bluuebunny/crossref_metadata_2025 huggingface dataset:
DAF-18 is required for the age-dependent increase in DAF-16 activity inCaenorhabditis elegans
Authors: Carrasco Kali , Youngman Matthew J.
Published: November 2020

The insulin/insulin-like growth factor signaling (IIS) pathway modulates growth, survival, and lifespan by regulating FOXO transcription factors. InCaenorhabditis elegans, IIS maintains DAF-16/FOXO in an inactive state unless animals are challenged by environmental stress. Recent evidence suggests that DAF-16 becomes activated as part of normal aging inC. elegans, yet the regulatory module responsible for this phenomenon is largely undefined. Embedded within IIS is phospholipid signaling in which PIP3produced by the PI3 kinase AGE-1 is an upstream event in DAF-16 inhibition. Countering AGE-1 is DAF-18, an ortholog of human PTEN phosphatase that dephosphorylates PIP3. Although it is required for normal lifespan inC. elegans, functional characterization of DAF-18 has primarily focused on its roles during development in the germline and neurons. In this study we asked whether DAF-18 plays a role in the age-dependent activation of DAF-16, and specifically in DAF-16-mediated immunity. Our data show that DAF-18 is expressed in multiple tissues during adulthood. We found that DAF-18 contributes to host defense in adult animals by functioning in the neurons and intestine, likely working through DAF-16 which acts in those same tissues to confer immunity. Supporting this possibility, DAF-18 was required for increased DAF-16 transcriptional activity during aging. Post-translational modifications including ubiquitination and sumoylation appear to be required for the function of DAF-18 during aging inC. elegans, indicating that strategies to modulate PTEN activity are evolutionarily conserved. Our results establish an important role for DAF-18 later in life and imply that it is a critical component of a neuroendocrine signaling circuit that governs the dynamic activity of DAF-16.
Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate
Authors: Brun Juliane , Vasiljevic Snežana , Gangadharan Bevin , Hensen Mario , Chandran Anu V. , Hill Michelle L. , Kiappes J.L. , Dwek Raymond A. , Alonzi Dominic S. , Struwe Weston B. , Zitzmann Nicole
Published: November 2020

Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of Nov 15, 2020 has claimed 1,319,946 lives worldwide. Vaccine development focuses on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralisation. Immunogen integrity is therefore important for glycoprotein-based vaccine candidates. Here we show how site-specific glycosylation differs between virus-derived spikes and spike proteins derived from a viral vectored SARS-CoV-2 vaccine candidate. We show that their distinctive cellular secretion pathways result in different protein glycosylation and secretion patterns, which may have implications for the resulting immune response and future vaccine design.
AStreptomyces venezuelaeCell-Free Toolkit for Synthetic Biology
Authors: Moore Simon J , Lai Hung-En , Chee Soo-Mei , Toh Ming , Coode Seth , Capel Patrick , Corre Christophe , de los Santos Emmanuel LC , Freemont Paul S
Published: November 2020

Prokaryotic cell-free coupled transcription-translation (TX-TL) systems are emerging as a powerful tool to examine natural product biosynthetic pathways in a test-tube. The key advantages of this approach are the reduced experimental timescales and controlled reaction conditions. In order to realise this potential, specialised cell-free systems in organisms enriched for biosynthetic gene clusters, with strong protein production and well-characterised synthetic biology tools, is essential. TheStreptomycesgenus is a major source of natural products. To study enzymes and pathways fromStreptomyces, we originally developed a homologousStreptomycescell-free system to provide a native protein folding environment, a high G+C (%) tRNA pool and an active background metabolism. However, our initial yields were low (36 μg/mL) and showed a high level of batch-to-batch variation. Here, we present an updated high-yield and robustStreptomycesTX-TL protocol, reaching up to yields of 266 μg/mL of expressed recombinant protein. To complement this, we rapidly characterise a range of DNA parts with different reporters, express high G+C (%) biosynthetic genes and demonstrate an initial proof of concept for combined transcription, translation and biosynthesis ofStreptomycesmetabolic pathways in a single ‘one-pot’ reaction.
Competition within low-density bacterial populations as an unexpected factor regulating carbon decomposition in bulk soil
Authors: Coche Alexandre , Babey Tristan , Rapaport Alain , Vieublé Gonod Laure , Garnier Patricia , Nunan Naoise , de Dreuzy Jean-Raynald
Published: November 2020

Bacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the access bacteria have to their substrate. The influence of bacterial traits on this control has, however, received little attention. Here, we develop a bioreactive transport model to screen the interactive impacts of dispersion and bacterial traits on mineralization. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the initial substrate location induced a significant increase in 2,4-D mineralization, revealing the existence of a regulation of mineralization by the bacterial decomposer density, in addition to the dilution of substrate. This regulation of degradation by density becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (a common feature of oligotrophs). The model output suggests that the distance between bacteria adapted to oligotrophic environments is a stronger regulator of degradation than the distance between these bacteria and the substrate initial location. Such oligotrophs, commonly found in soils, compete with each other for substrate even at remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, provide a more versatile representation than the substrate-dependent Monod model in these conditions. In view of their strong interactions, bioreactive and transport processes cannot be handled independently but should be integrated, in particular when reactive processes of interest are carried out by oligotrophs.

