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Lab Attendance

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Links

Cell_Biology_Introduction

TEDTALKS


Cells

Red White Blood cells 01.jpg


Individual Assignments

Lab 1

Composition of Mammalian Proteins.png

Figure 5. Functional domain composition of the mammalian midbody proteins. Pink sections represent proteins composed only of eukaryotic-specific functional domains (i.e. they have no homologues in prokaryotes, meaning that they probably appeared after the divergence of eukaryotes and prokaryotes); green sections represent proteins exclusively composed of domains shared by prokaryotes and eukaryotes (i.e. suggesting that these domains may have a more ancient origin since they may have arisen before eukaryotic divergence); yellow sections represent proteins composed by a combination of both types of domains. (A) Domain composition of 152 components of the mammalian midbody having detectable functional domains. The three remaining proteins have no functional domain detected above threshold. (B) Domain composition of 88 components inferred to be present in LECA having detectable functional domains. (C) Domain composition of the 64 Unikont-specific components. doi:10.1371/journal.pone.0005021.g005 [1]

Citation: Eme L, Moreira D, Talla E, Brochier-Armanet C (2009) A Complex Cell Division Machinery Was Present in the Last Common Ancestor of Eukaryotes. PLoS ONE 4(4): e5021. doi:10.1371/journal.pone.0005021

Editor: Jason E. Stajich, University of California, Berkeley, United States of America

Received: January 21, 2009; Accepted: March 2, 2009; Published: April 7, 2009

Copyright: © 2009 Eme 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

1.) Referencing image:

Refer to image above


2.) Task:Identify a recent research article (not review) that uses either confocal microscopy or super-resolution microscopy as one of the study's techniques. Explain briefly (1 paragraph) how the microscopy technique specifically contributed to the article's findings.

Chosen article (from PLOS ONE): Proteasome Particle-Rich Structures Are Widely Present in Human Epithelial Neoplasms: Correlative Light, Confocal and Electron Microscopy Study

With the use of confocal and electron microscopy, Necchi et al. have investigated the presence of proteasome-rich cytoplasmic structures (PaCS)in human neoplasms. Specifically, confocal microscopy allowed them to inspect a focal point of hyperplasia in a specimen of Helicobacter Pylori(H. pylori) infected gastric epithelium. The images obtained shoed that the neoplastic cells in question were enriched by SHP2 and ERK proteins. This information supports the known relationship between these proteins and H. pylori instigated gastric carcinoma. Though there is no direct link between PaCS and neoplasia further research may illuminated the role of PaCS systems in carcinogenesis.


Citation: Necchi V, Sommi P, Vanoli A, Manca R, Ricci V, et al. (2011) Proteasome Particle-Rich Structures Are Widely Present in Human Epithelial Neoplasms: Correlative Light, Confocal and Electron Microscopy Study. PLoS ONE 6(6): e21317. doi:10.1371/journal.pone.0021317

Editor: Per Westermark, Uppsala University, Sweden

Received: December 16, 2010; Accepted: May 30, 2011; Published: June 17, 2011

Copyright: © 2011 Necchi 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.


--Mark Hill (talk) 09:46, 30 April 2013 (EST) This is a good explanation. Next time please use the pubmed extension to insert the reference formatted as required on the website and as part of this assessment item (as shown below). shoed = showed, always check your spelling, small errors (typos) suggest to examiners that you have not read through your own work.

