User:Z3332327

From CellBiology

Lab Attendance

--Z3332327 15:20, 8 March 2012 (EST)

--Z3332327 14:11, 15 March 2012 (EST)

--Z3332327 14:09, 22 March 2012 (EST)

--Z3332327 14:13, 29 March 2012 (EST)

--Z3332327 14:06, 5 April 2012 (EST)

--Z3332327 14:07, 19 April 2012 (EST)

--Z3332327 14:16, 26 April 2012 (EST)

--Z3332327 14:16, 3 May 2012 (EST)

--Z3332327 14:11, 17 May 2012 (EST)

--Z3332327 14:12, 24 May 2012 (EST)

--Z3332327 14:17, 31 May 2012 (EST)

Lab Work

Lab 1

--Z3332327 15:20, 8 March 2012 (EST)

Internal Link: 2012 Group 2 Project

External Link: Sydney Morning Herald

Lab 2

1. Upload Image

Original Recycling Model.jpeg

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

Mudalige S Gunewardene, Fedor V Subach, Travis J Gould, Gregory P Penoncello, Manasa V Gudheti, Vladislav V Verkhusha, Samuel T Hess Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys. J.: 2011, 101(6);1522-8 PubMed 21943434


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

The article comments on the limitations of normal microscopy, ie. diffraction limits the resolution to around half the wavelenth of light (Ernst Abbe, 1873). It mentions a family of superresolution microscopy methods such as Flurorescene photoactivation localisation microscopy (FPALM), stochastic optical reconstruction microscopy (STORM)etc that have surpassed the limitation of normal microscopes. Consequently, increased resolution.

This is achieved by using conventional organic fluorophores that have a range of emission wavelengths. They are also capable of emitting many photos before photobleaching, which therefore help to improve precision and the visibility of single molecules.

--Mark Hill 18:17, 20 March 2012 (EST) Good paper.

Lab 3

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

SDS: Paraformaldehyde

Properties
Appearance Clear to white solid
Odour Pungent odour
pH 4.3
Vapour pressure (mm of Hg at °C) 1.4mmhg at 25°C
Vapour density(Air = 1) 1.03
Boiling point/range (°C) Slowly sublimes to formaldehyde gas
Freezing/melting point (°C) Melting point 120-170°C
Solubility Slightly soluble in cold water
Flash Point 70°C
Flammable (explosive) limits Lower limit: 7.0

Upper limit: 73

Ignition temperature 300°c


Hazards

  • Toxic by inhalation, in contact with skin and if swallowed.
  • Causes burns.
  • Limited evidence of a carcinogenic effect.
  • May cause sensitisation by skin contact.


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.


Articles

A vascular endothelial growth factor deficiency characterises scleroderma lung disease: This article is relatively current and explores the deleterious effects of VEGF deficiency in lung tissue in relation to scleroderma lung disease. This could be included under 'current research' or the 'abnormal function'.

Maria De Santis, Silvia Laura Bosello, Ettore Capoluongo, Rosanna Inzitari, Giusy Peluso, Paola Lulli, Gaetano Zizzo, Mario Bocci, Barbara Tolusso, Cecilia Zuppi, Massimo Castagnola, Gianfranco Ferraccioli A vascular endothelial growth factor deficiency characterises scleroderma lung disease. Ann. Rheum. Dis.: 2012, 71(9);1461-5 PubMed 22402140


Vascular endothelial growth factor B controls endothelial fatty acid uptake: This article explores the role of VEGF B which is mostly unclear in terms of angiogenesis and its involvement in endothelial cell physiology.

Carolina E Hagberg, Annelie Falkevall, Xun Wang, Erik Larsson, Jenni Huusko, Ingrid Nilsson, Laurens A van Meeteren, Erik Samen, Li Lu, Maarten Vanwildemeersch, Joakim Klar, Guillem Genove, Kristian Pietras, Sharon Stone-Elander, Lena Claesson-Welsh, Seppo Ylä-Herttuala, Per Lindahl, Ulf Eriksson Vascular endothelial growth factor B controls endothelial fatty acid uptake. Nature: 2010, 464(7290);917-21 PubMed 20228789


Vascular Endothelial Growth Factor: This article gives a great overview about the structure and function of VEGF.

Ian Zachary, Vascular endothelial growth factor, The International Journal of Biochemistry & Cell Biology, Volume 30, Issue 11, November 1998, Pages 1169-1174, ISSN 1357-2725, 10.1016/S1357-2725(98)00082-X.

Vascular Endothelial Growth factors: This paper reviews the role of VEGF and its role in clinical applications in cardiovascular medicine. There are some great summaries on the biology of the VEGF family.

