Difference between revisions of "Talk:2009 Group 4 Project"
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--[[User:Z3191358|Hamid Araghi]] 19:27, 2 June 2009 (EST)
--[[User:Z3191358|Hamid Araghi]] 19:27, 2 June 2009 (EST)
== bump! ==
== bump! ==
Revision as of 20:30, 2 June 2009
--Mark Hill 14:39, 3 May 2009 (EST) OK Guys, looks like you are back on track (get it?) so I will look back here in a while and see how you are getting on.
--Mark Hill 13:33, 19 March 2009 (EST)I fixed your topic layout and have moved microscopy assessment off your group project page to here.
A (was reviewed as a group)
- Content - incredibly dense and probably over the word limit. However, nevertheless in reading through i suppose there isn't really much that you guys could cut out as its all quite well thought out and laid out.
The structure looks good. You're structure looks good. Your content has a logical flow. It is easy to read and well spaced out. The timeline just needs to be completed or deleted from the page. The images on this page are well placed in relation to their respective text and they are all sourced except for the first. Is this the student drawn figure? Make sure you correct this.
- Good use of diagrams, the animations of the different pathways are quite impressive and a useful aid.
- The glossary is quite thorough, clear explanation of words. Will be better if you can improve the format so it's easier to refer to; such as making the main words bold, and using dashes " - " consistently.
- The youtube video link under "Ras-MAPK (mitogen-activated protein kinase) Pathway" is very helpful, the links to the individual member's pages were also placed appropiately.
B: Group 7
- Intro: Perhaps a little too in depth for an introduction - try to use 'easier to read' language.
- Structure + Function: A picture would help to illustrate what you're saying. Well set out.
- Dynamic process: "Phosphorylation of an additional seven tyrosines within this region promotes signalling by providing docking sides for adaptor proteins which regulate signalling-cascade couples." Include in the picture an explanation.
- Animations are great!
- PKC pathway: good but try to break the text up a bit with either dot points or numbers.
- Current research: Try to find research from the last couple of years. Dr. Hill might not think 2000 is 'recent' enough. For the second entry, which publication is referred to in "In a recent publication"? We, however, understand that you'll fill out that reference bracket after it.
- Overall: Great setting out and headings. The information is quite biochemical which you could probably condense into simpler, easier to read text. Picture legends and referencing need revision (they're a little short).
- All links present. Still missing references!
Location of Electron microscope facilities at UNSW:
Basement, Chemical Sciences Building (F10), Kensington UNSW Sydney NSW 2052
--Hamid/Arash Araghi 11:45, 09 March 2009 (EST)
So, I'll open the discussion with an invitation to group members to pick an area to specialise... the suggestion has be made that we each do receptor sub-classes and specificity... ideas?? thoughts?? suggestions??
also, has anyone had any luck tracking dow the mystery team member: (3189925? is it?)
That is all. --Peter Kehoe 10:22, 23 April 2009 (EST)
hey guys, yes, I eventually found the mystery number of our team member. Its a 'familiar face' who will be joining us from week 3; (I can't name him here on wiki). It seems that he has not loged into his wikim page yet.. Not sure if he has access yet/ he totally forgotten about it.. anyhow, it will be sorted out hopefully by thurs and so we can devide the group project between the members of the group... I'm still doing some readings on 'Trk receptors' to get an overal view of what we/ and I would want to take inpart for further info search...
--Hamid/Arash Araghi 17:25, 27 March 2009 (EST)
"self" individual assignments:
- 3187854 - P75NTK protein/receptor
- 3189925 - Trk A
- 3191358 - TrK B
- 3189168 - Trk C
A good guidline for these might be:
- what is it?
- How is it different from other proteins/receptors?
- Why is this so?
- what tissues might you find it in?
- what is the adaptive advantage of this?
that is all --Peter Kehoe 12:33, 26 March 2009 (EST)
Guys, just to clarify; The above topics are NOT part of the collaborative group assignment. the collaborative assignment covers the overall process of production, molecular interactions and signal transduction of Trk R.'s as well as the current field of research and diagnostic techniques etc etc etc.
