bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prunella vulgarisextract and suramin block SARS-coronavirus2virus Spike protein D614 and G614 variants mediated receptor association and virus entry in cell culture system
Authors: Ao Zhujun , Chan Mable , Ouyang Maggie Jing , Abiola Olukitibi Titus , Mahmoudi Mona , Kobasa Darwyn , Yao Xiaojian 
Published: August 2020

AbstractUntil now, no approved effective vaccine and antiviral therapeutic are available for treatment or prevention of SARS-coronavirus 2 (SCoV-2) virus infection. In this study, we established a SCoV-2 Spike glycoprotein (SP), including a SP mutant D614G, pseudotyped HIV-1-based vector system and tested their ability to infect ACE2-expressing cells. This study revealed that a C-terminal 17 amino acid deletion in SCoV-2 SP significantly increases the incorporation of SP into the pseudotyped viruses and enhanced its infectivity, which may be helpful in the design of SCoV2-SP-based vaccine strategies. Moreover, based on this system, we have demonstrated that an aqueous extract from the Chinese herbPrunella vulgaris(CHPV) and a compound, suramin, displayed potent inhibitory effects on both wild type and mutant (G614) SCoV-2 SP pseudotyped virus (SCoV-2-SP-PVs)-mediated infection. The 50% inhibitory concentration (IC50) for CHPV and suramin on SCoV-2-SP-PVs are 30, and 40 μg/ml, respectively. To define the mechanisms of their actions, we demonstrated that both CHPV and suramin are able to directly interrupt SCoV-2–SP binding to its receptor ACE2 and block the viral entry step. Importantly, our results also showed that CHPV or suramin can efficiently reduce levels of cytopathic effect caused by SARS-CoV-2 virus (hCoV-19/Canada/ON-VIDO-01/2020) infection in Vero cells. Furthermore, our results demonstrated that the combination of CHPV/suramin with an anti-SARS-CoV-2 neutralizing antibody mediated more potent blocking effect against SCoV2-SP-PVs. Overall, this study provides evidence that CHPV and suramin has anti-SARS-CoV-2 activity and may be developed as a novel antiviral approach against SARS-CoV-2 infection.
SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generatedin vitroduring propagation in TMPRSS2-deficient cells
Authors: Sasaki Michihito , Uemura Kentaro , Sato Akihiko , Toba Shinsuke , Sanaki Takao , Maenaka Katsumi , Hall William W. , Orba Yasuko , Sawa Hirofumi 
Published: August 2020

AbstractThe spike (S) protein of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) binds to a host cell receptor which facilitates viral entry. A polybasic motif detected at the cleavage site of the S protein has been shown to broaden the cell tropism and transmissibility of the virus. Here we examine the properties of SARS-CoV-2 variants with mutations at the S protein cleavage site that undergo inefficient proteolytic cleavage. Virus variants with S gene mutations generated smaller plaques and exhibited a more limited range of cell tropism compared to the wild-type strain. These alterations were shown to result from their inability to utilize the entry pathway involving direct fusion mediated by the host type II transmembrane serine protease, TMPRSS2. Notably, viruses with S gene mutations emerged rapidly and became the dominant SARS-CoV-2 variants in TMPRSS2-deficient cells including Vero cells. Our study demonstrated that the S protein polybasic cleavage motif is a critical factor underlying SARS-CoV-2 entry and cell tropism. As such, researchers should be alert to the possibility ofde novoS gene mutations emerging in tissue-culture propagated virus strains.
Differential adhesion regulates neurite placement via a retrograde zippering mechanism
Authors: Sengupta Titas , Koonce Noelle L. , Moyle Mark W. , Duncan Leighton H. , Vázquez-Martínez Nabor , Emerson Sarah E. , Han Xiaofei , Shao Lin , Wu Yicong , Santella Anthony , Fan Li , Bao Zhirong , Mohler William A. , Shroff Hari , Colón-Ramos Daniel A. 
Published: August 2020

AbstractDuring development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of theC. elegansbrain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificityin vivoin developing neuropil bundles.
Exploring the distribution of statistical feature parameters for natural sound textures
Authors: Mishra Ambika P. , Harper Nicol S. , Schnupp Jan W.H. 
Published: August 2020

