bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Authors: Karousis Evangelos D. , Gypas Foivos , Zavolan Mihaela , Mühlemann Oliver 
Published: May 2021

AbstractBackgroundNonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge.ResultsTo identify and analyze endogenous targets of NMD, we applied cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identified, most derive from alternative exon usage. The isoform-aware analysis revealed many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTRper sedoes not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD seems to be ridding the transcriptome of isoforms resulting from spurious splicing events.ConclusionsLong-read sequencing enabled the identification of many novel NMD-sensitive mRNAs and revealed both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.
New App knock-in mice that accumulate wild-type human Aβ as rapidly as AppNL-G-F mice exhibit intensive cored plaque pathology and neuroinflammation
Authors: Sato Kaori , Watamura Naoto , Fujioka Ryo , Mihira Naomi , Sekiguchi Misaki , Nagata Kenichi , Ohshima Toshio , Saito Takashi , Saido Takaomi C. , Sasaguri Hiroki 
Published: May 2021

AbstractWe previously developed single App knock-in mouse models of Alzheimer’s disease (AD), harboring the Swedish and Beyreuther/Iberian mutations with or without the Arctic mutation (AppNL-G-F and AppNL-F mice). These models showed amyloid β peptide (Aβ) pathology, neuroinflammation and cognitive impairment in an age-dependent manner. The former line exhibits extensive pathology as early as 6 months but is unsuitable for investigating Aβ metabolism and clearance because the Arctic mutation renders Aβ resistant to proteolytic degradation and prone to aggregation. In particular, it is inapplicable to preclinical immunotherapy studies due to its discrete affinity for anti-Aβ antibodies. The weakness of the latter model is that it may take as long as 18 months for the pathology to become prominent. We have thus generated a new model that exhibits early deposition of wild-type human Aβ by crossbreeding the AppNL-F line with the Psen1P117L/WT line. We show that the effects of the pathogenic mutations in the App and Psen1 genes are additive or synergistic. This new mouse model showed more cored plaque pathology and neuroinflammation than AppNL-G-F mice and will help accelerate the development of disease-modifying therapies to treat preclinical AD.
The adaptive potential of non-heritable somatic mutations
Authors: Majic Paco , Yagmur Erten E. , Payne Joshua L. 
Published: May 2021

AbstractNon-heritable somatic mutations are typically associated with deleterious effects such as in cancer and senescence, so their role in adaptive evolution has received little attention. However, most somatic mutations are harmless and some even confer a fitness advantage to the organism carrying them. We hypothesized that heritable, germline genotypes that are likely to express an advantageous phenotype via non-heritable somatic mutation will have a selective advantage over other germline genotypes, and this advantage will channel evolving populations toward more fit germline genotypes, thus promoting adaptation. We tested this hypothesis by simulating evolving populations of developing organisms with an impermeable germline-soma separation navigating a minimal fitness landscape. The simulations revealed the conditions under which non-heritable somatic mutations promote adaptation. Specifically, this can occur when the somatic mutation supply is high, when only very few cells with the advantageous somatic mutation are required to increase organismal fitness, and when the somatic mutation also confers a selective advantage to cells with that mutation. We therefore provide proof-of-principle that non-heritable somatic mutations can promote adaptive evolution via a process we call somatic genotypic exploration. We discuss the biological plausibility of this phenomenon, as well as its evolutionary implications.SignificanceThe immensity of non-heritable genetic diversity arising in the soma has been largely disregarded in evolutionary theory as a source of adaptation. Here, we introduce a model in which non-heritable somatic mutations arising during development confer an organismal fitness advantage. Analysis of this model shows how such mutations channel evolving populations toward adaptive germline genotypes. This is most likely to occur when somatic mutations confer a fitness benefit at both the cellular and organismal levels, evoking a synergistic form of multi-level selection that contrasts with the antagonistic forms typically associated with somatic mutations in cancer and senescence. As such, our study invites a new view of somatic genetic diversity in evolutionary theory as a potential source of adaptation.
Long-term sensitization of rat spinal neurons induced by adolescent psychophysical stress is further enhanced by a mild-nociceptive lumbar input
Authors: Singaravelu Sathish Kumar , Goitom Alexander Dawit , Surakka Akseli , Moerz Handan , Schilder Andreas , Hansson Anita C , Spanagel Rainer , Treede Rolf-Detlef 
Published: May 2021

