bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oecophyllibacter saccharovoransgen. nov. sp. nov., a bacterial symbiont of the weaver antOecophylla smaragdina
Authors: Chua Kah-Ooi , See-Too Wah-Seng , Tan Jia-Yi , Song Sze-Looi , Yong Hoi-Sen , Yin Wai-Fong , Chan Kok-Gan 
Published: February 2020

AbstractIn this study, bacterial strains Ha5T, Ta1 and Jb2 were isolated from different colonies of weaver antOecophylla smaragdina. They were distinguished as different strains based on matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15–37°C (optimum, 28–30°C) and in the presence of 0–1.5 % (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1ω7c, C16:0, C19:0ω8ccyclo, C14:0and C16:02-OH. Strains Ha5T, Ta1 and Jb2 shared highest 16S rRNA gene sequence similarity (94.56–94.63%) withNeokomagataea tanensisNBRC106556Tbut were phylogenetically closer toBombellaspp. andSaccharibacterfloricolaDSM15669T. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in familyAcetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa ofAcetobacteraceaeas they had low pairwise average nucleotide identity (≤70.7%),in silicoDNA-DNA hybridization (≤39.5%) and average amino acid identity (≤66.ü%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1 and Jb2 represent a novel species of a novel genus in familyAcetobacteraceae,for which we propose the nameOecophyllibacter saccharovoransgen. nov. sp. nov., and strain Ha5Tas the type strain.
LC/MS-QToF Profiling, Anti-Diabetic and Anti-Adipogenic potential of Divya MadhuKalp: A Novel Herbo-mineral Formulation
Authors: Balkrishna Acharya , Joshi Alpana , Das Subrata K. , Bisht Laxmi , Sakat Sachin , Sharma Vinamra , Sharma Niti , Joshi Khemraj , Verma Sudeep , Sharma Vinay K , Joshi CS 
Published: February 2020

AbstractThe incidence rate of diabetes mellitus is increasing worldwide. Herbal formulations have recently gained importance as an alternative therapeutic option in controlling diabetes without causing any side effects. In the present study, we have demonstrated maintenance of glycemic homeostasis and anti-adipogenic potential of a herbo-mineral formulation Divya MadhuKalp (DMK). Initially, we evaluated the presence of bioactive compounds in DMK using LC/MS-QToF analysis. In-vitro analysis of DMK in L6 (skeletal muscle) cells showed a significant increase in cellular glucose uptake. Similarly, a human equivalent dose of DMK significantly reduced blood glucose level in normoglycemic and oral glucose tolerance rat model. DMK extract also inhibited formation of advanced glycation end product and showed anti-α-glucosidase activity. Further analysis of DMK in 3T3 L1 pre-adipocytes demonstrated anti-adipogenic activity through reduction in intracellular lipid accumulation and triglyceride contents along with downregulation of major adipogenic transcriptional factors (PPAR-γ and C/EBPα) and, adipocytes marker genes (LPL, AP2 and adiponectin). In conclusion, DMK exhibited anti-diabetic and anti-adipogenic activities by synergistic effect of its bioactive compounds and can be considered as a potent herbo-mineral formulation for treating metabolic diseases.
A Bayesian nonparametric approach to super-resolution single-molecule localization
Authors: Gabitto Mariano I. , Marie-Nelly Herve , Pakman Ari , Pataki Andras , Darzacq Xavier , Jordan Michael I. 
Published: February 2020

We consider the problem of single-molecule identification in super-resolution microscopy. Super-resolution microscopy overcomes the diffraction limit by localizing individual fluorescing molecules in a field of view. This is particularly difficult since each individual molecule appears and disappears randomly across time and because the total number of molecules in the field of view is unknown. Additionally, data sets acquired with super-resolution microscopes can contain a large number of spurious fluorescent fluctuations caused by background noise.To address these problems, we present a Bayesian nonparametric framework capable of identifying individual emitting molecules in super-resolved time series. We tackle the localization problem in the case in which each individual molecule is already localized in space. First, we collapse observations in time and develop a fast algorithm that builds upon the Dirichlet process. Next, we augment the model to account for the temporal aspect of fluorophore photo-physics. Finally, we assess the performance of our methods with ground-truth data sets having known biological structure.
A novel voltage clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels
Authors: Gaete Pablo S. , Lillo Mauricio A. , López William , Liu Yu , Harris Andrew L. , Contreras Jorge E. 
Published: February 2020

