bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams
Authors: Busi Susheel Bhanu , Pramateftaki Paraskevi , Brandani Jade , Fodelianakis Stylianos , Peter Hannes , Halder Rashi , Wilmes Paul , Battin Tom J. 
Published: May 2020

AbstractGlacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecology, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a “mock” community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.
Personality, Subjective Well-Being, and the Serotonin 1a Receptor Gene in Common Marmosets (Callithrix jacchus)
Authors: Weiss Alexander , Yokoyama Chihiro , Hayashi Takuya , Inoue-Murayama Miho 
Published: May 2020

AbstractStudies of personality traits in common marmosets (Callithrix jacchus) indicate that there are five or six constructs—sociability, dominance, neuroticism, openness, and two related to conscientiousness—that define personality in common marmosets. The present study attempted to determine whether our earlier study of laboratory-housed individuals only yielded three domains—Dominance, Sociability, and Neuroticism—because of a low amount of between-subjects variance. We therefore increased our sample size from 77 to 128. In addition, we ascertained the reliability and validity of ratings and whether polymorphisms related to the serotonin 1a receptor were associated with personality. We found Sociability, Dominance, and Negative Affect factors that resembled three domains found in previous studies, including ours. We also found an Openness and Impulsiveness factor, the latter of which bore some resemblance to Conscientiousness, and two higher-order factors, Pro-sociality and Boldness. Further analyses could not exclude the possibility that Pro-sociality and Boldness represented a higher-level of personality organization. Correlations between personality factors and well-being were consistent with the definitions of the factors. There were no significant associations between personality and genotype. These results are consistent with the possibility that common marmoset personality structure varies as a function of rearing or housing variables that have not yet been investigated systematically.
Broad-spectrum antiviral activity of naproxen: from Influenza A to SARS-CoV-2 Coronavirus
Authors: Terrier Olivier , Dilly Sébastien , Pizzorno Andrés , Henri Julien , Berenbaum Francis , Lina Bruno , Fève Bruno , Adnet Frédéric , Sabbah Michèle , Rosa-Calatrava Manuel , Maréchal Vincent , Schwok Anny Slama 
Published: May 2020

AbstractThere is an urgent need for specific antiviral drugs directed against SARS-CoV-2 both to prevent the most severe forms of COVID-19 and to reduce viral excretion and subsequent virus dissemination; in the present pandemic context, drug repurposing is a priority. Targeting the nucleoprotein N of the SARS-CoV-2 coronavirus in order to inhibit its association with viral RNA could be a strategy to impeding viral replication and possibly other essential functions associated with viral N. The antiviral properties of naproxen, belonging to the NSAID family, previously demonstrated against Influenza A virus, were evaluated against SARS-CoV-2. Naproxen binding to the nucleoprotein of SARS-CoV2 was shown by molecular modeling. In VeroE6 cells and reconstituted human primary respiratory epithelium models of SARS-CoV-2 infection, naproxen inhibited viral replication and protected the bronchial epithelia against SARS-CoV-2 induced-damage. The benefit of naproxen addition to the standard of care is tested in an on-going clinical study.
Downregulation of Perilipin1 by IMD leads to LD reconfiguration and adaptation to bacterial infection inDrosophila
Authors: Wang Lei , Lin Jiaxin , Yu Junjing , Yang Kaiyan , Sun Li , Tang Hong , Pan Lei 
Published: May 2020

ABSTRACTLipid droplets (LDs) are dynamic intracellular organelles critical for lipid metabolism. Dynamic alterations in the configurations and functions of LDs during innate immune response to bacterial infections and the underlying mechanisms however, remain largely unknown. Herein, we trace the time-course morphology of LDs in fat bodies ofDrosophilaafter transient bacterial infection. Detailed analysis shows thatperilipin1(plin1), a core gene regulating lipid metabolism of LDs is suppressed by IMD/Relish, an innate immune signaling. During immune activation, downregulatedplin1promotes the enlargement of LDs, which in turn alleviates immune reaction-associated reactive oxygen species (ROS) stress. Thus, the growth of LDs is likely an active adaptation to maintain redox homeostasis in response to IMD activation. Therefore, our study provides evidence thatplin1serves as a modulator on LDs’ reconfiguration in regulating infection-induced pathogenesis, and Plin1 might be a potential therapeutic target for coordinating inflammation resolution and lipid metabolism.
Niche and neutral processes leave distinct structural imprints on indirect interactions in mutualistic networks
Authors: Simmons Benno I. , Beckerman Andrew P. , Hansen Katrine , Maruyama Pietro K. , Televantos Constantinos , Vizentin-Bugoni Jeferson , Dalsgaard Bo 
Published: May 2020

