User:Z3254598

From CellBiology

Lab Attendance

--Z3254598 15:29, 8 March 2012 (EST)Lab 1 - Introduction to Labs

--Z3254598 14:07, 15 March 2012 (EST)Lab 2 - Microscopy Methods

--Z3254598 15:08, 22 March 2012 (EST)Lab 3 - Preparation/Fixation

--Z3254598 14:14, 29 March 2012 (EST)

--Z3254598 14:14, 5 April 2012 (EST)

--Z3254598 14:07, 3 May 2012 (EST)

--Z3254598 14:42, 10 May 2012 (EST)

Was here on may 17, forgot to sign in, did quiz though so can be checked up! Was here on may 24th

--Z3254598 14:01, 31 May 2012 (EST)

Assessments

Lab 1

Lab 1 internal link

Mouse Skull external link

Lab 2

Modular kinetochores.jpg

1. Identify a reference article that uses the "superresolution" microscopy technique.

Lothar Schermelleh, Peter M Carlton, Sebastian Haase, Lin Shao, Lukman Winoto, Peter Kner, Brian Burke, M Cristina Cardoso, David A Agard, Mats G L Gustafsson, Heinrich Leonhardt, John W Sedat Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science: 2008, 320(5881);1332-6 PubMed 18535242


2. What did the paper show that normal microscopy could not show.

In this paper Schermelleh et al. noted that although normal fluorescence light microscopy permits the cellular components to be visualised in various colours, it is limited in providing adequate resolution.

They overcame this problem by applying the use of 3D-SIM. In this paper they use it to study the mammalian nucleus. In particular, with the use of 3D-SIM they were able to "resolve single NPCs"[1], "differentially localize distinct NPC components"[2] and "detect double-layered invaginations of the nuclear envelope"[3], all of which would not be possible with the use of conventional microscopy.

Schermelleh et al. notes that the use 3D-SIM will allow for a greater exploration of the subcellular structures "beyond the diffraction limit of the emitted light"[4]

Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy.

--Z3254598 00:52, 22 March 2012 (EST)


Lab 3

1. Locate a current SDS for one of the fixatives described in today's lab. Identify the properties and hazards associated with that chemical.

Paraformaldehyde SDS

Properties:

White powder Pungent Odor Freezes at 120deg C, Melts at 170deg C, Decomposes at 260deg C Slightly Soluble

Hazards:

Causes severe eye irritation and burns Causes skin irritation, contact with dust causes drying/cracking/scaling of the skin Harmful if inhaled, severe irritation of upper respiratory tract with pain burns and inflammation, may cause loss of smell May be harmful if ingested, may cause stomach pain and damage to digestive tract, may cause nausea, vomiting, diarrhea and possible loss of consciousness.


2. Identify 4 papers (articles or reviews) that relate to your topic. These should be added to the discussion page and also to your individual page (as part of this week's assessment).


K A Davies, V J Toothill, J Savill, N Hotchin, A M Peters, J D Pearson, C Haslett, M Burke, S K Law, N F Mercer A 19-year-old man with leucocyte adhesion deficiency. In vitro and in vivo studies of leucocyte function. Clin. Exp. Immunol.: 1991, 84(2);223-31 PubMed 1673876

This article shows the importance of CD11/18 molecules/antigens in neutrophil recruitment, this was done one a person with Leukocyte Adhesion Deficiency (LAD)


E C Mathew, J M Shaw, F A Bonilla, S K Law, D A Wright A novel point mutation in CD18 causing the expression of dysfunctional CD11/CD18 leucocyte integrins in a patient with leucocyte adhesion deficiency (LAD). Clin. Exp. Immunol.: 2000, 121(1);133-8 PubMed 10886250

This article again shows the importance of the CD11/18 antigens, by observing a patient with an "abnormal" form of LAD, however it still presents the involvemnt of a dysfunction in the CD11/18 antigens


D C Anderson, F C Schmalstieg, M A Arnaout, S Kohl, M F Tosi, N Dana, G J Buffone, B J Hughes, B R Brinkley, W D Dickey Abnormalities of polymorphonuclear leukocyte function associated with a heritable deficiency of high molecular weight surface glycoproteins (GP138): common relationship to diminished cell adherence. J. Clin. Invest.: 1984, 74(2);536-51 PubMed 6746906

This article shows that the functions of polymorphonuclear leukocyte are related to cell adhesive properties which are in turn affected by surface glycoproteins


H M DeLisser, M Christofidou-Solomidou, J Sun, M T Nakada, K E Sullivan Loss of endothelial surface expression of E-selectin in a patient with recurrent infections. Blood: 1999, 94(3);884-94 PubMed 10419878

This article shows the role that E-selectin plays in leukocyte recruitment, and how a problem with its expression can result in similar symptoms to a patient with Leukocyte Adhesion Deficiency, despite having normal functioning neutrophils and other adhesion molecules.

