Proteomics of E.coli Nissle 1917 in Responce to Cocos nucifera sap and Wine
Abstract:
In the present study, we described the protein profile experimentally by 2D-PAGE and MALDI analysis to understand the stress mechanisms of cocoti sap and wine on E.coli Nissle 1917. We isolated one newly expressed protein from cocoti wine treated gel which is not present in both control and cocoti sap treated sample i.e. P21 prophage-derived head-stabilizing proteinVG03_ECOL6 (3n1) also called as Head protein gp3. This protein mainly activities related to the viral life cycle. It helps to attach the viral gene into host. The growth rate was delayed in cocoti wine treated E.coli Nissle 1917 when compared to control and cocoti sap treated samples. Stress mechanism induce many proteins they are involved in metabolic process, hydrolase activity, lyase activity, quinone binding, phosphotransferase system, carbohydrate metabolism, DNA binding, DNA repair, transferase activity, oxidoreductase, purine metabolism, transcription anti-termination, transcription regulation and other related activities.We proved that the predicted protein structure quality, resolution, density and error plot values by QMEAN analysis. Based on these results, only two differentially expressed proteins under sap stress showed that the significant results, which were N-acetylgalactosamine-specific phosphotransferase enzyme IIB component 1, PTPB1_ECOLI and DinI-like protein Z3305/ECs2939 in prophage CP-933VDINI1_ECO57. In case of wine stress, the differentially expressed proteins were Transcription anti-termination protein RFAH- ECO57 NusA and PUR7-eco24- phosphoribosylamidazole-succinocarboxamide synthase showed significant results. ProtParam analysis indicating that the multiple physico-chemical characters of differentially expressed proteins were differed and compared. The phylogenetic tree represents the relationship in-between the differentially expressed proteins, were showed siblings (related) as well as monophytic clade.
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[1] Abbott A (1999). A Post-genomic challenge: learning to read patterns of protein synthesis. Nature, 402: 715-720.
DOI: 10.1038/45350
[2] Abola E, Kuhn P, Earnest T and Stevens RC (2002). Automation of X-ray Crystallography. Nature of Structural Biology, 7: 973-977.
DOI: 10.1038/80754
[3] Accolas JP, Bloquel R, Didienne R and Regnier J (1977). Proprirtes acidifiantes des bacteries lactiques thermopiles en relation avecla fabrication du Yoghourt. Dairy Science and Technology, 67: 1-23.
[4] Aebersold R and Goodlett DR (2001). Mass spectrometry in proteomics. Chemical Review, 101: 269-295.
[5] Agu RC (1993). Use of high ethanol resistant yeast isolates from Nigerian Palm wine in larger beer brewing. World Journal of Micro Biotechnology, 9 (6): 660-661.
DOI: 10.1007/bf00369575
[6] Agu RC, Okenchi MU, Ude CM, Onyia AI, Onwumelu AH and Ajiwe VIE (1999). Fermentation kinetic studies of Nigerian palm wines; Elaeis guinensis and Raphia hookeri for preservation by bottling. Journal of Food Science and Technology, 36 (3): 205-209.
[7] Aires J and Butel MJ (2011). Proteomics, human gut microbiota and probiotics. Expert Review of Proteomics, 8 (2): 279-288.
DOI: 10.1586/epr.11.5
[8] Aires J, Thouvenez M and Allano SandButel MJ (2011). Longitudinal analysis and genotyping of infant dominant bifidobacteria populations. Systematic and Applied Microbiology, 34: 536-541.
[9] Aldous D (2001). Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statistical Science, 16: 23-34.
DOI: 10.1214/ss/998929474
[10] Allali N, Afif H, Couturier M and Van Melderen L (2002). The highly conserved TldD and TldE proteins of Eschericia coli are involved in microcin B17 processing and in CcdA degredation. Journal of Bacteriology, 184 (12): 3224-3231.
[11] Amoa-Awua WK, Sampson E and Tano-Debrah K (2007). Growth of yeasts, lactic and acetic acid bacteria in plam wine during tapping and fermentation from felled oil palm (Elaeis guineensis) in Ghana. Journal of Applied Microbiology, 102: 599–606.
[12] Anderson NG and Anderson NL (1996). Twenty years of two-dimensional electrophoresis: past, present and future. Electrophoresis, 17: 443– 453.
[13] Anderson NL and Anderson NG (1998). Proteome and proteomics: new technologies, new concepts and new words. Electrophoresis, 19 (11): 1853-1861.
[14] Andrews JM (2001). Determination of minimum inhibitory concentrations. Journal of Antimicrobial Chemotherapy, 48 (1): 5-16.
[15] Armengaud J (2010). Proteo genomics and systems biology: quest for the ultimate missing parts. Expert Reviews of Proteomics, 7:65–77.
DOI: 10.1586/epr.09.104
[16] Armengaud J (2013). Microbiology and proteomics, getting the best of both worlds. Environmental Microbiology, 15:12–23.
[17] Arnold K, Bordoli L, Kopp J and Schwede T (2009). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22 (2): 195–201.
[18] Avaritt NL, Shalin S and Tackett AJ (2014). Decoding the Proteome in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues. Journal of Proteomics and Bioinformatics, 7(3):25-26.
DOI: 10.4172/jpb.10000e25
[19] Bach SJ, McAllister TA, Veira DM, Gannon VPJ and Holley RA (2003). Effects of a Saccharomyces cerevisiae feed supplement on Escherichia coli O157:H7 in ruminal fluid in vitro. Animal Feed Science Technology, 104: 179–189.
[20] Balamurugan R, Janardhan HP, George S, Chittaranjan SP and Ramakrishna BS (2008). Bacterial succession in the colon during childhood and adolescence: molecular studies in a southern Indian village. American Journal of Clinical Nutrition, 88:1643–1647.
[21] Baneyx F (1999). Recombinant Protein Expression in Escherichia coli. Opinion Biotechnology, 10: 411-421.
[22] Banks RE, Dunn MJ, Hochstrasser DF, Sanchez JC, Blackstock W and Pappin DJ (2000). Proteomics: New perspectives, new biomedical opportunities. Lancet, 356:1749 –1756.
[23] Bantscheff M, Schirle M, Sweetman G, Rick J and kuster B (2007). Quantitative mass spectrometry in proteomics: a critical review. Analytical and Bio-analytical Chemistry, 389 (4): 1017-1031.
[24] Bassir O (1962). Observations on the fermentation of palm wine. World African Journal of Biology and Chemistry, 6: 20-25.
[25] Baton Rouge LA (2007). Surface Water Quality Standards. Louisiana Administrative Code (LAC), 33 (11): IX.
[26] Begley M, Gahan CGM and Hill C (2005). The interaction between bacteria and bile. FEMS Microbiology reviews, 29: 625-651.
[27] Ben Thabet I, Besbes S, Attia H, Deroanne C, Francis F, Drira NE and Blecker C (2009). Physicochemical characteristics of date sap ''Lagmi" from Deglet Nour palm (Phoenix Dactylifera L.). International Journal of Food Properties, 12: 659–670.
[28] Benkert P, Schwede T and Tosatto SCE. (2009). QMEAN clust: Estimation of protein model quality by combining a composite scoring function with structural density information. BMC Structural Biology, 20: 9-35.
[29] Benkert P, Tosatto SCE and Schomburg D (2008). QMEAN: A comprehensive scoring function for model quality assessment. Proteins: Structure, Function, and Bioinformatics, 71 (1): 261-277.
DOI: 10.1002/prot.21715
[30] Berman HM (2008). The protein Data Bank: A historical perspective. Acta Crystallographica section A: Foundations of Crystallography A, 64 (1): 88-95.
