bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of a Replicon System for Bourbon Virus and Identification of Small Molecules that Efficiently Inhibit Virus Replication
Authors: Hao Siyuan , Ning Kang , Wang Xiaomei , Wang Jianke , Cheng Fang , Ganaie Safder S. , Tavis John E. , Qiu Jianming 
Published: April 2020

ABSTRACTBourbon virus (BRBV) was first isolated from a patient hospitalized at the University of Kansas Hospital in 2014. Since then, several deaths have been reported to be caused by BRBV infection in the Midwest and Southern United States. BRBV is a tick-borne virus that is widely carried by lone star ticks. It belongs to genusThogotovirusof theOrthomyxoviridaefamily. Currently, there are no treatments or vaccines available for BRBV or thogotovirus infection caused diseases. In this study, we reconstituted a replicon reporter system, composed of plasmids expressing the RNA-dependent RNA polymerase (RdRP) complex (PA, PB1 and PB2), nucleocapsid (NP) protein, and a reporter gene flanked by the 3’ and 5’ UTR of the envelope glycoprotein (GP) genome segment. By using the luciferase reporter, we screened a few small molecule compounds of anti-endonuclease that inhibited the nicking activity by parvovirus B19 (B19V) NS1, as well as FDA-approved drugs targeting the RdRP of influenza virus. Our results demonstrated that myricetin, and an anti-B19V NS1 nicking inhibitor, efficiently inhibited the RdRP activity of BRBV and virus replication. The IC50and EC50of myricetin are 2.22 μM and 4.6 μM, respectively, in cells. Myricetin had minimal cytotoxicity in cells, and therefore the therapeutic index of the compound is high. In conclusion, the BRBV replicon system is a useful tool to study viral RNA replication and to develop antivirals, and myricetin may hold promise in treatment of BRBV infected patients.
Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins
Authors: Bai Yunmeng , Jiang Dawei , Lon Jerome R , Chen Xiaoshi , Hu Meiling , Lin Shudai , Chen Zixi , Wang Xiaoning , Meng Yuhuan , Du Hongli 
Published: April 2020

AbstractObjectivesTo reveal epidemic trend and possible origins of SARS-CoV-2 by exploring its evolution and molecular characteristics based on a large number of genomes since it has infected millions of people and spread quickly all over the world.MethodsVarious evolution analysis methods were employed.ResultsThe estimated Ka/Ks ratio of SARS-CoV-2 is 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes, and the time to the most recent common ancestor (tMRCA) was inferred in late September 2019. Further 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating H3 and H4 might have existed for a long time, while H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time. Notably the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37).ConclusionsIn this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.
Latent defense response to non-pathogenic microbial factors impairs plant-rhizobacteria mutualism
Authors: Yang Yu , Chen Shenglan , Peng Li , Liu Xiaomin , Kaushal Richa , Yuan Fengtong , Singh Sunil K. , He Danxia , Lv Suhui , Vílchez Juan I. , Morcillo Rafael J. L. , Wang Wei , Huang Weichang , Lei Mingguang , Song Chun-Peng , Zhu Jian-Kang , Paré Paul W. , Zhang Huiming 
Published: April 2020

ABSTRACTUnlike pathogens that trigger plant defense responses, commensal or beneficial microbes are compatible with plants and do not elicit a defense response. An assumption underlying the compatibility is that plants are inert in mounting a defense response to non-pathogenic microbial factors. However, the mechanisms underlying this inertness in defense are unknown. Here a forward genetic screen led to the isolation of an Arabidopsis mutant displaying a new type of immunity which we named as latent defense response (LDR) to a beneficial rhizobacterium. The mutant, known asgp1forGrowth-Promotion 1, is impaired in rhizobacteria-induced plant growth-promotion due to disrupted oleic acid homeostasis and consequent activation of defense responses. Several bacterial volatile compounds trigger LDR ingp1but not wild type plants. GP1 dysfunction strongly represses colonization of the beneficial rhizobacterium and alters root-associated microbiota. Our findings reveal a hidden layer of plant defense, LDR, which is suppressed by GP1 to allow mutualistic association between plants and beneficial rhizobacteria.One Sentence SummaryA hidden layer of host immunity against non-pathogenic microbes leads to plant incompatibility with beneficial rhizobacteria.
SIRT1 ameliorates premature senescence-induced defenestration in hepatic sinusoidal endothelial cell
Authors: Luo Xiaoying , Bai Yangqiu , He Shuli , Jiang Xiaoke , Yang Zhiyu , Sun Suofeng , Lu Di , Wei Peiru , Liang Yuan , Peng Cong , Wang Yaru , Sheng Ruli , Han Shuangyin , Li Xiuling , Zhang Bingyong 
Published: April 2020

