User:Z3293029

From CellBiology

--Z3293029 15:13, 8 March 2012 (EST)

--Z3293029 14:12, 15 March 2012 (EST)

--Z3293029 14:43, 29 March 2012 (EST)

--Z3293029 14:38, 19 April 2012 (EST)

--Z3293029 14:23, 3 May 2012 (EST)

--Z3293029 14:22, 17 May 2012 (EST)

--Z3293029 15:29, 24 May 2012 (EST)

--Z3293029 13:50, 31 May 2012 (EST)


this is a heading

and this a subheading

text text text text text


internal link to timetable

external link to GOOGLE

Actin.jpg


Decoration of actin filaments is similar in muscle (left) and epithelial (right) cells.

reference

H Holtzer, H Weintraub, R Mayne, B Mochan The cell cycle, cell lineages, and cell differentiation. Curr. Top. Dev. Biol.: 1972, 7;229-56 PubMed 4264706


LAB 2 : microscopy

1) Steven M Wiltgen, Ian F Smith, Ian Parker Superresolution localization of single functional IP3R channels utilizing Ca2+ flux as a readout. Biophys. J.: 2010, 99(2);437-46 PubMed 20643061


2) This paper used "superresolution" techniques to localise Ca2+ ion channels in high proximity distribution that cannot be distinguished with other microscopic techniques. The "superresolution" technique used was “stochastic channel Ca2+ nanoscale resolution (SCCaNR)" which involves fluorescent dyes and high precision. Steven M Wiltgen, Ian F Smith, Ian Parker Superresolution localization of single functional IP3R channels utilizing Ca2+ flux as a readout. Biophys. J.: 2010, 99(2);437-46 PubMed 20643061


LAB 3: Fixation

1) Chemical Identity: Formalin Jars. Common Name(s): 10% Buffered Formalin Fixative

ingredients: Formaldehyde Solution (flammable) Potassium Dihydrogen Phosphate Disodium Hydrogen Orthophosphate Water

Physical and chemical properties: Appearance: Clear Liquid. Odour: Pungent Odour. Boiling point/range: BP ~ 100°C. MP ~ 0°C. Solubility: Soluble in all proportions. Specific gravity or density: About 1.02. Flash Point: 72°C.

health hazards: Acute and chronic health effects: Prolonged or repeated exposure may lead to irreversible damage to health and skin sensitisation. Possible routes of exposure: Inhalation, swallowing, skin/eye contact. Range of effects following exposure: Harmful if swallowed. May cause irritation to the mouth, throat and stomach with effects including mucous build up, irritation to tongue, lips and pains in the stomach. Eye, may cause irritation, with effects including: tearing, pain, stinging and blurred vision. Skin, will cause irritation with effects including: redness, itchiness, and posible dermatitis. Inhaled, may cause irritation to the nose, throat and respiratory system with effects including: dizziness, headache and possible confusion.

precautions: Disposal Methods: Refer to the appropriate authority in your state. Dispose of the material through a licenced waste contractor. Advise of flammable nature.

manufacturer: Supplier Name: ProSciTech Postal Address: PO Box 111, Thuringowa Central Qld. 4817 Australia Street Address: 1/11 Carlton Street, Kirwan, Qld. 4817 Australia Telephone Number: (07) 4773 9444

2) articles:

Kazunari Iwamoto, Hiroyuki Hamada, Masahiro Okamoto Mechanism of cell cycle disruption by multiple p53 pulses. Genome Inform: 2011, 25(1);12-24 PubMed 22230936

- this article's about the mechanism of p53 oscillation but also explains the signalling networks involved.

Manujendra N Saha, Hua Jiang, Yijun Yang, Xiaoyun Zhu, Xiaoming Wang, Aaron D Schimmer, Lugui Qiu, Hong Chang Targeting p53 via JNK pathway: a novel role of RITA for apoptotic signaling in multiple myeloma. PLoS ONE: 2012, 7(1);e30215 PubMed 22276160

-explores p53 in terms of JNK signalling pathway

Yanping Zhang, Hua Lu Signaling to p53: ribosomal proteins find their way. Cancer Cell: 2009, 16(5);369-77 PubMed 19878869

-about ribosomal involvement in p53 function (cell cycle arrest) - "ribosomal protein-MDM2-p53 signaling pathway"

Angela L McCleary-Wheeler, Robert McWilliams, Martin E Fernandez-Zapico Aberrant signaling pathways in pancreatic cancer: a two compartment view. Mol. Carcinog.: 2012, 51(1);25-39 PubMed 22162229


