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Lab Attendance

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lab Work

lab 1

eukaryote enternal

Vslides external

lab 2

Nuclear transport.jpg

Individual Task

Lab 2

Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules

Superresolution imaging techeniques are based on the localization of a single molecule. photoactivated localization microscopy and stochastic optical reconstruction microsocopy are examples of this technology. The two example mentioned above rely on the photoactivated proteins or photoswitching dyes, which makes them extermly difficult and challenging. This new technique which is called bleaching/blinking dose not rely on photoactive or photoswitching property of the protein. In this technique to detect the fluorophores (compounds that re-emit light up on light excitation) a series of fluorescence images are captured. Fluorophore bleach or blink off are detected by comparing the image with the images captured before. After this comparison the flurescence emission signals from the fluorophores are indentified and the localization determined. This technique also works with a range of different fluorescent molecules in the same sample. Therefore this technique extendes the single molecule based superresolution localization to multiple sample labeled with multiple fluorescent probes.



lab 3




Solubility (water): SOLUBLE


Specific gravity: 1.1 (Approximately)

pH: 2.4 to 4.0

% Volatiles: > 44 %

Vapour pressure: NOT AVAILABLE


Vapour density: 1.04 (Air = 1)

Flash Point: 85°C (Approximately)

Boiling point" < 100°C

Upper Explosion Limit: 73 %

Lower Explosion Limit: 7 %

Melting point: NOT AVAILABLE

Evaporation rate: NOT AVAILABLE

Autoignition temperature: 430°C

Decomposition temperature: NOT AVAILABLE

Partition coefficient: NOT AVAILABLE



Toxic - corrosive. This product has the potential to cause adverse health effects. Use safe work practices to avoid eye or skin contact and inhalation. Contact may result in burns with possible tissue damage. May cause sensitisation by skin contact. Formaldehyde is classified as a confirmed human carcinogen (IARC Group 1). Chronic exposure may result in cell mutations, reproductive system effects, liver damage and insomnia. Chronic exposure to methanol may result in optic nerve damage.


Corrosive - irritant. Contact may result in irritation, lacrimation, pain, redness, corneal burns and possible permanent damage.


Toxic - corrosive. Over exposure may result in mucous membrane irritation of the respiratory tract, coughing, chest pain and sensitisation with asthma-like symptoms, breathing difficulties, pulmonary oedema and convulsions at high levels. Chronic exposure may result in liver damage and fertility effects (sperm count and viability, increase in spontaneous abortions).


Corrosive. Contact may result in irritation, redness, pain, rash, dermatitis and possible burns. May cause sensitisation by skin contact.


Toxic - corrosive. Ingestion may result in gastrointestinal ulceration, nausea, vomiting, abdominal pain, acidosis and diarrhoea (bloody). Ingestion of large quantities may result in liver and kidney damage, pulmonary oedema, unconsciousness and death which may be delayed.

Toxicity Data


LDLo (intravenous): 30 mg/kg (cat)

TCLo (inhalation): 14300 ppb/6 hours/2 years (mouse - cancer)

LDLo (intraperitoneal): 16 mg/kg (mouse)

LC50 (inhalation): 81 ppm (rats)

LDLo (subcutaneous): 240 mg/kg (rabbit)

LD50 (ingestion): 42 mg/kg (rat)

LDLo (ingestion): 108 mg/kg (woman)

LD50 (subcutaneous): 300 mg/kg (mouse)


TCLo (inhalation): 300 ppm human (visual effects)

LC50 (inhalation): 50 g/m³/2 hours (mouse)

LCLo (inhalation): 1000 ppm (monkey)

TDLo (ingestion): 3429 mg/kg (man-visual change)

LD50 (ingestion): 5628 mg/kg (rat)

LDLo (ingestion): 143 mg/kg (human)

LD50 (skin): 15,800 mg/kg (rabbit)

LDLo (skin): 393 mg/kg (monkey)


CTRP3 is a molecule found in high concentration in adipose and causes increase in production of testosterone.

1. <pubmed>22342437</pubmed> This article explains how testosterone increase the muscle mass and circulation of GH and I-GFI in the blood.

2. <pubmed>21084444</pubmed>

Phthalic acid esters are used in production of plastic. studies shows that phthalates impair testicular testosterone production in the rat. This article looks at the effect of Phthalic in man.


This article looks at the effect of testosterone in older men and testosterone replacement therapy and its benefits.



Musashi (Msi) is an evolutionarily conserved gene family of RNA-binding proteins (RBPs) that is preferentially expressed in the nervous system. This protein plays an important role in regulating asymmetric cell division of the sensory organ precursor cells (stem cell). The gene for this protein is found on chromosome="12".



