bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of ESBL-producingEscherichia colidynamics in calf fattening farms: a modelling study
Authors: Bastard Jonathan , Haenni Marisa , Gay Emilie , Glaser Philippe , Madec Jean-Yves , Temime Laura , Opatowski Lulla 
Published: September 2020

AbstractThe contribution of bacteria in livestock to the global burden of antimicrobial resistance raises concerns worldwide. However, the dynamics of selection and diffusion of antimicrobial resistance in farm animals are not fully understood. Here, we used veal calf fattening farms as a model system, as they are a known reservoir of Extended Spectrum β-Lactamase-producingEscherichia coli(ESBL-EC). Longitudinal data of ESBL-EC carriage and antimicrobial use (AMU) were collected from three veal calf farms during the entire fattening process. We developed 18 agent-based mechanistic models to assess different hypotheses regarding the main drivers of ESBL-EC dynamics in calves. The models were independently fitted to the longitudinal data using Markov Chain Monte Carlo and the best model was selected. Within-farm transmission between individuals and sporadic events of contamination were found to drive ESBL-EC dynamics on farms. In the absence of AMU, the median carriage duration of ESBL-EC was estimated to be 19.6 days (95% credible interval: [12.7; 33.3]). In the best model, AMU was found to influence ESBL-EC dynamics, by affecting ESBL-EC clearance rather than acquisition. This effect of AMU was estimated to decrease gradually after the end of exposure and to disappear after 62.5 days [50.0; 76.9]. Moreover, using a simulation study, we quantified the efficacy of ESBL-EC mitigation strategies. Decreasing ESBL-EC prevalence by 50% on arrival at the fattening farm reduced prevalence at slaughter age by 33.3%. Completely eliminating the use of selective antibiotics had a strong effect on average ESBL-EC prevalence (relative reduction of 79.6%), but the effect was mild if this use was only decreased by 50% compared to baseline (relative reduction of 3.7%).
Flexible RSV prefusogenic fusion glycoprotein exposes multiple neutralizing epitopes that may collectively contribute to protective immunity
Authors: Patel Nita , Tian Jing-Hui , Flores Rhonda , Jacobson Kelsey , Walker Michelle , Portnoff Alyse , Gueber-Xabier Mimi , Massare Michael J. , Glenn Greg , Ellingsworth Larry , Smith Gale 
Published: September 2020

AbstractHuman respiratory syncytial virus (RSV) is a significant cause of lower respiratory tract infection in infants, young children, and older adults. There is no licensed vaccine and prophylactic treatment options are limited and not widely available in developing countries with the greatest disease burden. The RSV fusion (F) glycoprotein is a primary target of host immunity and thus a major focus for vaccine development. The native F glycoprotein structure is flexible and undergoes significant rearrangements from the metastable prefusion to a stable postfusion structure with neutralizing epitopes on intermediate structures. We hypothesize trimeric vaccine strategies that recapitulate the breathable F quaternary structure, and provide accessibility of B-cells to epitopes on intermediate conformations, may collectively contribute to protective immunity, while ridge prefusion F structures restrict access to key protective epitopes. To test this hypothesis, we used the near full-length native prefusogenic F as a backbone to construct three prefusion F variants with substitutions in the hydrophobic head cavity: 1) disulfide bond double mutant (DS), 2) space filling hydrophobic amino acid substitutions (Cav1), and 3) DS plus Cav1 substitutions (DS-Cav1). In this study, we compared the immunogenicity of prefusogenic F to the immunogenicity of the prefusion F variants in two animal models. Native prefusogenic F was significantly more immunogenic producing high titer antibodies to prefusogenic, prefusion, and postfusion F structures compared to animals immunized with prefusion F DS or DS-Cav1. Importantly, native prefusogenic F elicited antibodies that targeted neutralizing epitopes including prefusion-specific site zero (Ø) and V as well as conformation-independent neutralizing sites II and IV. Immunization with prefusion F DS or DS-Cav1 elicited antibodies primarily targeting antigenic sites Ø and V with little or no detectable antibodies to other key neutralizing sites. Animals immunized with native prefusogenic F also had significantly higher neutralizing antibodies that cross-neutralized RSV A and B subtypes while immunization with DS or DS-Cav1 elicited neutralizing antibodies primarily to the A subtype. We conclude that breathable trimeric vaccines that closely mimic the native F-structure, and incorporate strategies for B-cell accessibility to protective epitopes, are important considerations for vaccine design. F structures locked in a single conformation restrict B-cell access to neutralizing epitopes that may collectively contribute to destabilizing F-trimers important for broad protection. These results also have implications for vaccine strategies targeting other type 1 integral membrane proteins.
Computationally Grafting an IgE Epitope onto a Scaffold: Implications for a Pan Anti-Allergy Vaccine Design
Authors: Sabban Sari 
Published: September 2020

