Journal: Biotechnology for Biofuels

Article Title: Transporter engineering for improved tolerance against alkane biofuels in Saccharomyces cerevisiae

doi: 10.1186/1754-6834-6-21

Figure Lengend Snippet: Intracellular alkane levels of ABC2 and ABC3. S. cerevisiae BY4741 with and without ABC2/3 were cultured under exposure to 0.5% (vol/vol) alkane or 20% (vol/vol) undecane. After 48 h incubation, intracellular alkane levels were measured as described under “Methods”. Intracellular alkane levels were normalized to that of control cells carrying an empty plasmid. Data shown are the mean ± SD of four biological replicates.

Article Snippet: The yeast strains S. cerevisiae BY4741 (ATCC 201388) and Y. lipolytica CLIB122 (CIRM) were used for function characterization.

Techniques: Cell Culture, Incubation, Plasmid Preparation

Journal: PLoS ONE

Article Title: REAL-Select: Full-Length Antibody Display and Library Screening by Surface Capture on Yeast Cells

doi: 10.1371/journal.pone.0114887

Figure Lengend Snippet: Antigen specificities and KD-values of antibodies displayed on BJ5464 using REAL-Select.

Article Snippet: The yeast strain that harbored antibody light chains was S. cerevisiae strain BJ5464 (MATα URA3-52 trp1 leu2Δ1his3Δ200 pep4::HIS3 prb1Δ1.6R can1 GAL) obtained from the American Type Culture Collection (ATCC).

Techniques:

Journal: Microbial Cell Factories

Article Title: De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

doi: 10.1186/1475-2859-11-36

Figure Lengend Snippet: Overview of the reconstruction of the MAL2 locus in S. cerevisiae CEN.PK113-7D . A ) Depth of coverage analysis of MAL loci. Sequencing reads from the CEN.PK113-7D and S288C have been mapped onto the S288C genome sequence. Log 2 -ratio's of the average sequencing depth in 414-bp windows of CEN.PK113-7D over S288C have been plotted versus genomic position. Log 2 -ratio's were capped at -4. B ) Schematic representation of the paired-end linkage analysis that showed anomalous read pairs (red arrows) on the end of chromosome III that mapped to BIO2 on CHRVII. C ) Southern blots and karyotypes, denoted with 'b' and 'k', respectively, of S288C and CEN.PK113-7D, denoted with 'S' anc 'C', respectively. Probes for IMA1, BIO2 and MAL32 were amplified with the primers listed in Additional file : Table S8. Square boxes indicate hybridized chromosomes. Chromosomes marked with an asterisk (*) depicts cross-hybridization of the IMA1 probe to paralogs of IMA1 (see text). D ) Schematic organization of the MAL loci in CEN.PK113-7D. Loci marked with (#) were individually amplified, sequenced and assembled.

Article Snippet: The prototrophic S. cerevisiae strains CEN.PK113-7D [ ] and S288C (ATCC 204508) [ ] were grown in liquid cultures.

Techniques: Sequencing, Amplification, Hybridization

Journal: Microbial Cell Factories

Article Title: De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

doi: 10.1186/1475-2859-11-36

Figure Lengend Snippet: Copy number variation between the S288C and CEN.PK113-7D genomes was estimated by mapping CEN.PK and S288C reads to the S288C genome using BWA [ 45 ]

Article Snippet: The prototrophic S. cerevisiae strains CEN.PK113-7D [ ] and S288C (ATCC 204508) [ ] were grown in liquid cultures.

Techniques: Amplification

Journal: Microbial Cell Factories

Article Title: De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

doi: 10.1186/1475-2859-11-36

Figure Lengend Snippet: Occurrence analysis of three regions present in the CEN.PK113-7D genome, but not in the S288C genome . A) Venn diagram that represents the occurrence of the three regions over the available S. cerevisiae sequenced strains in Genbank (Additional file : Table S7). B and C) Annotation of the regions and RNA-seq expression profiles. RNA-seq data from glucose- and nitrogen limited anaerobic chemostat cultures (red and blue, respectively) were plotted (one bar every 10 th base) for the CEN.PK113-7D specific ENA locus ( B ) and the two specific contigs ( C ). Expression data, expressed as the number of times a base is covered by a read, are ranged from are [0-750] for contig379 and contig151 and [0-250] for contig596.

