bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative secretome analysis establishes the cell type-resolved mouse brain secretome
Authors: Tüshaus Johanna , Müller Stephan A. , Kataka Evans Sioma , Zaucha Jan , Monasor Laura Sebastian , Su Minhui , Güner Gökhan , Jocher Georg , Tahirovic Sabina , Frishman Dmitrij , Simons Mikael , Lichtenthaler Stefan F. 
Published: May 2020

AbstractTo understand how cells communicate in the nervous system, it is essential to define their secretome, which is challenging for primary cells because of large cell numbers being required. Here, we miniaturized secretome analysis by developing the high-performance secretome-protein-enrichment-with-click-sugars method (hiSPECS). To demonstrate its broad utility, hiSPECS was used to identify the secretory response of brain slices upon LPS-induced neuroinflammation and to establish the cell type-resolved mouse brain secretome resource using primary astrocytes, microglia, neurons and oligodendrocytes. This resource allowed mapping the cellular origin of CSF proteins and revealed that an unexpectedly high number of secreted proteinsin vitroandin vivoare proteolytically-cleaved membrane protein ectodomains. Two examples are neuronally secreted ADAM22 and CD200, which we identified as substrates of the Alzheimer-linked protease BACE1. hiSPECS and the brain secretome resource can be widely exploited to systematically study protein secretion, brain function and to identify cell type-specific biomarkers for CNS diseases.
Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm
Authors: Tourigny David S. , Goldberg Arthur P. , Karr Jonathan R. 
Published: May 2020

ABSTRACTStochasticity from gene expression in single cells is known to drive metabolic heterogeneity at the level of cellular populations, which is understood to have important consequences for issues such as microbial drug tolerance and treatment of human diseases like cancer. Despite considerable advancements in profiling the genomes, transcriptomes, and proteomes of single cells, it remains difficult to experimentally characterise their metabolism at genome-scale. Computational methods could bridge this gap toward a systems understanding of single-cell biology. To address this challenge, we developed stochastic simulation algorithm with flux-balance analysis embedded (SSA-FBA), a computational framework for simulating the stochastic dynamics of the metabolism of individual cells using genome-scale metabolic models with experimental estimates of gene expression and enzymatic reaction rate parameters. SSA-FBA extends the constraint-based modelling formalism of metabolic network modelling to the single-cell regime, enabling simulation when experimentation is intractable. We also developed an efficient implementation of SSA-FBA that leverages the topology of embedded FBA models to significantly reduce the computational cost of simulation. As a preliminary case study, we built a reduced single-cell model ofMycoplasma pneumoniae, and used SSA-FBA to illustrate the role of stochasticity on the dynamics of metabolism at the single-cell level.SIGNIFICANCEDue to fundamental challenges limiting the experimental characterisation of metabolism within individual cells, computational methods are needed to help infer the metabolic behaviour of single cells from information about their transcriptomes and proteomes. In this paper, we present SSA-FBA, the first systematic framework for modelling the stochastic dynamics of single cells at the level of genome-scale metabolic reaction networks. We provide a robust and efficient algorithm for simulating SSA-FBA models, and apply it to a case study involving the metabolism, RNA and protein synthesis and turnover of a singleMycoplasma pneumoniaecell.
SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in ovarian cancer
Authors: Winkler Claudia , Ferraioli Domenico , Garuti Anna , Grillo Federica , Rodriguez-Canales Jaime , Ferrando Lorenzo , Chopin Nicolas , Ray-Coquard Isabelle , Bedognetti Davide , Ballestrero Alberto , Leo Elisabetta , Zoppoli Gabriele 
Published: May 2020

AbstractLarge independent analyses on cancer cell lines followed by functional studies have identified Schlafen 11 (SLFN11), a putative DNA/RNA helicase, as the strongest predictor of sensitivity to DNA-damaging agents. However, its role as a prognostic biomarker is undefined, partially due to the lack of validated methods to score SLFN11 in human tissues. Here, we implemented a pipeline to quantify SLFN11 in human cancer samples. By analyzing a cohort of high-grade serous ovarian carcinoma specimens prior platinum-based chemotherapy treatment, we demonstrate that SLFN11 is expressed by infiltrating innate and adaptive immune cells. We show, for the first time, that SLFN11 density in both the neoplastic and microenvironmental components was independently associated with favorable outcome. Transcriptomic analyses suggested the presence of a hitherto modulation of the cancer-immunity cycle orchestrated by SLFN11. We propose SLFN11 as a dual biomarker capturing simultaneously interconnected immunological and cancercell-intrinsic functional dispositions associated with sensitivity to DNA damaging agents.
Benchmarking atlas-level data integration in single-cell genomics
Authors: Luecken MD , Büttner M , Chaichoompu K , Danese A , Interlandi M , Mueller MF , Strobl DC , Zappia L , Dugas M , Colomé-Tatché M , Theis FJ 
Published: May 2020