AbstractIndirect interactions are central to ecological and evolutionary dynamics in pollination communities, yet we have little understanding about the processes determining patterns of indirect interactions, such as those between pollinators through shared flowering plants. Instead, research has concentrated on the processes responsible for direct interactions and whole-network structures. This is partly due to a lack of appropriate tools for characterising indirect interaction structures, because traditional network metrics discard much of this information. The recent development of tools for counting motifs (subnetworks depicting interactions between a small number of species) in bipartite networks enable detailed analysis of indirect interaction patterns. Here we generate plant-hummingbird pollination networks based on three major assembly processes – neutral effects (species interacting in proportion to abundance), morphological matching and phenological overlap – and evaluate the motifs associated with each one. We find that different processes produce networks with significantly different patterns of indirect interactions. Neutral effects tend to produce densely-connected motifs, with short indirect interaction chains, and motifs where many specialists interact indirectly through a single generalist. Conversely, niche-based processes (morphology and phenology) produced motifs with a core of interacting generalists, supported by peripheral specialists. These results have important implications for understanding the processes determining indirect interaction structures.
Sex-specific vasopressin signaling buffers stress-dependent synaptic changes in female mice
Authors: Loewen Spencer P. , Baimoukhametova Dinara , Bains Jaideep S. 
Published: May 2020

AbstractIn many species, social networks provide benefit for both the individual and the collective. In addition to transmitting information to others, social networks provide an emotional buffer for distressed individuals. Our understanding about the cellular mechanisms that contribute to buffering is poor. Stress has consequences for the entire organism, including a robust change in synaptic plasticity at glutamate synapses onto corticotropin-releasing hormone (CRH) neurons in the paraventricular nucleus of the hypothalamus (PVN). In females, however, this stress-induced metaplasticity is buffered by the presence of a naïve partner. This buffering may be due to discrete behavioral interactions, signals in the context in which the interaction occurs (i.e. olfactory cues), or it may be influenced by local signaling events in the PVN. Here, we show that local vasopressin (VP) signaling in PVN buffers the short-term potentiation (STP) at glutamate synapses after stress. This social buffering of metaplasticity, which requires the presence of another individual, was prevented by pharmacological inhibition of the VP 1a receptor in female mice. Exogenous VP mimicked the effects of social buffering and reduced STP in CRHPVNneurons from females but not males. These findings implicate VP as a potential mediator of social buffering in female mice.Significance StatementIn many organisms, including rodents and humans, social groups are beneficial to overall health and well-being. Moreover, it is through these social interactions that the harmful effects of stress can be mitigated—a phenomenon known as social buffering. In the present study, we describe a critical role for the neuropeptide vasopressin in social buffering of synaptic metaplasticity in stress-responsive corticotropin-releasing hormone neurons in female mice. These effects of vasopressin do not extend to social buffering of stress behaviors, suggesting this is a very precise and local form of sex-specific neuropeptide signaling.
The Rotating Snake Illusion is a straightforward consequence of non-linearity in arrays of standard motion detectors
Authors: Bach Michael , Atala-Gérard Lea 
Published: May 2020

AbstractThe Rotating Snakes illusion is a motion illusion based on repeating, asymmetric luminance patterns. Recently, we found certain grey-value conditions where a weak, illusory motion occurs in the opposite direction. Of the four models for explaining the illusion, one (Backus and Oruç, 2005) also explains the unexpected perceived opposite direction. We here present a simple new model, without free parameters, based on an array of standard correlation-type motion detectors with a subsequent non-linearity (e.g., saturation) before summing the detector outputs. The model predicts (1) the pattern-appearance motion illusion for steady fixation, (2) an illusion under the real-world situation of saccades across or near the pattern (pattern shift), (3) a relative maximum of illusory motion for the same grey values where it is found psychophysically, and (4) the inverse illusion for certain luminance values. We submit that the model’s sparseness of assumptions justifies adding a fifth model to explain this illusion.
Is a Simple Sensorimotor Reaction Really Simple?
Authors: Kulakov Alexey A. 
Published: May 2020

