The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Yeasts are predominant in the ancient and complex process of winemaking. In spontaneous fermentations, there is a progressive growth pattern of indigenous yeasts, with the final stages invariably being dominated by the alcohol-tolerant strains of Saccharomyces cerevisiae. This species is universally known as the ‘wine yeast’ and is widely preferred for initiating wine fermentations. The primary role of wine yeast is to catalyze the rapid, complete and efficient conversion of grape sugars to ethanol, carbon dioxide and other minor, but important, metabolites without the development of off-flavours. However, due to the demanding nature of modern winemaking practices and sophisticated wine markets, there is an ever-growing quest for specialized wine yeast strains possessing a wide range of optimized, improved or novel oenological properties. This review highlights the wealth of untapped indigenous yeasts with oenological potential, the complexity of wine yeasts’ genetic features and the genetic techniques often used in strain development. The current status of genetically improved wine yeasts and potential targets for further strain development are outlined. In light of the limited knowledge of industrial wine yeasts’ complex genomes and the daunting challenges to comply with strict statutory regulations and consumer demands regarding the future use of genetically modified strains, this review cautions against unrealistic expectations over the short term. However, the staggering potential advantages of improved wine yeasts to both the winemaker and consumer in the third millennium are pointed out. Copyright # 2000 John Wiley & Sons, Ltd.

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Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking

Cloning and characterization of the

Wine is a highly complex mixture of compounds which largely define its appearance, aroma, flavour and mouth-feel properties. The compounds responsible for those attributes have been derived in turn from three major sources, viz. grapes, microbes and, when used, wood (most commonly, oak). The grape-derived compounds provide varietal distinction in addition to giving wine its basic structure. Thus, the floral monoterpenes largely define Muscat-related wines and the fruity volatile thiols define Sauvignon-related wines; the grape acids and tannins, together with alcohol, contribute the palate and mouth-feel properties. Yeast fermentation of sugars not only produces ethanol and carbon dioxide but a range of minor but sensorially important volatile metabolites which gives wine its vinous character. These volatile metabolites, which comprise esters, higher alcohols, carbonyls, volatile fatty acids and sulfur compounds, are derived from sugar and amino acid metabolism. The malolactic fermentation, when needed, not only provides deacidification, but can enhance the flavour profile.

The aroma and flavour profile of wine is the result of an almost infinite number of variations in production, whether in the vineyard or the winery. In addition to the obvious, such as the grapes selected, the winemaker employs a variety of techniques and tools to produce wines with specific flavour profiles. One of these tools is the choice of microorganism to conduct fermentation. During alcoholic fermentation, the wine yeast Saccharomyces cerevisiae brings forth the major changes between grape must and wine: modifying aroma, flavour, mouth-feel, colour and chemical complexity. The wine bacterium Oenococcus oeni adds its contribution to wines that undergo malolactic fermentation. Thus flavour-active yeasts and bacterial strains can produce desirable sensory results by helping to extract compounds from the solids in grape must, by modifying grape-derived molecules and by producing flavour-active metabolites. This article reviews some of the most important flavour compounds found in wine, and their microbiological origin.

Yeast and bacterial modulation of wine aroma and flavour

Acetic acid bacteria in traditional balsamic vinegar: Phenotypic traits relevant for starter cultures selection

The history of vinegar production, which dates back to around 2000 BC, has taught us a great deal about microbial biotransformation. However, vinegar has been always considered a ‘poor relation’ among fermented food products: it is not considered to be a ‘food’, it does not have great nutritional value, and it is made by the transformation of richer and more nutritive fermented foods. Vinegar is used as a flavouring agent, as a preservative and, in some countries, also as a healthy drink. It can be made from almost any fermentable carbohydrate source by a two-step fermentation process involving yeasts as the first agent, followed by acetic acid bacteria (AAB): the most common raw materials are apples, pears, grapes, honey, syrups, cereals, hydrolysed starches, beer and wine.

Vinegars of the World

Characterization of acetic acid bacteria in “traditional balsamic vinegar”

Application of denaturing gradient gel electrophoresis (DGGE) analysis to evaluate acetic acid bacteria in traditional balsamic vinegar.

The formation of hydrogen sulfide in wine has been shown to arise from fermentations of grape musts with nitrogenous deficiencies. This work was instigated to explore this formation with the use of a qualitative, but simple, rapid, and explicit method for hydrogen sulfide detection. Two yeast strains were used that showed representative high and low formations of sulfide from sulfite. In synthetic medium, without added sulfite, the formation of hydrogen sulfide was shown to come exclusively from reduction of sulfate and was dependent upon the limiting concentration of ammonia. The amount of n -propanol formed was also found to be dependent upon the yeast strain and upon the ammonia present. Under ammonia limitations, the addition of non-sulfur containing amino acids tended to inhibit the formation of hydrogen sulfide from sulfate but increased formation of sulfite. Added cysteine brought about increased sulfide but inhibited sulfite formation. Added methionine inhibited both sulfide and sulfite formation, as expected. These results, while preliminary, show that sulfate can be the main substrate for hydrogen sulfide production. The amount of n -propanol formed was explained by metabolic control by methionine.

Paolo Giudici

Papers

Acetic acid bacteria in traditional balsamic vinegar: Phenotypic traits relevant for starter cultures selection

Vinegars of the World

Characterization of acetic acid bacteria in “traditional balsamic vinegar”

Application of denaturing gradient gel electrophoresis (DGGE) analysis to evaluate acetic acid bacteria in traditional balsamic vinegar.

The Effect of Nitrogen Deficiency and Sulfur-Containing Amino Acids on the Reduction of Sulfate to Hydrogen Sulfide by Wine Yeasts