User:Z3370664

From CellBiology

Lab attendance

Lab 1 --Z3370664 (talk) 15:55, 14 March 2013 (EST)

Lab 2 --Z3370664 (talk) 15:34, 21 March 2013 (EST)

Lab 3 --Z3370664 (talk) 15:09, 28 March 2013 (EST)

Lab 4 --Z3370664 (talk) 15:17, 11 April 2013 (EST)

Lab 5 --Z3370664 (talk) 15:21, 18 April 2013 (EST)

Lab 6 --Z3370664 (talk) 15:20, 2 May 2013 (EST)

Lab 7 --Z3370664 (talk) 15:22, 9 May 2013 (EST)

Lab 8 --Z3370664 (talk) 15:12, 16 May 2013 (EST)

Lab 9 --Z3370664 (talk) 15:02, 23 May 2013 (EST)

Lab 10 --Z3370664 (talk) 15:08, 30 May 2013 (EST)

Lab 11 --Z3370664 (talk) 15:20, 6 June 2013 (EST)

Lab Assignments

Lab 1

Microtubules-bacteria-eukaryote.JPG


Structural model of “bacterial microtubules Bacteria are normally considered prokaryotic. This image shows the differences in the structures of microtubules in Eukaryotes and Bacteria (Prokaryotes)


Original legend:

Structural model of “bacterial microtubules.”

(A) 2-D schematic of the proposed architecture of bacterial microtubules built from BtubA (dark-blue) and BtubB (light-blue). Protofilaments are numbered 1–5. (B) 3-D comparison of the architectures of a bacterial microtubule (left; BtubA in dark-blue; BtubB in light-blue) and a 13-protofilament eukaryotic microtubule (right; β-tubulin in black; α-tubulin in white). Seams and start-helices are indicated as in (A).

Reference

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001213

Martin Pilhofer, Mark S Ladinsky, Alasdair W McDowall, Giulio Petroni, Grant J Jensen Microtubules in bacteria: Ancient tubulins build a five-protofilament homolog of the eukaryotic cytoskeleton. PLoS Biol.: 2011, 9(12);e1001213 PubMed 22162949


[1]


Copyright: © 2011 Pilhofer 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.


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 2

How confocal microscopy helped contribute to the following research article: [2]


Albert Pineda Rodó, Libuše Váchová, Zdena Palková In vivo determination of organellar pH using a universal wavelength-based confocal microscopy approach. PLoS ONE: 2012, 7(3);e33229 PubMed 22470445


Many of the significant cellular processes such as cellular transport and homeostasis are impacted by factors such as the gradient of electrolytes along the membranes, as well as the pH balance of each cell. The authors of this research article wanted to observe the pH of individual cellular components for their research. They decided to use confocal microscopy to aid their research, as this technique is non-invasive. They relied on the release of wavelength scans of single organelles to produce pH estimates based on the wavelength, which were reasonably accurate. With the aid of Green fluorescent protein, the authors were able to detect the internal pH and metabolic changes in subcellular components by studying the wavelengths emitted by the fluorescent protein through confocal fluorescent microscopy. The use of such confocal microscopy in this type of study is fairly new, and the authors have found advantages to using this method, rather than relying on the older conventional methods. Advantages of using confocal microscopy in this research includes being able to scan the subcellular components in high resolution, and being able to regularly monitor and detect the pH changes fairly accurately.

--Mark Hill (talk) 12:37, 11 April 2013 (EST) This reference and description meet the assessment criteria. You did though need to include the citation within your description, rather than as a separate heading, as below.

The authors of this research article[3]....




