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Physicomechanical Properties and Utilization of Hydrogels Prepared by Physical and Physicochemical Crosslinking Read chapter Read first chapter

2018 | OriginalPaper | Chapter

7. Gel-Based Approaches in Genomic and Proteomic Sciences

Authors : Rafael A. Baraúna, Diego A. Graças, Joriane T. C. Alves, Ana Lídia Q. Cavalcante, Artur Silva

Published in: Polymer Gels

Publisher: Springer Singapore

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Abstract

In the last few years, many advances have been made in genomic and proteomic sciences using gel-based technologies. Some of these technologies still have valuable applications for genomic and proteomic studies. Two-dimensional gel electrophoresis (2DE), for example, is a protein fractionation technique used to analyze the differential expression of genes and to characterize post-translational modifications. On the other hand, pulsed-field gel electrophoresis (PFGE) is used to determine the size of prokaryotic genomes, for the detection of plasmids, and in epidemiological studies of pathogenic microorganisms. In this context, this chapter aims to describe the functionality of gel-based techniques, such as 2DE and PFGE, as well as their pros and cons, and advances that have been made and their primary applications in the fields of genomics and proteomics of microorganisms.

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Literature
Aires J, Anglade P, Baraige F, Zagorec M, Champomier-Vergès M, Butel M (2010) Proteomic comparison of the cytosolic proteins of three Bifidobacterium longum human isolates and B. longum NCC2705. BMC Microbiol 10:29CrossRefPubMedPubMedCentral
Almácegui RJ, Navarro CA, Paradela A, Albar JP, von Bernath D, Jerez CA (2014) New copper resistance determinants in the extremophile Acidithiobacillus ferrooxidans: a quantitative proteomic analysis. J Proteome Res 13(2):946–960CrossRef
Bart-Delabesse E, Boiron P, Carlotti A, Dupont B (1993) Candida albicans genotyping in studies with patients with AIDS developing resistance to fluconazole. J Clin Microbiol 31(11):2933–2937PubMedPubMedCentral
Bengtsson S, Naseer U, Sundsfjord A, Kahlmeter G, Sundqvist M (2012) Sequence types and plasmid carriage of uropathogenic Escherichia coli devoid of phenotypically detectable resistance. J Antimicrob Chemother 67(1):69–73CrossRefPubMed
Caetano-Allóles G (1993) Amplyfing DNA with arbitrary oligonucleotide primers. Genome Res 3:85–94CrossRef
Carneiro AR, Ramos RTJ, Dall’Agnol H, Pinto AC, Soares SC, Santos AR, Guimarães LC, Almeida SS, Baraúna RA, Graças DA et al (2012) Genome sequence of Exiguobacterium antarcticum B7, isolated from a biofilm in Ginger Lake, King George Island, Antarctica. J Bacteriol 194(23):6689–6690
Dall’Agnol HPMB, Baraúna RA, de Sá PHCG, Ramos RTJ, Nóbrega F, Nunes CIP, Graças DA, Carneiro AR, Santos DM, Pimenta AMC et al. (2014) Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation. BMC Genomics 15:986
Davis MA, Hancock DD, Besser TE, Call DR (2003) Evaluation of pulsed-field gel electrophoresis as a tool for determining the degree of genetic relatedness between strains of Escherichia coli O157:H7. J Clin Microbiol 41(5):1843–1849CrossRefPubMedPubMedCentral
Dekker L, Arsène-Ploetze F, Santini JM (2016) Comparative proteomics of Acidithiobacillus ferrooxidans grown in the presence and absence of uranium. Res Microbiol 167(3):234–239CrossRefPubMed
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenza Rd. Science 269(5223):496–512CrossRefPubMed
Folster JP, Pecic G, Rickert R, Taylor J, Zhao S, Fedorka-Cray PJ, Whichard J, Mcdermott P (2012) Characterization of multi-resistant Salmonella enterica serovar Heidelberg from a ground Turkey-associated outbreak in the United States in 2011. Antimicrob Agents Chemother 56(6):3465–3466CrossRefPubMedPubMedCentral
García-Descalzo L, García-Lopez E, Alcázar A, Baquero F, Cid D (2014) Proteomic analysis of the adaptation to warming in the Antarctic bacteria Shewanella frigidimarina. Biochemica et Biophysica Acta (BBA)—Proteins Proteomics 1844(12):2229–2240
Ge Y, Wang DZ, Chiu JF, Cristobal S, Sheehan D, Silvestre F, Peng X, Li H et al (2013) Environmental OMICS: current status and future directions. J Integr OMICS 3(2):75–87CrossRef
