bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Powassan virus deletions and defective RNA in field collected ticks
Authors: Langsjoen Rose M. , Courtney Samantha J. , Trammell Chasity E. , Robich Rebecca M. , Goethert Heidi K. , McMinn Rebekah J. , Telford Sam R. , Ebel Gregory D. , Piantadosi Anne 
Published: October 2024

ABSTRACTPowassan virus (POWV) is a tick-borne flavivirus in the tick-borne encephalitis virus (TBEV) serogroup endemic to the United States, Canada, and parts of Russia. POWV remains an under-studied pathogen, despite the potential for serious and life-threatening neurologic complications following infection. While prior studies have characterized viral diversity due to single nucleotide polymorphisms, little is known about POWV recombination, defective RNAs (D-RNAs), and functional structural variants (SVs). Understanding POWV recombination in its natural vector can provide important insights into its replication and evolution. Thus, we analyzed POWV sequence data from 51 ticks collected from the Northeast United States to characterize deletion expression levels and patterns in naturally infected ticks, and we compared these results to single-passage isolates. We found that deletions were common in POWV RNA from ticks and that several areas of the genome were enriched for recombination junctions. Deletions were often associated with areas of microhomology. While most deletions were sample-specific, two major deletion archetypes were observed across multiple tick samples. The first consisted of small 19-50 base deletions in the methyltransferase domain of the ns5 RNA-dependent RNA-polymerase gene, resulting in a mixture of putative SVs and D-RNAs. The second consisted of approximately 1600 base deletions spanning the ns2a-ns3 genes, resulting in putative D-RNAs with abrogated viral protease function. Protease deletions were significantly enriched after one passage in baby hamster kidney cells despite a decrease in overall deletion expression. These results demonstrate the proclivity of POWV for recombination, with potential implications for immune evasion and persistence in ticks.IMPORTANCEPowassan virus is a tick-borne flavivirus that can cause serious, life-threatening neurological disease. Understanding how Powassan virus replicates and evolves within its tick vector may elucidate factors important in persistence, transmission, and human disease. Defective RNAs are replication-incompetent viral genomes generated through internal deletions, which have been associated with disease severity and persistent infection in other viruses but have not been described for Powassan virus. Here, we show that Powassan virus produces abundant defective RNAs in field-caught ticks, and that expression patterns of these defective RNAs changes after one passage in mammalian cells. Although the function of these defective RNAs remains unknown, this work establishes a critical framework for investigating the role of defective RNAs in Powassan virus replication and transmission.
Functional classification of tauopathy strains reveals the role of protofilament core residues
Authors: Vaquer-Alicea Jaime , Manon Victor A. , Bommareddy Vaibhav , Kunach Peter , Gupta Ankit , Monistrol Jim , Perez Valerie A. , Tran Hung Tri , Saez-Calveras Nil , Du Siling , Batra Sushobhna , White Charles L. , Joachimiak Lukasz A. , Shahmoradian Sarah H. , Diamond Marc I. 
Published: October 2024

AbstractDistinct tau amyloid assemblies underlie diverse tauopathies but defy rapid classification. Cell and animal experiments indicate tau functions as a prion, as different strains propagated in cells cause unique, transmissible neuropathology after inoculation. Strain amplification requires compatibility of the monomer and amyloid template. We used cryo-EM to study one cell-based YFP-tagged strain, resolving its amyloid nature. We then used sequential alanine (Ala) substitution (scan) within tau repeat domain (RD) to measure incorporation to pre-existing tau RD-YFP aggregates. This robustly discriminated strains, defining sequences critical for monomer incorporation. We then created 3R/4R or 4R WT RD (aa 246-408) biosensors. Ala scan of recombinant tau seeds with the Alzheimer’s Disease fold matched that of AD homogenate. We scanned 22 brain lysates comprising 4 tauopathies. This clustered cases by neuropathological syndrome, revealed the role of amino acids in protofilament folds, and allowed strain discrimination based on amino acid requirements for prion replication.TeaserDiscrimination of tau strains based on the relative contribution of each amino acid to templated propagation of the amyloid.
Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes
Authors: Chan Chun Kit , Nguyen Jonathan , Hryc Corey F. , Gupta Chitrak , Redding Kevin , Dowhan William , Baker Matthew L. , Perez Alberto , Mileykovskaya Eugenia , Singharoy Abhishek 
Published: October 2024