AbstractBackgroundNon-specific low back pain (LBP) is one of the most common chronic pain conditions and adverse childhood experiences (ACEs) are known mediators for chronicity of LBP. Sensitization of dorsal horn neurons (DHNs) is a significant element that contributes to chronic LBP. Repeated restraint stress in adult animals is known to cause manifest DHN sensitization when combined with a short-lasting nociceptive input.ObjectiveIn this study, we investigated whether repeated restraint stress in early adolescence leads to a long-term sensitization of DHNs and if an additional mild-nociceptive input by intramuscular nerve growth factor (NGF) leads to further sensitization.MethodsAdolescent Wistar rats were stressed repeatedly in a narrow plastic restrainer, 1 hour per day for 12 consecutive days. Control animals were handled but not restrained. In adulthood, rats were treated with intramuscular injections of saline or NGF (short-lasting mild-nociceptive input) into the lumbar multifidus muscle (L5). Behavioral tests for pain sensitivity were performed before, after stress and inconjunction with intramuscular injections. Rats were transcardially perfused and immunohistochemistry was performed on lumbar (L2) spinal segments.ResultsAdolescent restraint stress significantly lowered the low back pressure pain threshold (PPT) immediately after the stress (p<0.0001) and was maintained throughout adulthood (p<0.05). Additionally, paw withdrawal threshold (PWT) was significantly lowered by stress (p<0.0001) but normalized towards adulthood. An NGF injection in adulthood in previously stressed animals lowered the PPT (Cohen’sd=0.87) and increased microglia marker (Iba-1) immunoreactive area in the superficial DHN (p<0.01) with a trend in increased feret’s diameter of the immunoreactive cell (p=0.05).ConclusionsOur adolescence stress model induced behavioral signs of sensitization and enhanced sensitivity to further sensitization and dorsal horn microglia activation by subsequent mild nociceptive input (NGF injection). These findings help to understand certain aspects of how adolescent stress might predispose to exacerbation of pain with an additional insult.
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study
Authors: Arizmendi Cárdenas Yami Ommar , Neuenschwander Samuel , Malaspinas Anna-Sapfo 
Published: May 2021

AbstractOwing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown.In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers.Across most simulations, more than 228 out of the 233 simulated viruses are recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovers only around one third. Overall, Centrifuge and Kraken2 have the best performance with the highest values of sensitivity and precision. We found that deamination damage has little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieves the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend to verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.
Spiking activity in the visual thalamus is coupled to pupil dynamics across temporal scales
Authors: Crombie Davide , Spacek Martin A. , Leibold Christian , Busse Laura 
Published: May 2021

AbstractThe processing of sensory information, even at early processing stages, is influenced by the internal state of the animal. Internal states, such as arousal, are often characterized by relating neural activity to a single “level” of arousal, defined by a behavioral indicator such as pupil size. In this study, we expand the understanding of arousal-related modulations in sensory systems by uncovering multiple timescales of pupil dynamics and their relationship to neural activity. Specifically, we observed coupling between spiking activity in the mouse dorsal lateral geniculate nucleus (dLGN) of the thalamus and pupil dynamics across timescales spanning three orders of magnitude, from seconds to minutes. Throughout all of these timescales, two distinct spiking patterns – tonic spikes and bursts – preferred opposing phases of pupil dynamics. This multi-scale coupling captures modulations distinct from those captured by pupil sizeper se, transitions between locomotion and quiescence, or saccadic eye movements. Furthermore, coupling persisted even during viewing of a naturalistic movie, where it contributed to differences in how visual information was encoded. We conclude that dLGN spiking activity is influenced by arousal processes associated with pupil dynamics occurring simultaneously across a broad range of timescales, with implications for the transfer of sensory information to the cortex.
Imaging translational control by Argonaute with single-molecule resolution in live cells
Authors: Cialek Charlotte A. , Morisaki Tatsuya , Zhao Ning , Montgomery Taiowa A. , Stasevich Timothy J. 
Published: May 2021

