User:Z3374087

From CellBiology

Lab Attendance

Week 1

--Z3374087 (talk) 16:12, 14 March 2013 (EST)

Week 2

--Z3374087 (talk) 15:32, 21 March 2013 (EST)

Week 3

--Z3374087 (talk) 15:44, 28 March 2013 (EST)

Week 4

--Z3374087 (talk) 15:13, 11 April 2013 (EST)

Week 5

--Z3374087 (talk) 15:29, 18 April 2013 (EST)

Week 6

No lab because of ANZAC day

Week 7

--Z3374087 (talk) 15:23, 2 May 2013 (EST)

Week 8

--Z3374087 (talk) 16:49, 9 May 2013 (EST)

Week 9

--Z3374087 (talk) 16:20, 16 May 2013 (EST)

Week 10

--Z3374087 (talk) 16:34, 23 May 2013 (EST)

Week 11

--Z3374087 (talk) 16:27, 30 May 2013 (EST)

Week 13

--Z3374087 (talk) 15:21, 6 June 2013 (EST)

Individual Assessments

Lab 1

Photo illustrating the difference in the structure of a Prokaryotic and Eukaryotic RNA polymerase.png

Photo illustrating the difference in the structure of a Prokaryotic and Eukaryotic RNA polymerase.

This image shows the differences in the 3-D structure of Prokaryotic and Eukaryotic RNA polymerase. This relates to prokaryotic/eukaryotic cells because they both carry out DNA replication. However the structure of their respective DNA is different and it is therefore appropriate that they have differing RNA polymerase structures to compensate for this.

The three-dimensional structures of RNA polymerases from a prokaryote (Thermus aquaticus) and a eukaryote (Saccharoromyces cerevisiae). The two largest subunits for each structure are shown in dark red and dark blue. The similarity of these structures reveals that these enzymes have the same evolutionary origin and have many mechanistic features in common.

Reference

http://www.ncbi.nlm.nih.gov/books/NBK21189/

Copyright

2002, W. H. Freeman and Company (RNA Synthesis and Splicing)

Lab2

PART 1

Jeremy Berg, John Tymoczko, Lubert Stryer RNA Synthesis and Splicing. Biochemistry. 5th edition. New York: W H Freeman.: 2002, PMID: 23393914

PART 2

Ex vivo laser confocal microscopy findings of cultured Acanthamoeba trophozoites

In the following article, the researcher used confocal microscopy to identify the various shapes and sizes of cultured Acanthamoeba trophozoites obtained from Acanthamoeba keratitis patients. In the human body Acanthamoeba organisms grow within our epithelium and anterior stroma. It has severe effects on eyesight because it causes a potentially blinding corneal infection. Traditionally it would go misdiagnosed because ts basic structure is very similar to the herpes simplex infection. However the confocal microscopy techniques used in this article allowed the researchers to identify the particular structure of these organisms as being highly reflective, ovoid, and 10-25 microns in diameter. This was achieved by first culturing them on an agar plate and viewing them using this technique, then observing the same structures of these organisms from a sample of an infected human. This confocal microscopy technique allows us to identify these previously unidentifiable structures because it uses point illumination to increase the optical resolution and contrast of a micrograph.


--Mark Hill (talk) 13:25, 11 April 2013 (EST) Your explanation of the paper's findings and how CLSM contributed meet that part of the assessment criteria. You have not though inserted the reference correctly as explained in the class tutorial and online Project Referencing. I have pasted your paragraph again below and shown how referencing works, have a look at the paragraph in page edit mode.

In the following article[1], the researcher used confocal microscopy to identify the various shapes and sizes of cultured Acanthamoeba trophozoites obtained from Acanthamoeba keratitis patients. In the human body Acanthamoeba organisms grow within our epithelium and anterior stroma. It has severe effects on eyesight because it causes a potentially blinding corneal infection. Traditionally it would go misdiagnosed because ts basic structure is very similar to the herpes simplex infection. However the confocal microscopy techniques used in this article allowed the researchers to identify the particular structure of these organisms as being highly reflective, ovoid, and 10-25 microns in diameter. This was achieved by first culturing them on an agar plate and viewing them using this technique, then observing the same structures of these organisms from a sample of an infected human. This confocal microscopy technique allows us to identify these previously unidentifiable structures because it uses point illumination to increase the optical resolution and contrast of a micrograph.


