Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity.

Saccharomyces cerevisiae is the main actor of wine fermentation but at present, still little is known about the factors impacting its distribution in the vineyards. In this study, 23 vineyards and 7 cellars were sampled over 2 consecutive years in the Bordeaux and Bergerac regions. The impact of geography and farming system and the relation between grape and vat populations were evaluated using a collection of 1374 S.

Fast sequence-based microsatellite genotyping development workflow.

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability.

CReasPy-Cloning: A Method for Simultaneous Cloning and Engineering of Megabase-Sized Genomes in Yeast Using the CRISPR-Cas9 System.

Over the past decade, a new strategy was developed to bypass the difficulties to genetically engineer some microbial species by transferring (or "cloning") their genome into another organism that is amenable to efficient genetic modifications and therefore acts as a living workbench. As such, the yeast has been used to clone and engineer genomes from viruses, bacteria, and algae. The cloning step requires the insertion of yeast genetic elements in the genome of interest, in order to drive its replication and maintenance as an artificial chromosome in the host cell.

Correction for Rosa et al., "Draft Genome Sequence of the (syn., ) Type Strain CBS 9494".

[This corrects the article DOI: 10.1128/MRA.00872-18.

Draft Genome Sequence of the Candida zemplinina (syn., Starmerella bacillaris) Type Strain CBS 9494 [corrected].

Starmerella bacillaris is an ascomycetous yeast ubiquitously present in grapes and fermenting grape musts. In this report, we present the draft genome sequence of the S. bacillaris type strain CBS 9494, isolated from sweet botrytized wines, which will contribute to the study of this genetically heterogeneous wine yeast species.

MiR-10a and HOXB4 are overexpressed in atypical myeloproliferative neoplasms.

Background: Atypical Myeloproliferative Neoplasms (aMPN) share characteristics of MPN and Myelodysplastic Syndromes. Although abnormalities in cytokine signaling are common in MPN, the pathophysiology of atypical MPN still remains elusive. Since deregulation of microRNAs is involved in the biology of various cancers, we studied the miRNome of aMPN patients.

Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution.

Brettanomyces bruxellensis is a unicellular fungus of increasing industrial and scientific interest over the past 15 years. Previous studies revealed high genotypic diversity amongst B. bruxellensis strains as well as strain-dependent phenotypic characteristics.

Modulation of oncogenic miRNA biogenesis using functionalized polyamines.

MicroRNAs are key factors in the regulation of gene expression and their deregulation has been directly linked to various pathologies such as cancer. The use of small molecules to tackle the overexpression of oncogenic miRNAs has proved its efficacy and holds the promise for therapeutic applications. Here we describe the screening of a 640-compound library and the identification of polyamine derivatives interfering with in vitro Dicer-mediated processing of the oncogenic miR-372 precursor (pre-miR-372).

Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions.

Unlabelled: Understanding the mechanisms behind the typicity of regional wines inevitably brings attention to microorganisms associated with their production. Oenococcus oeni is the main bacterial species involved in wine and cider making. It develops after the yeast-driven alcoholic fermentation and performs the malolactic fermentation, which improves the taste and aromatic complexity of most wines.

Cellar-Associated Saccharomyces cerevisiae Population Structure Revealed High-Level Diversity and Perennial Persistence at Sauternes Wine Estates.

Unlabelled: Three wine estates (designated A, B, and C) were sampled in Sauternes, a typical appellation of the Bordeaux wine area producing sweet white wine. From those wine estates, 551 yeast strains were collected between 2012 and 2014, added to 102 older strains from 1992 to 2011 from wine estate C. All the strains were analyzed through 15 microsatellite markers, resulting in 503 unique Saccharomyces cerevisiae genotypes, revealing high genetic diversity and a low presence of commercial yeast starters.

Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering.

Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation (AF) which is usually performed by Saccharomyces species. The aim of this study was to characterize the genetic and phenotypic variability within the H. uvarum species.

Microsatellite analysis of Saccharomyces uvarum diversity.

Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated.

Over-five octaves wide Raman combs in high-power picosecond-laser pumped H(2)-filled inhibited coupling Kagome fiber.

