bluuebunny/crossref_metadata_2025_split huggingface dataset:
Populus D-type cyclin gene PsnCYCD1;1 accelerates cell division and participates in secondary growth of vascular bundles
Authors: Zheng Tangchun , Dai Lijuan , Li Shuang , Liu Yi , Zhao Zhongnan , Yang Chuanping , Qu Guanzheng 
Published: April 2023

Abstract
Plant growth and development rely heavily on cyclins, which comprise an important class of cell division regulators. D-type cyclins (CYCDs) are responsible for the rate-limiting step of G1 cells. In the plant kingdom, despite the importance of CYCDs in herbaceous plants, there is little knowledge of these proteins in perennial woody plants. Here, the gene of a nucleus-localized cyclin, PsnCYCD1;1, was cloned from Populus simonii × P. nigra. PsnCYCD1;1 was highly expressed in tissues with active cell division, especially the leaf buds, and could be induced by sucrose and phytohormones. Moreover, overexpression of PsnCYCD1;1 in poplar could stimulate cell division, resulting in the generation of small cells and causing severe morphological changes in the vascular bundles, resulting in ‘S’-shaped tortuous stems and curled leaves. Furthermore, transcriptomic analysis revealed that endogenous genes related to cell division and vascular cambium development were significantly up-regulated in the transgenic plants. In addition, using yeast two-hybrid and bimolecular fluorescence complementation assays PsnCDKA1, PsnICK3, and PsnICK5 were identified as proteins interacting with PsnCYCD1;1. Our study demonstrates that PsnCYCD1;1 accelerates plant cell division and participates in secondary growth of vascular bundles in poplar.
grgadget: an N-body TreePM relativistic code for cosmological simulations
Authors: Quintana-Miranda Eduardo , Monaco Pierluigi , Tornatore Luca 
Published: April 2023

ABSTRACT
We present the merging of the Particle-Mesh (PM) relativistic gevolution code with the TreePM gadget-4 code, with the aim of studying general relativity effects in cosmology. Our code, called grgadget, is able to track the evolution of metric perturbations in the weak field limit by using gevolution’s implementation of a relativistic PM in the Poisson gauge. To achieve this, starting from gevolution, we have written a c++ library called libgevolution, which allows a code to access and use the same abstractions and resources that gevolution uses for its PM-only N-body simulations. The code works under the assumption that particle interactions at short distances can be approximated as Newtonian, so that we can combine the forces computed with a Newtonian Tree with those computed with a relativistic PM. The result is a TreePM simulation code that represents metric perturbations at the scales where they are relevant while resolving non-linear structures. We validate our code by closely matching gadget-4 forces, computed with the Tree switched off, with those computed with libgevolution in the Newtonian limit. With grgadget, we obtain a matter power spectrum that is compatible with Newtonian gadget-4 at small scales and contains GR features at large scales that are consistent with results obtained with gevolution. We demonstrate that, due to the better resolution of the highly non-linear regime, the representation of the relativistic fields sampled on the mesh improves with respect to the PM-only simulations.
Polycyclic aromatic hydrocarbon emission model in photodissociation regions – II. Application to the polycyclic aromatic hydrocarbon and fullerene emission in NGC 7023
Authors: Sidhu Ameek , Tielens A G G M , Peeters Els , Cami Jan 
Published: April 2023

ABSTRACT
We present a charge distribution-based emission model that calculates the infrared spectrum of fullerenes (C60). Analysis of the modelled spectrum of C60 in various charge states shows that the relative intensity of the features in the 5–10 μm versus 15–20 μm can be used to probe the C60 charge state in interstellar spectra. We further used our model to simulate emission from polycyclic aromatic hydrocarbons (PAHs) and C60 at five positions in the cavity of reflection nebula NGC 7023. Specifically, we modelled the 6.2/11.2 band ratio for circumcoronene and circumcircumcoronene and the 7.0/19.0 band ratio for C60 as a function of the ionization parameter γ. A comparison of the model results with the observed band ratios shows that the γ values in the cavity do not vary significantly, suggesting that the emission in the cavity does not originate from locations at the projected distances. Furthermore, we find that the C60-derived γ values are lower than the PAH-derived values by an order of magnitude. We discuss likely scenarios for this discrepancy. In one scenario, we attribute the differences in the derived γ values to the uncertainties in the electron recombination rates of PAHs and C60. In the other scenario, we suggest that PAHs and C60 are not co-spatial resulting in different γ values from their respective models. We highlight that experiments to determine necessary rates will be required in validating either one of the scenarios.
Influence of the substrate on the density and infrared spectra of the adsorbed methanol ice of different thicknesses using molecular dynamics simulation
Authors: Nag Shubhadeep , Majumdar Jeet , Sivaraman Bhalamurugan , Yashonath Subramanian , Maiti Prabal K 
Published: April 2023

