bluuebunny/crossref_metadata_2025_split huggingface dataset:
The two-component system CopRS maintains femtomolar levels of free copper in the periplasm ofPseudomonas aeruginosausing a phosphatase-based mechanism
Authors: Novoa-Aponte Lorena , Soncini Fernando C. , Argüello José M. 
Published: May 2020

ABSTRACTTwo component systems control periplasmic Cu+homeostasis in Gram-negative bacteria. In characterized systems such asEscherichia coliCusRS, upon Cu+binding to the periplasmic sensing domain of CusS, a cytoplasmic phosphotransfer domain phosphorylates the response regulator CusR. This drives the expression of efflux transporters, chaperones, and redox enzymes to ameliorate metal toxic effects. Here, we show that thePseudomonas aeruginosatwo component sensor histidine kinase CopS exhibits a Cu-dependent phosphatase activity that maintains a non-phosphorylated CopR when the periplasmic Cu levels are below its activation threshold. Upon Cu+binding to the sensor, the phosphatase activity is blocked and the phosphorylated CopR activates transcription of the CopRS regulon. Supporting the model, mutagenesis experiments revealed that the ΔcopSstrain showed constitutive high expression of the CopRS regulon, lower intracellular Cu+levels, and larger Cu tolerance when compared to wild type cells. The invariant phospho-acceptor residue His235of CopS was not required for the phosphatase activity itself, but necessary for its Cu-dependency. To sense the metal, the periplasmic domain of CopS binds two Cu+ions at its dimeric interface. Homology modeling of CopS based on CusS structure (four Ag+binding sites) clearly explains the different binding stoichiometries in both systems. Interestingly, CopS binds Cu+/2+with 30 × 10−15M affinities, pointing to the absence of free (hydrated) Cu+/2+in the periplasm.IMPORTANCECopper is a micronutrient required as cofactor in redox enzymes. When free, copper is toxic, mismetallating proteins, and generating damaging free radicals. Consequently, copper overload is a strategy that eukaryotic cells use to combat pathogens. Bacteria have developed copper sensing transcription factors to control copper homeostasis. The cell envelope is the first compartment that has to cope with copper stress. Dedicated two component systems control the periplasmic response to metal overload. This manuscript shows that the copper sensing two component system present in Pseudomonadales exhibits a signal-dependent phosphatase activity controlling the activation of the response regulator, distinct from previously described periplasmic Cu sensors. Importantly, the data show that the sensor is activated by copper levels compatible with the absence of free copper in the cell periplasm. This emphasizes the diversity of molecular mechanisms that have evolved in various bacteria to manage the copper cellular distribution.
Single Cell Transcriptomics-guided Antisense Treatment Improves Endoderm Differentiation of iPSCs
Authors: Hor P. , Punj V. , Borok Z. , Ryan (Firth) A.L. , Ichida J.K. 
Published: May 2020

AbstractDirected differentiation of induced pluripotent stem cells (iPSCs) enables the production of relevant cell types for studies of human biology, disease-modeling, and efforts towards cellular therapy and transplantation. However, the low yield and purity of desired cell types can limit the utility of this approach. Enhancing differentiation purity can require extensive optimization of morphogen treatments, and this can still be ineffective for iPSC lines with biased or aberrant differentiation propensities. To address these limitations, we have developed a new approach for increasing the purity of iPSC directed differentiation cultures calledRNA sequencing andAntisense-assistedDifferentiation (RAD). We performed trajectory analysis of single cell RNA sequencing during iPSC differentiation into endoderm to identify transcription factors responsible for committing cells to undesired, non-endodermal fates. Specific suppression of these transcription factors using antisense oligonucleotides (ASOs) increased the percentage of endodermal cells by up to 20-fold in 3 different iPSC lines that exhibited poor endoderm differentiation. Moreover, this approach required minimal culture manipulation. Thus, RAD improves the utility of iPSCs for basic and translational studies.
Reprogramming of larval locomotory pattern during baculovirus-induced host manipulation
Authors: Hikida Hiroyuki , Katsuma Susumu 
Published: May 2020

