bluuebunny/crossref_metadata_2025 huggingface dataset:
The INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) Academy: a community resource for plant science
Authors: Tatout Christophe , Mougeot Guillaume , Parry Geraint , Baroux Célia , Pradillo Mónica , Evans David
Published: January 2022

This Community Resource paper introduces the range of materials developed by the INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) COST Action made available through the INDEPTH Academy. Recent rapid growth in understanding of the significance of epigenetic controls in plant and crop science has led to a need for shared, high-quality resources, standardization of protocols, and repositories for open access data. The INDEPTH Academy provides a range of masterclass tutorials, standardized protocols, and teaching webinars, together with a rapidly developing repository to support imaging and spatial analysis of the nucleus and deep learning for automated analysis. These resources were developed partly as a response to the COVID-19 pandemic, but also driven by needs and opportunities identified by the INDEPTH community of ~200 researchers in 80 laboratories from 32 countries. This community report outlines the resources produced and how they will be extended beyond the INDEPTH project, but also aims to encourage the wider community to engage with epigenetics and nuclear structure by accessing these resources.
A stress-associated protein OsSAP8 modulates gibberellic acid biosynthesis by reducing the promotive effect of transcription factor OsbZIP58 on OsKO2
Authors: Li Ming , Zhang Hui , He Dongli , Damaris Rebecca Njeri , Yang Pingfang
Published: January 2022

Gibberellic acid (GA) is a vital phytohormone for plant growth and development. GA biosynthesis is a complex pathway regulated by various transcription factors. Here we report a stress-associated protein 8 (OsSAP8), negatively involved in GA biosynthesis. Overexpression of OsSAP8 in rice resulted in a semi-dwarfism phenotype and reduced endogenous GA3 content. In contrast, an OsSAP8 knockout mutant exhibited higher endogenous GA3 content and slightly increased plant height. Sub-cellular localization analysis of OsSAP8 showed that it could enter the nucleus. Based on electrophoretic mobility shift assay and yeast one hybrid experiments, OsSAP8 was found to bind to the cis-acting regulatory element GADOWNAT of ent-kaurene oxidases (KO2, KO3, KO5). The results from dual-luciferase reporter assays showed that OsSAP8 does not activate LUC reporter gene expression. However, it could interact with basic leucine zipper 58 (OsbZIP58), which has strong transcriptional activation potential on OsKO2. Moreover, the interaction between OsSAP8, rice lesion simulating disease 1-like 1 (OsLOL1), and OsbZIP58 could reduce the promotive effect of transcription factor OsbZIP58 on OsKO2. These results provide some new insights on the regulation of GA biosynthesis in rice.
Iterative reconstruction excursions for Baryon Acoustic Oscillations and beyond
Authors: Seo Hee-Jong , Ota Atsuhisa , Schmittfull Marcel , Saito Shun , Beutler Florian
Published: January 2022

The density field reconstruction technique has been widely used for recovering the baryon acoustic oscillation (BAO) feature in galaxy surveys that has been degraded due to non-linearities. Recent studies advocated adopting iterative steps to improve the recovery much beyond that of the standard technique. In this paper, we investigate the performance of a few selected iterative reconstruction techniques focusing on the BAO and the broad-band shape of the two-point clustering. We include redshift-space distortions, halo bias, and shot noise and inspect the components of the reconstructed field in Fourier space and in configuration space using both density field-based reconstruction and displacement field-based reconstruction. We find that the displacement field reconstruction becomes quickly challenging in the presence of non-negligible shot noise and therefore present surrogate methods that can be practically applied to a much more sparse field such as galaxies. For a galaxy field, implementing a debiasing step to remove the Lagrangian bias appears crucial for the displacement field reconstruction. We show that the iterative reconstruction does not substantially improve the BAO feature beyond an aggressively optimized standard reconstruction with a small smoothing kernel. However, we find taking iterative steps allows us to use a small smoothing kernel more ‘stably’, i.e. without causing a substantial deviation from the linear power spectrum on large scales. In one specific example we studied, we find that a deviation of 13 per cent in $P(k\sim 0.1\, h{\rm \,\,Mpc^{-1}})$ with an aggressive standard reconstruction can reduce to 3–4 per cent with iterative steps.
Collisional fragmentation and bulk composition tracking in rebound
Authors: Childs Anna C , Steffen Jason H
Published: January 2022

We present a fragmentation module and a composition tracking code for the N-body code rebound. Our fragmentation code utilizes previous semi-analytical models and follows an implementation method similar to fragmentation for the N-body code mercury. In our N-body simulations with fragmentation, we decrease the collision and planet formation time-scales by inflating the particle radii by an expansion factor f and experiment with various values of f to understand how expansion factors affect the collision history and final planetary system. As the expansion factor increases, so do the rate of mergers which produces planetary systems with more planets and planets at larger orbits. Additionally, we present a composition tracking code which follows the compositional change of homogeneous bodies as a function of mass exchange and use it to study how fragmentation and the use of an expansion factor affects volatile delivery to the inner terrestrial disc. We find that fragmentation enhances radial mixing relative to perfect merging and that on average, as f increases so does the average water mass fraction of the planets. Radial mixing decreases with increasing f as collisions happen early on, before the bodies have time to grow to excited orbits and move away from their original location.
Filling the gap between synchronized and non-synchronized sdBs in short-period sdBV+dM binaries with TESS: TIC 137608661, a new system with a well-defined rotational splitting
Authors: Silvotti Roberto , Németh Péter , Telting John H , Baran Andrzej S , Østensen Roy H , Ostrowski Jakub , Sahoo Sumanta K , Prins Saskia
Published: January 2022