Lab 3

4 Research Articles For Spindle apparatus:


Article # 1:

R B Nicklas Measurements of the force produced by the mitotic spindle in anaphase. J. Cell Biol.: 1983, 97(2);542-8 PubMed 6885908


In this article[4], the author researched the measurements of force produced by spindles during anaphase of mitosis. A glass needle was used to measure the force that each spindle acts on each single moving chromosome. The use of the needle resulted in producing a force on the chromosome in opposition to the force produced by the spindle, and this was measured using the deflection of the needle tip. Twelve experiments were performed on grasshopper spermatocytes (which was chosen because the research ensured the surface of the cell did not interfere with the contents inside the cell). The results showed the relationship between the velocity of chromosomes and the opposing forces of the spindles. It was found that the spindles produce a large force, which shows that it can affect the stability and length of microtubules. This article is relevant in the spindle historical research section.


Article # 2:

D Szollosi, P Calarco, R P Donahue Absence of centrioles in the first and second meiotic spindles of mouse oocytes. J. Cell. Sci.: 1972, 11(2);521-41 PubMed 5076360


This article [5] discusses research in the topic of centrioles and their role in spindle apparatus formation. Centrioles are normally present in animal cells. Spindle apparatus originate from a 'center' which is called the centriole. It helps organise the spindles to originate from a single point. However centrioles are absent in many plant cells. Ovaries of rate, mice, hamster, Mongolian gerbils, and humans were used in this study. Oocyte samples were taken out of the ovaries, and examined. The results showed that centrioles were present in human oogonia, as well as the neonatal ovaries of rats. However, centrioles seem to be absent in later stages of oogenesis. It was not discovered what exactly happens to the centrioles, because there was no observation of breaking down. The results also show that an intact centriole is not needed for successful completion of meiosis. Mitotic spindles in early mouse embryos and many plants lack centrioles. This article will be helpful in the historical research section.


Article # 3:

R E Stephens A thermodynamic analysis of mitotic spindle equilibrium at active metaphase. J. Cell Biol.: 1973, 57(1);133-47 PubMed 4734864


This article [6] researches mitotic spindle thermodynamics and equilibrium during metaphase. Sea urchin eggs undergoing metaphase were used in this study. These eggs were observed using polarization microscopy. Spindle fibres were said to be 'labile' in nature, however the existence of spindle fibres were not confirmed until 1953 by Inoue, who was able to show their existence in living cells, using polarization microscopy. He also discovered that hypothermic treatment, as well as the antimitotic drug colchicine can abolish these spindle fibers. The author of this article investigated the equilibrium of spindle fibres that are dependent on temperature. Rise of temperature seems to cause an increase in birefringence. Birefringence is also related to the proportion of tubulin content of microtubules. This article is useful for the historical research section.



Article # 4:

K Watanabe, M S Hamaguchi, Y Hamaguchi Effects of intracellular pH on the mitotic apparatus and mitotic stage in the sand dollar egg. Cell Motil. Cytoskeleton: 1997, 37(3);263-70 PubMed 9227856


This article [7] researches the effect of intracellular pH on mitotic spindle apparatus. Fertilized eggs of Scaphechinus mirabilis and Clypeaster japonicus were used in this study. The pH of Scaphechinus mirabilis was 7.34, while the pH of Clypeaster japonicus was 7.31. The pH of both these egg species changed after their nucleus was broken down with the treatment of adding sea water which contained ammonia or acetate which had pH of variable values. The results showed that the mitotic spindles increased to their maximum size at pHi 6.70. However, the spindle length then decreased when the pHi was changed from 6.70 to 7.84. The increase in spindle size was found to also be related to the amount of microtubules present. Inhibition of the mitotic spindle organisation were observed at pHi 6.30. Most of the eggs of Scaphechinus mirabilis arrested at the metaphase stage when the pHi was 6.70. The main result found overall from this research was that a slightly acidic pH results in the stabilization of microtubules in the spindles, and the number of microtubules present were larger than it is in normal eggs. This article is useful for the historical research section.



