bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of the Batoidea Pectoral Fin Skeleton: Convergence, Modularity, and Integration Driving Disparity Trends
Authors: López-Romero Faviel A. , Villalobos-Segura Eduardo , Türtscher Julia , Berio Fidji , Stumpf Sebastian , Dearden Richard P. , Kriwet Jürgen , Maldonado Ernesto 
Published: June 2024

AbstractBatoids (skates and rays) are the most speciose group of cartilaginous fishes. Their body plan represents diverse ecologies and swimming modes. Early skeletal fossil remains, and recent phylogenetic analyses suggest that convergence has occurred within the batoids several times independently. The drivers for such disparity patterns and possible association with modularity and phenotypic integration among batoids are not fully understood. Here we used geometric morphometrics and phylogenetic comparative methods to characterize the evolutionary trends of the basal fin skeleton of batoids and sharks. Our analyses show that the morphological variation has a strong phylogenetic signal. Interestingly, the most speciose orders of batoids display low morphological disparity. Reef and freshwater species, show increased evolutionary rates. Meanwhile, the swimming mode shows different rates depending on the fin structure analyzed. A higher modularity and integration signal suggest that the pectoral fin of batoids has experienced mosaic evolution. The low morphological disparity might be associated with high integration. We find support for convergence between Jurassic, Cretaceous, and Extant guitarfishes, however, not completely between sharks and batoids. Our findings suggest that habitats and swimming mode have shaped the pectoral fin evolution among batoids, and at the same time batoids have constrained their basal fin skeleton.
EEG Electrodes and Where to Find Them: Automated Localization From 3D Scans
Authors: Tveter Mats , Tveitstøl Thomas , Nygaard Tønnes , Pérez T Ana S. , Kulashekhar Shrikanth , Bruña Ricardo , Hammer Hugo L. , Hatlestad-Hall Christoffer , Haraldsen Ira R. J. Hebold 
Published: June 2024

AbstractObjectiveThe accurate localization of electroencephalography (EEG) electrode positions is crucial for accurate source localization. Recent advancements have proposed alternatives to labor-intensive, manual methods for spatial localization of the electrodes, employing technologies such as 3D scanning and laser scanning. These novel approaches often integrate Magnetic Resonance Imaging (MRI) as part of the pipeline in localizing the electrodes. The limited global availability of MRI data restricts its use as a standard modality in several clinical scenarios. This limitation restricts the use of these advanced methods.ApproachIn this paper, we present a novel, versatile approach that utilizes 3D scans to localize EEG electrode positions with high accuracy. Importantly, while our method can be integrated with MRI data if available, it is specifically designed to be highly effective even in the absence of MRI, thus expanding the potential for advanced EEG analysis in various resource-limited settings. Our solution implements a two-tiered approach involving landmark/fiducials localization and electrode localization, creating an end-to-end framework.Main resultsThe efficacy and robustness of our approach have been validated on an extensive dataset containing over 400 3D scans from 278 subjects. The framework identifies pre-auricular points and achieves correct electrode positioning accuracy in the range of 85.7% to 91.0%. Additionally, our framework includes a validation tool that permits manual adjustments and visual validation if required.SignificanceThis study represents, to the best of the authors’ knowledge, the first validation of such a method on a substantial dataset, thus ensuring the robustness and generalizability of our innovative approach. Our findings focus on developing a solution that facilitates source localization, contributing to the critical discussion on balancing cost effectiveness with methodological accuracy to promote wider adoption in both research and clinical settings.
Evolutionary bursts drive morphological novelty in the world’s largest skinks
Authors: Brennan Ian G. , Chapple David G. , Scott Keogh J. , Donnellan Stephen 
Published: June 2024