AbstractThe biological significance of protein supercomplexes have remained contentious, particularly how they tune the shuttling of charge-carrier redox proteins across cell membranes during biological energy conversion. We employ multiscale modeling and single particle cryo-electron microscopy (cryo-EM) to determine the mechanisms of diffusive electron transfer in mitochondrial supercomplexes, composed of respiratory complexes III and IV (CIII and CIV). Using a combination of bioinformatic and entropy maximization tools, we model an ensemble of structures representing the conformational space of CIII’s disordered QCR6 ‘hinge’ within the yeast CIII2CIV2supercomplex. Molecular and Brownian Dynamics simulations of the entire supercomplex reveal a mechanism for electrostatic coupling between these negatively charged hinge conformations, and binding and directional diffusion of the redox proteins on the mitochondrial membrane, which is simulated over the millisecond timescale. Anionic lipids reinforce this conformationally-coupled recognition of the supercomplex by retaining a pool of the redox proteins in the vicinity of the membrane when the hinges are of a critical length. Cryo-EM models reveal a large-scale rearrangement of the ΔQCR6 supercomplex, which retains a surprisingly robust electrostatic environment for recognition of the redox protein, despite compromise in the supercomplex’s negative charge, still enabling a surface-mediated electron transfer in this CIII2CIV2variant. Altogether, the evolutionary need of confining electron carriers on the surface of bioenergetic membranes is found to give rise to a refolding-guided diffusion model of the redox proteins, which improves the energy conversion efficiency within the supercomplex by nearly 30%.
Single Nuclei Sequencing Reveals Intratumoral Cellular Heterogeneity and Replication Stress in Adrenocortical Carcinoma
Authors: Popova Liudmila V. , Garfinkle Elizabeth A. R. , Chopyk Daniel M. , Navarro Jaye B. , Rivaldi Adithe , Shu Yaoling , Lomonosova Elena , Phay John E. , Miller Barbra S. , Sattuwar Swati , Mullen Mary , Mardis Elaine R. , Miller Katherine E. , Dedhia Priya H. 
Published: October 2024

ABSTRACTAdrenocortical carcinoma (ACC) is a rare endocrine malignancy with a poor prognosis and limited treatment options. Bulk genomic characterization of ACC has not yielded obvious therapeutic or immunotherapeutic targets, yet novel therapies are needed. We hypothesized that elucidating the intratumoral cellular heterogeneity by single nuclei RNA sequencing analyses would yield insights into potential therapeutic vulnerabilities of this disease. In addition to characterizing the immune cell and fibroblast landscape, our analyses of single nuclei gene expression profiles identified an adrenal cortex cell cluster exhibiting a program of replication stress and DNA damage response in primary and metastatic ACC.In vitroassessment of replication stress and DNA damage response using an ACC cell line and a series of newly-derived hormonally active patient-derived tumor organoids revealed ATR sensitivity. These findings provide novel mechanistic insight into ACC biology and suggest that an underlying dependency on ATR may be leveraged therapeutically in advanced ACC.
Linking microscopy to diffusion MRI with degenerate biophysical models: an application of the Bayesian EstimatioN of CHange (BENCH) framework
Authors: Kor Daniel Z.L. , Rafipoor Hossein , Huszar Istvan N. , Smart Adele , Daubney Greg , Jbabdi Saad , Cottaar Michiel , Miller Karla L. , Howard Amy F.D. 
Published: October 2024