Seppo Ylä-Herttuala, Tuomas T Rissanen, Ismo Vajanto, Juha Hartikainen Vascular endothelial growth factors: biology and current status of clinical applications in cardiovascular medicine. J. Am. Coll. Cardiol.: 2007, 49(10);1015-26 PubMed 17349880


Lab 4

Musashi (Msi)is a group of RNA-binding proteins mainly expressed in the nervous system. There are various musashi isotopes, and are expressed in various cells such as

- sensory organ precursor cells

- expressed in beta cells

- expressed in stem cells

- involved in apoptosis (programmed cell death)

The article concludes that Msi1 plays roles in CNS development in vertebrates

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


Msi 1 antibody - Affinity Purified Polyclonal Rabbit Antibody

Catalogue no: RA14128

Size: 50ul

Price (USD): $250

Type: Rabbit IgG

Applications: Immunocytochemistry 1:100-1,000, Immunohistochemistry 1:100, Western blotting 1:100

Species Reactivity: Human, Mouse and Rat

Msi 1 Antibody Datasheet


Secondary Antibody

Product name Alexa Fluor® 488 goat anti-rabbit IgG (H+L) *2 mg/mL*

Product code A11008

Company: INVITROGEN AUSTRALIA PTY LIMITED 2A/14 LIONEL ROAD MOUNT WAVERLY VIC 3149 AUSTRALIA 011 61 3 8542 7400

MSDS Goat anti-rabbit IgG (H+L) *2 mg/mL

Lab 6

Tm4 overexpression Vs Control

Tm4 Overexpression.JPG

A. Do you see a difference in phenotype(morphology) between Tm4 overexpressing and control cells?

Yes.

B. If so, how could Tm4 overexpression lead to this difference?

In the pronged and stringed phenotypes, the Tm4 samples were relatively higher compared to the control groups. This may suggest that Tm4 causes increased expression.

In contrast, the pygnotic phenotype, shows relative lower Tm4 samples compared to the control. This suggests that Tm4 may have an inhibitory effect.

C. Differences between Genotype A and B (induced with cAMP)

Genotype A: rounder nuclei, short processes (also more abundant)

Genotype B: Processes appear longer, and nuclei appear dense

Lab 7

My contributions to the Group Project include:

  • History
Date Brief description
Late 1970s

Discovery of tumor-secreted protein that potently increased microvascular permeability to plasma proteins. [1]

1983

Senger and Dvorak were the first to discover a protein which increased vascular permeability in a number of vascular beds, including those of skin, subcutaneous tissue, peritoneum, pleura, mesentery, diaphragm, retina and skeletal muscle. This protein was named vascular permeability factor (VPF). [2]

1986

Dvorak proposed that by secreting VPF, tumors induce angiogenesis. Dvorak's scientific research greatly contributes to our current understanding of tumor growth and its blood supply. He noted that tumors were like wounds in their secretion of VPF, which caused blood vessels to leak plasma fibrinogen and hence induced angiogenesis. However, unlike wounds which heal and stop secretion of VPF, malignant tumors would continue to grow and spread. [3]

1989

VEGF-A was first cloned and isolated by Napoleone Ferrara and his colleagues at Genentech. [4] Subsequently, it was discovered that the DNA sequences of VEGF and VPF were identical.

Over the years, five VEGF-related genes have been identified (VEGF-A, VEGF-B, VEGF-C, VEGF-D and VEGF-E). There are five characterized VEGF-A isoforms of 121, 145, 165, 189 and 206 amino acids in mammals. [2]

1993

Ferrara reports that by inhibiting VEGF-induced angiogenesis with specific monoclonal antibodies, they were able to suppress the growth of a variety of tumours in vivo. [4]

  • Current Research

Cancer Therapy

GFP-positive metastatic tumor cells (B)More metastatic lesions were visible in lungs (after 9 days) of mice injected with cells expressing VEGF compared with cells expressing GFP alone]] In recent years, antiangiogenesis has been at the core of alternate cancer therapy research. This includes a variety of methods that prevent tumor angiogenesis and/or that attack tumor blood vessels. Alternate cancer therapy is desirable as these approaches are relatively non-toxic and are thought to prevent tumor cell regrowth with long-term administration.

In particular, therapies have been designed to target VEGF-A, which is known to initiate and promote tumor vasculature in humans and animals. There have been recent successes in treating mouse cancers. Evidence shows that by neutralising antibodies against VEGF-A, and antibodies that block VEGF-A receptors, tumor growth can be significantly reduced. More recently, antibodies have been designed to selectively recognise VEGF-A forms found on tumor vessels, hence avoiding side effects that might result from inactivation of free VEGF-A. [5]

  • Images
(A) Fresh lung tissue was examined using laser scanning confocal microscopy to detect GFP-positive metastatic tumor cells (B)More metastatic lesions were visible in lungs (after 9 days) of mice injected with cells expressing VEGF compared with cells expressing GFP alone

--Z3332327 16:07, 2 May 2012 (EST)

