bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional visualization of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads
Authors: Sheard Thomas M. D. , Hurley Miriam E. , Smith Andrew J. , Colyer John , White Ed , Jayasinghe Izzy 
Published: October 2022

Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery of intracellular calcium signalling in cardiomyocytes. While a range of optical super-resolution microscopy techniques have revealed the nanoscale structure of these clusters, the three-dimensional (3D) nanoscale topologies of the clusters have remained mostly unresolved. In this paper, we demonstrate the exploitation of molecular-scale resolution in enhanced expansion microscopy (EExM) along with various 2D and 3D visualization strategies to observe the topological complexities, geometries and molecular sub-domains within the RyR clusters. Notably, we observed sub-domains containing RyR-binding protein junctophilin-2 (JPH2) occupying the central regions of RyR clusters in the deeper interior of the myocytes (including dyads), while the poles were typically devoid of JPH2, lending to a looser RyR arrangement. By contrast, peripheral RyR clusters exhibited variable co-clustering patterns and ratios between RyR and JPH2. EExM images of dyadic RyR clusters in right ventricular (RV) myocytes isolated from rats with monocrotaline-induced RV failure revealed hallmarks of RyR cluster fragmentation accompanied by breaches in the JPH2 sub-domains. Frayed RyR patterns observed adjacent to these constitute new evidence that the destabilization of the RyR arrays inside the JPH2 sub-domains may seed the primordial foci of dyad remodelling observed in heart failure.This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Ontogeny of cardiomyocytes: ultrastructure optimization to meet the demand for tight communication in excitation–contraction coupling and energy transfer
Authors: Birkedal Rikke , Laasmaa Martin , Branovets Jelena , Vendelin Marko 
Published: October 2022

The ontogeny of the heart describes its development from the fetal to the adult stage. In newborn mammals, blood pressure and thus cardiac performance are relatively low. The cardiomyocytes are thin, and with a central core of mitochondria surrounded by a ring of myofilaments, while the sarcoplasmic reticulum (SR) is sparse. During development, as blood pressure and performance increase, the cardiomyocytes become more packed with structures involved in excitation–contraction (e-c) coupling (SR and myofilaments) and the generation of ATP (mitochondria) to fuel the contraction. In parallel, the e-c coupling relies increasingly on calcium fluxes through the SR, while metabolism relies increasingly on fatty acid oxidation. The development of transverse tubules and SR brings channels and transporters interacting via calcium closer to each other and is crucial for e-c coupling. However, for energy transfer, it may seem counterintuitive that the increased structural density restricts the overall ATP/ADP diffusion. In this review, we discuss how this is because of the organization of all these structures forming modules. Although the overall diffusion across modules is more restricted, the energy transfer within modules is fast. A few studies suggest that in failing hearts this modular design is disrupted, and this may compromise intracellular energy transfer.
This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Serial block face scanning electron microscopy reveals region-dependent remodelling of transverse tubules post-myocardial infarction
Authors: Perera Tharushi , Pius Charlene , Niort Barbara , Radcliffe Emma J. , Dibb Katharine M. , Trafford Andrew W. , Pinali Christian 
Published: October 2022

The highly organized transverse tubule (t-tubule) network facilitates cardiac excitation–contraction coupling and synchronous cardiac myocyte contraction. In cardiac failure secondary to myocardial infarction (MI), changes in the structure and organization of t-tubules result in impaired cardiac contractility. However, there is still little knowledge on the regional variation of t-tubule remodelling in cardiac failure post-MI. Here, we investigate post-MI t-tubule remodelling in infarct border and remote regions, using serial block face scanning electron microscopy (SBF-SEM) applied to a translationally relevant sheep ischaemia reperfusion MI model and matched controls. We performed minimally invasive coronary angioplasty of the left anterior descending artery, followed by reperfusion after 90 min to establish the MI model. Left ventricular tissues obtained from control and MI hearts eight weeks post-MI were imaged using SBF-SEM. Image analysis generated three-dimensional reconstructions of the t-tubular network in control, MI border and remote regions. Quantitative analysis revealed that the MI border region was characterized by t-tubule depletion and fragmentation, dilation of surviving t-tubules and t-tubule elongation. This study highlights region-dependent remodelling of the tubular network post-MI and may provide novel localized therapeutic targets aimed at preservation or restoration of the t-tubules to manage cardiac contractility post-MI.
This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Fast and Automated Protein-DNA/RNA Macromolecular Complex Modeling from Cryo-EM Maps
Authors: Nakamura Andrew , Meng Hanze , Zhao Minglei , Wang Fengbin , Hou Jie , Cao Renzhi , Si Dong 
Published: October 2022

ABSTRACTCryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fit residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/.
Reduction ofParaoxonaseexpression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization
Authors: Graham Allie M , Jamison Jerrica M , Bustos Marisol , Cournoyer Charlotte , Michaels Alexa , Presnell Jason S , Richter Rebecca , Crocker Daniel E. , Fustukjian Ari , Hunter Margaret E. , Rea Lorrie D. , Marsillach Judit , Furlong Clement E , Meyer Wynn K , Clark Nathan L 
Published: October 2022

ABSTRACTConvergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of theParaoxonase 1(Pon1) gene among aquatic mammal lineages -Pon1became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studyingPon1sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression ofPon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events inPon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss ofPon1function in aquatic/semiaquatic lineages is consistent with a benefit toPon1functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces ofPon1functional loss. We find that loss is best correlated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.
Stacked binding of a small molecule PET tracer to Alzheimer’s tau paired helical filaments
Authors: Merz Gregory E. , Chalkley Matthew J. , Tan Sophia , Tse Eric , Lee Joanne , Prusiner Stanley B. , Paras Nick A. , DeGrado William F. , Southworth Daniel R. 
Published: October 2022

AbstractNeurodegenerative diseases (NDs) are characterized by the formation of amyloid filaments that adopt disease-specific conformations in the brain. Recently developed small molecules hold promise as diagnostics and possible therapeutics for NDs, but their binding mechanisms to amyloid filaments remain unknown. Here, we used cryo–electron microscopy (cryo-EM) to determine a 2.7 Å structure of Alzheimer’s disease patient-derived tau paired-helical filaments incubated with the GTP-1 PET probe. GTP-1 is bound stoichiometrically along an exposed cleft of each protofilament in a stacked arrangement that matches the fibril’s symmetry. Multiscale modeling revealed favorable pi-pi aromatic stacking interactions between GTP-1 molecules that, together with small molecule–protein contacts, result in high affinity binding. This binding mode offers new insight into designing compounds for diagnosis and treatment of specific NDs.One Sentence SummaryCryo-EM structure reveals a novel stacked arrangement of the GTP-1 PET ligand bound to Alzheimer’s disease tau filaments.
Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal
Authors: Rancilhac Loïs , Miralles Aurélien , Geniez Philippe , Mendez-Aranda Daniel , Beddek Menad , Brito José Carlos , Leblois Raphaël , Crochet Pierre-André 
Published: October 2022

AbstractAimDiscontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting.LocationMoroccoTaxonSpiny-footed lizard (Acanthodactylus erythrurus), Squamata: LacertidaeMethodsUsing 325 samples from 40 localities, we identified genetic discontinuities withinA. erythrurusbased on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks).ResultA. erythrurusis characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases.Main conclusionsThe genetic diversity ofA. erythrurusoriginates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations withinA. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.
Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: comparison of experiments and computation
Authors: Pacheco-Garcia Juan Luis , Cagiada Matteo , Tienne-Matos Kelly , Salido Eduardo , Lindorff-Larsen Kresten , Pey Angel L. 
Published: October 2022

