Chapter XVIII Viable counts and Viability, Methods in Microbiology, pp.611-628, 1969. ,
Estimation of dormant Micrococcus luteus cells by penicillin lysis and by resuscitation in cell-free spent culture medium at high dilution, FEMS Microbiol Lett, vol.115, p.347, 1994. ,
Schrö dinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems, Microbiome, vol.5, p.28810907, 2017. ,
Survival strategies of bacteria in the natural environment, Microbiol Rev, vol.51, pp.365-379, 1987. ,
Nonculturable bacteria: programmed survival forms or cells at death's door?, BioEssays News Rev Mol Cell Dev Biol, vol.25, pp.204-211, 2003. ,
Recent findings on the viable but nonculturable state in pathogenic bacteria, FEMS Microbiol Rev, vol.34, pp.415-425, 2010. ,
Viable but Nonculturable and Persister Cells Coexist Stochastically and Are Induced by Human Serum, Infect Immun, vol.83, pp.4194-4203, 2015. ,
The importance of the viable but non-culturable state in human bacterial pathogens, Front Microbiol, vol.5, p.258, 2014. ,
Evidence for viable but nonculturable yeasts in botrytis-affected wine, J Appl Microbiol, vol.99, pp.85-93, 2005. ,
Characterization of the Viable but Nonculturable (VBNC) State in Saccharomyces cerevisiae, PloS One, vol.8, 2013. ,
Characterization of the "viable but nonculturable" (VBNC) state in the wine spoilage yeast Brettanomyces, Food Microbiol, vol.30, pp.438-447, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00939790
Reactivation of dormant/latent fungal infection, J Infect, vol.77, pp.463-468, 2018. ,
Pseudomonas aeruginosa displays a dormancy phenotype during long-term survival in water, PloS One, vol.13, p.198384, 2018. ,
Internalization of Salmonella by macrophages induces formation of nonreplicating persisters, Science, vol.343, pp.204-208, 2014. ,
Biological concepts in recurrent Plasmodium vivax malaria, Parasitology, vol.145, pp.1765-1771, 2018. ,
The normalcy of dormancy: common themes in microbial quiescence, Cell Host Microbe, vol.13, pp.643-651, 2013. ,
Epidemiological evidence for dormant Cryptococcus neoformans infection, J Clin Microbiol, vol.37, pp.3204-3209, 1999. ,
Isolation of Cryptococcus neoformans var. gattii from an Asian patient in France: evidence for dormant infection in healthy subjects, J Med Vet Mycol Bi-Mon Publ Int Soc Hum Anim Mycol, vol.30, pp.395-397, 1992. ,
Philadelphia : Lea & Febiger; 1992 ,
Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis, Lancet Infect Dis, vol.17, p.873, 2017. ,
The primary pulmonary lymph node complex of crytptococcosis, Am J Clin Pathol, vol.65, pp.83-92, 1976. ,
Pathogenesis of pulmonary Cryptococcus neoformans infection in the rat, Infect Immun, vol.62, pp.4755-4761, 1994. ,
Cryptococcus neoformans host adaptation: toward biological evidence of dormancy, mBio, vol.6, pp.2580-2594, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01405218
Skeletal muscle stem cells adopt a dormant cell state post mortem and retain regenerative capacity, Nat Commun, vol.3, p.903, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00711881
Nutrient-starved, non-replicating Mycobacterium tuberculosis requires respiration, ATP synthase and isocitrate lyase for maintenance of ATP homeostasis and viability, Microbiol Read Engl, vol.156, pp.81-87, 2010. ,
Evaluation of fluorescent dyes for measuring intracellular glutathione content in primary cultures of human neurons and neuroblastoma SH-SY5Y, Cytometry A, vol.51, pp.16-25, 2003. ,
A combination of flow cytometry and traditional screening using chemicals to isolate high glutathione-producing yeast mutants, Biosci Biotechnol Biochem, vol.76, pp.1085-1090, 2012. ,
