From allicindixvin from gmail.com Tue Sep 2 07:42:47 2008 From: allicindixvin from gmail.com (kyoli) Date: Tue Sep 2 10:56:01 2008 Subject: [Protein-analysis] gas chromatography Message-ID: <8ff0557f-8941-4122-a2c4-75c6e4aa43a2@p31g2000prf.googlegroups.com> hello to all, i am new in the field and trying to run my sample in GC. i have extracted my oil from seed in petroleum ether using soxhlet apparatus. to transesterifying it it is treated with methanolic KOH. the problem starts now as i don't know that how to prepare the standard sample. i have standards of linoleic acid and oleic acid from sigma aldrich. i don't know the exact procedure to prepare these standards so as to run into GC. can it be made by simply dissolving in methanol From dienoylcoa from hotmail.com Tue Sep 2 11:04:20 2008 From: dienoylcoa from hotmail.com (P Hubbard) Date: Tue Sep 2 17:32:05 2008 Subject: [Protein-analysis] New web service to help establish scientific collaborations Message-ID: Hi all=2C In an effort to help new PIs at smaller research institutes form collaborations=2C I=92ve made a Google Maps mashup designed for people to add push-pins for any specialist equipment they migh= t be willing to share/collaborate with. It=92s pretty basic at the moment=2C and currently covers only a small range of equipment that I=92ve needed for my = own research projects (however=2C I am happy to extend this much further). =20 http://www.pageforaday.com/xtalwizard/maps/ =20 To circumvent data protection issues=2C people who list equipment need only submit a webpage which includes suitable contact information rather than submitting a contact name/e-mail address/phone number. I=92m not sure if something like it already exists (please let me know if i= t does)=2C but if people find it useful I will try to fix any bugs and improv= e it with any user suggestions. Thanks=2C AGS _________________________________________________________________ Be the filmmaker you always wanted to be=97learn how to burn a DVD with Win= dows=AE. http://clk.atdmt.com/MRT/go/108588797/direct/01/= From otastan from gmail.com Fri Sep 5 17:33:53 2008 From: otastan from gmail.com (Oznur Tastan) Date: Fri Sep 5 22:15:08 2008 Subject: [Protein-analysis] Coarse functional protein classification Message-ID: <63aeb8db0809051533i44afef31m6848469beb25c0df@mail.gmail.com> Hi, is anyone aware of a database which provides functional protein classification in broad terms, for example "kinases", "receptors" would be two protein classes. I've just checked the root terms of InterPro, it was still too specific for my task. thanks - oznur From nick.theodorakis from gmail.com Sat Sep 6 10:12:51 2008 From: nick.theodorakis from gmail.com (Nick Theodorakis) Date: Sat Sep 6 13:21:48 2008 Subject: [Protein-analysis] Re: Coarse functional protein classification References: Message-ID: On Sep 5, 5:33 pm, "Oznur Tastan" wrote: > Hi, is anyone aware of a database which provides functional protein > classification in broad terms, for example "kinases", "receptors" would be > two protein classes. I've just checked the root terms of InterPro, it was > still too specific for my task. > Many receptors are also kinases, you know. There is the EC enzyme nomenclature for classifying enzymes by the type of reactions they catalyze, but it's only for enzymes and may not be exactly what you are looking for. Nick -- Nick Theodorakis nick_theodorakis@hotmail.com contact form: http://theodorakis.net/contact.html From holeung from berkeley.edu Sat Sep 6 15:42:06 2008 From: holeung from berkeley.edu (Ho-Leung Ng) Date: Sat Sep 6 20:12:30 2008 Subject: [Protein-analysis] Re: Coarse functional protein classification Message-ID: <6678762a0809061342v67c796f5n4f3714c8c3d26b6f@mail.gmail.com> How about the NCBI keywords? From otastan from gmail.com Sat Sep 6 13:31:19 2008 From: otastan from gmail.com (Oznur Tastan) Date: Sat Sep 6 20:12:40 2008 Subject: [Protein-analysis] Re: Coarse functional protein classification In-Reply-To: References: Message-ID: <63aeb8db0809061131o7fa0b754l1ace9d73aa648d4@mail.gmail.com> that is true, there is the receptor tyrosine kinases. thanks for the EC pointer, but it would been great if there were some nomenclanture that covers the whole human proteome. thanks oznur On Sat, Sep 6, 2008 at 11:12 AM, Nick Theodorakis < nick.theodorakis@gmail.com> wrote: > On Sep 5, 5:33 pm, "Oznur Tastan" wrote: > > Hi, is anyone aware of a database which provides functional protein > > classification in broad terms, for example "kinases", "receptors" would > be > > two protein classes. I've just checked the root terms of InterPro, it > was > > still too specific for my task. > > > > Many receptors are also kinases, you know. > > There is the EC enzyme nomenclature for classifying enzymes by the > type of reactions they catalyze, but it's only for enzymes and may > not be exactly what you are looking for. > > Nick > > -- > Nick Theodorakis > nick_theodorakis@hotmail.com > contact form: > http://theodorakis.net/contact.html > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > -- oznur From erik.flahive from pfizer.com Wed Sep 10 19:22:22 2008 From: erik.flahive from pfizer.com (Flahive, Erik) Date: Thu Sep 11 16:39:17 2008 Subject: [Protein-analysis] Endotoxin Removal Message-ID: <20E676E26D369946912FD7D7E347DE760CF4B25C@lajamrexm01.amer.pfizer.com> Dr. Balaal, I hope you do not mind for me contact you directly. I was searching on the internet for "endotoxin removal" methods and came across your discussion thread on www.indusbio.co.in . Do you know if the charged filter capsules (e.g. Pall, Millipore) that you mentioned, or any others that may be available, would be compatible/effective with a solution of a compound in an organic solvent (e.g. ethanol) from which we would wish to purge endotoxin, versus aqueous solutions? Thanks in advance for your advice - I appreciate it, Erik Erik Flahive Pfizer Global R&D - La Jolla Labs 10646 Science Center Drive San Diego, CA 92121 (858)-622-7541 From sittner from lkb.ens.fr Fri Sep 12 05:30:00 2008 From: sittner from lkb.ens.fr (assa sittner) Date: Fri Sep 12 07:30:15 2008 Subject: [Protein-analysis] Large Scale, native, periplasmic prep Message-ID: Hi everyone, I have been using an osmotic shock (20% sucrose and then water - taken from "current protocols" or the pET manual) - based protocol, for the extraction of a protein expressed with pET26b (periplasmic exp. with a pelB leader sequence). It looks fine on the small scale (>50ml culture), but I'm having trouble up-scaling it to ~1L. does anyone know a protocol designed for large scale periplasmic preparation (non-danaturing). cheers, -- Assa Sittner Optics & Biology group, Physics Dept. Ecole Normale Superieure, Paris From engelbert_buxbaum from hotmail.com Fri Sep 12 09:19:35 2008 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Fri Sep 12 16:02:21 2008 Subject: [Protein-analysis] Re: Coarse functional protein classification References: Message-ID: Am 05.09.2008, 18:33 Uhr, schrieb Oznur Tastan : > Hi, is anyone aware of a database which provides functional protein > classification in broad terms, for example "kinases", "receptors" would > be > two protein classes. I've just checked the root terms of InterPro, it > was > still too specific for my task. Enzymes are classified by the 6 fundamental reactions they may perform by the Enzyme Commission (kinases are transferases). You would then have to further classify non-enzyme proteins, e.g. receptors, structural proteins, hormons and so on. From mbabashir1 from yahoo.com Fri Sep 19 11:31:13 2008 From: mbabashir1 from yahoo.com (mba bashir) Date: Fri Sep 19 14:52:08 2008 Subject: [Protein-analysis] (no subject) Message-ID: <941845.55235.qm@web53910.mail.re2.yahoo.com> Dear Ashley, I am completing my PhD on production, characterization and application of alkaline phosphatase. However my HPLC experiments are still pending. As for GFC, i got quite good results and consitant activity. For further discussion, we can communicate through email. Regards Bashir Ahmad Ph.D Research Scholar Deptt.of Microbiology&Biotechnology Quaid i Azam University, Islamabad 45320 Pakistan. mbashir@bs.qau.edu.pk ? Visiting Research Fellow Uni of Waterloo, Ontario,Canada b2ahmed@scimail.uwaterloo.ca ? From otastan from gmail.com Sat Sep 20 14:06:28 2008 From: otastan from gmail.com (Oznur Tastan) Date: Sat Sep 20 18:06:42 2008 Subject: [Protein-analysis] UniRef clusters Message-ID: <63aeb8db0809201206g5a223e62g3197c0d74ddab3c@mail.gmail.com> Hi all, is anyone know where I could retrieve the members of each Uniref cluster. The fasta file I downloaded from uniprot ftp site, uniref90.fasta, includes only the Uniref cluster name and the representative sequence information but does not include which sequences belong the this cluster. thanks, oznur From sanjaysingh765 from gmail.com Tue Sep 30 01:18:59 2008 From: sanjaysingh765 from gmail.com (chunnu) Date: Tue Sep 30 08:51:38 2008 Subject: [Protein-analysis] highly expressed gene Message-ID: <2cc92d56-2062-414d-b8ef-96904a3f5294@k30g2000hse.googlegroups.com> I am a graduate student. I am looking for the highly and lowly expressed genes of rice and Arabidopsis gene ( say 10 % of whole genomes). I know that there is a database called MPSS for this purpose but due to lack of my knowledge I am not able to extract out the data of my interest from this database. So please help me in this regards.You can mail me at sanjaysingh765@gmail.com also. Best regards Sanjay From lisa.m.fasulo from pfizer.com Tue Sep 30 15:55:26 2008 From: lisa.m.fasulo from pfizer.com (Fasulo, Lisa M) Date: Tue Sep 30 17:43:12 2008 Subject: [Protein-analysis] Help with calculations for specific activity Message-ID: <3F4063B77CC1F445933078B93A0A0C720855F3CF@groamrexm05.amer.pfizer.com> I am trying to calculate the specific activity of my [3H]-ligand but don't know how to do it. The package insert for my radioligand states that the Specific Activity is 200 mCi/g but I need to know what the Specific Activity is in Ci/mmol. How do I calculate this? The molecular weight of the radioligand is 463.6 g/mol. Can anyone walk me through the calculations to give the specific activity in Ci/mmol? The only other info I have is the concentration of the radioligand which is 1mCi/mL. Lisa