pinecone/core-2020-05-10-deduplication huggingface dataset:
Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection

Within this study, we have used a set of computational techniques to relate the genotypes
and phenotypes of natural populations of Saccharomyces cerevisiae, using allelic
information from 11 microsatellite loci and results from 24 phenotypic tests. A group
of 103 strains was obtained from a larger S. cerevisiae winemaking strain collection
by clustering with self-organizing maps. These strains were further characterized
regarding their allelic combinations for 11 microsatellites and analysed in phenotypic
screens that included taxonomic criteria (carbon and nitrogen assimilation tests,
growth at different temperatures) and tests with biotechnological relevance (ethanol
resistance, H2S or aromatic precursors formation). Phenotypic variability was rather
high and each strain showed a unique phenotypic profile. The results, expressed as
optical density (A640) after 22 h of growth, were in agreement with taxonomic data,
although with some exceptions, since few strains were capable of consuming arabinose
and ribose to a small extent. Based on microsatellite allelic information, na¨ıve
Bayesian classifier correctly assigned (AUC = 0.81, p < 10−8) most of the strains to
the vineyard from where they were isolated, despite their close location (50–100 km).
We also identified subgroups of strains with similar values of a phenotypic feature
and microsatellite allelic pattern (AUC >0.75). Subgroups were found for strains
with low ethanol resistance, growth at 30 ◦C and growth in media containing galactose,
raffinose or urea. The results demonstrate that computational approaches can
be used to establish genotype–phenotype relations and to make predictions about a
strain’s biotechnological potential.JATOON softwareFundação para a Ciência e a Tecnologia (FCT) – POCI/AGR/56102/2004, PDTC/AGR-ALI/103392/2008, SFRH/BD/48591/2008União Europeia (EU). Fundo Europeu de Desenvolvimento Regional (FEDER)AGRO - ENOSAFE, Nº 762Slovenian Research Agency - P2-0209, J2-9699, L2-111
There is a steady-state transcriptome in exponentially growing yeast cells

The growth of yeast cells in batches in glucose-based media is a standard condition in most yeast laboratories. Most gene expression experiments are done by taking this condition as a reference. Presumably, cells are in a stable physiological condition that can be easily reproduced in other laboratories. With this assumption, however, it is necessary to consider that the average amount of the mRNAs per cell for most genes does not change during exponential growth. That is to say, there is a steady-state condition for the transcriptome. However, this has not been rigorously demonstrated to date. In this work we take several cell samples during the exponential phase growth to perform a kinetic study using the genomic run-on (GRO) technique, which allows simultaneous measurement of the amount of mRNA and transcription rate variation at the genomic level. We show here that the steady-state condition is fulﬁlled for almost all the genes during most exponential growth in yeast extract<br>peptone<br>dextrose medium (YPD) and, therefore, that simultaneous measures of the transcription rates and the amounts of mRNA can be used for indirect mRNA stability calculations. With this kinetic approach, we were also able to dermine the relative inﬂuence of the transcription rate and the mRNA stability changes for the mRNA variation for those genes that deviate from the steady state
Plasmids for in vivo construction of integrative Candida albicans vectors in saccharomyces cerevisiae

A general system has been devised for the in vivo construction of Candida albicans integrative vectors in Saccharomyces cerevisiae. The system is especially useful for the integration of genes in C. albicans that cannot be propagated in Escherichia coli possibly because of their toxic effects. The ligation of S. cerevisiae 2μ sequences to a C. albicans integrative vector permits in vivo maintenance and gap repair cloning within S. cerevisiae. After the vector assembly, it can be purified from S. cerevisiae or amplified by PCR and then used for transformation of C. albicans. The S. cerevisiae 2μ sequence is completely removed by linearization prior to C. albicans transformation, such that no unwanted DNA is transferred in the final construct. The system was successfully used to clone and reintegrate the C. albicans JEN2 gene, which encodes a membrane protein that is apparently toxic to E. coli. Three popular C. albicans integrative vectors CIp10, CIp20 and CIp30 are now available in versions that permit gap repair in S. cerevisiae.
GenBank Accession Nº: CIp10-2μ (GU550119), CIp20-2μ (GU550120) and CIp30-2μ (GU550121).This study was supported by FEDER, Portugal (Grant No. POCI/BIA-BCM/57812/2004; Eixo 2, Medida 45 2.3, QCAIII-FEDER). N.V. received a FCT PhD fellowship (Grant No. SFRH/BD/23503/2005). F. P. and B.J. were supported by European Union project NILE (Grant No. FP6-019882). AJPB was funded by the BBSRC (Grant Nos BB/F000111/1, BB/D009308/1, BB/F010826/1 and BB/FO0513X/1) and the European Commission (Grant Nos PITN-GA-2008-214004 and ERC-2009-AdG-249793)
Susceptibility and resistance to ethanol in Saccharomyces strains isolated from wild and fermentative environments