LAB 4: immunohistochemistry

musashi protein

Yoriko Sugiyama-Nakagiri, Masashi Akiyama, Shinsuke Shibata, Hideyuki Okano, Hiroshi Shimizu Expression of RNA-binding protein Musashi in hair follicle development and hair cycle progression. Am. J. Pathol.: 2006, 168(1);80-92 PubMed 16400011


- family of RNA binding proteins

- "involved with maintenance/asymmetric cell division of neural progenitor cells"

- mammalian Musashi protein is expressed in various epithelial stemn cells, also gut, stomach,mammary gland

- musashi-1, musashi-2


antibody:

primary antibody - "musashi-1 (D46A8) XP® Rabbit mAb detects endogenous levels of total Musashi-1 protein"

external link to cellsignal musashi antibody

-> "Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues surrounding Met190 of human Musashi-1 protein."


secondary antibody - "Affinity purified goat anti-rabbit IgG (H&L) antibody is conjugated to horseradish peroxidase"

external link to cellsignal secondary antibody


LAB 6

Bargraph.JPG


LAB 7

contribution to group project so far:


part of introduction + normal function

Through regulation of the cell cycle, the p53 gene plays an important role in suppressing tumour formation [1] . The p53 protein is tightly regulated in cells and responds to stress signals produced by DNA damage, oncogenic gene expression and anoxia [1][2]. It controls the activation of apoptosis or cell cycle arrest in response to damage, therefore maintaining integrity of the genome. Consequently, mutation or loss of p53 results in genomic instability that promotes risk and facilitates progression of tumours, and for that reason it is the most frequent genetic mutation in human tumours [1]


Normal Function

--Z3293029 11:28, 3 May 2012 (EST) P53 has a principal role in acting as a transcription factor to promote a range of functions that are critical in maintaining celllular integrity throughout proliferation [62]. However, apart from its main role in tumour suppression, p53 has recently been found to have a wider range of functions including those in cell membrane function and adhesion, DNA repair, cellular metabolism and motility [63]. In response to stress signals and DNA damage, p53 upregulates gene expression to bring about protective mechanisms including cell cycle arrest, DNA repair, senescence or apoptosis [64]. DNA DAMAGE The DNA-damage pathway is initiated by 2 associated protein kinases, ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia mutated related (ATR). These protein kinases activate analogous down-stream pathways in response to DNA damage, however the types of damage sensed by each ATM and ATR are different [2]. Upon activation by DNA stress signals, they phosphorylate various targets including p53 to initiate cell cycle arrest, and stimulate DNA repair pathways through the phosphorylation of DNA repair proteins [2]. CELL CYCLE ARREST Cell cycle arrest happens in the late G1 phase of the cell cycle and is induced by p53-mediated transcription of CDK1A (p21) gene [2]. The CDKN1A gene stops the cell cycle to allow time for DNA repair. It initiates cycle arrest by the inhibition of cyclin-CDK complexes and prevention of RB (retinoblastoma) gene phosphorylation, the latter of which is functionally required for cellular entry into G1 phase [2]. DNA REPAIR p53 induces transcription of certain mechanisms and proteins (eg. GADD45) to stimulate DNA repair [2]. Successful damage repair results in p53-initiated up-regulation of MDM2 which leads to p53 destruction and hence an end to cell cycle arrest [2].If repair does not occur, apoptosis or senescence may be initiated by p53 instead.

SENESCENCE senescence is referred to as a cell permanently in irreversible cell cycle arrest [2]. It is distinguished by particular differences in gene expression and morphological characteristics [2]. It is dissimilar to the reversible form of cell cycle arrest or quiescent cells in the G0 phase of the cell cycle (1). Senescence requires p53 or RB gene activation as well as expression of CDKIs or other mediators[2]. APOPTOSIS The pro-apoptotic pathway is the essential mechanism of protection against irreversible DNA damage and therefore effectively also against neoplasia(1). The induction of programmed cell death occurs in response to cellular aberration, including oncogenic stress, hence making it a crucial function in tumour suppression [65].Other cellular stress signals including interleukin-3 deprivation for example, may also induce apoptosis [66]. In response to stress signals, p53 is not degraded and therefore accumulates and binds to specific target sites of chromatin to initiate the apoptotic pathway [67]. Transcriptional activation of pro-apoptotic Bcl-2 genes is initiated by p53 at the sites of binding in chromatin [68]. The Bcl-2 genes which include BAX, Bbc3 PUMA and NOXA, are upregulated to mediate normal apoptotic function[69]. Jabbour et al. (2012) also state that in abnormal p53 function, it is not solely apoptotic failure that contributes to oncogenic potential, but depending on the cell and tumour type, p53-initiated apoptosis may promote tumour development [70]. For example, as suggested by Jabbour et al. (2012), T-cell lymphoma caused by irradiation requires a certain amount of cell death initiated by p53, in order to create a niche environment that encourages proliferation of the malignant cells [71]. [edit]

