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Hybridization capture approaches allow targeted high-throughput sequencing analysis at reduced costs compared to shotgun sequencing. Hybridization capture is particularly useful in analyses of genomic data from ancient, environmental, and forensic samples, where target content is low, DNA is fragmented and multiplex PCR or other targeted approaches often fail. Here, we describe a DNA bait synthesis approach for hybridization capture that we call Circular Nucleic acid Enrichment Reagent, or CNER (pronounced ‘snare’). The CNER method uses rolling-circle amplification followed by restriction digestion to discretize microgram quantities of hybridization probes. We demonstrate the utility of the CNER method by generating probes for a panel of 23 771 known sites of single nucleotide polymorphism in the horse genome. Using these probes, we capture and sequence from a panel of ten ancient horse DNA libraries, comparing CNER capture efficiency to a commercially available approach. With about one million read pairs per sample, CNERs captured more targets (90.5% versus 66.5%) at greater mean depth than an alternative commercial approach.

 

The most reliable single-epoch supermassive black hole mass (M_BH) estimates in quasars are obtained by using the velocity widths of low-ionization emission lines, typically the Hβλ4861 line. Unfortunately, this line is redshifted out of the optical band atz≈ 1, leavingM_BHestimates to rely on proxy rest-frame ultraviolet (UV) emission lines, such as Civλ1549 or Mgiiλ2800, which contain intrinsic challenges when measuring, resulting in uncertainM_BHestimates. In this work, we aim at correctingM_BHestimates derived from the Civand Mgiiemission lines based on estimates derived from the Hβemission line. We find that employing the equivalent width of Civin derivingM_BHestimates based on Mgiiand Civprovides values that are closest to those obtained from Hβ. We also provide prescriptions to estimateM_BHvalues when only Civ, only Mgii, and both Civand Mgiiare measurable. We find that utilizing both emission lines, where available, reduces the scatter of UV-basedM_BHestimates by ∼15% when compared to previous studies. Lastly, we discuss the potential of our prescriptions to provide more accurate and precise estimates ofM_BHgiven a much larger sample of quasars at 3.20 ≲z≲ 3.50, where both Mgiiand Hβcan be measured in the same near-infrared spectrum.

 

Quasars atz≳ 1 most often have redshifts measured from rest-frame ultraviolet emission lines. One of the most common such lines, Civλ1549, shows blueshifts up to ≈5000 km s⁻¹and in rare cases even higher. This blueshifting results in highly uncertain redshifts when compared to redshift determinations from rest-frame optical emission lines, e.g., from the narrow [Oiii]λ5007 feature. We present spectroscopic measurements for 260 sources at 1.55 ≲z≲ 3.50 having −28.0 ≲M_i≲ − 30.0 mag from the Gemini Near Infrared Spectrograph–Distant Quasar Survey (GNIRS-DQS) catalog, augmenting the previous iteration, which contained 226 of the 260 sources whose measurements are improved upon in this work. We obtain reliable systemic redshifts based on [Oiii]λ5007 for a subset of 121 sources, which we use to calibrate prescriptions for correcting UV-based redshifts. These prescriptions are based on a regression analysis involving Civfull-width-at-half-maximum intensity and equivalent width, along with the UV continuum luminosity at a rest-frame wavelength of 1350 Å. Applying these corrections can improve the accuracy and the precision in the Civ-based redshift by up to ∼850 km s⁻¹and ∼150 km s⁻¹, respectively, which correspond to ∼8.5 and ∼1.5 Mpc in comoving distance atz= 2.5. Our prescriptions also improve the accuracy of the best available multifeature redshift determination algorithm by ∼100 km s⁻¹, indicating that the spectroscopic properties of the Civemission line can provide robust redshift estimates for high-redshift quasars. We discuss the prospects of our prescriptions for cosmological and quasar studies utilizing upcoming large spectroscopic surveys.

 

Abstract Organ-on-a-chip systems combine microfluidics, cell biology, and tissue engineering to culture 3D organ-specific in vitro models that recapitulate the biology and physiology of their in vivo counterparts. Here, we have developed a multiplex platform that automates the culture of individual organoids in isolated microenvironments at user-defined media flow rates. Programmable workflows allow the use of multiple reagent reservoirs that may be applied to direct differentiation, study temporal variables, and grow cultures long term. Novel techniques in polydimethylsiloxane (PDMS) chip fabrication are described here that enable features on the upper and lower planes of a single PDMS substrate. RNA sequencing (RNA-seq) analysis of automated cerebral cortex organoid cultures shows benefits in reducing glycolytic and endoplasmic reticulum stress compared to conventional in vitro cell cultures. 

The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.

 

Weak emission-line quasars (WLQs) are a subset of type 1 quasars that exhibit extremely weak Lyα+ Nvλ1240 and/or Civλ1549 emission lines. We investigate the relationship between emission-line properties and accretion rate for a sample of 230 “ordinary” type 1 quasars and 18 WLQs atz< 0.5 and 1.5 <z< 3.5 that have rest-frame ultraviolet and optical spectral measurements. We apply a correction to the Hβ-based black hole mass (M_BH) estimates of these quasars using the strength of the optical Feiiemission. We confirm previous findings that WLQs’M_BHvalues are overestimated by up to an order of magnitude using the traditional broad-emission-line region size–luminosity relation. With thisM_BHcorrection, we find a significant correlation between Hβ-based Eddington luminosity ratios and a combination of the rest-frame Civequivalent width and Civblueshift with respect to the systemic redshift. This correlation holds for both ordinary quasars and WLQs, which suggests that the two-dimensional Civparameter space can serve as an indicator of accretion rate in all type 1 quasars across a wide range of spectral properties.

 

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function. 

Abstract The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears. 

Abstract We report the results of near-infrared spectroscopic observations of 37 quasars in the redshift range 6.3 < z ≤ 7.64, including 32 quasars at z > 6.5, forming the largest quasar near-infrared spectral sample at this redshift. The spectra, taken with Keck, Gemini, VLT, and Magellan, allow investigations of central black hole mass and quasar rest-frame ultraviolet spectral properties. The black hole masses derived from the Mg ii emission lines are in the range (0.3–3.6) × 10 9 M ⊙ , which requires massive seed black holes with masses ≳10 3 –10 4 M ⊙ , assuming Eddington accretion since z = 30. The Eddington ratio distribution peaks at λ Edd ∼ 0.8 and has a mean of 1.08, suggesting high accretion rates for these quasars. The C iv –Mg ii emission-line velocity differences in our sample show an increase of C iv blueshift toward higher redshift, but the evolutionary trend observed from this sample is weaker than the previous results from smaller samples at similar redshift. The Fe ii /Mg ii flux ratios derived for these quasars up to z = 7.6, compared with previous measurements at different redshifts, do not show any evidence of strong redshift evolution, suggesting metal-enriched environments in these quasars. Using this quasar sample, we create a quasar composite spectrum for z > 6.5 quasars and find no significant redshift evolution of quasar broad emission lines and continuum slope, except for a blueshift of the C iv line. Our sample yields a strong broad absorption line quasar fraction of ∼24%, higher than the fractions in lower-redshift quasar samples, although this could be affected by small sample statistics and selection effects.