From CellBiology


--Z3333427 15:13, 8 March 2012 (EST)



MUST -- external link

LAB1 -- internal link


--Z3333427 14:38, 15 March 2012 (EST)

Formation of cristae and crista junction

Cell biology image.png

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 After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at


PMID 19528297

Lab question week 2


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 After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at

In the past, both light and electron microscopy have been limited by low precision and sensitivity. This article discuss the potential of overcoming such limitations though direct mapping of signals. By using∼20 fluorescent protein molecules, and employing them to a 3D tomogram it has been demonstrated that unlike light microscopy, such method has been able to detect individual HIV particles.

--Z3333427 23:18, 16 March 2012 (EST)

--Mark Hill 12:45, 20 March 2012 (EST) You do not need to include the Rockefeller copyright information for the Lab 2 response. You are simply citing the paper and explaining in your own words what the paper has shown.

Lab 3

Current SDS for Paraformaldehyde

Paraformaldehyde (SDS)

Properties of Paraformaldehyde:

  • Flammable solid
  • Pungent odour
  • Forms a strong acidic soloution in water
  • Can potentially cause oxygen depletion in aquatic bath

Hazards of Paraformaldehyde:

  • Severe Irritant
  • result in irritation and blurring of vision
  • gastrointestinal irritation
  • Nausea
  • Vomitting and diarrhoea

Z3333427 14:16, 26 March 2012 (EST)

Lab question 2

1)<pubmed>7540611</pubmed> This article investigates the stimulation of 3T3-L adipocytes with insulin. It investigates the involvement of activation of tyrosine kinase for insulin signalling

2)<pubmed>10459021</pubmed> The primary article investigate the effect of nsulin-like growth factor (IGF) II and its over expression in human cancers.

3)<pubmed>7040416</pubmed> The study of this article provided evidence about the internalization of insulin in hepatocytes.


This article explains the step by step process of internalization of insulin in its target cell. Z3333427 21:21, 28 March 2012 (EST)

LAB 4 Z3333427 14:05, 29 March 2012 (EST)


Musashi is a real protein, which act as a stem cell marker in the nervous system. It binds RNA and is 118 amino acid long. It is roughly 10 kilo Dalton. The Musashi is a 39 kDa RNA binding protein, and is expressed in CNS stem and progenitor cells. It was discovered in 1998, and is a linear antibody. <pubmed>9790759</pubmed>


The company eBioscience supplies 14H1 monoclonal antibody which recognizes human Musashi-1 (MSI-1). It also recognizes mouse and rat Musashi - 1. The monoclonal antibody works with fluorescence immunochemistry and western blotting. Monoclonal antibody used at a concentration of 1 µg/ml.


Z3333427 15:02, 29 March 2012 (EST)

The secondary antibody against mouse with Alexa dye includes the Alexa Fluor 488 Mouse IgG1 supplied by life technologies. The price is $619 AUD, the indicative colour is green with the labeling scale between 1-20 µg. The target isotype includes the IgG1. The emission of the dye is between 495⁄519 nm, and uses fluorescent detection method.

Life Technologies

Z3333427 15:30, 29 March 2012 (EST)

Lab 5

Z3333427 14:08, 5 April 2012 (EST)

Lab 6

Tm4 over expression2.jpg

Z3333427 15:53, 19 April 2012 (EST)

1) What changes were observed between group a and b? The group that included overexpression of Tm4 favoured stumped and pronged phenotypes. The Tm4 group expressed a increase of 15% and 35% for stumped and pronged phenotype respectively. However, the overexpression to Tm4 resulted in a decrease of fan, broken fan and pygnotic phenotypes by 10%, 30% and 3% respectively.

2. What are the changes in phenotype that you observed between the two groups? Phenotype A - Tm4

  • increased branching
  • more connections between cells
  • shorter cells
  • wider diameter
  • more rounded cell body
  • mainly stringed and pronged phenotpyes

Phenotype B - Control

  • decreased branching
  • less amount of connections
  • longer cell bodies
  • thinner cell bodies
  • mnainly stringed phenotype

3. How does Tm4 mediate these changes?

Tropomyosin is a protein found throughout the body in various type of cells. In muscle cells, tropomyosin act by binding to actin, whereas in non muscle cells, tropomyosin isoform influence the regulation functional characteristics of actin filaments and the regulation of the cytoskeleton. The different diagrams provided in this week lab were of Tm4 isoform which were provided to show the important role Tm4 play in neurite development and synaptic plasticity 1)<pubmed>787636</pubmed>. In group A, Tm4 was overexpressed and the result indicated that there was an increase amount of branching and neurite development. In contrast to the control group, group A had more overlapping cells, and the result suggested that more connections were formed, assisting interactions and development between cells. The control group on the other hand had less overlapping cells, with less branching. The above diagram along with the results indicates that Tropomyosin 4 is responsible for phenotypic changes which lead to an increased number of interactions between cells.

