

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Iserman2020,
  title     = "Condensation of Ded1p Promotes a Translational Switch from
               Housekeeping to Stress Protein Production",
  author    = "Iserman, Christiane and Altamirano, Christine Desroches and
               Jegers, Ceciel and Friedrich, Ulrike and Zarin, Taraneh and
               Fritsch, Anatol W and Mittasch, Matth{\"a}us and Domingues,
               Antonio and Hersemann, Lena and Jahnel, Marcus and Richter,
               Doris and Guenther, Ulf-Peter and Hentze, Matthias W and Moses,
               Alan M and Hyman, Anthony A and Kramer, G{\"u}nter and Kreysing,
               Moritz and Franzmann, Titus M and Alberti, Simon",
  journal   = "Cell",
  publisher = "Elsevier",
  volume    =  0,
  number    =  0,
  month     =  apr,
  year      =  2020,
  keywords  = "phase separation; heat stress; evolutionary adaptation; heat
               shock response; 5′; UTR; ribosomal scanning; Ded1p; condensate;
               chaperone; cytosolic pH",
  language  = "en"
}


@ARTICLE{VandeVossenberg1999,
  title    = "Homeostasis of the membrane proton permeability in Bacillus
              subtilis grown at different temperatures",
  author   = "van de Vossenberg, J L and Driessen, A J and da Costa, M S and
              Konings, W N",
  journal  = "Biochim. Biophys. Acta",
  volume   =  1419,
  number   =  1,
  pages    = "97--104",
  month    =  jun,
  year     =  1999,
  language = "en"
}


@ARTICLE{Baler1992,
  title    = "Heat shock gene regulation by nascent polypeptides and denatured
              proteins: hsp70 as a potential autoregulatory factor",
  author   = "Baler, R",
  journal  = "J. Cell Biol.",
  volume   =  117,
  number   =  6,
  pages    = "1151--1159",
  year     =  1992,
  keywords = "Base Sequence; Cycloheximide; Cycloheximide: pharmacology; DNA;
              DNA-Binding Proteins; DNA-Binding Proteins: physiology; Gene
              Expression Regulation; HeLa Cells; Heat-Shock Proteins;
              Heat-Shock Proteins: genetics; Heat-Shock Proteins: metabolism;
              Homeostasis; Hot Temperature; Humans; Molecular Sequence Data;
              Peptides; Peptides: physiology; Protein Denaturation; Protein
              Synthesis Inhibitors; Protein Synthesis Inhibitors: pharmacology;
              Stress, Physiological; Transcription Factors; Transcription
              Factors: physiology"
}


@ARTICLE{Li2017,
  title    = "Rethinking {HSF1} in Stress, Development, and Organismal Health",
  author   = "Li, Jian and Labbadia, Johnathan and Morimoto, Richard I",
  journal  = "Trends Cell Biol.",
  volume   =  27,
  number   =  12,
  pages    = "895--905",
  month    =  dec,
  year     =  2017,
  keywords = "HSF1; cell proliferation; heat shock response (HSR); metabolism;
              organismal health; proteostasis",
  language = "en"
}


@ARTICLE{Christiaens2014,
  title   = "The Fungal Aroma Gene {ATF1} Promotes Dispersal of Yeast Cells
             through Insect Vectors",
  author  = "Christiaens, Joaquin F and Franco, Luis M and Cools, Tanne L and
             De Meester, Luc and Michiels, Jan and Wenseleers, Tom and Hassan,
             Bassem A and Yaksi, Emre and Verstrepen, Kevin J",
  journal = "Cell Rep.",
  volume  =  9,
  number  =  2,
  pages   = "425--432",
  year    =  2014
}

@ARTICLE{Shi1998,
  title    = "Molecular chaperones as {HSF1-specific} transcriptional
              repressors",
  author   = "Shi, Y and Mosser, D D and Morimoto, R I",
  journal  = "Genes Dev.",
  volume   =  12,
  number   =  5,
  pages    = "654--666",
  year     =  1998,
  language = "en"
}

@ARTICLE{Ritossa1962,
  title   = "A new puffing pattern induced by temperature shock and {DNP} in
             drosophila",
  author  = "Ritossa, F",
  journal = "Experientia",
  volume  =  18,
  number  =  12,
  pages   = "571--573",
  year    =  1962
}

@ARTICLE{Gidalevitz2011,
  title    = "The stress of protein misfolding: from single cells to
              multicellular organisms",
  author   = "Gidalevitz, Tali and Prahlad, Veena and Morimoto, Richard I",
  journal  = "Cold Spring Harb. Perspect. Biol.",
  volume   =  3,
  number   =  6,
  year     =  2011,
  language = "en"
}


@ARTICLE{Nicholls2011,
  title    = "Activation of the heat shock transcription factor Hsf1 is
              essential for the full virulence of the fungal pathogen Candida
              albicans",
  author   = "Nicholls, Susan and MacCallum, Donna M and Kaffarnik, Florian A R
              and Selway, Laura and Peck, Scott C and Brown, Alistair J P",
  journal  = "Fungal Genet. Biol.",
  volume   =  48,
  number   =  3,
  pages    = "297--305",
  year     =  2011,
  keywords = "Heat shock; Hsf1; Transcriptional activation; Phosphorylation;
              Pathogenesis"
}

@ARTICLE{Nicholls2004,
  title    = "Msn2- and {M}sn4-like transcription factors play no obvious roles
              in the stress responses of the fungal pathogen {C}andida albicans",
  author   = "Nicholls, Susan and Straffon, Melissa and Enjalbert, Brice and
              Nantel, Andr{\'e} and Macaskill, Susan and Whiteway, Malcolm and
              Brown, Alistair J P",
  journal  = "Eukaryot. Cell",
  volume   =  3,
  number   =  5,
  pages    = "1111--1123",
  year     =  2004,
  language = "en"
}


@ARTICLE{Salvado2011,
  title    = "Temperature adaptation markedly determines evolution within the
              genus {S}accharomyces",
  author   = "Salvad{\'o}, Z and Arroyo-L{\'o}pez, F N and Guillam{\'o}n, J M
              and Salazar, G and Querol, A and Barrio, E",
  journal  = "Appl. Environ. Microbiol.",
  volume   =  77,
  number   =  7,
  pages    = "2292--2302",
  year     =  2011,
  keywords = "Adaptation, Physiological; Biological Evolution; Cold
              Temperature; Hot Temperature; Phylogeny; Saccharomyces;
              Saccharomyces: classification; Saccharomyces: growth \&
              development; Saccharomyces: radiation effects"
}

@ARTICLE{CoxWalter1996,
  title    = "A novel mechanism for regulating activity of a transcription
              factor that controls the unfolded protein response",
  author   = "Cox, Jeffery S and Walter, Peter",
  journal  = "Cell",
  volume   =  87,
  number   =  3,
  pages    = "391--404",
  year     =  1996,
  language = "en"
}

@ARTICLE{Estruch2000,
  title    = "Stress-controlled transcription factors, stress-induced genes and
              stress tolerance in budding yeast",
  author   = "Estruch, Francisco",
  journal  = "FEMS Microbiol. Rev.",
  volume   =  24,
  number   =  4,
  pages    = "469--486",
  year     =  2000,
  language = "en"
}

@ARTICLE{Brown2010,
  title    = "The relevance of heat shock regulation in fungal pathogens of
              humans",
  author   = "Brown, Alistair J P and Leach, Michelle D and Nicholls, Susan",
  journal  = "Virulence",
  volume   =  1,
  number   =  4,
  pages    = "330--332",
  year     =  2010,
  language = "en"
}


@ARTICLE{Nicholls2009,
  title    = "Role of the heat shock transcription factor, {H}sf1, in a major
              fungal pathogen that is obligately associated with warm-blooded
              animals",
  author   = "Nicholls, Susan and Leach, Michelle D and Priest, Claire L and
              Brown, Alistair J P",
  journal  = "Mol. Microbiol.",
  volume   =  74,
  number   =  4,
  pages    = "844--861",
  year     =  2009,
  language = "en"
}


@ARTICLE{Diaz2016,
  title    = "Fever-range hyperthermia improves the anti-apoptotic effect
              induced by low p{H} on human neutrophils promoting a proangiogenic
              profile",
  author   = "D{\'\i}az, Fernando Erra and Dantas, Ezequiel and Cabrera, Maia
              and Ben{\'\i}tez, Constanza A and Delpino, Mar{\'\i}a V and
              Duette, Gabriel and Rubione, Julia and Sanjuan, Norberto and
              Trevani, Anal{\'\i}a S and Geffner, Jorge",
  journal  = "Cell Death Dis.",
  volume   =  7,
  number   =  10,
  pages    = "e2437",
  year     =  2016,
  language = "en"
}

@ARTICLE{Singh2013,
  title    = "Fever, hyperthermia and the heat shock response",
  author   = "Singh, Ishwar S and Hasday, Jeffrey D",
  journal  = "Int. J. Hyperthermia",
  volume   =  29,
  number   =  5,
  pages    = "423--435",
  year     =  2013,
  language = "en"
}

@ARTICLE{Morgenstern2012,
  title    = "A molecular phylogeny of thermophilic fungi",
  author   = "Morgenstern, Ingo and Powlowski, Justin and Ishmael, Nadeeza and Darmond, Corinne and
              Marqueteau, Sandrine and Moisan, Marie-Claude and Quenneville, Genevieve and Tsang, Adrian",
  journal  = "Fungal Biol.",
  volume   =  116,
  number   =  4,
  pages    = "489--502",
  year     =  2012,
  keywords = "*Industrial Microbiology; Cluster Analysis; DNA,
              Fungal/chemistry/genetics; DNA, Ribosomal
              Spacer/chemistry/genetics; DNA, Ribosomal/chemistry/genetics;
              Fungal Proteins/genetics; Fungi/*classification/genetics/*growth
              \& developme; Genes, rRNA; Hot Temperature; Molecular Sequence
              Data; Phylogeny; RNA, Fungal/genetics; RNA, Ribosomal,
              18S/genetics; RNA, Ribosomal, 5.8S/genetics; RNA,
              Ribosomal/genetics; Sequence Analysis, DNA"
}

@ARTICLE{Madden2018,
  title    = "The ecology of insect-yeast relationships and its relevance to
              human industry",
  author   = "Madden, Anne A and Epps, Mary Jane and Fukami, Tadashi and Irwin,
              Rebecca E and Sheppard, John and Sorger, D Magdalena and Dunn,
              Robert R",
  journal  = "Proc. Biol. Sci.",
  volume   =  285,
  number   =  1875,
  year     =  2018,
  keywords = "Ascomycota; diffuse mutualism; dispersal",
  language = "en"
}


@ARTICLE{Giglioli1897,
  title   = "Insects and Yeasts",
  author  = "Giglioli, Italo",
  journal = "Nature",
  volume  =  56,
  pages   = "575--577",
  year    =  1897
}

@ARTICLE{Francesca2010,
  title   = "Indigenous yeast communities in the environment of ``Rovello
             bianco'' grape variety and their use in commercial white wine
             fermentation",
  author  = "Francesca, Nicola and Chiurazzi, Mario and Romano, Raffaele and
             Aponte, Maria and Settanni, Luca and Moschetti, Giancarlo",
  journal = "World J. Microbiol. Biotechnol.",
  volume  =  26,
  number  =  2,
  pages   = "337--351",
  year    =  2010
}

@ARTICLE{DeHaven1981,
  title     = "Estimating Bird Damage from Damage Incidence in Wine Grape
               Vineyards",
  author    = "DeHaven, R W and Hothem, R L",
  journal   = "Am. J. Enol. Vitic.",
  publisher = "American Journal of Enology and Viticulture",
  volume    =  32,
  number    =  1,
  pages     = "1--4",
  year      =  1981,
  language  = "en"
}


@ARTICLE{Heck2010,
  title    = "Cytoplasmic protein quality control degradation mediated by
              parallel actions of the {E3} ubiquitin ligases {U}br1 and {S}an1",
  author   = "Heck, Jarrod W and Cheung, Samantha K and Hampton, Randolph Y",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  volume   =  107,
  number   =  3,
  pages    = "1106--1111",
  year     =  2010,
  keywords = "Cytoplasm; Cytoplasm: metabolism; Saccharomyces cerevisiae;
              Saccharomyces cerevisiae Proteins; Saccharomyces cerevisiae
              Proteins: metabolism; Saccharomyces cerevisiae: metabolism;
              Ubiquitin-Protein Ligases; Ubiquitin-Protein Ligases: metabolism"
}

@ARTICLE{Fredrickson2013,
  title    = "Substrate recognition in nuclear protein quality control
              degradation is governed by exposed hydrophobicity that correlates
              with aggregation and insolubility",
  author   = "Fredrickson, Eric K and Gallagher, Pamela S and Clowes Candadai,
              Sarah V and Gardner, Richard G",
  journal  = "J. Biol. Chem.",
  volume   =  288,
  number   =  9,
  pages    = "6130--6139",
  year     =  2013,
  keywords = "Hydrophobic and Hydrophilic Interactions; Nuclear Proteins;
              Nuclear Proteins: genetics; Nuclear Proteins: metabolism; Protein
              Folding; Proteolysis; Saccharomyces cerevisiae; Saccharomyces
              cerevisiae Proteins; Saccharomyces cerevisiae Proteins: genetics;
              Saccharomyces cerevisiae Proteins: metabolism; Saccharomyces
              cerevisiae: genetics; Saccharomyces cerevisiae: metabolism;
              Solubility; Ubiquitin-Protein Ligases; Ubiquitin-Protein Ligases:
              genetics; Ubiquitin-Protein Ligases: metabolism"
}

@ARTICLE{Somers2002,
  title   = "Birds and wine grapes: foraging activity causes small-scale damage
             patterns in single vineyards",
  author  = "Somers, Christopher M and Morris, Ralph D",
  journal = "J. Appl. Ecol.",
  volume  =  39,
  number  =  3,
  pages   = "511--523",
  year    =  2002
}