The individual assignments cover the specificinteractions and roles unique to the above proteins. Realistically there should be little to no overlap between the two despite the fact that they are, of course, inherently similar- The trick to the group assignments is to BE SPECIFIC, whereas the group work is a wholist generallised view of Trk R.'s
--Peter Kehoe 12:20, 2 April 2009 (EST)
some general information about signalling processes requiring Tyrosine Kinase receptors;(from molecular biology of the Cell/garland science text book)
"Table 15-4. Some Signaling Proteins That Act Via Receptor Tyrosine Kinases
SIGNALING LIGAND RECEPTORS SOME RESPONSES
Epidermal growth factor (EGF) EGF receptor stimulates proliferation of various cell types Insulin insulin receptor stimulates carbohydrate utilization and protein synthesis Insulin-like growth factors (IGF-1 and IGF-2) IGF receptor-1 stimulate cell growth and survival Nerve growth factor (NGF) Trk A stimulates survival and growth of some neurons Platelet-derived growth factors (PDGF AA, BB, AB) PDGF receptors (α and β) stimulate survival, growth, and proliferation of various cell types Macrophage-colony-stimulating (M-CSF) M-CSF receptor factor stimulates monocyte/macrophage proliferation and differentiation Fibroblast growth factors (FGF-1 to FGF-24) FGF receptors (FGF-R1-FGF- R4, plus multiple isoforms of each) stimulate proliferation of various cell types; inhibit differentiation of some precursor cells; inductive signals in development Vascular endothelial growth factor (VEGF) VEGF receptor stimulates angiogenesis Ephrins (A and B types) Eph receptors (A and B types) stimulate angiogenesis; guide cell and axon migration
more from this book at:
cheers, --Peter Kehoe 09:58, 9 April 2009 (EST)
additionally heres a cool link to Trk-B complexed with neurotrophin structure *Trk B... isnt that someones assignment? hint hint*
If you have difficulty understanding Trk concept, take a look at this animation; I will later on include this animation in our group project...
--Hamid/Arash Araghi 17:48, 15 April 2009 (EST)
Guys we're really lagging behind in posting things... i'll start posting on the main page tonight (hopefully) please do likewise. --Peter Kehoe 10:27, 23 April 2009 (EST)
arghhhhhhhhhhhhhhhhh Just before I hit the save page button, I wanted to see how this message would look like. My internet got disconnected and now I have to type it all again.
Very thanks to Peter for taking the initial step to post on the main page. Of course, there are parts in his post which need to be improved. I will start posting some material tonight and/or at the weekend. Most likely, I will make some minor changes to the other member's post. As Mark mentioned in the lecture today, he wants us to actively take a role in posting things on the main page and discussing over our project on this board. Please guys feel free to do some changes to my post in order to make yours to fit in. Also I will appreciate if you could comment on my postings.
As per our conservation in week 3 of the session, one of us will do the proof reading and make changes to our posts so that each of our own style of writing will connect from one point to another. Otherwise, our work may not flow, and look a bit clumsy. --Serkan Erkan 15:28, 29 April 2009 (EST)
Morning Guys, I need to address few important issues here.
Firstly, please make sure you do a thorough research on the topic before writing on the page. Believe me writing on the page is the easiest part. But finding and digesting the info, particularly in this topic is a little tough. The reason I said that is because ‘Tyrosin Receptor Kinases’ are not restricted only in Neural cells, also involved in normal cells. so perhaps you’d need to read more on that…?!!!
Secondly, in order to make the most out of this group project, I personally believe that we should divide the topic evenly between four members of the group. This way we’d ensure that 1) everybody has had a fair go. 2) Prevents further confusion. 3) Prevents waste of time and overlapping info. Hopefully during our peer-review session we can then follow members’ works easily without any confusion.
For Now, I’m advising everyone that I will be doing the Introduction that will include evolutionary info on Trk as well as its identification in human genome project. I will also create a distinct subheading talking about the cause of some cancers. eg: colon cancers and its relation to Trk receptors. Please avoid touching my assigned topic :-D thanks. :D
So there will still be function, structure, dynamic processes and current research left which needs to be assigned… so people hurry up and assign yourself…and let us know..
We also need to have a group deadline by which everyone will be done with their topic and so we can run a peer-review session, which we will basically review and make improvements on our project… I'd prefer by the end of Week 8 (next week).
Lastly, as a reminder we are doing our topic on Trk receptors Not Tm (Tropomycin) receptors… I changed it back to Trk.. just to avoid confusion.
--Hamid/Arash Araghi 08:27, 30 April 2009 (EST)
It seems like my last post has been deleted. As per our discussion in today's lab, I will do the "Function" section and add onto the "Structure" section on the weekend. Meanwhile, check this board daily to be up-to-date with the project.--Serkan Erkan 15:21, 30 April 2009 (EST)
Serkan, I remember you collected few good journals on 'K-Ras oncogene'. could you please forward them to my email as they are more related to my section?? thanks.