[31] Bhadoria PBS and Mahapatra SC (2011). Prospects, Technological Aspects and Limitations of Probiotics – A Worldwide Review. European Journal of Food Research & Review, 1 (2): 23-42.
[32] Blackstock WP and Weir MP (1999). Proteomics: quantitative and physical mapping of cellular proteins. Trends in Biotechnology, 17 (3): 121-127.
[33] Blum-OG, Oswald S, Eiteljorge K, Sonnenborn U, Schulze J, Kruis W and Hacker J (2003). Development of strain-specific PCR reactions for the detection of the probiotic E. coli strain Nissle 1917 in faecal samples. Research Microbiology, 154: 59–66.
[34] Bohm SK and Kruis W (2006). Probiotics: do they help to control intestinal inflammation. Annals of New York Academic Sciences, 1072: 339-350.
[35] Booth IR (2002). Stress and the single cell: intra-population diversity is a mechanism to ensure survival upon exposure to stress. International Journal of Food Microbiology, 78: 19-30.
[36] Borchers AT, Selmi C, Meyers FJ, Keen CL and Gershwin ME (2009). Probiotics and immunity. Journal of Gastroenterology, 44: 26-46.
[37] Bradford MM (1976). Rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Annals of Biochemistry, 72: 248–254.
[38] Breese CR, D'Costa A, Ingram R, Lenham J and Sonntag WE (1993). Long-term suppression of insulin like growth factor-1 in rats after in utero ethanol exposure-relationship to somatic growth. Journal of Pharmacology and Experimental Therapeutics, 264 (1): 448-456.
[39] Brinkkotter A, Kloss H, Alpert C and Lengeler JW (2000). Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli. Molecular Microbiology 37 (1): 125-135.
[40] Carl Zimmer (2012).Tending the Body's Microbial Garden. New York Times, 18.
[41] Casey EB, Zhao HR and Abraham EC (1995). Role of glycine 1 and lysine 2 in the glycation of bovine gamma-B-crystallin. Journal of Biological Chemistry, 270: 20781-20786.
[42] Champomier-Verges MC, Chailou S, Cornet M and Zagorec M (2002). Erratum to Lactobacillus sakei: recent developments and future prospects. Research in Microbiology, 153: 115-123.
[43] Champomier-Verges MC, Maguin E, Mistou MY, Anglade P and Chich JF (2002). Lactic acid bacteria and proteomics: current knowledge and perspectives. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Sciences, 771: 329–342.
[44] Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG and Thompson JD (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31 (13): 3497–3500.
DOI: 10.1093/nar/gkg500
[45] Chiang AC and Massague J (2008). Molecular basis of metastasis. The New England Journal of Medicine, 359 (26): 2814-2823.
[46] Chinarasa E (1968). The preservation and bottling of palm-wine. Research Report No.38. Federal Ministry of industries Logos, Nigeria.
[47] Chomczynski P and Sacchi N (1987). Single-step method of RNA isolation by acid guanidiumthiocyanate-phenol-chloroform extraction. Analytical Biochemistry, 162 (1): 156-159.
[48] Cohen DPA, Renes J, Bouwman FG, Zoetendal EG, Mariman Ede Vos WM and Vaughan EE (2006). Proteomic analysis of log to stationary growth phase Lactobacillus plantarum cells and a 2-DE database. Proteomics, 6: 6485–6493.
[49] Collins MD and Gibson GR (1999). Probiotics, Prebiotics and synbiotics: approaches for modulating the microbial ecology of the gut. American Journal of Clinical Nutrition, 69: 1052S-1057S.
[50] Collins, Francis and Alan Guttmacher (2002). Genomic Medicine – A primer. New England Journal of Medicine, 347: 1512-1520.
DOI: 10.1056/nejmra012240
[51] Cristalli G, Costanzi S, Lambertucci C, Lupidi G, Vittori S, Volpini R and Camaioni E (2001). Adenosine deaminase: Functional implications and different classes of inhibitors. Medicinal Research Reviews, 21 (2): 105–128.
DOI: 10.1002/1098-1128(200103)21:2<105::aid-med1002>3.0.co;2-u
[52] Curreli N, Sollai F, Massa L, Comandini O, Rufo A, Sanjust E, Rinaldi A and Rinaldi AC (2001). Effects of plant-derived naphthoquinones on the growth of Pleurotus sajor-caju and degradation of the compounds by fungal cultures. Journal of Basic Microbiology, 41: 253–259.
DOI: 10.1002/1521-4028(200110)41:5<253::aid-jobm253>3.0.co;2-r
[53] Dajana GS, Spomenka K and Djuro J (2010). Application of Proteomics in Food Technology and Food Nanotechnology: Process Development,Quality Control and Product Safety. Food Technology and Biotechnology, 48 (3): 284-295.
[54] Das UK, De D, Chatterjee K, Mallick C, Bera TK and Ghosh D (2009). Antigonadal effect induced by hydro-methanolic extract of leaf of Aelgle mermelos in male rat: Effect of hCG co-administration. Journal of Medicinal Plants Research, 3 (10): 728 – 735.
[55] Debmalya Barh BC and Mazumdar (2008). Comparative nutritive values of palm saps before and after their partial fermentation and effective use of wild date (Phoenix sylvestris Roxb.) sap in treatment of anemia. Research Journal of Medicine and Medical Sciences, 3: 173-176.
[56] Del Chierico F, Petrucca A and Vernocchi P (2014). Proteomics boosts translational and clinical microbiology. Journal of proteomics, 97: 69-87.
[57] Desroches D, Ehite SS and Denno RH (1987). Effects of acute alcohol administration on maternal Ca metabolism and fetal development in mice. Alcohol drug Research, 55: 443-462.
[58] Dicks LMT, Silvester M, Lawson PA and Collins MD (2000). Lactobacillus fornicalis sp.nov, isolated from the posterior fornix of the human vagina. International Journal of Systemic and Evolutionary Microbiology, 50 (3):1253-1258.
[59] Dominguez-Bello MG and Blaser MJ (2008). Do you have a probiotic in your future. Microbial Infections, 10: 1072-1076.
[60] Doron S and Gorbach SL (2006). Probiotics: their role in the treatment and prevention of disease. Expert Review of Anti-infective Therapy, 4 (2): 261-275.
[61] Dotan I and Rachmilewitz D (2005). Probiotics in inflammatory bowel disease: possible mechanisms of action. Current Opinion in Gastroenterology, 21: 426–430.
[62] Doustjalali SR, Bhuiyan M, Al-Jashamy K , Linn NH , Abdul Kadir SY, Appalanaidu V, Arzuman H, Krishnan A, Lin WM, Saraji A, Gopal K, Shankar EM, Fatemeh S and Sabet NS (2014). Two Dimensional Gel Electrophoresis: An Overview of Proteomic Technique in Cancer Research. Journal of Proteomics and Bioinformatics, 7(3): 077-081.
DOI: 10.4172/jpb.1000305
[63] Eluwa MA, Agarrey LE, Ekanem TB, Amabe OA, Agnes OE and Ekong MB (2010). Comaparative study of tetratogenic effects of brewed beer and palm wine on fetal femur bone of albino wistar rats. International Journal of Biomedical and health Sciences, 6 (4): 229-233.
[64] Eschie HA (1978). Effect of different preservatives on the major chemical constituents of bottled palm wine during storage. Nigerian agriculture Journal, 15: 158-167.
[65] Ezeronye OU and Okerentugba PO (2002). Focculation and mating behaviour in Saccharomyces yeast from palm wine. Nigerian Experimental and Applied Biology, 3 (1): 83-88.
[66] Faparusi SI and Bassir O (1972). Factors affecting the quality of palm wine Period of storage. West African Journal of Biology and Applied Chemistry, 15 (2): 17-28.