@ARTICLE{Dapporto2016,
  title    = "Social wasp intestines host the local phenotypic variability of
              {S}accharomyces cerevisiae strains",
  author   = "Dapporto, Leonardo and Stefanini, Irene and Rivero, Damariz and
              Polsinelli, Mario and Capretti, Paolo and De Marchi, Paolo and
              Viola, Roberto and Turillazzi, Stefano and Cavalieri, Duccio",
  journal  = "Yeast",
  volume   =  33,
  number   =  7,
  pages    = "277--287",
  year     =  2016,
  keywords = "ecology; phenotype; saccharomyces cerevisiae; social wasps",
  language = "en"
}

@ARTICLE{Francesca2012,
  title   = "Dissemination of wine-related yeasts by migratory birds",
  author  = "Francesca, Nicola and Canale, Domenica E and Settanni, Luca and
             Moschetti, Giancarlo",
  journal = "Environ. Microbiol. Rep.",
  volume  =  4,
  number  =  1,
  pages   = "105--112",
  year    =  2012
}

@ARTICLE{Prinzinger1991,
  title   = "Body temperature in birds",
  author  = "Prinzinger, R and Pre{\ss}mar, A and Schleucher, E",
  journal = "Comp. Biochem. Physiol. A Physiol.",
  volume  =  99,
  number  =  4,
  pages   = "499--506",
  year    =  1991
}

@INCOLLECTION{Moschetti2017,
  title     = "Yeasts in Birds",
  booktitle = "Yeasts in Natural Ecosystems: Diversity",
  author    = "Moschetti, Giancarlo and Alfonzo, Antonio and Francesca, Nicola",
  editor    = "Buzzini, Pietro and Lachance, Marc-Andr{\'e} and Yurkov, Andrey",
  publisher = "Springer International Publishing",
  pages     = "435--454",
  year      =  2017,
  address   = "Cham"
}

@ARTICLE{Mortimer1999,
  title    = "On the origins of wine yeast",
  author   = "Mortimer, R and Polsinelli, M",
  journal  = "Res. Microbiol.",
  volume   =  150,
  number   =  3,
  pages    = "199--204",
  year     =  1999,
  language = "en"
}


@ARTICLE{Klein2007,
  title    = "Dimorphism and virulence in fungi",
  author   = "Klein, Bruce S and Tebbets, Brad",
  journal  = "Curr. Opin. Microbiol.",
  volume   =  10,
  number   =  4,
  pages    = "314--319",
  year     =  2007,
  language = "en"
}


@ARTICLE{Grousl2009,
  title    = "Robust heat shock induces {eIF2alpha-phosphorylation-independent}
              assembly of stress granules containing {eIF3} and {40S} ribosomal
              subunits in budding yeast, Saccharomyces cerevisiae",
  author   = "Grousl, T and Ivanov, P and Frydlova, I and Vasicova, P and
              Janda, F and Vojtova, J and Malinska, K and Malcova, I and
              Novakova, L and Janoskova, D and Valasek, L and Hasek, J",
  journal  = "J. Cell Sci.",
  volume   =  122,
  number   = "Pt 12",
  pages    = "2078--2088",
  year     =  2009,
  keywords = "Cycloheximide/pharmacology; Cytoplasmic Granules/drug
              effects/*metabolism/phys; Down-Regulation/physiology; Eukaryotic
              Initiation Factor-2/*metabolism; Eukaryotic Initiation
              Factor-3/*metabolism; Heat-Shock Response/drug
              effects/*physiology; Organisms, Genetically Modified;
              Phosphorylation/physiology; Protein Biosynthesis/drug
              effects/physiology; Protein Synthesis Inhibitors/pharmacology;
              Protein-Serine-Threonine Kinases/physiology; Ribosome Subunits,
              Small, Eukaryotic/*metabolism; Saccharomyces cerevisiae
              Proteins/physiology; Saccharomyces
              cerevisiae/*metabolism/physiology; Tissue Distribution"
}

@ARTICLE{Anderson2002,
  title    = "Stressful initiations",
  author   = "Anderson, P and Kedersha, N",
  journal  = "J. Cell Sci.",
  volume   =  115,
  number   = "Pt 16",
  pages    = "3227--3234",
  year     =  2002,
  keywords = "*Protein Biosynthesis; Basal Metabolism/*physiology; Cell Line;
              Eukaryotic Initiation Factor-2/metabolism; Guanosine
              Triphosphate/metabolism; Inclusion Bodies/*metabolism;
              Macromolecular Substances; Models, Genetic;
              Polyribosomes/metabolism; RNA, Messenger/metabolism; RNA,
              Transfer, Met/metabolism"
}

@ARTICLE{Elsutohy2017,
  title    = "Real-time measurement of the intracellular pH of yeast cells
              during glucose metabolism using ratiometric fluorescent
              nanosensors",
  author   = "Elsutohy, Mohamed M and Chauhan, Veeren M and Markus, Robert and
              Kyyaly, Mohammed Aref and Tendler, Saul J B and Aylott, Jonathan
              W",
  journal  = "Nanoscale",
  volume   =  9,
  number   =  18,
  pages    = "5904--5911",
  year     =  2017,
  language = "en"
}

@ARTICLE{Walters2015,
  title    = "Differential effects of Ydj1 and Sis1 on Hsp70-mediated clearance
              of stress granules in Saccharomyces cerevisiae",
  author   = "Walters, Robert W and Muhlrad, Denise and Garcia, Jennifer and
              Parker, Roy",
  journal  = "RNA",
  volume   =  21,
  number   =  9,
  pages    = "1660--1671",
  year     =  2015,
  keywords = "Hsp70; Sis1; Ydj1; stress granules"
}

@ARTICLE{Kroschwald2018,
  title    = "Different Material States of {P}ub1 Condensates Define Distinct
              Modes of Stress Adaptation and Recovery",
  author   = "Kroschwald, Sonja and Munder, Matthias C and Maharana, Shovamayee
              and Franzmann, Titus M and Richter, Doris and Ruer, Martine and
              Hyman, Anthony A and Alberti, Simon",
  journal  = "Cell Rep.",
  volume   =  23,
  number   =  11,
  pages    = "3327--3339",
  year     =  2018,
  keywords = "Hsp104; condensate; cytosolic pH; molecular chaperone; phase
              separation; phase transition; protein aggregation; stress
              granule; stress response",
  language = "en"
}

@ARTICLE{Zilberstein1984,
  title    = "Escherichia coli intracellular pH, membrane potential, and cell
              growth",
  author   = "Zilberstein, D and Agmon, V and Schuldiner, S and Padan, E",
  journal  = "J. Bacteriol.",
  volume   =  158,
  number   =  1,
  pages    = "246--252",
  year     =  1984,
  language = "en"
}

@ARTICLE{Rudiger1997,
  title    = "Substrate specificity of the {DnaK} chaperone determined by
              screening cellulose-bound peptide libraries",
  author   = "R{\"u}diger, Stefan and Germeroth, Lothar and Schneider-Mergener, Jens and
              Bukau, Bernd",
  journal  = "EMBO J.",
  volume   =  16,
  number   =  7,
  pages    = "1501--1507",
  year     =  1997,
  language = "en"
}

@ARTICLE{Trotter2002,
  title    = "Misfolded proteins are competent to mediate a subset of the
              responses to heat shock in {S}accharomyces cerevisiae",
  author   = "Trotter, Eleanor W and Kao, Camilla M and Berenfeld, Ludmilla and Botstein, David and
              Petsko, Gregory A and Gray, Joseph V",
  journal  = "J. Biol. Chem.",
  volume   =  277,
  number   =  47,
  pages    = "44817--44825",
  year     =  2002,
}

@ARTICLE{Drummond1986,
  title    = "Large changes in intracellular pH and calcium observed during
              heat shock are not responsible for the induction of heat shock
              proteins in Drosophila melanogaster",
  author   = "Drummond, I A and McClure, S A and Poenie, M and Tsien, R Y and
              Steinhardt, R A",
  journal  = "Mol. Cell. Biol.",
  volume   =  6,
  number   =  5,
  pages    = "1767--1775",
  year     =  1986,
  language = "en"
}

@ARTICLE{Yang1993,
  title    = "On the p{H} dependence of protein stability",
  author   = "Yang, A S and Honig, B",
  journal  = "J. Mol. Biol.",
  volume   =  231,
  number   =  2,
  pages    = "459--474",
  year     =  1993,
  language = "en"
}


@ARTICLE{GeilerSamerotte2011,
  title    = "Misfolded proteins impose a dosage-dependent fitness cost and
              trigger a cytosolic unfolded protein response in yeast",
  author   = "Kerry A. Geiler-Samerotte and Michael F. Dion and Bogdan A. Budnik and Stephanie M. Wang and Daniel L. Hartl and D. Allan Drummond",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  volume   =  108,
  number   =  2,
  pages    = "680--685",
  year     =  2011,
  keywords = "Bacterial Proteins/chemistry; Cytosol/*chemistry/metabolism;
              Evolution, Molecular; Fungal Proteins/*chemistry; Hot
              Temperature; Luminescent Proteins/chemistry; Molecular
              Chaperones/chemistry; Protein Denaturation; Protein Folding;
              Proteins/chemistry; Proteomics/methods; Saccharomyces cerevisiae
              Proteins/chemistry; Saccharomyces cerevisiae/metabolism;
              Transcription, Genetic"
}


@ARTICLE{Anderson2008,
  title    = "Stress granules: the {T}ao of {RNA} triage",
  author   = "Anderson, Paul and Kedersha, Nancy",
  journal  = "Trends Biochem. Sci.",
  volume   =  33,
  number   =  3,
  pages    = "141--150",
  year     =  2008,
  keywords = "Animals; Cytoplasmic Granules/*metabolism; Humans; Models,
              Biological; Protein Binding; RNA, Messenger/*metabolism;
              RNA-Binding Proteins/*metabolism; Ribonucleoproteins/metabolism"
}

@ARTICLE{Hoyle2007,
  title   = "Stress-dependent relocalization of translationally primed {mRNPs}
             to cytoplasmic granules that are kinetically and spatially
             distinct from P-bodies",
  author  = "Hoyle, Nathaniel P and Castelli, Lydia M and Campbell, Susan G and
             Holmes, Leah E A and Ashe, Mark P",
  journal = "J. Cell Biol.",
  volume  =  179,
  number  =  1,
  pages   = "65--74",
  year    =  2007
}


@ARTICLE{Yao2004,
  title    = "Calcium and p{H} homeostasis in neurons during hypoxia and ischemia",
  author   = "Yao, Hang and Haddad, Gabriel G",
  journal  = "Cell Calcium",
  volume   =  36,
  number   = "3-4",
  pages    = "247--255",
  year     =  2004,
  language = "en"
}


