Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6× coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5× coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

Accurate detection of identity-by-descent segments in human ancient DNA.

Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers.

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

ancIBD - Screening for identity by descent segments in human ancient DNA.

Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.

Analyzing Construction Workers' Unsafe Behaviors in Hoisting Operations of Prefabricated Buildings Using HAZOP.

Along with the increasing number of prefabricated buildings being constructed in China each year, the incident rate of hoisting operations has been continuously rising. In order to improve construction safety in hoisting operations of prefabricated buildings, this paper analyzes the construction workers' unsafe behaviors using the Hazard and Operability (HAZOP) method. A questionnaire survey and a literature review were first performed to gather information on safety risks and influencing factors during each stage of hoisting operations, and the survey results were statistically analyzed using the SPSS software. Next, HAZOP was applied to identify the deviation and change of the unsafe behaviors as well as their causes, consequences, and countermeasures. Finally, a case study was presented to verify the effectiveness of the countermeasures through a comparison and evaluation method from experimental economics. This paper demonstrates the use of HAZOP to analyze construction workers' unsafe behaviors in hoisting operations of prefabricated buildings, and effective countermeasures in each stage of hoisting operations are proposed to mitigate unsafe behaviors. This paper therefore provides an innovative method and a theoretical foundation for reducing unsafe behaviors in hoisting operations of prefabricated buildings and serves as a reference for decision-making for hoisting safety policies in prefabricated construction projects.

An Optimized Ni-catalyzed Chan-Lam Type Coupling: Enantioretentive Access to Chiral N-Aryl Sulfinamides.

C-N bond formation takes on a critical significance in reactions of organic synthesis, material production and pharmaceutical manufactory. Chan-Lam has proposed a useful methodology to furnish secondary arylamides under mild conditions. However, when chiral sulfinamides serve as the coupling precursors, the Cu-catalyzed coupling reaction is found with low efficacy. Complex side-products are generated under classic conditions. Moreover, it led to the racemization of the coupling product. In this study, an optimized Ni-catalyzed Chan-Lam type coupling conditions were proposed, which resulted in clean conversion from chiral sulfinamides and arylboronic acids to offer N-aryl sulfinamides efficiently and enantioretentively. The trans-N1 ,N2 -dimethylcyclohexane-1,2-diamine was proven as the most efficient ligand. Under the optimized conditions, a series of chiral N-aryl sulfinamides was prepared with high chemical yield without racemization. Furthermore, a plausible and novel mechanism was proposed. Interestingly, the method could efficiently furnish a wide variety of C-X bonds by coupling arylboronic acids with different nucleophiles.

hapCon: estimating contamination of ancient genomes by copying from reference haplotypes.

MOTIVATION: Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches. RESULTS: We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1× for SNP capture data (1240k) and 0.02× for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25-30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45 000 and various global ancestries. AVAILABILITY AND IMPLEMENTATION: We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dynamically enhancing plaque targeting via a positive feedback loop using multifunctional biomimetic nanoparticles for plaque regression.

A paradigm shift from preventive therapy to aggressive plaque regression and eventual eradication is much needed to address increasing atherosclerotic burden and risks. Herein, we report a biologically inspired dual-targeting multifunctional recombinant high-density lipoprotein (rHDL)-mimicking core-shell nanoplatform. It is composed of an ATP-responsive ternary polyplexes core for SR-A siRNA and catalase complexation, and a phosphatidylserine-modified rHDL-based outer shell for SR-BI and CD36 targeting, in which pitavastatin is packaged. We demonstrated that dual-targeting biomimetic core-shell nanoparticles dynamically enhanced macrophage CD36 targeting in the plaques by establishing a positive feedback loop via the reciprocal regulation of SR-A and CD36. Positive feedback-enabled accumulation of the nanoparticles in the atherosclerotic plaques increased by 3.3-fold following 4-week repeated administration. A 3-month dosage regimen of the dual-targeting rHDL-mimicking nanoparticles reduced plaque areas by 65.8%, and decreased macrophages by 57.3%. Collectively, this work shows that dynamically enhancing plaque targeting via a positive feedback loop and dual action of cholesterol deposition inhibition and efflux enhancement accomplished with our novel multifunctional biomimetic nanoparticles provides a new way to regress plaques and alleviate the atherosclerotic burden.

ATP-Responsive Low-Molecular-Weight Polyethylenimine-Based Supramolecular Assembly via Host-Guest Interaction for Gene Delivery.

In this work, we report on an ATP-responsive low-molecular-weight polyethylenimine (LMW-PEI)-based supramolecular assembly. It formed via host-guest interaction between PEI (MW = 1.8 kDa)-α-cyclodextrin (α-CD) conjugates and PEI1.8k-phenylboronic acid (PBA) conjugates. The host-guest interaction between PEI1.8k-α-CD and PEI1.8k-PBA was confirmed by the 2D-NOESY chromatogram experiment and competition test. The ATP-responsive property of the supramolecular assembly was evaluated by a series of ATP-triggered degradation and siRNA release studies in terms of fluorescence resonance energy transfer, agarose gel electrophoresis assay, and the time course monitoring of the particle size and morphology. Confocal laser scanning microscopy confirmed the intracellular disassembly of the supramolecular polymer and the release of siRNA. The supramolecular assembly showed high buffering capability and was capable of protecting siRNA from RNase degradation. It had high cytocompatibility according to in vitro cytotoxicity and hemolysis assays. LMW-PEI-based supramolecular assembly facilitated cellular entry of siRNA via energy-dependent endocytosis. Moreover, the assembly/SR-A siRNA polyplexes at N/P ratio of 30 was most effective in knocking down SR-A mRNA and inhibiting uptake of modified LDL. Taken together, this work shows that ATP-responsive LMW-PEI-based supramolecular assembly is a promising gene vector and has potential application in treating atherosclerosis.