AbstractSounds like “running water” and “buzzing bees” are classes of sounds which are a collective result of many similar acoustic events and are known as “sound textures”. Recent psychoacoustic study using sound textures by [1] reported that natural sounding textures can be synthesized from white noise by imposing statistical features such as marginals and correlations computed from the outputs of cochlear models responding to the textures. The outputs being the envelopes of bandpass filter responses, the ‘cochlear envelope’. This suggests that the perceptual qualities of many natural sounds derive directly from such statistical features, and raises the question of how these statistical features are distributed in the acoustic environment. To address this question, we collected a corpus of 200 sound textures from public online sources and analyzed the distributions of the textures’ marginal statistics (mean, variance, skew, and kurtosis), cross-frequency correlations and modulation power statistics. A principal component analysis of these parameters revealed a great deal of redundancy in the texture parameters. For example, just two marginal principal components, which can be thought of as measuring the sparseness or burstiness of a texture, capture as much as 66% of the variance of the 128 dimensional marginal parameter space, while the first two principal components of cochlear correlations capture as much as 90% of the variance in over 1000 correlation parameters. Knowledge of the statistical distributions documented here may help guide the choice of acoustic stimuli with high ecological validity in future research.
miRNA-mediated loss of m6A increases nascent translation in glioblastoma
Authors: Zepecki John P. , Karambizi David , Fajardo J. Eduardo , Snyder Kristin M. , Guetta-Terrier Charlotte , Tang Oliver Y. , Chen Jia-Shu , Sarkar Atom , Fiser Andras , Toms Steven A. , Tapinos Nikos 
Published: August 2020

AbstractWithin the glioblastoma cellular niche, glioma stem cells (GSCs) can give rise to differentiated glioma cells (DGCs) and, when necessary, DGCs can reciprocally give rise to GSCs to maintain the cellular equilibrium necessary for optimal tumor growth. Here, using ribosome profiling, transcriptome and m6A RNA sequencing, we show that GSCs from patients with different subtypes of glioblastoma share a set of transcripts, which exhibit a pattern of m6A loss and increased protein translation during differentiation. The target sequences of a group of miRNAs overlap the canonical RRACH m6A motifs of these transcripts, many of which confer a survival advantage in glioblastoma. Ectopic expression of the RRACH-binding miR-145 induces loss of m6A, formation of FTO/AGO1/ILF3/miR-145 complexes on a clinically relevant tumor suppressor gene (CLIP3) and significant increase in its nascent translation. Inhibition of miR-145 maintains RRACH m6A levels of CLIP3 and inhibits its nascent translation. This study highlights a critical role of miRNAs in assembling complexes for m6A demethylation and induction of protein translation during GSC state transition.Author SummaryCellular plasticity and epigenetic adaptation of human glioblastoma stem cells to the tumor microenvironment is a hallmark of this devastating disease. With our present work, we discover the relationship between miRNAs and the RNA methylation machinery in human glioblastoma and show how miRNA-induced loss of m6A results in increase in protein translation of clinically important transcripts during glioblastoma stem cell differentiation. Leveraging the dynamic functions of these miRNAs can be important in the design of optimal therapeutics targeted at cancer cell plasticity.
Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase
Authors: Teixeira Raphael D. , Holzschuh Fabian , Schirmer Tilman 
Published: August 2020

AbstractDiguanylate cyclases (DGCs) synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR fromLeptospira biflexais a constitutively dimeric prototype of this class of DGCs. Full-length crystal structures revealed that BeF3-pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coilviaa localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many DGCs with N-terminal coiled-coil linkers.
Myomixer is expressed during embryonic and post-larval hyperplasia, muscle regeneration and fusion of myoblats in rainbow trout (Oncorhynchus mykiss)
Authors: Perello-Amoros Miquel , Rallière Cécile , Gutiérrez Joaquim , Gabillard Jean-Charles 
Published: August 2020

1.AbstractIn contrast to mice or zebrafish, trout exhibits post-larval muscle growth through hypertrophy and formation of new myofibers (hyperplasia). The muscle fibers are formed by the fusion of mononucleated cells (myoblasts) regulated by several muscle-specific proteins such as myomaker or myomixer. In this work, we identified a unique gene encoding a myomixer protein of 77 amino acids (aa) in the trout genome. Sequence analysis and phylogenetic tree, showed moderate conservation of the overall protein sequence across teleost fish (61% of aa identity between trout and zebrafish myomixer sequences). Nevertheless, the functionally essential motif, AxLyCxL is perfectly conserved in all studied sequences of vertebrates. Usingin situhybridization, we observed that myomixer was highly expressed in the embryonic myotome, particularly in the hyperplasic area. Moreover, myomixer remained readily expressed in white muscle of juvenile (1 and 20 g) although its expression decreased in mature fish. We also showed that myomixer is up-regulated during muscle regeneration andin vitromyoblasts fusion. Together, these data indicate that myomixer expression is consistently associated with the formation of new myofibers during somitogenesis, post-larval growth and muscle regeneration in trout.
SynapsEM: computer-assisted synapse morphometry
Authors: Watanabe Shigeki , Davis M Wayne , Kusick Grant F , Iwasa Janet , Jorgensen Erik M 
Published: August 2020

