bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary origins of epidemic potential among human RNA viruses
Authors: Lu Lu , Brierley Liam , Robertson Gail , Zhang Feifei , Lycett Samantha , Smith Donald , Chase-Topping Margo , Simmonds Peter , Woolhouse Mark 
Published: September 2019

AbstractTo have epidemic potential, a pathogen must be able to spread in human populations, but of human-infective RNA viruses only a minority can do so. We investigated the evolution of human transmissibility through parallel analyses of 1755 virus genome sequences from 39 RNA virus genera. We identified 57 lineages containing human-transmissible species and estimated that at least 74% of these lineages have evolved directly from non-human viruses in other mammals or birds, a public health threat recently designated “Disease X”. Human-transmissible viruses rarely evolve from virus lineages that can infect but not transmit between humans. This result cautions against focussing surveillance and mitigation efforts narrowly on currently known human-infective virus lineages and supports calls for a better understanding of RNA virus diversity in non-human hosts.
Hydrodynamic regime drives flow reversals in suction feeding larval fishes during early ontogeny
Authors: Krishnan Krishnamoorthy , Nafi Asif Shahriar , Gurka Roi , Holzman Roi 
Published: September 2019

AbstractFish larvae are the smallest self-sustaining vertebrates. As such, they face multiple challenge that stem from their minute size, and from the hydrodynamic regime in which they dwell. This regime of intermediate Reynolds numbers (Re) was shown to affect the swimming of larval fish and impede their ability to capture prey. Numerical simulations indicate that the flow fields external to the mouth in younger larvae result in shallower spatial gradients, limiting the force exerted on the prey. However, observations on feeding larvae suggest that failures in prey capture can also occur during prey transport, although the mechanism causing these failures is unclear. We combine high-speed videography and numerical simulations to investigate the hydrodynamic mechanisms that impede prey transport in larval fishes. Detailed kinematics of the expanding mouth during prey capture by larvalSparus auratawere used to parameterize age-specific numerical models of the flows inside the mouth. These models reveal that, for small larvae that slowly expand their mouth, not all the fluid that enters the mouth cavity is expelled through the gills, resulting in flow reversal at the mouth orifice. This efflux at the mouth orifice was highest in the younger ages, but was also high (>8%) in slow strikes produced by larger fish. Our modeling explains the observations of “in-and-out” events in larval fish, where prey enters the mouth but is not swallowed. It further highlights the importance of prey transport as an integral part in determining suction feeding success.
Purification of native CCL7 and its functional interaction with selected chemokine receptors
Authors: Goncharuk Marina V. , Roy Debarati , Dubinnyi Maxim A. , Nadezhdin Kirill D. , Srivastava Ashish , Baidya Mithu , Dwivedi-Agnihotri Hemlata , Arseniev Alexander S. , Shukla Arun K. 
Published: September 2019

AbstractChemokine receptors form a major sub-family of G protein-coupled receptors (GPCRs) and they are involved in a number of cellular and physiological processes related to our immune response and regulation. A better structural understanding of ligand-binding, activation, signaling and regulation of chemokine receptors is very important to design potentially therapeutic interventions for human disorders arising from aberrant chemokine signaling. One of the key limitations in probing the structural details of chemokine receptors is the availability of large amounts of purified, homogenous and fully functional chemokine ligands, and the commercially available products, are not affordable for in-depth structural studies. Moreover, production of uniformly isotope-labeled chemokines, for example, suitable for NMR-based structural investigation, also remains challenging. Here, we have designed a streamlined approach to express and purify the human chemokine CCL7 as well as its15N-,15N/13C-,2H/15N/13C-isotope-labeled derivatives, at milligram levels usingE. coliexpression system. Purified CCL7 not only maintains a well-folded three-dimensional structure as analyzed using circular dichroism and1H/15N NMR but it also induces coupling of heterotrimeric G-proteins and β-arrestins for selected chemokine receptors in cellular system. Our strategy presented here may be applicable to other chemokines and therefore, provide a potentially generic and cost-effective approach to produce chemokines in large amounts for functional and structural studies.
Active transport of brilliant blue FCF across theDrosophilamidgut and Malpighian tubule epithelia
Authors: Livingston Dawson B.H. , Patel Hirva , Donini Andrew , MacMillan Heath A. 
Published: September 2019