Z3333427 16:01, 26 April 2012 (EST)

Lab 7

Z3333427 21:28, 2 May 2012 (EST)

My contribution to the group work up until today

Structure of insulin.JPG

A three dimensional image of an insulin hexamer, in addition to the zinc ions holding it together and the histidine residues involved in zinc binding. This Computer generated image display insulin in it stored form (hexamer), whereas the active form is a monomer.


Insulin is a type of protein that compose of an A chain and B chain. The A chain consists of 21 amino acids while B chain consists 30 amino acids and they are linked together by sulfur atoms.

Signaling Pathway

Autophosphorylation of the IR causes a range of different signalling pathways that includes activation of PI(3) kinase important for glucose metabolism, the MAP kinase cascade required for cell growth and differentiation and the Cbl/CAP pathway required for transportation of glucose vesicles.

Consisting of two extracellular a subunits and two transmembrane b, linked together by disulphide bonds the insulin receptor dectects the presence of insulin which binds to the a subunit. The binding of insulin results in a conformational change, which in turn leads to the autophosphorylation of certain tyrosine residues located in the b subunit [5]. The phosphotyrosine-binding (PTB) domains of adaptor proteins recognises the phosphorylation of these residues The PTB domains are members of the insulin receptor substrate family (IRS) [6], and when phosphorylation of key tyrosine residues takes place on IRS proteins, it is recognised by the Src homology 2 (SH2) domain of the p85 regulatory subunit of PI 3-kinase (a lipid kinase). This in turn leads to the phosphorylation of phsophatidylinositol (4,5) bisphosphate (PtdIns(4,5)P2) by the p110, which the is the catalytic subunit of the PI 3-kinease. The phosphorylation of (PtdIns(4,5)P2) results in the formation of phsophatidylinositol (3,4,5) bisphosphate Ptd(3,4,5)P3. As a result, a downstream effector of Ptd(3,4,5)P3 known as AKT is reqruited to the plasma membrane, which then activates AKT with the aid of protein kinase 3-phosphoinositide-dependent protein kinase-1 (PDK1). After activation, AKT enters the cytoplasm and inactivates glycogen synthase kinase 3 (GSK3) by phosphorylation. The GSK3 then phosphorylates glycogen synthase, a major substrate of GSK3, and therefore promotes glucose storage as glycogen [7].

Z3333427 09:29, 21 April 2012 (EST)

Normal function

During normal function, insulin signalling regulate carbohydrate and fat metabolism in the body. The presence of the peptide results in the uptake of glucose from the blood by cells found in tissues such as liver, muscle and fat. The presence of Insulin inhibit the release of glucagon, and is added gradually into the bloodstream to regulate the blood glucose levels, which could be toxic.

The pancreas is responsible for the production of insulin, however, patients with type 1 diabetes who lack the ability to produce insulin in sufficent amount could still have a normal function of insulin signalling pathway by aquiring an external source of insulin, which in most cases is injected subcutaneously for a longer lasting effect.

Z3333427 21:19, 2 May 2012 (EST) [edit] Abnormal Function

Diabetes is one of many conditions which are a result of a dysfunctional insulin signaling pathway. Type 1 diabetes is a result of failure of producing insulin in the pancreas, and requires the injection of insulin. Type 1 diabetes can arise due to a number of reasons, most which are due to a problem with insulin signaling pathway. Type 2 diabetes is a result from insulin resistance where the cells does not respond to an increased blood glucose level.