[67] Farnworth ER (2008). The evidence to support health claims for probiotics. Journal of Nutrition, 138: 1250S-1254S.
[68] Fisher Box and Joan (1987). Guinness, Gosset, Fisher, and Small Samples. Statistical Science, 2 (1): 45–52.
[69] Fitzpatrick LR, Small J, Hoerr RA, Bostwick EF, Maines L and Koltun WA (2008). In vitro and in vivo effects of the probiotic Escherichia coli strain M-17: immunomodulation and attenuation of murine colitis. British Journal of Nutrition, 100 (3): 530-541.
[70] Fletcher SA, Rhodes D and Csonka LN (2001). Analysis of the effects of osmoprotectants on the high osmolality-dependent induction of increased thermotolerance in Salmonella typhimurium. Food Microbiology, 18: 345–354.
[71] Frank Rogerson and Charles Symington (2006). A Method for the Estimation of Alcohol in fortified wines using hydrometer baume and refractometer brix. American Journal of Enology and Viticulture, 57: 486-490.
[72] Fuller R (1989). Probiotics in man and animals. Journal of Applied bacteriology, 66 (5): 365-378.
[73] Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M and Bauer A (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415: 141– 147.
[74] Geoghegan KF, Dixon HBF, Rosner PJ, Hoth LR, Lanzetti AJ, Borzilleri KA, Marr ES, Pezullo LH, Martin LB, Lemotte PK, McColl AS, Kamath AV and Stroh JG (1999). Spontaneous alpha-N-6-phosphogluconoylation of a His tag in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Analytical Biochemistry, 267: 169-184.
[75] Georgopoulos C and Welch WJB (1993). Role of the major heat shock proteins as molecular chaperones. Annual Reviews of Cell and Developmental Biology, 9: 601-634.
[76] Gibson GR and Williams CM (1999). Gut fermentation and health advantages: myth or reality. British Journal of Nutrition, 8: 83-84.
[77] Gill SC and Von Hippel PH (1989). Calculation of protein extinction coefficients from amino acid sequence data. Annals of Biochemistry, 182: 319–326.
[78] Gilliland SE (1990). Health and nutritional benefits from Lactic Acid Bacteria. FEMS Microbiology Reviews, 87: 175-188.
[79] Gionchetti P, Rizzello F, Helwig U, Venturi A, Lammers KM, Brigidi P, Vitali B, Poggioli G, Miglioli M and Campieri M (2003). Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial. Gastroenterology, 124: 1202-1209.
[80] Gionchetti P, Rizzello F, Venturi A, Brigidi P, Matteuzzi D, Bazzocchi G, Poggioli G, Miglioli M and Campieri M (2000). Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. Gastro enterology, 119: 305-309.
[81] Gismondo MR, Drago L and Lombardi A (1999). Reviews of probiotics available to modify gastrointestinal flora. International Journal of Antimicrobial Agents, 12: 287-292.
[82] Glader BE, Backer K, Diamond LK (1983). Elevated Erythrocyte Adenosine Deaminase Activity in Congenital Hypoplastic Anemia. New England Journal of Medicine, 309 (24): 1486–1490.
[83] Gobom J, Schuerenberg M, Mueller M, Theiss D, Lehrach H and NordhoVE (2001). α-Cyano-4- hydroxycinnamic Acid Affinity Sample Preparation. A Protocol for MALDI-MS Peptide Analysis in Proteomics. Analytical Chemistry, 73: 434–438.
DOI: 10.1021/ac001241s
[84] Godovac-Zimmermann J and Brown LR (2001). Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Review, 20: 1-57.
[85] Gonzales C, Rubio J, Gasco M, Nieto J, Sandra Y and Gonzales GF (2006). Effect of short term and long-term tratments with three ecotypes of Lepidium meyenii (MACA) on spermatogenesis in rats. Journal of Ethno pharmacology, 103: 448-454.
[86] Gosselink MP, Schouten WR, van Lieshout LM, Hop WC, Laman JD and Ruseler-van Embden JG (2004). Delay of the first onset of pouchitis by oral intake of the probiotic strain Lactobacillus rhamnosus GG. Diseases of the Colon & Rectum, 47: 876-884.
[87] Grozdanov L, Raasch C, Schulze J, Sonnenborn U, Gottschalk G, Hacker J and Ulrich D (2004). Analysis of the genome structure of the non-pathogenic probiotic Escherichia coli strain Nissle 1917. Journal of Bacteriology, 186: 5432–5441.
[88] Guarner F and Schaafsma GJ (1998). Probiotics. International Journal of Food Microbiology, 39: 237-238.
[89] Guex N, Peitsch MC, and Schwede T (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis, 30 (1): S162–S173.
[90] Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP and Turnbaugh PJ (2013). Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science, 341 (6143): 295–298.
[91] Hamilton-Miller JMT (2001). Probiotics in the management of irritable bowel syndrome: A review of clinical trials. Microbial Ecology in Health and Disease, 13: 212-216.
[92] Han MJ and Lee SY. (2003). Proteome profiling and its use in metabolic and cellular engineering. Proteomics, 3: 2317–2324.
[93] Hart AL, Stagg AJ, Frame M, Graffner H, Glise H, Falk P, and Kamm MA ( 2002). The role of the gut flora in health and disease and its modification as therapy. Journal of Aliment Pharmacol Therapy, 16: 1383-1393.
[94] Havenaar R and Huisin't Veld JHJ (1992). Probiotics: A general view. In: Wood BJB: The Lactic Acid Bacteria: The Lactic Acid Bacteria in Health and Disease, Chapman & Hall, New York, NY, 1: 209–224.
[95] Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H and Horiuchi T (2006). Highly accurate genome sequences of Eschericia coli K-12 strain MG 1655 and W3110. Molecular System Biology, 2: E1-E5.
DOI: 10.1038/msb4100049
[96] Henker J, Laass M, Blokhin BM, Bolbot YK, Maydannik VG, Elze M, Wolff C and Schulze J (2007). The probiotic Escherichia coli strain Nissle 1917 (EcN) stops acute diarrhoea in infants and toddlers. European Journal of Paediatrics, 166: 311–318.
[97] Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C and Watanabe C (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proceedings of the National Academy of Sciences USA, 90 (11): 5011-5015.
[98] Hill C (2010). Probiotics and Pharmabiotics: alternative medicine or an evidence-based alternative. Bioengineered bugs, 1 (2): 79-84.
[99] Hinsby AM, Olsen JV, Bennett KL and Mann M (2003). Signalling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometry. Molecular Cell Proteomics, 2: 29-36.
[100] Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L and Adams SL (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415: 180– 183.
[101] Hoch JA and Varughese KI (2001). Keeping signals straight in phosphorelay signal transduction. Journal of Bacteriology, 183 (17): 4941–4949.
[102] Housecroft C and Constable E (2006). Chemistry: an introduction to organic, inorganic, and physical chemistry. Pearson Education, 3: 349-353.
[103] Ichida K, Amaya Y, Noda K, Minoshima S, Hosoya T, Sakai O, Shimizu N and Nishino T (1993). Cloning of the cDNA encoding human xanthine dehydrogenase (oxidase): structural analysis of the protein and chromosomal location of the gene, Gene 133 (2): 279–284.
[104] Ideker T, Thorsson V, Ranish A, Christmas R, Buhler J, Eng KG, Bumgarner R, Goodlett DR, Aebersold R and Hood L (2001). Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292: 929-934.
[105] Inoue T, Higuchi M, Hashimoto Y, Seki M, Kobayashi M ,Kato T, Tabata S, Shinozaki K, and Kakimoto T (2001). Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature, 409: 1060–1063.
