User:Z3333794

From CellBiology

--Z3333794 15:13, 8 March 2012 (EST)

Lab Attendance

LAB 1

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Lecture 2

My 1st lab in Cell Biology!

LAB 2

--Z3333794 14:40, 15 March 2012 (EST)

Actin and Microtubules lined together.jpg

Reference

L M Griffith, T D Pollard Evidence for actin filament-microtubule interaction mediated by microtubule-associated proteins. J. Cell Biol.: 1978, 78(3);958-65 PubMed 568144


Individual Task

Analysis of Replication Factories in Human cells using "Supperresolution" Microscopy

Using Stimulation Emission Depletion microscopy or STED scientists now have a better understanding of the way nuclear replicating factories work. In earlier works approximately 150 RPA factories were thought to exist in the S-phase of replication that gave rise to 3000 replicating forks but using the super resolution techniques it is established that as much as 1200 factories exist each giving rise to 2-3 forks.

Zoltan Cseresnyes, Ulf Schwarz, Catherine M Green Analysis of replication factories in human cells by super-resolution light microscopy. BMC Cell Biol.: 2009, 10;88 PubMed 20015367



Rockefeller University Press Copyright Policy 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/).

--Z3333794 14:03, 22 March 2012 (EST)

Lab 3

Possible references for Group Project

J Bass, G Chiu, Y Argon, D F Steiner Folding of insulin receptor monomers is facilitated by the molecular chaperones calnexin and calreticulin and impaired by rapid dimerization. J. Cell Biol.: 1998, 141(3);637-46 PubMed 9566965

The article uses pulse-chase labelling technique to follow the steps involved in the maturation process of the IR protein. This will make it more clear how the structure of the IR forms and binds to insulin.


J M Backer, S E Shoelson, M A Weiss, Q X Hua, R B Cheatham, E Haring, D C Cahill, M F White The insulin receptor juxtamembrane region contains two independent tyrosine/beta-turn internalization signals. J. Cell Biol.: 1992, 118(4);831-9 PubMed 1500426

This article describes the structure and function of tyrosine residues on the insulin receptor.


J L Carpentier, J P Paccaud, J Backer, A Gilbert, L Orci, C R Kahn, J ] Baecker J [corrected to Backer Two steps of insulin receptor internalization depend on different domains of the beta-subunit. J. Cell Biol.: 1993, 122(6);1243-52 PubMed 8376461

This article provides with information on different receptor domains required for different internalisation steps.


H U Haring, M F White, C R Kahn, M Kasuga, V Lauris, R Fleischmann, M Murray, J Pawelek Abnormality of insulin binding and receptor phosphorylation in an insulin-resistant melanoma cell line. J. Cell Biol.: 1984, 99(3);900-8 PubMed 6381509

This is an article from 1984 that describes activity of tyrosine kinase linked insulin receptor. It can help to outline the basic steps in insulin signalling.

Acetone

Physical and Chemical Properties

Physical state and appearance: Liquid.

Odor: Fruity. Mint-like. Fragrant. Ethereal

Taste: Pungent, Sweetish

Molecular Weight: 58.08 g/mole

Color: Colorless. Clear

pH (1% soln/water): Not available.

Boiling Point: 56.2°C (133.2°F)

Melting Point: -95.35 (-139.6°F)

Critical Temperature: 235°C (455°F)

Specific Gravity: 0.79 (Water = 1)p. 4

Vapor Pressure: 24 kPa (@ 20°C)

Vapor Density: 2 (Air = 1)

Volatility: Not available.

Odor Threshold: 62 ppm

Water/Oil Dist. Coeff.: The product is more soluble in water; log(oil/water) = -0.2

Ionicity (in Water): Not available.

Dispersion Properties: See solubility in water.

Solubility: Easily soluble in cold water, hot water.

Hazards

Potential Acute Health Effects: Hazardous in case of skin contact (irritant), of eye contact (irritant), of ingestion, of inhalation. Slightly hazardous in case of skin contact (permeator).

Potential Chronic Health Effects:

CARCINOGENIC EFFECTS: A4 (Not classifiable for human or animal.) by ACGIH. MUTAGENIC EFFECTS: Not available.

