bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying signal persistence in the T cell signaling network using an optically controllable antigen receptor
Authors: Harris Michael J , Fuyal Muna , James John R 
Published: October 2020

SUMMARYT cells discriminate between healthy and infected cells with remarkable sensitivity when mounting an immune response. It has been hypothesized that this efficient detection requires combining signals from discrete antigen-presenting cell interactions into a more potent response, requiring T cells to maintain a ‘memory’ of previous encounters. To quantify the magnitude of this phenomenon, we have developed an antigen receptor that is both optically and chemically tunable, providing control over the initiation, duration, and intensity of intracellular T-cell signaling within physiological cell conjugates. We observe very limited persistence within the T cell intracellular network on disruption of receptor input, with signals dissipating entirely in ~15 minutes, and directly confirm that sustained proximal receptor signaling is required to maintain active gene transcription. Our data suggests that T cells are largely incapable of integrating discrete antigen receptor signals but instead simply accumulate the output of gene expression. By engineering optical control in a clinically relevant chimeric antigen receptor, we show that this limited signal persistence can be exploited to increase the activation of primary T cells by ~3-fold by using pulsatile stimulation. Our results are likely to apply more generally to the signaling dynamics of other cellular networks.
Were Neoarchean atmospheric methane hazes and early Paleoproterozoic glaciations driven by the rise of oxygen in surface environments?
Authors: Swain Anshuman , Kaufman Alan J , Kalinowski Marcin , Yarwood Stephanie A , Fagan William F 
Published: October 2020

AbstractGeochemical evidence suggests methane was the predominant greenhouse gas in the Archean and early Proterozoic eons. Consequently, fluctuations in methane concentration in Earth’s atmosphere (i.e., ‘methane hazes’) would have contributed to climate change and influenced the flux of UV radiation reaching surface environments. If correct, understanding what factors (e.g., O2and/or resource concentration) drove the biological methane cycle might shed light on the repetition of biological, atmospheric and climatic events preserved in the sedimentary rock record from ~2.8 to 2.0 BYA. To explore these interdependencies, we developed a novel dynamical model of microbial ecological interactions to investigate the conditions under which methane is preferentially released to the atmosphere. We found that the interplay between resource and O2availability results in complex cyclic methane dynamics unrelated to the functional groups or efficiencies of microbial communities, to initial conditions, or to other model constraints. Based on these results, we propose that the cyclicity of methane haze events and glacial episodes in the Neoarchean and early Paleoproterozoic may have been linked to the progressive increase in oceanic and atmospheric O2through the interval.
DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized nucleotide insertion products and base excision repair intermediates with mismatches
Authors: Kamble Pradnya , Hall Kalen , Chandak Mahesh , Tang Qun , Çağlayan Melike 
Published: October 2020

ABSTRACTDNA ligase I (LIG1) completes base excision repair (BER) pathway at the last nick sealing step following DNA polymerase (pol) β gap filling DNA synthesis. We previously reported that pol β 8-oxo-2’-deoxyribonucleoside 5’-triphosphate (8-oxodGTP) insertion confounds LIG1 leading to the formation of ligation failure products with 5’-adenylate (AMP) block. Here, we report the mutagenic ligation of pol β 8-oxodGTP insertion products and an inefficient substrate-product channeling from pol β Watson-Crick like dG:T mismatch insertion to DNA ligation by LIG1 mutant with perturbed fidelity (E346A/E592A)in vitro. Moreover, our results revealed that the substrate discrimination of LIG1 for the nicked repair intermediates with preinserted 3’-8-oxodG or mismatches is governed by the mutations at both E346 and E592 residues. Finally, we found that Aprataxin (APTX) and Flap Endonuclease 1 (FEN1), as compensatory DNA-end processing enzymes, can remove 5’-AMP block from the abortive ligation products with 3’-8-oxodG or all possible 12 non-canonical base pairs. These findings contribute to understand the role of LIG1 as an important determinant of faithful BER, and how a multi-protein complex (LIG1, pol β, APTX and FEN1) can coordinate to hinder the formation of mutagenic repair intermediates with damaged or mismatched ends at the downstream steps of the BER pathway.
The DNA binding domain of theVibrio vulnificusSmcR transcription factor is flexible and recognizes diverse DNA sequences
Authors: Newman Jane D. , Russell Meghan M. , Gonzalez-Gutierrez Giovanni , van Kessel Julia C. 
Published: October 2020