Antibody: Anti-Musashi-1

Antibody Type: Polyclonal Antibody

Molecular Weight: 39 kDa

Species Reactivity: Human, rabbit, mouse

Host: Rabbit

Application notes:

Immunohistochemistry: 1:200-1:1,000 dilution from a previous lot was used.

Immunocytochemistry: 1:200-1:1,000 dilution from a previous lot was used.

Western blot: 1:200-1:1,000 using ECL.

Secondary antibody

Alexa Fluor 488 goat anti—rabbit IgG

Price: $347

color: bright, photostable, green-fluorescent

Dilution: 2 mg⁄mL






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

Phenotype A(FUN): no change in the number of cells seen in compare to the control group.

phenotype B(BROKEN FUN): there is a reduction in TM4 group about 15% which suggest TM4 may inhibit this cell phenotype.

Phenotype C(STUMPED): there is a small increase in TM4, the change is very small and it dose not suggest the TM4 caused this.

Phenotype D(PRONGED): expression of of TM4 increased about 11 percent, this suggest that TM4 is involved in growth of this phenotype.

Phenotype E(STRINGED): expression of of TM4 increased about 10 percent, this suggest that TM4 is involved in growth of this phenotype.

Genotype A (TM4):

more branching and process can be seen

this suggest more interaction between the cells

The processors seem to be shorter, wider, fluoresce more cheerfully

more stringed , pronged and stumped seen

they are seen as groups

the nuclei is round, pink blue in colour

lamella is yellow and the cytoskeleton is pink

Genotype B (control):

less branching and not many process

so less interaction between the cells

cells are process seems to be thinner

more broken fun, stumped and stringed

nuclei seems to be shiny

shape of nuclei is either round or spindle

lamella is red and the cytoskeleton is red

2. If so, how could Tm4 over-expression lead to this difference?

So from the compression of the two phenotype conclusion can be made that phenotype A and B have opposite characteristics. This suggest that TM4 is involved in the cell motility, these cell also show more branching and process which suggest more interaction of the cells. Tm based on its molecular shape twists around the actin filaments. It binds to the actin molecules and can form a barrier. This characteristics of the Tm come into play when when the muscle is relaxed, Tm blocks the myosin binding sites and so prevents the crossbridge between the myosin head and the actin filaments and the muscle wont contract. When ca2+ is released, they bind to the troponin and cell myosin binding site will be exposed again and the filaments can form the crossbridge and muscle can contract. There are many Tm isoform and one of them is Tm4. Tm4 isoform for striated muscle is necessary for conractile function in embryonic heart. This shows TM4 was expressed embryonically and was needed for normal structure and function of heart (ventricles). In addition TM4 may be is involved in motility of the neurite and syaptic plasticity. This was observed in the images for each phenotype of group A and group B. Tm4 group has more process branching which allows cell to cell interaction. Other results from new research indicates that TM4 plays a regulatory rule in the adhesion of osteclasts, the likely explanation is by stabilizing the actin filaments present in podosomes and the sealing zone.





3. What are the differences in phenotype (morphology) between cAMP over-expressing cells and control cells?


- More process

-so more interaction between cells

-shorter and wider process

-less dense and less fluorescent nuclei

-cells appear duller

-lamella appear yellow on the edges


-less process

-so less interaction

-longer thinner process

-denser and shiner(blue) nculei

-cells appear brighter

-lamella appears orange, red on the edges

How could cAMP over-expression lead to this difference?

cAMP is a second messenger important in many biological processes. cAMP is produced from ATP and is used for interacellular signaling many organisms. An example can be signal transduction, such the transfer of the effect of hormones like glucagon and adrenaline, which cant pass the cell membrane. cAMP is also has a rule in function of ion channels. for example activation of protein kinase.cAMP binds to regulatory units of protein kinase and dissociates the regulatory and catalytic subunits. so activiatin of 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

My contribution

Four related article about testosterone

CTRP3 is a molecule found in high concentration in adipose and causes increase in production of testosterone.

1. Masataka Otani, Mikihiko Kogo, Souhei Furukawa, Satoshi Wakisaka, Takashi Maeda The adiponectin paralog C1q/TNF-related protein 3 (CTRP3)

stimulates testosterone production through the cAMP/PKA signaling pathway. Cytokine: 2012; PMID:22342437 This article explains how testosterone increase the muscle mass and circulation of GH and I-GFI in the blood.

