bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of two microbial source tracking markers for detection of wastewater-associatedEscherichia coliisolates
Authors: Gomi Ryota , Haramoto Eiji , Wada Hiroyuki , Sugie Yoshinori , Ma Chih-Yu , Raya Sunayana , Malla Bikash , Nishimura Fumitake , Tanaka Hiroaki , Ihara Masaru 
Published: August 2022

ABSTRACTEscherichia colihas been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identifyE. colimicrobial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewaterE. coligenomes sequenced by us (n = 50) and RefSeq animalE. coligenomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewaterE. coligenomes and 3,318 RefSeq animalE. coligenomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associatedE. coliisolates. These two markers showed higher performance than the previously developed human wastewater-associatedE. colimarkers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9% and sensitivity of 25.7%. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detectingE. coliisolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.
Basins of attraction of microbiome structure and soil ecosystem functions
Authors: Fujita Hiroaki , Yoshida Shigenobu , Suzuki Kenta , Toju Hirokazu 
Published: August 2022

AbstractTheory predicts that biological communities can have multiple basins of attraction in terms of their species/taxonomic compositions. The presence of such basins of community structure has been examined in classic empirical studies on forest–savanna transitions and those on eutrophication in freshwater lakes. Nonetheless, it remains a major challenge to extend the investigations of multistability to species-rich microbial communities. By targeting soil microbiomes, we infer the stability landscapes of community structure based on the concepts of statistical physics. Our analysis on the compiled dataset involving 11 archaeal, 332 bacterial, and 240 fungal families detected from > 1,500 agroecosystem soil samples suggested that both prokaryotic and fungal community compositions could be classified into several basins of attraction. We also found that the basins differed greatly in their associations with crop disease prevalence in agroecosystems. A further analysis highlighted microbial taxa potentially playing key roles in transitions between basins with different ecosystem-scale functions. The statistical framework commonly applicable to diverse microbial and non-microbial communities will reorganize our understanding of relationship among community structure, stability, and functions.
snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling
Authors: Vallejo Andres F , Harvey Kate , Wang Taopeng , Wise Kellie , Butler Lisa M. , Polo Jose , Plummer Jasmine , Swarbrick Alex , Martelotto Luciano G 
Published: August 2022

AbstractFFPE (formalin-fixed, paraffin-embedded) tissue archives are the largest repository of clinically annotated human specimens. Despite numerous advances in technology, current methods for sequencing of FFPE-fixed single-cells are slow, labour intensive, insufficiently sensitive and have a low resolution, making it difficult to fully exploit their enormous research and clinical potential. Here we introduce single nuclei pathology sequencing (snPATHO-Seq), a sensitive and efficient high-throughput platform to profile the transcriptome of single nuclei extracted from formalin-fixed paraffin-embedded (FFPE) samples. snPATHO-Seq combines an optimised nuclei extraction protocol from archival samples with 10x Genomics probe-based technology targeting the whole transcriptome. We performed direct comparison of the Fixed RNA Profiling (FRP) and established 3’ single cell RNA-Sequencing (scRNA-Seq) workflows through a comprehensive bioinformatics analysis of matched fresh and fixed samples derived from the LNCaP prostate cancer cell line. FRP detected 2.1 times more transcripts in the fixed sample than the 3’ kit did in the fresh sample. Low mitochondrial genes detection using the FRP was translated into 99.9 percent of cells passing the QC filters, compared to 81.6 percent of cells using the v3.1 chemistry. We then optimized snPATHO-Seq and applied it to a human breast cancer metastasis to the liver collected at autopsy and preserved in FFPE, a particularly challenging sample type. Remarkably, at 28,000 reads/cell snPATHO-Seq was able to detect a median of 1850 genes/cell and 3,216 UMI counts/cell. Comparison of snPATHO-Seq with spatial transcriptomics data (10x Genomics Visium FFPE v1) derived from an adjacent section of the same sample revealed a strong correlation, validating the accuracy of the snPATHO-Seq data. Gene expression data from snPATHO-Seq was used to predict cell type composition within each spatial transcriptomic location via deconvolution. Overall, snPATHO-Seq enables high quality and sensitivity snRNA-Seq from preserved tissue samples, unlocking the vast archives of FFPE tissues and thereby allowing extensive retrospective clinical genomic studies.
EnterotoxigenicEscherichia coliheat-labile toxin drives enteropathic changes in small intestinal epithelia
Authors: Sheikh Alaullah , Tumala Brunda , Vickers Tim J. , Martin John C. , Rosa Bruce A. , Sabui Subrata , Basu Supratim , Simoes Rita D. , Mitreva Makedonka , Storer Chad , Tyksen Erik , Head Richard D. , Beatty Wandy , Said Hamid M. , Fleckenstein James M. 
Published: August 2022

