From CellBiology

Lab Attendance

--Z3333204 15:13, 8 March 2012 (EST)

--Z3333204 14:08, 15 March 2012 (EST)

--Z3333204 14:09, 22 March 2012 (EST)

--Z3333204 14:12, 29 March 2012 (EST)

--Z3333204 14:10, 19 April 2012 (EST)

--Z3333204 14:15, 26 April 2012 (EST)

--Z3333204 14:47, 3 May 2012 (EST)

--Z3333204 14:15, 10 May 2012 (EST)

--Z3333204 14:14, 17 May 2012 (EST)

--Z3333204 14:12, 30 May 2012 (EST) attended on 24 May 2012 but forgot to register my attendance

--Z3333204 15:18, 31 May 2012 (EST)

Lab 1

SMH - external link

group - internal link

Lab 2

DNA in chloroplasts and mitochondria.jpg

Title: Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions

Description: The paper looks at the experimental examination of a sample of PtK1 cells expressing a certain photo-activatable green fluorescent protein using the technology of the superresolution microscopy. Results show a total of 144 individual single molecules being identified in a sample, yielding 998 total localisation measurements. Unlike normal microscopic methods, this method of superresolution microscopy is not bound by the traditional limit of resolution set by diffraction but rather by the localisation precision of the individual molecules. Hence we are able to identify a greater number of individual molecules, and to an immense degree of precision.



Proceedings National Academy of Sciences (PNAS) Liberalization of PNAS copyright policy: Noncommercial use freely allowed Note original Author should be contacted for permission to reuse for Educational purposes. See also PNAS Author Rights and Permission FAQs

Cozzarelli NR, Fulton KR, Sullenberger DM. Liberalization of PNAS copyright policy: noncommercial use freely allowed. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12399. PMID15314225 "Our guiding principle is that, while PNAS retains copyright, anyone can make noncommercial use of work in PNAS without asking our permission, provided that the original source is cited."

Lab 3


<pubmed>21554430</pubmed> Description: The article talks about the effects of the use of anabolic androgenic steroids, mainly concerned with the regions in the brain that are being activated. This is related to our topic of testosterone signalling involving the neural pathways involved


<pubmed>21651570</pubmed> Description: The article talks about the importance of androgen signalling in the differentiation and function of adult Leydig cells. The synthesis of testosterone is dependent on the development of these Leydig cells, hence understanding the mechanisms involved is essential in grasping the idea of testosterone signalling


<pubmed>22319659</pubmed> Description: This article talks about testosterone signalling and its involvement in spermatogenesis. The article is mainly concerned with the main cellular target of testosterone signalling, being the Sertoli cells


<pubmed>22405892</pubmed> Description: The article talks about several molecules that are involved in the testosterone signalling pathway, such as seladin-1, in which its expression is severely moduled by the effect of testosterone


Physical and Chemical Properties


Solubility (water): SLIGHTLY SOLUBLE


Specific gravity: 1.48


% Volatiles: 100 %

Vapour pressure: 213 hPa @ 20°C

Flammability: NON FLAMMABLE

Vapour density: 4.25 (Air = 1)


Boiling point: 61°C to 62°C

Upper Explosion Limit: NOT RELEVANT

Melting point: -63.5°C (Approximately)

Lower Explosion Limit: NOT RELEVANT

Evaporation rate: 11.6 (Butyl acetate = 1)

Autoignition temperature: 982°C

Decomposition temperature: NOT AVAILABLE

Partition coefficient: 1.97 (Octanol/Water)



Toxic - irritant: This product has the potential to cause adverse health effects. Use safe work practices to avoid eye or skin contact and inhalation. Over exposure may result in nerve, liver, kidney and lung damage. Central nervous system and cardiac depressant. Experimental teratogen. Chloroform is classified as possibly carcinogenic to humans (IARC Group 2B).

Eye: Irritant. Contact may result in irritation, lacrimation, pain and redness. May result in burns with prolonged contact.

