bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular diversity of WNV within circulating avian peripheral blood mononuclear cells reveals host-dependent patterns of polyinfection
Authors: Talmi Frank Dalit , Byas Alex D. , Murrieta Reyes , Weger-Lucarelli James , Rückert Claudia , Gallichotte Emily , Yoshimoto Janna A. , Allen Chris , Bosco-Lauth Angela M. , Graham Barbara , Felix Todd A. , Brault Aaron , Ebel Gregory D. 
Published: January 2023

AbstractError-prone replication of RNA viruses generates the genetic diversity required for adaptation within rapidly changing environments. Thus, arthropod-borne virus (arbovirus) populations exist in nature as mutant swarms that are maintained between arthropods and vertebrates. Previous studies have demonstrated that West Nile virus (WNV) population dynamics are host dependent: In American crows, which experience extremely high viremia, purifying selection is weak and population diversity is high compared to American robins, which have 100 to 1000-fold lower viremia. WNV passed in robins experiences fitness gains, whereas that passed in crows does not. Therefore, we tested the hypothesis that high crow viremia allows higher genetic diversity within individual avian peripheral-blood mononuclear cells (PBMCs), reasoning that this could have produced the previously observed host-specific differences in genetic diversity and fitness. Specifically, we infected cells and birds with a novel, barcoded version of WNV and sequenced viral RNA from single cells to quantify the number of WNV barcodes that each contained. Our results demonstrate that the richness of WNV populations within crows far exceeds that in robins. Similarly, rare WNV variants were maintained by crows more frequently than by robins. Our results suggest that increased viremia in crows relative to robins leads to maintenance of defective genomes and less prevalent variants, presumably through complementation. Our findings further suggest that weaker purifying selection in highly susceptible crows is attributable to this higher viremia, polyinfections and complementation. These studies further document the role of particular, ecologically relevant hosts in shaping virus population structure.Author SummaryWNV mutational diversity in vertebrates is species-dependent. In crows, low frequency variants are common, and viral populations are more diverse. In robins, fewer mutations become permanent fixtures of the overall viral population. We infected crows, robins and a chicken cell line with a genetically marked (barcoded) WNV. Higher levels of virus led to multiple unique WNV genomes infecting individual cells, even when a genotype was present at low levels in the input viral stock. Our findings suggest that higher levels of circulating virus in natural hosts allow less fit viruses to survive in RNA virus populations through complementation by more fit viruses. This is significant as it allows less represented and less fit viruses to be maintained at low levels until they potentially emerge when virus environments change. Overall our data reveal new insights on the relationships between host susceptibility to high viremia and virus evolution.
Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions
Authors: Alyami R. Y. , Cleary D. W. , Forster J. , Feelisch M. , Ardern-Jones M. R. 
Published: January 2023

AbstractBackgroundThe skin microbiome is increasingly recognised as a critical component of the innate skin immune response and is central to the pathogenesis of many inflammatory skin disorders including atopic dermatitis. Previous studies have not looked in detail at the impact of changing both sampling methodology and hypervariable region sequencing for skin microbiome analysis.ObjectivesWe set out to undertake a detailed analysis comparing microbe population diversity and resolution at the single species level by swab, tape, scrape and scrape then swab sampling assayed by hypervariable region sequencing.MethodsIn triplicate samples from the antecubital fossa were taken from healthy volunteers for 16s RNA analysis by primer amplification for hypervariable regions 1-3, and 3-4.ResultsAlpha (phylogenetic) diversity was the greatest with tape sampling and V1-3 analysis, whereas for V4, tape and swab were equivalent. Scrape sampling showed lower alpha diversity at both V1-3 and V4. All measures of beta diversity showed the scrape methodology yielded a lesser diversity than the others. Phyla composition was similar across all sampling methodologies. Minor differences in composition were noted between V1-3 and V4 sequencing, but V1-3 was optimal for identification of firmicutes (including staphylococci).ConclusionsIn the methodological planning of skin microbiome analysis skin scientists need to consider the microbes of interest to choose the optimal hypervariable region to sequence, and harmonisation of methodological approaches would be beneficial to the field. For detection of staphylococci on flexural skin, we would recommend tape sampling with analysis of V1-3.What’s already known about this topic?Previous microbiome studies have utilised many different methodologies, but a detailed comparison of their utility in skin research has not been undertakenMethodological choices in skin microbiome analysis affect both sensitivity to detect diversity and sensitivity to identify at a species levelOptimisation to detect diversity and species identification can require different approachesWhat does this study add?Our study compared a matrix the four most widely utilised skin sampling methodologies and the two principle means for hypervariable gene analysis.We show that alpha diversity is optimal with tape samplingAdditionally, in contrast to gut microbiome analyses, in the skin hypervariable region V1-3 analysis is superior to V4 when the species of interest are staphylococci.
A First Ultrastructural and Immuno-Labelling Investigation of Western Red Cedar Leaves
Authors: Gowen Brent E. , Noshad David 
Published: January 2023