@article{Banani2017,
abstract = {In addition to membrane-bound organelles, eukaryotic cells feature various membraneless compartments, including the centrosome, the nucleolus and various granules. Many of these compartments form through liquid–liquid phase separation, and the principles, mechanisms and regulation of their assembly as well as their cellular functions are now beginning to emerge.},
author = {Banani, Salman F. and Lee, Hyun O. and Hyman, Anthony A. and Rosen, Michael K.},
doi = {10.1038/nrm.2017.7},
file = {:Users/Triandafillou/Downloads/papers/nrm.2017.7.pdf:pdf},
isbn = {2146456361},
issn = {14710080},
journal = {Nat. Rev. Mol. Cell Biol.},
number = {5},
pages = {285--298},
pmid = {28225081},
publisher = {Nature Publishing Group},
title = {{Biomolecular condensates: Organizers of cellular biochemistry}},
url = {http://dx.doi.org/10.1038/nrm.2017.7},
volume = {18},
year = {2017}
}
@article{Soifer2016,
abstract = {To maintain a constant cell size, dividing cells have to coordinate cell-cycle events with cell growth. This coordination has long been supposed to rely on the existence of size thresholds determining cell-cycle progression [1]. In budding yeast, size is controlled at the G1/S transition [2]. In agreement with this hypothesis, the size at birth influences the time spent in G1: smaller cells have a longer G1 period [3]. Nevertheless, even though cells born smaller have a longer G1, the compensation is imperfect and they still bud at smaller cell sizes. In bacteria, several recent studies have shown that the incremental model of size control, in which size is controlled by addition of a constant volume (in contrast to a size threshold), is able to quantitatively explain the experimental data on four different bacterial species [4-7]. Here, we report on experimental results for the budding yeast Saccharomyces cerevisiae, finding, surprisingly, that cell size control in this organism is very well described by the incremental model, suggesting a common strategy for cell size control with bacteria. Additionally, we argue that for S. cerevisiae the "volume increment" is not added from birth to division, but rather between two budding events.},
archivePrefix = {arXiv},
arxivId = {arXiv:1410.4771v2},
author = {Soifer, Ilya and Robert, Lydia and Amir, Ariel},
doi = {10.1016/j.cub.2015.11.067},
eprint = {arXiv:1410.4771v2},
file = {:Users/Triandafillou/Downloads/papers/1-s2.0-S0960982215015602-mmc2.pdf:pdf},
isbn = {1879-0445 (Electronic)$\backslash$r0960-9822 (Linking)},
issn = {09609822},
journal = {Curr. Biol.},
number = {3},
pages = {356--361},
pmid = {26776734},
publisher = {Elsevier Ltd},
title = {{Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy}},
url = {http://dx.doi.org/10.1016/j.cub.2015.11.067},
volume = {26},
year = {2016}
}
@article{Kuang2017,
abstract = {{\textless}p{\textgreater}Nutrient availability and stresses impact a cell's decision to enter a growth state or a quiescent state. Acetyl-CoA stimulates cell growth under nutrient-limiting conditions, but how cells generate acetyl-CoA under starvation stress is less understood. Here, we show that general stress response factors, Msn2 and Msn4, function as master transcriptional regulators of yeast glycolysis via directly binding and activating genes encoding glycolytic enzymes. Yeast cells lacking Msn2 and Msn4 exhibit prevalent repression of glycolytic genes and a significant delay of acetyl-CoA accumulation and reentry into growth from quiescence. Thus Msn2/4 exhibit a dual role in activating carbohydrate metabolism genes and stress response genes. These results suggest a possible mechanism by which starvation-induced stress response factors may prime quiescent cells to reenter growth through glycolysis when nutrients are limited.{\textless}/p{\textgreater}},
author = {Kuang, Zheng and Pinglay, Sudarshan and Ji, Hongkai and Boeke, Jef D.},
doi = {10.7554/eLife.29938},
file = {:Users/Triandafillou/Downloads/papers/elife-29938-v2.pdf:pdf},
issn = {2050084X},
journal = {Elife},
pages = {1--16},
pmid = {28949295},
title = {{Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth}},
volume = {6},
year = {2017}
}
@article{Krakowiak2018,
author = {Krakowiak, Joanna and Zheng, Xu and Patel, Nikit and Anandhakumar, Jayamani and Valerius, Kendra and Gross, David S and Khalil, Ahmad S and Pincus, David},
doi = {10.1101/183137},
file = {:Users/Triandafillou/Downloads/papers/elife-31668-v2.pdf:pdf},
issn = {2050-084X},
journal = {Elife},
keywords = {hsf1,hsp70,hsr,modeling},
mendeley-tags = {hsf1,hsp70,hsr,modeling},
pages = {1--17},
pmid = {29393852},
title = {{Hsf1 and Hsp70 constitute a two-component feedback loop that regulates the yeast heat shock response}},
url = {http://dx.doi.org/10.1101/183137},
volume = {7},
year = {2018}
}
@article{Mittasch2018,
abstract = {Recent advances in cell biology enable precise molecular perturbations. The spatiotemporal organization of cells and organisms, however, also depends on physical processes such as diffusion or cytoplasmic flows, and strategies to perturb physical transport inside cells are not yet available. Here, we demonstrate focused-light-induced cytoplasmic streaming (FLUCS). FLUCS is local, directional, dynamic, probe-free, physiological, and is even applicable through rigid egg shells or cell walls. We explain FLUCS via time-dependent modelling of thermoviscous flows. Using FLUCS, we demonstrate that cytoplasmic flows drive partitioning-defective protein (PAR) polarization in Caenorhabditis elegans zygotes, and that cortical flows are sufficient to transport PAR domains and invert PAR polarity. In addition, we find that asymmetric cell division is a binary decision based on gradually varying PAR polarization states. Furthermore, the use of FLUCS for active microrheology revealed a metabolically induced fluid-to-solid transition of the yeast cytoplasm. Our findings establish how a wide range of transport-dependent models of cellular organization become testable by FLUCS.},
author = {Mittasch, Matth{\"{a}}us and Gross, Peter and Nestler, Michael and Fritsch, Anatol W. and Iserman, Christiane and Kar, Mrityunjoy and Munder, Matthias and Voigt, Axel and Alberti, Simon and Grill, Stephan W. and Kreysing, Moritz},
doi = {10.1038/s41556-017-0032-9},
file = {:Users/Triandafillou/Downloads/papers/s41556-017-0032-9.pdf:pdf},
issn = {1465-7392},
journal = {Nat. Cell Biol.},
keywords = {Cancer Research,Cell Biology,Developmental Biology,Life Sciences,Stem Cells,general},
pages = {1},
title = {{Non-invasive perturbations of intracellular flow reveal physical principles of cell organization}},
url = {http://www.nature.com/articles/s41556-017-0032-9},
year = {2018}
}
@article{Delobel2014,
author = {Delobel, Pierre and Tesni{\`{e}}re, Catherine},
doi = {10.1371/journal.pone.0084645},
file = {:Users/Triandafillou/Downloads/papers/DelobelandTesnire2014.pdf:pdf},
journal = {PLoS One},
number = {1},
pages = {1--8},
title = {{A Simple FCM Method to Avoid Misinterpretation in Saccharomyces cerevisiae Cell Cycle Assessment between G0 and Sub-G1}},
volume = {9},
year = {2014}
}
@article{Johnston1980,
author = {Johnston, G.C. and Singer, R.A.},
doi = {10.1128/MCB.21.20.6972},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Johnston, Singer - 1980 - Ribosomal Precursor RNA Metabolism and Cell Division in the Yeast Saccharomyces cerevisiae.pdf:pdf},
journal = {Molec. gen. Genet.},
keywords = {cell cycle,heat shock},
mendeley-tags = {cell cycle,heat shock},
number = {20},
pages = {357--360},
title = {{Ribosomal Precursor RNA Metabolism and Cell Division in the Yeast Saccharomyces cerevisiae}},
volume = {178},
year = {1980}
}
@article{Hewitt2004,
author = {Hewitt, Christopher J. and Nebe-Von-Caron, Gerhard},
doi = {10.1007/b93997},
file = {:Users/Triandafillou/Downloads/papers/b93997.pdf:pdf},
isbn = {978-3-540-20311-7},
issn = {07246145},
journal = {Adv Biochem Engin/Biotechnol},
keywords = {cell cycle,cell size,flow cytometry},
mendeley-tags = {cell cycle,cell size,flow cytometry},
pages = {197--223},
pmid = {15217160},
title = {{The Application of Multi-Parameter Flow Cytometry to Monitor Individual Microbial Cell Physiological State}},
url = {http://www.springerlink.com/index/10.1007/b93997},
volume = {89},
year = {2004}
}
@article{Hottiger1992,
author = {Hottiger, Thomas and Virgilio, Claudio De and Bell, Walter and Boller, Thomas and Wiemken, Andres},
doi = {10.1111/j.1432-1033.1992.tb17399.x},
file = {:Users/Triandafillou/Downloads/papers/HOTTIGER{\_}et{\_}al-1992-European{\_}Journal{\_}of{\_}Biochemistry.pdf:pdf},
isbn = {0014-2956 (Print)$\backslash$r0014-2956 (Linking)},
issn = {14321033},
journal = {Eur. J. Biochem.},
keywords = {hsp70},
mendeley-tags = {hsp70},
number = {1},
pages = {125--132},
pmid = {1446665},
title = {{The 70-kilodalton heat-shock proteins of the SSA subfamily negatively modulate heat-shock-induced accumulation of trehalose and promote recovery from heat stress in the yeast, Saccharomyces cerevisiae}},
volume = {210},
year = {1992}
}
@article{Weinberg2016,
author = {Weinberg, David E and Shah, Premal and Eichhorn, Stephen W and Hussmann, Jeffrey A and Plotkin, Joshua B and Bartel, David P},
doi = {10.1016/j.celrep.2016.01.043},
file = {:Users/Triandafillou/Downloads/papers/PIIS2211124716300213.pdf:pdf},
issn = {2211-1247},
journal = {Cell Rep.},
keywords = {ribosome profiling},
mendeley-tags = {ribosome profiling},
number = {7},
pages = {1787--1799},
publisher = {The Authors},
title = {{Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation}},
url = {http://dx.doi.org/10.1016/j.celrep.2016.01.043},
volume = {14},
year = {2016}
}
@article{Putney2003,
author = {Putney, Luanna K. and Barber, Diane L.},
doi = {10.1074/jbc.M308099200},
file = {:Users/Triandafillou/Downloads/papers/J. Biol. Chem.-2003-Putney-44645-9.pdf:pdf},
isbn = {4464544649},
issn = {00219258},
journal = {J. Biol. Chem.},
number = {45},
pages = {44645--44649},
pmid = {12947095},
title = {{Na-H Exchange-dependent Increase in Intracellular pH Times G2/M Entry and Transition}},
volume = {278},
year = {2003}
}
@article {Franzmann2018,
	author = {Franzmann, Titus M. and Jahnel, Marcus and Pozniakovsky, Andrei and Mahamid, Julia and Holehouse, Alex S. and N{\"u}ske, Elisabeth and Richter, Doris and Baumeister, Wolfgang and Grill, Stephan W. and Pappu, Rohit V. and Hyman, Anthony A. and Alberti, Simon},
	title = {Phase separation of a yeast prion protein promotes cellular fitness},
	volume = {359},
	number = {6371},
	year = {2018},
	doi = {10.1126/science.aao5654},
	publisher = {American Association for the Advancement of Science},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/359/6371/eaao5654},
	eprint = {http://science.sciencemag.org/content/359/6371/eaao5654.full.pdf},
	journal = {Science}
}
@article{Benaglia2009,
author = {Benaglia, Tatiana and Chauveau, Didier and Hunter, David R and Young, Derek S},
doi = {10.18637/jss.v032.i06},
file = {:Users/Triandafillou/Downloads/papers/v32i06.pdf:pdf},
isbn = {1548-7660},
issn = {1548-7660},
journal = {J. Stat. Softw.},
keywords = {1,EM algorithm,R,and mixtools,cutpoint,em algorithm,introduction to finite mixtures,metric mixture,mixture of regressions,mo,model-based clustering,nonpara-,observe,often be divided into,populations of individuals may,semiparametric mixture,software,subgroups,unsupervised clustering,yet even when we},
mendeley-tags = {R,software},
number = {6},
pages = {1--29},
title = {{mixtools: An R package for analyzing mixture models}},
url = {https://www.jstatsoft.org/index.php/jss/article/view/v032i06},
volume = {32},
year = {2009}
}
@article{Ingolia2009,
author = {Ingolia, Nicholas T and Ghaemmaghami, Sina and Newman, John R S and Weissman, Jonathan S},
doi = {10.1126/science.1168978},
file = {:Users/Triandafillou/Downloads/papers/20493686.pdf:pdf},
issn = {1095-9203},
journal = {Science},
keywords = {5' Untranslated Regions,Codon,DNA,Fungal,Fungal: genetics,Fungal: metabolism,Gene Library,Genome,Introns,Messenger,Messenger: genetics,Messenger: metabolism,Peptide Chain Elongation,Peptide Chain Initiation,Protein Biosynthesis,RNA,Ribosomes,Ribosomes: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: biosynthesis,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Saccharomyces cerevisiae: physiology,Sequence Analysis,Translational,ribosome profiling,seq},
mendeley-tags = {ribosome profiling,seq},
number = {5924},
pages = {218--223},
pmid = {19213877},
title = {{Genome-wide analysis in vivo of Translation with Nucleotide Resolution Using Ribosome Profiling}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19213877},
volume = {324},
year = {2009}
}
@article{Shishkin2015,
archivePrefix = {arXiv},
arxivId = {15334406},
author = {Shishkin, Alexander A. and Giannoukos, Georgia and Kucukural, Alper and Ciulla, Dawn and Busby, Michele and Surka, Christine and Chen, Jenny and Bhattacharyya, Roby P. and Rudy, Robert F. and Patel, Milesh M. and Novod, Nathaniel and Hung, Deborah T. and Gnirke, Andreas and Garber, Manuel and Guttman, Mitchell and Livny, Jonathan},
doi = {10.1038/nmeth.3313},
eprint = {15334406},
file = {:Users/Triandafillou/Downloads/papers/documentasdf.pdf:pdf},
isbn = {1548-7091},
issn = {15487105},
journal = {Nat. Methods},
keywords = {methods,seq},
mendeley-tags = {methods,seq},
number = {4},
pages = {323--325},
pmid = {25730492},
title = {{Simultaneous generation of many RNA-seq libraries in a single reaction}},
volume = {12},
year = {2015}
}
@article{White2017,
annote = {Low pHi correlates with less proliferation - same as we see in yeast where cells that fail to recover intracellular pH are slower to re-enter the cell cycle.},
author = {White, Katharine A. and Grillo-Hill, Bree K. and Barber, Diane L.},
doi = {10.1242/jcs.195297},
file = {:Users/Triandafillou/Downloads/papers/663.full.pdf:pdf},
issn = {0021-9533},
journal = {J. Cell Sci.},
keywords = {cancer,cell cycle,growth rate,intracellular pH,mammalian cells,metabolism,metastasis,migration,ph,review},
mendeley-tags = {cancer,cell cycle,growth rate,intracellular pH,mammalian cells},
number = {4},
pages = {663--669},
title = {{Cancer cell behaviors mediated by dysregulated pH dynamics at a glance}},
url = {http://jcs.biologists.org/lookup/doi/10.1242/jcs.195297},
volume = {130},
year = {2017}
}
@article{Fels2009,
author = {Fels, Johannes and Orlov, Sergei N and Grygorczyk, Ryszard},
doi = {10.1016/j.bpj.2009.02.038},
file = {:Users/Triandafillou/Downloads/papers/PIIS0006349509006006.pdf:pdf},
issn = {0006-3495},
journal = {Biophys. J.},
keywords = {cell size,intracellular pH,mammalian cells},
mendeley-tags = {cell size,intracellular pH,mammalian cells},
number = {10},
pages = {4276--4285},
publisher = {Biophysical Society},
title = {{The Hydrogel Nature of Mammalian Cytoplasm Contributes to Osmosensing and Extracellular pH Sensing}},
url = {http://dx.doi.org/10.1016/j.bpj.2009.02.038},
volume = {96},
year = {2009}
}
@article{Zhong1999,
author = {Zhong, Min and Kim, Soon-jong and Wu, Carl},
file = {:Users/Triandafillou/Downloads/papers/J. Biol. Chem.-1999-Zhong-3135-40.pdf:pdf},
journal = {J. Biol. Chem.},
keywords = {HSF1,drosophila,heat shock,hsr,intracellular pH},
mendeley-tags = {HSF1,drosophila,heat shock,hsr,intracellular pH},
number = {5},
pages = {3135--3140},
title = {{Sensitivity of Drosophila Heat Shock Transcription Factor to Low pH}},
volume = {274},
year = {1999}
}
@article{Hussmann2015,
author = {Hussmann, Jeffrey A. and Patchett, Stephanie and Johnson, Arlen and Sawyer, Sara and Press, William H.},
doi = {10.1371/journal.pgen.1005732},
file = {:Users/Triandafillou/Downloads/journal.pgen.1005732.PDF:PDF},
isbn = {1553-7404},
issn = {15537404},
journal = {PLoS Genet.},
keywords = {modeling,ribosome profiling,seq},
mendeley-tags = {modeling,ribosome profiling,seq},
number = {12},
pages = {1--25},
pmid = {26656907},
title = {{Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast}},
volume = {11},
year = {2015}
}
@article{Hoffman2009,
author = {Hoffman, Robert A.},
doi = {10.1002/0471142956.cy0123s50},
isbn = {0471142956},
issn = {19349297},
journal = {Curr. Protoc. Cytom.},
pages = {1--17},
pmid = {19816921},
title = {{Pulse width for particle sizing}},
year = {2009}
}
@article{Bray2016,
archivePrefix = {arXiv},
arxivId = {1505.02710},
author = {Bray, Nicolas L and Pimentel, Harold and Melsted, P{\'{a}}ll and Pachter, Lior},
doi = {10.1038/nbt.3519},
eprint = {1505.02710},
file = {:Users/Triandafillou/Downloads/papers/nbt.3519.pdf:pdf},
isbn = {1087-0156$\backslash$r1546-1696},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {5},
pages = {525--527},
pmid = {27043002},
title = {{Near-optimal probabilistic RNA-seq quantification}},
url = {http://www.nature.com/doifinder/10.1038/nbt.3519},
volume = {34},
year = {2016}
}
@article{Shaner2004,
archivePrefix = {arXiv},
arxivId = {NIHMS183007},
author = {Shaner, Nathan C and Campbell, Robert E and Steinbach, Paul A and Giepmans, Ben N G and Palmer, Amy E and Tsien, Roger Y},
doi = {10.1038/nbt1037},
eprint = {NIHMS183007},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Shaner et al. - 2004 - Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein.pdf:pdf},
isbn = {1087-0156 (Print)$\backslash$r1087-0156 (Linking)},
issn = {1087-0156},
journal = {Nat. Biotechnol.},
number = {12},
pages = {1567--1572},
pmid = {15558047},
title = {{Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein}},
url = {http://www.nature.com/doifinder/10.1038/nbt1037},
volume = {22},
year = {2004}
}
@article{Gutierrez2017,
author = {Gutierrez, J. Ignacio and Brittingham, Greg and Want, Xuya and Fenyo, David and Holt, Liam J.},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Gutierrez et al. - 2017 - The largest SWISNF polyglutamine domain is a pH sensor.pdf:pdf},
journal = {bioRxiv},
title = {{The largest SWI/SNF polyglutamine domain is a pH sensor}},
year = {2017}
}
@article{Ashe2000,
author = {Ashe, Mark P and Long, Susan K De and Sachs, Alan B},
journal = {Mol. Biol. Cell},
keywords = {2DG,starvation,translation},
mendeley-tags = {2DG,starvation,translation},
pages = {833--848},
title = {{Glucose depletion rapidly inhibits translation initiation in yeast}},
volume = {11},
year = {2000}
}
@article{Schuller2017,
author = {Schuller, Anthony P. and Wu, Colin Chih-Chien and Dever, Thomas E. and Buskirk, Allen R. and Green, Rachel and Starosta, A.L. and Guydosh, N.R. and Johnson, W.E. and Wilson, D.N. and Buskirk, A.R. and Wilson, D.N.},
doi = {10.1016/j.molcel.2017.03.003},
issn = {10972765},
journal = {Mol. Cell},
keywords = {biochemistry,eIF5A,ribosome profiling,translation elongation,translation termination},
number = {0},
pages = {872--884},
pmid = {28392174},
publisher = {Elsevier Inc.},
title = {{eIF5A Functions Globally in Translation Elongation and Termination}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276517301703},
volume = {162},
year = {2017}
}
@article{Mohammad2016,
archivePrefix = {arXiv},
arxivId = {15334406},
author = {Mohammad, Fuad and Woolstenhulme, Christopher J. and Green, Rachel and Buskirk, Allen R.},
doi = {10.1016/j.celrep.2015.12.073},
eprint = {15334406},
isbn = {2211-1247},
issn = {22111247},
journal = {Cell Rep.},
number = {4},
pages = {686--694},
pmid = {26776510},
publisher = {The Authors},
title = {{Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling}},
url = {http://dx.doi.org/10.1016/j.celrep.2015.12.073},
volume = {14},
year = {2016}
}
@article{RibackKatanski2017,
author = {Riback, Joshua A and Katanski, Christopher D and Kear-Scott, Jamie L and Pilipenko, Evgeny V and Rojek, Alexandra E and Sosnick, Tobin R and Drummond, D Allan},
doi = {10.1016/j.cell.2017.02.027},
file = {:Users/Triandafillou/Downloads/papers/Article.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
pages = {1028--1040},
pmid = {28283059},
publisher = {Elsevier},
title = {{Stress-triggered phase separation is an adaptive, evolutionarily tuned response}},
url = {http://dx.doi.org/10.1016/j.cell.2017.02.027},
volume = {168},
year = {2017}
}
@article{Barnes1987,
author = {Barnes, C. A. and Singer, R. A. and Johnston, G. C.},
file = {:Users/Triandafillou/Downloads/papers/J. Bacteriol.-1987-Barnes-5622-5.pdf:pdf},
journal = {J. Bacteriol.},
keywords = {cell cycle,heat shock,induction},
mendeley-tags = {cell cycle,heat shock,induction},
number = {12},
pages = {5622--5625},
title = {{Production of heat shock protein is independent of cell cycle blockage in the yeast Saccharomyces cerevisiae}},
volume = {169},
year = {1987}
}
@article{Tzur2011,
abstract = {Cell size is a defining characteristic central to cell function and ultimately to tissue architecture. The ability to sort cell subpopulations of different sizes would facilitate investigation at genomic and proteomic levels of mechanisms by which cells attain and maintain their size. Currently available cell sorters, however, cannot directly measure cell volume electronically, and it would therefore be desirable to know which of the optical measurements that can be made in such instruments provide the best estimate of volume. We investigated several different light scattering and fluorescence measurements in several different cell lines, sorting cell fractions from the high and low end of distributions, and measuring volume electronically to determine which sorting strategy yielded the best separated volume distributions. Since we found that different optical measurements were optimal for different cell lines, we suggest that following this procedure will enable other investigators to optimize their own cell sorters for volume-based separation of the cell types with which they work.},
author = {Tzur, Amit and Moore, Jodene K. and Jorgensen, Paul and Shapiro, Howard M. and Kirschner, Marc W.},
doi = {10.1371/journal.pone.0016053},
file = {:Users/Triandafillou/Downloads/papers/Tzur2011.PDF:PDF},
isbn = {1932-6203 (Electronic)$\backslash$n1932-6203 (Linking)},
issn = {19326203},
journal = {PLoS One},
keywords = {flow cytometry},
mendeley-tags = {flow cytometry},
number = {1},
pages = {1--9},
pmid = {21283800},
title = {{Optimizing optical flow cytometry for cell volume-based sorting and analysis}},
volume = {6},
year = {2011}
}
@article{Bagar2009,
author = {Bagar, Tanja and Altenbach, Kirsten and Read, Nick D. and Ben{\v{c}}ina, Mojca},
doi = {10.1128/EC.00333-08},
file = {:Users/Triandafillou/Downloads/papers/Eukaryotic Cell-2009-Bagar-703-12.pdf:pdf},
issn = {15359778},
journal = {Eukaryot. Cell},
keywords = {pHluorin},
mendeley-tags = {pHluorin},
number = {5},
pages = {703--712},
pmid = {19286983},
title = {{Live-cell imaging and measurement of intracellular pH in filamentous fungi using a genetically encoded ratiometric probe}},
volume = {8},
year = {2009}
}
@article{Zheng2016,
author = {Zheng, Xu and Krakowiak, Joanna and Patel, Nikit and Beyzavi, Ali and Ezike, Jideofor and Khalil, Ahmad S and Pincus, David},
doi = {10.7554/eLife.18638},
file = {:Users/Triandafillou/Downloads/papers/e18638-download.pdf:pdf},
issn = {2050-084X},
journal = {Elife},
keywords = {general stress response,hsf1,hsp70,hsr,modeling},
mendeley-tags = {general stress response,hsf1,hsp70,hsr,modeling},
pages = {e18638},
pmid = {27831465},
title = {{Dynamic control of Hsf1 during heat shock by a chaperone switch and phosphorylation}},
url = {http://elifesciences.org/lookup/doi/10.7554/eLife.18638},
volume = {5},
year = {2016}
}
@article{Rowley1993,
annote = {START: p34 kinase complexes with cyclins to progress through the beginning of the cell cycle (START is a central control cycle in G1).

