User:Z3291200

From CellBiology

Lab Attendence

--Z3291200 15:13, 8 March 2012 (EST)

--Z3291200 14:07, 15 March 2012 (EST)

--Z3291200 14:11, 22 March 2012 (EST)

--Z3291200 14:46, 29 March 2012 (EST)

--Z3291200 14:13, 26 April 2012 (EST)

--Z3291200 14:18, 3 May 2012 (EST)

--Z3291200 14:48, 17 May 2012 (EST)

--Z3291200 14:12, 31 May 2012 (EST)

LAB ASSESSMENTS

Lab 1 - Online Work

ANAT3231 cell biology

External link JoVE: Journal of Visualized Experiments

External link see also [1]

Internal link Lecture 2

Internal link Lab 1


Lab 2 - Microscopy

A filamentous network.jpg


1. Identify a reference article that uses the "superresolution" microscopy technique.

Timothy A Brown, Ariana N Tkachuk, Gleb Shtengel, Benjamin G Kopek, Daniel F Bogenhagen, Harald F Hess, David A Clayton Superresolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction. Mol. Cell. Biol.: 2011, 31(24);4994-5010 PubMed 22006021


2. What did the paper show that normal microscopy could not show.

The difficulties of imaging small and highly compartmentalized mitochondria was over came by using superresolution florescence microscophy technique. Both two- and three- dimensional 'photoacticated localization microscopy' was practiced in this article to view the core dimensions and relative locations of mitochondrial nucleoids at an never yet seen resolution.


Lab 3 - Fixation

1. Locate a current SDS for one of the fixatives described in today's lab. Identify the properties and hazards associated with that chemical.

Methanol that is used in Precipitation fixation

Dangerous Good Class: 3 (Flammable liquid)

Subsidiary Risk(s): 6.1 (Toxic)

Risk:

- Highly flammable.

- Toxic by inhalation, in contact with skin and if swallowed.

- Toxic: danger of very serious irreversible effects through inhalation, in contact with skin and if swallowed.

Safety Phrases:

- Keep container tightly closed.

- Keep away from sources of ignition - No smoking.

- Avoid contact with skin.

- Wear suitable protective clothing and gloves.

- In case of accident or if you feel unwell seek medical advice immediately (show the label where possible).


2. Identify 4 papers required for your group work project. Cite on the Group Project discussion page and also on your own Individual page. Add one sentence for each as too why they are relevant to your group topic.


1) Kenneth Siddle Signalling by insulin and IGF receptors: supporting acts and new players. J. Mol. Endocrinol.: 2011, 47(1);R1-10 PubMed 21498522

I'm not sure if we can use this review as a reference but it covers basic details about insulin; what it does, its receptors, how is regulated and it's signaling pathways. So I thought that it will be good for just background information.


2) Sabine Uhles, Tilo Moede, Barbara Leibiger, Per-Olof Berggren, Ingo B Leibiger Isoform-specific insulin receptor signaling involves different plasma membrane domains. J. Cell Biol.: 2003, 163(6);1327-37 PubMed 14691140


3) B Leibiger, T Moede, T Schwarz, G R Brown, M Köhler, I B Leibiger, P O Berggren Short-term regulation of insulin gene transcription by glucose. Proc. Natl. Acad. Sci. U.S.A.: 1998, 95(16);9307-12 PubMed 9689076


4) Tine Glendorf, Carsten E Stidsen, Mathias Norrman, Erica Nishimura, Anders R Sørensen, Thomas Kjeldsen Engineering of insulin receptor isoform-selective insulin analogues. PLoS ONE: 2011, 6(5);e20288 PubMed 21625452


5) Crystal M Cordes, Robert G Bennett, Gerri L Siford, Frederick G Hamel Redox regulation of insulin degradation by insulin-degrading enzyme. PLoS ONE: 2011, 6(3);e18138 PubMed 21448434

This is not really about Insulin signaling but Insulin degrading Enzyme. I thought that because this mentions 'Alzheimer's disease' we might talk about it in abnormal section?