abstractEnterotoxigenicE. coli(ETEC), produce heat-labile (LT) and/or heat-stable (ST) enterotoxins, and are a common cause of diarrhea in children of resource-poor regions. ETEC have also been linked repeatedly to poorly understood sequelae including enteropathy, malnutrition, and growth impairment. While the cellular actions of ETEC enterotoxins leading to diarrhea are well-established, their potential contribution to subsequent pathology is unclear. LT stimulates cellular cAMP production to activate protein kinase A (PKA) which phosphorylates cellular ion channels that drive export of salt and water into the intestinal lumen resulting in diarrhea. However, as PKA exhibits broad kinase activity and its activated catalytic subunits modulate transcription of many genes, we interrogated the transcriptional profiles of LT-treated small intestinal epithelia. These studies demonstrated toxin-induced changes in hundreds of genes including those required for biogenesis and function of the brush border, the major site absorption of nutrients, and suppression of a key transcription factors, HNF4 and SMAD4, critical to differentiation of intestinal epithelia. Accordingly, LT treatment of intestinal epithelial cells significantly disrupted the absorptive microvillus architecture and altered transport of essential nutrients. In addition, challenge of neonatal mice with LT-producing ETEC recapitulated the architectural derangement of the brush border while maternal vaccination with LT prevented brush border disruption in ETEC-challenged neonatal mice. Finally, mice repeatedly challenged with toxigenic ETEC exhibited impaired growth recapitulating the multiplicative impact of recurring ETEC infections in children. These findings highlight impacts of ETEC enterotoxins beyond acute diarrheal illness and may inform approaches to mitigate and prevent major sequelae including malnutrition that impact millions of young children.
The fungal expel of 5-fluorocytosine derived fluoropyrimidines mitigates its antifungal activity and generates a cytotoxic environment
Authors: Sastré-Velásquez Luis Enrique , Dallemulle Alex , Kühbacher Alexander , Baldin Clara , Alcazar-Fuoli Laura , Niedrig Anna , Müller Christoph , Gsaller Fabio 
Published: August 2022

AbstractInvasive aspergillosis remains one of the most devastating fungal diseases and is predominantly linked to infections caused by the opportunistic human mold pathogen Aspergillus fumigatus. Major treatment regimens for the disease comprise the administration of antifungals belonging to the azole, polyene and echinocandin drug class. The prodrug 5-fluorocytosine (5FC), which is the only representative of a fourth class, the nucleobase analogs, shows unsatisfactory in vitro activities and is barely used for the treatment of aspergillosis. The main route of 5FC activation in A. fumigatus comprises its deamination into 5-fluorouracil (5FU) by FcyA, which is followed by Uprt-mediated 5FU phosphoribosylation into 5-fluorouridine monophosphate (5FUMP). In this study, we characterized and examined the role of a metabolic bypass that generates this nucleotide via 5-fluorouridine (5FUR) through uridine phosphorylase and uridine kinase activities. Resistance profiling of mutants lacking distinct pyrimidine salvage activities suggested a minor contribution of the alternative route in 5FUMP formation. We further analyzed the contribution of drug efflux in 5FC tolerance and found that A. fumigatus cells exposed to 5FC reduce intracellular fluoropyrimidine levels through their export into the environment. This release, which was particularly high in mutants lacking Uprt, generates a toxic environment for cytosine deaminase lacking mutants as well as mammalian cells. Employing the broad-spectrum fungal efflux pump inhibitor clorgyline, we demonstrate synergistic properties of this compound in combination with 5FC, 5FU as well as 5FUR.
The Ebola virus VP40 matrix undergoes endosomal disassembly essential for membrane fusion
Authors: Winter Sophie L. , Golani Gonen , Lolicato Fabio , Vallbracht Melina , Thiyagarajah Keerthihan , Ahmed Samy Sid , Lüchtenborg Christian , Fackler Oliver T. , Brügger Britta , Hoenen Thomas , Nickel Walter , Schwarz Ulrich S. , Chlanda Petr 
Published: August 2022

