The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it ...introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph-based models. Here, we survey various projects underway to build and apply these graph-based structures-which we collectively refer to as genome graphs-and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.
Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only one version of each locus, ignoring variation in the population. Poor ...representation of an individual's genome sequence impacts read mapping and introduces bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation across a population, including large-scale structural variation such as inversions and duplications. Previous graph genome software implementations have been limited by scalability or topological constraints. Here we present vg, a toolkit of computational methods for creating, manipulating, and using these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays, with improved accuracy over alignment to a linear reference, and effectively removing reference bias. These capabilities make using variation graphs as references for DNA sequencing practical at a gigabase scale, or at the topological complexity of de novo assemblies.
Biochar has been recently heralded as an amendment to revitalize degraded soils, improve soil carbon sequestration, increase agronomic productivity and enter into future carbon trading markets. ...However, scientific and economic technicalities may limit the ability of biochar to consistently deliver on these expectations. Past research has demonstrated that biochar is part of the black carbon continuum with variable properties, due to the net result of production (e.g., feedstock and pyrolysis conditions) and post-production factors (storage or activation). Therefore, biochar is not a single entity, but rather spans a wide range of black carbon forms. Biochar is black carbon, but not all black carbon is biochar. Agronomic benefits arising from biochar additions to degraded soils have been emphasized, but negligible and negative agronomic effects have also been reported. Fifty percent of the reviewed studies reported yield increases following black carbon or biochar additions, with the remainder of the studies reporting alarming decreases to no significant differences. Hardwood biochar (black carbon) produced by traditional methods (kilns or soil pits) possessed the most consistent yield increases when added to soils. The universality of this conclusion requires further evaluation due to the highly skewed feedstock preferences within existing studies. With global population expanding while the amount of arable land remains limited, restoring soil quality to nonproductive soils could be a vital key to meeting future global food production, food security and energy supplies; biochar may play a role in this endeavor. Biochar economics are often marginally viable and are tightly tied to the assumed duration of agronomic benefits. Further research is needed to determine the specific conditions under which biochar can provide real economic and agronomic benefits and to elucidate the fundamental mechanisms responsible for these benefits.
We examine the behaviour of the infrared-radio correlation (IRRC) over the range 0 <z ≲ 6 using new, highly sensitive 3 GHz observations with the Karl G. Jansky Very Large Array (VLA) and infrared ...data from the Herschel Space Observatory in the 2 deg2 COSMOS field. We distinguish between objects where emission is believed to arise solely from star-formation, and those where an active galactic nucleus (AGN) is thought to be present. We account for non-detections in the radio or in the infrared using a doubly-censored survival analysis. We find that the IRRC of star-forming galaxies, quantified by the infrared-to-1.4 GHz radio luminosity ratio (qTIR), decreases with increasing redshift: qTIR(z) = (2.88 ± 0.03)(1 + z)− 0.19 ± 0.01. This is consistent with several previous results from the literature. Moderate-to-high radiative luminosity AGN do not follow the same qTIR(z) trend as star-forming galaxies, having a lower normalisation and steeper decrease with redshift. We cannot rule out the possibility that unidentified AGN contributions only to the radio regime may be steepening the observed qTIR(z) trend of the star-forming galaxy population. We demonstrate that the choice of the average radio spectral index directly affects the normalisation, as well as the derived trend with redshift of the IRRC. An increasing fractional contribution to the observed 3 GHz flux by free-free emission of star-forming galaxies may also affect the derived evolution. However, we find that the standard (M82-based) assumption of the typical radio spectral energy distribution (SED) for star-forming galaxies is inconsistent with our results. This suggests a more complex shape of the typical radio SED for star-forming galaxies, and that imperfect K corrections in the radio may govern the derived trend of decreasing qTIR with increasing redshift. A more detailed understanding of the radio spectrum is therefore required for robust K corrections in the radio and to fully understand the cosmic evolution of the IRRC. Lastly, we present a redshift-dependent relation between rest-frame 1.4 GHz radio luminosity and star formation rate taking the derived redshift trend into account.