AbstractUnder conditions of stress, many animals suffer from epithelial barrier disruption that can cause molecules to leak down their concentration gradients, potentially causing a loss of organismal homeostasis, further injury or death.Drosophilais a common insect model, used to study barrier disruption related to aging, traumatic injury, or environmental stress. Net leak of a non-toxic dye (Brilliant blue FCF) from the gut lumen to the hemolymph is often used to identify barrier failure under these conditions, butDrosophilaare capable of actively transporting structurally-similar compounds. Here, we examined whether cold stress (like other stresses) causes Brilliant blue FCF (BB-FCF) to appear in the hemolymph of flies fed the dye, and if so whetherDrosophilaare capable of clearing this dye from their body following chilling. Usingin situmidgut leak and transport assays as well as Ramsay assays of Malpighian tubule transport, we tested whether these ionoregulatory epithelia can actively transport BB-FCF. In doing so, we found that theDrosophilamidgut and Malpighian tubules can mobilize BB-FCF via an active transcellular pathway, suggesting that elevated concentrations of the dye in the hemolymph may occur from increased paracellular permeability, reduced transcellular clearance, or both.Summary StatementDrosophilaare able to actively secrete Brilliant blue FCF, a commonly used marker of barrier dysfunction
Lysenin toxin insertion mechanism is Calcium-dependent
Authors: Munguira Ignacio L.B. 
Published: September 2019

AbstractPore Forming Toxins (PFTs), formed mainly by virulence factors of bacteria, belongs to Pore Forming Protein (PFP) family. Secreted as soluble monomers, they bind specific targets in membranes where their oligomerization and insertion place. Lysenin, a member of the PFTs, forms and oligomer after sphingomyelin binding, the so-called prepore, which become inserted forming a pore after a conformational change triggered by a pH decrease. In crowded conditions, oligomers tends to stay in prepore form because the prepore-to-pore transition is sterically blocked. In this study, we investigate the effect of calcium ions in those crowded conditions, finding that calcium act as a trigger for lysenin insertion. We localize the residues responsible for calcium sensitivity in a small α-helix. Our results are not only one of the few complete structural descriptions of prepore-to-pore transitions but the very first that involves a calcium triggering mechanism. The presence of glutamic or aspartic acids in the insertion domains could be an indication that calcium may be a general trigger for PFTs and more generally PFP.
An atypical DYRK kinase connects quorum-sensing with posttranscriptional gene regulation inTrypanosoma brucei
Authors: Cayla Mathieu , McDonald Lindsay , MacGregor Paula , Matthews Keith R. 
Published: September 2019

AbstractThe sleeping sickness parasite,Trypanosoma brucei, uses quorum sensing (QS) to balance proliferation and transmission potential in the mammal bloodstream. A signal transduction cascade regulates this process, a component of which is a divergent member of the DYRK family of protein kinases, TbDYRK. Phylogenetic and mutational analysis in combination with activity and phenotypic assays revealed that TbDYRK exhibits a pre-activated confirmation and an atypical HxY activation loop motif, unlike DYRK kinases in other eukaryotes. Phosphoproteomic comparison of TbDYRK null mutants with wild type parasites identified molecules that operate on both the inhibitory ‘slender retainer’ and activatory ‘stumpy inducer’ arms of the QS control pathway. One of these molecules, the RNA-regulator TbZC3H20, regulates parasite QS, this being dependent on the integrity of its TbDYRK phosphorylation site. This analysis reveals fundamental differences to conventional DYRK family regulation and links trypanosome environmental sensing, signal transduction and developmental gene expression in a coherent pathway.
Inter-Species Differences in the Response of Sinus Node Cellular Pacemaking to Changes of Extracellular Calcium
Authors: Loewe Axel , Lutz Yannick , Nagy Norbert , Fabbri Alan , Schweda Christoph , Varró András , Severi Stefano 
Published: September 2019

