User:Z3253205

From CellBiology

Anne-Marie Lauzon, Jason H T Bates, Graham Donovan, Merryn Tawhai, James Sneyd, Michael J Sanderson A multi-scale approach to airway hyperresponsiveness: from molecule to organ. Front Physiol: 2012, 3;191 PubMed 22701430


George Pyrgos, Trisevgeni Kapsali, Solbert Permutt, Alkis Togias Absence of deep inspiration-induced bronchoprotection against inhaled allergen. Am. J. Respir. Crit. Care Med.: 2003, 167(12);1660-3 PubMed 12796055


Takeshi Nabe, Fusa Hosokawa, Kouki Matsuya, Toyoko Morishita, Ayumu Ikedo, Masanori Fujii, Nobuaki Mizutani, Shin Yoshino, David D Chaplin Important role of neutrophils in the late asthmatic response in mice. Life Sci.: 2011, 88(25-26);1127-35 PubMed 21565205


Ok Hee Chai, Eui-Hyeog Han, Hern-Ku Lee, Chang Ho Song Mast cells play a key role in Th2 cytokine-dependent asthma model through production of adhesion molecules by liberation of TNF-α. Exp. Mol. Med.: 2011, 43(1);35-43 PubMed 21169725


Lars Jacobsen, Ulrich Wahn, M Beatrice Bilo Allergen-specific immunotherapy provides immediate, long-term and preventive clinical effects in children and adults: the effects of immunotherapy can be categorised by level of benefit -the centenary of allergen specific subcutaneous immunotherapy. Clin Transl Allergy: 2012, 2;8 PubMed 22500494


Lab 1

Tasks

ANAT3231 Home Page

PubMed

Lab 2

Attendance

--Z3253205 14:33, 15 March 2012 (EST)

Tasks

Microtubule Dynamics.jpg

Marked kinetochore microtubules flux poleward.


Rockefeller University Press Copyright Policy This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.jcb.org/misc/terms.shtml). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

T J Mitchison Polewards microtubule flux in the mitotic spindle: evidence from photoactivation of fluorescence. J. Cell Biol.: 1989, 109(2);637-52 PubMed 2760109

PMID 2760109

Homework Task

Task 1

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

PMID 22006021

Task 2

Brown, T. A. and his team used superresolution fluorescence microscopy techniques to investigate mitochondrial DNA. They employed two analysis of mitochondrial DNA. In a 2D and a 3D perspective using a technique called Photoactivated Localisation Microscopy, otherwise knows as PALM (2D) and iPALM (3D). Through this microscopic technique, Brown and his team were able to view the mitochondrial nucleoids in ways that have never been possible before. Their findings include that nucleoids are not uniform and through iPALM, the mtDNA inside the nucleoids were very highly condensed, more than expected. Amongst other findings, the Photoactivated Localisation Microscopy allowed Browns' team to further investigate Mitochondria and in particular the mtDNA that has previously been limited to the microscopic techniques available.

Lab 3

Attendance

--Z3253205

Homework Task

Task 1

Acetone
PPE

Wear splash-proof goggles and barrier or viton (R) or butyl gloves. When using large quantities or where heavy contamination is likely, wear: coveralls. Where an inhalation risk exists, wear: a Type A (Organic vapour) respirator. If spraying, wear: a Type A-Class P1 (Organic gases/vapours and Particulate) respirator.

Engineering Controls

Avoid inhalation. Use in well ventilated areas. Where an inhalation risk exists, mechanical explosion proof extraction ventilation is recommended. Flammable/explosive vapours may accumulate in poorly ventilated areas. Vapours are heavier than air and may travel some distance to an ignition source and flash back. Maintain vapour levels below the recommended exposure standard.

Poison Schedule

S5 - Classified as a Schedule 5 (S5) Poison using the criteria in the Standard for the Uniform Scheduling of Drugs and Poisons (SUSDP).

