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Specific targeting of plasmids with Argonaute enables genome editing
No full textProkaryotic Argonautes (pAgos) are programmable nucleases involved in cell defense against invading DNA. In vitro, pAgos can bind small single-stranded guide DNAs to recognize and cleave complementary DNA. In vivo, pAgos preferentially target plasmids, phages and multicopy genetic elements. Here, we show that CbAgo nuclease from Clostridium butyricum can be used for genomic DNA engineering in bacteria. We demonstrate that CbAgo loaded with plasmid-derived guide DNAs can recognize and cleave homologous chromosomal loci, and define the minimal length of homology required for this targeting. Cleavage of plasmid DNA at an engineered site of the I-SceI meganuclease increases guide DNA loading into CbAgo and enhances processing of homologous chromosomal loci. Analysis of guide DNA loading into CbAgo also reveals off-target sites of I-SceI in the Escherichia coli genome, demonstrating that pAgos can be used for highly sensitive detection of double-stranded breaks in genomic DNA. Finally, we show that CbAgo-dependent targeting of genomic loci with plasmid-derived guide DNAs promotes homologous recombination between plasmid and chromosomal DNA, depending on the catalytic activity of CbAgo. Specific targeting of plasmids with Argonautes can be used to integrate plasmid-encoded sequences into the chromosome thus enabling genome editing
Elemental Abundances of Kepler Objects of Interest in APOGEE DR17
No full textThe elemental abundances of planet host stars can shed light on the conditions of planet forming environments. We test if individual abundances of 130 known/candidate planet hosts in APOGEE are statistically different from those of a reference doppelgänger sample. The reference set comprises objects selected with the same T_(eff), log g, [Fe/H], and [Mg/H] as each Kepler Object of Interest (KOI). We predict twelve individual abundances (X = C, N, O, Na, Al, Si, Ca, Ti, V, Cr, Mn, Ni) for the KOIs and their doppelgängers using a local linear model of these four parameters, training on ASPCAP abundance measurements for a sample of field stars with high-fidelity (signal-to-noise ratio > 200) APOGEE observations. We compare element prediction residuals (model–measurement) for the two samples and find them to be indistinguishable, given a high-quality sample selection. We report median intrinsic dispersions of ∼0.038 dex and ∼0.041 dex, for the KOI and doppelgänger samples, respectively, for these elements. We conclude that the individual abundances at fixed T_(eff), log g, [Fe/H], and [Mg/H] are unremarkable for known planet hosts. Our results establish an upper limit on the abundance precision required to uncover any chemical signatures of planet formation in planet host stars
Local Geometry of Tetrahedrally Coordinated Boron Correlates with ¹¹B NMR Chemical Shifts in Borosilicate Minerals
No full textChemical shifts from the ¹¹B nuclear magnetic resonance (NMR) spectra of crystalline borosilicate minerals with highly ordered, tetrahedrally coordinated boron atoms (B) linearly correlate with the local geometric parameters related to the B–O–T angles (T denotes a tetrahedrally coordinated atom) obtained from single-crystal X-ray diffraction. The correlations between the ¹¹B NMR chemical shifts and structural parameters are similar in functional form to the well-known correlations of ²⁹Si and ²⁷Al NMR chemical shifts with structural features of silicates and aluminosilicates, respectively. These correlations enable the use of ¹¹B NMR chemical shifts to elucidate the local geometry of tetrahedrally coordinated B and aid in establishing B ordering among the crystallographic T-sites within crystalline borosilicates
Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts
No full textAn important question in evolutionary biology is whether (and in what ways) genotype–phenotype (GP) map biases can influence evolutionary trajectories. Untangling the relative roles of natural selection and biases (and other factors) in shaping phenotypes can be difficult. Because the RNA secondary structure (SS) can be analyzed in detail mathematically and computationally, is biologically relevant, and a wealth of bioinformatic data are available, it offers a good model system for studying the role of bias. For quite short RNA (length L ≤ 126), it has recently been shown that natural and random RNA types are structurally very similar, suggesting that bias strongly constrains evolutionary dynamics. Here, we extend these results with emphasis on much larger RNA with lengths up to 3000 nucleotides. By examining both abstract shapes and structural motif frequencies (i.e., the number of helices, bonds, bulges, junctions, and loops), we find that large natural and random structures are also very similar, especially when contrasted to typical structures sampled from the spaces of all possible RNA structures. Our motif frequency study yields another result, where the frequencies of different motifs can be used in machine learning algorithms to classify random and natural RNA with high accuracy, especially for longer RNA (e.g., ROC AUC 0.86 for L = 1000). The most important motifs for classification are the number of bulges, loops, and bonds. This finding may be useful in using SS to detect candidates for functional RNA within ‘junk’ DNA regions