We report on the generation of over 5 octaves wide Raman combs using inhibited coupling Kagome guiding hollow-core photonic crystal fiber filled with hydrogen and pumped with 22.7 W average power and 27 picosecond pulsed fiber laser. Combs spanning from ~321 nm in the UV to ~12.

The yeast Starmerella bacillaris (synonym Candida zemplinina) shows high genetic diversity in winemaking environments.

The yeast Candida zemplinina (Starmerella bacillaris) is frequently isolated from grape and wine environments. Its enological use in mixed fermentation with Saccharomyces cerevisiae has been extensively investigated these last few years, and several interesting features including low ethanol production, fructophily, glycerol and other metabolites production, have been described. In addition, molecular tools allowing the characterization of yeast populations have been developed, both at the inter- and intraspecific levels.

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods.

Highly efficient higher-order modes filtering into aperiodic very large mode area fibers for single-mode propagation.

We report here on the first experimental demonstration, to the best of our knowledge, of a new generation of very large mode area (VLMA) fibers intended to strengthen single-mode propagation. The originality of this work relies on an aperiodicity of the inner cladding microstructuration exacerbating the spatial rejection of higher-order-modes (HOMs) while preserving a significant confinement of the fundamental mode. The single-mode behavior was demonstrated using an optical low-coherence interferometry measurement based on the group-velocity dispersion.

Development of microsatellite markers for the rapid and reliable genotyping of Brettanomyces bruxellensis at strain level.

Although many yeasts are useful for food production and beverage, some species may cause spoilage with important economic loss. This is the case of Dekkera/Brettanomyces bruxellensis, a contaminant species that is mainly associated with fermented beverages (wine, beer, cider and traditional drinks). To better control Brettanomyces spoilage, rapid and reliable genotyping methods are necessary to determine the origins of the spoilage, to assess the effectiveness of preventive treatments and to develop new control strategies.

Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii.

The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect).

Amplification and compression of temporally shaped picosecond pulses in Yb-doped rod-type fibers.

We report on a new technique to produce high power sub-picosecond pulses from a fiber amplifier. We use parabolic pulse shaping of 27 ps transform-limited pulses in order to control nonlinear effects in the fiber amplifier. 63 MW, 780 fs pulses with 25 W average power were obtained, and ways to scale the technique to higher peak powers were identified.

Inner cladding microstructuration based on symmetry reduction for improvement of singlemode robustness in VLMA fiber.

Very large mode area, active optical fibers with a low high order mode content in the actively doped core region were designed by removing the inner cladding symmetry. The relevance of the numerical approach is demonstrated here by the investigation of a standard air-silica Large Pitch Fiber, used as a reference. A detailed study of all-solid structures is also performed.

Picosecond to femtosecond pulses from high power self mode-locked ytterbium rod-type fiber laser.

We have designed an ytterbium rod-type fiber laser oscillator with tunable pulse duration. This system that delivers more than 10 W of average power is self mode-locked. It yields femtosecond to picosecond laser pulses at a repetition rate of 74 MHz.

High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination.

Background: The availability of a large expressed sequence tags (EST) resource and recent advances in high-throughput genotyping technology have made it possible to develop highly multiplexed SNP arrays for multi-objective genetic applications, including the construction of meiotic maps. Such approaches are particularly useful in species with a large genome size, precluding the use of whole-genome shotgun assembly with current technologies.

Results: In this study, a 12 k-SNP genotyping array was developed for maritime pine from an extensive EST resource assembled into a unigene set.

Hybrid master oscillator power amplifier high-power narrow-linewidth nanosecond laser source at 257 nm.

We report on a high-power narrow-linewidth pulsed laser source emitting at a wavelength of 257 nm. The system is based on a master oscillator power amplifier architecture, with Yb-doped fiber preamplifiers, a Yb:YAG single crystal fiber power amplifier used to overcome the Brillouin limitation in glass fiber and nonlinear frequency conversion stages. This particularly versatile architecture allows the generation of Fourier transform-limited 15 ns pulses at 1030 nm with 22 W of average power and a diffraction-limited beam (M(2)<1.