ABSTRACT
In the interstellar medium, several complex organic molecules are found, and of these molecules, methanol is the simplest and the most ubiquitous one. By comparing the observed infrared (IR) spectra from astrochemical data, with laboratory experiments, one can deduce the composition and structure of these astrochemical ices. Computational studies are scarce, yet they could be greatly helpful in understanding the nature of these molecules. On that premise, the present study reports a molecular dynamics study of adsorbed methanol on the KBr substrate at 90 K and 130 K. After validating the potential parameters, two adsorbed phases differing in their thickness along the z-axis: 4 × 10 × 4 (4 layers) and 4 × 10 × 50 (50 layers) were simulated. Depending on this thickness, the IR spectra and density distribution functions were computed for the bottom and top 10 Å of the 4 layers of adsorbed methanol and the top, middle, and bottom 10 Å of the 50 layers of adsorbed methanol on the KBr substrate. The bottom 10 Å of the adsorbed phase exhibit considerable disorder. Additionally, the bands in the IR spectra of these bottom 10 Å show widening, referring to a heterogeneous environment. It is further reported that the slower heating and cooling of the adsorbed phase between 90 K and 130 K leads to a complete reversal of the changes seen in heating. Our findings here further clarify the recent observation of the amorphous phase of different astrochemical molecules seen at low temperatures and their crystalline phase seen at relatively higher temperatures.
Exotic baryons in hot neutron stars
Authors: Issifu A , Marquez K D , Pelicer M R , Menezes D P 
Published: April 2023

ABSTRACT
We study the nuclear isentropic equation of state for a stellar matter composed of nucleons, hyperons, and Δ-resonances. We investigate different snapshots of the evolution of a neutron star, from its birth as a lepton-rich proto-neutron star in the aftermath of a supernova explosion to a lepton-poor regime when the star starts cooling to a catalysed configuration. We use a relativistic model within the mean-field approximation to describe the hot stellar matter and adopt density-dependent couplings adjusted by the DDME2 parameterization. We use baryon–meson couplings for the spin-1/2 baryonic octet and spin-3/2 decuplet determined in a unified manner relying on SU(6) and SU(3) symmetry arguments. We observe that Λ is the dominant exotic particle in the star at different entropies for both neutrino-free and neutrino-trapped stellar matter. For a fixed entropy, the inclusion of new particles (hyperons and/or delta resonances) in the stellar matter decreases the temperature. Also, an increase in entropy per baryon (1–2) with decreasing lepton number density (0.4–0.2) leads to an increase in stellar radii and a decrease in its mass due to neutrino diffusion. In the neutrino transparent matter, the radii decrease from entropy per baryon 2 to $T\, =\, 0$ without a significant change in stellar mass.
A needle in a haystack? Catching Population III stars in the epoch of reionization: I. Population III star-forming environments
Authors: Venditti Alessandra , Graziani Luca , Schneider Raffaella , Pentericci Laura , Di Cesare Claudia , Maio Umberto , Omukai Kazuyuki 
Published: April 2023

