Biomoo Meeting held on 26/3/98 at 15:00GMT

Jim_Pitts turns the T-recorder on.


Jim Pitts says "Go"

ClareS says "Great! Up and running at last.. sorry for the late start"

Jim Pitts says "Sorry had to build a recorder quickly"

ClareS says "This meeting, and the one tonight, is specifically to discuss the questions (and answers) in the self-assessment exercises"

ClareS says "By the way, the confusion was my fault: I ran out of disk quota :("

ClareS blushes

Claudia finds her way in.

ClareS [to claudia] Hi - we've only just started

ClareS says "after this we will be going back to the previous pattern with BioMOOs discussing specific parts of the course material"

Claudia [to ClreS] "Hi

ClareS says "Before we start properly: can someone confirm that the answers to the self assessment questions, which I posted to the list earlier today, have arrived there"

Mikolaj finds his way in.

ClareS [to Mikolaj] Hi

BMD says "Yes, they're here"

Claudia says ", "Yes. I received them today"

Mikolaj says "Hi, sorry for beuing late"

Pawel [guest] says "Yes - I received the answers."

ClareS [to Mikolaj] you can catch up by reading the transcript on the tape called BIOMOO1 but we've only just started

ClareS is pleased they have arrived )

Mikolaj says "thanks. I just received the answers"

ClareS says "One general point first: very many of you really gave longer answers than we were expecting"

ClareS says "we don't mind getting nice long complete answers, but they must have taken some of you quite a long time"

ClareS says "the answers we have provided are very short, and in note form ;)"

ClareS says "How did you all find the exercise? Were the questions easy / difficult / just right / interesting?"

ClareS looks round expectantly

BMD says "I feel they were just right.....some concentrated more on reporting facts, some required some thinking."

Mikolaj says "I find the exercices generally O.K."

Claudia says "" I I found them quite interesting since I had to look for and to get deeper in some subjects and they were useful to understand I had not understood something before. "

ClareS . o O ( we aim to please ;) )

Pawel [guest] says "Some of the guestions were, hmm... VERY simple but some were interesting - e.g. I had some problems with the cations/anions bound to a-helices."

Mikolaj says "but I couldn,t find anything on peptide mapping, in the course mareriasay but "

ClareS [to Pawel] yes, that was partly *our* fault - typo in the original question

Mikolaj says "sorry : in the course material"

ClareS says "the one on peptide mapping *did* require some thought"

ClareS says "we aimed to have some simple and some not so..."

Mikolaj says "Yes?"

Claudia says " To tell the truth, I would like to have more books to read: it's difficult to find everything on the Net. For example the pepetide mapping question..."

BMD says "Jim, in the question 19, I mentioned trypsin might have a role...did you agree?"

Mikolaj says "could you explain it more precisely?"

NickyM says "I agree with Claudia, I spent a lot of time going through the course to retreive data which I thought I had understood but obviously hadn't."

ClareS [to claudia] yes.. a book list will be provided. It has been on our "to-do-list" for some time

ClareS makes a note of it

Claudia says "Thank you very much!"

Claudia says "ClareS, will we have our answers back with marks?"

ClareS [to claudia] yes... before very long, I hope!

Claudia says "Very nice!"

ClareS says "shall I go through the peptide mapping question?"

Jim Pitts [to BMD] The problem with amino acid repeats is that you can get esily confused if the peptide is cut often. You need a couple of specifities to sort it out. So it would be difficult. However sequencing the gene would not suffer the same problems but you have to clone it first.

ClareS [to Jim Pitts] please correct me if I over-simplify

BMD says "Jim, so you would agree that using trypsin for partial hydrolysis would create problems."

JudyH finds his/her way in.

ClareS says "the basic point is that peptide mapping will separate peptides on the basis of their charge and polarity. Histones, with repetitive sequences with many basic residues (with the same charge and similar polarity) will be difficult to sequence with this technique"

JudyH says "sorry I'm late"

Jim Pitts [to BMD] It would depend on each case. I would expect problems unless you could control or limit the cleavage. You may have partially buried sites due to the structure. The products may then be analysed by a sensitive method like mass spectroscopy.

Pawel [guest] says "In this problem with histones we can use other digestion reagents - e.g. CNRr or Asp-Pro digestion in strong acid. These procedures may generate longer and useful fragments."

ClareS [to JudyH] don't worry about it. we were late starting too

(Mikolaj has disconnected.)

BMD [to Jim Pitts] My point is that trypsin cleaves the peptide chain at Lys and Arg sites...

ClareS [to JudyH] you can catch up by reading the transcript on BIOMOOTAPE1

Pawel [guest] says "should be CNBr..."

ClareS . o O ( should be just BIOMOO1 )

BMD [to Jim Pitts], if there's a lot of them, you'll run into trouble.

Jim Pitts [to BMD] The best method I have used is to digest from either the N or c-terminussequentially

ClareS says "I agree you couldn't find out what peptide mapping was from the course material"

Jim Pitts [to BMD] however it depends again on the specific sequence present

Jim Pitts [to BMD] chemical methods are very good

ClareS says "but, assuming that you know this (or have access to a suitable techniques book) it is the *principles* of amino acid chemistry which you use to determine whether histones, with their unusual sequences, are sequenced easily using this technique"

BMD [to ClareS] I think the problem was that there seemed to be an emphasis on...

