bluuebunny/crossref_metadata_2025 huggingface dataset:
Frame-shift mutation ofInCOmight cause early flowering of Japanese morning glory and might have contributed to northward expansion
Authors: Katsuyama Hiroaki , Ito Takuro , Ezura Kyousuke , Haque Emdadul , Hoshino Atsushi , Nitasaka Eiji , Ono Michiyuki , Sato Shusei , Isobe Sachiko , Fukuoka Hiroyuki , Watanabe Nobuyoshi , Kuboyama Tsutomu
Published: September 2024

Japanese morning glory (Ipomoea nil), a short day plant, has been used for studying flowering times. Here, quantitative trait loci (QTL) analysis for days from sowing to flowering (DTF) of F2betweenI. nilvar. Tokyo Kokei Standard (TKS) andI. hederacealine var. Q65, an early flowering variety, revealed four QTLs:QTL Ipomoea Flowering 1–4(qIF1–4). The position ofqIF3, which had the most significant effect among the four QTLs, corresponds with that ofI. nil(orI. hederacea)CONSTANS(InCO/IhCO) in the linkage map. There is a single-base In/Del in the coding sequence ofInCO/IhCO. The single-base deletion (SBD) causes a frame-shift mutation and loss of function in TKS allele (inco-1).I. nilaccessions bearinginco-1tend to flower early, similarly to rice varieties bearing the loss of function allele ofCOortholog,hd1. Consequently,inco-1was inferred to reduce DTF. This inferred effect ofinco-1corresponds with the effect of the TKS allele ofqIF3. Becauseinco-1is found exclusively in Asian accessions, the SBD ininco-1might have played an important role in the expansion of Japanese morning glories, originally native to the tropical regions of the Americas, into temperate Asia.
Insights into the low-temperature adaptation of an enzyme as studied through ancestral sequence reconstruction
Authors: Cui Shuang , Furukawa Ryutaro , Akanuma Satoshi
Published: September 2024

For billions of years, enzymes have evolved in response to the changing environments in which their host organisms lived. Various lines of evidence suggest the earliest primitive organisms inhabited high-temperature environments and possessed enzymes adapted to such conditions. Consequently, extant mesophilic and psychrophilic enzymes are believed to have adapted to lower temperatures during the evolutionary process. Herein, we analyzed this low-temperature adaptation using ancestral sequence reconstruction. Previously, we generated the phylogenetic tree of 3-isopropylmalate dehydrogenases (IPMDHs) and reconstructed the sequence of the last bacterial common ancestor. The corresponding ancestral enzyme displayed high thermostability and catalytic activity at elevated temperatures but moderate activity at low temperatures (Furukawaet al.,Sci. Rep.10, 15493 (2020)). Here, to identify amino acid residues that are responsible for the low-temperature adaptation, we reconstructed and characterized all eleven evolutionary intermediates that sequentially connect the last bacterial common ancestor with extant mesophilic IPMDH fromEscherichia coli. A remarkable change in catalytic properties, from those suited for high reaction temperatures to those adapted for low temperatures, occurred between two consecutive evolutionary intermediates. Using a combination of sequence comparisons between ancestral proteins and site-directed mutagenesis analyses, three key amino acid substitutions were identified that enhance low-temperature catalytic activity. Intriguingly, amino acid substitutions that had the most significant impact on activity at low temperatures displayed no discernable effect on thermostability. However, these substitutions markedly reduced the activation energy for catalysis, thereby improving low-temperature activity. Our findings exemplify how ancestral sequence reconstruction can identify residues crucial for adaptation to low temperatures.
DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss
Authors: Parsons Rachel , Bansal Mukul S.
Published: September 2024

Accurate species tree reconstruction in the presence of widespread gene duplication and loss is a challenging problem in eukaryote phylogenomics. Many phylogenomics methods have been developed over the years to address this challenge; these range from older methods based on gene tree parsimony to newer quartet-based methods. In this work, we introduce improved software for gene tree parsimony-based species tree reconstruction under gene duplication and loss. The new software, DupLoss-2, uses an improved procedure for computing gene losses and is far more accurate and much easier to use than its previous version released over a decade ago. We thoroughly evaluate DupLoss-2 and eight other existing methods, including ASTRAL-Pro, ASTRAL-Pro 2, DISCO-ASTRAL, DISCO-ASTRID, FastMulRFS, and SpeciesRax, using existing benchmarking data and find that DupLoss-2 outperforms all other methods on most of the datasets. It delivers an average of almost 30% reduction in reconstruction error compared to iGTP-Duploss, the previous version of this software, and a 10% reduction compared to the best performing existing method. DupLoss-2 is written in C++ and is freely available open-source.
Segregation, Finite Time Elastic Singularities and Coarsening in Renewable Active Matter
Authors: Roychowdhury Ayan , Dasgupta Saptarshi , Rao Madan
Published: September 2024

