bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metals alter membership but not diversity of a headwater stream microbiome
Authors: Wolff Brian A. , Clements William H. , Hall Ed K. 
Published: May 2020

AbstractMetal contamination from mining or natural weathering is a common feature of surface waters in the American west. Traditionally, stream macroinvertebrate community metrics have been used for stream quality assessments. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination in a manner similar to what has been observed for stream macroinvertebrates, and if so, identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a 2×2 factorial design: 1) location (upstream or downstream of contaminating tributary), and 2) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.ImportanceOur results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Several results presented in this study are consistent with the idea that a microbial response to metals at the base of the food web may be affecting consumers one trophic level above. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystems health.
Alteration of epigenetic landscape by lamin A mutations: Hallmark of Dilated Cardiomyopathy
Authors: Banerjee Avinanda , Sengupta Kaushik 
Published: May 2020

AbstractMutations in lamin A have been reported to be associated with over 16 human diseases including dilated cardiomyopathy (DCM). We have focused on three such DCM causing mutants of lamin A which have to address the contribution of lamins in the pathogenesis of DCM at molecular level. We have elucidated the effect of these mutants for the first time on the epigenetic landscape of a myogenic fibroblast cell line C2C12. C2C12 cells expressing these mutant proteins exhibited alterations in some histone modification marks like H3K4me3, H3K9me3, H3K27me3, H3K36me3 and RNA Polymerase II activity compared to its wild type variants. This report paves the way for further studies involving epigenetic regulation in laminopathies which would be an important step in explaining the molecular mechanism and pathophysiology of the diseases like dilated cardiomyopathy.High Lightslamin A K97E mutation predominantly alters H3K9me3 histone modifications landscapelamin A K97E aggregates within nucleus also sequester the HP1γlamin A K97E mutation affects RNA polymerase II distribution pattern
All-Atom Simulation of the HET-s Prion Replication
Authors: Terruzzi Luca , Spagnolli Giovanni , Boldrini Alberto , Requena Jesús R. , Biasini Emiliano , Faccioli Pietro 
Published: May 2020

AbstractPrions are self-replicative protein particles lacking nucleic acids. Originally discovered for causing infectious neurodegenerative disorders, they have also been found to play several physiological roles in a variety of species. Functional and pathogenic prions share a common mechanism of replication, characterized by the ability of an amyloid conformer to propagate by inducing the conversion of its physiological, soluble counterpart. In this work, we focus on the propagation of the prion forming domain of HET-s, a physiological fungal prion for which high-resolution structural data are available. Since time-resolved biophysical experiments cannot yield a full reconstruction of prion replication, we resort to computational methods. To overcome the computational limitations of plain Molecular Dynamics (MD) simulations, we adopt a special type of biased dynamics called ratchet-and-pawl MD (rMD). The accuracy of this enhanced path sampling protocol strongly depends on the choice of the collective variable (CV) used to define the biasing force. Since for prion propagation a reliable reaction coordinate (RC) is not yet available, we resort to the recently developed Self-Consistent Path Sampling (SCPS). Indeed, in such an approach the CV where the biasing force is applied is not heuristically postulated but is calculated through an iterative refinement procedure. Our atomistic reconstruction of the HET-s replication shows remarkable similarities with a previously reported mechanism of mammalian PrPSc propagation obtained with a different computational protocol. Together, these results indicate that the propagation of prions generated by evolutionary distant proteins shares common features. In particular, in both these cases, prions propagate their conformation through a very similar templating mechanism.
Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories
Authors: Simmonds P. 
Published: May 2020

AbstractThe pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3×10−4substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5’U/A and 3’U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts.ImportanceThe evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations.
Non-muscle myosin-2 contractility-dependent actin turnover limits the length of epithelial microvilli
Authors: Chinowsky Colbie R. , Pinette Julia A. , Meenderink Leslie M. , Tyska Matthew J. 
Published: May 2020

ABSTRACTEpithelial brush borders are large arrays of microvilli that enable efficient solute uptake from luminal spaces. In the context of the intestinal tract, brush border microvilli drive functions that are critical for physiological homeostasis, including nutrient uptake and host defense. However, cytoskeletal mechanisms that regulate the assembly and morphology of these protrusions are poorly understood. The parallel actin bundles that support microvilli have their pointed-end rootlets anchored in a highly crosslinked filamentous meshwork referred to as the “terminal web”. Although classic EM studies revealed complex ultrastructure, the composition, organization, and function of the terminal web remains unclear. Here, we identify non-muscle myosin-2C (NM2C) as a major component of the brush border terminal web. NM2C is found in a dense, isotropic layer of puncta across the sub-apical domain, which transects the rootlets of microvillar actin bundles. Puncta in this network are separated by ∼210 nm, dimensions that are comparable to the expected size of filaments formed by NM2C. In primary intestinal organoid cultures, the terminal web NM2C network is highly dynamic and exhibits continuous remodeling. Using pharmacological and genetic perturbations to disrupt NM2C activity in cultured intestinal epithelial cells, we found that this motor controls the length of growing microvilli by regulating actin turnover in a manner that requires a fully active motor domain. Our findings answer a decades old question on the function of terminal web myosin and hold broad implications for understanding apical morphogenesis in diverse epithelial systems.
Disulfide reduction allosterically destabilizes the β-ladder sub-domain assembly within the NS1 dimer of ZIKV
Authors: Roy P , Roy S , Sengupta N 
Published: May 2020