2. Carlo Serra, Shalender Bhasin, Frances Tangherlini, Elisabeth R Barton, Michelle Ganno, Anqi Zhang, Janet Shansky, Herman H Vandenburgh, Thomas G Travison, Ravi Jasuja, Carl Morris The role of GH and IGF-I in mediating anabolic effects of testosterone on androgen-responsive muscle. Endocrinology: 2011, 152(1);193-206 PMID:21084444

Phthalic acid esters are used in production of plastic. studies shows that phthalates impair testicular testosterone production in the rat. This article looks at the effect of Phthalic in man.

3. C Desdoits-Lethimonier, O Albert, B Le Bizec, E Perdu, D Zalko, F Courant, L Lesné, F Guillé, N Dejucq-Rainsford, B Jégou Human testis steroidogenesis is inhibited by phthalates. Hum Reprod: 2012; PMID:22402212

This article looks at the effect of testosterone in older men and testosterone replacement therapy and its benefits.

4. N Nigro, M Christ-Crain Testosterone treatment in the aging male: myth or reality? Swiss Med Wkly: 2012, 142(); PMID:22430839


Normal function

testosterone acts on cells through intracellular receptors called ARs (androgen receptors). in this article the researchers show that a mouse type (IC-21) macrophage which lack the AR receptors but still shows specific responses to testosterone. as a response to testosterone there is rapid increase in ca2+ in the cells. this ca2+ is also achievable by plasma membrane-impermeable testosterone-BSA.It is not affected by the AR blockers cyproterone and flutamide, whereas it is completely inhibited by the phospholipase C inhibitor U-73122 and pertussis toxin. Binding sites for testosterone are detectable on the surface of intact IC-21 cells, which become selectively internalized independent on caveolae and clathrin-coated vesicles upon agonist stimulation. Internalization is dependent on temperature, ATP, cytoskeletal elements, phospholipase C, and G-proteins. Collectively, our data provide evidence for the existence of G-protein-coupled, agonist-sequestrable receptors for testosterone in plasma membranes, which initiate a transcription-independent signaling pathway of testosterone. [17]

Experimental and clinical studies have reported that testosterone has a critical role in the maintenance of homeostatic and morphologic corpus cavernosum components, essential for normal erectile physiology. Although the exact mechanisms mediated by testosterone in erectile function are still under investigation, recent research has suggested an important role in the regulation of endothelial cell (EC) biological functions. Besides stimulating the production of EC mediators, testosterone is also thought to promote the vasculogenic reendothelialization process, mediated by bone marrow-derived endothelial progenitor cells. Additionally, testosterone seems to modulate other erectile tissue components, including trabecular smooth muscle cells, nerve fibers, and tunica albuginea structure, all essential for the erectile process. This paper summarizes current data regarding testosterone-induced cellular and molecular mechanisms that regulate penile tissue components, focusing particularly on the role of testosterone in endothelial health and erectile function. Angela Castela, Pedro Vendeira, Carla Costa Testosterone, endothelial health, and erectile function. ISRN Endocrinol: 2011, 2011();839149 PMID:22363891

Abnormal function

Myxedema in men is thought to cause infertility and impotence. Testicular function was investigated in eight consecutive men with primary hypothyroidism (autoimmune thyroiditis in five patients and amiodarone therapy in three patients). All had impotence that preceded the onset of hypothyroidism and did not improve with thyroid therapy. Gonadal function tests showed a hypergonadotropic state in five patients and hypogonadotropic hypogonadism in three patients including one with no response to luteinizing hormone-releasing hormone. Luteinizing hormone bioactivity was decreased in six patients and increased in two subjects who also had increased luteinizing hormone immunoreactivity. Serum testosterone and testosterone/estradiol-binding globulin concentrations were low in four of the patients. It is concluded that abnormalities of gonadal function are common in men with primary hypothyroidism. J Wortsman, W Rosner, M L Dufau Abnormal testicular function in men with primary hypothyroidism. Am. J. Med.: 1987, 82(2);207-12 PMID:3101496

current research

this article discusses the results of low testosterone in middle age men and benefits of and some of the risk associated with the use of testosterone replacement therapy. this is a review article and the author gathered his information from many research about low testosterone. here is a summary of the main points 1. low testosterone is a very common condition in aging man and brings about medical conditions such as obesity, metabolic syndrom, type 2 diabetes and high blood pressure. 2. low testosterone levels increase the risk of death from cardiovascular disease in middle age men. 3. testosterone replacement therapy helps to reduce body fat and so is a good way of treating diabetes. 4. testosterone replacement therapy improves glucose control and reduces the amount of bad lipids and increase the good fats in the body. 5. testosterone replacement therapy increases sexual desire and erectile function. [27]

