Stefanini I.,University of Florence |
Dapporto L.,University of Florence |
Legras J.-L.,French National Institute for Agricultural Research |
Legras J.-L.,Montpellier SupAgro |
And 10 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2012
Saccharomyces cerevisiae is one of the most important model organisms and has been a valuable asset to human civilization. However, despite its extensive use in the last 9,000 y, the existence of a seasonal cycle outside human-made environments has not yet been described. We demonstrate the role of social wasps as vector and natural reservoir of S. cerevisiae during all seasons. We provide experimental evidence that queens of social wasps overwintering as adults (Vespa crabro and Polistes spp.) can harbor yeast cells from autumn to spring and transmit them to their progeny. This result is mirrored by field surveys of the genetic variability of natural strains of yeast. Microsatellites and sequences of a selected set of loci able to recapitulate the yeast strain's evolutionary history were used to compare 17 environmental wasp isolates with a collection of strains from grapes from the same region and more than 230 strains representing worldwide yeast variation. The wasp isolates fall into subclusters representing the overall ecological and industrial yeast diversity of their geographic origin. Our findings indicate thatwasps are a key environmental niche for the evolution of natural S. cerevisiae populations, the dispersion of yeast cells in the environment, and the maintenance of their diversity. The close relatedness of several wasp isolates with grape and wine isolates reflects the crucial role of human activities on yeast population structure, through clonal expansion and selection of specific strains during the biotransformation of fermented foods, followed by dispersal mediated by insects and other animals.
News Article | October 26, 2016
Satellite meetings for interested investigators will occur Nov. 28 and 30 at the Radiological Society of North America annual meeting in Chicago The Tomosynthesis Mammography Imaging Screening Trial (TMIST), the first large-scale breast cancer screening trial in nearly 25 years, is approved for funding by the National Cancer Institute (NCI). The ECOG-ACRIN Cancer Research Group (ECOG-ACRIN), leading the trial, is now recruiting medical facilities as it prepares to open the trial in mid-2017. TMIST will enroll 165,000 asymptomatic women in the US and Canada, between the ages of 45 and 74, to compare the incidence of advanced cancers in those screened for four years with digital breast tomosynthesis vs. standard digital mammography. The study aims to provide a modern basis for the continued use of mammography for breast cancer screening. Interested medical imaging providers can attend one of two TMIST informational sessions while at the upcoming Radiological Society of North America (RSNA) annual meeting in Chicago: No pre-registration is required to attend. To participate in TMIST, a medical facility must be (1) located in the US or Canada, (2) able to provide both imaging methods in the same location, and (3) a member of a research group in the NCI National Clinical Trials Network (NCTN), either directly or through the NCI Community Oncology Research Program (NCORP). TMIST will require nearly 100 sites, estimating that each will enroll about four to five women per day to reach the accrual goal in about three years. Available for interviews are the following spokespersons for TMIST: lead investigator Etta D. Pisano, MD at Beth Israel Deaconess Medical Center and Harvard Medical School; lead statistician Constantine A. Gatsonis, PhD at the ECOG-ACRIN Biostatistics and Data Management Center located at the Brown University Center for Statistical Sciences; and ECOG-ACRIN group co-chair Mitchell D. Schnall, MD, PhD at the University of Pennsylvania. TMIST image acquisition, storage, and sharing will be carried out at the ACR Center for Research and Innovation. Dr. Gatsonis will lead the TMIST statistical analysis. The NTCN research groups are the Alliance for Clinical Trials in Oncology, ECOG-ACRIN Cancer Research Group, NRG Oncology, and SWOG. Imaging providers can submit email inquiries at http://www. to check on their NCTN status or ask questions about the trial. The ECOG-ACRIN Cancer Research Group is a membership-based scientific organization that designs and conducts cancer research involving adults who have or are at risk of developing cancer. ECOG-ACRIN comprises nearly 1100 member institutions in the United States and around the world. Approximately 12,000 physicians, translational scientists, and associated research professionals from the member institutions are involved in Group research, which is organized into three scientific programs: Cancer Control and Outcomes, Therapeutic Studies, and Biomarker Sciences. ECOG-ACRIN is supported primarily through National Cancer Institute research grant funding, but also receives funding from private sector organizations through philanthropy and collaborations. It is headquartered in Philadelphia, Pa. For more information, visit http://www. or call 215.789.3631.