ABSTRACTA major challenge to our understanding of translational control has been deconvolving the individual impact specific regulatory factors have on the complex dynamics of mRNA translation. MicroRNAs (miRNAs), for example, guide Argonaute and associated proteins to target mRNAs, where they direct gene silencing in multiple ways that are not well understood. To better deconvolve these dynamics, we have developed technology to directly visualize and quantify the impact of human Argonaute2 (Ago2) on the translation and subcellular localization of individual reporter mRNAs in living cells. We show that our combined translation and Ago2 tethering system reflects endogenous miRNA-mediated gene silencing. Using the system, we find that Ago2 association leads to progressive silencing of translation at individual mRNA. The timescale of silencing was similar to that of translation, consistent with a role for Ago2 in blocking translation initiation, leading to ribosome runoff. At early time points, we observed occasional brief bursts of translational activity at Ago2-tethered mRNAs undergoing silencing, suggesting that translational repression may initially be reversible. At later time points, Ago2-tethered mRNAs cluster and coalesce with endogenous P-bodies, where a translationally silent state is maintained. These results provide a framework for exploring miRNA-mediated gene regulation in live cells at the single-molecule level. Furthermore, our tethering-based, single-molecule reporter system will likely have wide-ranging application in studying general RNA-protein interactions.
Identification and characterization of human CD34+and CD34dim/-neutrophil-committed progenitors
Authors: Calzetti Federica , Finotti Giulia , Tamassia Nicola , Bianchetto-Aguilera Francisco , Castellucci Monica , Cavallini Chiara , Mattè Alessandro , Gasperini Sara , Benedetti Fabio , Bonifacio Massimiliano , Tecchio Cristina , Scapini Patrizia , Cassatella Marco A. 
Published: May 2021

ABSTRACTWe report the identification of human CD66b−CD64dimCD115−neutrophil-committed progenitors within SSClowCD45dimCD34+and CD34dim/−bone marrow cells, that we named neutrophil myeloblast (NMs). CD34+and CD34dim/−NMs resulted as either CD45RA+or CD45RA−, with CD34+CD45RA−NMs found as selectively expanded in chronic-phase chronic myeloid leukemia patients. By scRNA-seq experiments, CD34+and CD34dim/−NMs were found to consist of combinations of four cell clusters, characterized by different maturation stages and distributed along two differentiation routes. Cell clusters were identified by neutrophil-specific gene profiles, one of them associated to an interferon-stimulated gene (ISG) signature, hence supporting recently identified expansions of mature neutrophil subsets expressing ISGs in blood of diseased individuals. Altogether, our data shed light on the very early phases of neutrophil ontogeny.
Prediction of Whole-Cell Transcriptional Response with Machine Learning
Authors: Eslami Mohammed , Borujeni Amin Espah , Doosthosseini Hamid , Vaughn Matthew , Eramian Hamed , Clowers Katie , Gordon D. Benjamin , Gaffney Niall , Weston Mark , Becker Diveena , Dorfan Yuval , Fonner John , Urrutia Joshua , Corbet Carolyn , Zheng George , Stubbs Joe , Cristofaro Alexander , Maschhoff Paul , Singer Jedediah , Voigt Christopher A , Yeung Enoch 
Published: May 2021