SummaryAnimal phenotypes evolve and diverge as a result of differing selective pressures and drift. These processes leave unique signatures in patterns of trait evolution, impacting the tempo and mode of morphological macroevolution. While there is a broad understanding of the history of some organismal traits (e.g. body size), there is little consensus about the evolutionary mode of most others. This includes the relative contribution of prolonged (Darwinian gradualist) and episodic (Simpsonian jump) changes towards the evolution of novel morphologies. Here we use new exon-capture and linear morphological datasets to investigate the tempo and mode of morphological evolution in Australo-Melanesian Tiliquini skinks. We generate a well-supported time-calibrated phylogenomic tree from ∼400 nuclear markers for more than 100 specimens including undescribed diversity, and provide unprecedented resolution of the rapid Miocene diversification of these lizards. By collecting a morphological dataset that encompasses the lizard body plan (19 traits across the head, body, limb, and tail) we are able to identify that most traits evolve conservatively but infrequent evolutionary bursts result in morphological novelty. These phenotypic discontinuities occur via rapid rate increases along individual branches, inconsistent with both gradualistic and punctuated equilibrial evolutionary modes. Instead, this ‘punctuated gradualism’ has resulted in the rapid evolution of blue-tongued giants and armored dwarves in the ∼20 million years since colonizing Australia. These results outline the evolutionary pathway towards new morphologies and highlight the heterogeneity of evolutionary tempo and mode, even within individual traits.
Widespread destabilization ofC. elegansmicroRNAs by the E3 ubiquitin ligase EBAX-1
Authors: Stubna Michael W. , Shukla Aditi , Bartel David P. 
Published: June 2024

ABSTRACTMicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that direct mRNA repression. miRNAs are also the subject of regulation. For example, some miRNAs are destabilized through a pathway in which pairing to specialized transcripts recruits the ZSWIM8 E3 ubiquitin ligase, which polyubiquitinates AGO, leading to its degradation and exposure of the miRNA to cellular nucleases. Here, we found that 22 miRNAs inC. elegansare sensitive to loss of EBAX-1, the ZSWIM8 ortholog in nematodes, implying that these 22 miRNAs might be subject to this pathway of target-directed miRNA degradation (TDMD). The impact of EBAX-1 depended on the developmental stage, with the greatest effect on the miRNA pool (14.5%) observed in L1 larvae and the greatest number of different miRNAs affected (17) observed in germline-depleted adults. The affected miRNAs included the miR-35–42 family, as well as other miRNAs among the least stable in the worm, suggesting that TDMD is a major miRNA-destabilization pathway in the worm. The excess miR-35–42 molecules that accumulated inebax-1mutants caused increased repression of their predicted target mRNAs and underwent 3′ trimming over time. In general, however, miRNAs sensitive to EBAX-1 loss had no consistent pattern of either trimming or tailing. Replacement of the 3′ region of miR-43 substantially reduced EBAX-1 sensitivity, a result that differed from that observed previously for miR-35. Together, these findings broaden the implied biological scope of TDMD-like regulation of miRNA stability in animals, and indicate that a role for miRNA 3′ sequences is variable in the worm.
Gut microbial profiling of COVID-19 patients in Uganda
Authors: Kateete David Patrick , Lubega Christopher , Galiwango Ronald , Nasinghe Emmanuel , Mbabazi Monica , Jjingo Daudi , Elliott Alison 
Published: June 2024

AbstractBackground:While COVID-19 spread globally, the role of the gut microbiota in patient outcomes has remained an area of exploration especially in resource limited settings. This study aimed to comprehensively profile the gut microbiome among Ugandan COVID-19 patients and infer potential implications.Methods:Nasopharyngeal swabs, stool, clinical and demographic data were collected from COVID-19 confirmed cases at the COVID-19 isolation and treatment centers in Kampala and Entebbe, Uganda, during the first and second waves of the pandemic in Uganda (i.e., 2020 and 2021, respectively). SARS-CoV-2 presence in the swab samples was confirmed by quantitative real-time RT-PCR assays. 16S rRNA metagenomic next-generation sequencing was performed on the DNA extracted from the stool samples, followed by bioinformatics analysis. Machine learning was used to determine microbes that were associated with disease severity.Results:We observed varied gut microbial composition between COVID-19 patients and healthy controls. Potentially pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Enrichment of opportunistic pathogens, such as Enterococcus species, and depletion of beneficial microbes, like Alphaproteobacteria, was observed between mild and severe cases. Machine learning identified age and microbes such as Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae, and Prevotella copri as predictive of severity.Conclusion:These findings suggest that the microbiome plays a role in the dynamics of SARS-CoV-2 infection in African patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population. Their direct or indirect roles in determining severity should be investigated further for potential therapeutic interventions.
Quantification ofSalmonella entericaserovar Typhimurium Population Dynamics in Murine Infection Using a Highly Diverse Barcoded Library
Authors: Hotinger Julia A. , Campbell Ian W. , Hullahalli Karthik , Osaki Akina , Waldor Matthew K. 
Published: June 2024