TIC 137608661/TYC 4544-2658-1/FBS 0938+788 is a new sdBV+dM reflection-effect binary discovered by the TESS space mission with an orbital period of 7.21 h. In addition to the orbital frequency and its harmonics, the Fourier transform of TIC 137608661 shows many g-mode pulsation frequencies from the subdwarf B (sdB) star. The amplitude spectrum is particularly simple to interpret as we immediately see several rotational triplets of equally spaced frequencies. The central frequencies of these triplets are equally spaced in period with a mean period spacing of 270.12 s, corresponding to consecutive l = 1 modes. From the mean frequency spacing of 1.25 μHz we derive a rotation period of 4.6 d in the deep layers of the sdB star, significantly longer than the orbital period. Among the handful of sdB+dM binaries for which the sdB rotation was measured through asteroseismology, TIC 137608661 is the non-synchronized system with both the shortest orbital period and the shortest core rotation period. Only NY Vir has a shorter orbital period but it is synchronized. From a spectroscopic follow-up of TIC 137608661 we measure the radial velocities of the sdB star, determine its atmospheric parameters, and estimate the rotation rate at the surface of the star. This measurement allows us to exclude synchronized rotation also in the outer layers and suggests a differential rotation, with the surface rotating faster than the core, as found in few other similar systems. Furthermore, an analysis of the spectral energy distribution of TIC 137608661, together with a comparison between sdB pulsation properties and asteroseismic models, gives us further elements to constrain the system.
Simultaneously constraining cosmology and baryonic physics via deep learning from weak lensing
Authors: Lu Tianhuan , Haiman Zoltán , Zorrilla Matilla José Manuel
Published: January 2022

Ongoing and planned weak lensing (WL) surveys are becoming deep enough to contain information on angular scales down to a few arcmin. To fully extract information from these small scales, we must capture non-Gaussian features in the cosmological WL signal while accurately accounting for baryonic effects. In this work, we account for baryonic physics via a baryonic correction model that modifies the matter distribution in dark matter-only N-body simulations, mimicking the effects of galaxy formation and feedback. We implement this model in a large suite of ray-tracing simulations, spanning a grid of cosmological models in Ωm−σ8 space. We then develop a convolutional neural network (CNN) architecture to learn and constrain cosmological and baryonic parameters simultaneously from the simulated WL convergence maps. We find that in a Hyper-Suprime Cam-like survey, our CNN achieves a 1.7× tighter constraint in Ωm−σ8 space (1σ area) than the power spectrum and 2.1× tighter than the peak counts, showing that the CNN can efficiently extract non-Gaussian cosmological information even while marginalizing over baryonic effects. When we combine our CNN with the power spectrum, the baryonic effects degrade the constraint in Ωm−σ8 space by a factor of 2.4, compared to the much worse degradation by a factor of 4.7 or 3.7 from either method alone.
Why hot Jupiters can be large but not too large
Authors: Hou Qiang , Wei Xing
Published: January 2022

Tidal heating is often used to interpret ‘radius anomaly’ of hot Jupiters (i.e. radii of a large fraction of hot Jupiters are in excess of 1.2 Jupiter radius which cannot be interpreted by the standard theory of planetary evolution). In this paper, we find that tidal heating induces another phenomenon ‘runaway inflation’ (i.e. planet inflation becomes unstable and out of control when tidal heating rate is above its critical value). With sufficiently strong tidal heating, luminosity initially increases with inflation, but across its peak it decreases with inflation such that heating is stronger than cooling and runaway inflation occurs. In this mechanism, the opacity near radiative-convective boundary (RCB) scales approximately as temperature to the fourth power and heat cannot efficiently radiate away from planet interior, which induces runaway inflation (similar to a tight lid on a boiling pot). Based on this mechanism, we find that radii of hot Jupiters cannot exceed 2.2RJ, which is in good agreement with the observations. We also give an upper limit for orbital eccentricity of hot Jupiters. Moreover, by comparison to the observations we infer that tidal heating locates near RCB.
Relic galaxy analogues in TNG50 simulation: the formation pathways of surviving red nuggets in a cosmological simulation
Authors: Flores-Freitas Rodrigo , Chies-Santos Ana L , Furlanetto Cristina , De Rossi María Emilia , Ferreira Leonardo , Zenocratti Lucas J , Alamo-Martínez Karla A
Published: January 2022

