bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish
Authors: Godivier Josepha , Lawrence Elizabeth A. , Wang Mengdi , Hammond Chrissy L. , Nowlan Niamh C. 
Published: January 2022

AbstractIn early limb embryogenesis, synovial joints acquire specific shapes which determine joint motion and function. The process by which the opposing cartilaginous joint surfaces are moulded into reciprocal and interlocking shapes, called joint morphogenesis, is one of the least understood aspect of joint formation and the cell-level dynamics underlying it are yet to be unravelled. In this research, we quantified key cellular dynamics involved in growth and morphogenesis of the zebrafish jaw joint and synthesised them in a predictive computational simulation of joint development. Cells in larval zebrafish jaw joints labelled with cartilage markers were tracked over a forty-eight hour time window using confocal imaging. Changes in distance and angle between adjacent cell centroids resulting from cell rearrangement, volume expansion and extracellular matrix (ECM) deposition were measured and used to calculate the rate and direction of local tissue deformations. We observed spatially and temporally heterogeneous growth patterns with marked anisotropy over the developmental period assessed. There was notably elevated growth at the level of the retroarticular process of the Meckel’s cartilage, a feature known to undergo pronounced shape changes during zebrafish development. Analysis of cell dynamics indicated a dominant role for cell volume expansion in growth, with minor influences from ECM volume increases and cell intercalation. Cell proliferation in the joint was minimal over the timeframe of interest. Synthesising the dynamic cell data into a finite element model of jaw joint development resulted in accurate shape predictions. Our biofidelic computational simulation demonstrated that zebrafish jaw joint growth can be reasonably approximated based on cell positional information over time, where cell positional information derives mainly from cell orientation and cell volume expansion. By modifying the input parameters of the simulation, we were able to assess the relative contributions of heterogeneous growth rates and of growth orientation. The use of uniform rather than heterogeneous growth rates only minorly impacted the shape predictions whereas isotropic growth fields resulted in altered shape predictions. The simulation results suggest that growth anisotropy is the dominant influence on joint growth and morphogenesis. This study addresses the gap of the cellular processes underlying joint morphogenesis, with implications for understanding the aetiology of developmental joint disorders such as developmental dysplasia of the hip and arthrogryposis.
Common Dynamic Determinants Govern Quorum Quenching Activity in N-terminal Serine Hydrolases
Authors: Surpeta Bartlomiej , Grulich Michal , Palyzová Andrea , Marešová Helena , Brezovsky Jan 
Published: January 2022

ABSTRACTGrowing concerns about microbial antibiotic resistance have motivated extensive research into ways of overcoming antibiotic resistance. Quorum quenching (QQ) processes disrupt bacterial communication via quorum sensing, which enables bacteria to sense the surrounding bacterial cell density and markedly affects their virulence. Due to its indirect mode of action, QQ is believed to exert limited pressure on essential bacterial functions and may thus avoid inducing resistance. Although many enzymes display QQ activity against various bacterial signaling molecules, their mechanisms of action are poorly understood, limiting their potential optimization as QQ agents. Here we evaluate the capacity of three N-terminal serine hydrolases to degrade N-acyl homoserine lactones that serve as signaling compounds for Gram-negative bacteria. Using molecular dynamics simulations of the free enzymes and their complexes with two signaling molecules of different lengths, followed by quantum mechanics/molecular mechanics molecular dynamics simulations of their initial catalytic steps, we clarify the molecular processes underpinning their QQ activity. We conclude that all three enzymes degrade bacterial signaling molecules via similar reaction mechanisms. Moreover, we experimentally confirmed the activity of two penicillin G acylases from Escherichia coli (ecPGA) and Achromobacter spp. (aPGA), adding these biotechnologically well-optimized enzymes to the QQ toolbox. We also observed enzyme- and substrate-dependent differences in the catalytic actions of these enzymes, arising primarily from the distinct structures of their acyl-binding cavities and the dynamics of their molecular gates. As a consequence, the first reaction step catalyzed by ecPGA with a longer substrate had an elevated energy barrier because its shallow acyl binding site could not accommodate a productive substrate-binding configuration. Conversely, aPGA in complex with both substrates exhibited unfavorable energetics in both reaction steps due to the dynamics of the residues gating the acyl binding cavity entrance. Finally, the energy barriers of the second reaction step catalyzed by Pseudomonas aeruginosa acyl-homoserine lactone acylase with both substrates were higher than in the other two enzymes due to the unique positioning of Arg297β in this enzyme. The discovery of these dynamic determinants will guide future efforts to design robust QQ agents capable of selectively controlling virulence in resistant bacterial species.
An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
Authors: Parey Elise , Louis Alexandra , Montfort Jérôme , Guiguen Yann , Crollius Hugues Roest , Berthelot Camille 
Published: January 2022

AbstractTeleost fishes are ancient tetraploids stemming from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to a diploid state through meiosis resolution and subsequent genetic divergence (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap to interpret their functional evolution. As legacy of the whole genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for over 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates.
Dissecting the interactions of PINK1 with the TOM complex in depolarized mitochondria
Authors: Maruszczak Klaudia K. , Jung Martin , Rasool Shafqat , Trempe Jean-François , Rapaport Doron 
Published: January 2022