Material renewability in active living systems, such as in cells and tissues, can drive the large-scale patterning of forces, with distinctive phenotypic consequences. This is especially significant in the cell cytoskeleton, where multiple species of myosin bound to actin, apply contractile stresses and undergo continual turnover, that result in patterned force channeling. Here we study the dynamical patterning of stresses that emerge in a hydrodynamic model of a renewable active actomyosin elastomer comprising two myosin species. We find that a uniform active contractile elastomer spontaneously segregates into spinodal stress patterns, followed by a finite-time collapse into tension carrying singular structures that display self-similar scaling and caustics. These singular structures move and merge, and gradually result in a slow coarsening dynamics in one dimension. In addition, the nonreciprocal nature of the underlying dynamics gives rise to exceptional points that are associated with a variety of travelling states – from peristalsis to swap and trains of regular and singular stress patterns, that may coexist with each other. Both the novel segregation and excitability are consequences of time reversal symmetry breaking of the underlying active dynamics. We discuss the implications of our findings to the emergence of stress fibers and the spatial patterning of myosin.
Chaperone-mediated heterotypic phase separation prevents the amyloid formation of the pathological Y145Stop variant of the prion protein
Authors: Arora Lisha , Bhowmik Dipankar , Sarkar Snehasis , Sarbahi Anusha , Rai Sandeep K. , Mukhopadhyay Samrat
Published: September 2024

Biomolecular condensates formed via phase separation of proteins and nucleic acids are crucial for the spatiotemporal regulation of a diverse array of essential cellular functions and the maintenance of cellular homeostasis. However, aberrant liquid-to-solid phase transitions of such condensates are associated with several fatal human diseases. Such dynamic membraneless compartments can contain a range of molecular chaperones that can regulate the phase behavior of proteins involved in the formation of these biological condensates. Here, we show that a heat shock protein 40 (Hsp40), Ydj1, exhibits a holdase activity by potentiating the phase separation of a disease-associated stop codon mutant of the prion protein (Y145Stop) either by recruitment into Y145Stop condensates or via Y145Stop-Ydj1 two-component heterotypic phase separation that prevents the conformational conversion of Y145Stop into amyloid fibrils. Utilizing site-directed mutagenesis, multicolor fluorescence imaging, single-droplet steady-state and picosecond time-resolved fluorescence anisotropy, fluorescence recovery after photobleaching, and fluorescence correlation spectroscopy, we delineate the complex network of interactions that govern the heterotypic phase separation of Y145Stop and Ydj1. We also show that the properties of such heterotypic condensates can further be tuned by RNA that promotes the formation of multicomponent multiphasic protein-RNA condensates. Our vibrational Raman spectroscopy results in conjunction with atomic force microscopy imaging reveal that Ydj1 effectively redirects the self-assembly of Y145Stop towards a dynamically-arrested non-amyloidogenic pathway, preventing the formation of typical amyloid fibrils. Our findings underscore the importance of chaperone-mediated heterotypic phase separation in regulating aberrant phase transitions and amyloid formation associated with a wide range of deadly neurodegenerative diseases.
The roles of lifestyle factors and genetic risk in the association between night shift work and cholelithiasis: a prospective cohort study
Authors: He Wangping , Mi Ningning , Jin Kecheng , Jin Boru , Zhong Ruyang , Liu Zhen , Lin Yanyan , Yue Ping , Xia Bin , He Qiangsheng , Smith Fang Gao , Zhen Jie , Yuan Jinqiu , Meng Wenbo
Published: September 2024

Background

Night shift work has been linked to various adverse health outcomes, but its relationship with incident cholelithiasis remains unclear. This study aims to investigate the association between night shift work and the risk of cholelithiasis, assess the potential modifying effects of genetic susceptibility, and explore the mediating roles of lifestyle factors.

Methods

A total of 219,810 subjects who were either in paid employment or self-employed were included in the UK Biobank. Information on current and lifetime employment were collected. Genetic risk was quantified and stratified by a polygenic risk score (PRS) incorporating 13 known cholelithiasis-associated loci. We used Cox proportional hazard models to investigate associations between night shift work and risk of cholelithiasis. Lifestyle factors measured at baseline were explored as potential mediators.

