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Group 8

Lab Attendance

--Z3217686 15:13, 8 March 2012 (EST)

--Z3217686 14:08, 15 March 2012 (EST)

--Z3217686 14:07, 22 March 2012 (EST)

--Z3217686 14:13, 29 March 2012 (EST)

--Z3217686 14:08, 5 April 2012 (EST)

--Z3217686 14:08, 19 April 2012 (EST)

--Z3217686 14:18, 26 April 2012 (EST)

--Z3217686 14:06, 3 May 2012 (EST)

--Z3217686 14:17, 10 May 2012 (EST)

--Z3217686 16:01, 17 May 2012 (EST)

--Z3217686 14:05, 24 May 2012 (EST)

--Z3217686 14:19, 31 May 2012 (EST)

First Lab

This is an EXTERNAL link: JOVE

This is an INTERNAL link: Lecture 2

This is my first lab in cell biology.

Second Lab

Dynein stain.jpg

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

Review article: Schermelleh, L. et al. A guide to super-resolution fluorescence microscopy J Cell Biol: 2010, 190:165-175. Published July 19, 2010, doi:10.1083/jcb.201002018

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

The paper shows us a much clearer view of cells with a sharper, more focused picture. Colours that show through because of the dyes are perfectly clear instead of blurred, allowing us to view more intricate parts of a cell. With super-resolution microscopy we can also gather a much better understanding of the 3D concept of the cell, as more views become available. There are, however, limitations on the varieties of super-resolution microscopy methods. For example, it is expensive, can be technically demanding and is not useful in certain situations such as imaging embryos in 3 dimensions over a long period of time.

Third Lab

MSDS Methanol

Methanol. Properties: Liquid at room temp. Appears colourless. Weak, alcohol-like odour.

Hazards: Poison: May be fatal or cause blindness if swallowed. Flammable liquid and vapour. Causes respiratory irritation if inhaled.

Protective methods: Chemical splash goggles; butyl rubber gloves, apron and/or clothing. Respirator.

Fourth Lab

Description: Musashi (Msi) is an evolutionarily conserved gene family of RNA-binding proteins (RBPs) that is preferentially expressed in the nervous system. Mammalian Msi1 contributes to self renewal of NS/PCs through translational regulation of several target mRNAs.

Basically promotes renewal and growth of neural stem and progenitor cells in the central nervous system.

Shinsuke Shibata, Masahiko Umei, Hironori Kawahara, Masato Yano, Shinji Makino, Hideyuki Okano Characterization of the RNA-binding protein Musashi1 in zebrafish. Brain Res.: 2012, 1462;162-73 PubMed 22429745


Size:


Antibody: Neuromics - musashi antibody accessed at 3:09pm 29/03/12. Rabbit antibody, reacts with Human, Rat and Mouse. Used for Immunocytochemistry, immunohistochemistry, western blotting. $250.00 per 50.0 microlitres.

anti-musashi1

Secondary antibody: Alexa Fluor 488 Goat Anti-Rabbit IgG

Fifth Lab

Transgenic mice: Random chromosomal integration of foreign DNA.

- Protein may become over-expressed

- Protein may become ectopically expressed

- Protein may be mutated e.g. gains or loses a function, or mimics another protein.

Because it is random, problems occur is the DNA affects normal production of normal proteins or does not create the desired phenotype at all.

Knock-out mouse:

- To understand function of genes.

- To study pathophysiology of disease and can test therapeutic approaches to disease.

- Mimic recessive disorders (loss of function mutations)

- [Traditional transgenics can be used for dominant disorders]

Homologous recombination: fragment of genomic DNA is introduced into a mammalian cell and it can locate and recombine with the endogenous homologous sequences (gene targeting). Occurs in yeast, bacteria etc. Just like natural homologous recombination, but with a controlled, specific DNA segment inserted.

Trypomyosin

Tm5NM1/2 knockout = eliminated in all tissues.

Organ weights (Fat, brain, kidneys)

Adipocyte Proliferation

Body weight

Histopathology

Food intake

Food utilisation

Glucose tolerance test: Glucose cleared quicker in a transgenic individual but not hugely affected in a knockout individual.