AbstractCell atlases often include samples that span locations, labs, and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration.Choosing a data integration method is a challenge due to the difficulty of defining integration success. Here, we benchmark 38 method and preprocessing combinations on 77 batches of gene expression, chromatin accessibility, and simulation data from 23 publications, altogether representing >1.2 million cells distributed in nine atlas-level integration tasks. Our integration tasks span several common sources of variation such as individuals, species, and experimental labs. We evaluate methods according to scalability, usability, and their ability to remove batch effects while retaining biological variation.Using 14 evaluation metrics, we find that highly variable gene selection improves the performance of data integration methods, whereas scaling pushes methods to prioritize batch removal over conservation of biological variation. Overall, BBKNN, Scanorama, and scVI perform well, particularly on complex integration tasks; Seurat v3 performs well on simpler tasks with distinct biological signals; and methods that prioritize batch removal perform best for ATAC-seq data integration. Our freely available reproducible python module can be used to identify optimal data integration methods for new data, benchmark new methods, and improve method development.
Long-term sterile immunity induced by an adjuvant-containing live-attenuated AIDS virus
Authors: Okamura Tomotaka , Shimizu Yuya , Kanuma Tomohiro , Tsujimura Yusuke , Asaka Masamitsu N , Matsuo Kazuhiro , Yamamoto Takuya , Yasutomi Yasuhiro 
Published: May 2020

AbstractAntigen 85B (Ag85B) is one of the most dominant proteins secreted from most mycobacterial species, and it induces Th1-type immune responses as an adjuvant. We genetically constructed a live attenuated simian human immunodeficiency virus to express the adjuvant molecule Ag85B (SHIV-Ag85B). SHIV-Ag85B could not be detected 4 weeks after injection in cynomolgus macaques, and strong SHIV-specific T cell responses were induced in these macaques. When these macaques in which SHIV-Ag85B had become undetectable were challenged with pathogenic SHIV89.6P at 37 weeks after SHIV-Ag85B became undetectable, SHIV89.6P could not be detected after the challenge. Eradication of SHIV89.6P was confirmed by adoptive transfer experiments and CD8-depletion studies. The SHIV-Ag85B-inoculated macaques showed enhancement of Gag-specific monofunctional and polyfunctional CD8+T cells in the acute phase of pathogenic SHIV challenge. The results suggest that SHIV-Ag85B elicited strong sterile immune responses against pathogenic SHIV and that it may lead to the development of a vaccine for AIDS virus infection.ImportanceDevelopment of an effective HIV vaccine has been a major priority to control the worldwide AIDS epidemic. The moderately attenuated prototypic vaccine strain SIVmac239Δnef has been used in various studies; however, it does not provide sufficient effects to prevent infection. The use of adjuvant in vaccination is thought to be useful for enhancing the immune responses to various pathogens. In the present study, we constructed a live attenuated SHIV virus expressing adjuvant molecule Ag85B and assessed vaccine effects in cynomolgus macaques. The present study shows that live-attenuated SHIV expressing Ag85B elicits viral antigen-specific polyfunctional CD8+T cell responses against pathogenic SHIV and provide the possibility of eradicating a pathogenic lentivirus from infected animals.
Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia
Authors: Álvarez-Díaz Diego A. , Franco-Muñoz Carlos , Laiton-Donato Katherine , Usme-Ciro José A. , Franco-Sierra Nicolás D. , Flórez Astrid C. , Rangel Sergio Gómez , Rodríguez Luz Dary , Barbosa Juliana , Ospitia Erika , Walteros Diana Marcela , Martínez Martha Lucia Ospina , Mercado-Reyes Marcela 
Published: May 2020

