From Heather.Vincent from manchester.ac.uk Thu Jan 1 05:38:46 2009 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Thu Jan 1 12:01:02 2009 Subject: [Protein-analysis] The Bioinformatics of Protein Structure, March 2009 Message-ID: <495C9D36.8010002@manchester.ac.uk> The Bioinformatics of Protein Structure, offered by the University of Leeds, is one of a number of online courses run jointly with The University of Manchester. Like all of our distance courses, it is delivered in a Virtual Learning Environment that allows us to extend the classroom into the web. Each course, which is paced to suit those in full-time employment, runs over 16 teaching weeks. The aim of this course is for the participant to first acquire a knowledge of the basic mechanisms of protein evolution. Students will then use their knowledge to inform and guide the process of relating protein structure, function and primary sequence data. The course is divided into 9 sections:- 1. Amino Acids and Molecular Interactions 2. Protein Secondary Structure 3. Domains, Folds and Motifs 4. Introduction to Protein Evolution 5. Classification of Protein Structure 6. Protein Sequence Alignment 7. Construction of Phylogenetic Trees 8. Prediction of Secondary Structure 9. Introduction to Comparative Modelling You will find information on all our courses, including fees and a link to the online application form, here : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk From novalidaddress from nurfuerspam.de Thu Jan 1 08:44:37 2009 From: novalidaddress from nurfuerspam.de (WS) Date: Thu Jan 1 12:01:17 2009 Subject: [Protein-analysis] Make Akta Prime Software work under Linux!? Message-ID: Dear Colleagues, I am about to make the ?kta Prime package run with Opensuse Linux 11.1 (WINE 1.1.9, Kernel 2.6.27.7-9-default). I already successfully have set up the Prime software to acquire data from the machine (for monitoring runs, "Csyscon.exe prime"). However, I have serious problems doing the same with the Evaluation software ("Emain.exe prime") that is used to analyze the data. Currently, I am figthing with DLLs (MFC42.DLL and MSVCRT.DLL in detail) as I get error messages pointing to unresolved functions, the app crashed after loading any data set. I already have tried all versions of these DLLs I could get hold of, but no success yet. Has anyone already solved the "problem" or wants to do the same and is willing to share her/his experience? Or is interested to team up? Best regards, Wolfgang (?kta/Akta Prime is an FPLC protein purification machine from Pharmacia/Amersham/GE-Healthcare) From ddloeb from gmail.com Fri Jan 2 12:45:29 2009 From: ddloeb from gmail.com (ddloeb@gmail.com) Date: Fri Jan 2 15:57:13 2009 Subject: [Protein-analysis] Re: Make Akta Prime Software work under Linux!? References: Message-ID: On Jan 1, 7:33?am, WS wrote: > Dear Colleagues, > > I am about to make the ?kta Prime package run with Opensuse Linux 11.1 > (WINE 1.1.9, Kernel 2.6.27.7-9-default). I already successfully have > set up the Prime software to acquire data from the machine (for > monitoring runs, "Csyscon.exe prime"). However, I have serious > problems doing the same with the Evaluation software ("Emain.exe > prime") that is used to analyze the data. Currently, I am figthing > with DLLs (MFC42.DLL and MSVCRT.DLL in detail) as I get error messages > pointing to unresolved functions, the app crashed after loading any > data set. I already have tried all versions of these DLLs I could get > hold of, but no success yet. I don't use Akta Prime (or Wine), but in general I have three suggestions: a) Have you tried Codeweavers Crossover-Linux? It is based on Wine, but is compatible with more Windows applications than Wine is. b) I use VMWare - haven't found a single application that doesn't work with it yet. But then again, they're running in a Windows XP guest session running on Linux. c) You could try Bochs. It is a little slower than VMWare - differences in virtualization routines, but Bochs is free Dan From novalidaddress from nurfuerspam.de Sat Jan 3 05:46:14 2009 From: novalidaddress from nurfuerspam.de (WS) Date: Sat Jan 3 15:56:07 2009 Subject: [Protein-analysis] Re: Make Akta Prime Software work under Linux!? References: Message-ID: Hi Dan, I just tried your suggestion with the Crossover Linux. I get the same problems as with wine. To make things run, I borrowed a PC with XP to be able to operate the ?KTA, while I consider the WINE port now as hobby project and I consider to run install a virtual Windows on the Linux Machine. I could resolve an issue where Emain asked for some 32bit alsa- pulse.so files by installing a 32bit library, but now I am running into lots of page faults which have not been displayed before. Then the known messages about stack/heap problems and MFC42.DLL show up. Best reagrds, Wolfgang From biospace from noster-it.com Sun Jan 18 02:25:50 2009 From: biospace from noster-it.com (biospace) Date: Sun Jan 18 15:28:32 2009 Subject: [Protein-analysis] Urinary Biomarkers For Coronary Disease Found Message-ID: <2bbeb179-5f31-45e7-8f68-8ee50befa0db@m22g2000vbl.googlegroups.com> A set of 15 proteins found in urine can distinguish healthy individuals from those who have coronary artery disease (CAD), a new study has found. Due to the ease of obtaining samples, urinary protein analysis is emerging as a powerful tool to detect and monitor disease. Anna Dominiczak and colleagues tested whether urine could provide useful biomarkers for coronary disease, one of the leading worldwide killers. They analyzed samples from 88 CAD patients and 282 controls and found a 15 protein "signature" indicative of disease. Several of the protein fragments were collagens, which are components of arterial walls. The researchers next examined how predictive their protein panel was and found it could identify the presence of CAD 83% of the time. The panel had a sensitivity of over 98%, which means the test produced almost no false positives and thus inaccuracies are primarily misdiagnosing CAD individuals as healthy. The researchers also observed that the protein signatures of CAD individuals became more normal after exercise, suggesting these biomarkers can be used to both help diagnose CAD and monitor the progress of treatment Tonny -------------- More bio-med news & videos Portal to share biological information-data between people http://biospace.ethz.ch From m.saidi from cnstn.rnrt.tn Thu Jan 22 07:28:07 2009 From: m.saidi from cnstn.rnrt.tn (Mouldi SAIDI) Date: Thu Jan 22 12:34:00 2009 Subject: [Protein-analysis] Protein precipitation in HPLC buffer Message-ID: <49786657.50305@cnstn.rnrt.tn> I would like to separate caseins using HPLC and it is known that acetonitrile precipitates proteins. Is it possible to use it Thank you very much From engelbert_buxbaum from hotmail.com Fri Jan 23 13:25:12 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Fri Jan 23 16:03:34 2009 Subject: [Protein-analysis] Re: Protein precipitation in HPLC buffer References: Message-ID: Am 22.01.2009, 08:28 Uhr, schrieb Mouldi SAIDI : > I would like to separate caseins using HPLC and it is known that > acetonitrile precipitates proteins. Is it possible to use it Sure. However, proteins - as opposed to small peptides - can not be separated by reverse phase chromatography (with a C18 column and acetonitrile gradient). You need other chromatographic principles. I have never worked with caseins, but consider ion exchange chromatography, chromatofocussing or hydrophobic interaction chromatography. A literature search on scholar.google.com may be a good first step. From sazadi from interchange.ubc.ca Sun Jan 25 12:40:19 2009 From: sazadi from interchange.ubc.ca (seifollah Azadi) Date: Sun Jan 25 18:20:41 2009 Subject: [Protein-analysis] help with a 20 kDa protein Message-ID: <5642757.25351232905219759.JavaMail.myubc2@brahms.my.ubc.ca> Hi all, I am working with a 20 kDa protein which is kind of novel and not that much work has been done on this protein. By western blot, I some times get the band and most of the times can?t. Last time I ran the same sample twice and side by side using DTT and 2ME. The lane that had been reduced by DTT showed a better result whereas the one with 2ME showed a kind of diffused band. I ran this western very short, like half an hour. I think this might be another reason that I got the band. I know that both 2ME and DTT do not run with the protein and they are left behind in the top of the gel and if the protein is sensitive to oxidation, will be gone. I heard there is other reducing agent which travels all the way with the running protein. So I would be extremely appreciated if you could help: 1) Do you know any other reducing agent which can be run with the sample along the gel? 2) Why do you think when I run the gel longer the band gets disappeared? Many thanks in advance Seifollah Azadi From biospace from noster-it.com Mon Jan 26 00:59:40 2009 From: biospace from noster-it.com (biospace) Date: Mon Jan 26 12:48:28 2009 Subject: [Protein-analysis] 'Jumping Gene' May Contribute To A Premature Aging Syndrome Message-ID: <637ebaca-e962-484d-8be1-36c7c1459ac1@g39g2000pri.googlegroups.com> Scientists have identified a fusion protein that may contribute to Cockayne syndrome, a devastating disease characterized by developmental defects, neurodegeneration, severe wasting, and premature aging. Genetic defects in certain DNA repair factors like the CSB protein have been known for some time to cause premature aging, but the reasons are still unclear. Most cases of Cockayne syndrome (CS) are caused by recessive mutations in the CSB gene, yet some individuals with inherited mutations that cause complete loss of the CSB protein are nearly unaffected. The implication is that CS is not caused solely by loss of functional CSB protein, but by continued expression of CSB- related proteins or protein fragments. The University of Washington researchers, led by Alan