Lab 4

Musashi is a protein that regulates insulin expression, apoptosis and proliferation. Found in 1998.

[5]

Musashi 1 antibody is available from neuromics for 250USD per 50ul http://www.neuromics.com/ittrium/visit/A1x66x1y1x85b1x1x9cy1x6217x1x96y1x581x1x82y1xed7x1x7f

Musashi 1 antibody is polyclonal, hosted in rabbit with race specificity human rat and mouse, can be applied to western blocks, immunohistochemistry and immunocytochemistry

http://www.neuromics.com/site/special/A8x1130x8x1.pdf

488 goat-anti-rabbit igg secondary anti-body, binds with musashi 1 rabbit antibody which has a fluorescent property of chromeosity 488 similar to that of Alexa 488 http://www.neuromics.com/site/special/A8x374bx8x1.pdf

From a different manufacturer, is another goat anti-rabbit secondary anti-body that is conjugated with alexa 488 and will fluoresce green. http://products.invitrogen.com/ivgn/product/A11008

--Z3254598 15:35, 28 March 2012 (EST)

Lab 7

Contribution to Group project to date.

I admit that my contribution to the group project has been fairly poor. I have gathered resources for my topic of the abnormal function of extravasation but have not done much with it. Due to personal family reasons I have been absent, and I know this is no excuse and am will now commit to contributing properly to my group assessment.


Links to Fellow Group Members

Z3288970

Z3217686

z3223095

In Group 8

Lab 8

1. monocyte/macrophage cell line designated as 'SC'

2.Human peripheral blood

3. The original paper was "Continuous mammalian cell lines having having monocyte/macrophage characteristics and their establishment in vitro [6]

Lab 12

1. A current technique for gene sequencing is Next Generation Sequencing

2. Amygdala 14-3-3ζ as a novel modulator of escalating alcohol intake in mice. [7]

3. Microarray analysis was used to determine the time period of the changed gene expression in the mice

Peer Assessments

Group 1

  • Introduction is clear and concise, giving the information I would expect from and intro – not too in-depth but giving a good overview however (take this with a grain of salt as I am uneducated in the topic) but perhaps more should be introduced about testosterone signaling as opposed to just the hormone testosterone. While the image provided has a link, it is missing copyright info.
  • The history section does draw you in, and the information contained therein is good, however while good on its own it does not really fit in with the rest of the page and I do not see any information/meaning of the history section being taken away if the colour was removed.
  • Information contained in the biosynthesis section is good from what I can see however the terms used here being put in the glossary would be good. The table format is quite unnecessary; you can simply list out the steps 1/2/3/4, no need for the table which squishes the info together.
  • I feel as if perhaps more information should be added to regulation, perhaps an elaboration on how it is regulated/more on why it needs to be regulated or what causes testosterone levels to be high or low.
  • Pathway section appears to have a good amount of information in a nice format with appropriate subheadings; images are useful however there is a second wiki image being used.

There are a few grammar issues in the normal function section, aside from this the information contained is good. If possible a few subheadings to easier group the information could be useful.

  • Abnormal function section is done well from the uneducated observer perspective.
  • Clinical uses, like abnormal function is done well, however perhaps putting them in the same format would be ideal given they are presented similarly, that is, perhaps put abnormal function info in a table like that of clinical uses, or simply take the clinical use table and have it as subheadings followed by relevant information – the table, although there is nothing wrong with it, is not necessary. The video is a good example of a useful external link.
  • The numbered points at the start of the research section are mildly confusing in their odd placing, perhaps cutting those points into an introduction as to why research is being done could be more useful. Aside from this, a few formatting edits could improve the section.
  • The glossary is decent and simply needs to be finished off.
  • Reference section has a few errors, 2nd reference is missing/broken. While I understand that the references for 20/22/26 are to a database, perhaps name the database, linking to the inserted link would be better, if not “date accessed” can be put in. For Ref 27, a reference for the paper as opposed to a link to the paper would be better.

