bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increasing marine trophic web knowledge through DNA analyses of fish stomach contents: a step towards an Ecosystem Based Approach to fisheries research
Authors: Canals Oriol , Lanzén Anders , Mendibil Iñaki , Bachiller Eneko , Corrales Xavier , Andonegi Eider , Cotano Unai , Rodríguez-Ezpeleta Naiara 
Published: December 2023

AbstractMultispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding (the simultaneous identification of all taxa in a sample by sequencing a short DNA region) could be used for speeding up large-scaled stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which is feasible to be incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomachs, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analysed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.
Resource selection at fine-scale: What drives the decision of a generalist herbivore?
Authors: Boyers Melinda , Parrini Francesca 
Published: December 2023

AbstractSpatial patterns in topography and forage distribution significantly influence the movements and choices of large herbivores. However, understanding the foraging strategies of free-grazing herbivores at different temporal and spatial scales remains limited, as different behavioural decisions can apply at different hierarchical levels, This study investigates the fine-scale foraging strategies of zebra (Equus quagga) in a South African savanna, with a specific focus on their selection of green vegetation at the plant and feeding patch levels. We used the Normalized Difference Vegetation Index (NDVI) as a proxy for vegetation productivity and quality. Our findings reveal that zebra adapted their foraging strategies according to the scale and season. During the late-dry season and early-wet season, selection for greenness was at both the grass tuft and feeding site levels. In contrast, during the mid-dry season, their selection was predominantly at the tuft level, focusing solely on greenness. These insights emphasize the importance of conducting multi-level studies when investigating factors influencing foraging decisions. Findings at one hierarchical level may not necessarily apply across other levels of investigation, highlighting the need for a nuanced and comprehensive approach to understanding the complex foraging behaviours of these animals.
Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation
Authors: Halblander Fabian N. , Meng Fanju W. , Murphy Patrick J. 
Published: December 2023

AbstractEpigenetic regulation of chromatin states is crucial for proper gene expression programs and progression during development, but precise mechanisms by which epigenetic factors influence differentiation remain poorly understood. Here we find that the histone variant H2A.Z accumulates at Sox motif-containing promoters during zebrafish gastrulation while neighboring genes become transcriptionally active. These changes coincide with reduced expression ofanp32e, the H2A.Z histone removal chaperone, suggesting that loss of Anp32e may lead to increases in H2A.Z during differentiation. Remarkably, genetic removal of Anp32e in embryos leads to H2A.Z accumulation prior to gastrulation, and precocious developmental transcription of Sox motif associated genes. Altogether, our results provide compelling evidence for a mechanism in which Anp32e restricts H2A.Z accumulation at Sox motif-containing promoters, and subsequent down-regulation of Anp32e enables temporal up-regulation of Sox motif associated genes.HighlightsAn early-developmental time course of zebrafish chromatin accessibility is achieved using an integrated UMAP analysis of datasets from two separate published studies.CUT&Tag sequencing is used to characterize the genomic localization for the histone chaperone ANP32E.Changes in Anp32e enrichment coincide with opposing changes in H2A.Z enrichment during zebrafish gastrulation.Precociously expressed genes in embryos lacking Anp32e are disproportionately Sox-marked and may represent H2A.Z-mediated developmental accelerations.
Glucocorticoid chrono-pharmacology unveils novel targets for the cardiomyocyte-specific GR-KLF15 axis in cardiac glucose metabolism
Authors: Durumutla Hima Bindu , Prabakaran Ashok Daniel , Soussi Fadoua El Abdellaoui , Akinborewa Olukunle , Latimer Hannah , McFarland Kevin , Piczer Kevin , Werbrich Cole , Jain Mukesh K , Haldar Saptarsi M , Quattrocelli Mattia 
Published: December 2023

