From CellBiology
Revision as of 07:50, 10 May 2016 by Z3461106 (talk | contribs)

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.


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Lab 1 Assessment

Search Pubmed

prokaryotic cytoskeleton

eukaryotic cytoskeleton

PMID 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

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.



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. <pubmed>26996201</pubmed>
  2. <pubmed>26756351</pubmed>


Carnegie stage table

Lecture 1

The Sydney Morning Herald

Student Image

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:

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: <pubmed>22532802</pubmed>

1. Antibody: Anti-Red Blood Cells antibody ab106101

2. Link:

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: <pubmed>18209093</pubmed>

Peer Reviews

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

Nice succinct introduction and history. All of it cited. Histologic picture of the Lymphocytic NK cells  nicely presented and labelled. NK cells in disease conditions in a table. Very comprehensive information on the involvement of the Natural Killer Cells in Disease.

However, more citations would be beneficial, especially in the Abnormalities in Disease area.

  1. 1.0 1.1 1.2 <pubmed>24516640</pubmed>
  2. <pubmed>24453417</pubmed>
  3. <pubmed>25676371</pubmed>
  4. <pubmed>25048613</pubmed>
  5. <pubmed>25280420</pubmed>