AbstractChanges of serum and extracellular ion concentrations occur regularly in patients with chronic kidney disease (CKD). Recently, hypocalcemia, i.e. a decrease of the extra-cellular calcium concentration [Ca2+]o, has been suggested as potential pathomechanism contributing to the unexplained high rate of sudden cardiac death (SCD) in CKD patients. In particular, there is a hypothesis that hypocalcaemia could slow down natural pacemaking in the human sinus node to fatal degrees. Here, we address the question whether there are inter-species differences in the response of cellular sinus node pacemaking to changes of [Ca2+]o. Towards this end, we employ computational models of mouse, rabbit and human sinus node cells. The Fabbri et al. human model was updated to consider changes of intracellular ion concentrations. We identified crucial inter-species differences in the response of cellular pacemaking in the sinus node to changes of [Ca2+]o with little changes of cycle length in mouse and rabbit models (<83 ms) in contrast to a pronounced bradycardic effect in the human model (up to > 1000 ms). Our results suggest that experiments with human sinus node cells are required to investigate the potential mechanism of hypocalcaemia-induced bradycardic SCD in CKD patients and small animal models are not well suited.
Establishing the phenotypic basis of adherent-invasiveEscherichia coli(AIEC) pathogenicity in intestinal inflammation
Authors: Kittana Hatem , Gomes-Neto João C. , Heck Kari , Sughroue Jason , Xian Yibo , Mantz Sara , Muñoz Rafael R. Segura , Cody Liz A. , Schmaltz Robert J. , Anderson Christopher L. , Moxley Rodney A. , Hostetter Jesse M. , Fernando Samodha C. , Clarke Jennifer , Kachman Stephen D. , Cressler Clayton E. , Benson Andrew K. , Walter Jens , Ramer-Tait Amanda E. 
Published: September 2019

AbstractBackground & AimsAdherent-invasiveEscherichia coli(AIEC) are enriched in ileal Crohn’s disease patients and implicated in disease etiology. However, AIEC pathogenesis is poorly understood, and it is unclear if the expansion of these organisms contributes to inflammatory bowel disease (IBD). Questions also remain as to what extent the variousin vitrophenotypes used to classify AIEC are pathologically relevant.MethodsWe utilized a combination ofin vitrophenotyping and a murine model of intestinal inflammation to systematically relate AIEC phenotypes to pathogenicity for 30 mucosa-associated human-derivedE. colistrains.In vitroassays used included survival/replication in and TNF-α production by J774 macrophages as well as invasion/replication in Caco2 intestinal epithelial cells.ResultsAIEC do not form a phenotypic group that is clearly separated from non-AIEC. However,E. colistrains displayingin vitroAIEC phenotypes caused, on average, more severe intestinal inflammation. Survival/replication of strains in J774 and Caco2 cells were positively correlated with diseasein vivo, while adherence to Caco2 cells and TNF-α production by J774 cells were not. Importantly, co-colonization with adherent non-AIEC strains ameliorated AIEC-mediated disease.ConclusionOur findings do not support the existence of an AIEC pathovar that can be clearly separated from commensalE. coli. However, intracellular survival/replication phenotypes do contribute to murine intestinal inflammation, suggesting that the AIEC overgrowth observed in human IBD makes a causal contribution to disease. The ability to differentiate pathologically-relevant AIEC phenotypes from those that are not provides an important foundation for developing strategies to predict, diagnose and treat human IBD through characterizing and modulating patientE. colipopulations.
Withdrawal from Chronic Ethanol Exposure Increases Postsynaptic Glutamate Function of Insular Cortex Projections to the Rat Basolateral Amygdala
Authors: McGinnis Molly M. , Parrish Brian C. , McCool Brian A. 
Published: September 2019