Inhalation: Toxic - irritant. Over exposure may result in irritation of the nose and throat, coughing, nausea, headache, fatigue, loss of appetite and vomiting. High level exposure may result in dizziness, breathing difficulties, pulmonary oedema and unconsciousness.

Skin: Irritant. Contact may result in drying and defatting of the skin, rash and dermatitis. May be absorbed through skin with harmful effects.

Ingestion: Toxic - irritant. Ingestion may result in nausea, vomiting, abdominal pain, dizziness, fatigue and diarrhoea. Ingestion of large quantities may result in liver and kidney damage, and unconsciousness. Aspiration may result in chemical pneumonitis and pulmonary oedema.

Toxicity Data: No LD50 data available for this product.

--Mark Hill 19:40, 26 March 2012 (EST) This meets the assessment criteria.

Lab 4

Musashi is an RNA binding protein expressed in the CNS and in Beta cells. Musashi is encoded by the MSI1 gene. Musashi is a stem cell marker

The size of the protein is 362 amino acids

There are varieties of Musashi, such as Musashi 1 and Musashi 2

Musachi discovered in 1998


description: Anti-Musashi 1 / Msi1 antibody

specie specificity: mouse, human


molecular weight: 39 kDa

tested applications: ICC/IF (immunochemistry), WB (western blotting)

concentration: 100 µg at 1-1.4mg/ml (use above this range will cause non-specific binding)\

Secondary antibody

Alexa Fluor 647 goat anti—rabbit IgG

price: $350

colour: bright, far-red

dilution factor: 2mg/ml

Lab 6


A: What are the differences in phenotype (morphology) between Tm4 over-expressing cells and control cells?

Tm4 cells vs control cells.png

It seems that the morphology of the control cells revealed the opposite characteristics compared with the Tm4 induced cells. Thus it can be established that Tm4 cells are involved in cell motility, hence exposing these defined characteristics.

B: If so, how could Tm4 over-expression lead to this difference?

Tropomyosin 4 is a member of the tropomyosin family of actin-binding proteins involved in the contractile system of striated and smooth muscles and the cytoskeleton of non-muscle cells. Tm4 studies have exposed its presence in the embryonic heart, neurites as well as osteoclasts.

Tropomyosins are dimers of coiled-coil proteins that polymerise end-to-end along the major groove in most actin filaments. They provide stability to the filaments and regulate access of other actin-binding proteins. In muscle cells, they regulate muscle contraction by controlling the binding of myosin heads to the actin filament. This occurs by the binding of Tm to actin hence acting as a molecular barrier by preventing the cross-bridge cycle from occurring, which is normally what occurs in relaxed muscle. After the release of calcium ions, their binding causes a conformational change to troponin, hence shifting Tm's position on the actin filament and exposing the myosin binding sites. As a result Tm4 cells result in altering the cells motility, hence exposing the observed characteristics.


C: What are the differences in phenotype (morphology) between cAMP over-expressing cells and control cells? CAMP induced vs control.png

D: If so, how could cAMP over-expression lead to this difference?

Cyclic adenosine monophosphate is a second messenger important in many biological processes. cAMP is derived from adenosine triphosphate and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway. cAMP is mainly used for intracellular signal transduction, such as transferring into cells the effects of hormones like glucagon and adrenaline, which cannot pass through the cell membrane. cAMP is also important in the binding and regulation of the function of specific ion channels. The main effect of cAMP in eukaryotic cells is its activation of protein kinase (which is normally inactive in the cell). cAMP binds to specific locations on the regulatory units of the protein kinase, causing dissociation between the regulatory and catalytic subunits, thus activating the catalytic units and enabling them to phosphorylate substrate proteins. Thus the differing characteristics of Genotype A are demonstrated, as a result of these stimulating effects of cAMP on the cell.

Lab 7

On the first week of assessment I posted up four papers that were related to out group work project, as well as listing their relevance to our group topic.