AbstractPremature senescence, linked to progerin, involves in endothelial dysfunction and liver diseases. Activating sirtuin 1 (SIRT1) ameliorates liver fibrosis. However, the potential mechanisms of premature senescence in defenestration in hepatic sinusoidal endothelial cells (HSECs) and how SIRT1 affects fenestrae remains elusive. Our study showed thatin vivo, premature senescence occurred, with decrease of SIRT1, during CCl4-induced defenestration in HSECs and liver fibrogenesis; whereas overexpressing SIRT1 with adenovirus vector lessened progerin-associated premature senescence to relieve CCl4-induced defenestration and liver fibrosis.In vitro, fenestrae in HSECs disappeared, with progerin-associated premature senescence; these effects aggravated by H2O2-induced oxidative damage. Nevertheless, knockdown of NOX2 or overexpression of SIRT1 with adenovirus vector reduced progerin-associated premature senescence to maintain fenestrae through deacetylating p53. Furthermore, more Ac p53 K381 and progerin co-localized with accumulation of actin filament (F-actin) in the nuclear envelope of H2O2-treated HSECs; in contrast, these effects were rescued by overexpressing SIRT1. In conclusion, NOX2-dependent oxidative damage aggravates defenestration in HSECs via progerin-associated premature senescence; SIRT1-mediated deacetylation of p53 maintains fenestrae and attenuates liver fibrogenesis through inhibiting premature senescence.
Identification and characterization of the hypoxia response regulatory elements in the accessible genome
Authors: Lu Xi , Chen Xingqi 
Published: April 2020

AbstractHypoxia is commonly observed in the solid tumor and contributes to the drug resistance in cancer therapy. Deciphering the epigenetic feature under the hypoxia condition in the solid tumor is critical for us to understand the tumorigenesis and design the precision therapy. Using the time series of ATAC-seq data under the hypoxia treatment from the epithelia cells, we identified the hypoxia response regulatory elements (HRREs) in the accessible genome. We found that these different HRREs have unique genomic features and are enriched with different transcriptional factors (TFs). Our study provides insights into the chromatin structure response to the hypoxia treatment and identifies useful genomic features for a better understanding of the hypoxia biology in the solid tumor.
Biochemical, structural insights of newly isolated AA16 family of Lytic Polysaccharide Monooxygenase (LPMO) fromAspergillus fumigatusand investigation of its synergistic effect using biomass
Authors: Hossain Musaddique , Dodda Subba Reddy , Kapoor Bishwajit Singh , Aikat Kaustav , Mukhopadhyay Sudit S. 
Published: April 2020

