bluuebunny/crossref_metadata_2025 huggingface dataset:
High glucose attenuates Ca2+influx in cytotoxic T lymphocytes upon target recognition
Authors: Zou Huajiao , Schwär Gertrud , Zhao Renping , Alansary Dalia , Yin Deling , Schwarz Eva C. , Niemeyer Barbara , Qu Bin
Published: April 2020

The killing efficiency of cytotoxic T lymphocytes (CTLs) is tightly regulated by intracellular Ca2+concentration. Glucose is the key energy source for CTLs, lack of which significantly impairs CTL activation, proliferation and effector functions. The impact of high glucose on Ca2+influx in CTLs remains largely elusive. In this work, we stimulated primary human CD8+T cells in medium containing either 25 mM (high glucose, HG) or 5.6 mM glucose (normal glucose, NG). We found that store-operated calcium entry (SOCE) induced by thapsigargin (Tg) is elevated in HG-cultured CTLs compared to their counterparts in NG. Unexpectedly, the Ca2+influx elicited by recognition of target cells is reduced in HG-cultured CTLs. Under HG condition,STIM1andSTIM2, the calcium sensors in the endoplasmic reticulum (ER), were down-regulated;ORAI1, the main structural component of calcium-release activated channels, remained unchanged, whereasORAI2andORAI3were up-regulated. The fraction of necrosis of HG-cultured CTLs was enhanced after killing without affecting glucose uptake. Thus, our findings reveal that HG has a distinctive impact on Tg-evoked SOCE and target recognition-induced Ca2+influx in CTLs and causes more CTL death after killing, suggesting a novel regulatory role of high glucose on modulating CTL functions.
Protein Kinase D promotes activity-dependent AMPA receptor endocytosis in hippocampal neurons
Authors: Oueslati Morales Carlos O. , Ignácz Attila , Bencsik Norbert , Rátkai Anikó Erika , Lieb Wolfgang S. , Eisler Stephan A. , Szűcs Attila , Schlett Katalin , Hausser Angelika
Published: April 2020

AMPA type glutamate receptors (AMPARs) mediate the majority of fast excitatory neurotransmission in the brain. The continuous trafficking of AMPARs into and out of synapses is a core feature of synaptic plasticity, which is considered as the cellular basis of learning and memory. The molecular mechanisms underlying the postsynaptic AMPAR trafficking, however, are still not fully understood. In this work, we demonstrate that the Protein Kinase D (PKD) family promotes basal and activity-induced AMPAR endocytosis in primary hippocampal neurons. Pharmacological inhibition of PKD increased synaptic levels of GluA1-containing AMPARs, slowed down their endocytic trafficking and increased neuronal network activity. By contrast, ectopic expression of constitutive active PKD decreased the synaptic level of AMPARs, while increasing their co-localization with early endosomes. Our results thus establish an important role for PKD in the regulation of postsynaptic AMPAR trafficking during synaptic plasticity.
3D genome evolution and reorganization in theDrosophila melanogasterspecies group
Authors: Torosin Nicole S. , Anand Aparna , Golla Tirupathi Rao , Cao Weihuan , Ellison Christopher E.
Published: April 2020

Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin. TADs play an important role in regulating gene expression by constraining enhancer-promoter contacts; there is evidence that deletion of TAD boundaries leads to aberrant expression of neighboring genes. While the mechanisms of TAD formation have been well-studied, current knowledge on the extent of TAD conservation across species is inconclusive. Due to the integral role TADs play in gene regulation, their structure and organization is expected to be conserved during evolution. However, more recent research suggests that TAD structures diverge relatively rapidly. We use Hi-C chromosome conformation capture to measure evolutionary conservation of whole TADs and TAD boundary elements betweenD. melanogasterandD. triauraria, two early-branching species from themelanogasterspecies group which diverged ~15 million years ago. We find that 75% of TAD boundaries are orthologous while only 25% of TAD domains are conserved and these are enriched for Polycomb-repressed chromatin. Our results show that TADs have been reorganized since the common ancestor ofD. melanogasterandD. triauraria, yet the sequence elements that specify TAD boundaries remain highly conserved. We propose that evolutionary divergence in 3D genome organization results from shuffling of conserved boundary elements across chromosomes, breaking old TADs and creating new TAD architectures. This result supports the existence of distinct TAD subtypes: some may be evolutionarily flexible while others remain highly conserved due to their importance in restricting gene-regulatory element interactions.
Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis
Authors: Kumar Nilesh , Mishra Bharat , Mehmood Adeel , Athar Mohammad , Mukhtar M. Shahid
Published: April 2020

COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrated multiomics data pertaining to lung epithelial cells-specific coexpression network and human interactome to generateCalu-3-specific human-SARS-CoV-2Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity.
The preservative sorbic acid targets respiration, explaining the resistance of fermentative spoilage-yeast species
Authors: Stratford M. , Vallières C. , Geoghegan I.A. , Archer D.B. , Avery S.V.
Published: April 2020