     J G Oberlander, D M Porter, C A A Penatti, L P Henderson Anabolic androgenic steroid abuse: multiple mechanisms of regulation of GABAergic synapses in neuroendocrine control regions of the rodent forebrain. J. Neuroendocrinol.: 2012, 24(1);202-14 PMID:21554430
     Description: The article talks about the effects of the use of anabolic androgenic steroids, mainly concerned with the regions in the brain that are being activated. This is related to our topic of testosterone signalling involving the neural pathways involved
     M Welsh, L Moffat, K Belling, L R de França, T M Segatelli, P T K Saunders, R M Sharpe, L B Smith Androgen receptor signalling in peritubular myoid cells is essential for normal differentiation and function of adult Leydig cells. Int. J. Androl.: 2012, 35(1);25-40 PMID:21651570
     Description: The article talks about the importance of androgen signalling in the differentiation and function of adult Leydig cells. The synthesis of testosterone is dependent on the development of these Leydig cells, hence understanding the mechanisms involved is essential in grasping the idea of testosterone signalling
     William H Walker Testosterone signaling and the regulation of spermatogenesis. Spermatogenesis: 2011, 1(2);116-120 PMID:22319659
     Description: This article talks about testosterone signalling and its involvement in spermatogenesis. The article is mainly concerned with the main cellular target of testosterone signalling, being the Sertoli cells
     Hengbing Zu, Junfeng Wu, Jianfeng Zhang, Min Yu, Zhen Hong Testosterone up-regulates seladin-1 expression by iAR and PI3-K/Akt signaling pathway in C6 cells. Neurosci Lett: 2012; PMID:22405892
     Description: The article talks about several molecules that are involved in the testosterone signalling pathway, such as seladin-1, in which its expression is severely moduled by the effect of testosterone

From the second week of assessment I had an image posted up, with appropriate referencing attached. This image was related to a study on testosterone signalling


After this I mapped out several pages in my exercise book about the points necessary for our group task, mainly to give myself an idea on the extend of work required for the entire task.

I then started on building some information on the introduction part of the group task.

    Testosterone is an androgen*. Androgens are synthetic compounds that stimulate or control the development or maintenance of male characteristics in vertebrates by binding to androgen receptors*. Testosterone in particular has very strong affinity for the Androgen receptor*
    Androgen receptors are 'nuclear receptors' which are activated by the binding or adrenergic hormones in the cytoplasm and then translocating into the nucleus.
    Testosterone has two main pathways, Androgenic; which is mainly responsible for the development of sex differences, and Anabolic which is the metabolic pathway, responsible for muscle and bone growth.

I then did most of my research on the 'biosynthesis' as well as the 'signalling pathway' for testosterone signalling. This included the posting of several important notes and attaching their relevant references. Throughout this I also posted some important images relavent to this research.

    Like other steroid hormones, testosterone is derived from cholesterol (see figure to the left).[98] The first step in the biosynthesis involves the oxidative cleavage of the sidechain of cholesterol by CYP11A, a mitochondrial cytochrome P450 oxidase with the loss of six carbon atoms to give pregnenolone. In the next step, two additional carbon atoms are removed by the CYP17A enzyme in the endoplasmic reticulum to yield a variety of C19 steroids.[99] In addition, the 3-hydroxyl group is oxidized by 3-β-HSD to produce androstenedione. In the final and rate limiting step, the C-17 keto group androstenedione is reduced by 17-β hydroxysteroid dehydrogenase to yield testosterone.
    M R Waterman, D S Keeney Genes involved in androgen biosynthesis and the male phenotype. Horm. Res.: 1992, 38(5-6);217-21 PMID:1307739
    M X Zuber, E R Simpson, M R Waterman Expression of bovine 17 alpha-hydroxylase cytochrome P-450 cDNA in nonsteroidogenic (COS 1) cells. Science: 1986, 234(4781);1258-61 PMID:3535074

I also did some research into the structure of the testosterone molecule, as well as posting an image of the structure.

Testosterone Structure
    Testosterone Structure
    Molecular formula: C19H28O2
    Molecular weight: 288.42442

Furthermore I recently added a gallery of the images at the bottom of the page, mainly as a collection of all the images used in our assessment for ease of inspection.

