Supernova cosmology: legacy and future

The discovery of dark energy by the first generation of high-redshift supernova surveys has generated enormous interest beyond cosmology and has dramatic implications for fundamental physics. Distance measurements using supernova explosions are the most direct probes of the expansion history of the Universe, making them extremely useful tools to study the cosmic fabric and the properties of gravity at the largest scales. The past decade has seen the confirmation of the original results. Type Ia supernovae are among the leading techniques to obtain high-precision measurements of the dark energy equation of state parameter, and in the near future, its time dependence. The success of these efforts depends on our ability to understand a large number of effects, mostly of astrophysical nature, influencing the observed flux at Earth. The frontier now lies in understanding if the observed phenomenon is due to vacuum energy, albeit its unnatural density, or some exotic new physics. Future surveys will address the systematic effects with improved calibration procedures and provide thousands of supernovae for detailed studies.Comment: Invited review, Annual Review of Nuclear and Particle Science (submitted version

Yeast cell death caused by nutrient desequilibrium during alcoholic fermentation is impacted by nitrogen sources

Nutrients availability is a key factor for controlling wine alcoholic fermentation. Among them, nitrogen has been identified as an essential parameter, controlling both the fermentation rate and the durationof the fermentation. However, nitrogen is not sufficient to ensure a correct fermentation and other nutrients such as vitamins and lipids, present in lower quantities, are required. Furthermore, we showed in a previous study that an excess of nitrogen combined with a depletion in certain micronutrients can lead to cell death and sluggish or stuck fermentation. In this study, we provide evidence of the mechanism controlling cell death and we show that all the nitrogen sources are not equivalent in the initiation of this phenomenon.Fermentations limited in oleic acid, pantothenic acid and nicotinic acid showed yeast cell death linked to a high nitrogen content. In each case, lowering the nitrogen level restored yeast viability. We evidenced that yeast cell lack of a correct stress response to those micronutrient starvations in presence of high levels of nitrogen. A transcriptional analysis showed a correct stress response suggesting that the lack of resistance originates from a post-transcriptional control mechanism. We then provide evidence that the nitrogen Tor/Sch9 signaling pathway is involved in triggering cell death.Yeast cell viability was then monitored and compared during fermentation starting at different nitrogen levels, with the addition of different nitrogen sources (19 amino acids and NH4+) and two different timing of NH4+ addition. We observed that cell death was triggered with different intensities.Yeast cell death associated to disequilibrium between micronutrients and nitrogen has been evidenced and its implication on fermentations highlighted. We showed a strong impact of both the nature of the nitrogen source and time of addition on yeast cell death and fermentation outcome

Genetic bases of nitrogen requirement in wine yeast assessed trhrough QTL analysis

In grape must, nitrogen content is ofteninsufficient for the completion of alcoholic fermentation by yeast. For Saccharomyces cerevisiae, response to nitrogen deficiency is strain-dependent, some strains being able to complete fermentation despite nitrogen deficiency whereas others are not and result in sluggish or stuck fermentation. Thus, it is of high interest to study the mechanisms behind those different responses and exploit them to improve yeast strain for wine fermentation when nitrogen content is low. Previous study highlighted different genomic regions involved in nitrogen requirement through BSA (Bulk Segregant Analysis), and the contributions of three genes: MDS3, GCN1, and ARG81 have been shown (1). However, many other large genomic regions were also defined for which we could not find evident candidate genes. In addition, BSA did not provide any information on possible interactions between loci. In order to explore further the genetic bases of nitrogen requirement, we applied a QTL analysis to the fermentation rate in nitrogen deficient medium, on a population of 131 individually genotyped segregants obtained from the same cross as (1). The dense genetic map available for the segregant population (3727 markers) enabled us to perform single and multiple map QTL and thus define genomic regions which could be implied in low nitrogen requirement. In order to further validate the impact of candidate genes on the phenotype, alleles were “swapped” by CRISPR-Cas9 technique and phenotype was evaluated in comparison with haploid parent strains.Several regions with high LOD scores were identified, some above the significance threshold, and others below, among which the regions containing the genes identified by (1), probably in relation with the multigenic character of the trait. In the region with the highest LOD score, two candidate genes in relation with nitrogen metabolism (namely, Target of Rapamycin (TOR) pathwayand lifespan regulation) were identified. In addition, in order to reveal possible interaction between genes, strains carrying different combinations of GCN1 and MDS3 parental alleles (implied in TOR pathway) have been evaluated. These constructions confirm their role on the fermentation rate in low-nitrogen conditions and indicate dependence on the genetic background. These results confirm the complexity of mechanisms involved in nitrogen requirement during alcoholic fermentation and will permit to optimise wine yeast strain selection in response to winemaking industry demands

