bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brequinar and Dipyridamole in Combination Exhibits Synergistic Antiviral Activity Against SARS-CoV-2 in vitro: Rationale for a host-acting antiviral treatment strategy for COVID-19
Authors: Demarest James F. , Kienle Maryline , Boytz RuthMabel , Ayres Mary , Kim Eun Jung , Chung Donghoon , Gandhi Varsha , Davey Robert , Sykes David B. , Shohdy Nadim , Pottage John C. , Kumar Vikram S. 
Published: April 2022

ABSTRACTThe continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised the efficacy of currently available vaccines and monoclonal antibody (mAb)-based treatment options for COVID-19. The limited number of authorized small-molecule direct-acting antivirals present challenges with pill burden, the necessity for intravenous administration or potential drug interactions. There remains an unmet medical need for effective and convenient treatment options for SARS-CoV-2 infection. SARS-CoV-2 is an RNA virus that depends on host intracellular ribonucleotide pools for its replication. Dihydroorotate dehydrogenase (DHODH) is a ubiquitous host enzyme that is required for de novo pyrimidine synthesis. The inhibition of DHODH leads to a depletion of intracellular pyrimidines, thereby impacting viral replication in vitro. Brequinar (BRQ) is an orally available, selective, and potent low nanomolar inhibitor of human DHODH that has been shown to exhibit broad spectrum inhibition of RNA virus replication. However, host cell nucleotide salvage pathways can maintain intracellular pyrimidine levels and compensate for BRQ-mediated DHODH inhibition. In this report, we show that the combination of BRQ and the salvage pathway inhibitor dipyridamole (DPY) exhibits strong synergistic antiviral activity in vitro against SARS-CoV-2 by enhanced depletion of the cellular pyrimidine nucleotide pool. The combination of BRQ and DPY showed antiviral activity against the prototype SARS-CoV-2 as well as the Beta (B.1.351) and Delta (B.1.617.2) variants. These data support the continued evaluation of the combination of BRQ and DPY as a broad-spectrum, host-acting antiviral strategy to treat SARS-CoV-2 and potentially other RNA virus infections.
Reducing societal impacts of SARS-CoV-2 interventions through subnational implementation
Authors: Dekker Mark M. , Coffeng Luc E. , Pijpers Frank P. , Panja Debabrata , de Vlas Sake J. 
Published: April 2022

AbstractTo curb the initial spread of SARS-CoV-2, many countries relied on nation-wide implementation of non-pharmaceutical intervention measures, resulting in substantial socio-economic impacts. Potentially, subnational implementations might have had less of a societal impact, but comparable epidemiological impact. Here, using the first COVID-19 wave in the Netherlands as a case in point, we address this issue by developing a high-resolution analysis framework that uses a demographically-stratified population and a spatially-explicit, dynamic, individual contact-pattern based epidemiology, calibrated to hospital admissions data and mobility trends extracted from mobile phone signals and Google. We demonstrate how a subnational approach could achieve similar level of epidemiological control in terms of hospital admissions, while some parts of the country could stay open for a longer period. Our framework is exportable to other countries and settings, and may be used to develop policies on subnational approach as a better strategic choice for controlling future epidemics.
Mesenchymal Stem Cells Sense the Toughness of Nanomaterials and Interfaces
Authors: Peng Lihui , Matellan Carlos , del Rio Hernandez Armando , Gautrot Julien E. 
Published: April 2022

