User:Z5059696

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

Z5059696 (talk) 16:05, 7 March 2017 (AEDT)

Z5059696 (talk) 15:07, 14 March 2017 (AEDT)

Z5059696 (talk) 15:14, 21 March 2017 (AEDT)

Z5059696 (talk) 15:25, 28 March 2017 (AEDT)

Z5059696 (talk) 15:07, 4 April 2017 (AEST)

Z5059696 (talk) 14:54, 11 April 2017 (AEST)

Z5059696 (talk) 15:00, 16 May 2017 (AEST)

Tutorial

Student Image Template

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.

Referencing

Pubmed

Plasma membrane search

  • PMID: 28260162
  • PMID 28260162

Marjut Niinivirta, Gunilla Enblad, Per-Henrik Edqvist, Fredrik Pontén, Anca Dragomir, Gustav J Ullenhag Tumoral cubilin is a predictive marker for treatment of renal cancer patients with sunitinib and sorafenib. J. Cancer Res. Clin. Oncol.: 2017; PubMed 28260162


Image

Human R3 RPTP members.png

Reference

Javier U Chicote, Rob DeSalle, Antonio García-España Phosphotyrosine phosphatase R3 receptors: Origin, evolution and structural diversification. PLoS ONE: 2017, 12(3);e0172887 PubMed 28257417


Image

Fmr1 mutants.jpg

The phagocytic activity of hemocytes in Drosophila melanogaster Fmr1 mutants is defective. There are lower levels of phagocytosis by immune blood cells in the mutant Drosophilia than the wild type.


Phagocytosis by circulating immune cells is defective in Fmr1 mutants. (A) Fmr1 mutants (blue, n = 6) exhibit reduced total phagocytosis by immune blood cells (hemocytes) relative to wild types (gray, n = 6), as shown by internalization of dead S. aureus labeled with pHrodo, a pH-sensitive dye. Shown here are representative fluorescence images and quantifications. (B and C) Fmr1 mutants exhibit less phagocytic activity per hemocyte. Hemocytes were genetically labeled by hemlΔ-Gal4 driving UAS-GFP expression in both control and Fmr1 mutants. Shown here are representative fluorescence images (B) and quantification of pHrodo fluorescence (C; wild type, n = 10; Fmr1, n = 9), hemocyte-specific GFP, and phagocytic activity normalized to hemocyte-specific GFP. a.u., arbitrary units. (D) Fmr1 mutants also exhibit a defect in hemocyte engulfment of S. aureus, an early stage of phagocytosis, as measured by the injection of Alexa Fluor 594–labeled dead S. aureus, followed by Trypan blue quench (controls, n = 10; Fmr1 mutants, n = 10). **, P < 0.01; ****, P < 0.0001; not significant (n.s.), P > 0.05. P-values were obtained by Mann-Whitney U test. Means ± SEM are shown, and variance is shown by scatter plot. (A, B, and D) Bars: (A and D) 100 µm; (B) 50 µm.


Reference

Reed M O'Connor, Elizabeth F Stone, Charlotte R Wayne, Emily V Marcinkevicius, Matt Ulgherait, Rebecca Delventhal, Meghan M Pantalia, Vanessa M Hill, Clarice G Zhou, Sophie McAllister, Anna Chen, Jennifer S Ziegenfuss, Wesley B Grueber, Julie C Canman, Mimi M Shirasu-Hiza A Drosophila model of Fragile X syndrome exhibits defects in phagocytosis by innate immune cells. J. Cell Biol.: 2017, 216(3);595-605 PubMed 28223318


Copyright Statement


Rockefeller University Press Copyright Policy This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.jcb.org/misc/terms.shtml). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

Student Image Template

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.

Mark Hill (talk) 14:56, 20 April 2017 (AEDT) Good image upload, all required associated information provided here, but you needed this to be in the image summary box associated with the image, not on your student page here. This was shown in my tutorial example. The file name (Fmr1 mutants.jpg) could have also been more descriptive ( Fmr1 Fly mutant immune cells.jpg). (4/5)

Lab 1:Preperation and Fixation

Lead Lead Safety Data Sheet

Mark Hill (talk) 19:20, 24 April 2017 (AEST) Identify a chemical SDS and the risks and hazards of that chemical in text. Add a link to the original SDS. Where are the risks and hazards, they were supposed to be added here as well as the link, as described in the lab question.

