bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brain-wide mapping of oligodendrocyte organization and oligodendrogenesis across the murine lifespan
Authors: Xu Yu Kang T. , Bush Abigail , Musheyev Ephraim , Kim Anya A. , Zhang Sen , von Bernhardi Jaime Eugenin , Sulam Jeremias , Bergles Dwight E. 
Published: September 2024

SUMMARYInsulating sheaths of myelin accelerate neuronal signaling in complex networks of the mammalian brain. In the CNS, myelin sheaths are exclusively produced by oligodendrocytes, which continue to be generated throughout life to change patterns of myelination. However, a brain-wide analysis of oligodendrocyte dynamics across the lifespan has not been performed. We developed a rapid, robust cellular mapping pipeline involving tissue clearing, lightsheet microscopy, atlas alignment, and automated segmentation to define the location of all oligodendrocytes in the mouse brain. This analysis demonstrated the remarkable consistency of oligodendrocyte patterns between hemispheres, individuals, and sexes, and established that oligodendrocyte maps estimate myelin coverage. We trained a vision transformer to identify newly generated oligodendrocytes from millions of mature cells, highlighting age- and region-specific differences in oligodendrogenesis, and revealing areas of enhanced oligodendrocyte resilience and regenerative capacity following demyelination, demonstrating the utility of this pipeline for uncovering brain-wide oligodendrocyte dynamics in health and disease.
Patch-leaving decisions and pupil-linked arousal systems
Authors: Marzecová Anna , Vernaillen Brent , Hoxhaj Drita , Kaiser Luca F. , Verguts Tom , Jocham Gerhard 
Published: September 2024

AbstractDeciding when to abandon a depleting resource in favour of potentially richer alternatives is fundamental to adaptive behaviour. Such patch-leaving decisions require balancing the expected advantage of leaving against both the cost of moving and the reward foregone in the current environment. Previous research suggests that activity of noradrenergic (NE) neurons in the locus coeruleus (LC) underpins patch-leaving. In the current study, we used pupil dilation as a time-resolved readout of subcortical neuromodulation during patch-leaving. We hypothesised that leave decisions will be preceded by a transient pupil dilation. Participants harvested from exponentially depleting patches (blueberry bushes) with three initial reward values, in two environments, which differed in the variability of initial reward values. Behavioural results show that, as predicted by the mathematically optimal solution, participants adjusted their decisions based on the instantaneous reward rate, but also displayed a bias to overharvest (stay longer in compared to the optimum), which was more pronounced in the high variability environment. Pupil size was overall larger in the high variability environment, associated with increased uncertainty. Importantly, we observed an increased transient pupil dilation in response to reward outcomes immediately preceding leave compared to stay decisions, as well as an increase in pupil dilation (and RT) across successive stay trials, leading up to leave decisions, presumably indicating an increased LC-NE activity associated with abandoning current options to explore alternatives.
Fitness effects of killer virus infection on wildSaccharomyces paradoxus
Authors: Unni Rahul , Kavlak Onur Erk , Stukenbrock Eva H. , Boynton Primrose J. 
Published: September 2024

AbstractEndosymbioses, the intimate relationships between smaller symbionts and larger hosts, have profound impacts on eukaryotic organisms. However, symbiont effects on host fitness in natural conditions are difficult to study, especially for microbial hosts. We used killer viruses and the wild yeastSaccharomyces paradoxusto study a symbiotic virus’s effect on its host’s fitness in oak litter. We cured hosts of naturally-occurring killer viruses and compared killer and cured individuals’ fitnesses in laboratory medium and oak litter using a unique field chamber design to house competingS. paradoxus. In the laboratory, the impact of virus loss on host fitness could be positive, negative, or neutral, depending on host identity. Trends in the forest were similar to those in the lab, although only overall strain fitness differences were significant and curing impacts differed between the forest and laboratory. These results demonstrate the importance of incorporating environmental context into studies of host-symbiont interactions.
Comprehensive Characterization of BTK Inhibitor Specificity, Potency, and Biological Effects: Insights into Covalent and Non-covalent Mechanistic Signatures
Authors: Darragh Antonia C. , Hanna Andrew M. , Lipner Justin H. , Servant Nicole B. , King Alastair J. , Jahic Mirza 
Published: September 2024