AbstractMurine models are often used to study the pathogenicity and dissemination of the enteric pathogenSalmonella entericaserovar Typhimurium. Here, we quantifiedS.Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverseS. Typhimurium barcoded library containing ∼55,000 unique strains distinguishable by genomic barcodes by enumeratingS. Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen’s colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed thatSalmonellare-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding ofSalmonellapopulation dynamics.Significance StatementSalmonellais a prevalent food-borne pathogen that infects hundreds of millions of people worldwide. Here, we created a highly complex barcodedSalmonella entericaserovar Typhimurium library containing ∼55,000 barcodes to further understand and quantifySalmonellapopulation dynamics in experimental murine infection. Through comparisons of barcode abundance and frequency in different samples and following different routes of inoculation, we quantify key facets ofSalmonellainfection, including bottleneck sizes and dissemination patterns, and uncover hidden routes of spread that drive heterogeneity in infection outcome. These observations provide a detailed map ofSalmonellainfection and demonstrate the power of high-diversity barcoded libraries in deciphering microbial population dynamics.
Codon bias, nucleotide selection, and genome size predictin situbacterial growth rate and transcription in rewetted soil
Authors: Chuckran Peter F. , Estera-Molina Katerina , Nicolas Alexa M. , Sieradzki Ella T. , Dijkstra Paul , Firestone Mary K. , Pett-Ridge Jennifer , Blazewicz Steven J. 
Published: June 2024

ABSTRACTIn soils, the first rain after a prolonged dry period greatly impacts soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils—however this is often through measurements in culture. Here, we used metagenome-assembled genomes in combination with metatranscriptomics and18O- water stable isotope probing to track genomic traits associated with transcriptional activity and growth of soil microorganisms over the course of one week following rewetting of a grassland soil. We found that the codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also observed higher growth rates in bacteria with smaller genomes, demonstrating that reduced genome size contributes to bacterial growth responses to sudden changes in water or nutrient availability—potentially explaining why smaller genomes are more prevalent in arid and carbon poor systems. High levels of codon bias corresponded to faster transcriptional upregulation of ribosomal protein genes. In early transcribing taxa, nucleotides requiring less energy to produce were more common at synonymous substitution sites—where nucleotide substitutions did not change the encoded amino acid. We found several of these relationships also existed within a phylum, suggesting that association between genomic traits and activity could be a generalized characteristic of soil bacteria. These results providein situevidence that following rewetting, certain genomic characteristics affect soil microbial growth rate and transcription, and points towards the fitness advantages that these traits might pose for bacteria under changing conditions in soil.
Structural and functional analysis ofPseudomonas aeruginosaPelA provides insight into the modification of the Pel exopolysaccharide
Authors: Van Loon Jaime C. , Le Mauff François , Vargas Mario A. , Gilbert Stephanie , Pfoh Roland , Morrison Zachary A. , Razvi Erum , Nitz Mark , Sheppard Donald C. , Howell P. Lynne 
Published: June 2024

ABSTRACTA major biofilm matrix determinant ofPseudomonas aeruginosais the partially deacetylated α-1,4 linkedN-acetylgalactosamine polymer, Pel. After synthesis and transport of the GalNAc polysaccharide across the inner membrane, PelA partially deacetylates and hydrolyzes Pel before its export out of the cellviaPelB. While the Pel modification and export proteins are known to interact in the periplasm, it is unclear how the interaction of PelA and PelB coordinates these processes. To determine how PelA modifies the polymer, we determined its structure to 2.1 Å and found a unique arrangement of four distinct domains. We have shown previously that the hydrolase domain exhibits endo-α-1,4-N-acetylgalactosaminidase activity. Characterization of the deacetylase domain revealed that PelA is the founding member of a new carbohydrate esterase family, CE#. Further, we found that the PelAB interaction enhances the deacetylation ofN-acetylgalactosamine oligosaccharides. Using the PelA structure in conjunction with AlphaFold2 modelling of the PelAB complex, we propose a model wherein PelB guides Pel to the deacetylase domain of PelA and subsequently to the porin domain of PelB for export. Perturbation or loss of the PelAB interaction would result in less efficient deacetylation and potentially result in increased Pel hydrolysis. In PelA homologues across many phyla, the predicted structure and active sites are conserved, suggesting that there is a common modification mechanism in Gram-negative bacterial species that contain a functionalpeloperon.
A versatile platform for single fluorescent protein-based fluorescence lifetime biosensors
Authors: Zhong Chongxia , Arai Satoshi , Okada Yasushi 
Published: June 2024

