User:Z3376548

From CellBiology

Attendance

--Z3376548 (talk) 15:57, 14 March 2013 (EST)

I was in the lab on 21 March but forgot to mark myself off for this lab, have talked about the issue with Mark and got his consent.

--Z3376548 (talk) 15:14, 28 March 2013 (EST)

--Z3376548 (talk) 15:06, 11 April 2013 (EST)

--Z3376548 (talk) 15:06, 18 April 2013 (EST)

--Z3376548 (talk) 15:06, 2 May 2013 (EST)

--Z3376548 (talk) 15:13, 9 May 2013 (EST)

--Z3376548 (talk) 15:08, 16 May 2013 (EST)

--Z3376548 (talk) 15:01, 23 May 2013 (EST)

--Z3376548 (talk) 15:11, 30 May 2013 (EST)

--Z3376548 (talk) 15:22, 6 June 2013 (EST)

Individual Assessments

Lab 1

Transporters' differences in cells

Citation: Ren Q, Paulsen IT (2005) Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes. PLoS Comput Biol 1(3): e27. doi:10.1371/journal.pcbi.0010027

Editor: Peer Bork, EMBL Heidelberg, Germany

Received: March 24, 2005; Accepted: July 8, 2005; Published: August 19, 2005

Copyright: © 2005 Ren and Paulsen. 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

1st task

PMID 16118665

Qinghu Ren, Ian T Paulsen Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput. Biol.: 2005, 1(3);e27 PubMed 16118665


[1]

2nd task

The researcher of the article "Biofilm Matrix Regulation by Candida albicans Zap1" found a specific gene ZAP 1 that controls the formation of biofilm from the organism called Candida albicans. They manipulate this gene in order to see how the production of biofilm changes. However, the researcher need to precisely observe the biomass or thickness of the biofilm and this could not be done by using the normal microscope. Therefore, they used confocal microscopy which contribute to this experiment process that it enables the 3D image of the biofilm to be observed thus helps the researcher to understand more about how the ZAP 1 gene regulate the appearance of the biofilm.

PMID 19529758

Clarissa J Nobile, Jeniel E Nett, Aaron D Hernday, Oliver R Homann, Jean-Sebastien Deneault, Andre Nantel, David R Andes, Alexander D Johnson, Aaron P Mitchell Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol.: 2009, 7(6);e1000133 PubMed 19529758


[2]


--Mark Hill (talk) 10:25, 11 April 2013 (EST) Referencing is formatted correctly, but not positioned correctly. The research article does also use CLSM in its findings, as you have described here.

Lab 3

1st task

Article 1: This article searches the roles of actin filaments (F-actin) and F-actin-based motors (myosins) which are required components of mitotic spindles. In their research, they found out that myosin-10 (Myo10) is important for assembly of meiotic spindles. In more detail, Myo10 set themselves to mitotic spindle poles and is very important for proper spindle anchoring, normal spindle length, spindle pole integrity as well as progression through metaphase. They also found out the antagonistic relationship between F-actin and Myo10 in maintenance of spindle length and that they work independently.[3] Actin filaments (F-actin) and F-actin-based motors (myosins) are essential components in the proper functioning of spindle apparatus. They are required for correct positioning of the spindle towards the anchor point.

Sarah Woolner, Lori L O'Brien, Christiane Wiese, William M Bement Myosin-10 and actin filaments are essential for mitotic spindle function. J. Cell Biol.: 2008, 182(1);77-88 PubMed 18606852


Article 2: Their finding found out the function of the long-tailed class-1 myosin myosin-1C from Dictyostelium discoideum during mitosis. They use the data obtained as back up, suggested that myosin-1C binds to microtubules and play parts in maintenance of spindle stability during chromosome separation and that the association of myosin-1C with microtubules is mediated through the tail domain. Further data has leaded to another suggestion that myosin-1C tail can inhibit kinesin motor activity, strengthen the stability of microtubules as well as forming crosslinks between microtubules and F-actin. [4] Myosin-1C motor and tail-domain-mediated MT-F-actin are required for the relocalization of certain protein from the cell periphery to the spindle. Therefore, both contribute to the formation and stability of spindle apparatus in considerable amount.

