User:Z3290558

From CellBiology

Lab Attendance:

w2 --Z3290558 15:13, 8 March 2012 (EST)

w3 --Z3290558 14:15, 15 March 2012 (EST)

w4 --Z3290558 14:08, 22 March 2012 (EST)

w5 --Z3290558 14:09, 29 March 2012 (EST)

w6 --Z3290558 14:42, 5 April 2012 (EST)

w7 --Z3290558 14:26, 19 April 2012 (EST)

w8 --Z3290558 14:16, 26 April 2012 (EST)

W9 --Z3290558 14:53, 3 May 2012 (EST)

w10 --Z3290558 14:27, 10 May 2012 (EST)

w12 --Z3290558 14:26, 24 May 2012 (EST)

w13 -- --Z3290558 15:16, 31 May 2012 (EST)


Lab 1

Online Work

External Link:

http://www.jove.com/basic [1]


Internal Link:

Lecture 2


Heterochromatin shown in a spermatocyte.jpg


Lab 2 - Microscopy

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.

This article is a summary of a review article from the American Society for Microbiology. It showed that by using various superresolution microscopy techniques, more details and greater insight into mitochondrial nucleoids could be found. Some of these included:

- ability to visualise the main dimensions and locations of the mitochondrial nucleoids

- size and shape of nucleoids

- dimensions of the mitochondria (to see if the size of the nucleoids caused any restraints upon the space within the mitochondria)

- nucleoid's association with its inner membrane


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.

Formalin (Synonyms: Formalin, Formol, Morbicid) SDS

Properties:

  • Clear liquid
  • Pungent odour
  • Boiling Point: ~96°C
  • pH: 2.8-4.0

Hazards:

  • Vapour is irritant to mucous membranes and respiratory tract
  • Toxic if inhaled, swallowed or with skin contact
  • Carcinogen potential


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.

a) Atsuhiko Ichimura, Yoshinao Ruike, Kazuya Terasawa, Gozoh Tsujimoto miRNAs and regulation of cell signaling. FEBS J.: 2011, 278(10);1610-8 PubMed 21395975

This review article talks about the target genes required for notch signalling and how it is regulated.


b) Donal MacGrogan, Meritxell Nus, José Luis de la Pompa Notch signaling in cardiac development and disease. Curr. Top. Dev. Biol.: 2010, 92;333-65 PubMed 20816401

This review article outlines a type of notch signalling - endocardial notch, and its roles and activities it plays in this particular notch.


c) Simon D Gerber, Ruth Amann, Stefan Wyder, Beat Trueb Comparison of the gene expression profiles from normal and Fgfrl1 deficient mouse kidneys reveals downstream targets of Fgfrl1 signaling. PLoS ONE: 2012, 7(3);e33457 PubMed 22432025

The research article above highlights the requirement of the notch signalling pathway involved in the proximal and distal tubules of the kidney, and the genes involved.


(d) Rui Du, Wenjuan Sun, Lin Xia, Ali Zhao, Yan Yu, Lijuan Zhao, Hanmin Wang, Chen Huang, Shiren Sun Hypoxia-induced down-regulation of microRNA-34a promotes EMT by targeting the Notch signaling pathway in tubular epithelial cells. PLoS ONE: 2012, 7(2);e30771 PubMed 22363487

This research article provides results of what would happen if specific changes occurred in the notch pathway.


Lab 4 - Immunochemistry

What is musashi? What does it do? And is it a real protein?

  • it's an RNA binding protein
  • expressed in neural stem cells and neural lineage cells
  • exists in isoforms: Musashi-1, Musashi-2

Sayaka Higuchi, Tetsutaro Hayashi, Hiroshi Tarui, Osamu Nishimura, Kaneyasu Nishimura, Norito Shibata, Hiroshi Sakamoto, Kiyokazu Agata Expression and functional analysis of musashi-like genes in planarian CNS regeneration. Mech. Dev.: 2008, 125(7);631-45 PubMed 18440787


M Szabat, T B Kalynyak, G E Lim, K Y Chu, Y H Yang, A Asadi, B K Gage, Z Ao, G L Warnock, J M Piret, T J Kieffer, J D Johnson Musashi expression in β-cells coordinates insulin expression, apoptosis and proliferation in response to endoplasmic reticulum stress in diabetes. Cell Death Dis: 2011, 2;e232 PubMed 22113197


  • Antibody against Musashi:

- Source: polyclonal rabbit

- Using Western Blotting, at a concentration of 1 µg/ml, 1:1000 dilution, it detects a band of a predicted molecular weight of 39kDa. However can be blocked by the Musashi1 peptide.