SUMMARYThe COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main inhouse methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3′ end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3’ end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.HIGHLIGHTSColombian SARS-CoV-2 sequences displayed genetic variability in some target regions used for COVID-19 diagnosis.Mismatches in critical primer regions could impact their performance and the rate of false negative results.
Brain orchestration of pregnancy and maternal behavior in mice
Authors: Barrière David André , Ella Arsène , Szeremeta Frédéric , Adriaensen Hans , Même William , Chaillou Elodie , Migaud Martine , Même Sandra , Lévy Frédéric , Keller Matthieu 
Published: May 2020

AbstractReproduction induces changes within the brain to prepare for gestation and motherhood. However, the dynamic of these central changes and their relationships with the development of maternal behavior remain poorly understood. Here, we describe a longitudinal morphometric neuroimaging study in female mice between pre-gestation and weaning, using new magnetic resonance imaging (MRI) resources comprising a high-resolution brain template, its associated tissue priors (60-μm isotropic resolution) and a corresponding mouse brain atlas (1320 regions of interest). Using these tools, we observed transient hypertrophies not only within key regions controlling gestation and maternal behavior (medial preoptic area, bed nucleus of thestria terminalis), but also in the amygdala, caudate nucleus and hippocampus. Additionally, unlike females exhibiting lower levels of maternal care, highly maternal females developed transient hypertrophies in somatosensory, entorhinal and retrosplenial cortices among other regions. Therefore, coordinated and transient brain modifications associated with maternal performance occurred during gestation and lactation.
Dopamine-gated memory selection during slow wave sleep
Authors: Isotalus Hanna , Carr Will J , Averill George G , Radtke Oliver , Selwood James , Williams Rachel , Ford Elizabeth , McCullagh Liz , McErlane James , O’Donnell Cian , Durant Claire , Bartsch Ullrich , Jones Matt W , Muñoz-Neira Carlos , Wearn Alfie R , Grogan John P , Coulthard Elizabeth J 
Published: May 2020

AbstractThe human brain selectively stores knowledge of the world to optimise future behaviour, automatically rehearsing, contextualising or discarding information to create a robust record of experiences. Storage or forgetting evolves over time, particularly during sleep. We have previously shown that dopamine given in the form of L-DOPA tablets improves long-term memory in Parkinson’s disease, but only when given overnight. L-DOPA is already prescribed widely with a good safety profile and could potentially be rapidly repurposed to improve cognitive performance and improve quality of life in, for example, early Alzheimer’s Disease, if we understood the best time of day to prescribe. Therefore, we sought to test how dopamine shaped long-term memory formation before and during sleep in a double-blind randomised placebo-controlled cross-over trial of healthy older adults (n = 35). We administered L-DOPA after word-list learning to be active during repeat exposure to a proportion of the words and during subsequent nocturnal sleep. Nocturnal dopamine accelerated forgetting for words presented once but it did not affect memory for words presented twice. During slow wave sleep, L-DOPA also increased spindle amplitude around slow oscillation peaks. Larger dopamine-induced difference in word memory was associated with a larger increase in spindle amplitude. Dopamine-dependent memory processing may therefore modulate spindles dependent on slow-oscillation phase. Further, overnight dopamine increased total slow wave sleep duration by approximately 11%. This pharmaceutical modification of slow wave sleep may have potential health-enhancing benefits in old age that could include cognitive enhancement and Alzheimer’s prevention.One Sentence SummaryDopamine before sleep promotes forgetting of weak memory traces associated with increased spindle amplitude around the peak of a slow oscillations.
Dependence of the stimulus-driven microsaccade rate signature on visual stimulus polarity
Authors: Malevich Tatiana , Buonocore Antimo , Hafed Ziad M. 
Published: May 2020