  1. Natsuko Yamazaki, Akira Kobayashi, Hideaki Yokogawa, Yasuhisa Ishibashi, Yosaburo Oikawa, Masaharu Tokoro, Kazuhisa Sugiyama Ex vivo laser confocal microscopy findings of cultured Acanthamoeba trophozoites. Clin Ophthalmol: 2012, 6;1365-8 PubMed 22973090

Lab 3

--Z3374087 (talk) 20:22, 10 April 2013 (EST)

My topic for group assignment: Process and mechanism of cytokinesis.

Andrew G Clark, Jenny R Sider, Koen Verbrugghe, Gabriel Fenteany, George von Dassow, William M Bement Identification of small molecule inhibitors of cytokinesis and single cell wound repair. Cytoskeleton (Hoboken): 2012, 69(11);1010-20 PubMed 23125193


Relevance to topic: Investigates the inhibitory effects of particular 'small molecules'. Can use this information to identify factors and biological processes that prevent these inhibitory effects.

Findings: 1990 compounds were obtained from the National Cancer Institute and screened and tested to identify any inhibitory effects on cytokinesis in sand dollar embryos and on single cell wound repair in frog oocytes. It was found that two restriction enzymes in Sph1 and Sph2 reduce Rho (family of G-proteins) activation in wound repair and prevent spindly formation during cytokinesis.


Juan Pablo Fededa, Daniel W Gerlich Molecular control of animal cell cytokinesis. Nat. Cell Biol.: 2012, 14(5);440-7 PubMed 22552143


Relevance to topic: Investigates recent research into the particular steps of cytokinesis and the effects of these after it has completed on the next cell cycle.

Findings: Article did not find or prove anything new in particular. It only reinforced common research findings that cytokinesis contributed to anaphase spindle reorganization, division plane specification, actomyosin ring assembly, contraction and abscission. These processes are all integral to completing the final stages of the cell cycle which ultimately allows the two daughter cells to successfully split from one another and undergo their own metabolic pathways.


Runsheng He, Qixi Wu, Haining Zhou, Ning Huang, Jianguo Chen, Junlin Teng Cep57 protein is required for cytokinesis by facilitating central spindle microtubule organization. J. Biol. Chem.: 2013, 288(20);14384-90 PubMed 23569207


Relevance to topic:Investigates the effects of C57 in cytokinesis. Relevant because c57 will be an integral part of my description of the cell cycle and this provides great and reliable information in relation to this.

Findings: Lack of Cep57 microtubule distribution and Assembly led to cytokinesis failure of the central spindle. Bi nuclear cells also formed as a result of unnatural distribution of MKLP1, Plk1 and Aurora B. Cep57 was also found to directly regulate the microtubule organization in spindle formation.


YuKyung Lee, Sunglan Chung, In Keol Baek, Tae H Lee, Soon-Yong Paik, JooHun Lee UNC119a bridges the transmission of Fyn signals to Rab11, leading to the completion of cytokinesis. Cell Cycle: 2013, 12(8);1303-15 PubMed 23535298


Relevance to topic: Research focuses on the metabolic processes that facilitate the completion of cytokinesis. Can use to summarize and finish my description.

Findings: UNC119a activates Src family kinases (SFKs) through a signalling pathway. This is achieved by UNC119a localizing to the centrosome within cells undergoing interphase. After this is translocates from the spindle pole to the spindle mid zone after the subsequent process of mitosis is complete. This process activates the Fyn signal transduction pathway (T cell receptor signaling pathway) to allow cytokinesis to complete.


Image upload:

File:HeLa cell in the final stage of cytokinesis.jpg
PIP2 localizes to the midbody (white arrow). HeLa cells were transfected with An external file that holds a picture, illustration, etc. Object name is nihms166533ig4.jpg (vector kindly provided by Tamas Balla, NIH). An external file that holds a picture, illustration, etc. Object name is nihms166533ig1.jpg (red) were stained with anti-tubulin (Sigma T6199), An external file that holds a picture, illustration, etc. Object name is nihms166533ig3.jpg (blue) with DAPI.

--Mark Hill (talk) 19:18, 10 June 2013 (EST) This image has been deleted for copyright reasons.

Lab 4

Work completed during the lab

Antibody of interest: Anti-alpha 2 Catenin antibody

Datasheet website: [1]

Type of antibody: Rabbit monoclonal antibody. It is a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system.