1 Image for Current Research on Spindles, from this article:

Aurélien Courtois, Melina Schuh, Jan Ellenberg, Takashi Hiiragi The transition from meiotic to mitotic spindle assembly is gradual during early mammalian development. J. Cell Biol.: 2012, 198(3);357-70 PubMed 22851319


Spindle-transition-meiosis-mitosis.jpg


This image shows spindle assembly during the the gradual transition from meiosis to mitosis in the mouse embryo during preimplantation stage. [8] This image is relevant to the research article in the current research section.




Lab 4

1.Identify an antibody against an adhesion junction protein that is commercially available.

Answer: Rabbit anti-connexin-43 polyclonal antibody

Source: http://products.invitrogen.com/ivgn/product/710700


2.Add a link to the original data sheet page and identify the type of adhesion junction.

Answer: Type of adhesion junction is: gap junction, made of connexin proteins.

Link To original data sheet: https://tools.invitrogen.com/content/sfs/msds/2007/710700_MTR-AUIV_BE.pdf

Link to manual: http://tools.invitrogen.com/content/sfs/manuals/710700_Rev1008.pdf


3.Include the following information: type of antibody (polyclonal, monoclonal), species raised in, species reacts against, types of application uses, and if available any reference using that antibody.

Answer:

Type of antibody: Polyclonal

Species raised in: Rabbit

Species reacts against: Human, Rat, Mouse.

Types of application uses: Western Blot, Immunofluorescence, Immunohistochemistry, Immunoassay (ELISA).

A reference of a journal article using this antibody [9] :

Richard Francis, Xin Xu, Hyunsoo Park, Chin-Jen Wei, Stephen Chang, Bishwanath Chatterjee, Cecilia Lo Connexin43 modulates cell polarity and directional cell migration by regulating microtubule dynamics. PLoS ONE: 2011, 6(10);e26379 PubMed 22022608


Source of full journal article: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026379





Lab 6

Experiment Result Graph:

Tm4-graph.JPG


Part 1: Questions for Undifferentiated B35 Cells:

Question 1. Do you see any changes in phenotypes between Group A and B?

Answer: Yes i do see a difference in phenotype percentages present in group A and B. Group A which is the Tropomyosin 4 overexpressing group, shows a smaller percentage of phenotypes Fan, Broken Fan, Pygnotic, and Stumped. Group A also shows a larger percentage of phenotypes Pronged and Stringed. Group B has less pronged and stringed phenotypes compared to A.


Question 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 why that could be.

Answer: Tropomyosin is associated with actin. Since Tropomyosin 4 was overexpressed in group A, we can conclude that it has a role in causing different phenotypes in the B35 cell morphology. Since Group A shows a larger number of pronged and stringed phenotypes, which have long neurites, it may imply that tropomyosin 4 causes an increase in the length or outgrowths of neurites, due to the organisation of actin cytoskeleton.



Part 2: Questions for differentiated B35 Cells:

Question 1. Do you see any changes in phenotypes between Group A and B?

Answer: Yes i see a difference in the group A and B. Genotype A appears to have a large number of stringed and pronged phenotypes. Other phenotypes are not clearly visible. Genotype B appears to also have a large number of stringed and pronged phenotypes, although the majority seem to be stringed, and the stalks appear very elongated. Genotype B group seems to have a lesser concentration of the phenotypes compared to the Genotype A group. Perhaps Genotype A group is the overexpressed group or is simply showing the effect of the different genotype for tropomyosin.


Question 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 why that could be.

Answer: Perhaps the different genes for tropomyosin caused the difference in function of the tropomyosin, resulting in the different morphologies of the B35 cells, particularly, the increased length of neurites and their branching.





Group Project Peer Review

Group 1- Regulation of Cell Division

The introductory paragraph is a good start, but needs some more work. Perhaps a little bit more description briefly summarising the other sections of the wiki page in the introduction would make it more substantial. It’s good to see that you have added some references with appropriate formatting in the introduction. There is also no image in this section, it would be nice to add an image or two to support the text. I’m curious to see what video you wanted to upload which you’re checking the copyright clearance for. It’s good you haven’t uploaded it yet since you’re not sure of the copyright.