AbstractA first morphological analysis of the leaves ofThuja plicata(Western Red Cedar, WRC), a commercially valuable tree species, is presented. The ultrastructural and immuno-labelling analyses were only possible after applying modifications to standard transmission electron microscopy (TEM) preparatory methodology to fully embed cedar leaves. We demonstrate an application of the technique after leaf exposure to the fungiDidymascella thujina(cedar leaf blight, CLB). The leaves resulting defence response was visualized to two plant defence proteins, β-1,3 Glucanase and Chitinase. The TEM methodology modifications presented may generally apply to other plant species resistant to morphological analyses due to their thick leaf cuticles. The technique requires no more equipment than found in any basic Transmission Electron Microscopy Facility.
Identification of levoglucosan degradation pathways in bacteria and sequence similarity network analysis
Authors: Kaur Arashdeep , Scott Nichollas E. , Herisse Marion , Goddard-Borger Ethan D. , Pidot Sacha , Williams Spencer J. 
Published: January 2023

AbstractLevoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degradingPaenarthrobacterspp. (Paenarthrobacter nitrojuajacolisLG01 andPaenarthrobacter histidinolovoransLG02) that were isolated from soil by metabolic enrichment using levoglucosan as the sole carbon source. Genome sequencing and proteomics analysis revealed the expression of a series of genes encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan β-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and an associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident, while the expressed genes contained a range of putative sugar phosphate isomerases/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbours of LgdA revealed that homologues of LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One group of sugar phosphate isomerase/xylose isomerase homologues (named LgdB3) was identified with limited distribution that is mutually exclusive with LgdB2, and we propose that they may fulfill a similar function. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds, suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight diversity within the LGDH pathway, through which bacteria utilize levoglucosan as a nutrient source.
Amphiphiles formed from synthetic DNA-nanomotifs mimic the step-wise dispersal of transcriptional clusters in the cell nucleus
Authors: Tschurikow Xenia , Gadzekpo Aaron , Tran Mai P. , Chatterjee Rakesh , Sobucki Marcel , Zaburdaev Vasily , Göpfrich Kerstin , Hilbert Lennart 
Published: January 2023

AbstractStem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Low amphiphile concentrations induce rounding of droplets, followed by splitting and, ultimately, full dispersal at higher concentrations. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of the complex organization of transcription in biological cells using relatively simple, DNA sequence-programmable nanostructures, opening novel ways to control mesoscopic organization of synthetic nanomaterials.GRAPHICAL ABSTRACT
Kar4 is Required for the Normal Pattern of Meiotic Gene Expression
Authors: Park Zachory M. , Remillard Matthew , Rose Mark D. 
Published: January 2023

AbstractKar4p, the yeast homolog of the mammalian methyltransferase subunit METTL14, is required for the initiation of meiosis and has at least two distinct functions in regulating the meiotic program. Cells lacking Kar4p can be driven to sporulate by co-overexpressing the master meiotic transcription factor,IME1, and the translational regulator,RIM4, suggesting that Kar4p functions at both the transcriptional and translational level to regulate meiosis. Using microarray analysis and RNA sequencing, we found thatkar4Δ/Δ mutants have a largely wild type transcriptional profile with the exception of two groups of genes that show delayed and reduced expression: (1) a set of Ime1p-dependent early genes as well asIME1, and (2) a set of late genes dependent on the mid-meiotic transcription factor, Ndt80p. The early gene expression defect is rescued by overexpressingIME1, but the late defect is only suppressed by overexpression of bothIME1andRIM4. Mass spectrometry analysis identified several genes involved in meiotic recombination with strongly reduced protein levels, but with little to no reduction in transcript levels inkar4Δ/Δ afterIME1overexpression. The low levels of these proteins were rescued by overexpression ofRIM4andIME1, but not by the overexpression ofIME1alone. These data expand our understanding of the role of Kar4p in regulating meiosis and provide key insights into a potential mechanism of Kar4p’s later meiotic function that is independent of mRNA methylation.Author SummaryKar4p is required at two stages during meiosis. Cells lacking Kar4p have a severe loss of mRNA methylation and arrest early in the meiotic program, failing to undergo either pre-meiotic DNA synthesis or meiotic recombination. The early block is rescued by overexpression of the meiotic transcription factor,IME1. Thekar4Δ/Δ cells show delayed and reduced expression of a set of Ime1p-dependent genes expressed early in meiosis as well as a set of later genes that are largely Ndt80p-dependent. Overexpression ofIME1rescues the expression defect of these early genes and expedites the meiotic program in the wild type S288C strain background. However,IME1overexpression is not sufficient to facilitate sporulation inkar4Δ/Δ. Completion of meiosis and sporulation requires the additional overexpression of a translational regulator,RIM4.Analysis ofkar4Δ/Δ’s proteome during meiosis withIME1overexpression revealed that proteins important for meiotic recombination have reduced levels that cannot be explained by equivalent reductions in transcript abundance.IME1overexpression by itself rescues the defect associated with a catalytic mutant of Ime4p, implying that the early defect reflects mRNA methylation. The residual defects in protein levels likely reflect the loss of a non-catalytic function of Kar4p, and the methylation complex, which requires overexpression ofRIM4to suppress.
Transcriptomic impacts and potential routes of detoxification in a lampricide-tolerant teleost exposed to TFM and niclosamide
Authors: Lawrence M.J. , Grayson P. , Jeffrey J.D. , Docker M.F. , Garroway C.J. , Wilson J.M. , Manzon R.G. , Wilkie M.P. , Jeffries K.M. 
Published: January 2023

