bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycorrhization and chemical seed priming boost tomato stress tolerance by changing primary and defence metabolic pathways
Authors: Giovannini Luca , Pagliarani Chiara , Cañizares Eva , Sillo Fabiano , Chitarra Walter , De Rose Silvia , Zampieri Elisa , Ioannou Andreas , Spanos Alexandros , Vita Federico , González-Guzmán Miguel , Fotopoulos Vasileios , Arbona Vicent , Balestrini Raffaella 
Published: November 2024

Abstract
Priming modulates plant stress responses before the stress appears, increasing the ability of the primed plant to endure adverse conditions and thrive. In this context, we investigated the effect of biological (i.e. arbuscular mycorrhizal fungi, AMF) agents and natural compounds (i.e. salicylic acid applied alone or combined with chitosan) against water deficit and salinity on a commercial tomato genotype (cv. Moneymaker). Effects of seed treatments on AMF colonization were evaluated, demonstrating the possibility of using them in combination. Responses to water and salt stresses were analysed on primed plants alone or in combination with the AMF inoculum in soil. Trials were conducted on potted plants by subjecting them to water deficit or salt stress. The effectiveness of chemical seed treatments, both alone and in combination with post-germination AMF inoculation, was investigated using a multidisciplinary approach that included ecophysiology, biochemistry, transcriptomics, and untargeted metabolomics. Results showed that chemical seed treatment and arbuscular mycorrhizal symbiosis modified the tomato response to water deficit and salinity triggering a remodelling of both transcriptome and metabolome, which ultimately elicited the plant antioxidant and osmoprotective machinery. The plant physiological adaptation to both stress conditions improved, confirming the success of the adopted approaches in enhancing stress tolerance.
A New Polyphonic Source from Sixteenth-Century Scotland
Authors: Newton-Jackson Paul , Coney David , Cook James 
Published: November 2024

ABSTRACT
This article discusses a new source of sacred polyphonic music from sixteenth-century Scotland, one which had remained hidden for more than five centuries as marginalia within a printed book. Despite containing only a small amount of music, this source can tell us a great deal about cultures of written and improvised liturgical music in pre-Reformation Scotland, a time and place from which very little notated music survives. The music in this source has no text, title, or attribution. However, we reveal the identity of the music as the tenor part of a faburden on the Office hymn Cultor Dei memento and we determine that it was most likely written down in Aberdeenshire, in the north-east of Scotland. Finally, by analysing the book’s non-musical annotations, we explore a series of likely owners of the book—and what it might have meant to own such an object—during the turbulent period in Scotland from the early sixteenth century to the late seventeenth.
Are all models wrong? Falsifying binary formation models in gravitational-wave astronomy using exceptional events
Authors: Passenger Lachlan , Thrane Eric , Lasky Paul , Payne Ethan , Stevenson Simon , Farr Ben 
Published: November 2024

ABSTRACT
As the catalogue of gravitational-wave transients grows, several entries appear ‘exceptional’ within the population. Tipping the scales with a total mass of $\sim 150 \,{\rm M}_\odot$, GW190521 likely contained black holes in the pair-instability mass gap. The event GW190814, meanwhile, is unusual for its extreme mass ratio and the mass of its secondary component. A growing model-building industry has emerged to provide explanations for such exceptional events, and Bayesian model selection is frequently used to determine the most informative model. However, Bayesian methods can only take us so far. They provide no answer to the question: does our model provide an adequate explanation for exceptional events in the data? If none of the models we are testing provide an adequate explanation, then it is not enough to simply rank our existing models – we need new ones. In this paper, we introduce a method to answer this question with a frequentist p-value. We apply the method to different models that have been suggested to explain the unusually massive event GW190521: hierarchical mergers in active galactic nuclei and globular clusters. We show that some (but not all) of these models provide adequate explanations for exceptionally massive events like GW190521.
Deep drilling in the time domain with DECam – II: characterizing the light curves of candidates in the extragalactic fields
Authors: Graham Melissa L , Rollins Midori , Knop Robert A , Dhawan Suhail , Fonseca Alvarez Gloria , Phillips Christopher A , Nir Guy , Ramey Emily , Nugent Peter E 
Published: November 2024