Task 2

Jihed Boubaker, Wissem Bhouri, Mohamed Ben Sghaier, Ines Bouhlel, Ines Skandrani, Kamel Ghedira, Leila Chekir-Ghedira Leaf extracts from Nitraria retusa promote cell population growth of human cancer cells by inducing apoptosis. Cancer Cell Int.: 2011, 11(1);37 PubMed 22040460

PMID 22040460

Hiroshi Moro, Dennis C Otero, Yoshinari Tanabe, Michael David T cell-intrinsic and -extrinsic contributions of the IFNAR/STAT1-axis to thymocyte survival. PLoS ONE: 2011, 6(9);e24972 PubMed 21949815

PMID 21949815

Emanuele Marzetti, Riccardo Calvani, Roberto Bernabei, Christiaan Leeuwenburgh Apoptosis in skeletal myocytes: a potential target for interventions against sarcopenia and physical frailty - a mini-review. Gerontology: 2012, 58(2);99-106 PubMed 21952604

PMID 21952604

Ognoon Mungunsukh, Autumn J Griffin, Young H Lee, Regina M Day Bleomycin induces the extrinsic apoptotic pathway in pulmonary endothelial cells. Am. J. Physiol. Lung Cell Mol. Physiol.: 2010, 298(5);L696-703 PubMed 20154224

PMID 20154224

Susan Elmore Apoptosis: a review of programmed cell death. Toxicol Pathol: 2007, 35(4);495-516 PubMed 17562483


Roy,  Nicholson Cross-talk in cell death signaling J. Exp. Med.: 2000, 192(8);21-6 PubMed 11034597


R M Locksley, N Killeen, M J Lenardo The TNF and TNF receptor superfamilies: integrating mammalian biology. Cell: 2001, 104(4);487-501 PubMed 11239407


Lab 4

Attendance

--Z3253205 15:07, 29 March 2012 (EST)

Task

Musashi Protein

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

PMID 22113197

Musashi Protein expresses in neural stem cell populations in the adult central nervous system. Found in 1998

Musashi Antibody

Musashi Antibody Msi1 (69-Q) Antibody: sc-135721 Data Sheet

Msi1 (69-Q) is a mouse monoclonal antibody raised against recombinant Msi1 of human origin. Msi1 (69-Q) is recommended for detection of Msi1 of mouse, rat and human origin by Western Blotting (starting dilution 1:200, dilution range 1:100-1:1000)

Anti-Msi1 (69-Q) Antibody

Alexa Fluor® 488 Goat Anti-Mouse IgG Manuals & Protocols (Goat Anti–Mouse IgG Antibodies)

Lab 6

Attendance

--Z3253205 14:13, 19 April 2012 (EST)

Task

Lab 6 (percentage).png

Lab 7

Attendance

--Z3253205 16:02, 26 April 2012 (EST)

Task

Signalling Pathway

- include other proteins, molecules, receptors that may be involved with the pathway

Some of the proteins involved in Extrinsic Apoptosis include;

  1. TNF-α (Tumor necrosis factor alpha)
  2. TNFR1 (Tumor necrosis factor receptor 1)
  3. FasL (Fatty acid synthetase ligand)
  4. FasR (Fatty acid synthetase receptor)
  5. Apo3L (Apo3 ligand)
  6. DR3 (Death receptor 3)
  7. Apo2L (Apo2 ligand)
  8. DR4 (Death receptor 4)
  9. DR5 (Death receptor 5)
  10. FADD (Fas-associated death domain )
  11. TRADD (TNF receptor-associated death domain)
  12. RIP (Receptor-interacting protein)
  13. DED (Death effector domain)
  14. caspase-8 (Cysteinyl aspartic acid-protease 8)
  15. c-FLIP (FLICE-inhibitory protein)


Fas-mediated apoptosis

'The Fas receptor (also known as CD95 and APO-1) is a member of the tumor necrosis factor α-family of death receptors that mediate T-cell responses. Here, we show that Fas receptor signaling requires a functional T-cell receptor (TCR) complex. Fas receptor directly binds to and activates TCR components in a stimulus-dependent manner. Fas receptor stimulation does not activate canonical downstream TCR pathways, but instead the TCR complex is required specifically for Fas-mediated calcium release.'