AbstractThe simple sensorimotor reaction (SSR) is widely used in psychophysiological research. It was previously shown, that the SSR latency is not constant. We studied changes in the SSR latency as a function of the waiting time from the moment of the previous response to the moment of the start of the stimulation. We performed the stimulation using light, sound and air impulse. As a response, we used a “labial sound”, a finger touch and blinking of the eyes. In all cases, where the objects of the study were humans, the SSR latency had constant and variable components. The constant SSR component was the shortest in response to closing the eyes to sound (120 ms). For “lip reaction” and finger response to sound it was 174–178 ms and 178–182 ms, respectively, but for “lip reaction” and finger response to light it was 220–226 ms. The variable SSR component represented exponential latency decay with an increase in the waiting time interval. In this case, the decay consisted of at least two components, with an apparent relaxation time in the range 30–150 ms and 600–1300 ms. Alternating stimulation of paired organs of the reception or alternating fingers reduced the apparent relaxation time of the SSR latency decay. Moreover, the latency of the human corneal reflex during eye stimulation with an air pulse also had the latency decay with three components of apparent relaxation time 9.5, 68.2 and 1,086 ms and the constant latency of 34.2 ms.The latency of the corneal reflex in a young cat was constant and had a value of 14.6 ms. Thus, it has been shown, that the SSR latency has a complex structure and, like any conditioned reflex, is strongly influenced by the cortex. We believe that a choice is made in the centers for analysis of receiving signals from reception organs and centers sending signals to reacting organs, i.e. essentially, the SSR is also a choice reaction.
Analysis of circulating protein aggregates reveals pathological hallmarks of amyotrophic lateral sclerosis
Authors: Adiutori Rocco , Puentes Fabiola , Bremang Michael , Lombardi Vittoria , Zubiri Irene , Leoni Emanuela , Aarum Johan , Sheer Denise , McArthur Simon , Pike Ian , Malaspina Andrea 
Published: May 2020

AbstractBlood-based biomarkers can be informative of brain disorders where protein aggregation play a major role. The proteome of plasma and circulating protein aggregates (CPA) reflect the inflammatory and metabolic state of the organism and can be predictive of system-level and/or organ-specific pathologies. CPA are enriched with heavy chain neurofilaments (NfH), key axonal constituents involved in brain aggregates formation and biomarkers of the fatal neurodegenerative disorder amyotrophic lateral sclerosis (ALS). Here we show that CPA and brain protein aggregates (BPA) from ALS differ in protein composition and appear as a combination of electron-dense large globular and small filamentous formations on transmission electron microscopy. CPA are highly enriched with proteins involved in the proteasome and energy metabolism. Compared to the human proteome, proteins within aggregates show distinct and tissue-dependent chemical features of aggregation propensity. The use of a TMTcalibrator™ proteomics workflow with ALS brain as calibrant reveals 4973 brain-derived low-abundance proteins in CPA, including the products of translation of 24 ALS risk genes. 285 of these (5.7%) are regulated in ALS CPA including FUS (p<0.05). CPA from both ALS and healthy controls affect cell viability when testing endothelial and PC12 neuronal cell lines, while CPA from ALS exert a more toxic effect at lower concentrations. The analysis of resistance to protease enzymes hydrolysis indicates an ALS-specific digestion pattern for NfH using enterokinase. This study reveals how peripheral protein aggregates are significantly enriched with brain proteins which are highly representative of ALS pathology and a potential alternative source of biomarkers and therapeutic targets for this incurable disorder.Significance StatementMolecular mechanism of neurodegeneration like protein aggregation are important brain-specific alterations which need to be addressed therapeutically. Recently described fluid biomarkers of neurodegenerative disorders provide means for stratification and monitoring of disease progression. Here we show that circulating protein aggregates are easily accessible in blood and reproduce important features of brain pathology for an incurable disorder like amyotrophic lateral sclerosis. They represent a source of biomarkers and of novel therapeutics for ALS.
Experience-dependent inhibitory plasticity is mediated by CCK+ basket cells in the developing dentate gyrus
Authors: Feng Ting , Alicea Christian , Pham Vincent , Kirk Amanda , Pieraut Simon 
Published: May 2020