AbstractMany parasites manipulate host behaviour to enhance their transmission. Baculovirus induces enhanced locomotory activity (ELA) combined with subsequent climbing behaviour in lepidopteran larvae, which facilitates viral dispersal. Previously, larval locomotion during ELA was summarized as the distance travelled for a few minutes at several time points. However, as ELA continues for several hours, these methods are unlikely to evaluate larval locomotion precisely during ELA. We developed a novel method to continuously trace the locomotion ofBombyx morilarvae using time-lapse imaging. This method successfully quantified the locomotory activities of larvae infected withBombyx mori nucleopolyhedrovirus(BmNPV) for 24 h. We found that both mock- and BmNPV-infected larvae periodically repeated moving and pausing with a similar frequency. In contrast, BmNPV-infected larvae showed fast and long-lasting locomotion compared with mock-infected larvae, which resulted in longer locomotory distances in infected larvae. Moreover, BmNPV-infected larvae exhibited biphasic behaviour. Initially, BmNPV-infected larvae showed longer locomotory distances, but the locomotory pattern was similar to mock-infected larvae. However, during the second phase, the locomotory pattern was drastically altered, with an extremely larger locomotory area. These results indicate that BmNPV reprograms host locomotory pattern, which is a turning point for the process of BmNPV-induced host manipulation.
Regularity extraction under stress: boosted statistical learning but unaffected sequence learning
Authors: Tóth-Fáber Eszter , Janacsek Karolina , Szőllősi Ágnes , Kéri Szabolcs , Németh Dezső 
Published: May 2020

AbstractAcute stress can crucially influence learning and memory processes. One of the key processes underlying human learning and memory is the ability of our brain to rapidly detect and extract regularities from sensory input across time and space leading to effective predictive processing. Here, we aimed to get an in-depth look into the effect of stress on the acquisition of two aspects of regularity extraction. We examined whether and how stress affects (1) processes and learning of probability-based, statistical regularities and (2) serial order-based, sequential regularities in the same experimental design, and (3) explicit access to the acquired information. Considering that the acquisition of statistical regularities is a rapid process, we primarily focused on the early phases of the task. We induced stress with the Socially Evaluated Cold Pressor Test in 27 young adults, while 26 participants were enrolled in the control group. Salivary cortisol levels and subjective ratings of affective states showed successful stress induction. After the stress induction, we measured regularity extraction with the cued Alternating Serial Reaction Time task. We found that stress promoted the acquisition of statistical regularities and did not alter the learning of sequential regularities. Post-block reports showed weaker explicit access to the sequential regularities in the stress group. Our results give a process-level understanding on how stress alters learning and memory functions related to predictive processes.
Automatic Wake-Sleep Stages Classification using Electroencephalogram Instantaneous Frequency and Envelope Tracking
Authors: Rahbar Alam Mahdi , Sameni Reza 
Published: May 2020

AbstractBackgroundThe study of cerebral activity during sleep using the electroencephalograph (EEG) is a major research field in neuroscience. Despite the rich literature in this field, the automatic and accurate categorization of wake-sleep stages remains an open problem.New MethodA robust model-based Kalman filtering scheme is proposed for tracking the poles of a second order time-varying autoregressive model fitted over the EEG acquired during different wake/sleep stages. The pole angle/phase is regarded as the dominant frequency of the EEG spectrum (known as the instantaneous frequency in literature). The frequency resolution is improved by splitting the wide frequency band to subbands corresponding to well-known brain rhythms. Using recent findings in field of EEG phase/frequency tracking, the instantaneous envelope of the narrow-band signal’s analytic form is also tracked as a complementary feature.ResultsThe minimal set of instantaneous frequency and envelope features is employed in three classification schemes, using training labels from R&k and AASM sleep scoring standards. The LDA classifier resulted in the highest performance using the proposed feature set.Comparison with Existing MethodsThe proposed method resulted in a higher mean decoding accuracy and a lower standard deviation on the entire dataset, as compared with state-of-the-art techniques.ConclusionsThe accurate tracking of the instantaneous frequency and envelope are highly informative for sleep stage scoring. The proposed method is shown to have additional applications, including the prediction of wake-sleep transition, which can be used for drowsiness detection from the EEG.
Energy dynamics for systemic configurations of virus-host co-evolution
Authors: Romano Alessandra , Casazza Marco , Gonella Francesco 
Published: May 2020