ABSTRACT
In this second paper on the DECam deep-drilling field (DDF) program, we release 2020 optical $gri$-band light curves for transients and variables in the extragalactic COSMOS and ELAIS fields based on time series observations with a 3-d cadence from semester 2021A through 2023A. In order to demonstrate the wide variety of time domain events detected by the program and encourage others to use the data set, we characterize the sample by presenting a brief analysis of the light-curve parameters such as time span, amplitude, and peak brightness. We also present preliminary light-curve categorizations, and identify potential stellar variables, active galactic nuclei, tidal disruption events, supernovae (SNe) (such as Type Ia, Type IIP, superluminous, and gravitationally lensed SNe), and fast transients. Where relevant, the number of identified transients is compared to the predictions of the original proposal. We also discuss the challenges of analyzing DDF data in the context of the upcoming Vera C. Rubin Observatory and its Legacy Survey of Space and Time, which will include DDFs. Images from the Dark Energy Camera DDF program are available without proprietary period and the light curves presented in this work are publicly available for analysis.
Late-time non-thermal emission from mildly relativistic tidal ejecta of compact objects merger
Authors: Sadeh Gilad 
Published: November 2024

ABSTRACT
Mergers of compact objects [binary neutron stars or neutron star-black hole (NSBH)] with a substantial mass ratio ($q\gt 1.5$) are expected to produce a mildly relativistic ejecta within $\sim 20^\circ$ from the equatorial plane. We present a semi-analytic approach to calculate the expected synchrotron emission observed from various viewing angles, along with the corresponding radio maps, that are produced by a collisionless shock driven by such ejecta into the interstellar medium. This method reproduces well (up to $\sim 30~{{\ \rm per\ cent}}$ deviations) the observed emission produced by 2D numerical calculations of the full relativistic hydrodynamics. We consider a toroidal ejecta with an opening angle of $15^\circ \le \theta _ \text{open}\le 30^\circ$ and broken power-law mass distribution, $M(\gt \gamma \beta)\propto (\gamma \beta)^{-s}$ with $s=s_{\rm KN}$ at $\gamma \beta \lt \gamma _0\beta _0$ and $s=s_{\rm ft}$ at $\gamma \beta \gt \gamma _0\beta _0$ (where $\gamma$ is the Lorentz factor). The parameter values are chosen to characterize merger calculation results – a ‘shallow’ mass distribution, $1\lt s_{\rm KN}\lt 3$, for the bulk of the ejecta (at $\gamma \beta \approx 0.2$), and a steep, $s_{\rm ft}\gt 5$, ‘fast tail’ mass distribution. While the peak flux is dimmer by a factor of $\sim$2–3, and the peak time remains roughly the same (within 20 per cent), for various viewing angles compared to isotropic equivalent ejecta ($\theta _\text{open}=90^\circ$) considered in preceding papers, the radio maps are significantly different from the spherical case. The semi-analytic method can provide information on the ejecta geometry and viewing angle from future radio map observations and, consequently, constrain the ejection mechanism. For NSBH mergers with a significant mass ejection ($\sim 0.1\,{\rm M}_\odot$), this late non-thermal signal can be observed to distances of $\lesssim 200$ Mpc for typical parameter values.
Evolution of Sex-linked Genes and the Role of Pericentromeric Regions in Sex Chromosomes: Insights from Diploid Willows
Authors: Wang Yi , Zhang Ren-Gang , Hörandl Elvira , Zhang Zhi-Xiang , Charlesworth Deborah , He Li 
Published: November 2024

Abstract
The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sex-linkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex linkage.
Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles
Authors: Zhu Chenglong , Li Shengyou , Zhang Daizhen , Zhang Jinjin , Wang Gang , Zhou Botong , Zheng Jiangmin , Xu Wenjie , Wang Zhengfei , Gao Xueli , Liu Qiuning , Xue Tingfeng , Zhang Huabin , Li Chunhui , Ge Baoming , Liu Yuxuan , Qiu Qiang , Zhang Huixian , Huang Jinghui , Tang Boping , Wang Kun 
Published: November 2024