Monitoring the spreading of industrial yeast populations in the winery environment

Resumo e poster da comunicação apresentada no "22nd International Specialized Symposium on Yeasts", em 2002, Kwa Maritane, África do Sul.Nowadays, about 50% of the European wine production is based on the use of active dried wine yeast. These strains were selected due to their good fermentation performance and to their capacity to produce a wine with desirable organoleptical characteristics. From an ecological point of view, they are non-indigenous, mostly S. cerevisiae strains that are annually introduced in the ecosystem surrounding the winery. The fate of those yeasts in the natural environment in different geographical localizations is totally unknown. The present study aims to evaluate the industrial starter yeasts’ ability to survive and spread in nature, and become part of the natural microflora of musts. A large-scale sampling plan was elaborated, including 6 different vineyards (3 in Portugal 3 in France), that use the same industrial yeast strain continuously in the last 5 years, being the winery located in close proximity to the vine. In each vineyard, 6 sampling sites were chosen depending on the predominating wind direction and the relative position to the winery. From each site, before and after the harvest, a sufficient amount of grapes was collected to perform small-scale fermentations (0,5 l). Must samples were plated when 30 g/l and 70g/l of CO2 were released, and in both cases, 30 randomly selected colonies were collected. The identification of the industrial yeast strains, Zymaflore VL1 from Laffort Oenologie and a labelled starter yeast, were performed by PCR-amplification of ∂-sequences [1, 2], pulse field electrophoresis and by the use of appropriate antibiotics containing media, respectively. The overall duration of those studies is 3 years, and preliminary results of the first year will be presented

Family dispute: do Type IIP supernova siblings agree on their distance?

Context: Type II supernovae provide a direct way to estimate distances through the expanding photosphere method, which is independent of the cosmic distance ladder. A recently introduced Gaussian process-based method allows for a fast and precise modelling of spectral time series, which puts accurate and computationally cheap Type II-based absolute distance determinations within reach. Aims: The goal of the paper is to assess the internal consistency of this new modelling technique coupled with the distance estimation empirically, using the spectral time series of supernova siblings, i.e. supernovae that exploded in the same host galaxy. Methods: We use a recently developed spectral emulator code, which is trained on \textsc{Tardis} radiative transfer models and is capable of a fast maximum likelihood parameter estimation and spectral fitting. After calculating the relevant physical parameters of supernovae we apply the expanding photosphere method to estimate their distances. Finally, we test the consistency of the obtained values by applying the formalism of Bayes factors. Results: The distances to four different host galaxies were estimated based on two supernovae in each. The distance estimates are not only consistent within the errors for each of the supernova sibling pairs, but in the case of two hosts they are precise to better than 5\%. Conclusions: Even though the literature data we used was not tailored for the requirements of our analysis, the agreement of the final estimates shows that the method is robust and is capable of inferring both precise and consistent distances. By using high-quality spectral time series, this method can provide precise distance estimates independent of the distance ladder, which are of high value for cosmology.Comment: 20 pages, 20 figures, 6 tables, Accepted in A&

Deciphering the Molecular Basis of Wine Yeast Fermentation Traits Using a Combined Genetic and Genomic Approach