ABSTRACTCircadian time-of-intake gates the cardioprotective effects of glucocorticoid administration in both healthy and infarcted hearts. The cardiomyocyte-specific glucocorticoid receptor (GR) and its co-factor, Krüppel-like factor (Klf15), play critical roles in maintaining normal heart function in the long-term and serve as pleiotropic regulators of cardiac metabolism. Despite this understanding, the cardiomyocyte-autonomous metabolic targets influenced by the concerted epigenetic action of GR-Klf15 axis remain undefined. Here, we demonstrate the critical roles of the cardiomyocyte-specific GR and Klf15 in orchestrating a circadian-dependent glucose oxidation program within the heart. Combining integrated transcriptomics and epigenomics with cardiomyocyte-specific inducible ablation of GR or Klf15, we identified their synergistic role in the activation of adiponectin receptor expression (Adipor1) and the mitochondrial pyruvate complex (Mpc1/2), thereby enhancing insulin-stimulated glucose uptake and pyruvate oxidation. Furthermore, in obese diabetic (db/db) mice exhibiting insulin resistance and impaired glucose oxidation, light-phase prednisone administration, as opposed to dark-phase prednisone dosing, effectively restored cardiomyocyte glucose oxidation and improved diastolic function towards control-like levels in a sex-independent manner. Collectively, our findings uncover novel cardiomyocyte-autonomous metabolic targets of the GR-Klf15 axis. This study highlights the circadian-dependent cardioprotective effects of glucocorticoids on cardiomyocyte glucose metabolism, providing critical insights into chrono-pharmacological strategies for glucocorticoid therapy in cardiovascular disease.GRAPHICAL ABSTRACTBrief summaryDepending on when it is taken during the day, the drug prednisone activates the heart to
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference
Authors: Dong Xiaoru , Leary Jack R. , Yang Chuanhao , Brusko Maigan A. , Brusko Todd M. , Bacher Rhonda 
Published: December 2023

AbstractSingle-cell RNA sequencing (scRNA-seq) experiments have become instrumental in developmental and differentiation studies, enabling the profiling of cells at a single or multiple time-points to uncover subtle variations in expression profiles reflecting underlying biological processes. Benchmarking studies have compared many of the computational methods used to reconstruct cellular dynamics, however researchers still encounter challenges in their analysis due to uncertainties in selecting the most appropriate methods and parameters. Even among universal data processing steps used by trajectory inference methods such as feature selection and dimension reduction, trajectory methods’ performances are highly dataset-specific. To address these challenges, we developed Escort, a framework for evaluating a dataset’s suitability for trajectory inference and quantifying trajectory properties influenced by analysis decisions. Escort navigates single-cell trajectory analysis through data-driven assessments, reducing uncertainty and much of the decision burden associated with trajectory inference. Escort is implemented in an accessible R package and R/Shiny application, providing researchers with the necessary tools to make informed decisions during trajectory analysis and enabling new insights into dynamic biological processes at single-cell resolution.
Enhancing Rice Growth and Yield with Weed Endophytic BacteriaAlcaligenes faecalisandMetabacillus indicusUnder Reduced Chemical Fertilization
Authors: Fatema Kaniz , Mahmud Nur Uddin , Gupta Dipali Rani , Siddiqui Md. Nurealam , Sakif Tahsin Islam , Sarker Aniruddha , Sharpe Andrew G , Islam Tofazzal 
Published: December 2023

AbstractEndophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified asAlcaligenes faecalis(BTCP01) from Eleusine indica (Goose grass) andMetabacillus indicus(BTDR03) fromCynodon dactylon(Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection ofnifHandipdCgenes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.
Extracellular vesicles propagate aging in COPD airway epithelial cells by transfer of microRNA-34a
Authors: Devulder Justine V. , Baker Jonathan R. , Fenwick Peter S. , Odqvist Lina , Donnelly Louise E. , Barnes Peter J. 
Published: December 2023

AbstractRationaleChronic obstructive pulmonary disease (COPD) is associated with the acceleration of lung aging, demonstrated by the accumulation of senescent cells in lung tissue. MicroRNA (miR)-34a is induces senescence by suppressing the key anti-aging molecule, sirtuin-1 (SIRT1). Senescent cells spread senescence to neighboring and distant cells, which favors the progression of COPD and its comorbidities. The mechanisms for spreading senescence remain undetermined but may be mediated by the transfer of microRNAs in extracellular vesicles.ObjectivesTo analyze the miRNA content of extracellular vesicles in COPD and explore their effect on cellular senescence of healthy cellsMethodsEVs were isolated from small airway epithelial cells (SAEC) from healthy donors or COPD patients. Recipient healthy SAEC were cultured with EVs and the expression of miR-34a and markers of cellular senescence, p21CIP1and SIRT1, were measured.Main ResultsEVs from COPD cells induce senescence in healthy recipient cells via the selective transfer of miR-34a. We showed that COPD SAEC produce increased numbers of EVs enriched with miR-34a. EVs are taken up by healthy cells, resulting in reduced expression of the anti-aging molecule sirtuin-1 and increased expression of markers of senescence, such as p21CIP1and positive staining for senescence-associated β-galactosidaseConclusionsOur findings provide evidence of the mechanism by which EVs spread cellular senescence in human primary cells via miR-34a, rather than via soluble mediators. EVs enriched with miR-34a may spread senescence locally, accounting for disease progression, but also provide a mechanism for distant spread to account for comorbidities and multimorbidity of the elderly.
Male-specific features ofC. elegansneuronal aging
Authors: Weng Yifei , Murphy Coleen T. 
Published: December 2023