AbstractThe quorum-sensing regulon in vibrios is controlled by the LuxR/HapR family of transcriptional regulators. InVibrio vulnificus, this regulator is called SmcR, and it controls expression of numerous virulence behaviors, including biofilm formation and elastase production. The consensus binding site ofVibrioLuxR/HapR/SmcR proteins is palindromic, as is common for regulators that bind as dimers with helix-turn-helix N-terminal DNA binding domains. However, the LuxR/HapR/SmcR consensus site is highly degenerate and asymmetric with variations in sequence at each promoter. To determine the mechanism of DNA site recognition, we generated separation-of-function mutants of SmcR that either repress or activate transcription but not both. The SmcR N55I protein is defective at transcription activation due to loss of binding to most DNA binding sites in activated promoters but retains interaction with RNA polymerase (RNAP) alpha. SmcR S76A, L139R, and N142D are defective for interaction with RNAP alpha but retain functional DNA binding activity. Using X-ray crystallography, we show that the wild-type SmcR dimer and the three RNAP-interaction mutants exhibit two conformations of the helix-turn-helix DNA binding domain. Conversely, the SmcR N55I X-ray crystal structure is limited to only one conformation and is restricted in recognition of single base-pair variations in DNA binding site sequences. These data support a model in which two mechanisms drive SmcR transcriptional activation: interaction with RNA polymerase and a multi-conformational DNA binding domain that permits recognition of variable DNA sites. Thus, the LuxR/HapR/SmcR proteins balance specificity for quorum-sensing targets and diversity to accommodate binding at hundreds of sites genome-wide.SignificanceThe cell-cell communication system called quorum sensing controls expression of genes required for virulence inVibriobacteria species, including the potent human pathogenVibrio vulnificus. The master transcriptional regulator of quorum-sensing genes in vibrios belongs to the LuxR/HapR/SmcR family. These regulators directly activate and repress transcription of >100 genes via binding to degenerate sites in promoter regions. We used X-ray crystallography to determine the structure of mutant SmcR proteins. Our experiments reveal that SmcR recognizes diverse sequences via a DNA binding domain that samples multiple conformations to accommodate variations in palindromic DNA sequences. Significantly, the DNA binding domain of SmcR is completely conserved in LuxR/HapR/SmcR family proteins, suggesting that this mechanism is representative of quorum-sensing regulation in other vibrios.
Elucidating dynamics and regulation of alternative splicing in osteogenic differentiation
Authors: Wang Yuanyuan , Chun Rene F , Adhikari Samir , Lopez Christopher M , Henrich Mason , Yacoubian Vahe , Lin Lan , Adams John S. , Xing Yi 
Published: October 2020