Abstract
Limbs are a defining characteristic of tetrapods, yet numerous taxa, primarily among amphibians and reptiles, have independently lost limbs as an adaptation to new ecological niches. To elucidate the genetic factors contributing to this convergent limb loss, we present a 12 Gb chromosome-level assembly of the Banna caecilian (Ichthyophis bannanicus), a limbless amphibian. Our comparative analysis, which includes the reconstruction of amphibian karyotype evolution, reveals constrained gene length evolution in a subset of developmental genes across 3 large genomes. Investigation of limb development genes uncovered the loss of Grem1 in caecilians and Tulp3 in snakes. Interestingly, caecilians and snakes share a significantly larger number of convergent degenerated conserved noncoding elements than limbless lizards, which have a shorter evolutionary history of limb loss. These convergent degenerated conserved noncoding elements overlap significantly with active genomic regions during mouse limb development and are conserved in limbed species, suggesting their essential role in limb patterning in the tetrapod common ancestor. While most convergent degenerated conserved noncoding elements emerged in the jawed vertebrate ancestor, coinciding with the origin of paired appendage, more recent degenerated conserved noncoding elements also contribute to limb development, as demonstrated through functional experiments. Our study provides novel insights into the regulatory elements associated with limb development and loss, offering an evolutionary perspective on the genetic basis of morphological specialization.
Diversity of Transcriptional Regulatory Adaptation in E. coli
Authors: Dalldorf Christopher , Hefner Ying , Szubin Richard , Johnsen Josefin , Mohamed Elsayed , Li Gaoyuan , Krishnan Jayanth , Feist Adam M , Palsson Bernhard O , Zielinski Daniel C 
Published: November 2024

Abstract
The transcriptional regulatory network (TRN) in bacteria is thought to rapidly evolve in response to selection pressures, modulating transcription factor (TF) activities and interactions. In order to probe the limits and mechanisms surrounding the short-term adaptability of the TRN, we generated, evolved, and characterized knockout (KO) strains in Escherichia coli for 11 regulators selected based on measured growth impact on glucose minimal media. All but one knockout strain (Δlrp) were able to recover growth and did so requiring few convergent mutations. We found that the TF knockout adaptations could be divided into four categories: (i) Strains (ΔargR, ΔbasR, Δlon, ΔzntR, and Δzur) that recovered growth without any regulator-specific adaptations, likely due to minimal activity of the regulator on the growth condition, (ii) Strains (ΔcytR, ΔmlrA, and ΔybaO) that recovered growth without TF-specific mutations but with differential expression of regulators with overlapping regulons to the KO’ed TF, (iii) Strains (Δcrp and Δfur) that recovered growth using convergent mutations within their regulatory networks, including regulated promoters and connected regulators, and (iv) Strains (Δlrp) that were unable to fully recover growth, seemingly due to the broad connectivity of the TF within the TRN. Analyzing growth capabilities in evolved and unevolved strains indicated that growth adaptation can restore fitness to diverse substrates often despite a lack of TF-specific mutations. This work reveals the breadth of TRN adaptive mechanisms and suggests these mechanisms can be anticipated based on the network and functional context of the perturbed TFs.
WD-repeat containing protein-61 regulates endometrial epithelial cell adhesion indicating an important role in receptivity
Authors: Downing Poppy , Howe Madeleine , Sacco Michaela , Santos Leilani L , Menkhorst Ellen , Teh Wan Tinn , Lucky Tarana , Zhou Wei , Dimitriadis Evdokia 
Published: November 2024

