User:Z5061522

From CellBiology

Welcome to Cell Biology 2017!

Lab 1 Assessment

Lab 2 Assessment

  1. Identify a chemical SDS and the risks and hazards of that chemical in text. Add a link to the original SDS
  2. Select 4 reference papers papers related to your selected group project topic sub-section. Read the research papers and write a brief description of their findings and relevance to the selected topic sub-section. The reference along with your description should then be pasted on both your group discussion page and your own personal page.

Lab 3 Assessment - Endo/Exo worksheet questions.

Lab 4 Assessment

  1. Identify a cytoskeletal antibody.
  2. Identify the species deriving the antibody.
  3. Identify the working concentration for the antibody.
  4. Identify a secondary antibody that could be used with this antibody.
  5. Identify a paper that has used this antibody.

This assessment will be due by the next lab (Lab 5).

Lab 7 Assessment

The following peer assessment exercise should be completed before next lab (Lab 8 - 2 May) as your individual assessment for this week (lab missed due to public holiday).

Your answer should be pasted in 2 places

  1. onto each project discussion page (Note you should add anonymously to the discussion page)
  2. your own individual student page for my assessment.

Each individual will provide a brief assessment of the other groups projects. This should take the form of a brief critical (balanced) assessment identifying both the positive (good) and negative (bad) aspects of the project page as it currently exists online.

You may if you choose, use the final project assessment criteria as a guide. Though you are also welcome to use your own 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.

Practical Attendance

Z5061522 (talk) 16:05, 7 March 2017 (AEDT)

Z5061522 (talk) 15:36, 14 March 2017 (AEDT)

Z5061522 (talk) 15:40, 28 March 2017 (AEDT)

Z5061522 (talk) 15:07, 4 April 2017 (AEST)

Z5061522 (talk) 15:09, 11 April 2017 (AEST)

Z5061522 (talk) 15:01, 2 May 2017 (AEST)

Z5061522 (talk) 15:24, 9 May 2017 (AEST)

Z5061522 (talk) 16:19, 16 May 2017 (AEST)

Z5061522 (talk) 15:08, 23 May 2017 (AEST)

Individual Assessments

Lab 1

Silver-intensified cationic gold nanoparticle on cell membrane.png

Diagram of a cationic charged gold nanoparticle, with silver intensification, on a cell membrane.

Fogarty SW, Patel II, Martin FL, Fullwood NJ (2014) Surface-Enhanced Raman Spectroscopy of the Endothelial Cell Membrane. PLoS ONE 9(9): e106283. doi:10.1371/journal.pone.0106283

© 2014 Fogarty et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Lab 2

Part 1:

Chemical: Toluene

Hazards:

1. Flame (GHS02): Flammable

2. Exclamation Mark (GHS07): Acute Toxicity, Skin & Eye Irritant, Skin Sensitisation, Specific Target Organ Toxicity

3. Health Hazard (GHS08): Respiratory Sensitization, Germ Cell Mutagenicity, Carcinogenicity, Reproductive Toxicity, Specific Target Organ Toxicity, Aspiration Hazard

Hazard Statements: H225: Highly flammable liquid and vapour.

H304: May be fatal if swallowed and enters airways

H315: Causes skin irritation

H336: May cause drowsiness or dizziness

H361d: Suspected of damaging the unborn child

H373: May cause damage to organs through prolonged or repeated exposure

Website Address/Link: http://www.sigmaaldrich.com/catalog/product/sial/244511?lang=en&region=AU&cm_sp=Insite-_-prodRecCold_xviews-_-prodRecCold10-7


Part 2:

Article 1:

Article Title: Resveratrol and curcumin enhance pancreatic β-cell function by inhibiting phosphodiesterase activity

Article Description: The key aim of this study is to determine the relationship between pancreatic β-cell function, resveratrol (RES) and curcumin (CUR), to examine whether or not RES and CUR enhances pancreatic β-cell function. RES and CUR are polyphenols, found predominately within fruits and turmeric, which have been previously reported to contain medicinal properties that are beneficial to diabetes mellitus patients. Previously published studies claim that the therapeutic properties of RES and CUR can be attributed to their anti-inflammatory effects and protection against β-cell dysfunction. This study thus seeks to examine such reported phenomenon by examining the mechanism/s of action of RES and CUR in β-cells. Results indicate that RES and CUR regulate insulin secretion under glucose-stimulated conditions, and increase intracellular levels of cAMP, which plays an important role in insulin secretion and pancreatic β-cell health. The study also showcases that RES and CUR inhibit the activity of phosphodiesterases, which degrade cAMP. The polyphenols RES and CUR thus indeed enhance pancreatic β-cell function and have therapeutic benefits to diabetic patients.