AbstractBiophysical modelling of diffusion MRI (dMRI) is used to non-invasively estimate microstructural features of tissue, particularly in the brain. However, meaningful description of tissue requires many unknown parameters, resulting in a model that is often ill-posed. The Bayesian EstimatioN of CHange (BENCH) framework was specifically designed to circumvent parameter fitting for ill-conditioned models when one is simply interested in interpreting signal changes related to some variable of interest. To understand the biological underpinning of some observed change in MR signal between different conditions, BENCH predicts which model parameter, or combination of parameters, best explains the observed change, without having to invert the model. BENCH has been previously used to identify which biophysical parameters could explain group-wise dMRI signal differences (e.g. patients vs. controls); here, we adapt BENCH to interpret dMRI signal changes related to continuous variables. We investigate how parameters from the dMRI standard model of white matter, with an additional sphere compartment to represent glial cell bodies, relate to tissue microstructure quantified from histology. We validate BENCH using synthetic dMRI data from numerical simulations. We then apply it to ex-vivo macaque brain data with dMRI and microscopy metrics of glial density, axonal density, and axonal dispersion in the same brain. We found that (i) increases in myelin density are primarily associated with an increased intra-axonal volume fraction and (ii) changes in the orientation dispersion derived from myelin microscopy are linked to variations in the orientation dispersion index. Finally, we found that the dMRI signal is sensitive to changes in glial cell soma in the WM, but that no parameter in the extended standard model was able to explain this observed signal change, suggesting model inadequacy.
Do pollinators play a role in shaping the essential amino acids found in nectar?
Authors: Parkinson Rachel H. , Power Eileen F. , Walter Kieran , McDermott-Roberts Alex E. , Pattrick Jonathan G. , Wright Geraldine A. 
Published: October 2024

SummaryPlants produce floral nectar as a reward for pollinators, which contains carbohydrates and amino acids (AAs). We designed experiments to test whether pollinators could exert selection pressure on the profiles of AAs in nectar.We used HPLC to measure the free amino acids and sugars in the nectar of 102 UK plant species. Six distinct profiles of essential amino acids (EAAs) were defined using the relative proportions of AAs with a clustering algorithm; we then tested bumblebee (Bombus terrestris) preferences for the EAA profiles and proline using a two-choice assay.We found a phylogenetic signal for the proportions of phenylalanine, methionine and proline as well as the total concentrations of essential and non-essential AAs. However, there was no phylogenetic signal for EAA profile. Bumblebees did not exhibit a preference for any of the six EAA nectar profiles, however, four of the EAA profiles stimulated feeding. In contrast, bumblebees avoided proline in an inverse concentration-dependent manner.Our data indicate that bees are likely to have mechanisms for the post-ingestive evaluation of free AAs in solution but are unlikely to taste EAAs at nectar-relevant quantities. We predict that EAAs increase nectar value to bumblebees post-ingestively.
Inferring Time-Varying Internal Models of Agents Through Dynamic Structure Learning
Authors: James Ashwin , Bethus Ingrid , Muzy Alexandre 
Published: October 2024

AbstractReinforcement learning (RL) models usually assume a stationary internal model structure of agents, which consists of fixed learning rules and environment representations. However, this assumption does not allow accounting for real problem solving by individuals who can exhibit irrational behaviors or hold inaccurate beliefs about their environment. In this work, we present a novel framework called Dynamic Structure Learning (DSL), which allows agents to adapt their learning rules and internal representations dynamically. This structural flexibility enables a deeper understanding of how individuals learn and adapt in real-world scenarios. The DSL framework reconstructs the most likely sequence of agent structures—sourced from a pool of learning rules and environment models—based on observed behaviors. The method provides insights into how an agent’s internal structure model evolves as it transitions between different structures throughout the learning process. We applied our framework to study rat behavior in a maze task. Our results demonstrate that rats progressively refine their mental map of the maze, evolving from a suboptimal representation associated with repetitive errors to an optimal one that guides efficient navigation. Concurrently, their learning rules transition from heuristic-based to more rational approaches. These findings underscore the importance of both credit assignment and representation learning in complex behaviors. By going beyond simple reward-based associations, our research offers valuable insights into the cognitive mechanisms underlying decision-making in natural intelligence. DSL framework allows better understanding and modeling how individuals in real-world scenarios exhibit a level of adaptability that current AI systems have yet to achieve.
Computational Analysis of Zn2+Mediated Non-Competitive Inhibition to Caspase-3
Authors: Tian Xinyu Erya , Zang Min , Wang Xiaoyu , Dong Hao 
Published: October 2024