Lab 8

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

CHO-K1 ATCC CHO-K1

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

Ovary - Cricetulus griseus (epithelial-like)

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

T T PUCK, S J CIECIURA, A ROBINSON Genetics of somatic mammalian cells. III. Long-term cultivation of euploid cells from human and animal subjects. J. Exp. Med.: 1958, 108(6);945-56 PubMed 13598821


Lab 9 - Peer Assessments

Group 1- Testosterone Signaling

  • Introduction: Well summarised and good use of sources. Need to add copyright info for the image.
  • History: very informative and research is quite extensive. I like the table format, not too sure about the colour. But it does make the website more inviting and interesting.
  • Biosynthesis: this section is overwhelming with scientific jargon. Perhaps adding some of the words such as hydrogenation to the glossary could really help people to understand. Include copyright information for the image.
  • Signaling pathway: i like the layout of this section and the use of appropriate images (both of which are correctly cited. I also noticed there are two wiki images?)
  • Normal function: appears very dense and full of information. Maybe consider playing with the layout by adding images/tables
  • Clinical Uses: table is very useful in summarising and organising the information. The video is a great touch!
  • Current and ongoing research: I think this section needs a little introduction before diving into the research content. It could really benefit from some sub-headings or in-text citations just to reinforce the studies already summarised.
  • Glossary: bit short, but coming along well. Don't forget to arrange them in alphabetical order.
  • References: double check some of your references. E.g. No. 2 is a dead link and also 20, 22, 26-27 need proper references.

Overall the page was very interesting and generally well presented. Just a few changes needed.

Group 3 – Extrinsic Apoptosis

  • Introduction: Incomplete, maybe too much info for an introduction. An image would help break up that block of text. No references?
  • History: Information is fine, though placing it in a table would make it easier to read. No other sources used?
  • Signalling Pathway: Formatting the referencing would make the “Fas-Mediated Apoptosis” section cleaner to read. Section looks too bare! Images?
  • Function: No referencing, content looks incomplete, but some solid effort.
  • Current Research: Could image be formatted to be incorporated beside the block of text?
  • Glossary: nothing there.
  • References: In some of the text, nothing here though!

Overall the page appears to be incomplete and still needs to be formatted.

Group 4 - Notch Signaling

There is no title!

  • Introduction: Very brief, addition of image if possible?
  • History: Table is fine, though did nothing happen between 1930-78? Feels like more info could be added.
  • Pathway: Is there such thing as notch 2 and 3? Concise information, any images to support?
  • Proteins and Receptors: Well done, very appealing with all the formatting. Good work!
  • Function: A lot of information, but set out neatly, which make it much easier to read. Enjoyed it.
  • External links: the “Further Research” section could have some text in regards to the future research besides just having a link.
  • Glossary: Kind of short, but mostly well done.
  • References: Good work, looks great!

Overall the page seems a little short. It’s looking great so far, but I think it just lacks a bit more information and possibly an image in the introduction.

Group 5

  • Introduction: I would explain what a Wnt/β Signalling pathway first, then go on about the 30th anniversary. Only one reference is used here.
  • History: Although, preferably have it in a table, it seems to be neat and easy to read! Great use of resources, and it is evident that a lot of research has been put into this section. The Image could be slightly larger to be easily read.
  • Mechanism of Action: Maybe a short summary or paragraph about the MoA instead of dot points? The hand drawn image is very well done. Its a great summary of the pathway as opposed to a wall of text.
  • Diseases Associated with Wnt/β-catenin signalling: Excellent work! Short, concise, great images, great formatting.
  • Key Players in Wnt/β-catenin Signalling: Table looks really well set out. I’m not 100% sure about the copyright for the images. Technically this website is available to the world wide web – not just university students etc.
  • Embryonic Development: Short, but informative. Possible to explain a bit more?
  • Future directions: This section is difficult to understand. Instead of just a list of possible directions, maybe you can elaborate on the points and provide some sources/articles/research.
  • Glossary: Looks good, some formatting to clean it up is all that’s really needed.
  • References: Excellent referencing, though 64 needs to be fixed. And also you have many instances where references appear twice. Such as 74&73 and 77&79 and 105&106.

Group 6

  • Introduction: Its a good introduction, however I’m not sure the use of subheadings is very appropriate here. The youtube video is a nice touch, but perhaps that should be added to the Insulin section. The link also needs a caption. The introduction is also lacking in references.
  • Structure of Insulin: This section is very short, and the image contains no copyright or reference information. I don’t particularly find the formatting of this section appealing. Maybe the image could be smaller, or changed to a thumbnail so at least there isn’t all this blank space on the page.
  • History: The history section is extensive, but some of the dates are missing references. And the external link to the Nobel Prize of Dorothy Hodgkin needs a better caption. Or if you like, add it to the end of the section as External Links: [Nobel Prize Winner]
  • Insulin Receptor: Once again, the image is too big. It breaks up the page and leaves a lot of blank space. The image info also requires a reference. Copyright information is correct.
  • Signalling Pathway: The formatting of this section is very well done with the subheadings to break up the text. The image needs copyright information.
  • Normal function: Short, any more referencing? Maybe drop the “Introduction” title!
  • Abnormal function: Well researched section and appealing layout.
  • Current Research: any reference for “Wilson Research Institute” and what they are doing?
  • Glossary: short, more could be added!
  • References: everything seems to be there, good job.