Results

During a median follow-up of 13.76 years, 6450 incidents of cholelithiasis were documented. Compared with day workers, the hazard ratio (HR) and 95% confidence interval (CI) of cholelithiasis was 1.09 (1.01, 1.17) for individuals with rarely/some night shifts and 1.18 (1.04, 1.35) for those with usual/permanent night shifts. Among the 62,558 participants who had reports on lifetime experience of night shift work, those with a higher frequency of night shifts and a longer length of each night shift were associated with an increased risk of cholelithiasis. Notably, individuals with usual/permanent night shifts and high genetic risk exhibited the highest risk of cholelithiasis (HR: 1.48, 95% CI: 1.21, 1.81), with day workers at low genetic risk serving as the reference. Mediation analysis indicated that a substantial portion (24.6%) of the association was mediated by BMI, followed by unhealthy alcohol intake (4.5%) and sedentary time (1.8%).

Conclusions

Night shift work is associated with an increased risk of cholelithiasis, with this relationship being largely mediated by lifestyle factors. These findings suggest that reducing the frequency and duration of night shifts may help mitigate the incidence of cholelithiasis among night shift workers, particularly for those with heightened genetic susceptibility.
Neural Representations of Extrasystoles: A Predictive Coding Perspective
Authors: Reinfeld Pia , Steinfath Tim Paul , Ku Pei-Hsin , Nikulin Vadim , Neumann Jane , Villringer Arno
Published: September 2024

The coordinated interplay between brain and body is essential for survival, with the heart-brain axis playing a fundamental role in perceptual, cognitive and motor processes. Central to this interaction, the heart-evoked potential (HEP) represents a neural correlate of the heart activity. Further, the HEP is thought to represent a neuronal prediction for each heartbeat, raising questions about its role in arrhythmia. Yet, previous studies have primarily focused on regular heart rhythms, with only a few investigations delving into arrhythmias and, notably, none into extrasystoles, a form of benign arrhythmias that disrupt the regular heart rhythm. Extrasystoles represent a unique possibility for investigating brain responses to unexpected pronounced alterations in heart rhythm. We took advantage of the largest dataset (103 subjects with 3000 extrasystoles), including both EEG and ECG recordings, and analysed the neural response to both types of extrasystoles (supraventricular and ventricular) using multiverse approaches and control analysis in time and source space. We found that the HEP was significantly reduced for ventricular extrasystoles with underlying sources in the left insular. For the postextrasystolic beat of both types of extrasystoles, we found a significantly earlier and increased HEP originating from sources in the left frontal orbital cortex and the anterior cingulate gyri. The reduced HEP response to the ventricular extrasystole might result from inactive interoceptive cardiac pathways. In contrast, increased HEP of the postextrasystolic beat along with the anatomical neural HEP generators may reflect an interoceptive prediction error arising from a naturally occurring discrepancy between the predicted and actual heart rhythm, with a main source in the anterior cingulate gyri, a primary location for prediction error processing.
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

Insulating 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

Deciding 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

Endosymbioses, 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

Abstract

Uncovering 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
Improved Genomic Prediction Performance with Ensembles of Diverse Models
Authors: Tomura Shunichiro , Wilkinson Melanie J , Cooper Mark , Powell Owen M.
Published: September 2024

The improvement of selection accuracy of genomic prediction is a key factor in accelerating genetic gain for crop breeding. Traditionally, efforts have focused on developing superior individual genomic prediction models. However, this approach has limitations due to the absence of a consistently "best" individual genomic prediction model, as suggested by the No Free Lunch Theorem. The No Free Lunch Theorem states that the performance of an individual prediction model is expected to be equivalent to the others when averaged across all prediction scenarios. To address this, we explored an alternative method: combining multiple genomic prediction models into an ensemble. The investigation of ensembles of prediction models is motivated by the Diversity Prediction Theorem, which indicates the prediction error of the many-model ensemble should be less than the average error of the individual models due to the diversity of predictions among the individual models. To investigate the implications of the No Free Lunch and Diversity Prediction Theorems, we developed a naïve ensemble-average model, which equally weights the predicted phenotypes of individual models. We evaluated this model using two traits influencing crop yield - days to anthesis and tiller number per plant - in the Teosinte Nested Association Mapping dataset. The results show that the ensemble approach increased prediction accuracies and reduced prediction errors over individual genomic prediction models. The advantage of the ensemble was derived from the diverse predictions among the individual models, suggesting the ensemble captures a more comprehensive view of the genomic architecture of these complex traits. These results are in accordance with the expectations of the Diversity Prediction Theorem and suggest that ensemble approaches can enhance genomic prediction performance and accelerate genetic gain in crop breeding programs.
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

Messenger 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

Dinoflagellates 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

Brain-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

Endogenous 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 Implementation

detectEVEis 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

Objective

Chronic 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.