AbstractCaspase-3, a critical mediator of apoptosis, is implicated in neurodegenerative diseases and cancer, making it an attractive therapeutic target. Here, we elucidated the molecular mechanisms of caspase-3 inhibition through computational methods. We first investigated the binding of the canonical substrate DEVD and novel peptidomimetic inhibitors, characterizing their competitive inhibition mechanisms. Using AlphaFold3 and molecular dynamics simulations, we then identify Zn2+-binding sites and characterize conformational changes induced by Zn2+chelation, revealing a mechanism for non-competitive inhibition. Our results provide atomic-level insights into both competitive and Zn2+-mediated non-competitive inhibition of caspase-3, enhancing our understanding of apoptotic pathways. These findings could help guide the development of targeted therapies for apoptosis-related disorders, encompassing both competitive inhibitors and non-competitive modulators.
Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
Authors: Ferraz Matheus V. F. , Adan W. Camilla S. , Lima Tayná E. , Santos Adriele J. C. , de Paula Sérgio O. , Dhalia Rafael , Wallau Gabriel L. , Wade Rebecca C. , Viana Isabelle F. T. , Lins Roberto D. 
Published: October 2024

AbstractThe design of proteins capable to effectively bind to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining regions (CDRs)-grafting approach for designing nanobodies (Nbs) that target specific epitopes, with the aid of computer simulation and machine learning. As a proof-of-concept, we designed, evaluated, and characterized a high-affinity Nb against the spike protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. The designed Nb, referred to as Nb Ab.2, was synthesized and displayed high-affinity for both the purified receptor-binding domain protein and to the virus-like particle, demonstrating affinities of 9 nM and 60 nM, respectively, as measured with microscale thermophoresis. Circular dichroism showed the designed protein’s structural integrity and its proper folding, whereas molecular dynamics simulations provided insights into the internal dynamics of Nb Ab.2. This study shows that our computational pipeline can be used to efficiently design high affinity Nbs with diagnostic and prophylactic potential, which can be tailored to tackle different viral targets.Author summaryIn this study, we present a pipeline for designing a high-affinity nanobody (Nb) targeting the SARS-CoV-2 spike protein using enhanced sampling molecular dynamics simulations and CDR-grafting. To address the challenges of CDR grafting in Nbs, including the need for structural similarity between the CDR motif of interest and the scaffold region, we utilized the Nb scaffold cAbBCII10, known for its versatility in accommodating various CDRs. We generated a library based on the cAbBCII10 framework with diverse, unrelated CDRs and applied machine learning to identify the most promising candidates. Our approach enabled successful engineering of a Nb that binds to the SARS-CoV-2 spike protein with high affinity, demonstrating the effectiveness of our design pipeline for potential therapeutic applications.
Detection of positive selection driving antimicrobial resistance in the core genome ofStaphylococcus epidermidis
Authors: Rimmer Callum O. , Thomas Jonathan C. 
Published: October 2024

