Summary
Application of whole‐genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing.
We compared the performance of two recent WGC methods in ...enriching human aDNA within Illumina libraries built using both double‐stranded and single‐stranded build protocols. Although both methods effectively enriched aDNA, we observed consistent differences between the methods, providing the opportunity to further explore parameters influencing WGC experiments.
Our results suggest bait length has a potential influence on library enrichment. Moreover, we show WGC biases against shorter molecules that are enriched in single‐stranded libraries preparation protocols. Lastly, we document the effect of WGC on features including clonality, GC composition and repetitive DNA content.
Our findings provide insights relevant to those planning WGC on aDNA and suggest future tests and optimization to improve WGC efficiency.
Although endogenous retroviruses are common across vertebrate genomes, the koala retrovirus (KoRV) is the only retrovirus known to be currently invading the germ line of its host. KoRV is believed to ...have first infected koalas in northern Australia less than two centuries ago. We examined KoRV in 28 koala museum skins collected in the late 19th and 20th centuries and deep sequenced the complete proviral envelope region from five northern Australian specimens. Strikingly, KoRV env sequences were conserved among koalas collected over the span of a century, and two functional motifs that affect viral infectivity were fixed across the museum koala specimens. We detected only 20 env polymorphisms among the koalas, likely representing derived mutations subject to purifying selection. Among northern Australian koalas, KoRV was already ubiquitous by the late 19th century, suggesting that KoRV evolved and spread among koala populations more slowly than previously believed. Given that museum and modern koalas share nearly identical KoRV sequences, it is likely that koala populations, for more than a century, have experienced increased susceptibility to diseases caused by viral pathogenesis.
Abstract
Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico’s Indigenous population is ...highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.
In the past three decades, Fenton and photo-Fenton processes have been the subject of a large number of research studies aimed at developing a low-cost and robust alternative to treat complex ...wastewater. Aspects such as installation and operating costs and technical complexity of reactors have limited the commercial applications of Fenton processes. In this study, we evaluated the potential of solar pond reactors to carry out degradation of the dye reactive orange 16 (RO16). Decolorization (D = 99 ± 0.6%), chemical oxygen demand reduction (COD = 55 ± 2%), total organic carbon removal (TOC = 28 ± 0.5%), and biocompatibilization can be accomplished using 15% peroxide (0.6 mg H2O2/mg RO16), which is theoretically required to mineralize the dye. Under dark conditions, decolorization and aromatic removal were scarcely affected (2%), whereas COD and TOC removal were reduced to 37% and 16%, respectively. The application of multivariable analysis and the use of low-cost reactors may lead to a reduction in annual treatment costs of colored effluents to 0.76 (US/m3). Furthermore, the treatment capacity can be increased from 0.6 m3 wastewater/m2 reactor surface to 1.7 m3 wastewater/m2 reactor surface without compromising process efficiency or the biodegradability (BOD5/COD ratio) of the effluent. Dyeing auxiliaries, mainly NaCl, appreciably reduced the decolorization performance in Fenton (13 ± 0.4%) and photo-Fenton (83 ± 0.5%) processes due to the formation of iron-chloride complexes and less powerful oxidants. To reduce the impact of auxiliary agents on process performance and treatment capacity, the Fe2+ concentration should be increased from 5 mg/L to 15 mg/L. The results seem promising; however, additional studies at pilot and semi-industrial scales should be conducted to demonstrate the potential of low-cost reactors to carry out colored wastewater treatment.
•Fenton processes are considered the most suitable technologies for treatment of dyes.•Costs and complexity of reactors have limited applications of Fenton processes.•Dyeing auxiliaries reduced the decolorization performance in Fenton and photo-Fenton.•Inhibitory effect of dyeing auxiliaries can be circumvented by solar radiation.•Solar pond reactors have been successfully applied for the treatment of dyes.
The circumstellar disk density distributions for a sample of 63 Be southern stars from the BeSOS survey were found by modeling their H emission line profiles. These disk densities were used to ...compute disk masses and disk angular momenta for the sample. Average values for the disk mass are 3.4 × 10−9 and 9.5 × 10−10 M for early (B0-B3) and late (B4-B9) spectral types, respectively. We also find that the range of disk angular momentum relative to the star is (150-200)J /M and (100-150)J /M , again for early- and late-type Be stars, respectively. The distributions of the disk mass and disk angular momentum are different between early- and late-type Be stars at a 1% level of significance. Finally, we construct the disk mass distribution for the BeSOS sample as a function of spectral type and compare it to the predictions of stellar evolutionary models with rapid rotation. The observed disk masses are typically larger than the theoretical predictions, although the observed spread in disk masses is typically large.