Fault Slip Rates and Seismic Moment Deficits on Major Faults in Ordos Constrained by GPS Observation.

The Ordos Block, surrounded by numerous active faults, is a relatively rigid but dangerous area with many strong historical earthquakes. We derive the block rotation velocity and fault slip rates in this area by using GPS data recorded from 1999 to 2007 and implementing an elastic block model. Instead of assuming vertical faults, as did most previous studies in and around Ordos, we use an improved method to invert for the fault dip angles and construct a closed 3-D fault system in our inversion. The predicted slip rates range from <1 mm/yr to ~ 10 mm/yr. Our results are roughly consistent with geological and other geodetic observations. Using the estimated slip rates, we also calculate the cumulative seismic moment due to fault locking and the released moment from historical earthquake catalogues. A comparison of the two quantities indicates that the Hetao Rift has an unreleased seismic moment equal to a Mw 7.9 earthquake, which is also indicated by frequent earthquakes above M6 after 1900.

Rapid determination of ginkgolic acids in Ginkgo biloba kernels and leaves by direct analysis in real time-mass spectrometry.

A novel method based on direct analysis in real time integrated with mass spectrometry was established and applied into rapid determination of ginkgolic acids in Ginkgo biloba kernels and leaves. Instrument parameter settings were optimized to obtain the sensitive and accurate determination of ginkgolic acids. At the sample introduction speed of 0.2 mm/s, high intensity of [M-H]- ions for ginkgolic acids were observed in the negative ion mode by utilization of high-purity helium gas at 450°C. Two microliters of methanol extract of G. biloba kernels or leaves dropped on the surface of Quick-Strip module was analyzed after solvent evaporated to dryness. A series of standard solutions of ginkgolic acid 13:0 in the range of 2-50 mg/L were analyzed with a correlation coefficient r = 0.9981 and relative standard deviation (n = 5) from 12.5 to 13.7%. The limit of detection was 0.5 mg/L. The results of direct analysis in real time-mass spectrometry were in agreement with those observed by thermochemolysis gas chromatography. The proposed method demonstrated significant potential in the application of the high-throughput screening and rapid analysis for ginkgolic acids in dietary supplements.

Determination of methacrylic acid in food simulants by pyrolytic butylation-gas chromatography.

An on-line pyrolytic butylation approach was proposed to determine methacrylic acid (MA) in food simulants by gas chromatography (GC) without an expensive pyrolyzer. MA in food simulants was converted into butyl methacrylate in the presence of tetrabutylammonium hydroxide (TBAH) without any pretreatment at 330°C in the injection-port, contributing to high GC signal response. The derivatizing conditions for the proposed method were optimized, namely the injection-port temperature, type and amount of the organic alkaline used for derivatization. A series of standard solutions of MA in the range of 1.0-50mg/kg were analyzed with correlation coefficient r≥0.9975. The limits of detection (LODs) were less than 0.15mg/kg for MA in four matrix simulants (distilled water, 3%w/v acetic acid, 10%v/v ethanol, and isooctane). Relative standard deviations (RSDs) for retention time, peak height and peak area were all less than 3.88%. The technique was successfully applied to the analysis of MA migrating from plastic cup samples, with recoveries of added MA in the range of 96.5-123.0%. Direct injection of the simulants into the GC system after migration tests, without any pretreatment step, makes the developed method of great value for rapid screening analysis of samples in bulks.

Derivatization following hollow-fiber microextraction with tetramethylammonium acetate as a dual-function reagent for the determination of benzoic acid and sorbic acid by GC.

Derivatization at the injection port following hollow-fiber-based liquid-liquid-liquid microextraction with tetramethylammonium acetate as a dual-function reagent, i.e. an acceptor and derivatization reagent, for the determination of benzoic acid (BA) and sorbic acid (SA) in real samples by GC was developed. BA and SA were extracted from aqueous samples to an organic phase impregnated into the pores of the hollow fiber wall, and then back-extracted to the acceptor solution located inside the lumen of the hollow fiber. Upon injection, the extracted analytes were quantitatively derivatized to their methyl esters with tetramethylammonium acetate in the GC injection port. Several parameters related to the derivatization and extraction efficiency were optimized. The linearity was satisfactory over a concentration range of 0.1-50 mg/L with r > 0.993 for both analytes. The LODs were 2.0 µg/L for SA and 20 µg/L for BA. The recoveries (83-116%) and precisions (RSDs of 1.2-11.4% (n = 3)) were examined by analyzing real spiked samples. The enrichment factors of BA and SA were 300 and 425. The results demonstrated that this is a simple, rapid, accurate, and sensitive method for the determination of BA and SA in various samples.