In Vitro Analysis of Metabolites Secreted during Infection of Lung Epithelial Cells by Cryptococcus neoformans, PloS One, vol.11, p.153356, 2016. ,
Quorum sensing-mediated, cell density-dependent regulation of growth and virulence in Cryptococcus neoformans, mBio, vol.5, pp.986-999, 2013. ,
Tissue Changes and Tissue Diagnosis in Cryptococcosis: A Study of 26 Cases, Am J Clin Pathol, vol.25, p.14, 1955. ,
The Pulmonary Lesions in Cryptococcosis with Special References to Subpleural Nodules, Am J Clin Pathol, vol.24, p.1381, 1954. ,
Deciphering the model pathogenic fungus Cryptococcus neoformans, Nat Rev Microbiol, vol.3, pp.753-764, 2005. ,
The essence of yeast quiescence, FEMS Microbiol Rev, vol.36, p.21658086, 2012. ,
Hypoxia and fungal pathogenesis: to air or not to air?, Eukaryot Cell, vol.11, pp.560-570, 2012. ,
An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence, Infect Immun, vol.64, pp.2062-2069, 1996. ,
Deletion of Cryptococcus neoformans AIF ortholog promotes chromosome aneuploidy and fluconazole-resistance in a metacaspase-independent manner, PLoS Pathog, vol.7, 2011. ,
Changes in membrane fatty acid composition during entry of Vibrio vulnificus into the viable but nonculturable state, J Microbiol Seoul Korea, vol.42, pp.69-73, 2004. ,
Yeast Transcriptome and In Vivo Hypoxia Detection Reveals Histoplasma capsulatum Response to Low Oxygen Tension, Med Mycol, vol.54, pp.40-58, 2016. ,
Immunometabolism within the tuberculosis granuloma: amino acids, hypoxia, and cellular respiration, Semin Immunopathol, vol.38, pp.139-152, 2016. ,
Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach, Front Cell Infect Microbiol, vol.6, 2016. ,
Modulating the stem cell niche for tissue regeneration, Nat Biotechnol, vol.32, pp.795-803, 2014. ,
Hypoxia-inducible factors have distinct and stage-specific roles during reprogramming of human cells to pluripotency, Cell Stem Cell, vol.14, pp.592-605, 2014. ,
Apoptosis-Resistance of Hypoxic Cells: Multiple Factors Involved and a Role for IAP-2, Am J Pathol, vol.163, issue.10, pp.63693-63693, 2003. ,
PR39 inhibits apoptosis in hypoxic endothelial cells: role of inhibitor apoptosis protein-2, Circulation, vol.109, pp.1660-1667, 2004. ,
Hypoxia-mediated selection of cells with diminished apoptotic potential in solid tumours, Nature, vol.379, pp.88-91, 1996. ,
Inability of Escherichia coli to resuscitate from the viable but nonculturable state, FEMS Microbiol Ecol, vol.62, p.17908096, 2007. ,
The importance of the viable but non-culturable state in human bacterial pathogens, Front Microbiol, vol.5, p.258, 2014. ,
Understanding and Teaching the Most Probable Number Technique, J Milk Food Technol, vol.38, pp.540-545, 1975. ,
Thirty years of viable but nonculturable state research: unsolved molecular mechanisms, Crit Rev Microbiol, vol.41, pp.61-76, 2013. ,
Modifications to methods for the enumeration and detection of injured Escherichia coli O157:H7 in foods, Int J Food Microbiol, vol.55, pp.285-290, 2000. ,
On substrate-accelerated death in Klebsiella aerogenes, J Gen Microbiol, vol.70, pp.115-122, 1972. ,
Adoption of the transiently non-culturable state -a bacterial survival strategy?, 2003. ,
mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein, Mol Cell, vol.67, pp.936-946, 2017. ,
Cryptococcus neoformans interactions with amoebae suggest an explanation for its virulence and intracellular pathogenic strategy in macrophages, Proc Natl Acad Sci U S A, vol.98, pp.15245-15250, 2001. ,
Abu Kwaik Y. Acanthamoeba polyphaga resuscitates viable non-culturable Legionella pneumophila after disinfection, Environ Microbiol, vol.9, p.17472639, 2007. ,
Resuscitation of viable but nonculturable Legionella pneumophila Philadelphia JR32 by Acanthamoeba castellanii, Appl Environ Microbiol, vol.63, pp.2047-2053, 1997. ,