AbstractUncovering a drug’s mechanism of action and possible adverse effects are critical components in drug discovery and development. Moreover, it provides evidence for why some drugs prove more effective than others, and how to design better drugs altogether. Here we demonstrate the utility of a high- throughputin vitroscreening platform along with a comprehensive panel to aid in the characterization of fifteen BTK inhibitors that are either approved by the FDA or presently under clinical evaluation. To compare the potency of these drugs, we measured the binding affinity of each to wild-type BTK, as well as a clinically relevant resistance mutant of BTK (BTK C481S). In doing so, we discovered a considerable difference in the selectivity and potency of these BTK inhibitors to the wild-type and mutant proteins. Some of this potentially contributes to the adverse effects experienced by patients undergoing therapy using these drugs. Overall, non-covalent BTK inhibitors showed stronger potency for both the wild-type and mutant BTK when compared with that of covalent inhibitors, with the majority demonstrating a higher specificity and less off-target modulation. Additionally, we compared biological outcomes for four of these inhibitors in human cell-based models. As expected, we found different phenotypic profiles for each inhibitor. However, the two non-covalent inhibitors had fewer off-target biological effects when compared with the two covalent inhibitors. This and similar in-depth preclinical characterization of drug candidates can provide critical insights into the efficacy and mechanism of action of a compound that may affect its safety in a clinical setting.Table of Contents/Abstract Graphic
Deep Generative Optimization of mRNA Codon Sequences for Enhanced Protein Production and Therapeutic Efficacy
Authors: Li Yupeng , Wang Fan , Yang Jiaqi , Han Zirong , Chen Linfeng , Jiang Wenbing , Zhou Hao , Li Tong , Tang Zehua , Deng Jianxiang , He Xin , Zha Gaofeng , Hu Jiekai , Hu Yong , Wu Linping , Zhan Changyou , Sun Caijun , He Yao , Xie Zhi 
Published: September 2024

ABSTRACTMessenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboCode, a deep learning framework that generates mRNA codon sequences for enhanced protein production. RiboCode introduces several advances, including direct learning from large-scale ribosome profiling data, context-aware mRNA optimization and generative exploration of a large sequence space.In silicoanalysis demonstrate RiboCode’s robust predictive accuracy for unseen genes and cellular environments.In vitroexperiments show substantial improvements in protein expression, with up to a 72-fold increase, significantly outperforming past methods. In addition, RiboCode achieves cell-type specific expression and demonstrates robust performance across different mRNA formats, including m1Ψ-modified and circular mRNAs, an important feature for mRNA therapeutics.In vivomouse studies show that optimized influenza hemagglutinin mRNAs induce ten times stronger neutralizing antibody responses against influenza virus compared to the unoptimized sequence. In an optic nerve crush model, optimized nerve growth factor mRNAs achieve equivalent neuroprotection of retinal ganglion cells at one-fifth the dose of the unoptimized sequence. Collectively, RiboCode represents a paradigm shift from rule-based to data-driven, context-sensitive approach for mRNA therapeutic applications, enabling the development of more potent and dose-efficient treatments.
Resolving Symbiodiniaceae diversity across coral microhabitats and reef niches
Authors: Million Wyatt C. , Voolstra Christian R. , Perna Gabriela , Puntin Giulia , Rowe Katherine , Ziegler Maren 
Published: September 2024