A small number (10-20) of yeast species cause major spoilage in foods. Spoilage yeasts of soft drinks are resistant to preservatives like sorbic acid and they are highly fermentative, generating large amounts of carbon dioxide gas. Conversely, many yeast species derive energy from respiration only and most of these are sorbic acid-sensitive, so prevented from causing spoilage. This led us to hypothesize that sorbic acid may specifically inhibit respiration. Tests with respiro-fermentative yeasts showed that sorbic acid was more inhibitory to bothSaccharomyces cerevisiaeandZygosaccharomyces bailiiduring respiration (of glycerol) compared with fermentation (of glucose). The respiration-only speciesRhodotorula glutiniswas equally sensitive when growing on either carbon source, suggesting that ability to ferment glucose specifically enables sorbic acid-resistant growth. Sorbic acid inhibited the respiration process more strongly than fermentation. We present a dataset supporting a correlation between the level of fermentation and sorbic acid resistance across 191 yeast species. Other weak acids, C2 – C8, inhibited respiration in accordance with their partition coefficients, suggesting that effects on mitochondrial respiration were related to membrane localization rather than cytosolic acidification. Supporting this, we present evidence that sorbic acid causes production of reactive oxygen species, the formation of petite (mitochondria-defective) cells, and Fe-S cluster defects. This work rationalises why yeasts that can grow in sorbic acid-preserved foods tend to be fermentative in nature. This may inform more-targeted approaches for tackling these spoilage organisms, particularly as the industry migrates to lower-sugar drinks, which could favour respiration over fermentation in many spoilage yeasts.

IMPORTANCE

Spoilage by yeasts and moulds is a major contributor to food and drink waste, which undermines food security. Weak acid preservatives like sorbic acid help to stop spoilage but some yeasts, commonly associated with spoilage, are resistant to sorbic acid. Different yeasts generate energy for growth by the processes of respiration and/or fermentation. Here we show that sorbic acid targets the process of respiration, so fermenting yeasts are more resistant. Fermentative yeasts are also those usually found in spoilage incidents. This insight helps to explain the spoilage of sorbic acid-preserved foods by yeasts and can inform new strategies for effective control. This is timely as sugar content of products like soft drinks is being lowered, which may favour respiration over fermentation in key spoilage yeasts.
Photosynthetic sea slugs inflict protective changes to the light reactions of the chloroplasts they steal from algae
Authors: Havurinne Vesa , Tyystjärvi Esa
Published: April 2020

Sacoglossan sea slugs are able to maintain functional chloroplasts inside their own cells, and mechanisms that allow preservation of the chloroplasts are unknown. We found that the slugElysia timidainflicts changes to the photosynthetic light reactions of the chloroplasts it steals from the algaAcetabularia acetabulum. Working with a large continuous laboratory culture of both the slugs (>500 individuals) and their prey algae, we show that the plastoquinone pool of slug chloroplasts remains oxidized, which can suppress reactive oxygen species formation. Slug chloroplasts also rapidly build up a strong proton motive force upon a dark-to-light transition, which helps them to rapidly switch on photoprotective non-photochemical quenching of excitation energy. Finally, our results suggest that chloroplasts insideE. timidarely on flavodiiron proteins as electron sinks during rapid changes in light intensity. These photoprotective mechanisms are expected to contribute to the long-term functionality of the chloroplasts inside the slugs.
Selection and gene flow define polygenic barriers between incipient butterfly species
Authors: Van Belleghem Steven M. , Cole Jared M. , Montejo-Kovacevich Gabriela , Bacquet Caroline N. , McMillan W. Owen , Papa Riccardo , Counterman Brian A.
Published: April 2020

Characterizing the genetic architecture of species boundaries remains a difficult task. Hybridizing species provide a powerful system to identify the factors that shape genomic variation and, ultimately, identify the regions of the genome that maintain species boundaries. Unfortunately, complex histories of isolation, admixture and selection can generate heterogenous genomic landscapes of divergence which make inferences about the regions that are responsible for species boundaries problematic. However, as the signal of admixture and selection on genomic loci varies with recombination rate, their relationship can be used to infer their relative importance during speciation. Here, we explore patterns of genomic divergence, admixture and recombination rate among hybridizing lineages across theHeliconius eratoradiation. We focus on the incipient species,H. eratoandH. himera, and distinguish the processes that drive genomic divergence across three contact zones where they frequently hybridize. Using demographic modeling and simulations, we infer that periods of isolation and selection have been major causes of genome-wide correlation patterns between recombination rate and divergence between these incipient species. Upon secondary contact, we found surprisingly highly asymmetrical introgression between the species pair, with a paucity ofH. eratoalleles introgressing into theH. himeragenomes. We suggest that this signal may result from a current polygenic species boundary between the hybridizing lineages. These results contribute to a growing appreciation for the importance of polygenic architectures of species boundaries and pervasive genome-wide selection during the early stages of speciation with gene flow.
Choosing representative proteins based on splicing structure similarity improves the accuracy of gene tree reconstruction
Authors: Kamela Esaie Kuitche , Degen Marie , Wang Shengrui , Ouangraoua Aïda
Published: April 2020

