer. The subjects used in this experiment were all ensured to be healthy, however, were diagnosed with Periodontitis, a common chronic inflammation disease. Through this paper, insight can be drawn as to how RBC saturated fat levels can lead to inflammation.

Lab 5 Assessment

Group 2 Tm4 Vs. Control Graph Capture.PNG


Lab 6 Assessment

1. Antibody: Anti-Red Blood Cells antibody ab34858


2. Link: http://www.abcam.com/Red-Blood-Cells-antibody-ab34858.pdf

Group Blood Cell Protein: Red Blood Cells (Erythrocytes)


3. Type of Antibody: Polyclonal

Species raised in: Rabbit

Species it reacts against: Human

Types of application uses: Agglutination

Reference of Antibody: Ashfaq Ghumra, Jean-Philippe Semblat, Ricardo Ataide, Carolyne Kifude, Yvonne Adams, Antoine Claessens, Damian N Anong, Peter C Bull, Clare Fennell, Monica Arman, Alfred Amambua-Ngwa, Michael Walther, David J Conway, Lalla Kassambara, Ogobara K Doumbo, Ahmed Raza, J Alexandra Rowe Induction of strain-transcending antibodies against Group A PfEMP1 surface antigens from virulent malaria parasites. PLoS Pathog.: 2012, 8(4);e1002665 PubMed 22532802



1. Antibody: Anti-Red Blood Cells antibody ab106101


2. Link: http://www.abcam.com/Red-Blood-Cells-antibody-ab106101.pdf

Group Blood Cell Protein: Red Blood Cells (Erythrocytes)


3. Type of Antibody: Monoclonal

Species raised in: Mouse

Species it reacts against: Mouse

Types of application uses: Functional Studies, Flow Cytometry

Reference of Antibody: Lucie Baudino, Falk Nimmerjahn, Samareh Azeredo da Silveira, Eduardo Martinez-Soria, Takashi Saito, Michael Carroll, Jeffrey V Ravetch, J Sjef Verbeek, Shozo Izui Differential contribution of three activating IgG Fc receptors (FcgammaRI, FcgammaRIII, and FcgammaRIV) to IgG2a- and IgG2b-induced autoimmune hemolytic anemia in mice. J. Immunol.: 2008, 180(3);1948-53 PubMed 18209093


Assessment - I would have liked the "Types of application uses" to be more specific with research techniques, though this is how it is identified in the product information. (5/5)

Peer Reviews

  • Z8600021 Your peer review feedback shows a good balance of critical analysis identifying the best aspects and also areas where the project could be improved. I do like the specific features/sections you have identified, as this helps the groups review their project. You have also been able to provide your feedback in a brief format. I hope this now also makes you think about your own project in the context of how you have assessed all the other class group projects. Well done (18/20)


Group 1

Group 1 introduced the topic of Megakaryocytes in a simple and succinct manner whilst taking care to elaborate on acronyms and define scientific terms. A great example of this was in the Platelets subheading in which the group usefully defined the term α-granules. The history of the Megakaryocyte is very comprehensive, detailed and chronologically structured. Much of the headings were well thought out, allowing the wiki page to embrace a logical structure. Some of the histological images provided a great visual representation that allowed me to have an insight of how Megakaryocytes would look like under the microscope. In addition, great thought has been given to the flow of text in paragraphs. For instance, the maturation of Megakaryocytes through endomitosis was clearly elaborated upon in the following sentences and intuitively evoked me to ask questions while reading and also being provided the answers in the latter sentences.

However, more references must be cited in the introduction and structural information, especially when introducing the fundamental definitions and history of Megakaryocytes. This is not only to ensure that the information is accurate, but to also ensure reliability of findings. For example, in the Structure section, only two references to the literature were cited. Admittedly, through having an overview of these references, I found that these were great as they had comprehensive information pertaining to Megakaryocyte structure, however, greater research depth can be obtained only through citing more sources. Further, a diagram of the Megakaryocyte would be highly beneficial in providing readers with easier understanding of the structure, in accompaniment with the descriptive language employed. This would also have been beneficial in regards to the structure of the platelets. Overall, Group 1 has made a solid attempt in providing good depth of information and flow of text, but will be able to reach a higher standard of work if more care is given in citing sources as well as increased diagrams.


