bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus
Authors: Souza-Borges Carolina Heloisa , Utsunomia Ricardo , Varani Alessandro M , Uliano-Silva Marcela , Lira Lieschen Valeria G , Butzge Arno J , Gomez Agudelo John F , Manso Shisley , Freitas Milena V , Ariede Raquel B , Mastrochirico-Filho Vito A , Penaloza Carolina , Barria Agustín , Porto-Foresti Fábio , Foresti Fausto , Hattori Ricardo , Guiguen Yann , Houston Ross D , Hashimoto Diogo Teruo 
Published: November 2024

Abstract

Background
Megaleporinus macrocephalus (piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex determination system and thus constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool sequencing of males and females to characterize its sex system, and RNA sequencing to highlight candidate genes of M. macrocephalus sex determination.

Results
The reference genome of M. macrocephalus is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. In the sex chromosome, based on patterns of recombination suppression, coverage, FST, and sex-specific SNPs, we distinguished a putative W-specific region that is highly differentiated, a region where Z and W still share some similarities and is undergoing degeneration, and the PAR. The sex chromosome gene repertoire includes genes from the TGF-β family (amhr2, bmp7) and the Wnt/β-catenin pathway (wnt4, wnt7a), some of which are differentially expressed.

Conclusions
The chromosome-level genome of piauçu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.
Successful collaborative trials of simple gear modifications to reduce entanglement of whales and other megafauna in Scotland’s static pot (creel) fisheries
Authors: Calderan Susannah , Cisternino Bianca , De Noia Michele , Leaper Russell , MacLennan Ellie , Philp Bally 
Published: November 2024

Abstract
Entanglement in ropes associated with static fishing gear (pots/traps/creels) is a welfare and conservation concern for minke whales (Balaenoptera acutorostrata), humpback whales (Megaptera novaeangliae), basking sharks (Cetorhinus maximus), and other megafauna in Scottish waters. The Scottish Entanglement Alliance estimated that six humpback whales and 30 minke whales become entangled annually. Where entanglement type was known, 83% of minke whales, 50% of humpback whales, and 76% of basking sharks were caught in floating groundlines between pots. We collaborated with fishers on Scotland’s west coast to trial sinking groundline (which lies on the seabed) to assess its practicality. A total of 15 Nephrops (langoustine) and crab fishers re-roped 61 sets of creel gear and fished the gear for ∼15 months, reporting on each haul. Over 1500 hauls were reported; the fishers encountered few problems, in some cases preferring the modified gear. We also deployed depth sensors/accelerometers and filmed a range of sinking and floating rope configurations with a Remotely Operated Vehicle (ROV) to collect data on performance underwater. This project is encouraging, both because of its results—that there may be a simple option to greatly reduce entanglement risk—and because of the successful, bottom-up, partnership approach with Scottish creel fishers.
The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species
Authors: DuBose James G , Crook Thomas Blake , Matzkin Luciano M , Haselkorn Tamara S 
Published: November 2024

Abstract
Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host–microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.
COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database
Authors: Chandrasekhar Venkata , Rajan Kohulan , Kanakam Sri Ram Sagar , Sharma Nisha , Weißenborn Viktor , Schaub Jonas , Steinbeck Christoph 
Published: November 2024

Abstract
The COCONUT (COlleCtion of Open Natural prodUcTs) database was launched in 2021 as an aggregation of openly available natural product datasets and has been one of the biggest open natural product databases since. Apart from the chemical structures of natural products, COCONUT contains information about names and synonyms, species and organism parts in which the natural product has been found, geographic information about where the respective sample has been collected and literature references, where available. COCONUT is openly accessible at https://coconut.naturalproducts.net. Users can search textual information and perform structure, substructure, and similarity searches. The data in COCONUT are available for bulk download as SDF, CSV and a database dump. The web application for accessing the data is open-source. Here, we describe COCONUT 2.0, for which the web application has been completely rewritten, and the data have been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways.
Phosphorylation-mediated disassembly of C-terminal binding protein 2 tetramer impedes epigenetic silencing of pluripotency in mouse embryonic stem cells
Authors: Lee Han-Teo , Kim Young Ah , Lee Sangho , Jung Ye-Eun , Kim Hanbyeol , Kim Tae Wan , Kwak Sojung , Kim Jaehyeon , Lee Chul-Hwan , Cha Sun-Shin , Choi Jinmi , Cho Eun-Jung , Youn Hong-Duk 
Published: November 2024

