4,052 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
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
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.
İmmün Süpresif Hastalarda Progresif Multifokal Lökoensefalopati Etkeni Olarak JC Virus
No full textGiriş: Progresif multifokal lökoensefalopati (PML), santral sinir sisteminde John Cunningham (JC) virüsün neden olduğu demiyelinizan bir hastalıktır. Primer veya sekonder immünyetersizlik bulunan olgularda, çeşitli nörolojik bulgularla ortaya çıkabilir.Olgu 1: Dokuz yıldır atopik dermatit tanısı ile izlenen hasta burunda herpetik lezyonlar ile başvurdu. Uygun tedaviye rağmen lezyonları devam eden hastada yapılan tetkiklerde DOC 8 eksikliği tanısı kondu. Üç haftada bir IVIG tedavi ile takip edilmekte olan hasta tonik klonik nöbet ile başvurduğunda alınan BOS örneğinde JC virüs 23600 kopya/mL saptandı. Radyolojik olarak da PML ile uyumlu bulguları olan hastaya sidofovir tedavisi başlandı. Yirmi sekiz doz sonrasında klinik ve radyolojik regresyonu olan hastanın tedavisi kesilerek kemik iliği nakil ünitesine yönlendirildi.Olgu 2: Başvurudan 1,5 ay önce ilk nöbetinin geçiren ve sonrasında sol kol ve bacakta güçsüzlük ile sol fasiyal paralizisi olan 6,5 yaş erkek hasta sağlık merkezine başvurmuş. Nörolojik bulguların yanında tam kan sayımında ağır lenfopenisi de saptanan hastada bakılan anti-HIV testi pozitif sonuçlanmış. Kraniyal görüntülemede PML ile uyumlu lezyonları olan hastanın BOS örneğinde JC virus 13,700,000 kopya/mL saptandı. Uygun antiretroviral tedavi ve antimikrobiyal tedavinin yanında sidofovir de başlandı. Antiretroviral tedaviye immünolojik yanıtı gelişmeyen, üç doz sidofovir alan hastanın radyolojik bulguları progrese oldu. Gelişen solunum arresti ile yoğun bakım ünitesine nakledilen hasta takibinin altıncı gününde kaybedildi.Sonuç: İmmunsuprese hastalarda gelişen nörolojik bulgulara eşlik eden radyolojik tutulumların varlığında latent bir virüs olan JC akla gelmelidir. Tedavi sürecinde; kanıt düzeyi yüksek tedavi önerileri bulunmadığından mevcut literatür bilgileri vaka bazında değerlendirilmelidir
Perancangan Sistem Informasi Pengelola Barang/Inventaris Di Jc Komp
No full textInventory information system is a system used to enter inventory data into the database, so that there are no errors in input, output data, and reporting based on the desired data. based on surveys and interviews with jc comp personnel, information was obtained that the existing system in the jc comp warehouse section is still manual. therefore, the system that will be created by the author is the result of a replication of the existing system in the jc comp warehouse section. in addition to the process of input and output of goods, this information system is also equipped with features for creating data reports, input and output of goods, and searching for goods data by item name. with the inventory information system is expected to be useful for the warehouse parts jc comp. By implementing this system in the jc comp warehouse, it is hoped that it can reduce errors that may occur. this system is also expected to further speed up the process of input, output, and report generation, which in turn will help the jc comp warehouseSistem Informasi Persediaan Barang adalah sebuah sistem yang digunakan untuk memasukkan data-data persediaan barang ke dalam database, sehinggga tidak terjadi kesalahan dalam input, output data, dan pembuatan laporan berdasarkan data yang diinginkan. Berdasarkan survey dan wawancara dengan bagian personalia Jc Komp, didapatkan informasi bahwa sistem yang ada dibagian gudang Jc Komp masih manual. Oleh karena itu, sistem yang akan dibuat oleh penulis adalah hasil replikasi dari sistem yang telah ada dibagian gudang Jc Comp. Selain proses input dan output barang, pada sistem informasi ini juga dilengkapi fitur pembuatan laporan data, input, dan output barang, dan pencarian data barang berdasarkan nama barang. Dengan adanya Sistem Informasi persediaan barang ini diharapkan dapat bermanfaat bagi bagian gudang Jc Komp. Dengan diterapkannya sistem ini pada bagian gudang Jc Comp, maka diharapkan dapat mengurangi kesalahan-kesalahan yang mungkin terjadi. Sistem ini juga diharapkan dapat lebih mempercepat proses input, output, dan pembuatan laporan yang pada akhirnya dapat membantu bagian gudang Jc Komp
