bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a single-step, single-tube reverse transcription-loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA
Authors: Lee Jean Y. H. , Best Nickala , McAuley Julie , Porter Jessica L. , Seemann Torsten , Schultz Mark B. , Sait Michelle , Orlando Nicole , Mercoulia Karolina , Ballard Susan A. , Druce Julian , Tran Thomas , Catton Mike G. , Pryor Melinda J. , Cui Huanhuan L. , Luttick Angela , McDonald Sean , Greenhalgh Arran , Kwong Jason C. , Sherry Norelle L. , Graham Maryza , Hoang Tuyet , Herisse Marion , Pidot Sacha J. , Williamson Deborah A. , Howden Benjamin P. , Monk Ian R. , Stinear Timothy P. 
Published: April 2020

2.AbstractIntroductionThe SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues.AimTo establish and validate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs.MethodologyWe used a commercial RT-LAMP mastermix from OptiGene Ltd in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby as little as 1 μL of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65°C for 30 minutes and measure fluorescence in the FAM channel at one-minute intervals.ResultsAssay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87% and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 minutes (SD ±7 minutes). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50mL−1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay.ConclusionWith a simplified workflow, N1-STOP-LAMP is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.3.Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Imaging translation dynamics in live embryos reveals spatial heterogeneities
Authors: Dufourt Jeremy , Bellec Maelle , Trullo Antonio , Dejean Matthieu , De Rossi Sylvain , Lagha Mounia 
Published: April 2020

AbstractThe translation of individual mRNA molecules is a key biological process, yet this multi-step process has never been imaged in living multicellular organisms. Here we deploy the recently developed Suntag method to visualize and quantify translation dynamics of single mRNAs in livingDrosophilaembryos. By focusing on the translation of the conserved major epithelial-mesenchymal transition (EMT)-inducing transcription factor Twist, we identified spatial heterogeneity in mRNA translation efficiency and reveal the existence of translation factories, where clustered mRNAs are co-translated preferentially at basal perinuclear regions. Simultaneous visualization of transcription and translation dynamics in a living multicellular organism opens exciting new avenues for understanding of gene regulation during development.
Investigating DNA methylation as a potential mediator between pigmentation genes, pigmentary traits and skin cancer
Authors: Bonilla Carolina , Bertoni Bernardo , Min Josine L , Hemani Gibran ,   Genetics of DNA Methylation Consortium, Elliott Hannah R 
Published: April 2020

AbstractBackgroundIncidence rates for melanoma and non-melanoma skin cancer (NMSC), which includes basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), have been steadily increasing in all populations. Populations of European ancestry exhibit the highest rates and therefore, have been widely studied. Pigmentation characteristics are well-known risk factors for skin cancer, particularly fair skin, red hair, blue eyes and the inability to tan. Polymorphisms in established pigmentation-related genes have been associated with these traits and with an increased risk of malignancy. However, the functional relationship between genetic variation and disease is still unclear, with the exception of red hair colour variants in the melanocortin 1 receptor (MC1R) gene.ObjectivesThe aim of this study was to explore the possibility that non-coding pigmentation SNPs are associated with pigmentary traits and skin cancer via DNA methylation (DNAm).Methods and ResultsUsing a meta-GWAS of whole blood DNAm from 36 European cohorts (N=27,750; the Genetics of DNA Methylation Consortium, GoDMC), we found that 19 out of 27 pigmentation-associated SNPs distributed within 10 genes (ASIP, BNC2, IRF4, HERC2, MC1R, OCA2, SLC24A4, SLC24A5, SLC45A2, TYR) were associated with 391 DNAm sites across 30 genomic regions. We selected 25 DNAm sites for further analysis.We examined the effect of the chosen DNAm sites on pigmentation traits, sun exposure phenotypes, and skin cancer, and on gene expression in whole blood. We found an association of decreased DNAm at cg07402062 with red hair in the Avon Longitudinal Study of Parents and Children (ALSPAC), and a strong positive association of DNAm at this and correlated sites with higher expression ofSPIRE2. Additionally, we investigated the association of gene expression in skin with pigmentation traits and skin cancer. The expression ofASIP,FAM83C,NCOA6,CDK10, andEXOC2was associated with hair colour, whilst that ofASIPandCDK10also had an effect on melanoma and BCC.ConclusionsOur results indicate that DNAm and expression of genes in the 16q24.3 and 20q11.22 regions, deserve to be further investigated as potential mediators of the relationship between genetic variants, pigmentation/sun exposure phenotypes, and some types of skin cancer.
Unequivocal mapping of molecular ether lipid species by LC-MS/MS in plasmalogen-deficient mice
Authors: Koch Jakob , Lackner Katharina , Wohlfarter Yvonne , Sailer Sabrina , Zschocke Johannes , Werner Ernst R. , Watschinger Katrin , Keller Markus A. 
Published: April 2020