SummaryAging is a complex biological process, with sexually dimorphic aspects. For example, men and women differ in their vulnerabilities in cognitive decline, suggesting biological sex may contribute to the heterogeneous nature of aging. Although we know a great deal about the cognitive aging of hermaphrodites of the model systemC. elegans,less is known about cognitive decline in males. Through behavioral analyses, we found that the cognitive aging process has both sex-shared and sex-dimorphic characteristics. Through neuron-specific sequencing, we identified neuronal age-associated sex-differential targets. In addition to sex-shared neuronal aging genes, males differentially downregulate mitochondrial metabolic genes and upregulate GPCR genes with age. In addition, the X chromosome exhibits increased gene expression in hermaphrodites and altered dosage compensation complex expression with age, indicating possible X-chromosomal dysregulation that contributes to sexual dimorphism in cognitive aging. Finally, we found that the sex-differentially expressed genehrg-7, which encodes an aspartic-type endopeptidase, regulates male behavior during cognitive aging but does not affect hermaphrodites’ behaviors. Overall, these results suggest that males and hermaphrodites exhibit different age-related neuronal changes. This study will strengthen our understanding of sex-specific vulnerability and resilience and help identify new pathways to target with novel treatments that could benefit both sexes.
Early Intervention with Electrical Stimulation Reduces Neural Damage After Stroke in Non-human Primates
Authors: Zhou Jasmine , Khateeb Karam , Yazdan-Shahmorad Azadeh 
Published: December 2023

AbstractIschemic stroke is a neurological condition that results in significant mortality and long-term disability for adults, creating huge health burdens worldwide. For stroke patients, acute intervention offers the most critical therapeutic opportunity as it can reduce irreversible tissue injury and improve functional outcomes. However, currently available treatments within the acute window are highly limited. Although emerging neuromodulation therapies have been tested for chronic stroke patients, acute stimulation is rarely studied due to the risk of causing adverse effects related to ischemia-induced electrical instability. To address this gap, we combined electrophysiology and histology tools to investigate the effects of acute electrical stimulation on ischemic neural damage in non-human primates. Specifically, we induced photothrombotic lesions in the monkey sensorimotor cortex while collecting electrocorticography (ECoG) signals through a customized neural interface. Gamma activity in ECoG was used as an electrophysiological marker to track the effects of stimulation on neural activation. Meanwhile, histological analysis including Nissl, cFos, and microglial staining was performed to evaluate the tissue response to ischemic injury. Comparing stimulated monkeys to controls, we found that theta-burst stimulation administered directly adjacent to the ischemic infarct at 1 hour post-stroke briefly inhibits peri-infarct neuronal activation as reflected by decreased ECoG gamma power and cFos expression. Meanwhile, lower microglial activation and smaller lesion volumes were observed in animals receiving post-stroke stimulation. Together, these results suggest that acute electrical stimulation can be used safely and effectively as an early stroke intervention to reduce excitotoxicity and inflammation, thus mitigating neural damage and enhancing stroke outcomes.
RLKdb: A comprehensive curated receptor-like kinase family database
Authors: Yin Zhiyuan , Liu Jinding , Dou Daolong 
Published: December 2023