- Target: RNA binding protein

RNA binding protein that regulates the expression of target mRNAs at the translation level.


  • Secondary antibody against Musashi using Alexa:

- Source: Goat, polyclonal secondary antibody to the rabbit

- pre-adsorbed, dilution of 1/5000


http://www.abcam.com/Musashi-1-Msi1-antibody-ab21628.html [2]


Lab 6 (week 7)

Week 7 lab.JPG


Lab 7 (week 8)

Sections I worked on mainly for the group project:

  • Introduction
  • History

'Other minor parts contributed:

  • Normal function of notch


Lab 8 - Tissue Culture (week 9 hwk)

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

MDA-MB-231 [3]


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

Derived from a Homo sapien mammary gland (breast), from the adenocarcinoma disease. It's cell type is an epithelial cell.


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

M J Siciliano, P E Barker, R Cailleau Mutually exclusive genetic signatures of human breast tumor cell lines with a common chromosomal marker. Cancer Res.: 1979, 39(3);919-22 PubMed 427779


Lab 9, Week 10 homework

Group 1

  • Introduction: check grammar – ‘Androgens, with testosterone in particular, have strong affinity for the androgen receptor.’

The introduction is a little clunky and has no smooth flow from one sentence to the next. I’m also left unsure of what you’re going to talk about in your project. Nice picture but if you aren’t going to talk about it and simply dot point out the molecular properties, not describe it, then I think that seems a little awkward for an introduction.

  • History: nice table, nice use of different colours but colour choice seems slightly awkward. Makes the page seem untogether and the history part stands out too much.
  • Biosynthesis: I’m a little unsure of why you bolded certain words. I thought they would be in the glossary but it isn’t. great picture, but should you be referencing from Wikipedia? Maybe find the same thing in a text book, modify it and draw it. Could also be worthwhile mentioning where cholesterol or testosterone comes from in the steroidogenesis pathway so the picture is being useful instead of just looking pretty.
  • Signalling pathway – great section, easy to understand and flows well.
  • Normal function – proof read this section – second paragraph, second sentence ‘…. fertility.if testosterone ‘. Also might want to separate this section into having a few subheadings. A massive piece of text with no pictures makes it a little boring and hard to read.
  • Clinical uses – love this section and how you’ve written it and put it into a table. Love the video, made it easy to understand.
  • Glossary – putting it in alphabetical order would make it easier to find the words
  • Images: I like how you did this and put them altogether.
    1. note: I noticed you didn’t have a student drawn image in the project which doesn’t fit the marking criteria. Please remember to do this!

Group 2

  • Intro: bit brief, and seems a little vague. I’m left unsure of what Vascular endothelial growth factor is about. Maybe even put more terms in the glossary that people of non-scientific background can understand too, such as embryogenesis, and proliferation. Even a picture to help describe what VEGF is all about.
  • History: great. But did nothing happen between 1993-2004? Also in 2004, might be good to put ‘antiangiogenic effect’ and ‘metastatic’ in the glossary.
  • Normal function: easy and clear to read. Great work. Might want to fix up your hormones section, don’t quite understand the question mark at the end of steroids? And lack of references for oncogenes…
  • Abnormal function: love the table. Made it clear, interesting and easy to read
    1. overall: not many terms in the glossary, remember that a good way to look at it would be to imagine a person with no scientific background came and looked at your page, write any science-y words in your glossary. Some I found I mentioned, others worth noting are: thromboembolic, dehiscence etc. Also love what you’ve done with adding hyperlinks to words to link straight to the glossary words at the bottom. Also, you need a student drawn image to fit the marking criteria, so make sure you draw one up and include it! Otherwise great work, some sections at the beginning could do with a bit more detail cos it seems very vague.

Group 3

  • Intro: in the first paragraph you referred to your project page as a ‘paper’ which is kinda weird. Also if you are not going to talk about the minor apoptotic pathways in the rest of the project, you might want to leave that out of the introduction and briefly mention it in the major pathways as a side thing.
  • Great introduction, interesting, flows well and leads onto the project page well, but I think you gave a little too much detail for the intro (perhaps leave the second paragraph out but keep the first and last one). Other than that, well done!
  • Signalling pathway – bit unclear of how you’re structuring this. Perhaps have a paragraph explaining what you’re talking about and then lead onto talking about Fas-mediated apoptosis etc.
  • Overall: a few pictures could brighten up your page. your references are a little weird. You might want to go to another project page and see what they’ve done and copy their computer codes if you’re not sure how to reference it properly. Your glossary looks empty so please add to your glossary list, words in alphabetical order of any technical terms that someone from a non-science background may not understand. You also don’t have the student drawn image which is part of the marking criteria. Don’t forget to include this!