The genetic basis of the phenotypic diversity of yeast is still poorly understood. Wine yeast strains have specific abilities to grow and ferment under stressful conditions compared with other strains, but the genetic basis underlying these traits is unknown. Understanding how sequence variation influences such phenotypes is a major challenge to address adaptation mechanisms of wine yeast. We aimed to identify the genetic basis of fermentation traits and gain insight into their relationships with variations in gene expression among yeast strains. We combined fermentation trait QTL mapping and expression profiling of fermenting cells in a segregating population from a cross between a wine yeast derivative and a laboratory strain. We report the identification of QTL for various fermentation traits (fermentation rates, nitrogen utilization, metabolites production) as well as expression QTL (eQTL). We found that many transcripts mapped to several eQTL hotspots and that two of them overlapped with QTL for fermentation traits. A QTL controlling the maximal fermentation rate and nitrogen utilization overlapping with an eQTL hotspot was dissected. We functionally demonstrated that an allele of the ABZ1 gene, localized in the hotspot and involved in p-aminobenzoate biosynthesis, controls the fermentation rate through modulation of nitrogen utilization. Our data suggest that the laboratory strain harbors a defective ABZ1 allele, which triggers strong metabolic and physiological alterations responsible for the generation of the eQTL hotspot. They also suggest that a number of gene expression differences result from some alleles that trigger major physiological disturbances

Supernova Cosmology and the ESSENCE project

The proper usage of Type Ia supernovae (SNe Ia) as distance indicators has revolutionized cosmology, and added a new dominant component to the energy density of the Universe, dark energy. Following the discovery and confirmation era, the currently ongoing SNe Ia surveys aim to determine the properties of the dark energy. ESSENCE is a five year ground-based supernova survey aimed at finding and characterizing 200 SNe Ia in the redshift domain z=[0.2-0.8]. The goal of the project is to put constraints on the equation of state parameter, w, of the dark energy with an accuracy of <10%. This paper presents these ongoing efforts in the context of the current developments in observational cosmology.Comment: Submitted to EPS1

Spectroscopy of High-Redshift Supernovae from the ESSENCE Project: The First Two Years

We present the results of spectroscopic observations of targets discovered during the first two years of the ESSENCE project. The goal of ESSENCE is to use a sample of ~200 Type Ia supernovae (SNe Ia) at moderate redshifts (0.2 < z < 0.8) to place constraints on the equation of state of the Universe. Spectroscopy not only provides the redshifts of the objects, but also confirms that some of the discoveries are indeed SNe Ia. This confirmation is critical to the project, as techniques developed to determine luminosity distances to SNe Ia depend upon the knowledge that the objects at high redshift are the same as the ones at low redshift. We describe the methods of target selection and prioritization, the telescopes and detectors, and the software used to identify objects. The redshifts deduced from spectral matching of high-redshift SNe Ia with low-redshift SNe Ia are consistent with those determined from host-galaxy spectra. We show that the high-redshift SNe Ia match well with low-redshift templates. We include all spectra obtained by the ESSENCE project, including 52 SNe Ia, 5 core-collapse SNe, 12 active galactic nuclei, 19 galaxies, 4 possibly variable stars, and 16 objects with uncertain identifications.Comment: 38 pages, 9 figures (many with multiple parts), submitted to A

23 High Redshift Supernovae from the IfA Deep Survey: Doubling the SN Sample at z>0.7

We present photometric and spectroscopic observations of 23 high redshift supernovae spanning a range of z=0.34-1.03, 9 of which are unambiguously classified as Type Ia. These supernovae were discovered during the IfA Deep Survey, which began in September 2001 and observed a total of 2.5 square degrees to a depth of approximately m=25-26 in RIZ over 9-17 visits, typically every 1-3 weeks for nearly 5 months, with additional observations continuing until April 2002. We give a brief description of the survey motivations, observational strategy, and reduction process. This sample of 23 high-redshift supernovae includes 15 at z>0.7, doubling the published number of objects at these redshifts, and indicates that the evidence for acceleration of the universe is not due to a systematic effect proportional to redshift. In combination with the recent compilation of Tonry et al. (2003), we calculate cosmological parameter density contours which are consistent with the flat universe indicated by the CMB (Spergel et al. 2003). Adopting the constraint that Omega_total = 1.0, we obtain best-fit values of (Omega_m, Omega_Lambda)=(0.33, 0.67) using 22 SNe from this survey augmented by the literature compilation. We show that using the empty-beam model for gravitational lensing does not eliminate the need for Omega_Lambda > 0. Experience from this survey indicates great potential for similar large-scale surveys while also revealing the limitations of performing surveys for z>1 SNe from the ground.Comment: 67 pages, 12 figures, 12 tables, accepted for publication in the Astrophysical Journa