AbstractSea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America often relies on the application of 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide mixtures to kill larval sea lamprey. Selectivity of TFM against lampreys appears to be due to differential detoxification ability in these jawless fishes compared to bony fishes, particularly teleosts. However, the proximate mechanisms of tolerance to the TFM and niclosamide mixture and the mechanisms of niclosamide toxicity on its own are poorly understood, especially among non-target fishes. Here, we used RNA sequencing to identify specific mRNA transcripts and functional processes that responded to niclosamide or a TFM:niclosamide mixture in bluegill (Lepomis macrochirus). Bluegill were exposed to niclosamide or TFM:niclosamide mixture, along with a time-matched control group, and gill and liver tissues were sampled at 6, 12, and 24 h. We summarized the whole-transcriptome patterns through gene ontology (GO) term enrichment and through differential expression of detoxification genes. The niclosamide treatment resulted in an upregulation of several transcripts associated with detoxification (cyp, ugt, sult, gst), which may help explain the relatively high detoxification capacity in bluegill. Conversely, the TFM:niclosamide mixture resulted in an enrichment of processes related to arrested cell cycle and growth, and cell death alongside a diverse detoxification gene response. Detoxification of both lampricides likely involves the use of phase I and II biotransformation genes. Our findings strongly suggest that the unusually high tolerance of bluegill to lampricides is due to these animals having an inherently high capacity and flexible detoxification response to such compounds.
Economic policy uncertainty, geopolitical risk and cash holdings: evidence from Saudi Arabia
Authors: Guizani Moncef , Talbi Dorra , Abdalkrim Gaafar 
Published: January 2023

PurposeThis study aims to investigate the influence of economic policy uncertainty (EPU) and geopolitical risk (GPR) on corporate cash holding level and speed of adjustment (SOA) in one of the most important emerging markets in the Middle East and North Africa, Saudi Arabia. It also investigates whether Shariah-compliance as well as financial constraints affect the relationship between both EPU and GPR and corporate cash holdings.Design/methodology/approachThe study employs GMM regression considering a sample of 140 nonfinancial firms drawn from the Saudi stock market over the period 2002 to 2019.FindingsThe authors find evidence in support of the precautionary motive hypothesis. Facing costly external financing induced by economic policy-related uncertainty and geopolitical tension, Saudi firms tend to accumulate cash as a buffer against negative shocks to their cash flows. The results also show that the positive impact of EPU and GPR on the level of cash holding is less pronounced in Shariah-compliant firms, whereas it is more pronounced in more financially constrained firms. Evidence also reveals that the estimated adjustment coefficients show that Saudi firms adjust more quickly toward their target cash ratio in periods of high economic instability and geopolitical risks.Practical implicationsThis study has important implications for managers, policymakers and regulators. For managers, the study is an important reference to understand and design cash management policies by considering factors measured at the country level. More specifically, managers should pay more attention to periods of heightened uncertainties and geopolitical tensions in which the availability of funds is reduced. For policymakers and regulators, this study may be useful in assessing the effect of economic instability on firm’s cash holding decision. Therefore, in an effort to increase the supply of external financing available to firms, policymakers may devise investment friendly environment by controlling country-specific factors.Originality/valueThis paper shows how EPU and GPR as institutional environment factors affect cash holding decision in an oil-rich country.
Digital content marketing consumption motives in the age of social media: an investigation of relational and monetary outcomes
Authors: Izogo Ernest Emeka , Mpinganjira Mercy 
Published: January 2023

