Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ~2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection

Applicability of Ammonia Sensors for Controlling Environmental Parameters in Accommodations for Lamb Fattening

Electrochemical ammonia sensors were used to analyse the existing relationship between the ammonia concentration and ambient levels of both temperature and relative humidity in commercial lamb fattening housing equipped with mechanical ventilation and straw-bedded pens. In the first stage of the experiment, sensors were placed over straw beds covered in lamb urine and analysed under laboratory conditions in order to determine ammonia emission evolution over time; three control temperatures (25, 35, and 50 degrees C) were used. A HOBO H8 temperature and relative humidity logger and a Drager NH3LC-6809680 electrochemical ammonia sensor placed in a Drager Polytron 7000 gas detector were utilized as sensors. A positive correlation was established between both ammonia emission time and emitted amount with temperature. Additionally, tests were performed in a commercial lamb housing to determine ammonia concentration variation with respect to height from the ground; three ammonia sensors placed at 50, 90, and 135 cm above the ground were used simultaneously. The ammonia concentration significantly decreased as height increased. A 90 cm height was selected, and three ammonia probes were placed in three different pens inside the livestock housing, along with temperature and relative humidity sensors; four different housing ventilation rates were then tested under real conditions over a time period of 4 months. An adjustment polynomial equation between the housing ambient temperature and the ammonia concentration was obtained with R-2 = 0.632. In conclusion, a relationship can be established between temperature and ammonia concentration in commercial lamb housing under certain handling conditions, which in turn allows for estimating the ammonia concentration adequately based on the ambient internal temperature

Do agri-food market incentives improve food security and nutrition indicators? a microsimulation evaluation for Kenya

The sustainable development goal #2 aims at ending hunger and malnutrition by 2030. Given the numbers of food insecure and malnourished people on the rise, the heterogeneity of nutritional statuses and needs, and the even worse context of COVID-19 pandemic, this has become an urgent challenge for food-related policies. This paper provides a comprehensive microsimulation approach to evaluate economic policies on food access, sufficiency (energy) and adequacy (protein, fat, carbohydrate) at household level. The improvement in market access conditions in Kenya is simulated as an application case of this method, using original insights from households’ surveys and biochemical and nutritional information by food item. Simulation’s results suggest that improving market access increases food purchasing power overall the country, with a pro-poor impact in rural areas. The daily energy consumption per capita and macronutrients intakes per capita increase at the national level, being the households with at least one stunted child under 5 years old, and poor households living areas outside Mombasa and Nairobi, those which benefit the most. The developed method and its Kenya's application contribute to the discussion on how to evaluate nutrition-sensitive policies, and how to cover most households suffering food insecurity and nutrition deficiencies in any given country

Decoherence in a Josephson junction qubit

The zero-voltage state of a Josephson junction biased with constant current consists of a set of metastable quantum energy levels. We probe the spacings of these levels by using microwave spectroscopy to enhance the escape rate to the voltage state. The widths of the resonances give a measurement of the coherence time of the two states involved in the transitions. We observe a decoherence time shorter than that expected from dissipation alone in resonantly isolated 20 um x 5 um Al/AlOx/Al junctions at 60 mK. The data is well fit by a model including dephasing effects of both low-frequency current noise and the escape rate to the continuum voltage states. We discuss implications for quantum computation using current-biased Josephson junction qubits, including the minimum number of levels needed in the well to obtain an acceptable error limit per gate.Comment: 4 pages, 6 figure

Validation of a CFD model by using 3D sonic anemometers to analyse the air velocity generated by an air-assisted sprayer equipped with two axial fans

A computational fluid dynamics (CFD) model of the air flow generated by an air-assisted sprayer equipped with two axial fans was developed and validated by practical experiments in the laboratory. The CFD model was developed by considering the total air flow supplied by the sprayer fan to be the main parameter, rather than the outlet air velocity. The model was developed for three air flows corresponding to three fan blade settings and assuming that the sprayer is stationary. Actual measurements of the air velocity near the sprayer were taken using 3D sonic anemometers. The workspace sprayer was divided into three sections, and the air velocity was measured in each section on both sides of the machine at a horizontal distance of 1.5, 2.5, and 3.5 m from the machine, and at heights of 1, 2, 3, and 4 m above the ground The coefficient of determination (R2) between the simulated and measured values was 0.859, which demonstrates a good correlation between the simulated and measured data. Considering the overall data, the air velocity values produced by the CFD model were not significantly different from the measured values

Untargeted metabolomic analysis of thoracic blood from badgers indicate changes linked to infection with bovine tuberculosis (Mycobacterium bovis):A pilot study

INTRODUCTION: Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB) in cattle, represents a major disease burden to UK cattle farming, with considerable costs associated with its control. The European badger (Meles meles) is a known wildlife reservoir for bTB and better knowledge of the epidemiology of bTB through testing wildlife is required for disease control. Current tests available for the diagnosis of bTB in badgers are limited by cost, processing time or sensitivities. MATERIALS AND METHODS: We assessed the ability of flow infusion electrospray—high-resolution mass spectrometry (FIE-HRMS) to determine potential differences between infected and non-infected badgers based on thoracic blood samples obtained from badgers found dead in Wales. Thoracic blood samples were autoclaved for handling in a containment level 2 (CL2) hazard laboratory. RESULTS: Here we show the major differences associated with with M. bovis infection were changes to folate, pyrimidine, histidine, glycerophospholipid and phosphonate metabolism. CONCLUSIONS: Our studies have indicated differences in the metabolomic signature of badgers found dead in relation to their infection status, suggesting metabolomics could hold potential for developing novel diagnostics for bTB in badgers. As well as highlighting a potential way to handle samples containing a highly pathogenic agent at CL2 for metabolomics studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11306-022-01915-6

Systemic chimerism in human female recipients of male livers

We have previously reported data from clinical and laboratory animal observations which suggest that organ tolerance after transplantation depends on a state of balanced lymphodendritic cell chimerism between the host and donor graft. We have sought further evidence to support this hypothesis by investigating HLA-mismatched liver allograft recipients. 9 of 9 female recipients of livers from male donors had chimerism in their allografts and extrahepatic tissues, according to in-situ hybridisation and molecular techniques 10 to 19 years post-transplantation. In 8 women with good graft function, evidence of the Y chromosome was found in the blood (6/8), skin (8/8), and lymph nodes (7/8). A ninth patient whose transplant failed after 12 years from recurrent chronic viral hepatitis had chimerism in her lymph nodes, skin, jejunum, and aorta at the time of retransplantation. Although cell migration is thought to take place after all types of transplantation, the large population of migratory cells in, and the extent of their seeding from, hepatic grafts may explain the privileged tolerogenicity of the liver compared with other organs. © 1992

Dynamics of Robertson-Walker spacetimes with diffusion

We study the dynamics of spatially homogeneous and isotropic spacetimes containing a fluid undergoing microscopic velocity diffusion in a cosmological scalar field. After deriving a few exact solutions of the equations, we continue by analyzing the qualitative behavior of general solutions. To this purpose we recast the equations in the form of a two dimensional dynamical system and perform a global analysis of the flow. Among the admissible behaviors, we find solutions that are asymptotically de-Sitter both in the past and future time directions and which undergo accelerated expansion at all times.Fundação para a Ciência e a Tecnologia (FCT

Computational fluid dynamics: the analysis of drag coefficient during the gliding phase

The aim of the current study was to analyse the effect of depth on hydrodynamic drag coefficient during the underwater gliding, using computational fluid dynamics.This work was supported by FCT (PTDC/DES/098532/2008