--Hamid/Arash Araghi 02:04, 2 May 2009 (EST)
Arash, not a problem. I have forwarded the items to your unimail. I hope they will be useful for yor section.--Serkan Erkan 12:00, 2 May 2009 (EST)
Each of the seven subfamilies of the Trk receptors are distinct in their own ways. We can describe their structures. Please see the link http://www.ncbi.nlm.nih.gov/books/bv.fcgi?&rid=mboc4.figgrp.2848
I also did some posting on Function and a minor contribution to Structure, and added two references. I will do further posting for the Function and Structure by the end of the weekend --Serkan Erkan 17:26, 2 May 2009 (EST)
Hey guys, I've been watching the posts go up over the weekend but have been unable to contributed signifcantly due to demands of other projects/exams- I will do so tomorrow night and continue my signal-transduction diagram. You guys are doing fantastic work... things seem to be working smoothly now :)
K-ras oncogene require disambiguation i think... could you clarify for me... K-ras is definately a known oncogene and a common element in many signal transductive pathways... the K-ras proteins is structurally and functionally distinct from TrK, however they do participate in some cascade pathways... I was of the understanding from other studies that the TrK oncogene and K-ras oncogenes are not interrelated(loci?)... it is also notable that although K-ras and Trk DISfuction can contribute to cancerous cell formation they are not the only factors, the presence of significant mutation at these loci does not define a cancerous cell but it does contribute to oncogenesis I'm interested to see how you are tieing these two oncogenes together.
Cheers, --Peter Kehoe 23:49, 3 May 2009 (EST)
important notice: after many episode of discussion and confusion, it has finally been decided that we are definitely doing the TrK pathway - the tyrosine kinase pathway specifically known as tropomyosin-related kinase. Confusion arose from disambiguation between conversations in class relating to TKR's and Trk's. So, we are DEFINITELY doing a Trk pathway. Sorry for the confusion.
Thanks to all members and Mark for working on this to alleviate the confusion!!!
A lot of the beginnings of these processes are already done on the wiki site but cleanup needs to be done to make sure all processes related to Trk's and not TKRs. The dynamic processes, etc are the same however the ligand specificity and dimerisation structure is more specific for Trks.
the workload is as follows (as we have a lot of catching up to do since the confusion has put us WAY behind other groups)
Intro+current research(oncogene)+ K-ras (not sure where this fits yet)+ assorted- Arash
Structure+ function(A,B,C specific)+ (PL3 summary and individual) - Serkan
Timeline+ Glossary of terms+ PKC (summary and individual) - Dan
Dynamic Process + Structure + disambiguation explaination+ P75NTR - Peter
--Daniel Manassa 12:59, 7 May 2009 (EST)
Intro has now been added... Lots of ideas are flowing on my mind!!!
I am removing K-ras as it would be irrelevant to our current topic... (Peter and I discussed this yesterday). Instead I'll be talking about oncogene...
Also, I was thinking of giving a background info about Neurotrophines. Though I'm not sure if anybody is covering this explicitly ??!!! if Not, then It'd be a good idea to throw it in. think about it and we'll discuss it in the lab.
see ya soon. Arash --Hamid Araghi 08:54, 14 May 2009 (EST)
i'm happy to do a neurotrophin summary as i've already covered most of that to do my individual work. let me know if you'd like me to do this. No doubt i'll discuss in lab today, will be arriving an hour late. --Peter Kehoe 10:50, 14 May 2009 (EST)
my part is almost ready. I am busy with another assignment right now, which is due on monday. I will post my part on the weekend.--Serkan Erkan 11:53, 14 May 2009 (EST)
just talking to Serkan realised that we don't have an image of the receptor pathways. I will work on it this weekend and make one. if anyone else is doing it let me know before Friday. I will start the glossary tonight, but will finish once all text is uploaded. The Time line is pretty complex, but it is an image. I wont upload until finished.
excellent... yes as long as you cover that in your section, it'd suffice...
--Hamid Araghi 12:17, 14 May 2009 (EST)
the 2nd above post is not me.. it think its Daniel? in anycase, i'm already working on an image... only just got the message
--Peter Kehoe 20:46, 15 May 2009 (EST)
The two topics "Mechanism of Trk Activation via multiple Signalling pathways" and "current research" have now been partially added. There are parts, which have been tagged, would need to be completed by members...
So, please for time being keep things that have been added so-far unchanged. once everybodys done with their parts, we'll then run a thorough editing/proofreading
One of my youtube animation doesnt work.. dunno why.. i'd need to fix that prob..
Nevertheless, we are getting there... :D
--Hamid Araghi 11:23, 20 May 2009 (EST)
okay guys, we're slowly getting there... the diagram is coming together though ive still got alot to addd to it and need to post up dynamics... iguess the point is here that we dont have much time for post-completion editing so everyone post as finals over the weekend and if nescessary the typos etc can be edited out by us as we read through eachothers....
Take care all
okay guys, as per our discussion in lab this week we need to make the final edits on our page... please post as you complete ASAP and comment on eachothers edits
Goodluck guys--Peter Kehoe 15:34, 30 May 2009 (EST)
Put a new intro on, let me know - yes or no? --Peter Kehoe 16:31, 30 May 2009 (EST)
Peter,New intro will do. Also, i thought of the hand-drawn image if it should be moved somewhere else? like function/structure???
Guys,I changed the orientation of some image.. see if you like it that way.