Lab 8

Mammalian cell line CHO-K1


Original tissue of origin From the Ovary of the species Cricetulus griseus (epithelial-like)
Original paper characterising the properties of that cell line <pubmed>13598821</pubmed>

Lab 9

Group 2

First of all I am very impressed with the overall layout and structure of the page. It is very easy on the eye, simple to follow, and very neatly arranged. The use of tables is quite impressive, especially in certain sections demanding structure and organisation.

  • The introduction is quite succinct, however maybe a bit more information about the depth of the overall scope of the topic would be interesting to add, such as all the deferent types of VEGFs, despite basing your research on a VEGF-A.
  • The History is set out very neatly, however I do sense there must be some more discoveries about VEGF
  • The Normal function section doesn't seem to be complete yet so I can't say too much about it, however I do hope citations to be added. Also the addition of images should enhance the interactivity
  • The section for Abnormal function is done very well and there is not much that I could criticise about it appart from the origin of the images.
  • The Glossary section must be filled with more terms, as there were many terms within the text that I did not initially comprehend
  • I appreciate the use of an interactive image at the top of the page, which seems to heighten the readers intrest (as it did with me). Most images seem to have the correct copyright information displayed, however I realised the use of more than one wikipedia image, which is against the specification of the assessment.
  • The addition of related study links seem to be very useful. Also Internal links for the glossary was a very intelligent addition
  • Some extra points:
    • Adding some more citations to support your information would enhance the validity of your research
    • There are some minor grammer and punctuation errors, however I am assuming these woud be corrected towards the end
    • Appart from the subsection for 'signalling pathway', maybe you can also add a subheading describing the 'Formation of VEGF'
    • There still doesn't seem to be any sketch relating to your research

Group 3

  • Introduction seems to be way too detailed. This section should look mainly at introducing the topics that will be discussed later on in the page. This information is far too detailed to comprehend at the beginning of the text. Also maybe the inclusion of an interactive image at the top would be a good addition.
  • The History section seems ok, off course in terms of the content displayed. However I will strongly stress the point of referencing, as it is very important to enhance the validity of the information, as well as the origin of the information.
  • Under signalling pathways I find that the listing of proteins involved in the pathway should rather be added in a separate section, such as 'proteins involved'. Otherwise the information on 'Fas-Mediated Apoptosis' seems to be great, and I can see that the references have been added. Please make sure to hyperlink these references, hence to display numbering after the writing and to have a list of references at the bottom of the page.
  • For the Function section the information seems to make good sense, however I found that making large slabs of information is rather not very appealing for the reader and quite difficult to follow. Therefore it would be nice to have the information organised more succinctly, such as through the use of tables or bullets. Also in terms of the appeal, look into the addition of several images relating to the study.
  • Under the Current research it seems there is some interesting study collected about your topic, however once again this should be organised more neatly. Please include referencing as stated earlier. Furthermore when adding images, it would be useful to incorporate thumbnails rather than just dumping the image, as it causes too much distortion to the surrounding text.
  • There seems to be a lot of information displayed, but the biggest blunder is that there seems to be a great lack in references. Hopefully this issue is addressed because it is going to be the most crucial aspect of the assessment.
  • Unfortunately it seems that not too much time was spent on this assessment til date, however it is never to late to get everything patched up. Look into other small additions such as additional subheadings (such as glossary) as well as a 'gallery' of the images placed at the bottom of the page. If you are not very sure on how to do most of these things, just google: how to do on wikipedia, and you will most likely be able to answer your query.