AbstractThe efficient conversion of lignocellulosic biomass into fermentable sugar is a bottleneck for the cheap production of bio-ethanol. The recently identified enzyme Lytic Polysaccharide Monooxygenase (LPMO) family has brought new hope because of its boosting capabilities of cellulose hydrolysis. In this report, we have identified and characterized a new class of auxiliary (AA16) oxidative enzyme LPMO from the genome of a locally isolated thermophilic fungusAspergillus fumigatus(NITDGPKA3) and evaluated its boosting capacity of biomass hydrolysis. TheAfLPMO16 is an intronless gene and encodes the 29kDa protein. While Sequence-wise, it is close to the C1 type ofAaAA16 and cellulose-active AA10 family of LPMOs, but the predicted three-dimensional structure shows the resemblance with the AA11 family of LPMO (PDB Id: 4MAH). The gene was expressed under an inducible promoter (AOX1) with C-terminal His tag in thePichia pastoris. The protein was purified using Ni-NTA affinity chromatography, and we studied the enzyme kinetics with 2,6-dimethoxyphenol. We observed polysaccharides depolymerization activity with Carboxymethyl cellulose (CMC) and Phosphoric acid swollen cellulose (PASC). Moreover, the simultaneous use of cellulase cocktail (commercial) andAfLPMO16 enhances lignocellulosic biomass hydrolysis by 2-fold, which is highest so far reported in the LPMO family.ImportanceThe auxiliary enzymes, such as LPMOs, have industrial importance. These enzymes are used in cellulolytic enzyme cocktail due to their synergistic effect along with cellulases. In our study, we have biochemically and functionally characterized the new AA16 family of LPMO fromAspergillus fumigatus(NITDGPKA3). The biochemical characterization is the fundamental scientific elucidation of the newly isolated enzyme. The functional characterization, biomass degradation activity ofAfLPMO16, and cellulase cocktail (commercial) combination enhancing the activity by 2-fold. This enhancement is the highest reported so far, which gives the enzymeAfLPMO16 enormous potential for industrial use.
Inhibitory effect of eslicarbazepine acetate and S-licarbazepine on Nav1.5 channels
Authors: Leslie Theresa K. , Brückner Lotte , Chawla Sangeeta , Brackenbury William J. 
Published: April 2020

AbstractEslicarbazepine acetate (ESL) is a dibenzazepine anticonvulsant approved as adjunctive treatment for partial-onset epileptic seizures. Following first pass hydrolysis of ESL, S-licarbazepine (S-Lic) represents around 95 % of circulating active metabolites. S-Lic is the main enantiomer responsible for anticonvulsant activity and this is proposed to be through the blockade of voltage-gated Na+channels (VGSCs). ESL and S-Lic both have a voltage-dependent inhibitory effect on the Na+current in N1E-115 neuroblastoma cells expressing neuronal VGSC subtypes including Nav1.1, Nav1.2, Nav1.3, Nav1.6 and Nav1.7. ESL has not been associated with cardiotoxicity in healthy volunteers, although a prolongation of the electrocardiographic PR interval has been observed, suggesting that ESL may also inhibit cardiac Nav1.5 isoform. However, this has not previously been studied. Here, we investigated the electrophysiological effects of ESL and S-Lic on Nav1.5 using whole-cell patch clamp recording. We interrogated two model systems: (1) MDA-MB-231 metastatic breast carcinoma cells, which endogenously express the ‘neonatal’ Nav1.5 splice variant, and (2) HEK-293 cells stably over-expressing the ‘adult’ Nav1.5 splice variant. We show that both ESL and S-Lic inhibit transient and persistent Na+current, hyperpolarise the voltage-dependence of fast inactivation, and slow the recovery from channel inactivation. These findings highlight, for the first time, the potent inhibitory effects of ESL and S-Lic on the Nav1.5 isoform, suggesting a possible explanation for the prolonged PR interval observed in patients on ESL treatment. Given that numerous cancer cells have also been shown to express Nav1.5, and that VGSCs potentiate invasion and metastasis, this study also paves the way for future investigations into ESL and S-Lic as potential invasion inhibitors.
eCovSens-Ultrasensitive Novel In-House Built Printed Circuit Board Based Electrochemical Device for Rapid Detection of nCovid-19 antigen, a spike protein domain 1 of SARS-CoV-2
Authors: Mahari Subhasis , Roberts Akanksha , Shahdeo Deepshikha , Gandhi Sonu 
Published: April 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or nCovid-19) outbreak has become a huge public health issue due to its rapid transmission and global pandemic. Currently, there are no vaccines or drugs available for nCovid-19, hence early detection is crucial to help and manage the outbreak. Here, we report an in-house built biosensor device (eCovSens) and compare it with a commercial potentiostat for the detection of nCovid-19 spike antigen (nCovid-19Ag) in spiked saliva samples. A potentiostat based sensor was fabricated using fluorine doped tin oxide electrode (FTO) with gold nanoparticle (AuNPs) and immobilized with nCovid-19 monoclonal antibody (nCovid-19Ab) to measure change in the electrical conductivity. Similarly, eCovSens was used to measure change in electrical conductivity by immobilizing nCovid-19 Ab on screen printed carbon electrode (SPCE). The performances of both sensors were recorded upon interaction of nCovid-19Ab with its specific nCovid-19Ag. Under optimum conditions, the FTO based immunosensor and eCovSens displayed high sensitivity for detection of nCovid-19Ag, ranging from 1 fM to 1 μM. Our in-house developed device can successfully detect nCovid-19Ag at 10 fM concentration in standard buffer that is in close agreement with FTO/AuNPs sensor. The limit of detection (LOD) was found to be 90 fM with eCovSens and 120 fM with potentiostst in case of spiked saliva samples. The proposed portable eCovSens device can be used as a diagnostic tool for the rapid (within 10-30 s) detection of nCovid-19Ag traces directly in patient saliva in a non-invasive manner.
Zika virus-based immunotherapy enhances long-term survival of rodents with brain tumors through upregulation of memory T-cells
Authors: Crane Andrew T. , Chrostek Matthew R. , Krishna Venkatramana D. , Shiao Maple , Toman Nikolas G. , Pearce Clairice , Tran Sarah K. , Sipe Christopher J. , Guo Winston , Voth Joseph P. , Vaid Shivanshi , Xie Hui , Lu Wei-Cheng , Swanson Will , Grande Andrew W. , Schleiss Mark R. , Bierle Craig J. , Cheeran Maxim C-J. , Low Walter C. 
Published: April 2020