Group 5

  • History – it might look nicer if you put this into a table and under one certain year, write everything that happened in dot point instead of writing the same year several times.
  • Mechanism of action: great stuff, but simply writing it in dot form made me a little confused. Maybe write a little paragraph explaining the basic idea of whats happening and then have the dot points after it.
  • Overall: great project. Just a few touch ups with adding a little more info here and there but overall it was a clear and easy project to follow through. Loved the table with the pictures making everything easier to follow and understand. Great work.

Group 6

  • No heading!
  • Intro- I don’t think its necessary to write about each subsection and talk about it. Instead just talk about the insulin pathway and summarise everything into one or two paragraphs. I think this would be more effective and easier to understand and introduces us to the whole project rather than subsections cos this doesn’t make anything seem whole.
  • Structure – proof read! ‘Computer’ shouldn’t be written like this midsentence. Perhaps the structure could be pieced together inside of the introduction because it seem very brief. Possibly even reduce the side of the image into a thumbnail for easier viewing.
  • History – in 1980, 1985 and 1988 do we know who discovered these?

Insulin receptor – I don’t think this part is that necessary to put into its own subheading. Reducing of the image would be a lot nicer as well.

  • Glossary – Your glossary looks empty so please add to your glossary list, words in alphabetical order of any technical terms that someone from a non-science background may not understand.
  • I liked your images section but make sure you copy the copyright info for each image you use!

Group 7

  • Intro – please proof-read. 3rd paragraph, last sentence ‘when the process IN not working correctly.’ And also the sentence after it, involced* spelling error. Also ‘the main the main’…. Mistakes like these in the intro, please proof read..

I think also you got a little carried away with the intro, we want a general summary of the whole thing not a summary of each section. Otherwise great intro, interesting to read, summarised what I’m about to read. Good stuff.

  • The receptor agonist section seems unfinished…
  • Overall: as it is a project report that you’d probably see on a wiki page, its not necessary to add your signature after each section. Also some of you didn’t do in-cite referencing, so please be sure to do this instead of writing all the references at the bottom of the subsection.

very well written project with enough detail, however please add to your glossary. Remember to put in any words that someone from a non-science background may not understand.


Group 8

  • Intro – great intro, straight to the point and easy to follow. Perhaps talk about what you will be talking about in the paper though
  • Pathway – maybe introduce it a little better of what a leukocyte extravasation does and when and how it does it. Or readers may find it confusing to just read it that way. Great picture to go with the supporting text however make sure you reference it (even if it’s a student drawn image, mention it).
  • History – no text??
  • Normal function: don’t think its necessary to have that first line written there, just get straight into the intro of it. I think include the pathway part into the normal function instead of separating them into two headings. The intro of the normal function already sounds like what I’d like to read before I read about the pathways section. It’d make it transition better and sound nicer. Also the intro here sounds very clunky and doesn’t flow from sentence to sentence. Please also proof read.
  • Overall: you have no references before abnormal function! For your glossary, remember to put in any words that someone from a non-science background may not understand.

Group 9

  • Intro – clear and easy to understand. Not necessary having signature marks though
  • History – easy to read and follow, great table.
  • Glossary - Remember to put in any words that someone from a non-science background may not understand.
  • Overall: project seems unfinished. Abnormal function is very brief, also note that you haven’t yet done a student drawn image which needs to be included for the marking criteria.


--Mark Hill 13:15, 17 May 2012 (EST) You have made some good critical analysis and related comments for each project, some have more detail that others.

Lab 12, week 13 - Microarray

1. Identify a current technique used in gene sequencing.

Next generation Gene Sequencing.

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

Markus Kaller, Sven-Thorsten Liffers, Silke Oeljeklaus, Katja Kuhlmann, Simone Röh, Reinhard Hoffmann, Bettina Warscheid, Heiko Hermeking Genome-wide characterization of miR-34a induced changes in protein and mRNA expression by a combined pulsed SILAC and microarray analysis. Mol. Cell Proteomics: 2011, 10(8);M111.010462 PubMed 21566225


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

This research paper described changes in proteins and in mRNA expression on the encoding gene of miR-34a microRNA which was found to cause inactivation in colon cancer and other tumours. Microarray analysis of mRNA levels was performed after ectopic expression to determine the miRNA targets and expressions, which resulted in only minor changes caused by the miR-34a-specific gene that was present.