Group 4

  • The Introduction is succinct and well structured. It also makes reference to topics that are going to be covered in the project. There is a remark about specific ligands and their families, and it seems this piece of information is missing a citation. Maybe the addition of an image to this section would enhance the appeal.
  • The History section is set out very neatly and is easy to follow. citations have also been appropriately attached.
  • The Pathway section is probably the most important element of the project. Unfortunately it feels that this section is still incomplete. The language used is quite difficult to follow, and the author has made no attempt to explain the jargon. Furthermore, there is only one citation made, so it seems that many citations are missing. Because of the elaborate nature of this section of the project, it would be better to incorporate the use of bullets to organise the information, hence the text would be easier to follow.
  • The section for Proteins and Receptors has been done very well. The information is organised very neatly incorporating bullets and subheadings. The image used is very useful and entirely relevant to the topic. A related video has been recommended, with is an impressive addition, however it would be easier for the reader if a hyperlink was made within the same section of the project, rather than mention the video is located under another section. In addition it would be a pleasant addition if you would incorporate further readings for specific proteins or receptors.
  • The section for Normal function is very impressive. The information provided is extremely relevant, and has been set out neatly. Subheadings allowed for good organisation of the various roles of Notch in various tissues. The image of the flow chart is a great summary of the information, however this image needs to have a copyright notice. Furthermore, the information has been well cited.
  • Under the heading for External links, the subheading ‘Further research’ should probably be done under its own separate heading. Also the author should make reference to further readings, rather than just videos.
  • Glossary is on the right path, but should incorporate more terms.
  • References have been done correctly, but again there should be more present.

Group 5

  • The Introduction is very interesting. The introduction also makes good reference to the more elaborate topics that are going to be discussed in the report. The image used at the top creates a good sense of appeal.
  • The History section is quite elaborate, and very detailed. Despite this, it remains very easy to follow. Citations have been used correctly. On the downside, I haven’t found the image used any relevant to the history, hence this could be rather incorporated to the introduction
  • Under the section Mechanism of action, the author has made a clever distinction between the signalling pathway in the presence and absence of Wnt, which allows for a more logical understanding. I usually find the use of bullets as a great way of organising information, however in this instance, the use of too many bullets has caused confusion to the reader. Hence it would be easier to provide a paragraph of information, and then follow it with some bullets. Furthermore, the sketch provided is also very useful and relevant to the topic.
  • The section for associated diseases has been done magnificently, and there is little criticism to follow. The range of associated diseases have been organised into a table, and are very easy to follow. Furthermore the author has made a great attempt at providing the treatment options for specific mutations, and this leads as an example for other groups to follow. This section has been referenced correctly, and the images used have greatly enhanced the appeal of the page
  • The section for embryonic development is a great addition to the project
  • The section for Future directions contains an long list of future research for Wnt, however no specific research has been elaborated upon.
  • The Glossary is well organised. The division between the abbreviations and other terms makes it easy to follow
  • A good list of external links have been provided
  • References have been done correctly, and the list is also quite elaborate.

Group 6

  • The Introduction doesn’t really need to be set out in subheadings. It feels that the information provided it too elaborate for an introduction, which should be more succinct. Look into rather introducing the topics that are going to be addressed in the project, rather than explain these. Including an image would be a good addition.
  • The section for structure of insulin is a good addition to the project. However the image hasn’t been referenced correctly and no copyright is provided. Also it is probably better to add this section directly below the History section.
  • History section is set out neatly and is easy to follow. The image used enhances the appeal of this section. On the downside it seems that some citations are missing for several key dates.
  • The heading for insulin receptor is a good addition, however I feel that this section is better conjoint with the section for the structure of insulin. Hence you will be able to demonstrate the interaction of the protein with the receptor.
  • The signalling pathway has been done fairly well. The author has established two main pathways and elaborated upon these, following the introduction. However it does feel that the introduction is too detailed. The image used is quite relevant, yet the author has failed to attach the copyright information.
  • Normal function: It feels that there is no need to include the subheading ‘introduction’ under individual headings, you can simply dive into the information. Due to the brief nature of this section, it would probably be a better idea combining this section with ‘signalling pathway’ section.
  • The section for Abnormal function contains a good load of vital information, however it is not structured very well, hence difficult to follow. It would probably be better of organising this information into a table. Furthermore including several images would make this section far more interactive.
  • Current research has been done well, however some extra citations need to be added.
  • The Glossary is a good addition, however this will certainly require more terms.
  • The Gallery is also a clever way to organise the images into a single section.
  • References seem to be done correctly.