AbstractNearly all human multi-exonic genes undergo alternative splicing (AS) via regulation by RNA-binding proteins (RBPs), but few studies have examined the temporal dynamics of AS and its regulation during cell differentiation in the bone niche. We sought to evaluate how AS, under the control of RBPs, affects cell fate commitment during induced osteogenic differentiation of human bone marrow-derived multipotent stem/stromal progenitor cells (MSPCs). We generated a time-course RNA sequencing (RNA-seq) dataset representative of induced MSPC differentiation to osteoblasts. Our analysis revealed widespread AS changes, coordinated with differential RBP expression, at multiple time points, including many AS changes in non-differentially expressed genes. We also developed a computational approach to profile the dynamics and regulation of AS by RBPs using time-course RNA-seq data, by combining temporal patterns of exon skipping and RBP expression with RBP binding sites in the vicinity of regulated exons. In total we identified nine RBPs as potential key splicing regulators during MSPC osteogenic differentiation. Perturbation of one candidate,KHDRBS3, inhibited osteogenesis and bone formationin vitro, validating our computational prediction of “driver” RBPs. Overall, our work highlights a high degree of complexity in the splicing regulation of MSPC osteogenic differentiation. Our computational approach may be applied to other time-course data to explore dynamic AS changes and associated regulatory mechanisms in other biological processes or disease trajectories.
Rhythmic modulation of visual perception by continuous rhythmic auditory stimulation
Authors: Bauer Anna-Katharina R. , van Ede Freek , Quinn Andrew J. , Nobre Anna C. 
Published: October 2020

AbstractAt any given moment our sensory systems receive multiple, often rhythmic, inputs from the environment. Processing of temporally structured events in one sensory modality can guide both behavioural and neural processing of events in other sensory modalities, but whether this occurs remains unclear. Here, we used human electroencephalography (EEG) to test the cross-modal influences of a continuous auditory frequency-modulated (FM) sound on visual perception and visual cortical activity. We report systematic fluctuations in perceptual discrimination of brief visual stimuli in line with the phase of the FM sound. We further show that this rhythmic modulation in visual perception is related to an accompanying rhythmic modulation of neural activity recorded over visual areas. Importantly, in our task, perceptual and neural visual modulations occurred without any abrupt and salient onsets in the energy of the auditory stimulation and without any rhythmic structure in the visual stimulus. As such, the results provide a critical validation for the existence and functional role of cross-modal entrainment and demonstrates its utility for organising the perception of multisensory stimulation in the natural environment.Significance StatementOur sensory environment is filled with rhythmic structures that are often multi-sensory in nature. Here we show that the alignment of neural activity to the phase of an auditory frequency-modulated sound has cross-modal consequences for vision: yielding systematic fluctuations in perceptual discrimination of brief visual stimuli that is mediated by accompanying rhythmic modulation of neural activity recorded over visual areas. These cross-modal effects on visual neural activity and perception occurred without any abrupt and salient onsets in the energy of the auditory stimulation and without any rhythmic structure in the visual stimulus. The current work shows that continuous auditory fluctuations in the natural environment can provide a pacing signal for neural activity and perception across the senses.
Mechanosensitive Expression of Lamellipodin Governs Cell Cycle Progression and Intracellular Stiffness
Authors: Brazzo Joseph A. , Lee Kwonmoo , Bae Yongho 
Published: October 2020

SUMMARYCells exhibit pathological behaviors in response to increased extracellular matrix (ECM) stiffness, including accelerated cell proliferation and migration [1–9], which are correlated with increased intracellular stiffness and tension [2, 3, 10–12]. The biomechanical signal transduction of ECM stiffness into relevant molecular signals and resultant cellular processes is mediated through multiple proteins associated with the actin cytoskeleton in lamellipodia [2, 3, 10, 11, 13]. However, the molecular mechanisms by which lamellipodial dynamics regulate cellular responses to ECM stiffening remain unclear. Previous work described that lamellipodin, a phosphoinositide- and actin filament-binding protein that is known mostly for controlling cell migration [14–21], promotes ECM stiffness-mediated early cell cycle progression [2], revealing a potential commonality between the mechanisms controlling stiffness-dependent cell migration and those controlling cell proliferation. However, i) whether and how ECM stiffness affects the levels of lamellipodin expression and ii) whether stiffness-mediated lamellipodin expression is required throughout cell cycle progression and for intracellular stiffness have not been explored. Here, we show that the levels of lamellipodin expression in cells are significantly increased by a stiff ECM and that this stiffness-mediated lamellipodin upregulation persistently stimulates cell cycle progression and intracellular stiffness throughout the cell cycle, from the early G1 phase to M phase. Finally, we show that both Rac activation and intracellular stiffening are required for the mechanosensitive induction of lamellipodin. More specifically, inhibiting Rac1 activation in cells on stiff ECM reduces the levels of lamellipodin expression, and this effect is reversed by the overexpression of activated Rac1 in cells on soft ECM. We thus propose that lamellipodin is a critical molecular lynchpin in the control of mechanosensitive cell cycle progression and intracellular stiffness.
Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella
Authors: Bruchmann Sebastian , Feltwell Theresa , Parkhill Julian , Short Francesca L. 
Published: October 2020

