bluuebunny/crossref_metadata_2025 huggingface dataset:
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps
Authors: Nepal Roshan , Houtak Ghais , Shaghayegh Gohar , Bouras George , Shearwin Keith , Psaltis Alkis James , Wormald Peter-John , Vreugde Sarah
Published: December 2021

Prophages affect bacterial fitness on multiple levels. These include bacterial infectivity, toxin secretion, virulence regulation, surface modification, immune stimulation and evasion and microbiome competition. Lysogenic conversion arms bacteria with novel accessory functions thereby increasing bacterial fitness, host adaptation and persistence, and antibiotic resistance. These properties allow the bacteria to occupy a niche long term and can contribute to chronic infections and inflammation such as chronic rhinosinusitis (CRS). In this study, we aimed to identify and characterize prophages present in

Staphylococcus aureus

from patients suffering from CRS in relation to CRS disease phenotype and severity. Prophage regions were identified using PHASTER. Various in silico tools like ResFinder and VF Analyzer were used to detect virulence genes and antibiotic resistance genes respectively. Progressive MAUVE and maximum likelihood were used for multiple sequence alignment and phylogenetics of prophages respectively. Disease severity of CRS patients was measured using computed tomography Lund–Mackay scores. Fifty-eight

S. aureus

clinical isolates (CIs) were obtained from 28 CRS patients without nasal polyp (CRSsNP) and 30 CRS patients with nasal polyp (CRSwNP). All CIs carried at least one prophage (average=3.6) and prophages contributed up to 7.7 % of the bacterial genome. Phage integrase genes were found in 55/58 (~95 %)

S. aureus

strains and 97/211 (~46 %) prophages. Prophages belonging to Sa3int integrase group (phiNM3, JS01, phiN315) (39/97, 40%) and Sa2int (phi2958PVL) (14/97, 14%) were the most prevalent prophages and harboured multiple virulence genes such as sak, scn, chp, lukE/D, sea. Intact prophages were more frequently identified in CRSwNP than in CRSsNP (P=0.0021). Intact prophages belonging to the Sa3int group were more frequent in CRSwNP than in CRSsNP (P=0.0008) and intact phiNM3 were exclusively found in CRSwNP patients (P=0.007). Our results expand the knowledge of prophages in

S. aureus

isolated from CRS patients and their possible role in disease development. These findings provide a platform for future investigations into potential tripartite associations between bacteria-prophage-human immune system,

S. aureus

evolution and CRS disease pathophysiology.
Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment
Authors: Weiss Andy , Lopez Christopher A. , Beavers William N. , Rodriguez Jhoana , Skaar Eric P.
Published: December 2021

Clostridioides difficile

(formerly

Clostridium difficile

) colonizes the gastrointestinal tract following disruption of the microbiota and can initiate a spectrum of clinical manifestations ranging from asymptomatic to life-threatening colitis. Following antibiotic treatment, luminal oxygen concentrations increase, exposing gut microbes to potentially toxic reactive oxygen species. Though typically regarded as a strict anaerobe,

C. difficile

can grow at low oxygen concentrations. How this bacterium adapts to a microaerobic environment and whether those responses to oxygen are conserved amongst strains is not entirely understood. Here, two

C. difficile

strains (630 and CD196) were cultured in 1.5% oxygen and the transcriptional response to long-term oxygen exposure was evaluated via RNA-sequencing. During growth in a microaerobic environment, several genes predicted to protect against oxidative stress were upregulated, including those for rubrerythrins and rubredoxins. Transcription of genes involved in metal homeostasis was also positively correlated with increased oxygen levels and these genes were amongst the most differentially transcribed. To directly compare the transcriptional landscape between

C. difficile

strains, a ‘consensus-genome’ was generated. On the basis of the identified conserved genes, basal transcriptional differences as well as variations in the response to oxygen were evaluated. While several responses were similar between the strains, there were significant differences in the abundance of transcripts involved in amino acid and carbohydrate metabolism. Furthermore, intracellular metal concentrations significantly varied both in an oxygen-dependent and oxygen-independent manner. Overall, these results indicate that

C. difficile

adapts to grow in a low oxygen environment through transcriptional changes, though the specific strategy employed varies between strains.
Local adaptation, geographical distance and phylogenetic relatedness: assessing the drivers of siderophore-mediated social interactions in natural bacterial communities
Authors: Butaitė Elena , Kramer Jos , Kümmerli Rolf
Published: December 2021