Group 2

  • The introduction has good information, however it is a bit short and perhaps informal/has odd language for a wiki “fortunately” perhaps use the word however here, as it is an information giving wiki. If you really feel the need to introduce your page as well as your topic consider rewording your language as “here we will examine” is something I’d expect from an essay, but not necessarily in a wiki page.
  • The history section is good, with the table format being of particular note as it is of the same format of the other tables on the page, giving the entire page a feel of continuity.
  • Normal function begins well, however it is evident by the broken information and lack of citation that it is not yet finished
  • What is done on the signaling pathway section appears good, the use of table and image under VEGFR receptors convey information well. There is nothing under the VEGF subheading however, and it appears that the section VEGFR-3 is unfinished [if it is not, perhaps a “not much is known except that….” Would be useful here”]. Oddly enough this ‘unfinished’ section is cited while the previous sections are not.
  • Abnormal function section has a good layout however captions would be a good addition to the image section.
  • Research section again provides decent information, however it appears significantly more cluttered than the rest of the wiki page, and could perhaps benefit from some formatting edits.
  • References appear ok, and the use of external linking to the glossary is a nice touch, once finished would be very good

Group 3

  • Introduction appears to have good information, although it appears you have yet to finish/edit through it
  • History is done as appropriate, shows that while the history-in-a-table format [groups 1 &2] was not a bad thing, it is not a necessity. For added ‘flair’ though you may wish to consider such a format.
  • Signaling pathway section appears to be unfinished, with despite the rather large list, it only talks about one protein on the list, perhaps after more has been completed the direction of the section may make more sense. The referencing appears to be more a result of simply unfinished work as the format of referencing used here is normally followed by the full citation in the reference list – regardless, it is not the referencing required of the wiki page
  • Function section is a good starting collection of information that looks to be promising once filled out with language made more appropriate for a wiki info page, with a sentence such as “The next link in the chain is how do these effectors contribute to cellular disassembly?” seeming to belong more to an essay than a wiki page
  • the introduction to the Current Research section is good with a bit more expansion possibly needed on the section on cardiovascular disease.
  • throughout the page, citations are not present, although I acknowledge that it appears they have technological issues with such and so I cannot say much for the referencing other than that it is currently missing. Overall more imagery would be a good idea.

Group 4

  • The introduction is short, however it appears to lead that the rest of the page will provide all the information – perhaps some brief generalized info here would be good.
  • The history is formatted well, however again it appears to be too brief – this could simply be because there is not much history on notch signaling but I am unsure
  • There could be more information/elaboration in the pathway section, and there appears to be a distinct lack of citations in this section as well.
  • Again the proteins and receptors section seems fairly unfinished, esp. with the inclusion of the dead internal links. The sections also need to be expanded upon past simple dotpoints as it provides generic and basic information, but not much beyond that. There is also a lack of citations in this section.
  • The normal function section appears very well done, with an appropriate use of subheadings to differentiate the information given, a helpful image as well as a decent amount of citation.
  • The further research section is clearly unfinished, and so not much comment can be given here.

Group 5

  • The introduction is short and concise with the expected generalized basic info needed, although perhaps citations for the end of the 2nd paragraph are needed
  • The history section is well detailed with a fair bit of history and citation for each point. However I am unsure about the need for the figure that is included in the history section – perhaps it would be better placed elsewhere
  • The mechanism of action appears to have a lot of information and be well cited, however I do not believe the dot point format is appropriate for a wiki page – you do not normally see an entire section on a wiki page in dot point format. You could perhaps have an introductory paragraph that leads into further dotpoints, but as of now it seems as if you merely have the outline of the format done
  • The table in the disease section provides nice summarized information, however perhaps more detail as to the mutation would be helpful. Perhaps integrating the treatment options into the table would also be useful, or perhaps make it more clear that the 4 treatment options you have shown are linked to the disease you have shown, as the table is not numbered while your treatment options are.
  • The Key players section is well cited for the most part, and the table format is quite useful for conveying such a large amount of information. Structure is missing for a few of the proteins, making it seem a bit odd. You have also neglected the citation for the structure of the APC protein.
  • Embryonic development section is a nice touch and well cited.
  • Future directions seems to be lacking in citation, and again is in full dot point format, which is probably not the best idea for a wiki page.
  • You have a format error for ref 64

Group 6

  • The introduction section is missing a lot of citation, and not entirely sure if the different subheadings are needed in the introduction.
  • Citation needed for specifications of insulin. Image also missing copyright information
  • History is brief, perhaps more detail can be added, for example “discovery of….” By who? Etc. Also missing a large amount of citations in this section.
  • Good hand-drawn image in the Insulin receptor section, although maybe more information aside from the structures could be useful here
  • The signaling pathway section seems well done with good use of an image, with proper citation, although unsure if perhaps more citation within the paragraphs would be necessary, for example in the last sub-section CAP/Cbl pathway with 2 citations at the end, were the ideas contained therein from both articles and mixed?
  • Normal function section appears to be too brief and lacking in citations
  • Abnormal function section appears to be much more filled out than the normal function, and have a concise bit of information of a variety of defects; however citations would be nice for the Diabetes subsections.
  • Missing citations for 1st sub section of current research section, and perhaps misplaced citations for the Mediterranean research sub section, with the same citations within the paragraph and not at the end – also suggesting earlier on in the page that paragraphs with only citations at the end are not cited mid paragraph
  • Glossary should be expanded