► Pyrolysis of a range of manures yields alkaline inorganic nutrient-rich biochars. ► Properties similar for turkey and poultry litter, feedlot and dairy, but different for swine biochars. ► ...Concentration of non-volatile minerals may prove beneficial for manure biochar use as a fertilizer alternative. ► FTIR confirmed increased aromatic C-structures with N and P-group contributions.
While pyrolysis of livestock manures generates nutrient-rich biochars with potential agronomic uses, studies are needed to clarify biochar properties across manure varieties under similar controlled conditions. This paper reports selected physicochemical results for five manure-based biochars pyrolyzed at 350 and 700°C: swine separated-solids; paved-feedlot manure; dairy manure; poultry litter; and turkey litter. Elemental and FTIR analyses of these alkaline biochars demonstrated variations and similarities in physicochemical characteristics. The FTIR spectra were similar for (1) turkey and poultry and (2) feedlot and dairy, but were distinct for swine biochars. Dairy biochars contained the greatest volatile matter, C, and energy content and lowest ash, N, and S contents. Swine biochars had the greatest P, N, and S contents alongside the lowest pH and EC values. Poultry litter biochars exhibited the greatest EC values. With the greatest ash contents, turkey litter biochars had the greatest biochar mass recoveries, whereas feedlot biochars demonstrated the lowest.
We present the VLA-COSMOS 3 GHz Large Project based on 384 h of observations with the Karl G. Jansky Very Large Array (VLA) at 3 GHz (10 cm) toward the two square degree Cosmic Evolution Survey ...(COSMOS) field. The final mosaic reaches a median rms of 2.3 μJy beam-1 over the two square degrees at an angular resolution of 0.75″. To fully account for the spectral shape and resolution variations across the broad (2 GHz) band, we image all data with a multiscale, multifrequency synthesis algorithm. We present a catalog of 10 830 radio sources down to 5σ, out of which 67 are combined from multiple components.Comparing the positions of our 3 GHz sources with those from the Very Long Baseline Array (VLBA)-COSMOS survey, we estimate that the astrometry is accurate to 0.01″ at the bright end (signal-to-noise ratio, S/N3 GHz > 20). Survival analysis on our data combined with the VLA-COSMOS 1.4 GHz Joint Project catalog yields an expected median radio spectral index of α = −0.7. We compute completeness corrections via Monte Carlo simulations to derive the corrected 3 GHz source counts. Our counts are in agreement with previously derived 3 GHz counts based on single-pointing (0.087 square degrees) VLA data. In summary, the VLA-COSMOS 3 GHz Large Project simultaneously provides the largest and deepest radio continuum survey at high (0.75″) angular resolution to date, bridging the gap between last-generation and next-generation surveys.
Haplotype-aware graph indexes Sirén, Jouni; Garrison, Erik; Novak, Adam M ...
Bioinformatics,
01/2020, Letnik:
36, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Abstract
Motivation
The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely ...recombinations of true haplotypes.
Results
We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows–Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.
Availability and implementation
Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2.
Supplementary information
Supplementary data are available at Bioinformatics online.
Summary Population density is known to influence acute measures of hypothalamic-pituitary-adrenal (HPA) axis activity in a variety of species, including fish, deer, birds, and humans. However, the ...effects of population density on levels of chronic stress are unknown. Given the fact that exposure to chronically elevated levels of circulating glucocorticoids results in a host of health disparities in animals and humans alike, it is important to understand how population density may impact chronic stress. We assessed hair cortisol concentrations (HCCs), which are reliable indicators of chronic HPA axis activity, in rhesus monkeys ( Macaca mulatta ) to determine the influence of population density on these values. In Experiment 1, we compared HCCs of monkeys living in high-density (HD; 1 monkey/0.87 m2 ) and low-density (LD; 1 monkey/63.37 m2 ) environments ( N = 236 hair samples) and found that HD monkeys exhibited higher hair cortisol across all age categories (infant, juvenile, young adult, adult, and aged) except infancy and aged ( F(5) = 4.240, p = 0.001), for which differences were nearly significant. HD monkeys also received more severe fight wounds than LD monkeys ( χ2 = 26.053, p < 0.001), though no effects of dominance status emerged. In Experiment 2, we examined how HCCs change with fluctuating population levels across 5 years in the adult LD monkeys ( N = 155 hair samples) and found that increased population density was significantly positively correlated with HCCs in this semi-naturalistic population ( r(s) = 0.975, p = 0.005). These are the first findings to demonstrate that increased population density is associated with increased chronic, endogenous glucocorticoid exposure in a nonhuman primate species. We discuss the implications of these findings with respect to laboratory research, population ecology, and human epidemiology.