In heterogenous, spatially structured habitats, individuals within populations can become adapted to the prevailing conditions in their local environment. Such local adaptation has been reported for animals and plants, and for pathogens adapting to hosts. There is increasing interest in applying the concept of local adaptation to microbial populations, especially in the context of microbe-microbe interactions. Here, we tested whether cooperation and cheating on cooperation can spur patterns of local adaptation in soil and pond communities ofPseudomonasbacteria, collected across a geographical scale of 0.5 to 50 meters. We focused on the production of pyoverdines, a group of secreted iron-scavenging siderophores that often differ among pseudomonads in their chemical structure and the receptor required for their uptake. A combination of supernatant-feeding and competition assays between isolates from four distance categories revealed tremendous variation in the extent to which pyoverdine non- and low-producers can benefit from pyoverdines secreted by producers. However, this variation was not explained by geographical distance, but primarily depended on the phylogenetic relatedness between interacting isolates. A notable exception occurred in local pond communities, where the effect of phylogenetic relatedness was eroded in supernatant assays, probably due to the horizontal transfer of receptor genes. While the latter result could be a signature of local adaptation, our results overall indicate that common ancestry and not geographical distance is the main predictor of siderophore-mediated social interactions among pseudomonads.
Safe and easy evaluation of tmRNA-SmpB-mediatedtrans-translation in ESKAPE pathogenic bacteria
Authors: Thépaut Marion , Da Silva Rodrigo Campos , Renard Eva , Barloy-Hubler Frédérique , Ennifar Eric , Boujard Daniel , Gillet Reynald
Published: December 2021

Bacteria cope with ribosome stalling thanks totrans-translation, a major quality control system of protein synthesis that is mediated by tmRNA, an hybrid RNA with properties of both a tRNA and an mRNA, and the small protein SmpB. Becausetrans-translation is absent in eukaryotes but necessary for bacterial fitness or survival, it is a promising target for the development of novel antibiotics. To facilitate screening of chemical libraries, various reliablein vitroandin vivosystems have been created for assessingtrans-translational activity. However, none of these permits the safe and easy evaluation oftrans-translation in pathogenic bacteria, which are obviously the ones we should be targeting. Based on green fluorescent protein (GFP) reassembly during activetrans-translation, we have created a cell-free assay adapted to the rapid evaluation oftrans-translation in ESKAPE bacteria, with 24 different possible combinations. It can be used for easy high-throughput screening of chemical compounds as well as for exploring the mechanism oftrans-translation in these pathogens.
Adolescent vaccination with BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine and effectiveness against COVID-19: national test-negative case-control study, England
Authors: Powell Annabel A , Kirsebom Freja , Stowe Julia , McOwat Kelsey , Saliba Vanessa , Ramsay Mary E , Lopez-Bernal Jamie , Andrews Nick , Ladhani Shamez N
Published: December 2021

Adolescents in the UK were recommended to have their first dose of mRNA vaccine during a period of high community transmission due to the highly transmissible Delta variant, followed by a second dose at an extended interval of 8-12 weeks. We used national SARS-CoV-2 testing, vaccination and hospitalisation data to estimate vaccine effectiveness (VE) using a test-negative case-control design, against PCR-confirmed symptomatic COVID-19 in England. BNT162b2 vaccination in 12-15-year-olds and 16-17-year-olds was associated with lower VE against symptomatic COVID-19 caused by Omicron compared to Delta. Data shows a rapid increase in VE against symptomatic COVID-19 after the second dose for both Delta and Omicron, although this declines to 23% against Omicron after 70+ days. Very high protection was achieved for Delta against hospitalisation after one dose. Our data highlight the importance of the second vaccine dose for protection against symptomatic COVID-19 and raise important questions about the objectives of an adolescent immunisation programme. If prevention of infection is the primary aim, then regular COVID-19 vaccine boosters will be required.
Echinacea purpurea for the Long-term Prevention of Viral Respiratory Tract Infections during COVID-19 Pandemic: A Randomized, Open, Controlled, Exploratory Clinical Study
Authors: Kolev Emil , Mircheva Lilyana , Edwards Michael R. , Johnston Sebastian L. , Kalinov Krassimir , Stange Rainer , Gancitano Giuseppe , Berghe Wim Vanden , Kreft Samo
Published: December 2021

Introduction

SARS-CoV-2 vaccination is effective in preventing severe COVID-19, but efficacy in reducing viral load and transmission wanes over time. In addition, the emergence of novel SARS-CoV-2 variants increases the threat of uncontrolled dissemination and additional antiviral therapies are urgently needed for effective containment. In previous in vitro studies Echinacea purpurea demonstrated strong antiviral activity against enveloped viruses, including SARS-CoV-2. In this study, we examined the potential of Echinacea purpurea in preventing and treating respiratory tract infections (RTIs) and in particular, SARS-CoV-2 infections.

Methods

120 healthy volunteers (m,f, 18 – 75 years) were randomly assigned to Echinacea prevention or control group without any intervention. After a run-in week, participants went through 3 prevention cycles of 2, 2 and 1 months with daily 2’400mg Echinacea purpurea extract (Echinaforce®, EF). The prevention cycles were interrupted by breaks of 1 week. Acute respiratory symptoms were treated with 4’000 mg EF for up to 10 days, and their severity assessed via a diary. Naso/oropharyngeal swabs and venous blood samples were routinely collected every month and during acute illnesses for detection and identification of respiratory viruses, including SARS-CoV-2 via RT-qPCR and serology.

