bluuebunny/crossref_metadata_2025_split huggingface dataset:
NtrC expression at lag-phase improves competitive fitness under low and fluctuating nutrient condition
Authors: Mishra L K , Shashidhar R 
Published: March 2022

AbstractThe enteric pathogens cycle between nutrient rich host and nutrient poor external environment. These pathogens compete for nutrients in the host as well as in external environment and also often experience starvation. In this context, we have studied the role of a global nitrogen regulator (NtrC) of Salmonella Typhimurium. The ntrC mutation caused extended lag phase and slow growth in minimal media. In lag phase the wild-type cells showed ∼60 fold more expression of ntrC as compared to log phase cells. The role of ntrC gene is often studied with respect to nitrogen scavenging in a low nitrogen growing condition. However, our observation indicates that, even in the adequate supply of nitrogen, the ntrC null mutants failed to adapt to new nutrient conditions and were slow to exit from the lag phase. Gene expression studies at lag phase showed down-regulation of the genes involved in carbon/nitrogen transportation and metabolism in ΔntrC mutant. In the co-culture competition studies, we observed that ntrC knockout was unable to survive with the wild-type Salmonella and E. coli. We also observed that the ΔntrC mutant did not survive long term nitrogen starvation (150 days). Critical analysis of starvation survival revealed that, ntrC gene is essential for recycling of nutrients from the dead cells. The nutrient recycling efficiency of ΔntrC mutant was ∼ 12 times less efficient than wild-type. Hence, the current work establishes that ntrC expression at the lag phase is essential for competitive fitness of Salmonella to survive in an environment having low and fluctuating nutrient conditions.ImportanceSalmonella Typhimurium, both inside or outside of the host organism face enormous competition from other microorganisms. The competition may take place either in steady or in fluctuating climatic conditions. Thus, how Salmonella Typhimurium survive under such overlapping stress conditions, remained unclear. Therefore, here we report that, a global regulator NtrC, which is also a part of two-component system, activates the set of genes and operons involved in rapid adaptation and efficient nutrient recycling/scavenging. These properties, make cell able to compete with other microbes, under characteristic feast- or-famine life style of Salmonella Typhimurium. Therefore, this piece of work helps us to understand the starvation physiology of enteric bacterial pathogen Salmonella Typhimurium.
Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid
Authors: Lee Jonathan T. , Yang Qingyi , Gribenko Alexey , Perrin B. Scott , Zhu Yuao , Cardin Rhonda , Liberator Paul A. , Anderson Annaliesa S. , Hao Li 
Published: March 2022

AbstractSARS-CoV-2 continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid™. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from ∼4,892,000 high-quality SARS-CoV-2 genomes in GISAID. Any mutations identified from comparison to the reference sequence (Wuhan-hu-1) were cataloged and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (alpha-, beta-, and gamma-coronaviruses). Additionally, we showed that over time the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the EUA approval of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals.ImportanceThe recent authorization of oral SARS-CoV-2 antivirals, such as Paxlovid, has ushered in a new era of the COVID-19 pandemic. Emergence of new variants, as well as selective pressure imposed by antiviral drugs themselves, raise concern for potential escape mutations in key drug binding motifs. To determine the potential emergence of antiviral resistance in globally circulating isolates and its implications for the clinical response to the COVID-19 pandemic, sequencing of SARS-CoV-2 viral isolates before, during, and after the introduction of new antiviral treatments is critical. The infrastructure built herein for active genetic surveillance of Mpro evolution and emergent mutations will play an important role in assessing potential antiviral resistance as the pandemic progresses and Mpro inhibitors are introduced. We anticipate our framework to be the starting point in a larger effort for global monitoring of the SARS-CoV-2 Mpro mutational landscape.
Characterizing Photosynthetic Biofuel Production: Isotopically non-stationary13C metabolic flux analysis (INST-13CMFA) on limonene producingSynechococcussp. PCC 7002
Authors: Newman Darrian M. , Sake Cara L. , Metcalf Alex J. , Davies Fiona K. , Boyle Nanette R. 
Published: March 2022