Lab 4

Musashi (RNA binding protein):

It is involved with Post transcriptional gene regulation. And it is important when it comes to cell fate determination. It plays role in maintaining the stem cell state, differentiation and in creating tumors.


Antibodies that binds to Musashi: [Musashi-1 ABfinity™ Recombinant Rabbit Oligoclonal Antibody]

Host: rabbit

It is recognised in Western Blot, Immunocytochemistry and indirect ELISA. And it reacts with only Human species. Concentration: 0.5 mg⁄ml


Secondary Antibody: [Alexa Fluor® 488 Goat Anti-Rabbit IgG (H+L) *Highly Cross-Adsorbed* *2 mg⁄mL]

Host: Goat


Lab 6

Tropomyosin 4 vs Control.JPG

A) Do you see difference in Phenotype (morphology) between Tm4 over expressing and control cells?

Fan: Controls 4% more than Tm4

Broken Fan: Tm4 <1% more than Control

Stumped: Tm4 17% more than Control

Stringed: Control 20% more than Tm4

Pronged: Tm4 1% more than Control

The obvious differences are observed in "Stumped" and "Stringed" phenotype between control and Tm4 expressed cells.

B) If so, how could Tm4 over expression lead to this difference


Lab 7

  • Introduction of insulin pathway; what it is, what it does and basic defect related to it
  • trying to figure out the sequence in the studies of insulin through timeline


Lab 8

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

VR-805 [link]

  • Identify the original tissue of origin of that cell line.

Human rhabdomyosarcoma cell line (RD) growing in cat

  • Identify the original paper that characterised the properties of that cell line.

1. V Klement, R M McAllister Syncytial cytopathic effect in KB cells of a C-type RNA virus isolated from human rhabdomyosarcoma. Virology: 1972, 50(1);305-8 PubMed 4343115

2. R M McAllister, W A Nelson-Rees, E Y Johnson, R W Rongey, M B Gardner Disseminated rhabdomyosarcomas formed in kittens by cultured human rhabdomyosarcoma cells. J. Natl. Cancer Inst.: 1971, 47(3);603-11 PubMed 5157579


Lab 9

-Group 1 Testosterone Signaling-

  • Introduction: very interesting, short but distict!
  • History: love the table and detailing but may be to bright??? Good Job!
  • Biosynthesis: I love the table and the image but seems abit hard to understand with all the names that I am not familar with
  • Regulation: very simple, distinct and easy to understand
  • Signalling Pathway: love the structure, love the sub heading, love the diagram and it was very easy to read and understand.
  • Normal Function: May be put them under sub headings or bullet point? It repeats 'Testosterone has many functions...' quite few times and it is confusing to read
  • Abnormla Function: like the detail. It is very easy and simple to read and love the heading.
  • Clinical Uses: Like the overal structure, like how it is put in a table. Easy to read and easily distinguishable.
  • Current & Ongoing Research: I like how it has many ongoing researches but thought it would be better if it had details of where the reseach is happening.


-Group 2 Vascular Endothelial Growth Factor (VEGF)- I think this page is by far the best organised page

  • Introduction: like the simplicity of it but seems might want to add a image to make it look better?
  • History: love the table! love the detail!
  • Normal Function: maybe this should be with abnormal function.
  • Signalling Pathway: love the page, love the table and image, adequate amount of information
  • Abnormal Function: love what you've done with it! the table makes details more distinguishable and easy to read, well done!
  • Research: Therapeutic Applications: love the whole structure of this section! the tables, images and the description about Cancer therapy and Age Related Macular Degeneration (AMD) is great!


-Group 3 Extrinsic Apoptosis- There is no reference and I can't believe it! More sub headings and images will brighten up your group project. And there is nothing on the Glossary! Plus it seems to be too short compared to other groups and there is no 'abnormal' and 'normal' function??