AbstractDeficient ether lipid biosynthesis in rhizomelic chondrodysplasia punctata and other disorders is associated with a wide range of severe symptoms including small stature with proximal shortening of the limbs, contractures, facial dysmorphism, congenital cataracts, ichthyosis, spasticity, microcephaly, and mental disability. Mouse models are available but show less severe symptoms. In both humans and mice it has remained elusive which of the symptoms can be attributed to lack of plasmanyl or plasmenyl ether lipids. The latter compounds, better known as plasmalogens, harbor a vinyl ether double bond conferring special chemical and physical properties. Discrimination between plasmanyl and plasmenyl ether lipids is a major analytical challenge, especially in complex lipid extracts with many isobaric species. Consequently, these lipids are often neglected also in recent lipidomic studies. Here we present a comprehensive LC-MS/MS based approach that allows unequivocal distinction of these two lipid subclasses based on their chromatographic properties. The method was validated using a novel plasmalogen-deficient mouse model which lacks plasmanylethanolamine desaturase and therefore cannot form plasmenyl ether lipids. We demonstrate that plasmanylethanolamine desaturase deficiency causes an accumulation of plasmanyl species, a little studied but biologically important substance class.
Biochemically diverse CRISPR-Cas9 orthologs
Authors: Gasiunas Giedrius , Young Joshua K. , Karvelis Tautvydas , Kazlauskas Darius , Urbaitis Tomas , Jasnauskaite Monika , Grusyte Mantvyda , Paulraj Sushmitha , Wang Po-Hao , Hou Zhenglin , Dooley Shane K. , Cigan Mark , Alarcon Clara , Chilcoat N. Doane , Bigelyte Greta , Curcuru Jennifer L. , Mabuchi Megumu , Sun Zhiyi , Fuchs Ryan T. , Schildkraut Ezra , Weigele Peter R. , Jack William E. , Robb G. Brett , Venclovas Česlovas , Siksnys Virginijus 
Published: April 2020

ABSTRACTCRISPR-Cas9 nucleases are abundant in microbes. To explore this largely uncharacterized diversity, we applied cell-free biochemical screens to rapidly assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) requirements of novel Cas9 proteins. This approach permitted the characterization of 79 Cas9 orthologs with at least 7 distinct classes of gRNAs and 50 different PAM sequence requirements. PAM recognition spanned the entire spectrum of T-, A-, C-, and G-rich nucleotides ranging from simple di-nucleotide recognition to complex sequence strings longer than 4. Computational analyses indicated that most of this diversity came from 4 groups of interrelated sequences providing new insight into Cas9 evolution and efforts to engineer PAM recognition. A subset of Cas9 orthologs were purified and their activities examined further exposing additional biochemical diversity. This constituted both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for longer stretches of homology between gRNA and DNA target to function robustly. In all, the diverse collection of Cas9 orthologs presented here sheds light on Cas9 evolution and provides a rich source of PAM recognition and other potentially desirable properties that may be mined to expand the genome editing toolbox with new RNA-programmable nucleases.
Fluorogenic probe for fast 3D whole-cell DNA-PAINT
Authors: Chung Kenny KH , Zhang Zhao , Kidd Phylicia , Zhang Yongdeng , Williams Nathan D , Rollins Bennett , Yang Yang , Lin Chenxiang , Baddeley David , Bewersdorf Joerg 
Published: April 2020

AbstractDNA-PAINT is an increasingly popular super-resolution microscopy method that can acquire high-fidelity images at nanometer resolution. It suffers, however, from high background and very slow imaging speed, both of which can be attributed to the presence of unbound fluorophores in solution. We present a fluorogenic DNA-PAINT probe that solves these problems and demonstrate 3D imaging without the need for optical sectioning and a 26-fold increase in imaging speed over regular DNA-PAINT.
Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax
Authors: Daron J. , Boissière A. , Boundenga L. , Ngoubangoye B. , Houze S. , Arnathau C. , Sidobre C. , Trape J.-F. , Durant P. , Renaud F. , Fontaine M.C. , Prugnolle F. , Rougeron V. 
Published: April 2020

