User:Z5019526

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.

Attendance

Z5019526 (talk) 16:04, 7 March 2017 (AEDT)

Z5019526 (talk) 15:27, 14 March 2017 (AEDT)

Z5019526 (talk) 15:25, 21 March 2017 (AEDT)

Z5019526 (talk) 15:36, 28 March 2017 (AEDT)

Z5019526 (talk) 17:06, 4 April 2017 (AEST)

Z5019526 (talk) 15:07, 11 April 2017 (AEST)

(Attended May 2 lab on Flourescent Dye but forgot to take down attendance)

Z5019526 (talk) 15:21, 9 May 2017 (AEST)

Z5019526 (talk) 15:42, 16 May 2017 (AEST)


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


Individual Assessments

Lab 1

Top (A) and bottom (B) view and size (C) of the cell membrane.jpeg

Top and bottom view and size of the cell membrane. [1] 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.


Mark Hill (talk) 12:21, 28 March 2017 (AEDT) All good with the image upload. You only needed to add the image a title and the reference to your page (as you have above) the additional information goes with the actual image file. Note, try a simpler name and if you had looked ahead you would have seen this image has already been added to the Wiki. (5/5)

Lab 2

Ethanol is a clear, colourless liquid that is highly flammable and extremely irritant. To prevent the hazardous effects of ethanol, it is important to:

  • Keep it away from heat, open flames and hot surfaces
  • Keep the container tightly sealed/closed
  • Use explosive-proof electrical/ventilating equipment
  • Use only non-sparking tools and avoid sources of ignition
  • Wear protective gloves/clothing and eye/face protection.

If ethanol comes into contact with the skin, immediately take off all contaminated clothing and flush affected area with water for 15 minutes. In the case of a fire, use dry sand, dry chemical or alcohol-resistant foam for extinction. It is important to keep it cool and store it in a well-ventilated place, as well as dispose its contents to an approved waste disposal plant.

Safety Data Sheet for Ethanol http://sydney.edu.au/medicine/medsci/whs/msds/e/ethanol__Sigma__20130416.pdf


Research papers on duct cells

Tetsuyuki Miyazaki, Yoshihiro Ohishi, Yoshihiro Miyasaka, Yasunori Oda, Shinichi Aishima, Keigo Ozono, Atsushi Abe, Eishi Nagai, Masafumi Nakamura, Yoshinao Oda Molecular Characteristics of Pancreatic Ductal Adenocarcinomas with High-Grade Pancreatic Intraepithelial Neoplasia (PanIN) Are Different from Those without High-Grade PanIN. Pathobiology: 2017; PubMed 28291966

Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and develops from cells lining the ducts. It was reported that a patient suffering from PDAC without high-grade pancreatic intraepithelial neoplasia (PanIN) in the surrounding areas had worse prognoses than a patient with PDAC with high-grade PanIN. This paper researches the molecular characteristics of PDACs with and without high-grade PanIN. They divided 100 patients with PDAC in 2 groups: one group with the PDACs with PanIN-2 or PanIN-3 in the background and the other group without PanIN-2 and PanIN-3. Immunohistological staining was used to evaluate SMAD4, p53 and p16 expressions in the invasive ductal carcinoma. The results showed that the group without PanIN-2 and -3 had sufficiently more continual high p53 and low SMAD4 expression, concluding that PDACs without high-grade PanIN may develop through an alternative pathway besides the PANIN-carcinoma sequence. Therefore, the molecular characteristics in the pancreatic ductal adenocarcinomas with high-grade PanIN were significantly different from those in the pancreatic ductal adenocarcinomas without high-grade PanIN.


Junpei Yamaguchi, Andrew S Liss, Alexandra Sontheimer, Mari Mino-Kenudson, Carlos Fernández-Del Castillo, Andrew L Warshaw, Sarah P Thayer Pancreatic duct glands (PDGs) are a progenitor compartment responsible for pancreatic ductal epithelial repair. Stem Cell Res: 2015, 15(1);190-202 PubMed 26100232

Pancreatic duct glands (PDGs) are the main site of proliferation of pancreatic ductal epithelium, and one of its molecular features includes marking stem cell niches, however, their function remains unknown. The purpose of this research was to explore the role of PDGs as a progenitor niche using human and mouse models. This was done by grouping the cells by immunohistochemistry and microarray analysis. It was found that PDGs are the principal site of proliferative activity in the epithelium of the pancreas as a response to acute inflammatory injury. The proliferative cells would then relocate to the pancreatic duct and obtain a more mature pancreatic ductal phenotype, while losing their PDG-specific markers. This suggests that the pancreatic duct glands are an epithelial progenitor compartment that makes way for mature differentiated progeny and is important in pathways for embryonic and stem cell niches. This leads to the conclusion that pancreatic duct glands amount to an epithelial progenitor niche important in the repair of the pancreatic duct after inflammatory injury.


