Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations

Saccharomyces cerevisiae and its sibling species S. paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1,200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus as well as small number of S. kudriavzevii strains from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance

わが国の臨床看護技術に関するランダム化比較試験のシステマティックレビュー

目的:わが国の臨床看護技術に関する過去5年間のランダム化比較試験(RCT)のシステマティックレビューを行い,品質が保証された研究成果を明らかにする.方法:医学中央雑誌Web版を含む8つの文献検索サイトを用いて検索し,キーワードは「看護」,論文種類は原著論文とし,その中でわが国の臨床看護技術を研究し,日本語表記の論文を対象とした.そして,RCTの妥当性,再現性の評価と,研究成果を抽出した.結果:58件の論文を得た.3件の論文は妥当性が評価されたが,対照群の介入の再現性に差がみられた.得られた研究成果は,心臓カテーテル検査初回患者に対する検査説明リラクセーションプログラムの睡眠時間延長効果と,手術予定幼児に対するビデオを用いた家庭でのプレパレーションの体温,心拍数,心理面への安定効果,の2件(3.4%)であった.結論:品質が保証された研究成果は僅か2件であり,妥当性の向上に努める必要がある.Objectives : This study was conducted to produce a systematic review of randomized controlled trials (RCTs) over the past five years of clinical nursing skills in Japan and identify studies based on RCTs with proven quality. Methods : Eight websites for literature searches, including the web version of Japana Centra Revuo Medicina, were used. Using the keyword "Nursing Care", we searched for original papers written in Japanese on clinical nursing skills. We then assessed the validity and reproducibility of RCTs and identified the results of related studies with proven quality. Results : We retrieved 58 papers. In three studies, the validity of which had been verified, there were differences in the reproducibility of data in the intervention and control groups. Research results with proven quality were generated by two studies (3.4%), "The effects of a relaxation program, including sleep extension, designed to explain the examination procedures for patients undergoing the first cardiac catheterization test" and "Preparation at home using videos for infants undergoing surgery - Its effects to maintain their body temperature, heart rate, and psychological stability". Conclusions : We identified only two studies yielding results with proven quality, which indicated that efforts should be made to increase the validity of RCTs.報

Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms

We analyzed 192 strains of the pathogenic yeast Candida glabrata from patients, mainly suffering from systemic infection, at Danish hospitals during 1985-1999. Our analysis showed that these strains were closely related but exhibited large karyotype polymorphism. Nine strains contained small chromosomes, which were smaller than 0.5 Mb. Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes). We suggest that at least two mechanisms could participate in their origin: (i) through a segmental duplication which covered the centromeric region, or (ii) by a translocation event moving a larger chromosome arm to another chromosome that leaves the centromere part with the shorter arm. The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable. Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment"

Assembly and analysis of the genome sequence of the yeast Brettanomyces naardenensis CBS 7540

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis

Alcohol dehydrogenase gene ADH3 activates glucose alcoholic fermentation in genetically engineered Dekkera bruxellensis yeast

Dekkera bruxellensis is a non-conventional Crabtree-positive yeast with a good ethanol production capability. Compared to Saccharomyces cerevisiae, its tolerance to acidic pH and its utilization of alternative carbon sources make it a promising organism for producing biofuel. In this study, we developed an auxotrophic transformation system and an expression vector, which enabled the manipulation of D. bruxellensis, thereby improving its fermentative performance. Its gene ADH3, coding for alcohol dehydrogenase, was cloned and overexpressed under the control of the strong and constitutive promoter TEF1. Our recombinant D. bruxellensis strain displayed 1.4 and 1.7 times faster specific glucose consumption rate during aerobic and anaerobic glucose fermentations, respectively; it yielded 1.2 times and 1.5 times more ethanol than did the parental strain under aerobic and anaerobic conditions, respectively. The overexpression of ADH3 in D. bruxellensis also reduced the inhibition of fermentation by anaerobiosis, the "Custer effect". Thus, the fermentative capacity of D. bruxellensis could be further improved by metabolic engineering