Viability of bacteria from different aquatic habitats. I. Environmental conditions and productivity, Aquat Microb Ecol, vol.32, pp.121-135, 2003. ,
Exploring the metabolic and genetic control of gene expression on a genomic scale, Science, vol.278, pp.680-686, 1997. ,
Protein synthesis during transition and stationary phases under glucose limitation in Saccharomyces cerevisiae, J Bacteriol, vol.161, pp.385-392, 1985. ,
Protein synthesis in long-term stationary-phase cultures of Saccharomyces cerevisiae, J Bacteriol, vol.176, pp.5802-5813, 1994. ,
Ribosome synthesis during the growth cycle of Saccharomyces cerevisiae, Yeast Chichester Engl, vol.10, pp.151-157, 1994. ,
Autophagy, mitochondria and oxidative stress: cross-talk and redox signalling, Biochem J, vol.441, pp.523-540, 2012. ,
Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence, Eukaryot Cell, vol.7, pp.58-67, 2008. ,
Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A, BMC Microbiol, vol.15, p.26453029, 2015. ,
Identification of Aph1, a phosphate-regulated, secreted, and vacuolar acid phosphatase in Cryptococcus neoformans, mBio, vol.5, pp.1649-1663, 2014. ,
Vesicle-associated melanization in Cryptococcus neoformans, Microbiol Read Engl, vol.155, pp.3860-3867, 2009. ,
Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence, Eukaryot Cell, vol.7, pp.58-67, 2007. ,
Unravelling secretion in Cryptococcus neoformans: more than one way to skin a cat, Mycopathologia, vol.173, p.21898146, 2012. ,
Lipid raft-associated protein sorting in exosomes, Blood, vol.102, pp.4336-4344, 2003. ,
Intracellular Action of a Secreted Peptide Required for Fungal Virulence, Cell Host Microbe, vol.19, pp.849-864, 2016. ,
TUP1 disruption in Cryptococcus neoformans uncovers a peptide-mediated density-dependent growth phenomenon that mimics quorum sensing, Mol Microbiol, vol.64, p.591, 2007. ,
Regulatory diversity of TUP1 in Cryptococcus neoformans, Eukaryot Cell, vol.8, pp.1901-1908, 2009. ,
Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry, Clin Proteomics, vol.11, p.24484775, 2014. ,
Characterization of host response to Cryptococcus neoformans through quantitative proteomic analysis of cryptococcal meningitis co-infected with HIV, Mol Biosyst, vol.11, pp.2529-2540, 2015. ,
Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus, PLoS Genet, vol.11, p.1005490, 2015. ,
Oxidative stress responses of the yeast Saccharomyces cerevisiae, Yeast Chichester Engl, vol.14, pp.1511-1527, 1998. ,
The TOR signalling network from yeast to man, Int J Biochem Cell Biol, vol.38, pp.1476-1481, 2006. ,
The TOR kinases link nutrient sensing to cell growth, J Biol Chem, vol.276, pp.9583-9586, 2001. ,
Capsule growth in Cryptococcus neoformans is coordinated with cell cycle progression, mBio, vol.5, p.24939886, 2014. ,
Coenzyme A biosynthetic machinery in mammalian cells, Biochem Soc Trans, vol.42, pp.1112-1117, 2014. ,
Coenzyme A, more than "just" a metabolic cofactor, Biochem Soc Trans, vol.42, pp.1075-1079, 2014. ,
Peroxisomal and mitochondrial ?-oxidation pathways influence the virulence of the pathogenic fungus Cryptococcus neoformans, Eukaryot Cell, vol.11, pp.1042-1054, 2012. ,
Changes of Lipid Composition with Growth Phase of Cryptococcus neoformans, Agric Biol Chem, vol.39, pp.2365-2371, 1975. ,
Transcriptional response of Candida albicans upon internalization by macrophages, Eukaryot Cell, vol.3, pp.1076-1087, 2004. ,
Metabolic adaptation in Cryptococcus neoformans during early murine pulmonary infection, Mol Microbiol, vol.69, pp.1456-1475, 2008. ,