Results

Summarized over all phases of prevention, 21 and 29 samples tested positive for any virus in the EF and control group, of which 5 and 14 samples tested SARS-CoV-2 positive (RR=0.37, Chi-square test, p=0.03). Overall, 10 and 14 symptomatic episodes occurred, of which 5 and 8 were COVID-19 (RR=0.70, Chi-square test, p>0.05). EF treatment when applied during acute episodes significantly reduced the overall virus load by at least 2.12 log10 or approx. 99% (t-test, p<0.05), the time to virus clearance by 8.0 days for all viruses (Wilcoxon test, p=0.02) and by 4.8 days for SARS-CoV-2 (p>0.05) in comparison to control. Finally, EF treatment significantly reduced fever days (1 day vs 11 days, Chi-square test, p=0.003) but not the overall symptom severity. There were fewer COVID-19 related hospitalizations in the EF treatment group (N=0 vs N=2).

Discussion/Conclusion

EF exhibited antiviral effects and reduced the risk of viral RTIs, including SARS-CoV-2. By substantially reducing virus loads in infected subjects, EF offers a supportive addition to existing mandated treatments like vaccinations. Future confirmatory studies are warranted.

Clinical Trials registration Nr

NCT05002179
A new animal model signifying a decisive bridge between innate immunity and the pathognomonic morphological characteristics of Type 1 Diabetes
Authors: Angie Tegehall , Sofie Ingvast , Åsa Melhus , Oskar Skog , Olle Korsgren
Published: December 2021

Available animal models for Type 1 Diabetes (T1D) show limited similarities with the human disease and have no predictive value in screening for effective intervention therapies. Heat-inactivated bacteria instilled in the ductal compartment of the pancreas in healthy rats rapidly cause periductal inflammation and accumulation of mainly granulocytes and monocytes in the exocrine pancreas and in the peri-islet area mimicking the acute pancreatic inflammation in subjects with recent onset T1D. After three weeks, the triggered exocrine inflammation had vanished and pancreases showed normal morphology. However, a distinct accumulation of both CD4+ and CD8+ T cells within and adjacent to affected islets was found in one third of the rats, mimicking the pathognomonic insulitis in T1D. As in human T1D, the insulitis affected a fraction of all islets and was observed only in certain lobes of the pancreases. The presented animal model for T1D will allow detailed mechanistic studies to unravel a previously unknown interplay between bacteria-activated innate immunity and an acquired cellular immunity forming the immunopathological events described in humans at different stages of T1D.

Summary Statement

The results presented signify a previously unknown decisive bridge between innate immunity and formation of the pathognomonic immunopathological events described in subjects with recent onset T1D.
Develop an efficient and specific AAV based labeling system for Muller glia in mice
Authors: Gao Yanxia , Fang Kailun , Yan Zixiang , Zhang Haiwei , Geng Guannan , Wu Weiwei , Xu Ding , Zhang Heng , Zhong Na , Wang Qifang , Cai Minqing , Zuo Erwei , Yang Hui
Published: December 2021

Cell degeneration in the retina leads to several ocular diseases and vision loss. Considerable research efforts focus on reprogramming Muller glia (MG) into functional cells to rescue vision as a promising therapeutic strategy, although whether MG can convert into functional bipolar cells, retinal ganglia cells (RGCs), rods or cones in mammals remains controversial. The broad applicability of tracking MG differentiation thus presents a need for improved labeling efficiency and specificity. Here, we compared AAV-based labeling strategies with conventional lineage-tracking by crossing transgenic mouse lines. We found that reporter expression was weak and not MG-specific in mGFAP-Cre transgenic mice. Different AAV serotypes showed a range of efficiency and specificity in labeling MG, leading us to optimize a human GFAP-Cre reporter system packaged in the AAV9 serotype with the WPRE (WPRE, woodchuck hepatitis virus post-transcriptional regulatory element) removed. The hGFAP-Cre- ΔWPRE reporter could label 20-73.8% MGs, with non-specific RGC labeling rates ranging from 0-0.08% at doses of 1 × 108 to 1010 vector genomes (vg) per eye, an approximate 40-fold reduction compared with the AAV9-hGFAP-Cre-WPRE labeling system. Furthermore, we validated the availability of the label system to trace MG reprogramming and also detected false-positive results reported previously. The AAV9-hGFAP-Cre-ΔWPRE system thus represents a highly efficient and specific labeling system for MG, providing a valuable tool for tracking cell fate in vivo.
Using network analysis to illuminate the intergenerational transmission of adversity in the ALSPAC cohort
Authors: Hemady Chad Lance , Speyer Lydia Gabriela , Kwok Janell , Meinck Franziska , Melendez-Torres G.J. , Fry Deborah , Auyeung Bonnie , Murray Aja Louise
Published: December 2021

Objective

The effects of maternal exposure to adverse childhood experiences (ACEs) may be transmitted to subsequent generations through various biopsychosocial mechanisms. However, studies tend to focus on exploring one or two focal pathways with less attention paid to links between different pathways. Using a network approach, this paper explores a range of core prenatal risk factors that may link maternal ACEs to infant preterm birth (PTB) and low birthweight (LBW).

Methods

We used data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 8 379) to estimate two mixed graphical network models: Model 1 was constructed using adverse infant outcomes, biopsychosocial and environmental risk factors, forms of ACEs, and sociodemographic factors. In Model 2, ACEs were combined to represent a threshold ACEs score (≥ 4). Network indices were estimated to determine the shortest pathway from ACEs to infant outcomes, and to identify the risk factors that are most vital in bridging these variables.