A 5 kb intergenic region containing oril in the mitochondrial DNA of Saccharomyces cerevisiae is dispensable for expression of the respiratory phenotype

AbstractA mutant mitochondrial DNA of Saccharomyces cerevisiae strain R 0.54 has been shown to have a 5 kb deletion which removes the oril sequence and its surrounding intergenic sequences between the pro tRNA and 15 S rRNA genes. The deleted DNA has been sequenced and is found to be flanked by two 11 bp direct repeats. The deletion mutant displays a normal phenotype in non-fermentable media. This implies that the intergenic sequence is not required for expression of the respiratory phenotype

Sensitivity of intergenic regions of yeast mitochondrial DNA to single-strand-specific nucleases

AbstractThe reactivity of mitochondrial DNA (mtDNA) sequences from Torulopsis glabrata and Saccharomyces cerevisiae towards single-strand-specific nucleases has been examined. AT-rich stretches located in intergenic sequences from both yeasts were cleaved by nucleases when the sequences were contained in supercoiled plasmid DNA. In particular ori/rep sequences from the mtDNA of S. cerevisiae were shown to be sensitive to the single-strand-specific nucleases. The locations of the sensitive sites were related to the organisation of the sequence domains of ori/rep and the superhelicity of the DNA, as well as the presence of particular sequences. It is proposed that distortions of the DNA duplex could be generated in mtDNA molecules in vivo and that these distortions may provide a substrate for enzymes involved in transmission, recombination and/or transcription of mtDNA

Complex Nature of the Genome in a Wine Spoilage Yeast, Dekkera bruxellensis▿ †

When the genome organizations of 30 native isolates belonging to a wine spoilage yeast, Dekkera (Brettanomyces) bruxellensis, a distant relative of Saccharomyces cerevisiae, were examined, the numbers of chromosomes varied drastically, from 4 to at least 9. When single gene probes were used in Southern analysis, the corresponding genes usually mapped to at least two chromosomal bands, excluding a simple haploid organization of the genome. When different loci were sequenced, in most cases, several different haplotypes were obtained for each single isolate, and they belonged to two subtypes. Phylogenetic reconstruction using haplotypes revealed that the sequences from different isolates belonging to one subtype were more similar to each other than to the sequences belonging to the other subtype within the isolate. Reanalysis of the genome sequence also confirmed that partially sequenced strain Y879 is not a simple haploid and that its genome contains approximately 1% polymorphic sites. The present situation could be explained by (i) a hybridization event where two similar but different genomes have recently fused together or (ii) an event where the diploid progenitor of all analyzed strains lost a regular sexual cycle, and the genome started to accumulate mutations

Aggregated DNA in ethanol solution

AbstractA recently developed mechanochemical method has provided a new, efficient tool for studies on the thermal stability and structure of aggregated DNA in ethanol-water solutions. At low ethanol concentrations DNA is fully soluble and is in the B form. However, with increasing ethanol concentration the melting temperature of DNA, Tm, decreases. At a critical ethanol concentration dependent on the nature and concentration of the counterion, aggregation of the DNA molecules sets in. This is reflected in a marked increase in Tm indicating that the aggregated DNA molecules are thermally more stable than the dissolved ones. However, they are still in the B form. In general, Tm of aggregated DNA also decreases with further increasing ethanol concentration and is dependent on the nature of the counterion, but Tm is not affected by the concentration of the counterion (excess salt) in the ethanol-water solution. When the ethanol concentration reaches the range of 70–80% (v/v), the B-to-A conformational transition occurs in the case of Na-, K- and CsDNA. Above this transition point the A form is more stable than the B form due to the reduced water activity and to increased interhelical interactions. At very high ethanol concentrations, above 85% and dependent on the nature of the counterion, a drastic change in the thermal behaviour is observed. Apparently such a strong interhelical interaction is induced in the aggregated DNA that the DNA is stabilized and cannot adopt a random coil state even at very high temperatures. This stability of DNA in the P form is fully reversed if the ethanol concentration is lowered and the activity of water, thereby, is restored