- 1 My student page
- 2 Attendance
- 3 Lab 1 assessment
- 3.1 Search PubMed
- 3.2 How to make an in-text citation
- 3.3 Links
- 3.4 Learnt today
- 3.5 Student image
- 3.6 Lab 2 assessment: Summary of Article
- 3.7 Lab 3 assesment
- 3.7.1 Article Source: study of mast cells and granules from Primo Nodes using Scanning Ionic conductance microscopy
- 3.7.2 Article Source: A method for detailed analysis of the structure of mast cell secretory granules by negative contrast imaging
- 3.7.3 Article Source: Phospholipase D2: A Pivotal Player Modulating RBL-2H3 Mast Cell Structure
- 3.7.4 Article Source: NOD1 and NOD2 Interact with the Phagosome Cargo in Mast Cells: A Detailed Morphological Evidence
- 4 Lab 5 assessment
- 5 Lab 6 assessment
- 6 Peer reviews
My student page
|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)
|Group Assessment Criteria|
Group Assessment Criteria
|Individual Lab Assessments|
- Z8600021 attende 11 (eleven) practical classes.
Lab 1 assessment
<pubmed>26756351</pubmed> eukaryotic cytoskeleton
How to make an in-text citation
Bacterial division protein Ftz. 
In this lab, I learnt how to create and edit a wiki page. I learnt how to format a page and log my attendance for each lab. I also learnt how to create headings and different types of subheadings and the coding involved in achieving that, as well as how to put in text under these particular headings. Two equal signs are used for headers, i.e. ==Title== and subsequent subheadings are created by adding an extra equal sign, e.g. ===subheading===. This lab also enabled me to learn how to search for scientific articles on various research databases such as PubMed and BioMed central, and use filters on these websites in order to find articles of interest. Furthermore, I learn the importance of copyright declarations on these articles, and which papers can and cannot be used in assignments. These databases were then used to be linked into the wiki, and I learnt the ways in which specific articles could be formatted to be linked into the wiki page. Coding was also used such as using [url] to link specific searches on the database, and the coding of <article database> article number </article database> was used to link to the specific article of choice, as well as provide additional information regarding the authors and publication date of the articles. In addition, coding was learnt to link specific pages within the wiki by using two square brackets, title of page, and for pages outside of this particular wiki, the coding of [URL] would be used. In order to give the link a title, the coding of [URL/ title] is used.
- Z8600021 - you needed to set a defined size for its appearance on the page. 600, or 800px otherwise it appears too large.
Energetics and genetics across the prokaryote-eukaryote divide.
Lab 2 assessment: Summary of Article
Platelet functions are dependent upon the release of bioactive molecules from their granules, traditionally studied and classified in groups through electron microscopy techniques. These granules are essential for secondary haemostasis, and any deficiencies in number, shape or content leads to bleeding. In genetic disorders such as Hermansky-Pudlak syndrome (HPS), the absence of dense granules immensely slows down the rate of hemostasis at the site of injury. In normal circumstances, dense granules have been identified with EM techniques through the presence of an electron-dense core. However, these EM methods are time consuming and lead to differences in identification of the granules depending on different analysis types. As a result, the recent developments in super resolution microscopy (SRM) allow for structures to be resolved in the 10-200nm range, leading to individual platelet granules easily being resolved. SRM methods coupled with current automated image analysis methods allow for quantitative data of platelet granules to be obtained.