Vittorio Necchi, Patrizia Sommi, Alessandro Vanoli, Rachele Manca, Vittorio Ricci, Enrico Solcia Proteasome particle-rich structures are widely present in human epithelial neoplasms: correlative light, confocal and electron microscopy study. PLoS ONE: 2011, 6(6);e21317 PubMed 21695063


Lab 3

4 Articles and their summaries:

1.) Who Needs Microtubules? Myogenic Reorganization of MTOC, Golgi Complex and ER Exit Sites Persists Despite Lack of Normal Microtubule Tracks

This article aims to better understand the process of structural reorganization which occurs during skeletal muscle differentiation. The focus is placed on the Golgi complex, endoplasmic reticulum exit sites and their ability to move and differentiate despite their lack of normal microtubule tracks. The lack of knowledge is attributed to the fact that these changes to the secretory pathway happen almost simultaneously. By using taxol, nocodazole and GSK3-beta inhibitor it was possible to interrupt the microtubule network and uncouple the reorganization. This investigation has revealed new insight into the structure and functional reorganization of both the Golgi complex and ER during myogenisis.

Citation: Zaal KJM, Reid E, Mousavi K, Zhang T, Mehta A, et al. (2011) Who Needs Microtubules? Myogenic Reorganization of MTOC, Golgi Complex and ER Exit Sites Persists Despite Lack of Normal Microtubule Tracks. PLoS ONE 6(12): e29057. doi:10.1371/journal.pone.0029057

Editor: Michael Klymkowsky, University of Colorado, Boulder, United States of America

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.


2.)The Golgin Tether Giantin Regulates the Secretory Pathway by Controlling Stack Organization within Golgi Apparatus

This article looks at the connection between Giantin (a regulation protein) and the function and structure of the Golgi apparatus. By using of drugs (nocodazole) which inhibits the action on Giantin it was found that there was a notable difference in the movement of the Golgi. The Golgi partitioned into a ribbon like form rather than the normal stacks. It was also found that in area where there was a deficiency in Giantin there was a notable increase in transport of cell surface proteins. Furthermore, Drosophila cells known to lack Giantin show the organisation of the Golgi to be dispersed. Ultimately this information suggests that the Giantin protein in the Golgi can be at least partially responsible for the regulation of transport and structure of the Golgi apparatus.

Citation: Koreishi M, Gniadek TJ, Yu S, Masuda J, Honjo Y, et al. (2013) The Golgin Tether Giantin Regulates the Secretory Pathway by Controlling Stack Organization within Golgi Apparatus. PLoS ONE 8(3): e59821. doi:10.1371/journal.pone.0059821

Copyright: © 2013 Koreishi 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.


3.) Golgi Cisternal Unstacking Stimulates COPI Vesicle Budding and Protein Transport

In this article Wang et al. compare the efficiency at which the Golgi transports proteins to the cell surface when it is varying degrees of compactness. Through the use of an assay it was found that more protein was transported when the Golgi was unstacked. This information can suggest that the amount of stacking within the cisternae of the Golgi could be directly related to the rate of protein transport. In addition, it implies that transport could in fact be maximized in cells by unpacking the Golgi.

Citation: Wang Y, Wei J-H, Bisel B, Tang D, Seemann J (2008) Golgi Cisternal Unstacking Stimulates COPI Vesicle Budding and Protein Transport. PLoS ONE 3(2): e1647. doi:10.1371/journal.pone.0001647

Copyright: © 2008 Wang 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.

4.)Polarization of the Golgi apparatus and the microtubule-organizing center in cultured fibroblasts at the edge of an experimental wound.

In this article Kupfer et al. explore the movement of the Golgi apparatus and microtubule organising centre in experimentally wounded fibroblasts through the use of immunolabelling. They compare the orientation of these two organelles to each other in two positions; at the edge of the wound and in a culture of cells that have been removed from the wound. In the prior the two were relatively close to the face of the wound and in the latter they were randomly orientated. This change in position suggests that the ma play a role in the cell movement.