DOI: 10.1038/35059117
[106] Isaac DD, Pinkner JS, Hultgren SJ and Silhavy TJ (2005). The extra cytoplasmic adaptor protein CpxP is degraded with substrate by DegP. Proceedings of the National Academy of Sciences, 102:17775–17779.
[107] Jakob H and Waterborg (2002). The Lowry Method for Protein Quantitation. The Protein Protocols Handbook. 7-9.
[108] Jensen William B (2006). The Origins of the Hirsch and Buchner Vacuum Filtration Funnels. Journal of Chemical Education, 83 (9): 1283.
DOI: 10.1021/ed083p1283
[109] John JL, Sreeranjit kumar CV and Indira M (2006). A study on the chemical and biological composition of coconut palm wine. Journal of Ecotoxicology and Environmental Monitoring, 5 (2): 163-165.
[110] John M. Walker (2005). The Proteomics Protocols Handbook. Humana Press. 571-607.
[111] Kaczanowski S and Zielenkiewicz P (2010). Why similar protein sequences encode similar three- dimensional structures. Theoretical Chemistry Accounts, 125: 543-550.
[112] Kadere TT, Miyamoto T, Oniang ORK, Kutima PM and Njoroge SM (2008). Isolation and identification of the genera Acetobacter and Gluconobacter in coconut toddy (mnazi). African Journal of Biotechnology, 7: 2963-2971.
[113] Karas M and Hillenkampp F (1988). Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons. Analytical chemistry, 60: 259-280.
DOI: 10.1021/ac00171a028
[114] Kau AL, Ahern PP, Griffin NW, Goodman AL and Gordon JI (2011). Human nutrition, the gut microbiome and the immune system. Nature, 474: 327-336.
DOI: 10.1038/nature10213
[115] Kaufmann R, Kirsch D and Spengler B (1994). Sequencing of peptides in a time-of-flight mass spectrometer: evaluation of post source decay following matrix-assisted laser desorption ionisation (MALDI). International Journal of Mass Spectrometry and Ion Processes, 131: 355-364.
[116] Kawano M, Oshima T, Kasai H and Mori H (2002). Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Molecular Microbiology, 45: 333-349.
[117] Kelley LA and Sternberg MJE (2009). Protein Structure prediction on the Web: A case study using the Phyre server. Nature Protocols, 4 (3): 363-371.
DOI: 10.1038/nprot.2009.2
[118] Khan AA, Shrivastava A and Khurshid M. (2012). Normal to cancer microbiome transformation and its implication in cancer diagnosis. Biochimica et Biophysica Acta, 1826: 331–337.
[119] Kim HJ, Song EJ and Lee KJ (2002). Proteomic analysis of protein phosphorylation in heat shock response and thermotolerence. Journal of Biological Chemistry, 277 (26): 23193-23207.
[120] Kim KM, Yi EC, Baker D and Zhang KYJ (2001). Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase. Acta Crystallographica Section D, 57: 759-762.
[121] Kitchen DB, Decornez H, Furr JR and Bajorath J (2004). Docking and scoring in virtual screening for drug discovery: methods and applications. Nature reviews. Drug discovery, 3 (11): 935–949.
DOI: 10.1038/nrd1549
[122] Klaenhammer TR and Russell WM (1999). Lactobacillus acidophilus. Encyclopedia of Food Microbiology. Academic Press, San Diego, CA, 2: 1151-1157.
[123] Klein G, Pack A and Bonaparte C and Reuter G (1998). Taxonomy and physiology of probiotic lactic acid bacteria. International journal of Food Microbiology, 41: 103–125.
[124] Koenig T, Menze BH, Kirchner M, Monigatti F, Parker KC, Patterson T, Steen JJ, Hamprecht FA and Steen H (2008). Robust prediction of the MASCOT scores for an improved quality assessment in mass spectrometric proteomics. Journal of Proteome Research, 7 (9): 3708–3717.
DOI: 10.1021/pr700859x
[125] Koistinen KM, Plumed-Ferrer C, Lehesranta SJ, Kärenlampi SO and Von Wright A (2007). Comparison of growth-phase-dependent cytosolic proteomes of two Lactobacillus plantarum strains used in food and feed fermentations. FEMS Microbiology Letter, 273: 12–21.
[126] Koistinen KM, Plumed-Ferrer C, Lehesranta SJ, Kärenlampi SO and Von Wright A (2007). Comparison of growth-phase-dependent cytosolic proteomes of two Lactobacillus plantarum strains used in food and feed fermentations. FEMS MicrobiologyLetter, 273: 12–21.
[127] Krebs and Feder (2003). Hsp70 and larval thermo tolerance in Drosophila melanogaster: how much is enough and when is more too much. Journal of Insect Physiology, 44 (11): 1091-1101.
[128] Krishnamoorthy M and Arjun P (2012). Probiotic and antimicrobial activity of bacteria from fermented toddy of Cocus nucifera. Journal of Academic and Industrial Research, 1 (3): 127-131.
[129] Krishnan P, Kruger NJ and Ratcliffe RG (2005). Metabolite fingerprinting and profiling in plants using NMR. Journal of Experimental Botany, 56: 255-265.
DOI: 10.1093/jxb/eri010
[130] Kruis W, Fric P, Pokrotnieks J, Lukas M, Fixa B Kascak M, Kamm MA, Weismuller J, Beglinger C, Stolte M, Wolff C and Schulze J (2004). Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine. Gut, 53: 1617–1623.
[131] Kruis W, Schutz E, Fric P, Fixa B and Judmaier G (1997). Double-blind comparision of an oral Escherichia coli Nissle preparation and mesalazine in maintain remission of ulcerative colitis. Alimentary Pharmacology & Therapeutics Journal, 11: 853-858.
[132] Kumar, Abbas and Fausto (1999). Pathology Bases of Disease, 7th edition, China: Elsevier Saunders, 122.
[133] Kumarathasana K, Vincentb R, Dasa D, Mohottalagea S, Blaisa E, Blanka K, Karthikeyanb S, Vuongb NQ, Arbucklec TE and Fraserd WD (2014). Applicability of a high-throughput shotgun plasma protein screening approach in understanding maternal biological pathways relevant to infant birth weight outcome. Journal of Proteomics, 100: 136-146.
[134] Kurnosenko S and Moskovets E (2010). On the high-resolution mass analysis of the product ions in tandem time-of-flight (TOF/TOF) mass spectrometers using a time- dependant re-acceleration technique. Rapid Communications in Mass Spectrometry, 24 (1): 63-74.
DOI: 10.1002/rcm.4356
[135] Kyte J and Doolittle RF (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular biology, 157: 105–132.
[136] Lal JJ, Sreeranjit kumar CV, Indira M and Vijayammal PL (1997). Effect of coconut palm wine (Toddy) on carbohydrate metabolism in pregnant rats and foetuses. Plant Foods and Human Nutrition, 50: 71-79.
DOI: 10.1007/bf02436045
[137] Larkin MA, Blackshields G, Brown NP, Chenna R, Mc Gettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ and Higgins DG (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23: 2947-2948.
[138] Lasekan O, Buettner A and Christlbauer M (2007). Investigation of important odorants of palm wine (Elaeis guineensis). Food Chemistry, 105: 15-23.
[139] Laugesen S and Roepstor VP (2003). Combination of two matrices results in improved performance of MALDI MS for peptide mass mapping and protein analysis. Journal of American Society of Mass Spectrom, 14: 992–1002.
[140] Lbu Jo, Dick TT and Ogan SF (1986). Effect of Nigerian bottled palm wine on gastric acid secretion. Scandinavian journal of gastroenterology. Supplement, 124: 89-93.