Lab 2: Group Project Articles

R H Unger, E Aguilar-Parada, W A Müller, A M Eisentraut Studies of pancreatic alpha cell function in normal and diabetic subjects. J. Clin. Invest.: 1970, 49(4);837-48 PubMed 4986215


This article is relevant to our group project because it discusses the function of the alpha cell and also explores its relationship with diabetes. The glucagon levels of patients (diabetic and non diabetic) were raised through arginine exposure. The patients were given glucose and this induced hyperglycemia resulted in the decrease of the glucagon levels. It was found that the diabetic patients resulted in a significantly higher rise in glucagon when the arginine was present compared with the non-diabetic patients. The article observed raised glucagon levels in severe diabetic ketoacidosis prior to the patient being administered with insulin. This article suggests that in diabetes mellitus alpha cell function is increased, which results in raised glucose concentration in the blood which could be playing a role in the disease.


J Jensen, R S Heller, T Funder-Nielsen, E E Pedersen, C Lindsell, G Weinmaster, O D Madsen, P Serup Independent development of pancreatic alpha- and beta-cells from neurogenin3-expressing precursors: a role for the notch pathway in repression of premature differentiation. Diabetes: 2000, 49(2);163-76 PubMed 10868931

This article is relevant to our alpha cell group project as it explains the origin and development of the alpha cell. The article states that the notch pathway is involved in preventing the alpha cell to differentiate prematurely.

Pancreatic duodenal homeobox factor 1 (PXD1) is a transcription factor involved in pancreatic development. The study states that PXD1+ epithelial cells are a class of these transcription factors that are distinct by their expression of the Neurogenin3 (Ngn3) protein. Ngn3 is a transcription factor which, in a basic helix- loop- helix cascade, acts upstream of NeuroD. And NeuroD+ cells form rapidly from Ngn3 expressing cells.

The study shows that Ki-67 ,a proliferating cell marker, is found in Ngn3+ cells which supports that Ngn3+ cells are endocrine precursor cells. This highlights the idea that PXD1+/Ngn3+ epithelial cells develop into alpha cells. Activation of NeuroD expression begins alpha cell development through gene activation and inhibition. The expression of Notch1 in PDX epithelial cells inhibits the Ngn-NeuroD cascade. This notch signaling represses early endocrine cell differentiation.


E Vieira, A Salehi, E Gylfe Glucose inhibits glucagon secretion by a direct effect on mouse pancreatic alpha cells. Diabetologia: 2007, 50(2);370-9 PubMed 17136393

This article is relevant and important to the project as it discusses the function (and lack of function) of the alpha cell. This article discusses the inhibitory effect of glucose on the secretion of glucagon in mouse subjects. The article suggests that this inhibitory effect is due to direct impact on alpha cells. Incubated mouse islet cells were exposed to different levels of glucagon, insulin and somatostatin. The concentrations of cytoplasmic calcium (Ca2+) in the alpha cells were measured. It was found that neither insulin (beta cell factor) nor somatostatin facilitate glucose inhibition of glucagon secretion. Glucose lowers the Ca2+ levels of the alpha cells independently through the enzyme sarco(endo)plasmic reticulum Ca(2+)-ATPase, which prevents depolarizing in the cells, inhibiting glucagon secretion.


H Heimberg, A De Vos, K Moens, E Quartier, L Bouwens, D Pipeleers, E Van Schaftingen, O Madsen, F Schuit The glucose sensor protein glucokinase is expressed in glucagon-producing alpha-cells. Proc. Natl. Acad. Sci. U.S.A.: 1996, 93(14);7036-41 PubMed 8692940

This article is relevant to our group project as it explains the mechanism of the role of alpha cells in glucose homeostasis. Using rat models, the study states that glucokinase expression occurs in alpha cells when they produce glucagon. Glucokinase acts as a sensor to glucose levels in the blood, when the glucose levels rise glucokinase signals that glucagon must be released to decrease this hyperglycemia. The study also reported that Glut2 and glucokinase were not both expressed during this signaling process suggesting co-expression is not necessary for the regulation mechanism.