Cyclins are downregulated during heat stress (this makes sense)
-{\textgreater} cells in G1 are unbudded - they will appear smaller by flow/microscopy?

40-60 minutes at elevated temperature is sufficient to return to proliferation

CLN2 is required for re-entry into the cell cycle - if low pH inhibits the production of CLN2 but degradation is not imparied, we would expect to see a failure to resume growth},
author = {Rowley, Adele and Johnston, Gerald C and Butler, Braeden and Werner-Washburne, Margaret and Singer, Richard A},
doi = {10.1128/MCB.13.2.1034},
file = {:Users/Triandafillou/Downloads/papers/molcellb00014-0318.pdf:pdf},
isbn = {0270-7306 (Print)},
issn = {0270-7306},
journal = {Mol. Cell. Biol.},
keywords = {cell cycle,growth rate,heat shock},
mendeley-tags = {cell cycle,growth rate,heat shock},
number = {2},
pages = {1034--1041},
pmid = {8380888},
title = {{Heat shock-mediated cell cycle blockage and G1 cyclin expression in the yeast Saccharomyces cerevisiae.}},
url = {http://mcb.asm.org/content/13/2/1034.abstract},
volume = {13},
year = {1993}
}
@article{Mosser1990,
abstract = {The transcription of heat shock genes in response to physiological stress requires activation of heat shock transcription factor (HSF). Although the transcriptional response is most commonly induced by temperature elevation, the biochemical events involved in HSF activation in vivo can also be triggered at normal physiological temperatures by chemicals that inhibit metabolic processes. We have used a HeLa cell-free system in which HSF DNA-binding is activated by conditions that affect protein conformation, including increasing concentrations of hydrogen ions, urea, or nonionic detergents. Treatment with calcium ions also results in a concentration- and time-dependent activation of HSF in vitro. Pretreatment with each of these biochemical conditions reduces the temperature dependence for HSF activation in vitro. These results suggest that HSF is activated either directly by undergoing a conformational change or indirectly through interactions with unfolded proteins.},
author = {Mosser, D D and Kotzbauer, P T and Sarge, K D and Morimoto, R I},
doi = {10.1073/pnas.87.10.3748},
file = {:Users/Triandafillou/Downloads/papers/pnas01035-0122.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
number = {10},
pages = {3748--3752},
pmid = {2339118},
title = {{In vitro activation of heat shock transcription factor DNA-binding by calcium and biochemical conditions that affect protein conformation.}},
volume = {87},
year = {1990}
}
@article{Al-Sady2016,
annote = {gal1 system in s cer could replace urg system in s pombe.

