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Volumn 10, Issue 3, 2015, Pages

Protocols and programs for high-throughput growth and aging phenotyping in yeast

Author keywords

[No Author keywords available]

Indexed keywords

AGING; ANALYTICAL PARAMETERS; ARTICLE; BACTERIUM CULTURE; BIOASSAY; CELL AGING; CHRONOLOGICAL LIFE SPAN; COLONY FORMING UNIT; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DOUBLING TIME; FUNGAL BIOMASS; FUNGAL GENETICS; FUNGUS CULTURE; FUNGUS GROWTH; GROWTH CURVE; LAG TIME; MICROBIOLOGICAL PARAMETERS; MICROPLATE READER; NONHUMAN; OPTICAL DENSITY; PHENOTYPE; SACCHAROMYCES CEREVISIAE; YEAST; ASCOMYCETES; BIOMASS; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SCREENING; KINETICS; MYCOLOGY; PROCEDURES; SALINITY; SOFTWARE; STATISTICS AND NUMERICAL DATA; VALIDATION STUDY;

EID: 84926305675     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0119807     Document Type: Article
Times cited : (58)

References (49)
  • 2
    • 34249053477 scopus 로고    scopus 로고
    • Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae
    • PMID: 17194785
    • Hu XH, Wang MH, Tan T, Li JR, Yang H, Leach L, et al. Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae. Genetics. 2007; 175: 1479-1487. PMID: 17194785
    • (2007) Genetics , vol.175 , pp. 1479-1487
    • Hu, X.H.1    Wang, M.H.2    Tan, T.3    Li, J.R.4    Yang, H.5    Leach, L.6
  • 3
    • 84860571592 scopus 로고    scopus 로고
    • Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooledsegregant whole-genome sequence analysis
    • PMID: 22399573
    • Swinnen S, Schaerlaekens K, Pais T, Claesen J, Hubmann G, Yang Y, et al. Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooledsegregant whole-genome sequence analysis. Genome Res. 2012; 22: 975-984. doi: 10.1101/gr. 131698.111 PMID: 22399573
    • (2012) Genome Res , vol.22 , pp. 975-984
    • Swinnen, S.1    Schaerlaekens, K.2    Pais, T.3    Claesen, J.4    Hubmann, G.5    Yang, Y.6
  • 5
    • 0033604566 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast genome by transposon tagging and gene disruption
    • PMID: 10586881
    • Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 1999; 402: 413-418. PMID: 10586881
    • (1999) Nature , vol.402 , pp. 413-418
    • Ross-Macdonald, P.1    Coelho, P.S.2    Roemer, T.3    Agarwal, S.4    Kumar, A.5    Jansen, R.6
  • 6
    • 84867088439 scopus 로고    scopus 로고
    • Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology
    • PMID: 22882838
    • Voordeckers K, De Maeyer D, van der Zande E, Vinces MD, Meert W, Cloots L, et al. Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology. Molecular Microbiol. 2012; 86: 225-239. doi: 10.1111/j.1365-2958.2012.08192.x PMID: 22882838
    • (2012) Molecular Microbiol , vol.86 , pp. 225-239
    • Voordeckers, K.1    De Maeyer, D.2    Van Der Zande, E.3    Vinces, M.D.4    Meert, W.5    Cloots, L.6
  • 8
    • 34248666071 scopus 로고    scopus 로고
    • High-throughput and sensitive assay to measure yeast cell growth: A bench protocol for testing genotoxic agents
    • Toussaint M, Conconi A. High-throughput and sensitive assay to measure yeast cell growth: a bench protocol for testing genotoxic agents. Nature Protoc. 2006; 1: 1922-1928.