[141] Lebeer S, Vanderleyden J and De Keersmaecker SCJ (2008). Genes and molecules of Lactobacilli supporting probiotic action. Microbial Molecular biology, 72: 728-764.
[142] Lengauer T and Rarey M (1996). Computational methods for biomolecular docking. Current Opinion Structural Biolology, 6 (3): 402–406.
[143] Leonhatsbergrer S, Huber A, Lottapeich F and Bock A (2001). The hydH/G Genes from Escherichia coli code for zinc lead responsive two-component regulatory system. Journal of Molecular Biology, 307(1):93-105.
[144] Lewis TS, Hunt JB, Aveline LD, Jonscher KR, Louie DF and Yeh JM (2000). Identification of novel MAP kinase pathway signalling targets by functional proteomics and mass spectrometry. Molecular Cell, 6: 1343– 1354.
[145] Li J, Zhang Z, Rosenzweig J, Wang YY and Chan DW (2002). Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clinical Chemistry, 48 (8): 1296-1304.
[146] Li M, Rosenshine I, Tung SL, Wang XH, Friedberg D, Hew CL and Leung KY (2004). Comparative Proteomic analysis of extracellular proteins of Enterohemorrhagic and Enteropathogenic Escherichia coli Strains and their ihf and ler Mutants. Applied and Environmental Microbiology, 70: 5274–5282.
[147] Li S, Peari DK and Doss H (2000). Phylogenetic tree construction using meme. Journal of the American statistical Association. 95: 493-503.
[148] Liddell HG, Robert S; Stuart JH (1968). A Greek-English lexicon (9 ed). Oxford: Clarendon Press. p.1961.
[149] Lilly DM and Stillwell RH (1965). Probiotics: growth-promoting factors produced by microorganisms. Science, 147: 747-748.
[150] Linder CR and Warnow T (2005). An overview of phylogeny reconstruction. In the Handbook of Computational Molecular Biology, Chapman and Hall/CRC Computer & Information Science.
[151] Lindsay RM, Smith W, Lee WK, Dominiczak MH and Baird JD (1997). The effect of delta-gluconolactone, an oxidised analogue of glucose, on the non-enzymatic glycation of human and rat haemoglobin. Clinica Chimica Acta, 263: 239-247.
[152] Ljungh, Asa, Wadstrom, Torkel and Eds (2009). Lactobacillus Molecular Biology: from Genomics to Probiotics. Caister Academic Press. p-206. ISBN: 978-1-904455-41-7
[153] Lorca GL and Font de Valdez G (2001). Acid tolerance mediated by membrane ATPases in Lactobacillus acidophilus. Biotechnology Letters, 23: 777–780.
[154] Lovell SC, Davis IW, Arendall III WB, De Bakker PIW, Word JM, Prisant MG, Richardson JS and Richardson DC (2002). Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins: Structure, Function and Genetics, 50: 437-450.
DOI: 10.1002/prot.10286
[155] Ly M, Wang Z, Laremore TN, Zhang F, Zhong W, Pu D, Zagorevski DV, Dordick JS and Linhardt RJ (2011). Analysis of E. coli K5 capsular polysaccharide heparosan. Analytical and Bio-analytical Chemistry, 399: 737–745.
[156] Mac Kerell AD, Bashford D, Bellott RL, Dunbrack RL and Evanseck JD (1998). All-Atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry, 102: 3586−3616.
[157] Mach T (2006). Clinical usefulness of probiotics in inflammatory bowel diseases. Journal of Physiology and Pharmacology, 57 (9): 23-33.
[158] Magalon A and Bock A (2000). Dissection of the maturation reactions of the [NiFe] hydrogenase 3 from Escherichia coli taking place after nickel incorporation. FEBS Letters, 473 (2): 254-258.
[159] Makarova K, Slesarey A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A and Pavlov N (2006). Comparative genomics of the lactic acid bacteria. Proceedings of the National Academy of Sciences, 103 (42): 15611-15616.
[160] Maloney and Chris (2011). pH calculation of a very small concentration of a strong acid.
[161] Manna S, Bhattacharrya D, Mandal TK and Das S (2005). Repeated dose toxicity of deltamethrin in rats. India Journal of Pharmacology, 37: 160-164.
[162] Mark O, Collinsa 1, James C. Wrighta C, Matthew J, Raynerb JC and Choudharya JS (2014). Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation. Journal of Proteomics, 103:1-14.
[163] Marti-Renom MA, Ilyin VA and Sali A (2001). DBALI: a database of protein structure alignments. Bioinformatics, 17: 746−747.
[164] Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F and Sali A (2000). Comparative protein structure modelling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29: 291-325.
[165] Mary P, Sautour M, Chihib NE, Tierny Y, and Hornez JP (2003). Tolerance and starvation induced cross-protection against different stresses in Aeromonas hydrophila. International journal of food microbiology, 87 (1-2): 121-30.
[166] Mascher T, Helmann JD and Unden G (2006). Stimulus perception in bacterial signal-transducing histidine kinases. Microbiology and Molecular Biology Review, 70 (4): 910–938.
[167] Mateos JA (2004). Yoghurt: a probiotic Mediterranean food. Journal Archivos Latinoamericanos de Nutrition, 54 (2): 76-78.
[168] Matto J, Malinen E, Suihko ML, Alander M, Palva A, Saarela M. (2004). Genetic heterogeneity and functional properties of intestinal Bifidobacterium. Journal of Applied Microbiology 97: 459–470.
[169] Mayo B, Van S and Douwe EDS (2010). Bifidobacteria: Genomics and Molecular Aspects. Caister Academic Press, ISBN 978-1-904455-68-4.
[170] Meijerink M, Mercenier A and Wells JM (2013). Challenges in translational research on probiotic Lactobacilli: from in vitro assays to clinical trials. Beneficial Microbes, 4 (1): 83–100.
DOI: 10.3920/bm2012.0035
[171] Melo F, Sanchez R and Sali A (2002). Statistical potentials for fold assessment. Protein Sciences, 11: 430-448.
DOI: 10.1002/pro.110430
[172] Metchnikoff E (1907). The prolongation of life. London, UK: William Heinemann.
[173] Mikkelsen S and Cortón E (2004). Bioanalytical Chemistry. John Wiley & Sons, Inc. p.224.
[174] Mimura T, Rizzello F, Helwig U, Poggioli G, Schreiber S, Talbot IC, Nicholls RJ, Gionchetti P, Campieri M and Kamm MA (2004). Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis. Gut, 53: 108-114.
DOI: 10.1136/gut.53.1.108
[175] Mironova R, Niwa T, Dimitrova R, Bosanova M and Ivanov I (2003). Glycation and post-translational processing of human interferon-gamma expressed in Escherichia coli. Journal of Biological Chemistry, 278: 51068-51074.
[176] Moco S, Bino RJ, Vorst O, Verhoeven HA, De Groot J, Van Beek TA, VerVoort J and Devos CHR (2006). A liquid chromatography-mass spectrometry based metabolome database for tomato. Plant Physiology, 141: 1205-1218.
[177] Mohammed OA and Ameen SBB (2007). Testicular histopathological alternations in rats treated with sumithion NP 25/2.5 EC, insecticide. Journal of Biological Sciences, 7 (3): 520-525.
[178] Montelione GT, Zheng d, Huang Y and Szyperski T (2000). Protein NMR spectroscopy in structural genomics. Nature of Structural Biology, 7: 982-984.
[179] Morah FNI (1995). Effect of metasulphite on alcohol production in palm wine. Food Chemistry, 53: 153-156.
[180] Mottet C and Michetti P (2005). Probiotics: wanted dead or alive. Digestive and Liver Diseases, 37: 3–6.
[181] Muth T (2010). jTraqX: a Free, Platform independent tool for isobaric tag Quantitation at the protein level. Proteomics, 10 (6): 1223-1225.
