bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution and diversity of the TopoVI and TopoVI-like subunits with extensive divergence of the TOPOVIBL subunit
Authors: Brinkmeier Julia , Coelho Susana M. , de Massy Bernard , Bourbon Henri-Marc 
Published: May 2022

AbstractType II DNA topoisomerases regulate topology by double-stranded DNA cleavage and ligation. The TopoVI family of DNA topoisomerase, first identified and biochemically characterized in Archaea, represents, with TopoVIII and mini-A, the type IIB family. TopoVI has several intriguing features in terms of function and evolution. TopoVI has been identified in some eucaryotes, and a global view is lacking to understand its evolutionary pattern. In addition, in eucaryotes, the two TopoVI subunits (TopoVIA and TopoVIB) have duplicated and evolved to give rise to Spo11 and TopoVIBL, forming TopoVI-like (TopoVIL), a complex essential for generating DNA breaks that initiation homologous recombination during meiosis. TopoVIL is essential for sexual reproduction. How the TopoVI subunits have evolved to ensure this meiotic function is unclear. Here, we investigated the phylogenetic conservation of TopoVI and TopoVIL. We demonstrate that BIN4 and RHL1, potentially interacting with TopoVIB, have co-evolved with TopoVI. Based on model structures, this observation supports the hypothesis for a role of TopoVI in decatenation of replicated chromatids and predicts that in eucaryotes the TopoVI catalytic complex includes BIN4 and RHL1. For TopoVIL, the phylogenetic analysis of Spo11, which is highly conserved among Eukarya, highlighted a eukaryal-specific N-terminal domain that may be important for its regulation. Conversely, TopoVIBL was poorly conserved and rapidly evolving, giving rise to ATP hydrolysis-mutated or -truncated protein variants, or was undetected in some species. This remarkable plasticity of TopoVIBL provides important information for the activity and function of TopoVIL during meiosis.
Developmentally regulated alternate 3’ end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage
Authors: Berry Cameron W. , Olivares Gonzalo H. , Gallicchio Lorenzo , Ramaswami Gokul , Glavic Alvaro , Olguín Patricio , Li Jin Billy , Fuller Margaret T. 
Published: May 2022

AbstractAlternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3’ cleavage site, resulting in the production of mRNA isoforms with different length 3’UTRs. Although widespread, the role of APA in the biology of cells, tissues and organisms has been controversial. We identified over 500Drosophilagenes that express mRNA isoforms with a long 3’UTR in proliferating spermatogonia but a short 3’UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3’ end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3’UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed over 250 genes where the long 3’UTR versus short 3’UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3’end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.
A comparison of marker gene selection methods for single-cell RNA sequencing data
Authors: Pullin Jeffrey M. , McCarthy Davis J. 
Published: May 2022

AbstractThe development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalogue and probe the transcriptional heterogeneity of individual cells in unprecedented detail. A common step in the analysis of scRNA-seq data is the selection of so-called marker genes, most commonly to enable annotation of the biological cell types present in the sample. In this paper we benchmarked 56 computational methods for selecting marker genes in scRNA-seq data. The performance of the methods was compared using 10 real scRNA-seq datasets and over 170 additional simulated datasets. Methods were compared on their ability to recover simulated and expert-annotated marker genes, the predictive performance and characteristics of the gene sets they select, their memory usage and speed and their implementation quality. In addition, various case studies were used to scrutinise the most commonly used methods, highlighting issues and inconsistencies. Overall, we present a comprehensive evaluation of methods for selecting marker genes in scRNA-seq data. Our results highlight the efficacy of simple methods, especially the Wilcoxon rank-sum test, Student’s t-test and logistic regression. All code used in the evaluation, including an extensible Snakemake pipeline, is available at:https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking.
Primate sympatry shapes the evolution of their brain architecture
Authors: Robira Benjamin , Perez-Lamarque Benoît 
Published: May 2022