AbstractRecent advances in DNA sequencing technologies are revealing a large variability in the human genome. Our capacity to establish genotype-phenotype correlations in such large-scale is, however, limited. This task is particularly challenging due to the multifunctional nature of proteins. Here we describe an extensive analysis of the stability and function of naturally-occurring variants (found in the COSMIC and gnomAD databases) of the cancer-associated human NAD(P)H: quinone oxidoreductase 1 (NQO1). First, we performed in silico saturation mutagenesis studies (>5000 substitutions) aimed to identify regions in NQO1 important for stability and function. We then experimentally characterized twenty-two naturally-occurring variants in terms of protein levels during bacterial expression, solubility, thermal stability and coenzyme binding. These studies showed a good overall correlation between experimental analysis and computational predictions; also the magnitude of the effects of the substitutions are similarly distributed in variants from the COSMIC and gnomAD databases. Outliers in these experimental-computational genotype-phenotype correlations remain, and we discuss these on the grounds and limitations of our approaches. Our work represents a further step to characterize the mutational landscape of NQO1 in the human genome and may help to improve high-throughput in silico tools for genotype-phenotype correlations in multifunctional proteins associated with disease.
CNHplus: the chromosomal copy number heterogeneity which respects biological constraints
Authors: Grendár Marian , Martínek Petr , Loderer Dušan , Ondič Ondrej 
Published: October 2022

ABSTRACTMotivationIntra-Tumor Heterogeneity (ITH) is a hallmark of cancer. ITH influences evolution of tumors and hence also affects patients survival. There are several methods for quantifying ITH. Recently, van Dijk et al. (Nat. Commun. 12(1):1-12, 2021) introduced Copy Number Heterogeneity (CNH) method for quantifying ITH from a single tumor sample, based on a copy number profile. The authors demonstrated capability of CNH to stratify patients for survival, across cancers. We aimed to reproduce the authors’ study.ResultsA deficiency in CNH is pointed out. The absolute copy number (ACN) profile obtained by solving the CNH optimization problem may contain negative number of copies. For a large portion of samples from The Cancer Genome Atlas (TCGA) studies considered by the authors the CNH-recovered ACN profiles are faulty. CNHplus corrects the flaw by imposing the non-negativity constraint. CNHplus is applied to survival stratification of patients from the TCGA studies. Also, it is discussed which other biological constraints should be incorporated into CNHplus. CNHplus estimates of the tumor purity, tumor ploidy are compared with those of the ABSOLUTE method.Availability and implementationR library CNHplus can be accessed here:https://github.com/grendar/CNHplus
Intermediately Synchronised Brain States optimise trade-off between Subject Identifiability and Predictive Capacity
Authors: Sasse Leonard , Larabi Daouia I. , Omidvarnia Amir , Jung Kyesam , Hoffstaedter Felix , Jocham Gerhard , Eickhoff Simon B. , Patil Kaustubh R. 
Published: October 2022

AbstractFunctional connectivity (FC) refers to the statistical dependencies between activity of distinct brain areas. To study temporal fluctuations in FC within the duration of a functional magnetic resonance imaging (fMRI) scanning session, researchers have proposed the computation of an edge time series (ETS) and their derivatives. Evidence suggests that FC is driven by a few time points of high-amplitude co-fluctuation (HACF) in the ETS, which may also contribute disproportionately to interindividual differences. However, it remains unclear to what degree different time points actually contribute to brain-behaviour associations. Here, we systematically evaluate this question by assessing the predictive utility of FC estimates at different levels of co-fluctuation using machine learning (ML) approaches. We demonstrate that time points of lower and intermediate co-fluctuation levels provide overall highest subject specificity as well as highest predictive capacity of individual-level phenotypes.
Notes on the data quality of bibliographic records from the MEDLINE database
Authors: Bramley Robin , Howe Stephen , Marmanis Haralambos 
Published: October 2022

AbstractThe US National Library of Medicine has created and maintains the PubMed®database, a collection of over 33.8 million records that contain citations and abstracts from the biomedical and life sciences literature. That database is an important resource for researchers and information service providers alike. As part of our work related to the creation of an author graph for coronaviruses, we encountered several data quality issues with records from a curated subset of the PubMed database called MEDLINE. We provide a data quality assessment for records selected from the MEDLINE database and report on several issues ranging from parsing issues (e.g., character encodings and schema definition weaknesses) to low scores against several data quality metrics (e.g., identifier completeness, validity, and uniqueness).
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
Authors: Chiou Kenneth L. , Huang Xingfan , Bohlen Martin O. , Tremblay Sébastien , O’Day Diana R. , Spurrell Cailyn H. , Gogate Aishwarya A. , Zintel Trisha M. ,   Cayo Biobank Research Unit, Andrews Madeline G. , Martínez Melween I. , Starita Lea M. , Montague Michael J. , Platt Michael L. , Shendure Jay , Snyder-Mackler Noah 
Published: October 2022

AbstractCataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. Altogether, we profiled 2.58M transcriptomes and 1.59M epigenomes from single nuclei sampled from 30 regions across the adult brain. Cell composition differed extensively across the brain, revealing cellular signatures of region-specific functions. We also identified 1.19M candidate regulatory elements, many novel, allowing us to explore the landscape ofcis-regulatory grammar and neurological disease risk in a cell-type-specific manner. Together, this multi-omic atlas provides an open resource for investigating the evolution of the human brain and identifying novel targets for disease interventions.
Pro-tumor and prothrombotic activities of hepsin in colorectal cancer cells and suppression by venetoclax
Authors: Rodenas Maria Carmen , Peñas-Martínez Julia , Pardo-Sánchez Irene , Zaragoza-Huesca David , Ortega-Sabater Carmen , Peña-García Jorge , Espín Salvador , Ricote Guillermo , Montenegro Sofía , de la Peña Francisco Ayala , Luengo-Gil Ginés , Nieto Andrés , García-Molina Francisco , Vicente Vicente , Bernardi Francesco , Lozano Maria Luisa , Mulero Victoriano , Pérez-Sánchez Horacio , Carmona-Bayonas Alberto , Martínez-Martínez Irene 
Published: October 2022

ABSTRACTHepsin is a type II transmembrane serine protease whose expression has been linked to greater tumorigenicity and worse prognosis in different tumors such as prostate and gastric cancer. Recently, our group described hepsin expression in the primary biopsy as a potential biomarker of thrombosis and metastasis in localized colorectal cancer patients. Here we explored the role of hepsin in this tumor. Hepsin overexpression increased Caco-2 cell migration and invasion, higher phosphorylation of Erk1/2 and STAT3 and led to more thrombin generation in plasma. Indeed, our study revealed higher plasma levels of hepsin in metastatic colorectal cancer patients, which was associated with a greater tendency toward thrombosis. By virtual screening of a FDA-approved drug library, we identified venetoclax as a potent hepsin inhibitor, reducing the metastatic and prothrombotic phenotype of Caco-2 cells, but not of other colorectal cancer cells without hepsin expression. Interestingly, pre-treating Caco-2 cells overexpressing hepsin with venetoclax reduced its in vivo invasiveness. Taken together, our results demonstrate that elevated hepsin levels correlate with a more aggressive and prothrombotic tumor phenotype. Likewise, they evidence an antitumor role for venetoclax as a hepsin inhibitor. This lays the groundwork for molecular targeted therapy for colorectal cancer.
Biophysical analysis of Gaussia Luciferase bioluminescence mechanisms using a non-oxidizable coelenterazine
Authors: Takatsu Kyoko , Kobayashi Naohiro , Wu Nan , Janin Yves L. , Yamazaki Toshio , Kuroda Yutaka 
Published: October 2022

AbstractGaussia luciferase (GLuc 18.2kDa; 168 residues) is a marine copepod luciferase that emits a bright blue light when oxidizing coelenterazine (CTZ). It is a helical protein where two homologous sequential repeats form two anti-parallel bundles, each made of four helices. We previously identified a hydrophobic cavity as a prime candidate for the catalytic site, but Gluc’s fast bioluminescence reaction hampered a detailed analysis. Here, we used azacoelenterazine, a non-oxidizable coelenterazine analog, as a probe to investigate its binding mode to GLuc. Interestingly, the biochemical studies of GLuc inhibition by azacoelenterazine also led us to find that salt, and monovalent anions, are required for GLuc’s bioluminescence, which seems reasonable for a sea-dwelling creature. The NMR-based investigation, using chemical shift perturbations monitored by 15NH-HSQC, suggested that CTZ binds to residue in or near the hydrophobic cavity. Of note is that these NMR data are in line with a recent structural prediction of GLuc, hypothesizing that large structural changes occur in regions remote from the hydrophobic cavity upon the addition of CTZ. Interestingly, these results point toward a unique mode of catalysis to achieve CTZ oxidative decarboxylation.