Agrani Rump, Tim Scholz, Claudia Thiel, Falk K Hartmann, Petra Uta, Maike H Hinrichs, Manuel H Taft, Georgios Tsiavaliaris Myosin-1C associates with microtubules and stabilizes the mitotic spindle during cell division. J. Cell. Sci.: 2011, 124(Pt 15);2521-8 PubMed 21712373


Article 3: This article states thoroughly for the process of spindle assembly, spindle positioning and separation of the nascent spindle poles in relation to cortical dynein-based pulling on astral microtubules, and kinesin-based sliding of polar microtubules. They talked about the motors and microtubule binding proteins at kinetochores which provide attachment sites for microtubule to the chromosomes. They also states that there is a complicated mechanism that which perform pushing and pulling action to chromosomes that puts them in metaphase plate position. Kinetochore motors and microtubule binding proteins can also give signal to the cell cycle regulatory machinery for on time advance passing the cell cycle phrases. [5] Dynein-based pulling and kinesin-based sliding of microtubules is very important in spindle assembly and positioning. Motors and microtubule binding proteins will aid spindle for its function to separate sister chromatids.

Joshua C Sandquist, Angela M Kita, William M Bement And the dead shall rise: actin and myosin return to the spindle. Dev. Cell: 2011, 21(3);410-9 PubMed 21920311


Article 4: By combine the use of force-calibrated needles, high-resolution microscopy, and biochemical perturbations, the researcher analyze the vertebrate metaphase spindle and found that spindle viscosity is dependent on microtubule density and cross-linking. Spindle elasticity are said to be relating to kinetochore and non-kinetochore microtubule rigidity, and also to spindle pole organization by kinesin-5 and dynein. [6] The data obtain in their research provides micromechanics modal insight of this cytoskeletal architecture and provide insight into how structural and functional stability is maintained for proper control of spindle function.

Yuta Shimamoto, Yusuke T Maeda, Shin'ichi Ishiwata, Albert J Libchaber, Tarun M Kapoor Insights into the micromechanical properties of the metaphase spindle. Cell: 2011, 145(7);1062-74 PubMed 21703450


2nd task

Knockdown of Myo10 leads to mitotic spindle defects

Description: The researcher use combination of Western blot and Confocal microscopy determine the cause of spindle defects has strong relation to Myo10 malfunction.

Citation: Sarah Woolner, Lori L O'Brien, Christiane Wiese, William M Bement Myosin-10 and actin filaments are essential for mitotic spindle function. J. Cell Biol.: 2008, 182(1);77-88 PMID:18606852

Copyright: Copyright © 2008 Woolner et al.

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/).

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.

Lab 4

http://www.pierce-antibodies.com/Catenin-beta-antibody-clone-6F9-Monoclonal--MA1300.html

Beta catenin takes partin in cell-cell communication and adhesion junction. Furthermore, beta Catenin can also activate a family of Lef/Tcf transcription factors which stimulate transcription of the genes that encode cyclin D and c-myc. Cyclin D and c-myc do the job to promote cell proliferation. Therefore, the protein is important for both cell adhesion as well as interacting with tumorgenesis.

The antibody, Catenin beta Antibody, is able to recognise and bind to this protein. Catenin beta Antibody, according to the data sheet, is raised in mouse and it can react against human as well as non-human primate. It is a monoclonal antibody. It can be used in Western Blot, Immunohistochemistry as well as Immunofluorescence.

Lab 6

Analysis of phenotypes in tropomyosin 4 over-expressing b35 neuro-epithelial cells

Question 1 A. Yes, there is changes. B. Genotype A is believed to be the over-expressing Tm4 cells because the cell phenotypes are almost all stringed and prolonged shape. In comparison, the cell phenotypes of genotype B are more evenly distributed. Tm4 expression was thought to be focusing on the growth of neuron cells. The stretch shape might had it involved more in the neurosystem where the cell there all mainly stretched shape.