AbstractEarly postnatal experience shapes both inhibitory and excitatory networks in the hippocampus. However, the underlying circuit plasticity is unclear. Using an enriched environment (EE) paradigm, we assessed the circuit plasticity of inhibitory cell-types in the hippocampus. We found that cholecystokinin (CCK)-expressing basket cells strongly increased somatic inhibition on the excitatory granular cells (GC) following EE while another pivotal inhibitory cell-type, parvalbumin (PV)-expressing cells did not show changes. By inhibiting activity of the entorhinal cortex (EC) using a chemogenetic approach, we demonstrate that the projections from the EC is responsible for the developmental plasticity of CCK+ basket cells. Our measurement of the input decorrelation by DG circuit suggests that EE has little effect on pattern separation despite of the altered CCK+ basket cell circuit. Altogether, our study places the activity-dependent remodeling of CCK+ basket cell innervation as a central process to adjust inhibition in the DG, while maintaining the computation in the circuit.
An effective cold storage method for stockpilingHalyomorpha halyseggs for field surveys and laboratory rearing ofTrissolcus japonicus
Authors: Wong Warren H. L. , Walz Matt A. , Oscienny Angela B. , Sherwood Jade L. , Abram Paul K. 
Published: May 2020

AbstractAn effective stockpiling method for egg masses of the invasive brown marmorated stink bug (Halyomorpha halys[Stål]; Hemiptera: Pentatomidae) would be useful for rearing and field studies of its egg parasitoidTrissolcus japonicus(Ashmead) (Hymenoptera: Scelionidae). The current method of stockpilingH. halysegg masses at sub-zero temperatures has lethal and sublethal fitness consequences forT. japonicus. We show that parasitoid emergence from egg masses refrigerated at 8°C for up to two months before parasitism is higher than from frozen egg masses and usually has minimal or no sublethal fitness effects (sex ratio, development time, activity, fecundity, longevity, and weight) on emergingT. japonicus. Only after two months of host egg refrigeration did the emergence ofT. japonicusbegin to decrease significantly (by 9.6% relative to untreated viable egg masses), whereas egg masses previously frozen at -80°C had a 58.8% reduction in parasitoid emergence after 14 days of storage. Refrigerated egg masses that were subsequently exposed to average field temperatures (warm: 22.9°C; cool: 13.2°C) were still suitable forT. japonicusparasitism after 7 days, while viable egg masses exposed to warm temperatures for 7 days before parasitism had 24.1% lower parasitoid emergence. Our results demonstrate that refrigeration at 8°C, while resulting in complete mortality ofH. halysembryos after 10 days, are more suitable forT. japonicusparasitism than those stored at sub-zero temperatures. The quantity and quality ofH. halyseggs that can be stockpiled with this method could facilitateT. japonicuslaboratory colony maintenance, field monitoring, and releases.
A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs
Authors: Callahan Tiffany J. , Tripodi Ignacio J. , Hunter Lawrence E. , Baumgartner William A. 
Published: May 2020

ABSTRACTMotivationAlthough knowledge graphs (KGs) are used extensively in biomedical research to model complex phenomena, many KG construction methods remain largely unable to account for the use of different standardized terminologies or vocabularies, are often difficult to use, and perform poorly as the size of the KG increases in scale. We introduce PheKnowLator (Phenotype Knowledge Translator), a novel KG framework and fully automated Python 3 library explicitly designed for optimized construction of semantically-rich, large-scale biomedical KGs. To demonstrate the functionality of the framework, we built and evaluated eight different parameterizations of a large semantic KG of human disease mechanisms. PheKnowLator is available at:https://github.com/callahantiff/PheKnowLator.
Genome mapping resolves structural variation within segmental duplications associated with microdeletion/microduplication syndromes
Authors: Mostovoy Yulia , Yilmaz Feyza , Chow Stephen K. , Chu Catherine , Lin Chin , Geiger Elizabeth A. , Meeks Naomi J. L. , Chatfield Kathryn. C. , Coughlin Curtis R. , Kwok Pui-Yan , Shaikh Tamim H. 
Published: May 2020

AbstractSegmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams-Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. These three genomic regions, and the SDs within them, have been previously analyzed in a small number of individuals. However, population-level studies have been lacking because most techniques used for analyzing these complex regions are both labor- and cost-intensive. In this study, we present a high-throughput technique to genotype complex structural variation using a single molecule, long-range optical mapping approach. We identified novel structural variants (SVs) at 7q11.23, 15q13.3 and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising 5 super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we refined the microdeletion breakpoints located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.