AbstractThe Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the non-structural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major roleviasymmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intra-monomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intra-monomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability and asymmetric salt bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (Sconf), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state. Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher ordered oligomerization, and thereby affect crucial replication pathways.Statement of significanceControlling viral pathogenesis remains a challenge in the face of modern-day epidemics. Though cumbersome and fraught with misleads, most therapeutic endeavors lean towards the design of drug molecules targeting specific proteins involved in viral pathogenesis. This work demonstrates an alternative approach, namely the usage of allosteric intervention to disrupt the binding integrity of the primary domain of the non-structural NS1 protein dimer crucially important in ZIKV virulence. The intervention, triggered by symmetric reduction of the internal monomeric disulfide bonds, results in weakening and distortion of the distal binding interfaces. It further introduces marked structural and entropic asymmetry within the homooligomeric unit, precluding the formation of higher ordered oligomers of high symmetry. The results have important ramifications for consolidated efforts at limiting ZIKV virulence.
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Authors: Utter Daniel R. , Borisy Gary G. , Eren A. Murat , Cavanaugh Colleen M. , Welch Jessica L. Mark 
Published: May 2020

AbstractBackgroundThe increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.ResultsHere, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa,Haemophilus parainfluenzaeand the genusRothia, metapangenomes revealed distinct genomic groups based on shared genome content.H. parainfluenzaegenomes separated into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identified an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genusRothia, grouping by shared genome content recapitulated species-level taxonomy and habitat preferences. However, while mostR. mucilaginosawere restricted to the tongue as expected, two genomes represented a cryptic population ofR. mucilaginosain many buccal mucosa samples. For bothH. parainfluenzaeand the genusRothia, we identified not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences were absent or ubiquitous.ConclusionsOur findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.
Shifting trust in construction supply chains through blockchain technology
Authors: Qian Xiaoning (Alice) , Papadonikolaki Eleni 
Published: May 2020

PurposeBlockchain technology is booming in many industries. Its application in supply chain management is also gradually increasing. Supply chain management (SCM) has long been committed to reducing costs and increasing efficiency and is trying to optimise resources and reduce the sector's fragmentation. Trust has always been an important factor in managing supply chain relationships, and it also affects the efficiency of supply chain operations. To this end, this study aims to examine how trust is affected by the introduction of blockchain technology in construction supply chain management.Design/methodology/approachThis study is based on semi-structured interviews and publicly available information from experts in blockchain and construction supply chain management. Through content analysis, the data are analysed thematically to explore how various types of trust, such as system-based, cognition-based and relation-based, are affected by blockchain technology.FindingsBlockchain technology provides solutions for data tracking, contracting and transferring resources in supply chain management. These applications help enhance the various sources of trust in SCM and provide supply chain partners with protection mechanisms to avoid the risks and costs of opportunistic behaviour in collaboration, shifting trust from relational to system-based and cognition-based.Research limitations/implicationsThis study focuses only on inter-organisational rather than interpersonal trust and empirical data from experts whose knowledge and cognition could be subjective.Practical implicationsLeveraging the potential of digitalisation to manage trust requires that leaders and managers actively try to improve contractual arrangements, information sharing and being open to new innovative technologies like blockchain.Social implicationsFrom a relational view of supply chain management, the extent to which blockchain technology can develop and spread depends on the readiness of the social capital to accept decentralised governance structures.Originality/valueThis study builds upon an original data set and discusses features and applications of blockchain technology, explores the sources and dimensions of trust in supply chain management and explains the impact of blockchain technology on trust.
Explicating innovation-based human resource management's influence on employee satisfaction and performance
Authors: Lasisi Taiwo Temitope , Ozturen Ali , Eluwole Kayode Kolawole , Avci Turgay 
Published: May 2020

PurposeThis study aims to build and test an empirical model that investigates the mechanism with which innovation-based human resource management (HRM) impacts employee satisfaction and performance in Nigerian international airports.Design/methodology/approachA time-lagged approach that involved three-waves was used to collect data from passenger-contact employees and their immediate managers for three-month period starting from January to March 2019. A total of 247 dyads of passenger-contact employees and managers were used for the data analysis.FindingsResults from data analysis showed that coworker support and absorptive capacity mediate the impact of innovation-based HRM on employee satisfaction and performance. Innovation-based human resource effort is best applied when coworker support is evident in the workplace.Originality/valueThe development and application of innovation-driven human resources in the Nigerian aviation context encourage satisfaction with assigned task roles, leading to employee performance. Theory-based implications for managing passenger-contact employees were also given. A significant strength of this study is that it is among the forerunners of scholars that investigated innovation-based HRM as a continuum rather than different aspects of broader management issues.
Simulated home: an effective cross-cultural adjustment model for Chinese expatriates
Authors: Huang Hao , Liu Hong , Huang Xin , Ding Yusen 
Published: May 2020