Is qPCR necessary? For calibration maybe},
author = {Al-Sady, Bassem and Greenstein, Rachel A. and El-Samad, Hana J. and Braun, Sigurd and Madhani, Hiten D.},
doi = {10.1371/journal.pone.0159292},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Al-Sady et al. - 2016 - Sensitive and quantitative three-color protein imaging in fission yeast using spectrally diverse, recoded fluore.pdf:pdf},
issn = {19326203},
journal = {PLoS One},
keywords = {compensation,flow cytometry,fluorophores,single-cell,translation},
mendeley-tags = {compensation,flow cytometry,fluorophores,single-cell,translation},
number = {8},
pages = {1--20},
title = {{Sensitive and quantitative three-color protein imaging in fission yeast using spectrally diverse, recoded fluorescent proteins with experimentally-characterized in vivo maturation kinetics}},
volume = {11},
year = {2016}
}
@article{Solis2016,
author = {Solis, Eric J. and Pandey, Jai P and Zheng, Xu and Jin, Dexter X and Gupta, Piyush B and Airoldi, Edoardo M and Pincus, David and Denic, Vladimir},
doi = {10.1016/j.molcel.2016.05.014},
file = {:Users/Triandafillou/Downloads/papers/1-s2.0-S1097276516301514-main.pdf:pdf},
issn = {10972765},
journal = {Mol. Cell},
keywords = {hsf1},
mendeley-tags = {hsf1},
pages = {60--71},
pmid = {27320198},
title = {{Defining the essential function of yeast Hsf1 reveals a compact transcriptional program for Maintaining eukaryotic proteostasis}},
year = {2016}
}
@article{Coote1994,
author = {Coote, P J and Jones, M V and Seymour, I J and Rowe, D L and Ferdinando, D P and McArthur, A J and Cole, M B},
file = {:Users/Triandafillou/Downloads/papers/mic-140-8-1881.pdf:pdf},
issn = {1350-0872},
journal = {Microbiology},
keywords = {Adaptation,Cell Membrane Permeability,Fungal,Fungal Proteins,Fungal Proteins: physiology,Gene Expression Regulation,Glucose,Glucose: pharmacology,Heat-Shock Proteins,Heat-Shock Proteins: biosynthesis,Hot Temperature,Hydrogen-Ion Concentration,Intracellular Fluid,Intracellular Fluid: chemistry,Physiological,Proton-Translocating ATPases,Proton-Translocating ATPases: physiology,Protons,Saccharomyces cerevisiae,Saccharomyces cerevisiae: drug effects,Saccharomyces cerevisiae: enzymology,Saccharomyces cerevisiae: physiology,intracellular pH,membrane permeability,pma1,thermotolerance},
mendeley-tags = {intracellular pH,membrane permeability,pma1,thermotolerance},
number = {1},
pages = {1881--1890},
pmid = {7921241},
title = {{Activity of the plasma membrane H(+)-ATPase is a key physiological determinant of thermotolerance in Saccharomyces cerevisiae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/7921241},
volume = {140},
year = {1994}
}
@article{DeNadal2011,
author = {de Nadal, Eul{\`{a}}lia and Ammerer, Gustav and Posas, Francesc},
doi = {10.1038/nrg3055},
file = {:Users/Triandafillou/Downloads/papers/documsdgacent.pdf:pdf},
isbn = {1471-0064 (Electronic)$\backslash$r1471-0056 (Linking)},
issn = {1471-0056},
journal = {Nat. Rev. Genet.},
keywords = {gsr},
mendeley-tags = {gsr},
number = {12},
pages = {833--845},
pmid = {22048664},
title = {{Controlling gene expression in response to stress}},
url = {http://dx.doi.org/10.1038/nrg3055},
volume = {12},
year = {2011}
}
@article{Mendillo2012,
abstract = {Heat-Shock Factor 1 (HSF1), master regulator of the heat-shock response, facilitates malignant transformation, cancer cell survival, and proliferation in model systems. The common assumption is that these effects are mediated through regulation of heat-shock protein (HSP) expression. However, the transcriptional network that HSF1 coordinates directly in malignancy and its relationship to the heat-shock response have never been defined. By comparing cells with high and low malignant potential alongside their nontransformed counterparts, we identify an HSF1-regulated transcriptional program specific to highly malignant cells and distinct from heat shock. Cancer-specific genes in this program support oncogenic processes: cell-cycle regulation, signaling, metabolism, adhesion and translation. HSP genes are integral to this program, however, many are uniquely regulated in malignancy. This HSF1 cancer program is active in breast, colon and lung tumors isolated directly from human patients and is strongly associated with metastasis and death. Thus, HSF1 rewires the transcriptome in tumorigenesis, with prognostic and therapeutic implications. ?? 2012 Elsevier Inc.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Mendillo, Marc L. and Santagata, Sandro and Koeva, Martina and Bell, George W. and Hu, Rong and Tamimi, Rulla M. and Fraenkel, Ernest and Ince, Tan A. and Whitesell, Luke and Lindquist, Susan},
doi = {10.1016/j.cell.2012.06.031},
eprint = {NIHMS150003},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Mendillo et al. - 2012 - HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers.pdf:pdf},
isbn = {1097-4172; 0092-8674},
issn = {00928674},
journal = {Cell},
number = {3},
pages = {549--562},
pmid = {22863008},
title = {{HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers}},
volume = {150},
year = {2012}
}
@article{Zuleta2014,
abstract = {Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary to dissect cellular homeostatic strategies. Here we report the development of an automated flow cytometry robotic setup that enables real-time measurement of precise and simultaneous relative growth and protein synthesis rates of multiplexed microbial populations across many conditions. These measurements generate quantitative profiles of dynamically evolving protein synthesis and degradation rates. We demonstrate this setup in the context of gene regulation of the unfolded protein response (UPR) of Saccharomyces cerevisiae and uncover a dynamic and complex landscape of gene expression, growth dynamics and proteolysis following perturbations.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Zuleta, Ignacio A and Aranda-D{\'{i}}az, Andr{\'{e}}s and Li, Hao and El-Samad, Hana},
doi = {10.1038/nmeth.2879},
eprint = {NIHMS150003},
file = {:Users/Triandafillou/Downloads/papers/nmeth.2879.pdf:pdf},
isbn = {1548-7105},
issn = {1548-7105},
journal = {Nat. Methods},
keywords = {Automation,Flow Cytometry,Flow Cytometry: instrumentation,Flow Cytometry: methods,Fungal Proteins,Fungal Proteins: genetics,Fungal Proteins: metabolism,Gene Expression Regulation, Fungal,Gene Expression Regulation, Fungal: physiology,Saccharomyces cerevisiae,Saccharomyces cerevisiae: growth {\&} development,Saccharomyces cerevisiae: metabolism},
number = {4},
pages = {443--8},
pmid = {24608180},
title = {{Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry.}},
url = {http://dx.doi.org/10.1038/nmeth.2879},
volume = {11},
year = {2014}
}
@article{Munder2016,
author = {Munder, Matthias Christoph and Midtvedt, Daniel and Franzmann, Titus and Nuske, Elisabeth and Otto, Oliver and Herbig, Maik and Ulbricht, Elke and M{\"{u}}ller, Paul and Taubenberger, Anna and Maharana, Shovamayee and Malinovska, Liliana and Richter, Doris and Guck, Jochen and Zaburdaev, Vasily and Alberti, Simon},
doi = {10.7554/eLife.09347},
file = {:Users/Triandafillou/Downloads/papers/elife-09347-v1.pdf:pdf},
issn = {2050-084X},
journal = {Elife},
keywords = {crowding,intracellular pH,pHluorin,starvation},
mendeley-tags = {crowding,intracellular pH,pHluorin,starvation},
pages = {1--30},
title = {{A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy}},
url = {http://elifesciences.org/lookup/doi/10.7554/eLife.09347},
volume = {5},
year = {2016}
}
@article{Joyner2016,
annote = {Cells under continual acid loading by potassium sorbate do not show dramatic changes in cellular ATP concentration

Can we measure cellular volume?

Does treatment with 2,4 DNP change cellular volume?

Track the last author

Changing pH without changing cell volume? 2,4 DNP in pH 7.4 without glucose? What effect does glucose concentration have?},
author = {Joyner, Ryan P and Tang, Jeffrey H and Helenius, Jonne and Dultz, Elisa and Brune, Christiane and Holt, Liam J and Huet, Sebastien and Muller, Daniel J and Weis, Karsten},
doi = {10.7554/eLife.09376},
file = {:Users/Triandafillou/Downloads/papers/elife-09376-v2.pdf:pdf},
issn = {2050-084X},
journal = {Elife},
keywords = {intracellular pH},
mendeley-tags = {intracellular pH},
pages = {1--26},
title = {{A glucose-starvation response regulates the diffusion of macromolecules}},
volume = {5},
year = {2016}
}
@article{Parry2014,
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Parry, Bradley R. and Surovtsev, Ivan V. and Cabeen, Matthew T. and O'Hern, Corey S. and Dufresne, Eric R. and Jacobs-Wagner, Christine},
doi = {10.1016/j.cell.2013.11.028},
eprint = {NIHMS150003},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Parry et al. - 2014 - The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity.pdf:pdf},
isbn = {1097-4172 (Electronic)$\backslash$n0092-8674 (Linking)},
issn = {00928674},
journal = {Cell},
number = {1-2},
pages = {183--194},
pmid = {24361104},
publisher = {Elsevier Inc.},
title = {{The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity}},
url = {http://dx.doi.org/10.1016/j.cell.2013.11.028},
volume = {156},
year = {2014}
}
@article{Dechant2010,
author = {Dechant, Reinhard and Binda, Matteo and Lee, Sung Sik and Pelet, Serge and Winderickx, Joris and Peter, Matthias},
doi = {10.1038/emboj.2010.138},
file = {:Users/Triandafillou/Downloads/papers/2515.full.pdf:pdf},
isbn = {1460-2075 (Electronic)$\backslash$r0261-4189 (Linking)},
issn = {0261-4189},
journal = {EMBO J.},
keywords = {24DNP,cytosolic ph,glucose sensing,intracellular pH,metabolism,pH,pka,starvation},
mendeley-tags = {24DNP,intracellular pH,pH,starvation},
number = {15},
pages = {2515--2526},
pmid = {20581803},
publisher = {Nature Publishing Group},
title = {{Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V-ATPase.}},
url = {http://dx.doi.org/10.1038/emboj.2010.138},
volume = {29},
year = {2010}
}
@article{Miesenbock1998,
author = {Miesenb{\"{o}}ck, Gero and {De Angelis}, Dino A and Rothman, James E},
doi = {10.1038/28190},
file = {:Users/Triandafillou/Downloads/papers/394192a0.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$n0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
keywords = {Animals,Cells,Cultured,Cytoplasmic Granules,Cytoplasmic Granules: physiology,Exocytosis,Fluorescent Dyes,Green Fluorescent Proteins,HeLa Cells,Hippocampus,Hippocampus: cytology,Humans,Hydrogen-Ion Concentration,Indicators and Reagents,Luminescent Proteins,Luminescent Proteins: genetics,Molecular Sequence Data,Mutagenesis,Rats,Recombinant Fusion Proteins,Synaptic Transmission,Synaptic Vesicles,Synaptic Vesicles: physiology,pHluorin},
mendeley-tags = {pHluorin},
number = {6689},
pages = {192--5},
pmid = {9671304},
title = {{Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9671304},
volume = {394},
year = {1998}
}
@article{Martinez-Munoz2008,
author = {Mart{\'{i}}nez-Mu{\~{n}}oz, Gloria a. and Kane, Patricia},
doi = {10.1074/jbc.M710470200},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Mart{\'{i}}nez-Mu{\~{n}}oz, Kane - 2008 - Vacuolar and plasma membrane proton pumps collaborate to achieve cytosolic pH homeostasis in yeast.pdf:pdf},
isbn = {0021-9258 (Print)$\backslash$r0021-9258 (Linking)},
issn = {00219258},
journal = {J. Biol. Chem.},
keywords = {intracellular pH,pma1,vma1},
mendeley-tags = {intracellular pH,pma1,vma1},
number = {29},
pages = {20309--20319},
pmid = {18502746},
title = {{Vacuolar and plasma membrane proton pumps collaborate to achieve cytosolic pH homeostasis in yeast}},
volume = {283},
year = {2008}
}
@article{Valkonen2013,
author = {Valkonen, Mari and Mojzita, Dominik and Penttil{\"{a}}, Merja and Bencina, Mojca},
doi = {10.1128/AEM.02515-13},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Valkonen et al. - 2013 - Noninvasive high-throughput single-cell analysis of the intracellular pH of Saccharomyces cerevisiae by ratiome.pdf:pdf},
isbn = {0099-2240},
issn = {1098-5336},
journal = {Appl. Environ. Microbiol.},
keywords = {Cytosol,Cytosol: chemistry,Flow Cytometry,Flow Cytometry: methods,Fluorescent Dyes,Fluorescent Dyes: metabolism,Green Fluorescent Proteins,Green Fluorescent Proteins: metabolism,Hydrogen-Ion Concentration,Saccharomyces cerevisiae,Saccharomyces cerevisiae: chemistry,Single-Cell Analysis,Single-Cell Analysis: methods,Staining and Labeling,Staining and Labeling: methods,flow cytometry,intracellular pH,pHluorin},
mendeley-tags = {flow cytometry,intracellular pH,pHluorin},
number = {23},
pages = {7179--87},
pmid = {24038689},
title = {{Noninvasive high-throughput single-cell analysis of the intracellular pH of Saccharomyces cerevisiae by ratiometric flow cytometry.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3837762{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {79},
year = {2013}
}
@article{Petrovska2014,
author = {Petrovska, Ivana and N{\"{u}}ske, Elisabeth and Munder, Matthias C and Kulasegaran, Gayathrie and Malinovska, Liliana and Kroschwald, Sonja and Richter, Doris and Fahmy, Karim and Gibson, Kimberley and Verbavatz, Jean-Marc and Alberti, Simon},
doi = {10.7554/eLife.02409},
issn = {2050-084X},
journal = {Elife},
keywords = {glycolytic enzymes,intracellular pH,polymerization,starvation},
mendeley-tags = {glycolytic enzymes,intracellular pH,polymerization,starvation},
pages = {1--19},
title = {{Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation}},
url = {http://elifesciences.org/lookup/doi/10.7554/eLife.02409},
volume = {3},
year = {2014}
}
@article{Brett2005,
author = {Brett, Christopher L. and Tukaye, Deepali N. and Mukherjee, Sanchita and Rao, Rajini},
doi = {10.1091/mbc.E04},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Brett et al. - 2005 - The Yeast Endosomal Na(K)H Exchanger Nhx1 Regulates Cellular pH to Control Vesicle Trafficking.pdf:pdf},
isbn = {1059-1524 (Print)},
issn = {1059-1524},
journal = {Mol. Biol. Cell},
keywords = {NASA Discipline Evolutionary Biology,Non-NASA Center,intracellular pH,pHluorin},
mendeley-tags = {intracellular pH,pHluorin},
pages = {1396--1405},
pmid = {15509653},
title = {{The Yeast Endosomal Na+(K+)/H+ Exchanger Nhx1 Regulates Cellular pH to Control Vesicle Trafficking}},
volume = {16},
year = {2005}
}
@article{Dechant2014,
abstract = {Regulation of cell growth by nutrients is governed by highly conserved signaling pathways, yet mechanisms of nutrient sensing are still poorly understood. In yeast, glucose activates both the Ras/PKA pathway and TORC1, which coordinately regulate growth through enhancing translation and ribosome biogenesis and suppressing autophagy. Here, we show that cytosolic pH acts as a cellular signal to activate Ras and TORC1 in response to glucose availability. We demonstrate that cytosolic pH is sensitive to the quality and quantity of the available carbon source (C-source). Interestingly, Ras/PKA and TORC1 are both activated through the vacuolar ATPase (V-ATPase), which was previously identified as a sensor for cytosolic pH in vivo. V-ATPase interacts with two distinct GTPases, Arf1 and Gtr1, which are required for Ras and TORC1 activation, respectively. Together, these data provide a molecular mechanism for how cytosolic pH links C-source availability to the activity of signaling networks promoting cell growth.},
author = {Dechant, Reinhard and Saad, Shady and Ib{\'{a}}{\~{n}}ez, Alfredo J. and Peter, Matthias},
doi = {10.1016/j.molcel.2014.06.002},
file = {:Users/Triandafillou/Downloads/papers/1-s2.0-S1097276514004845-main.pdf:pdf},
isbn = {1097-4164 (Electronic)$\backslash$r1097-2765 (Linking)},
issn = {1097-4164},
journal = {Mol. Cell},
keywords = {ADP-Ribosylation Factor 1,ADP-Ribosylation Factor 1: metabolism,ADP-Ribosylation Factor 1: physiology,Cytosol,Cytosol: metabolism,Fungal,Gene Expression Regulation,Glucose,Glucose: metabolism,Monomeric GTP-Binding Proteins,Monomeric GTP-Binding Proteins: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: metabolism,Signal Transduction,TOR,Transcription Factors,Transcription Factors: metabolism,Vacuolar Proton-Translocating ATPases,Vacuolar Proton-Translocating ATPases: metabolism,growth rate,intracellular pH,metabolism,ras Proteins,ras Proteins: metabolism},
mendeley-tags = {TOR,growth rate,intracellular pH,metabolism},
number = {3},
pages = {409--21},
pmid = {25002144},
title = {{Cytosolic pH regulates cell growth through distinct GTPases, Arf1 and Gtr1, to promote ras/PKA and TORC1 activity}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25002144},
volume = {55},
year = {2014}
}
@article{Richter2010,
author = {Richter, Klaus and Haslbeck, Martin and Buchner, Johannes},
doi = {10.1016/j.molcel.2010.10.006},
file = {:Users/Triandafillou/Downloads/papers/1-s2.0-S1097276510007823-main.pdf:pdf},
issn = {10972765},
journal = {Mol. Cell},
number = {2},
pages = {253--266},
publisher = {Elsevier Inc.},
title = {{The Heat Shock Response: Life on the Verge of Death}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1097276510007823},
volume = {40},
year = {2010}
}
@article{Weigert2009,
author = {Weigert, Claudia and Steffler, Fabian and Kurz, Tomas and Shellhammer, Thomas H. and Methner, Frank J{\"{u}}rgen},
doi = {10.1128/AEM.00650-09},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Weigert et al. - 2009 - Application of a short intracellular pH method to flow cytometry for determining Saccharomyces cerevisiae vitali.pdf:pdf},
isbn = {4930314275},
issn = {00992240},
journal = {Appl. Environ. Microbiol.},
keywords = {flow cytometry,intracellular pH,pHluorin},
mendeley-tags = {flow cytometry,intracellular pH,pHluorin},
number = {17},
pages = {5615--5620},
pmid = {19581482},
title = {{Application of a short intracellular pH method to flow cytometry for determining Saccharomyces cerevisiae vitality}},
volume = {75},
year = {2009}
}
@article{Weitzel1985,
author = {Weitzel, G. and Pilatus, U. and Rensing, L.},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Weitzel, Pilatus, Rensing - 1985 - Similar Does Response of Heat Shock Protein Synthesis and Intracellular pH Change in Yeast.pdf:pdf},
journal = {Exp Cell Res},
keywords = {intracellular pH},
mendeley-tags = {intracellular pH},
pages = {252--256},
title = {{Similar Dose Response of Heat Shock Protein Synthesis and Intracellular pH Change in Yeast}},
year = {1985}
}
@article{Weitzel1987,
title = "The cytoplasmic pH, ATP content and total protein synthesis rate during heat-shock protein inducing treatments in yeast",
journal = "Exp. Cell Res.",
volume = "170",
number = "1",
pages = "64 - 79",
year = "1987",
issn = "0014-4827",
doi = "https://doi.org/10.1016/0014-4827(87)90117-0",
url = "http://www.sciencedirect.com/science/article/pii/0014482787901170",
author = "Gabriele Weitzel and Ulrich Pilatus and Ludger Rensing"
}
@article{Gasch2000,
author = {Gasch, Audrey P. and Spellman, Paul T. and Kao, Camilla M. and Carmel-Harel, Orna and Eisen, Michael B and Storz, Gisela and Botstein, David and Brown, Patrick O},
doi = {10.1091/mbc.11.12.4241},
file = {:Users/Triandafillou/Downloads/papers/mk004241.pdf:pdf},
isbn = {1059-1524},
issn = {1059-1524},
journal = {Mol. Biol. Cell},
number = {12},
pages = {4241--4257},
pmid = {11102521},
title = {{Genomic expression programs in the response of yeast cells to environmental changes.}},
volume = {11},
year = {2000}
}
@article{Coote1991,
abstract = {Incubation of Saccharomyces cerevisiae at sub-lethal temperatures results in an increase in thermotolerance. This process is dependent not only on the sub-lethal temperature but also on the duration of sub-lethal heating. This indicates that the mechanism inducing thermotolerance is a time/temperature dose response. Other factors that induce thermotolerance include exposure to ethanol, sorbic acid and low external pH values. These factors induce thermotolerance after incubation in the presence of protein synthesis inhibitors, and they are all known to affect the intracellular pH (pH(i)). The acquisition of increased thermotolerance is minimal with sub-lethal heating under neutral external pH conditions. However, when the external pH is reduced to 4.0 the level of induced thermotolerance increases to a maximum value. Using a specific ATPase inhibitor, diethylstilboestrol (DES), ATPase activity was shown to be essential for the cell to survive heat stress. In addition, measurement of acid efflux, or ATPase activity, revealed that proton pumping from the cell increased by approximately 50{\%} at sublethal temperatures that induce thermotolerance. This work has clearly implicated pH(i), perturbation as the triggering mechanism conferring thermotolerance on S. cererisiae.},
annote = {Seems to indicate cross-protection between both acid stress and alkaline stress with thermal stress.