Constructing accurate gene trees is important, as gene trees play a key role in several biological studies, such as species tree reconstruction, gene functional analysis and gene family evolution studies. The accuracy of these studies is dependent on the accuracy of the input gene trees. Although several methods have been developed for improving the construction and the correction of gene trees by making use of the relationship with a species tree in addition to multiple sequence alignment, there is still a large room for improvement on the accuracy of gene trees and the computing time. In particular, accounting for alternative splicing that allows eukaryote genes to produce multiple transcripts/proteins per gene is a way to improve the quality of multiple sequence alignments used by gene tree reconstruction methods. Current methods for gene tree reconstruction usually make use of a set of transcripts composed of one representative transcript per gene, to generate multiple sequence alignments which are then used to estimate gene trees. Thus, the accuracy of the estimated gene tree depends on the choice of the representative transcripts. In this work, we present an alternative-splicing-aware method called Splicing Homology Transcript (SHT) method to estimate gene trees based on wisely selecting an accurate set of homologous transcripts to represent the genes of a gene family. We introduce a new similarity measure between transcripts for quantifying the level of homology between transcripts by combining a splicing structure-based similarity score with a sequence-based similarity score. We present a new method to cluster transcripts into a set of splicing homology groups based on the new similarity measure. The method is applied to reconstruct gene trees of the Ensembl database gene families, and a comparison with current EnsemblCompara gene trees is performed. The results show that the new approach improves gene tree accuracy thanks to the use of the new similarity measure between transcripts. An implementation of the method as well as the data used and generated in this work are available athttps://github.com/UdeS-CoBIUS/SplicingHomologGeneTree/.
The impact of di-2-ethylhexyl phthalate on sperm fertility
Authors: Gabelev Khasin Liliya , Della Rosa John , Petersen Natalie , Moeller Jacob , Kriegsfeld Lance J. , Lishko Polina V.
Published: April 2020

A growing number of studies point to reduced fertility upon chronic exposure to endocrine-disrupting chemicals (EDCs) such as phthalates and plasticizers. These toxins are ubiquitous and are often found in food and beverage containers, medical devices, as well as in common household and personal care items. Animal studies with EDCs, such as phthalates and bisphenol A have shown a dose-dependent decrease in fertility and embryo toxicity upon chronic exposure. However, limited research has been conducted on the acute effects of these EDCs on male fertility. Here we used a murine model to test the acute effects of four ubiquitous environmental toxins: bisphenol A (BPA), di-2-ethylhexyl phthalate (DEHP), diethyl phthalate (DEP), and dimethyl phthalate (DMP) on sperm fertilizing ability and pre-implantation embryo development. The most potent of these toxins, di-2-ethylhexyl phthalate (DEHP), was further evaluated for its effect on sperm ion channel activity, capacitation status, acrosome reaction and generation of reactive oxygen species (ROS). DEHP demonstrated a profound hazardous effect on sperm fertility by producing an altered capacitation profile, impairing the acrosome reaction, and, interestingly, also increasing ROS production. These results indicate that in addition to its known chronic impact on reproductive potential, DEHP also imposes acute and profound damage to spermatozoa, and thus, represents a significant risk to male fertility.
Estimating the Probability of Early Afterdepolarization and Predicting Arrhythmic Risk associated with Long QT Syndrome Type 1 Mutations
Authors: Jin Qingchu , Greenstein Joseph L. , Winslow Raimond L.
Published: April 2020

Early after-depolarizations (EADs) are action potential (AP) repolarization abnormalities that can trigger lethal arrhythmias. Simulations using biophysically-detailed cardiac myocyte models can reveal how model parameters influence the probability of these cellular arrhythmias, however such analyses can pose a huge computational burden. We have previously developed a highly simplified approach in which logistic regression models (LRMs) map parameters of complex cell models to the probability of ectopic beats (EBs). Here, we extend this approach to predict the probability of early after-depolarizations (P(EAD)). We use the LRM to investigate how changes in parameters of the slow-activating delayed rectifier current (IKs) affect P(EAD) for 17 different Long QT syndrome type 1 (LQTS1) mutations. We compare P(EAD) for these 17 LQTS1 mutations with two other recently proposed model-based arrhythmia risk metrics. These three model-based risk metrics yield similar prediction performance; however, they all fail to predict relative clinical risk for a significant number of the 17 studied LQTS1 mutations. The consistent successes and failures of all three risk metrics suggest that important functional characteristics of LQTS1 mutations may not yet be fully known.