PurposeThe purpose of this study is to explore the adjustment model of expatriates in overseas projects by studying two overseas projects of a Chinese state-owned enterprise.Design/methodology/approachBased on the grounded theory, qualitative analysis was performed based on data compiled from 116 pieces of project briefings, 105 questionnaires answered by expatriate workers and 21 interviews conducted to those workers based on briefings and questionnaires.FindingsThe study found that the simulated home is a standard cross-cultural adjustment model for expatriates in Chinese engineering projects, which are project-oriented and often inattentive to employees' individual rights. The simulated home creates a unique work-place and social environment similar to that of expatriates' home country in the cultural setting of the host country, but it also establishes a cultural barrier, limiting the communication between expatriates and the local people, which is not conducive to the cultural exchange between the two sides, causing cultural clashes and consequently hindering the progress of projects.Originality/valueThis research puts forward the model of “simulated home.” And this study bears significance to the cross-cultural adjustment of expatriate workers in Chinese overseas projects.
Harsh environmental regimes increase the functional significance of intraspecific variation in plant communities
Authors: Niu Kechang , Zhang Shiting , Lechowicz Martin J. 
Published: May 2020

Abstract

The relative importance of intraspecific trait variation (rITV) for functional diversity (FD) in plant communities is increasingly apparent, but the influence of abiotic factors on the balance between intraspecific and interspecific effects in contrasting environments is uncertain. Drawing on a novel conceptual and analytic framework, we quantified rITV as the ratio of FD associated with between‐population ITV (Intra_FD) and the interspecific variation (Inter_FD) due to species turnover across sites.
We predicted that rITV would increase with environmental harshness as a result of decreasing interspecific variation and concomitant increases in between‐population ITV. We empirically tested this prediction in a comparison of rITV for five traits (mature plant height, SLA, leaf dry matter content and the foliar concentrations of nitrogen and phosphorus (P)) characterizing species in Tibetan alpine meadow communities from contrasting environmental regimes.
We found that across sites: (a) rITV for all five traits increased with environmental harshness not only through decreasing Inter_FD but also through increasing Intra_FD; (b) increases in rITV were mostly attributable to declines in soil resources, especially soil P, with lower soil P significantly associated with lower Inter_FD but higher Intra_FD for most traits; and (c) although neither Intra_FD nor Inter_FD was significantly impacted by species richness for any traits, a higher rITV for SLA was significantly associated with low species richness.
Taken together, these results support our hypothesis that the functional significance of ITV in plant communities increases with environmental harshness. Moreover, in the Tibetan alpine meadows we studied, the opposing intraspecific and interspecific responses along a gradient of P availability appear to act as a buffering mechanism stabilizing the functional structure of communities on P deficient soils. Our novel conceptual and analytical framework provides a template for evaluating the generality of this favourable mismatch between intraspecific and interspecific responses in FD along environmental gradients.

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Cause of intrauterine and neonatal death in twin pregnancies (CoDiT): development of a novel classification system
Authors: Gulati N , Mackie FL , Cox P , Marton T , Heazell AEP , Morris RK , Kilby MD 
Published: May 2020

ObjectiveTwin pregnancies have a significantly higher perinatal mortality than singleton pregnancies. Current classification systems for perinatal death lack twin‐specific categories, potentially leading to loss of important information regarding cause of death. We introduce and test a classification system designed to assign a cause of death in twin pregnancies (CoDiT).DesignRetrospective cross‐sectional study.SettingTertiary maternity unit in England with a perinatal pathology service.PopulationTwin pregnancies in the West Midlands affected by fetal or neonatal demise of one or both twins between 1 January 2005 and 31 December 2016 in which postmortem examination was undertaken.MethodsA multidisciplinary panel designed CoDiT by adapting the most appropriate elements of singleton classification systems. The system was tested by assigning cause of death in 265 fetal and neonatal deaths from 144 twin pregnancies. Cause of death was validated by another obstetrician blinded to the original classification.Main outcome measuresInter‐rater, intra‐rater, inter‐disciplinary agreement and cause of death.ResultsCohen’s Kappa demonstrated ‘strong’ (>0.8) inter‐rater, intra‐rater and inter‐disciplinary agreement (95% CI 0.70–0.91). The commonest cause of death irrespective of chorionicity was the placenta; twin‐to‐twin transfusion syndrome (TTTS) was the commonest placental cause in monochorionic twins and acute chorioamnionitis in dichorionic twins.ConclusionsThis novel classification system records causes of death in twin pregnancies from postmortem reports with high inter‐user agreement. We highlight differences in aetiology of death between monochorionic and dichorionic twins.Tweetable abstractNew classification system for #twin cause of death ‘CoDiT’ shows high rater agreement.