Mark Hill (talk) 19:20, 24 April 2017 (AEST) These papers are relevant and could be used in the group project. You have lost marks for not completing the first part of the assessment (6/10).

Lab 3

Vinculin antibody

species- human, mouse

host- Rabbit

IgG

Monoclonal


Anti Vinculin antibody

Species- Mouse, Rat, Hamster, Human

Host- mouse

Isotype- IgG1 kappa

Monoclonal

Paper that has used antibody

Mark Hill (talk) 20:43, 24 April 2017 (AEST) Good (3.5/5) You have not described the antibody by its name (42H89L44) and not included the working concentration (shown below)

  • Flow Cytometry (Flow) 2-4µg/10^6 cells
  • Immunocytochemistry (ICC) 2-4µg
  • Immunofluorescence (IF) 2-4µg
  • Western Blot (WB) 1-3µg/ml


You should have used the referencing technique (below) shown in the lab tutorial, as your link is not informative, and you should have at least included the paper name.

Daniel J T Kyle, Antonios Oikonomou, Ernie Hill, Ardeshir Bayat Development and functional evaluation of biomimetic silicone surfaces with hierarchical micro/nano-topographical features demonstrates favourable in vitro foreign body response of breast-derived fibroblasts. Biomaterials: 2015, 52;88-102 PubMed 25818416


Lab 5

Neuron phenotypes and Tm4.png

Lab 7: Peer reviews

Group 1

Overall it appears you have a lot of information and the page is well structured with different headings and subheadings. The background information was a good general summary and included the function of all the secretary cells in the pancreas. However it focused a lot on the percentages of the cells in the Langerhans too extensively. I recommend choosing just one of the stated percentages. I think a history section would be beneficial rather than the background paragraph. The development information was brief, however was all very relevant and succinct information. I did see that you discussed more developmental information further in the page under the signaling heading. I recommend joining this information together so they are under one heading. I can see that there is more information to come for the structure section, but what you do have is very well layed out and well described. I liked how you referred to another section of the page so it all comes together. The functions information was very thorough and detailed and well referenced. I recommend including a diagram so it is easier to follow. The pathology section was super informative and easy to follow. I liked the inclusion of the videos and the tables. However I do recommend having a summary of each video and some more information about the pathological processes of each disease. Overall, well done, your project is very progressed and top quality.

Group 2

Overall, the project appears very neat and well layed out. It is not very extensive so far but it is a good start. The introduction is very succinct; it gives a great summary of the whole project. The structure section includes a great description of the ductal cells. However, the paragraph veered off track and there is a lot of information that doesn’t come under the structure heading such as development and cancers. I recommend including the developmental information under the development heading. The image was useful, however a description and reference to it in the text would be beneficial. The function section was informative and well referenced, but could be more in depth. The history section had core information; I recommend a table with dates and text so it is neater and easier to read. The developmental heading was very extensive and had great information. I recommend a diagram or flow chart to back up the text. The signaling and interactions section is informative; I do think it could be a subheading under development. The image was good but needs to be explained. I can see you have found articles for the pathology/ abnormalities section, which is a good start. Overall it is a good draft, I only had minor recommendations.

Group 3

At first glance your project seems very organised and neat, it is appealing to read. The introduction section is very extensive and gives a very detailed and informative description of beta cells. I can also see you guys discussing and helping each other, which is great. I loved the table for the history section, it is well layed out and has useful information. The structure information and mice comparison headings are super detailed and useful. I would recommend maybe breaking the text up into smaller paragraphs or use sub headings because it is a big block of text. Also more images would make it more eye catching. The function, development and signalling information is brief, but it is a good start and just needs to be drawn-out. The role in disease section and treatments heading were very well done. The collapsible video is a nice addition; a description of the video would be useful. The information is detailed and well referenced. The subheadings made it easy to follow. Good use of referencing, you have clearly done lots of research. Overall, well done you guys have progressed well. Most of the headings are almost done, I would recommend including more images.


Good banged feedback (8/10)

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. 00098GMark 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.