In order to effectively study the abilities of SRM, one such method- structured illumination microscopy (SIM)- was utilised in this study to distinguish between a group of healthy control patients and three patients with platelet storage disorders, in particular HPS. Of interest was the CD63 marker, as it is present in dense granules and has an altered distribution in HPS patients. The SRM techniques were used to reconstruct images from a sequence of raw images of the sample. In this study, SIM methods proved to be efficient, compatible with the routinely used fluorescent labels and achieved fast image-acquisition rates. The number of CD63-positive markers per platelet was determined through staining techniques, and this method enabled a more sensitive analysis of granules per platelet through SIM due to its improved resolution and removal of out of focus backgrounds. Samples of platelets were taken from healthy controls as well as HPS patients and SIM was used to differentiate between the two groups. Through this it was found that the mean number of dense granules in the controls (3.5) was far higher than that of the patients (0.07). Blood samples were consequently tested using SRM, counting the number of CD63-positive structures through SIM, and once again it was found that the number of CD63-positive structures per platelet was higher in the controls than in the patients. Thus, these results indicate that SIM is a rapid and successful method of identifying those with platelet bleeding disorders, and SRM can act as an effective determinant of a dense-granule disorder. 
Lab 3 assesment
Structure/ morphology of mast cells
Article Source: study of mast cells and granules from Primo Nodes using Scanning Ionic conductance microscopy
<pubmed> 26742911 </pubmed>
In this article, scanning ion conductance microscopy (SICM) is used to study the three dimensional structure of live mast cells, and the distribution of mast cell granules in each of their four developmental stages. This was done in the in the primo node (PN) of the primo vascular system from the surfaces of the large and small intestines, abdominal walls and bladder of rats, as mast cells are found to be in abundance here. Through the use of SICM, the mast cells were easily observed through the presence of their granule structures, and by the use of toludine blue stain. SICM methods were able to obtain a 3D image of these mast cells, with the surface of the cells densely covered with granules. Through this, it was able to be determined that the structure of the mast cell included 74 granules, with an average diameter of 1.2 micrometers. Upon further analysis, early stages of degranulation of the mast cell in stage 2 showed a granule-free region in the middle upper portion of the cell. In addition, the mast cell in stage 3 showed very sparse remnants of granules on the upper most parts of the cell surface. Here, SICM picked up the disintegrated boundary of the mast cell as having an appearance of laced patches, with a diameter of 1.6 micrometers. It was observed that the height of the mast cell progressively decreased with each stage, while the round shape and diameters of the granules remained the same.
This article was useful to the subtopic of mast cell structure, as it provided a detailed analysis of the structure and appearance of mast cells in their various developmental stages, with a focus on the mast cell granules during these stages. The graunles are an essential component of mast cell structure as these are secreted when mast cells are triggered, thus making it important to understand its structure. Hence, this article was useful in the research of the structure and morphology of mast cells. 
Article Source: A method for detailed analysis of the structure of mast cell secretory granules by negative contrast imaging
<pubmed> 26997316 </pubmed>
An essential aspect of mast cell structure is the large number of secretory granules (SG) found in the cytoplasm. These elicit inflammation through molecules including histamine and serotonin. Several models suggest that a single mast cell has a large number of different types of secretory granules, all in various stages of development. Secretory granules also contain lysosomal proteins and markers such as CD63, and are hence lysosomal granules.
In order properly study the structure of mast cells, this study aims to gain insight into the structure and organisation of SGs via negative contrast imaging (NCI). Within the mast cell, organelles such as SGs are separated from the cytoplasm by a lipid bilayer, and this method uses microscopy techniques in order to visualise negatively stained organelles. These NCI techniques highlight the presence of small outlines in the perinuclear region surrounded by large, spherical shapes. NCI usage in this study also identified key structures such as the cell body, nucleoli, nuclear membrane as well as the mitochondria. The structural appearance of mast cell SGs was found to be either single elongated structures or a cluster of multiple spherical structures strung together. Experimental data indicated SGs are cylindrical in shape, and fuse along the vertical axis, highlighting polarity in structure. Further, time lapse observation during the cell cycle showed that SGs increase in abundance with cell size, but are under continuous control to maintain size distribution. This data is important as mast cell proliferation in peripheral tissues is an issue of interest in allergy treatment.
