Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

N-acetyltransferase 2 (NAT2), an important enzyme in clinical pharmacology, metabolizes antibiotics such as isoniazid and sulfamethoxazole, and catalyzes the transformation of aromatic and heterocyclic amines from the environment and diet into carcinogenic intermediates. Polymorphisms in NAT2 account for variability in the acetylator phenotype and the pharmacokinetics of metabolized drugs. Native Americans, settled in rural areas and large cities of Latin America, are under-represented in pharmacogenetics studies; therefore, we sequenced the coding region of NAT2 in 456 chromosomes from 13 populations from the Americas, and two from Siberia, detecting nine substitutions and 11 haplotypes. Variants *4 (37%), *5B (23%) and *7B (24%) showed high frequencies. Average frequencies of fast, intermediate and slow acetylators across Native Americans were 18, 56 and 25%, respectively. NAT2 intra-population genetic diversity for Native Americans is higher than East Asians and similar to the rest of the world, and NAT2 variants are homogeneously distributed across native populations of the continent

Ion-Exchange Chromatographic Method for the Determination of the Free Amino Acid Composition of Cheese and Other Dairy Products : an Inter-Laboratory Validation Study

Although free amino acids (FAAs) represent a significant component of ripened cheeses and can provide useful information for their characterization, no inter-laboratory validated analytical method exists which allows a reliable comparison of data obtained by different laboratories and the adoption of quality control schemes based on FAA pattern. The objective of the present work was to test the effectiveness of an analytical protocol for the determination of the FAA composition of cheese and to verify the adequateness of this type of analysis for quality control procedures of Grana Padano PDO cheese as well as for research purposes. After an initial test to compare performances of ion-exchange chromatography (IEC) and HPLC techniques, an inter-laboratory collaborative study (seven laboratories, four samples) was organized to validate an IEC method with post-column ninhydrin derivatization and using l-norleucine as an internal standard. Determined amounts of individual FAA ranged from 8 to over 1380 mg/100 g cheese, with relative standard deviation of repeatability (RSDr) ranging from 0.5 to 4.6%, and relative standard deviation of reproducibility (RSDR) ranging from 1.3 to 9.9% for FAA concentrations over 100 mg/100 g. For lower concentrations, RSDr and RSDR were about thrice as high. On the basis of the results of this investigation, at present, the validated method is adopted as the official method for the determination of FAA patterns in the quality control of Grana Padano PDO cheese

Can child injury prevention include healthy risk promotion?

To reflect on the role of risk-taking and risky play in child development and consider recommendations for the injury prevention field, a symposium was held prior to the November 2013 Canadian Injury Prevention and Safety Promotion Conference. Delegates heard from Canadian and international researchers, practitioners and play safety experts on child development, play space design and playground safety, provision of recreation, and legal and societal perceptions of risk and hazard. The presenters provided multidisciplinary evidence and perspectives indicating the potential negative effect on children’s development of approaches to injury prevention that prioritise safety and limit children’s opportunities for risky play. Delegates considered the state of the field of injury prevention and whether alternative approaches were warranted. Each presenter prepared a discussion paper to provide the opportunity for dialogue beyond attendees at the symposium. The resulting discussion papers provide a unique opportunity to consider and learn from multiple perspectives in order to develop a path forward

Mutations in blind cavefish target the light-regulated circadian clock gene, period 2

Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors

Multiple Advantageous Amino Acid Variants in the NAT2 Gene in Human Populations

Background: Genetic variation at NAT2 has been long recognized as the cause of differential ability to metabolize a wide variety of drugs of therapeutic use. Here, we explore the pattern of genetic variation in 12 human populations that significantly extend the geographic range and resolution of previous surveys, to test the hypothesis that different dietary regimens and lifestyles may explain inter-population differences in NAT2 variation. Methodology/Principal Findings: The entire coding region was resequenced in 98 subjects and six polymorphic positions were genotyped in 150 additional subjects. A single previously undescribed variant was found (34T>C; 12Y>H). Several aspects of the data do not fit the expectations of a neutral model, as assessed by coalescent simulations. Tajima's D is positive in all populations, indicating an excess of intermediate alleles. The level of between-population differentiation is low, and is mainly accounted for by the proportion of fast vs. slow acetylators. However, haplotype frequencies significantly differ across groups of populations with different subsistence. Conclusions/Significance: Data on the structure of haplotypes and their frequencies are compatible with a model in which slow-causing variants were present in widely dispersed populations before major shifts to pastoralism and/or agriculture. In this model, slow-causing mutations gained a selective advantage in populations shifting from hunting-gathering to pastoralism/agriculture. We suggest the diminished dietary availability of folates resulting from the nutritional shift, as the possible cause of the fitness increase associated to haplotypes carrying mutations that reduce enzymatic activity. © 2008 Luca et al