    • (2006) Nature Protoc , vol.1 , pp. 1922-1928
    • Toussaint, M.1    Conconi, A.2
  • 9
    • 62649089109 scopus 로고    scopus 로고
    • Population genomics of domestic and wild yeasts
    • PMID: 19212322
    • Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, et al. Population genomics of domestic and wild yeasts. Nature. 2009; 458: 337-341. doi: 10.1038/nature07743 PMID: 19212322
    • (2009) Nature , vol.458 , pp. 337-341
    • Liti, G.1    Carter, D.M.2    Moses, A.M.3    Warringer, J.4    Parts, L.5    James, S.A.6
  • 11
    • 79959847334 scopus 로고    scopus 로고
    • Trait variation in yeast is defined by population history
    • PMID: 21698134
    • Warringer J, Zorgo E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, et al: Trait variation in yeast is defined by population history. PLoS Genet. 2011; 7: e1002111. doi: 10.1371/journal.pgen.1002111 PMID: 21698134
    • (2011) PLoS Genet , vol.7
    • Warringer, J.1    Zorgo, E.2    Cubillos, F.A.3    Zia, A.4    Gjuvsland, A.5    Simpson, J.T.6
  • 12
    • 33646757567 scopus 로고    scopus 로고
    • A high-throughput method to measure the sensitivity of yeast cells to genotoxic agents in liquid cultures
    • PMID: 16713735
    • Toussaint M, Levasseur G, Gervais-Bird J, Wellinger RJ, Elela SA, Conconi A. A high-throughput method to measure the sensitivity of yeast cells to genotoxic agents in liquid cultures. Mutat Res. 2006; 606: 92-105. PMID: 16713735
    • (2006) Mutat Res , vol.606 , pp. 92-105
    • Toussaint, M.1    Levasseur, G.2    Gervais-Bird, J.3    Wellinger, R.J.4    Elela, S.A.5    Conconi, A.6
  • 13
    • 0037438569 scopus 로고    scopus 로고
    • Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae
    • PMID: 12489126
    • Warringer J, Blomberg A. Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast. 2003; 20: 53-67. PMID: 12489126
    • (2003) Yeast , vol.20 , pp. 53-67
    • Warringer, J.1    Blomberg, A.2
  • 14
    • 84884682741 scopus 로고    scopus 로고
    • Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype
    • PMID: 24068968
    • Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, et al. Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype. PLoS Genet. 2013; 9: e1003803. doi: 10.1371/journal.pgen.1003803 PMID: 24068968
    • (2013) PLoS Genet , vol.9
    • Gagneur, J.1    Stegle, O.2    Zhu, C.3    Jakob, P.4    Tekkedil, M.M.5    Aiyar, R.S.6
  • 15
    • 84891767235 scopus 로고    scopus 로고
    • Growth rates made easy
    • PMID: 24170494
    • Hall BG, Acar H, Nandipati A, Barlow M. Growth rates made easy. Mol Biol Evol. 2014; 31: 232-238. doi: 10.1093/molbev/mst187 PMID: 24170494
    • (2014) Mol Biol Evol , vol.31 , pp. 232-238
    • Hall, B.G.1    Acar, H.2    Nandipati, A.3    Barlow, M.4
  • 16
    • 84875976775 scopus 로고    scopus 로고
    • A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespan
    • PMID: 23505383
    • Kwan EX, Foss EJ, Tsuchiyama S, Alvino GM, Kruglyak L, Kaeberlein M, et al. A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespan. PLoS Genet. 2013; 9: e1003329. doi: 10.1371/journal.pgen.1003329 PMID: 23505383
    • (2013) PLoS Genet , vol.9
    • Kwan, E.X.1    Foss, E.J.2    Tsuchiyama, S.3    Alvino, G.M.4    Kruglyak, L.5    Kaeberlein, M.6
  • 17
    • 84867190452 scopus 로고    scopus 로고
    • Natural genetic variation in yeast longevity
    • PMID: 22955140
    • Stumpferl SW, Brand SE, Jiang JC, Korona B, Tiwari A, Dai J, et al. Natural genetic variation in yeast longevity. Genome Res. 2012; 22: 1963-1973. doi: 10.1101/gr.136549.111 PMID: 22955140
    • (2012) Genome Res , vol.22 , pp. 1963-1973
    • Stumpferl, S.W.1    Brand, S.E.2    Jiang, J.C.3    Korona, B.4    Tiwari, A.5    Dai, J.6
  • 18
    • 84863524526 scopus 로고    scopus 로고