Scaling Law for Impact Resistance of Amorphous Alloys Connecting Atomistic Molecular Dynamics with Macroscale Experiments
No full textEstablishing scaling laws for amorphous alloys is of critical importance for describing their mechanical behavior at different size scales. In this paper, taking Ni₂Ta amorphous metallic alloy as a prototype materials system, we derive the scaling law of impact resistance for amorphous alloys. We use laser-induced supersonic micro-ballistic impact experiments to measure for the first time the size-dependent impact response of amorphous alloys. We also report the results of molecular dynamics (MD) simulations for the same system but at much smaller scales. Comparing these results, we determined a law for scaling both length and time scales based on dimensional analysis. It connects the time and length scales of the experimental results on the impact resistance of amorphous alloys to that of the MD simulations, providing a method for bridging the gap in comparing the dynamic behavior of amorphous alloys at various scales and a guideline for the fabrication of new amorphous alloy materials with extraordinary impact resistance
UID: The uranium isotope database
No full textAs the parent element in the U-Pb and Pb-Pb radiochronometers, uranium (U) was one of the first heavy elements whose isotopic composition was carefully determined. Thought to be constant until the end of the 20th century, the ratio of the long-lived isotopes of U (²³⁸8U/²³⁵U) has since been shown to be variable at the permil to sub-permil levels in natural materials. Today, the study of U isotopes has found applications in a variety of fields including geo/cosmochronology, oceanic paleoredox reconstruction, magmatic differentiation, environmental remediation, and forensic studies. With thousands of newly reported U isotopic data each year, a real need exists for a comprehensive U isotope database.
Here, we introduce a global, updatable, U isotope database (UID), which not only contains the most expansive, internally consistent U isotopic dataset to date (14,591 entries from more than 320 papers), but also includes all other sample data from the original publications, as well as the relevant metadata and sample information to facilitate further analysis. The UID is freely accessible and will be updated regularly. All data are normalized to the widely-used CRM-145 standard, and all assumptions used to convert the published data are explicitly detailed in the paper and the database itself. New data can be easily formatted and submitted for incorporation into the database. Using the UID we provide new recommended δ238U values for certified U standards and geostandards and discuss important applications and future directions for U isotope studies
TTV constraints on additional planets in the WD 1856+534 system
No full textWD 1856+534 b (or WD 1856 b for short) is the first known transiting planet candidate around a white dwarf star. WD 1856 b is about the size of Jupiter, has a mass less than about 12 Jupiter masses, and orbits at a distance of about 2 per cent of an astronomical unit. The formation and migration history of this object is still a mystery. Here, we present constraints on the presence of long-period companions (where we explored eccentricity, inclination, mass, and period for the possible companion) in the WD 1856+534 planetary system from transit timing variations. We show that existing transit observations can rule out planets with orbital periods less than about 500 d. With additional transit observations over the next decade, it will be possible to test whether WD 1856 also hosts additional long-period planets that could have perturbed WD 1856 b into its current close-in orbit
A semi-analytic study of self-interacting dark-matter haloes with baryons