AbstractA key feature of alcohol use disorder (AUD) is negative affect during withdrawal, which often contributes to relapse and is thought to be caused by altered brain function, especially in circuits that are important mediators of emotional behaviors. Both the agranular insular cortex (AIC) and the basolateral amygdala (BLA) regulate emotions and are sensitive to ethanol-induced changes in synaptic plasticity. The AIC and BLA are reciprocally connected, however, and the effects of chronic ethanol exposure on this circuit have yet to be explored. Here, we use a combination of optogenetics and electrophysiology to examine the pre- and postsynaptic changes that occur to AIC – BLA synapses following withdrawal from 7- or 10-days of chronic intermittent ethanol (CIE) exposure. While CIE/withdrawal did not alter presynaptic glutamate release probably from AIC inputs, withdrawal from 10, but not 7, days of CIE increased AMPA receptor-mediated postsynaptic function at these synapses. Additionally, NMDA receptor-mediated currents evoked by electrical stimulation of the external capsule, which contains AIC afferents, were also increased during withdrawal. Notably, a single subanesthetic dose of ketamine administered at the onset of withdrawal prevented the withdrawal-induced increases in both AMPAR and NMDAR postsynaptic function. Ketamine also prevented the withdrawal-induced increases in anxiety-like behavior measured using the elevated zero maze. Together, these findings suggest that chronic ethanol exposure increases postsynaptic function within the AIC – BLA circuit and that ketamine can prevent ethanol withdrawal-induced alterations in synaptic plasticity and negative affect.
DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition
Authors: Chantarachot Thanin , Sorenson Reed S. , Hummel Maureen , Ke Haiyan , Kettenburg Alek T. , Chen Daniel , Aiyetiwa Karen , Dehesh Katayoon , Eulgem Thomas , Sieburth Leslie E. , Bailey-Serres Julia 
Published: September 2019

AbstractGene transcription is counterbalanced by mRNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA HELICASEs ofArabidopsis thalianacontrol the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. These RHs function to limit the precocious accumulation and translation of stress-responsive mRNAs associated with autoimmunity and growth inhibition under non-stress conditions. Given the conservation of this RH subfamily, they may control basal levels of conditionally-regulated mRNAs in diverse eukaryotes, accelerating responses without penalty.
Direct, sensitive and specific detection of individual single- or double-strand DNA breaks by fluorescence microscopy
Authors: Kordon Magdalena , Zarębski Mirosław , Solarczyk Kamil , Ma Hanhui , Pederson Thoru , Dobrucki Jurek 
Published: September 2019

ABSTRACTWe here describe a technique termed STRIDE (SensiTive Recognition of Individual DNA Ends), which enables highly sensitive, specific, direct in situ detection of single- or double-strand DNA breaks (sSTRIDE or dSTRIDE), in nuclei of single cells, using fluorescence microscopy. Sensitivity of STRIDE was tested using specially developed CRISPR/Cas9 DNA damage induction system, capable of inducing small clusters or individual single- or double-strand breaks. STRIDE exhibits significantly higher sensitivity and specificity of detection of DNA breaks than the commonly used TUNEL assay or methods based on monitoring of recruitment of repair proteins or histone modifications at the damage site (e.g. γH2AX). Even individual genome site-specific DNA double-strand cuts induced by CRISPR/Cas9, as well as individual single-strand DNA scissions induced by the nickase version of Cas9, can be detected by STRIDE and precisely localized within the cell nucleus. We further show that STRIDE can detect low-level spontaneous DNA damage, including age-related DNA lesions, DNA breaks induced by several agents (bleomycin, doxorubicin, topotecan, hydrogen peroxide, UV, photosensitized reactions), and fragmentation of DNA in human spermatozoa. STRIDE methods are potentially useful in studies of mechanisms of DNA damage induction and repair in cell lines and primary cultures, including cells with impaired repair mechanisms.
Atlas of the Neuromuscular System in the TrachymedusaAglantha digitale: Insights from the advanced hydrozoan
Authors: Norekian Tigran P. , Moroz Leonid L. 
Published: September 2019