Oxidative status on Bos indicus and Bos taurus semen under seasonal tropical conditions
No full textA utilização de raças Bos taurus nos rebanhos brasileiros tem aumentado a fim de atender às novas demandas de mercado e de consumo da carne bovina. Entretanto, quando criados em climas mais quentes, esses animais não apresentam as mesmas capacidades adaptativas em comparação aos Bos indicus. Dentre os problemas associados a essa diferença, destaca-se o estresse térmico, que pode comprometer não só a saúde do animal mas também seu potencial reprodutivo, devido principalmente à maior formação de EROs (espécies reativas de oxigênio) relacionada a este fenômeno. Quando isso ocorre em touros utilizados em programas de reprodução o impacto é maior, uma vez que distúrbios reprodutivos podem passar despercebidos ao exame andrológico comum. Um exemplo disso é a alteração no DNA espermático, que pode resultar em perdas embrionárias até doenças transgeracionais, prejudicando a produtividade e, consequentemente, causando grandes prejuízos a setor. Diante disso, foram utilizados 10 touros da raça Nelore (Bos taurus indicus) e oito da raça Simental (Bos taurus taurus) criados a pasto, na região de Dourados, Mato Grosso do Sul, para conduzir o estudo visando verificar o perfil oxidativo e o DNA espermático em cada raça (Simental e Nelore) e estação do ano (verão e inverno), formando um arranjo fatorial 2x2. As amostras foram descongeladas e analisadas por meio dos testes de susceptibilidade ao estresse oxidativo (TBARS), mensuração da atividade de enzimas intracelulares (SOD e GPx), susceptibilidade à fragmentação do DNA espermático (SCSA), atividade mitocondrial (DAB), potencial de membrana mitocondrial (JC-1), integridade de membranas plasmática e acrossomal (E/N;FITC-PSA), motilidade (CASA) e deficiência de protaminação (CMA3). Observou-se efeito de estação sobre a variável potencial de membrana mitocondrial (85.55 ± 2.21% e 74.58 ± 3.30%, verão e inverno respectivamente; p = 0.0175) e efeito raça na deficiência de protaminação (0.52 ± 0.09% e 0.20 ± 0.10%, Simental e Nelore respectivamente; p = 0.0376). Verificou-se, no inverno, correlações entre variáveis relacionadas à motilidade com variáveis de potencial de membrana mitocondrial e TBARS com SOD. Já no verão, as variáveis de motilidade correlacionam com os níveis de atividade mitocondrial e o TBARS com SOD e GPx. Na análise de componentes principais, tanto no efeito estação quanto na raça, os loadings com maior valor selecionados foram apenas de variáveis relacionadas ao metabolismo energético e ao perfil oxidativo. Esses dados evidenciam a importância do metabolismo energético e o possível efeito negativo do calor no seu funcionamento. Os resultados sugerem que a maior deficiência de protaminação no Bos taurus não esteja relacionada ao estresse térmico, mas sim a uma característica de raça. A inda que esta deficiência não esteja acompanhada de estresse oxidativo, a mesma parece não afetar a susceptibilidade à fragmentação do DNA espermático. Além disso, o caráter multifatorial e dinâmico dos parâmetros do sê men proporcionou desafios para a identificação dos efeitos estudados, uma vez que elementos como a nutrição ou até mecanismos compensatórios do espermatozóide podem ter amenizado as diferenças esperadas.The use of Bos taurus breeds in Brazilian herds has increased in order to meet new market demands and beef consumption. However, when raised in warmer climates, these animals do not present the same adaptive capabilities compared to Bos indicus. Among the problems associated with this difference, heat stress stands out, which can compromise not only the animals’ health but also its reproductive potential, mainly due to the greater formation of ROS (reactive oxygen species) related to this phenomenon. When it affects bulls used in breeding programs the impact is even more significant, since reproductive disorders can go unnoticed by the common andrological examination. An example is the alteration in sperm DNA, which can result in embryonic lethality to