Askar M Akimzhanov, Xinmin Wang, Jiaren Sun, Darren Boehning T-cell receptor complex is essential for Fas signal transduction. Proc. Natl. Acad. Sci. U.S.A.: 2010, 107(34);15105-10 PubMed 20696918

'Fas-induced death in T cells is strongly dependent on activation of phospholipase C-γ1 (PLC-γ1) (9). As PLC-γ1 activation is a key upstream event in TCR signaling, these observations suggest that activation of Fas and TCR pathways might not be triggered independently in different phases of AICD, but rather directly collaborate during initiation of Fas-mediated apoptosis.'

Askar M Akimzhanov, Xinmin Wang, Jiaren Sun, Darren Boehning T-cell receptor complex is essential for Fas signal transduction. Proc. Natl. Acad. Sci. U.S.A.: 2010, 107(34);15105-10 PubMed 20696918


Lab 8

Attendance

--Z3253205 14:17, 10 May 2012 (EST)

Task

1. Hepatoma Cell Line - Hepa 1-6 (CRL-1830) Hepatoma Cell Line - ATCC

2. Organ: liver, Strain: C57L , Disease: hepatoma

3. G J Darlington Liver cell lines. Meth. Enzymol.: 1987, 151;19-38 PubMed 3431441


Homework Task

--Mark Hill 13:24, 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.

1. Overall I think that the wiki is presented well. Some small issues I can see include:

  • Small amounts of grammatical errors (which are expected and I’m sure I have some of my own). In the Regulation subheading, a double use of ‘from’ and in Normal Function, ‘development of sexual organs in male fetal‘ could be rephrased.
  • The timeline finishes in 1994, there must be more recent studies into testosterone or clinical cases that relate, even if less relevant to testosterone signaling, it would be nice to have something up to or near current date.
  • Again in the Normal Function section, possibly looking into a different way of conveying the information. It is a big slab of writing; maybe some images or diagrams to break it up a little bit will help with the flow when being read. Possibly this is where the hand drawn images can come into play and help explain the message at the same time.
  • Lines like ‘Testosterone has many function during puberty in males, even though it has similar function in females but the effect is much more significant in males than in females’ could be condensed into something a little easier to read.

Otherwise I think the page is informative, it is not too difficult to understand, key points are covered, layout is as required and research seems to be vast and in depth. I think with some small amendments, the wiki will serve the purpose that is needed.

2. In short, the wiki is done well, with some small adjustments it will become very strong. Some small issues include:

  • Try to utilise the introduction a bit more. It is a section where you can establish a good description about VEGF and grab any readers attention. It is quite vague and although, in some respects, introductions should be, going into more detail can further validate you page to a prospective researcher entering the field.
  • Most of the project has a very effective and flowing layout to it with use of tables, images and subheadings appropriately. The Normal Function section looks as though it doesn’t belong in that regard. Although the concepts there are reasonably simple and difficult to write a lot about, possible some images or some form of filler to aid in the flow of the entire wiki as a whole.

Other than a few small issues, I feel the wiki read very well, a strong understanding of VEGF is shown, research appears to be well done and the layout has been very well thought out and makes reading the wiki an easier task for a peer.

4. The wiki currently is quite good, it highlights the role of the Notch Signaling Pathway. Some small areas to improve can include:

  • An individual title. I think it was just overlooked but a main heading ‘Notch Signaling Pathway’ tells the reader exactly what the page is about. Saving them searching for whether they are on the correct page or not.
  • As I advised before to another group. Try to utilise the introduction a bit more. It is strong way to give a good first impression on a reader and captivate their attention. There is a fine line between too much information in an introduction but other groups have managed to find it.

In some sections, assumed knowledge is a little high. I like the way in which the information in condensed, eliminating big slabs of writing, but be careful that some sections need a little more explanation. Others go into some depth that could be left out. This could help in keeping the size nice and condensed at the same time.

  • It also appears to be a bit short in size but I don’t feel it is lacking content, possible just some filler to give the page some size.

Overall, I believe the wiki is strong, very good portrayal of the pathway, research is very well done given the content, and layout is good so far. With some small adjustments I think it will become a very good and informative page for researchers to begin.