The defective responsiveness of cells to insulin uptake in diabetes type 2 is thought to be due the insulin receptor not responding adequately to insulin signaling pathway. [11] [12]

Other conditions that are associated with abnormal signalling pathway include

  • Type 1 Diabetes Mellitus
  • Type 2 Diabetes Mellitus
  • Obesity
  • Hyperlipidemia
  • Hypertension
  • Hyperinsulinemia

Z3333427 20:53, 2 May 2012 (EST) [edit] Current Research

The Wilson Research institute has been active in the research on Insulin and insulin-like growth factor's fundamental roles in nutrient-regulated metabolism and growth. Signals which are defective are known to be factors which contribute to diabetes and a number of human cancer. Links have also been recently found between defective insulin signalling and diseases such as Parkinson's and Alzheimer's disease. However, What remains to be identified are the genes which regulate cellular response to insulin and also the mechanism by which they work.

Z3333427 21:05, 2 May 2012 (EST)


   ↑ X Chang, A M Jorgensen, P Bardrum, J J Led Solution structures of the R6 human insulin hexamer,. Biochemistry: 1997, 36(31);9409-22 PMID:9235985
   ↑ 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 PMID:8376461
   ↑ Y Kawazoe, T Naka, M Fujimoto, H Kohzaki, Y Morita, M Narazaki, K Okumura, H Saitoh, R Nakagawa, Y Uchiyama, S Akira, T Kishimoto Signal transducer and activator of transcription (STAT)-induced STAT inhibitor 1 (SSI-1)/suppressor of cytokine signaling 1 (SOCS1) inhibits insulin signal transduction pathway through modulating insulin receptor substrate 1 (IRS-1) phosphorylation. J. Exp. Med.: 2001, 193(2);263-9 PMID:11208867
   ↑ M F White The insulin signalling system and the IRS proteins. Diabetologia: 1997, 40 Suppl 2();S2-17 PMID:9248696
   ↑ Toru Akune, Naoshi Ogata, Kazuto Hoshi, Naoto Kubota, Yasuo Terauchi, Kazuyuki Tobe, Hideko Takagi, Yoshiaki Azuma, Takashi Kadowaki, Kozo Nakamura, Hiroshi Kawaguchi Insulin receptor substrate-2 maintains predominance of anabolic function over catabolic function of osteoblasts. J. Cell Biol.: 2002, 159(1);147-56 PMID:12379806
   ↑ D E James, R C Piper Insulin resistance, diabetes, and the insulin-regulated trafficking of GLUT-4. J. Cell Biol.: 1994, 126(5);1123-6 PMID:8063851
   ↑ 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 PMID:1500426
   ↑ L M Chuang, S F Hausdorff, M G Myers, M F White, M J Birnbaum, C R Kahn Interactive roles of Ras, insulin receptor substrate-1, and proteins with Src homology-2 domains in insulin signaling in Xenopus oocytes. J. Biol. Chem.: 1994, 269(44);27645-9 PMID:7961682
   ↑ A Kimura, C A Baumann, S H Chiang, A R Saltiel The sorbin homology domain: a motif for the targeting of proteins to lipid rafts. Proc. Natl. Acad. Sci. U.S.A.: 2001, 98(16);9098-103 PMID:11481476
   ↑ R C Feldhoff, T Peters Fragments of bovine serum albumin produced by limited proteolysis. Isolation and characterization of peptic fragments. Biochemistry: 1975, 14(20);4508-14 PMID:1100106
   ↑ Celia Pender, Ira D Goldfine, Jennifer L Kulp, Charles J Tanner, Betty A Maddux, Kenneth G MacDonald, Joseph A Houmard, Jack F Youngren Analysis of insulin-stimulated insulin receptor activation and glucose transport in cultured skeletal muscle cells from obese subjects. Metab. Clin. Exp.: 2005, 54(5);598-603 PMID:15877289
   ↑ L Mosthaf, B Vogt, H U Häring, A Ullrich Altered expression of insulin receptor types A and B in the skeletal muscle of non-insulin-dependent diabetes mellitus patients. Proc. Natl. Acad. Sci. U.S.A.: 1991, 88(11);4728-30 PMID:1711209
  • not certain of which references are mine, but 7 of the 12 are references from my work
Annotation of work

The group project seems to be build upon at a steady rate, and I am pleased with my contribution. The last few weeks would require more team work, however, the basic information have been included and more detailed information is continously being added to the page.