Author summary

An early after-depolarization (EAD) is an abnormal cellular electrical event which can trigger dangerous arrhythmias in the heart. We use our previously developed method to build a simple logistic regression model (LRM) that estimates the probability of EAD (P(EAD)) as a function of myocyte model parameters. Using this LRM along with two other recently published model-based arrhythmia risk predictors, we estimate risk of arrhythmia for 17 Long QT syndrome type 1 (LQTS1) mutations. Results show that all approaches have similar prediction performance in that there are a set of mutations whose relative clinical risk for arrhythmia are well estimated using these metrics, but that relative risk is consistently over- or under-estimated across all approaches for a significant number of other mutations. We believe this indicates that the functional characterization of the LQTS1 phenotype is incomplete.
Hierarchical fear: parental behaviour and corticosterone release mediate nestling growth in response to predation risk
Authors: de Zwaan Devin R. , Martin Kathy
Published: April 2020

Nestling development, a critical life-stage for altricial songbirds, is highly vulnerable to predation, particularly for open-cup nesting species. Since nest predation risk increases cumulatively with time, rapid growth may be an adaptive response that promotes early fledging. However, greater predation risk can reduce parental provisioning rate as a risk aversion strategy and subsequently constrain nestling growth, or directly elicit a physiological response in nestlings with adaptive or detrimental effects on development rate. Despite extensive theory, evidence for the relative strength of these effects on nestling development in response to prevailing predation risk and the underlying mechanisms remain unclear. For an alpine population of horned lark (Eremophila alpestris), we elevated perceived predation risk (decoys/playback) during the nestling stage to assess the influence of predator cues and parental care on nestling wing growth and the glucocorticoid hormone corticosterone. We used piecewise path analysis to test a hypothesized causal response structure composed of direct and indirect pathways. Nestlings under greater perceived predation risk reduced corticosterone and increased wing growth, resulting in an earlier age at fledge. This represented both a direct response that was predator-specific, and an indirect response dependent on parental provisioning rate. Parents that reduced provisioning rate most severely in response to predator cues had smaller nestlings with greater corticosterone. Model comparisons indicated the strongest support for a directed, causal influence of corticosterone on nestling wing growth, highlighting corticosterone as a potential physiological mediator of the nestling growth response to predation risk. Finally, cold temperatures prior to the experiment constrained wing growth closer to fledge, illustrating the importance of considering the combined influence of weather and predation risk across developmental stages. We present the first study to separate the direct and indirect effects of predation risk on nestling development in a causal, hierarchical framework that incorporates corticosterone as an underlying mechanism and provides experimental evidence for an adaptive developmental response to predation risk in ground-nesting songbirds.
The regulation of a pigmentation gene in the formation of complex color patterns inDrosophilaabdomens
Authors: Raja Komal K. B. , Shittu Mujeeb O. , Nouhan Peter M. E. , Steenwinkel Tessa. E. , Bachman Evan A. , Kokate Prajakta P. , McQueeney Alexander H. , Mundell Elizabeth A. , Armentrout Alexandri A. , Nugent Amber M. , Werner Thomas
Published: April 2020

Changes incis-regulatory modules (CRMs) that control developmental gene expression patterns have been implicated in the evolution of animal morphology1-6. However, the genetic mechanisms underlying complex morphological traits remain largely unknown. Here we investigated the molecular mechanisms that induce the pigmentation geneyellow(y) in a complex spot and shade pattern on the abdomen of the quinaria group speciesDrosophila guttifera. We show that theyexpression pattern is controlled by only one CRM, which contains a stripe-inducing CRM at its core. We identified several developmental genes that may collectively interact with the CRM to orchestrate the patterning in the pupal abdomen ofD. guttifera. We further show that the core CRM is conserved amongD. guttiferaand the closely related quinaria group speciesDrosophila deflecta, which displays a similarly spotted abdominal pigment pattern. Our data suggest that besides direct activation of patterns in distinct spots, abdominal spot patterns inDrosophilaspecies may have evolved through partial repression of an ancestral stripe pattern, leaving isolated spots behind. Abdominal pigment patterns of extant quinaria group species support the partial repression hypothesis and further emphasize the modularity of theD. guttiferapattern.
Comparative ACE2 variation and primate COVID-19 risk
Authors: Melin Amanda D. , Janiak Mareike C. , Marrone Frank , Arora Paramjit S. , Higham James P.
Published: April 2020

The emergence of the novel coronavirus SARS-CoV-2, which in humans is highly infectious and leads to the potentially fatal disease COVID-19, has caused hundreds of thousands of deaths and huge global disruption. The viral infection may also represent an existential threat to our closest living relatives, the nonhuman primates, many of which are endangered and often reduced to small populations. The virus engages the host cell receptor, angiotensin-converting enzyme-2 (ACE2), through the receptor binding domain (RBD) on the spike protein. The contact surface of ACE2 displays amino acid residues that are critical for virus recognition, and variations at these critical residues are likely to modulate infection susceptibility across species. While infection studies are emerging and have shown that some primates, such as rhesus macaques and vervet monkeys, develop COVID-19-like symptoms when exposed to the virus, the susceptibility of many other nonhuman primates is unknown. Here, we show that all apes, including chimpanzees, bonobos, gorillas, and orangutans, and all African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at significant contact residues, and protein modeling predicts that these differences should greatly reduce the binding affinity of the ACE2 for the virus, hence moderating their susceptibility for infection. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, as well as some lemurs are all likely to be highly susceptible to SARS-CoV-2, representing a critical threat to their survival. Urgent actions have been undertaken to limit the exposure of Great Apes to humans, and similar efforts may be necessary for many other primate species.
Classical drug digitoxin inhibits influenza cytokine storm, with implications for COVID-19 therapy
Authors: Pollard Bette S. , Blanco Jorge C. , Pollard John R. , Prince Gregory A.
Published: April 2020