ABSTRACT
Despite extensive search efforts, direct observations of the first [Population III (Pop III)] stars have not yet succeeded. Theoretical studies have suggested that late Pop III star formation is still possible in pristine clouds of high-mass galaxies, co-existing with Pop II stars, down to the epoch of reionization. Here, we re-assess this finding by exploring Pop III star formation in six 50 h−1 cMpc simulations performed with the hydrodynamical code dustyGadget. We find that Pop III star formation (∼10−3.4–10−3.2 M⊙ yr−1 cMpc−3) is still occurring down to z ∼ 6–8, i.e. well within the reach of deep JWST surveys. At these epochs, $\gtrsim\!{10}~{{\ \rm per\ cent}}$ of the rare massive galaxies with M⋆ ≳ 3 × 109 M⊙ are found to host Pop III stars, although with a Pop III/Pop II mass fraction $\lesssim\!0.1~{{\ \rm per\ cent}}$ . Regardless of their mass, Pop III-hosting galaxies are mainly found on the main sequence, at high star-formation rates, probably induced by accretion of pristine gas. This scenario is also supported by their increasing star-formation histories and their preferential location in high-density regions of the cosmic web. Pop III stars are found both in the outskirts of metal-enriched regions and in isolated, pristine clouds. In the latter case, their signal may be less contaminated by Pop IIs, although its detectability will strongly depend on the specific line of sight to the source, due to the complex morphology of the host galaxy and its highly inhomogeneous dust distribution.
On the hosts of neutron star mergers in the nearby Universe
Authors: Cavallo L , Greggio L 
Published: April 2023

ABSTRACT
Recently, the characterization of binary systems of neutron stars has become central in various fields such as gravitational waves, gamma-ray bursts (GRBs), and the chemical evolution of galaxies. In this work, we explore possible observational proxies that can be used to infer some characteristics of the delay time distribution (DTD) of neutron star mergers (NSMs). We construct a sample of model galaxies that fulfils the observed galaxy stellar mass function, star formation rate versus mass relation, and the cosmic star formation rate density. The star formation history of galaxies is described with a log-normal function characterized by two parameters: the position of the maximum and the width of the distribution. We assume a theoretical DTD that mainly depends on the lower limit and the slope of the distribution of the separations of the binary neutron star systems at birth. We find that the current rate of NSMs ($\mathcal {R}=320^{+490}_{-240}$ Gpc−3 yr−1) requires that ∼0.3 per cent of neutron star progenitors lives in binary systems with the right characteristics to lead to an NSM within a Hubble time. We explore the expected relations between the rate of NSMs and the properties of the host galaxy. We find that the most effective proxy for the shape of the DTD of NSMs is the current star formation activity of the typical host. At present, the fraction of short-GRBs observed in star-forming galaxies favours DTDs with at least ${\sim}40~{{\ \rm per\ cent}}$ of mergers within 100 Myr. This conclusion will be put on a stronger basis with larger samples of short-GRBs with host association (e.g. 600 events at z ≤ 1).
Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo
Authors: Lisitskaya Lidiya , Kropocheva Ekaterina , Agapov Aleksei , Prostova Maria , Panteleev Vladimir , Yudin Denis , Ryazansky Sergei , Kuzmenko Anton , Aravin Alexei A , Esyunina Daria , Kulbachinskiy Andrey 
Published: April 2023

Abstract
Prokaryotic Argonaute proteins (pAgos) are homologs of eukaryotic Argonautes (eAgos) and are also thought to play a role in cell defense against invaders. However, pAgos are much more diverse than eAgos and little is known about their functional activities and target specificities in vivo. Here, we describe five pAgos from mesophilic bacteria that act as programmable DNA endonucleases and analyze their ability to target chromosomal and invader DNA. In vitro, the analyzed proteins use small guide DNAs for precise cleavage of single-stranded DNA at a wide range of temperatures. Upon their expression in Escherichia coli, all five pAgos are loaded with small DNAs preferentially produced from plasmids and chromosomal regions of replication termination. One of the tested pAgos, EmaAgo from Exiguobacterium marinum, can induce DNA interference between homologous sequences resulting in targeted processing of multicopy plasmid and genomic elements. EmaAgo also protects bacteria from bacteriophage infection, by loading phage-derived guide DNAs and decreasing phage DNA content and phage titers. Thus, the ability of pAgos to target multicopy elements may be crucial for their protective function. The wide spectrum of pAgo activities suggests that they may have diverse functions in vivo and paves the way for their use in biotechnology.
DNA strand asymmetry generated by CpG hemimethylation has opposing effects on CTCF binding
Authors: Thomas Stacey L , Xu Ting-Hai , Carpenter Brittany L , Pierce Steven E , Dickson Bradley M , Liu Minmin , Liang Gangning , Jones Peter A 
Published: April 2023