Abstract
Endometrial receptivity is crucial for successful embryo implantation during early pregnancy. The human endometrium undergoes remodeling within each menstrual cycle to prepare or become receptive to an implanting blastocyst in the mid-secretory phase. However, the mechanisms behind these changes are not fully understood. Recently, using hormone-treated endometrial organoids to model receptivity, we identified that the transcriptional regulator WD-repeat-containing protein-61 (WDR61) was reduced in organoids derived from infertile women. In this study, we aimed to determine the role of WDR61 in endometrial receptivity. Here, we demonstrated that WDR61 immunolocalizes in the nuclei and cytosol of endometrial glandular epithelium, luminal epithelium, and stroma. The staining intensity of WDR61 was significantly higher during the receptive mid-secretory phase compared to the non-receptive proliferative phase in fertile women. In a functional experiment to model blastocyst adhesion to the endometrial epithelium, we found that adhesion of cytotrophoblast progenitor spheroids was blocked when siRNA was used to knockdown WDR61 in primary endometrial epithelial cells. Similarly, in Ishikawa cells (a receptive human endometrial epithelial cell line), siRNA knockdown of WDR61 significantly reduced the cell adhesive and proliferative capacities. qPCR revealed that WDR61 knockdown reduced expression of key genes involved in receptivity including HOXD10, MMP2, and CD44. Chromatin immunoprecipitation sequencing demonstrated that WDR61 directly targeted 2022 genes in Ishikawa cells, with functions including focal adhesion, intracellular signaling and epithelial-mesenchymal transition. Overall, these findings suggest that WDR61 promotes endometrial receptivity by modulating epithelial cell focal adhesions, proliferation, and epithelial–mesenchymal transition.
ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures
Authors: Yang Yuntao , Kumar Himansu , Xie Yuhan , Li Zhao , Li Rongbin , Chen Wenbo , Diala Chiamaka S , Ali Meer A , Xu Yi , Wu Albon , Hosseini Sayed-Rzgar , Bi Erfei , Zhao Hongyu , Kim Pora , Zheng W Jim 
Published: November 2024

Abstract
Alternative splicing is a crucial cellular process in eukaryotes, enabling the generation of multiple protein isoforms with diverse functions from a single gene. To better understand the impact of alternative splicing on protein structures, protein–protein interaction and human diseases, we developed ASpdb (https://biodataai.uth.edu/ASpdb/), a comprehensive database integrating experimentally determined structures and AlphaFold 2-predicted models for human protein isoforms. ASpdb includes over 3400 canonical isoforms, each represented by both experimentally resolved and predicted structures, and &gt;7200 alternative isoforms with AlphaFold 2 predictions. In addition to detailed splicing events, 3D structures, sequence variations and functional annotations, ASpdb uniquely offers comparative analyses and visualization of structural alterations among isoforms. This resource is invaluable for advancing research in alternative splicing, structural biology and disease mechanisms.
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species
Authors: Liu Fuyun , Cai Bingcheng , Lian Shanshan , Chang Xinyao , Chen Dongsheng , Pu Zhongqi , Bao Lisui , Wang Jing , Lv Jia , Zheng Hongkun , Bao Zhenmin , Zhang Lingling , Wang Shi , Li Yuli 
Published: November 2024

Abstract
Mollusca represents the second-largest animal phylum but remains less explored genomically. The increase in high-quality genomes and diverse functional genomic data holds great promise for advancing our understanding of molluscan biology and evolution. To address the opportunities and challenges facing the molluscan research community in managing vast multi-omics resources, we developed MolluscDB 2.0 (http://mgbase.qnlm.ac), which integrates extensive functional genomic data and offers user-friendly tools for multilevel integrative and comparative analyses. MolluscDB 2.0 covers 1450 species across all eight molluscan classes and compiles ∼4200 datasets, making it the most comprehensive multi-omics resource for molluscs to date. MolluscDB 2.0 expands the layers of multi-omics data, including genomes, bulk transcriptomes, single-cell transcriptomes, proteomes, epigenomes and metagenomes. MolluscDB 2.0 also more than doubles the number of functional modules and analytical tools, updating 14 original modules and introducing 20 new, specialized modules. Overall, MolluscDB 2.0 provides highly valuable, open-access multi-omics platform for the molluscan research community, expediting scientific discoveries and deepening our understanding of molluscan biology and evolution.
CRISPRepi: a multi-omic atlas for CRISPR-based epigenome editing
Authors: Shi Leisheng , Li Shasha , Zhu Rongyi , Lu Chenyang , Xu Xintian , Li Changzhi , Huang Xinyue , Zhao Xiaolu , Mao Fengbiao , Li Kailong 
Published: November 2024

