The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of milk and meat. Much like cattle and ...horses, the camel may be found in industrial farming conditions as well as used in sporting. Camel racing is a multi-million dollar industry, with some specimens being valued at upward of 9.5 million USD. Despite its apparent value to humans, the dromedary camel is a neglected species in genomics. While cattle and other domesticated species have had much attention in terms of genome assembly, the camel has only been assembled to scaffold level, which does not give a clear indication of the order or chromosomal location of sequenced fragments. In this study, the Reference Assistant Chromosome Assembly (RACA) algorithm was implemented to use read-pair information of camel scaffolds, aligned with the cattle and human genomes in order to organize and orient these scaffolds in a near-chromosome level assembly. This method generated 72 large size fragments (N50 54.36 Mb). These predicted chromosome fragments (PCFs) were then compared with comparative maps of camel and cytogenetic map of alpaca chromosomes, allowing us to further upgrade the assembly. This dromedary camel assembly will be an invaluable tool to verify future camel assemblies generated with chromatin conformation or/and long read technologies. This study provides the first near-chromosome assembly of the dromedary camel, thus adding this economically important species to a growing pool of knowledge regarding the genome structure of domesticated livestock.
The speed of muscle contraction is related to body size; muscles in larger species contract at slower rates. Since contraction speed is a property of the myosin isoform expressed in a muscle, we ...investigated how sequence changes in a range of muscle myosin II isoforms enable this slower rate of muscle contraction. We considered 798 sequences from 13 mammalian myosin II isoforms to identify any adaptation to increasing body mass. We identified a correlation between body mass and sequence divergence for the motor domain of the 4 major adult myosin II isoforms (β/Type I, IIa, IIb, and IIx), suggesting that these isoforms have adapted to increasing body mass. In contrast, the non-muscle and developmental isoforms show no correlation of sequence divergence with body mass. Analysis of the motor domain sequence of β-myosin (predominant myosin in Type I/slow and cardiac muscle) from 67 mammals from 2 distinct clades identifies 16 sites, out of 800, associated with body mass (padj < 0.05) but not with the clade (padj > 0.05). Both clades change the same small set of amino acids, in the same order from small to large mammals, suggesting a limited number of ways in which contraction velocity can be successfully manipulated. To test this relationship, the 9 sites that differ between human and rat were mutated in the human β-myosin to match the rat sequence. Biochemical analysis revealed that the rat-human β-myosin chimera functioned like the native rat myosin with a 2-fold increase in both motility and in the rate of ADP release from the actin-myosin crossbridge (the step that limits contraction velocity). Thus, these sequence changes indicate adaptation of β-myosin as species mass increased to enable a reduced contraction velocity and heart rate.
We determined the feasibility of abdominal aortic aneurysm (AAA) screening program led by family physicians in public primary healthcare setting using hand-held ultrasound device. The potential study ...population was 11,214 men aged ≥ 60 years attended by three urban, public primary healthcare centers. Participants were recruited by randomly-selected telephone calls. Ultrasound examinations were performed by four trained family physicians with a hand-held ultrasound device (Vscan®). AAA observed were verified by confirmatory imaging using standard ultrasound or computed tomography. Cardiovascular risk factors were determined. The prevalence of AAA was computed as the sum of previously-known aneurysms, aneurysms detected by the screening program and model-based estimated undiagnosed aneurysms. We screened 1,010 men, with mean age of 71.3 (SD 6.9) years; 995 (98.5%) men had normal aortas and 15 (1.5%) had AAA on Vscan®. Eleven out of 14 AAA-cases (78.6%) had AAA on confirmatory imaging (one patient died). The total prevalence of AAA was 2.49% (95%CI 2.20 to 2.78). The median aortic diameter at diagnosis was 3.5 cm in screened patients and 4.7 cm (p<0.001) in patients in whom AAA was diagnosed incidentally. Multivariate logistic regression analysis identified coronary heart disease (OR = 4.6, 95%CI 1.3 to 15.9) as the independent factor with the highest odds ratio. A screening program led by trained family physicians using hand-held ultrasound was a feasible, safe and reliable tool for the early detection of AAA.
By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing ...question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.
We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.
Our data suggest that adaptive alleles - in this case, genes involved in the immune response - might have been favored by genome rearrangements in the macaque lineage.
Due to the high prevalence of dementia, health care needs are increasing beyond existing formal resources. In Spain, it is the family that takes care of this disease.
To analyze the direct (health ...and non-health) and indirect economic costs related to care of people with dementia living with their informal caregiver in the home care/community environment, from the perspective of illness severity, associated comorbidity and social impact.
Multicentric, descriptive study.
Three primary care public health centers associated with Hospital Clínic, Barcelona (Spain).
Patients over 65 years old with a diagnosis of dementia, and included in a home care program.
People with a diagnosis of dementia made by a specialist neurologist; aged 65 years or older; a score ≤24 on the Mini-Mental State Examination, and identification of an informal caregiver.
Patients unable to identify an informal caregiver, and those with primary psychiatric pathology or Korsakoff's syndrome.
