Talk:2009 Group 4 Project

From CellBiology

--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

  1. Intro: Perhaps a little too in depth for an introduction - try to use 'easier to read' language.
  2. Structure + Function: A picture would help to illustrate what you're saying. Well set out.
  3. 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.
  4. Animations are great!
  5. PKC pathway: good but try to break the text up a bit with either dot points or numbers.
  6. 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.
  7. 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).
  8. All links present. Still missing references!


Location of Electron microscope facilities at UNSW:

Basement, Chemical Sciences Building (F10), Kensington UNSW Sydney NSW 2052

Link to electron microscopy Unit,UNSW

--Hamid/Arash Araghi 11:45, 09 March 2009 (EST)

Thanks Mark...

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


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*,_Issue_12,_Pages_1127-1263_(December_2001)%23tagged%23Volume%23first%3D9%23Issue%23first%3D12%23Pages%23first%3D1127%23last%3D1263%23date%23(December_2001)%23&view=c&_gw=y&wchp=dGLzVtb-zSkzS&md5=8f23b4fd824036c481d16d3f9b09b5c3&ie=/sdarticle.pdf


Hey Guys,

If you have difficulty understanding Trk concept, take a look at this animation; I will later on include this animation in our group project...

TK Receptor Animation

--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

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)

Morning guys,

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)

hey guys,

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)

Hi everyone,

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

cheers Arash

--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

final edits

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)

hey guys,

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)

final edits

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. [1]

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)

hmm im not sure if Dan has deleted that section or...

i dont get why my references are doubling up :S any help??

F**K what happened!! :S references exploded... all i did was add a couple in my text --- okay fixed lol


I think we are gonna have a big crisis if you keep referencing. you can undo what you have done by going to "history" and undo.

please stop referencing until I get Dan or Serkan to fix it


Should be fine now yeah?? i think i've figured it out lol--Peter Kehoe 20:26, 2 June 2009 (EST)

it actually made me laugh.. :D glad u got it sorted.. but im still worried about disappearance of PLC-Y1 pathway... --Hamid Araghi 20:32, 2 June 2009 (EST)

me too can you add it back in... i think i've done everyhting now, are you happy wiht my contributions? anyhting i've missed?--Peter Kehoe 20:48, 2 June 2009 (EST)

Also, a group reflection needs to be added... a bit hard when not all of the group have finished thier contributions. ideas?--Peter Kehoe 20:57, 2 June 2009 (EST)

hmm, I'm not sure if I'd be able to find it amongst all changes being made recently. also, im not sure if I still should add proto-oncogens? thought I'd add it to the current research section but then its discovery is not very recent. it goes back to 1991 If im not mistaken. but where would u recommend to stick it in?

you have done a great job. many thanks..

Reflection: well I think it'd be a good idea to start from what we went through to sort out the difference between (TK) and Trk receptors :D

--Hamid Araghi 21:06, 2 June 2009 (EST)

im freaking out, cant find the PLC pathway in any of the old versions, what the heck... who wrotie it originally??

Daniel did... i dunno if he took it away... I know that he fixed some referencing today but dunno if he deleted PLC pathway.. meh anywho, for now I have emailed Serkan and Dan to do their fair bit on reflection. you can also write your bit. Im happy to put them all together. how lengthy should it be?

btw, I will not be online until 11:30 when I get home.

--Hamid Araghi 21:23, 2 June 2009 (EST)


Overall, the assignment was "interesting". I did very much enjoy being left to our own devices and, despite some problems with discoordination of the group due to a confusion between Trk and Tyrosine kinases and which of the two we were actually being asked to do, i'm happy with the product. I found the experience of delegation an extremely useful tool, with each group member contributing only in areas where they felt comfortable- thus the best product was produced. Overall, I am very proud of the group and our ability to resolve the conflict which arose half way through the assesment period in a rational and level-headed way. Particularlly, since our topic was rather dense and complex I am quite satisfied with the level of langauge and depth which, i feel, is sufficiently expressed to be aimed at a cohort of our undergraduate peers. This was initially quite a challange for us but i feel the page has evolved significantly to this point due to our consideration of peer responses. Overall, a satisfying experience(I hope the marks will reflect this!).--Peter Kehoe 22:15, 2 June 2009 (EST)

Due to other commitments on week 2, I was not able to attend the lab class when my group chose Trk as our group project. I was happy to work with my group members as they were all willing to share their knowledge. Unfortunately, we were all confused between Trk and Tyrosine kinases. After vigorous discussion among the members, we figured that they are not the same. It was already week 8 when we were able to choose that Trk should be our project topic. Meanwhile, we all posted items on Tyrosine kinases on our page. It was quite frustrating to restart from a scratch when all the group members were busy with other exams and assignments during that time. Nevertheless, we productively worked together to produce a high quality assignment. Everyone chose an area which they were comfortable with. Each member commented on each other’s work to make sure our work is at its best. Overall, I am satisfied with what we achieved in this project. We didn’t only produce a high quality work but also learnt from each other. The aim of the group projects is often to encourage collaboration among the group members. This project has definitely achieved its aim.--Serkan Erkan 23:11, 2 June 2009 (EST)

PLC thats the link for the last page before PLC is missing.... i dont know why dan deleted but if he lets us know we can throw it back on or not?? i felt that section was short enough already and not needing to be cut out --Peter Kehoe 22:18, 2 June 2009 (EST)

Hey guys, i didnt delete it. Dnt know what happened. If you see the edit page. It is still there. Im trying to fix it. When i last signed out both my parts were still there. WEIRD. Im also getting this WARNING: This page is 33 kilobytes long; some browsers may have problems editing pages approaching or longer than 32kb. Please consider breaking the page into smaller sections. when trying to edit. Anyone have a clue? Dan

yes i had the same warning as well. I only edit the section on which i am working. Hamid asked me to write a reflection. I am writing it now. I have shortened PI3K but i still need to talk about the mechanism in which neuronal survival occurs --Serkan Erkan 22:54, 2 June 2009 (EST)

Ok i got it back on. I dnt know how, but i pasted it twice within the edit page and now it works. Is this due tomorrow? Dan

I think the answer is YES - it s due tomorrow ! Serk

Protooncogenes are normal genes which are prone to mutation. They regulate some key functions of the cells such as growth and differentiation. When protooncogenes get mutated, it will result in the proliferation of the undifferentiated or poorly differentiated cells in the absence of normal growth-promoting signals. Mutation to one allele of the protooncogene will lead to cellular transformation. Hence, they are considered to be dominant. Trk is one of the protooncogenes through which growth promoting signals will activate number of cellular functions. Growth factors binding on the receptors will cause cell proliferation. Many cancer cells possess the ability to produce the growth factors which will act upon them for permanent signaling. For instance, many glioblastoma secrete Platelet- derived growth factor and express the PDGF receptor. This will lead to an autocrine loop of cell proliferation.

--Serkan Erkan 04:20, 3 June 2009 (EST)

Great job guys! good luck with exams

--Hamid Araghi 12:08, 4 June 2009 (EST)

  1. Kapeller R, and Cantley LC. Phosphatidylinositol 3-kinase. Bioessays. 1994;16(8):565-576. Retrieved May 16, 2009, from [1]