AbstractStem cells are known to sense and respond to a broad range of physical stimuli arising from their extra-cellular environment. In particular, the role of the mechanical properties (Youngs or shear modulus, viscoelasticity) of biomaterials has extensively been shown to have a significant impact on the adhesion, spreading, expansion and differentiation of stem cells. In turn, cells exert forces on their environment that can lead to striking changes in shape, size and contraction of associated tissues, and may result in mechanical disruption and functional failure. However, no study has so far correlated stem cell phenotype and biomaterials toughness. Indeed, disentangling toughness-mediated cell response from other mechanosensing processes has remained elusive as it is particularly challenging to uncouple Youngs’ or shear moduli from toughness, within a range relevant to cell-generated forces. In this report, we show how the design of macromolecular architecture of polymer nanosheets regulates interfacial toughness, independently to interfacial shear storage modulus, and how this, in turn, controls the expansion of mesenchymal stem cells at liquid interfaces.
Affective enhancement of episodic memory is associated with widespread patterns of intrinsic functional connectivity across the adult lifespan
Authors: Katsumi Yuta , Moore Matthew 
Published: April 2022

AbstractSubjectively arousing experiences tend to be better remembered than neutral ones. While numerous task-related neuroimaging studies have revealed the neural mechanisms associated with this phenomenon, it remains unclear how variability in the extent to which individuals show superior memory for subjectively arousing stimuli is associated with theintrinsicfunctional organization of their brains. Here, we addressed this issue using functional magnetic resonance imaging data collected at rest from a sample drawn from the Cambridge Centre for Ageing Neuroscience cohort (N= 269, 18-86 years). Specifically, we performed multi-voxel pattern analysis of intrinsic functional connectivity, an unbiased, data-driven approach to examine whole-brain voxel-wise connectivity patterns. This technique allowed us to reveal the most important features from the high-dimensional, whole-brain connectivity structure without a priori hypotheses about the topography and direction of functional connectivity differences. Behaviorally, both item and associative memory accuracy were enhanced for trials with affectively arousing (positive or negative) stimuli than those with neutral ones. Whole-brain multi-voxel pattern analysis of functional connectivity revealed that the affective enhancement of memory was associated with intrinsic connectivity patterns of spatially distributed brain regions belonging to several functional networks in the cerebral cortex. Post hoc seed-based brain-behavior regression analysis and principal component analysis of the resulting correlation maps showed that these connectivity patterns were in turn primarily characterized by the involvement of heteromodal association (dorsal attention, salience, and default mode) networks as well as select subcortical structures (striatum, thalamus, and cerebellum). Collectively, these findings suggest that the affective enhancement of episodic memory may be characterized as a whole-brain phenomenon, possibly supported by intrinsic functional interactions across several networks and structures in the brain.
Characterization of EDS1-independent plant defense responses against bacterial pathogens using Duckweed/Pseudomonaspathosystems
Authors: Baggs E.L , Tiersma M.B , Abramson B.W , Michael T.P , Krasileva K.V 
Published: April 2022

AbstractENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) mediates the induction of defense responses against pathogens in most land plants. However, it has recently been shown that a few species have lost EDS1. It is unknown how defense against disease unfolds and evolves in the absence of EDS1. Here we utilize duckweeds; a collection of aquatic species that lack EDS1, to investigate this question. We successfully established duckweed-Pseudomonaspathosystems and were able to characterize pathogen-induced responses in an immune system that lacks the EDS1 signaling pathway. We show that the copy number of infection-associated genes and the infection-induced transcriptional responses of duckweeds differ from that of other model species. Moreover, we show that the conservation of canonical Microbe Triggered Immunity and Effector Triggered Immunity pathways varies between duckweed species. This work shows that pathogen defense has evolved along different trajectories and uncovers alternative genomic and transcriptional reprogramming. Specifically, the miAMP1 domain containing proteins, which are absent in Arabidopsis, show pathogen responsive upregulation in duckweeds. Despite such divergence between Arabidopsis and duckweed species, we find evidence for the conservation of upregulation of certain genes and the role of hormones in response to disease. Our work highlights the importance of expanding the pool of model species to study defense responses that have evolved in the plant kingdom, including those independent of EDS1.
Temporal and Spatial Resolution of a Protein Quake that Activates Hydrogen Tunneling in Soybean Lipoxygenase
Authors: Zaragoza Jan Paulo T. , Offenbacher Adam R. , Hu Shenshen , Gee Christine L. , Firestein Zachary M. , Minnetian Natalie , Deng Zhenyu , Fan Flora , Iavarone Anthony T. , Klinman Judith P. 
Published: April 2022