ABSTRACTChannels that are permeable to small molecules such as ATP, in addition to atomic ions, are emerging as important regulators in health and disease. Nonetheless, mechanisms of molecular permeation and selectivity of these channels remain mostly unexplored due to the lack of quantitative methodologies. To address this need, we developed a novel two-electrode voltage clamp (TEVC)/dye uptake assay to examine the kinetics of molecular permeation of channels formed by human connexins (hCx), and the calcium homeostasis modulator (hCALHM1). We expressed hCx26, hCx30, and hCALHM1 individually inXenopus laevisoocytes. To quantify the uptake of small molecular dyes through these channels, we developed a protocol that renders oocytes translucent – thereby amenable to optical detection techniques – without affecting the functional properties of the expressed channels. To control membrane potential and to determine functional channel expression accurately, dye uptake was evaluated in conjunction with TEVC. Using this methodology, we found that: (1) CALHM1 and Cx30 hemichannels display saturable transport of molecules that could be described by Michaelis-Menten kinetics, with apparent KMand Vmax; (2) Kinetic parameters for molecular transport through CALHM1 are sensitive to voltage and extracellular calcium; (3) Significant transport of molecules occurs through CALHM1 when there are little or no ionic currents through the channels; (4) Cx mutations in the N-terminal region significantly affect kinetics of transport and permselectivity. Our results reveal that molecular flux through these channels has a rate-limiting step, that the kinetic parameters of molecular transport are sensitive to modulators of channel gating and that molecular transport and ionic currents can be differentially affected. Our methodology allows the analysis of how human mutations causing diseases affect kinetic properties and permselectivity of molecular signaling and enables the study of molecular mechanisms, including selectivity and saturability, associated with molecular transport in large-pore channels.
North-westward range expansion of the bumblebeeBombus haematurusinto Central Europe is associated with warmer winters and niche conservatism
Authors: Biella Paolo , Ćetković Aleksandar , Gogala Andrej , Neumayer Johann , Sárospataki Miklós , Šima Peter , Smetana Vladimir 
Published: February 2020

AbstractRange expansions of naturally spreading species are crucial for understanding how species interact with the environment and build their niche. Here, we studied the bumblebeeBombus haematurusKriechbaumer, 1870, a species historically distributed in the eastern Mediterranean area which has very recently started expanding northwards into Central Europe. After updating the global distribution of this species, we investigated if niche shifts took place during this range expansion between colonized and historical areas. In addition, we have explored which climatic factors have favoured the natural range expansion of the species. Our results indicated thatBombus haematurushas colonized large territories in 7 European countries outside the historical area in the period from the 1980s to 2018, a natural expansion over an area that equals the 20% of the historical distribution. In addition, this bumblebee performs generalism in flower visitation and habitat use, although a preference for forested areas emerges. The land-use associated with the species in the colonized areas is similar to the historical distribution, indicating that no major niche shifts occurred during the spread. Furthermore, the component of climate change that favoured this colonization is the warming of winter temperatures and similar warming rates took place during both overwintering and queen’s emergence phases. These findings document a case of natural range expansion due to environmental change rather than due to niche shifts, and specifically they indicate that warmer winters are playing a major role in the process of natural colonization of new areas.
Analysis of variance when both input and output sets are high-dimensional
Authors: de los Campos Gustavo , Pook Torsten , Gonzalez-Raymundez Agustin , Simianer Henner , Mias George , Vazquez Ana I. 
Published: February 2020