Relic galaxies are massive compact quiescent galaxies that formed at high-redshift and remained almost unchanged since then. In this work, we search for analogues to relic galaxies in the TNG50 cosmological simulations to understand relic formation and test the ability of TNG50 to reproduce such rare objects. Using stellar mass, age, radius, quiescence, and stellar assembly criteria, we find five subhaloes in TNG50 that could be potential relic analogues. We compare their properties with other constraints imposed by a sample of 13 observed relic galaxies. We find one analogue in TNG50 that simultaneously satisfies most of the available observational constraints, such as metallicity and morphology. It also shows similarities to the confirmed relic NGC 1277, regarding environment and dark matter fraction. By taking into account a degree of relicness, a second relic analogue may also be considered. However, the central parts of the brightness and density profiles of the analogues are less steep than that of real relic galaxies, possibly due to limited numerical resolution. We identify two formation pathways of relic analogues in TNG50 depending on their environment: they either have their remaining gas stripped during the infall into a cluster at z ≲ 1.2 or consume it before z > 1.5. They are then deprived of significant star formation, leaving their stellar populations almost unaltered during the last 9 Gyr. We also find that the analogue progenitors at z ∼ 4 inhabit more massive haloes than progenitors of quiescent galaxies with similar stellar mass at z ∼ 0.
Nebular-phase spectra of Type Ia supernovae from the Las Cumbres Observatory Global Supernova Project
Authors: Graham M L , Kennedy T D , Kumar S , Amaro R C , Sand D J , Jha S W , Galbany L , Vinko J , Wheeler J C , Hsiao E Y , Bostroem K A , Burke J , Hiramatsu D , Hosseinzadeh G , McCully C , Howell D A , Diamond T , Hoeflich P , Wang X , Li W
Published: January 2022

The observed diversity in Type Ia supernovae (SNe Ia) – the thermonuclear explosions of carbon–oxygen white dwarf stars used as cosmological standard candles – is currently met with a variety of explosion models and progenitor scenarios. To help improve our understanding of whether and how often different models contribute to the occurrence of SNe Ia and their assorted properties, we present a comprehensive analysis of seven nearby SNe Ia. We obtained one to two epochs of optical spectra with Gemini Observatory during the nebular phase (>200 d past peak) for each of these events, all of which had time series of photometry and spectroscopy at early times (the first ∼8 weeks after explosion). We use the combination of early- and late-time observations to assess the predictions of various models for the explosion (e.g. double-detonation, off-centre detonation, stellar collisions), progenitor star (e.g. ejecta mass, metallicity), and binary companion (e.g. another white dwarf or a non-degenerate star). Overall, we find general consistency in our observations with spherically symmetric models for SN Ia explosions, and with scenarios in which the binary companion is another degenerate star. We also present an in-depth analysis of SN 2017fzw, a member of the subgroup of SNe Ia which appear to be transitional between the subluminous ‘91bg-like’ events and normal SNe Ia, and for which nebular-phase spectra are rare.
Constraining tidal quality factor using spin period in eclipsing binaries
Authors: Patel Ruskin , Penev Kaloyan
Published: January 2022

Evolution of binary objects under the influence of tides drastically affects the expected observational properties of the system. With the discovery of a large number of close-in hot Jupiter systems and eclipsing binaries from missions such as Kepler and Transiting Exoplanet Survey Satellite, it has become imperative to understand the extent of tidal influence on their formation and observed properties. In the case of binary systems, an efficient tidal dissipation can lead to either spin-up or spin-down of the stars and/or spin–orbit synchronization, depending upon the exchange of angular momentum between the star and the orbit. We combine the eclipsing binary systems from the Kepler mission with stellar and orbital parameters available in the literature to create a catalogue of 41 eclipsing binaries suitable for analysis of tidal dissipation. Empirically, the efficiency of tidal dissipation is parametrized using a modified tidal quality factor ($Q_{\star }^{\prime }$). We find constraints on $Q_{\star }^{\prime }$ using the observed rotation period of the primary star in the eclipsing binary systems. We calculate detailed evolutions of binary systems under the combined influence of tides, stellar evolution, and loss of stellar angular momentum to magnetic winds, and perform Markov chain Monte Carlo simulations to account for the uncertainties in the observed data. Our analysis shows that $\log _{10}{Q^{\prime }_{\star }}=7.818\pm 0.035$ can reproduce the observed primary star spin in almost all systems in our sample.
UOCS – VII. Blue straggler populations of open cluster NGC 7789 with UVIT/AstroSat
Authors: Vaidya Kaushar , Panthi Anju , Agarwal Manan , Pandey Sindhu , Rao Khushboo K , Jadhav Vikrant , Subramaniam Annapurni
Published: January 2022

NGC 7789 is a ∼1.6 Gyr old, populous open cluster located at ∼2000 pc. We characterize the blue straggler stars (BSS) of this cluster using the Ultraviolet (UV) data from the UVIT/AstroSat. We present spectral energy distributions (SED) of 15 BSS candidates constructed using multiwavelength data ranging from UV to IR wavelengths. In 8 BSS candidates, a single temperature SED is found to be satisfactory. We discover hot companions in 5 BSS candidates. The hot companions with Teff ∼ 11750–15500 K, R ∼ 0.069–0.242 R⊙, and L ∼ 0.25–1.55 L⊙, are most likely extremely low mass (ELM) white dwarfs (WDs) with masses smaller than ∼0.18 M⊙, and thereby confirmed post mass transfer systems. We discuss the implication of this finding in the context of BSS formation mechanisms. Two additional BSS show excess in one or more UV filters, and may have a hot companion, however we are unable to characterize them. We suggest that at least 5 of the 15 BSS candidates (33 per cent) studied in this cluster have formed via the mass-transfer mechanism.
Collisional excitation of isotopologs of H2S by molecular hydrogen: D2S and HDS
Authors: Dagdigian Paul J
Published: January 2022