Possible use of a chemical permeant (H+ pump ATPase inhibitor) to achieve intracellular acidification as well.},
author = {Coote, P. J. and Cole, M. B. and Jones, M. V.},
file = {:Users/Triandafillou/Downloads/papers/Coote et al. 1991 - Induction of increased thermotolerance in Saccharomyces cerevisiae may be triggered by a mechanism involving intracellular pH.pdf:pdf},
isbn = {0022-1287 (Print)$\backslash$r0022-1287 (Linking)},
issn = {00221287},
journal = {J. Gen. Microbiol.},
keywords = {induced thermotolerance,intracellular pH},
mendeley-tags = {induced thermotolerance,intracellular pH},
number = {7},
pages = {1701--1708},
pmid = {1835495},
title = {{Induction of increased thermotolerance in Saccharomyces cerevisiae may be triggered by a mechanism involving intracellular pH}},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0025894783{\&}partnerID=tZOtx3y1},
volume = {137},
year = {1991}
}
@article{Hahn2004,
author = {Hahn, Ji-sook and Hu, Zhanzhi and Thiele, Dennis J and Iyer, Vishwanath R},
doi = {10.1128/MCB.24.12.5249},
file = {:Users/Triandafillou/Downloads/papers/Mol. Cell. Biol.-2004-Hahn -5249-56.pdf:pdf},
isbn = {0270-7306 (Print)},
issn = {0270-7306},
journal = {Mol. Cell. Biol.},
keywords = {general stress response,hsf1,microarray},
mendeley-tags = {general stress response,hsf1,microarray},
number = {12},
pages = {5249--5256},
pmid = {15169889},
title = {{Genome-Wide Analysis of the Biology of Stress Responses through Heat Shock Transcription Factor}},
volume = {24},
year = {2004}
}
@article{Causton2001,
annote = {"Acid" stress - really intracellular pH stress I'd guess.

Environmental stress response - upregulation (2x - 5x) of well-detected transcripts in five or more time courses during 7 stress conditions (heat, small organic acid, alkali, oxidative stress, salt, osmolarity, diauxic shift).

Looking beyond the transcriptional response - response during recovery and how translation resumes normalcy

Induction of acid-induced genes depends on Msn2/Msn4. Msn2/4 are transported from cytoplasm to nucleus upon phosphorylation by PKA, Hog1, or TOR, depending on the stress.},
author = {Causton, H C and Ren, B and Koh, S S and Harbison, C T and Kanin, E and Jennings, E G and Lee, T I and True, H L and Lander, E S and Young, R A},
doi = {10.1091/mbc.12.2.323},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Causton et al. - 2001 - Remodeling of yeast genome expression in response to environmental changes.pdf:pdf},
isbn = {1059-1524 (Print)$\backslash$r1059-1524 (Linking)},
issn = {1059-1524},
journal = {Mol Biol Cell},
keywords = {*Gene Expression Regulation,*Saccharomyces cerevisiae Proteins,Adaptation,DNA-Binding Proteins/genetics,Enzymes/genetics,Enzymologic,Fungal,Fungal/drug effects,Gene Expression Profiling,Gene Expression Regulation,Genome,Heat-Shock Response/genetics,Hydrogen Peroxide/pharmacology,Hydrogen-Ion Concentration,Mutation,Non-U.S. Gov't,Osmotic Pressure,P.H.S.,Physiological/*genetics,Research Support,Salts/pharmacology,Transcription Factors/genetics,U.S. Gov't,Yeasts/drug effects/*physiology,gsr,transcriptomics},
mendeley-tags = {gsr,transcriptomics},
number = {2},
pages = {323--337},
pmid = {11179418},
title = {{Remodeling of yeast genome expression in response to environmental changes}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}dopt=Citation{\&}list{\_}uids=11179418},
volume = {12},
year = {2001}
}
@article{Swamy2014,
author = {Swamy, Krishna B S and Lin, Chih-Hsu and Yen, Ming-Ren and Wang, Chuen-Yi and Wang, Daryi},
doi = {10.1186/1471-2164-15-521},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Swamy et al. - 2014 - Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus.pdf:pdf},
issn = {1471-2164},
journal = {BMC Genomics},
keywords = {Antisense RNA,Evolution,Budding yeast,Stress,antisense rna,budding yeast,evolution,stress},
number = {1},
pages = {521},
title = {{Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus}},
url = {http://www.biomedcentral.com/1471-2164/15/521},
volume = {15},
year = {2014}
}
@article{Morano2012,
annote = {Transcription in yeast: driven by HSF1 (always present in the nucleus and constitutively bound to targets), MSN2/4 which are recruited to the nucleus upon oxidation of thioredoxin proteins, or when repression by nutrient-sensing proteins such as Snf1 and PKA are relieved.

Heat induced transcription factors (MSN2/4) are degraded in the nucles during constitutive activation, indicating a mechanism for capping the concentration of stress transcripts in the cytosol.

Here the close relationship between heat stress and ethanol stress is commented on. Yet some cross-protection studies have shown no degree of cross-protection between ethanol and heat.

Genes that are upregulated during heat shock: disaggregases, chaperones, small heat shock proteins, proteins associated with cell wall integrity, as well as selected glycolytic enzymes, hexose transporters, and metal-binding proteins.



Msn2/4 is blocked from entry to the nucleus by phosphorylation during log growth. This phosphorylation is in part done by Snf1

Yak1 activates HSF1 under low glucose conditions.

Heat shocked cells arrest in G1},
author = {Morano, Kevin A. and Grant, Chris M. and Moye-Rowley, W. Scott},
doi = {10.1534/genetics.111.128033},
file = {:Users/Triandafillou/Downloads/papers/1157.full.pdf:pdf},
isbn = {1943-2631 (Electronic)$\backslash$n0016-6731 (Linking)},
issn = {1943-2631},
journal = {Genetics},
keywords = {Cell Division,Chromatin Assembly and Disassembly,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Fungal,Fungal: genetics,Fungal: metabolism,Gene Expression Regulation,Genes,Heat-Shock Proteins,Heat-Shock Proteins: genetics,Heat-Shock Proteins: metabolism,Heat-Shock Response,Oxidative Stress,Protein Transport,RNA,Reactive Oxygen Species,Reactive Oxygen Species: metabolism,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Saccharomyces cerevisiae Proteins: genetics,Saccharomyces cerevisiae Proteins: metabolism,Saccharomyces cerevisiae: enzymology,Saccharomyces cerevisiae: genetics,Saccharomyces cerevisiae: metabolism,Trans-Activators,Trans-Activators: genetics,Trans-Activators: metabolism,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism,Transcriptional Activation,hsr,review},
mendeley-tags = {hsr,review},
pages = {1157--1195},
pmid = {22209905},
title = {{The response to heat shock and oxidative stress in Saccharomyces cerevisiae}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3316637{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {190},
year = {2012}
}
@article{Castells-Roca2011,
annote = {Trends during heat shock (mild, short):

-total poly-A RNA increases},
author = {Castells-Roca, Laia and Garc{\'{i}}a-Mart{\'{i}}nez, Jos{\'{e}} and Moreno, Joaqu{\'{i}}n and Herrero, Enrique and Bell{\'{i}}, Gemma and P{\'{e}}rez-Ort{\'{i}}n, Jos{\'{e}} E.},
doi = {10.1371/journal.pone.0017272},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Castells-Roca et al. - 2011 - Heat Shock Response in Yeast Involves Changes in Both Transcription Rates and mRNA Stabilities.pdf:pdf},
issn = {1932-6203},
journal = {PLoS One},
number = {2},
pages = {e17272},
title = {{Heat Shock Response in Yeast Involves Changes in Both Transcription Rates and mRNA Stabilities}},
url = {http://dx.plos.org/10.1371/journal.pone.0017272},
volume = {6},
year = {2011}
}
@article{Orij2009,
annote = {External pH in the media is 5.0.
Internal pH (cytosol) is close to neutral (6.9) under these conditions. Starved cells in the same conditions have an internal pH of 6

Internal pH of cells does not vary within external shifts from pH 3.0 to pH 7.5 as long as acidification is performed with small inorganic acids.

Treatment with sorbic acid (2mM) -{\textgreater} decrease from 7 to 6},
author = {Orij, Rick and Postmus, Jarne and Beek, Alex Ter and Brul, Stanley and Smits, Gertien J.},
doi = {10.1099/mic.0.022038-0},
file = {:Users/Triandafillou/Downloads/papers/268.pdf:pdf},
isbn = {1350-0872},
issn = {13500872},
journal = {Microbiology},
keywords = {intracellular pH,pHluorin},
mendeley-tags = {intracellular pH,pHluorin},
number = {1},
pages = {268--278},
pmid = {19118367},
title = {{In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth}},
volume = {155},
year = {2009}
}
@article{Orij2011,
annote = {How does the cell 'sense' pH? There are specific interactions that are perturbed in a pH-dependent manner (example: Opi1 and a lipid binding partner - Opi1 is released at acidic pH and travels to the nucleus to change transcription); there are also changes in the overall state of the cell, including solidification and crowding.