Use of Resources in Dementia to assess costs; Mini-Mental State Examination to evaluate cognitive capacity; Katz-Index to measure functional capacity; Neuropsychiatric Index for neuropsychiatric symptoms, and the Charlson-Index for comorbidity. Data collection took place between November, 2010 and April, 2012.
The average estimated monthly care costs for people with dementia in the home setting are 1956.2€ (SD 1463.9). Informal care was the major contributor to this with a mean estimated cost of 1214.86 (SD 902.68)€/month. Greater illness severity, dependency in activities of daily living, comorbidity and behavioral disturbance are associated with higher costs. Behavioral disturbance appeared as the only factor independently associated with cost in dementia care. The group of people with dementia with severe behavioral disturbance requires the most care resources with an average cost of 2545.2 (SD 1753.2)€/month.
There is a direct association between dementia severity and increased costs. In addition, informal caregivers looking after people with dementia in Spain represent an important social cost. The independent factor associated with an increase in the total costs of patient care was neuropsychiatric symptoms.
Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to ...evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal.
Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements.
Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.
En el ámbito del aceite de oliva conviven, actualmente, dos modelos de construcción de la calidad. Un modelo de calidad que se sustenta en los atributos específicos de cada territorio y en el ...conocimiento tradicional, y otro modelo de calidad basado en normas, estándares y en el conocimiento científico-técnico. La implantación de este segundo modelo implica que las diferentes calidades del aceite de oliva se determinen, por normativa, a través de un análisis sensorial, siguiendo parámetros organolépticos. Este artículo analiza las transformaciones operadas en los territorios olivareros para adaptarse a este modelo de calidad <<científico-técnica>>. Estudia los procesos diferenciales de apropiación de esa <<nueva cultura del aceite>> en diferentes zonas de Andalucía (España) con una arraigada tradición en la producción de aceite de oliva de calidad. La investigación se ha centrado en tres Sistemas Oleícolas Locales con Denominación de Origen Protegida (Estepa y Puente Genil, Priego de Córdoba y Montoro-Adamuz). En el estudio se ha aplicado una metodología cualitativa, basada en el trabajo de campo realizado durante 12 meses entre 2015-2016. Las técnicas utilizadas han sido la observación participante y las entrevistas semiestructuradas realizadas a 178 actores claves de los tres territorios. Los resultados obtenidos indican que el éxito en el proceso de conversión a esa <<nueva cultura del aceite>> está vinculado a la territorialización del conocimiento <>. Resulta fundamental que el panel de cata pase a ser un actor activo del territorio y que se genere un conocimiento accesible que se retroalimente con el conocimiento vernáculo del territorio. PALABRAS CLAVE Calidad alimentaria, aceite de oliva, identidad territorial, Denominación de Origen Protegida, Andalucía. In the field of olive oil, two quality construction models currently coexist. One quality model based on the specific attributes of each territory and the traditional knowledge and other quality model based on rules and standards and on scientific-technical knowledge. The implementation of this second model implies that the different qualities of olive oil are determined, by regulation, through a sensory analysis, following organoleptic parameters. This article analyzes the transformations carried out in the olive oil territories to adapt to this model of regulated quality. Study the differential processes of appropriation of this "new olive oil culture" in different areas of Andalusia with a tradition rooted in the production of quality oil. The research has focused on three Local Olive Oil Systems of Andalusia that have a Protected Designation of Origin (Estepa y Puente Genil, Priego de Córdoba y Montoro-Adamuz). In the study, qualitative methodology has been applied based on fieldwork carried out during 12 months between 2015-2016. The techniques used were participant observation and semi-structured interviews with 178 key actors from the three territories. Results show that the success in the process of conversion to the "new olive oil culture" is linked to the territorialization of "expert" knowledge. It is essential that the tasting panel becomes an active actor of the territory and that the knowledge generated is accessible and feedback with the vernacular knowledge of the territory. KEYWORDS Food quality, olive oil, territorial identity, Protected Designation of Origin, Andalusia.
Approximately one million in vitro produced (IVP) cattle embryos are transferred worldwide each year as a way to improve the rates of genetic gain. The most advanced programmes also apply genomic ...selection at the embryonic stage by SNP genotyping and the calculation of genomic estimated breeding values (GEBVs). However, a high proportion of cattle embryos fail to establish a pregnancy. Here, we demonstrate that further interrogation of the SNP data collected for GEBVs can effectively remove aneuploid embryos from the pool, improving live births per embryo transfer (ET). Using three preimplantation genetic testing for aneuploidy (PGT-A) approaches, we assessed 1713 cattle blastocysts in a blind, retrospective analysis. Our findings indicate aneuploid embryos have a 5.8% chance of establishing a pregnancy and a 5.0% chance of given rise to a live birth. This compares to 59.6% and 46.7% for euploid embryos (p < 0.0001). PGT-A improved overall pregnancy and live birth rates by 7.5% and 5.8%, respectively (p < 0.0001). More detailed analyses revealed donor, chromosome, stage, grade, and sex-specific rates of error. Notably, we discovered a significantly higher incidence of aneuploidy in XY embryos and, as in humans, detected a preponderance of maternal meiosis I errors. Our data strongly support the use of PGT-A in cattle IVP programmes.
Abstract
Background
The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when ...faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts.
Findings
Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions.
Conclusions
Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
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