AbstractDinoflagellates of the family Symbiodiniaceae are main symbionts of diverse marine animals. A large diversity of Symbiodiniaceae also occur beyond the bounds of their multicellular hosts, occupying environmental niches on coral reefs. The link between spatial diversity at ecosystem scale to microhabitats of Symbiodiniaceae within the coral holobiont are largely unknown. Using ITS2 amplicon sequencing, we compared Symbiodiniaceae communities across four environments (seawater, near-reef and distant sediments, and turf algae mats) and two coral microhabitats (tissue and mucus) on a coral reef in the Red Sea. Analysis of ITS2 sequences revealed that coral and environmental habitats were both dominated by the generaSymbiodinium,Cladocopium, andDurusdinium, but environmental habitats additionally harboredFugacium,Gerakladium, andHalluxium. Each environmental habitat harbored a distinct Symbiodiniaceae community, with 14-27 % exclusive ITS2 sequences. Nonetheless, 17 ITS2 sequences were shared among all habitat types and were variants defining nearly half of the ITS2 type profiles used to further resolve Symbiodiniaceae identity of coral-based communities. Tissues and surface mucus layers of 49 coral colonies from 17 genera had largely identical Symbiodiniaceae communities. Together with the large difference between environmental Symbiodiniaceae communities and those in the mucus, our results indicate a clear barrier between host-associated and environmental Symbiodiniaceae communities marked by only few shared complete type profiles under normal conditions. It remains to be determined how Symbiodiniaceae community dynamics between coral microhabitats and environmental reservoirs change during coral bleaching events. Monitoring coral colonies after mucus sampling confirmed its suitability for repeated long-term monitoring of coral-associated Symbiodiniaceae communities.
Typical development of synaptic and neuronal properties can proceed without microglia in the cortex and thalamus
Authors: O’Keeffe Mary , Booker Sam A , Walsh Darren , Li Mosi , Henley Chloe , de Oliveira Laura Simões , Liu Mingshan , Wang Xingran , Banqueri-Lopez Maria , Ridley Katherine , Dissanyake Kosala , Martinez-Gonzales Cristina , Craigie Kirsty , Vasoya Deepali , Leah Tom , He Xin , Hume David A , Duguid Ian , Nolan Matthew F , Qiu Jing , Wyllie David J. A. , Dando Owen R , Gonzales-Sulsar Alfredo , Gan Jian , Pridans Clare , Kind Peter C , Hardingham Giles E 
Published: September 2024

AbstractBrain-resident macrophages, microglia, have been proposed to play an active role in synaptic refinement and maturation, influencing plasticity and circuit-level connectivity. Here we show that a variety of neurodevelopmental processes previously attributed to microglia can proceed without them. Using a genetically modified mouse which lacks microglia (Csf1rΔFIRE/ΔFIRE) we find that intrinsic properties, synapse number and synaptic maturation are largely normal in the hippocampal CA1 region and somatosensory cortex at stages where microglia have been implicated. Seizure susceptibility and hippocampal-prefrontal cortex coherence in awake behaving animals, processes disrupted in mice deficient in microglia-enriched genes, are also normal. Similarly, eye-specific segregation of inputs into the lateral geniculate nucleus proceeds normally in the absence of microglia. Single cell/nucleus transcriptomic analyses of neurons and astrocytes did not uncover any substantial perturbation due to microglial absence. Thus, the brain possesses remarkable adaptability to execute developmental synaptic refinement, maturation and connectivity in the absence of microglia.
detectEVE: fast, sensitive and precise detection of endogenous viral elements in genomic data
Authors: Brait Nadja , Hackl Thomas , Lequime Sebastian 
Published: September 2024

AbstractSummaryEndogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs due to their genomic integration during their life cycle, however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr)EVEs. Detecting nrEVEs poses challenges due to their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection.Here, we introducedetectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies.detectEVEdeviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows thatdetectEVEis computationally efficient and accurate, as well as considerably faster than existing approaches, due to its resource-efficient parallel execution.Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.Availability and ImplementationdetectEVEis implemented as snakemake workflow, available with detailed documentation athttps://github.com/thackl/detectEVEand can be easily installed using conda.
Enhancing HBV-specific T cell responses through a combination of epigenetic modulation and immune checkpoint inhibition
Authors: Urbanek-Quaing Melanie , Chou Yin-Han , Gupta Manoj Kumar , Steppich Katja , Bremer Birgit , Schmaus Hagen , Deterding Katja , Maasoumy Benjamin , Wedemeyer Heiner , Xu Cheng-Jian , Kraft Anke R M , Cornberg Markus 
Published: September 2024