The transcriptional response of Cryptococcus neoformans to ingestion by Acanthamoeba castellanii and macrophages provides insights into the evolutionary adaptation to the mammalian host, Eukaryot Cell, vol.12, pp.761-774, 2013. ,
The depletion of nuclear glutathione impairs cell proliferation in 3t3 fibroblasts, PloS One, vol.4, p.6413, 2009. ,
Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators, PLoS Pathog, vol.14, p.1006982, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01854297
Vectorial acylation in Saccharomyces cerevisiae. Fat1p and fatty acyl-CoA synthetase are interacting components of a fatty acid import complex, J Biol Chem, vol.278, pp.16414-16422, 2003. ,
The role of oxidative and nitrosative bursts caused by azoles and amphotericin B against the fungal pathogen Cryptococcus gattii, J Antimicrob Chemother, vol.68, pp.1801-1811, 2013. ,
grofit: Fitting Biological Growth Curves withR, J Stat Softw, vol.33, 2010. ,
Dynamics of Cryptococcus neoformans-macrophage interactions reveal that fungal background influences outcome during cryptococcal meningoencephalitis in humans, mBio, vol.2, pp.158-169, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01405254
Molecular and idiotypic analysis of antibodies to Cryptococcus neoformans glucuronoxylomannan, Infect Immun, vol.62, pp.3864-3872, 1994. ,
Cryptococcus neoformans {alpha} strains preferentially disseminate to the central nervous system during coinfection, Infect Immun, vol.73, pp.4922-4933, 2005. ,
Phenotype microarrays for high-throughput phenotypic testing and assay of gene function, Genome Res, vol.11, pp.1246-1255, 2001. ,
UGE1 and UGE2 regulate the UDP-glucose/UDPgalactose equilibrium in Cryptococcus neoformans, Eukaryot Cell, vol.7, pp.2069-2077, 2008. ,
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes ,
, Genome Biol, vol.3, p.34, 2002.
A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Res, vol.29, 2001. ,
Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis, Nat Protoc, vol.9, pp.362-374, 2014. ,
Andromeda: a peptide search engine integrated into the MaxQuant environment, J Proteome Res, vol.10, pp.1794-1805, 2011. ,
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat Biotechnol, vol.26, pp.1367-1372, 2008. ,
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics, Nat Protoc, vol.11, pp.2301-2319, 2016. ,
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction ,
, Mol Cell Proteomics MCP, vol.13, pp.2513-2526, 2014.
LSimpute: accurate estimation of missing values in microarray data with least squares methods, Nucleic Acids Res, vol.32, 2004. ,
Some distance properties of latent root and vector methods used in multivariate analysis, Biometrika, pp.325-363, 1966. ,
limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, vol.43, 2015. ,
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, J R Stat Soc Ser B Methodol, vol.57, pp.289-300, 1995. ,
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species, Bioinforma Oxf Engl, vol.31, pp.445-446, 2014. ,
jvenn: an interactive Venn diagram viewer, BMC Bioinformatics, vol.15, p.25176396, 2014. ,
STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-52, 2014. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. journal, vol.17, pp.10-12, 2011. ,
STAR: ultrafast universal RNAseq aligner, Bioinformatics, vol.29, pp.15-21, 2013. ,
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinforma Oxf Engl, vol.30, pp.923-930, 2014. ,
MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, vol.32, pp.3047-3048, 2016. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes, J Fungi Basel Switz, vol.4, 2018. ,
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017. ,
Predicting Secretory Proteins with SignalP, Methods Mol Biol Clifton NJ, vol.1611, pp.59-73, 2017. ,