Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential

A current trend in winemaking has highlighted the beneficial contribution of non-Saccharomyces yeasts to wine quality. Hanseniaspora uvarum is one of the more represented non-Saccharomyces species onto grape berries and plays a critical role in influencing the wine sensory profile, in terms of complexity and organoleptic richness. In this work, we analyzed a group of H. uvarum indigenous wine strains as for genetic as for technological traits, such as resistance to SO2 and beta-glucosidase activity. Three strains were selected for genome sequencing, assembly and comparative genomic analyses at species and genus level. Hanseniaspora genomes appeared compact and contained a moderate number of genes, while rarefaction analyses suggested an open accessory genome, reflecting a rather incomplete representation of the Hanseniaspora gene pool in the currently available genomes. The analyses of patterns of functional annotation in the three indigenous H. uvarum strains showed distinct enrichment for several PFAM protein domains. In particular, for certain traits, such as flocculation related protein domains, the genetic prediction correlated well with relative flocculation phenotypes at lab-scale. This feature, together with the enrichment for oligo-peptide transport and lipid and amino acid metabolism domains, reveals a promising potential of these indigenous strains to be applied in fermentation processes and modulation of wine flavor and aroma. This study also contributes to increasing the catalog of publicly available genomes from H. uvarum strains isolated from natural grape samples and provides a good roadmap for unraveling the biodiversity and the biotechnological potential of these non-Saccharomyces yeasts

Rtg signaling sustains mitochondrial respiratory capacity in hog1-dependent osmoadaptation

Mitochondrial RTG-dependent retrograde signaling, whose regulators have been characterized in Saccharomyces cerevisiae, plays a recognized role under various environmental stresses. Of special significance, the activity of the transcriptional complex Rtg1/3 has been shown to be modu-lated by Hog1, the master regulator of the high osmolarity glycerol pathway, in response to osmotic stress. The present work focuses on the role of RTG signaling in salt-induced osmotic stress and its interaction with HOG1. Wild-type and mutant cells, lacking HOG1 and/or RTG genes, are compared with respect to cell growth features, retrograde signaling activation and mitochondrial function in the presence and in the absence of high osmostress. We show that RTG2, the main upstream regulator of the RTG pathway, contributes to osmoadaptation in an HOG1-dependent manner and that, with RTG3, it is notably involved in a late phase of growth. Our data demonstrate that impairment of RTG signaling causes a decrease in mitochondrial respiratory capacity exclusively under os-mostress. Overall, these results suggest that HOG1 and the RTG pathway may interact sequentially in the stress signaling cascade and that the RTG pathway may play a role in inter-organellar metabolic communication for osmoadaptation

LOCUS: A Multi-Sensor Lidar-Centric Solution for High-Precision Odometry and 3D Mapping in Real-Time

A reliable odometry source is a prerequisite to enable complex autonomy behaviour in next-generation robots operating in extreme environments. In this work, we present a high-precision lidar odometry system to achieve robust and real-time operation under challenging perceptual conditions. LOCUS (Lidar Odometry for Consistent operation in Uncertain Settings), provides an accurate multi-stage scan matching unit equipped with an health-aware sensor integration module for seamless fusion of additional sensing modalities. We evaluate the performance of the proposed system against state-of-the-art techniques in perceptually challenging environments, and demonstrate top-class localization accuracy along with substantial improvements in robustness to sensor failures. We then demonstrate real-time performance of LOCUS on various types of robotic mobility platforms involved in the autonomous exploration of the Satsop power plant in Elma, WA where the proposed system was a key element of the CoSTAR team's solution that won first place in the Urban Circuit of the DARPA Subterranean Challenge.Comment: Accepted for publication at IEEE Robotics and Automation Letters, 202

Yeast between life and death: a summary of the Ninth International Meeting on Yeast Apoptosis in Rome, Italy, 17–20 September 2012

Remembering the ancient latin saying omnes viae Romam ducunt, the yeast cell death community came to the eternal city to attend the 9th International Meeting on Yeast Apoptosis (IMYA), from 17–20 September 2012. More than one hundred investigators from around the world presented and discussed their researches on programmed cell death (PCD) and its role in stress responses, aging and development employing yeast as model organism. On the first day, the meeting took place at the historical Angelicum Congress Center, sharing its opening session with the last session of the 20th Euroconference on Apoptosis (ECDO)

A Gradient-Based Approach for Breast DCE-MRI Analysis

Breast cancer is the main cause of female malignancy worldwide. Effective early detection by imaging studies remains critical to decrease mortality rates, particularly in women at high risk for developing breast cancer. Breast Magnetic Resonance Imaging (MRI) is a common diagnostic tool in the management of breast diseases, especially for high-risk women. However, during this examination, both normal and abnormal breast tissues enhance after contrast material administration. Specifically, the normal breast tissue enhancement is known as background parenchymal enhancement: it may represent breast activity and depends on several factors, varying in degree and distribution in different patients as well as in the same patient over time. While a light degree of normal breast tissue enhancement generally causes no interpretative difficulties, a higher degree may cause difficulty to detect and classify breast lesions at Magnetic Resonance Imaging even for experienced radiologists. In this work, we intend to investigate the exploitation of some statistical measurements to automatically characterize the enhancement trend of the whole breast area in both normal and abnormal tissues independently from the presence of a background parenchymal enhancement thus to provide a diagnostic support tool for radiologists in the MRI analysis