Thus, this article was beneficial in facilitating knowledge in the sub topic of mast cell morphology as it sheds light on the structure of mast cell SGs, including their organelle volume, size and number using NCI techniques. These methods can ultimately provide more information on the detailed molecular mechanisms of SG biogenesis in mast cells. 
Article Source: Phospholipase D2: A Pivotal Player Modulating RBL-2H3 Mast Cell Structure
<pubmed> 22344748 </pubmed>
This article examines the role of PLD2 in mast cell structure maintenance. It is thought that PLD plays a key role in mast cell degranulation, and PLD2 is essential in maintaining the structure of mast cells. The study examined if differences in PLD2 expression reflected upon alternations in morphology of the mast cells, with different cell lines being used, and was found that the inactive form of PLD2 has a dramatic effect on the morphology of these cells. The morphology of secretory granules was also determined, with these granules being heterogeneous in some cell lines include PDL2Ca, but having an electron lucid content in others. It was thus found through this study that the overexpression of the inactive form of PLD2 has a dramatic effect on the structure of mas cells, thus suggesting that the production of PA by PLD2 assists in the structural maintenance of the cytoskeleton, golgi complex as well as influencing the distribution of lysosomes and secretory granules in mast cells.
This article is hence relevant to the sub topic of mast cell structure as it highlights the specific role of PLD2 in the maintenance of the structure and morphology of the mast cell, as well as the structures within the cell. Thus, this article is beneficial as it provides a background knowledge regarding the way in which the specific structure of the cell is maintained. 
Article Source: NOD1 and NOD2 Interact with the Phagosome Cargo in Mast Cells: A Detailed Morphological Evidence
<pubmed> 25502289 </pubmed>
This article analyses the detailed structure of the mast cell, and in particular, the mast cell phagosome, as it has key functions in triggering the inflammatory process and has phagocytic properties. The mast cells express NOD1 and NOD2 proteins whose role is to recognize intracellular foreign components and initiate cytokine synthesis. In this study, five experiments were conducted in which mast cells were incubated with E. coli and at least 100 cells were analysed in order to determine the main morphology in each cell population. The maturation of the paghosome structure of the mast cells was also followed closely, and the outside leaflet of the mast cell plasma membrane was able to be distinguished. As structure was analysed, it was seen that many granules were interacting with the phagosome, with the phagosome membrane structure undergoing remodeling over time. It was also established that the phagosome membrane is interrupted in places in direct contact with the granule components, and these interruptions were observed at sites of granule-phagosome interaction. Additionally, NOD1 and NOD2 were found to be associated with granule surface or the granule matrix of the mast cell. The article was thus useful for this particular subtopic as it analyses the structure and morphology of the various components of the mast cell, such as the phagosome. It is beneficial to gain some perspective on the structure of the phagosome that is heavily involved in inflammatory processes, which is a key function of the mast cell. 
Lab 5 assessment
Lab 6 assessment
1. Identify an antibody against your group blood cell protein that is commercially available.
Anti-Mast Cell Tryptase antibody [AA1], commerically availble from abcam
2. Add a link to the original data sheet page and identify the type of group blood cell protein.
http://www.abcam.com/mast-cell-tryptase-antibody-aa1-ab2378.html, It is mouse monoclonal [AA1] to Mast Cell Tryptase
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.
This antibody is monoclonal, and is raised in the mouse species. It reacts against cat, donkey and monkey. It's main application include uses in immunocytochemistry (ICC), WB, ICH-P, ICC/ IF, ICH-R and the ELISA techniques.