Gulez G, Altintaş A, Fazli M, Dechesne A, Workman CT, Tolker-Nielsen T, Smets BF (2014) Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate of all EPS synthesis under controlled matric potentials. MicrobiologyOpen 3(4):457–469CrossRefPubMedPubMedCentral
Heintz N, Gong S (2001) Working with bacterial artificial chromosomes and other high-capacity vectors. In: Green MR, Sambrook J (eds) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York, p 301
Hoogland C, Mostaguir K, Appel RD, Lisacek F (2008) The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server. J Proteomics 71(2):245–248CrossRefPubMed
Ichiyama S, Ohta M, Shimokata K, Kato N, Takeuchi J (1991) Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus. J Clin Microbiol 29(12):2690–2695PubMedPubMedCentral
Kuska B (1998) Beer, Bethesda, and biology: how “genomics” came into being. J Natl Cancer Inst 90(2):93CrossRefPubMed
Mangold S, Jonna V, Dopson M (2013) Response of Acidithiobacillus caldus toward suboptimal pH conditions. Extremophiles 17(4):689–696CrossRefPubMed
Marouga R, David S, Hawkins E (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382:669–678CrossRefPubMed
Morimoto H, Kuwano M, Kasahara Y (2013) Gene expression profiling of Pseudomonas putida F1 after exposure to aromatic hydrocarbon in soil by using proteome analysis. Arch Microbiol 195(12):805–813CrossRefPubMed
Nair S, Poh CL, Lim YS, Tay L, Goh KT (1994) Genome fingerprinting of Salmonella typhi by pulsed-field gel electrophoresis for subtyping common phage types. Epidemiol Infect 113(3):391–402CrossRefPubMedPubMedCentral
Najdenski H, Iteman I, Carniel E (1994) Efficient subtyping of pathogenic Yersinia enterocolitica strains by pulsed-field gel electrophoresis. J Clin Microbiol 32:2913–2920PubMedPubMedCentral
O’Farrell (1975) High resolution two-dimensional electrophoresis of protein. J Biol Chem 250(10):4007–4021
Ouyang J, Liu Q, Li B, Ao J, Chen X (2013) Proteomic analysis of differential protein expression in Acidithiobacillus ferroxidans grown on ferrous iron or elemental sulfur. Ind J Microbiol 53(1):56–62CrossRef
Petrak J, Ivanek R, Toman O, Cmejla R, Cmejlova J, Vyoral D, Zivny J, Vulpe CD (2008) Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins. Proteomics 8(9):1744–1749CrossRefPubMed
Poirier I, Hammann P, Kuhn L, Bertrand M (2013) Strategies developed by the marine bacterium Pseudomonas fluorescens BA3SM1 to resist metals: a proteome analysis. Aquat Toxicol 128:215–232CrossRefPubMed
Pooideh M, Jabbarzadeh I, Ranjbar R, Saifi M (2015) Molecular epidemiology of Mycobacterium tuberculosis isolates in 100 patients with tuberculosis using pulsed field gel electrophoresis. Jundishapur J Microbiol 8(7):e18274PubMedPubMedCentral
Ray P, Girard V, Gault M, Job C, Bonneu M, Mandrand-Berthelot MA, Singh SS, Job D, Rodrigue A (2013) Pseudomonas putida KT2440 response to nickel or cobalt induced stress by quantitative proteomics. Metallomics 5:68–79CrossRefPubMed
Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37(1):67–75CrossRefPubMed
Soll DR (2000) The ins and outs of DNA fingerprinting the infectious fungi. Clin Microbiol Rev 13:322–370CrossRef
Sommer MO, Church GM, Dantas G (2010) A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol Syst Biol 6:360CrossRefPubMedPubMedCentral
Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329(5991):533–538CrossRefPubMedPubMedCentral
Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B (1995) Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 33(9):2233–2239PubMedPubMedCentral
Vera M, Krok B, Bellenberg S, Sand W, Poetsch A (2013) Shotgun proteomics study of early biofilm formation process of Acidithiobacillus ferrooxidans ATCC 23270 on pyrite. Proteomics 13(7):1133–1144CrossRefPubMed
Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL (1995) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
Ying BW, Yama K, Kitahara K, Yomo T (2016) The Escherichia coli transcriptome linked to growth fitness. Genom Data 7:1–3CrossRefPubMed
Metadata
Title
Gel-Based Approaches in Genomic and Proteomic Sciences
Authors
Rafael A. Baraúna
Diego A. Graças
Joriane T. C. Alves
Ana Lídia Q. Cavalcante
Artur Silva
Copyright Year
2018
Publisher
Springer Singapore
Book
Polymer Gels

Print ISBN: 978-981-10-6082-3

Electronic ISBN: 978-981-10-6083-0

Copyright Year: 2018

DOI
https://doi.org/10.1007/978-981-10-6083-0_7

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