Question 2 A. yes, there is some minor changes. B. Genotype A seems to be all stringed shape cell. In comparison, genotype B cells although have majority number of stringed cell, have a number of cells that looks pronged. Therefore, it seems db-CAMP acts to induce the differentiation of B35 cells which causing Tm4 expression to be silenced. Therefore, the reverse of Tm4 expression happen as length decreases.

Lab 8

Peer Review

Group 1 Regulation of cell division

1. Regulation of cell division is a relative large area to talk about. At this level, it will be more a good idea to briefly address different regulatory components at each cell division phase. Therefore, key ideas will be more apparent. 2. I found my understanding of this article rather fragmented. The sub-headings are relevant but the flow is inconsistent. A nice structured cell division break down will be more impressive. Therefore it will help understanding. The animated picture is good for understanding. 3. Content is correctly cited and referenced. 4. Some diagram is helpful to understand the relevant concepts. I can see tables that are nicely layout that break information into parts that really helps peer to understand their study area. The information is rather informative than innovative. 5. There is limited evidence of significant research relating to basic and applied sciences. There should be some advance research is disease and complications involved. There are some concepts like tropomyosin are mentioned in future research. It will be more sophisticated to reference certain articles that have mentioned same as well. 6. This group topic is very relevant to cell biology. It helps to understand the need of regulatory components during cell division. The mentions of spindle check out and Anaphase Promoting Complex as well as mitogens is interesting related to cell biology study.

Group 2 Cytokinesis

1. Cytokinesis is a focused area to talk about. At this level, I can see there is a focus explanation at mechanism of action which is the key point and it is well addressed. 2. The group has managed to break mechanism of action down into different small steps in sequence. The sub-headings are relevant and the flow is consistent. A nice structured table can be used to make the differences in cytokinesis between animal and plant more clear. Therefore it will help understanding. More animated picture should be placed in the mechanism section which will be good for understanding. 3. Content is correctly cited and referenced. 4. Some diagram is helpful to understand the relevant concepts. I can see tables that are nicely layout that break information into parts that really helps peer to understand their study area. The information is rather informative than innovative. 5. There are many evidences of significant research relating to basic and applied sciences. There are advance researches in cytokenesis failure but it will be a good idea to include some disease and complications in relation. There are detail concepts mentioned in future research. It is sophisticated as many referenced articles are mentioned. 6. This group topic is very relevant to cell biology. It helps to understand the detailed mechanism of action in cytokinesis. The mentions of midbody, abscission and contractile ring are interesting related to cell biology study.

Group 3 The Golgi Apparatus

1. Golgi Apparatus is a focused area to talk about. At this level, I can see there is a detailed explanation at morphology of Golgi Apparatus throughout cell division. The other key points like function and structure are addressed therefore It has covered all the key points. 2. The group has managed to break morphology of Golgi Apparatus down into different phase of cell division. The sub-headings are relevant and the flow is consistent. The display will be improved if history part is moved upward to the top. Therefore it will help audience to gain a basic understanding of history before going into depth. There are sufficient number of animated pictures displayed which are good for understanding. 3. Content is correctly cited and referenced. 4. Some diagram is helpful to understand the relevant concepts. I can see tables that are nicely layout that break information into parts that really helps peer to understand their study area. The information is rather informative than innovative. 5. There are many evidences of significant research relating to basic and applied sciences. There are vast researches in mophology but it will be a good idea to include some disease and complications too. 6. This group topic is very relevant to cell biology. It helps to understand the Golgi Apparatus. The focus on morphology really goes in depth very much. It helps audience understand morphology of Golgi Apparatus in each step of cell division.