Abstract
CpG methylation generally occurs on both DNA strands and is essential for mammalian development and differentiation. Until recently, hemimethylation, in which only one strand is methylated, was considered to be simply a transitory state generated during DNA synthesis. The discovery that a subset of CCCTC-binding factor (CTCF) binding sites is heritably hemimethylated suggests that hemimethylation might have an unknown biological function. Here we show that the binding of CTCF is profoundly altered by which DNA strand is methylated and by the specific CTCF binding motif. CpG methylation on the motif strand can inhibit CTCF binding by up to 7-fold, whereas methylation on the opposite strand can stimulate binding by up to 4-fold. Thus, hemimethylation can alter binding by up to 28-fold in a strand-specific manner. The mechanism for sensing methylation on the opposite strand requires two critical residues, V454 and S364, within CTCF zinc fingers 7 and 4. Similar to methylation, CpG hydroxymethylation on the motif strand can inhibit CTCF binding by up to 4-fold. However, hydroxymethylation on the opposite strand removes the stimulatory effect. Strand-specific methylation states may therefore provide a mechanism to explain the transient and dynamic nature of CTCF-mediated chromatin interactions.
Phase-separated DropCRISPRa platform for efficient gene activation in mammalian cells and mice
Authors: Ma Shufeng , Liao Kaitong , Li Mengrao , Wang Xinlong , Lv Jie , Zhang Xin , Huang Hongxin , Li Lian , Huang Tao , Guo Xiaohua , Lin Ying , Rong Zhili 
Published: April 2023

Abstract
Liquid–liquid phase separation (LLPS) plays a critical role in regulating gene transcription via the formation of transcriptional condensates. However, LLPS has not been reported to be engineered as a tool to activate endogenous gene expression in mammalian cells or in vivo. Here, we developed a droplet-forming CRISPR (clustered regularly interspaced short palindromic repeats) gene activation system (DropCRISPRa) to activate transcription with high efficiency via combining the CRISPR-SunTag system with FETIDR–AD fusion proteins, which contain an N-terminal intrinsically disordered region (IDR) of a FET protein (FUS or TAF15) and a transcription activation domain (AD, VP64/P65/VPR). In this system, the FETIDR–AD fusion protein formed phase separation condensates at the target sites, which could recruit endogenous BRD4 and RNA polymerase II with an S2 phosphorylated C-terminal domain (CTD) to enhance transcription elongation. IDR-FUS9Y&gt;S and IDR-FUSG156E, two mutants with deficient and aberrant phase separation respectively, confirmed that appropriate phase separation was required for efficient gene activation. Further, the DropCRISPRa system was compatible with a broad set of CRISPR-associated (Cas) proteins and ADs, including dLbCas12a, dAsCas12a, dSpCas9 and the miniature dUnCas12f1, and VP64, P65 and VPR. Finally, the DropCRISPRa system could activate target genes in mice. Therefore, this study provides a robust tool to activate gene expression for foundational research and potential therapeutics.
RNAcanvas: interactive drawing and exploration of nucleic acid structures
Authors: Johnson Philip Z , Simon Anne E 
Published: April 2023

Abstract
Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher's own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app.
Macroprudential policy implementation in a heterogeneous monetary union
Authors: Rubio Margarita 
Published: April 2023