Results

In both models, childhood and prenatal risk factors were highly interrelated. Childhood physical abuse, but not threshold ACEs, was directly linked to LBW. Further, exposure to second-hand smoke, developing gestational hypertension, prenatal smoking, first time pregnancy, not being White, and older age were directly linked to LBW, while developing gestational diabetes, having previous pregnanc(ies), and lower educational attainment were associated with PTB. Only pre-eclampsia was directly linked to both outcomes. Network indices and shortest pathways plots indicate that sexual abuse played a central role in bridging ACEs to other risks and poor infant outcomes. Overall, prenatal smoking was determined as the most influential bridge node.

Conclusions

As child physical abuse was directly linked to low birthweight, and child sexual abuse and prenatal smoking were the most influential bridge nodes, they can be considered priority candidate targets for interventions to disrupt intergenerational risk transmission. Further, our study demonstrates the promise of network analysis as an approach for illuminating the intergenerational transmission of adversity in its full complexity.
Chromosome-level genome assembly of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni)
Authors: Wang Gaojianyong , Brändl Björn , Rohrandt Christian , Hong Karl , Pang Andy , Lee Joyce , Lewin Harris A. , Migliorelli Giovanna , Stanke Mario , Schwab Remy , Ford Sarah , Pollmann Iris , Schuldt Bernhard M. , Houck Marlys , Ryder Oliver A. , Meissner Alexander , Loring Jeanne F. , Müller Franz-Josef , Korody Marisa L.
Published: December 2021

The northern white rhinoceros (NWR; Ceratotherium simum cottoni) is functionally extinct, with only two females remaining alive. Efforts to rescue the NWR have inspired the exploration of unconventional conservation methods, including the generation of artificial gametes from induced pluripotent stem cells and somatic cell nuclear transfer. To enable the technologies required for these approaches, we used complementary sequencing and mapping methods to generate a NWR chromosome-level reference genome that meets or exceeds the metrics proposed by the Vertebrate Genome Project. It represents 40 autosomes, an X and a partially-resolved Y chromosome, and the mitochondrial genome. We compared the NWR reference genome to the southern white rhinoceros (SWR) population that has been physically separated from the NWR for tens of thousands of years. Using short-read data from the SWR and optical mapping, we found that the two populations are very similar on both the chromosome level and mitochondrial genome level. The results of this study are encouraging for the efforts underway to rescue the NWR.
Pre-Operative Kidney Biomarkers and Risks for Death, Cardiovascular and Chronic Kidney Disease Events: The TRIBE-AKI Study
Authors: Vasquez-Rios George , Moledina Dennis G. , Jia Yaqi , McArthur Eric , Mansour Sherry G. , Thiessen-Philbrook Heather , Shlipak Michael G. , Koyner Jay L. , Garg Amit X. , Parikh Chirag R. , Coca Steven G. ,   TRIBE-AKI Consortium
Published: December 2021

Background

Soluble tumor necrosis factor receptor (sTNFR)1, sTNFR2, and plasma kidney injury molecule-1 (KIM-1) are associated with kidney events in patients with and without diabetes. However, their associations with clinical outcomes when obtained pre-operatively have not been explored.

Methods

The TRIBE-AKI cohort study is a prospective, multicenter, cohort study of high-risk adults undergoing cardiac surgery. We assessed the associations between pre-operative concentrations of plasma sTNFR1, sTNFR2, and KIM-1 and post-operative long-term outcomes including mortality, cardiovascular events, and chronic kidney disease (CKD) incidence or progression, ascertained after discharge.

Results

Among 1378 participants included in the analysis with a median follow-up period was 6.7 (IQR 4.0-7.9), 434 (31%) patients died, 256 (19%) experienced cardiovascular events and out of 837 with available long-term kidney function data, 30% developed CKD. After adjustment for clinical covariates, each log increase in biomarker concentration was independently associated with mortality with 95%CI adjusted hazard ratios (aHRs) of 3.0 (2.3-4.0), 2.3 (1.8-2.9) and 2.0 (CI 1.6-2.4) for sTNFR1, sTNFR2 and KIM-1, respectively. For cardiovascular events, the 95%CI aHRs were 2.1 (1.5 – 3.1), 1.9 (1.4 – 2.6) and 1.6 (1.2 – 2.1) for sTNFR1, sTNFR2 and KIM-1, respectively. For CKD events, the aHRs were 2.2 (1.5 – 3.1) for sTNFR1, 1.9 (1.3 – 2.7) for sTNFR2, and 1.7 (1.3 – 2.3) for KIM-1. Despite the associations, each of the biomarkers alone or in combination failed to result in robust discrimination on an absolute basis or compared to a clinical model.