AbstractEbola viruses (EBOVs) are filamentous particles, whose shape and stability are determined by the VP40 matrix. Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40-lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH-driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.
JNK signalling regulates self-renewal of proliferative urine-derived renal progenitor cells via inhibition of ferroptosis
Authors: Nguyen Lisa , Westerhoff Michelle , Thewes Leonie , Wruck Wasco , Reichert Andreas S. , Berndt Carsten , Adjaye James 
Published: August 2022

SummaryWith a global increase in chronic kidney disease patients, alternatives to dialysis and organ transplantation are needed. Stem cell-based therapies could be one possibility to treat chronic kidney disease. Here, we used multipotent urine-derived renal progenitor cells (UdRPCs) to study nephrogenesis. UdRPCs treated with the JNK inhibitor-AEG3482, displayed decreased proliferation and downregulated transcription of cell cycle-associated genes as well as the kidney progenitor markers -SIX2, CITED1, and SALL1. In addition, levels of activated SMAD2/3, which is associated with the maintenance of self-renewal in UdRPCs, were decreased. JNK inhibition resulted in less efficient oxidative phosphorylation and more lipid peroxidation via ferroptosis-an iron-dependent non-apoptotic cell death pathway linked to various forms of kidney disease. Our study reveals the importance of JNK signalling in maintaining self-renewal as well as protection against ferroptosis in SIX2-positive UdRPCs. We propose that UdRPCs can be used for modelling ferroptosis-induced kidney diseases.
Rotavirus NSP1 subverts the antiviral OAS-RNase L pathway by inducing RNase L degradation
Authors: Dai Jin , Yi Guanghui , Philip Asha A. , Patton John T. 
Published: August 2022

ABSTRACTThe interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS) - RNase L pathway plays a critical role in antiviral immunity. Group A rotaviruses, including the simian SA11 strain, inhibit this pathway through two activities: an E3-ligase related activity of NSP1 that degrades proteins necessary for IFN signaling, and a phosphodiesterase (PDE) activity of VP3 that hydrolyzes the RNase L-activator 2′,5′-oligoadenylate. Unexpectedly, we found that a recombinant (r) SA11 double-mutant virus deficient in both activities (rSA11-VP3H797R-NSP1ΔC17) retained the ability to prevent RNase L activation. Mass spectrometry led to the discovery that NSP1 interacts with RNase L in rSA11-infected MA104 cells. This interaction was confirmed through co-pulldown assay of cells transiently expressing NSP1 and RNase L. Immunoblot analysis showed that infection with wild type rSA11 virus, rSA11-VP3H797R-NSP1ΔC17 double-mutant virus, or single mutant forms of the latter virus, all resulted in the depletion of endogenous RNase L. The loss of RNase L was reversed by addition of the neddylation inhibitor MLN4924, but not the proteasome inhibitor MG132. Analysis of additional mutant forms of rSA11 showed that RNase L degradation no longer occurred when either the N-terminal RING domain of NSP1 was mutated or the C-terminal 98 amino acids of NSP1 were deleted. The C-terminal RNase L degradation domain is positioned upstream and is functionally independent of the NSP1 domain necessary for inhibiting IFN expression. Our studies reveal a new role for NSP1 and its E3-ligase related activity as an antagonist of RNase L and uncover a novel virus-mediated strategy of inhibiting the OAS-RNase L pathway.IMPORTANCEFor productive infection, rotavirus and other RNA viruses must suppress interferon (IFN) signaling and the expression of IFN-stimulated antiviral gene products. Particularly important is inhibiting the interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS) - RNase L pathway, as activated RNase L can direct the nonspecific degradation of viral and cellular RNAs, thereby blocking viral replication and triggering cell death pathways. In this study, we have discovered that the simian SA11 strain of rotavirus employs a novel strategy of inhibiting the OAS-RNase L pathway. This strategy is mediated by SA11 NSP1, a nonstructural protein that hijacks E3 cullin-RING ligases, causing the ubiquitination and degradation of host proteins essential for IFN induction. Our analysis shows that SA11 NSP1 also recognizes and causes the ubiquitination of RNase L, an activity resulting in depletion of endogenous RNase L. These data raise the possibility of using therapeutics targeting cellular E3 ligases to control rotavirus infections.
Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding
Authors: Thakur Shivani , Verma Rajaneesh Kumar , Kepp Kasper Planeta , Mehra Rukmankesh 
Published: August 2022