Zhong Y.,Nanjing Agricultural University |
Yin H.,Nanjing Agricultural University |
Sargent D.J.,Center for Research and Innovation |
Malnoy M.,Center for Research and Innovation |
And 2 more authors.
BMC Genomics | Year: 2015
Background: Disease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosaceae species because several Rosaceae genome sequences have only recently become available. Results: Since most disease resistance genes encode NBS-LRR proteins, we performed a systematic genome-wide survey of NBS-LRR genes between five Rosaceae species, namely Fragaria vesca (strawberry), Malus×domestica (apple), Pyrus bretschneideri (pear), Prunus persica (peach) and Prunus mume (mei) which contained 144, 748, 469, 354 and 352 NBS-LRR genes, respectively. A high proportion of multi-genes and similar Ks peaks (Ks=0.1-0.2) of gene families in the four woody genomes were detected. A total of 385 species-specific duplicate clades were observed in the phylogenetic tree constructed using all 2067 NBS-LRR genes. High percentages of NBS-LRR genes derived from species-specific duplication were found among the five genomes (61.81% in strawberry, 66.04% in apple, 48.61% in pear, 37.01% in peach and 40.05% in mei). Furthermore, the Ks and Ka/Ks values of TIR-NBS-LRR genes (TNLs) were significantly greater than those of non-TIR-NBS-LRR genes (non-TNLs), and most of the NBS-LRRs had Ka/Ks ratios less than 1, suggesting that they were evolving under a subfunctionalization model driven by purifying selection. Conclusions: Our results indicate that recent duplications played an important role in the evolution of NBS-LRR genes in the four woody perennial Rosaceae species. Based on the phylogenetic tree produced, it could be inferred that species-specific duplication has mainly contributed to the expansion of NBS-LRR genes in the five Rosaceae species. In addition, the Ks and Ka/Ks ratios suggest that the rapidly evolved TNLs have different evolutionary patterns to adapt to different pathogens compared with non-TNL resistant genes. © Zhong et al.
Kreisinger J.,Center for Research and Innovation |
Bastien G.,Center for Research and Innovation |
Hauffe H.C.,Center for Research and Innovation |
Marchesi J.,Imperial College London |
And 2 more authors.
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2015
The gut microbiota is vital to host health and, as such, it is important to elucidate the mechanisms altering its composition and diversity. Intestinal helminths are host immunomodulators and have evolved both temporally and spatially in close association with the gut microbiota, resulting in potential mechanistic interplay. Host–helminth and host–microbiota interactions are comparatively well-examined, unlike microbiota–helminth relationships, which typically focus on experimental infection with a single helminth species in laboratory animals. Here, in addition to a review of the literature on helminth– microbiota interactions, we examined empirically the association between microbiota diversity and composition and natural infection of multiple helminth species in wild mice (Apodemus flavicollis), using 16S rRNA gene catalogues (metataxonomics). In general, helminth presence is linked with high microbiota diversity, which may confer health benefits to the host. Within our wild rodent system variation in the composition and abundance of gut microbial taxa associated with helminths was specific to each helminth species and occurred both up- and downstream of a given helminth’s niche (gut position). The most pronounced helminth–microbiota association was between the presence of tapeworms in the small intestine and increased S24–7 (Bacteroidetes) family in the stomach.Helminths clearly have the potential to alter gut homeostasis. Free-living rodentswith a diverse helminth community offer a useful model system that enables both correlative (this study) and manipulative inference to elucidate helminth–microbiota interactions. © 2015 The Authors.
Cornetti L.,Center for Research and Innovation |
Cornetti L.,University of Ferrara |
Menegon M.,Museo di Science |
Giovine G.,Stazione Sperimentale Regionale per lo Studio e la Conservazione degli Anfibi in Lombardia |
And 2 more authors.