AbstractThe main hypotheses on the evolution of animal cognition emphasise the role of conspecifics in affecting the socio-ecological environment shaping cognition. Yet, space is often simultaneously occupied by multiple species from the same ecological guild. These sympatric species can compete for food, which may thereby stimulate or hamper cognition. Considering brain size as a proxy for cognition, we tested whether species sympatry impacted the evolution of cognition in frugivorous primates. We first retraced the evolutionary history of sympatry between frugivorous primate lineages. We then fitted phylogenetic models of the evolution of the size of several brain regions in frugivorous primates, considering or not species sympatry. We found that the evolution of the whole brain or brain regions used in immediate information processing was best fitted with models not considering sympatry. By contrast, models considering species sympatry best predicted the evolution of brain regions related to long-term memory of interactions with the socio-ecological environment, with a decrease in their size the higher the sympatry. We speculate that species sympatry, by generating intense food depletion, might lead to an over-complexification of resource spatiotemporality that counteracts the benefits of high cognitive abilities and/or might drive niche partitioning and specialisation, thereby inducing lower brain region sizes. In addition, we reported that primate species in sympatry diversify more slowly. This comparative study suggests that species sympatry significantly contributes to shaping primate evolution.
spSeudoMap: Cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data
Authors: Bae Sungwoo , Choi Hongyoon , Lee Dong Soo 
Published: May 2022

AbstractWith advances in computational models, the cellular landscape can be tracked in various tissues using spatial transcriptomics. Since many single-cell RNA-seq (scRNA-seq) data have been obtained after cell sorting, such as when investigating immune cells, integrating these singlecell data with spatial data is limited due to a mismatch of cell types composing the two datasets. Here, we present a method, spSeudoMap, which utilizes sorted scRNA-seq data to train a model for predicting cell types of spatial spots by creating virtual cell mixtures that closely mimic the gene expression profile of spatial transcriptomic data. To overcome the mismatch issue, the cell type exclusively present in the spatial data, pseudotype, was defined. The proportion of pseudotype cells and virtual expression profiles in the cell mixture was determined by pseudobulk transcriptomes. The simulated cell mixture was considered a reference dataset, and the model that predicts the cell composition of the mixture was trained to predict the cell fraction of the spatial data using domain adaptation. First, spSeudoMap was evaluated in human and mouse brain tissues, and the main region-specific neuron types extracted from single-cell data could be precisely mapped to the expected anatomical locations. Moreover, the method was applied to human breast cancer data and described the spatial distribution of immune cell subtypes and their interactions in heterogeneous tissue. Taken together, spSeudoMap is a platform that predicts the spatial composition of cell subpopulations using sorted scRNA-seq data, and it may help to clarify the roles of a few but crucial cell types.
Real-time single-molecule observation of chaperone-assisted protein folding
Authors: Marzano Nicholas , Paudel Bishnu , van Oijen Antoine , Ecroyd Heath 
Published: May 2022

SummaryThe ability of Hsp70 molecular chaperones to remodel the conformation of their clients is central to their biological function; however, questions remain regarding the precise molecular mechanisms by which Hsp70 machinery interacts with the client and how this contributes towards efficient protein folding. Here, we used Total Internal Reflection Fluorescence (TIRF) microscopy and single-molecule Fluorescence Resonance Energy Transfer (smFRET) to temporally observe the conformational changes that occur to individual firefly luciferase (Fluc) proteins as they are folded by the bacterial Hsp70 system. For the first time, we observed multiple cycles of chaperone binding-and-release to an individual client during refolding and that high rates of chaperone cycling improves refolding yield. Furthermore, we demonstrate that DnaJ remodels misfolded proteins via a conformational selection mechanism whereas DnaK resolves misfolded states via mechanical unfolding. This study illustrates that the temporal observation of chaperone-assisted folding enables the elucidation of key mechanistic details inaccessible using other approaches.
Evidence for increased parallel information transmission in human brain networks compared to macaques and mice
Authors: Griffa Alessandra , Mach Mathieu , Dedelley Julien , Gutierrez-Barragan Daniel , Gozzi Alessandro , Allali Gilles , Grandjean Joanes , Van De Ville Dimitri , Amico Enrico 
Published: May 2022