transgenerational diseases, impairing productivity and, consequently, causing great losses to the industry. Therefore, 10 bulls of the Nelore breed (Bos indicus) and eight of the Simmental breed (Bos taurus) bred on pasture in the region of Dourados, Mato Grosso do Sul, were used to conduct the study to verify the oxidative profile and the Sperm DNA in each breed (Simmental and Nellore) and season of the year (summer and winter) forming a 2x2 factorial arrangement. The samples were thawed and analyzed through oxidative stress susceptibility (TBARS), measurement of intracellular enzyme activity (SOD and GPx), sperm DNA fragmentation susceptibility (SCSA), mitochondrial activity (DAB), mitochondrial membrane potential (JC-1), plasma membrane and acrosome integrity (E/N;FITC-PSA), motility (CASA) and protamination deficiency (CMA3). There was an seasonal effect on the mitochondrial membrane potential variable (85.55 ± 2.21% and 74.58 ± 3.30%, summer and winter respectively; p = 0.0175) and breed showed an effect on protamination deficiency (0.52 ± 0.09% and 0.20 ± 0.10%, Simmental and Nellore respectively; p = 0.0376). During winter, correlations were found between variables related to motility with mitochondrial membrane potential variables and TBARS with SOD. In summer, motility variables correlate with levels of mitochondrial activity and TBARS with SOD and GPx. In the principal component analysis, for the season and breed effects, the selected higher loadings were only of variables related to energy metabolism and oxidative profile. These data show the importance of energy metabolism and the possible negative effect of heat upon its functioning. The results suggest that the greater protamination deficiency in Bos Taurus is not related to heat stress, but to a breed trait. Although not accompanied by oxidative stress, it does not seem to affect the susceptibility to sperm DNA fragmentation. Furthermore, the multifactorial and dynamic features of the semen parameters provided challenges to identify the aimed effects, since elements such as nutrition or even sperm compensatory mechanisms may have mitigated the expected differences
Amenable L-2-Theoretic Methods and Knot Concordance
No full textWe reveal new structures in the topological knot concordance group. As a key ingredient, we develop obstructions using L-2-theoretic methods for amenable groups in Strebel's class recently introduced by Orr and the author. Concerning (h)-solvable knots, which are defined in terms of certain Whitney towers of height h in bounding 4-manifolds, we show the following: for any n>1, there are (n)-solvable but non-(n. 5)-solvable (and therefore nonslice) knots, which are not detected by prior methods using Cochran-Orr-Teichner L-2-signature obstructions as well as Levine algebraic obstructions and Casson-Gordon invariants.X1197sciescopu
Dynamics of Network Formation Processes in the Co-Author Model
No full textThis article studies the dynamics in the formation processes of a mutual consent network in game theory setting: the Co-Author Model. In this article, a limited observation is applied and analytical results are derived. Then, 2 parameters are varied: the number of individuals in the network and the initial probability of the links in the network in its initial state. A simulation result shows a finding that is consistent with an analytical result for a state of equilibrium while it also shows different possible equilibria.Dynamics, Network, Game Theory, Model,Simulation, Equilibrium, Complexity
High-level polyomavirus JC viruria following long-term steroid therapy
No full textCASE REPORT JC virus is a highly seroprevalent ubiquitous polyomavirus which is acquired at an early age through respiratory or oral route, Thereafter JCV establishes persistent, but mainly asymptomatic, infections in various tissues, including the genitourinary tract and brain Corresponding author Cristina Costa, MD S.C.D.U. Virologia Azienda Ospedaliero-Universitaria San Giovanni Battista di Torino Via Santena, 9 -10126 Torino E-mail: [email protected] increasing with age, with adult prevalence rate often between 15% and 60
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