Group 5 The Nuclear Envelope during Cell Division

1. The Nuclear Envelope during cell division is a focused area to talk about. At this level, I can see there is a detailed steps describing how nuclear envelop reacts during cell division. The other key points like structure and history are addressed therefore It has covered all the key points. 2. The group has managed to break detailed step of nuclear envelop during cell division down into relevant subheading which is very impressive. The sub-headings are relevant and the flow is consistent. There are sufficient number of animated pictures displayed which are good for understanding. 3. Content is correctly cited and referenced. 4. Some diagram is helpful to understand the relevant concepts. I can see tables that are nicely layout that break information into parts that really helps peer to understand their study area. The information is rather informative than innovative. 5. There are many evidences of significant research relating to basic and applied sciences. There are detail concepts mentioned in future research. It is sophisticated as many referenced articles are mentioned. They have included some disease and complications too. 6. This group topic is very relevant to cell biology. It helps to understand the nuclear envelop in cell division process. The focus on each stage really goes in depth very much. It helps audience understand how nuclear envelop reacts in each step of cell division.

Group 6 Anaphase

1. Anaphase is a focused area to talk about. At this level, I can see there is a focus explanation at detail components of anaphase which is the key point and it is well addressed. 2. The group has managed to break anaphase down into different small steps in sequence. The sub-headings are relevant and the flow is consistent. Tables and figures have been used effectively to demonstrate teaching at a peer level. 3. Some of the images have not been correctly cited 4. Tables and figures have been used effectively to demonstrate teaching at a peer level. I can see tables that are nicely layout that break information into parts that really helps peer to understand their study area. The information is rather informative than innovative. 5. There are many evidences of significant research relating to basic and applied sciences. There are detail concepts mentioned in future research. It is sophisticated as many referenced articles are mentioned. 6. This group topic is very relevant to cell biology. It helps to understand the detailed mechanism of anaphase.

Group 7 Mitochondria

1. Mitochondria are a focused area to talk about. At this level, I can see there is a detailed explanation at morphology of Mitochondria throughout cell division. The other key points like function and structure are addressed therefore It has covered all the key points. 2. The group has managed to break morphology of Mitochondria down into different phase of cell division. The sub-headings are relevant and the flow is consistent. The display will be improved if history part is moved upward to the top. Therefore it will help audience to gain a basic understanding of history before going into depth. There are sufficient number of animated pictures displayed which are good for understanding. 3. Content is correctly cited and referenced. 4. Some diagram is helpful to understand the relevant concepts. I can see tables that are nicely layout that break information into parts that really helps peer to understand their study area. The information is rather informative than innovative. 5. There are many evidences of significant research relating to basic and applied sciences. There are vast researches in mophology but it will be a good idea to include some disease and complications too. 6. This group topic is very relevant to cell biology. It helps to understand the Mitochondria.

References

  1. Qinghu Ren, Ian T Paulsen Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput. Biol.: 2005, 1(3);e27 PubMed 16118665
  2. Clarissa J Nobile, Jeniel E Nett, Aaron D Hernday, Oliver R Homann, Jean-Sebastien Deneault, Andre Nantel, David R Andes, Alexander D Johnson, Aaron P Mitchell Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol.: 2009, 7(6);e1000133 PubMed 19529758
  3. Sarah Woolner, Lori L O'Brien, Christiane Wiese, William M Bement Myosin-10 and actin filaments are essential for mitotic spindle function. J. Cell Biol.: 2008, 182(1);77-88 PubMed 18606852
  4. Agrani Rump, Tim Scholz, Claudia Thiel, Falk K Hartmann, Petra Uta, Maike H Hinrichs, Manuel H Taft, Georgios Tsiavaliaris Myosin-1C associates with microtubules and stabilizes the mitotic spindle during cell division. J. Cell. Sci.: 2011, 124(Pt 15);2521-8 PubMed 21712373
  5. Joshua C Sandquist, Angela M Kita, William M Bement And the dead shall rise: actin and myosin return to the spindle. Dev. Cell: 2011, 21(3);410-9 PubMed 21920311
  6. Yuta Shimamoto, Yusuke T Maeda, Shin'ichi Ishiwata, Albert J Libchaber, Tarun M Kapoor Insights into the micromechanical properties of the metaphase spindle. Cell: 2011, 145(7);1062-74 PubMed 21703450

links

First Lecture

SMH