5. A very good effort and interesting read. Minor things that could do with some adjustments include:

  • Introduction is very intriguing and definitely engages readers but could do with a bit more of a clear definition as to what the Wnt signaling pathway is.
  • Although effective, the description of the mechanism of the pathway in bullet point style can be confusing to follow at times. In order to keep things short and sweat, the bullet points are great but can lead to miscellaneous information that looks like it doesn’t belong. In the Tumor Cell section, continuous use of the sub bullet point can throw off readers.
  • Protein table used in Key Players… segment looks like it doesn’t fit. I think there are too many columns. Possibly integrating the inhibitors column with the function column as the inhibitors themselves, play a role in the pathway.

My comments may seem petty at times but I think it was a very well done piece and that forces minor criticisms to be made. Hopefully they help. Otherwise a very well researched, very well written wiki. It is well aimed at peers in that field of research and will serve as a strong basis for further research.

6. A fairly interesting read, covers what I wiki about insulin should cover. A few little things that could be amended include:

  • As expected with all drafts, some grammatical errors. Some I spotted include ‘Ones the alpha subunit binds’ that I think should say ‘Once..’ and the heading ‘RAS-MAP kinease pathway’. Not a major problem but things that can be touched up.
  • The Introduction with the subtitles was a bit questionable for me. As it sits, I would even go as far to say possible removing the titles and just use the sections as paragraphs would rectify it. I don’t think it needs subtitles at all.
  • Layout of the wiki could be rearranged. Some of the other wiki’s (not my own and just something I picked up) have a very nice flow to them with neatly placed images and tables. That’s something that my group is looking into fixing as well.

Otherwise I believe that the wiki has good potential. Strong research is evident, content is well aimed at peers in the field, well related to the concepts of cell biology.

7. In short, the wiki is done well, with some small adjustments it will become very strong. Some small issues include

  • Some small grammatical errors that are expected and found in my own page. Include ‘Nevertheless the main the main process ‘ repeating ‘the main’.
  • I found there to be large slabs of information that can be difficult to sort through at times. Possibly breaking up the information with images and paragraphs or condensing down points with more simple descriptions.
  • More for aesthetics, most of the other groups have put their history into table form. It isn’t a big problem but I believe it helps with the flow of the page overall.

In summary, I believe the wiki is strong, very good portrayal G-protein coupled receptors, research is very well done given the content, and layout can be fine tuned. With some small adjustments I think it will become a very good and informative page for researchers to begin.

8. Overall I think that the wiki is presented well. Some small issues I can see include:

  • One problem I found when reading through the project was that I felt as though there was too much information being thrown at me in one hit.
  • Try to condense the information, move away from the writing found in an article aimed at experts in the area, aim for peer level. The way you were before reading anything about the topic.
  • Integrate some tables and positioning of images between text. It involves some coding, ask around the lab or even have a look at other groups coding on their page to get an idea.

Otherwise I think the page is informative, key points are covered, layout could do with some work and research seems to be in depth in some areas, make sure to complete it with the normal function sectoin. I think with some small amendments, the wiki will serve the purpose that is needed.

9. A good effort and interesting read. Some things that could do with some adjustments include:

  • Completion of all sections to the project is required. I came to the understanding that this is not near completion and it is something that should be a major concern. It leaves questions to be asked about the validity of some of the better-written sections.
  • I believe some more depth in research is required and shows when going through some of the more difficult sections of the page. Normal Function especially as I believe this is at the top of the list when someone is researching anything to do with p53.
  • Layout is definitely something that needs to be rectified. Like I have advised to other groups, jump on some of the better-presented pages and have a look at their coding for positioning images and tables. This can help the page look the part at the very least.

In closing, I believe that the page does require some work to get it to the required standard. It is not out of reach by a long shot but will require some good group work and discussion. Take on board the advise given from myself and others, remove the crap from it and tackle what is left.

Lab 10

Attendance

--Z3253205 15:49, 17 May 2012 (EST)

Lab 11

Attendance

--Z3253205 14:52, 31 May 2012 (EST)

Lab 12

Attendance

--Z3253205 14:52, 31 May 2012 (EST)

Task

1. Next Generation Gene Sequencing

2. PMID 22564414 'miR-34s inhibit osteoblast proliferation and differentiation in the mouse by targeting SATB2.'

3. Microarrays have been used to analyse pre-osteoblasts and mature osteoblasts, between a set time period, to assess the expression of miR-34s throughout the investigation.