Rate coefficients for transitions between the lower rotational levels of two isotopologs of hydrogen sulphide, specifically HDS and D2S, induced by collisions with para-H2 and ortho-H2 are presented in this work. The availability of these rate coefficients will allow accurate estimates to be made of the abundance of these species in the interstellar medium to be made from astronomical observations. The rate coefficients were computed in close-coupling calculations using potential energy surfaces (PESs) obtained by transformation of the H2S–H2 PES previously calculated with the explicitly correlated CCSD(T)-F12a coupled-cluster method. Rate coefficients for transitions between rotational levels with energies less than 196 cm−1 and temperatures from 5 to 400 K have been calculated for HDS, ortho-D2S, and para-D2S. The rate coefficients for the H2S–H2, HDS–H2, and D2S–H2 systems are compared
ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions – VIII. A search for hot cores by using C2H5CN, CH3OCHO, and CH3OH lines
Authors: Qin Sheng-Li , Liu Tie , Liu Xunchuan , Goldsmith Paul F , Li Di , Zhang Qizhou , Liu Hong-Li , Wu Yuefang , Bronfman Leonardo , Juvela Mika , Lee Chang Won , Garay Guido , Zhang Yong , He Jinhua , Hsu Shih-Ying , Shen Zhi-Qiang , Lee Jeong-Eun , Wang Ke , Tang Ningyu , Tang Mengyao , Zhang Chao , Yue Yinghua , Xue Qiaowei , Li Shanghuo , Peng Yaping , Dutta Somnath , Ge Jixing , Xu Fengwei , Chen Long-Fei , Baug Tapas , Dewangan Lokesh , Tej Anandmayee
Published: January 2022

Hot cores characterized by rich lines of complex organic molecules are considered as ideal sites for investigating the physical and chemical environments of massive star formation. We present a search for hot cores by using typical nitrogen- and oxygen-bearing complex organic molecules (C2H5CN, CH3OCHO, and CH3OH), based on ALMA Three-millimeter Observations of Massive Star-forming regions (ATOMS). The angular resolutions and line sensitivities of the ALMA observations are better than 2 arcsec and 10 mJy beam−1, respectively. A total of 60 hot cores are identified with 45 being newly detected, in which the complex organic molecules have high gas temperatures (> 100 K) and hot cores have small source sizes (< 0.1 pc). So far, this is the largest sample of hot cores observed with similar angular resolution and spectral coverage. The observations have also shown nitrogen and oxygen differentiation in both line emission and gas distribution in 29 hot cores. Column densities of CH3OH and CH3OCHO increase as rotation temperatures rise. The column density of CH3OCHO correlates tightly with that of CH3OH. The pathways for production of different species are discussed. Based on the spatial position difference between hot cores and ultracompact H ii (UC H ii) regions, we conclude that 24 hot cores are externally heated, while the other hot cores are internally heated. The observations presented here will potentially help establish a hot core template for studying massive star formation and astrochemistry.
Emission-line diagnostics of H ii regions using conditional invertible neural networks
Authors: Kang Da Eun , Pellegrini Eric W , Ardizzone Lynton , Klessen Ralf S , Koethe Ullrich , Glover Simon C O , Ksoll Victor F
Published: January 2022

Young massive stars play an important role in the evolution of the interstellar medium (ISM) and the self-regulation of star formation in giant molecular clouds (GMCs) by injecting energy, momentum, and radiation (stellar feedback) into surrounding environments, disrupting the parental clouds, and regulating further star formation. Information of the stellar feedback inheres in the emission we observe, however inferring the physical properties from photometric and spectroscopic measurements is difficult, because stellar feedback is a highly complex and non-linear process, so that the observational data are highly degenerate. On this account, we introduce a novel method that couples a conditional invertible neural network (cINN) with the WARPFIELD-emission predictor (WARPFIELD-EMP) to estimate the physical properties of star-forming regions from spectral observations. We present a cINN that predicts the posterior distribution of seven physical parameters (cloud mass, star formation efficiency, cloud density, cloud age which means age of the first generation stars, age of the youngest cluster, the number of clusters, and the evolutionary phase of the cloud) from the luminosity of 12 optical emission lines, and test our network with synthetic models that are not used during training. Our network is a powerful and time-efficient tool that can accurately predict each parameter, although degeneracy sometimes remains in the posterior estimates of the number of clusters. We validate the posteriors estimated by the network and confirm that they are consistent with the input observations. We also evaluate the influence of observational uncertainties on the network performance.
Dark matter haloes in interacting dark energy models: formation history, density profile, spin, and shape
Authors: Liu Yun , Liao Shihong , Liu Xiangkun , Zhang Jiajun , An Rui , Fan Zuhui
Published: January 2022