AbstractBrain communication, defined as information transmission through white-matter connections, is at the foundation of the brain’s computational capacities that subtend almost all aspects of behavior: from sensory perception shared across mammalian species, to complex cognitive functions in humans. How did communication strategies in macroscale brain networks adapted across evolution to accomplish increasingly complex functions? By applying a graph- and information-theory approach to assess information-related pathways in mouse, macaque and human brains, we show a brain communication gap between selective information transmission in non-human mammals, where brain regions share information through single polysynaptic pathways, and parallel information transmission in humans, where regions share information through multiple parallel pathways. In humans, parallel transmission acts as a major connector between unimodal and transmodal systems. The layout of information-related pathways is unique to individuals across different mammalian species, pointing at the individual-level specificity of information routing architecture. Our work provides evidence that different communication patterns are tied to the evolution of mammalian brain networks.
Cryo-EM structure ofex vivofibrils associated with extreme AA amyloidosis prevalence in a cat shelter
Authors: Schulte Tim , Chaves-Sanjuan Antonio , Mazzini Giulia , Speranzini Valentina , Lavatelli Francesca , Ferri Filippo , Palizzotto Carlo , Mazza Maria , Milani Paolo , Nuvolone Mario , Vogt Anne-Cathrine , Palladini Giovanni , Merlini Giampaolo , Bolognesi Martino , Ferro Silvia , Zini Eric , Ricagno Stefano 
Published: May 2022

ABSTRACTAA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at high SAA serum levels during chronic inflammation. The disease can be transmitted horizontally, likely facilitated by prion-like mechanism, in captive animals leading to extreme disease prevalence, e.g. 70% in captive cheetah and 57-73% in domestic short hair (DSH) cats kept in shelters.Herein, we present the 3.3 Å cryo-EM structure of an AA amyloid extractedpost-mortemfrom the kidney of a DSH cat with renal failure. The structure reveals a cross-β architecture assembled from two 76-residue long proto-filaments. Despite >70% sequence homology to mouse and human SAA, the cat SAA variant adopts a distinct amyloid fold. Based on shared disease profiles and almost identical protein sequences, we propose a similar amyloid fold of deposits identified previously in captive cheetah.
Individual Differences in Audio-Visual Binding Can Predict the Varied Severity of Motion Sickness
Authors: Zilka Revital , Bonneh Yoram 
Published: May 2022

In neuroscience, research often focuses on the group, while ignoring large individual differences, which are left poorly understood. One such example is the large individual variability in the susceptibility to motion-sickness (MS), the feeling of sickness that typically occurs during travel or movement. Current explanations of MS focus on the sensory conflict in the perception of motion, primarily between the vestibular and the visual systems, e.g., when feeling motion but not seeing it. To account for the large individual differences in MS, we hypothesized that people feel motion sickness only when the conflicting stimuli are perceived as bound together, and their tendency to bind conflicting multi-sensory information is an individual trait. To test this hypothesis, we measured the persistence of audio-visual binding using the McGurk effect in which watching a moving mouth alters the auditory perception of phonemes. We used a temporal audio-visual mismatch to probe the persistence of binding and computed a temporal binding window for each individual (n=21) in 3 tasks: syllable Identification (McGurk), simultaneity judgement, and syllable synchronization judgement. To assess the severity of MS, we used 2 subjective symptom questionnaires. We found that the temporal binding window of the McGurk stimuli in two of the tasks varied across individuals and was positively correlated (R>0.8) with the MS questionnaire severity scores. These results support our hypothesis and shed new light on the enigmatic differences between individuals regarding their susceptibility to motion-sickness. They also highlight the potential strength of studies focusing on individual differences and neurological diversity.Significance StatementMotion sickness is the feeling of sickness that typically occurs during travel or movement. Although it is commonly linked to a sensory mismatch, the large differences in its susceptibility across people remains poorly understood. In the current study, we link these individual differences to a multi-modal temporal binding window, which measures the persistence of perceiving multi-modal stimuli as coming from the same source despite temporal discrepancies. We demonstrated this link by finding a high correlation between the temporal binding window of an audio-visual illusion (the McGurk effect) and the subjective reports of the susceptibility to motion sickness. These results shed new light on the enigmatic differences between individuals regarding their susceptibility to motion sickness and highlight the potential strength of studies focusing on individual differences and neurological diversity.
High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer
Authors: Salcher Stefan , Sturm Gregor , Horvath Lena , Untergasser Gerold , Fotakis Georgios , Panizzolo Elisa , Martowicz Agnieszka , Pall Georg , Gamerith Gabriele , Sykora Martina , Augustin Florian , Schmitz Katja , Finotello Francesca , Rieder Dietmar , Sopper Sieghart , Wolf Dominik , Pircher Andreas , Trajanoski Zlatko 
Published: May 2022