    • Replicative and chronological aging in Saccharomyces cerevisiae
    • PMID: 22768836
    • Longo VD, Shadel GS, Kaeberlein M, Kennedy B. Replicative and chronological aging in Saccharomyces cerevisiae. Cell Metab. 2012; 16: 18-31. doi: 10.1016/j.cmet.2012.06.002 PMID: 22768836
    • (2012) Cell Metab , vol.16 , pp. 18-31
    • Longo, V.D.1    Shadel, G.S.2    Kaeberlein, M.3    Kennedy, B.4
  • 19
    • 84866360129 scopus 로고    scopus 로고
    • Chronological aging in Saccharomyces cerevisiae
    • PMID: 22094419
    • Longo VD, Fabrizio P. Chronological Aging in Saccharomyces cerevisiae. Subcell Biochem. 2012; 57: 101-121. doi: 10.1007/978-94-007-2561-4-5 PMID: 22094419
    • (2012) Subcell Biochem , vol.57 , pp. 101-121
    • Longo, V.D.1    Fabrizio, P.2
  • 20
    • 0032831936 scopus 로고    scopus 로고
    • Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae
    • PMID: 10512855
    • Kim S, Benguria A, Lai CY, Jazwinski SM. Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell. 1999; 10: 3125-3136. PMID: 10512855
    • (1999) Mol Biol Cell , vol.10 , pp. 3125-3136
    • Kim, S.1    Benguria, A.2    Lai, C.Y.3    Jazwinski, S.M.4
  • 21
    • 0033214237 scopus 로고    scopus 로고
    • The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms
    • PMID: 10521401
    • Kaeberlein M, McVey M, Guarente L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 1999; 13: 2570-2580. PMID: 10521401
    • (1999) Genes Dev , vol.13 , pp. 2570-2580
    • Kaeberlein, M.1    McVey, M.2    Guarente, L.3
  • 22
    • 19344374925 scopus 로고    scopus 로고
    • Sir2-independent life span extension by calorie restriction in yeast
    • PMID: 15328540
    • Kaeberlein M, Kirkland KT, Fields S, Kennedy BK. Sir2-independent life span extension by calorie restriction in yeast. PLoS Biol. 2004; 2: E296. PMID: 15328540
    • (2004) PLoS Biol , vol.2 , pp. E296
    • Kaeberlein, M.1    Kirkland, K.T.2    Fields, S.3    Kennedy, B.K.4
  • 24
    • 27744511769 scopus 로고    scopus 로고
    • Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients
    • PMID: 16293764
    • Kaeberlein M, PowersRW 3rd, Steffen KK, Westman EA, Hu D, Dang N, et al. Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science. 2005; 310: 1193-1196. PMID: 16293764
    • (2005) Science , vol.310 , pp. 1193-1196
    • Kaeberlein, M.1    Powers, R.W.2    Steffen, K.K.3    Westman, E.A.4    Hu, D.5    Dang, N.6
  • 25
    • 84893760820 scopus 로고    scopus 로고
    • Yeast sirtuins and the regulation of aging
    • PMID: 24164855
    • Wierman MB, Smith JS. Yeast sirtuins and the regulation of aging. FEMS Yeast Res. 2014; 14: 73-88. doi: 10.1111/1567-1364.12115 PMID: 24164855
    • (2014) FEMS Yeast Res , vol.14 , pp. 73-88
    • Wierman, M.B.1    Smith, J.S.2
  • 26
    • 0004760134 scopus 로고
    • Life span of individual yeast cells
    • PMID: 13666896
    • Mortimer RK, Johnston JR. Life span of individual yeast cells. Nature. 1959; 183: 1751-1752. PMID: 13666896
    • (1959) Nature , vol.183 , pp. 1751-1752
    • Mortimer, R.K.1    Johnston, J.R.2
  • 27
    • 84859463277 scopus 로고    scopus 로고
    • Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform
    • PMID: 22421136
    • Lee SS, Avalos Vizcarra I, Huberts DH, Lee LP, Heinemann M. Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform. Proc of the Natl Acad Sci USA. 2012; 109: 4916-4920. doi: 10.1073/pnas.1113505109 PMID: 22421136
    • (2012) Proc of the Natl Acad Sci USA , vol.109 , pp. 4916-4920
    • Lee, S.S.1    Avalos Vizcarra, I.2    Huberts, D.H.3    Lee, L.P.4    Heinemann, M.5
  • 28
    • 84869051816 scopus 로고    scopus 로고
    • Single cell analysis of yeast replicative aging using a new generation of microfluidic device
    • PMID: 23144860