Conclusion

sTNFR1, sTNFR2, and KIM-1 were independently associated with longitudinal outcomes after discharge from a cardiac surgery hospitalization including death, cardiovascular and CKD events when obtained pre-operatively in high-risk individuals. Pre-operative plasma biomarkers could serve to assist during the evaluation of patients in whom cardiac surgery is planned.
Guiding ATR and PARP inhibitor combinations with chemogenomic screens
Authors: Zimmermann Michal , Bernier Cynthia , Kaiser Beatrice , Fournier Sara , Li Li , Desjardins Jessica , Skeldon Alexander , Rimkunas Victoria , Veloso Artur , Young Jordan T. F. , Roulston Anne , Zinda Michael
Published: December 2021

Combinations of inhibitors of Ataxia Telangiectasia- and Rad3-related kinase (ATRi) and poly(ADP-ribose) polymerases (PARPi) synergistically kill tumor cells through modulation of complementary DNA repair pathways, but their tolerability is limited by hematological toxicities. To address this we performed a genome-wide CRISPR/Cas9 screen to identify genetic alterations that hypersensitize cells to a combination of the ATRi RP-3500 with PARPi, including deficiency in RNase H2, RAD51 paralog mutations or the Alternative Lengthening of Telomeres telomere maintenance mechanism. We show that RP-3500 and PARPi combinations kill cells carrying these genetic alterations at doses sub-therapeutic as single agents. We also demonstrate the mechanism of combination hypersensitivity in RNase H2-deficient cells, where we observe an irreversible replication catastrophe, allowing us to design a highly efficacious and tolerable in vivo dosing schedule. Altogether, we present a comprehensive dataset to inform development of ATRi and PARPi combinations and an experimental framework applicable to other drug combination strategies.
Identifying long-range synaptic inputs using genetically encoded labels and volume electron microscopy
Authors: Ayuso-Jimeno Irene P. , Ronchi Paolo , Wang Tianzi , Gallori Catherine , Gross Cornelius T.
Published: December 2021

Enzymes that facilitate the local deposition of electron dense reaction products have been widely used as labels in electron microscopy (EM). Peroxidases, in particular, can efficiently metabolize 3,3’-diaminobenzidine tetrahydrochloride hydrate (DAB) to produce precipitates with high contrast under EM following heavy metal staining, and can be genetically encoded to facilitate the labeling of specific cell-types or organelles. Nevertheless, the peroxidase/DAB method has so far not been reported to work in combination with 3D volume EM techniques (e.g. Serial blockface electron microscopy, SBEM; Focused ion beam electron microscopy, FIBSEM) because the surfactant treatment needed for efficient reagent penetration disrupts tissue ultrastructure and because these methods require the deposition of large amounts of heavy metals that can obscure DAB precipitates. However, a recently described peroxidase with enhanced enzymatic activity (dAPEX2) appears to successfully deposit EM-visible DAB products in thick tissue without surfactant treatment. Here we demonstrate that multiplexed dAPEX2/DAB tagging is compatible with both FIBSEM and SBEM volume EM approaches and use them to map long-range genetically identified synaptic inputs from the anterior cingulate cortex to the periaqueductal gray in the mouse brain.
PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
Authors: Patz S. , Gautam A. , Becker M. , Ruppel S. , Rodríguez-Palenzuela P. , Huson DH.
Published: December 2021

Plant-beneficial microorganisms are gaining importance for sustainable plant production and phytosanitary practices. Yet there is a lack of computational approaches targeting bacterial traits associated with plant growth-promotion (PGP), which hinders the in-silico identification, comparison, and selection of phytostimulatory bacterial strains. To address this problem, we have developed the new web resource PLaBAse (v1.01, http://plabase.informatik.uni-tuebingen.de/pb/plabase.php), which provides a number of services, including (i) a database for screening 5,565 plant-associated bacteria (PLaBA-db), (ii) a tool for predicting plant growth-promoting traits (PGPTs) of single bacterial genomes (PGPT-Pred), and (iii) a tool for the prediction of bacterial plant-association by marker gene identification (PIFAR-Pred). The latter was developed by Martínez-García et al. and is now hosted at University of Tuebingen. The PGPT-Pred tool is based on our new PGPT ontology, a literature- and OMICs-curated, comprehensive, and hierarchical collection of ∼6,900 PGPTs that are associated with 6,965,955 protein sequences. To study the distribution of the PGPTs across different environments, we applied it to 70,540 bacterial strains associated with (i) seven different environments (including plants), (iii) five different plant spheres (organs), and (iii) two bacteria-induced plant phenotypes. This analysis revealed that plant-symbiotic bacteria generally have a larger genome size and a higher count of PGPT-annotated protein encoding genes. Obviously, not all reported PGPTs are restricted to -or only enriched in-plant-associated and plant symbiotic bacteria. Some also occur in human- and animal-associated bacteria, perhaps due to the transmission of PGP bacteria (PGPBs) between environments, or because some functions are involved in adaption processes to various environments. Here we provide an easy-to-use approach for screening of PGPTs in bacterial genomes across various phyla and isolation sites, using PLaBA-db, and for standardized annotation, using PGPT-Pred. We believe that this resource will improve our understanding about the entire PGP processes and facilitate the prediction of PGPB as bio-inoculants and for biosafety strategies, so as to help to establish sustainable and targeted bacteria-incorporated plant production systems in the future.
A calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome
Authors: Jiang Connie , Richardson Ebony , Farr Jessica , Hill Adam P. , Ullah Rizwan , Kroncke Brett M. , Harrison Steven M. , Thomson Kate L. , Ingles Jodie , Vandenberg Jamie I. , Ng Chai-Ann
Published: December 2021

Purpose

Modern sequencing technologies have revolutionised our detection of gene variants. In most genes, including KCNH2, the majority of missense variants are currently classified as variants of uncertain significance (VUS). The aim of this study is to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in the KCNH2 gene.