The history section is lacking content. You need to add more years and descriptions of the discoveries in those years. Some of the spaces are still blank. It’s good that you have added correct references for each of the 5 discoveries you’ve mentioned so far. Perhaps adding some images to support some of the discoveries would make this section look more interesting. The table format is a good idea.

Entry into M-phase section is a good start, but it would be better to add a bit more detail. There is also a lack of references used, I only see 1 reference. The grey image from 1992 is not referenced correctly on the file page, you need to add the source and copyright information. The other colourful image of the cyclins is referenced correctly.

Metaphase to Anaphase transition is a good start with appropriate referencing, but needs a bit more description and you need to add some images to support the text to make it more interesting. Mitogens and Cell Division section is the best section so far in this wiki page. So far the information is sufficient with appropriate referencing. The image is also a good choice, however it does not have appropriate referencing, you need to add information about the copyright, whether reuse is allowed or not. You also need to add the student image template. The last two lines in this section I assume are points you are intending to elaborate more on.

The disease section significantly lacks information; there is only a 1 line description of one disease. You need to add more diseases and bit more detailed description, not just 1 line. The table format is a good idea.

Current and future research section also lacks information. Current research only has 1 line from only 1 reference to a research paper. There are no other references and no detailed description. You need to find some current research papers and describe their findings. Future research also needs some references, perhaps describe some relevant research done already and then talk about what more topics can be researched in the future based on those findings. The cell division phases image at the bottom of the current research section seems a bit out of place. The image however is nice and has the appropriate referencing. I think it would be more suitable in the introduction section.

Overall the project is a good start but needs more work.



Group 2 – Cytokinesis

The introductory paragraph significantly lacks information. Perhaps a little bit more description briefly summarising the other sections of the wiki page in the introduction would make it more substantial. The image in this section is nice and appropriate, with correct referencing. The history section is lacking content. You need to add more years and descriptions of the discoveries in those years. It’s good that you have added correct references for each of the 3 discoveries you’ve mentioned so far. Perhaps adding some images to support some of the discoveries would make this section look more interesting. The colourful table format is a good idea.

The mechanisms section is the best so far in this wiki page. There is a good amount of content with appropriate referencing. There is only 1 image in this section and it has appropriate referencing. It would be nice to add maybe two more images to support the text, as there is a lot of text. I also like the clickable links to the words in the glossary.

The microfilament organisation sections seems a little brief, perhaps you should add a bit more information and also use an image to support the text to make it more interesting.

The plant vs animal cells section seems good and clear and to the point. However, there are no references, you need to add references. It would also be good to add some images to support the text as it’s difficult to read so much text with no supporting images.

Cytokinesis failure section is reasonably good so far, with appropriate referencing for the text and images. It has a good balance of text and images.

The “current/future research” section heading should be edited to get rid of the slash and just put “Current and Future Research”. So far the content is relevant with good descriptions of the research findings. You need to add the proper reference for the papers though, not just external links to the papers.

The external links has links to good images and videos that are relevant and appropriate to the topic. Add a template for the external links disclaimer to say that some of the links may not work in future if those websites take down that content.

The glossary list has appropriate choice of words and is good so far.



Group 3 – Golgi Apparatus

The introductory paragraph is a good start, but needs some more work. Perhaps a little bit more description briefly summarising the other sections of the wiki page in the introduction would make it more substantial. I only see 1 reference in the introduction. The image in this section has the reference in it, but you need to also put the student image disclaimer.

Structure section is concise with appropriate referencing. The image in this section is also relevant.

Function section is also concise with appropriate referencing. However there is no image, it would be nice to add an image to support the text.

The history section is a reasonably good start, with appropriate referencing for the discoveries. You need to add a few more years and descriptions of the discoveries in those years. Perhaps adding some images to support some of the discoveries would make this section look more interesting. The table format is a good idea.