Group 7

  • Introduction has a decent amount of information and nice images [although these are lacking copyright info], however it is evident the formatting has yet to be cleaned up, with the citations not placed correctly – they should be put after the ideas, or at the very least at the end of the paragraph [not best situation] not in a line after the paragraph. The signatures lying around also suggest a need for a clean up
  • History section is well cited, with good use of external links; however a bit of a cleanup is needed here as well
  • Gene description is brief [this may have been what you are aiming for] again however it seems less like a wiki page if you keep saying “this group project” , while this is a group project, the page itself is a wiki not an essay/presentation. Fix up citations as opposed to giving external links
  • Section seems unfinished, perhaps some text to accompany the table would be good, as it stands to the uneducated observer the table seems to say nothing much at all
  • Receptor structure section shows promise, however there appears to be a lack of citations, especially earlier in the section, and a need for a cleanup here as well
  • Pathway and normal function section seems well done, being one of the cleaner sections, however the 1st paragraph under inhibitory pathway section is missing citations, and there are still a few signatures lying around
  • Abnormal function section is nice, apart from the cleanup still required, brief summarizing table, followed by more in-depth, well cited information is very good. Bit of formatting required near the 1st image to fix up aesthetics, including the citation which needs to be fixed up.

Group 9

  • Clean concise introduction, need a bit of a cleanup here with the signatures
  • Pathway section is missing a lot of citation, if all the information is obtained all from ref 6, you should still multi ref throughout the section
  • Receptor and proteins sections empty – the project is not finished so that’s alright, however cannot comment on anything
  • History section done in an easy to read layout, and is well cited for each point with an adequate brief description for most points, however some are confusing and simply require a few more words to make sense /be put into conext for example “p53 is cloned in Drosophila and C. elegans” do you mean that it was discovered/established it did this? Right now it seems as if in the year 2000/2001 this just happened as an event
  • Current research section may be better positioned nearer to the end of the page
  • Normal function is well cited however the sub section titles should be altered for a more aesthetic appeal further elaboration/expansion of information could be helpful
  • Abnormal function too brief if it is finished, citation format error evident


--Mark Hill 13:33, 17 May 2012 (EST) This is a detailed critical analysis of each project, well done. It includes both comments about the scientific content and the project layout.

References

  1. Lothar Schermelleh, Peter M Carlton, Sebastian Haase, Lin Shao, Lukman Winoto, Peter Kner, Brian Burke, M Cristina Cardoso, David A Agard, Mats G L Gustafsson, Heinrich Leonhardt, John W Sedat Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science: 2008, 320(5881);1332-6 PubMed 18535242
  2. Lothar Schermelleh, Peter M Carlton, Sebastian Haase, Lin Shao, Lukman Winoto, Peter Kner, Brian Burke, M Cristina Cardoso, David A Agard, Mats G L Gustafsson, Heinrich Leonhardt, John W Sedat Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science: 2008, 320(5881);1332-6 PubMed 18535242
  3. Lothar Schermelleh, Peter M Carlton, Sebastian Haase, Lin Shao, Lukman Winoto, Peter Kner, Brian Burke, M Cristina Cardoso, David A Agard, Mats G L Gustafsson, Heinrich Leonhardt, John W Sedat Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science: 2008, 320(5881);1332-6 PubMed 18535242
  4. Lothar Schermelleh, Peter M Carlton, Sebastian Haase, Lin Shao, Lukman Winoto, Peter Kner, Brian Burke, M Cristina Cardoso, David A Agard, Mats G L Gustafsson, Heinrich Leonhardt, John W Sedat Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science: 2008, 320(5881);1332-6 PubMed 18535242
  5. M Szabat, T B Kalynyak, G E Lim, K Y Chu, Y H Yang, A Asadi, B K Gage, Z Ao, G L Warnock, J M Piret, T J Kieffer, J D Johnson Musashi expression in β-cells coordinates insulin expression, apoptosis and proliferation in response to endoplasmic reticulum stress in diabetes. Cell Death Dis: 2011, 2;e232 PubMed 22113197
  6. Collins GW, Largen MT. Continuous mammalian cell lines having monocyte/macrophage characteristics and their establishment in vitro. US Patent 5,447,861 dated Sep 5 1995
  7. Heidi M B Lesscher, Julia M Houthuijzen, Marian J Groot Koerkamp, Frank C P Holstege, Louk J M J Vanderschuren Amygdala 14-3-3ζ as a novel modulator of escalating alcohol intake in mice. PLoS ONE: 2012, 7(5);e37999 PubMed 22629472