Influenza viruses, corona viruses and related pneumotropic viruses cause sickness and death partly by inducing a hyper-proinflammatory response by immune cells and cytokines in the host airway. Here we show that the cardiac glycoside digitoxin suppresses this response induced by influenza virus strain A/Wuhan/H3N2/359/95 in the cotton rat lung. The cytokines TNFα, GRO/KC, MIP2, MCP1, TGFβ, and IFNγ. are significantly and differentially reduced. Since the hyper-proinflammatory expression of cytokines is a host response, we suggest that digitoxin may have therapeutic potential for not only influenza and but also for coronavirus infections.
Dynamical effects of dendritic pruning implicated in aging and neurodegeneration: Towards a measure of neuronal reserve
Authors: Kirch Christoph , Gollo Leonardo L.
Published: April 2020

Aging is a main risk factor for neurodegenerative disorders including Alzheimer’s disease. It is often accompanied by reduced cognitive functions, gray-matter volume, and dendritic integrity. Although age-related brain structural changes have been observed across multiple scales, their functional implications remain largely unknown. Here we simulate the aging effects on neuronal morphology as dendritic pruning and characterize its dynamical implications. Utilizing a minimal computational modeling approach, we simulate the dynamics of detailed digitally reconstructed pyramidal neurons of humans obtained from the online repository Neuromorpho.org. We show that as aging progressively affects neuronal integrity, neuronal firing rate is reduced, which causes a reduction in energy consumption, energy efficiency, and dynamic range. Pruned neurons require less energy but their function is often impaired, which can explain the diminished ability to distinguish between similar experiences (pattern separation) in older people. Our measures indicate that the resilience of neuronal dynamics is neuron-specific, heterogeneous, and strongly affected by dendritic topology and the centrality of the soma. Based on the emergent neuronal dynamics, we propose to classify the effects of dendritic deterioration, and put forward that soma centrality measures neuronal reserve. Moreover, our findings suggest that increasing dendritic excitability could partially mitigate the dynamical effects of aging.
Membrane Insertion ofMycobacterium tuberculosisEsxA in Cultured Lung Epithelial Cells
Authors: Zhang Qi , Aguilera Javier , Reyes Salvador Vazquez , Sun Jianjun
Published: April 2020

EsxA has long been recognized as an important virulence factor ofMycobacterium tuberculosis(Mtb) that plays an essential role in Mtb cytosolic translocation presumably by penetrating phagosomal membranes with its acidic pH-dependent membrane permeabilizing activity (MPA). However, current data suggest that the observed cytolytic activity of EsxA at neutral pH is due to contamination of ASB-14, a detergent used in EsxA protein purification, and the role of EsxA MPA in Mtb cytosolic translocation is also questionable. Here, we have obtained evidence that it is ASB-14, not EsxA that causes cytolysis at neutral pH. Quantitative liquid chromatography and mass spectrometry showed that even after gel filtration, dialysis, or passing through detergent removal column, the remaining ASB-14 in the EsxA protein solution was still at a concentration enough to kill cultured lung epithelial cells. When treated with trypsin or proteinase K, the digested EsxA protein solution with ASB-14 was still cytotoxic. Interestingly, however, we have found that the exogenously added EsxA is endocytosed into lung epithelial cells and inserts into the host membranes within acidic subcellular compartments, which can be blocked by cytochalasin D and bafilomycin A. It is for the first time EsxA is found to insert into the host membranes within acidic subcellular compartments.

Importance

EsxA has long been recognized as an important virulence factor ofMycobacterium tuberculosis(Mtb) that plays an essential role in Mtb virulence. However, current data regarding to its role in Mtb virulence are controversial. Here, we have obtained evidence showing that the cytolytic activity of EsxA at neutral pH is due to contamination of ASB-14, a detergent used in EsxA preparation. Moreover, it is for the first time we have found that EsxA protein is endocytosed into lung epithelial cells and inserts into the host membranes within acidic subcellular compartments, implicating an important role of the acidic pH-dependent membrane permeabilizing activity of EsxA in Mtb virulence.
Evaluation of nine commercial SARS-CoV-2 immunoassays
Authors: Lassaunière Ria , Frische Anders , Harboe Zitta B. , Nielsen Alex C.Y. , Fomsgaard Anders , Krogfelt Karen A. , Jørgensen Charlotte S.
Published: April 2020