AbstractSynechococcussp. PCC 7002 is a unicellular cyanobacterium capable of fast growth, even under high light intensity and high salinity. These attributes along with genetic tractability makeSynechococcussp. PCC 7002 an attractive candidate for industrial scale production of specialty and commodity chemicals. One such strain produces limonene, an energy dense diesel jet fuel drop-in additive, at a titer of 4 mg/L over a four-day incubation period. In this study, we use the state-of-the-art whole-cell characterization tool, isotopically non-stationary13C metabolic flux analysis (INST-13CMFA) to determine intracellular fluxes through the pathways of central metabolism for the limonene producing strain and wild type strain ofSynechococcussp. PCC 7002. We find similar flux distribution in the Calvin-Benson-Bassham cycle, photorespiration, oxidative pentose phosphate pathway, and reductive tricarboxylic acid cycle. The key difference between strains is observed in the production of pyruvate. The limonene producing strain displays significantly higher flux through the amphibolic pathways of phosphoenolpyruvate carboxylase and the malic enzyme to synthesize pyruvate, while the wild type strain uses pyruvate kinase in a single step. Our findings suggest that this flux distribution is a mechanism to recover a physiologically optimal ratio of ATP to NADPH. The upregulation of this amphibolic pathway may act to restore the physiological ATP:NADPH ratio that has been disturbed by limonene biosynthesis.
Multiethnic Polygenic Risk Prediction in Diverse Populations through Transfer Learning
Authors: Tian Peixin , Chan Tsai Hor , Wang Yong-Fei , Yang Wanling , Yin Guosheng , Zhang Yan Dora 
Published: March 2022

AbstractPolygenic risk scores (PRS) leverage the genetic contribution of an individual’s genotype to a complex trait by estimating disease risk. Traditional PRS prediction methods are predominantly for European population. The accuracy of PRS prediction in non-European populations is diminished due to much smaller sample size of genome-wide association studies (GWAS). In this article, we introduced a novel method to construct PRS for non-European populations, abbreviated as TL-Multi, by conducting transfer learning framework to learn useful knowledge from European population to correct the bias for non-European populations. We considered non-European GWAS data as the target data and European GWAS data as the informative auxiliary data. TL-Multi borrows useful information from the auxiliary data to improve the learning accuracy of the target data while preserving the efficiency and accuracy. To demonstrate the practical applicability of the proposed method, we applied TL-Multi to predict the risk of systemic lupus erythematosus (SLE) in Asian population and the risk of asthma in Indian population by borrowing information from European population. TL-Multi achieved better prediction accuracy than the competing methods including Lassosum and meta-analysis in both simulations and real applications.
Proteomic characterization of spinal cord synaptoneurosomes from Tg-SOD1/G93A mice supports a role for MNK1 and local translation in the early stages of amyotrophic lateral sclerosis
Authors: Casañas Juan José , Montesinos María Luz 
Published: March 2022

ABSTRACTThe isolation of synaptoneurosomes (SNs) represents a useful means to study synaptic events. However, the size and density of synapses varies in different regions of the central nervous system (CNS), and this also depends on the experimental species studied, making it difficult to define a generic protocol for SNs preparation. To characterize synaptic failure in the spinal cord (SC) in the Tg-SOD1/G93A mouse model of amyotrophic lateral sclerosis (ALS), we applied a method we originally designed to isolate cortical and hippocampal SNs to SC tissue. Interestingly, we found that the SC SNs were isolated in a different gradient fraction to the cortical/hippocampal SNs. We compared the relative levels of synaptoneurosomal proteins in control (Tg-SOD1) animals, with Tg-SOD1/G93A mice at onset and those that were symptomatic using iTRAQ proteomics. The results obtained suggest that an important regulator of local synaptic translation, MNK1 (MAP kinase interacting serine/threonine kinase 1), might well influence the early stages of ALS.
The Structural and Biochemical Basis for FER Receptor Kinase Early Signaling Initiation in Arabidopsis
Authors: Kong Yanqiong , Chen Jia , Chen Hong , Shen Yanan , Wang Lifeng , Yan Yujie , Zhou Huan , Zheng Heping , Yu Feng , Ming Zhenhua 
Published: March 2022