TERATOGENIC EFFECTS: Not available. DEVELOPMENTAL TOXICITY: Classified Reproductive system/toxin/female,

Reproductive system/toxin/male [SUSPECTED]. The substance is toxic to central nervous system (CNS). The substance may be toxic to kidneys, the reproductive system, liver, skin. Repeated or prolonged exposure to the substance can produce target organs damage

--Z3333794 14:35, 29 March 2012 (EST)

Lab 4

--Z3333794 14:58, 29 March 2012 (EST)

Musashi (homo sapiens) homologe 1 is a a neural RNA-binding protein putatively expressed in CNS stem cells and neural progenitor cells. It is a stem cell marker. It is 362 amino acids long and is about 10 KD heavy.

Musashi Protein

P Good, A Yoda, S Sakakibara, A Yamamoto, T Imai, H Sawa, T Ikeuchi, S Tsuji, H Satoh, H Okano The human Musashi homolog 1 (MSI1) gene encoding the homologue of Musashi/Nrp-1, a neural RNA-binding protein putatively expressed in CNS stem cells and neural progenitor cells. Genomics: 1998, 52(3);382-4 PubMed 9790759


A monoclonal antibody found for Musashi is found in Rabbits IgG supplied by Cell Signalling technology (XP® Rabbit mAb #5663). The antibody works with Immunofluorescence and Western Blotting and reacts with humans, mouse ans rats.

Musashi Antibody

Musashi-1 (D46A8) XP™ Rabbit mAb Data Sheet

The Anti-IgG Antibody is The Alexa Fluor 633 rabbit anti—goat IgG is labeled with our bright far-red—fluorescent Alexa Fluor 633 dye. It is available in 2mg/mL dilutions.

Anti IgG antibody

Lab 5

--Z3333794 14:06, 5 April 2012 (EST)

The use of genetically modified mouse models to study Cytoskeleton

Lab 6

--Z3333794 14:07, 19 April 2012 (EST)

Cytoskeleton Lab Exercise - In this exercise the difference in phenotype morphology between over-expressing and control cells was oberserved.

Dofference in phenotype morphology of control and tropomyosin 4 over-expressing cells.jpg

Do you see a difference in phenotype morphology between TM4 over expressing and control cells?

Group a represents overexpression while group b represents the control group. The graph exhibits that the control group shows more fan and broken fan phenotypes whereas cells with overexpressing TM4 show a greater amount of stumped, pronged, stringed phenotypes and pygnotic phenotypes.

If so how could TM4 over expression lead to this difference?

Since later developing phenotypes like stumped, pronged and stringed are highly expressed in cells containing excess TM4 we can conclude that TM4 has a role in growth of neuritis including neurite motility and synaptic plasticity. Tropomyosin is suggested to play a role in actin based motility which explains why TM4, an isoform of tropomyosin when overexpressed in cells exhibits more of the latter phenotypes

Beáta Bugyi, Dominique Didry, Marie-France Carlier How tropomyosin regulates lamellipodial actin-based motility: a combined biochemical and reconstituted motility approach. EMBO J.: 2010, 29(1);14-26 PubMed 19893490


Lab 7

--Z3333794 14:17, 26 April 2012 (EST) So far in my group project for group 6 I have done the following things:


1. Insulin receptor structure - description and diagram

2. Insulin signalling pathway - Ras pathway and CAP pathway

3. Organised the references system

Lab 8

According to ATCC mammalian cell line is HeLa S3 [1]. It is derived from Homo sapiens from the cervix epithelium. The first paper to characterize its properties is T T Puck, P I Marcus A RAPID METHOD FOR VIABLE CELL TITRATION AND CLONE PRODUCTION WITH HELA CELLS IN TISSUE CULTURE: THE USE OF X-IRRADIATED CELLS TO SUPPLY CONDITIONING FACTORS. Proc. Natl. Acad. Sci. U.S.A.: 1955, 41(7);432-7 PubMed 16589695

.

Lab 9

--Z3333794 14:05, 10 May 2012 (EST)

Review the group project

Paste Assessment on discussion page

Do not put signature

Strengths and weakness

Do not use 'spectacular, magnificent' etc.

Not extreme judgment

Examples from their page

Group 1 - The overall group work is constructed very well as it is easy to understand the content. The project page demonstrates a good structure as well as satisfying the requirement of the assessment. The use of purple in the history section adds brightness to the page and draws attention to the text. In the biosynthesis section however, I do not see the point of clustering the information into a table as adds messiness to the page. You can simply present the information as dot points. Although the project page obeys the given criteria, one aspect is not followed; Mark clearly indicated that only one wiki image could be referenced in our projects however the images of Testosterone binding to androgen receptor and Steroidogenesis, are both referenced from Wiki. There was no student drawn image on the page.