AbstractSingle fluorescent protein (FP)-based FLIM (fluorescence lifetime imaging) biosensors are potent tools for quantitatively imaging intracellular processes with high spatial and temporal resolution. They only require a single wavelength for detection, which facilitates multi-color imaging. However, the development of single FP-based FLIM biosensors has been limited by the absence of a general design framework and the complexity of the screening process. In this study, we engineered FLIM biosensors capable of detecting ATP (adenosine triphosphate), cAMP (cyclic adenosine monophosphate), citrate, and glucose by inserting each sensing domain into the mTurquoise2 fluorescent protein between Tyr-145 and Phe-146 using peptide linkers. Through efficient linker screening, we successfully developed FLIM biosensors exhibiting an effective dynamic range from 0.5 to 1.0 ns upon analyte binding. This demonstrates that the qmTQ2-ATP-0 backbone is a universal platform for developing mTQ2-based biosensors. As a proof-of-concept, we demonstrated the capabilities of these FLIM biosensors in monitoring the intracellular dynamics of ATP and cAMP alongside dual-color imaging. Therefore, our work presents an accessible methodology for establishing a single FP-based FLIM biosensor platform for quantitative imaging.
Functional metagenomic discovery of novel tetracycline and acarbose resistance genes from low biomass samples using METa assembly
Authors: Allman HM , Bernate EP , Franck E , Oliaro FJ , Hartmann EM , Crofts TS 
Published: June 2024

ABSTRACTA significant challenge in the field of microbiology is the functional annotation of sequence novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offer a sequence-naïve and cultivation-independent solution. This forward genetics approach relies on the creation of functional metagenomic libraries (aka shotgun cloning) in which a microbial host such asE. coliis transformed with vectors containing metagenomic DNA fragments and, optimally, expresses any captured genes into a corresponding phenotype. These libraries can be screened or selected for a function of interest, such as antibiotic resistance, allowing the captured metagenomic DNA to be linked to a phenotype regardless of the sequence’s novelty. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types off limits to this toolset. Here, we show that our recently developed functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA masses. Standard methods of functional metagenomic library preparation generally call for 5 μg to 60 μg of input metagenomic DNA. Here, we demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a three-log decrease from prior art. These functional metagenomic libraries, prepared using between 30.5 ng and 100 ng of metagenomic DNA, nonetheless were sufficient to link three MFS efflux pumps to tetracycline resistance and capture two potential genes for degradation or resistance to the antidiabetic pharmaceutical acarbose. Our preparation of functional metagenomic libraries from aquatic samples and a model fecal swab demonstrate that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach. Functional metagenomic screens and selections are one of the few high-throughput methods that can link novel genes to functions and here we show that one of their significant drawbacks, a requirement for large amounts of metagenomic DNA, can now be overcome.
Cellular function of the GndA small open reading frame-encoded polypeptide during heat shock
Authors: Mohsen Jessica J. , Mohsen Michael G. , Jiang Kevin , Landajuela Ane , Quinto Laura , Isaacs Farren J. , Karatekin Erdem , Slavoff Sarah A. 
Published: June 2024

AbstractOver the past 15 years, hundreds of previously undiscovered bacterial small open reading frame (sORF)-encoded polypeptides (SEPs) of fewer than fifty amino acids have been identified, and biological functions have been ascribed to an increasing number of SEPs from intergenic regions and small RNAs. However, despite numbering in the dozens inEscherichia coli, and hundreds to thousands in humans, same-strand nested sORFs that overlap protein coding genes in alternative reading frames remain understudied. In order to provide insight into this enigmatic class of unannotated genes, we characterized GndA, a 36-amino acid, heat shock-regulated SEP encoded within the +2 reading frame of thegndgene inE. coliK-12 MG1655. We show that GndA pulls down components of respiratory complex I (RCI) and is required for proper localization of a RCI subunit during heat shock. At high temperature GndA deletion (ΔGndA) cells exhibit perturbations in cell growth, NADH+/NAD ratio, and expression of a number of genes including several associated with oxidative stress. These findings suggest that GndA may function in maintenance of homeostasis during heat shock. Characterization of GndA therefore supports the nascent but growing consensus that functional, overlapping genes occur in genomes from viruses to humans.Significance StatementSame-strand overlapping, or nested, protein coding sequences optimize the information content of size-constrained viral genomes, but were previously omitted from prokaryotic and eukaryotic genome annotations. It was therefore surprising when dozens of nested sORFs were recently discovered in bacteria. Our case study ofE. coliGndA supports the hypothesis that overlapping genes may exist because they encode proteins with related functions. More broadly, characterization of nested sORFs may revise our understanding of the architecture of bacterial and eukaryotic genes.