Abstract
CRISPR-based epigenome editing integrates the precision of CRISPR with the capability of epigenetic mark rewriting, offering a tunable and reversible gene regulation strategy without altering the DNA sequences. Various epigenome editing systems have been developed and applied in different organisms and cell types; however, the detailed information is discrete, making it challenging to evaluate the precision of different editing systems and design the optimal sgRNAs for further functional studies. Herein, we developed CRISPRepi (http://crisprepi.maolab.org/ or http://crisprepi.lilab-pkuhsc.org/), a pioneering platform that consolidates extensive sequencing data from 671 meticulously curated RNA-seq, ChIP-seq, Bisulfite-seq and ATAC-seq datasets in 87 cell types manipulated by 74 epigenome editing systems. In total, we have curated 5962 sgRNAs associated with 283 target genes from 2277 samples across six species. CRISPRepi incorporates tools for analyzing editing outcomes and assessing off-target effects by analyzing gene expression changes pre- and post-editing, along with the details of multi-omic epigenetic landscapes. Moreover, CRISPRepi supports the investigation of editing potentials for newly designed sgRNA sequences in a cell/tissue-specific context. By providing a user-friendly interface for searching and selecting optimal editing designs across multiple organisms, CRISPRepi serves as an integrated resource for researchers to evaluate editing efficiency and off-target effects among diverse CRISPR-based epigenome editing systems.
PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data
Authors: Moon Youngbin , Herrmann Christina J , Mironov Aleksei , Zavolan Mihaela 
Published: November 2024

Abstract
The broadly used 10X Genomics technology for single-cell RNA sequencing (scRNA-seq) captures RNA 3′ ends. Thus, some reads contain part of the non-templated polyadenosine tails, providing direct evidence for the sites of 3′ end cleavage and polyadenylation on the respective RNAs. Taking advantage of this property, we recently developed the SCINPAS workflow to infer polyadenylation sites (PASs) from scRNA-seq data. Here, we used this workflow to construct version 3.0 (v3.0, https://polyasite.unibas.ch/) of the PolyASite Atlas from a big compendium of publicly available human, mouse and worm scRNA-seq datasets obtained from healthy tissues. As the resolution of scRNA-seq was too low for robust detection of cell-level differences in PAS usage, we aggregated samples based on their tissue-of-origin to construct tissue-level catalogs of PASs. These provide qualitatively new information about PAS usage, in comparison to the previous PAS catalogs that were based on bulk 3′ end sequencing experiments primarily in cell lines. In the new version, we document stringency levels associated with each PAS so that users can balance sensitivity and specificity in their analysis. We also upgraded the integration with the UCSC Genome Browser and developed track hubs conveniently displaying pooled and tissue-specific expression of PASs.
TranscriptDB: a transcript-centric database to study eukaryotic transcript conservation and evolution
Authors: Ouedraogo Wend Yam D D , Ouangraoua Aida 
Published: November 2024

Abstract
Eukaryotic genes can encode multiple distinct transcripts through the alternative splicing (AS) of genes. Interest in the AS mechanism and its evolution across different species has stimulated numerous studies, leading to several databases that provide information on AS and transcriptome data across multiple eukaryotic species. However, existing resources do not offer information on transcript conservation and evolution between genes of multiple species. Similarly to genes, identifying conserved transcripts—those from homologous genes that have retained a similar exon composition—is useful for determining transcript homology relationships, studying transcript functions and reconstructing transcript phylogenies. To address this gap, we have developed TranscriptDB, a database dedicated to studying the conservation and evolution of transcripts within gene families. TranscriptDB offers an extensive catalog of conserved transcripts and phylogenies for 317 annotated eukaryotic species, sourced from Ensembl database version 111. It serves multiple purposes, including the exploration of gene and transcript evolution. Users can access TranscriptDB through various browsing and querying tools, including a user-friendly web interface. The incorporated web servers enable users to retrieve information on transcript evolution using their own data as input. Additionally, a REST application programming interface is available for programmatic data retrieval. A data directory is also available for bulk downloads. TranscriptDB and its resources are freely accessible at https://transcriptdb.cobius.usherbrooke.ca.