[182] Nakamura S, Watanabe A, Chongpraditnum P, Suzui N, Hayashi H, Hattori H and Chino M (2004). Analysis of phloem exudates collected from fruit-bearing stems of coconut palm: Palm trees as a source of molecules circulating in sieve tubes. Soil Science and Plant Nutrition, 50: 739–745.
[183] Naven T and Westermeier R (2002). Proteomics in Practice: A Laboratory Manual of Proteome Analysis. Weinheim: Wiley-VCH. ISBN 3-527-30354-5.
DOI: 10.1086/377836
[184] Nelson RJ (2005). Introduction to Behaviral Endocrinology.Sinauer Associates: Massachusetts.P-115.
[185] Nelson SW, Binkowski DJ, Honzatko RB, and Fromm HJ (2005). Mechanism of Action of Escherichia coli Phosphoribosylaminoimidazole-succinocarboxamide Synthetase. Biochemistry, 44: 766-774.
DOI: 10.1021/bi048191w
[186] Nikolov M, Schmidt C and Urlaub H (2012). Quantitative mass spectrometry-based proteomics: An Overview. Methods in Molecular Biology, 893: 85-100.
[187] Nordin S, Broman DA, Olofsson JK and Wulff M (2004). A longitudinal descriptive study of self-reported abnormal smell and taste perception. Chemical Senses, 29 (5): 391-402.
[188] Nwokeke NV (2001). Palm wine preservation using Traditional plants that have preservation bases. B.Sc. Thesis. Imo State University, Owerri, Nigeria.
[189] O'Hara AM and Shanahan F (2006). The gut flora as a forgotten organ. European Molecular Biology journal, 7: 688-693.
[190] Ogbulie TE, Ogbulie TN and Njokuho (2007). Comparative study on the shelf life stability of palm wine from Elaeis guineesis and Raphia hookeri obtained from Okigure. Nigeria, African Journal of Biotechnology, 6 (7): 914-922.
[191] OHara AM and Shanahan F (2007). Mechanisms of action of probiotics in intestinal disease. Scientific World Journal, 7: 31-46.
[192] Ojimelukwe PC (2000). Effect of preservation with Sacglottis gabonensis on the biochemistry and sensory evaluation of fermenting palm wine. Journal of Food biochemistry, 25: 411-424.
[193] Okafor N (1972). Microbiology and Bio-chemistry of oil palm wine. Advanced Applied Microbilogy, 24: 237-255.
[194] Okafor N (1977). The microbiological method for palm wine preservation. Journal of Applied Bacteriology, 43: 159-161.
[195] Okafor N (1978). Microbiology and Biochemistry of oil palm wine. Advanced applied Microbiology, 24: 237-255.
[196] Okagbue RN (1998). A note on the leavening activity of yeasts associate with palm wine. Journal of Applied Bacteriology, 64: 235-240.
[197] Olsen BJ and Markwell J (2007). Assays for the determination of protein concentration. Current Protocols in Protein Science, 3: 14–17.
[198] OShea EF, Cotter PD, Stanton C, Ross RP and Hill C (2012). Production of bioactive substances by intestinal bacteria as a basis for explaining probiotic mechanisms: Bacteriocins and conjugated linoleic acid. International Journal of Food Microbialogy, 152 (3): 189-205.
[199] Oyedeji Ko, Bolarinwa AF and M.A and Hamzat MA (2012). Effect of palm wine on reproductive functions in male albino rats. Research Journal of Biological Sciences, 7 (9-12): 340-344.
[200] Pandey A, Fernandez MM, Stehen H, Blagoev B, Nielsen MM and Roche S (2000). Identification of a novel immuno receptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signalling pathways. Journal of Biology and Chemistry, 275: 38633-38639.
[201] Pappin DJ, Hojrup P and Bleasby AJ (1993). Rapid identification of proteins by peptide mass finger printing. Current Biology, 3 (6): 327-332.
[202] Parracho H, McCartney AL and Gibson GR (2007). Probiotics and prebiotics in infant nutrition. Proceedings of the Nutrition Society, 66: 405-411.
[203] Parvez S, Malik KA, Kang KA and Kim HY (2006). Probiotics and their fermented food products are beneficial for health-review. Journal of Applied Microbiology, 100: 1171– 1185.
[204] Pataky Z, Bobbiono-Harsch E, Hadengue A, Carpentier A and Golay A (2009). Gut microbiota responsible for our body weight. Journal of Revue Médicale Suisse, 5 (196): 662-664.
[205] Peng Jian and Jinbo Xu (2011). RaptorX: Exploiting structure information for protein alignment by statistical inference. Proteins, 79: 161-171.
DOI: 10.1002/prot.23175
[206] Purves, William Kirkwood S, David O and Gordon H (2004). Life-the science of biology. Macmillan Publishers, 7 Th Edition.
[207] Qin Y, Song W, Xiao S, Yin G, Zhu Y, Yan Y and Hu Y (2014). Stress-related genes distinctly expressed in unfertilized wheat ovaries under both normal and water deficit conditions whereas differed in fertilized ovaries. Journal of Proteomics, 102: 11-27.
[208] Raja A, Gajalakshmi P, Raja MMM and Imran MM (2009). Effect of Lactobacillus lactis cremoris isolated from kefir against food spoilage bacteria. American Journal of Food Technology, 4: 201-209.
[209] Ramakrishnan S (1973). Effect of intake of excess alcohol on metabolism of glucose in rat. Indian Journal of Biochemistry and Biophysics, 10: 276-278.
[210] Ramakrishnan S (1983). Deleterious effect of alcoholism and aldehydism on metabolism and tissue function. Biochemical Reviews, 53: 1-7.
[211] Ramakrishnan S, Prasanna CV and Balasubramanian A (1976). Effect of alcohol intake on rat hepatic enzyme and thyroid function. Indian Journal of Biochemistry and Biophysics, 13: 49-51.
[212] Ramirez BE, Voloshin ON, Camerini-Otero RD and Bax A (2000). Solution structure of DinI provides insight into its mode of RecA inactivation. Protein Science, 9 (11): 2161–2169.
DOI: 10.1110/ps.9.11.2161
[213] Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V and Ravel JJ (2008). The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates. Bacteriology, 190:6881-6893.
DOI: 10.1128/jb.00619-08
[214] Ratsch Christian (1998). The Encyclopaedia of Psychoactive plants: Ethno pharmacology and its applications. Rochester: Park Street Press.
[215] Rauch M and Lynch S (2011). The potential for probiotic manipulation of the gastrointestinal microbiome. Current Opinion Biotechnology, 23 (1): 192-201.
[216] Ray WK and Larson TJ (2004). Application of Agar repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12. Molecular Microbiology, 51 (3): 813-826.
[217] Rehm J,Giesbrecht N, Patra J and Roerecke M (2002). Estimating chronic Disease deaths and hospitalization due to alcohol use in Canada: Implication for Policy and Preservation strategies. Preventing Chronic Disease: Public Health research, practice and policy, 3: 1-19.
[218] Rembacken BJ, Snelling AM, Hawkey PM, Chalmers DM and Axon ATR (1999). Non-pathogenic Eschericia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet, 354: 635-639.
[219] Resta-Lenert S and Barrett KE (2003). Live probiotics protect intestinal epithelial cells from the effects of infection with enteroinvasive Escherichia coli (EIEC). Gut, 52: 988–997.
DOI: 10.1136/gut.52.7.988
[220] Retrived (2006). Serratia marcescens section implant infection and orbital cellulitis. Eye Rounda.org.-04-06.