AbstractPlasmodium vivaxis the most prevalent and widespread human malaria parasite, with almost three billion people living at risk of infection. With the discovery of its closest genetic relatives in African great apes (Plasmodium vivax-like), the origin ofP. vivaxhas been proposed to be located in the sub-Saharan African area. However, the limited number of genetic markers and samples investigated questioned the robustness of this result. Here, we examined the population genomic variation of 447 humanP. vivaxstrains and 19 apeP. vivax-likestrains originating from 24 different countries across the world. We identified 2,005,455 high quality single-nucleotide polymorphism loci allowing us to conduct an extensive characterization to date ofP. vivaxworldwide genetic variation. Phylogenetic relationships between human and apePlasmodiumrevealed thatP. vivaxis a sister clade ofP. vivax-like, not included within the radiation ofP. vivax-like. By investigating a variety of aspects ofP. vivaxvariation, we identified several striking geographical patterns in summary statistics as function of increasing geographic distance from Southeast Asia, suggesting thatP. vivaxmay derived from serial founder effects from a single origin located in Asia.
InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes
Authors: Karpe Snehal D. , Tiwari Vikas , Ramanathan Sowdhamini 
Published: April 2020

AbstractInsect Olfactory Receptors (ORs) are diverse family of membrane protein receptors responsible for most of the insect olfactory perception and communication, and hence they are of utmost importance for developing repellents or pesticides. Hence, accurate gene prediction of insect ORs from newly sequenced genomes is an important but challenging task. We have developed a dedicated web-server, ‘insectOR’, to predict and validate insect OR genes using multiple gene prediction algorithms, accompanied by relevant validations. It is possible to employ this sever nearly automatically and perform rapid prediction of the OR gene loci from thousands of OR-protein-to-genome alignments, resolve gene boundaries for tandem OR genes and refine them further to provide more complete OR gene models. InsectOR outperformed the popular genome annotation pipelines (MAKER and NCBI eukaryotic genome annotation) in terms of overall sensitivity at base, exon and locus level, when tested on two distantly related insect genomes. It displayed more than 95% nucleotide level precision in both tests. Finally, given the same input data and parameters, InsectOR missed less than 2% gene loci, in contrast to 55% loci missed by MAKER forDrosophila melanogaster. The web-server is freely available on the web athttp://caps.ncbs.res.in/insectOR/. All major browsers are supported. Website is implemented in Python with Jinja2 for templating and bootstrap framework which uses HTML, CSS and JavaScript/Ajax. The core pipeline is written in Perl.
Empowering Virus Sequences Research through Conceptual Modeling
Authors: Bernasconi Anna , Canakoglu Arif , Pinoli Pietro , Ceri Stefano 
Published: April 2020

AbstractThe pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology).VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research.In addition to VCM, we also illustrate the data dictionary for patient’s phenotype used by the COVID-19 Host Genetic Initiative. Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information.
Cryo-EM of mammalian PA28αβ-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ
Authors: Chen Jinhuan , Wang Yifan , Xu Cong , Peng Chao , Ding Zhanyu , Cong Yao 
Published: April 2020

AbstractThe proteasome activator PA28αβ affects MHC class-I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determined the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures revealed a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gate-keeper α2/3/4 subunits, resulting in a partial open iCP gate. We found that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptamericTbPA26 orPfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.
MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data
Authors: Gatto Laurent , Gibb Sebastian , Rainer Johannes 
Published: April 2020

AbstractWe present version 2 of theMSnbaseR/Bioconductor package.MSnbaseprovides infrastructure for the manipulation, processing and visualisation of mass spectrometry data. We focus on the newon-diskinfrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for elegant data processing, method development, and visualisation.
Persistent thermal input controls steering behavior inCaenorhabditis elegans
Authors: Ikeda Muneki , Matsumoto Hirotaka , Izquierdo Eduardo J. 
Published: April 2020