Abstract (no-technical summary)Virus cause multiple outbreaks, for which comprehensive tailored therapeutic strategies are still missing. Virus and host cell dynamics are strictly connected, and convey in virion assembly to ensure virus spread in the body. Study of the systemic behavior of virus-host interaction at the single-cell level is a scientific challenge, considering the difficulties of using experimental approaches and the limited knowledge of the behavior of emerging novel virus as a collectivity. This work focuses on positive-sense, single-stranded RNA viruses, like human coronaviruses, in their virus-individual host interaction, studying the changes induced in the host cell bioenergetics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. We found that reducing the energy flow which fuels virion assembly is the most affordable strategy to limit the virus spread, but its efficacy is mitigated by the contemporary inhibition of other flows relevant for the system.SummaryPositive-single-strand ribonucleic acid ((+)ssRNA) viruses can cause multiple outbreaks, for which comprehensive tailored therapeutic strategies are still missing. Virus and host cell dynamics are strictly connected, generating a complex dynamics that conveys in virion assembly to ensure virus spread in the body.This work focuses on (+)ssRNA viruses in their virus-individual host interaction, studying the changes induced in the host cell bioenergetics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the energy dynamics of the system.By means of a computational simulator based on the systemic diagramming, we identifid host protein recycling and folded-protein synthesis as possible new leverage points. These also address different strategies depending on time setting of the therapeutic procedures. Reducing the energy flow which fuels virion assembly is addressed as the most affordable strategy to limit the virus spread, but its efficacy is mitigated by the contemporary inhibition of other flows relevant for the system. Counterintuitively, targeting RNA replication or virion budding does not give rise to relevant systemic effects, and can possibly contribute to further virus spread. The tested combinations of multiple systemic targets are less efficient in minimizing the stock of virions than targeting only the virion assembly process, due to the systemic configuration and its evolution overtime. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics.As a whole, our work points out the need for a systemic approach to design effective therapeutic strategies that should take in account the dynamic evolution of the system.
In Vitro Inhibition of SARS-CoV-2 Infection by Bovine Lactoferrin
Authors: de Carvalho Carlos Alberto Marques , da Rocha Matos Aline , Caetano Braulia Costa , de Sousa Junior Ivanildo Pedro , da Costa Campos Samir Pereira , Geraldino Barbara Rodrigues , Barros Caroline Augusto , de Almeida Matheus Augusto Patricio , Rocha Vanessa Pimenta , da Silva Andréa Marques Vieira , Melgaço Juliana Gil , da Costa Neves Patrícia Cristina , da Costa Barros Tamiris Azamor , Ano Bom Ana Paula Dinis , Siqueira Marilda Mendonça , Missailidis Sotiris , Gonçalves Rafael Braga 
Published: May 2020