Overall I feel the sections don’t really flow, I think this could avoided if you removed the subheading “Introduction” which appears in Signalling pathway, normal and abnormal function. However, it is evident that a lot of research has been put into this page. The page is nicely formatted with the use of appropriate images. I would suggest reconsidering the size of the images and look at how it breaks up the text a little too much.

Group 7

  • Introduction: I am very impressed by the hand drawn image. It’s a good diagram to accompany the intro which is also very well written. Just note you should probably remove the student tags, and also the references should be in text rather than a bunch at the end of the section.
  • History: Well researched, however it would be easier to read if it were in a table format.
  • Receptor Structure: Very easy to read, and understandable. I like the colourful images, they break up the text very well. I’m not sure what the limit on wiki images are, but just be aware you have two in this section.
  • Pathway and Normal function: I like the use of external links, however I think it would look better if you put them at the end of the section. Overall the layout is very appealing with the use of bright coloured images and subheadings. The information is also easy to understand.
  • Abnormal function, Diseases and Treatments: The table is a great way of summarising the information. Just a suggestion about the referencing, I noticed that you have used the same reference and tagged each sentence. This isn’t very necessary, just simply add the reference at the END of the paragraph rather than at the end of each sentence. Overall, very well researched section.
  • Glossary: I suggest adding internal links, it makes it easier for the reader to understand the text without having to scroll down and look for the word.
  • References: a few need to be corrected and properly referenced: 5,7,8

Group 8

  • Introduction: nicely summarised.
  • Pathway: Clearly set out and easy to understand. However I noticed neither of these sections had any references.
  • History: needs to be started at least
  • Normal Function: check your spelling and grammar. Some of the sentences are a bit hard to follow. This section is very dense and needs images or bullet points to break it up. There are also no references.
  • Abnormal function: very well researched. However you might consider using a table to format this section because it needs to be organised in such a way that is easier to read.
  • Proteins: Good use of resources, however there is a lot of text to comprehend.
  • New or Current Research: nothing.
  • References: appears to be correct!

Group 9

  • Introduction: Please remove student signatures. I think the introduction is well written and easy to understand. Maybe you could summarise it a little bit more.
  • Pathway: This section only has one reference. The information is understandable however the reader would appreciate some subheadings just to break up the text.
  • Receptor: Incomplete
  • Proteins: Incomplete
  • History: Unusual placement of the History section. Usually placed after introduction, which I think is more appropriate. However this section is very well researched and up-to-date.
  • Current Research: a very short paragraph, I am sure there is more research going on.
  • Normal function: I think this section should come earlier in the page. Good use of subheadings, this section could benefit from an image though.
  • Abnormal function: Appears incomplete. However the image is correctly referenced.

Overall, the page still needs a lot more work to be done.


--Mark Hill 13:39, 17 May 2012 (EST) You have made an assessment for all projects and included specific comments about content. The comments about layout are useful to each group, but you should also consider in detail the scientific content within the project.
  1. Harold F Dvorak Vascular permeability factor/vascular endothelial growth factor: a critical cytokine in tumor angiogenesis and a potential target for diagnosis and therapy. J. Clin. Oncol.: 2002, 20(21);4368-80 PubMed 12409337
  2. 2.0 2.1 D R Senger, S J Galli, A M Dvorak, C A Perruzzi, V S Harvey, H F Dvorak Tumor cells secrete a vascular permeability factor that promotes accumulation of ascites fluid. Science: 1983, 219(4587);983-5 PubMed 6823562
  3. Domenico Ribatti The contribution of Harold F. Dvorak to the study of tumor angiogenesis and stroma generation mechanisms. Endothelium: 2007, 14(3);131-5 PubMed 17578706
  4. 4.0 4.1 Napoleone Ferrara From the discovery of vascular endothelial growth factor to the introduction of avastin in clinical trials - an interview with Napoleone Ferrara by Domenico Ribatti. Int. J. Dev. Biol.: 2011, 55(4-5);383-8 PubMed 21858763
  5. Harold F Dvorak Vascular permeability factor/vascular endothelial growth factor: a critical cytokine in tumor angiogenesis and a potential target for diagnosis and therapy. J. Clin. Oncol.: 2002, 20(21);4368-80 PubMed 12409337