Article Reference: Michael Rouse, Antoine Younès, Josephine M Egan Resveratrol and curcumin enhance pancreatic β-cell function by inhibiting phosphodiesterase activity. J. Endocrinol.: 2014, 223(2);107-17 PubMed 25297556


Article 2:

Article Title: Ultrastructural Alterations of Pancreatic Beta Cells in Human Diabetes Mellitus

Article Description: The aim of this article is to investigate the correlation between pancreatic beta cells and diabetes mellitus, within humans. This is done by focusing on the ultrastructural alterations of beta cells in human diabetes. Throughout the study, beta cells have been retrieved from the pancreas of eight non-diabetic, five type 1 diabetic and eight type 2 diabetic organ donors, and analysed under morphometric electron microscopy. Results have indicated that lower quantities of beta cells are present in patients suffering type 1 and 2 diabetes, compared to non-diabetic patients. Additionally, insulin granules are more represented in non-diabetic patients than in type 2 diabetic patients, while type 1 diabetic patients show minimal changes. Pancreatic beta cells within diabetic patients have also showcased greater apoptosis than beta cells in non-diabetics. These results are expected to improve therapeutic measures for diabetes.

Article Reference: Matilde Masini, Luisa Martino, Lorella Marselli, Marco Bugliani, Ugo Boggi, Franco Filipponi, Piero Marchetti, Vincenzo De Tata Ultrastructural Alterations of Pancreatic Beta Cells in Human Diabetes Mellitus. Diabetes Metab. Res. Rev.: 2017; PubMed 28303682


Article 3:

Article Title: Impairment of pancreatic β-cell function by chronic intermittent hypoxia

Article Description: The central purpose of this study is to demonstrate the link between chronic intermittent hypoxia (CIH) and pancreatic β-cell function. Via experimentation on rodents, the results of this study indicate that mitochondrial oxidative stress, which is produced by CIH, causes decreased pancreatic β-cell function, or increased pancreatic β-cell dysfunction. This is demonstrated by augmented basal insulin secretion, insulin resistance, defective proinsulin processing and impaired glucose-stimulated insulin secretion. This study thus contains direct evidence that CIH impacts β-cell function. As CIH is a hallmark of sleep apnoea, this study also indicates that CIH-impacted β-cell dysfunction could be a possible contributor to type 2 diabetes within sleep apnoea patients. It thus encourages possible future research in this area.

Article Reference: Ning Wang, Shakil A Khan, Nanduri R Prabhakar, Jayasri Nanduri Impairment of pancreatic β-cell function by chronic intermittent hypoxia. Exp. Physiol.: 2013, 98(9);1376-85 PubMed 23709585


Article 4:

Article Title: Protein tyrosine phosphatase-1B modulates pancreatic β-cell mass

Article Description: The goal of this study is to analyse the action/s of protein tyrosine phosphatase 1B (PTP1B), which is an endoplasmic reticulum bound phosphatase that has been previously documented to negatively regulate insulin signalling, in pancreatic islets. Through experimental procedures on rodents and morphometric analysis of their pancreatic cells, the results of this study indicate that mice with PTP1B exhibit increased β-cell area, higher β-cell proliferation and decreased β-cell apoptosis, compared to their wild-type counterparts. This study thus sheds light on the involvement of PTP1B in β-cell physiology, and encourages the potential of PTP1B as a therapeutical target for the treatment of β-cell failure, which is characteristic of type 2 diabetes.

Article Reference: Rebeca Fernandez-Ruiz, Elaine Vieira, Pablo M Garcia-Roves, Ramon Gomis Protein tyrosine phosphatase-1B modulates pancreatic β-cell mass. PLoS ONE: 2014, 9(2);e90344 PubMed 24587334


Lab 4

Antibody: beta Actin Polyclonal Antibody

Host/Isotope: Rabbit / IgG

Working Concentration: 1mg/ml

Tested Application: Western Blot (WB) 1:5000-1:15,000

Secondary Antibody: Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 555

Paper mentioning beta Actin Polyclonal Antibody: Viviana R Lopes, Vesa Loitto, Jean-Nicolas Audinot, Narges Bayat, Arno C Gutleb, Susana Cristobal Dose-dependent autophagic effect of titanium dioxide nanoparticles in human HaCaT cells at non-cytotoxic levels. J Nanobiotechnology: 2016, 14;22 PubMed 27001369


Lab 5

Graph showing the effect of Tm4 on phenotype expression

Lab assessment 5.PNG

Mark Hill (talk) 20:51, 24 April 2017 (AEST) This lab assessment will be marked by the guest presenter and the mark added here when I have received.