Article Snippet: The prototrophic S. cerevisiae strains CEN.PK113-7D [ ] and S288C (ATCC 204508) [ ] were grown in liquid cultures.

Techniques: RNA Sequencing Assay, Expressing

Journal: Microbial Cell Factories

Article Title: De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

doi: 10.1186/1475-2859-11-36

Figure Lengend Snippet: Biotin biosynthesis characterization in CEN.PK113-7D and S288C . A) Biotin biosynthesis pathway in CEN.PK113-7D. B) Southern blotting of S288C and CEN.PK113-7D chromosomes using specific probes for BIO1 and BIO6 genes. C) Maximal specific growth rate of CEN.PK113-7D and S288C in shake flask cultivations with synthetic medium in absence (white bar), and presence (grey bar) of biotin. Growth rates were calculated from biomass measurements expressed as optical density measured at 660 nm.

Article Snippet: The prototrophic S. cerevisiae strains CEN.PK113-7D [ ] and S288C (ATCC 204508) [ ] were grown in liquid cultures.

Techniques: Southern Blot

Journal: Microbial Cell Factories

Article Title: De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

doi: 10.1186/1475-2859-11-36

Figure Lengend Snippet: Mosaic CEN.PK113-7D genome . CEN.PK chromosomes colored by their identity to S. cerevisiae genomes, which were divided into the groups: laboratory (lab) (FL100:PRJNA60147, S288C:PRJNA128, Sigma1278b:PRJNA39317), industrial (e.g. wine, beer, bio-ethanol) (AWRI1631:PRJNA30553, AWRI796:PRJNA48559, CBS7960:PRJNA60391, CLIB382:PRJNA60145, EC1118:PRJEA37863, FostersB:PRJNA48569, FostersO:PRJNA48567, JAY291:PRJNA32809, Kyokai no. 7:PRJNA45827, Lalvin QA23:PRJNA48561, M22:PRJNA28815, PW5:PRJNA60181, RM11-1a:PRJNA13674, T73:PRJNA60195, UC5:PRJNA60197, Vin13:PRJNA48563, VL3:PRJNA48565, YJM269:PRJNA60389) and other (CLIB215:PRJNA60143, CLIB324:PRJNA60415, EC9-8:PRJNA73985, T7:PRJNA60387, Y10:PRJNA60201, YJM789:PRJNA13304, YPS163:PRJNA28813) (Additional file : Table S7). Each group was assigned one of the color channels of the RGB figure (red: lab, green: other and blue: industrial). The genome was divided in non-overlapping fragments of 1000 base pairs, represented by one pixel in the figure, which were aligned to the available S. cerevisiae genomes in GenBank (Additional file : Table S7). The identity of the best alignment in a group was set to be the value of the corresponding color channel. These values were scaled between 0 and 1; 0 meaning a maximal identity of 97% or lower, 1 meaning a maximal identity of 100%. For example, a white pixel color means 100% conservation of the fragment in all three groups. Blue and cyan mean conservation in industrial strains, but not in laboratory strains.

Article Snippet: The prototrophic S. cerevisiae strains CEN.PK113-7D [ ] and S288C (ATCC 204508) [ ] were grown in liquid cultures.

Techniques:

Journal: Biotechnology for Biofuels

Article Title: Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

doi: 10.1186/1754-6834-6-44

Figure Lengend Snippet: S. cerevisiae 311 batch cultures grown A) anaerobically B) aerobically and C) at a k L a of 5.5 h -1 . Data points are experimental measurements, while solid lines are dynamic model predictions.

Article Snippet: S. cerevisiae 311 (ATCC 42511), a mutant that was created by treating a wild-type strain with ethidium bromide [ ], was chosen as the respiratory-deficient S. cerevisiae strain.

Techniques:

Journal: Biotechnology for Biofuels

Article Title: Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

doi: 10.1186/1754-6834-6-44

Figure Lengend Snippet: S. cerevisiae / S. stipitis batch co-cultures grown with an equal inoculum and aerated at A) 5.5 h -1 B) 9.6 h -1 and C) 7.6 h -1 . Individual cell concentrations are shown in the inset. Dynamic model predictions are indicated by solid lines. Three separate fermentations were performed at each aeration level to compute average values indicated by the symbols and coefficients of variation indicated by the error bars.