11 pages, 3 figures, 3 tables.-- Article first published online: 8 SEP 2010In this work, we apply statistical modelling techniques to study the influence of increasing concentrations of ethanol on the overall growth of 29 yeast strains belonging to different Saccharomyces and non-Saccharomyces species. A modified Gompertz equation for decay was used to objectively estimate the noninhibitory concentration (NIC) and minimum inhibitory concentration (MIC) for the assayed strains to ethanol, which are related to the susceptibility and resistance of yeasts to this compound, respectively. A first ANOVA analysis, grouping strains as a function of their respective Saccharomyces species, revealed that S. cerevisiae was the yeast with the highest, and statistically significant, ethanol resistance value. Then, a second factorial ANOVA analysis, using the origin of strains (wild or fermentative) and their taxonomic classification (S. cerevisiae, S. paradoxus or S. bayanus var. uvarum) as categorical predictor variables, showed that no significant differences for the NIC and MIC parameters were found between both ecological niches within the same species, indicative that these physiological characteristics were presumably not modified throughout the adaptation to human-manipulated fermentative environments. Finally, differences among selected strains with respect to ethanol tolerance were correlated to the initial contents of unsaturated fatty acids, mainly oleic acid.This work was supported by Generalitat Valenciana (project PROMETEO/2009/019) and the Spanish Government (projects AGL2009-12673-CO2-01, AGL2009-12673-CO2-02 and AGL2007-65498-C02-02, to A.Q., E.B. and J.M.G., respectively). F.N. Arroyo-López also thanks the Spanish Government (MICINN) for his ‘Juan de la Cierva’ postdoctoral research contract.Peer reviewe
Measuring oxidative DNA damage and DNA repair using the yeast comet assay

Chromosomal DNA damage can be a result of several processes and agents of endogenous or exogenous origin. These cause strand breaks or oxidized bases that lead to strand breaks, which relax the normally supercoiled genomic DNA and increase its electrophoretic mobility. The extent of DNA damage can be assessed by single cell gel electrophoresis, where the chromosomal DNA migration distance correlates with the extent of DNA damage. This technique has been used for a variety of applications with several organisms, but only a few studies have been reported for Saccharomyces cerevisiae. A possible reason for this absence is that low cellular DNA content could hamper visualization. Here we report an optimization of the comet assay protocol for yeast cells that is robust and sensitive enough to reproducibly detect background DNA damage and oxidative damage caused by hydrogen peroxide. DNA repair was observed and quantified as diminishing comet tail length with time after oxidative stress removal in a process well described by first-order kinetics with a tail length half-life of 11 min at 37 °C. This is, to our knowledge, the first quantitative measurement of DNA repair kinetics in S. cerevisiae by this method. We also show that diet antioxidants protect from DNA damage, as shown by a three-fold decrease in comet tail length. The possibility of assessment of DNA damage and repair in individual cells applied to the model organism S. cerevisiae creates new perspectives for studying genotoxicity and DNA repair
Cassettes for PCR-mediated gene tagging in Candida albicans utilizing nourseothricin resistance

addresses: Biosciences, College of Life and Environmental Sciences, University of Exeter, UK.types: Journal Article; Research Support, Non-U.S. Gov't; Validation StudiesThis is the author's post-print version of an article published in Yeast, 2011, Vol. 28, Issue 12, pp. 833 – 841 Copyright © Wiley-Blackwell 2011. The definitive version is available at www3.interscience.wiley.comIn recent years a number of molecular tools have been reported for use in the human fungal pathogen Candida albicans, including PCR-mediated approaches for gene disruption, conditional expression and epitope tagging. Traditionally these methods have utilized auxotrophic markers; however, the availability of auxotrophic markers can be limiting and in some instances their use may also impact on the interpretation of results. As a result, the use of positive selection markers has now become more commonplace. Here we report the development and validation of a set of cassettes for PCR-mediated gene tagging and overexpression studies utilizing the nourseothricin resistance (CaNAT1) positive selection marker. In particular we have produced cassettes containing yeast-enhanced GFP, YFP, CFP, RFP and a combined V5-6xHis epitope tag. The cassettes are engineered for use in PCR-mediated gene tagging strategies where insertion is targeted to the 3' end of the gene of interest. In addition, to facilitate protein functional analysis and genetic suppression studies through the use of overexpression, we have also constructed a promoter replacement cassette containing the ENO1 promoter which is known to be expressed at a high level. These cassettes expand on the range of molecular tools available for working with C. albicans and may also be used in other Candida species that display sensitivity to nourseothricin
MyLabStocks: a web-application to manage molecular biology materials.