AbstractMotivationModern genomic data sets often involve multiple data-layers (e.g., DNA-sequence, gene expression), each of which itself can be high-dimensional. The biological processes underlying these data-layers can lead to intricate multivariate association patterns.ResultsWe propose and evaluate two methods for analysis variance when both input and output sets are high-dimensional. Our approach uses random effects models to estimate the proportion of variance of vectors in the linear span of the output set that can be explained by regression on the input set. We consider a method based on orthogonal basis (Eigen-ANOVA) and one that uses random vectors (Monte Carlo ANOVA, MC-ANOVA) in the linear span of the output set. We used simulations to assess the bias and variance of each of the methods, and to compare it with that of the Partial Least Squares (PLS)–an approach commonly used in multivariate-high-dimensional regressions. The MC-ANOVA method gave nearly unbiased estimates in all the simulation scenarios considered. Estimates produced by Eigen-ANOVA and PLS had noticeable biases. Finally, we demonstrate insight that can be obtained with the of MC-ANOVA and Eigen-ANOVA by applying these two methods to the study of multi-locus linkage disequilibrium in chicken genomes and to the assessment of inter-dependencies between gene expression, methylation and copy-number-variants in data from breast cancer tumors.AvailabilityThe Supplementary data includes an R-implementation of each of the proposed methods as well as the scripts used in simulations and in the real-data analyses.Contactgustavoc@msu.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
SARS-CoV-2 and SARS-CoV Spike-RBD Structure and Receptor Binding Comparison and Potential Implications on Neutralizing Antibody and Vaccine Development
Authors: Sun Chunyun , Chen Long , Yang Ji , Luo Chunxia , Zhang Yanjing , Li Jing , Yang Jiahui , Zhang Jie , Xie Liangzhi 
Published: February 2020

AbstractSARS-CoV-2 and SARS-CoV share a common human receptor ACE2. Protein-protein interaction structure modeling indicates that spike-RBD of the two viruses also has similar overall binding conformation and binding free energy to ACE2.In vitroassays using recombinant ACE2 proteins and ACE2 expressing cells confirmed the two coronaviruses’ similar binding affinities to ACE2. The above studies provide experimental supporting evidences and possible explanation for the high transmissibility observed in the SARS-CoV-2 outbreak. Potent ACE2-blocking SARS-CoV neutralizing antibodies showed limited cross-binding and neutralizing activities to SARS-CoV-2. ACE2-non-blocking SARS-CoV RBD antibodies, though with weaker neutralizing activities against SARS-CoV, showed positive cross-neutralizing activities to SARS-CoV-2 with an unknown mechanism. These findings suggest a trade-off between the efficacy and spectrum for therapeutic antibodies to different coronaviruses, and hence highlight the possibilities and challenges in developing broadly protecting antibodies and vaccines against SARS-CoV-2 and its future mutants.
Full cell infiltration and thick tissue formationin vivoin tailored electrospun scaffolds
Authors: Zonderland Jip , Rezzola Silvia , Gomes David , Espinosa Sandra Camarero , Lourenço Ana Henriques Ferreira , Serafim Andrada , Stancu Izabela Cristina , Koper David , Liu Hong , Habibovic Pamela , Kessler Peter , Peters Marloes , Emans Peter , Bouvy Nicole , Wieringa Paul , Moroni Lorenzo 
Published: February 2020

AbstractElectrospun (ESP) scaffolds are a promising type of tissue engineering constructs for large defects with limited depth. To form new functional tissue, the scaffolds need to be infiltrated with cells, which will deposit extracellular matrix. However, due to dense fiber packing and small pores, cell and tissue infiltration of ESP scaffolds is limited. Here, we combine two established methods, increasing fiber diameter and co-spinning sacrificial fibers, to create a porous ESP scaffold that allows robust tissue infiltration. Full cell infiltration across 2 mm thick scaffolds is seen 3 weeks after subcutaneous implantation in rats. After 6 weeks, the ESP scaffolds are almost fully filled withde novotissue. Cell infiltration and tissue formationin vivoin this thickness has not been previously achieved. In addition, we propose a novel method forin vitrocell seeding to improve cell infiltration and a model to study 3D migration through a fibrous mesh. This easy approach to facilitate cell infiltration further improves previous efforts and could greatly aid tissue engineering approaches utilizing ESP scaffolds.Statement of significanceElectrospinning creates highly porous scaffolds with nano- to micrometer sized fibers and are a promising candidate for a variety of tissue engineering applications. However, smaller fibers also create small pores which are difficult for cells to penetrate, restricting cells to the top layers of the scaffolds. Here, we have improved the cell infiltration by optimizing fiber diameter and by co-spinning a sacrificial polymer. We developed novel culture technique that can be used to improve cell seeding and to study cytokine driven 3D migration through fibrous meshes. After subcutaneous implantation, infiltration of tissue and cells was observed up to throughout up to 2 mm thick scaffolds. This depth of infiltrationin vivohad not yet been reported for electrospun scaffolds. The scaffolds we present here can be used forin vitrostudies of migration, and for tissue engineering in defects with a large surface area and limited depth.
Circadian Rhythm Analysis Using Wearable Device Data: A Novel Penalized Machine Learning Approach
Authors: Li Xinyue , Kane Michael , Zhang Yunting , Sun Wanqi , Song Yuanjin , Dong Shumei , Lin Qingmin , Zhu Qi , Jiang Fan , Zhao Hongyu 
Published: February 2020