How does pH affect transcription/translation of heat shock genes?
- cells that express a mutant version of Pma1 (presumably less effective, whether that leads to lower intracellular pH unclear - need to look into that) produce less molecular chaperones during heat stress: whether this is because they already have high levels of chaperones becasuse they're constitutively stressed, or if it's because pH-change dynamics are perturbed during stress is not determined.
- cells that have mutated, less-effective Pma1 fail to grow at low pH, and grow slower overall, suggesting that they have a lower internal pH. However, additional experiments showed that the ability of these mutants to efflux protons was not signficiantly affected; may instead be related to resting membrane potential},
author = {Orij, Rick and Brul, Stanley and Smits, Gertien J.},
doi = {10.1016/j.bbagen.2011.03.011},
file = {:Users/Triandafillou/Downloads/papers/1-s2.0-S0304416511000602-main.pdf:pdf},
isbn = {0304-4165},
issn = {03044165},
journal = {Biochim. Biophys. Acta - Gen. Subj.},
keywords = {Cytosolic pH,Dynamic regulation,Homeostasis,Nutrient signalling,Second messenger,intracellular pH,review},
mendeley-tags = {intracellular pH,review},
number = {10},
pages = {933--944},
pmid = {21421024},
publisher = {Elsevier B.V.},
title = {{Intracellular pH is a tightly controlled signal in yeast}},
url = {http://dx.doi.org/10.1016/j.bbagen.2011.03.011},
volume = {1810},
year = {2011}
}
@article{Wallace2015,
author = {Wallace, Edward W.J. and Kear-Scott, Jamie L. and Pilipenko, Evgeny V. and Schwartz, Michael H. and Laskowski, Pawel R. and Rojek, Alexandra E. and Katanski, Christopher D. and Riback, Joshua A. and Dion, Michael F. and Franks, Alexander M. and Airoldi, Edoardo M. and Pan, Tao and Budnik, Bogdan A. and Drummond, D. Allan},
doi = {10.1016/j.cell.2015.08.041},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Wallace et al. - 2015 - Reversible, Specific, active aggregates of endogenous proteins assemble upon heat stress.pdf:pdf},
issn = {00928674},
journal = {Cell},
number = {6},
pages = {1286--1298},
publisher = {Elsevier Inc.},
title = {{Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867415010934},
volume = {162},
year = {2015}
}
@article{Liu2013,
abstract = {Cell survival in changing environments requires appropriate regulation of gene expression, including translational control. Multiple stress signaling pathways converge on several key translation factors, such as eIF4F and eIF2, and rapidly modulate messenger RNA (mRNA) translation at both the initiation and the elongation stages. Repression of global protein synthesis is often accompanied with selective translation of mRNAs encoding proteins that are vital for cell survival and stress recovery. The past decade has seen significant progress in our understanding of translational reprogramming in part due to the development of technologies that allow the dissection of the interplay between mRNA elements and corresponding binding proteins. Recent genome-wide studies using ribosome profiling have revealed unprecedented proteome complexity and flexibility through alternative translation, raising intriguing questions about stress-induced translational reprogramming. Many surprises emerged from these studies, including wide-spread alternative translation initiation, ribosome pausing during elongation, and reversible modification of mRNAs. Elucidation of the regulatory mechanisms underlying translational reprogramming will ultimately lead to the development of novel therapeutic strategies for human diseases. For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Liu, Botao and Qian, Shu-Bing},
doi = {10.1002/wrna.1212},
eprint = {NIHMS150003},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Liu, Qian - 2013 - Translational reprogramming in cellular stress response.pdf:pdf},
isbn = {2122633255},
issn = {1757-7012},
journal = {Wiley Interdiscip. Rev. RNA},
number = {June},
pages = {301--315},
pmid = {24375939},
title = {{Translational reprogramming in cellular stress response.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24375939},
volume = {5},
year = {2013}
}

@article{Cherkasov2013,
abstract = {Background Exposure of cells to severe heat stress causes not only misfolding and aggregation of proteins but also inhibition of translation and storage of mRNA in cytosolic heat stress granules (heat-SGs), limiting newly synthesized protein influx into overloaded proteome repair systems. How these two heat stress responses connect is unclear. Results Here, we show that both S. cerevisiae and D. melanogaster heat-SGs contain mRNA, translation machinery components (excluding ribosomes), and molecular chaperones and that heat-SGs coassemble with aggregates of misfolded, heat-labile proteins. Components in these mixed assemblies exhibit distinct molecular motilities reflecting differential trapping. We demonstrate that heat-SG disassembly and restoration of translation activity during heat stress recovery is intimately linked to disaggregation of damaged proteins present in the mixed assemblies and requires Hsp104 and Hsp70 activity. Conclusions Chaperone-driven protein disaggregation directly coordinates timing of translation reinitiation with protein folding capacity during cellular protein quality surveillance, enabling efficient protein homeostasis. ?? 2013 Elsevier Ltd.},
author = {Cherkasov, Valeria and Hofmann, Sarah and Druffel-Augustin, Silke and Mogk, Axel and Tyedmers, Jens and Stoecklin, Georg and Bukau, Bernd},
doi = {10.1016/j.cub.2013.09.058},
file = {:Users/Triandafillou/Library/Application Support/Mendeley Desktop/Downloaded/Cherkasov et al. - 2013 - Coordination of translational control and protein homeostasis during severe heat stress.pdf:pdf},
isbn = {1879-0445 (Electronic)$\backslash$r0960-9822 (Linking)},
issn = {09609822},
journal = {Curr. Biol.},
number = {24},
pages = {2452--2462},
pmid = {24291094},
publisher = {Elsevier Ltd},
title = {{Coordination of translational control and protein homeostasis during severe heat stress}},
url = {http://dx.doi.org/10.1016/j.cub.2013.09.058},
volume = {23},
year = {2013}
}


@ARTICLE{Cherkasov2015,
  title    = "Systemic control of protein synthesis through sequestration of
              translation and ribosome biogenesis factors during severe heat
              stress",
  author   = "Cherkasov, Valeria and Grousl, Tomas and Theer, Patrick and
              Vainshtein, Yevhen and Gl{\"a}{\ss}er, Christine and Mongis,
              Cyril and Kramer, G{\"u}nter and Stoecklin, Georg and Knop,
              Michael and Mogk, Axel and Bukau, Bernd",
  journal  = "FEBS Lett.",
  month    =  oct,
  year     =  2015,
  keywords = "Chaperones; Heat shock; Protein sequestration; Ribosome
              biogenesis; Stress granules; Translation"
}


@ARTICLE{Yoo2019,
  title    = "Cellular sensing by phase separation: Using the process, not just
              the products",
  author   = "Yoo, Haneul and Triandafillou, Catherine and Drummond, D Allan",
  journal  = "J. Biol. Chem.",
  volume   =  294,
  number   =  18,
  pages    = "7151--7159",
  year     =  2019,
  keywords = "Sup35; biophysics; biosensor; cell biology; cellular regulation;
              cyclic GMP-AMP synthase; phase separation; phase transition;
              poly(A)-binding protein; stress response",
  language = "en"
}

@ARTICLE{Hentze2016,
  title    = "Molecular mechanism of thermosensory function of human heat shock
              transcription factor Hsf1",
  author   = "Hentze, Nikolai and Le Breton, Laura and Wiesner, Jan and Kempf,
              Georg and Mayer, Matthias P",
  journal  = "Elife",
  volume   =  5,
  month    =  jan,
  year     =  2016,
  keywords = "biochemistry; biophysics; conformational dynamics; heat shock
              response; heat shock transcription factor; hydrogen exchange mass
              spectrometry; none; structural biology; temperature response;
              thermosensor",
  language = "en"
}


@ARTICLE{Rikhvanov2014,
  title    = "Mechanism of Saccharomyces cerevisiae yeast cell death induced by
              heat shock. Effect of cycloheximide on thermotolerance",
  author   = "Rikhvanov, E G and Fedoseeva, I V and Varakina, N N and Rusaleva,
              T M and Fedyaeva, A V",
  journal  = "Biochemistry",
  volume   =  79,
  number   =  1,
  pages    = "16--24",
  month    =  jan,
  year     =  2014,
  language = "en"
}


@ARTICLE{Tanabe1997,
  title    = "Different thresholds in the responses of two heat shock
              transcription factors, {HSF1} and {HSF3}",
  author   = "Tanabe, M and Nakai, A and Kawazoe, Y and Nagata, K",
  journal  = "J. Biol. Chem.",
  volume   =  272,
  number   =  24,
  pages    = "15389--15395",
  month    =  jun,
  year     =  1997,
  language = "en"
}



@Manual{R,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2017},
  url = {https://www.R-project.org/},
}


@ARTICLE{Beckmann1992,
  title    = "Examining the function and regulation of hsp 70 in cells
              subjected to metabolic stress",
  author   = "Beckmann, R P and Lovett, M and Welch, W J",
  journal  = "J. Cell Biol.",
  volume   =  117,
  number   =  6,
  pages    = "1137--1150",
  month    =  jun,
  year     =  1992,
  language = "en"
}


@ARTICLE{Albert2019,
  title     = "A ribosome assembly stress response regulates transcription to
               maintain proteome homeostasis",
  author    = "Albert, Benjamin and Kos-Braun, Isabelle C and Henras, Anthony K
               and Dez, Christophe and Rueda, Maria Paula and Zhang, Xu and
               Gadal, Olivier and Kos, Martin and Shore, David",
  journal   = "Elife",
  publisher = "eLife Sciences Publications, Ltd",
  volume    =  8,
  pages     = "e45002",
  month     =  may,
  year      =  2019
}



@Book{ggplot,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2009},
  isbn = {978-0-387-98140-6},
  url = {http://ggplot2.org},
}

@Manual{tidyverse,
  title = {tidyverse: Easily Install and Load the 'Tidyverse'},
  author = {Hadley Wickham},
  year = {2017},
  note = {R package version 1.2.1},
  url = {https://CRAN.R-project.org/package=tidyverse},
}


@article{Carja2017,
author = {Carja, Oana and Xing, Tongji and Wallace, Edward W.J. and Plotkin, Joshua B. and Shah, Premal},
doi = {10.1186/s12859-017-1873-8},
file = {:Users/Triandafillou/Downloads/papers/riboviz.pdf:pdf},
isbn = {1285901718738},
issn = {14712105},
journal = {BMC Bioinformatics},
keywords = {Database,Ribosome profiling,Translation quantification,Visualization and comparison tool-kit},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {1},
pages = {10--13},
pmid = {29070028},
publisher = {BMC Bioinformatics},
title = {{Riboviz: Analysis and visualization of ribosome profiling datasets}},
volume = {18},
year = {2017}
}

@ARTICLE{Martin2011Cutadapt,
  author = {Marcel Martin},
  title = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
  journal = {EMBnet.journal},
  year = 2011,
  volume = 17,
  pages = {10--12},
  number = 1,
  doi = {http://dx.doi.org/10.14806/ej.17.1.200},
  url = {http://journal.embnet.org/index.php/embnetjournal/article/view/200}
}

@article{Orij2012,
author = {Orij, Rick and Urbanus, Malene L and Vizeacoumar, Franco J and Giaever, Guri and Boone, Charles and Nislow, Corey and Brul, Stanley and Smits, Gertien J},
doi = {10.1186/gb-2012-13-9-r80},
file = {:Users/Triandafillou/Downloads/papers/gb-2012-13-9-r80.pdf:pdf},
isbn = {1465-6914 (Electronic)$\backslash$n1465-6906 (Linking)},
issn = {1465-6906},
journal = {Genome Biol.},
keywords = {growth rate,intracellular pH},
mendeley-groups = {Grad School/Research,Grad School/Research/intracellular pH,Grad School/Research/intracellular pH/constitutive,Grad School/Research/work/stress-ph-paper},
mendeley-tags = {growth rate,intracellular pH},
number = {9},
pages = {R80},
pmid = {23021432},
publisher = {BioMed Central Ltd},
title = {{Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pHc in Saccharomyces cerevisiae.}},
url = {http://genomebiology.com/2012/13/9/R80},
volume = {13},
year = {2012}
}


@article{Glover1998,
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Glover, John R. and Lindquist, Susan},
doi = {10.1016/S0092-8674(00)81223-4},
eprint = {NIHMS150003},
isbn = {0092-8674 (Print)$\backslash$r0092-8674 (Linking)},
issn = {00928674},
journal = {Cell},
number = {1},
pages = {73--82},
pmid = {9674429},
title = {{Hsp104, Hsp70, and Hsp40: A novel chaperone system that rescues previously aggregated proteins}},
volume = {94},
year = {1998}
}

@article{Vabulas2010,
author = {Vabulas, R Martin and Raychaudhuri, Swasti and Hayer-Hartl, Manajit and Hartl, F Ulrich},
doi = {10.1101/cshperspect.a004390},
isbn = {1943-0264},
issn = {19430264},
journal = {Cold Spring Harb. Perspect. Biol.},
pages = {1--19},
pmid = {21123396},
title = {{Protein folding in the cytoplasm and the heat shock response}},
year = {2010}
}

@article{Lindquist1986,
author = {Lindquist, Susan},
journal = {Ann. Rev. Biochem},
pages = {1151--91},
title = {{The Heat-Shock Response}},
volume = {55},
year = {1986}
}


@article{Molliex2015,
author = {Molliex, Amandine and Temirov, Jamshid and Lee, Jihun and Coughlin, Maura and Kanagaraj, Anderson P. and Kim, Hong Joo and Mittag, Tanja and Taylor, J Paul},
doi = {10.1016/j.cell.2015.09.015},
issn = {0092-8674},
journal = {Cell},
pages = {123--133},
title = {{Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization}},
url = {http://dx.doi.org/10.1016/j.cell.2015.09.015},
volume = {163},
year = {2015}
}


@article{Kroschwald2015,
author = {Kroschwald, Sonja and Maharana, Shovamayee and Mateju, Daniel and Malinovska, Liliana and N{\"{u}}ske, Elisabeth and Poser, Ina and Richter, Doris and Alberti, Simon},
doi = {10.7554/eLife.06807},
issn = {2050-084X},
journal = {Elife},
pages = {1--32},
title = {{Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules}},
url = {http://elifesciences.org/lookup/doi/10.7554/eLife.06807},
volume = {4},
year = {2015}
}

