Mining livestock genome datasets for an unconventional characterization of animal DNA viromes

Whole genome sequencing (WGS) datasets, usually generated for the investigation of the individual animal genome, can be used for additional mining of the fraction of sequencing reads that remains unmapped to the respective reference genome. A significant proportion of these reads contains viral DNA derived from viruses that infected the sequenced animals. In this study, we mined more than 480 billion sequencing reads derived from 1471 WGS datasets produced from cattle, pigs, chickens and rabbits. We identified 367 different viruses among which 14, 11, 12 and 1 might specifically infect the cattle, pig, chicken and rabbit, respectively. Some of them are ubiquitous, avirulent, highly or potentially damaging for both livestock and humans. Retrieved viral DNA information provided a first unconventional and opportunistic landscape of the livestock viromes that could be useful to understand the distribution of some viruses with potential deleterious impacts on the animal food production systems

Identification of mutations in the bovine KIT gene, a candidate for the Spotted locus in cattle

AbstractIn mammals, abnormal migration of melanoblasts from the neural crest during embryonic development may be the reason of the pielbaldism phenotype that is a mixture of pigmented and unpigmented areas in the coat. Several cattle breeds, like for example Holstein, show the piebald spotted coat colour phenotype, that, according to crossbreeding studies, is due to a recessive allele (s), member of the allele series of the Spotted (S) locus. Dominant alleles at this locus act as suppressors of the spotted pattern and produce uniformly pigmented animals while others determine the colour-sided pattern known, for example, in the Hereford breed. The bovine v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene (KIT) gene was localized in the region of chromosome 6 where the Spotted locus was mapped. KIT plays a major role during the embryonic development in directing the migration of the melanoblasts from the neural crest. Mutations in this gene cause different coat colour patterns in mouse and human. In pigs..

Control of polymorphism in coronene by the application of magnetic fields

Coronene, a polyaromatic hydrocarbon, has been crystallized for the first time in a different polymorph using a crystal growth method that utilizes magnetic fields to access a unit cell configuration that was hitherto unknown. Crystals grown in magnetic field of 1 T are larger, have a different appearance to those grown in zero field and retain their structure in ambient conditions. We identify the new form, beta-coronene, as the most stable at low temperatures. As a result of the new supramolecular configuration we report significantly altered electronic, optical and mechanical properties.Comment: 32 pages, 17 figure

Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Polymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions

Aumento da sustentabilidade da produção de raças suínas locais através do uso de rótulos de qualidade - Estudo de caso e desenvolvimento de uma marca comercial no projecto TREASURE

The interest for traditional genetic resources, here comprised local pig breeds, has been increased in the last decades. Yet, at the time being, majority of local pig breeds still need to be supported with subsidies to ensure their conservation. However, the best strategy is if breeds could reach self-sustainability which is possible by an efficient marketing strategy of their products. The majority of studied breeds in project TREASURE are untapped, so the ambition is to develop an “umbrella” collective trademark that would gather together all breeds and that would create added values for their products. Major socio-economic aspects related to the implementation of the collective trademark include rights, responsibilities and expected added value for end-users. Based on the results obtained by an internal survey conducted in TREASURE, we have identified the main features of the collaborative trademark: 1) it should attract end-users such as farmers, breeders associations and meat processors; 2) it should be developed and promoted by an operational committee of end-users, under the coordination and supervision of TREASURE Consortium; 3) it should emphasize local pig genetic resources as the key common point, considering also production systems and nutrition; 4) it should explore possible collaboration or conflict with existing EU protected products (PDO, PGI, TSG) in order to optimally promote local products. An overview of intellectual property rights (IPR) in the context of pork value chains existing in the European Union is presented and prospects for TREASURE trademark analysed

Low-Cost Potentiometric Sensor for Chloride Measurement in Continuous Industrial Process Control

Recently, the new updates in legislation about drinking water control and human health have increased the demand for novel electrochemical low-cost sensors, such as potentiometric ones. Nowadays, the determination of chloride ion in aqueous solutions has attracted great attention in several fields, from industrial processes to drinking water control. Indeed, chloride plays a crucial role in corrosion, also influencing the final taste of beverages, especially coffee. The main goal is to obtain devices suitable for continuous and real-time analysis. For these reasons, we investigated the possibility to develop an easy, low-cost potentiometric chloride sensor, able to perform analysis in aqueous mediums for long immersion time and reducing the need of periodic calibration. We realized a chloride ion selective electrode made of Ag/AgCl sintered pellet and we tested its response in model solutions compatible with drinking water. The sensor was able to produce a stable, reproducible, and accurate quantification of chloride in 900 s, without the need for a preliminary calibration test. This opens the route to potential applications of this sensor in continuous, in situ, and real time measurement of chloride ions in industrial processes, with a reduced need for periodic maintenance

Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds

Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources

On the oxygen reduction reaction mechanism catalyzed by pd complexes on 2d carbon. A theoretical study

Oxygen Reduction Reaction (ORR) is the bottle-neck strategic reaction ruling the fuel cell efficiency process. The slow kinetics of the reaction require highly effective electrocatalysts for proper boosting. In this field, composite catalysts formed by carbon nanotubes functionalized with palladium(II) complexes showed surprising catalytic activity comparable to those of a commercial Pt electrode, but the catalytic mechanisms of these materials still remain open to discussion. In this paper, we propose the combination of experimental and theoretical results to unfold the elementary reaction steps underlying the ORR catalysis