Methods

We 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.

Results

Treatment 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.

Conclusions

The 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 Abstract

Highlights

Remodeling 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

DNA 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

Antibiotic 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

L-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 Statement

Coupling 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.
New evidence for the presence and function of phosphoinositides (PPIs) in the chloroplast
Authors: Sedaghatmehr Mastoureh , Rößler Frieda , Hertle Alexander P.
Published: September 2024

Essential proteins involved in thylakoid formation, including chloroplast-localized Sec14-like protein (CPSFL1) and the vesicle-inducing protein in plastids (VIPP1), bind PPIsin vitrowith high affinity. PPIs are a class of phospholipids characterized by a phosphorylated inositol head group. Although PPIs constitute a relatively small proportion of the total phospholipids, they play essential roles in various regulatory processes. The exact subcellular localization of most PPI species in plants is incomplete due to their rapid turnover and low abundance. Currently there is no documented evidence for the presence and function of phosphoinositides (PPIs) in chloroplasts. In our study, we developed genetically encoded biosensors targeted into plastids, enabling the detection of various PPI isoforms (PI3P, PI4P, PI5P, PI(4,5)P2and PI(3,5)P2) within the chloroplasts. We effectively demonstrated the specificity of our PPI biosensors in detection of PPIs, as evidenced by the alterations in PPI biosensor distribution patterns upon co-expression of PPI modifying enzymes (cTP-SAC7,cTP-PTEN, andcTP-dOCRL). Additionally, our research confirmed the capability of the generated PPI biosensors to detect PPIs within the chloroplasts of both tobacco andArabidopsisin a concentration-dependent manner. Furthermore, we unveiled the association and potential interaction of PI3P with VIPP1. We could show that the increased PPI flux within the cell during heat stress affects PPI levels in the chloroplasts, resulting in different distribution patterns of the PPI biosensors. Finally, plants expressing PPI modifierscTP-SAC7,cTP-PTEN, andcTP-dOCRL,in the chloroplast, showed increased sensitivity to drought stress, likely due to impaired PPI signaling.
Genome composition predicts physiological response to environmental change in polyploid salamanders
Authors: Burger Isabella , Itgen Michael , Tan Lynn , Woodward Parker , Rivas Linet , Hunt Tamyra , Ready Hailey , Martin Geronimo Xochitl , Denton Robert , Riddell Eric
Published: September 2024

Multi-trait analyses can be used to measure the differential performance of phenotypic traits in species complexes. Hybridization within these complexes can result in a mismatch between mitochondrial and nuclear DNA that may lead to reduced performance and acclimation capacity in hybrids. To test the effect of this mismatch on physiology, we compared physiological performance and acclimation capacity of metabolic rate (VCO2) and total resistance to water loss (rT) between two sexual Ambystoma species and a closely related unisexual lineage. We also separated unisexuals by their unique biotypes to determine how physiology varies with subgenomic composition. We found that unisexual biotypes exhibited phenotypes more like their related sexual species than to other unisexuals. We also found a trade-off between rT and VCO2, with increasing rT resulting in a decrease in VCO2. This trade-off was stronger in unisexuals than either sexual species, indicating that unisexuals may be more sensitive to environmental change. While we did not find evidence for mitonuclear mismatch, our results show that genomic composition of hybrids is more indicative of trait performance than other metrics (e.g., ploidy). Multi-trait analyses are imperative for understanding variation in phenotypic diversity, providing insight into how this diversity affects species responses to environmental change.
Dynamics and Determinants of the Gut Mobilome in Early Life
Authors: Fernández-Pato Asier , Sinha Trishla , Garmaeva Sanzhima , Gulyaeva Anastasia , Kuzub Nataliia , Roux Simon , Fu Jingyuan , Kurilshikov Alexander , Zhernakova Alexandra
Published: September 2024