Due to urgency and demand, numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoassays are rapidly being developed and placed on the market with limited validation on clinical samples. Thorough validation of serological tests are required to facilitate their use in the accurate diagnosis of SARS-CoV-2 infection, confirmation of molecular results, contact tracing, and epidemiological studies. This study evaluated the sensitivity and specificity of nine commercially available serological tests. These included three enzyme-linked immunosorbent assays (ELISAs) and six point-of-care (POC) lateral flow tests. The assays were validated using serum samples from: i) SARS-CoV-2 PCR-positive patients with a documented first day of disease; ii) archived sera obtained from healthy individuals before the emergence of SARS-CoV-2 in China; iii) sera from patients with acute viral respiratory tract infections caused by other coronaviruses or non-coronaviruses; and iv) sera from patients positive for dengue virus, cytomegalovirus and Epstein Barr virus. The results showed 100% specificity for the Wantai SARS-CoV-2 Total Antibody ELISA, 93% for the Euroimmun IgA ELISA, and 96% for the Euroimmun IgG ELISA with sensitivities of 90%, 90%, and 65%, respectively. The overall performance of the POC tests according to manufacturer were in the rank order of AutoBio Diagnostics > Dynamiker Biotechnology = CTK Biotech > Artron Laboratories > Acro Biotech ≥ Hangzhou Alltest Biotech. Overall, these findings will facilitate selection of serological assays for the detection SARS-CoV-2-specific antibodies towards diagnosis as well as sero-epidemiological and vaccine development studies.
“Mental health status of the general population, healthcare professionals, and university students during 2019 coronavirus disease outbreak in Jordan: a cross-sectional study”
Authors: Naser Abdallah Y , Dahmash Eman Zmaily , Al-Rousan Rabaa , Alwafi Hassan , Alrawashdeh Hamzeh Mohammad , Ghoul Imene , Abidine Anwer , Bokhary Mohammed A. , AL-Hadithi Hadeel T. , Ali Dalia , Abuthawabeh Rasha , Abdelwahab Ghada Mohammad , Alhartani Yosra J , Muhaisen Haneen Al , Dagash Ayah
Published: April 2020

Background

The emergence of COVID-19 global pandemic coupled with high transmission rate and mortality has created an unprecedented state of emergency worldwide. This global situation may have a negative impact on the psychological well-being of individuals which in turn impacts individuals’ performance.

Methods

A cross-sectional study using an online survey was conducted in Jordan between 22nd and 28th of March 2020 to explore the mental health status (depression and anxiety) of the general population, healthcare professionals, and university students during the COVID-19 outbreak. The Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7) were used to assess depression and anxiety among the study participants. Logistic regression analysis was used to identify predictors of depression and anxiety.

Results

The prevalence of depression and anxiety among the entire study participants was 23.8% and 13.1%, respectively. Anxiety was most prevalent across university students 21.5%, followed by healthcare professionals 11.3%, and general population 8.8%. Females among healthcare professionals and university students, divorced healthcare professionals, pulmonologists, and university students with history of chronic disease were at higher risk of developing depression. Females, divorced participants among the general population, and university students with history of chronic disease and those with high income (≥1500 JD) were at higher risk of developing anxiety.

Conclusions

During outbreaks, individuals are put under extreme stressful condition resulting in higher risk of developing anxiety and depression particularly for students and healthcare professionals. Policymakers and mental healthcare providers are advised to provide further mental support to these vulnerable groups during this pandemic.
Assessing the risk of spread of COVID-19 to the Asia Pacific region
Authors: Shearer Freya M. , Walker James , Tellioglu Nefel , McCaw James M. , McVernon Jodie , Black Andrew , Geard Nic
Published: April 2020

During the early stages of an emerging disease outbreak, governments are required to make critical decisions on how to respond appropriately, despite limited data being available to inform these decisions. Analytical risk assessment is a valuable approach to guide decision-making on travel restrictions and border measures during the early phase of an outbreak, when transmission is primarily contained within a source country. Here we introduce a modular framework for estimating the importation risk of an emerging disease when the direct travel route is restricted and the risk stems from indirect importation via intermediary countries. This was the situation for Australia in February 2020. The framework was specifically developed to assess the importation risk of COVID-19 into Australia during the early stages of the outbreak from late January to mid-February 2020. The dominant importation risk to Australia at the time of analysis was directly from China, as the only country reporting uncontained transmission. However, with travel restrictions from mainland China to Australia imposed from February 1, our framework was designed to consider the importation risk from China into Australia via potential intermediary countries in the Asia Pacific region. The framework was successfully used to contribute to the evidence base for decisions on border measures and case definitions in the Australian context during the early phase of COVID-19 emergence and is adaptable to other contexts for future outbreak response.
Super-rapid quantitation of the production of HIV-1 harboring a luminescent peptide tag
Authors: Ozono Seiya , Zhang Yanzhao , Tobiume Minoru , Kishigami Satoshi , Tokunaga Kenzo
Published: April 2020