Methods

The assay was designed according to recommendations of the ClinGen sequence variant interpretation framework. Thirty-one control variants of known clinical significance (17 pathogenic/likely pathogenic, 14 benign/likely benign) were heterozygously expressed in Flp-In HEK293 cells. Variants were analysed for effects on current density and channel gating. A panel of 44 VUS was then assessed for reclassification.

Results

All 17 pathogenic variant controls had reduced current density and 13/14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying moderate or supporting evidence strength for variant classification. Inclusion of KCNH2 functional assay evidence enabled us to reclassify 6 out of 44 VUS as likely pathogenic.

Conclusion

The high-throughput patch clamp assay can provide moderate strength evidence for clinical interpretation of clinical KCNH2 variants and demonstrates the value proposition for developing automated patch clamp assays for other ion channel genes.
The Geometry of Representational Drift in Natural and Artificial Neural Networks
Authors: Aitken Kyle , Garrett Marina , Olsen Shawn , Mihalas Stefan
Published: December 2021

Neurons in sensory areas encode/represent stimuli. Surprisingly, recent studies have suggested that, even during persistent performance, these representations are not stable and change over the course of days and weeks. We examine stimulus representations from fluorescence recordings across hundreds of neurons in the visual cortex using in vivo two-photon calcium imaging and we corroborate previous studies finding that such representations change as experimental trials are repeated across days. This phenomenon has been termed “representational drift”. In this study we geometrically characterize the properties of representational drift in the primary visual cortex of mice in two open datasets from the Allen Institute and propose a potential mechanism behind such drift. We observe representational drift both for passively presented stimuli, as well as for stimuli which are behaviorally relevant. Across experiments, the drift most often occurs along directions that have the most variance, leading to a significant turnover in the neurons used for a given representation. Interestingly, despite this significant change due to drift, linear classifiers trained to distinguish neuronal representations show little to no degradation in performance across days. The features we observe in the neural data are similar to properties of artificial neural networks where representations are updated by continual learning in the presence of dropout, i.e. a random masking of nodes/weights, but not other types of noise. Therefore, we conclude that a potential reason for the representational drift in biological networks is driven by an underlying dropout-like noise while continuously learning and that such a mechanism may be computational advantageous for the brain in the same way it is for artificial neural networks, e.g. preventing overfitting.
Structure-guided optimization of light-activated chimeric G-protein coupled receptors
Authors: Tichy Alexandra-Madelaine , So Wang Lok , Gerrard Elliot J. , Janovjak Harald
Published: December 2021

G-protein coupled receptors (GPCRs) are the largest human receptor family and involved in virtually every physiological process. One hallmark of GPCR function is the specific coupling of activated receptors to selected downstream signaling pathways. The ability to tune this coupling would permit the development of receptors with new capabilities. GPCRs and G-proteins have been recently resolved structurally at high resolution, but this information was in only very few cases harnessed for a rational engineering of these protein complexes. Here, we demonstrate the structure-guided optimization of coupling in chimeric light-activated GPCRs (OptoXRs). Our hypothesis was that the incorporation of structural GPCR-Gα contacts will lead to improved receptor activity. We first evaluated structure-based alignments as complements to existing sequence-based methods for generation of chimeric receptors. We then show in a prototypical light-activated β2AR that inclusion of α-helical residues forming structural contacts to Gα resulted in receptors with 7- to 20-fold increased function compared to other design strategies. In turn, elimination of GPCR-Gα contacts diminished function. Finally, the efficient receptor design served as a platform for the optimization of a further light-activated receptor and spectral tuning of the photoreceptor core domain. Our work exemplifies how increased OptoXR potency and new functionalities can be achieved through structure-based design towards targeted inputs into cells and cellular networks.
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion
Authors: Garb Jeremy , Lopatina Anna , Bernheim Aude , Zaremba Mindaugas , Siksnys Virginijus , Melamed Sarah , Leavitt Azita , Millman Adi , Amitai Gil , Sorek Rotem
Published: December 2021

Defense-associated sirtuins (DSR) comprise a family of proteins that defend bacteria from phage infection via an unknown mechanism. These proteins are common in bacteria and harbor an N-terminal sirtuin (SIR2) domain. In this study we report that DSR proteins degrade nicotinamide adenine dinucleotide (NAD+) during infection, depleting the cell of this essential molecule and aborting phage propagation. Our data show that one of these proteins, DSR2, directly identifies phage tail tube proteins and then becomes an active NADase in Bacillus subtilis. Using a phage mating methodology that promotes genetic exchange between pairs of DSR2-sensitive and DSR2–resistant phages, we further show that some phages express anti-DSR2 proteins that bind and repress DSR2. Finally, we demonstrate that the SIR2 domain serves as an effector NADase in a diverse set of phage defense systems outside the DSR family. Our results establish the general role of SIR2 domains in bacterial immunity against phages.
Key features of inhibitor binding to the human mitochondrial pyruvate carrier hetero-dimer
Authors: Tavoulari Sotiria , Schirris Tom J.J. , Mavridou Vasiliki , Thangaratnarajah Chancievan , King Martin S. , Jones Daniel T.D. , Ding Shujing , Fearnley Ian M. , Kunji Edmund R.S.
Published: December 2021