Abstract
Cells need to overcome both intrinsic and extrinsic threats. Although pluripotency is associated with damage responses, how stem cells respond to DNA damage remains controversial. Here, we elucidate that DNA damage activates Chk2, leading to the phosphorylation of serine 164 on C-terminal binding protein 2 (Ctbp2). The phosphorylation of Ctbp2 induces the disruption of Ctbp2 tetramer, weakening interactions with zinc finger proteins, leading to the dissociation of phosphorylated Ctbp2 from chromatin. This transition to a monomeric state results in the separation of histone deacetylase 1 from Ctbp2, consequently slowing the rate of H3K27 deacetylation. In contrast to the nucleosome remodeling and deacetylase complex, phosphorylated Ctbp2 increased binding affinity to polycomb repressive complex (PRC)2, interacting through the N-terminal domain of Suz12. Through this domain, Ctbp2 competes with Jarid2, inhibiting the function of PRC2. Thus, the phosphorylation of Ctbp2 under stress conditions represents a precise mechanism aimed at preserving stemness traits by inhibiting permanent transcriptional shutdown.
The Natural Products Atlas 3.0: extending the database of microbially derived natural products
Authors: Poynton Ella F , van Santen Jeffrey A , Pin Matthew , Contreras Marla Macias , McMann Emily , Parra Jonathan , Showalter Brandon , Zaroubi Liana , Duncan Katherine R , Linington Roger G 
Published: November 2024

Abstract
The Natural Products Atlas is a database of microbially derived natural products that contains structures, producing organism taxonomy, biosynthetic and chemical ontology classifications, grouping by compound classes and cross-links to a suite of other natural product-related data resources. The database is supported by a web server that includes functionality to browse the collection, search the database using both chemical structures and text/numerical terms and visualize the chemical diversity it contains using interactive dashboards. In the current database release, we have curated 1347 papers, increasing the number of compounds to 36 545. In addition, we have initiated a large-scale effort to incorporate data from papers reporting structural reassignments and revisions to previously published structures. This effort led to the incorporation of 590 corrections to existing entries, significantly improving the accuracy of the dataset. The Natural Products Atlas may be accessed at www.npatlas.org.
STK39-mediated amplification of γ-H2A.X promotes homologous recombination and contributes to PARP inhibitor resistance
Authors: Xu Yi , Li Changying , Yin Huan , Nowsheen Somaira , Xu Xin , Kang Wenjuan , Liu Xin , Chen Lifeng , Lou Zhenkun , Yi Junlin , Deng Min 
Published: November 2024

Abstract
The phosphorylation of histone H2A.X into γH2A.X is a crucial early event in the DNA damage response, marking DNA damage sites and initiating repair processes. While ATM kinase is traditionally recognized as the primary mediator of H2A.X phosphorylation, our study identifies serine/threonine kinase 39 (STK39) as a novel enhancer of this critical signaling pathway. We demonstrate that after DNA damage, STK39 undergoes phosphorylation by the ATM kinase, facilitating its interaction with the Mre11-Rad50-Nbs1 complex and subsequent recruitment to chromatin. This recruitment enables STK39 to further phosphorylate H2A.X, thus amplifying γH2A.X production and promoting homologous recombination repair. Notably, we observe a significant upregulation of STK39 in pancreatic adenocarcinoma (PAAD) tissues, correlating with heightened resistance to PARPi therapy. Furthermore, we demonstrate the synergistic efficacy of combining STK39 inhibition with PARP inhibitors in suppressing and reversing PAAD growth. This study not only provides new insights into the molecular dynamics of H2A.X phosphorylation but also highlights the therapeutic potential of targeting STK39 to enhance PARPi sensitivity in PAAD (created with BioRender).
Circular oligomeric particles formed by Ros/MucR family members mediate DNA organization in α-proteobacteria
Authors: Chaves-Sanjuan Antonio , D’Abrosca Gianluca , Russo Veronica , van Erp Bert , Del Cont-Bernard Alessandro , Capelli Riccardo , Pirone Luciano , Slapakova Martina , Sgambati Domenico , Fattorusso Roberto , Isernia Carla , Russo Luigi , Barton Ian S , Roop Roy Martin , Pedone Emilia M , Bolognesi Martino , Dame Remus T , Pedone Paolo V , Nardini Marco , Malgieri Gaetano , Baglivo Ilaria 
Published: November 2024

Abstract
The transcriptional regulator MucR from Brucella species controls the expression of many genes, including those involved in virulence, by binding AT-rich DNA regions. MucR and its homologs belong to the Ros/MucR family, whose members occur in α-proteobacteria. MucR is a recent addition to the family of histone-like nucleoid structuring (H-NS) proteins. Indeed, despite the lack of sequence homology, MucR bears many functional similarities with H-NS and H-NS-like proteins, structuring the bacterial genome and acting as global regulators of transcription. Here we present an integrated cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance, modeling and biochemical study shedding light on the functional architecture of MucR from Brucella abortus and its homolog Ml5 from Mesorhizobium loti. We show that MucR and Ml5 fold in a circular quaternary assembly, which allows it to bridge and condense DNA by binding AT-rich sequences. Our results show that Ros/MucR family members are a novel type of H-NS-like proteins and, based on previous studies, provide a model connecting nucleoid structure and transcription regulation in α-proteobacteria.
Chemotherapeutic agents and leucine deprivation induce codon-biased aberrant protein production in cancer
Authors: Kochavi Adva , Nagel Remco , Körner Pierre-Rene , Bleijerveld Onno B , Lin Chun-Pu , Huinen Zowi , Malka Yuval , Proost Natalie , van de Ven Marieke , Feng Xiaodong , Navarro Jasmine Montenegro , Pataskar Abhijeet , Peeper Daniel S , Champagne Julien , Agami Reuven 
Published: November 2024