“Morphology and Molecular Mechannisms” section title needs to be fixed, you spelt ‘mechanisms’ wrong. Other than that, this section is very detailed and has appropriate referencing and images to support the text, thus making it the best section in this page so far.

Current Model for Behaviour during Mitosis section is also very good so far, with appropriate referencing and relevant image. However the image is not really referenced correctly and you need to add the copyright information and the student disclaimer. Limitations of Current Models section has sufficient content so far, with appropriate referencing. It may be a good idea to add another image to support the text, as it is hard to read so much text with no image.

There is no current research section in your page. You should have this section and summarise some recent research papers on golgi apparatus.

The glossary is lacking in words, and the words that are there are not bolded. You need to make the words bold.

Overall the project is good so far but needs a little bit more work.


Group 5 – Nuclear Envelope

The introduction section is very good and detailed, with appropriate referencing. I also like the image, which also has the correct referencing.

The history section is a reasonably good start, with appropriate referencing for the discoveries. You need to add a few more years and descriptions of the discoveries in those years. Perhaps adding some images to support some of the discoveries would make this section look more interesting. The table format is a good idea. However the table is going off the page on the right side, you need to fix that.

Structure of the nuclear envelope section is very detailed with appropriate referencing. However I only see 1 line for the outer nuclear membrane. It would be good to add a little bit more information. There is only 1 image in this whole section, and although it has the correct referencing, the thumbnail image does not have a description. I noticed you have the 1 line description at the bottom of the section. You need to add that under the thumbnail. It would be good to also add another image in this section to support the text to make it easier to understand. The Nuclear Envelope At the Onset of Mitosis section is also very detailed with appropriate referencing. However there are no images in this section. It would be good to add an image in this section to support the text to make it more interesting and easier to understand.

Breakdown of the Nuclear Envelope section is also very detailed with appropriate referencing. There is only 1 image in this whole section, and it has the correct referencing. It would be appropriate to add some more images to support the text as there is a lot of text to read but insufficient image to support it. There are also two subheadings “The Disassociation of the Nuclear Envelope From Chromatin” and “The Dispersal of Nuclear Envelope Components into the Endoplasmic Reticulum” with no content under it. You need to add some content under those subheadings.

"Mitotic Functions of Nuclear Envelope Components" and "Reformation of the Nuclear Envelope" sections are very detailed with appropriate referencing. However there are no images in this section. It would be appropriate to add some images to support the text as there is a lot of text to read but no image to support it.

Open vs. Closed/Semi-closed Mitosis section is also very detailed with appropriate referencing. The image is also relevant and has appropriate referencing.

“Abnormalities in Nuclear Envelope Breakdown and Reformation” section does not have much information. It would be good to list a few more complications and their descriptions.

Current and Future research section is very good so far. It would be good to add one or two more images from the research papers you were discussing, to support the text.

The glossary section is significantly lacking in words.

Overall the project is excellent so far.



Group 6 – Anaphase

The introductory paragraph is a good start, but needs some more work. Perhaps a little bit more description briefly summarising the other sections of the wiki page in the introduction would make it more substantial. There are also no references. There is a nice image in this section, but it does not have the reference.

“Meiosis versus mitosis” section is very brief. You need to add some more detail and perhaps add some images to support the text.

The history section is lacking content. You need to add more years and descriptions of the discoveries in those years. It’s good that you have added references for each of the discoveries you’ve mentioned so far. However the references are external links. You need to make the references on the actual wiki page so that they appear at the bottom of the wiki page in the references section. Perhaps adding some images to support some of the discoveries would make this section look more interesting. The table format is a good idea.

Metaphase to anaphase transition (MAT) section is also quite brief.

Process of sister chromatid separation is detailed and has appropriate referencing. However there are no images in this section. It would be good to add an image to support the text.

“Anaphase to telophase”, “Chromosomal motors” and “Molecular aspect of anaphase” sections are all reasonably detailed so far, and has appropriate referencing. However there are no images to support the text. It would be good to add some images.

Kinetochores section has a good image with the correct referencing.