Junpei Yamaguchi, Mari Mino-Kenudson, Andrew S Liss, Sanjib Chowdhury, Timothy C Wang, Carlos Fernández-Del Castillo, Keith D Lillemoe, Andrew L Warshaw, Sarah P Thayer Loss of Trefoil Factor 2 From Pancreatic Duct Glands Promotes Formation of Intraductal Papillary Mucinous Neoplasms in Mice. Gastroenterology: 2016, 151(6);1232-1244.e10 PubMed 27523981

There is an insignificant amount of information regarding the origin of pancreatic intraductal papillary mucinous neoplasms (IPMN). Characteristics of side-branch IPMNs are found in pancreatic duct glands (PDG) that also convey gastric mucins. The aim of this research was to discover whether pancreatic duct glands were a precursor compartment for IPMNs, as well as to explore the role of TFF2 and the gastric mucosa - as both are involved in epithelial repair and tumour suppression (TFF2 stands for Trefoil factor family 2 and is a protein expressed by PDGs). In the study, they obtained pancreatectomy specimens taken from 20 patients with chronic pancreatitis. These samples were analyzed by immunohistochemistry to detect TFF2 and cell proliferation. In the histologic analyses of human IPMNs, the results showed that proliferation mainly took place in the basal segments containing pancreatic duct glands. This led to the conclusion that PDGs form the basal segment and can potentially work as a progenitor compartment. In addition, it was discovered that TFF2 has tumor-suppressor activity in the mouse pancreas and prevents formation of mucinous neoplasms.


Xuejun Xu, Zhiping Zhao, Sixiang Guo, Jian Li, Songsong Liu, Yu You, Bing Ni, Huaizhi Wang, Ping Bie Increased semaphorin 3c expression promotes tumor growth and metastasis in pancreatic ductal adenocarcinoma by activating the ERK1/2 signaling pathway. Cancer Lett.: 2017; PubMed 28315433

Pancreatic ductal adenocarcinoma (PDAC) is classified by neural changes and abnormal expression of neural-specific factors. Semaphorins, a bearer of signals, is a main contributor in axon guidance, the immune response and tumor progression. The clinical importance of Semaphorin 3c and its role in the growth and metastasis of pancreatic ductal adenocarcinoma remains unknown. This study found that overexpression of Semaphorin 3c inhibited cell apoptosis, thus promoted pancreatic cancer proliferation and regulated pancreatic cancer cell EMT by activating the ERK1/2 signalling pathway. Aberrant Semaphorin 3c expression was unmistakeably related with a specific tumor stage and correlated with poor survival of PDAC patients. Therefore, it was concluded that Semaphorin 3c is overexpressed and was linked with tumor stage in pancreatic cancer as it promoted tumor growth and metastasis by activating ERK1/2 signaling pathway.


Mark Hill (talk) 19:20, 24 April 2017 (AEST) Very good (10/10) For the SDS you could have also identified the Globally Harmonized System and the signal words and P280 Response P303 + P361 + P353. The 4 papers are relevant, hopefully they can be used in the final group project. You should also look at the OMIM entry for some of the proteins mentioned in these papers.

Lab 3

In class quiz

Lab 4

1. Identify a cytoskeletal antibody: Spectrin beta-1 Monoclonal Antibody (4C3)

2. Identify the species deriving the antibody: Human, Mouse, Rat

3. Identify the working concentration for the antibody: Monoclonal antibody

4. Identify a secondary antibody that could be used with this antibody: Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488

5. Identify a paper that has used this antibody.

Ceylan Polat, Ahmet Karataş, Mustafa Sözen, Ferhat Matur, Hakan Abacıoğlu, Mehmet Ali Öktem [Optimization of ELISA and immunoblot methods for the detection of IgG antibodies against old world hantaviruses in wild rodents]. [Yabani kemiricilerde Eski Dünya hantavirus IgG antikorlarının saptanması için ELISA ve immünoblot yöntemlerinin optimizasyonu.] Mikrobiyol Bul: 2016, 50(2);245-55 PubMed 27175497