AbstractSince its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing a serious threat to public health worldwide as the causative agent of coronavirus disease 2019 (COVID-19). Now distributed in a pandemic pattern, this disease still lacks an effective drug treatment with low toxicity, leading pharmaceutical companies and research labs to work against time to find a candidate molecule to efficiently treat the affected patients. Due to the well-known broad-spectrum antimicrobial activity of the lactoferrin protein, we sought to verify whether its bovine form (bLf) would also be effective in vitro against SARS-CoV-2. Using an antiviral assay based on quantitative reverse transcription-polymerase chain reaction (qRT-PCR), we found that bLf reduced progeny virus yield by up to ∼84,6% in African green monkey kidney epithelial cells (Vero E6) and ∼68,6% in adenocarcinomic human alveolar basal epithelial cells (A549) at 1 mg/mL, a concentration previously shown to have low cytotoxicity. Therefore, our preliminary data suggest that bLf has the potential to constitute a biochemical approach to fight the new coronavirus pandemic.
Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity
Authors: Masoli Stefano , Ottaviani Alessandra , D’Angelo Egidio 
Published: May 2020

AbstractThe Golgi cells are the main inhibitory interneurons of the cerebellar granular layer. Although recent works have highlighted the complexity of their dendritic organization and synaptic inputs, the mechanisms through which these neurons integrate complex input patterns remained unknown. Here we have used 8 detailed morphological reconstructions to develop multicompartmental models of Golgi cells, in which Na, Ca, and K channels were distributed along dendrites, soma, axonal initial segment and axon. The models faithfully reproduced a rich pattern of electrophysiological and pharmacological properties and predicted the operating mechanisms of these neurons. Basal dendrites turned out to be more tightly electrically coupled to the axon initial segment than apical dendrites. During synaptic transmission, parallel fibers caused slow Ca-dependent depolarizations in apical dendrites that boosted the axon initial segment encoder and Na-spike backpropagation into basal dendrites, while inhibitory synapses effectively shunted backpropagating currents. This oriented dendritic processing set up a coincidence detector controlling voltage-dependent NMDA receptor unblock in basal dendrites, which, by regulating local calcium influx, may provide the basis for spike-timing dependent plasticity anticipated by theory.Author SummaryThe Golgi cells are the main inhibitory interneurons of the cerebellum granular layer and play a fundamental role in controlling cerebellar processing. However, it was unclear how spikes are processed in the dendrites by specific sets of ionic channels and how they might contribute to integrate synaptic inputs and plasticity. Here we have developed detailed multicompartmental models of Golgi cells that faithfully reproduced a large set of experimental findings and revealed the nature of signal interchange between dendrites and axo-somatic compartments. A main prediction of the models is that synaptic activation of apical dendrites can effectively trigger spike generation in the axonal initial segment followed by rapid spike backpropagation into basal dendrites. Here, incoming mossy fiber inputs and backpropagating spikes regulate the voltage-dependent unblock of NMDA channels and the induction of spike timing-dependent plasticity (STDP). STDP, which was predicted by theory, may therefore be controlled by contextual information provided by parallel fibers and integrated in apical dendrites, supporting the view that spike timing is fundamental to control synaptic plasticity at the cerebellar input stage.
The effect of respiratory gases and incubation temperature on early stage embryonic development in sea turtles
Authors: Booth David Terrington , Archibald-Binge Alexander , Limpus Colin James 
Published: May 2020

AbstractSea turtle embryos at high density nesting beaches experience relative high rates of early stage embryo death. One hypothesis to explain this high dead rate is that there is an increased probability that newly constructed nests are located close to maturing clutches whose metabolising embryos cause low oxygen levels, high carbon dioxide levels, and high temperatures. Although these altered environmental conditions are well tolerated by mature embryos, early stage embryos may not be as tolerant leading to an increase in their mortality. To test this hypothesis, we incubated newly laid sea turtle eggs for a week over a range of temperatures in different combinations of oxygen and carbon dioxide concentrations and assessed embryo development and death rates. We found that gas mixtures of decreased oxygen and increased carbon dioxide, similar to those found in natural sea turtle nest containing mature embryos, slowed embryonic development but did not influence embryo mortality of early stage embryos. In contrast, high incubation temperature not only decreased embryo development rate, but prolonged incubation at 34°C was fatal.
Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences
Authors: Nour Islam , Alanazi Ibrahim O. , Hanif Atif , Kohl Alain , Eifan Saleh 
Published: May 2020