Abdulmaged M Traish, Martin M Miner, Abraham Morgentaler, Michael Zitzmann Testosterone deficiency. Am. J. Med.: 2011, 124(7);578-87 PMID:21683825

This study compares the effect of two forms of testosterone, injection with oral testosterone in the form of capsule. These two forms of testosterone was given to middle age men with symptoms of low testosterone and type 2 diabetes. The study was done on 52 men, they were divided into three groups, the ones who were injected, capsule and a control group that was given placebo drugs. after 6 months the group that was given the capsule, was given the injection form and the other groups remain the same. Below is some of the key findings of this study after 1 year.

name 1.Improved the body’s sensitivity to insulin 2.Had a beneficial effect on waist circumference and body fat 3.Improved sexual function 4.After switching from oral testosterone to the testosterone injection for the second 6 months of the study, testosterone levels, insulin sensitivity, waist circumference and levels of body fat all improved. This study is important because it shows that not all forms of testosterone are equally effective. This study showed for the first time that oral testosterone is not effective in men with low testosterone and diabetes. Unlike the oral form, the injection form of testosterone brings back the level of testosterone to the right level and only needs about five injection a year to keep in the right level. Low testosterone levels can increase the risk of cardiovascular disease, diabetes, MetS and narrowing of arteries, returning the testosterone to its normal range helps to improve all the conditions mentioned above. This study suggest testosterone replacement therapy have a role in preventing, MetS, cardiovascular disease, diabetes and narrowing of arteries. reference A Aversa, R Bruzziches, D Francomano, G Spera, A Lenzi Efficacy and safety of two different testosterone undecanoate formulations in hypogonadal men with metabolic syndrome. J. Endocrinol. Invest.: 2010, 33(11);776-83 PMID:20220293

This article is about testosterone effect on bone of elderly men. I n this study initially researchers compared a group of elderly men with normal testosterone levels and a group with low testosterone levels. Their data showed that the group with lower testosterone have a higher weight and body fat. Some muscle functioning tests were done and it was found that the group with normal testosterone levels performed much better than other group. Bone Mineral density was measured but no significant difference was found, they also found that metabolic rate of group with low testosterone was not as good as the other group. Men in the low testosterone group were less satisfied with overall quality of life, but no difference in quality of their sexual life in compare to the other group. Men in the low testosterone group were then randomly divided into two groups and treated with testosterone or a placebo drug. After one year this is what they found. Bone mass density was increased significantly in the group treated with testosterone and there was a significant difference between the two groups at the end of the study.Testosterone treatment did not increase handgrip strength or strength in the knee, but in the placebo group handgrip strength was reduced such that at the end of the study there were significant differences between the groups. This suggests that testosterone can maintain handgrip strength that would otherwise have declined in elderly men. J Svartberg, I Agledahl, Y Figenschau, T Sildnes, K Waterloo, R Jorde Testosterone treatment in elderly men with subnormal testosterone levels improves body composition and BMD in the hip. Int. J. Impot. Res.: , 20(4);378-87 PMID:18480825

Testosterone has anti depressant properties but the exact mechanism is still unknown. Studies have discovered that a specific pathway in the hippocampus, a region of the brain involve in regulation of stress and memory formation plays an important role in mediating testosterone effects. women are twice as likely to be affect by depression disorders. Men with hypogonadism also suffer from depression and anxiety more than other men with normal levels of testosterone. Testosterone replacement therapy has shown to reduce depression and anxiety. To observe the exact mechanism multiple experiment was done on adult male rat. With withdraw of testosterone from the rats they developed depressive like behaviors that was reversed with testosterone replacement. A pathway called MAPK/ERK2 plays a major rule in mediating the effects mentioned above. This suggest proper functioning of this pathway is needed before antidepressant effects of testosterone, this pathway can also help to produce antidepressant drugs based on testosterone.

Nicole Carrier, Mohamed Kabbaj Extracellular signal-regulated kinase 2 signaling in the hippocampal dentate gyrus mediates the antidepressant effects of testosterone. Biol. Psychiatry: 2012, 71(7);642-51 PMID:22265242

Lab 8

Name of Mammalian cell : V79-4

Source: Lung

Isolation: This cell line was developed by Ford and Yerganian in 1958 from lung tissue of a young male Chinese hamster, and was originally designated Strain V.



Lab 9

group two


The introduction is short and provides a good brief summary of the topic but it needs more information.


History is well organised, use of table makes it interesting for the table, but enough referencing and can be worked on more, needs more expansion.

Normal function

The language used in normal function section is too complicated for general people to understand, being a science student I found the information a little too hard to understand. This section is not complete and needs more research, referencing not complete.