Species it is raised in: Rabbit

How it can be used: 1) Western blot 2) Immunoprecipitation

Publication about it: [2]


Lab 7

Graphs completed at home using the information gathered by the Phenotype A and B photograph slides.

Phenotype A & B Homework data

Other observations with regard to cell morphology

The pronged and stumped morphologies appear very similar and are had to differentiate from one another in the slides.

Question: Description of phenotypes in sample images (differentiated b35 cells with either genotype A or B)

Genotype A: Phenotypes D (pronged) and E (stringed) were more prevalent in this group with counted amounts of 60 and 48 respectively. This is indicative that this group has a significant amount of branching and long processes.

Genotype B: Phenotypes C (stumped) and D (pronged) were the most prevalent. Phenotype E (stringed)levels was also high aswell although not as high as the other two respective groups. This indicates that there is branching and processes in this gropu although the branching is not as long and plentiful as in genotype A.

Lab 10 work (peer assessments)

Group 1: At first glance the history provided seems to short and brief but this may be attributed to the fact that they haven’t finished it yet. Seeing as this topic is on cell division it is very broad and the introduction seems too short and does not address the topic sufficiently. The entry into M-phase and ‘metaphase to anaphase transition’ both address the topics very well and are very descriptive. Sufficient visual pictures are presented to keep the viewers engaged and understanding what the content means. The mitogens section however requires 1 or 2 more related pictures so that the viewer understands what the specific content means. The current and future research seems a bit too short. It would be good if they provided 203 more examples along with external links and a short description of the aims and results of these research articles. The references seem fine and referenced correctly. Overall this is project has come along greatly. With s few more pictures and specific content I can see this getting a Distinction at least for sure.


Group 3: The introduction addresses the topic well with a combination of a brief history, structure and function of the golgi apparatus. The structure and function are very descriptive and address the all content required however it would be good to ad a picture under the function heading regarding a metabolic pathway involving the golgi apparatus. Having the history after these topics is great because they allow the reader to appreciate the function of the golgi apparatus before learning about its history. Although the “during cell division” content is very descriptive and informative it is very bunched up. The use of paragraphs and pictures will allow it to flow better and maintain the reader’s interest. The external links section detailing some current research needs descriptions for the research under the links so the reader can understand what they are about and how they relate to the group page. The references are all correct and plentiful. This is a very detailed assignment overall. With a bit more paragraph reorganisation and pictures detailing what is described it can achieve a HD for sure.


Group 4: Having a picture immediately is great as it allows the reader to understand what this structure looks like before reading about the page. This will help greatly with visualising what is occurring later on throughout the descriptions. The introduction is exceptional. It is short, sharp and succinct and the use of a picture is also great as a visual aid. Especially the pictures illustrating the different structures of the spindle apparatuses during the different stages of mitosis. The history is exceptional and in my opinion is the best section of the entire project. It details all the research into the spindle apparatus including its structure and function. Again the use of pictures is great in accompanying the information and maintaining the reader’s interest. The ‘structure’ section is detailed and has great pictures addressing all aspects of the information however the function section needs work. The paragraphs need restructuring so that they flow better and visual aids are required. This is because throughout all of the group project to that point the use of visual aid has been extensive then all of a sudden it stops. Therefore to maintain the exceptional flow of the projects pictures are needed that accompany and support the information that is being relayed to the reader. Again the current research section is very descriptive however the use of links may be required. The glossary is extensive and addresses all major words used throughout the project. Referencing is also extensive and quite impressive. Overall this is definitely a HD worthy group project. Only paragraph restructuring and pictures are required in the ‘function’ section.


Group 5: First off from the very outset I can see that this is an extremely detailed and extensive group project however pictures are lacking significantly and in particular throughout the middle of the page. The introduction is extensive detailing all necessary aspects of the nuclear envelope during cell division including the structure, function, a brief history and a reference to what the project is going to talk about. The history is sharp and succinct with all references relating to the project. The description of the “structure” is great however more information is needed regarding the outer membrane structure. Although there is not much information detailing the structure one sentence is not sufficient to address it properly. Pictures are needed especially in this section ASAP because the reader has to face this enormous amount of information without any visual aid to maintain their interest in the information. You cannot expect the reader to just real giant slabs of information. Again the “nuclear envelope” and “breakdown of nuclear envelope” sections have great and solid information regarding these topics with some interesting references but pictures are required because it just looks like information piled on top of information. Break it up with pictures every 500-600 words. The same can be said for the rest of the project up to the “glossary”. It seems very boring to read due to the mass amounts of information and I am sure Mark Hill is not going to be very impressed sitting at his computer and looking at this vast amount of content without any visual stimulus. The glossary needs extensive work and is too short. The references are absolutely outstanding. I can tell alot of information has gone into researching and extracting all necessary information for this project. Overall this is worth a HD if much more pictures are added and the glossary is lengthened. Great work.