Lab 7

Peer Review:

Group 1: Delta Cells

Upon first glance, it is evident that this group has made a lot of consistent progress on the project, which is definitely commendable. A quick check of the history page further reveals that all three team members have been fulfilling their delegated tasks and contributing towards the project, which is also very great to see and a testament to this group’s cooperation and successful interaction. With regards to the contents of the page, indeed I agree with the listed subheadings and do believe that it is important to explain the ‘background’, ‘structure’, ‘function’, etc. of delta cells. However, I would recommend researching additional information regarding the ‘history’ of the delta cell – i.e., when it was first discovered and in which organism, what was it first named, who first named it and so on. The inclusion of this would allow audiences from a non-science background to gain a deeper understanding of the origins of the delta cell. I am glad to see comparisons between humans and animals in the ‘functions’ section of the project, as I do believe that there is a lot of insight to be gained by comparing delta cells across two organisms. I would definitely recommend a similar comparison in the ‘structure’ section so that audiences can be informed whether or not the morphology of the delta cell is congruent throughout different organisms. The inclusion of videos and images within the latter half of the project adds an interactive dimension to the project, which I personally believe is a good thing as it provides readers with a break from reading dense information. The text to visual-aid ratio throughout the first half of the project (‘background’ to ‘pathology’) however, is uneven and in favour of text so I would encourage more images or tables here – ideally a few anatomical pictures of the delta cell should be included in the ‘structure’ section. In regards to referencing, I believe this has been done correctly so well done. In comparison to all of the other groups, this group also has the highest amount of references, a sizeable 20, which is quite good at this stage and additionally an indication of broad research conducted for the topic. While the readability of the project is mostly well, some sentences are weak and require revision. I do believe that editing previously completed work and rephrasing certain fragments of information can add a level of sophistication to the project. For example, a sentence in the ‘background’ section currently reads: “However, more current studies have significantly shown a decrease in numbers of β cells and an increase in numbers of α cells.” I recommend revising this sentence to improve its coherency. Perhaps something along the lines: “Nonetheless, recent studies have revealed a substantial decrease in the quantity of beta cells present within pancreatic Islets of Langerhans alongside a sizeable increase in the number of alpha cells.” To further improve the sentence, one could disclose the specific percentage by which the cells increased or decreased rather than mentioning a general trend. Nevertheless, on a positive note, the general flow of the project, and the order in which information is presented, is great. I would like to congratulate this group on their good work so far and while there is a large amount of work still required to be done before the project can be considered complete, thus far this group has the most content on their page and therefore, by extension, is overall the most informative and highest-quality project of the three projects which I am peer-reviewing. Solid work so far.

Group 2: Ductal Cells

My initial observation of this group’s project is that it does not contain as much information as some of the other groups. Unfortunately, this is an indication of inconsistent contributions by team members, which can be confirmed by browsing through the history page of the project, which reveals a period of inactivity from April 11 – May 1 2017. Nevertheless, I am a supporter of the ‘quality over quantity’ mindset and do understand that it can be difficult to contribute to the project when other assessments are due. The quality of the information presented on the page thus far is good, however a bit too generalised in my personal opinion. While there is mention of ductal cells in the ‘structure’ section of the project, I believe that the pancreas is fixated upon more so than it should be. I would definitely recommend adding a lot more information about the structure of the ductal cells themselves with a strong focus on answering specific questions such as – what is the diameter of the ductal cells, which membrane-enclosed organelles do they have, are they only present in the pancreas, etc. I also believe it would be beneficial for the audience if a comparison was made between the ductal cells within humans and those within animals – do they have the same structure, function and location? Additionally, an anatomical image of ductal cells would be ideal alongside the anatomical image of the pancreas in the ‘structure’ section. I also believe that the following sentence in the introduction: “[The pancreas] makes a number of different enzymes, each of which is responsible for breaking down the different types of food into small particles suitable for absorption” is also too generalised. I would personally list which specific ‘enzymes’ are synthesised so that audiences from a non-science background are informed better and not disadvantaged when reading the project. I also recommend more research and information in the ‘functions’ section of the project, as it seems slightly brief at the moment. The inclusion of pictures or flow diagrams would be useful in this section as well as it would allow readers to follow a diagram alongside written text. On a positive note, it’s great to see that a ‘history’ section has been included. I personally believe that this is quite important for audiences to acquire an understanding of the background and origins of ductal cells. My only two recommendations regrading the ‘history’ section would be to relocate its position in the project, as I don’t think it fits well beneath ‘functions’. I would also encourage another method of formatting the key dates, perhaps a table, as the present dot points make the section appear rather informal and disorganised. Referencing has been done well in this project so great job there however I would definitely encourage using a wider range of resources from hereon as it is hard to find all necessary information within the 5 resources that have been used up until now. I did notice that there is a full reference, rather than hyperlink, following the first sentence in the ‘structure’ section. I assume that this is to remind the team members of the article that has been used for this section. If not, then I would advise removing it from there as a hyperlinked reference is all that is required. The overall coherency and readability of this project is good. Clearly, the project is still in its early stages however it is encouraging to see information or dot points in most sections. The work so far is commendable and no major errors have been made, so well done on that. From the three projects, which I have peer-reviewed, I would say that this project ranks second- highest in terms of both quality and content. Nevertheless, I would definitely encourage more frequent contributions to the project to ensure that it becomes more informative. Congratulations to the team members on their good work so far.