Signalling pathway

Good use of table and pictures, although the picture is not referenced. The information is clear and easy to follow but again referencing is not done properly and seems not enough research is done, as I can see only one reference.

Abnormal function

Good use of table, good referencing and easy to follow and understand.

Research: Therapeutic Application pictures are well referenced, as well as the information in this section.

group 3


Good summary of the topic, but not referenced. The introduction provides good information about the apoptosis and it’s easy to understand, use of pictures in the section could have made the intro more interesting and easier for the reader to understand and follow.


History is done, it highlights some of the important discoveries, but again no referencing, at the end of this section there is a link to an article which leads to an article on pubmed that highlights the history of apoptosis, but shows lack of research.

Signalling pathway

This section is not complete yet, the group simply listed a bunch of proteins but no info about how the signalling pathway works. No referencing. Use of pictures and diagrams can help improve this section.


This section has lots of information as it explain some of the function of apoptosis, but the information is not well organised, information is scattered and that makes it hard to follow and understand, no referencing, no use of pictures and diagrams.

Current research

This section highlights importance of the topic,

As a whole this group has to spend more time on their project as there is only one week left to the deadline. Information in all the sections need to be edited, referenced and more research should be done in all areas. Use more subheadings and use of glossary of terms can help the readers to understand the topic better.

group 4 Introduction

Very brief and easy to understand, but seems too short maybe adding a few more subheading to the project and adding some info to the introduction help to make the whole project better.


History is done and it well referenced but again it seems too short with big gaps between each important discovery. More research should help fill up some of the gaps in this section.


Too short, information is scatter and don’t follow a logical order, this because not enough research was done.

Proteins and receptors

This section is fairly well organised but not referenced. The picture used is not referenced too.

Normal function

This section is done very well, well organised and good use of picture and well referenced.

group 5


Wnt/B-catenin signalling pathway subheading is there before the introduction without any further information to explain the process. The introduction is done good easy to understand but lack of referencing, there is only one reference which shows lack of research by the group. The picture used is not proper with no referencing, the picture is not proper because it does not explain anything related to the topic.


Extensive research is done, good referencing.

Mechanism of action

This section starts with dot points from the beginning; the group should include a good explanation of the paragraphs.

Diseases associated with Wnt/β-catenin signalling

Good use of table, well referenced.

Treatment options

Well organised but the pictures used in the table are not referenced.

Embryonic development

Well explained, easy to understand

Future direction

Needs editing, if change from dot point to easy paragraph to explain the future studies, will be easier for the reader to understand.

group 6


Good and simple intro but suffers lack of research as there is only one reference. Not sure if the subheading is a good idea. Adding pictures and graphs may help make the page more interesting and catchy for the reader.

Structure of insulin

The picture lacks referencing; more information regarding the structures and properties is needed.


History is done properly with good referencing

Insulin receptors

Patchy information from everywhere, hard to follow, the picture used is not referenced.

Signalling pathway

This section is done properly, information is structured well and easy to follow and understand, picture used is not referenced.

Normal function

Needs more information, lack of referencing.

Abnormal function

Is done well but lacks referencing, use of pictures and graphs could make the page more interesting.

Current research Needs more work, not information is available at this point.

group 7


Extensive well organised information, the pictures used lack referencing, and students have their signature all over the page.


This section meets the criteria too, but I don’t know why students put their signature on the page.

Gene description

Well organised information, but lacks proper referencing. Good use of table

Receptor structure

This section is done properly, meets the criteria.

Pathway and normal function

Well structure well referenced

The whole projects is done properly, just needs a general editing to correct a few grammatical mistakes.

group 8


provides a good summary of how the pathway works but does not introduce the whole project. The introduction should be a good summary of whats to come for the whole project. No referencing


this section is a good summary of the molecules works but need more research, a picture would be useful for this section, and needs referencing.


this section is not complete and needs to be done.

Normal and Abnormal function

these two sections is clear and discusses some of the functions and where they can abnormally function but yet it again its not referenced.


this section is very well done, but no referencing and the picture used is not referenced.

group 9


Easy to read and understand with good referencing. A picture can help make the intro interesting. I don’t know why students in this group put their signature all over the page.


The information is easy to read and understand but lacks referencing. The picture used is not referenced.

Receptor and protein

These two sections are not done.


Well done, good use of table and well referenced.

Current research

Needs more research, not complete.

Normal function

Well done well referenced

Abnormal function

This section is not complete needs more research.

This project is not complete needs more research. In general the group should consider using more pictures and graphs.

--Mark Hill 13:06, 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.