Group 3

Information is in great depth. Great command in language and flow of text, especially when explaining the role of calcium recruitment in T-cell independent activation. This allowed me to link my understanding to how B cells induce differentiation without the dependent need of T-cell activation. It is also presented in a concise manner, especially in the Differentiated B cells section in which it provides information of their origins and important functions after B cells are differentiated from hematopoietic stem cells. That is, that they act as APCs and present the antigens to CD4+ T cells. The tabulation of the B-cell surface molecules was a spectacular idea as it nicely summarised which those that exist on the surface and provides a brief explanation of their respective functions.

However, other information such as the Antibody Isotypes, whilst also equally concisely explained, can be tabulated so that it is aesthetically pleasing to the reader and easy to distinguish, comparing them by their prominence in the stage of immune response (i.e. primary or secondary) and their respective half-lives. In addition, more sources need to be cited throughout the whole wiki page, particularly in the Introduction, History, Structure, Function and Role in Disease sections. Furthermore, despite the history of the B cells being short and succinct, extra detail can still be added to provide a profound and broader timeline into the discoveries of the B-cell, which is representative of the amount of information depicted in your wiki. Take advantage of paragraphing. For example, when describing the two distinct pathways of B Cell differentiation. Lastly, utilising more diagrams, especially structure of B cells and their activation would be advantageous, so please consider this during your edits. e.g. When B cells are organised into follicles and exposure leads to germinal centres. Overall, Group 3 has made an excellent effort in the explanation of B cells, however, need to take greater emphasis in using headings, diagrams and citing sources.


Group 4

Group 4 has started off the wiki with a relatively strong introduction in terms of the functions of the Natural Killer Cells, however, extra detail must be added such as where it originates from and other general information such as its size. Otherwise, it is a nice succinct introduction and the History provided is concise and cited. Perhaps more history can be added from the time span of 1980- 2000 because it is quite doubtful that there were no developments on Natural Killer cells during these two decades.

The inclusion of a histological diagram of the large granular lymphocyte was a brilliant idea as it helped to provide me with a visual representation of how a large granular lymphocyte looks like under a microscope and their relative sizes compared to other cells. It would be great though to include a scale in the picture. It certainly is very good that the group has added a label to the picture and mentioned that it was a blood smear.

In addition, the addition of “NK Cells in Disease Conditions” in a tabulated format assisted in simplifying the layout making it easier to understand how NK cells play a role, the level/type of activity that it stimulates and also possible therapeutic approaches. This is wonderfully expanded upon in the following paragraphs which has provided an increased depth of information regarding each disease. Again, it would be very beneficial if the group could add more citations to ensure that their information is reliable and that these findings have been demonstrated and replicated by other scientists.

Overall, Group 4 has made a very solid attempt in providing information at a profound level. However, more citations and a stronger introduction would definitely be highly beneficial in allowing readers to attain a stronger grasp to NK cells.


Group 5

Group 5 has composed a brief overview that has perfectly summarised what a mast cells is, and have included a nicely formatted History table which comprehensively covers the developments of the Mast cell. The addition of a histological image of Mast cells stained in Toluidine Blue is very useful in understanding the visual structure and also contains a scale which is useful to know more about the size. A comprehensive list of references has been used throughout the wiki page, demonstrating a large amount of research that has been executed. Information has also been presented with logical flow, progressively developing upon the subsection. A great example of this was in Function whereby the process of Mast cell activation is outlined. Furthermore, there has been extensive use of diagrams and flow charts which assisted in explaining the origins and migrations of Mast cells. In particular, the adapted diagram of the Activations and Simplified Signalling Pathways allowed increased focus of explanation. On the other hand, I feel that the diagram could be improved by utilising pre-drawn arrows and pre-loaded fonts to make it more professional.

Although a glossary is very helpful in defining important terms, I believe that defining scientific terms should be incorporated within the main body of texts as it is more convenient to for the reader instead of having to scroll down to refer to definitions.Furthermore, some acronyms such as FcεRI need further expansion.

Overall, Group 5 has made an excellent wiki page that has used a good balance of clear and concise information, diagrams, videos and tables to represent the Mast cell in its entirety. However, the glossary could possibly be integrated with the main body text and some of the acronyms require expansion.