Lab 6

Gif Cell bio lab 19.GIF

Proteins_in_leukocyte_extravasation.gif


Lab 7

Everything under the "Proteins" heading is my own work. References are yet to be inserted.

Lab 8

Fibroblast (NRK-49F) Cell Line

Source: Mouse Kidney (Rattus norvegicus)

J E de Larco, G J Todaro Epithelioid and fibroblastic rat kidney cell clones: epidermal growth factor (EGF) receptors and the effect of mouse sarcoma virus transformation. J. Cell. Physiol.: 1978, 94(3);335-42 PubMed 304450

K F Sachsenmeier, N Sheibani, S J Schlosser, B L Allen-Hoffmann Transforming growth factor-beta 1 inhibits nucleosomal fragmentation in human keratinocytes following loss of adhesion. J. Biol. Chem.: 1996, 271(1);5-8 PubMed 8550610

S Schultz-Cherry, V S Hinshaw Influenza virus neuraminidase activates latent transforming growth factor beta. J. Virol.: 1996, 70(12);8624-9 PubMed 8970987

K Panneerselvam, H H Freeze Mannose enters mammalian cells using a specific transporter that is insensitive to glucose. J. Biol. Chem.: 1996, 271(16);9417-21 PubMed 8621609

M Centrella, C Ji, S Casinghino, T L McCarthy Rapid flux in transforming growth factor-beta receptors on bone cells. J. Biol. Chem.: 1996, 271(31);18616-22 PubMed 8702513


Peer reviews

Group 1:

Intro

  • Good relevant information.
  • Could use more on the actual pathway and to make it flow easier.
  • Image needs a copyright notice.

History

  • Good use of a table.
  • Well referenced.

Biosynthesis

  • Nice step to introduce how we get testosterone.
  • Well referenced again.

Regulation

  • Very simple, may need a little more expansion.
  • Good use of steps to show method.

Signalling Pathway

  • As this is the main area of the study, it could use more info across the board.
  • How do the proteins actually do what they do?
  • Classical and Non-classical pathway could use much more info.
  • Also, try to get images from other places, not so much wikipedia.

Normal Function

  • Good amount of info.
  • Just needs to be read through so that the sentences make sense (a lot of full stops in the wrong place and missing commas and spelling mistakes).
  • Could use an image or two.

Abnormal Function

  • Good topics for discussion.
  • Just needs a little more on each section.
  • Images are always good, could use some.

Clinical Uses

  • Good use of a table.
  • Well referenced.
  • Good succinct information.

Current & Ongoing research

  • Just needs a little bit of tidying up.
  • Good Glossary and References.

Group 2: Intro

  • Doesn't introduce the VEGF pathway. Just a sentence on what it actually does, i.e what moves from where to where, it sends what to where?
  • Good image, could use a little visible description of what it is though.

History

  • Nice table format.
  • Needs more info (if there is more history that is).

Normal Function

  • needs more info on the hormones that influence VEGF.
  • Suggest this section comes after signalling pathway.

Signalling pathway.

  • This section needs tidying up.
  • Table looks great.
  • Image is great also.
  • More info as this is a major element of the study.

Abnormal Function

  • Great table.
  • Great images (all with references and copyright).

Research

  • This section needs tidying up, just to make it flow.
  • Info is good.

References

  • Looks good, could always use a few more though.

Group 3: Intro

  • Sentences definitely cover the topic, but seem to be almost too direct and overwhelming for an intro.
  • Could use an image to help show your topic (images are nearly always good). Plus it can help break up the text to not make it so clumsy to read.

History

  • Table this section to ease readability.

Signalling Pathway

  • Could use a little expanding as this is the main topic of your research.
  • Maybe some more points on the proteins used.
  • Images definitely needed.

Function

  • Needs more information.
  • Needs to flow a little more, seems to be a whole lot of info put together without sorting through it.

Current Research

  • Good information here.
  • Needs to be properly referenced.
  • Could expand the second paragraph: ...Extrinsic apoptosis also plays a critical role.

Glossary

  • Obviously needs to be filled in.

References

  • Included and properly cited throughout the report.

Group 4: Introduction

  • Little lacking in info.
  • Could use a good picture.