ABSTRACTAccumulating evidence has indicated that receptor-like kinase (RLK) autophosphorylation and substrate phosphorylation triggered by RLK are early and essential events for RLK function. However, the structural and biochemical basis for these early events is largely unclear. Herein, we used RLK FERONIA (FER) as a model and crystallized its core kinase domain (FER-KD) in the dephosphorylated state. We found that FER-KD adopts an active conformation in its crystal structure. Moreover, FER-KD mutants with reduced or no catalytic activity also adopt an active conformation before phosphorylation. Collectively, these observations suggest that FER employs a phosphorylation-independent active state before ligand-induced phosphorylation and full activation. We further demonstrated that FER is a dual-specificity kinase and that autophosphorylation on Tyr residues lags somewhat behind Ser/Thr phosphorylation. More importantly, Tyr phosphorylation is essential for FER-KD to initiate substrate GRP7 phosphorylation. Our work provides a paradigm to study the mechanisms of the early steps of RLK signaling initiation and highlights its “active” form and Tyr phosphorylation-gated roles in response to signaling stimuli.
TGFβ limits Myc-dependent TCR-induced metabolic reprogramming in CD8+ T cells
Authors: Hope Helen Carrasco , Pickersgill Gabriella , Ginefra Pierpaolo , Vannini Nicola , Cook Graham P. , Salmond Robert J. 
Published: March 2022

AbstractT cell activation is dependent upon the integration of antigenic, costimulatory and cytokine-derived signals and the availability and acquisition of nutrients from the environment. Furthermore, T cell activation is accompanied by reprogramming of cellular metabolism to provide the energy and building blocks for proliferation, differentiation and effector function. Transforming growth factor β (TGFβ) has pleiotropic effects on T cell populations, having both an essential role in the maintenance of immune tolerance but also context-dependent pro-inflammatory functions. We set out to define the mechanisms underpinning the suppressive effects of TGFβ on mouse CD8+ T cell activation. RNA-sequencing analysis of TCR-stimulated T cells determined that Myc-regulated genes were highly enriched within gene sets downregulated by TGFβ. Functional analysis demonstrated that TGFβ impeded TCR-induced upregulation of amino acid transporter expression, amino acid uptake and protein synthesis. Furthermore, TCR-induced upregulation of Myc-dependent glycolytic metabolism was substantially inhibited by TGFβ treatment with minimal effects on mitochondrial respiration or mTOR activation. Thus, our data suggest that inhibition of Myc-dependent metabolic reprogramming represents a major mechanism underpinning the suppressive effects of TGFβ on CD8+ T cell activation.
Comparative Structural and Dynamics Study of Free and gRNA-bound FnCas9 and SpCas9 Proteins
Authors: Panda Gayatri , Ray Arjun 
Published: March 2022

AbstractThe introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation, thereby hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates of on-target DNA cleavage. Here, we have compared the dynamics of a more specific naturally occurring Cas9 from Francisella novicida (FnCas9) to the most widely used, SpCas9 protein. Long-scale atomistic MD simulations of free and gRNA-bound forms of both the Cas9 proteins were performed, and their domain rearrangements and binding affinity with gRNA were compared to decipher the possible reason behind the enhanced specificity of FnCas9 protein. The greater binding affinity with gRNA, high domain electrostatics, and more volatility of FnCas9 than SpCas9 may explain its increased specificity and lower tolerance for mismatches.HighlightsThe gRNA binding led to the opening of the structure of Cas9 endonuclease and exposure of hydrophobic residues to accommodate it.Concerted domain movement was observed in both SpCas9 (HNH-REC2 domains, CTD-Topo domains, and REC3-RuvC) and FnCas9 (HNH-REC3-REC1 and PI-WED-RuvC).Both Cas9s have shown a decrease in percentage helicity and an increase in the percentage of structurally dynamic residues (more secondary structural transitions) post gRNA binding.In the gRNA-bound form of FnCas9, the PAM-interacting domain was found to have a larger structural transition and increased coil%.Electrostatic interactions have a major contribution to the high binding affinity of FnCas9 with gRNA.Arginine-helix has shown a pivotal role in the binding of gRNA in FnCas9 protein.
A conserved PLK1 docking site in TopBP1 maintains genome integrity during mitosis
Authors: Li Jiayi , Bagge Jonas , Lisby Michael , Nilsson Jakob , Oestergaard Vibe H. 
Published: March 2022