[221] Richard Coico, Geoffrey, Sunshine and Eli Benjamini (2003). Immunology: a short course. New York: Wiley- Liss. ISBN- 0-471-22689-0.
[222] Riffle Robert L and craft Paul (2003). An encyclopedia of cultivated palms Portland. Timber press, 405-406.
[223] Roger S and James MW (1995). RasMol: Bio-molecular graphics for all. Trend in Biochemical Sciences, 20 (9): 374-382.
[224] Roland JS, Frank HJE, Michiel K and Bas T (2004). Genome data mining of lactic acid bacteria: the impact of bioinformatics. Current Opinion in Biotechnology, 15 (2): 105-115.
[225] Rossell S (2006). Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces Cerevisiae. Proceedings of the National Academy of Sciences, 103: 2166-2171.
[226] Rundel, Philip W (2002). The Chilean Wine palm in the Mildred E. Mathias Botanical Garden Newsletter, 5 (4).
[227] Sali A and Overington JP (1994). Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sciences, 3: 1582−1596.
[228] Sanchez B, Champomier-Verges MC, Stuer-Lauridsen B, Ruas-Madiedo P and Anglade P (2007). Adaptation and response of Bifidobacterium animalis subsp. lactis to bile: A proteomic and physiological approach. Applied Environmental Microbiology, 73 (21): 6757–6767.
DOI: 10.1128/aem.00637-07
[229] Sanchez R and Sali A (1998). Large-scale protein structure modeling of the Saccharomyces Cerevisiae genome. Proceedings of the National Academy of Sciences, 95 (23): 13597-13602.
[230] Sanders ME (2008). Probiotics: definition, source, selection and uses. Clinical Infections and Diseases, 46 (2): S58–S61.
DOI: 10.1086/523341
[231] Sanders ME, Morelli L and Tompkins TA (2003). Spore Formers as Human Probiotics: Bacillus, Sporolactobacillus and Brevibacillus. Comprehensive Review in Food Science and Food Safety, 2: 101-110.
[232] Sangha JS, Chen YH, Kaur Jatinder, Khan Wajahatullah, Abduljaleel Zainularifeen, Alanazi Mohammaed S, Mills Aaron, Adalla candida B and Bennett John (2013). Proteome analysis of rice (Oryza sativa L.) mutants reveals differentially induced proteins during brown Planthopper (Nilaparvata lugens) infestation. International Journal of Molecular Sciences, 14 (2): 3921-3945.
DOI: 10.3390/ijms14023921
[233] Santos DKV, Diniz CG, Veloso Lde C, de Andrade HM, Giusta Mda S, Pires Sda F, Santos AV, Apolônio AC, de Carvalho MA and Farias Lde M (2010). Proteomic analysis of E. coli with experimentally induced resistance topiperacillin/ tazobactam. Research in Microbiology, 161: 268-275.
[234] Sawers G (1994). The hydrogenases and formate dehydrogenases of Escherichia coli. Antonie Van Leeuwenhoek, 66 (1-3):57-88.
DOI: 10.1007/bf00871633
[235] Schell Mark A, Karmirantzou M, Snel B, Vilanova D, Bernard B, Pessi G, Zwahlen MC, Desiere and Frank (2002). The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proceedings of the National Acadamy of Sciences, 99 (22): 14422–14427.
[236] Schuerenberg M, Luebbert C, EickhoVH, Kalkum M, Lehrach H and NordhoVE (2003). Pre-structured MALDI-MS sample supports. Analytical Chemistry, 72: 3436–3442.
DOI: 10.1021/ac000092a
[237] Schultz M (2008). Clinical use of E.coli Nissle 1917 in inflammatory bowel disease. Inflammatory Bowel Disease, 14 (7): 127-131.
DOI: 10.1002/ibd.20377
[238] Schwede T, Kopp J, Guex N and Peitsch MC (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31(13): 3381–3385.
DOI: 10.1093/nar/gkg520
[239] Sekhon, B and Jairath S (2010). Prebiotics, probiotics and synbiotics: an overview. Journal of Pharmaceutical Education & Research, 1 (2): 13-36.
[240] Sekirov I, Russell SL, Antunes LC and Finlay BB (2010). Gut microbiota in health and disease. Physiological Reviews, 90: 859-904.
[241] Shah NP (2000). Probiotic bacteria: selective enumeration and survival in dairy foods. Journal of Dairy Science, 83: 894-907.
[242] Shalon D, Smith SJ and Brown PO (1996). A DNA microarray system for analysing complex DNA samples using two-colour fluorescent probe hybridization. Genome Research. 6: 639-645.
DOI: 10.1101/gr.6.7.639
[243] Shanahan F (2011). The colonic microflora probiotic therapy in health and disease. Current Opinion Gastroenterology, 27 (1): 61-65.
[244] Shevchenko A, Jensen ON, Podtelejnikov AV, Saglioco F, Wilm Vorm O, Mortensen P, Shevchenko A, Boucherie H and Mann M (1996). Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proceedings of the National Academy of Sciences, 93 (25): 14440-14445.
[245] Shi J, Blundell L and Mizuguchi K (2001). FUGUE: Sequence-structure homology recognition using environment- specific substitution tables and structure-dependent gap penalties. Journal of Molecular Biology, 310: 243-257.
[246] Smith T (2000). A new era. Nature of Structural Biology and Structural genomics, 7: 927-933.
[247] Sonnenborn U and Schulze J (2009). The non-pathogenic Escherichia coli strain Nissle 1917 features of a versatile probiotic. Microbial Ecology and Health Diseases. 21:122–158.
[248] Sparkman O David (2000). Mass spectrometry desk reference. Pittsburgh: global View Publications, ISBN 0-9660813-2-3.
[249] Stephen A, Gravina, Gregory L, Yep and Mehmood Khan (2013). Invited review: Human Biology of Taste. Annals of Saudi Medicine, 33 (3): 217-222.
[250] Stitt AW (2005). Maillard reaction in eye disease. Annals of the New York Academy of Sciences, 1043: 582-597.
[251] Stojancevic M, Bojic G, Salami HA and Mikov M (2013). The influence of intestinal tract and probiotics on the fate of orally administered drugs. Current Issues on Molecular Biology, 16 (2): 55–68.
[252] Storz G and Zheng M (2000). Oxidative stress. Current Opinion in Microbiology, 2: 188-194.
[253] Sun J, Gunzer F, Westendorf AM, Buer J, Scharfe M, Jarek M, Gössling F, Blöcker H and Zeng AP (2005). Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. Journal of Biotechnology. 117: 147–161.
[254] Suzuki T, Miwa K, Ishikawa K, Yamada H, Aiba H, and Mizuno T (2001). The Arabidopsis sensor His-kinase, AHK4, can respond to cytokinins. Plant and Cell Physiology, 42: 107–113.
DOI: 10.1093/pcp/pce037
[255] Swings J and De Ley J (1977). The biology of Zymomonas. Bacteriology reviews, 41: 1-46.
[256] Tang N, Tornatore P and Weinberger SR (2004). Current developments in SELDI affinity technology. Mass spectrometry reviews, 23 (1): 34-44.
DOI: 10.1002/mas.10066
[257] Tannock GW (1999). Analysis of the intestinal microflora: A renaissance. Antonie van Leenwenhoek, 76: 265-278.
[258] Todd RK and Martin JK (1999). Selection and design of probiotics. International Journal of Food Microbiology, 50 (1–2): 45–57.
[259] Tomar SK, Knauer SH, Nandymazumdar M, Rosch P and Artsimovitch I (2013). Interdomain contacts control folding of transcription factor RfaH. Nucleic Acids Resarch, 41 (22): 10077-10085.
DOI: 10.1093/nar/gkt779
[260] Twyman RM (2004). Principles of Proteomics (Advanced text Series). Oxford,UK: BIOS Scientific publishers. ISBN 1-85996-273-4.