AbstractThe enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen deuterium exchange experiments to detect a radiating cone of aliphatic side chains that extends from the iron active site of SLO to the protein-solvent interface. Employing eight variants of SLO, nanosecond fluorescence Stokes shifts have been measured using a probe appended to the identified surface loop. We report a remarkable identity of the enthalpies of activation for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within the identified thermal network. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, these new data implicate a thermally initiated, cooperative protein quake as the source of the activation of SLO. These findings indicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis.
Active Anemosensing Hypothesis: How Flying Insects Could Estimate Ambient Wind Direction Through Sensory Integration & Active Movement
Authors: van Breugel Floris , Jewell Renan , Houle Jaleesa 
Published: April 2022

AbstractEstimating the direction of ambient fluid flow is a crucial step during chemical plume tracking for flying and swimming animals. How animals accomplish this remains an open area of investigation. Recent calcium imaging with tethered flying Drosophila has shown that flies encode the angular direction of multiple sensory modalities in their central complex: orientation, apparent wind (or airspeed) direction, and direction of motion. Here we describe a general framework for how these three sensory modalities can be integrated over time to provide a continuous estimate of ambient wind direction. After validating our framework using a flying drone, we use simulations to show that ambient wind direction can be most accurately estimated with trajectories characterized by frequent, large magnitude turns. Furthermore, sensory measurements and estimates of their derivatives must be integrated over a period of time that incorporates at least one of these turns. Finally, we discuss approaches that insects might use to simplify the required computations, and present a list of testable predictions. Together, our results suggest that ambient flow estimation may be an important driver underlying the zigzagging maneuvers characteristic of plume tracking animals’ trajectories.
Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping
Authors: Kaat Rubben , Laurentijn Tilleman , Koen Deserranno , Olivier Tytgat , Dieter Deforce , Van Nieuwerburgh Filip 
Published: April 2022

AbstractCYP2D6 is one of the most challenging pharmacogenes to genotype due to the high similarity with its neighboring pseudogenes and the frequent occurrence of CYP2D6-CYP2D7 hybrids. Unfortunately, most current genotyping methods are therefore not able to correctly determine the complete CYP2D6-CYP2D7 sequence. Therefore, we developed a genotyping assay to generate complete allele-specific consensus sequences of complex regions by optimizing the PCR-free nanopore Cas9-targeted sequencing (nCATS) method combined with adaptive sequencing, and developing a new comprehensive long read genotyping (CoLoRGen) pipeline. The CoLoRGen pipeline first generates consensus sequences of both alleles and subsequently determines both large structural and small variants to ultimately assign the correct star-alleles. In reference samples, our genotyping assay confirms the presence of CYP2D6-CYP2D7 large structural variants, single nucleotide variants (SNVs), and small insertions and deletions (INDELs) that go undetected by most current assays. Moreover, our results provide direct evidence that the CYP2D6 genotype of the NA12878 DNA should be updated to include the CYP2D6-CYP2D7 *68 hybrid and several additional single nucleotide variants compared to existing references. Ultimately, the nCATS-CoLoRGen genotyping assay additionally allows for more accurate gene function predictions by enabling the possibility to detect and phase de novo mutations in addition to known large structural and small variants.Author SummaryDuring the last decades, the usefulness of personalized medicine has become increasingly apparent. Directly linked to that is the need for accurate genotyping assays to determine the pharmacogenetic profile of patients. Continuing research has led to the development of genotyping assays that perform quite robustly. However, complex genes remain an issue when it comes to determining the complete sequence correctly. An example of such a complex but very important pharmacogene is CYP2D6. Therefore, we developed a genotyping assay in an attempt to generate complete allele-specific consensus sequences of CYP2D6, by optimizing a targeted amplification-free long-read sequencing method and developing a new analysis pipeline. In reference samples, we showed that our genotyping assay performed accurately and confirmed the presence of variants that go undetected by most current assays. However, the implementation of this assay in practice is still hampered as the selected enrichment strategies inherently lead to a low percentage of on-target reads, resulting in low on-target sequencing depths. Further optimization and validation of the assay is thus needed, but definitely worth considering for follow-up research as we already demonstrated the added value for generating more complete genotypes, which on its turn will result in more accurate gene function predictions.
Padé SSA: A frequency domain method for estimating the dynamics of stochastic reaction networks
Authors: Gupta Ankit , Khammash Mustafa 
Published: April 2022