Z3333427 21:32, 2 May 2012 (EST)

Lab 8

Z3333427 14:12, 3 May 2012 (EST)

Z3333427 14:25, 10 May 2012 (EST)

1)Identify a mammalian cell line in the ATCC catalogue (and add a link)

Designation: CHO-K1 ATCC Number is CCL -61

Mammalian Cell Line

2)Identify the original tissue of origin of that cell line

Organism: Cricetulus griseus (Chinese hamster) Tissue: Ovary

3)Identify the original paper that characterised the properties of that cell line


Lab 9

--Mark Hill 13:12, 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.

Group 1:

The whole page seems very organised, and is very easy to follow throughout.

The first thing I noticed was the explicit use of tables which made the information easy to comprehend.

The subheadings in particular for signaling pathway along with the bullet points make the paragraph organized.

It would be great to see the same thing under the heading "normal function" as it is difficult to read the extensively long paragraph without any subheadings.

The Science behind "clinical uses" seems to be accurate, and quite understandable.

All the words which I thought should be in the glossary were explained in a way that could be understood by everyone.

The referencing and copyright all seem to be accurate, and very well done. An excellent page.

However, what I would like to see is which institutes are carrying out the research.

Although it is thoroughly explained, it fails to name who is taking part in the study and who is conducting the study.

A few internal and external links would be good to add in this assignment.

Group 2:

The first thing i noticed was the excellent layout of the page, everything seemed organised. The images seem very intriguing, but it seems that many of them are from Wikipedia.

If you found the original sources for the images, or if some of them were hand drawn it would make the page look excellent. The layout for the abnormal function is great, it is so easy to follow and the information is succinct.

The introduction is also to the point, and so is the history. The research section is great, and very interesting.

The whole page is eye catching and invites the reader to continue reading. The copyright and referencing is correct. The external link makes the page interactive, a few more would be great.

The downside however is mainly in the short glossary of terms which needs to be worked on. There are a large number of words that are difficult to comprehend which I couldn't find in the glossary of terms. Another thing I failed to find is the research groups or institutes which are responsible for the current research.

Group 3:

The basic outline of this page seems ok.

The information is good, but it needs to be put into subheadings and organised better.

My suggestion is to include a few tables and use diagrams/images to explain some of the concepts.

The History is great, I really enjoyed reading it.

The Signal pathway is also descent. The information is all there, it just needs to be organised.

The glossary and referencing needs to be worked on.

There is nothing under the two headings.

The Image has correct referencing as well as copyright information so well done.

A description would go along really well with the image.

Current research has been done very well. I really enjoyed seeing the reference made to the group currently doing the research the "MRC Toxicology Unit in the United Kingdom" which is really great.

Overall, try to work on the referencing, layout of the page, and glossary.

Group 4:

I know that it has already been mentioned, but it is very important that you have a heading for your page.

The introduction seems good and succinct. A picture would be nice at the top of the page.

Using a table for the history is a great idea, but it seems rather to simplistic and incomplete. However, the referencing for the information within the table is good.

The information about the pathway is really informative and detailed. Diagrams and labeled images would be great to explain it further.

Protein receptors, Normal function and Glossary had very good information, and the use of subheadings made everything so much more organised, and easy to follow. However, I realised a number of the links did not work, and I was not quite sure as to what the problem was, something worth figuring out.

The images were did attract my eyes, and did aid me in understanding a number of the concepts.

However, what I failed to find was information about current/future research.

References seems to be correct, and overall the information is quite detailed.

Having said this, the page probably needs more expanding, as the information seems quite limited.

Group 5:

A very well written introduction, in addition to the image at top makes the reader wanting to read more, so well done. The History is extensive, and organised which is great. However, what is "Figure 2 doing next to the history.

Overall structure of the β-catenin/XAxin-CBD complex" doing next to the history?? The referencing for the history is great though.

The mechanism of action is extensive, and the detailed referencing makes the section look complete. I am glad to see that you have included a hand drawn image next to mechanism of action, and it easy to understand which is great. The external link which leads to the movie is a great idea, adding another movie for the history or a different section would also be beneficial.

However, the subheading tumor cells does not belong under the mechanism of action heading. It is good to see that you have included both the on and off state, and have explained the difference pathways

The use of tables and images to explain Diseases associated with Wnt/β-catenin signalling is a great idea. The images found here all have correct references and the right copyright information which is great to see. The Glossary makes everything clear, and it seems to be a great idea to include the abbreviation.