Abstract Figure

Highlights

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The impact of spatial distributions on decomposition depends on bacterial traits

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Decomposition can be reduced by competition between bacteria even at low densities

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Bacterial density regulation counterbalances substrate accessibility regulation

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Regulation of decomposition by bacterial density is more acute for oligotrophs
Extracellular Matrix Remodeling Associated with Bleomycin-Induced Lung Injury Supports Pericyte-To-Myofibroblast Transition
Authors: Hannan Riley T. , Miller Andrew E. , Hung Ruei-Chun , Sano Catherine , Peirce Shayn M. , Barker Thomas H.
Published: November 2020

Of the many origins of pulmonary myofibroblasts, microvascular pericytes are a known source. Prior literature has established the ability of pericytes to transition into myofibroblasts, but provide limited insight into molecular cues that drive this process during lung injury repair and fibrosis. Fibronectin and RGD-binding integrins have long been considered pro-fibrotic factors in myofibroblast biology, and here we test the hypothesis that these known myofibroblast cues coordinate pericyte-to-myofibroblast transitions. Specifically, we hypothesized that αvβ3 integrin engagement on fibronectin induces pericyte transition into myofibroblastic phenotypes in the murine bleomycin lung injury model. Myosin Heavy Chain 11 (Myh11)-CreERT2 lineage tracing in transgenic mice allows identification of cells of pericyte origin and provides a robust tool for isolating pericytes from tissues for further evaluation. We used this murine model to track and characterize pericyte behaviors during tissue repair. The majority of Myh11 lineage-positive cells are positive for the pericyte surface markers, PDGFRβ (55%) and CD146 (69%), and display typical pericyte morphology with spatial apposition to microvascular networks. After intratracheal bleomycin treatment of mice, Myh11 lineage-positive cells showed significantly increased contractile and secretory markers, as well as αv integrin expression. According to RNASeq measurements, many disease and tissue-remodeling genesets were upregulated in Myh11 lineage-positive cells in response to bleomycin-induced lung injury. In vitro, blocking αvβ3 binding through cyclo-RGDfK prevented expression of the myofibroblastic marker αSMA relative to controls. In response to RGD-containing provisional matrix proteins present in lung injury, pericytes may alter their integrin profile. This altered matrix-integrin axis contributes to pericyte-to-myofibroblastic transition and represents a possible therapeutic target for limiting the myofibroblastic burden in lung fibrosis.

Highlights

Pericyte lineage model enables study of transdifferentiating pericytes

High dimensional flow cytometry used to characterize pulmonary stromal cells

Pulmonary pericytes express matrix-remodeling genes and proteins in lung injury

Myofibroblasts derived from pericytes have active αvβ3 integrin

In vitro assay reveals necessity of RGD for pericyte transdifferentiation
Divergent profiles of fentanyl withdrawal and associated pain in mice and rats
Authors: Uddin Olivia , Jenne Carleigh , Fox Megan E. , Arakawa Keiko , Keller Asaf , Cramer Nathan
Published: November 2020

Opioid abuse has devastating effects on patients, their families, and society. Withdrawal symptoms are severely unpleasant, prolonged, and frequently hinder recovery or lead to relapse. The sharp increase in abuse and overdoses arising from the illicit use of potent and rapidly-acting synthetic opioids, such as fentanyl, highlights the urgency of understanding the withdrawal mechanisms related to these drugs. Progress is impeded by inconsistent reports on opioid withdrawal in different preclinical models. Here, using rats and mice of both sexes, we quantified withdrawal behaviors during spontaneous and naloxone-precipitated withdrawal, following two weeks of intermittent fentanyl exposure. We found that both mice and rats lost weight during exposure and showed increased signs of distress during spontaneous and naloxone precipitated withdrawal. However, these species differed in their expression of withdrawal associated pain, a key contributor to relapse in humans. Spontaneous or ongoing pain was preferentially expressed in rats in both withdrawal conditions, while no change was observed in mice. In contrast, withdrawal associated thermal hyperalgesia was found only in mice. These data suggest that rats and mice diverge in how they experience withdrawal and which aspects of the human condition they most accurately model. These differences highlight each species’ strengths as model systems and can inform experimental design in studies of opioid withdrawal.
MED1 is a lipogenesis coactivator required for postnatal adipose expansion
Authors: Jang Younghoon , Park Young-Kwon , Lee Ji-Eun , Tran Nhien , Gavrilova Oksana , Ge Kai
Published: November 2020