LAB 8

ATCC catalogue:

CRL-2638

colon carcinoma cell

from mouse

original tissue: "CT26 is an N-nitroso-N-methylurethane-(NNMU) induced, undifferentiated colon carcinoma cell line. It was cloned to generate the cell line designated CT26.WT"

external link

M Wang, V Bronte, P W Chen, L Gritz, D Panicali, S A Rosenberg, N P Restifo Active immunotherapy of cancer with a nonreplicating recombinant fowlpox virus encoding a model tumor-associated antigen. J. Immunol.: 1995, 154(9);4685-92 PubMed 7722321


LAB 9

peer reviews

Group1:

- effect use of tables throughout

- clear and concise information in the regulation, pathway and abnomal function sections

- normal function section is a bit wordy and still has some spelling and grammatical errors, subheadings might be useful to organise the info here

- current research section is a bit confusing and hard to read, i would suggest using subsections for each study you mention to help with the format and perhaps some external links

- still require sstudent drawn image

- referencing is inconsistent and lacking in some areas

Group2:

- very well formatted except for maybe the normal function section which needs more work, particularly with organisation of the information and in text referencing. You should perhaps also expand on some points

- excellent use of images, make your page very engaging

- the abnormal function and research sections are particularly interesting

- referencing could be improved in the section on signaling pathway

- lacks glossary

Group3:

- referencing and glossary missing

-history could be put in a table to break up text and be visually more appealling

- proteins section may also benefit from being put into a table with a functions column

- layout of the page in general could be improved, re-organise blocks of text for easier reading

- function section especially could perhaps include normal and abnormal subsections, further editing and paraphrasing also needed

- more images including self drawn

Group4:

-external links are relevant and useful

- normal function section is excellent. well-described and interesting plus good layout

- pathway, proteins and receptors sections could be expanded a little more and organised hopefully like the normal function section

- history section could be expanded a bit with other related significant events

- more images required including student drawn

Group5:

- history section is comprehensive and well-researched

- mechanism of action section is well written and concise but perhaps a summarising introductory paragraph may be useful

- good work on the student drawn diagram, detailed but precise

-treatment section could be organised into headings and expanded on a bit more

- the key players section should perhaps be placed about diseases for better flow

-good use of images, especially in the key players section

-future direction still needs work but ideas are good so far

- perhaps embryonic development should a part of the function section

Group6:

- tiltle should be more striking

- intro could benefit from being more a cohesive paragraph that introduces concepts and is still precise with subheadings and details left for the function section. also needs proper in text referencing

- history section is well-researched and interesting

- simple but effective use of images

-pathway section is excellent. well-researched, informative and concise with effective use of images

-normal function should maybe precede the pathway section. also needs work on referencing

- very interesting current research section but it would probably benefit from external links

Group7:

- excellent student drawn images

-very good use of subheadings to organise your information

- use of a table for the history section may be useful to break up text and be visually pleasing

- the external links used throughout are effective and helpful

- a separate intro that is more general and precise may be useful

- perhaps save the detailed receptor descriptions for a separate section coupled with information about the structure

- abnormal function section is well researched and comprehensive

- make glossary words bold

- maybe work on formatting in the current research section

Group8:

- still need student image

- perhaps include a history and current research section

- pathway section might benefit from more focus on signaling as opposed to function

- interesting well thought out abnormal function section but it might benefit from use of tables and images

- comprehensive protein section with effective use of diagrams

- pathway section could be expanded on a bit more


LAB 12

1. Identify a current technique used in gene sequencing.

DNA microarray is a technique used to facilitate gene sequencing. It involves analyzing RNA hybridization to identify gene expression. It consists of a small glass surface containing DNA material in a pattern of spots and can be used to assess expression of a large number of genes.


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

Neda Mosakhani, Mohamed Guled, Gayle Leen, Silvia Calabuig-Fariñas, Tarja Niini, Isidro Machado, Suvi Savola, Katia Scotlandi, José Antonio López-Guerrero, Antonio Llombart-Bosch, Sakari Knuutila An integrated analysis of miRNA and gene copy numbers in xenografts of Ewing's sarcoma. J. Exp. Clin. Cancer Res.: 2012, 31;24 PubMed 22429812


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

RNA microarray techniques were used in this study to examine mRNA expression within xenograft tumours. The study demonstrated the successful use of microarray technology in the identification of new genetic biomarkers within the xenografts. This showed the role of RNA and genetic involvement in tumourigenesis,as well the ability for xenografts to reflect gene structure of its original tumour.



--Mark Hill 13:45, 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.