The mitochondrial pyruvate carrier (MPC) has emerged as a promising drug target for metabolic disorders, including non-alcoholic steatohepatitis and diabetes, metabolically dependent cancers and neurodegenerative diseases. Human MPC is a protein complex, but the composition of its active form is debated and the mechanisms of transport and inhibition are not resolved. We have recombinantly expressed and purified the human hetero-complex MPC1L/MPC2 and demonstrate that it is a functional hetero-dimer, like the yeast MPC hetero-dimers. Unlike the latter, human MPC1L/MPC2 binds the known inhibitors with high potencies. We identify the essential chemical features shared between these structurally diverse inhibitors and demonstrate that high affinity binding is not attributed to covalent bond formation with MPC cysteines, as previously thought. We also identify 14 new inhibitors of MPC, one outperforming the most potent compound UK5099 by tenfold. Two of them are the commonly prescribed drugs entacapone and nitrofurantoin, suggesting possible off-target mechanisms associated with their adverse effects. This work advances our understanding of MPC inhibition and will accelerate the development of clinically relevant MPC modulators.
Control of G2 phase duration by CDC25B modulates the switch from direct to indirect neurogenesis in the neocortex
Authors: Roussat Mélanie , Jungas Thomas , Audouard Christophe , Medevielle Francois , Davy Alice , Pituello Fabienne , Bel-Vialar Sophie
Published: December 2021

During development, cortical neurons are produced in a temporally regulated sequence from apical progenitors, directly, or indirectly through the production of intermediate basal progenitors. The balance between these major progenitors’ types is determinant for the production of the proper number and types of neurons and it is thus important to decipher the cellular and molecular cues controlling this equilibrium. Here we address the role of a cell cycle regulator, the CDC25B phosphatase, in this process. We show that deleting CDC25B in apical progenitors leads to a transient increase of the production of TBR1+ neurons at the expense of TBR2+ basal progenitors in mouse neocortex. This phenotype is associated with lengthening of the G2 phase of the cell cycle, the total cell cycle length being unaffected. Using in utero electroporation and cortical slice cultures, we demonstrate that the defect in TBR2+ basal progenitor production requires interaction with CDK1 and is due to the G2 phase lengthening in CDC25B mutants. Altogether, this study identifies a new role for CDC25B and the length of the G2 phase in direct versus indirect neurogenesis at early stages of the cortical development.
The role of initiative climate as a resource caravan passageway in developing proactive service performance
Authors: Aslam Muhammad Zia , Fateh Adnan , Omar Safiah , Nazri Mohammad
Published: December 2021

Purpose

The study aims to examine the role of initiative climate as a resource caravan passageway in engaging employees and developing a proactive frontline service workforce to identify the mechanisms whereby scarce resources efficiently yielding the desired outcomes can help organizations improve productivity and gain competitive advantage, thereby helping clarify the leadership–performance relationship in service organizations.

Design/methodology/approach

The study employed a quantitative research design with a cross-sectional survey conducted among frontline hospitality employees in Malaysia. Partial least squares structural equation modeling (PLS-SEM) was used to examine the hypothesized relationships.

Findings

The initiative climate is significant as a resource caravan passageway to transmit the positive impact of interpersonal leadership onto the engagement and proactive performance of frontline hospitality employees in whom initiative climate and employee engagement sequentially mediated the relationship between interpersonal leadership and proactive service performance.

Research limitations/implications

The online data collection procedure conducted through LinkedIn and Facebook and cross-sectional, self-reported survey method are significant limitations of the current study.

Practical implications

The findings of the study will aid in developing organizational interventions for an engaged and proactive frontline service workforce, as interpersonal leadership can positively impact the engagement and proactive behavior of frontline service employees via initiative climate. Therefore, hospitality managers should value interpersonal leadership and initiative climate as coexisting organizational resources.

Originality/value

The study shows the significance of initiative climate in the relationships between interpersonal leadership, employee engagement and the proactive performance of frontline service employees.
Sensitivity analysis for automotive EMC measurements using quasistatic Darwin model
Authors: Bingler Arnold , Bilicz Sándor , Csörnyei Márk
Published: December 2021

Purpose

The purpose of this paper is performing a global sensitivity analysis for automotive electromagnetic compatibility (EMC) measurements related to the CISPR 25 setup in order to examine the effect of the setup uncertainties on the resonance phenomenon.

Design/methodology/approach

An integral equation formulation is combined with Darwin model and special Green’s functions to model the configuration. The method of Sobol’ indices is used to gain sensitivity factors enhanced with a polynomial chaos metamodel.

Findings

The proposed model resulted in by orders of magnitude lower number of degrees of freedom and runtime compared to popular numerical methods, e.g. finite element method. The result of the sensitivity study is in good agreement with the underlying physical phenomena and improves the understanding of the resonances.

Practical implications

The fast model supplemented by the sensitivity factors can be used in EMC design and optimization.