PLoS ONE | Year: 2014
The European common lizard Zootoca vivipara exhibits reproductive bimodality, with populations being either viviparous or oviparous. In the central-eastern Italian Alps oviparous populations (Z. v. carniolica) and viviparous populations (Z. v. vivipara) partly overlap geographically. Studying the evolutionary relationship between these taxa presents an interesting opportunity to gain insight into the evolution of this trait. We aim to: i) test whether Z. v. carniolica, which is endangered, constitutes an ESU (Evolutionary Significant Unity); ii) infer mtDNA divergence time between the Z. v. carniolica clade and all the other Z. vivipara subspecies with the aid of an external calibration point; and iii) describe the phylogeographical and demographic scenarios in the area. To do so we sequenced about 200 individuals for mitochondrial variation; 64 of them were also analysed for three nuclear genes. Furthermore, we analysed the same nuclear markers in 17 individuals from the other oviparous subspecies Z. v. louislantzi and 11 individuals of Z. v. vivipara from widespread geographical origins. The mtDNA and nDNA loci that we examined supported the monophyly of Z. v. carniolica. The mtDNA-based estimate of divergence time between Z. v. carniolica and all the other subspecies indicated a separation at 4.5 Mya (95% CI 6.1-2.6), with about 5% of sequence divergence. Considering that Z. v. carniolica harbours higher genetic diversity, while Z. v. vivipara from central-eastern Alps shows a signature of recent population and spatial expansion, we argue that Z. v. carniolica represents a distinct evolutionary unit, with a presumably long-term evolutionary history of separation. Z. v. carniolica populations, occurring at higher latitudes and altitudes than insofar supposed, live in peat bogs, a seriously threatened habitat: taking into account also its evolutionary distinctness, specific conservation measures should be considered. © 2014 Cornetti et al.
Wehrens R.,Center for Research and Innovation |
Carvalho E.,Center for Research and Innovation |
Masuero D.,Center for Research and Innovation |
De Juan A.,University of Barcelona |
Martens S.,Center for Research and Innovation
Analytical and Bioanalytical Chemistry | Year: 2013
We present automated data analysis of high-throughput high-performance liquid chromatography with diode array detection (HPLC-DAD) data using multivariate curve resolution. This technique provides spectra and elution profiles of all UV-Vis active compounds present in the mixture. The specifics of using this method in noninteractive fashion are discussed. A case study on the stability of isoprenoids in grape extracts under two different experimental regimes serves to illustrate the potential of the method: quantitative results clearly show that the addition of triethylamine is beneficial in that carotenoid, chlorophyll, and tocopherol compounds are much more stable and in this way can be kept up to at least 30 days without any sign of degradation. © 2012 Springer-Verlag Berlin Heidelberg.
Bloemberg T.G.,Radboud University Nijmegen |
Gerretzen J.,Radboud University Nijmegen |
Lunshof A.,Radboud University Nijmegen |
Wehrens R.,Center for Research and Innovation |
Buydens L.M.C.,Radboud University Nijmegen
Analytica Chimica Acta | Year: 2013
Warping methods are an important class of methods that can correct for misalignments in (a.o.) chemical measurements. Their use in preprocessing of chromatographic, spectroscopic and spectrometric data has grown rapidly over the last decade. This tutorial review aims to give a critical introduction to the most important warping methods, the place of warping in preprocessing and current views on the related matters of reference selection, optimization, and evaluation. Some pitfalls in warping, notably for liquid chromatography-mass spectrometry (LC-MS) data and similar, will be discussed. Examples will be given of the application of a number of freely available warping methods to a nuclear magnetic resonance (NMR) spectroscopic dataset and a chromatographic dataset. As part of the Supporting Information, we provide a number of programming scripts in Matlab and R, allowing the reader to work the extended examples in detail and to reproduce the figures in this paper. © 2013 Elsevier B.V.