AbstractBackgroundWearable devices have been widely used in clinical studies to study daily activity patterns, but the analysis remains the major obstacle for researchers.Study ObjectiveThis study proposed a novel method to characterize sleep-activity rhythms using actigraphy and further used it to describe early childhood daily rhythm formation and examine its association with physical development.MethodsWe developed a machine learning-based Penalized Multi-band Learning (PML) algorithm to sequentially infer dominant periodicities based on Fast Fourier Transform (FFT) and further characterize daily rhythms. We implemented and applied the algorithm to Actiwatch data collected from a 262 healthy infant cohort at 6-, 12-, 18-, and 24-month old, with 159, 101, 111, and 141 subjects participating at each time point respectively. Autocorrelation analysis and Fisher’s test for harmonic analysis with Bonferroni correction were applied to compare with PML. The association between activity rhythm features and early childhood motor development, assessed by Peabody Developmental Motor Scales-Second Edition (PDMS-2), was studied through linear regression.ResultsPML results showed that 1-day periodicity is most dominant at 6 and 12 months, whereas 1-day, 1/3-day, and 1/2-day periodicities are most dominant at 18 and 24 months. These periodicities are all significant in Fisher’s test, with 1/4-day periodicity also significant at 12 months. Autocorrelation effectively detected 1-day periodicity but not others. At 6 months, PDMS-2 is associated with assessment seasons. At 12 months, PDMS-2 is associated with seasons and FFT signals at 1/3-day periodicity (P<.001) and 1/2-day periodicity (P=.04). In particular, subcategories of stationary, locomotion, and gross motor are associated with FFT signals at 1/3-day periodicity (P<.001).ConclusionsThe proposed PML algorithm can effectively conduct circadian rhythm analysis using time-series wearable device data. Application of the method effectively characterized sleep-wake rhythm development and identified the association between daily rhythm formation and motor development during early childhood.
Evolution of multicellularity by collective integration of spatial information
Authors: Colizzi Enrico Sandro , Vroomans Renske M.A. , Merks Roeland M.H. 
Published: February 2020

AbstractAt the origin of multicellularity, cells may have evolved aggregation in response to predation, for functional specialisation or to allow large-scale integration of environmental cues. These group-level properties emerged from the interactions between cells in a group, and determined the selection pressures experienced by these cells.We investigate the evolution of multicellularity with an evolutionary model where cells search for resources by chemotaxis in a shallow, noisy gradient. Cells can evolve their adhesion to others in a periodically changing environment, where a cell’s fitness solely depends on its distance from the gradient source.We show that multicellular aggregates evolve because they perform chemo-taxis more efficiently than single cells. Only when the environment changes too frequently, a unicellular state evolves which relies on cell dispersal. Both strategies prevent the invasion of the other through interference competition, creating evolutionary bi-stability. Therefore, collective behaviour can be an emergent selective driver for undifferentiated multicellularity.
Control of Systemic Iron Homeostasis by the 3’ Iron-Responsive Element of Divalent Metal Transporter 1 in Mice
Authors: Tybl Elisabeth , Gunshin Hiromi , Gupta Sanjay , Barrientos Tomasa , Bonadonna Michael , Nos Ferran Celma , Palais Gael , Karim Zoubida , Sanchez Mayka , Andrews Nancy C. , Galy Bruno 
Published: February 2020