AbstractMotile organisms actively detect environmental signals and migrate to a preferable environment. Especially, small-size animals convert subtle difference in sensory input into orientation behavioral output for directly steering toward a destination, but the neural mechanisms underlying steering behavior remain elusive. Here, we analyze aC. elegansthermotactic behavior in which a small number of neurons are shown to mediate steering toward a destination temperature. We construct a neuroanatomical model and use an evolutionary algorithm to find configurations of the model that reproduce empirical thermotactic behavior. We find that, in all the evolved models, steering rates are modulated by persistent thermal signals sensed through forward locomotion. Persistent temperature increment lessens steering rates resulting in straight movement of model worms, whereas temperature decrement enlarges steering rates resulting in curvy movement. This relationship between temperature change and steering rates reproduces the empirical thermotactic migration up thermal gradients and steering bias toward higher temperature. Further, spectrum decomposition of neural activities in model worms show that thermal signals are transmitted from a sensory neuron to motor neurons on the longer time scale than sinusoidal locomotion ofC. elegans. Our results suggest that employments of persistent sensory signals enable small-size animals to steer toward a destination in natural environment with variable, noisy, and subtle cues.Author summaryA free-living nematodeCaenorhabditis elegansmemorizes an environmental temperature and steers toward the remembered temperature on a thermal gradient. How does theC. elegansbrain, consisting of 302 neurons, achieve this thermotactic steering behavior? Here, we address this question through neuroanatomical modeling and simulation analyses. We find that persistent thermal input modulates steering rates of model worms; worms run straight when they move up to a destination temperature, whereas run crookedly when move away from the destination. As a result, worms steer toward the destination temperature as observed in experiments. Our analysis also shows that persistent thermal signals are transmitted from a thermosensory neuron to dorsal and ventral neck motor neurons, regulating the balance of dorsoventral muscle contractions of model worms and generating steering behavior. This study indicates thatC. eleganscan steer toward a destination temperature without processing acute thermal input that informs to which direction it should steer. Such indirect mechanism of steering behavior is potentially employed in other motile organisms.
A Model Selection Approach to Hierarchical Shape Clustering with an Application to Cell Shapes
Authors: Mirshahi Mina , Partovi-Nia Vahid , Asgharian Masoud 
Published: April 2020

AbstractShape is an important phenotype of living species that contain different environmental and genetic information. Clustering living cells using their shape information can provide a preliminary guide to their functionality and evolution. Hierarchical clustering and dendrograms, as a visualization tool for hierarchical clustering, are commonly used by practitioners for classification and clustering. The existing hierarchical shape clustering methods are distance based. Such methods often lack a proper statistical foundation to allow for making inference on important parameters such as the number of clusters, often of prime interest to practitioners. We take a model selection perspective to clustering and propose a shape clustering method through linear models defined on Spherical Harmonics expansions of shapes. We introduce a BIC-type criterion, called CLUSBIC, and study consistency of the criterion. Special attention is paid to the notions of over- and under-specified models, important in studying model selection criteria and naturally defined in model selection literature. These notions do not automatically extend to shape clustering when a model selection perspective is adopted for clustering. To this end we take a novel approach using hypothesis testing. We apply our proposed criterion to cluster a set of real 3D images from HeLa cell line.
Toward the pathogenicity of the SLC26A4 p.C565Y variant using a genetically driven mouse model
Authors: Hu Chin-Ju , Lu Ying-Chang , Yang Ting-Hua , Chan Yen-Hui , Tsai Cheng-Yu , Yu I-Shing , Lin Shu-Wha , Liu Tien-Chen , Cheng Yen-Fu , Wu Chen-Chi , Hsu Chuan-Jen 
Published: April 2020

AbstractRecessive variants of the SLC26A4 gene are a common cause of hearing impairment worldwide. In the past, cell lines and transgenic mice have been widely used to investigate the pathogenicity associated with the SLC26A4 variants. However, discrepancies in the pathogenicity between humans and cell lines or transgenic mice have been documented for some of the SLC26A4 variants. For instance, the p.C565Y variant, which has been reported to be pathogenic in humans, did not exhibit functional pathogenic consequences in cell lines. To address the pathogenicity of p.C565Y, we used a genotype-based approach in which we generated knock-in mice heterozygous (Slc26a4+/C565Y), homozygous (Slc26a4C565Y/C565Y), and compound heterozygous (Slc26a4919-2A>G/C565Y) for this variant. Subsequent phenotypic characterization revealed that mice segregating these genotypes demonstrated normal auditory and vestibular functions and normal inner ear morphology and expression of pendrin. These findings indicate that the p.C565Y variant is non-pathogenic for mice and that a single p.C565Y allele is sufficient to maintain normal inner ear physiology in mice. Our results highlight the differences in the pathogenicity associated with certain SLC26A4 variants between transgenic mice and humans, which should be taken into consideration while interpreting the results of animal studies for SLC26A4-related deafness.