Effects of a feeding strategy to increase intramuscular fat content of pork under the conditions of organic farming

In an ongoing study, the effect of the implementation of a specific feeding strategy using a high portion of home-grown grain legumes on the intramuscular fat (IMF) content of pork, is assessed under different conditions on organic farms in Germany and Austria. Preliminary results indicate that variation in the IMF content seems to be higher between farms than between treatments within each farm

ESPACIOS, TRADICIONES Y CAMBIOS EN CONCHUCOS. Ecos desde la Escuela de etnografía del Proyecto “Antonio Raimondi”, Ancash Perú

Este volumen nace con dos finalidades precisas. La primera, dar a conocer los trabajos de investigación etnográfica que un grupo de nueve estudiantes de la Universidad de Bologna (Italia) y otro de la Pontificia Universidad Católica del Perú han desarrollado en la provincia de Huari, Ancash, Perú, durante seis años, entre 2003 y 2008 en el marco del Proyecto Arqueológico y Antropológico “Antonio Raimondi”. La segunda finalidad es realizar la difusión de las únicas miradas etnográficas que hasta hoy se han producido sobre la región Conchucos. Otro objetivo, más teórico y más implícito, es desplegar a lo largo del camino de la lectura de los casos etnográficos, una visión processual y dinamista de la escritura etnográfica y de la especulación antropológica, procedente de una manera precisa de hacer trabajo de campo. Los artículos aquí propuestos presentan, mediante varios estilos y diferentes acercamientos, una realidad sociocultural en movimiento, en constante cambio. Construyendo cuadros de varios aspectos sociales, políticos y culturales de la provincia de Huari, los autores delinean un escenario en proceso en el cual diferentes actores, ámbitos y dinámicas socioculturales se interrelacionan, participando de maneras diferents en la transformación

From forensics to clinical research: expanding the variant calling pipeline for the precision ID mtDNA whole genome panel

Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS’s variants (TSS found 57.92% of PCP’s variants), with a significant correlation between the variant levels of variants found with both pipelines

Strategies for keeping dairy cows and calves together - a cross-sectional survey study

Although it is still most common to rear dairy calves separately from adult cattle, the interest in pro-longed contact between dairy calves and lactating cows during early life is increasing. Previous research has documented positive effects of cow-calf contact (CCC) on for example early calf growth and udder health of suckled cows, but also negative effects such as increased separation distress and reduced weight gains after weaning. The aim of this study was to use information from European farms with prolonged cow-calf contact to identify innovative solutions to common challenges for CCC farms. Commercial dairy farms that kept calves with adult lactating cows for seven days or more after birth were invited to participate, and interviews were performed with 104 farmers from six countries. During interviews, information about farm management, calf rearing, farmers' perception of animal health on their farm, and farmers' drivers and barriers for implementing CCC were collected. We found that CCC was practised in a large variety of housing and management systems, and that calves could be reared together with their dam, with foster cows, or using a combination of the two. The contact period varied considerably (7-305 days) between farms and about 25% of the farms manually milk fed the calves during parts of the milk feeding period. Daily contact time varied between farms, from 30 minutes per day to permanent contact except at milking. Behaviours indicative of separation distress, most commonly vocalisation in cows and calves, were reported by 87% of the farmers. Strategies to alleviate separation distress, for example simultaneous gradual weaning and separation, were used on some farms. Building constraints were most often mentioned as a barrier for implementing CCC. Our findings suggest that CCC is practised in a variety of commonly used husbandry systems. Reported challenges were primarily related to weaning and separation, and to building constraints; these aspects should be areas of future research.@2022 The Authors. Published by Elsevier B.V. on behalf of The Animal Consortium. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

Paper 5: How can we assess physical literacy?

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Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination

Discovery and population genomics of structural variation in a songbird genus

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping