bluuebunny/crossref_metadata_2025_split huggingface dataset:
Memory loss at sleep onset
Authors: Lacaux Célia , Andrillon Thomas , Arnulf Isabelle , Oudiette Delphine 
Published: May 2022

ABSTRACTEvery night, we pass through a transitory zone at the borderland between wakefulness and sleep, named the first stage of non-rapid eye movement sleep (N1). N1 sleep is associated with an increased hippocampal activity and dreamlike experiences that incorporate recent wake materials, suggesting that it may be associated with memory processing. Here, we investigated the specific contribution of N1 sleep in the processing of memory traces. Participants were asked to learn the precise locations of 48 objects on a grid and were then tested on their memory for these items before and after a 30-minute rest during which participants either stayed fully awake, transitioned toward N1 or deeper (N2) sleep. We showed that memory recall was lower (10% forgetting) after a resting period including only N1 sleep compared to N2 sleep. Furthermore, the ratio of alpha/theta power (an EEG marker of the transition towards sleep) correlated negatively with the forgetting rate when taking into account all sleepers (N1 and N2 groups combined), suggesting a physiological index for memory loss that transcends sleep stages. Our findings suggest that interrupting sleep onset at N1 may alter sleep-dependent memory consolidation and promote forgetting.
Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology
Authors: Velsko Irina M. , Semerau Lena , Inskip Sarah A. , García-Collado Maite Iris , Ziesemer Kirsten , Ruber Maria Serrano , Benítez de Lugo Enrich Luis , García Jesús Manuel Molero , Valle David Gallego , Ruiz Ana Cristina Peña , Salazar García Domingo C. , Hoogland Menno L.P. , Warinner Christina 
Published: May 2022

AbstractDental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed inter-individual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.Research HighlightsNo associations between calculus species profiles and oral health metrics were detected in a single large populationA minority of individuals have a dental calculus species profile characterized by low levels ofStreptococcusand high levels of anaerobic taxa
Epigenetic Control of Hundreds of Chromosome-Associated lncRNA Genes Essential for Replication and Stability
Authors: Heskett Michael B. , Vouzas Athanasios E. , Smith Leslie G. , Yates Phillip A. , Boniface Christopher , Bouhassira Eric E. , Spellman Paul , Gilbert David M. , Thayer Mathew J. 
Published: May 2022

AbstractASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilized a set of distinctive ASAR characteristics that allowed for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci resulted in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain “Inactivation/Stability Centers” that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
Method for quantifying the metabolic boundary fluxes of cell cultures in large cohorts by high resolution hydrophilic liquid chromatography mass spectrometry
Authors: Groves Ryan A. , Mapar Maryam , Aburashed Raied , Ponce Luis F. , Bishop Stephanie L. , Rydzak Thomas , Drikic Marija , Bihan Dominique G. , Benediktsson Hallgrimur , Clement Fiona , Gregson Daniel B. , Lewis Ian A. 
Published: May 2022

AbstractMetabolomics is a mainstream approach for investigating the metabolic underpinnings of complex biological phenomena and is increasingly being applied to large scale studies involving hundreds or thousands of samples. Although metabolomics methods are robust in smaller scale studies, they can be challenging to apply in larger cohorts due to the inherent variability of liquid chromatography mass spectrometry (LC-MS). Much of this difficulty results from the time-dependent changes in the LC-MS system, which affects both the qualitative and quantitative performance of the instrument. Herein, we introduce an analytical strategy for addressing this problem in large-scale microbial studies. Our approach quantifies microbial boundary fluxes using two zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) columns that are plumbed to enable offline column equilibration. Using this strategy, we show that over 360 common metabolites can be resolved in 4.5 minutes per sample and that metabolites can be quantified with a median coefficient of variation of 0.127 across 1,100 technical replicates. We illustrate the utility of this strategy via an analysis of 960 strains of Staphylococcus aureus isolated from blood stream infections. These data capture the diversity of metabolic phenotypes observed in clinical isolates and provide an example of how large-scale investigations can leverage our novel analytical strategy.
Isoform-specific O-glycosylation dictates Ebola virus infectivity
Authors: Bagdonaite Ieva , Abdurahman Samir , Mirandola Mattia , Frank Martin , Narimatsu Yoshiki , Vakhrushev Sergey Y. , Salata Cristiano , Mirazimi Ali , Wandall Hans H. 
Published: May 2022

SummaryEbola virus glycoprotein is one of the most heavily O-glycosylated viral envelope glycoproteins. Using glycoengineered cell lines we demonstrate that O-linked glycan truncation and perturbed initiation retarded the production of viral particles and decreased infectivity of progeny virus. Next, using TMT isobaric labelling, we performed quantitative differential O-glycoproteomics on proteins produced in wild type HEK293 cells and cell lines ablated for three key GalNAc-transferases, GalNAc-T1, -T2, and -T3, as well as compared it to patterns on wild type virus-like particles. We demonstrate selective initiation of a subset of O-glycosites by each enzyme, with GalNAc-T1 having the largest contribution. This work represents a comprehensive site-specific analysis of EBOV GP, with 47 O-glycosites identified, and sheds light on differential regulation of EBOV GP glycosylation initiated by host GalNAc-Ts. Together with the effect on viral propagation it opens prospective avenues for tailored intervention approaches and means for modulating immunogen O-glycan density.
Geographic Name Resolution Service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling
Authors: Boyle Brad L. , Maitner Brian S. , Barbosa George G. C. , Sajja Rohith K. , Feng Xiao , Merow Cory , Newman Erica A. , Park Daniel S. , Roehrdanz Patrick R. , Enquist Brian J. 
Published: May 2022

AbstractMassive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data and analysis of erroneous observations can lead to flawed results.Here, we present the Geographic Name Resolution Service (GNRS), an application for the correction, standardization and indexing of world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In an assessment of geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a major data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and can be accessed via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.
Great-tailed Grackles (Quiscalus mexicanus) as a tolerant host of avian malaria parasites
Authors: Pacheco M. Andreína , Ferreira Francisco C. , Logan Corina J. , McCune Kelsey B. , MacPherson Maggie P. , Miranda Sergio Albino , Santiago-Alarcon Diego , Escalante Ananias A. 
Published: May 2022

AbstractGreat-tailed Grackles (Quiscalus mexicanus) are a social, polygamous bird species whose populations have rapidly expanded their geographic range across North America over the past century. Before 1865, Great-tailed Grackles were only documented in Central America, Mexico, and southern Texas in the USA. Given the rapid northern expansion of this species, it is relevant to study its role in the dynamics of avian blood parasites. Here, 87 Great-tailed grackles in Arizona (a population in the new center of the range) were screened for haemosporidian parasites using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene. Individuals were caught in the wild from January 2018 until February 2020. Haemosporidian parasite prevalence was 60.9% (53/87). A high Plasmodium prevalence was found (59.8%, 52/87), and one grackle was infected with Haemoproteus (Parahaemoproteus) sp. (lineage SIAMEX01). Twenty-one grackles were infected with P. cathemerium, sixteen with P. homopolare, four with P. relictum (strain GRW04), and eleven with three different genetic lineages of Plasmodium spp. that have not been characterized to species level (MOLATE01, PHPAT01, and ZEMAC01). Gametocytes were observed in birds infected with three different Plasmodium lineages, revealing that grackles are competent hosts for some parasite species. This study also suggests that grackles are highly susceptible and develop chronic infections consistent with parasite tolerance, making them competent to transmit some generalist haemosporidian lineages. It can be hypothesized that, as the Great-tailed Grackle expands its geographic range, it may affect local bird communities by increasing the transmission of local parasites but not introducing new species into the parasite species pool.
Spatial organization of Dectin-1 and TLR2 during synergistic crosstalk revealed by super-resolution imaging
Authors: Li Miao , Vultorius Christopher , Bethi Manisha , Yu Yan 
Published: May 2022

AbstractInnate immune cells recognize and elicit responses against pathogens by integrating signals from different types of cell-surface receptors. How the receptors interact in the membrane to enable their signaling crosstalk is poorly understood. Here, we reveal the nanoscale organization of TLR2 and Dectin-1, a receptor pair known to cooperate in regulating antifungal immunity, through their synergistic signaling crosstalk at macrophage cell membranes. Using super-resolution single-molecule localization microscopy, we show that discrete non-colocalized nanoclusters of Dectin-1 and TLR2 are partially overlapped during their synergistic crosstalk. Compared to when one type of receptor is activated alone, the simultaneous activation of Dectin-1 and TLR2 leads to a higher percentage of both receptors being activated by their specific ligands, and consequently an increased level of tyrosine phosphorylation. Our results depict, in nanoscale detail, how Dectin-1 and TLR2 achieve synergistic signaling through the spatial organization of their receptor nanoclusters.
DNA-based detection of Aphanomyces cochlioides in soil and sugar beet plants
Authors: Botkin Jacob R. , Hirsch Cory D. , Martin Frank N. , Chanda Ashok K. 
Published: May 2022

AbstractAphanomyces cochlioides, the causal agent of seedling damping-off and Aphanomyces root rot (ARR) of sugar beet, causes yield losses in major sugar beet growing regions. Currently, a 4-week soil bioassay and a 2-day culture-based assay are used to diagnose presence of A. cochlioides. However, these assays can be time-consuming and lack sensitivity. In this study we developed a sensitive, specific, and rapid assay to detect and quantify DNA of A. cochlioides. We developed a TaqMan qPCR assay targeting a region of the mitochondrial genome of A. cochlioides representing a unique gene order for Aphanomyces with genus-specific primers and a species-specific probe. The qPCR assay detected A. cochlioides in 12 naturally infested field soil samples with disease severity index (DSI) values of 48-100, in sugar beet seedlings 5-7 days after planting, and with as little as 1 fg of pure A. cochlioides DNA. Adult sugar beet roots with ARR symptoms were sampled to further validate this qPCR assay. Aphanomyces cochlioides was detected in 95% of these samples using this qPCR assay, while only 23% of the same samples were positive using a culture-based assay. This shows the improved sensitivity of this qPCR assay for disease diagnosis and could provide growers with ARR risk of a field, which would help them make informed disease management decisions. However, further research is required to translate the results of this study to growers’ fields to quantify A. cochlioides with a high degree of accuracy.
CLASP2 stabilizes GDP-associated terminal tubulins to prevent microtubule catastrophe
Authors: Luo Wangxi , Demidov Vladimir , Shen Qi , Girão Hugo , Chakraborty Manas , Maiorov Aleksandr , Ataullakhanov Fazly I. , Lin Chenxiang , Maiato Helder , Grishchuk Ekaterina L. 
Published: May 2022

AbstractCLASPs are ubiquitous stabilizers of microtubule dynamics but their molecular targets at the microtubule plus-end are not understood. Using DNA origami-based reconstructions we show that clusters of human CLASP2 form a load-bearing bond with terminal GDP-tubulins at the stabilized microtubule tip. This activity relies on the unconventional TOG2 domain of CLASP2, which releases its high-affinity bond with the GDP-dimers upon their conversion into polymerization-competent GTP-tubulin. By tethering dynamic microtubule ends near immobilized CLASP2, we show that the targets for CLASP2 binding at the polymerizing tip arise stochastically, leading to nanoscale disruptions in microtubule tip integrity. The ability of CLASP2 to recognize nucleotide-specific tubulin conformation and stabilize the catastrophe-promoting GDP-tubulins intertwines with the previously underappreciated exchange between GDP and GTP at terminal tubulins, providing a distinct molecular mechanism to suppress microtubule catastrophe without affecting tubulin incorporation.
Episodic memory retrieval affects the onset and dynamics of evidence accumulation during value-based decisions
Authors: Kraemer Peter M. , Gluth Sebastian 
Published: May 2022

AbstractIn neuroeconomics, there is much interest in understanding simple value-based choices where agents choose between visually presented goods, comparable to a shopping scenario in a supermarket. However, many everyday decisions are made in the physical absence of the considered goods, requiring agents to recall information about the goods from memory. Here, we asked whether and how this reliance on an internal memory representation affects the temporal dynamics of decision making on a cognitive and neural level. Participants performed a remember-and-decide task, in which they made simple purchasing decisions between money offers and snack items while undergoing EEG. Snack identity was presented either visually (value trials) or had to be recalled from memory (memory trials). Behavioral data indicated comparable choice consistency across both trial types, but considerably longer response times (RT) in memory trials. Drift-diffusion modeling suggested that this RT difference was due to longer non-decision time of decision processes as well as altered evidence accumulation dynamics (lower accumulation rate and higher decision threshold). The non-decision time effect was supported by a delayed onset of the lateralized readiness potential. These results show that both, decision and non-decision processes are prolonged when participants need to resort to internal memory representations during value-based decisions.
The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi)
Authors: de Miranda Gustavo S. , Kulkarni Siddharth S. , Tagliatela Jéssica , Baker Caitlin M. , Giupponi Alessandro P.L. , Labarque Facundo M. , Gavish-Regev Efrat , Rix Michael G. , Carvalho Leonardo S. , Fusari Lívia Maria , Wood Hannah M. , Sharma Prashant P. 
Published: May 2022

AbstractAsymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or “living fossils” when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi (“whip spiders”), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous “whips”). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report several individuals of a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of “dark taxa”, and especially phylogenetic relicts in tropical and subtropical habitats.
Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
Authors: Poterek Marya L. , Vogels Chantal B.F. , Grubaugh Nathan D. , Ebel Gregory D. , Perkins T. Alex , Cavany Sean M. 
Published: May 2022

ABSTRACTThough instances of arthropod-borne (arbo)virus co-infection have been documented clinically, the overall incidence of arbovirus co-infection and its drivers are not well understood. Now that dengue, Zika, and chikungunya viruses are all in circulation across tropical and subtropical regions of the Americas, it is important to understand the environmental and biological conditions that make co-infections more likely to occur. To understand this, we developed a mathematical model of cocirculation of two arboviruses, with transmission parameters approximating dengue, Zika, and/or chikungunya viruses and co-infection possible in both humans and mosquitoes. We examined the influence of seasonal timing of arbovirus cocirculation on the extent of co-infection. By undertaking a sensitivity analysis of this model, we examined how biological factors interact with seasonality to determine arbovirus co-infection transmission and prevalence. We found that temporal synchrony of the co-infecting viruses and average temperature were the most influential drivers of co-infection incidence. For seasonal patterns typical of a tropical region, we observed non-negligible incidence irrespective of arrival time when two arboviruses arrived simultaneously. Under our default parameter settings, this corresponded to a maximum co-infection cumulative incidence of 83 per 1,000 individuals and a minimum cumulative incidence of 32 per 1,000 individuals in the year following arrival. For seasonal patterns typical of a more temperate region, co-infections only occurred if arrivals took place near the seasonal peak, and even then, did not reach 0.01 co-infections per 1,000 individuals. Our model highlights the synergistic effect of co-transmission from mosquitoes, which leads to more than double the number of co-infections than would be expected in a scenario without co-transmission. Our results show that arbovirus co-infections are unlikely to occur in appreciable numbers unless epidemics overlap in space and time and in a tropical region.