  • Introduction: detailed but too much information and it should be referenced
  • History: like the detail and the information but it should also be referenced
  • Signalling Pathway: Lack of information, very difficult to read and to understand... may be more image to understand the pathway? And again Reference
  • Function: seems unfinished and need referencing
  • Current Research: like the description about the research but more structure would be better (like sub headings or bullet points)


-Group 4- There is no title to show what your page is about! and thought it was relatively short page

  • Introduction: too short and lack of information
  • History: like the table and the content but you should find more information...
  • Pathway: too brief and lack of image to help understand the reader
  • Proteins and Receptors: like the overal lay out and t but...) but it is not referenced.
  • Normal Fuction: love the orientation, it was easy to read and understand!


-Group 5 Wnt/β-catenin Signalling Pathway- I love how this page had its unique headings.

  • History: love the amount of information but there is no recognition of who conducted it
  • Mechanism of action: it shows the understanding of the writer and it is well detailed and organized. And I love the hand drawn diagram!
  • Diseases associated with Wnt/β-catenin signalling: love the table and the structure but perhaps put treatment option with the table?
  • Key players in Wnt/β-catenin Signalling: Fabulous work. very detailed and easy to understand
  • Embryonic development: nice addition of information may be out more of this information in the introduction page.
  • Future directions: may be make it more formal and detail about things that should be researched on


-Group 7 G-protein coupled receptors- I think the page will look more complete without the student signatures

  • Introduction: I think this is too detailed and hard to read
  • History of pathway: love the details
  • Gene description: like the detail.
  • Receptor Agonists: I think there should be more information. The Beta 1,2,3 seems to have same natural Agonist, Synthetic Agonist, Non-specific Beta-blocker(nothing under this) and I don't see the point why this page is necessary. It can be simplified and added in to different section in one sentence.
  • Receptor Structure: like the overall detail
  • Pathway and Normal function: love the detail and the images that help to understand
  • Abnormal Function, Diseases and Treatments: like the structure, detail!


-Group 8- I think this page was somewhat incomplete and need more work

  • Introduction: like the flow of it but is too precise and need more detail
  • Pathway: Very clear and easy to read... may be make the image bigger so people dont have to click on the image to compare it with explanation
  • History: Nothing here! write something or get rid of it!
  • Normal Function: Nice details but there is no referencing and may be more images
  • Abnormal Function: no referencing and need more images
  • Proteins: I don't think this much information is needed on the protein.
  • New or Current Research: There is nothing here!


-Group 9 p53 Signalling Pathway- I think this page was somewhat incomplete and need more work

  • Introduction: I dont think there should be student signiture but I like the overal content
  • Pathway: The content was fine but may be break them up? and I think the image is too complicated. And need mroe referencing
  • Receptor: there is nothing here
  • Proteins: there is nothing here
  • History: like the length of it but it doesnt include who conducted the research
  • Current Research: There should be more researches
  • Normal Function: very clear and sufficient amount of information. But try putting more images
  • Abnormal Function: seems incomplete! more detail and referencing needed!


--Mark Hill 13:18, 17 May 2012 (EST) You have useful comments for each of the projects you have assessed.

Lab 12

Microarray Laboratory

1. Identify a current technique used in gene sequencing.

Next-generation sequencing (Illumina MiSeq system), that allow the sequence of not only DNA but RNA as well.


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

Miguel Angel Rodriguez-Milla, Isabel Mirones, Luis Mariñas-Pardo, Gustavo J Melen, Isabel Cubillo, Manuel Ramírez, Javier García-Castro Enrichment of neural-related genes in human mesenchymal stem cells from neuroblastoma patients. Int. J. Mol. Med.: 2012, 30(2);365-73 PubMed 22641458


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

Mesenchymal stem cells are known to interact with cancer cells, the relationship between mesenchymal stem cell and metastatic neuroblastoma cancer cells in bone marrow is unknown. The microarray was used to sequence the different gene expression between the bone marrow mesechymal stem cells in children compared to the normal control. The result showed 496 differently expressed genes showing either a 2-fold upregulation or downregulation between both groups of samples. this finding led to conclusion that there are genetic evidence that there are interactions between mesenchymal stem cell and neuroblastoma.