[261] Uzochukwu SVA, Balogh E, Tucknot OG, Lewis MJ and Ngoddy PO (1994). Volatiles Constituents of Palm wine and palm sap. Journal of the Science of Food and Agriculture, 94: 405-411.
[262] VanBogelen RA (2003). Probing the molecular physiology of the microbial organism, Escherichia coli using proteomics. Advances in Biochemical Engineering / Biotechnology, 83: 27–55.
[263] Varughese KI (2002). Molecular recognition of bacterial phosphorelay proteins. Current Opinion in Microbiology, 5 (2): 142–148.
[264] Vattanaviboon P, Panmanee W, and Mongkolsuk S (2003). Induction of peroxide and super-oxide protective enzymes and physiological cross-protection against peroxide killing by a super-oxide generator in Vibrio harveyi. Federation of European Microbiological Societies, microbiology letters, 221 (1): 89-95.
[265] Vaughan EE, Heilig HG and Ben-Amor K (2005). Diversity, vitality and activities of intestinal lactic acid bacteria and Bifidobacterium assessed by molecular approaches. FEMS Microbiology Review, 29: 477–490.
[266] Velculescu VE, Zhang L, Vogelstein B and Kinzler KW (1995). Serial analysis of gene expression. Science, 270: 484-487.
[267] Verma PK, Sharma A, Annu M, Prachi S, Gupta RS, Joshi SC and Dixit VP (2002). Effect of Sarcostemma acidum stem extract on spermatogenesis in male albino rats. Journal of Andrology, 4 (1): 43-47.
[268] Von Roepenack-Lahaye E, Degenkolb T, Zerjeski M, Roth U, Wessjohann L, Schmidt J, Scheel D and Clements S (2004). Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ioniation quadrupole time-of-flight mass spectrometry. Plant physiology, 134: 548-559.
[269] Walz C, Giavalisco P, Schad M, Juenger M, Klose J and Kehr J (2004). Proteomics of cucurbit phloem exudate reveals a network of defence proteins. Phytochemistry, 65: 1795–1804.
[270] Wang W, Sun J, Nimtz M, Deckwer WD and Zeng AP (2003). Protein identification from two-dimentional gel electrophoresis analysis of Klebshiella Pneumoniae by combined use of mass spectrometry data and raw genome sequences. Proteome science, 1 (1): 6-15.
[271] Wasinger VC, Cordwell SJ, Cerpa-Poljak A Yan JX, Gooley AA, Wilkins MR, Dencan MW, Harris R, Williams KL and Humphery-smith I (1995). Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalism. Electrophoresis, 16: 1090-1094.
[272] Weber H, Polen T, Heuveling J, Wendisch VF, and Hengge R ( 2005). Genome-wide analysis of the general stress response network in Escherichia coli: sigma S-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology, 187:1591–1603.
[273] Weese JS (2002). Microbial evaluation of commercial probiotics. Journal of the American Veterinary Medical Association, 220 (6): 794-797.
[274] Weese JS and Martin H (2011). Assessment of commercial probiotic bacterial contents and label accuracy. Canadian Veterinary Journal, 52 (1): 43-46.
[275] Westendorf AM, Gunzer F, Deppenmeier S, Tapadar D, Hunger JK, Schmidt MA, Buer J and Bruder D (2005). Intestinal immunity of Escherichia coli Nissle 1917: A safe carrier for therapeutic molecules. FEMS Immunology and Medical Microbiology, 43: 373–384.
[276] Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-smith I, Hochstrasser DF and Williams KL (1995). Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnology and Genetic Engineering Reviews, 13: 19-50.
[277] Williamson AR (2000). Creating a structural genomics consortium. Nature Structural and Molecular Biology, 7 (S1 (11s)): 953.
[278] Wilson ML (1996). General principles of specimen collection and transport. Clinical Infectious Diseases, 22 (5): 766-777.
[279] Witek Janusek L (1986). Maternal alcohol ingestion: Effect on maternal and neonatal glucose balance. American Journal of Physiology, 25 (2): 178-184.
[280] Wolf KM (1997). Occurrence, distribution and associations of O and H serogroups, colonization factor antigens and toxins of entero toxigenic Escherichia coli. Clinical Microbiology Review, 10: 569-584.
DOI: 10.1128/cmr.10.4.569
[281] Wu KJ, Shaler TA and Becker CH (1994). Time-of-flight mass spectrometry of underivatized single-stranded DNA oligomers by matrix-assisted laser desorption. Analytical Chemistry, 66 (10): 1637–1645.
DOI: 10.1021/ac00082a007
[282] Wu R, Sun Z, Wu J, Meng H and Zhang H (2010). Effect of bile salts stress on protein synthesis of Lactobacillus casei Zhang revealed by 2-dimensional gel electrophoresis. Journal of Dairy Sciences, 93: 3858–3868.
[283] Wu R, Sun Z, Wu J, Meng H and Zhang H (2010). Effect of bile salts stress on protein synthesis of Lactobacillus casei Zhang revealed by 2-dimensional gel electrophoresis. Journal of Dairy Sciences, 93: 3858–3868.
[284] Yamada H, Suzuki T, Terada K, Takei K, Ishikawa K, Miwa K, Yamashino T, and Mizuno T (2001). The Arabidopsis AHK4 histidine kinase is a cytokinin-binding receptor that transduces cytokinin signals across the membrane. Plant and Cell Physiology, 42: 1017–1023.
DOI: 10.1093/pcp/pce127
[285] Yan Z, Caldwell GW and McDoell PA (1999). Identification of a gluconic acid derivative attached to the N-terminus of histidine-tagged proteins expressed in bacteria. Biochemical and Biophysical Research Communications, 262: 793-800.
[286] Yi EC (2005). Increased quantitative proteome coverage with (13) C/ (12) C-based, acid- cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics, 5 (2): 380-387.
[287] Yildirin Z and Johnson MG (1998). Characterization and antimicrobial spectrum of bifidocin B, a bacteriocin produced by Bifidobacterium bifidum NCFB 1454. Journal of Food Protocols, 61: 47-51.
[288] Yohannes E, Barnhart DM and Slonczewski JL (2004). pH-Dependent Catabolic Protein Expression during Anaerobic Growth of Escherichia coli K-12. Journal of Bacteriology, 186: 192–199.
[289] Yokoyama S, Hirota H and Kigawa T (2000). Structural genomics projects in Japan. Nature of Structural Biology, 7: 943–945.
[290] Yoshimasu M, Aihara H, Ito Y, Rajesh S, Ishibe S, Mikawa T, Yokoyama S and Shibata T (2003). An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes. Nucleic Acids Research, 31 (6): 1735–1743.
DOI: 10.1093/nar/gkg256
[291] Yuan Liu, Rajendra Prasad, William A. Beard, Padmini S. Kedar, Esther W. Hou, David D. Shock, and Samuel HW (2007). Coordination of steps in single-nucleotide Base excision repair mediated by Apurinic/ Apyrimidinic endonuclease 1 and DNA polymerase β. Journal of Biological Chemistry, 282 (18): 13532–13541.
[292] Zieske LR (2006). A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. Journal of Experimental Botany, 57 (7): 1501-1508.
DOI: 10.1093/jxb/erj168
[293] Zoetendal EG, Vaughan EE and De Vos WM (2006). A microbial world within us. Molecular Microbiology, 59: 1639-1650.
[294] Zuowei Wu, Orhan Sahin, Fei Wang and Qijing Zhang (2014). Proteomic identification of immuno dominant membrane-related antigens in Campylobacter jejuni associated with sheep abortion. Journal of Proteomics, 99: 111-122.