Group 6: The introduction provides a brief structure and function of anaphase however it is too short and needs to address a bit more topics to be complete. I suggest including a very brief history and description of what the project is going to talk about. The meiosis vs mitosis section is a bit too short and needs more detail Also it is structured too early in the page. Put is after a description of what anaphase is and the overall function so that the viewer understands this process of cell division before making comparisons and contrasts between them. The history is too short and requires more research and relations to anaphase. It also needs to be reorganised before the “meiosis vs mitosis” section. The information provided from “metaphase to anaphase transition” to ‘chromosomal motors” is extensive and well described. They are backed up with sufficient visual aid however these pictures are too small. Even though the viewer can click on them it is good to make them larger to not only break up the paragraphs and allow the information to flow better but also to make it more visually appealing. This ultimately will maintain the reader’s attention while reading. The chromosomal motors section does identify the two (+ and -) motors however the information regarding them is insufficient and required diagrams especially in this section. Think of describing the structure, function and role of these molecular motors and getting pictures that illustrate this. It is great that in the “molecular aspect of anaphase” section you have described different molecular components and their contribution to the completion of the overall process. It is also good that you left this for later in the group page because the reader would have understood the overall process by then before looking at these components and their responsibilities. The defects section is very descriptive however the paragraphs need more spacing apart because it appears to convoluted and content heavy. The current research section is great because it shows an example in chronological order from 2008 to 2011 so that the reader can understand research the path that is being followed for anaphase and where we are heading in the future. The glossary is not long enough and requires much more terms used throughout the project. The referencing however is exceptional and extensive giving the reader the understanding that alot of research went into this group assignment. Overall this is definitely a HD worthy group project with a few more visual stimuli added.


Group 7: The introduction is extensive and concisely addresses all aspects of the groups “cell division” project including structure and function however it requires a brief history and what the project is going to address in regards to cell division. The “structure” subsection is very detailed but just one huge chunk of information. Try putting this into bullet form to break up the information and not let the reader become uninterested right at the beginning of the page. The “function section” is absolutely perfect. It is divided into short paragraphs which allow the information to flow and is supported by relevant pictures that aid in understanding these processes detailing cell division. The “history section” is also perfect and contains all relevant information however it needs to be relocated right to the beginning of the page because it is in the middle of nowhere. By having at the beginning it will provide a general background for the information that is going to follow and allow the reader to gain an appreciation for the research that has gone into cell division. For the “during cell division” section the retrograde content requires more information and accompanying pictures. A picture is also required for the anterogade heading which is very detailed. The “fusion and fission” sections address all necessary information however the picture provided does not have much reference to the steps provided. Try finding pictures that detail the steps during fusion and fission and don’t forget to add a caption under the picture describing what the picture is illustrating. The picture provided does not have a caption. Add a heading describing the diseases associated with mitochondrial division along with pictures illustrating the ultimate physical outcome of the diseases. A glossary is required. The references are plentiful and some really great sources are used. Overall this assignment needs many pictures and some restructuring of headings and paragraphs but is definitely at a Distinction level at the moment.

Work completed during introductory lab 1

Lab 1 - Introduction to Lab (understanding how to use Wikipedia)

Internal Link

Cell_Biology_Introduction

Shawn ray link

A reference reference

<Identification of small molecule inhibitors of cytokinesis and single cell wound repair="PMID23125193"> Andrew G Clark, Jenny R Sider, Koen Verbrugghe, Gabriel Fenteany, George von Dassow, William M Bement Identification of small molecule inhibitors of cytokinesis and single cell wound repair. Cytoskeleton (Hoboken): 2012, 69(11);1010-20 PubMed 23125193

</ref>


Cells

blood cells


  • Bullet point
    • Subheading list
      • subheading subheading list