AbstractMicrosaccades have a steady rate of occurrence during maintained gaze fixation, which gets transiently modulated by abrupt sensory stimuli. Such modulation, characterized by a rapid reduction in microsaccade frequency followed by a stronger rebound phase of high microsaccade rate, is often described as the microsaccadic rate signature, owing to its stereotyped nature. Here we investigated the impacts of stimulus polarity (luminance increments or luminance decrements relative to background luminance) and size on the microsaccadic rate signature. We presented brief visual flashes consisting of large or small white or black stimuli over an otherwise gray image background. Both large and small stimuli caused robust early microsaccadic inhibition, but only small ones caused a subsequent increase in microsaccade frequency above baseline microsaccade rate. Critically, small black stimuli were always associated with stronger modulations in microsaccade rate after stimulus onset than small white stimuli, particularly in the post-inhibition rebound phase of the microsaccadic rate signature. Because small stimuli were also associated with expected direction oscillations to and away from their locations of appearance, these stronger rate modulations in the rebound phase meant higher likelihoods of microsaccades opposite the black flash locations relative to the white flash locations. Our results demonstrate that the microsaccadic rate signature is sensitive to stimulus polarity, and they point to dissociable neural mechanisms underlying early microsaccadic inhibition after stimulus onset and later microsaccadic rate rebound at longer times thereafter. These results also demonstrate early access of oculomotor control circuitry to sensory representations, particularly for momentarily inhibiting saccade generation.New and noteworthyMicrosaccades are small saccades that occur during gaze fixation. Microsaccade rate is transiently reduced after sudden stimulus onsets, and then strongly rebounds before returning to baseline. We explored the influence of stimulus polarity (black versus white) on this “rate signature”. We found that small black stimuli cause stronger microsaccadic modulations than white ones, but primarily in the rebound phase. This suggests dissociated neural mechanisms for microsaccadic inhibition and subsequent rebound in the microsaccadic rate signature.
Flow-Mediated Olfactory Communication in Honey Bee Swarms
Authors: Nguyen Dieu My T. , Iuzzolino Michael L. , Mankel Aaron , Bozek Katarzyna , Stephens Greg J. , Peleg Orit 
Published: May 2020

AbstractHoney bee swarms are a landmark example of collective behavior. To become a coherent swarm, bees locate their queen by tracking her pheromones, but how can distant individuals exploit these chemical signals which decay rapidly in space and time? Here, we combine a novel behavioral assay with the machine vision detection of organism location and scenting behavior to track the search and aggregation dynamics of the honey beeApis melliferaL. We find that bees collectively create a communication network to propagate pheromone signals, by arranging in a specific spatial distribution where there is a characteristic distance between individuals and a characteristic direction in which individuals broadcast the signals. To better understand such a flow–mediated directional communication strategy, we connect our experimental results to an agent–based model where virtual bees with simple, local behavioral rules, exist in a flow environment. Our model shows that increased directional bias leads to a more efficient aggregation process that avoids local equilibrium configurations of isotropic communication, such as small bee clusters that persist throughout the simulation. Our results highlight a novel example of extended classical stigmergy: rather than depositing static information in the environment, individual bees locally sense and globally manipulate the physical fields of chemical concentration and airflow.
Intercalative DNA binding governs fluorescence enhancement of SYBR Gold
Authors: Kolbeck Pauline J. , Vanderlinden Willem , Nicolaus Thomas , Gebhardt Christian , Cordes Thorben , Lipfert Jan 
Published: May 2020

ABSTRACTSYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its binding mode to DNA remains controversial. Here, we quantitate SYBR Gold binding to DNA using two complementary approaches. We use mechanical micromanipulation with magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length, twist, and mechanical properties. The MT assay reveals systematic lengthening and unwinding of DNA upon SYBR Gold binding, consistent with an intercalative binding mode where every SYBR Gold molecule unwinds DNA by 19.1° ± 0.7°. We complement the MT data with a spectroscopic characterization of SYBR Gold fluorescence upon addition to DNA. The data are well described by a global binding model for dye concentrations ≤1 μM, with binding parameters that quantitatively agree with the MT results. The fluorescence signal increases linearly with the number of intercalated SYBR Gold molecules. At dye concentrations >1 μM, fluorescence quenching and inner filter effects become relevant and it is required to correct the SYBR Gold fluorescence signals for quantitative assessment of DNA concentrations. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.
Fevers Are Rarer in the Morning—Could We Be Missing Infectious Disease Cases by Screening for Fever Then?
Authors: Harding Charles , Pompei Francesco , Bordonaro Samantha F , McGillicuddy Daniel C , Burmistrov Dmitriy , Sanchez Leon D 
Published: May 2020

AbstractWe retrospectively studied US emergency department visits (n=295,406), including nationally representative results. Patients were less likely to have detectable fevers during mornings, with especially large morning-evening differences during influenza outbreaks (national RR=0.56, 95%CI=0.47-0.66). This suggests morning screenings could miss otherwise-detectable cases. Twice-daily screenings could be a simple solution. However, similar COVID-19 research is needed.Article Summary LineFevers were about half as common in the morning as in the evening during influenza outbreaks, suggesting that mornings may be a bad time to perform once-daily fever screenings for infectious diseases, and that twice-daily screenings could be preferable.