The interacting dark energy (IDE) model, which considers the interaction between dark energy and dark matter, provides a natural mechanism to alleviate the coincidence problem and can also relieve the observational tensions under the ΛCDM model. Previous studies have put constraints on IDE models by observations of cosmic expansion history, cosmic microwave background, and large-scale structures. However, these data are not yet enough to distinguish IDE models from ΛCDM effectively. Because the non-linear structure formation contains rich cosmological information, it can provide additional means to differentiate alternative models. In this paper, based on a set of N-body simulations for IDE models, we investigate the formation histories and properties of dark matter haloes and compare with their ΛCDM counterparts. For the model with dark matter decaying into dark energy and the parameters being the best-fitting values from previous constraints, the structure formation is markedly slowed down, and the haloes have systematically lower mass, looser internal structure, higher spin, and anisotropy. This is inconsistent with the observed structure formation, and thus this model can be safely ruled out from the perspective of non-linear structure formation. Moreover, we find that the ratio of halo concentrations between IDE and ΛCDM counterparts depends sensitively on the interaction parameter and is independent of halo mass. This can act as a powerful probe to constrain IDE models. Our results concretely demonstrate that the interaction of the two dark components can affect the halo formation considerably, and therefore the constraints from non-linear structures are indispensable.
Grids of stellar models with rotation VII: models from 0.8 to 300 M⊙ at supersolar metallicity (Z = 0.020)
Authors: Yusof Norhasliza , Hirschi Raphael , Eggenberger Patrick , Ekström Sylvia , Georgy Cyril , Sibony Yves , Crowther Paul A , Meynet Georges , Kassim Hasan Abu , Harun Wan Aishah Wan , Maeder André , Groh Jose H , Farrell Eoin , Murphy Laura
Published: January 2022

We present a grid of stellar models at supersolar metallicity (Z = 0.020) extending the previous grids of Geneva models at solar and sub-solar metallicities. A metallicity of Z = 0.020 was chosen to match that of the inner Galactic disc. A modest increase of 43 per cent (= 0.02/0.014) in metallicity compared to solar models means that the models evolve similarly to solar models but with slightly larger mass-loss. Mass-loss limits the final total masses of the supersolar models to 35 M⊙ even for stars with initial masses much larger than 100 M⊙. Mass-loss is strong enough in stars above 20 M⊙ for rotating stars (25 M⊙ for non-rotating stars) to remove the entire hydrogen-rich envelope. Our models thus predict SNII below 20 M⊙ for rotating stars (25 M⊙ for non-rotating stars) and SNIb (possibly SNIc) above that. We computed both isochrones and synthetic clusters to compare our supersolar models to the Westerlund 1 (Wd1) massive young cluster. A synthetic cluster combining rotating and non-rotating models with an age spread between log10(age/yr) = 6.7 and 7.0 is able to reproduce qualitatively the observed populations of WR, RSG, and YSG stars in Wd1, in particular their simultaneous presence at $\log _{10}(L/\mathit {\mathrm{ L}}_{\odot })$ = 5–5.5. The quantitative agreement is imperfect and we discuss the likely causes: synthetic cluster parameters, binary interactions, mass-loss and their related uncertainties. In particular, mass-loss in the cool part of the HRD plays a key role.
Catalogues of voids as antihaloes in the local Universe
Authors: Desmond Harry , Hutt Maxwell L , Devriendt Julien , Slyz Adrianne
Published: January 2022

A recently proposed algorithm identifies voids in simulations as the regions associated with haloes when the initial overdensity field is negated. We apply this method to the real Universe by running a suite of constrained simulations of the 2M++ volume with initial conditions inferred by the BORG algorithm, along with the corresponding inverted set. Our 101 inverted and uninverted simulations, spanning the BORG posterior, each identify ∼150 000 ‘voids as antihaloes’ with mass exceeding 4.38 × 1011 M⊙ (100 particles) at z = 0 in a full-sky sphere of radius 155 Mpc h−1 around the Milky Way. We calculate the size function, volume filling fraction, ellipticity, central density, specific angular momentum, clustering, and stacked density profile of the voids, and cross-correlate them with those produced by VIDE on the same simulations. We make our antihalo and VIDE catalogues publicly available.
A genuine Large Magellanic Cloud age gap star cluster
Authors: Piatti Andrés E
Published: January 2022

We confirm the existence of a second Large Magellanic Cloud (LMC) star cluster, KMHK 1592, with an age that falls in the middle of the so-called LMC star cluster age gap, a long period of time (∼4–11 Gyr) where no star cluster had been uncovered, except ESO 121-SC 03. The age (8.0 ± 0.5 Gyr) and the metallicity ([Fe/H] = −1.0 ± 0.2 dex) of KMHK 1592 were derived from the fit of theoretical isochrones to the intrinsic star cluster colour–magnitude diagram sequences, which were unveiled using a robust star-by-star membership probability procedure. Because of the relative low brightness of the star cluster, deep GEMINI GMOS images were used. We discuss the pros and cons of three glimpsed scenarios that could explain the presence of both LMC age gap star clusters in the outskirts of the LMC, namely: in situ star cluster formation, capture from the Small Magellanic Cloud, or accretion of a small dwarf galaxy.
Approximate Bayesian Computation Untangles Signatures of Contemporary and Historical Hybridization between Two Endangered Species
Authors: Dittberner Hannes , Tellier Aurelien , de Meaux Juliette
Published: January 2022

