User:Z5015719

From CellBiology
Revision as of 12:11, 7 April 2016 by Z5015719 (talk | contribs) (Attendance)

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

Z5015719 (talk) 11:53, 10 March 2016 (AEDT)

Z5015719 (talk) 11:11, 17 March 2016 (AEDT)

Z5015719 (talk) 11:11, 24 March 2016 (AEDT)

Z5015719 (talk) 11:10, 7 April 2016 (AEST)

Lab 1 assessment

Search PubMed

prokaryotic cytoskeleton

PMID 26756351

<pubmed>26756351</pubmed> eukaryotic cytoskeleton

Biomed Central

How to make an in-text citation

Bacterial division protein Ftz. [1]

  1. <pubmed>26756351</pubmed>

Links

Testz8600021

Cell Biology Introduction

Lecture 1

SMH Sydney Paper

Learnt today

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.

Student image

Prokaryotic genomes and membranes.jpg Energetics and genetics across the prokaryote-eukaryote divide.[1]

Lab 2 assessment: Summary of Article

SIM images and graphs compared with other imaging techniques demonstrating the beneifits of SIM in platelet imaging for various diseases including HPS[2]

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. [3]

References

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. [4]


Article Source: A method for detailed analysis of the structure of mast cell secretory granules by negative contrast imaging

<pubmed> 26997316 </pubmed>

A 3d Image of the mast cell. Secretory granules are illustrated in white, and the nucleus and cell body are shown in the cyan and grey areas.[5]

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. [6]

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. [7]

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. [8]

  1. <pubmed>21714941</pubmed>
  2. <pubmed>26806224</pubmed>
  3. <pubmed> 26806224 </pubmed>
  4. <pubmed>26742911</pubmed>
  5. <pubmed>26997316</pubmed>
  6. <pubmed>26997316</pubmed>
  7. <pubmed>22344748</pubmed>
  8. <pubmed>25502289</pubmed>