MED1 often serves as a surrogate of the general transcription coactivator complex Mediator for identifying active enhancers. MED1 is required for phenotypic conversion of fibroblasts to adipocytes in vitro but its role in adipose development and expansion in vivo has not been reported. Here we report that MED1 is dispensable for adipose development in mice. Instead, MED1 is required for postnatal adipose expansion and the induction of de novo lipogenesis (DNL) genes after pups switch diet from high-fat maternal milk to carbohydrate-based chow. During adipogenesis, MED1 is dispensable for induction of lineage-determining transcription factors (TFs) PPARγ and C/EBPα but is required for lipid accumulation in the late phase of differentiation. Mechanistically, MED1 controls the induction of DNL genes by facilitating lipogenic TF ChREBP-dependent recruitment of Mediator to active enhancers. Together, our findings identify a cell- and gene-specific regulatory role of MED1 as a lipogenesis coactivator required for postnatal adipose expansion.
Genetic manipulation of the Brassicaceae smut fungusThecaphora thlaspeos
Authors: Plücker Lesley , Bösch Kristin , Geißl Lea , Hoffmann Philipp , Göhre Vera
Published: November 2020

Investigation of plant-microbe interactions greatly benefits from genetically tractable partners to address molecularly the virulence and defense mechanisms. The smut fungusUstilago maydisis a model pathogen in that sense: efficient homologous recombination and a small genome allow targeted modification. On the host side, maize is limiting with regard to rapid genetic alterations. By contrast, the model plantArabidopsis thalianais an excellent model with a vast amount of information and techniques as well as genetic resources. Here, we present a transformation protocol for the Brassicaceae smut fungusThecaphora thlaspeos. Using the well-established transformation of protoplasts, we generated the first reporter strains expressing fluorescent proteins to follow mating. As a proof-of-principle for homologous recombination, we deleted the pheromone receptorpra1. As expected, this mutant cannot mate. Further analysis will contribute to our understanding of the role of mating for infection biology in this novel model fungus. From now on, the genetic manipulation ofT. thlaspeos, which is able to colonize the model plantA. thaliana,provides us with a pathosystem, in which both partners are genetically amenable to study smut infection biology.
Mutations in the juxtamembrane segment of the cholesterol-binding site of APP alter its processing and promotes production of shorter, less toxic Aβ peptides
Authors: Hanbouch Linda , Schaack Béatrice , Kasri Amal , Fontaine Gaëlle , Gkanatsiou Eleni , Brinkmalm Gunnar , Portelius Erik , Blennow Kaj , Mourier Gilles , Gilles Nicolas , Millan Mark J , Marquer Catherine , Zetterberg Henrik , Boussicault Lydie , Potier Marie-Claude
Published: November 2020

Background

The brains of patients with Alzheimer’s disease (AD) reveal increased cellular membrane levels of cholesterol. Correspondingly, we previously showed that elevating levels of membrane cholesterol in neuronal cultures recapitulates early AD phenotypes including excessive cleavage of amyloid β (Aβ) peptides from the amyloid precursor protein (APP). Here we aimed to evaluate how the presence of a cholesterol-binding site (CBS) in the transmembrane and juxtamembrane regions of APP regulates its processing.

Methods

We generated seven single and two double APP mutants at amino acid positions 22, 26, 28, 29, 33, 39 of the Aβ sequence changing the charge and/or hydrophobicity of the targeted amino acids. HEK293T cells were transfected with APP constructs and secreted Aβ peptides were measured using ELISA and mass spectrometry (MS). APP processing in normal and high cholesterol condition, and endocytosis were assessed in stably expressing APPwtand APPK28AHEK293T clones. Finally, we measured the binding of synthetic peptides derived from the Aβ sequence to cholesterol-rich exosomes purified from control HEK293T cells.

Results

Most mutations triggered a reduction in the production of Aβ40 and Aβ42 peptides, whereas only juxtamembrane mutants resulted in the generation of shorter Aβ peptides. We confirmed by mass spectrometry this specific change in the profile of secreted Aβ peptides for the most characteristic APPK28Amutant. A transient increase of plasma membrane cholesterol enhanced the production of Aβ40 by APPWT, an effect absent with APPK28A. The enzymatic activity of α-, β- and γ-secretases remained unchanged in cells expressing APPK28A. Similarly, APPK28Asubcellular localization in early endosomes did not differ to APPWT. Finally, WT but not CBS mutant Aβ derived peptides bound to cholesterol-rich exosomes.