Contemporary gene flow, when resumed after a period of isolation, can have crucial consequences for endangered species, as it can both increase the supply of adaptive alleles and erode local adaptation. Determining the history of gene flow and thus the importance of contemporary hybridization, however, is notoriously difficult. Here, we focus on two endangered plant species, Arabis nemorensis and A. sagittata, which hybridize naturally in a sympatric population located on the banks of the Rhine. Using reduced genome sequencing, we determined the phylogeography of the two taxa but report only a unique sympatric population. Molecular variation in chloroplast DNA indicated that A. sagittata is the principal receiver of gene flow. Applying classical D-statistics and its derivatives to whole-genome data of 35 accessions, we detect gene flow not only in the sympatric population but also among allopatric populations. Using an Approximate Bayesian computation approach, we identify the model that best describes the history of gene flow between these taxa. This model shows that low levels of gene flow have persisted long after speciation. Around 10 000 years ago, gene flow stopped and a period of complete isolation began. Eventually, a hotspot of contemporary hybridization was formed in the unique sympatric population. Occasional sympatry may have helped protect these lineages from extinction in spite of their extremely low diversity.
Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation
Authors: Hanna Courtney W , Huang Jiahao , Belton Christian , Reinhardt Susanne , Dahl Andreas , Andrews Simon , Stewart A Francis , Kranz Andrea , Kelsey Gavin
Published: January 2022

Histone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 (KMT2B) are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) oocytes using ultra-low input ChIP-seq, with comparisons to DNA methylation and gene expression analyses. H3K4me3 was redistributed in Setd1b cKO oocytes showing losses at active gene promoters associated with downregulated gene expression. Remarkably, many regions also gained H3K4me3, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich, which are hallmarks of MLL2 targets. Consequently, loss of SETD1B disrupts the balance between MLL2 and de novo DNA methyltransferases in determining the epigenetic landscape during oogenesis. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression and MLL2 to CpG content.
RBFOX2 is required for establishing RNA regulatory networks essential for heart development
Authors: Verma Sunil K , Deshmukh Vaibhav , Thatcher Kaitlyn , Belanger KarryAnne K , Rhyner Alexander M , Meng Shu , Holcomb Richard Joshua , Bressan Michael , Martin James F , Cooke John P , Wythe Joshua D , Widen Steven G , Lincoln Joy , Kuyumcu-Martinez Muge N
Published: January 2022

Human genetic studies identified a strong association between loss of function mutations in RBFOX2 and hypoplastic left heart syndrome (HLHS). There are currently no Rbfox2 mouse models that recapitulate HLHS. Therefore, it is still unknown how RBFOX2 as an RNA binding protein contributes to heart development. To address this, we conditionally deleted Rbfox2 in embryonic mouse hearts and found profound defects in cardiac chamber and yolk sac vasculature formation. Importantly, our Rbfox2 conditional knockout mouse model recapitulated several molecular and phenotypic features of HLHS. To determine the molecular drivers of these cardiac defects, we performed RNA-sequencing in Rbfox2 mutant hearts and identified dysregulated alternative splicing (AS) networks that affect cell adhesion to extracellular matrix (ECM) mediated by Rho GTPases. We identified two Rho GTPase cycling genes as targets of RBFOX2. Modulating AS of these two genes using antisense oligos led to cell cycle and cell-ECM adhesion defects. Consistently, Rbfox2 mutant hearts displayed cell cycle defects and inability to undergo endocardial-mesenchymal transition, processes dependent on cell-ECM adhesion and that are seen in HLHS. Overall, our work not only revealed that loss of Rbfox2 leads to heart development defects resembling HLHS, but also identified RBFOX2-regulated AS networks that influence cell-ECM communication vital for heart development.
Commonality and diversity in tRNA substrate recognition in t6A biogenesis by eukaryotic KEOPSs
Authors: Wang Jin-Tao , Zhou Jing-Bo , Mao Xue-Ling , Zhou Li , Chen Meirong , Zhang Wenhua , Wang En-Duo , Zhou Xiao-Long
Published: January 2022