AbstractInfections caused by Klebsiella pneumoniae are a major public health threat. Extensively drug-resistant and even pan-resistant strains have been reported. Understanding K. pneumoniae pathogenesis is hampered by the fact that murine models of infection offer limited resolution for the non-hypervirulent strains which cause the majority of infections. We have performed genome-scale fitness profiling of a multidrug-resistant K. pneumoniae ST258 strain during infection of the insect Galleria mellonella, with the aim to determine if this model is suitable for large-scale virulence factor discovery in this pathogen. Our results demonstrated a dominant role for surface polysaccharides in infection, with contributions from siderophores, cell envelope proteins, purine biosynthesis genes and additional genes of unknown function. Comparison with a hypervirulent strain, ATCC 43816, revealed substantial overlap in important infection-related genes, as well as additional putative virulence factors that may be specific to ST258. Our analysis also identified a role for the metalloregulatory protein NfeR (also called YqjI) in virulence. Overall, this study offers new insight into the infection fitness landscape of K. pneumoniae ST258, and provides a framework for using the highly flexible, scalable G. mellonella infection model to dissect the molecular virulence mechanisms of K. pneumoniae and other bacterial pathogens.
Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids
Authors: Umemura Yasuhiro , Koike Nobuya , Tsuchiya Yoshiki , Watanabe Hitomi , Kondoh Gen , Kageyama Ryoichiro , Yagita Kazuhiro 
Published: October 2020

AbstractIn mammals, circadian clocks are strictly suppressed during early embryonic stages as well as pluripotent stem cells, by the lack of CLOCK/BMAL1 mediated circadian feedback loops. During ontogenesis, the innate circadian clocks emerge gradually at a late developmental stage, then, with which the circadian temporal order is invested in each cell level throughout a body. Meanwhile, in the early developmental stage, a segmented body plan is essential for an intact developmental process and somitogenesis is controlled by another cell-autonomous oscillator, the segmentation clock, in the posterior presomitic mesoderm (PSM). In the present study, focusing upon the interaction between circadian key components and the segmentation clock, we investigated the effect of the CLOCK/BMAL1 on the segmentation clockHes7oscillation, revealing that the expression of functional CLOCK/BMAL1 severely interferes with the ultradian rhythm of segmentation clock in induced PSM and gastruloids. RNA sequencing analysis showed that the premature expression of CLOCK/BMAL1 affects theHes7transcription and its regulatory pathways. These results suggest that the suppression of CLOCK/BMAL1-mediated transcriptional regulation during the somitogenesis may be inevitable for intact mammalian development.
Inducible Directed Evolution of Complex Phenotypes in Bacteria
Authors: Al’Abri Ibrahim S. , Haller Daniel J. , Crook Nathan 
Published: October 2020