@Inbook{Ishizawa2014,
author="Ishizawa, Kimiharu",
editor="van Dongen, Joost T. and Licausi, Francesco",
title="Intracellular pH Regulation of Plant Cells Under Anaerobic Conditions",
bookTitle="Low-Oxygen Stress in Plants: Oxygen Sensing and Adaptive Responses to Hypoxia",
year="2014",
publisher="Springer Vienna",
address="Vienna",
pages="59--74",
isbn="978-3-7091-1254-0",
doi="10.1007/978-3-7091-1254-0_4",
url="https://doi.org/10.1007/978-3-7091-1254-0_4"
}

@article{Hedges2015,
archivePrefix = {arXiv},
arxivId = {1412.4312v1},
author = {Hedges, S. Blair and Marin, Julie and Suleski, Michael and Paymer, Madeline and Kumar, Sudhir},
doi = {10.1093/molbev/msv037},
eprint = {1412.4312v1},
file = {:Users/Triandafillou/Downloads/papers/msv037.pdf:pdf},
isbn = {1537-1719 (Electronic)$\backslash$r0737-4038 (Linking)},
issn = {15371719},
journal = {Mol. Biol. Evol.},
keywords = {biodiversity,diversification,speciation,timetree,tree of life},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {4},
pages = {835--845},
pmid = {25739733},
title = {{Tree of life reveals clock-like speciation and diversification}},
volume = {32},
year = {2015}
}
@article{Tombaugh1993,
author = {Tombaugh, Geoffrey C. and Sapolsky, Robert M.},
doi = {10.1111/j.1471-4159.1993.tb03589.x},
isbn = {0022-3042 (Print)$\backslash$r0022-3042 (Linking)},
issn = {14714159},
journal = {J. Neurochem.},
keywords = {Enerav metabolism,Excitotoxicity,Hippocampus,Infarction,Ischemia,Lactic acidosis,Selective neuronal necrosis},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {3},
pages = {793--803},
pmid = {8360684},
title = {{Evolving concepts about the role of acidosis in ischemic neuropathology}},
volume = {61},
year = {1993}
}
@article{Bright1992,
author = {Bright, Catherine M. and Ellis, David},
doi = {10.1113/expphysiol.1992.sp003570},
issn = {1469445X},
journal = {Exp. Physiol.},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
pages = {165--175},
pmid = {1311938},
title = {{Intracellular pH changes induced by hypoxia and anoxia in isolated sheep heart Purkinje fibres}},
volume = {77},
year = {1992}
}
@article{Jain2014,
author = {Jain, Kanika and Suryakumar, Geetha and Ganju, Lilly and Singh, Shashi Bala},
doi = {10.1007/s12192-014-0504-9},
isbn = {1466-1268 (Electronic)$\backslash$r1355-8145 (Linking)},
issn = {14661268},
journal = {Cell Stress Chaperones},
keywords = {Heart,Heat shock response,Hsp70,Hypoxia,NF-$\kappa$B,Nitric oxide},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {6},
pages = {801--812},
pmid = {24590457},
title = {{Differential hypoxic tolerance is mediated by activation of heat shock response and nitric oxide pathway}},
volume = {19},
year = {2014}
}
@article{Michaud2011,
author = {Michaud, M. Robert and Teets, Nicholas M. and Peyton, Justin T. and Blobner, Brandon M. and Denlinger, David L.},
doi = {10.1016/j.jinsphys.2010.11.007},
isbn = {0022-1910},
issn = {00221910},
journal = {J. Insect Physiol.},
keywords = {Heat shock factor,Heat shock proteins,Hypoxia,Sirtuin},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {1},
pages = {203--210},
pmid = {21075112},
title = {{Heat shock response to hypoxia and its attenuation during recovery in the flesh fly, Sarcophaga crassipalpis}},
url = {http://dx.doi.org/10.1016/j.jinsphys.2010.11.007},
volume = {57},
year = {2011}
}


@article{Zid2014,
annote = {Upregulated mRNA =$\backslash$ upregulated protein!!},
author = {Zid, Brian M. and O'Shea, Erin K.},
doi = {10.1038/nature13578},
isbn = {0028-0836},
issn = {0028-0836},
journal = {Nature},
keywords = {HSF1,PBs,SGs,starvation,translation},
number = {7520},
pages = {117--121},
pmid = {25119046},
publisher = {Nature Publishing Group},
title = {{Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast}},
url = {http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13578.html?WT.ec{\_}id=NATURE-20140807},
volume = {514},
year = {2014}
}

@article{Farny2009,
author = {Farny, Natalie G and Kedersha, Nancy L and Silver, Pamela A},
doi = {10.1261/rna.1684009.initiation},
journal = {RNA},
keywords = {arsenite,drosophila,eif2a,heat shock,stress granules},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
pages = {1814--1821},
title = {{Metazoan stress granule assembly is mediated by P-eIF2$\alpha$-dependent and -independent mechanisms}},
volume = {15},
year = {2009}
}






@article{Thomas1979,
author = {Thomas, John A. and Buchsbaum, Robert N. and Zimniak, Andrzej and Racker, Efraim},
doi = {10.1021/bi00578a012},
file = {:Users/Triandafillou/Downloads/papers/bi00578a012.pdf:pdf},
isbn = {0006-2960},
issn = {15204995},
journal = {Biochemistry},
keywords = {intracellular pH,nigericin,pH manipulation},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
mendeley-tags = {intracellular pH,nigericin,pH manipulation},
number = {11},
pages = {2210--2218},
pmid = {36128},
title = {{Intracellular pH measurements in Ehrlich Ascites tumor cells utilizing spectroscopic probes generated in situ}},
volume = {18},
year = {1979}
}
@article{Christen1982,
author = {Christen, Richard; and Schackmann, Robert W; and Shapiro, Bennett M;},
file = {:Users/Triandafillou/Downloads/papers/14881.full.pdf:pdf},
isbn = {0021-9258 (Print)$\backslash$r0021-9258 (Linking)},
issn = {0021-9258},
journal = {J Biol Chem},
keywords = {ionophore,nigericin,pH manipulation},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
mendeley-tags = {ionophore,nigericin,pH manipulation},
number = {24},
pages = {14881--14890},
pmid = {7174670},
title = {{Elevation of the intracellular pH activates respiration and motility of sperm of the sea urchin, Strongylocentrotus purpuratus}},
volume = {257},
year = {1982}
}
@article{Nakata2010,
author = {Nakata, Eiji and Yukimachi, Yoshihiro and Nazumi, Yoshijiro and Uto, Yoshihiro and Maezawa, Hiroshi and Hashimoto, Toshihiro and Okamoto, Yasuko and Hori, Hitoshi},
doi = {10.1039/c003167d},
file = {:Users/Triandafillou/Downloads/papers/c003167d.pdf:pdf},
isbn = {1359-7345},
issn = {1359-7345},
journal = {Chem. Commun.},
keywords = {nigericin,pH manipulation},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
mendeley-tags = {nigericin,pH manipulation},
number = {20},
pages = {3526},
pmid = {20379600},
title = {{A newly designed cell-permeable SNARF derivative as an effective intracellular pH indicator}},
url = {http://xlink.rsc.org/?DOI=c003167d},
volume = {46},
year = {2010}
}
@incollection{Freedman2012,
author = {Freedman, Jeffrey C.},
booktitle = {Cell Physiol. Source B.},
chapter = {4},
doi = {10.1016/B978-0-12-387738-3.00004-4},
isbn = {9780123877383},
pages = {61--66},
title = {{Ionophores in planar lipid bilayers}},
year = {2012}
}

@article{Modi2009,
author = {Modi, Souvik and {M G}, Swetha and Goswami, Debanjan and Gupta, Gagan D and Mayor, Satyajit and Krishnan, Yamuna},
doi = {10.1038/nnano.2009.83},
file = {:Users/Triandafillou/Downloads/papers/document.pdf:pdf},
isbn = {1748-3387},
issn = {1748-3387},
journal = {Nat. Nanotechnol.},
keywords = {nigericin},
mendeley-tags = {nigericin},
number = {5},
pages = {325--330},
pmid = {19421220},
title = {{A DNA nanomachine that maps spatial and temporal pH changes inside living cells.}},
volume = {4},
year = {2009}
}

@article {Pincus2018,
	author = {Pincus, David and Anandhakumar, Jayamani and Thiru, Prathapan and Guertin, Michael J and Erkine, Alexander M. and Gross, David S},
	title = {Genetic and Epigenetic Determinants Establish a Continuum of {H}sf1 Occupancy and Activity Across the Yeast Genome},
	year = {2018},
	doi = {10.1101/306704},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2018/04/23/306704},
	eprint = {https://www.biorxiv.org/content/early/2018/04/23/306704.full.pdf},
	journal = {bioRxiv}
}

@article{Hartwell1974,
abstract = {Images:},
author = {Hartwell, L H},
doi = {38(2): 164–198.},
file = {:Users/Triandafillou/Downloads/papers/bactrev00045-0058.pdf:pdf},
isbn = {0005-3678 (Print)$\backslash$r0005-3678 (Linking)},
issn = {0005-3678},
journal = {Bacteriol. Rev.},
number = {2},
pages = {164--198},
pmid = {4599449},
title = {{Saccharomyces cerevisiae cell cycle.}},
volume = {38},
year = {1974}
}

@article{Rosebrock2017,
author = {Rosebrock, Adam P.}, 
title = {Analysis of the Budding Yeast Cell Cycle by Flow Cytometry},
volume = {2017}, 
number = {1}, 
pages = {pdb.prot088740}, 
year = {2017}, 
doi = {10.1101/pdb.prot088740}, 
abstract ={DNA synthesis is one of the landmark events in the cell cycle: G1 cells have one copy of the genome, S phase cells are actively engaged in DNA synthesis, and G2 cells have twice as much nuclear DNA as G1 cells. Cellular DNA content can be measured by staining with a fluorescent dye followed by a flow-cytometric readout. This method provides a quantitative measurement of cell cycle position on a cell-by-cell basis at high speed. Using flow cytometry, tens of thousands of single-cell measurements can be generated in a few seconds. This protocol details staining of cells of the budding yeast Saccharomyces cerevisiae for flow cytometry using Sytox Green dye in a method that can be scaled widely—from one sample to many thousands and operating on inputs ranging from 1 million to more than 100 million cells. Flow cytometry is preferred over light microscopy or Coulter analyses for the analysis of the cell cycle as DNA content and cell cycle position are being directly measured.}, 
URL = {http://cshprotocols.cshlp.org/content/2017/1/pdb.prot088740.abstract}, 
eprint = {http://cshprotocols.cshlp.org/content/2017/1/pdb.prot088740.full.pdf+html}, 
journal = {Cold Spring Harbor Protocols} 
}

@article{Panaretou1990,
author = {Panaretou, B. and Piper, P. W.},
doi = {10.1099/00221287-136-9-1763},
issn = {0022-1287},
journal = {J. Gen. Microbiol.},
keywords = {pma1},
pages = {1763--1770},
title = {{Plasma-membrane ATPase action affects several stress tolerances of Saccharomyces cerevisiae and Schizosaccharomyces pombe as well as the extent and duration of the heat shock response}},
volume = {136},
year = {1990}
}

@article{Chowdhary2017,
author = {Chowdhary, Surabhi and Kainth, Amoldeep S and Gross, David S},
journal = {Mol. Cell. Biol.},
keywords = {3c,budding yeast,chromatin,chromosome,conformation capture,gene coalescence,gene looping,genes,heat shock protein,hsf1,interchromosomal clustering,live cell imaging,nuclear architecture,received 26 may 2017,returned for,transcription factories},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {24},
pages = {1--22},
title = {{Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress}},
volume = {37},
year = {2017}
}

@article{Chowdhary2018,
author = {Chowdhary, Surabhi and Kainth, Amoldeep S and Pincus, David and Gross, David S},
doi = {10.1101/400499},
journal = {bioRxiv},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
title = {{Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci Upon Heat Shock}},
url = {http://dx.doi.org/10.1101/400499},
year = {2018}
}

@article{Masser2019,
author = {Masser, Anna E and Kang, Wenjing and Roy, Joydeep and Kaimal, Jayasankar M and Quintana-Cordero, Jany and Friedl{\"{a}}nder, Marc R and Andr{\'{e}}asson, Claes},
doi = {10.7554/eLife.47791},
issn = {2050-084X},
journal = {Elife},
pages = {1--27},
pmid = {31552827},
title = {{Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/31552827},
volume = {8},
year = {2019}
}


@article{DeBoer2012,
author = {{De Boer}, Carl G. and Hughes, Timothy R.},
doi = {10.1093/nar/gkr993},
file = {:Users/Triandafillou/Downloads/papers/gkr993.pdf:pdf},
issn = {03051048},
journal = {Nucleic Acids Res.},
mendeley-groups = {Grad School/thesis/methods},
pages = {D169--D179},
title = {{YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities}},
volume = {40},
year = {2012}
}

@article{Venters2011,
author = {Venters, Bryan J. and Wachi, Shinichiro and Mavrich, Travis N. and Andersen, Barbara E. and Jena, Peony and Sinnamon, Andrew J. and Jain, Priyanka and Rolleri, Noah S. and Jiang, Cizhong and Hemeryck-Walsh, Christine and Pugh, B. Franklin},
doi = {10.1016/j.molcel.2011.01.015},
file = {:Users/Triandafillou/Downloads/papers/PIIS1097276511000426.pdf:pdf},
issn = {10972765},
journal = {Mol. Cell},
mendeley-groups = {Grad School/Research/work/stress-ph-paper},
number = {4},
pages = {480--492},
pmid = {21329885},
publisher = {Elsevier Inc.},
title = {{A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces}},
url = {http://dx.doi.org/10.1016/j.molcel.2011.01.015},
volume = {41},
year = {2011}
}
@article{Triandafillou2020,
author = {Triandafillou, Catherine G and Drummond, D. Allan},
doi = {10.21769/BioProtoc.3653},
file = {:Users/Triandafillou/Downloads/papers/Bio-protocol3653.pdf:pdf},
journal = {bio-protocol},
number = {12},
pages = {1--14},
title = {{Live Cell Measurement of the Intracellular pH of Yeast by Flow Cytometry Using a Genetically-Encoded Fluorescent Reporter Catherine}},
volume = {10},
year = {2020}
}