AbstractZika virus (ZIKV) exhibits a tropism for brain tumor cells and has been used as an oncolytic virus to target brain tumors in mice with modest effects on extending median survival. Recent studies have highlighted the potential for combining virotherapy and immunotherapy to target cancer. We postulated that ZIKV could be used as an adjuvant to enhance the long-term survival of mice with malignant glioblastoma and generate memory T-cells capable of providing long-term immunity against cancer remission. To test this hypothesis mice bearing malignant intracranial GL261 tumors were subcutaneously vaccinated with irradiated GL261 cells previously infected with the ZIKV. Mice also received intracranial injections of live ZIKV, irradiated ZIKV, or irradiated GL261 cells previously infected with ZIKV. Long-term survivors were rechallenged with a second intracranial tumor to examine their immune response and look for the establishment of protective memory T-cells. Mice with subcutaneous vaccination plus intracranial irradiated ZIKV or intracranial irradiated GL261 cells previously infected with ZIKV exhibited the greatest extensions to overall survival. Flow cytometry analysis of immune cells within the brains of long-term surviving mice after tumor rechallenge revealed an upregulation in the levels of T-cells, including CD4+and tissue-resident memory CD4+T-cells, in comparison to long-term survivors that were mock-rechallenged, and in comparison to naïve untreated mice challenged with intracranial gliomas. These results suggest that ZIKV can serve as an adjuvant to subcutaneous tumor vaccines that enhance long-term survival and generate protective tissue-resident memory CD4+T-cells.
High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains
Authors: Flament-Simon Saskia-Camille , de Toro María , Chuprikova Liubov , Blanco Miguel , Moreno-González Juan , Salas Margarita , Blanco Jorge , Redrejo-Rodríguez Modesto 
Published: April 2020

AbstractSelf-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB).We have now surveyed the presence of pipolins in a collection of 2238 human and animal pathogenicEscherichia colistrains and found that, although detected in only 25 new isolates (1.1%), they are present inE. colistrains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belongs to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring strains from GenBank further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons.In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulatingE. coliand possibly also among other pathogenic bacteria.
Analyzing Genomic Data Using Tensor-Based Orthogonal Polynomials with Application to Synthetic RNAs
Authors: Nafees Saba , Rice Sean H. , Wakeman Catherine A. 
Published: April 2020