SUMMARYNon-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with diverse immune cell infiltration patterns, which has been linked to both, therapy sensitivity and resistance. However, full understanding of how immune cell phenotypes vary across different patient and tumor subgroups is lacking. Here, we dissect the NSCLC tumor microenvironment at high resolution by integrating 1,212,463 single-cells from 538 samples and 309 patients across 29 datasets, including our own dataset capturing cells with low mRNA content. Based on the cellular composition we stratified patients into immune deserted, B cell, T cell, and myeloid cell subtypes. Using bulk samples with genomic and clinical information, we identified specific cellular components associated with tumor histology and genotypes. Analysis of cells with low mRNA content uncovered distinct subpopulations of tissue-resident neutrophils (TRNs) that acquire new functional properties in the tissue microenvironment, providing evidence for the plasticity of TRNs. TRN-derived gene signature was associated with anti-PD-L1 treatment failure in a large NSCLC cohort.In briefSalcher, Sturm, Horvath et al. integrate single-cell datasets to generate the largest transcriptome atlas in NSCLC, refining patient stratification based on tumor immune phenotypes, and revealing associations of histological subtypes and genotypes with specific cellular composition patterns.Coverage of cells with low mRNA content by single-cell sequencing identifies distinct tissue-resident neutrophil subpopulations, which acquire new properties within the tumor microenvironment. Gene signature from tissue-resident neutrophils is associated with immune checkpoint inhibitor treatment failure. The integrated atlas is publicly available online (https://luca.icbi.at), allowing the dissection of tumor-immune cell interactions in NSCLC.HighlightsHigh-resolution single-cell atlas of the tumor microenvironment (TME) in NSCLC.Histological tumor subtypes and driver genes imprint specific cellular TME patterns.scRNA-seq of cells with low transcript count identifies distinct tissue-resident neutrophil (TRN) subpopulations and non-canonical functional properties in the TME niche.TRN gene signature identifies patients who are refractory to treatment with PD-L1 inhibitors.Abstract Figure
Liquid-like VASP condensates drive actin polymerization and dynamic bundling
Authors: Graham Kristin , Chandrasekaran Aravind , Wang Liping , Ladak Aly , Lafer Eileen M. , Rangamani Padmini , Stachowiak Jeanne C. 
Published: May 2022