AbstractTopBP1 is a large scaffold protein with multiple functions in genome integrity. We previously identified a novel role for TopBP1 during M phase by showing that TopBP1 reduces carry-over of DNA damage to daughter cells. This function emerges as a critical backup pathway in BRCA deficient cells, yet many aspects of TopBP1 regulation during mitosis are unclear. The mitotic kinase PLK1 has been reported to interact with TopBP1 but the functional relevance of this is unclear. Here, we identify and characterize a conserved PLK1 docking site in TopBP1. Endogenous deletion of the PLK1 docking site in TopBP1 results in increased number of mitotic TopBP1 foci, increased DNA damage in daughter cells, deficient mitotic DNA repair synthesis and increased frequency of binucleation. At the same time, cell cycle distribution and ATR activation are normal in cells with the PLK1 docking site deletion in TopBP1. Interestingly, mutation of this site in TopBP1 renders cells sensitive to PARP inhibitors but not to camptothecin hinting to different cellular effects of the two chemotherapeutics. Altogether, our data indicate that the PLK1-TopBP1 interaction is critical for the mitotic function of TopBP1.
Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway
Authors: Xue Jan Y , Hind Katy , Lemay Matthew A. , Mcminigal Andrea , Jourdain Emma , Chan Cheong Xin , Martone Patrick T. 
Published: March 2022

AbstractThe discovery of lignins in the coralline red alga Calliarthron tuberculosum raised new questions about the deep evolution of lignin biosynthesis. Here we present the transcriptome of C. tuberculosum supported with newly generated genomic data to identify gene candidates from the monolignol biosynthetic pathway using a combination of sequence similarity-based methods. We identified candidates in the monolignol biosynthesis pathway for the genes 4CL, CCR, CAD, CCoAOMT, and CSE but did not identify candidates for PAL, CYP450 (F5H, C3H, C4H), HCT, and COMT. In gene tree analysis, we present evidence that these gene candidates evolved independently from their land plant counterparts, suggesting convergent evolution of a complex multistep lignin biosynthetic pathway in this red algal lineage. Additionally, we provide tools to extract metabolic pathways and genes from the newly generated transcriptomic and genomic datasets. Using these methods, we extracted genes related to sucrose metabolism and calcification. Ultimately, this transcriptome will provide a foundation for further genetic and experimental studies of calcifying red algae.
Species Distribution Modeling of Aedes aegypti in Maricopa County, Arizona from 2014-2020
Authors: Holeva-Eklund Whitney M. , Young Steven J. , Will James , Busser Nicole , Townsend John , Hepp Crystal M. 
Published: March 2022

AbstractAedes aegypti mosquitoes, which are of great importance to public health, have recently and rapidly expanded their global range; however, little is understood about the distribution of these mosquitoes in desert environments. Trapping records for Ae. aegypti in Maricopa County, Arizona from 2014-2020 were used to construct species distribution models using Maxent. Satellite imagery and socioeconomic factors were used as predictors. Maps of predicted habitat suitability were converted to binary presence/absence maps, and consensus maps were created that represent “core” habitat for the mosquito over six years of time. Generally, population density was the most important predictor in the models while median income was the least important. This study is the first step toward understanding the distribution of the vector in a desert environment.One-Sentence SummaryThis study uses satellite imagery and socioeconomic factors to identify core habitat over six years in a desert environment.
Liquid droplet aging and fibril formation of the stress granule protein TIA1 low complexity domain
Authors: Wittmer Yuuki , Jami Khaled M. , Stowell Rachelle K. , Le Truc , Hung Ivan , Murray Dylan T. 
Published: March 2022