In virological studies using HIV-1 proviral clones, virus production is normally monitored by either an RT assay or a p24 antigen capture ELISA. However, these assays are costly and time-consuming for routine handling of a large number of HIV-1 samples. In addition, sample dilution is always required in ELISA to determine p24 protein levels because of the very narrow range of detectable concentrations in this assay. Here, we establish a novel HIV-1 production assay system to solve the aforementioned problems by using a recently developed small peptide tag called HiBiT. First, we constructed a novel full-length proviral HIV-1 DNA clone and a lentiviral packaging vector in which the HiBiT tag was added to the C terminus of the integrase. Tagging the integrase with the HiBiT sequence did not impede the production or infectivity of the resultant viruses. Electron microscopy revealed normal morphology of the virus particles. Most importantly, by comparing between ELISA and the HiBiT luciferase assay, we successfully obtained an excellent linear correlation between p24 concentrations and HiBiT-based luciferase activity. Overall, we conclude that HiBiT-tagged viruses can replace the parental HIV-1 and lentiviral vectors, which enables us to perform a super-rapid, inexpensive, convenient, simple, and highly accurate quantitative assay for HIV-1 production.
Combining sample expansion and light sheet microscopy for the volumetric imaging of virus-infected cells with optical super-resolution
Authors: Mascheroni Luca , Scherer Katharina M. , Manton James D. , Ward Edward , Dibben Oliver , Kaminski Clemens F.
Published: April 2020

Expansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution owing to their physical magnification, which is achieved through water-absorbing polymers. The technique uses readily available chemicals and does not require sophisticated equipment, thus offering super-resolution to laboratories that are not microscopy-specialised. Here we present a protocol combining sample expansion with light sheet microscopy to generate high-contrast, high-resolution 3D reconstructions of whole virus-infected cells. The results are superior to those achievable with comparable imaging modalities and reveal details of the infection cycle that are not discernible before expansion. An image resolution of approximately 95 nm could be achieved in samples labelled in 3 colours. We clearly resolve the concentration of viral nucleoprotein on the surface of vesicular structures within the cell and their positioning relative to cellular organelles. We provide detailed guidance and a video protocol for the optimal application of the method and demonstrate its potential to study virus-host cell interactions.
XAB2 prevents abortive recombinational repair of replication-associated DNA double-strand breaks and its loss is synthetic lethal with RAD52 inhibition
Authors: Sharma Abhishek B. , Erasimus Hélène , Pinto Lia , Caron Marie-Christine , Neumann Katrin , Nazarov Petr V. , Klink Barbara , Fritah Sabrina , Herold-Mende Christel C. , Niclou Simone P. , Calsou Patrick , Masson Jean-Yves , Britton Sébastien , Van Dyck Eric
Published: April 2020

Unrepaired O6-methylguanine lesions induced by the alkylating chemotherapy agent temozolomide lead to replication-associated single-ended DNA double-strand breaks (seDSBs) that are repaired predominantly through RAD51-mediated homologous recombination (HR). Here, we show that loss of the pre-mRNA splicing and DNA repair protein XAB2 leads to increased temozolomide sensitivity in glioblastoma cells, which reflects abortive HR due to Ku retention on resected seDSBs. XAB2-dependent Ku eviction also occurred at seDSBs generated by the topoisomerase I poison campthotecin and operated in parallel to an ATM-dependent pathway previously described. Although Ku retention elicited by loss of XAB2 did not prevent RAD51 focus formation, the resulting RAD51-ssDNA associations were unproductive, leading to increased engagement of non-homologous-end-joining in S/G2 and genetic instability. Overexpression of RAD51 or the single-stranded DNA annealing factor RAD52 rescued the XAB2 defects. RAD52 depletion led to severe temozolomide sensitivity, whereas a synthetic lethality interaction was observed between RAD52 and XAB2.
Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments
Authors: Chen Zhijie , Shaw Alan , Wilson Hugh , Woringer Maxime , Darzacq Xavier , Marqusee Susan , Wang Quan , Bustamante Carlos
Published: April 2020

Theoretical and experimental observations that catalysis enhances the diffusion of enzymes have generated exciting implications about nanoscale energy flow, molecular chemotaxis and self-powered nanomachines. However, contradictory claims on the origin, magnitude, and consequence of this phenomenon continue to arise. Experimental observations of catalysis-enhanced enzyme diffusion, to date, have relied almost exclusively on fluorescence correlation spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an Anti-Brownian ELectrokinetic (ABEL) trap and in-solution spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an Anti-Brownian ELectrokinetic (ABEL) trap and in-solution single-particle tracking (SPT), we show that catalysis does not increase the diffusion of alkaline phosphatase (ALP) at the single-molecule level, in sharp contrast to the ~20% enhancement seen in parallel FCS experiments usingp-nitrophenyl phosphate (pNPP) as substrate. Combining comprehensive FCS controls, ABEL trap, surface-based single-molecule fluorescence, and Monte-Carlo simulations, we establish thatpNPP-induced dye blinking at the ~10 ms timescale is responsible for the apparent diffusion enhancement seen in FCS. Our observations urge a crucial revisit of various experimental findings and theoretical models––including those of our own––in the field, and indicate that in-solution SPT and ABEL trap are more reliable means to investigate diffusion phenomena at the nanoscale.