AbstractDirected evolution is a powerful method for engineering biology in the absence of detailed sequence-function relationships. To enable directed evolution of complex phenotypes encoded by multigene pathways, we require large library sizes for DNA sequences >5-10kb in length, elimination of genomic hitchhiker mutations, and decoupling of diversification and screening steps. To meet these challenges, we developed Inducible Directed Evolution (IDE), which uses a temperate bacteriophage to package large plasmids and transfer them to naive cells after intracellular mutagenesis. To demonstrate IDE, we evolved a 5-gene pathway from Bacillus licheniformis that accelerates tagatose catabolism in Escherichia coli, resulting in clones with 65% shorter lag times during growth on tagatose after only two rounds of evolution.
Phylogenomics reveals thatAsaiasymbionts from insects underwent convergent genome reduction, preserving an insecticide-degrading gene
Authors: Comandatore Francesco , Damiani Claudia , Cappelli Alessia , Ribolla Paulo , Gasperi Giuliano , Gradoni Francesco , Capelli Gioia , Piazza Aurora , Montarsi Fabrizio , Mancini Maria Vittoria , Rossi Paolo , Ricci Irene , Bandi Claudio , Favia Guido 
Published: October 2020

AbstractThe mosquito microbiota is composed by several lineages of microorganisms whose ecological roles and evolutionary histories have yet to be investigated in depth. Among these microorganisms,Asaiabacteria play a prominent role, given its abundance in the gut, reproductive organs and salivary glands of different mosquito species, while its presence has also been reported in several other insects. Notably,Asaiahas great potential as a tool for the control of mosquito-borne diseases. Here, we present a wide phylogenomic analysis ofAsaiastrains isolated from different species of mosquito vectors and from different populations of the Mediterranean fruit fly (medfly)Ceratitis capitata, an insect pest of worldwide economic importance. We show that phylogenetically distant lineages ofAsaiaexperienced independent genome reductions, despite following a common pattern, characterized by the early loss of genes involved in genome stability. This result highlights the role of specific metabolic pathways in the symbiotic relationship betweenAsaiaand the insect host. Finally, we discovered that all but one of theAsaiastrains included in the study possess the pyrethroid hydrolase gene. Phylogenetic analysis revealed that this gene is ancestral inAsaia, strongly suggesting that it played a role in the establishment of the symbiotic association between these bacteria and the mosquito hosts. We propose that this gene from the symbiont contributed to initial pyrethroid resistance in insects harboringAsaia, also considering the widespread production of pyrethrins by several plants.ImportanceWe have studied genome reduction within several strains of the insect symbiontAsaia, isolated from different species/strains of mosquito and medfly. Phylogenetically distant strains ofAsaia, despite following a common pattern involving the loss of genes related to genome stability, have undergone independent genome reductions, highlighting the peculiar role of specific metabolic pathways in the symbiotic relationship betweenAsaiaand its host. We also show that the pyrethroid hydrolase gene is present in all theAsaiastrains isolated except for the South American malaria vectorAn. darlingi, for which resistance to pyrethroids has never been reported, suggesting a possible involvement ofAsaiain determining the resistance to insecticides.
Innovations for potential entrepreneurs in service quality and customer loyalty in the hospitality industry
Authors: Satti Zoya Wajid , Babar Samreen Fahim , Parveen Shagufta , Abrar Kashif , Shabbir Asma 
Published: November 2020

Purpose
This study aims to investigate the role of moderated mediation between innovation in service quality and customer loyalty in the hospitality industry for potential entrepreneurs in the hospitality industry.

Design/methodology/approach
The authors have collected data from customers of the hospitality industry of significant cities of Pakistan using 362 structured questionnaires. Structural equation modelling was used to find out moderated mediation between innovation in service quality and customer loyalty in the hospitality industry for potential entrepreneurs in the hospitality industry.

Findings
The results showed that the role of customer satisfaction as a mediator and the role of perceived price fairness as a moderator between service quality and customer loyalty is statistically significant. Customers are influenced by price, and it leads to their satisfaction in the hospitality industry.

Research limitations/implications
The results of this study can be used by managers of the restaurant industry to enhance customer loyalty by focusing on customer satisfaction and perceived price.

Originality/value
The evidence documented in this paper is first known to measure the role of a mediator and moderator between service quality and customer loyalty for potential entrepreneurs. This paper will add to the literature of service quality in the hospitality industry concerning the role of customer satisfaction and perceived price fairness for future and potential entrepreneurs.