Citation: Kupfer A, Louvard D, Singer S-J (1982)Polarization of the Golgi apparatus and the microtubule-organizing center in cultured fibroblasts at the edge of an experimental wound. Proc Natl Acad Sci U S A 79(8): 2603–2607/PMC346248

Copyright:All of the material available from the PMC site is provided by the respective publishers or authors. Almost all of it is protected by U.S. and/or foreign copyright laws, even though PMC provides free access to it. (See Public Domain Material below, for one exception.) The respective copyright holders retain rights for reproduction, redistribution and reuse. Users of PMC are directly and solely responsible for compliance with copyright restrictions and are expected to adhere to the terms and conditions defined by the copyright holder. Transmission, reproduction, or reuse of protected material, beyond that allowed by the fair use principles of the copyright laws, requires the written permission of the copyright owners. U.S. fair use guidelines are available from the Copyright Office at the Library of Congress.

Upload a relevant image:

The relationship between the Golgi and microtubules.png

Lab 4

Product name (antibody):E-Selectin

Data sheet link: [E-Selectin Data Sheet] --Mark Hill 13:40, 12 June 2013 (EST) This should only have a single bracket for external links.

type of adhesion junction it act against: adhesion junctions in endothelial cells

type of antibody: monoclonal

species it is raised in: mice

species it reacts against: involved in cellular interactions with leukocytes

types of application uses:

  • detection of E-Selectin of human origin by Western Blotting (starting dilution 1:200, dilution range 1:100- 1:1000)
  • immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml of cell lysate)]
  • immunofluorescence (starting dilution 1:50, dilution range 1:50-1:500)
  • flow cytometry(1 µg per 1 x 10 6 cells)
  • solid phase ELISA (starting dilution 1:30, dilution range 1:30-1:3000)

references using antibody:

1. Varki, A. 1994. Selectin ligands. Proc. Natl. Acad. Sci. USA 91: 7390-7397.

2.Lasky,L.A. 1995. Selectin-carbohydrate interactions and the initiation of the inflammatoryresponse. Annu. Rev. Biochem. 64: 113-139.

3. Tedder, T.F., et al. 1995. The selectins:vascular adhesion molecules. FASEB J. 10: 866-873.

4. Pavalko, R.M., et al. 1995. The cytoplasmic domain ofL-Selectin interacts with cytoskeletal proteinsvia α-actinin: receptor positioning inmicrovilli does not require interactionwith α-actinin. J. Cell Biol. 129: 1155-1164.

5.Frenette, P.S., et al. 1996. Susceptibilityto infection and altered hematopoiesisinmice deficient in both P- and E-Selectins. Cell 84: 563-574.

6. Rosen, S.D. and Bertozzi, C.R. 1996. Two selectinsconverge on sulphate. Leukocyte adhesion. Curr. Biol. 6: 261-264.

7.McEver, R.P., et al. 1996.Leukocyte trafficking mediated byselectincarbohydrate interactions. J. Biol. Chem. 270: 11025-11028.

8.Diacovo, T.G., et al. 1996. Platelet-mediated lymphocyte deliveryto high endothelialvenules. Science 273: 252-255.

9.Alcaide, P., et al. 2007. The 130 kDa glycoform of CD43 functions as an E-Selectin ligand for activated Th1 cellsin vitro and in delayed-type hypersensitivityreactionsin vivo. J. Invest. Dermatol. 127: 1964-1972.


--Mark Hill 13:44, 12 June 2013 (EST) This ref list is fine, but it is not what was asked. You needed to use the pubmed ref format, as I have added below for the last reference.

Pilar Alcaide, Sandra L King, Charles J Dimitroff, Yaw-Chyn Lim, Robert C Fuhlbrigge, Francis W Luscinskas The 130-kDa glycoform of CD43 functions as an E-selectin ligand for activated Th1 cells in vitro and in delayed-type hypersensitivity reactions in vivo. J. Invest. Dermatol.: 2007, 127(8);1964-72 PubMed 17392823


Lab 5

Analysis of morophological phenotypes.JPG


Lab 6

Lab 6 hw graph.jpg


1.)Do you see any change in phenotypes between group A and B

There are two significant differences between group A and B. Group A has a greater percentage of pronged cells where as Group B has a great percentage of Broken fan cell. The pronged cells seem to have more branching and the processes appear to be longer. The changes between the groups in regards to the other phenotypes is relatively small.