Abstract
Messenger RNA (mRNA) translation is a tightly controlled process frequently deregulated in cancer. Key to this deregulation are transfer RNAs (tRNAs), whose expression, processing and post-transcriptional modifications are often altered in cancer to support cellular transformation. In conditions of limiting levels of amino acids, this deregulated control of protein synthesis leads to aberrant protein production in the form of ribosomal frameshifting or misincorporation of non-cognate amino acids. Here, we studied leucine, an essential amino acid coded by six different codons. Surprisingly, we found that leucine deprivation leads to ribosomal stalling and aberrant protein production in various cancer cell types, predominantly at one codon, UUA. Similar effects were observed after treatment with chemotherapeutic agents, implying a shared mechanism controlling the downstream effects on mRNA translation. In both conditions, a limitation in the availability of tRNALeu(UAA) for protein production was shown to be the cause for this dominant effect on UUA codons. The induced aberrant proteins can be processed and immune-presented as neoepitopes and can direct T-cell killing. Altogether, we uncovered a novel mode of interplay between DNA damage, regulation of tRNA availability for mRNA translation and aberrant protein production in cancer that could be exploited for anti-cancer therapy.
High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq
Authors: Choudhary Aanchal , Ammari Moonia , Yoon Hyuk Sung , Zander Mark 
Published: November 2024

Abstract
Assessing the dynamics of chromatin features and transcription factor (TF) binding at scale remains a significant challenge in plants. Here, we present PHILO (Plant HIgh-throughput LOw input) ChIP-seq, a high-throughput ChIP-seq platform that enables the cost-effective and extensive capture of TF binding and genome-wide distributions of histone modifications. The PHILO ChIP-seq pipeline is adaptable to many plant species, requires very little starting material (1mg), and provides the option to use MNase (micrococcal nuclease) for chromatin fragmentation. By employing H3K9ac PHILO ChIP-seq on eight Arabidopsis thaliana jasmonic acid (JA) pathway mutants, with the simultaneous processing of over 100 samples, we not only recapitulated but also expanded the current understanding of the intricate interplay between the master TFs MYC2/3/4 and various chromatin regulators. Additionally, our analyses brought to light previously unknown histone acetylation patterns within the regulatory regions of MYC2 target genes in Arabidopsis, which is also conserved in tomato (Solanum lycopersicum). In summary, our PHILO ChIP-seq platform demonstrates its high effectiveness in investigating TF binding and chromatin dynamics on a large scale in plants, paving the way for the cost-efficient realization of complex experimental setups.
Implications of sociodemographic and clinical factors on symptom burden: Age-specific survivorship care in the primary central nervous system tumor population
Authors: Robins Kimberly R , Kunst Tricia , Reyes Jennifer , Acquaye-Mallory Alvina , Grajkowska Ewa , Ozer Byram H , Penas-Prado Marta , Wu Jing , Burton Eric , Boris Lisa , Panzer Marissa , Pillai Tina , Polskin Lily , Gilbert Mark R , Vera Elizabeth , Armstrong Terri S 
Published: November 2024

Abstract

Background
This analysis aims to provide insight into differences in symptom burden and general health status between young adults (YA; 18–39 years old) and older adults (OA; ≥40 years old) with primary central nervous system tumors.

Methods
Data were retrospectively analyzed from the National Cancer Institute Neuro-Oncology Branch’s Natural History Study (NCT02851706 PI: T.S. Armstrong) to determine differences in patient-reported outcomes (general health status [EQ-5D-3L], symptom burden [MDASI-BT and MDASI-SP], anxiety/depression [Patient-Reported Outcomes Measurement Information System], and perceived cognition [Neuro-QOL]) and demographic and clinical data using chi-square, one-way ANOVA, and Student’s t-tests. Linear regression with backward elimination determined which characteristics impacted perceived symptom burden and general health status.