SIGNIFICANCE STATEMENT

Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase, ALP). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single ALP enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy (FCS), the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.
The development of a novel diagnostic PCR forMadurella mycetomatisusing a comparative genome approach
Authors: Lim Wilson , Eadie Kimberly , Siddig Emmanuel , Nyuykonge Bertrand , Ahmed Sarah , Fahal Ahmed H. , Verbon Annelies , Smit Sandra , van de Sande Wendy WJ
Published: April 2020

Eumycetoma is a neglected tropical disease characterized by large tumorous lesions. It is most commonly caused by the fungusMadurella mycetomatiswhich accounts for more than 70% of cases in central Africa. Currently, identification of the causative agent can only be reliably performed by a species-specific PCR. However, we recently demonstrated that ourM. mycetomatisspecific PCR can cross-react withMadurella pseudomycetomatis.We therefore used a comparative genome approach to develop a newM. mycetomatisspecific PCR for species identification. For this we compared the publishedM. mycetomatisgenome to genomes of other organisms in BLASTCLUST to identify uniqueM. mycetomatispredicted protein coding sequences. Based on 16 of these unique sequences, PCR primers were developed. The specificity of these primers was further evaluated in other eumycetoma causing agents including theMadurellasibling species. Out of the 16 tested sequences, only one was unique forM. mycetomatisand this should be used as a novel diagnostic marker forM. mycetomatis.
Predication of Pandemic COVID-19 situation in Maharashtra, India
Authors: Kumar Sunny
Published: April 2020

Presently, the world is infected by COVID 19 virus which has created an emergency for public health. For controlling the spreading of the virus, we have to prepare for precaution and futuristic calculation for infection spreading. The coronavirus affects the population of the world including Inia. Here, we are the study the virus spreading rate on the Maharashtra state which is part of India. We are predicting the infected people by the SIR model. SIR model is one of the most effective models which can predict the spreading rate of the virus. We have validated the model with the current spreading rate with this SIR model. This study will help to stop the epidemic spreading because it is in the early stage in the Maharashtra region.
#50+ fashion Instagram influencers: cognitive age and aesthetic digital labours
Authors: McFarlane Ashleigh , Samsioe Emma
Published: April 2020

Purpose

This paper demonstrates how #50+ fashion Instagram influencers contribute to the social construction of cognitive age through their aesthetic digital labours.

Design/methodology/approach

Non-participative netnography was used in the form of visual and textual analysis of over 300 Instagram posts including images, captions and comments.

Findings

Findings reveal how outfit selection, background choices and bodily poses redefine expressions of look age through forms of aesthetic labour. Post-construction, hashtag and emoji usage illustrates how influencers refrain from directly posting about the fashion brands that they endorse. Instead, image and personality work visually attracts followers to politically charged posts which directly impact upon the social and cultural contexts where influencers are active. This ties into present-day wider societal discourses.

Practical implications

50+ fashion influencers have high spending power. Fashion brands should refrain from using #brand and collaborate in more subtle ways and concentrate on challenging the negativity of the old-age cliché.

Originality/value

The study advances theory on the social construction of age in fashion studies by combining cognitive age with aesthetic labour to identify the characteristics of the social phenomenon of the 50+ Instagram influencer. It applies principles from critical visual analysis to digital context, thereby advancing the qualitative netnographic toolkit.
Selection of Value-at-Risk models for MENA Islamic indices
Authors: Ben Ayed Wassim , Fatnassi Ibrahim , Ben Maatoug Abderrazak
Published: April 2020

Purpose

The purpose of this study is to investigate the performance of Value-at-Risk (VaR) models for nine Middle East and North Africa Islamic indices using RiskMetrics and VaR parametric models.

Design/methodology/approach

The authors test the performance of several VaR models using Kupiec and Engle and Manganelli tests at 95 and 99 per cent levels for long and short trading positions, respectively, for the period from August 10, 2006 to December 14, 2014.

Findings

The authors’ findings show that the VaR under Student and skewed Student distribution are preferred at a 99 per cent level VaR. However, at 95 per cent level, the VaR forecasts obtained under normal distribution are more accurate than those generated using models with fat-tailed distributions. These results suggest that VaR is a good tool for measuring market risk. The authors support the use of RiskMetrics during calm periods and the asymmetric models (Generalized Autoregressive Conditional Heteroskedastic and the Asymmetric Power ARCH model) during stressed periods.

Practical implications

These results will be useful to investors and risk managers operating in Islamic markets, because their success depends on the ability to forecast stock price movements. Therefore, because a few Islamic financial institutions use internal models for their capital calculations, the regulatory committee should enhance market risk disclosure.

Originality/value

This study contributes to the knowledge in this area by improving our understanding of market risk management for Islamic assets during the stress periods. Then, it highlights important implications regarding financial risk management. Finally, this study fills a gap in the literature, as most empirical studies dealing with evaluating VaR prediction models have focused on quantifying the model risk in the conventional market.