91,867 research outputs found
Complete mitochondrial genomes of Bos taurus and Bos indicus provide new insights into intraspecies variation taxonomy and domestication
No full textThe taurine and zebuine cattle breeds comprise the majority of the world cattle population but their taxonomic status is still controversial. The two forms of cattle are currently classified as Bos taurus and Bos indicus species and are differentiated primarily by the presence or absence of a hump. However, these two species hybridize readily, producing fully fertile offspring. We have determined and analyzed complete B. taurus and B. indicus mitochondrial genome sequences to investigate the extent of sequence divergences and to study their taxonomic status by molecular dating. The sequences encompassed 16,338 and 16,339 nucleotides, respectively, and differed at 237 positions. Estimated divergence times indicated that the two cattle lineages separated 1.7-2.0 million years ago. Combined phylogenetic analyses of 18 new and 130 previously reported extant B. taurus and B. indicus control region sequences with data from 32 archaeological specimens of the extinct wild aurochs (Bos primigenius) identified four major maternal lineages. B. primigenius haplotypes were present in all but the B. indicus lineage, and one B. taurus sequence clustered with B. primigenius P haplotypes that were not previously linked with domestic cattle. The B. indicus cluster and a recently reported new B. primigenius haplotype that represents a new lineage were approximately equidistant from the B. taurus cluster. These data suggest domestications from several differentiated populations of B. primigenius and a subspecies status for taurine (B. primigenius taurus) and zebuine (B. primigenius indicus) cattle.S. Hiendleder, H. Lewalski, A. Jank
Immunological profiles of Bos taurus and Bos indicus cattle infested with the cattle tick, Rhipicephalus (Boophilus) microplus
No full textThe cattle tick, Rhipicephalus (Boophilus) microplus, is a major threat to the improvement of cattle production in tropical and subtropical countries worldwide. Bos indicus cattle are naturally more resistant to infestation with the cattle tick than are Bos taurus breeds, although considerable variation in resistance occurs within and between breeds. It is not known which genes contribute to the resistant phenotype, nor have immune parameters involved in resistance to R. microplus been fully described for the bovine host. This study was undertaken to determine whether selected cellular and antibody parameters of the peripheral circulation differed between tick-resistant Bos indicus and tick-susceptible Bos taurus cattle following a period of tick infestations. This study demonstrated significant differences between the two breeds with respect to the percentage of cellular subsets comprising the peripheral blood mononuclear cell population, cytokine expression by peripheral blood leukocytes, and levels of tick-specific immunoglobulin G1 (IgG1) antibodies measured in the peripheral circulation. In addition to these parameters, the Affymetrix bovine genome microarray was used to analyze gene expression by peripheral blood leukocytes of these animals. The results demonstrate that the Bos indicus cattle developed a stabilized T-cell-mediated response to tick infestation evidenced by their cellular profile and leukocyte cytokine spectrum. The Bos taurus cattle demonstrated cellular and gene expression profiles consistent with a sustained innate, inflammatory response to infestation, although high tick-specific IgG1 titers suggest that these animals have also developed a T-cell response to infestation
Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation
No full textBACKGROUND: Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS: Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS: We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.
On the Uniqueness of an Orthogonality Property of the Legendre Polynomials
No full textWe prove uniqueness of an orthogonality of the Legendre polynomials discussed elsewhere
Du Bos e l'estetica francese del Settecento
No full textIl saggio analizza l'influenza e la fortuna critica di Du Bos in Francia presso i principali autori del periodo illuminista, da Voltaire a Diderot, da D'Alembert a Batteux e Rousseau. Nel contempo si prospetta una teoria storiografica volta a delineare il percorso di una "estetica dell'interessante" di cui Du Bos appare come uno dei principali capostipiti nella modernità
The structure of particle gels as studied with confocal microscopy and computer simulations.
