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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. Source

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. Source

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. Source

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. Source

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. Source

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