N 6-Threonylcarbamoyladenosine (t6A) is a universal and pivotal tRNA modification. KEOPS in eukaryotes participates in its biogenesis, whose mutations are connected with Galloway-Mowat syndrome. However, the tRNA substrate selection mechanism by KEOPS and t6A modification function in mammalian cells remain unclear. Here, we confirmed that all ANN-decoding human cytoplasmic tRNAs harbor a t6A moiety. Using t6A modification systems from various eukaryotes, we proposed the possible coevolution of position 33 of initiator tRNAMet and modification enzymes. The role of the universal CCA end in t6A biogenesis varied among species. However, all KEOPSs critically depended on C32 and two base pairs in the D-stem. Knockdown of the catalytic subunit OSGEP in HEK293T cells had no effect on the steady-state abundance of cytoplasmic tRNAs but selectively inhibited tRNAIle aminoacylation. Combined with in vitro aminoacylation assays, we revealed that t6A functions as a tRNAIle isoacceptor-specific positive determinant for human cytoplasmic isoleucyl-tRNA synthetase (IARS1). t6A deficiency had divergent effects on decoding efficiency at ANN codons and promoted +1 frameshifting. Altogether, our results shed light on the tRNA recognition mechanism, revealing both commonality and diversity in substrate recognition by eukaryotic KEOPSs, and elucidated the critical role of t6A in tRNAIle aminoacylation and codon decoding in human cells.
Does rapid sequence divergence preclude RNA structure conservation in vertebrates?
Authors: Seemann Stefan E , Mirza Aashiq H , Bang-Berthelsen Claus H , Garde Christian , Christensen-Dalsgaard Mikkel , Workman Christopher T , Pociot Flemming , Tommerup Niels , Gorodkin Jan , Ruzzo Walter L
Published: January 2022

Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA’s structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can change through evolution while conserving its structure. Specifically, we consider predicted and known structures in vertebrate genomes. After careful control of false discovery rates, we obtain 13 de novo structures (and three known Rfam structures) that we predict to have rapidly evolving sequences—defined as structures where the primary sequences of human and mouse have diverged at least twice as fast (1.5 times for Rfam) as nearby neutrally evolving sequences. Two of the three known structures function in translation inhibition related to infection and immune response. We conclude that rapid sequence divergence does not preclude RNA structure conservation in vertebrates, although these events are relatively rare.
Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism
Authors: Dörner Kerstin , Badertscher Lukas , Horváth Bianka , Hollandi Réka , Molnár Csaba , Fuhrer Tobias , Meier Roger , Sárazová Marie , van den Heuvel Jasmin , Zamboni Nicola , Horvath Peter , Kutay Ulrike
Published: January 2022

Ribosome assembly is an essential process that is linked to human congenital diseases and tumorigenesis. While great progress has been made in deciphering mechanisms governing ribosome biogenesis in eukaryotes, an inventory of factors that support ribosome synthesis in human cells is still missing, in particular regarding the maturation of the large 60S subunit. Here, we performed a genome-wide RNAi screen using an imaging-based, single cell assay to unravel the cellular machinery promoting 60S subunit assembly in human cells. Our screen identified a group of 310 high confidence factors. These highlight the conservation of the process across eukaryotes and reveal the intricate connectivity of 60S subunit maturation with other key cellular processes, including splicing, translation, protein degradation, chromatin organization and transcription. Intriguingly, we also identified a cluster of hits comprising metabolic enzymes of the polyamine synthesis pathway. We demonstrate that polyamines, which have long been used as buffer additives to support ribosome assembly in vitro, are required for 60S maturation in living cells. Perturbation of polyamine metabolism results in early defects in 60S but not 40S subunit maturation. Collectively, our data reveal a novel function for polyamines in living cells and provide a rich source for future studies on ribosome synthesis.
RAD51 protects against nonconservative DNA double-strand break repair through a nonenzymatic function
Authors: So Ayeong , Dardillac Elodie , Muhammad Ali , Chailleux Catherine , Sesma-Sanz Laura , Ragu Sandrine , Le Cam Eric , Canitrot Yvan , Masson Jean Yves , Dupaigne Pauline , Lopez Bernard S , Guirouilh-Barbat Josée
Published: January 2022

Selection of the appropriate DNA double-strand break (DSB) repair pathway is decisive for genetic stability. It is proposed to act according to two steps: 1-canonical nonhomologous end-joining (C-NHEJ) versus resection that generates single-stranded DNA (ssDNA) stretches; 2-on ssDNA, gene conversion (GC) versus nonconservative single-strand annealing (SSA) or alternative end-joining (A-EJ). Here, we addressed the mechanisms by which RAD51 regulates this second step, preventing nonconservative repair in human cells. Silencing RAD51 or BRCA2 stimulated both SSA and A-EJ, but not C-NHEJ, validating the two-step model. Three different RAD51 dominant-negative forms (DN-RAD51s) repressed GC and stimulated SSA/A-EJ. However, a fourth DN-RAD51 repressed SSA/A-EJ, although it efficiently represses GC. In living cells, the three DN-RAD51s that stimulate SSA/A-EJ failed to load efficiently onto damaged chromatin and inhibited the binding of endogenous RAD51, while the fourth DN-RAD51, which inhibits SSA/A-EJ, efficiently loads on damaged chromatin. Therefore, the binding of RAD51 to DNA, rather than its ability to promote GC, is required for SSA/A-EJ inhibition by RAD51. We showed that RAD51 did not limit resection of endonuclease-induced DSBs, but prevented spontaneous and RAD52-induced annealing of complementary ssDNA in vitro. Therefore, RAD51 controls the selection of the DSB repair pathway, protecting genome integrity from nonconservative DSB repair through ssDNA occupancy, independently of the promotion of CG.
Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription
Authors: Minisini Martina , Di Giorgio Eros , Kerschbamer Emanuela , Dalla Emiliano , Faggiani Massimo , Franforte Elisa , Meyer-Almes Franz-Josef , Ragno Rino , Antonini Lorenzo , Mai Antonello , Fiorentino Francesco , Rotili Dante , Chinellato Monica , Perin Stefano , Cendron Laura , Weichenberger Christian X , Angelini Alessandro , Brancolini Claudio
Published: January 2022