Abstract
In this article, I develop a two-country new Keynesian general equilibrium model with housing and collateral constraints to explore how macroprudential policies should be conducted in a heterogeneous monetary union. I consider several types of cross-country heterogeneity: asymmetric shocks, different leveraged countries, and mortgage contract heterogeneity (fixed and variable rates). As a macroprudential tool, I propose a Taylor-type rule for the loan-to-value ratio, which responds to deviations in output and house prices. This policy can be applied at a national or union level. Results show that structural asymmetries matter for the implementation of macroprudential policies, especially when the heterogeneity delivers differences in economic and financial volatilities. It seems then adequate to delegate macroprudential policies to national authorities. However, a supranational institution could also help stabilize the whole union when there are asymmetric shocks.
Lineage diversity in a widely distributed New World passerine bird, the House Wren
Authors: Klicka John , Epperly Kevin , Smith Brian Tilston , Spellman Garth M , Chaves Jaime A , Escalante Patricia , Witt Christopher C , Canales-del-Castillo Ricardo , Zink Robert M 
Published: April 2023

Abstract
We explored the evolutionary radiation in the House Wren complex (Troglodytes aedon and allies), the New World’s most widely distributed passerine species. The complex has been the source of ongoing taxonomic debate. To evaluate phenotypic variation in the House Wren complex, we collected 81,182 single-nucleotide polymorphisms (SNPs) from restriction site associated loci (RADseq) and mitochondrial DNA (mtDNA) from samples representing the taxonomic and geographic diversity of the complex. Both datasets reveal deep phylogeographic structuring, with several topological discrepancies. The trees highlight the evolutionary distinctiveness of eastern and western T. aedon, which were sister taxa in the SNP tree and paraphyletic on the mtDNA tree. The RADseq data reveal a distinct T. a. brunneicollis group, although STRUCTURE plots suggest admixture between western T. aedon and northern Mexican samples of T. a. brunneicollis. MtDNA data show a paraphyletic arrangement of T. a. musculus on the tree, whereas the SNP tree portrays them as monophyletic. Island taxa are distinct in both datasets, including T. a. beani (Isla Cozumel), which appears derived from T. a. musculus in eastern Mexico, and T. sissonii (Isla Socorro) and T. tanneri (Isla Clarión) although the 2 datasets disagree on their overall phylogenetic placement. Although we had only mtDNA data for T. a. martinicensis from the Lesser Antilles, we found at least 4 distinct and paraphyletic taxa from Trinidad, Granada, St. Vincent islands, and Dominica. The House Wren complex showed strong differentiation in mtDNA and RADseq datasets, with conflicting patterns likely arising from some combination of sex-biased dispersal, incomplete lineage sorting, or selection on mtDNA. The most glaring discrepancies between these 2 datasets, such as the paraphyly of eastern and western North American House Wrens in the mtDNA tree, present excellent opportunities for follow-up studies on evolutionary mechanisms that underpin phylogeographic patterns.
A multifunctional true caffeoyl coenzyme A O-methyltransferase enzyme participates in the biosynthesis of polymethoxylated flavones in citrus
Authors: Liao Zhenkun , Liu Xiaojuan , Zheng Juan , Zhao Chenning , Wang Dengliang , Xu Yang , Sun Chongde 
Published: April 2023

Abstract
Polymethoxylated flavones (PMFs) have received extensive attention due to their abundant bioactivities. Citrus peels specifically accumulate abundant PMFs, and methylation modification is a key step in PMF biosynthesis; however, the function of reported O-methyltransferase (OMT) in citrus is insufficient to elucidate the complete methylation process of PMFs. In this study, we analyzed the accumulation pattern of PMFs in the flavedo of the sweet orange (Citrus sinensis) cultivar “Bingtangcheng” at different developmental stages. We found that accumulation of PMFs was completed at the early stage of fruit development (60-d after flowering). Furthermore, we characterized a true caffeoyl-CoA O-methyltransferase (named CsCCoAOMT1) from C. sinensis. Functional analysis in vitro showed that CsCCoAOMT1 preferred flavonoids to caffeoyl-CoA and esculetin. This enzyme efficiently methylated the 6-, 7- 8-, and 3′-OH of a wide array of flavonoids with vicinal hydroxyl groups with a strong preference for quercetin (flavonol) and flavones. The transient overexpression and virus-induced gene silencing experiments verified that CsCCoAOMT1 could promote the accumulation of PMFs in citrus. These results reveal the function of true CCoAOMTs and indicate that CsCCoAOMT1 is a highly efficient multifunctional O-methyltransferase involved in the biosynthesis of PMFs in citrus.