Grzeskowiak L.,Center for Research and Innovation |
Costantini L.,Center for Research and Innovation |
Lorenzi S.,Center for Research and Innovation |
Grando M.S.,Center for Research and Innovation
Theoretical and Applied Genetics | Year: 2013
Key message: In this study, we identified several genes, which potentially contribute to phenological variation in the grapevine. This may help to maintain consistent yield and suitability of particular varieties in future climatic conditions. The timing of major developmental events in fruit crops differs with cultivar, weather conditions and ecological site. This plasticity results also in diverse levels of fruitfulness. Identifying the genetic factors responsible for phenology and fertility variation may help to improve these traits to better match future climates. Two Vitis vinifera populations, an F1 progeny of Syrah × Pinot Noir and a phenological core collection composed of 163 cultivars, were evaluated for phenology and fertility subtraits during three to six growing seasons in the same geographical location. The phenotypic variability in the core collection mostly overlapped with that observed in the F1 progeny and several accessions had exceeding values of phenological response. The progeny population was used together with SSR and SNP markers to map quantitative trait loci (QTLs). This allowed us to detect nine QTLs related to budburst, flowering beginning, the onset of ripening (véraison) and total fertility, explaining from 8 to 44 % of phenotypic variation. A genomic region on chromosome 15 was associated with budburst and véraison and two QTLs for fruitfulness were located on chromosomes 3 and 18. Several genes potentially affecting fertility and the timing of fruit development were proposed, based on their position and putative function. Allelic variation at these candidate loci may be explored by sampling accessions from the core collection. © 2013 The Author(s).
Wehrens R.,Center for Research and Innovation |
Franceschi P.,Center for Research and Innovation
Molecular BioSystems | Year: 2012
Biomarker selection is an important topic in the omics sciences, where holistic measurement methods routinely generate results for many variables simultaneously. Very often, only a small fraction of these variables are really associated with the phenomena of interest. Selection and identification of these biomarkers is essential for obtaining an understanding of the complex biological processes under study. Finding biomarkers, however, is a difficult task. Even if a relative order can be established, e.g., on the basis of p values, it is usually hard to determine where to stop including candidates in the final set. Higher Criticism is an approach for finding data-dependent cutoff values when comparing two distinct groups of samples. Here, we extend its use to multivariate data, providing a principled approach to compromise between not selecting too many variables and catching as many true positives as possible. The results show a marked improvement in biomarker selection, compared to the standard settings available for some methods. Interestingly, HC thresholds can differ considerably from what has been suggested in literature before, again showing that it is not possible to use the same cutoff value for all data sets. The data-specific cutoff values provided by HC also open the way to more fair comparisons between biomarker selection methods, not biased by unlucky or suboptimal threshold choices. © 2012 The Royal Society of Chemistry.
Hauffe H.C.,University of York |
Hauffe H.C.,Center for Research and Innovation |
Gimenez M.D.,University of York |
Garagna S.,University of Pavia |
Searle J.B.,University of York
Chromosome Research | Year: 2010
Laboratory house mice (Mus musculus) with the XXY condition can be generated with ease and have been used as a biomedical model. However, although the XXY constitution has been described in humans and many domestic and wild mammal species, and a very large number of wild house mice have been karyotyped previously, no wild individuals of M. musculus with an XXY karyotype have ever been reported. Therefore, it is rather extraordinary that two wild XXY house mice were caught by us on two different farms in northern Italy in 2008. Except for the extra X chromosome, one male had a standard karyotype (2n=40) and the other, the karyotype of the Cremona metacentric population (2n=22). In this paper, the phenotype of these two individuals is described. Observations for both of these wild males agree with those of laboratory XXY mice, i.e., they had a normal body mass and appearance, but significantly smaller testes than normal, and no visible germ cells. The incidence of the XXY chromosome anomaly in wild mice (two among 5,123 wild mice surveyed by us and our colleagues, i.e., approximately 0.08% among wild-caught males) is intermediate between that found in male laboratory mice (approximately 0.04%) and that found in male humans (0.2%). © 2010 Springer Science+Business Media B.V.