Conclusions

Taken together, these data reveal a major role of the juxtamembrane region of APP in binding to cholesterol and accordingly in the regulation of APP processing. Binding of cholesterol to K28 could staple APP to the juxtamembrane region thereby permitting access to γ-secretase cleavage at positions 40-42. The APPK28 mutant would lie deeper in the membrane, facilitating the production of shorter Aβ peptides and unveiling this specific region as a novel target for reducing the production of toxic Aβ species.
Comparison of changes in electrical activity, in isolated andin vivohearts, induced by voluntary exercise in female rats
Authors: Stones Rachel , Drinkhill Mark , White Ed
Published: November 2020

Regular mild exercise is recommended to the general population as beneficial to health. Regular exercise typically leads to structural and electrical remodelling of the heart but in human studies it is difficult to relate the extrinsic and intrinsic influences on intact hearts to changes seen at the single cell level. In this study we wished to test whether changes in electrical activity in intact hearts, in response to voluntary wheel running exercise training, were consistent with our previous observations in single cardiac myocytes and whether these changes resulted in altered susceptibility to arrhythmic stimuli.

Female rats performed 5 weeks of voluntary wheel running. Implanted telemetry transmitters were used to measure electrocardiograms (ECGs) and determine heart rate variability (HRV) in conscious, unrestrained, trained (TRN) and sedentary (SED) animals. In isolated hearts, left ventricular epicardial monophasic action potentials (MAPs) were recorded and the responses to potentially arrhythmic interventions were assessed.

Exercise training caused cardiac hypertrophy, as indexed by a significantly greater heart weight to body weight ratio. Consistent with previous measurements of action potential duration in single myocytes, MAPs were significantly longer at 50%, 75% and 90% repolarization. Arrhythmic susceptibility was not different between SED and TRN hearts. Trained animals displayed significantly altered HRV by week 5, in a manner consistent with reduced sympathetic tone, however resting ECG parameters, including those most associated with repolarisation duration, were unaltered. We conclude that intrinsic changes to cellular cardiac electrophysiology, induced by mild voluntary exercise, are not attenuated by the electronic loading that occurs in intact hearts. However,in vivo,extrinsic neuro-hormonal control of the heart may minimize the effects of intrinsic alterations in electrical activity.
Genetic variation at the species and population levels in the Rocky Mountain ridged mussel (Gonidea angulata)
Authors: Mock Karen E. , Walton James A. , Brownlee Steven F. R. , Mageroy Jon H. , Wilson Greg , Walker Ian R.
Published: November 2020

Freshwater mussels in western North America are threatened by water diversions, climate change, loss of required host fish, and other factors, and have experienced marked decline in the past several decades. All four of the primary lineages (potentially species) of freshwater mussels in the western U.S. and Canada are widespread and have somewhat generalist host fish requirements. Of these lineages, perhaps the most poorly understood and of greatest conservation concern isGonidea angulata(Rocky Mountain ridged mussel).Gonideais a monotypic genus occurring only in the western continental U.S. and southern Canada. Here we describe the patterns of genetic variation across the species range, including several populations in the Okanagan Valley at the northern edge of the range. We detected only ten mitochondrial cytochrome oxidase I haplotypes, three of which ere commonly found across major hydrologic basins, and the remainder of which were basin-specific variants. Haplotypes differed by a maximum of 5 of 537 nucleotides. New microsatellite loci were developed forG. angulataas a part of this study. Data from these microsatellite loci indicated that the population in the Chehalis River, Washington, was distinct from other locations, and that the Okanagan lake population was somewhat diverged from the remaining populations in the Columbia River and Klamath Lake. Only low levels of inbreeding were detected, in contrast to previous findings inMargartifera falcata,suggesting that hermaphroditism is not common. The population with the least diversity, according to microsatellite data, was the northernmost known population in Okanagan Lake We discuss the biogeographic and conservation implications of our findings.
High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
Authors: Garrett Meghan E. , Galloway Jared , Chu Helen Y. , Itell Hannah L. , Stoddard Caitlin I. , Wolf Caitlin R. , Logue Jennifer K. , McDonald Dylan , Matsen Frederick A. , Overbaugh Julie
Published: November 2020

Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia
Authors: Souilmi Yassine , Lauterbur M. Elise , Tobler Ray , Huber Christian D. , Johar Angad S. , Enard David
Published: November 2020

The current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that likely started more than 20,000 years ago. These adaptive events were limited to the population ancestral to East Asian populations. Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics. An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions as coronaviruses with human hosts, may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to better predict the pandemics of the future. Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points toward an overwhelming impact of socioeconomic factors in the case of COVID-19.
Examining the Persistence of Human Coronaviruses on Fresh Produce
Authors: Blondin-Brosseau Madeleine , Harlow Jennifer , Doctor Tanushka , Nasheri Neda
Published: November 2020