History

  • Again, little lacking in information.
  • Good use of a table.

Pathway

  • As this is the main topic of the study, this needs the most attention.
  • NEEDS an image to help show the pathway.
  • Could use steps to show order and help readability.

Proteins and Receptors

  • Don't know why the videos and such are referred in here. Should be in pathway.
  • Little more written info on each of the major proteins.
  • Image needs a copyright notice.

Normal Function

  • Good section, well referenced and plenty of info and good use of an image.
  • Image needs reference and copyright notice.
  • Could maybe link each subsection together at the end with a small paragraph.

External links

  • This section should come after Further Research.
  • Further Research needs more information.

Glossary

  • Looks good, but there should probably be more words in there from your report.

References

  • Properly referenced, just need more done to it.

Group 5: Intro

  • Good length, long enough to provide enough info but short enough to be interesting.
  • Good relevant image.

History

  • Image is in the wrong section, I feel.
  • Definitely could use a table.
  • Well referenced.

Mechanism

  • Maybe some sections could be paragraphs while others stay bullet points? Just for ease of readability.
  • Good , hand-drawn image.

Diseases

  • Good little section, has both normal and abnormal function.
  • nice use of tables and images.

Key players

  • Table could use some light borders between cells to separate everything.

Future

  • Needs to be referenced a little more.

Great glossary, external links and referencing!


Group 6: Intro

  • Don't need subheadings, these break up the flow of what should be just a summary.
  • Good information, good overall summary of the report.

Structure

  • Good image, just needs reference and copyright notice. Also doesn't need to be that big.

History

  • Should come before Structure.
  • Should be in a table.
  • Good referencing and links to Nobel prizewinners.
  • Good image of important scientist.

Insulin receptor

  • Image is good, just doesn't need to take up half the page.
  • maybe mention a little more on the alpha subunit, only has 1 sentence.

Signaling pathway

  • Lots of information, well referenced.
  • Good image, could be a thumb on the side with a caption.

Normal Function

  • Lack of information + references.
  • Sentences are a bit lengthy, could use some breaking up.

I like the introduction into each section, good standard to follow.


Group 7: Introduction

  • Seems to be a whole lot for just a summary of the report.
  • Image used here could be in the pathway section and needs a description and copyright notice.
  • Need to work on referencing

History

  • Should be in a table.
  • Good links to Nobel prizewinners.

Gene description

  • Good section for aiding your report. (this section not usual in other reports)
  • Maybe a little more description in this section.

Receptor Agonists

  • Description of what is happening here.
  • Nice use of table.

Receptor Structure

  • Good section, plenty of information.
  • Images are used very well here.

Pathway and Normal function

  • Great section.

Abnormal function

  • Good section, just needs tidying up.

A little more work into tidying everything up and fixing images and tables.


Group 9: Intro

  • Don't need signatures.
  • Definitely needs an image to start things rolling.

Pathway

  • Needs more info.
  • Image is good.
  • Maybe have steps involved.

Receptors and Proteins

  • Obviously need info.

History

  • Not a great table format, needs borders around all cells to help separate info.
  • Plenty of info and good referencing.

Current research

  • More info needed.
  • Can also do this as a table.

Normal function

  • Again, can be a table.
  • Good concepts but needs more information.
  • Info that is there is well referenced.

Abnormal function

  • More info needed.
  • Should have similar amount to normal function.
  • Nice image.

Good references and glossary.


--Mark Hill 12:40, 17 May 2012 (EST) You have assessed each project and provided coverage of each sub-heading. My only comment would be that while you have given a good review of how the sections appear (with specific comments), it would have been good if you had applied the project assessment criteria as well.

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.

Paul M Ruegger, Elizabeth Bent, Wei Li, Daniel R Jeske, Xinping Cui, Jonathan Braun, Tao Jiang, James Borneman Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. J. Microbiol. Methods: 2012, 90(3);235-40 PubMed 22640891


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

"Polony microarrays were created by adding DNA template to an acrylamide gel mixture, casting the mixture onto a prepared microscope slide, and then performing solid-phase PCR in the cured gel." The microarray technique was therefore used to allow the use of a PCR technique to be done on the required substance.