ABSTRACTThe organization of actin filaments into bundles is required for cellular processes such as motility, morphogenesis, and cell division. Filament bundling is controlled by a network of actin binding proteins. Recently, several proteins that comprise this network have been found to undergo liquid-liquid phase separation. How might liquid-like condensates contribute to filament bundling? Here, we show that the processive actin polymerase and bundling protein, VASP, forms liquid-like droplets under physiological conditions. As actin polymerizes within VASP droplets, elongating filaments partition to the edges of the droplet to minimize filament curvature, forming an actin-rich ring within the droplet. The rigidity of this ring is balanced by the droplet’s surface tension, as predicted by a continuum-scale computational model. However, as actin polymerizes and the ring grows thicker, its rigidity increases and eventually overcomes the surface tension of the droplet, deforming into a linear bundle. The resulting bundles contain long, parallel actin filaments that grow from their tips. Significantly, the fluid nature of the droplets is critical for bundling, as more solid droplets resist deformation, preventing filaments from rearranging to form bundles. Once the parallel arrangement of filaments is created within a VASP droplet, it propagates through the addition of new actin monomers to achieve a length that is many times greater than the initial droplet. This droplet-based mechanism of bundling may be relevant to the assembly of cellular architectures rich in parallel actin filaments, such as filopodia, stress fibers, and focal adhesions.
Design of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography
Authors: Du Daniel X. , Fitzpatrick Anthony W. P. 
Published: May 2022

AbstractPonderomotive phase plates have shown temporally consistent phase contrast is possible within electron microscopes via high fluence static laser modes resonating in Fabry-Perot cavities. Here, we explore using pulsed laser beams as an alternative method of generating high fluences. We find through forward-stepping finite element models that picosecond-or-less interactions are required for meaningful fluences phase shifts, with higher pulse energies and smaller beam waists leading to the predicted higher fluences. An additional model based on quasiclassical assumptions is used to discover the shape of the phase plate by incorporating the oscillatory nature of the electric field. From these results, we find the transient nature of the laser pulses removes the influence of Kapitza-Dirac diffraction patterns that appear in the static resonator cases. The addition of a second laser aligned 90° to the first induces anisotropy to the shape of the phase plate. By incorporating a shifting-electron-beam algorithm, the effects of a finite electron beam crossover are also simulated. A total pulse energy of 8.7 μJ is enough to induce the required π/2 phase shift for Zernike-like phase microscopy. As a brief thought experiment, we also explore the usage of high frequency lasers in a standard electron emission scheme to see if a pulsed electron beam is even necessary. Ultimately, frequency requirements limit the laser to nanosecond pulse durations, causing the required pulse energies to reach unreasonable levels before adequate phase shifts are achieved.
Functional substitutions of amino acids that differ between GDF11 and GDF8 impact skeletal development and skeletal muscle
Authors: Lian John , Walker Ryan G. , D’Amico Andrea , Vujic Ana , Mills Melanie J. , Messemer Kathleen A. , Mendello Kourtney R. , Goldstein Jill M. , Leacock Krystynne A. , Epp Soraya , Stimpfl Emma V. , Thompson Thomas B. , Wagers Amy J. , Lee Richard T. 
Published: May 2022

AbstractGrowth differentiation factor 11 (GDF11) and GDF8 (MSTN) are closely related TGFβ family proteins that interact with nearly identical signaling receptors and antagonist proteins. However, GDF11 appears to activate SMAD2/3in vitroandin vivomore potently than GDF8. The ligands possess divergent structural properties, whereby substituting unique GDF11 amino acids into GDF8 enhanced activity of the resulting chimeric GDF8. We investigated potentially distinct endogenous activities of GDF11 and GDF8in vivoby genetically modifying their mature signaling domains. Full recoding of the GDF8 mature domain to that of GDF11 yielded mice lacking GDF8, with GDF11 levels ∼50-fold higher than normal, and exhibiting modestly decreased muscle mass, with no apparent negative impacts on health or survival to adulthood. Substitution of two specific amino acids in the fingertip region of GDF11 with the corresponding GDF8 residues resulted in prenatal axial skeletal transformations, consistent withGdf11-deficient mice, without apparent perturbation of skeletal or cardiac muscle development or homeostasis. These experiments uncover distinctive features between the GDF11 and GDF8 mature domainsin vivoand identify specific requirement for GDF11 in early-stage skeletal development.Summary StatementReplacement of amino acids unique to GDF11 and GDF8 into the native locus of the other ligand yields measurable, differential skeletal and muscle phenotypes, revealing distinct features between the ligands.