Results
The sample included 271 YA (82% with a primary brain tumor (PBT); median age 31 [range, 18–39]) and 516 OA (88% with a PBT; median age 54 [range, 40–85]). YA were more likely to be single (P &lt; .001), employed (P &lt; .001), and make &lt; $50 000 per year (P = .014). More YA reported pain (P = .008), nausea (P &lt; .001), drowsiness (P = .043), and vomiting (P = .001) than OA. Among demographic and clinical characteristics, when controlling for age, Karnofsky Performance Scale score (P &lt; .001) and employment status (P &lt; .001) were predictors of symptom interference, activity- and mood-related interference in patients with PBTs. Compared to OA with spinal tumors, YA reported more moderate-severe anxiety (P = .050) and moderate-severe perceived cognitive deficits (P = .023).

Conclusions
Significant differences in characteristics and symptom burden exist between YA and OA. Developmentally tailored survivorship programs providing additional psychosocial support and resources to address symptom presentation in YA are needed.
Effectiveness of the 2023–2024 Omicron XBB.1.5-containing mRNA COVID-19 Vaccine (mRNA-1273.815) in Preventing COVID-19–related Hospitalizations and Medical Encounters Among Adults in the United States
Authors: Kopel Hagit , Araujo Andre B , Bogdanov Alina , Zeng Ni , Winer Isabelle , Winer-Jones Jessamine P , Lu Tianyi , Marks Morgan A , Bonafede Machaon , Nguyen Van Hung , Martin David , Mansi James A 
Published: November 2024

Abstract

Background
This study aimed to evaluate the vaccine effectiveness (VE) of mRNA-1273.815, a 2023–2024 Omicron XBB.1.5-containing mRNA COVID-19 vaccine, at preventing COVID-19–related hospitalizations and any medically attended COVID-19 in adults.

Methods
In a linked electronic health record–claims dataset, we identified US adults (≥18 years) who received the mRNA-1273.815 vaccine (exposed cohort) between 12 September and 15 December 2023, matched 1:1 to individuals who did not receive a 2023–2024 updated COVID-19 vaccine (unexposed cohort). Cohorts were balanced using inverse probability of treatment weighting on demographics, vaccination and infection history, and underlying medical conditions. Study cohorts were followed until 31 December 2023 for COVID-19–related hospitalizations and medically attended COVID-19. Cox regression was used to estimate hazard ratios and VE. Subgroup analyses were performed for adults ≥50 years, adults ≥65 years, and individuals with underlying medical conditions.

Results
Overall, 859 335 matched pairs of mRNA-1273.815 recipients and unexposed adults were identified. The mean (standard deviation) age was 63 (16) years. More than 60% of individuals in both cohorts had an underlying medical condition. Among the overall adult population, VE was 60.2% (95% confidence interval, 53.4–66.0) against COVID-19–related hospitalization and 33.1% (30.2–35.9) against medically attended COVID-19 over a median follow-up of 63 (interquartile range: 44–78) days. VE estimates by age and underlying medical conditions were similar.

Conclusions
These results demonstrate the significant protection provided by mRNA-1273.815 against COVID-19–related hospitalizations and any medically attended COVID-19 in adults, regardless of vaccination history, and support Centers for Disease Control and Prevention recommendations to stay up-to-date with COVID-19 vaccination to prevent COVID-19–related outcomes, including hospitalizations.
Maize unstable factor for orange1 encodes a nuclear protein that affects redox accumulation during kernel development
Authors: Chatterjee Debamalya , Zhang Ziru , Lin Pei-Yu , Wang Po-Hao , Sidhu Gurpreet K , Yennawar Neela H , Hsieh Jo-Wei Allison , Chen Pao-Yang , Song Rentao , Meyers Blake C , Chopra Surinder 
Published: November 2024

Abstract
The basal endosperm transfer layer (BETL) of the maize (Zea mays L.) kernel is composed of transfer cells for nutrient transport to nourish the developing kernel. To understand the spatiotemporal processes required for BETL development, we characterized 2 unstable factor for orange1 (Zmufo1) mutant alleles. The BETL defects in these mutants were associated with high levels of reactive oxygen species, oxidative DNA damage, and cell death. Interestingly, antioxidant supplementation in in vitro cultured kernels alleviated the cellular defects in mutants. Transcriptome analysis of the loss-of-function Zmufo1 allele showed differential expression of tricarboxylic acid cycle, redox homeostasis, and BETL-related genes. The basal endosperms of the mutant alleles had high levels of acetyl-CoA and elevated histone acetyltransferase activity. The BETL cell nuclei showed reduced electron-dense regions, indicating sparse heterochromatin distribution in the mutants compared with wild-type. Zmufo1 overexpression further reduced histone methylation marks in the enhancer and gene body regions of the pericarp color1 (Zmp1) reporter gene. Zmufo1 encodes an intrinsically disordered nuclear protein with very low sequence similarity to known proteins. Yeast two-hybrid and luciferase complementation assays established that ZmUFO1 interacts with proteins that play a role in chromatin remodeling, nuclear transport, and transcriptional regulation. This study establishes the critical function of Zmufo1 during basal endosperm development in maize kernels.