Originality/value

The proposed method is original in the sense of combining a polynomial chaos metamodel with a low-cost integral equation model to reduce the computational demand for the sensitivity study.
A solution to the problem of brand definition
Authors: Avis Mark , Henderson Isaac Levi
Published: December 2021

Purpose

This paper aims to critically evaluate the definition of the brand concept, support the critique with an empirical study and provide a definition to resolve the problems that have been identified.

Design/methodology/approach

This paper combines a conceptual critique with empirical research using a sample of 730 journal papers to analyse the scope and number of brand-related concepts in extant literature.

Findings

The brand concept has evolved to become problematic with no clarity of definition. There has been an explosion in the number of brand-related concepts that make the brand concept opaque and unwieldy. Based upon the findings, the authors argue that it is necessary to return to a “label and associations model” of the brand concept to ameliorate these issues.

Research limitations/implications

The empirical research presented examines only 730 papers from a much wider body of brand literature. Nonetheless, it illustrates the fact that researchers and theorists are not talking about the same concept when using the term “brand”.

Practical implications

Practitioners are not being served by academic branding literature because no two researchers appear to be studying the same entity. This prevents a body of research from being built to guide practitioners.

Originality/value

This paper makes an original contribution by combining a conceptual critique and empirical study to examine the problems arising from the absence of an agreed definition of the brand concept and uses this as a foundation for creating a resolution to the problems.
How location-based messages influence customers' store visit attitudes: an integrative model of message value
Authors: Verhagen Tibert , Meents Selmar , Merikivi Jani , Moes Anne , Weltevreden Jesse
Published: December 2021

Purpose

This study aims to develop an understanding of how customers of a physical retail store valuate receiving location-based mobile phone messages when they are in proximity of the store. It proposes and tests a model relating two benefits (personalization and location congruency) and two sacrifices (privacy concern and intrusiveness) to message value perceptions and store visit attitudes.

Design/methodology/approach

The study uses a vignette-based survey to collect data from a sample of 1,225 customers of a fashion retailer. The postulated research model is estimated using SmartPLS 3.0 with the consistent-PLS algorithm and further validated via a post-hoc test.

Findings

The empirical testing confirms the predictive validity and robustness of the model and reveals that location congruency and intrusiveness are the location-based message characteristics with the strongest effects on message value and store visit attitude.

Originality/value

The paper adds to the underexplored field of store entry research and extends previous location-based messaging studies by integrating personalization, location congruency, privacy concern and intrusiveness into one validated model.
Framing and conflict: the case of the Asante Akyem North district’s farmer-herder conflict in Ghana
Authors: Appiah-Boateng Sabina , Kendie Stephen B.
Published: December 2021

Purpose

The purpose of this paper is to explore how framing of conflict in different phases is constructed and how the specific framing affects the development of the conflict and its management in the farmer–herder conflict in the Asante Akyem North District of Ghana.

Design/methodology/approach

The study area is Agogo which falls within the Asante Akyem North District in Ghana. The study used a qualitative approach whose philosophical ontology and epistemology believe that meaning is constructed (interpretivism). It further used a case study design using in-depth interviews, focus group discussion and observation guide. Purposive and snowball sampling techniques were used to select the respondents. The data were analysed using the thematic analysis approach. Ethical considerations such as informed consent, willingness and anonymity of respondents were duly respected.

Findings

The findings highlighted that the conflict actors formed frames such as identity-relational, affective-intellectual and negotiation-win frames as the drivers of the conflict. In this conflict, the farmers who are indigenes and custodians of the land feel more potent over the transnational migrants who are pastoralists and argue that the herdsmen be flushed out without negotiation.

Originality/value

To the best of the authors’ knowledge, this is one of the papers that bring to light the psychological dimension of the causes of the farmer–herder conflict in Ghana.
Investigating the relationship between bank performance and accounting standards: evidence from M&As in European banking
Authors: Akgün Ali İhsan
Published: December 2021

Purpose

The study aims to identify whether international financial reporting standards (IFRS) or local generally accepted accounting principles (GAAP) reporting provides investors and senior management of acquirer banks with superior information on target banks under post-merger bank performance.

Design/methodology/approach

The authors examine the claim that IFRS improves corporate transparency and increases financial reporting quality in European Bank merger and acquisitions (M&As). The authors compare the financial performance of merged banks where the target and acquirer banks employed the same reporting system (up to 305 merged banks) to the performance of a control group of banks not engaged in M&A activity (up to 1,690 European banks).

Findings

Local GAAP reporting allows a more transparent assessment of financial performance using traditional indicators, making it a superior tool for assessing potential acquisition targets.

Practical implications

Overall, the empirical findings are consistent with prior studies and indicate a significant relationship between local GAAP and post-merger performance, while IFRS does not contribute to post-merger bank performance.

Originality/value

The study is one of the very few studies to investigate the relationship between bank performance, M&A activity and accounting standards in EU-28 countries. The primary contribution the finding of poor performance of IFRS reporting merged banks compared to local GAAP banks in EU-28 countries in line with prior results of Huian (2012). In addition, several deal- and bank-specific characteristics that affect accounting standards influence M&A transactions in European banks.