Weiner, had been investigating the normal function of the CSB gene when co-author John Newman stumbled across hints that the human CSB gene harbored a previously unsuspected guest. The guest was a "domesticated" PiggyBac transposon -- a formerly selfish "jumping gene" that had settled into the CSB gene over 40 million years ago before marmosets diverged from humans. Tonny -------------- More bio-med news & videos Portal to share biological information-data between people http://biospace.ethz.ch From allicindixvin from gmail.com Mon Jan 26 12:06:49 2009 From: allicindixvin from gmail.com (kyoli) Date: Mon Jan 26 14:38:53 2009 Subject: [Protein-analysis] lowry estimation Message-ID: <88c9d6f7-ed23-4e62-ad85-718920cbd0c0@r15g2000prd.googlegroups.com> hi, all i m doing lowry estimation of protein and o.d. is coming sometimes above 1. may i dilute it bt i can't understand when i dilute it o.d. comes to be very low and in determinig protein content there is no volume term so how can i specify the amount From engelbert_buxbaum from hotmail.com Fri Jan 30 09:26:47 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Fri Jan 30 11:28:32 2009 Subject: [Protein-analysis] Re: help with a 20 kDa protein References: Message-ID: Am 25.01.2009, 13:40 Uhr, schrieb seifollah Azadi : > Last time I ran the same sample twice and side by side using DTT and > 2ME. The lane that had been reduced by DTT showed a better result > whereas the one with 2ME showed a kind of diffused band. I ran this > western very short, like half an hour. I think this might be another > reason that I got the band. That is not untypical, DTT (Cleland's reagent) was designed specifically to have the right redox potential for this purpose. bME is only a poor mans substitute. > I know that both 2ME and DTT do not run with the protein and they are > left behind in the top of the gel and if the protein is sensitive to > oxidation, will be gone. > I heard there is other reducing agent which travels all the way with the > running protein. Both are uncharged and hence do not move in an electrical field. Usually proteins run fine once they have been reduced, for the few cases where re-oxidation by air is a problem you can use TCEP (tris-(2-carboxyethyl)phosphine) to permanently modify the SH-groups. Note that this can not be used prior to IEF. > 2) Why do you think when I run the gel longer the band gets disappeared? I assume you use SDS-PAGE for separation. This is not an equilibrium technique (unlike IEF), all proteins leave the gel eventually if you run it long enough. From engelbert_buxbaum from hotmail.com Fri Jan 30 09:27:39 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Fri Jan 30 11:28:37 2009 Subject: [Protein-analysis] Re: lowry estimation References: <88c9d6f7-ed23-4e62-ad85-718920cbd0c0@r15g2000prd.googlegroups.com> Message-ID: Am 26.01.2009, 13:06 Uhr, schrieb kyoli : > hi, all > i m doing lowry estimation of protein and o.d. is coming sometimes > above 1. may i dilute it bt i can't understand when i dilute it o.d. > comes to be very low and in determinig protein content there is no > volume term so how can i specify the amount Dilute the protein sample before doing the assay. From satya from csmcri.org Fri Jan 30 12:14:42 2009 From: satya from csmcri.org (Satyabrata Das) Date: Fri Jan 30 13:10:13 2009 Subject: [Protein-analysis] Query about the price Message-ID: <000601c982fe$44549df0$ccfdd9d0$@org> I want to purchase a Innova 42R & 43R orbital shaker with the photosynthetic light Option. I just want to know about the approx. price of these two models. Help please Regards Satyabrata Das ---------------------------------------------------------------------------- -- Satyabrata Das, PhD Scientist (Fellow) Analytical Sciences Central Salt & Marine Chemicals Research Institute Gijubhai Badheka Marg, Bhavnagar - 364 002 (INDIA) Phone(off): +91-0278-2567760 (extn. 679 / 662) mobile: +91-9275174842 FAX: +91-0278-2567562 / 2566970 / 2572354 e-mail: satya@csmcri.org; satyabratadas@yahoo.com; satya.csmcri@gmail.com -------------------------------------------------------------------------- From Andrey.Kajava from crbm.cnrs.fr Tue Jan 20 05:41:57 2009 From: Andrey.Kajava from crbm.cnrs.fr (Andrey Kajava) Date: Sat Feb 7 17:13:24 2009 Subject: [Protein-analysis] (no subject) Message-ID: <4975AA36.4010306@crbm.cnrs.fr> International Jacques Monod Conference: “Protein folds in infectious and neurodegenerative diseases” Aussois (Savoie), France, 25-29 April 2009. The deadline for applications to attend this conference is February 15th 2009. Please email the application(s) and abstract(s) to Andrey Kajava (andrey.kajava@crbm.cnrs.fr). The conference will be held in Aussois (http://www.caes.cnrs.fr/Vacances/Explorer/Aussois. Registration fee includes board and lodging (385 € for PhD students; 575 € for other participants). More information: http://www.cnrs.fr/sdv/cjm/2009/steven_e.html -- passerelle antivirus du campus CNRS de Montpellier --