AbstractDynamic analysis and control of living cells relies on mathematical representations of cellular processes that are themselves modelled as biomolecular reaction networks. Stochastic models for biomolecular reaction networks are commonly employed for analysing intracellular networks having constituent species with low-copy numbers. In such models, the main object of interest is the probability distribution of the state vector of molecular counts which evolves according to a set of ordinary differential equations (ODEs) called the Chemical Master Equation (CME). Typically this set is very large or even infinite, making the CME practically unsolvable in most cases. Hence the outputs based on the CME solution, like the statistical moments of various state components, are generally estimated with Monte Carlo (MC) procedures by simulating the underlying Markov chain with Gillespie’s Stochastic Simulation Algorithm (SSA). However to obtain statistical reliability of the MC estimators, often a large number of simulated trajectories are required, which imposes an exorbitant computational burden. The aim of this paper is to present a frequency domain method for mitigating this burden by exploiting a small number of simulated trajectories to robustly estimate certain intrinsic eigenvalues of the stochastic dynamics. This method enables reliable estimation of time-varying outputs of interest from a small number of sampled trajectories and this estimation can be carried out for several initial states without requiring additional simulations. We demonstrate our method with a couple of examples.
Effect of tempol on post-thaw semen parameters and fertility during chicken semen cryopreservation
Authors: Shanmugam M. , Mahapatra R.K. 
Published: April 2022

ABSTRACTThe present study evaluated addition of tempol during chicken semen cryopreservation on post-thaw semen parameters and fertility. Adult PD-1 line semen was cryopreserved using 4% dimethyl sulfoxide (DMSO) in Sasaki diluent (SD). In the semen cryomixture tempol (1 and 5 mM) was added at final concentrations. The semen with additives were filled in 0.5 ml French straws and exposed to liquid nitrogen vapours for 30 min and then stored in liquid nitrogen. The semen straw was thawed at 5°C for 100 sec and evaluated for sperm motility, live, abnormal and acrosome intact sperm. The seminal plasma was evaluated for lipid peroxidation. Fertilizing potential of the cryopreserved sperm was evaluated after insemination in the PD-1 line hens. The post-thaw sperm parameters were significantly (P<0.05) lower in the cryopreserved groups. The lipid peroxidation was significantly (P<0.05) higher in cryopreserved groups. The fertility was significantly (P<0.05) lower in all the cryopreserved groups. In conclusion, addition of tempol to cryopreservation mixture did not improve the post-thaw semen parameters or fertility.
Spatial modeling reveals nuclear phosphorylation and subcellular shuttling of YAP upon drug-induced liver injury
Authors: Wehling Lilija , Keegan Liam , Fernández-Palanca Paula , Hassan Reham , Ghallab Ahmed , Schmitt Jennifer , Schirmacher Peter , Kummer Ursula , Hengstler Jan G. , Sahle Sven , Breuhahn Kai 
Published: April 2022