Human coronaviruses (HCoVs) are mainly associated with respiratory infections. However, there is evidence that highly pathogenic HCoVs, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome (MERS-CoV), infect the gastrointestinal (GI) tract and are shed in the fecal matter of the infected individuals. These observations have raised questions regarding the possibility of fecal-oral route as well as foodborne transmission of SARS-CoV-2 and MERS-CoV. Studies regarding the survival of HCoVs on inanimate surfaces demonstrate that these viruses can remain infectious for hours to days, however, to date, there is no data regarding the viral survival on fresh produce, which is usually consumed raw or with minimal heat processing. To address this knowledge gap, we examined the persistence of HCoV-229E, as a surrogate for highly pathogenic HCoVs, on the surface of commonly consumed fresh produce, including: apples, tomatoes and cucumbers. Herein, we demonstrated that viral infectivity declines within a few hours post-inoculation (p.i) on apples and tomatoes, and no infectious virus was detected at 24h p.i, while the virus persists in infectious form for 72h p.i on cucumbers. The stability of viral RNA was examined by droplet-digital RT-PCR (ddRT-PCR), and it was observed that there is no considerable reduction in viral RNA within 72h p.i.
The metabolic pace of life histories across fishes
Authors: Wong Serena , Bigman Jennifer S. , Dulvy Nicholas K.
Published: November 2020

All life acquires energy through metabolic processes and that energy is subsequently allocated to life-sustaining functions such as survival, growth, and reproduction. Thus, it has long been assumed that metabolic rate is related to the life history of an organism. Indeed, metabolic rate is commonly believed to set the pace of life by determining where an organism is situated along a fast-slow life history continuum. However, empirical evidence of a relationship between metabolic rate and life histories is lacking, especially for ectothermic organisms. Here, we ask whether three life history traits – maximum body mass, generation length, and growth performance – explain variation in resting metabolic rate (RMR) across fishes. We found that growth performance, which accounts for the trade-off between growth rate and maximum body size, explained variation in RMR, yet maximum body mass and generation length did not. Our results suggest that measures of life history that encompass trade-offs between life history traits, rather than traits in isolation, explain variation in RMR across fishes. Ultimately, understanding the relationship between metabolic rate and life history is crucial to metabolic ecology and has the potential to improve prediction of the ecological risk of data-poor species.
Synaptic vesicle pools are a major hidden resting metabolic burden of nerve terminals
Authors: Pulido Camila , Ryan Timothy Aidan
Published: November 2020

The human brain is a uniquely vulnerable organ as interruption in fuel supply leads to acute cognitive impairment on rapid time scales. The reasons for this vulnerability are not well understood, but nerve terminals are likely loci of this vulnerability as they do not store sufficient ATP molecules and must synthesize them on-demand during activity or suffer acute degradation in performance. The requirements for on-demand ATP synthesis however depends in part on the magnitude of resting metabolic rates. We show here that, at rest, synaptic vesicle (SV) pools are a major source of presynaptic basal energy consumption. This basal metabolism arises from SV-resident V-ATPases compensating for a hidden resting H+ efflux from the SV lumen. We show that this steady-state H+ efflux is 1) mediated by vesicular neurotransmitter transporters, 2) independent of the SV cycle, 3) accounts for ~half of the resting synaptic energy consumption and 4) contributes to nerve terminal intolerance of fuel deprivation.
Multiscale Invasion Assay for Probing Macrophage Response to Bacteria
Authors: Wodzanowski Kimberly A. , Kloxin April M. , Grimes Catherine L.
Published: November 2020

The immune system is a complex network of various cellular components that must differentiate between pathogenic bacteria and the commensal bacteria of the human microbiome, where misrecognition is linked to inflammatory disorders. Fragments of bacterial cell wall peptidoglycan bind to pattern recognition receptors within macrophages, leading to immune activation. To study this complex process, an approach for three-dimensional (3D) culture of human macrophages and their invasion with relevant bacteria in a well-defined hydrogel-based synthetic matrix inspired by the gut was established. Workflows were developed for monocyte encapsulation and differentiation into macrophages in 3D culture with high viability. Bacteria invaded into macrophages permittedin situpeptidoglycan labeling. Macrophages exhibited biologically-relevant cytokine release in response to bacteria. This multi-dimensional bacteria-macrophage co-culture system will prove useful in future studies to observe bacterial fragment production and localization in the cell at the carbohydrate level for insights into how our immune system properly senses bacteria.