Group 4: Alpha Cells

Upon first glance, this project has the least amount of information present on its page when compared against the other projects. Observing the history page, frequent contributions have been made by team members however the sizes of the contributions are relatively small, contributing to the overall progress of the page. On a positive note, the subheadings on the page are very relevant to the topic which definitely suggests a good start. Most sections also have dot points under them thus implying that a draft of the section is slowly being constructed, which is also encouraging. The inclusion of a table and numerous images is commendable as it portrays a range of visual aids, which I believe is necessary to actively capture the audience’s attention. I would encourage the inclusion of a video to further captivate audiences and reinforce what is written in text as videos usually provide clearer and more colloquial explanations, which would be valuable for readers without a science background. The general readability and flow of the ‘disease and abnormalities’ section, which is the only section with paragraphs of information, is good. It is encouraging to see that the image has been integrated with, and referred to, in the text. Though, I would recommend figure captions as currently the section reads “As seen in figure 2…” however there is no indication of which image ‘figure 2’ is. The 4 references used thus far have been formatted correctly, but I advise the use of more references so that a broader range of information can be disclosed on the page. Overall, this project has made significantly less progress than the other projects although it is off to a good start. I would encourage team members to conduct more research and contribute larger amounts of information towards the project. A possible suggestion for further research would be to compare the role, structure and function of alpha cells across different organisms, such as humans and animals. Overall, a large amount of work is still required to be done before the project can be considered complete. When compared to the other projects I have peer-reviewed, I would say that this project is presently the least informative.

Excellent (9/10)

Tutorial 1

Image

Human R3 RPTP members.png

Student Image Template

Reference Styles:

https://www.ncbi.nlm.nih.gov/pubmed or PubMed

Search Plasma Membrane

PMID: 28260084 NO LINK

PMID 28260084 LINK

Si Shi, Kunbin Guo, Xiangyu Wang, Hao Chen, Jianbin Min, Shuhua Qi, Wei Zhao, Weirong Li Toxicity study of oxalicumone A, derived from a marine-derived fungus Penicillium oxalicum, in cultured renal epithelial cells. Mol Med Rep: 2017; PubMed 28260084


Note - This image was originally uploaded as part of a student project and may contain inaccuracies in either description or acknowledgements. Please contact the site coordinator if the uploaded content does not meet the original copyright permission or requirements, for immediate removal.

Tutorial 2

Toluene

Webpage: http://www.sigmaaldrich.com/catalog/product/sial/244511?lang=en&region=AU&cm_sp=Insite-_-prodRecCold_xviews-_-prodRecCold10-7

Biological Hazards of Toluene:

1. Flammable

2. Acute Toxicity; Skin Irritant, Eye Irritant

3. Respiratory Sensitization, Germ Cell Mutagenicity, Carcinogenicity, Reproductive Toxicity

Tutorial 4

Task:

Antibody: Monoclonal Anti-Cytokeratin

Host: Produced in mice

Isotype: IgG1

Species Reactivity: Bovine, frog, human, rat, kangaroo rat, mouse

Reference: http://www.sigmaaldrich.com/catalog/product/sigma/c2931?lang=en&region=AU

Secondary Antibody: PE anti-mouse IgG1

Secondary Antibody Description: The RMG1-1 monoclonal antibody reacts with immunoglobulin G1 (IgG1) in all tested mouse haplotype (Igh-a and b),

Reference: https://www.biolegend.com/en-us/products/pe-anti-mouse-igg1-6494


2017 Course Content

Moodle

Lectures: Cell Biology Introduction | Cells Eukaryotes and Prokaryotes | Cell Membranes and Compartments | Cell Nucleus | Cell Export - Exocytosis | Cell Import - Endocytosis | Cytoskeleton Introduction | Cytoskeleton - Microfilaments | Cytoskeleton - Microtubules | Cytoskeleton - Intermediate Filaments | Cell Mitochondria | Cell Junctions | Extracellular Matrix 1 | Extracellular Matrix 2 | Cell Cycle | Cell Division | Cell Death 1 | Cell Death 2 | Signal 1 | Signal 2 | Stem Cells 1 | Stem Cells 2 | Development | 2017 Revision

2017 Laboratories: Introduction to Lab | Fixation and Staining |


2017 Projects: Group 1 - Delta | Group 2 - Duct | Group 3 - Beta | Group 4 - Alpha

Dr Mark Hill 2015, UNSW Cell Biology - UNSW CRICOS Provider Code No. 00098G