Article Snippet: S. cerevisiae 311 (ATCC 42511), a mutant that was created by treating a wild-type strain with ethidium bromide [ ], was chosen as the respiratory-deficient S. cerevisiae strain.

Techniques:

Journal: Biotechnology for Biofuels

Article Title: Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

doi: 10.1186/1754-6834-6-44

Figure Lengend Snippet: S. cerevisiae / S. stipitis batch co-cultures grown at the optimal conditions identified in silico . The co-culture was inoculated with 0.1 g/L S. cerevisiae 311 and 0.9 g/L S. stipitis and aerated at a k L a of 10.1 h -1 . Individual cell concentrations are shown in the inset. Dynamic model predictions are indicated by solid lines. Three separate fermentations were performed to compute average values indicated by the symbols and coefficients of variation indicated by the error bars.

Article Snippet: S. cerevisiae 311 (ATCC 42511), a mutant that was created by treating a wild-type strain with ethidium bromide [ ], was chosen as the respiratory-deficient S. cerevisiae strain.

Techniques: In Silico, Co-Culture Assay

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: Specific rates during growth on glucose of the reference strain S. cerevisiae BY4742 and the used deletion strains pat1Δ , dhh1Δ and lsm1Δ .

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques:

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: GC/MS spectrum of a S. cerevisiae BY4742 pat1Δ cell extract. The numerical labels of the identified compounds are specified in Table . (A) whole intensity rage, (B) 0 -1% of abundance range.

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques: Gas Chromatography-Mass Spectrometry

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: Peak areas of detected metabolites normalized to total peak area in BY4742 and the three deletion strains pat1Δ , dhh1Δ and lsm1Δ using GC/MS.

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques:

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: Comparison of intracellular metabolites of S. cerevisiae strains analyzed by GC/MS using normalized peak areas, I i . (A) dhh1Δ mutant versus reference BY4742, (B) pat1Δ versus reference BY4742, (C) lsm1Δ versus reference BY4742. The solid line indicates identical concentrations in both strains. Data points denote the mean of the normalized areas taken from six independent samples. Error bars in both directions indicate the corresponding standard deviations. The numerical labels of the single metabolites are defined in Table .

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques: Gas Chromatography-Mass Spectrometry, Mutagenesis

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: Strain comparison based on intracellular metabolites extracted form S. cerevisiae BY4742 and the tree deletion strains pat1Δ, dhh1Δ and lsm1Δ and analyzed using GC/MS. A – full data set; B – data without metabolites not observed in human as indicated in Table ; C – same as B but with additional removal of essential amino acids that are not synthesized in human. The distances between the four strains correspond to the Euclidian distance calculated by using the normalized areas of the extracted metabolites of the four strains.

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques: Gas Chromatography-Mass Spectrometry, Synthesized

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: PCA scores plot based on normalised peak areas from GC/MS analysis of cell extracts and the four strains BY4742 (reference), pat1Δ, dhh1Δ and lsm1Δ (each one n=6). Analysis was conducted using SIMCA-P+ 11.5 (Umetrics, Malmö, Sweden). Data were pareto scaled and the first two components were autofitted.

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques: Gas Chromatography-Mass Spectrometry

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: Heat map of 47 metabolites that show statistically significant changes between the reference strain (n=6) and the three deletion strains pat1Δ, dhh1Δ and lsm1Δ (each one n=6). Red color denotes lower concentrations in the deletion strains; green color indicates higher concentrations in the deletion strains. Statistically significant metabolites were identified using the loading plots shown in Figure . G6P, glucose-6-phosphate; G1P, glycerol-1- phosphate; X5P, xylulose-5-phosphate; u. m.; unknown metabolite; WT, reference strain BY4742.

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques:

Journal: Microbial Cell Factories

Article Title: Metabolite profiling studies in Saccharomyces cerevisiae : an assisting tool to prioritize host targets for antiviral drug screening

doi: 10.1186/1475-2859-8-12

Figure Lengend Snippet: Metabolites identified in the cell extracts of BY4742 and the used deletion mutants using the software AMDIS v2.0 and a TMS library.