ABSTRACTCnidaria is the sister taxon to bilaterian animals, and therefore, represents a key reference lineage to understand early origins and evolution of the neural systems. The hydromedusaAglantha digitaleis arguably the best electrophysiologically studied jellyfish because of its system of giant axons and unique fast swimming/escape behaviors. Here, using a combination of scanning electron microscopy and immunohistochemistry together with phalloidin labeling, we systematically characterize both neural and muscular systems inAglantha, summarizing and expanding further the previous knowledge on the microscopic neuroanatomy of this crucial reference species. We found that the majority, if not all (∼2500) neurons, that are labeled by FMRFamide antibody are different from those revealed by anti-α-tubulin immunostaining, making these two neuronal markers complementary to each other and, therefore, expanding the diversity of neural elements inAglanthawith two distinct neural subsystems. Our data uncovered the complex organization of neural networks forming a functional ‘annulus-type’ central nervous system with three subsets of giant axons, dozen subtypes of neurons, muscles and a variety of receptors fully integrated with epithelial conductive pathways supporting swimming, escape and feeding behaviors. The observed unique adaptations within theAglanthalineage (including giant axons innervating striated muscles) strongly support an extensive and wide-spread parallel evolution of integrative and effector systems across Metazoa.
Whole Cell Phenotypic Screening Of MMV Pathogen Box identifies Specific Inhibitors of Plasmodium falciparum merozoite maturation and egress
Authors: Patra Alok Tanala , Hingmire Tejashri Bhimashankar , Belekar Meenakshi , Xiong Aoli , Subramanian Gowtham , Bozdech Zbynek , Preiser Peter , Shanmugam Dhanasekaran , Chandramohanadas Rajesh 
Published: September 2019

AbstractWe report a systematic, cellular phenotype-based antimalarial screening of the MMV Pathogen Box collection, which facilitated the identification of specific blockers of late stage intraerythrocytic Plasmodium falciparum maturation. First, from standard growth inhibition asays, we discovered 62 additional antimalarials (EC50 ≤ 10μM) over previously known antimalarial candidates from Pathogen Box. A total of 90 potent molecules (EC50 ≤ 1μM) were selected for evaluating their stage-specific effects during the intra-erythrocytic development of P. falciparum. None of these molecules had significant effect on ring-trophozoite transition, 10 molecules inhibited trophozoite-schizont transition, and 21 molecules inhibited schizont-ring transition at 1μM. These compounds were further validated in secondary assays by flow cytometry and microscopic imaging of treated cells to prioritize 12 molecules as potent and selective blockers of schizont-ring transition. Seven of these were found to strongly inhibit calcium ionophore induced egress of Toxoplasma gondii, a related apicomplexan parasite, suggesting that the inhibitors may be acting via similar mechanism in the two parasites, which can be further exploited for target identification studies. Two of these molecules, with previously unknown mechanism of action, MMV020670 and MMV026356, were found to induce fragmentation of DNA in developing merozoites. Further mechanistic studies would facilitate therapeutic exploitation of these molecules as broadly active inhibitors targeting development and egress of apicomplexan parasites relevant to human health.
Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community
Authors: Bono Lisa M. , Orton Richard J. , Peredo Elena L. , Morrison Hilary G. , Sistrom Mark , Simmons Sheri , Turner Paul E. 
Published: September 2019

AbstractAlthough metagenomics reveals that natural virus communities harbor vast genetic diversity, the spatiotemporal dynamics of viral diversity in the wild are seldom tested, especially across small geographic scales. This problem is usefully examined in the above-ground phyllosphere, because terrestrial plants are frequently infected by taxonomically-diverse RNA viruses, whose elevated mutation rates generate abundant allele diversity. Here, we studied the problem by comparative analysis of RNA virus samples over time from three spatially-separated patches of a common perennial legume, white clover (Trifolium repens L.), growing in a grassy lawn in Woods Hole Village (Falmouth, MA, USA). We predicted that clover samples would show similarly high levels of virus species (alpha) diversity across space, but differing among-patch diversity of non-dominant virus taxa over time (4 samples spanning 6 weeks). Results showed that recognizable alpha diversity in clover patches was consistently dominated by RNA virus family Alphaflexiviridae across space, but that all patches showed inconsistent spatiotemporal presence of a diversity of minority virus families. Also, we observed that white clover mosaic virus (WClMV) dominated all patches across space and time. The high coverage of WClMV fostered an haplotype analysis, which revealed that two strains of the virus consistently infected clover plants during the 6-week period.