Diamond Detectors for the TOTEM Timing Upgrade

This paper describes the design and the performance of the timing detector developed by the TOTEM Collaboration for the Roman Pots (RPs) to measure the Time-Of-Flight (TOF) of the protons produced in central diffractive interactions at the LHC. The measurement of the TOF of the protons allows the determination of the longitudinal position of the proton interaction vertex and its association with one of the vertices reconstructed by the CMS detectors. The TOF detector is based on single crystal Chemical Vapor Deposition (scCVD) diamond plates and is designed to measure the protons TOF with about 50 ps time precision. This upgrade to the TOTEM apparatus will be used in the LHC run 2 and will tag the central diffractive events up to an interaction pileup of about 1. A dedicated fast and low noise electronics for the signal amplification has been developed. The digitization of the diamond signal is performed by sampling the waveform. After introducing the physics studies that will most profit from the addition of these new detectors, we discuss in detail the optimization and the performance of the first TOF detector installed in the LHC in November 2015.Comment: 26 pages, 18 figures, 2 tables, submitted for publication to JINS

Evidence for non-exponential elastic proton-proton differential cross-section at low |t| and sqrt(s) = 8 TeV by TOTEM

The TOTEM experiment has made a precise measurement of the elastic proton-proton differential cross-section at the centre-of-mass energy sqrt(s) = 8 TeV based on a high-statistics data sample obtained with the beta* = 90 optics. Both the statistical and systematic uncertainties remain below 1%, except for the t-independent contribution from the overall normalisation. This unprecedented precision allows to exclude a purely exponential differential cross-section in the range of four-momentum transfer squared 0.027 < |t| < 0.2 GeV^2 with a significance greater than 7 sigma. Two extended parametrisations, with quadratic and cubic polynomials in the exponent, are shown to be well compatible with the data. Using them for the differential cross-section extrapolation to t = 0, and further applying the optical theorem, yields total cross-section estimates of (101.5 +- 2.1) mb and (101.9 +- 2.1) mb, respectively, in agreement with previous TOTEM measurements.Comment: Final version published in Nuclear Physics

A Non-Death Role of the Yeast Metacaspase: Yca1p Alters Cell Cycle Dynamics

Caspase proteases are a conserved protein family predominantly known for engaging and executing apoptotic cell death. Nevertheless, in higher eukaryotes, caspases also influence a variety of cell behaviors including differentiation, proliferation and growth control. S. cerevisiae expresses a primordial caspase, yca1, and exhibits apoptosis-like death under certain stresses; however, the benefit of a dedicated death program to single cell organisms is controversial. In the absence of a clear rationale to justify the evolutionary retention of a death only pathway, we hypothesize that yca1 also influences non-apoptotic events. We report that genetic ablation and/or catalytic inactivation of Yca1p leads to a longer G1/S transition accompanied by slower growth in fermentation conditions. Downregulation of Yca1p proteolytic activity also results in failure to arrest during nocodazole treatment, indicating that Yca1p participates in the G2/M mitotic checkpoint. 20s proteasome activity and ROS staining of the Δyca1 strain is indistinguishable from its isogenic control suggesting that putative regulation of the oxidative stress response by Yca1p does not instigate the cell cycle phenotype. Our results demonstrate multiple non-death roles for yca1 in the cell cycle

Plasmodium falciparum metacaspase PfMCA-1 triggers a z-VAD-fmk inhibitable protease to promote cell death.

Activation of proteolytic cell death pathways may circumvent drug resistance in deadly protozoan parasites such as Plasmodium falciparum and Leishmania. To this end, it is important to define the cell death pathway(s) in parasites and thus characterize proteases such as metacaspases (MCA), which have been reported to induce cell death in plants and Leishmania parasites. We, therefore, investigated whether the cell death function of MCA is conserved in different protozoan parasite species such as Plasmodium falciparum and Leishmania major, focusing on the substrate specificity and functional role in cell survival as compared to Saccharomyces cerevisae. Our results show that, similarly to Leishmania, Plasmodium MCA exhibits a calcium-dependent, arginine-specific protease activity and its expression in yeast induced growth inhibition as well as an 82% increase in cell death under oxidative stress, a situation encountered by parasites during the host or when exposed to drugs such as artemisins. Furthermore, we show that MCA cell death pathways in both Plasmodium and Leishmania, involve a z-VAD-fmk inhibitable protease. Our data provide evidence that MCA from both Leishmania and Plasmodium falciparum is able to induce cell death in stress conditions, where it specifically activates a downstream enzyme as part of a cell death pathway. This enzymatic activity is also induced by the antimalarial drug chloroquine in erythrocytic stages of Plasmodium falciparum. Interestingly, we found that blocking parasite cell death influences their drug sensitivity, a result which could be used to create therapeutic strategies that by-pass drug resistance mechanisms by acting directly on the innate pathways of protozoan cell death

Ammonium Toxicity and Potassium Limitation in Yeast

DNA microarray analysis of gene expression in steady-state chemostat cultures limited for potassium revealed a surprising connection between potassium and ammonium: potassium limits growth only when ammonium is the nitrogen source. Under potassium limitation, ammonium appears to be toxic for Saccharomyces cerevisiae. This ammonium toxicity, which appears to occur by leakage of ammonium through potassium channels, is recapitulated under high-potassium conditions by over-expression of ammonium transporters. Although ammonium toxicity is well established in metazoans, it has never been reported for yeast. To characterize the response to ammonium toxicity, we examined the filtrates of these cultures for compounds whose excretion might serve to detoxify the ammonium (such as urea in mammals). Using liquid chromatography–tandem mass spectrometry to assay for a wide array of metabolites, we detected excreted amino acids. The amounts of amino acids excreted increased in relation to the severity of growth impairment by ammonium, suggesting that amino acid excretion is used by yeast for ammonium detoxification