Article Snippet: A comparison of the reference strain S. cerevisiae BY4742 with the non-auxotrophic wild type S. cerevisiae ATCC 32167 revealed that the intracellular concentrations of leucine, histidine and lysine were always higher than in the non-auxotrophic wild type strain.

Techniques: Software

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Illumina/Solexa genome sequencing and annotation results

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Genome sequencing and metabolic SNP detection

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques: Sequencing, Software

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Gene Ontology (GO) process terms for the nonsynonymous SNPs identified in CEN.PK113-7D compared to S288c . The x -axis in log-scale displays both the significance of each category ( p < 0.01, symbol: solid black), and the number of genes from the total of 85 containing nonsynonymous SNPs (symbol: solid white). GO process characterization performed using the Saccharomyces Genome Database (SGD).

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques:

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: An example of amino acid properties change of CEN. PK113-7D compared to S288c: the gene ERG8 of the ergosterol synthesis pathway . The gene ERG8 of the ergosterol synthesis pathway contains a total of 4 nonsynonymous SNPs, two of which, located at nucleotide positions 192 and 75, are analyzed here. The top plots show the CEN.PK Match Frequency, Dominanat AA Frequency, S288c Match Frequency, and Conversation Distance. The middle plots show the frequency (fraction) of each categorization across the amino acid sequences resulting from Pfam multi-sequence alignment. The bottom plots shows the characterization of the original S288c amino acid (symbol: blue bar) and the CEN.PK113-7D amino acid (symbol: red bar). The gene ERG8 contained a total of 4 nonsynonymous SNPs, and Additional file 1, Figure S5 includes the other 2 nonsynonymous SNPs (nucleotide positions 49 and 247).

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Physiological characterization of S. cerevisiae strains S288c and CEN.PK113-7D

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques:

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Physiological characterization of S. cerevisiae S288c and CEN.PK113-7D . The plots above show the carbon dioxide evolution rate and oxygen uptake rate as a function of cultivation time for the strains S288c and CEN.PK113-7D supplemented with glucose and galactose, respectively. Glucose fermentation (GF), ethanol respiration (ER), galactose respiro-fermentation (GaRF). The black arrow in the S288c Galactose plot indicates when 10 g L -1 glucose was supplemented (25 h) when no growth was observed on galactose. The red arrows in all plots indicates when biomass samples were taken for subsequent transcriptome analysis.

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques:

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Ergosterol measurements in S. cerevisiae strains S288c and CEN.PK113-7D . Ergosterol composition (mg g-DCW -1 ) was measured for different samples taken during S288c and CEN.PK113-7D fermentations, supplemented with glucose and galactose. Transcriptome sample was taken during the mid-exponential fermentation phase on glucose or respiration phase on galactose. For glucose fermentations, early ethanol, mid-ethanol, and stationary ethanol samples were taken post-diauxic shift to charcterize the change in ergosterol during growth on ethanol. Error bars are ± SD ( n = 2).

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques:

Journal: BMC Genomics

Article Title: Whole genome sequencing of Saccharomyces cerevisiae : from genotype to phenotype for improved metabolic engineering applications

doi: 10.1186/1471-2164-11-723

Figure Lengend Snippet: Summary of Differential Gene Expression

Article Snippet: S. cerevisiae strain S288c (American Type Culture Collection, ATCC ® ) and strain CEN.PK113-7D (Scientific Research and Development, SRD GmbH were used in this study.

Techniques: Expressing

Journal: Database: The Journal of Biological Databases and Curation

Article Title: The challenge of increasing Pfam coverage of the human proteome

doi: 10.1093/database/bat023

Figure Lengend Snippet: Pfam-A coverage of H. sapiens , S. cerevisiae and E. coli . Sequence coverage (blue) is calculated as the percentage of the proteome (Methods) that matches at least one Pfam-A family. Residue coverage (red) is the percentage of amino acids in the proteome that are covered by a Pfam-A family.

Article Snippet: We downloaded the UniProtKB/Swiss-Prot-reviewed protein sequences for Homo sapiens (taxonomic identifier 9606; 20 234 sequences), S. cerevisiae strain ATCC 204508 /S288c (taxonomic identifier 559292; 6621 sequences) and E. coli strain K12 (taxonomic identifier 83333; 4431 sequences) from the UniProt website ( http://www.uniprot.org/ ) ( ).

Techniques: Sequencing