ABSTRACT
The theory of line-driven winds can explain many observed spectral features in early-type stars, though our understanding the winds of B supergiants remains incomplete. The hydrodynamic ...equations for slowly rotating stellar winds predict two regimes based on the line-force parameter δ: the fast and the δ-slow solution. In this paper, we aim to explore the capability of the latter to explain the observed properties of B supergiant winds. We calculate Hα line profiles, the most sensitive wind diagnostics in the optical, for both fast and δ-slow wind models. We fit them to observed data from a well-studied sample of B supergiants, by adapting the line-force parameters (k, α, and δ) of the hydrodynamic model. Unexpectedly, the observed Hα spectra can be reproduced by both hydrodynamic wind regimes with similar precision. We argue that this similarity results from the similar shape of the normalized velocity law produced by both regimes in the lower, Hα-forming wind region. Our findings raise a dichotomy, because mass-loss rates and terminal velocities (v∞) for each solution are quite different. The δ-slow solution predicts maximum values for v∞ that are systematically lower than those measured in the ultraviolet, whereas the v∞ values of the fast solution are closer, and probably more appropriate. However, our results also indicate that the δ-slow solution might better describe the dense winds of B hypergiants. Multiwavelength analyses and a larger sample of stars are needed to reach a definitive conclusion.
The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and ...capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method in combination with a bioinformatic tool designed specifically to analyze sequence lengths and frequencies, we found that GS FLX STR sequence data are comparable to conventional capillary electrophoresis-based STR typing. Furthermore, we found DNA base substitutions and repeat sequence variations that would not have been identified using conventional STR typing
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division ...between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
Pine wilt disease (PWD) is a devastating forest disease caused by the pinewood nematode (PWN), Bursaphelenchus xylophilus, a migratory endoparasite that infects several coniferous species. During the ...last 20 years, advances have been made for understanding the molecular bases of PWN-host trees interactions. Major advances emerged from transcriptomic and genomic studies, which revealed some unique features related to PWN pathogenicity and constituted fundamental data that allowed the development of postgenomic studies. Here we review the proteomic approaches that were applied to study PWD and integrated the current knowledge on the molecular basis of the PWN pathogenicity. Proteomics has been useful for understanding cellular activities and protein functions involved in PWN-host trees interactions, shedding light into the mechanisms associated with PWN pathogenicity and being promising tools to better clarify host trees PWN resistance/susceptibility.
Background Anisakis spp. are nematode parasites found in a wide range of marine organisms. Human beings may accidentally become infected, showing the symptoms of anisakiasis and allergic responses. ...There has been evidence of increased intestinal permeability in A. simplex-sensitized subjects and that specific IgE titres increase in some allergic patients when fishery products are re-introduced into their diet. The aims of this work were to study the effect of A. simplex crude extract on the intestinal integrity and permeability by using Caco-2 cell monolayer. To analyse the capacity of Ani s 4 allergen to cross the epithelial barrier. Methodology/Principal findings Cellular bioenergetics, transepithelial electrical resistance, viability, permeability, reactive oxygen species generation and immunofluorescent staining of tight junction proteins were analysed. A. simplex crude extract compromises the Caco-2 cell monolayer integrity in a dose-dependent manner. This effect is detected at 1 hour of culture and integrity is recovered after 24 hours of culture. The epithelial barrier disruption is accompanied by an increase in paracellular permeability and reactive oxygen species production and by a delocalization of occludin and zonula occludens-1. Finally, Ani s 4, a thermostable and resistant to digestion allergen with cystatin activity, is able to cross the epithelial barrier in Caco-2 monolayer and reach a cumulative mean percentage of 22.7% of total concentration in the basolateral side after 24 hours of culture. Conclusions/Significance Our results demonstrate that A. simplex induces an early and reversible alteration of integrity and permeability of Caco-2 cell monolayer and that an underlying mechanism of this effect would involve the oxidative stress and disruption of epithelial tight junctions. Additionally, it has been shown that Ani s 4 allergen is able to cross the epithelial barrier. These findings could explain the increased intestinal permeability observed in Anisakis-sensitized patients, the changes over time in IgE sensitization to A. simplex allergens, and the specific IgE persistence in Anisakis allergy.
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