As mobile genetic elements (MGE) are critical yet understudied determinants of gut microbiome composition, we characterized the gut virome and plasmidome in 195 samples from 28 mother–infant dyads delivered by caesarean section. Infant mobilome increased in richness over the first 6 postnatal weeks, demonstrating high individual-specificity and temporal stability, establishing a personal persistent mobilome. Formula-fed infants exhibited greater mobilome richness than breastfed infants, with plasmid composition influenced by antibiotic exposure and birth weight. Plasmids constituted a significant reservoir of antibiotic resistance genes (ARG), with around 5% of infant gut plasmid taxonomic units carrying ARG. Notably, ARG profiles did not differ with antibiotic exposure at birth. We found that mother–infant sharing of viral and plasmid strains primarily occurred after 6 months of age. Overall, our integrative analysis offers novel insights into the dynamics, modulation, origin, and clinical implications of MGE in the developing gut microbiome.
Two-photon driven photoprotection mechanism in echinenone-functionalized Orange Carotenoid Protein
Authors: Niziński Stanisław , Hartmann Elisabeth , Shoeman Robert L. , Wilson Adjélé , Reinstein Jochen , Kirilovsky Diana , Sliwa Michel , Burdziński Gotard , Schlichting Ilme
Published: September 2024

Orange carotenoid protein (OCP) is a photoactive protein that mediates photoprotection in cyanobacteria. OCP binds different ketocarotenoid chromophores such as echinenone (ECN), 3’- hydroxyechinenone (hECN) and canthaxanthin (CAN). In the dark, OCP is in an inactive orange form known as OCPO; upon illumination, a red active state is formed, referred to as OCPR, that can interact with the phycobilisome. Large gaps still exist in the mechanistic understanding of the events between photon absorption and formation of the OCPRstate. Recent studies suggested that more than one photon may be absorbed during the photocycle. Using a two-pulse excitation setup with variable time delays we demonstrate that canthaxanthin-functionalized OCPOforms the OCPRsignature after absorption of a single photon. By contrast, OCPOcomplexed with hECN or ECN does not photoconvert to OCPRupon single photon absorption. Instead, OCPRis formed only upon absorption of a second photon, arriving roughly one second after the first one, implying the existence of a metastable light-sensitive OCP1hvintermediate. To the best of our knowledge, a sequential 2-photon absorption mechanism in a single biological photoreceptor chromophore is unique. It results in a non-linear response function with respect to light intensity, effectively generating a threshold switch. In the case of OCP, this prevents down regulation of photosynthesis at low light irradiance.
Outbreak of Western equine encephalitis virus infection associated with neurological disease in horses following a nearly 40-year intermission period in Argentina
Authors: Vissani Maria Aldana , Alamos Florencia , Tordoya Maria Silvia , Minatel Leonardo , Schammas Juan Manuel , Dus Santos María José , Trono Karina , Barrandeguy Maria E. , Balasuriya Udeni B.R. , Carossino Mariano
Published: September 2024

Western equine encephalitis virus (WEEV) is a mosquito-borne arbovirus (genusAlphavirus, familyTogaviridae) that has reemerged in South America in late 2023 causing severe disease in both horses and humans after a nearly 40-year intermission period. We describe the virological, serological, pathological and molecular features of WEEV infection in horses during the 2023- 2024 outbreak in Argentina. WEEV-infected horses developed neurological signs with mild to severe encephalitis associated with minimal to abundant WEEV-infected cells as demonstrated by WEEV-specificin situhybridization. The distribution of viral RNA was multifocal with predominance within neuronal bodies, neuronal processes, and glial cells in the medulla oblongata and thalamic regions. Phylogenetic analysis of partial nsP4 sequences from three viral isolates obtained from three different provinces of Argentina support grouping with other temporally current WEEV strains from Uruguay and Brazil under a recently proposed novel lineage.
Catalytic relevance of quinol anion in biological energy conversion by respiratory complex I
Authors: Zdorevskyi Oleksii , Laukkanen Johannes , Sharma Vivek
Published: September 2024

Redox chemistry of quinones is an essential component of life on earth. In the mitochondrial electron transport chain, ubiquinone molecule is reduced to ubiquinol by respiratory complex I to drive the synthesis of ATP. By performing both classical and hybrid QM/MM simulations on high-resolution cryo-EM structures, including quantitative free energy calculations, we show that semiquinone species in complex I is anionic in nature and is trapped in the active site chamber for its subsequent reduction. Two-electron reduction of ubiquinone yields a metastable ubiquinol anion, which is electrostatically pushed by 15-20 Å towards the exit of the ubiquinone binding chamber to drive the proton pump of complex I. As part of the two-electron reduction of ubiquinone, protonic rearrangements take place in the active site in which a highly conserved histidine converts from its one tautomeric state to another. The combined findings provide a detailed and testable mechanistic picture of proton-coupled electron transfer reaction at the active site of complex I in wild-type as well as mutant conditions.