Another issue, make sure u label ur images with well description of what they represent.. and if necessary refrence them.
btw, I thought we'd need to write a reflection on our work?!!! can somebody clarify this?
--Hamid Araghi 18:15, 30 May 2009 (EST)
Not sure about the reflection... :S thoughts anyone??? please contribute to the discussion so we know what ypu're doing... Also, as per our discussion in lab, the sections that overlap with your individual projects are too lengthy! Please shorten them and contribute further to other sections... you should be doing stuff! if you're not sure what you need to be doing then ask someone on here!!
Please guys, we need this finalised.
Hamid, I'm aware i've been naughty wiht my images, i'll clean up the tags.
Cheers and all that!
--Peter Kehoe 11:18, 1 June 2009 (EST)
I agree with peter about the overlap with individual projects. I will shorten the section, PI3K pathways. Instead of stating its function and mechanism, I will talk about the relevance of the pathway in Trks.
I will try to fix the "Function" and talk about the ways in which receptors interact with the ligands.
Is there anything else? Hmm Peter, do you think structure should be left the way it is or we should talk more about it? it looks concise the way it is. Any thoughts? I will check the discussion every few hours until wednesday.
--Serkan Erkan 14:32, 1 June 2009 (EST)
I've done a bit on structure today, i might change the formatting a bit and add a picture. I was going to mess around a bit with function and talk about knockout mice in a sub section, but because it's partitioned it should be okay... also i'm continuing work on dynamic processes so dont sweat that part... anyhting else?--Peter Kehoe 17:08, 1 June 2009 (EST)
daniel, still waiting on the timeline stuff... i'm adding knockout mouse stuff tomorrow as i left my article for it at home...
can someone talk me through the referencing component as i'm still not solid on it and my paragraphs are not referenced
--Peter Kehoe 19:59, 1 June 2009 (EST)
Send all your referenced paragraphs to Dan. He is responsible for the arrangement of reference section. here is the email of his: [I deleted his email address as it is not appropriate to post it here without his permission. PETER, I will email it to your unimail.--Serkan Erkan 21:16, 1 June 2009 (EST)]
--Hamid Araghi 20:54, 1 June 2009 (EST)
This is how you reference it. Click edit to view it. 
if you do referencing this way, then you dont need to order it. it ll happen automatically.
i had a read of structure. very well done. i ll do the function late tonight. you can all peruse it tomorrow. --Serkan Erkan 21:16, 1 June 2009 (EST)
Peter, I see you have talked about selectivity and specificity of receptors and that it’s because of distinct variations in the receptors. [This is good] But it is worth mentioning where all these variations in extra/intracellular receptor domain arise from??!! Just that you can be more specific but really depends on how well in depth you'd want to dig into. I have found a paper that describes ‘splice variants of Trk receptors” mainly originated from genetic allele, and that it is the main cause of variation between Trk receptors and moreover influential by being selective/specific toward their target substrate. For instance, TrkB lacks exon9 in the extracellular domain,which decreases its interaction with NT4/5 and NT3. Also, apparently, splice variants of TrkC have been found lacking the tyrosine kinase domain. This can be linked well to both figures 1 and 2 I guess!.
Here is the paper I have attached in:
Bibel,M, Barde,Y,A. “Neurotrophins: key regulators of cell fate and cell shape in the vertebrate nervous system”.Genes Dev. (2000).14(23):2919-37. PMID: 11114882
another issue in introduction is that we say "Trk's are commonly found throughout mammalian tissue types and bear particular signifcance in embryological development and maintainence and growth of neuronal cell types." Although, trks are found commonly throughout variety of mammalian tissue types,they are in very low abundance in vivo. Conversely, we can find them in high abundance in neuronal cells. perhaps we'd need to fix this too?? hope I haven't made you guys confused ;)
--Hamid Araghi 10:47, 2 June 2009 (EST)
Hamid, I dont have time to read, comprehend, integrate and potentially edit on relationn to those issues, please feel free to add within my sections wherever you feel it might help. At this point i feel my tampering in articles i dont yet understand may do more harm than good. Thoughts>? --Peter Kehoe 17:17, 2 June 2009 (EST)
is there any reason for deleting PLC-Y1 pathway?
--Hamid Araghi 19:27, 2 June 2009 (EST)
if i deleted it, it was an accident because i havent touched anything other than my own intentionally :S--Peter Kehoe 19:30, 2 June 2009 (EST)
okay so all my text is in, im just adding some referencing now and we should be golden....
Does anyone know whats happened ot Dan and the timeline?? the individual-overlap sections still need to be cut down by thier respective authors.... *pulls out hair*--Peter Kehoe 19:29, 2 June 2009 (EST)
- Kapeller R, and Cantley LC. Phosphatidylinositol 3-kinase. Bioessays. 1994;16(8):565-576. Retrieved May 16, 2009, from