AbstractStaphylococcus epidermidisis a commensal skin organism and leading cause of medical-device associated infections. Although previous research has investigated the phylogenetic diversity of the species, the level of positive selection on the core genome has yet to be explored. Here, we present the first core genome-wide screen of positive selection in the species. A curated dataset of 1003 whole-genome sequences (WGS) was created which represented the global diversity of the species, including all previously identified clades and genetic clusters (GCs). A 100-strain subset, which retained the diversity of the collection, was created by pruning the species-level tree with treemmer; core genes present in all genomes were extracted with Roary and used for positive selection analysis (n = 826). Site-level analysis was performed using PAML with omegaMap for confirmation. Selection along branches separating clades A and B were also investigated using PAML branch-site models and HyPhy. PAML site analysis revealed 17 genes under selection, including six hypothetical genes, most of which were linked to metabolism or transport. Several genes were associated with antimicrobial resistance, such asileSwhich confers resistance to mupirocin.cysGandsirC, which catalyse the first two steps in the synthesis of siroheme, were also under selection. Two genes were found to be under selection at the branch-site level by both PAML and HyPhy, of which only one,rhtC, has been functionally characterised. Our analysis reveals the extent to which positive selection is operating on the core genome and identifies candidate genes which may have important roles in the fitness of the species.
Modulation of the ATP-adenosine signaling axis combined with radiotherapy facilitates anti-cancer immunity in brain metastasis
Authors: Salamero-Boix Anna , Schulz Michael , Anthes Julian , Mayer Jens , Möckl Aylin , Tsoukala Ioanna , Menger Dominic , Mosa Mohammed H. , Hetzer Jenny , Macas Jadranka , Hehlgans Stephanie , Schuck Jonas , Roller Bastian , Reiss Yvonne , Hochart Guillaume , Bonnel David , Medyouf Hind , Rodriguez Mariana Barcenas , Broggini Thomas , Czabanka Marcus , Plate Karl H. , Heikenwälder Mathias , Rödel Franz , Harter Patrick N. , Imkeller Katharina , Sevenich Lisa 
Published: October 2024

SummaryThe immunosuppressive microenvironment in the brain poses a major limitation to successful therapy for brain metastases. Here we report that blockade of the ATP-to-adenosine-converting enzymes CD39 and CD73 and the adenosine receptor A2AR in combination with radiotherapy attenuates tumor progression in a breast-to-brain metastasis model by facilitating anti-cancer immunity. Immunophenotyping revealed loss of exhausted T cells and higher abundance of anti-cancer effector T cell populations. This effect was accompanied by a decrease of immunosuppressive lipid-laden macrophages and an expansion of CD14CD33high macrophages associated with antigen presentation. Analyses of human brain metastases samples supports a role of the ATP-adenosine signaling axis in modulating tumor inflammation and identified expression of CD39 and adenosine deaminase as predictive markers for patient survival and/or immune infiltration. Our findings demonstrate that the adenosine axis represents a druggable pathway to achieve local immunomodulation and treatment response, opening a new therapeutic avenue for brain metastases patients.
Sporadic distribution of a new archaeal genetic code with all TAG codons as pyrrolysine
Authors: Kivenson Veronika , Peters Samantha L. , Borrel Guillaume , Kivenson Aleksandr , Roe Leah T. , Hamlish Noah X. , Fadhlaoui Khaled , Schepartz Alanna , Gribaldo Simonetta , Hettich Robert L. , Banfield Jillian F. 
Published: October 2024

AbstractNumerous genetic codes developed during the evolution of Eukaryotes and three are known in Bacteria, yet no alternative genetic code has been established for Archaea. Some bacterial and archaeal proteins include selenocysteine or pyrrolysine, the 21stand 22ndamino acids, but no evidence establishes the adoption of a genetic code in which a stop codon universally encodes either amino acid. Here, we used proteomics to confirm the prediction that certain Archaea consistently incorporate pyrrolysine at TAG codons, supporting a new archaeal genetic code which we designate Genetic Code 34. This genetic code has 62 sense codons encoding 21 amino acids, and only two stop codons. In contrast with monophyletic genetic code distributions in bacteria, Code 34 occurs sporadically. This, combined with evidence for lateral gene transfer of the code change machinery and anticipated barriers to code reversal, suggests Code 34 arose independently in multiple lineages. TAG codon distribution patterns in Code 34 genomes imply a wide range in time since code switch. We identified many new enzymes containing Pyl residues, raising questions about potential roles of this amino acid in protein structure and function. We used five new PylRS/tRNAPylpairs from Code 34 archaea to introduce new-to-nature pyrrolysine analogs into proteins inE. coli, demonstrating their utility for genetic code expansion.Graphical abstract