The Triggerless Data Acquisition System of the XENONnT Experiment

The XENONnT detector uses the latest and largest liquid xenon-based timeprojection chamber (TPC) operated by the XENON Collaboration, aimed atdetecting Weakly Interacting Massive Particles and conducting other rare eventsearches. The XENONnT data acquisition (DAQ) system constitutes an upgraded andexpanded version of the XENON1T DAQ system. For its operation, it reliespredominantly on commercially available hardware accompanied by open-source andcustom-developed software. The three constituent subsystems of the XENONnTdetector, the TPC (main detector), muon veto, and the newly introduced neutronveto, are integrated into a single DAQ, and can be operated both independentlyand as a unified system. In total, the DAQ digitizes the signals of 698photomultiplier tubes (PMTs), of which 253 from the top PMT array of the TPCare digitized twice, at $\times10$ and $\times0.5$ gain. The DAQ for the mostpart is a triggerless system, reading out and storing every signal that exceedsthe digitization thresholds. Custom-developed software is used to process theacquired data, making it available within $\mathcal{O}\left(10\text{ s}\right)$for live data quality monitoring and online analyses. The entire system withall the three subsystems was successfully commissioned and has been operatingcontinuously, comfortably withstanding readout rates that exceed $\sim500$ MB/sduring calibration. Livetime during normal operation exceeds $99\%$ and is$\sim90\%$ during most high-rate calibrations. The combined DAQ system hascollected more than 2 PB of both calibration and science data during thecommissioning of XENONnT and the first science run.<br

Worldwide distribution of NAT2 diversity: Implications for NAT2 evolutionary history

<p>Abstract</p> <p>Background</p> <p>The N-acetyltransferase 2 (<it>NAT2</it>) gene plays a crucial role in the metabolism of many drugs and xenobiotics. As it represents a likely target of population-specific selection pressures, we fully sequenced the <it>NAT2 </it>coding region in 97 Mandenka individuals from Senegal, and compared these sequences to extant data on other African populations. The Mandenka data were further included in a worldwide dataset composed of 41 published population samples (6,727 individuals) from four continental regions that were adequately genotyped for all common <it>NAT2 </it>variants so as to provide further insights into the worldwide haplotype diversity and population structure at <it>NAT2</it>.</p> <p>Results</p> <p>The sequencing analysis of the <it>NAT2 </it>gene in the Mandenka sample revealed twelve polymorphic sites in the coding exon (two of which are newly identified mutations, C345T and C638T), defining 16 haplotypes. High diversity and no molecular signal of departure from neutrality were observed in this West African sample. On the basis of the worldwide genotyping survey dataset, we found a strong genetic structure differentiating East Asians from both Europeans and sub-Saharan Africans. This pattern could result from region- or population-specific selective pressures acting at this locus, as further suggested in the HapMap data by extremely high values of <it>F</it>_STfor a few SNPs positions in the <it>NAT2 </it>coding exon (T341C, C481T and A803G) in comparison to the empirical distribution of <it>F</it>_STvalues accross the whole 400-kb region of the <it>NAT </it>gene family.</p> <p>Conclusion</p> <p>Patterns of sequence variation at <it>NAT2 </it>are consistent with selective neutrality in all sub-Saharan African populations investigated, whereas the high level of population differentiation between Europeans and East Asians inferred from SNPs could suggest population-specific selective pressures acting at this locus, probably caused by differences in diet or exposure to other environmental signals.</p

Searching for Heavy Dark Matter near the Planck Mass with XENON1T

Multiple viable theoretical models predict heavy dark matter particles with a mass close to the Planck mass, a range relatively unexplored by current experimental measurements. We use 219.4 days of data collected with the XENON1T experiment to conduct a blind search for signals from multiply interacting massive particles (MIMPs). Their unique track signature allows a targeted analysis with only 0.05 expected background events from muons. Following unblinding, we observe no signal candidate events. This Letter places strong constraints on spin-independent interactions of dark matter particles with a mass between 1×10$^{12}$ and 2×10$^{17}$  GeV/c$^2$. In addition, we present the first exclusion limits on spin-dependent MIMP-neutron and MIMP-proton cross sections for dark matter particles with masses close to the Planck scale

Detector signal characterization with a Bayesian network in XENONnT

We developed a detector signal characterization model based on a Bayesian network trained on the waveform attributes generated by a dual-phase xenon time projection chamber. By performing inference on the model, we produced a quantitative metric of signal characterization and demonstrate that this metric can be used to determine whether a detector signal is sourced from a scintillation or an ionization process. We describe the method and its performance on electronic-recoil (ER) data taken during the first science run of the XENONnT dark matter experiment. We demonstrate the first use of a Bayesian network in a waveform-based analysis of detector signals. This method resulted in a 3% increase in ER event-selection efficiency with a simultaneously effective rejection of events outside of the region of interest. The findings of this analysis are consistent with the previous analysis from XENONnT, namely a background-only fit of the ER data