    • Zhang Y, Luo C, Zou K, Xie Z, Brandman O, Ouyang Q, et al. Single cell analysis of yeast replicative aging using a new generation of microfluidic device. PloS One. 2012; 7: e48275. doi: 10.1371/journal.pone.0048275 PMID: 23144860
    • (2012) PloS One , vol.7
    • Zhang, Y.1    Luo, C.2    Zou, K.3    Xie, Z.4    Brandman, O.5    Ouyang, Q.6
  • 29
    • 84890980868 scopus 로고    scopus 로고
    • Aging yeast cells undergo a sharp entry into senescence unrelated to the loss of mitochondrial membrane potential
    • PMID: 24332850
    • Fehrmann S, Paoletti C, Goulev Y, Ungureanu A, Aguilaniu H, Charvin G. Aging yeast cells undergo a sharp entry into senescence unrelated to the loss of mitochondrial membrane potential. Cell Rep. 2013; 5: 1589-1599. doi: 10.1016/j.celrep.2013.11.013 PMID: 24332850
    • (2013) Cell Rep , vol.5 , pp. 1589-1599
    • Fehrmann, S.1    Paoletti, C.2    Goulev, Y.3    Ungureanu, A.4    Aguilaniu, H.5    Charvin, G.6
  • 30
    • 84893792592 scopus 로고    scopus 로고
    • Maximising the yeast chronological lifespan
    • PMID: 22094421
    • Piper PW. Maximising the yeast chronological lifespan. Subcell Biochem. 2012; 57: 145-159. doi: 10. 1007/978-94-007-2561-4-7 PMID: 22094421
    • (2012) Subcell Biochem , vol.57 , pp. 145-159
    • Piper, P.W.1
  • 31
    • 42449147944 scopus 로고    scopus 로고
    • A method for high-throughput quantitative analysis of yeast chronological life span
    • PMID: 18314444
    • Murakami CJ, Burtner CR, Kennedy BK, Kaeberlein M. A method for high-throughput quantitative analysis of yeast chronological life span. J Geront A Biol Sci Med Sci. 2008; 63: 113-121. PMID: 18314444
    • (2008) J Geront a Biol Sci Med Sci , vol.63 , pp. 113-121
    • Murakami, C.J.1    Burtner, C.R.2    Kennedy, B.K.3    Kaeberlein, M.4
  • 32
    • 80055111017 scopus 로고    scopus 로고
    • Quantifying yeast chronological life span by outgrowth of aged cells
    • Murakami C, Kaeberlein M. Quantifying yeast chronological life span by outgrowth of aged cells. J Vis Exp. 2009.
    • (2009) J Vis Exp
    • Murakami, C.1    Kaeberlein, M.2
  • 34
    • 0027996945 scopus 로고
    • Estimation of bacterial growth rates from turbidimetric and viable count data
    • PMID: 7873339
    • Dalgaard P, Ross T, Kamperman L, Neumeyer K, McMeekin TA. Estimation of bacterial growth rates from turbidimetric and viable count data. Int J Food Microbiol. 1994; 23: 391-404. PMID: 7873339
    • (1994) Int J Food Microbiol , vol.23 , pp. 391-404
    • Dalgaard, P.1    Ross, T.2    Kamperman, L.3    Neumeyer, K.4    McMeekin, T.A.5
  • 35
    • 0343673773 scopus 로고    scopus 로고
    • Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates
    • PMID: 10831450
    • Duetz WA, Ruedi L, Hermann R, O'Connor K, Buchs J, Witholt B. Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates. Appl Environ Microbiol. 2000; 66: 2641-2646. PMID: 10831450
    • (2000) Appl Environ Microbiol , vol.66 , pp. 2641-2646
    • Duetz, W.A.1    Ruedi, L.2    Hermann, R.3    O'Connor, K.4    Buchs, J.5    Witholt, B.6
  • 36
    • 0030925208 scopus 로고    scopus 로고
    • Physiology and genetics of the dimorphic fungus Yarrowia lipolytica
    • PMID: 9167256
    • Barth G, Gaillardin C. Physiology and genetics of the dimorphic fungus Yarrowia lipolytica. FEMS Microbiol Rev. 1997; 19: 219-237. PMID: 9167256
    • (1997) FEMS Microbiol Rev , vol.19 , pp. 219-237
    • Barth, G.1    Gaillardin, C.2
  • 37
    • 34247500374 scopus 로고    scopus 로고
    • Python for scientific computing
    • Oliphant TE. Python for scientific computing. Comput Sci Eng. 2007; 9: 10-20.
    • (2007) Comput Sci Eng , vol.9 , pp. 10-20
    • Oliphant, T.E.1
  • 38
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: A 2D graphics environment
    • Hunter JD. Matplotlib: A 2D graphics environment. Comput Sci Eng. 2007; 9: 90-95.
    • (2007) Comput Sci Eng , vol.9 , pp. 90-95
    • Hunter, J.D.1
  • 39
    • 77952308176 scopus 로고    scopus 로고
    • YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast
    • PMID: 20298554
    • Olsen B, Murakami CJ, Kaeberlein M. YODA: software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. BMC Bioinformatics. 2010; 11: 141. doi: 10.1186/1471-2105-11-141 PMID: 20298554
    • (2010) BMC Bioinformatics , vol.11 , pp. 141
    • Olsen, B.1    Murakami, C.J.2    Kaeberlein, M.3
  • 40
    • 0042887624 scopus 로고    scopus 로고
    • Physiological characterization of osmotolerant yeast Pichia sorbitophila and comparison with a putative synonym Pichia farinosa
    • PMID: 12800505
    • Maresova L, Sychrova H. Physiological characterization of osmotolerant yeast Pichia sorbitophila and comparison with a putative synonym Pichia farinosa. Folia Microbiol (Praha). 2003; 48: 211-217. PMID: 12800505
    • (2003) Folia Microbiol (Praha) , vol.48 , pp. 211-217
    • Maresova, L.1    Sychrova, H.2
  • 41
    • 78649318096 scopus 로고    scopus 로고
    • Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species
    • PMID: 20830585
    • Jung PP, Friedrich A, Souciet JL, Louis V, Potier S, de Montigny J, et al. Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species. Curr Genet. 2010; 56: 507-515. doi: 10.1007/s00294-010-0318-y PMID: 20830585
    • (2010) Curr Genet , vol.56 , pp. 507-515
    • Jung, P.P.1    Friedrich, A.2    Souciet, J.L.3    Louis, V.4    Potier, S.5    De Montigny, J.6
  • 43
    • 67349272355 scopus 로고    scopus 로고
    • The absence of a mitochondrial genome in rho0 yeast cells extends lifespan independently of retrograde regulation
    • PMID: 19285548
    • Woo DK, Poyton RO. The absence of a mitochondrial genome in rho0 yeast cells extends lifespan independently of retrograde regulation. Exp Gerontol. 2009; 44: 390-397. doi: 10.1016/j.exger.2009.03.001 PMID: 19285548
    • (2009) Exp Gerontol , vol.44 , pp. 390-397
    • Woo, D.K.1    Poyton, R.O.2
  • 44
    • 84863527085 scopus 로고    scopus 로고
    • Mitochondrial respiratory thresholds regulate yeast chronological life span and its extension by caloric restriction
    • PMID: 22768839
    • Ocampo A, Liu J, Schroeder EA, Shadel GS, Barrientos A. Mitochondrial respiratory thresholds regulate yeast chronological life span and its extension by caloric restriction. Cell Metab. 2012; 16: 55-67. doi: 10.1016/j.cmet.2012.05.013 PMID: 22768839
    • (2012) Cell Metab , vol.16 , pp. 55-67
    • Ocampo, A.1    Liu, J.2    Schroeder, E.A.3    Shadel, G.S.4    Barrientos, A.5
  • 45
    • 65949122940 scopus 로고    scopus 로고
    • A molecular mechanism of chronological aging in yeast
    • PMID: 19305133
    • Burtner CR, Murakami CJ, Kennedy BK, Kaeberlein M. A molecular mechanism of chronological aging in yeast. Cell Cycle. 2009; 8: 1256-1270. PMID: 19305133
    • (2009) Cell Cycle , vol.8 , pp. 1256-1270
    • Burtner, C.R.1    Murakami, C.J.2    Kennedy, B.K.3    Kaeberlein, M.4
  • 46
    • 50649099122 scopus 로고    scopus 로고
    • Aging and survival: The genetics of life span extension by dietary restriction
    • PMID: 18373439
    • Mair W, Dillin A. Aging and survival: the genetics of life span extension by dietary restriction. Annu Rev Biochem. 2008; 77: 727-754. doi: 10.1146/annurev.biochem.77.061206.171059 PMID: 18373439
    • (2008) Annu Rev Biochem , vol.77 , pp. 727-754
    • Mair, W.1    Dillin, A.2
  • 49
    • 84922373440 scopus 로고    scopus 로고
    • Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast
    • PMID: 25349286
    • Friedrich A, Jung P, Reisser C, Fischer G, Schacherer J. Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast. Mol Biol Evol. 2015; 32: 184-192. doi: 10.1093/ molbev/msu295 PMID: 25349286
    • (2015) Mol Biol Evol , vol.32 , pp. 184-192
    • Friedrich, A.1    Jung, P.2    Reisser, C.3    Fischer, G.4    Schacherer, J.5


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