AbstractThe Hippo signaling pathway controls cell proliferation and tissue regeneration via its transcriptional effectors yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). In this context, the canonical pathway topology is characterized by sequential phosphorylation of kinases in the cytoplasm that define the subcellular localization of YAP and TAZ. However, the molecular mechanisms controlling the nuclear/cytoplasmic shuttling dynamics of both factors under physiological and tissue-damaging conditions are poorly understood. By implementing experimental data, partial differential equation (PDE) modeling, as well as automated image analysis, we demonstrate that nuclear phosphorylation contributes to differences between YAP and TAZ localization in the nucleus and cytoplasm. Treatment of hepatocyte-derived cells with hepatotoxic acetaminophen (APAP) overdose induces a biphasic protein phosphorylation eventually leading to nuclear protein enrichment of YAP but not TAZ. APAP-dependent regulation of nuclear/cytoplasmic YAP shuttling is not an unspecific cellular response but relies on the sequential induction of reactive oxygen species (ROS), RAC-alpha serine/threonine-protein kinase (AKT, synonym: protein kinase B), as well as elevated nuclear interaction between YAP and AKT. Mouse experiments confirm this consecutive sequence of events illustrated by the expression of ROS-, AKT-, and YAP-specific gene signatures upon APAP administration. In summary, our data illustrate the importance of nuclear processes in the regulation of Hippo pathway activity. YAP and TAZ exhibit different shuttling dynamics, which explains distinct cellular responses of both factors under physiological and tissue-damaging conditions.SignificanceWe show that canonical view on the Hippo pathway must be extended by additional regulatory processes in cell nuclei. These processes significantly contribute to the activity of YAP and TAZ under unchallenged conditions (e.g., with cell density as physiological regulator of the Hippo kinase cassette) or under cell damaging conditions (e.g., after administration of APAP overdose). APAP-induced cellular damage activates YAP via distinct molecular processes as part of a cell-protective response.
Does Tesla valve work for microscale active swimmers? – a computational study
Authors: Rogers Ariel , Wang Yong 
Published: April 2022

AbstractAlthough the Tesla valve is well-known for its diodicity for fluid flows and pressure drops, it is not clear whether and how the resistances experienced by active swimmers in the forward and reverse directions are different. Here we carried out a computational study on the diodicity of the Tesla valve for active swimmers in the absence of fluid flows. We simulated the active Brownian motion of the swimmers in a Tesla valve, followed by examining their trajectories and quantifying the fraction of active swimmers reaching the left or right end of the Tesla valve (in the forward or reverse direction, respectively). We also estimated the first passage time of the swimmers reaching the valve ends. We confirmed that, in the absence of fluid flows, the Tesla valve shows much higher resistance to active swimmers in the reverse direction than the forward direction. The current study provides a better understanding of the interaction of the Tesla valve with active swimmers and gives insight into potential applications of the Tesla valve in the filtering and sorting of motile microbes.
Autophagy slows the aging of Germline stem cells in Drosophila through modulation of E-cadherin
Authors: Murmu Nidhi , Shravage Bhupendra V. 
Published: April 2022

AbstractAutophagy is a conserved process that degrades cytoplasmic components and organelles in metazoan cells including germline stem cells. Although autophagy is implicated in the aging of stem cells, the precise mechanism are still unknown. Here we show that elevating autophagy by overexpressing (OE) Drosophila Autophagy-related gene 8a (Atg8a) in the female Germline stem cells (GSCs) delays their loss due to aging. However, sustained elevated autophagy levels in old flies promote GSC loss due to cell death. In contrast, knockdown of Atg8a (Atg8aRNAi) in GSCs accelerates their loss. Atg8aOE GSCs show elevated autophagy flux, and increased mitotic activity even at 8 weeks of age. Atg8aOE GSCs possess smaller-sized mitochondria and exhibit reduced mitochondrial oxidative stress in the GSCs. However, in contrast Atg8aRNAi GSCs have elevated mitochondrial ROS and possess larger mitochondria. Finally, our data show that Atg8aOE GSCs occupy the stem cell niche for longer duration with the aid of elevated E-cadherin at the GSC-cap cell contact sites. Our data suggests that elevated autophagy promotes GSC maintenance and activity, and delays their aging.Graphical abstract