Mark Hill (talk) 20:43, 24 April 2017 (AEST) You have not understood the questions correctly here (3/5)

  • You should have included a link to the original resource Spectrin beta-1 Monoclonal Antibody (4C3).
  • Species deriving the antibody is mouse, that is what animal was the original antibody raised in. It reacts with the protein from Human, Mouse, Rat.
  • The working concentration is just that, a working concentration or dilution factor for the original antibody. Flow Cyt 1/50., IHC-P 1/200, ICC/IF 1/10 - 1/200, WB 1/100, IHC-P 1/20 - 1/200.
  • You have identifed correct secondary antibodies and a related reference.

Lab 5

Lab 5 Assessment.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

Group 1, you guys have done an amazing job so far. Your project is well structured with its appropriate headings such as Structure, Signalling and Current Research, as well as subheadings underneath certain sections such as Cell-Matrix Interactions 'Cholecystokinin B receptor (CKKBR)'. The organization of your page is very helpful for the viewer as they scroll through your page. I do however, suggest that you add a brief Introduction or Outline at the beginning of your page, so that the viewer has an idea of the contents of your page. Furthermore, a 'History' section of delta cells, with each point referenced, would be a good start to your page as well. Reading through the information, I can see that it is concise and easy to understand, providing a good understanding of delta cells. With the amount of references that have been correctly citied at the bottom of your page, it is clear that you guys have thoroughly researched your topic so far. The visual elements of your page, such as the videos and pictures, are great as it gives the viewer a break from big blocks of text. The consistency of the videos underline a flow to the project, however I suggest that you guys add a few more pictures (preferably around the top of your page) so there is a balance between text and pictures. It would be good to add a few more definitions in the glossary as well - for example, what is somatostatin? - and your page would be awesome once you have completed the empty subheadings and tables. Overall, your project is well underway for receiving excellent marks. Great job, Group 1!

Group 3

Group 3, you are off to a great start. The Introduction is helpful, but I think you should focus more specifically on Beta cells rather than elaborating on the human pancreas. There should also be a brief outline stating what topics your project will cover. Just a heads up that there is a discussion section where your group can talk about problems with the project (instead of on your actual project page, where viewers can see it). The table in the 'History' section has been made excellently, as each point is concise and correctly referenced, definitely providing a great tool of learning for the viewer. As with the pictures added in the project, they should have a caption underneath or beside it, briefly explaining what it shows. Scrolling through your project, I noticed that there is plenty of text (which is good), however as a whole, the text looks too dense. I suggest breaking your big blocks of text every now and then by dividing it into subheadings or inserting a relevant picture or a video. Though there is still plenty of information to add, Group 3 is on the right track - placing subheadings and dot points under headings that have not been covered yet is a good method in making sure relevant information is covered, which is what you guys have done. I believe this project has the potential to receive good marks.

Group 4

Group 4 - while your project is well underway, there is still a substantial amount of work that needs to be done in order to make it great. A positive aspect of your project is the use of visual elements. It is good that you have added various pictures throughout the project, however, each picture requires a caption describing what it is about. Some also seem out of place, so I suggest inserting a few paragraphs of text accompanying the picture next to it. There is no need to hide the videos that you have uploaded and I suggest that you put them out in the open, otherwise viewers can miss it. I would suggest also adding text underneath the video - just a short description of what the video is about. Various subheadings lack any bit of information, such as Introduction, Structure and Current Research. The dot point structure of information in particular sections such as Pancreas Development, Endocrine Cells and Notch Signalling should be edited to full sentences to achieve flow of content. It also will make it easier to understand. Significantly more detail and content is needed throughout the project. Furthermore, the reference list at the bottom of the page is incorrectly referenced, as there should be a blue PubMed link that takes us to the article (however, there is none). There should be no website links, which is what I see under 'Regeneration'. It would also be helpful to add terms in the glossary, such as PDX1and Progenitor. Overall Group 4, it is a solid start to the project but more work definitely needs to be done.

(8/10)


  1. Weidong Zhao, Yongmei Tian, Mingjun Cai, Feng Wang, Jiazhen Wu, Jing Gao, Shuheng Liu, Junguang Jiang, Shibo Jiang, Hongda Wang Studying the nucleated mammalian cell membrane by single molecule approaches. PLoS ONE: 2014, 9(5);e91595 PubMed 24806512