PurposeAlthough digital content marketing (DCM) research and industry-wide expenditure is growing very rapidly owing to the positive outcomes associated with this new pull marketing strategy, research has not completely mapped how DCM activities can be optimized in the social media brand community context. This paper seeks to understand how social media DCM activities can be optimized to achieve greater relational and monetary outcomes for different products.Design/methodology/approachA structural equation modeling procedure was used to analyze 416 survey responses obtained from members of Facebook brand communities in South Africa.FindingsThe results reveal that social media DCM consumption motives exert significant differential effects on both relational and monetary marketing outcomes in search and experience product contexts while also demonstrating the mechanism through which social media DCM consumption motives lead to contributing social media engagement behaviors.Practical implicationsThe study findings call for the need for firms to understand the motives that drive the consumption of DCM in social media brand communities. Specifically, marketers of search products should deploy more of hedonic contents such as images while simultaneously keeping highly textual DCM to a minimum in Facebook brand communities as this works better for experience products. Finally, more authentic SM-DCM activities that effectively address the authenticity SM-DCM consumption motive can result from the DCM activities of social media opinion leaders and genuine consumer–brand interactions in the context of Facebook brand communities.Originality/valueThis paper broke new grounds in three unique directions in terms of: (1) the relative salience of SM-DCM consumption motives in enhancing WTP and different aspects of SMBE; (2) the contextual influence of product type on SM-DCM activities optimization and (3) the mechanisms that underlie the effects of SM-DCM consumption motives on contributing SMBE in the Facebook brand community context.
Examining the determinants of consumer support for corporate social advocacy
Authors: Kim Joon Kyoung , Overton Holly , Alharbi Khalid , Carter Jackson , Bhalla Nandini 
Published: January 2023

PurposeUsing the theory of planned behavior (TPB) as a theoretical framework, this study investigates individual level psychological determinants of individuals word-of-mouth (WOM) intentions as a way to support corporate social advocacy (CSA).Design/methodology/approachAn online survey (N = 505) using a Qualtrics panel was conducted.FindingsIndividuals' attitudes towards WOM, subjective norms, and self-efficacy was positively associated with their positive WOM intention, whereas perceived controllability over WOM behaviors was not associated with WOM intention. Age was negatively associated with WOM intention.Originality/valueThis study is one of the early attempts to test individual level factors in shaping individuals' WOM intention in response to CSA. This study also employed recent TPB argument and tested the role of self-efficacy and perceived controllability on behavioral intentions in the context of corporate communication. The findings of this study offer theoretical and practical insights to corporations when developing CSA campaigns and designing CSA messages.
Chinese sentiment analysis model by integrating multi-granularity semantic features
Authors: Liu Zhongbao , Zhao Wenjuan 
Published: January 2023

PurposeIn recent years, Chinese sentiment analysis has made great progress, but the characteristics of the language itself and downstream task requirements were not explored thoroughly. It is not practical to directly migrate achievements obtained in English sentiment analysis to the analysis of Chinese because of the huge difference between the two languages.Design/methodology/approachIn view of the particularity of Chinese text and the requirement of sentiment analysis, a Chinese sentiment analysis model integrating multi-granularity semantic features is proposed in this paper. This model introduces the radical and part-of-speech features based on the character and word features, with the application of bidirectional long short-term memory, attention mechanism and recurrent convolutional neural network.FindingsThe comparative experiments showed that the F1 values of this model reaches 88.28 and 84.80 per cent on the man-made dataset and the NLPECC dataset, respectively. Meanwhile, an ablation experiment was conducted to verify the effectiveness of attention mechanism, part of speech, radical, character and word factors in Chinese sentiment analysis. The performance of the proposed model exceeds that of existing models to some extent.Originality/valueThe academic contribution of this paper is as follows: first, in view of the particularity of Chinese texts and the requirement of sentiment analysis, this paper focuses on solving the deficiency problem of Chinese sentiment analysis under the big data context. Second, this paper borrows ideas from multiple interdisciplinary frontier theories and methods, such as information science, linguistics and artificial intelligence, which makes it innovative and comprehensive. Finally, this paper deeply integrates multi-granularity semantic features such as character, word, radical and part of speech, which further complements the theoretical framework and method system of Chinese sentiment analysis.