No full textThis thesis contains the results of a PhD-study on the structure of particle gels. Part of it is directed at a quantification of this structure from measured data, part of it at modelling the aggregation processes that lead to particle gels. Chapter 1 of this thesis is a general introduction describing the aim of this study.Chapter 2 introduces aggregation and gelation of particles. As to the modelling of aggregation we conclude that there are two types of approach: one based on thermodynamics and one based on fractal aggregation (Diffusion Limited Cluster Aggregation or DLCA). The former is appropriate for reversible aggregation, the latter for irreversible aggregation. For all types of colloidal aggregation which are in between these two extremes, an understanding based on both approaches is needed. We use fractal aggregation models as a starting point, but recognise the importance of cluster reorganisation, which will cause gels with structures different than predicted in DLCA. As to quantification of fractal structure, a lower cutoff length scale r <sub>0</sub> is suggested as a valuable addition to the fractal dimensionality d <sub>f</sub> .Chapter 3 describes Confocal Scanning Laser Microscopy (CSLM) as a tool to study the structure of various particle gels. An in-depth optical treatment of imaging in CSLM is presented, along with a new way of image enhancement using calculated three dimensional point spread functions. It is concluded that image enhancement is essential in order to get useful results from an analysis of CSLM micrographs.Chapter 4 shows the results on the fractal structure of particle gels derived from CSLM micrographs of colloidal model systems. It explains thoroughly the details of the image analysis procedure and identifies possible problems, most notably background intensities. From the results it appears that all fractal dimensionalities are about equal, with values larger than the DLCA limit. The values of r <sub>0</sub> show that there are significant differences between gel structures despite the similarities in d <sub>f</sub> . These differences are difficult to connect with properties of the colloidal model systems. A hypothesis about a ' pre- aggregation stage' is formulated which might serve as a starting point for further research.In Chapters 5 and 6 Brownian Dynamics simulations are used as a tool for forming a better connection between aggregation and gel structure. For aggregating Lennard-Jones systems (Chapter 5) we find percolating networks at high volume fractions; these appear to be formed by reorganisation of large aggregates, during which branched strands are formed with voids in between. The gel structure is influenced by both cluster growth and cluster reorganisation; fractal analysis gives non-universal, i.e. time dependent results. For the Lennard-Jones potential, the aggregation is dominated by cluster reorganisation. Aggregating particles with a shorter potential range (Chapter 6) also show time dependent fractal results, but by decreasing the potential range the balance between cluster growth and cluster reorganisation becomes more subtle. Reorganisation of clusters occurs at a lower rate when the potential range is decreased. A large potential well depth εboth promotes reorganisation and inhibits it because of irreversible clustering. A thermodynamical analysis shows that this effect will become more pronounced for shorter ranged potentials.Chapter 7 generalises the conclusions of all previous chapters and gives suggestions for further research. All results in this thesis have used available computing resources up to the maximum. Given the ever growing computing power, significantly more sophisticated techniques for simulation or image analysis will become available within years.The work described in this thesis has led to the following publications:J.H.J. van Opheusden, M.T.A. Bos, 'Induced flocculation of casein micelles - a Brownian Dynamicssimulation on the Parsytec Gcel MPP', Future. Gener. Comp. Sy. 11123-133, 1995BE. Bijsterbosch, M.T.A. Bos, E. Dickinson, J.H.J. van Opheusden, P. Walstra, "Brownian dynamics simulation of particle gel formation: From argon to yoghurt", Faraday Discuss. 10151-64, 1995M.T.A. Bos, J.H.J van Opheusden, "Brownian dynamics simulation of gelation and aging in interacting colloidal systems", Phys Rev E 53 5044-5050, 199
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
No full textBackground
Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.
Results
Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle.
Conclusions
This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought
A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius)
No full textBackground
The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample.
Methodology
DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738±68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences.
Conclusions
For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle
Iberian Odonata distribution: data of the BOS Arthropod Collection (Univ. Oviedo, Spain)
No full textDataset of Odonata specimens of BOS Arthropod Collection (BOS-Odo) of University of Oviedo, available on IPT of GBIF (doi asigned to dataset: https://doi.org/10.15468/5chm8b ), and published in Torralba-Burrial, A., & Ocharan, F. J. (2013). Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain). ZooKeys, 06, 37–58 https://doi.org/10.3897/zookeys.306.5289 (please cited the paper when use the dataset).Odonata are represented from the Iberian Peninsula by 79 species. However, there exists a significant gap in accessible knowledge about these species, especially regarding their distribution. This data paper describes the specimen-based Odonata data of the Arthropod Collection of the Department of Biología de Organismos y Sistemas (BOS), University of Oviedo, Spain. The specimens were mainly collected from the Iberian Peninsula (98.63% of the data records), especially the northern region. The earliest specimen deposited in the collection dates back to 1950, while the 1980’s and 2000’s are the best-represented time periods. Between 1950 and 2009, 16, 604 Odonata specimens were deposited and are documented in the dataset. Approximately 20% of the specimens belong to the families Coenagrionidae and Calopterygidae. Specimens include the holotype and paratypes of the Iberian subspecies Calopteryx haemorrhoidalis asturica Ocharan, 1983 and Sympetrum vulgatum ibericum Ocharan, 1985. The complete dataset is also provided in Darwin Core Archive format.Spanish National R+D+i Plan (MICINN, Spanish Government, grant ref. PTA2010-4108-I) and PCTI Asturias (Asturias Regional Government, ref. COF11-38)
Analysis of limitations of tomographic BOS measurements in a lean H2-air premixed flame
No full textBackground Oriented Schlieren (BOS) is an optical technique that visualizes and quantifies refractive index gradients in transparent media, used extensively in studying compressible flows, heat transfer, and combustion. The refractive index field can be converted to a density field using the Lorentz-Lorenz or Gladstone-Dale equations. Recently, the tomographic version of BOS has gained attention for its application in these fields. Sipkens et al. proposed the ARAP method for tomographic BOS, which improves reconstruction accuracy by accounting for light rays converging at the camera pinhole, a common setup with entocentric lenses. This study aims to assess the limitations of tomographic BOS reconstruction using numerical simulations of an axisymmetric hydrogen Bunsen flame, comparing the results with experimental BOS measurements. It has been observed that the constant composition assumption (i.e., assuming a unique value
of the Gladstone-Dale constant independently from composition) may introduce some limited errors, whereas the implementation of the ARAP algorithm has a negligible impact on the computation of temperature distribution
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