AbstractThe structural features of a synapse, in part, determine its output. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified using morphometry. Three parameters are typically assessed from each specimen: 1) the sizes of individual vesicles and organelles, 2) the absolute number and densities of organelles, and 3) distances between organelles and key features at synapses such as active zone membranes and dense projections. For data to be valid, the analysis must be repeated from hundreds or thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze these features: SynapsEM. In short, we developed macros for ImageJ/Fiji to record x,y-coordinates of segmented structures; the coordinates are then exported as text files. Independent investigators can reload the images and text files to confirm or re-evaluate the segmentation using ImageJ. The Matlab program calculates and reports key synaptic parameters from the coordinates. Since the values are calculated, rather than measured from each micrograph, other parameters can be extracted in Matlab by additional scripting. Thus, this program can accelerate morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.
Long-read sequencing resolves structural variants inSERPINC1causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methods
Authors: de la Morena-Barrio Belén , Stephens Jonathan , de la Morena-Barrio María Eugenia , Stefanucci Luca , Padilla José , Miñano Antonia , Gleadall Nicholas , García Juan Luis , López-Fernández María Fernanda , Morange Pierre-Emmanuel , Puurunen Marja K , Undas Anetta , Vidal Francisco ,   NIHR BioResource, Raymond F Lucy , García Vicente Vicente , Ouwehand Willem H , Corral Javier , Sanchis-Juan Alba 
Published: August 2020

AbstractThe identification and characterization of structural variants (SVs) in clinical genetics have remained historically challenging as routine genetic diagnostic techniques have limited ability to evaluate repetitive regions and SVs. Long-read whole-genome sequencing (LR-WGS) has emerged as a powerful approach to resolve SVs. Here, we used LR-WGS to study 19 unrelated cases with type I Antithrombin Deficiency (ATD), the most severe thrombophilia, where routine molecular tests were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs and resolved 10 cases. For the first time, we identified a germline complex rearrangement involved in ATD previously misclassified as a deletion. Additionally, we provided molecular diagnoses for two unresolved individuals that harbored a novel SINE-VNTR-Alu retroelement insertion that we fully characterized byde novoassembly and confirmed by PCR amplification in all affected relatives. Finally, the nucleotide-level resolution achieved for all the SVs allowed breakpoint analysis, which revealed a replication-based mechanism for most of the cases. Our study underscores the utility of LR-WGS as a complementary diagnostic method to identify, characterize, and unveil the molecular mechanism of formation of disease-causing SVs, and facilitates decision making about long-term thromboprophylaxis in ATD patients.
Neoplastic and immune single cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma
Authors: Riemondy Kent A. , Venkataraman Sujatha , Willard Nicholas , Nellan Anandani , Sanford Bridget , Griesinger Andrea M. , Amani Vladimir , Mitra Siddhartha , Hankinson Todd C. , Handler Michael H. , Sill Martin , Ocasio Jennifer , Weir Seth J. , Malawsky Daniel S , Gershon Timothy R. , Garancher Alexandra , Wechsler-Reya Robert J. , Hesselberth Jay R. , Foreman Nicholas K. , Donson Andrew M. , Vibhakar Rajeev 
Published: August 2020

AbstractMedulloblastoma (MB) is a heterogeneous disease in which neoplastic cells and associated immune cells contribute to disease progression. To better understand cellular heterogeneity in MB we use single-cell RNA sequencing, immunohistochemistry and deconvolution of transcriptomic data to profile neoplastic and immune populations in childhood MB samples. Neoplastic cells cluster primarily according to individual sample of origin which is in part due to the effect of chromosomal copy number gains and losses. Harmony alignment reveals novel MB subgroup/subtype-associated subpopulations that recapitulate neurodevelopmental processes and are associated with clinical outcomes, including discrete photoreceptor-like cells in MB subgroups GP3 and GP4 and nodule-associated neuronally-differentiated cells in subgroup SHH. We definitively chart the spectrum of MB immune cell infiltrates, which include subgroup/subtype-associated developmentally-related neuron-pruning and antigen presenting myeloid cells. MB cellular diversity is recapitulated in genetically engineered mouse subgroup-specific models of MB. These findings provide a clearer understanding of both the neoplastic and immune cell heterogeneity in MB.
Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection
Authors: Kreger Jesse , Garcia Josephine , Zhang Hongtao , Komarova Natalia L. , Wodarz Dominik , Levy David N. 
Published: August 2020