SUMMARYProtein domains biased toward a few amino acid types are vital for the formation of biomolecular condensates in living cells. These membraneless compartments are formed by molecules exhibiting a range of molecular motions and structural order. Missense mutations increase condensate persistence lifetimes or structural order, properties that are thought to underlie pathological protein aggregation. We examined seeded fibrils of the T-cell restricted intracellular antigen-1 low complexity domain and determined residues 338–357 compose the rigid fibril core. Aging of wild-type and P362L mutant low complexity domain liquid droplets resulted in fibril assemblies that are structurally distinct from the seeded fibril preparation. The results show that most disease mutations lie outside the region that forms homogeneous fibril structure, the droplets age into conformationally heterogenous fibrils, and the P362L disease mutation does not favor a specific fibril conformation.
The customer experience in Thailand's multichannel retail environments
Authors: Sombultawee Kedwadee , Tansakul Thanchanok 
Published: March 2022

PurposeThe purpose of this paper is to investigate cognitive and affective customer service in Thailand's maltichannel retail environment. The research used the stimulus–organism–response model of consumer behaviour. The study's theoretical framework incorporated the multichannel service quality framework (Sousa and Voss, 2006) and a decomposed measure of customer experience, including cognitive and affective customer experience (Gao et al., 2021). Outcomes investigated included repurchase intention and word-of-mouth intention.Design/methodology/approachA quantitative survey of Thai consumers (aged 18 and over) who had purchased from multichannel retailers at least one time in the past year (n = 502) was conducted. Data were collected online and analysed using a structural equation modelling approach.FindingsSignificant factors in cognitive customer experience and affective customer experience included breadth of channel choice, transparency of channel, content consistency and process consistency. Effects differed in strength on these effects. Cognitive customer experience and affective customer experience influenced repurchase intention and word-of-mouth intention, with a stronger effect from affective customer experience.Originality/valueThis research presents an integrative model for customer experience in multichannel marketing, incorporating a well-established model of multichannel service quality and a decomposed measure of customer experience. It also illustrates the difference between cognitive customer experience and affective customer experience, which have different effect sizes from antecedents and different effects on outcome variables. This finding is a significant theoretical advancement.
Leader humility and team effectiveness: a moderated mediation model of leader-member exchange and employee satisfaction
Authors: Sheikh Aarif Mohd 
Published: March 2022

PurposeThis research study examines the impact of leader humility (LH) on team effectiveness (TE) via the mediating mechanism of leader-member exchange (LMX). It also proposes employee satisfaction (ES) as a moderating variable in the relationship between LH and TE.Design/methodology/approachThis study examines relationships among the study variables in the Indian context, using a sample of 589 employees serving the banking sector in Jammu and Kashmir, India. The data analysis was carried out via confirmatory factor analysis and structural equation modeling.FindingsThe results showed a significant positive influence of LH on TE. The results also posit a partial mediating effect of LMX on LH and TE interplay, and ES acts as a moderator between LH and TE. Thus, the results supported the hypothesized moderated mediation model and suggested implications for theory and practice. Further, the potential limitations and future directions are placed at the end.Research limitations/implicationsOrganizational implications include that organizations should develop attractive organizational mechanisms to ensure better LMX and ES for enhancing employee effectiveness. Besides, organizations should attract and retain effective and humble leaders; and leaders should use humble attitude and behavior in dealing with employees, eventually ensuring higher TE.Originality/valueThis study tested LMX and job satisfaction as intervening variables in the relationship between LH and TE in the Indian context; the framework under context has received scarce research attention. The results suggest that organizations that focus on producing humble leaders succeed in enhancing and maintaining higher organizational effectiveness.