Group 7

  • The Introduction contains some vital information, however it is too long, hence this section kills the reader attention. The student sketch is a great addition as it provides a great summary of the overall process of the GPCR. The table of the adrenoceptors is quite useful, however it would seem more relevant under an alternate subsection of the project.
  • The History provided is not specified to a specific date, but rather narrowed down to a span of several decades. References have been provided, however in some cases a hyperlink of text is provided rather than simply numbering it.
  • The section for Gene description doesn’t seem entirely useful. This section could be made more appealing by incorporating images
  • The section for Receptor agonists doesn’t seem complete, or otherwise any relevant.
  • Receptor structure: The information seems to overlap. Furthermore, the information is not organised very well and is quite difficult to follow. Images used seem quite relevant and useful.
  • The section for Pathway and normal function is far too elaborate. The information doesn’t feel to be well structured. The information feels far too detailed and the jargon is too difficult to comprehend. On the other hand the images used are quite useful and easy to follow, particularly the student image.
  • Under Abnormal function, the table provides a great summary. The information within the table is also cited very well. However the information below the table was far too detailed once again. On the bottom line it doesn’t feel that this section has been completed yet.
  • Glossary of terms is a good addition.
  • References done correctly, yet still seems incomplete.

In summary it feels that a lot of work has been done gathering information, however this information is not yet set out that well.

Group 8

  • The Introduction is quite succinct and this is a good note, however it feels that this section doesn’t encapsulate the entire spectrum of the project. Thus this section should look to introduce the topics of discussion, rather than simply provide a brief summary of the pathway. Including an interactive image would certainly enhance the appeal.
  • The History section should probably be located directly below the introduction. There has yet been no attempt made on this section.
  • The pathway section provides a very good summary of the overall process, however I do feel that this section should be somewhat more detailed, as this section is the main part of the project. No references have been made. The image used is a great conceptualisation of the process, however this also hasn’t been referenced, and no reference of the copyright has been made.
  • The normal function section contains a great deal of information, and this would have taken up a lot of time to find, however, once again the author has failed to make citations as to the origin of the information.
  • The section for Abnormal function seems to be cited appropriately. On the downside this information is quite difficult to follow mainly due to the poor structure of the text. The incorporation of table will most likely solve this problem
  • The section for proteins contain far too much information, especially considering the scope of the research. It would probably be enough to list the proteins involved and include a small description. Also this section should be located directly before the pathway section.
  • No attempt has yet been made on the New or current research
  • The Glossary of terms is a good addition, however should contain more terms
  • The references seem to be done correctly

Group 9

  • The Introduction seems to be done quite well. The intro is not to brief yet not too detailed to comprehend. I feel that an image would provide a good addition to page.
  • The Pathway section contains very important information. However regardless of the quality of information, it is quite difficult for the reader to follow paragraphs of information. It would be better to incorporate subheadings and bullets which will more neatly arrange the text.
  • The sections for receptor and proteins have yet not been attempted. I would recommend joining both of these headings together, mainly because they are interrelated.
  • The history section has been accomplished to a very high quality. The tabular form is very easy to follow. The colours chosen are also very comfortable. Citation have also been used correctly.
  • Current research seems a bit too brief.
  • Normal Function doesn’t seem to be complete yet in terms of structure, however the information seems to be high-grade. The use of subheadings provides great organisation to the page.
  • Abnormal function does seem to be too brief, however I will assume this section is yet not complete.
  • The Glossary is a great addition, however it is not yet complete.
  • References seem to be done correctly.

On a separate note, signatures should probably be removed by this stage of the project.

--Mark Hill 12:28, 17 May 2012 (EST) Well done, this seems to be good feedback for the projects. Still one to do?

Lab 12

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>7569999</pubmed> 3) What aspect of the research findings were contributed by the microarray technique.

- The microarray technique allowed for differential expression measurements of various Arabidopsis genes. The microarray technique enabled the detection of these rare transcripts. Analysis of these genes thus allows entails a greater understanding of the expression of these genes providing clues to their biological roles.