AbstractAllergy is becoming an intensifying disease among the world population, particularly in the developed world. Once allergy develops, sufferers are permanently trapped in a hyper-immune response that makes them sensitive to innocuous substances, such as the protein cupin in peanuts. The immune pathway concerned with developing allergy is the Th2immune pathway where the IgE antibody (targeting innocuous substances) binds to its FcεRI receptor on Mast and Basophil cells. Currently, there is not a permanent treatment for allergies. This paper discusses a strategy and a protocol that could disrupt the binding between the antibody and its receptor for a potential permanent treatment. Ten proteins were computationally designed to display a human IgE motif very close in proximity to the IgE antibodies’s FcεRI receptor’s binding site in an effort for these proteins to be used as a vaccine against our own IgE antibody. The motif of interest was the FG motif and it was excised and grafted onto aStaphylococcus aureusprotein (PDB ID 1YN3). The new structures (motif + scaffold) had their sequences re-designed around the motif to find an amino acid sequence that would fold to the designed structures correctly. These ten computationally designed proteins showed successful folding when simulated using Rosetta’s AbinitioRelax folding simulation and the IgE epitope was clearly displayed in its native three-dimensional structure in all of them. These designed proteins have the potential to be used as a pan anti-allergy vaccine by guiding the immune system towards developing antibodies against the body’s own IgE antibody, thus neutralising it, and presumably permanently shutting down a major aspect of the Th2immune pathway. This work employedin silicobased methods for designing the proteins and did not include any experimental verifications.
Stationary Ca2+nanodomains in the presence of buffers with two binding sites
Authors: Chen Y. , Matveev V. 
Published: September 2020

ABSTRACTWe examine closed-form approximations for the equilibrium Ca2+concentration near a point Ca2+source representing a Ca2+channel, in the presence of a mobile Ca2+buffer with 2:1 Ca2+binding stoichiometry. We consider buffers with two Ca2+binding sites activated in tandem and possessing distinct binding affinities and kinetics. This allows to model the impact on Ca2+nanodomains of realistic endogenous Ca2+buffers characterized by cooperative Ca2+binding, such as calretinin. The approximations we present involve a combination or rational and exponential functions, whose parameters are constrained using the series interpolation method that we recently introduced for the case of 1:1 Ca2+buffers. We conduct extensive parameter sensitivity analysis and show that the obtained closed-form approximations achieve reasonable qualitative accuracy for a wide range of buffer’s Ca2+binding properties and other relevant model parameters. In particular, the accuracy of the newly derived approximants exceeds that of the rapid buffering approximation in large portions of the relevant parameter space.STATEMENT OF SIGNIFICANCEClosed-form approximations describing equilibrium distribution of Ca2+in the vicinity of an open Ca2+channel proved useful for the modeling of local Ca2+signals underlying secretory vesicle exocytosis, muscle contraction and other cell processes. Such approximations provide an efficient method for estimating Ca2+and buffer concentrations without computationally expensive numerical simulations. However, while most biological buffers have multiple Ca2+binding sites, much of prior modeling work considered Ca2+dynamics in the presence of Ca2+buffers with a single Ca2+binding site. Here we extend modeling work on equilibrium Ca2+nanodomains to the case of Ca2+buffers with two binding sites, allowing to gain deeper insight into the impact of more realistic Ca2+buffers, including cooperative buffers, on cell Ca2+dynamics.
High fidelity reconstitution of stress granules and nucleoli in mammalian cellular lysate
Authors: Freibaum Brian D. , Messing James , Yang Peiguo , Kim Hong Joo , Taylor J. Paul 
Published: September 2020