In leiomyosarcoma class IIa HDACs (histone deacetylases) bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Disruption of this complex with small molecules should antagonize cancer growth. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, which is used as a docking site by class IIa HDACs. However, NKL54 could also act as HDAC inhibitor (HDACI). Therefore, it is unclear which activity is predominant. Here, we show that NKL54 and similar derivatives are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these molecules as HDACIs strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACIs, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the transcription start site (TSS). Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot outcompete MEF2 from binding to class IIa HDACs, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.
Deuterium magnetic resonance spectroscopy enables noninvasive metabolic imaging of tumor burden and response to therapy in low-grade gliomas
Authors: Taglang Céline , Batsios Georgios , Mukherjee Joydeep , Tran Meryssa , Gillespie Anne Marie , Hong Donghyun , Ronen Sabrina M , Artee Luchman Hema , Pieper Russell O , Viswanath Pavithra
Published: January 2022

Background

The alternative lengthening of telomeres (ALT) pathway is essential for tumor proliferation in astrocytomas. The goal of this study was to identify metabolic alterations linked to the ALT pathway that can be exploited for noninvasive magnetic resonance spectroscopy (MRS)-based imaging of astrocytomas in vivo.

Methods

Genetic and pharmacological methods were used to dissect the association between the ALT pathway and glucose metabolism in genetically engineered and patient-derived astrocytoma models. 2H-MRS was used for noninvasive imaging of ALT-linked modulation of glycolytic flux in mice bearing orthotopic astrocytomas in vivo.

Results

The ALT pathway was associated with higher activity of the rate-limiting glycolytic enzyme phosphofructokinase-1 and concomitantly elevated flux of glucose to lactate in astrocytoma cells. Silencing the ALT pathway or treating with the poly(ADP-ribose) polymerase inhibitor niraparib that induces telomeric fusion in ALT-dependent astrocytoma cells abrogated glycolytic flux. Importantly, this metabolic reprogramming could be non-invasively visualized by 2H-MRS. Lactate production from [6,6′-2H]-glucose was higher in ALT-dependent astrocytoma tumors relative to the normal brain in vivo. Furthermore, treatment of orthotopic astrocytoma-bearing mice with niraparib reduced lactate production from [6,6′-2H]-glucose at early timepoints when alterations in tumor volume could not be detected by anatomical imaging, pointing to the ability of [6,6′-2H]-glucose to report on pseudoprogression in vivo.

Conclusions

We have mechanistically linked the ALT pathway to elevated glycolytic flux and demonstrated the ability of [6,6′-2H]-glucose to non-invasively assess tumor burden and response to therapy in astrocytomas. Our findings point to a novel, clinically translatable method for metabolic imaging of astrocytoma patients.
Predictors of Secondhand Smoke Exposure During Pregnancy in Costa Rica, the Dominican Republic, and Honduras
Authors: Quiñones Zahira , Li Dongmei , McIntosh Scott , Avendaño Esteban , Sánchez José Javier , DiMare-Hering Carmen , Flores-Golfin Daniel , Wang Sijiu , Pérez-Ramos José G , Dye Timothy D V , Ossip Deborah J
Published: January 2022

Introduction

Secondhand smoke (SHS) exposure poses risks to pregnant women and children. Though smoking among pregnant women in many low- and middle-income countries is low, exposure to SHS might be higher. We examined the prevalence and predictors of SHS among pregnant women from Costa Rica, the Dominican Republic, and Honduras.

Methods

Postpartum women 18+ years old who completed pregnancy in past 5 years were surveyed in health care and community settings.

Results

Data for 1,081 women indicated low tobacco use (1.0%–3.7%), frequent exposure to active smokers (29.0%–34.0%), often being close enough to breathe others’ smoke (49.4%–66.5%), and most having smoke-free home policies (70.8%–76.2%). Women reporting unintended pregnancy (adjusted odds ratio [aOR]: 1.44, 95% confidence interval [CI] 1.03, 2.00) and alcohol consumption (aOR: 1.92, 95% CI 1.34, 2.77) were more likely to be close enough to breathe others’ smoke. Women with health problems during pregnancy (aOR: 1.48 95% CI 1.07, 2.06) were more likely to have home smoking policies. Tobacco use was associated with all SHS exposure outcomes.

Conclusions

SHS exposure was high during pregnancy; women with higher risk variables, that is, tobacco use, alcohol consumption, and unintended pregnancy were more likely to be exposed. Addressing SHS exposure in pregnancy in low- and middle-income countries can improve maternal health outcomes in vulnerable populations.

Implications

The study results suggest a cluster of multiple risk factors associated with a high prevalence of exposure to SHS among pregnant women in LIMCs from Latin America and Caribbean Region. Interventions, regulations, and policies need to address specific high-risk factors to change behaviors and improve maternal and child health outcomes especially in vulnerable populations.