No full textWe combine the isothermal Jeans model and the model of adiabatic halo contraction into a semi-analytic procedure for computing the density profile of self-interacting dark-matter (SIDM) haloes with the gravitational influence from the inhabitant galaxies. The model agrees well with cosmological SIDM simulations over the entire core-forming stage up to the onset of gravothermal core-collapse. Using this model, we show that the halo response to baryons is more diverse in SIDM than in CDM and depends sensitively on galaxy size, a desirable feature in the context of the structural diversity of bright dwarfs. The fast speed of the method facilitates analyses that would be challenging for numerical simulations – notably, we quantify the SIDM halo response as functions of the baryonic properties, on a fine mesh grid spanned by the baryon-to-total-mass ratio, M_b/M_(vir), and galaxy compactness, r1/2/Rvir; we show with high statistical precision that for typical Milky-Way-like systems, the SIDM profiles are similar to their CDM counterparts; and we delineate the regime of core-collapse in the Mb/Mvir − r1/2/Rvir space, for a given cross section and concentration. Finally, we compare the isothermal Jeans model with the more sophisticated gravothermal fluid model, and show that the former yields faster core formation and agrees better with cosmological simulations. We attribute the difference to whether the target CDM halo is used as a boundary condition or as the initial condition for the gravothermal evolution, and thus comment on possible improvements of the fluid model. We have made our model publicly available at https://github.com/JiangFangzhou/SIDM
A red giant orbiting a black hole
No full textWe report spectroscopic and photometric follow-up of a dormant black hole (BH) candidate from Gaia DR3. The system, which we call Gaia BH₂, contains a ∼1 M_⊙ red giant and a dark companion with mass M₂ = 8.9 ± 0.3 M_⊙ that is very likely a BH. The orbital period, P_(orb) = 1277 d, is much longer than that of any previously studied BH binary. Our radial velocity (RV) follow-up over a 7-month period spans >90 per cent of the orbit’s RV range and is in excellent agreement with the Gaia solution. UV imaging and high-resolution optical spectra rule out plausible luminous companions that could explain the orbit. The star is a bright (G = 12.3), slightly metal-poor [Fe/H] = -0.22) low-luminosity giant T_(eff) = 4600 K; R = 7.8 R_⊙ }; log [g/(cm s⁻²)] = 2.6). The binary’s orbit is moderately eccentric (e = 0.52). The giant is enhanced in α-elements, with [α/Fe] = +0.26, but the system’s Galactocentric orbit is typical of the thin disc. We obtained X-ray and radio non-detections of the source near periastron, which support BH accretion models in which the net accretion rate at the horizon is much lower than the Bondi–Hoyle–Lyttleton rate. At a distance of 1.16 kpc, Gaia BH2 is the second-nearest known BH, after Gaia BH1. Its orbit – like that of Gaia BH1 – seems too wide to have formed through common envelope evolution. Gaia BH1 and BH2 have orbital periods at opposite edges of the Gaia DR3 sensitivity curve, perhaps hinting at a bimodal intrinsic period distribution for wide BH binaries. Dormant BH binaries like Gaia BH1 and Gaia BH2 significantly outnumber their close, X-ray bright cousins, but their formation pathways remain uncertain
Non-bonding interaction of dual atom catalysts for enhanced oxygen reduction reaction
No full textWe demonstrate the design of graphene-supported dual atom catalysts (DACs) for the four-electron oxygen reduction reaction (ORR), by utilizing the non-bonding interaction of counterpart metals (M) that synergistically tune the electronic properties and catalytic activity of the Fe active site in FeMN₆-DAC and FeMN₈-DAC systems, where M stands for Fe, Co, Ni, Cu, and Zn. More specifically, for Fe-M distances below 15 Å, the non-bonding interaction is significant, making the system act as the DAC. We predicted that FeNiN₆-DAC and FeNiN₈-DAC exhibit a low ORR overpotential (η^(ORR)) of 0.28 V and 0.47 V, respectively, which are at the summits of volcano plots. This low η^(ORR) originates from the high Bader charge transfer coupled with high spin density at the Fe site in both the FeNiN₆-DAC and FeNiN₈-DAC systems, which weakens the adsorption of OH* intermediate while enhancing its desorption to H₂O. Guided by these density functional theory (DFT) computational results, we synthesized FeCoN₈-DAC and FeNiN₈-DAC along with N-doped graphene and confirmed their structures with scanning transmission electron microscopy (STEM), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and electron spin resonance (ESR). We verify experimentally the catalytic activities and find that FeNiN₈-DAC has the low experimental overpotential of 0.39 V with a Tafel slope of 47 mVdec⁻¹. Based on these results, we propose a DFT-guided strategy to tune the charge transfer and spin population of the active site toward designing DACs for electrochemical ORR