From zzhao from vcu.edu Fri Jun 5 09:59:26 2009 From: zzhao from vcu.edu (Zhongming Zhao) Date: Fri Jun 5 12:48:34 2009 Subject: [Protein-analysis] Call for Papers: Computational Analysis of Biological Networks in Journal Advances in Bioinformatics Message-ID: <4A2932CE.5020809@vcu.edu> Deadline: August 1, 2009 Computational Analysis of Biological Networks Call for Papers One of the fundamental goals of bioinformatics is to understand the biological processes that are the driving forces behind organisms' functions. Biological networks such as metabolic, gene regulatory, and protein interaction networks show how various biochemical entities interact with each other to perform vital functions that they cannot perform alone. A critical common property of biological networks is that although the individual entities of a pathway may have specific functions, they play additional roles in the entire network by communicating with other entities. This Special Issue focuses on novel computational approaches and methods for understanding biological networks. This issue will publish original, high-quality research articles. High-risk/high-gain ideas for understanding biological networks are welcome. Manuscripts should include biological impact and validation as well as technical depth. The topics that are included (but not limited to) in this issue are: * Pathway reconstruction * Comparison and querying of biological networks * Annotation of functional subnetworks * Motif discovery in networks * Steady-state analysis of networks and the whole cell model * Analysis of network-disease family relationships Before submission, authors should carefully read over the journal's Author Guidelines, which are located at http://www.hindawi.com/journals/abi/guidelines.html. Prospective authors should submit an electronic copy of their complete manuscripts through the journal manuscript tracking system at http://mts.hindawi.com/, according to the following timetable: Manuscript Due August 1, 2009 First Round of Reviews November 1, 2009 Publication Date February 1, 2010 Lead Guest Editor * Tamer Kahveci , Computer and Information Sciences and Engineering Department, University of Florida, FL 32610, USA Guest Editors * Tolga Can , Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey * Limsoon Wong , School of Computing, National University of Singapore, Room 3-34, Building COM1, 13 Computing Drive, Singapore, Singapore 117417 * Zhongming Zhao , Virginia Commonwealth University, VA 23284, USA -- ============================================ Zhongming Zhao, Ph.D. Asst. Professor of Bioinformatics Depts. Psychiatry and Human Genetics and Center for the Study of Biological Complexity Virginia Commonwealth University PO Box 980126, Richmond VA 23298-0126 Phone: (804) 828-8129 Fax: (804) 828-1471 http://bioinfo.vipbg.vcu.edu/ From ajbr.acadjourn from gmail.com Mon Jun 8 10:50:02 2009 From: ajbr.acadjourn from gmail.com (African Jourmal Biochemistry Research) Date: Mon Jun 8 13:43:09 2009 Subject: [Protein-analysis] Invitation to Review: AJBR-08-041 Message-ID: African Journal of Biochemistry Research www.academicjournals.org/ajbr Dear Collegue, We received a manuscript titled: ** The contribution of Ser463 residue to the enzymatic and autoprocessing activities of *Escherichia coli *=83=D7-glutamyltranspeptidase Below you will find the abstract A serine residue, Ser463, required for the proper function of *Escherichia coli* g-glutamyltranspeptidase (*Ec*GGT) was identified by site-directed mutagenesis on the basis of sequence alignment of human, pig, rat, and thre= e bacterial enzymes. Thr-, Asp-, and Lys-substituted variants were overexpressed in *E. coli *M15 cells and the recombinant proteins were purified to near homogeneity by nickel-chelate chromatography. With the exception of S463T, the other two variants completely lost GGT activity, implying the importance of this residue in *Ec*GGT. Moreover, substitution of Ser463 with either Lys or Asp impaired the capability of autocatalytic processing of the precursor into a- and b-subunit. Computer modeling showed that the critical bonding distance of Gln390 C-Thr391 OG1 is significantly increased in S463D and S463K, indicating that these distance changes might be responsible for the lack of enzyme maturation. Measurements of intrinsic tryptophan fluorescence revealed alteration of the microenvironment of aromatic amino acid residues in S463D and S463K, while circular dichroism spectra were nearly identical for wild-type and all mutant enzymes. The temperature-dependent signal in the far-UV region for S463T was consistent with that of wild-type enzyme but S463D and S463K showed a different sensitivity towards temperature-induced denaturation. These results imply that a significant conformational change occurred as a result of Asp- and Lys-substitution. Key words: *Escherichia coli*, g-glutamyltranspeptidase, site-specific mutagenesis, autocatalytic processing, tryptophan emission fluorescence, circular dichroism i am looking forward to your response if you are interested in reviewing. Best regards, Prof. Johnson Lin Editor, African Journal of Biochemistry Research E-mail: * **ajbr.acadjourn@gmail.com* http://www.academicjournals.org/AJBR From eleguinea from gmail.com Thu Jun 11 11:20:08 2009 From: eleguinea from gmail.com (elena guinea) Date: Fri Jun 12 07:31:35 2009 Subject: [Protein-analysis] HPLC Troubleshooting question Message-ID: <4f9863e0906110920nb9eec45i6d3e51f522010a37@mail.gmail.com> Hello; I have a 486 Waters detector, and last day an erros message apears in were the wavelnght should apear. We looked up what does the message means and was related with change the battery. We open the instrumente, and change it and the message disapears but now, there is no back comunication between the detector and the computer, we can controll the flow and the parametres, but we can?t see the chrommatogram. I don?t know how can help me, thanks a lot. I would be pleasure if you could help me or send me information about where I can look it up. Elena Guinea University of Guelph, On From Peggy.Willemarck from ablynx.com Thu Jun 18 06:30:05 2009 From: Peggy.Willemarck from ablynx.com (Peggy Willemarck) Date: Thu Jun 18 09:53:58 2009 Subject: [Protein-analysis] Concentration Protein after fluorescent labeling Message-ID: <1676D4A332BFF34CA3A07ACDF801FF67886610E666@posix.lan.ablynx.com> Does anyone knows how the concentration of labeled protein with Alexa 647 can be determined? Normal methods such as OD280, Bradford and coomassie stain have to much interference with the dye to give a good concentrations. Peggy ________________________________
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