AbstractApplications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments to cover all possible combinations of perturbations is infeasible. In this paper, we present the host response model (HRM), a machine learning approach that takes the cell response to single perturbations as the input and predicts the whole cell transcriptional response to the combination of inducers. We find that the HRM is able to qualitatively predict the directionality of dysregulation to a combination of inducers with an accuracy of >90% using data from single inducers. We further find that the use of known prior, known cell regulatory networks doubles the predictive performance of the HRM (an R2from 0.3 to 0.65). This tool will significantly reduce the number of high-throughput sequencing experiments that need to be run to characterize the transcriptional impact of the combination of perturbations on the host.
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data
Authors: Lyu Wenyang , Dai Xiaoyang , Beaumont Mark , Yu Feng , He Zhangyi 
Published: May 2021

AbstractWith the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured, which can result in overestimation of the effect of natural selection. To address these issues, we introduce a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.
Same but different: New insights on the correspondence between subjective affective experience and physiological responses from representational similarity analyses
Authors: Ventura-Bort C. , Wendt J. , Weymar M. 
Published: May 2021

AbstractClassical views suggest that experienced affect is related to a specific bodily response (Fingerprint hypothesis), whereas recent perspectives challenge this view postulating that similar affective experiences rather evoke different physiological responses. To further advance this debate in the field, we used representational similarity analysis (N= 64) to investigate the correspondence between subjective affect (arousal and valence ratings) and physiological reactions (skin conductance response [SCR], startle blink response, heart rate and corrugator activity) across various emotion induction contexts (picture viewing task, sound listening task and imagery task). Significant similarities were exclusively observed between SCR and arousal in the picture viewing task. However, none of the other physiological measures showed a significant relation with valence and arousal ratings in any of the tasks. These findings tend to support thepopulations hypothesis, suggesting that there is no clear match between the evoked physiological responses and the experienced subjective affect between individuals.Statement of relevanceThe subjective affective experience evoked by an event is accompanied by physiological responses. The correspondence between physiological response patterns and the experienced affect, however, is still under debate. Classical views (Fingerprint hypothesis) suggest that affect is related to a specific physiological response, whereas recent perspectives (Populations hypothesis) challenge this view, postulating rather different physiological responses. In the current study, we used representational similarity analysis (RSA) to examine the relation between affective experience, assessed using valence and arousal ratings, and the evoked physiological reactivity across three affect-inducing contexts. Results showed significant similarities exclusively between SCR and arousal in the passive picture viewing task. However, none of the other physiological measures showed a significant relation with valence and arousal ratings in any of the tasks, supporting the populations hypothesis. These findings invite to reframe the relation between physiology and affect from invariant and homogeneous to variant and context-dependent.
Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients
Authors: Sanchez-Burgos Ignacio , Joseph Jerelle A. , Collepardo-Guevara Rosana , Espinosa Jorge R. 
Published: May 2021

ABSTRACTBiomolecular condensates are liquid-like membraneless compartments that contribute to the spatiotemporal organization of proteins, RNA, and other biomolecules inside cells. Some membraneless compartments, such as nucleoli, are dispersed as different condensates that do not grow beyond a certain size, or do not present coalescence over time. In this work, using a minimal protein model, we show that phase separation of binary mixtures of scaffolds and low-valency clients that can act as surfactants—i.e., that significantly reduce the droplet surface tension—can yield either a single drop or multiple droplets that conserve their sizes on long timescales (herein ‘multidroplet size-conserved’), depending on the scaffold to client ratio. Our simulations demonstrate that protein connectivity and condensate surface tension regulate the balance between these two scenarios. Multidroplet size-conserved behavior spontaneously arises at increasing surfactant-to-scaffold concentrations, when the interfacial penalty for creating small liquid droplets is sufficiently reduced by the surfactant proteins that are preferentially located at the interface. In contrast, low surfactant-to-scaffold concentrations enable continuous growth and fusion of droplets without restrictions. Overall, our work proposes one potential thermodynamic mechanism to help rationalize how size-conserved coexisting condensates can persist inside cells—shedding light on the roles of general biomolecular features such as protein connectivity, binding affinity, and droplet composition in this process.