TOC Figure
Revisiting the Notion of Deleterious Sweeps
Authors: Johri Parul , Charlesworth Brian , Howell Emma K. , Lynch Michael , Jensen Jeffrey D.
Published: November 2020

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites - both in the presence and absence of interference amongst deleterious mutations - and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value ofFSTafter a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.
Computer Designed PRC2 Inhibitor, EBdCas9, Reveals Functional TATA boxes in Distal Promoter Regions
Authors: Levy Shiri , Somasundaram Logesh , Raj Infencia Xavier , Ic-Mex Diego , Schmidt Sven , Alghadeer Ammar , Honkanen Henrik , Hawkins R. David , Mathieu Julie , Wang Yuliang , Baker David , Bomsztyk Karol , Ruohola-Baker Hannele
Published: November 2020

The critical process in development, bifurcation of cellular fates, requires epigenetic H3K27me3 marks propagated by PRC2 complex. However, the precise chromatin loci of functional H3K27me3 marks are not yet known. Here we identify critical PRC2 functional sites at a single nucleosome resolution. We fused a computationally designed protein, EED binder (EB) that competes with EZH2 and thereby disrupts PRC2 function, to dCas9 (EBdCas9) to direct PRC2 inhibition at a precise locus using gRNA. We targeted EBdCas9 to 4 different genes (TBX18, p16, CDX2 and GATA3) and observed epigenetic remodeling at a single nucleosome resolution resulting in gene activation. Remarkably, while traditional TATA box is located 30bp upstream of TSS, we identified a functional TATA box, >500bp of TSS, normally repressed by PRC2 complex. Deletion of this TATA box eliminates EBdCas9 dependent TBP recruitment and transcriptional activation. Targeting EBdCas9 to CDX2 and GATA3 results in trophoblast trans-differentiation. EBdCas9 technology is broadly applicable for epigenetic regulation at a single locus to control gene expression.

Graphical Abstract
Proteomic analysis reveals Utf1 as a neurogenesis-associated new Sumo target
Authors: Correa-Vázquez Juan F. , Juárez-Vicente Francisco , García-Gutiérrez Pablo , Barysch Sina V. , Melchior Frauke , García-Domínguez Mario
Published: November 2020

Post-translational modification by covalent attachment of Sumo regulates numerous processes in vertebrates. Despite demonstrated roles of Sumo in development and function of the nervous system, the identification of key factors displaying a sumoylation-dependent activity during neurogenesis remains elusive. Based on SILAC, we have identified the Sumo proteome of proliferating and neuronal-differentiating cells. More than 300 putative Sumo targets differentially associated with one or the other condition. Among these, Utf1 revealed as a new Sumo target. Gain-of-function experiments demonstrated marked differences between the effects on neurogenesis of wild type and sumoylation mutant versions of selected proteins. While sumoylation of Prox1, Sall4a, Trim24 and Utf1 associated with a positive effect on neurogenesis, sumoylation of Kctd15 associated with a negative effect. Similar results were observed in embryos. Finally, detailed analysis of Utf1 showed sumoylation-dependent control of bivalent genes expression. This effect relies on two mechanisms: sumoylation modulates Utf1 chromatin binding and mediates recruitment of the mRNA-decapping enzyme Dcp1a through a conserved SIM. Altogether, our results indicate that combined sumoylation status of key proteins determine proper progress of neurogenesis.

Sumo/transcription/chromatin/neurogenesis/Utf1
Two salts of the 6,6-difluoro-6H-dibenzo[c,e][1,2]oxaborinin-6-ide anion with different cations
Authors: Budanow Alexandra , Lerner Hans-Wolfram , Bolte Michael
Published: November 2020

The crystal structures are reported of the 6,6-difluoro-6H-dibenzo[c,e][1,2]oxaborinin-6-ide (or 9,9-difluoro-10-oxa-9-boraphenanthren-9-ide) anion with two different cations, namely, potassium 6,6-difluoro-6H-dibenzo[c,e][1,2]oxaborinin-6-ide, K+·C12H8BF2O−, (II), featuring a polymeric structure, and bis(tetraphenylphosphonium) bis(6,6-difluoro-6H-dibenzo[c,e][1,2]oxaborinin-6-ide) acetonitrile trisolvate, 2C24H20P+·2C12H8BF2O−·3CH3CN, (III), which is composed of discrete cations, anions and acetonitrile solvent molecules linked by C—H...O, C—H...N and C—H...F hydrogen bonds. There are only minor differences in the geometrical parameters of the anions in these structures.
Investigating the antecedents of e-commerce satisfaction in social commerce context
Authors: Attar Razaz Waheeb , Shanmugam Mohana , Hajli Nick
Published: November 2020

Purpose

Social media is still influencing consumers and is extending social commerce (S-Commerce) use. Different social media activities can influence the users' trust and e-satisfaction at different levels, which in turn influence the purchase intentions. This is evident for the food and beverage industry as S-Commerce mediated by social media can help realise a shorter time to market and meet buyer demands. In addition, credibility factors may influence trust and purchase intentions. Understanding the various factors of influence such as social constructs, namely ratings, reviews and referrals; design constructs such as credibility and features and behavioural constructs such as trust, satisfaction and motivation; and analysing the relationship between these factors and how they influence purchase intentions can provide deeper insights into S-Commerce research, decision-making process and purchase intentions particularly from a food and beverage context.