ABSTRACTThe recently emerged SARS-CoV-2 (Coronaviridae; Betacoronavirus) is the underlying cause of COVID-19 disease. Here we assessed SARS-CoV2 from the Kingdom of Saudi Arabia alongside sequences of SARS-CoV, bat SARS-like CoVs and MERS-CoV, the latter currently detected in this region. Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer proximity to bat SARS-like CoVs, followed by SARS-CoVs, however quite distant to MERS-CoV. Moreover, genome recombination analysis revealed two recombination events between SARS-CoV-2 and bat SARS-like CoVs. This was further assessed by S gene recombination analysis. These recombination events may be relevant to the emergence of this novel virus. Moreover, positive selection pressure was detected between SARS-CoV-2, bat SL-CoV isolates and human SARS-CoV isolates. However, the highest positive selection occurred between SARS-CoV-2 isolates and 2 bat-SL-CoV isolates (Bat-SL-RsSHC014 and Bat-SL-CoVZC45). This further indicates that SARS-CoV-2 isolates were adaptively evolved from bat SARS-like isolates, and that a virus with originating from bats triggered this pandemic. This study thuds sheds further light on the origin of this virus.AUTHOR SUMMARYThe emergence and subsequent pandemic of SARS-CoV-2 is a unique challenge to countries all over the world, including Saudi Arabia where cases of the related MERS are still being reported. Saudi SARS-CoV-2 sequences were found to be likely of the same or similar origin. In our analysis, SARS-CoV-2 were more closely related to bat SARS-like CoVs rather than to MERS-CoV (which originated in Saudi Arabia) or SARS-CoV, confirming other phylogenetic efforts on this pathogen. Recombination and positive selection analysis further suggest that bat coronaviruses may be at the origin of SARS-CoV-2 sequences. The data shown here give hints on the origin of this virus and may inform efforts on transmissibility, host adaptation and other biological aspects of this virus.
Mitochondrial nicotinic acetylcholine receptors form complexes with Bax upon apoptosis induction
Authors: Kalashnyk Olena , Lykhmus Olena , Uspenska Kateryna , Izmailov Mykhailo , Komisarenko Sergiy , Skok Maryna 
Published: May 2020

AbstractNicotinic acetylcholine receptors (nAChRs) mediate fast synaptic transmission in muscles and autonomic ganglia and regulate cytokine and neurotransmitter release in the brain and nonexcitable cells. The nAChRs expressed in the outer membrane of mitochondria control the early events of mitochondria-driven apoptosis like cytochrome c release by affecting intramitochondrial kinase pathways. However, the mechanisms through which nAChRs influence mitochondrial permeability remain obscure. Previously we demonstrated that mitochondrial nAChRs interact with voltage-dependent anion channels (VDAC) involved in forming the pore in mitochondria membrane. Here we put an aim to explore the connection of nAChRs to pro-apoptotic protein Bax and its changes in the course of apoptosis induction. By using molecular modeling in silico, it was shown that both Bax and VDAC bind within the 4thtransmembrane portion of nAChR subunits. Experimentally, α7 nAChR-Bax and α7 nAChR-VDAC complexes were identified by sandwich ELISA in mitochondria isolated from astrocytoma U373 cells. Stimulating apoptosis of U373 cells by 1μM H2O2disrupted α7-VDAC complexes and favored formation of α7-Bax complexes. α7-selective agonist PNU282987 and type 2 positive allosteric modulator PNU120596 disrupted α7-Bax and returned α7 nAChR to complex with VDAC. It is concluded that mitochondrial nAChRs regulate apoptosis-induced mitochondrial channel formation by modulating the interplay of apoptosis-related proteins in mitochondria outer membrane.