AbstractObjectiveChronic hepatitis B virus (HBV) infection results in the exhaustion of HBV-specific T cells and the development of epigenetic imprints that impair immune responses and limit the effectiveness of immune checkpoint inhibitor (ICI) monotherapy, such as αPD-L1. This study aimed to determine whether the DNA methyltransferase inhibitor decitabine (DAC) can reverse these epigenetic imprints and enhance the efficacy of ICI in restoring HBV-specific T cell responses.MethodsWe investigated HBV-specific CD4+and CD8+T cell responses by 10-dayin vitrostimulation of peripheral blood mononuclear cells (PBMCs) from patients with chronic HBV infection. PBMCs were stimulated with HBV core-specific overlapping peptide pools and HLA-A*02-restricted peptides, including core18and pol455. The immunomodulatory effect of the combination of DAC/αPD-L1 was assessed via flow cytometry. Responder stratification was investigated by comparison of clinical characteristics,ex vivoDNA methylation analysis of PBMCs, and determination of IFNγ plasma levels.ResultsTreatment with DAC and αPD-L1 enhanced HBV-specific CD4+T cell responses in a significant proportion of 53 patients, albeit with variability. The effect was independent of the HBcrAg level.Ex vivoDNA methylation revealed hypermethylation of key genes likeIFNGamong DAC-responders versus non-responders, supported by alteredex vivoIFNγ plasma levels. Further analysis of HBV-specific CD8+T cell responses in 22 HLA-A*02-positive patients indicated distinct response patterns between HBV-core18- and HBV-pol455-specific T cells, with pol455-specific CD8+T cells showing increased susceptibility to DAC/αPD-L1, surpassing αPD-L1 monotherapy response.ConclusionsThe combination of DAC and αPD-L1 shows promising effects in improving HBV-specific T cell responsesin vitro. Our study highlights the potential of remodeling exhaustion-associated epigenetic signatures to enhance HBV-specific T cell restoration, suggesting a novel immunotherapeutic avenue for chronic HBV infections.Graphic AbstractHighlightsRemodeling epigenetic signatures with a DNA methyltransferase inhibitor enhances the effectiveness of immune checkpoint inhibition in restoring HBV-specific T cell responses.Responsiveness is associated with specific IFNγ DNA methylation patterns and plasma levels.Epigenetic remodeling had distinct effects on two CD8 T cell epitopes, with more pronounced effects on HBV-pol455-specific CD8+T cell responses.
Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine
Authors: Krude Torsten , Bi Jiaming , Doran Rachel , Jones Rebecca A. , Smith James C 
Published: September 2024

SummaryDNA replication initiates at tens of thousands of sites on the human genome during each S phase. However, no consensus DNA sequence has been found that specifies the locations of these replication origins. Here, we investigate modifications of human genomic DNA by density equilibrium centrifugation and DNA sequencing. We identified short discrete sites with increased density during quiescence and G1 phase that overlap with DNA replication origins before their activation in S phase. The increased density is due to the oxidation of 5-methyl-deoxycytidines by TET enzymes at GC-rich domains. Reversible inhibition of de novo methylation and of subsequent oxidation of deoxycytidines results in a reversible inhibition of DNA replication and of cell proliferation. Our findings suggest a mechanism for the epigenetic specification and semiconservative inheritance of DNA replication origin sites in human cells that also provides a stable integral DNA replication licence to support once-per-cell cycle control of origin activation.
Multiplexing bacteriocin synthesis to kill and prevent antimicrobial resistance
Authors: Quintero-Yanes Alex , Petit Kenny , Rodriguez-Villalobos Hector , Vande Capelle Hanne , Masschelein Joleen , Borrero Juan , Gabant Philippe 
Published: September 2024