We study the composition of the faint radio population selected from the Karl G. Jansky Very Large Array Cosmic Evolution Survey (VLA-COSMOS) 3 GHz Large Project, which is a radio continuum survey ...performed at 10 cm wavelength. The survey covers a 2.6 square degree area with a mean rms of ~ 2.3 μJy/beam, cataloging 10 830 sources above 5σ, and enclosing the full 2 square degree COSMOS field. By combining these radio data with optical, near-infrared (UltraVISTA), and mid-infrared (Spitzer/IRAC) data, as well as X-ray data (Chandra), we find counterparts to radio sources for ~93% of the total radio sample reaching out to z ≲ 6; these sources are found in the unmasked areas of the COSMOS field, i.e., those not affected by saturated or bright sources in the optical to near-infrared (NIR) bands. We further classify the sources as star-forming galaxies or AGN based on various criteria, such as X-ray luminosity; observed mid-infrared color; UV–far-infrared spectral energy distribution; rest-frame, near-UV optical color that is corrected for dust extinction; and radio excess relative to that expected from the star formation rate of the hosts. We separate the AGN into subsamples dominated by low-to-moderate and moderate-to-high radiative luminosity AGN, i.e., candidates for high-redshift analogs to local low- and high-excitation emission line AGN, respectively. We study the fractional contributions of these subpopulations down to radio flux levels of ~11 μJy at 3 GHz (or ~20 μJy at 1.4 GHz assuming a spectral index of –0.7). We find that the dominant fraction at 1.4 GHz flux densities above ~200 μJy is constituted of low-to-moderate radiative luminosity AGN. Below densities of ~100 μJy the fraction of star-forming galaxies increases to ~ 60%, followed by the moderate-to-high radiative luminosity AGN (~ 20%) and low-to-moderate radiative luminosity AGN (~ 20%). Based on this observational evidence, we extrapolate the fractions down to sensitivities of the Square Kilometer Array (SKA). Our estimates suggest that at the faint flux limits to be reached by the (Wide, Deep, and UltraDeep) SKA1 surveys, a selection based only on radio flux limits can provide a simple tool to efficiently identify samples highly (>75%) dominated by star-forming galaxies.
The mechanism(s) by which bacterial communities impact susceptibility to infectious diseases, such as HIV, and maintain female genital tract (FGT) health are poorly understood. Evaluation of FGT ...bacteria has predominantly been limited to studies of species abundance, but not bacterial function. We therefore sought to examine the relationship of bacterial community composition and function with mucosal epithelial barrier health in the context of bacterial vaginosis (BV) using metaproteomic, metagenomic, and in vitro approaches. We found highly diverse bacterial communities dominated by Gardnerella vaginalis associated with host epithelial barrier disruption and enhanced immune activation, and low diversity communities dominated by Lactobacillus species that associated with lower Nugent scores, reduced pH, and expression of host mucosal proteins important for maintaining epithelial integrity. Importantly, proteomic signatures of disrupted epithelial integrity associated with G. vaginalis-dominated communities in the absence of clinical BV diagnosis. Because traditional clinical assessments did not capture this, it likely represents a larger underrepresented phenomenon in populations with high prevalence of G. vaginalis. We finally demonstrated that soluble products derived from G. vaginalis inhibited wound healing, while those derived from L. iners did not, providing insight into functional mechanisms by which FGT bacterial communities affect epithelial barrier integrity.
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