BMD [to ClareS] Lys and your arguments it seems that peptide mapping would readily...

Jim Pitts says "Methods to cleave polypeptides have become important in the application of Biotechnolgy because many expressed proteins are produced as fusions, etc. and these may need to be removed without damage to the "native part""

BMD [to ClareS] into difficulties the moment there is too much of any one class of AA...right?

ClareS [to BMD] yes, I'm not a molecular biologist ;) but from basic principles I would guess so

BMD [to ClareS] That is why I thought of trypsin..'cause it cleaves at Lys and Arg sites specifically.

ClareS says "you need a sequence with a wide range of AA types and no short repeats for peptide mapping to be really successful"

BMD [to ClareS] The mere high frequency of basic AAs did not seem to do justice to the perceived emphasis on Lys and Arg.

The housekeeper arrives to cart Mikolaj off to bed.

ClareS says "Jim is lagging: is anyone else having serious problems with the connection?"

BMD says "No"

Claudia says "No, it's all right with my connection (hopefully...)"

Jim Pitts says "That is a bit better"

ClareS says "I hope you are clearer about peptide mapping now.. are there any other questions which you would like to discuss?"

ClareS [to Jim Pitts] it seems to be OK now

Mikolaj finds his way in.

ClareS [to Mikolaj] Hi - welcome back ;)

Pawel [guest] says "The discussion arrives to my computer as the long "packets" "

ClareS [to Mikolaj] you can catch up with what you missed by reading the transcript - read BIOMOO1

ClareS says "do you all know the unix traceroute command?"

ClareS says "you can use this to trace the route taken by data from one computer on the Net to another"

Claudia says "Would you please repeat it?"

ClareS says "it can sometimes be useful when everything goes slow and you are interested in finding out why"

ClareS says "on a unix box the command is something like /usr/etc/traceroute or /usr/sbin/traceroute"

Claudia says "Thank you"

ClareS says "and you can find out which with the command "whereis traceroute""

Pawel [guest] says "I use Win95, I do not have Unix..."

ClareS says "if traceroute isn't implemented, or if you're using a PC or Mac, you can still use traceroute via the Net"

Pawel [guest] says "How ?"

ClareS says "there are various pages.. there is one at the Weizmann (useful for tracing routes to BioMOO) but I can't remember the URL off hand"

ClareS fires up Netscape

Claudia says "Sorry, but I have got a work meeting. I must go. Bye, you all. "

Claudia says "And thank you very much"

(Claudia has disconnected.)

ClareS waits...

ClareS says "while we are waiting: any more questions on the self-assessment questions?"

BMD says "My modem is playing up"

(BMD has disconnected.)

NickyM says "Question 13 is a puzzle to me. Are these numbers just memorised or do you have to go to drawings / images / rasmol and work them out. "

The housekeeper arrives to cart claudia off to bed.

ClareS says "you don't need to remember them off by heart - but there's a better way of finding them than with Rasmol: read them off the Ramachandran plot"

ClareS says "there's one in the course material (somewhere ;)"

The housekeeper arrives to cart BMD off to bed.

ClareS says "You can quite easily read the required phi and psi angles off from the plot at"

NickyM says "Is then the Ramachandran plot set in stone. I have assumed that it would change depending on what AAs were present"

ClareS says "about that traceroute URL at the Weizmann: they seem to have moved it ;)"

ClareS says "I've found several in Israel tho' via a simple search of Yahoo with "traceroute""

ClareS [to NickyM] it depends on what you're using the plot for ;)

Pawel [guest] says "Is the traceroute a unix command or the server function ?..."

ClareS [to NickyM] the phi, psi angles for helices and strands are *always* the same...

ClareS [to NickyM] the angles which can be accessed by polypeptide chains at low energy will depend to an extent on AA type...

ClareS [to NickyM] only Gly and Pro are significantly different

ClareS [to Pawel] traceroute is a unix command but it has been implemented as a tool on many servers

ClareS [to Pawel] they typically provide a tool to show the number of hops and speed of packets from their server to your browser...

ClareS [to Pawel] so you can find out just why it's taking forever to download a little software tool from

ClareS would like to close the meeting and stop the recorder at 1630GMT

ClareS would therefore like to know if there are any more questions ;)

ClareS says "Before we finish the meeting, I would like to remind you all that the next time we have a meeting will be in Summer Time (BST)"

NickyM says "Thank you, that is a lot clearer"

JudyH says "I haven't had a chance to see the answers, so I don't know which ones will be clearer when I do, but I found no 20 difficult, I couldn,t visualize the R?S from the course material"

ClareS says "We will still post the times in GMT, but those of you in the UK will need to know that BST is one hour later and other people will probably be on different time zones too"

ClareS [to JudyH] it can be difficult to visualise this

ClareS [to JudyH] it's much better (if *much* harder ;) to work it out from first principles using Rasmol etc. as you did

ClareS says "Thanks to you all for taking part: sorry about the tape mix-up (my fault) and the slow line (*not* my fault ;)"

ClareS says "I hope that you are all clearer about some things now"

ClareS says "Best of luck with your studies in the second semester!"

NickyM says "Cheerio"

Jim_Pitts turns the T-recorder off.