AbstractLiquid-liquid phase separation (LLPS) is an important mechanism of intracellular organization that underlies the assembly of a variety of distinct RNP granules. Fundamental biophysical principles governing LLPS during RNP granule assembly have been revealed by simple in vitro systems consisting of several components, but these systems have limitations when studying the biology of complex, multicomponent RNP granules. Visualization of RNP granules in live cells has validated key principles revealed by simple in vitro systems, but this approach presents difficulties for interrogating biophysical features of RNP granules and provides limited ability to manipulate protein, nucleic acid, or small molecule concentrations. Here we introduce a system that builds upon recent insights into the mechanisms underlying RNP granule assembly and permits high fidelity reconstitution of stress granules and the granular component of nucleoli in mammalian cellular lysate. This system fills the gap between simple in vitro systems and live cells, and allows for a wide variety of studies of membraneless organelles.
High yield preparation of outer-membrane protein efflux pumps byin vitrorefolding is concentration dependent
Authors: Budiardjo S. Jimmy , Ikujuni Ayotunde Paul , Firlar Emre , Cordova Andrés , Kaelber Jason T. , Slusky Joanna S.G. 
Published: September 2020

AbstractOverexpression of tripartite efflux pump systems in gram-negative bacteria are a principal component of antibiotic resistance. High-yield purification of the outer membrane component of these systems will enable biochemical and structural interrogation of their mechanisms of action and allow testing of compounds that target them. However, preparation of these proteins is typically hampered by low yields requiring laborious large-scale efforts. If refolding conditions can be found, refolding these proteins from inclusion bodies can lead to increased yields as compared to membrane isolations. Here, we develop a concentration-dependent folding protocol for refolding TolC, the outer membrane component of the antibiotic efflux pump fromEscherichia coli. We show that by our method of re-folding, homotrimeric TolC remains folded in SDS-PAGE, retains binding to an endogenous ligand, and recapitulates the known crystal structure by single particle cryoEM analysis. We find that a key factor in successful re-folding is a concentration dependence of TolC oligomerization. We extended the scheme to CmeC, a homologous protein fromCampylobacter jejuni, and find that concentration-dependent oligomerization is a general feature of these systems. Because outer-membrane efflux pump components are ubiquitous across gram-negative species, we anticipate that incorporating a concentration step in re-folding protocols will promote correct refolding allowing for reliable, high-yield preparation of this family of proteins.
Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors
Authors: Olgun Gulden , Tastan Oznur 
Published: September 2020

AbstractThe dysregulation of long non-coding RNAs’ (lncRNAs) expressions has been implicated in cancer. Since most of the lncRNAs’ are not functionally characterized well, investigating the set of perturbed lncRNAs are is challenging. Existing methods that inspect lncRNAs functionally rely on the co-expressed coding genes, which are far better characterized functionally. LncRNAs can be known to act as transcriptional regulators; they may activate or repress the neighborhood’s coding genes on the genome. Based on this, in this work, we aim to analyze the deregulated lncRNAs in cancer by taking into account their ability to regulate nearby loci on the genome. We perform functional analysis on differentially expressed lncRNAs for 28 different cancers considering their adjacent coding genes. We identify that some deregulated lncRNAs are cancer-specific, but a substantial number of lncRNAs are shared across cancers. Next, we assess the similarities of the cancer types based on the functional enrichment of the deregulated lncRNA sets. We find some cancers are very similar in the functions and biological processes related to the deregulated lncRNAs. We observe that some of the cancers for which we find similarity can be linked through primary, metastatic site relations. We investigate the similarity of enriched functional terms for the deregulated lncRNAs and the mRNAs. We further assess the enriched functions’ similarity to the functions and processes that the known cancer driver genes take place. We believe that our methodology help to understand the impact of the lncRNAs in cancer functionally.
Structural characterization and evolutionary analyses of theCoccidioides immitisandCoccidioides posadasiimitochondrial genomes
Authors: de Melo Teixeira Marcus , Lang B. Franz , Matute Daniel R. , Stajich Jason E. , Barker Bridget 
Published: September 2020