Group 6

Group 6 has composed an excellent introduction that has set out to briefly explain the origins and naming of T-cells. Through brief explanation of how T cells function, followed by a listing of what the wiki page will explain, has provided a nice structural overview. In addition, the History is tabulated with comprehensive information and citations which shows that the topic has been thoroughly researched, including important modern developments/ discoveries. There is an abundance of information which has been conveniently hidden in order to ensure that the main points are not construed. Diagrams have been extensively used which contain labels which assist with the visual representations of T cells and how they function. A great example of this is the APC-T cell interaction through explanations of the T cell receptor structure which interacts with the MHCII receptor of the antigen.

However, information can be further simplified through the use of tables, such as when outlining the differences between the subtypes of different T cells. In addition, to maintain professionalism of wikis, I believe that the text should not contain third person pronouns such as “we”.

Overall, Group 6 has maintained a fantastic effort in providing a simple understanding with great depth of research detail whilst also balancing diagrams and videos. Some potential tips to take onboard could be increased use of tables to illustrate and compare subtypes of T cells.

Group 7

Group 7 has provided a great amount of information and has presented them in a concise and simply understood format. Histological diagrams of eosinophils have been cleverly utilised which has assisted in visually representing the cell. The amount of citations that have been utilised is a sufficient amount to demonstrate profound depth of research in regards to the subject of eosinophils. They have also expanded upon acronyms very well.

Mechanisms for Contents Release has been explained briefly, however, it would benefit from being incorporated into a table. The same applies for contents for the Granules. Instead of simply listing the contents of the cytokines as “preformed chemokines”, “preformed cytokines”, etc., it may help to tabulate this information. On another column, examples of the types of cytokines and chemokines can be listed to demonstrate a deeper understanding of eosinophils. In addition, group 7 will also further benefit by opening with a solid introduction that provides a basic overview of eosinophils with further entries made to the History table. I believe that there are more modern developments/discoveries that have happened in the past, especially in the 20th and 21st centuries when there has been huge advancements in technology.

I also further recommend the group to ensure that the use of their Youtube video is appropriate as some online videos are not available under the Creative Commons License, but the Standard Youtube License instead.

Some terms such as “Respiratory Syncytial Virus” can be further detailed by just a sentence in regards to the main pathogenesis of the disease as opposed to simply listing it as an example. This will provide readers with a more significant link between the eosinophil granules play a part in viruses.

Overall, Group 7 has made a solid attempt at demonstrating the knowledge of Eosinophils through information presented in a great depth but clever structure. But, more care needs to be given when linking to copyrighted content.
  1. 1.0 1.1 1.2 Tianju Liu, Hongfeng Yu, Matthew Ullenbruch, Hong Jin, Toshihiro Ito, Zhe Wu, Jianhua Liu, Sem H Phan The in vivo fibrotic role of FIZZ1 in pulmonary fibrosis. PLoS ONE: 2014, 9(2);e88362 PubMed 24516640
  2. Lucia Ciccoli, Claudio De Felice, Eugenio Paccagnini, Silvia Leoncini, Alessandra Pecorelli, Cinzia Signorini, Giuseppe Belmonte, Roberto Guerranti, Alessio Cortelazzo, Mariangela Gentile, Gloria Zollo, Thierry Durand, Giuseppe Valacchi, Marcello Rossi, Joussef Hayek Erythrocyte shape abnormalities, membrane oxidative damage, and β-actin alterations: an unrecognized triad in classical autism. Mediators Inflamm.: 2013, 2013;432616 PubMed 24453417
  3. John M Higgins Red blood cell population dynamics. Clin. Lab. Med.: 2015, 35(1);43-57 PubMed 25676371
  4. Othoniel Hugo Aragon-Martinez, Othir Galicia, Mario Alberto Isiordia-Espinoza, Flavio Martinez-Morales A novel method for measuring the ATP-related compounds in human erythrocytes. Tohoku J. Exp. Med.: 2014, 233(3);205-14 PubMed 25048613
  5. Lin Mu, Kenneth J Mukamal, Asghar Z Naqvi Erythrocyte saturated fatty acids and systemic inflammation in adults. Nutrition: 2013, 30(11-12);1404-8 PubMed 25280420