AbstractThe binding affinity of the SARS-CoV-2 spike (S)-protein ΔΔGbind to the human membrane protein ACE2 is critical for virus function and evolution. Computational structure-based screening of new S-protein mutations for ACE2 binding lends promise to rationalize virus function directly from protein structure and ideally aid early detection of potentially concerning variants. We used a computational protocol based on cryo-electron microscopy structures of the S-protein to estimate the ACE2-binding that gave good trend agreement with experimental ACE2 affinities. We then expanded predictions to all possible S-protein mutations in 21 different S-protein-ACE2 complexes (400,000 ΔΔGbind data points in total), using mutation group comparisons to reduce systematic errors. We show that mutations that have arisen in major variants as a group maintain ACE2 affinity significantly more than random mutations in the total protein, at the interface, and at evolvable sites, with differences between variant mutations being small relative to these effects. Omicron mutations as a group had a modest change in binding affinity compared to mutations in other major variants. The single-mutation effects are consistent with ACE2 binding being optimized and maintained in omicron, despite increased importance of other selection pressures (antigenic drift). As epistasis, glycosylation and in vivo conditions will modulate these effects, computational predictive SARS-CoV-2 evolution remains far from achieved, but the feasibility of large-scale computation is substantially aided by using many structures and comparison of mutation groups rather than single mutation effects, which are very uncertain. Our results demonstrate substantial challenges but indicate ways to improve the quality of computer models for assessing SARS-CoV-2 mutation effects.
Exploring India’s Generation Z perspective on AI enabled internet banking services
Authors: Hameed Shaheema , Nigam Abhinav 
Published: August 2022

Purpose
India is a rapidly developing economy with a rapidly expending internet infrastructure and among the largest Generation Z population. This generation is tech savvy and the access to technology and network creates a conducive environment for such usage. Internet banking for the same reasons is growing leaps and bounds. The introduction of artificial intelligence (AI) has created disruptions in the traditional banking also. This paper aims to analyze the comfort level and usage of AI-enabled banking services by Generation Z.

Design/methodology/approach
The data is collected from 272 Generation Z members. The differential aspects, that is, the relationship of independent variables with dependent variables (AI-enabled internet banking), were analyzed using the structural equation modeling approach.

Findings
Defining factors for AI-enabled internet banking were identified. The results of factors were consistent with previous studies. It was found that the usage of AI-enabled internet banking services is insignificant, indicating that Generation Z does not perceive any advantage in using AI-enabled internet banking services.

Research limitations/implications
This paper does not incorporate age groups other than Generation Z. Further research could throw light on the difference based on age groups. Further research is required to deeply understand why Generation Z does not perceive AI-enabled internet services as very important.