AbstractRecombination has been shown to contribute to HIV-1 evolutionin vivo, but the underlying dynamics are extremely complex, depending on the nature of the fitness landscapes and of epistatic interactions. A less well-studied determinant of recombinant evolution is the mode of virus transmission in the cell population. HIV-1 can spread by free virus transmission, resulting largely in singly infected cells, and also by direct cell-to-cell transmission, resulting in the simultaneous infection of cells with multiple viruses. We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models toin vitroexperimental data on the growth of fluorescent reporter viruses under static conditions (where both transmission pathways operate), and under gentle shaking conditions, where cell-to-cell transmission is largely inhibited. The parameterized mathematical models are then used to extrapolate the viral evolutionary dynamics beyond the experimental settings. Assuming a fixed basic reproductive ratio of the virus (independent of transmission pathway), we find that recombinant evolution is fastest if virus spread is driven only by cell-to-cell transmission, and slows down if both transmission pathways operate. Recombinant evolution is slowest if all virus spread occurs through free virus transmission. This is due to cell-to-cell transmission (i) increasing infection multiplicity, (ii) promoting the co-transmission of different virus strains from cell to cell, and (iii) increasing the rate at which point mutations are generated as a result of more reverse transcription events. This work further resulted in the estimation of various parameters that characterize these evolutionary processes. For example, we estimate that during cell-to-cell transmission, an average of 3 viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to free virus transmission. In general, our study points towards the importance of infection multiplicity and cell-to-cell transmission for HIV-evolution.
Comprehensive synthetic genetic array analysis of alleles that interact with mutation of theSaccharomyces cerevisiaeRecQ helicases Hrq1 and Sgs1
Authors: Sanders Elsbeth , Nguyen Phoebe A. , Rogers Cody M. , Bochman Matthew L. 
Published: August 2020

ABSTRACTMost eukaryotic genomes encode multiple RecQ family helicases, including five such enzymes in humans. For many years, the yeastSaccharomyces cerevisiaewas considered unusual in that it only contained a single RecQ helicase, named Sgs1. However, it has recently been discovered that a second RecQ helicase, called Hrq1, resides in yeast. Both Hrq1 and Sgs1 are involved in genome integrity, functioning in processes such as DNA inter-strand crosslink repair, double-strand break repair, and telomere maintenance. However, it is unknown if these enzymes interact at a genetic, physical, or functional level as demonstrated for their human homologs. Thus, we performed synthetic genetic array (SGA) analyses ofhrq1Δandsgs1Δmutants. As inactive alleles of helicases can demonstrate dominant phenotypes, we also performed SGA analyses on thehrq1-K318Aandsgs1-K706AATPase/helicase-null mutants, as well as all combinations of deletion and inactive double mutants. We crossed these eight query strains (hrq1Δ, sgs1Δ, hrq1-K318A, sgs1-K706A, hrq1Δ sgs1Δ, hrq1Δ sgs1-K706A, hrq1-K318A sgs1Δ, andhrq1-K318A sgsl-K706A) to theS. cerevisiaesingle gene deletion and temperature-sensitive allele collections to generate double and triple mutants and scored them for synthetic positive and negative genetic effects based on colony growth. These screens identified hundreds of synthetic interactions, supporting the known roles of Hrq1 and Sgs1 in DNA repair, as well as suggesting novel connections to rRNA processing, mitochondrial DNA maintenance, transcription, and lagging strand synthesis during DNA replication.
The genetic and physical interactomes of theSaccharomyces cerevisiaeHrq1 helicase
Authors: Rogers Cody M. , Sanders Elsbeth , Nguyen Phoebe A. , Smith-Kinnaman Whitney , Mosley Amber L. , Bochman Matthew L. 
Published: August 2020

ABSTRACTThe human genome encodes five RecQ helicases (RECQL1, BLM, WRN, RECQL4, and RECQL5) that participate in various processes underpinning genomic stability. Of these enzymes, the disease-associated RECQL4 is comparatively understudied due to a variety of technical challenges. However,Saccharomyces cerevisiaeencodes a functional homolog of RECQL4 called Hrq1, which is more amenable to experimentation and has recently been shown to be involved in DNA inter-strand crosslink (ICL) repair and telomere maintenance. To expand our understanding of Hrq1 and the RecQ4 subfamily of helicases in general, we took a multi-omics approach to define the Hrq1 interactome in yeast. Using synthetic genetic array analysis, we found that mutations of genes involved in processes such as DNA repair, chromosome segregation, and transcription synthetically interact with deletion ofHRQ1and the catalytically inactivehrq1-K318Aallele. Pull-down of tagged Hrq1 and mass spectrometry identification of interacting partners similarly underscored links to these processes and others. Focusing on transcription, we found thathrq1mutant cells are sensitive to caffeine and that mutation ofHRQ1alters the expression levels of hundreds of genes. In the case ofhrq1-K318A, several of the most highly upregulated genes encode proteins of unknown function whose expression levels are also increased by DNA ICL damage. Together, our results suggest a heretofore unrecognized role for Hrq1 in transcription, as well as novel members of the Hrq1 ICL repair pathway. These data expand our understanding of RecQ4 subfamily helicase biology and help to explain why mutations in human RECQL4 cause diseases of genomic instability.