<pubmed>24831942</pubmed> <pubmed> 25361058</pubmed>
- Z8600021 (5/5)
- Z8600021 (18/20)
This page is well detailed and provides comprehensive information about megakaryocytes and their structure and function. The introduction and history are well detailed, providing a good overview of the basic information regarding the cell, and the table format of the history allows the information to be presented in an organised and easy to follow manner. While the structure of the cell is well detailed, the majority of this section only uses one source, and I believe it may be able to be improved by using additional articles (which are perhaps a more recent). The development section is thoroughly done, with the information presented in an organised, easy to understand manner. The histological image is also very useful in supplementing the information, as was the image regarding the maturation of the megakaryocyte. However, the section regarding thrombopoietin receptors under the signalling topic does not appear to have any references, and this should be fixed whenever possible. The function and role section is well detailed, with clear subheadings organising the information into distinct sections, and the images also help to substantiate this information. The video in the pathology section is a useful tool of providing an overview of the topic. However, the references for the essential thrombocytosis section appear to be separate, and not within the standard reference list at the end of the page. This seems to be a little disorganised, as the drop down table showcasing the references doesn’t allow for the specific citations/ reference numbers to be used within the body of information like the rest of the page. In addition, the osteoporosis section doesn’t appear to be complete, but this can be fixed in the near future. The future of megakaryocytes section was well detailed, with well structured information about each of the different areas of research. In addition to this, while this is a minor point, I found that the numbering of the images throughout the page is out of order, with some numbers doubling up (such as there being more than one figure 4), and this can cause some confusion on the page.
Overall, I found this page to be quite informative and education regarding megakaryocytes. The information is well presented, with distinct sections showcasing different aspects of the cell. The images are also well chosen, and supplement the information very well. Some areas require a little more work in terms of referencing and providing more substantial information, as well as the formatting of the images. However, on the whole this is a good page that is very educational regarding megakaryocytes.
This page is well structure and extremely well detailed, providing substantial information about red blood cells in a clear and concise manner. The introduction provides a strong overview of the cell, and is well detailed. However, the final sentence of this section seems to be unfinished (ending with “such as…”), and I am assuming a brief overview of current research should have been added there to complete the sentence. All the different subsections are extensively detailed, and the information is presented in an easy to read and understand manner. The structure and function sections are particularly well done, with the corresponding electron micrograph image of a red blood cell further facilitating ths information. However, one suggestion would be to add more images or visuals on the page, in order to balance out the substantial amount of information, as well as to make it more interesting and user friendly. All of the information is referenced appropriately and thoroughly, and the synthesis and regulation subtopic in particular provides unique information about the cell. The drop down tables in the diseases section was also a good touch, providing extra information if desired.
Overall, this group page is very well done with extremely detailed and well presented information regarding red blood cells. There is an extensive use of citations and references, indicating the group has undertaken a significant amount of research, and the information has been presented in an easy to understand manner. The page could benefit from more images, however, which can help to solidify the information being presented. In addition, the information within the sections could be broken down into smaller chunks (possibly through the use of more visual aids), as there is currently an extensive amount of paragraphs of text on the page. On the whole however, this group page was very well done.
This page provides sufficient information regarding B cells, with its respective sections providing a solid amount of detail to educate those reading the page. However, the history section requires a lot more detail, and more information regarding events that occurred in more recent years as well. Further, the vast majority of the page does not seem to be referenced in the required manner, and thus the reference list at the end of the page has 18 links only. While there are in text citations throughout the page, I am assuming that they need to be properly referenced so that they get added to the reference list. The actual information is detailed and thorough, with the subsections helping to make it flow and appear organised and informative. The function and the types of B cell sections in particular are very detailed, and extremely educational. The images also provide extra supplementary information to the text, however, I believe that the images need to be edited so that there is a title and small summary (on the actual page) of what the pictures are displaying. The page could also be improved through the addition of more images to break up the long paragraphs of text, especially in areas such as the different B cell types, as well as the function section. Further, some images don’t have the copyright information, or a description of the image when it is clicked on. The applications section is quite unique and a good way to end the page, providing information on the diagnostic uses of the cell type. However, once again, this section is not referenced either, and no in text citations are provided. Additionally, the immunodeficiency section is not completed yet.