However, what you might consider is adding the meaning of the abbreviation within brackets after the word within the text. At least that way readers wont have to continually scroll up and down.

The external links are great sources. They had some information which I believe you could benefit from. One thing I failed to find is current and future research. Please include that section, as the rest seems very good.

And the reference list is extensive.

Group 6:

My own group

Group 7:

The outline is great and organised. The way the information continues to flow in order make the page easy to follow. The hand drawn images make everything easy to understand. I find these simple diagrams better than complicated images.

More tables and dot points would benefit your page as it would make the information easier to follow. Having said that, don't alter the information too much as it is very detailed and informative.

It is great to see that you have included information under each diagram and image. The explanation you have provided sometimes seem to be too simplistic. Considering that you have the glossary of term at the bottom which explain the words, do not hesitate to include jargon when explaining these images.

The referencing and copyright information for the images seem to be correct. What was particularly good was that you referenced what the hand drawn images were based on.

The external links provide with good information. Using these links, I found that some information could be beneficial for your page. The identification of drugs make the page even more interesting.

Where is your current and future research information. Please include information about research groups and institutes which are leading the way in today's research, and their accomplishment.

Overall great work, it really does show that you have put in a lot of work.

Group 8:

Both the introduction and pathway is clearly explained, and have been written in a logical manner. However, what I did notice is the lack of referencing in the pathway section. Surely you must have got this information from somewhere.

What happened to the history?? Please complete this section as it would benefit your page.

The subheadings used for normal function, abnormal function and proteins is really well done. The glossary needs to be extended as there are a number of abbreviations could not be understood.

I did notice that a number of things were missing in your page. External links, I couldn't find any. A number of links could be great to include. A link to a movie which would explain the signaling pathway would also be great.

Current and Future research is left blank. Please include information about what research is taking place and which research groups/institute are responsible for it.

overall the content is correctly cited and referenced, and the layout of the page is really good. The first image, and a few others don't have the copyright information. It would be a good idea to include it. A few tables and more diagrams would make the information easier to understand.

Group 9:

The introduction seems to go into too much detail. This is not necessary for an introduction. Some of the information provided seem to relate more to other part of the page including normal, and abnormal function. A large image or diagram would go well at the top of the page as colour would attract the reader to continue down the page.

The information and referencing in the pathway section seems fairly good, but it is so disorganized. I did not want to continue to read because it was just a paragraph with sentences. Employing more tables, dot points and even subheadings would make the information stick out much better, and become easier to read.

Why is there so little/no information under the heading of protein, abnormal function, and current research. It makes the page look incomplete. In order to attract the readers eye, you need to include more text, images and links. You need to make this page more interactive. Try to include some links which direct the reader to a movie which explains the signaling pathway or abnormal function.

The images are way to small. I cannot make any sense of them without having to click into the images. I would at least want to have some sort of an idea of what im looking into before i open a larger image. There seems to be a mismatch between the order of the sentences, maybe include history after introduction, and current/future research right before the glossary of terms.

The table about the History is really informative, and the detailed referencing gives a sense of reliability. It is good to see content correctly referenced and the copyright information available in each image.

The referencing looks really good. However I did notice that same reference have been repeated a number of times with a different number. Why is that? Have you used the wrong reference? Overall the page looks decent. Some colour, images, links and subheadings would make the page look better/

Z3333427 14:19, 17 May 2012 (EST)

LAB 10

Z3333427 14:04, 24 May 2012 (EST)

LAB 11

Z3333427 15:00, 31 May 2012 (EST)

Lab 12 - Microarray

1. Identify a current technique used in gene sequencing.

  • next generation sequencing

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

  • <pubmed>22081366</pubmed>

3. What aspect of the research findings were contributed by the microarray technique.

  • Phylogenetic Microarray technology was used to characterize intestinal microbiota, a genus of evergreen coniferous shrub in the cypress family Cupressaceae. In order to characterize microbiota it is necessary to use high throughput 16S rRNA gene based microarray analysis <pubmed>22081366</pubmed>. In this research paper, Phylogenetic Microarray technology was compared and contrasted with barcoded pyrosequencing (a technique to test bacterial composition from a large number of samples by looking at their 16S rRNA genes) in order to analyse the bacterial composition in fecal and small intestinal samples<pubmed>17932070</pubmed>.