Design/methodology/approach

Drawing on trust through social media activities and surface credibility as well as e-commerce satisfaction, the authors have proposed a research model to investigate the purchase intention of consumers in S-Commerce platforms. Survey data were collected from six countries in Asia and analysed using SEM-PLS.

Findings

Results indicated that both trust and surface credibility significantly influence e-commerce satisfaction leading to purchase intention. Furthermore, surface credibility, which is a novel predictor for purchase intention in S-Commerce context, is highly significant on e-commerce satisfaction. Besides, encouraged by surface credibility, it was identified that trust significantly affects e-commerce satisfaction and results in purchase intention. This research adds contribution to theory and practice in S-Commerce stream as discussed at the end of the paper.

Originality/value

The results of this research contribute to the S-Commerce literature and have practical implications for practitioners in the food and beverage industry. As such, focussing on these constructs, this paper analyses the relationship between the social media activities, trust, e-commerce satisfaction, surface credibility and intention to buy.
Higher education in Japan: internationalization, the Sustainable Development Goals and survivability
Authors: Edwards Sachi , Ashida Akemi
Published: November 2020

Purpose

This paper reviews the national and institutional internationalization activities in Japan's higher education sector and considers the extent to which these efforts have attempted to incorporate and/or contribute to meeting the Sustainable Development Goals (SDGs).

Design/methodology/approach

This paper was developed based on a review of available demographic data on internationalization in Japan (in both English and Japanese), a survey of recent scholarly literature on this topic and conversations with numerous faculty and staff members working on internationalization issues in a wide range of higher education institutions throughout the country.

Findings

There are substantial internationalization efforts being made at both national and institutional levels, yet scholars and practitioners of higher education question the extent to which genuine internationalization is occurring. Moreover, the metrics used to track internationalization are somewhat limited and the available data, in many cases, can be complicated to interpret. A bit of tension also exists in Japanese universities between those who support the movement to internationalize and those who see it as a passing fad, an intrusion on their academic freedom and/or as a guise for Westernization – a tension that some cite, along with language barriers and system misalignment, as a challenge to internationalization.

Originality/value

Numerous scholars discuss the internationalization of higher education in Japan. The originality of this paper is in the comparison of Japan's higher education internationalization efforts to the movement to achieve the SDGs – both in Japan and as a global effort.
Organizational change and job insecurity: the moderating role of employability
Authors: Çalışkan Nurgül , Özkoç Aziz Gökhan
Published: November 2020

Purpose

The purpose of this study is to examine the relationship between characteristics of change (frequency of change [FC], impact of change [IC], planning involved in change [PC]) and job insecurity (JIS), as well as the moderating role of employability (EMP) within these relationships.

Design/methodology/approach

Data were obtained from a sample of 361 permanent employees working at four- and five-star hotels. The hypothesized relationships were tested via structural equation modeling.

Findings

The findings revealed that employees’ perceptions of JIS are affected positively by FC and IC and negatively by PC. Additionally, this study confirmed that the perception of EMP moderates the relationships between the characteristics of organizational change (FC, IC, PC) and JIS.

Research limitations/implications

No causal inference can be made with regard to the relationships in this study by virtue of the cross-sectional data used in the study. Hence, further studies with longitudinal design and wider samples covering different regions and/or tourism destinations need to be carried out to validate the results of this study and to further clarify the direction of the relationships presented here.

Originality/value

To the best of authors’ knowledge, this study presents the first empirical evidence on the moderating role of EMP in accounting for the JIS resulting from FC, IC and PC, the characteristics of organizational change. Also, the significance of this study lies in the fact that its subject has not been addressed before from the perspective of the hospitality industry.
The behavioral analysis of choice difficulty states during clothing online shopping
Authors: Chen Yumiao , Yang Zhongliang
Published: November 2020

Purpose

Choice overload in e-commerce induces choice difficulty, which is detrimental to shopping decision-making. The purpose of this paper is to provide relatively simple and effective methods and indicators to detect and assess the choice difficulty states of customers during clothing online shopping.

Design/methodology/approach

In order to find out the behavioral performance of choice difficulty states during clothing online shopping, the authors performed the following steps: at first, the authors conducted an experiment to record the videos of the purchasing process during clothing online shopping. Then, the authors carried out the behavioral analysis of customers, correlating each behavioral index to choice difficulty states.