On the whole, this group’s page provides well detailed information regarding this cell type, and allows readers to gain a sound understanding of the details of B cells. The accompanying images further enhance the content, and allow for a deeper understand of the topic. However, some sections need to be worked on and completed, and the references need to be added so that the enter page is properly cited and referenced. The addition of more images could also positively benefit this page.
This page is well detailed and informative on the whole and well structured, providing readers with a good understanding of natural killer cells. However, the history section appears to require more information, as there are not enough dates on the timeline outlining the history of the cell. The specific subtopics are quite informative and well structured, although a few additional images would help to supplement the text. Additionally, while the images are a good visual aid and help to supplement the information on the page (especially images such as the effector function diagram), a few of them are not properly structured, as some are missing the image descriptions and others do not have copyright statements. The abnormalities in disease section is well done, with good descriptions of specific diseases. The table at the start of the section is a good addition, as it provides a nice overview of the role of natural killer cells in disease. However, this section requires more references, as in many cases there is only one article being referenced for each paragraph or section (such as in sections like rheumatoid arthritis and cancer). Additionally, on the whole, this page requires a few more references, and I believe this can be achieved by added more of these into the abnormalities in disease section. The current research and glossary sections are a good addition to the page, however the glossary needs to be completed.
Overall, this group page provides a lot of well detailed information regarding natural killer cells and is very informative on this topic. While this information is presented in a concise manner, the page could be further improved with the addition of more images and visual aids, and a more detailed explanation of these images. The references of this page also needs to be added to and improved upon. However, on the whole this is an informative and well done page.
This page is extremely detailed and it is evident that a lot of thought and work went into the way in which the information is presented. The introduction is well done and provides a good overview of T cells in an educational manner. The video placed in the introduction is also a good touch to make the page interesting from the very start. All of the individual sections are very well done and show a high level of detail, and the section of the different types of T cells is extremely thorough and provides good detail on the entire range of T cells. All of the drop down tables are also a nice touch to the page, with links to videos such as Khan Academy further helping to solidify knowledge on the subject. Additionally, the supplementing images are well picked out as they serve to solidify the information that is being provided. However, while looking through the images, the diagram of CD4 and CD8 co-receptors doesn’t seem to include a copyright statement (it only includes the fact that it is copyrighted from the British Pharmacological Society), so that is something that needs to be fixed. While the extensive number of references indicates the high level of research that has been put into the page, some of them seem to be links to websites and not articles, and I am not sure if those websites can be used as a source of information in this assignment. The research at UNSW section is a nice, unique touch to add to the page, as is the glossary, although it needs to be filled out.
On the whole, this page is very well done and it is evident that a lot of effort went into creating it. All of the information is well structured and constructed, and all of the additional touches such as images and drop down sections are extremely informative. Some improvements could be made regarding the references and the images, but overall this page is very well done.
On the whole, this page provides a good amount of information regarding eosinophils in a clear and engaging manner. However, I feel that the page would benefit from including an introduction/ overview of the cell at the beginning, instead of starting immediately from the history of eosinophils. Additionally, while the history section is well detailed, It could benefit from having information from more recent dates as well (as it stops at 1879), as well as information from more sources than just one article. The use of images is well done and it complements the information in the structure and birth, life and death in the body sections well. Furthermore, the text itself in these sections is well presented and easy to follow. The section on role in allergy and disease provides a lot of good detail, however, some sections seem a little on the short side, such as the sections on viral, fungal and bacterial infection, and might benefit from adding more information there. The addition of the drop down videos was a good aspect on the page, and allows for a more interesting read. One other minor point would be the fact that the last two references in the reference list don’t appear to be linked properly as there is no pubmed reference for them.
Overall, this page is well done with a lot of good information provided. However, I do believe that it can be improved by the addition of more text to make the different sections more comprehensive. There is a nice balance of images and texts, and this could benefit even more by the addition of more information.
- <pubmed> 26806224 </pubmed>