2.)If you see a difference speculate about a potential molecular mechanism that has led to the change, if you don’t see a change speculate as to why that could be.

The differences between the cells could be because the treated cells are evolved in more actions requiring movement. They appear to be more motile or have a greater capability for motility. Also this accounts for the wider lamella fans. When compared to control group where there is a large percentage of broken fans, the treated epithelial cells have developed better structural and motile abilities.

Peer Review

Group 1

The key points of regulation during cell division have been addressed. The textual formatting is clear and uncluttered. It is clear that the group has done a significant amount of research. Their content is informative and relevant. Their use of informative diagrams (flow diagrams) makes it much easier to grasp the concepts being presented (e.g. bacterial destruction, neutrophil activation and adaptive immune responses).

In general the formatting could be improved by adding a few more images and arranging them on the page in a more visually pleasing way (e.g. change the positions of the images, don’t just put them to the right of the text).There are several areas of the page which may require referencing, in particularly there are a few images which lack copyright information. Also, adding a brief description to the images could make the page more viewer friendly.


Group 2

The key points are very thoroughly addressed and the choice of headings and sub headings is excellent. The categorisation of the content into its relevant headings demonstrates that the group has done a significant amount of research. The glossary is a particularly useful section for viewers who are not familiar with the topic area. The formatting from ‘Cytokinesis Failure’ onwards is really good. The referencing of the text and images is well done.

There is a significantly large portion of the page which lacks images. This makes the test/image images and balance of the entire page uneven. Also adding a brief statement of what is happening in the diagram in relation to cytokinesis instead of just a description may make the images make more of an impact.


Group 4

The Key points concerning the spindle apparatus throughout cell division seem to be addresses. The images supplement the text very well. The content is very thorough and informative- it demonstrates the completion of a significant amount of research. The referencing for both the text and images is done well.

A few of the headings seem excessively long. The formatting in some areas (Introduction and mechanisms of formation) is a little clumsy. Adjusting the balancing/position of images and text can easily fix this. The history table is a little overwhelming. Maybe condense the information or write a briefer summary for the articles presented.


Group 5

The key points are accurately and thoroughly addressed. This page presents a very detailed explanation of the nuclear envelope throughout cell division. The formatting of the headings, images and text is good. The referencing of images and text is well done. Overall the entire page demonstrates that the group has done a significant amount of research and translated it in a way that the viewer can clearly understand it.

The images could be improved by adding a statement describing the image and linking it to the processes it is illustrating. Also there is a section of the page which is very text heavy. Adding a few more images to supplement the text may make the page more enjoyable to read.


Group 6

The key points of Anaphase are presented in the headings. The images supplement the text very well. The text is referenced properly. The balance of text and images is good. The glossary makes understanding the rest of the content much easier. The group has shown that they have done a significant amount of research-particularly the current research.

Though the key points are present, a bit more content in some areas would be good (meiosis vs mitosis, history and molecular aspects of anaphase). Several of the images lack proper referencing and a description. The general formatting of the page could be improved by changing the position of the text and images.


Group 7

Most of key points concerning mitochondria during cell division are thoroughly addressed. The content is informative and relevant to each section. This demonstrates that the group has conducted a significant amount of research. The images supplement the text well. The text and images has been referenced well.

The balance between texts and images could be improved by adding a few more images (specifically to the introduction and structure sections). Also changing the positions of some of the images and adding a brief statement to describe the illustrated processes will improve the formatting. Finally, adding a section for current and future research may improve the page.

Reference

  1. Laura Eme, David Moreira, Emmanuel Talla, Céline Brochier-Armanet A complex cell division machinery was present in the last common ancestor of eukaryotes. PLoS ONE: 2009, 4(4);e5021 PubMed 19352429