Group 2 - The organisation of the page is very simple and easy to follow. I like the use of table and the image in the beginning attracts the readers and the table summarises the history nicely. There is generally a good balance between content and pictures but the sigannling section need more information like interaction of certain proteins that cause the interaction perhaps. You could also describe the receptor structure and how that helps in the signalling process. Your abnormal section is exceptionally good with the table. The research part is very interesting to read as well especially with the pictures. Overall the page itself is very well organised and intriguing to read but a bit more information will be good to clear the pathway.


Group 3 - ntroduction is well detailed and gives a reader a sense of the rest of the page. The history is also a good overview because there is not an overload of information. In the signalling pathway section the proteins listed should be in the glossary because some of them are not in the actual summary and the reader does not know why they are there. The signalling pathway itself is very technical a digram or picture will make it easier to follow. There is too much information in the normal function and having sections will make it easier to read. I liked the current research section is very interesting. There are no references on the page or any glossary so you should get cracking on that and you dont have a self drawn digram either. You need to add more pictures illustrating the signalling process. You could add an abnormal functioning part as well and add some diseases that are caused due abnormal apaptosis.


Group 4 - You need to put up a title heading on the page.

The introduction is nice and brief.

Your use of colour in the history table is very eye catching and not straining on the eyes so it is very inviting.

The actual pathway is easy to understand but it would be good if you specified which notch pathway it is.

The normal functioning part is the most well done...enough info and nice use of headings.

Also the use of videos is also ingenious to explain the pathway.

In the future research u should really explain what and how the research is being done and the benefits.

Don't forget to put a self made drawing on the page.


Group 7 - A very well planned and researched page...seems like all the group members have put effort into it.

Fine tuning of the page is required by getting rid of the signs.

The balance between pictures and text is good to.

The introduction should be brief and an overview...you have too much information in it. Make it a little concise if you can because it makes it very tedious to read.

The self drawn diagram is very good and all the pictures have correct citations.

For all the information provided the journal articles used are very less for e.g. the 1st para of inhibitory pathway has no citation at all and the regulation of beta arrestin has one article ref. Maybe you should have another article that just confirms the studies of this one.

There is no future perspective part...I dont know if that is compulsory but adding that will highlight your paper more.


Group 8 - Hey guys! it looks like your page is coming together well.

First thing i noticed is the heading but you should put down that its the signalling pathway that ull be discussing on the page.

The normal and abnormal function are very well done. With the proteins section you have done bring it into context so we know why ur talking about them....maybe try to include them in the siganlling section.

The balance between text and pictures is very skewed so try add more pictures and I also noticed that u havnt put up a self drawn image yet.

The parts written so far just need minor adjustments with the punctuations but overall well written.

The history and current research part is what you should start writing soon.


Group 9 - Overall the page is very rough and a little unorganized.

I found that the order in which the page is set out is very illogical...if u can put the history up the top we know the order in which the signaling pathway is been progressing. also current research should follow all the normal functioning and can be the climax of the page rather than being in the middle.

You need to get rid of all the signatures and provide details under the headings like and protein.

Normal functioning is well done but you need to correct the formatting especially with the spaces after each headings.

Abnormal functioning does not have enough text in it so you need to expand upon that.

You can make the page more inviting by adding more pictures in and you have to put a self drawn image in there so don't forget that.


--Mark Hill 13:23, 17 May 2012 (EST) You have not completed the peer assessment process yet. If you have made comments on each project page they need also to be pasted here today for me to include in your individual assessment.


Lab 10

--Z3333794 14:56, 17 May 2012 (EST)

Lab 11

--Z3333794 14:05, 24 May 2012 (EST)

Working on group project.

Student Number 3291300 not present today.

Lab 12

--Z3333794 14:04, 31 May 2012 (EST)

Microarray Questions

Identify a current technique used in gene sequencing?

Next generation microarray sequencing provides a current, highly competent technique in gene sequencing. Following the human genome project there is a high technological advance in the way gene sequencing is done. Next Gen Sequencing provides a user friendly and highly accurate technology which has opened many avenues for cancer research, diabetes and other diseases that have a great impact on human life. The following review article lists the benefits of Next Gen Sequencing.

<pubemd>18262675</pubmed>


Identify a recent cell biology research paper that has used microarray technology?

What aspect of the research findings were contributed by the microarray technique?

http://www.sciencedirect.com/science/article/pii/S0167701212001911?v=s5