AbstractFungal mitochondrial genomes encode for genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and these genes have been used as molecular markers for population genetics studies.Coccidioides immitisandC. posadasiiare endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, almost one hundredCoccidioidesstrains have been sequenced. The focus of these studies has been exclusively to infer patterns of variation of nuclear genomes (nucDNA). However, their mitochondrial genomes (mtDNA) have not been studied. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains ofC. posadasiiandC. immitis, as well as assess population variation among 77 published genomes. The circular-mapping mtDNA molecules are 68.2 Kb inC. immitisand 75.1 Kb inC. posadasii. We identified the fourteen mitochondrial protein-coding genes common to most fungal mitochondria, including genes encoding the small and large ribosomal RNAs (rnsandrnl), the RNA subunit of RNAse P (rnpB), and 26 tRNAs organized in polycistronic transcription units, which are mostly syntenic across different populations and species ofCoccidioides. BothCoccidioidesspecies are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparison of the mtDNA and nucDNA genomes shows discordance, possibly due to differences in patterns of inheritance. In summary, this work represents the first complete assessment of mitochondrial genomes among several isolates of both species ofCoccidioides, and provides a foundation for future functional work.
Tracking strains predicts personal microbiomes and reveals recent adaptive evolution
Authors: Zhao Shijie , Dai Chengzhen L. , Evans Ethan D. , Lu Ziyu , Alm Eric J. 
Published: September 2020

AbstractAn individual’s microbiome consists of a diverse set of bacterial strains that encode rich information on its colonization and evolutionary history. Here, we introduce a versatile and straightforward reference-based strain tracking approach (StrainTrack) that determines whether distinct metagenomes carry closely-related strains based on gene presence and absence profiles. We show that StrainTrack can predict whether two metagenomes originate from the same donor via counting the number of species sharing closely-related strains, achieving >96% specificity, and ∼100% sensitivity. When applied to the metagenomes of adult twins in the TwinsUK registry, we identify six cases of closely-related strains carried by both twins, potentially over decades of colonization.
Controlling T cells shape, mechanics and activation by micropatterning
Authors: Sadoun A. , Biarnes-Pelicot M. , Ghesquiere-Dierickx L. , Wu A. , Théodoly O. , Limozin L. , Hamon Y. , Puech P.-H. 
Published: September 2020

AbstractWe designed a strategy, based on a careful examination of the activation capabilities of proteins and antibodies used as substrates for adhering T cells, coupled to protein microstamping. This allowed us to control at the same time the position, shape, mechanics and activation state of T cells. Once adhered on shaped patterns we examined the capacities of T cells to be activated with soluble aCD3, in comparison to T cells adhered to a continuously decorated substrate with the same density of ligands. We show that, in our hand, adhering onto an anti CD45 (aCD45) antibody decorated surface is not affecting T cell calcium fluxes, even adhered on variable size micro-patterns. We further demonstrate this by expressing MEGF10 as a non immune adhesion receptor in T cells to obtain the very same spreading area on PLL substrates and Young modulus than immobilized cells on aCD45, while retaining similar activation capabilities using soluble aCD3 or through model APC contacts. We propose that our system is a way to test activation or anergy of T cells with defined adhesion and mechanical characteristics, and may allow to dissect fine details of these mechanisms since it allows to observe homogenised populations in standardized T cell activation assays.
The evolution of phenotypic plasticity in response to temperature stress
Authors: Mallard Francois , Nolte Viola , Schlötterer Christian 
Published: September 2020

AbstractPhenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to environmental variation. The importance of phenotypic plasticity in natural populations and its contribution to phenotypic evolution during rapid environmental change is widely debated. Here, we show that thermal plasticity of gene expression in natural populations is a key component of its adaptation: evolution to novel thermal environments increases ancestral plasticity rather than mean genetic expression. We determined the evolution of plasticity in gene expression by conducting laboratory natural selection on aDrosophila simulanspopulation in hot and cold environments. After more than 60 generations in the hot environment, 325 genes evolved a change in plasticity relative to the natural ancestral population. Plasticity increased in 75% of these genes, which were strongly enriched for several well-defined functional categories (e.g. chitin metabolism, glycolysis and oxidative phosphorylation). Furthermore, we show that plasticity in gene expression of populations exposed to different temperatures is rather similar across species. We conclude that most of the ancestral plasticity can evolve further in more extreme environments.
How do food consumption motivations and emotions affect the experiential values and well-being of foodies?
Authors: Chang Janet , Morrison Alastair M. , Lin Sean Hsin-Hung , Ho Ching-Yen 
Published: September 2020

PurposeTravellers who love to try different foods and who frequently follow up on food-related news and topics consider themselves to be “foodies”. The main aim of this research was to identify the relationships among food consumption motivations, experiential values and well-being of foodies.Design/methodology/approachA questionnaire survey was distributed to foodies from the Chinese mainland, Hong Kong and Macao in March–May 2019 who were aged 18 and above and who had visited Taiwan within the prior two years. Some 480 valid responses were received based on intercepts at airports and the data, based on a conceptual model, were analysed through structural equation modelling (SEM).FindingsThree paths among the key variables showed significant and positive relationships. Additionally, the mediating effect of food experiential values on emotions and well-being was identified.Research limitations/implicationsThe findings provide insights for food and hospitality scholars and the related literature since “foodie” is a rather new concept that is lacking in sufficient empirical and conceptual research. The research examines the relationships among experiential values, motivations and emotions and their influences on the well-being of foodies. In past studies on food consumption motivations and emotions, food experiential values were not included as a variable of potential influence. The research subjects were confined to foodies from the Chinese mainland (including Hong Kong and Macao) who were in Taiwan. Hence, the generalisation based on the sample may be limited.Practical implicationsThis research produces useful information on the behaviour of Chinese foodies when they are travelling. Preparers of food and beverages and tourism retailers should supply food that represents local cultural characteristics and design relevant local food souvenirs with the appropriate packaging.Social implicationsCommunities need to realise that not all visitors are alike and that some have a deeper interest in local foods and their historical and cultural roots.Originality/valueAlthough numerous studies on the behaviours of Chinese tourists have been conducted, the research on their food consumption characteristics is limited. To date, no empirical studies have examined the relationships among foodies, food consumption motivations, food experiential values, emotions and well-being of mainland Chinese tourists, which is a knowledge gap in understanding this important market segment.
Learning solutions to a Cauchy problem for the modified Helmholtz equations using LS-SVM
Authors: Wu Ziku , Han Xiaoming , Li GuoFeng 
Published: September 2020

Purpose
The purpose of this paper is to develop a mesh-free algorithm based on the least square support vector machines method for numerical simulation of the modified Helmholtz equations.

Design/methodology/approach
The proposed method deals with a Cauchy problem for the modified Helmholtz equations. The algorithm converts the problem into a quadratic programming. It can be divided into three steps. First, some training points are allocated. Then, an approximate function is constructed. Finally, the shape parameters are estimated.

Findings
The proposed method's stability is discussed. Numerical experiments are conducted to check the efficiency of the algorithm. The proposed method is found to feasible for the ill-posed problems of the modified Helmholtz equations.

Originality/value
The originality lies in that the proposed method is applied to solve the modified Helmholtz equations for the first time, and the expected results are obtained.