Dear Editor,Since the first plant receptor-like kinase (RLK) geneZmPK1was cloned fromZea maysin 1990 (Walker & Zhang, 1990), this large gene family has been extensively studied and shown to play crucial roles in growth, development, and immunity (Tanget al., 2017). RLKs are widespread in the plant kingdom, while the biological functions of most RLKs remain largely elusive (Dievartet al., 2020). Given RLKs share a conserved monophyletic RLK/Pelle kinase domain, RLKs in several model plants are classified into distinct families by extracellular domains (ECDs) (Shiu & Bleecker, 2001). However, independent domain shuffling in specific lineages drives the origin of novel families, which raises a question: how about the landscape of RLKs in the whole plant kingdom? Previously, sequence homology-based methods have been widely used for RLK identification and classification, which probably will miss the distantly related proteins but with similar structures and potential novel families unmentioned in the literature. The academic community urgently requires a dedicated database for a systematic overview of the RLK gene family, providing data support for in-depth research on RLK genes. Here, we used a topology-based method to accurately isolate the RLKomes from proteomes. The obtained RLKomes were further classified into (sub)families based on ECD domains. We constructed a comprehensively curated plant RLK database (https://biotec.njau.edu.cn/rlkdb/), which contains valuable resources for investigating the origin and evolution of the RLK family and multiple online tools for personalized analysis.
Cell-based production of Fc-GlcNAc and Fc-alpha-2,6 sialyl glycan enriched antibody with improved effector functions through glycosylation pathway engineering
Authors: Huang Han-Wen , Shivatare Vidya S. , Tseng Tzu-Hao , Wong Chi-Huey 
Published: December 2023

ABSTRACTGlycosylation of antibody plays an important role in Fc-mediated killing of tumor cells and virus-infected cells through effector functions such as antibody-dependent cellular cytotoxicity (ADCC), antibody dependent cell-mediated phagocytosis (ADCP) and vaccinal effect. Previous studies showed that therapeutical humanized antibodies with α2-6 sialyl complex type (SCT) glycan attached to Fc-Asn297 exhibited optimal binding to the Fc receptors on effector cells associated with ADCC, ADCP and vaccinal effect. However, the production of antibodies with homogeneous Fc-SCT needs multiplein vitroenzymatic and purification steps. In this study, we report two different approaches to shorten the processes to produce SCT-enriched antibodies. First, we expressed a bacterial endoglycosidase in GNT1-KO EXPI293 cells to trim allN-glycans to mono-GlcNAc glycoforms forin vitrotransglycosylation to generate homogeneous SCT antibody. Second, we engineered the glycosylation pathway of HEK293 cells through knockout of the undesired glycosyltransferases and expression of the desired glycosyltransferases to produce SCT enriched antibodies with similar binding affinity to Fc receptors and ADCC activity to homogenous SCT antibody.
The impact of speaker accent on discourse processing: a frequency investigation
Authors: Thomas Trisha , Martin Clara D. , Caffarra Sendy 
Published: December 2023

AbstractPrevious studies show that there are differences in native and foreign speech processing (Lev-Ari, 2018) while mixed evidence has been found regarding differences between dialectal and foreign accent processing (see: Adank et al., 2009; Floccia et al. 2006 but see also: Floccia et al., 2009; Girard et al., 2008). Within this field, two theories have been proposed. The Perceptual Distance Hypothesis states that the mechanisms underlying dialectal accent processing are attenuated versions of those of foreign (Clarke & Garrett, 2004). While, the Different Processes Hypothesis argues that the mechanisms of foreign and dialectal accent processing are qualitatively different (Floccia et al, 2009). A recent study looking at single-word EEG data, suggested that there may be flexibility in processing mechanisms (Thomas et al., 2022). The present study deepens this investigation by addressing in which frequency bands native, dialectal and foreign accent processing differ when listening to extended speech. Electroencephalographic data was recorded from 30 participants who listened to dialogues of approximately six minutes spoken in native, dialectal and foreign accents. Power spectral density estimation (1-35 hz) was performed. Linear mixed models were done in frequency windows of particular relevance to discourse processing. Frequency bands associated with phoneme [gamma], syllable [theta], and prosody [delta] were considered along with those of general cognitive mechanisms [alpha and beta]. Results show power differences in the Gamma frequency range. While in higher frequency ranges foreign accent processing is differentiated from power amplitudes of native and dialectal accent processing, in low frequencies we do not see any accent-related power amplitude modulations. This suggests that there may be a difference in phoneme processing for native accent types and foreign accent, while we speculate that top-down mechanisms during discourse processing may mitigate the effects observed with short units of speech.
Predicting stop codon reassignment improves functional annotation of bacteriophages
Authors: Cook Ryan , Telatin Andrea , Bouras George , Camargo Antonio Pedro , Larralde Martin , Edwards Robert A. , Adriaenssens Evelien M. 
Published: December 2023

AbstractThe majority of bacteriophage diversity remains uncharacterised, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as theCrassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokkagv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome medians) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased mean coding density from 66.8% to 90.0%, and from 69.0% to 89.8% for UHGV and INPHARED sequences. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.