Open AccessLaboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks under an open source licence. © 2014 Laboratoire de Biologie Moleculaire de la Cellule CNRS. Yeast published by John Wiley & Sons, Ltd
Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae

Genome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large-scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross-validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection. Copyright (C) 2014 John Wiley & Sons, Ltd.Ricardo Franco-Duarte and Ines Mendes are the recipients of fellowships from the Portuguese Science Foundation (FCT; Grant Nos SFRH/BD/74798/2010 and SFRH/BD/48591/2008, respectively) and Joao Drumonde-Neves is the recipient of a fellowship from the Azores Government (Grant No. M3.1.2/F/006/2008; DRCT). Financial support was obtained from FEDER funds through the programme COMPETE and by national funds through FCT by Project Nos FCOMP-01-0124-008775 (PTDC/AGR-ALI/103392/2008) and PTDC/AGR-ALI/121062/2010. Lan Umek and Blaz Zupan acknowledge financial support from the Slovene Research Agency (Grant No. P2-0209). The authors would like also to thank all the researchers who kindly provided yeast strains: Gianni Liti, Institute of Genetics, UK; Laura Carreto, CESAM and Biology Department, Portugal; Goto Yamamoto, NRIB, Japan; Cletus Kurtzman, Microbial Properties Research, USA; Rogelio Brandao, Laboratorio de Fisologia e Bioquimica de Microorganismos, Brazil; and Huseyin Erten, Cukurova University, Turkey.info:eu-repo/semantics/publishedVersio
Quantitative analysis of morphological changes in yeast\ud
colonies growing on solid medium: the eccentricity and\ud
Fourier indices

The colony shape of four yeast species growing on agar medium was measured for 116 days by image analysis. Initially, all the colonies are circular, with regular edges. The loss of circularity can be quantitatively estimated by the eccentricity index, Ei, calculated as the ratio between their orthogonal vertical and horizontal diameters. Ei can increase from 1 (complete circularity) to a maximum of 1.17–1.30, depending on the species. One colony inhibits its neighbour only when it has reached a threshold area. Then, Ei of the inhibited colony increases proportionally to the area of the inhibitory colony. The initial distance between colonies affects those threshold values but not the proportionality, Ei /area; this inhibition affects the shape but not the total surface of the colony. The appearance of irregularities in the edges is associated, in all the species, not with age but with nutrient exhaustion. The edge irregularity can be quantified by the Fourier index, Fi , calculated by the minimum number of Fourier coefficients that are needed to describe the colony contour with 99% fitness. An ad hoc function has been developed in Matlab v. 7.0 to automate the computation of the Fourier coefficients. In young colonies, Fi has a value between 2 (circumference) and 3 (ellipse). These values are maintained in mature colonies of Debaryomyces, but can reach values up to 14 in Saccharomyces. All the species studied showed the inhibition of growth in facing colony edges, but only three species showed edge irregularities associated with substrate exhaustion
New cassettes for single-step drug-resistance and prototrophic marker switching in fission yeast

Copyright © 2015 John Wiley & Sons, Ltd. Funded by College of Life Science and Medicine, University of Aberdeen, UK This work was funded by a start-up grant from the College of Life Science and Medicine, University of Aberdeen, UK. I am grateful to J. Bähler, E. Hartsuiker, F. Klein, J. Kohli, K. Nasmyth, M. C. Whitby, the Leibniz Institute – German Collection of Microorganisms and Cell Cultures (DMSZ) and the National BioResource Project Japan (NBRP) for providing materials used in this study. I thank Alistair J. P. Brown and Takashi Kubota for critically reading this manuscript.Peer reviewedPostprin
Yeast biota of naturally fermented black olives in different brines made from cv. Gemlik grown in various districts of the Cukurova region of Turkey