AbstractAntibiotic resistance represents an emergency for global public health. This calls for using alternative drugs and developing innovative therapies based on a clear understanding of their mechanisms of action and resistance in bacteria. Bacteriocins represent a unique class of natural molecules selectively eliminating bacteria. These secreted proteins exhibit a narrower spectrum of activity compared to conventional broad-spectrum antimicrobials by interacting with specific protein and lipid receptors on bacterial cell envelopes. Despite their diverse molecular structures, the commonality of being genetically encoded makes bacteriocins amenable to synthetic biology design. In using cell-free gene expression (CFE) and continuous-exchange CFE (CECFE), we produced controlled combinations (cocktails) of bacteriocins in single synthesis reactions for the first time. A first set of bacteriocin cocktails comprising both linear and circular proteins allowed the targeting of different bacterial species. Other cocktails were designed to target one bacterial species and considering bacteriocins pathways to cross the cell-envelope. Such combinations demonstrated efficient bacterial eradication and prevention of resistance. We illustrate the effectiveness of these bacteriocin mixtures in eradicating various human pathogenic-multiresistant—isolates. Finally, we highlight their potential as targeted and versatile tools in antimicrobial therapy by testing a combination of bacteriocins for treatmentin vivoin the animal modelGalleria mellonella.
Abnormal hyperactivity of specific striatal ensembles encodes distinct dyskinetic behaviors revealed by high-resolution clustering
Authors: Alcacer Cristina , Klaus Andreas , Mendonça Marcelo , Abalde Sara F. , Cenci Maria Angela , Costa Rui M. 
Published: September 2024

AbstractL-DOPA-induced dyskinesia (LID) is a debilitating complication of dopamine replacement therapy in Parkinsońs disease and the most common hyperkinetic disorder of basal ganglia origin. Abnormal activity of striatal D1 and D2 spiny projection neurons (SPNs) is critical for LID, yet the link between SPN activity patterns and specific dyskinetic movements remains unknown. To explore this, we developed a novel method for clustering movements based on high-resolution motion sensors and video recordings. In a mouse model of LID, this method identified two main dyskinesia types and pathological rotations, all absent during normal behavior. Using single-cell resolution imaging, we found that specific sets of both D1 and D2-SPNs were abnormally active during these pathological movements. Under baseline conditions, the same SPN sets were active during behaviors sharing physical features with LID movements. These findings indicate that ensembles of behavior-encoding D1- and D2-SPNs form new combinations of hyperactive neurons mediating specific dyskinetic movements.
Modelling how lamellipodia-driven cells maintain persistent migration and interact with external barriers
Authors: Sadhukhan Shubhadeep , Martinez-Torres Cristina , Penič Samo , Beta Carsten , Iglič Aleš , Gov Nir 
Published: September 2024

Cell motility is fundamental to many biological processes, and cells exhibit a variety of migration patterns. Many motile cell types follow a universal law that connects their speed and persistency, a property that can originate from the intracellular transport of polarity cues due to the global actin retrograde flow. This mechanism was termed the “Universal Coupling between cell Speed and Persistency”(UCSP). Here we implemented a simplified version of the UCSP mechanism in a coarse-grained “minimal-cell” model, which is composed of a three-dimensional vesicle that contains curved active proteins. This model spontaneously forms a lamellipodia-like motile cell shape, which is however sensitive and can depolarize into a non-motile form due to random fluctuations or when interacting with external obstacles. The UCSP implementation introduces long-range inhibition, which stabilizes the motile phenotype. This allows our model to describe the robust polarity observed in cells and explain a large variety of cellular dynamics, such as the relation between cell speed and aspect ratio, cell-barrier scattering, and cellular oscillations in different types of geometric confinements.Significance StatementCoupling curved membrane proteins to active protrusive forces that arise from recruited actin polymerization, can lead, in the presence of adhesion, to self-organization of a leading-edge cluster and a motile “minimal-cell”. However, this polarized and motile shape can become unstable, and due to fluctuations or interactions with external perturbations transform to an immotile, symmetric shape. Here we couple the spatial organization of the curved active proteins to a global advection of a polarity cue along the cell’s activity axis. Introducing long-range inhibition, the resultant gradient of the polarity-cue stabilizes the motile, polarized “minimal-cell” vesicle. We thereby present a robust model of cell motility that can explain a variety of cellular shape-migration relations, cell-barrier scattering and spontaneous oscillations of confined cells.