Practical implications
It has been observed that internet banking is important for Generation Z, but they also place greater importance on interpersonal communication. Banks need to consider this in designing their internet banking services.

Originality/value
This paper addresses the gap between comfort with and usage of AI-enabled internet banking services, by Generation Z. This paper indicates that the comfort with AI-enabled internet banking services does not translate to usage.
Post COVID-19's opportunities for customer-centric green supply chain management and customers' resilience; the moderate effect of corporate social responsibility
Authors: Kholaif Moustafa Mohamed Nazief Haggag Kotb , Ming Xiao , Getele Gutama Kusse 
Published: August 2022

PurposeThis research aims to profoundly investigate the post-COVID-19's opportunities for customer-centric green supply chain management (GSCM) and perceived customer resilience by studying the correlation between fear-uncertainty of COVID-19, customer-centric GSCM, and the perceived customers' resilience. Moreover, to examine how the perceived corporate social responsibility (CSR) activities moderates the relationship among the variables.Design/methodology/approachIn this study partial least squares structural equation modeling (PLS-SEM) was adopted on a sample of 298 managers and customers in the Egyptian small and medium enterprises (SMEs) market for data analysis and hypotheses testing.FindingsPreliminary results indicate that the fear-uncertainty of COVID-19 positively affects customer-centric GSCM. Also, external CSR moderates the association between fear-uncertainty towards COVID-19 and customer-centric GSCM. However, internal CSR does not moderate this relationship. Customer-centric GSCM has a significant positive impact on the perceived environmental and social resilience. However, it has an insignificant effect on the perceived financial resilience. Also, customer-centric GSCM has a significant mediation outcome on the relation between fear-uncertainty of COVID-19 and the perceived environmental and social resilience. However, this relation is insignificant regarding the perceived financial resilience.Practical implicationsManagers could develop a consistent strategy for applying CSR practices, providing clear information and focusing on their procedures to meet their customer needs during COVID-19. Governments and managers should develop a consistent strategy to apply customer-oriented green practices to achieve customers' resilience, especially during the pandemic.Originality/valueBased on the “social-cognitive,” “stakeholder” and “consumer culture” theories, this study shed light on the optimistic side of the COVID-19 pandemic, as it also brings the concepts of social responsibility, resilience and green practices back into the light, which helps in solving customers' issues and help to achieve their resilience.
Impact of corona virus outbreak on travellers’ behaviour: scale development and validation
Authors: Ansari Zaid Ahmad , Bashir Makhmoor , Pradhan Sudeepta 
Published: August 2022

PurposeThe purpose of this paper is to develop an instrument to measure the influence of coronavirus (COVID-19) on international travellers’ behaviour.Design/methodology/approachData were collected from 500 respondents in the Kingdom of Saudi Arabia to develop and validate a multi-item scale to measure international travel behaviour post-COVID-19. The initial pool of items was validated by using exploratory factor analysis. The first-order reflective and the assessment of hierarchical factor structure were done through structural equation modelling by using SmartPLS 3.FindingsFindings revealed a hierarchical three-level scale for measuring international traveller’s behaviour. The first level consists of six sub-dimensions of 19 items. These six sub-dimensions can be used as a formative measure of three dimensions of general impact, attitude and preference and cleanliness and safety. These three dimensions form the third level for the meta construct of traveller’s behaviour.Research limitations/implicationsThe proposed scale will provide policymakers and managers with an improved understanding of the change in travellers’ behaviour due to the COVID-19 crisis or any future pandemic.Practical implicationsThe scale can be used by the tourism and hospitality industry to access the impact of COVID-19 or any other future pandemic on traveller’s behaviour.Originality/valueSince the outbreak of the novel COVID-19, almost all international travel has come to halt. A diverse measuring instrument to measure traveller’s behaviour is not available in extant literature. To the best of the authors’ knowledge, this study is the first of its kind which has developed and validated a scale for measuring traveller’s behaviour during and post COVID-19.