In this study, the yeast microbiota of naturally fermented black olives made from cv. Gemlik, grown in three different districts of the Çukurova region of Turkey, were investigated. Fermentations were conducted for 180 days in three different brines, including NaCl 10% w/v, NaCl 8% w/v and NaCl 8% w/v added with glucose 0.5%. In total, 223 yeasts were isolated and then identified by PCR–RFLP analysis of the 5.8S ITS rRNA region and sequence information for the D1/D2 domains of the 26S rRNA gene. A broad range of yeast biodiversity was identified, including eight genera and nine species. Candida boidinii (41%), Wickerhamomyces anomalus (32%) and Saccharomyces sp. (18%) were predominant yeasts throughout the fermentations. To a lesser extent, the other species, Candida aaseri, Meyerozyma sp., Zygoascus hellenicus, Pichia kudriavzevii, Schwanniomyces etchellsii and Candida atlantica were also members of the olive-fermenting microbiota. In Tarsus and Bahçe districts C. boidinii and in Serinyol district Saccharomyces sp. were the most frequently identified species. W. anomalus was the most frequently isolated species (by 48% of total yeasts) in NaCl 10% brines. C. boidinii was the most dominant species in the brines, including NaCl 8% and NaCl 8% + glucose 0.5%, with frequencies of 42% and 61%, respectively. At the end of the 180 days of fermentation, total acidity values of the brines were in the range 1.04–8.1 g/l lactic acid. Copyright © 2016 John Wiley & Sons, Ltd
Protein phosphorylation in yeast mitochondria

We describe the identification and submitochondrial localization of four protein kinases and of their target proteins in derepressed yeast mitochondria. The activity of one of the kinases depends on the presence of cyclic AMP (cAMP). It is soluble and localized in the mitochondrial intermembrane space. Its natural target is a polypeptide of 40 kDa molecular mass, which is bound to the inner membrane. Besides this natural target this kinase phosphorylates acidic heterologous proteins, like casein, with high efficiency. The other protein kinases identified so far are cAMP-independent. At least one is localized in the matrix having its natural substrates (49 and 24 kDa) in the same compartment. Two others are firmly bound to the inner membrane phosphorylating target proteins in the inner membrane (52·5 kDa) and in the intermembrane space (17·5 kDa), respectively.
Galactose inhibition of the constitutive transport of hexoses in Saccharomyces cerevisiae

The relationship between the pathways of glucose and galactose utilization in Saccharomyces cerevisiae has been studied. Galactose (which is transported and phosphorylated by inducible systems) is a strong inhibitor of the utilization of glucose, fructose and mannose (which have the same constitutive transport and phosphorylation systems). Conversely, all these three hexoses inhibit the utilization of galactose, though with poor efficiency. These cross-inhibitions only occur in yeast adapted to galactose or in galactose-constitutive mutants. The efficiency of galactose as inhibitor is even greater than the efficiencies of each of the other three hexoses to inhibit the utilization of each other. Phosphorylation is not involved in the inhibition and transport of sugars is the affected step. The cross-inhibitions between galactose and either glucose, fructose or mannose do not implicate utilization of one hexose at the expense of the other, as it occurs in the mutual interactions between the latter three sugars. it seems that, by growing the yeast in galactose, a protein component is synthesized, or alternatively modified, that once bound to either galactose or any one of the other three hexoses (glucose, fructose or mannose), cross-interacts respectively with the constitutive or the inducible transport systems, impairing their function.This work was supported by a grant (PB87-0206) from the DGICYT, Promoción General del Conocimiento.Peer Reviewe
The regulatable MAL32 promoter in S. cerevisiae: characteristics and tools to facilitate its use

Here we describe a set of tools to facilitate the use of maltose and the MAL32 promoter for regulated gene expression in yeast, alone or in combination with the GAL1 promoter. Using fluorescent protein reporters we find that under non-inducing conditions the MAL32 promoter exhibits a low basal level of expression, similar to the GAL1 promoter, and that both promoters can be induced independently of each other using the respective sugars, maltose and galactose. While their repression upon glucose addition is immediate and complete, we found that the MAL32 and GAL1 promoter each exhibit distinct induction kinetics. A set of plasmids is available to facilitate the application of the MAL32 promoter for chromosomal modifications using PCR targeting and for plasmid based gene expression. This article is protected by copyright. All rights reserved.status: publishe
Disruption and phenotypic analysis of six open reading frames from chromosome VII of Saccharomyces cerevisiae reveals one essential gene

Six open reading frames (ORFs) located on chromosome VII of Saccharomyces cerevisiae
(YGR205w, YGR210c, YGR211w, YGR241c, YGR243w and YGR244c) were disrupted in two different genetic backgrounds using short-flanking homology (SFH) gene replacement. Sporulation and tetrad analysis showed that YGR211w, recently identified as the yeast ZPR1 gene, is an essential gene. The other five genes are non-essential, and no phenotypes could be associated to their inactivation. Two of these genes have recently been further characterized: YGR241c (YAP1802) encodes a yeast adaptor protein and YGR244c (LSC2) encodes the b-subunit of the succinyl-CoA ligase. For each ORF, a replacement cassette with long flanking regions homologous to the target locus was cloned in pUG7, and the cognate wild-type gene was cloned in pRS416