AbstractDivalent metal transporter 1 (DMT1) is essential for dietary iron assimilation and erythroid iron acquisition. The 3’ untranslated region of the murine DMT1 mRNA contains an iron responsive element (IRE) that is conserved in humans but whose functional role remains unclear. We generated and analyzed mice with targeted disruption of the DMT1 3’IRE. These animals display hypoferremia during the suckling period, associated with a reduction of DMT1 mRNA and protein in the intestine. In contrast, adult mice exhibit hyperferremia, accompanied by enlargement of hepatic and splenic iron stores. Intriguingly, disruption of the DMT1 3’IRE in adult animals augments intestinal DMT1 expression, in part due to increased mRNA translation. Hence, during postnatal growth, the DMT1 3’IRE promotes intestinal DMT1 expression and secures iron sufficiency; in adulthood, it suppresses DMT1 and prevents systemic iron loading. This work demonstrates that the 3’IRE of DMT1 plays a role in the control of DMT1 expression and systemic iron homeostasis, and reveals an age-dependent switch in its activity.Key pointsTargeted mutagenesis of the 3’IRE of DMT1 in mice reveals its importance for maintenance of systemic iron homeostasis.The 3’IRE stimulates intestinal DMT1 expression and prevents hypoferremia during early life, but exerts opposite effects in adulthood
Tasting the differences: microbiota analysis of different insect-based novel food
Authors: Frigerio Jessica , Agostinetto Giulia , Galimberti Andrea , De Mattia Fabrizio , Labra Massimo , Bruno Antonia 
Published: February 2020

AbstractTraceability, quality and safety of edible insects are important both for the producers and the consumers. Today, alongside the burst of edible insects in western countries, we are facing a gap of knowledge of insect microbiota associated with the microbial ecosystems of insect-based products. Recent studies suggest that the insect microbiota can vary between insect species and that can be shaped by additional factors, such as rearing conditions. Also, the production processes of raw materials (i.e. insect flour) into final food products can affect the insect microbiota too. This has consequences for the evaluation of food safety and food traceability. In this context, High-Throughput DNA Sequencing (HTS) techniques can give insight into the carryover of insect microbiota into final food products. In this study, we investigated the microbiota composition of insect-based commercial food products, applying HTS techniques coupled with bioinformatic analysis. The aim of this work was to analyse the microbiota variability of different categories of insect-based products made ofA. domesticus(house cricket),T. molitor(mealworm beetle), andA. diaperinus(lesser mealworm or litter beetle), including commercial raw materials and processed food items, purchased via e-commerce from different companies. Our data revealed that samples cluster per insect species based on microbiota profile and preliminary results suggested that a small number of prevalent bacteria formed a “core microbiota” characterizing the products depending on the insect, suggesting that a resident microbiota is conserved. This microbial signature can be recognized despite the different food processing levels, rearing conditions selling companies. We showed that differences exist when comparing raw vs processed food made of the same insect, or similar products produced by different companies as well, laying the groundwork for further analyses. These results support the application of HTS analysis for studying the composition of processed insect food in a wider perspective, for food traceability and food quality control.
Comprehensive cell surface proteomics defines markers of classical, intermediate and non-classical monocytes
Authors: Ravenhill Benjamin J. , Soday Lior , Houghton Jack , Antrobus Robin , Weekes Michael P. 
Published: February 2020

AbstractMonocytes are a critical component of the cellular innate immune system, and can be subdivided into classical, intermediate and non-classical subsets on the basis of surface CD14 and CD16 expression. Classical monocytes play the canonical role of phagocytosis, and account for the majority of circulating cells. Intermediate and non-classical cells are known to exhibit varying levels of phagocytosis and cytokine secretion, and are differentially expanded in certain pathological states. Characterisation of cell surface proteins expressed by each subset is informative not only to improve understanding of phenotype, but may also provide biological insights into function. Here we use highly multiplexed Tandem-Mass-Tag (TMT)-based mass spectrometry with selective cell surface biotinylation to characterise the classical monocyte surface proteome, then interrogate the phenotypic differences between each monocyte subset to identify novel protein markers.