ABSTRACTAn important goal in molecular biology is to quantify both the patterns across a genomic sequence and the relationship between phenotype and underlying sequence. We propose a multivariate tensor-based orthogonal polynomial approach to characterize nucleotides or amino acids in a given sequence and map corresponding phenotypes onto the sequence space. We have applied this method to a previously published case of small transcription activating RNAs (STARs). Covariance patterns along the sequence showcased strong correlations between nucleotides at the ends of the sequence. However, when the phenotype is projected onto the sequence space, this pattern doesn’t emerge. When doing second order analysis and quantifying the functional relationship between the phenotype and pairs of sites along the sequence, we identified sites with high regressions spread across the sequence, indicating potential intramolecular binding. In addition to quantifying interactions between different parts of a sequence, the method quantifies sequence-phenotype interactions at first and higher order levels. We discuss the strengths and constraints of the method and compare it to computational methods such as machine learning approaches. An accompanying command line tool to compute these polynomials is provided. We show proof of concept of this approach and demonstrate its potential application to other biological systems.
Validation and standardization of a new radial-arm water maze protocol using a murine model of mild closed head traumatic brain injury
Authors: Macheda Teresa , Roberts Kelly N. , Bachstetter Adam D. 
Published: April 2020

AbstractCognitive impairments can be a significant problem after a traumatic brain injury (TBI), which affects millions worldwide each year. There is a need for establish reproducible cognitive assays in rodents to better understand disease mechanisms and to develop therapeutic interventions towards treating TBI-induced impairments. Our goal was to validate and standardize the radial arm water maze (RAWM) test as an assay to screen for cognitive impairments caused by TBI. RAWM is a visuo-spatial learning test, originally designed for use with rats, and later adapted for mice. The present study investigates whether test procedures, such us the presence of extra-maze cues influences learning and memory performance. C57BL/6 mice were tested in an 8-arm RAWM using a four-day protocol. We demonstrated that two days of training, exposing the mice to extra-maze cues and a visible platform, influenced learning and memory performance. Mice that did not receive training performed poorer compared to mice trained. To further validate our RAWM protocol, we used scopolamine. We, also, demonstrated that a single mild closed head injury (CHI) caused deficits in this task at two weeks post-CHI. Our data supported the use of 7 trials per day and a spaced training protocol as key factor to unmask memory impairment following CHI. Here, we provide a detailed standard operating procedure for RAWM test, which can be applied to a variety of mouse models including neurodegenerative diseases and pathology, as well as when pharmacological approaches are used.
Greenhouse conditions in lower Eocene coastal wetlands? – Lessons from Schöningen, Northern Germany
Authors: Lenz Olaf K. , Riegel Walter , Wilde Volker 
Published: April 2020

AbstractThe Paleogene succession of the Helmstedt Lignite Mining District in Northern Germany includes coastal peat mire records from the latest Paleocene to the middle Eocene at the southern edge of the Proto-North Sea. Therefore, it covers the different long- and short-term climate perturbations of the Paleogene greenhouse. 56 samples from three individual sections of a lower Eocene seam in the record capture the typical succession of the vegetation in a coastal wetland during a period that was not affected by climate perturbation. This allows facies-dependent vegetational changes to be distinguished from those that were climate induced. Cluster analyses and NMDS of well-preserved palynomorph assemblages reveal four successional stages in the vegetation during peat accumulation: (1) a coastal vegetation, (2) an initial mire, (3) a transitional mire, and (4) a terminal mire. Biodiversity measures show that plant diversity decreased significantly in the successive stages. The highly diverse vegetation at the coast and in the adjacent initial mire was replaced by low diversity communities adapted to wet acidic environments and nutrient deficiency. The palynomorph assemblages are dominated by elements such asAlnus(Betulaceae) orSphagnum(Sphagnaceae). Typical tropical elements which are characteristic for the middle Eocene part of the succession are missing. This indicates that a more warm-temperate climate prevailed in northwestern Germany during the early lower Eocene.