Findings

The results of the behavioral analysis in this study have indicated that three types of behavior were significantly correlated to the choice difficulty states of customers.

Practical implications

It is expected that it would be possible to use the threshold values of behavioral indicators to determine whether and when the customer is suffering from choice phobia disorder. Based on the findings, a recommender system with timely interventions to help customers with choice difficulty to make shopping decisions will be developed in the future.

Originality/value

This is the first reported study that explores the possibility of using behavioral indicators to detect choice difficulty, which will remain helpful to the scientific community to start further customer-centered research work and development of clothing online shopping.
Sustainability of Brazilian public debt: a structural break analysis
Authors: Campos Eduardo Lima , Cysne Rubens Penha
Published: November 2020

Purpose

The objective of this work is to investigate the existence of structural breaks in multicointegration models estimated for Brazilian fiscal variables and to identify their effects on the sustainability or not of this country`s fiscal policy between December 1997 and June 2018.

Design/methodology/approach

The authors apply the econometric multicointegration method, in order to analyze long-term relationships between accumulated revenue and expenses of Brazilian central government and the stock of its debt, incorporating structural breaks, over the study period.

Findings

The unsustainability of the debt/GDP ratio is found here, as in a previous work, but now considering a structural break. As one of the contributions, the present work makes it possible to identify the date as of which Brazilian fiscal policy may have become unsustainable: May 2014.

Originality/value

The work points out the worsening of Brazilian fiscal situation as of 2014. The authors adapted original methodologies both in model specification and in the stationarity test used. The estimated parameters before and after structural break allow for identifying changes in fiscal variables that may have led to unsustainability, thus providing possible guidance for fiscal policy.
The impact of ownership structure and the board of directors’ composition on tax avoidance strategies: empirical evidence from Jordan
Authors: Alkurdi Amneh , Mardini Ghassan H.
Published: November 2020

Purpose

Adopting agency theory, the purpose of this study is to explore the impact of ownership structure and board of directors’ composition on the extent of tax avoidance strategies.

Design/methodology/approach

The sample included all of the Jordanian first market companies listed on the Amman Stock Exchange from 2012 to 2017, comprising 348 observations.

Findings

The main finding of the paper is that tax avoidance is negatively related to managerial and institution ownership structures, which reduces the usage of tax avoidance strategies. Foreign ownership, however, has a positive relation that increases the likelihood of adopting tax avoidance strategies.

Practical implications

This study has policy implications for policymakers in relation to designing future tax systems to reduce the possibility of engaging in tax avoidance practices.

Originality/value

To the best of the authors’ knowledge, this study is the first of its kind that investigates the effects of the managerial, foreign and institutional ownership classes and board composition on tax avoidance for Jordanian listed companies.
The application of social innovation as it relates to older people and the implications for future policymaking: a scoping review
Authors: Crossen-White Holly Louise , Hemingway Ann , Ladkin Adele
Published: November 2020

Purpose

Social innovation has received increasing attention in recent decades (Agostini et al., 2017). This study aims to consider how the concept has been applied to the issue of ageing and what can be learnt about effective policy responses.

Design/methodology/approach

The acknowledged lack of understanding generally about the concept makes it timely to undertake a scoping review of the current evidence from social innovation projects associated with older people. A scoping review is considered appropriate where there is a need to “identify and analyse knowledge gaps” (Munn et al., 2018, p. 2).

Findings

Findings from the scoping review indicate that, as yet, the concept of social innovation is not fully defined. However, it has widespread appeal across a diverse range of disciplines and has the potential to generate innovative policy responses.

Originality/value

A key argument identified is the need to change the public’s perceptions of ageing and devise public policies that encourage and nurture age-friendly communities. In summation, although social innovation has the potential to act as a policy driver, but to be effective, it is necessary to devise robust strategies to ensure full user-engagement and active involvement of communities. Therefore, it is the process of delivery that needs urgent attention in any future research into social innovation.
Stronger together? Intergenerational connection and Covid-19
Authors: Burke Stephen
Published: November 2020

Purpose

This paper aims to review how intergenerational connections and relationships have been affected to date by COVID-19. It provides lessons for the future.

Design/methodology/approach

This paper is a review of policy and practice.

Findings

Although there are some excellent examples of creative approaches such as online strategies to bring generations together in the face of social distancing, there remain barriers to building stronger communities. Many people of all ages remain lonely and isolated. Community projects are under-funded and will struggle to maintain connections beyond the immediate crisis. Inequalities and the digital divide have been exacerbated by COVID-19. Intergenerational relations are likely to be further strained by the economic impact.

Originality/value

None of us have known anything like COVID-19 and its impact on all aspects of our lives. It will continue to affect generations to come, and we need to learn the lessons as we move forward.