“Defects resulting from anaphase malformation” section is very good so far, with correct referencing. However, the text are all too close together, it would be better to put some spaces between the dot point paragraphs. The two images in this section have correct referencing. Current research section is reasonably good so far. You need to add some more images to support the research papers you were summarising.

The glossary list has some words with no definitions next to them. Please add the definitions soon. Overall the project is moderately good but needs some more work.


Group 7 – Mitochondria

The introduction is appropriate and concise and has appropriate referencing. There is an ‘error’ for the thumbnail image, you need to fix it soon.

The structure section is a good start but is a little brief. Perhaps you should add a bit more information and an image to support the text.

The function section is very detailed and has appropriate referencing. The images are also relevant and support the text and has appropriate referencing.

The history section is reasonably good so far, with appropriate referencing for the discoveries. Perhaps adding some images to support some of the discoveries would make this section look more interesting. The table format is a good idea. However the table is going off the page on the right side, you need to fix that.

“During Cell Division” section is reasonably detailed and has appropriate referencing. It would be good to add an image to support the text, as there is a lot of text to read.

“ Mitochondrial Fission and Fusion” section is also very detailed and has correct referencing. However the thumbnail image in this section does not have a label to describe what it is. After clicking on it, i can see the description then. The referencing for the image is correct.

“Physiological Significance of Mitochondrial Division” is also very detailed with correct referencing. However there is only 1 image in this whole section. Perhaps you should add another image to balance the text.

There is no current research section in your page. You should have this section and summarise some recent research papers on mitochondria, along with some images from those papers.

There is also no glossary section in your page, you need to have a glossary to make it easier for people to understand some words that are difficult to understand.

Overall the project is very good, but needs a bit more work.



References

  1. Martin Pilhofer, Mark S Ladinsky, Alasdair W McDowall, Giulio Petroni, Grant J Jensen Microtubules in bacteria: Ancient tubulins build a five-protofilament homolog of the eukaryotic cytoskeleton. PLoS Biol.: 2011, 9(12);e1001213 PubMed 22162949
  2. Albert Pineda Rodó, Libuše Váchová, Zdena Palková In vivo determination of organellar pH using a universal wavelength-based confocal microscopy approach. PLoS ONE: 2012, 7(3);e33229 PubMed 22470445
  3. Albert Pineda Rodó, Libuše Váchová, Zdena Palková In vivo determination of organellar pH using a universal wavelength-based confocal microscopy approach. PLoS ONE: 2012, 7(3);e33229 PubMed 22470445
  4. R B Nicklas Measurements of the force produced by the mitotic spindle in anaphase. J. Cell Biol.: 1983, 97(2);542-8 PubMed 6885908
  5. D Szollosi, P Calarco, R P Donahue Absence of centrioles in the first and second meiotic spindles of mouse oocytes. J. Cell. Sci.: 1972, 11(2);521-41 PubMed 5076360
  6. R E Stephens A thermodynamic analysis of mitotic spindle equilibrium at active metaphase. J. Cell Biol.: 1973, 57(1);133-47 PubMed 4734864
  7. K Watanabe, M S Hamaguchi, Y Hamaguchi Effects of intracellular pH on the mitotic apparatus and mitotic stage in the sand dollar egg. Cell Motil. Cytoskeleton: 1997, 37(3);263-70 PubMed 9227856
  8. Aurélien Courtois, Melina Schuh, Jan Ellenberg, Takashi Hiiragi The transition from meiotic to mitotic spindle assembly is gradual during early mammalian development. J. Cell Biol.: 2012, 198(3);357-70 PubMed 22851319
  9. Richard Francis, Xin Xu, Hyunsoo Park, Chin-Jen Wei, Stephen Chang, Bishwanath Chatterjee, Cecilia Lo Connexin43 modulates cell polarity and directional cell migration by regulating microtubule dynamics. PLoS ONE: 2011, 6(10);e26379 PubMed 22022608