AbstractMitochondria dysfunction is involved in the pathomechanism of many illnesses including Parkinson’s disease. PINK1, which is mutated in some cases of familiar Parkinsonism, is a key component in the degradation of damaged mitochondria by mitophagy. The accumulation of PINK1 on the mitochondrial outer membrane (MOM) of compromised organelles is crucial for the induction of mitophagy, but the molecular mechanism of this process is still unresolved. Here, we investigate the association of PINK1 with the TOM complex. We demonstrate that PINK1 heavily relies on the import receptor TOM70 for its association with mitochondria and directly interacts with this receptor. The structural protein TOM7 appears to play only a moderate role in PINK1 association with the TOM complex, probably due to its role in stabilizing this complex. PINK1 requires the TOM40 pore lumen for its stable interaction with the TOM complex and apparently remains there during its further association with the MOM. Overall, this study provides new insights on the role of the individual TOM subunits in the association of PINK1 with the MOM of depolarized mitochondria.
Histopathological analysis of selected organs of Oreochromis niloticus due to sub-lethal industrial effluents exposure
Authors: Jabeen Ghazala , Ishaq Sarwat , Manzoor Farkhanda 
Published: January 2022

AbstractOn a daily basis, our environment is exposed to tons of a composite of industrial effluents, which has a negative impact on commercial fish production and, as a result, on humans. Present study was designed to evaluate the acute, sub-chronic, and chronic toxicity of a composite of raw industrial effluent from Sunder Industrial Estate in the freshwater fish Oreochromis niloticus biosystem by investigating at the histopathological changes in different organs such as heart, kidney, and muscle after exposure. Fish was exposed to 1/3rd, 1/5th and 1/10th of predetermined LC50. Significant histopathological alterations in heart (myocarditis, pericardium bending and lifting) kidney (renal tube degeneration, glomerulus structural alteration and necrotic proximal tubule) and muscle (inflammation, atrophy and tumor) were observed in treated groups. After the sub-lethal exposure histological alteration index (HAI) was highest in chronic group as compared to the acute and sub-chronic group as HAI group D> HAI group C> HAI group B. Moreover physicchemical parameters of water were found to be out of the range of the APHA standard approach.
The impact of national culture on COVID-19 pandemic outcomes
Authors: He Zhaochen , Jiang Yixiao , Chakraborti Rik , Berry Thomas D. 
Published: January 2022

PurposeThis study aims to uncover the extent to which cultural traits may explain the puzzling international divergence in COVID-19 outcomes, and how those traits interact with state action to produce compliance with pandemic health policy.Design/methodology/approachA theoretical framework illustrates the surprising possibility that culture and state action may not reinforce each other but rather act as substitutes in eliciting anti-pandemic behavior. This possibility is tested empirically in two specifications: a cross-sectional regression that includes several novel COVID-related measures, and a panel model that controls for contemporaneous disease burden. Across these models, we use the measures of national culture developed by Hofstede (1984) and a newer metric developed by Schwartz (1990).FindingsIndividualism and egalitarianism have a positive effect on disease prevalence, while cultural heterogeneity was associated with a more robust public health response. Consistent with our model, we find that culture and state action served as substitutes in motivating compliance with COVID-19 policy.Practical implicationsThe results of this study imply that culture and state interact in determining the effectiveness of public health measures aimed at combating COVID-19; these results recommend culturally aware state intervention when combating pandemics.Originality/valueThis study offers several new contributions. First, it proposes a model to help contextualize the empirical analysis. Second, it examines a wider range of traits than previous studies, including cultural homogeneity and the Schwartz variables. Third, it employs a richer econometric specification that explores the interaction between state and culture in a panel context.
Research on the reliable test range of four-point supported piezoelectric dynamometer
Authors: Zhang Jun , Ma Yixuan , Ren Zongjin , Bai Tao , Hu Peikai , Wang Zunhao 
Published: January 2022

Purpose
The purpose of this paper is to improve the reliability of the force measurement system by determining the reliable test range of dynamometer.

Design/methodology/approach
Based on the principle of leverage and moment balance, a general force distribution model is applicable in where the test point is located either inside or outside the support region of four three-component force links of dynamometer is established. After corroborating the correctness of the model through verification experiments, the boundary conditions that each three-component force link should satisfy are analyzed by considering the characteristic of the dynamometer components comprehensively. Furthermore, the reliable test range of dynamometer is determined, followed by a calibration experiment to verify its rationality.

Findings
The relationships between the reliable test range and the tested force, the bolt pre-tightening force and the bearing capacity of quartz wafers are clarified. Further, the experimental calibration results show that when the test point is within the reliable test range, the three-directional output voltage of dynamometer has excellent linearity and repeatability. The nonlinearity and repeatability in X-, Y- and Z-directions are all less than 1.1%.

Originality/value
A general mathematical model of force distribution of four three-component force links is constructed, which provides a theoretical basic for the mechanical analysis of multi-sensors’ dynamometer. Comprehensively considering the performance of dynamometer components, the value of measured force and the pre-tightening force, the simultaneous equations of reliable test range are deduced, which limits the boundary of allowable test position of piezoelectric dynamometer.
Functional Traits 2.0: The power of the metabolome for ecology
Authors: Walker Tom W. N. , Alexander Jake M. , Allard Pierre‐Marie , Baines Oliver , Baldy Virginie , Bardgett Richard D. , Capdevila Pol , Coley Phyllis D. , David Bruno , Defossez Emmanuel , Endara María‐José , Ernst Madeleine , Fernandez Catherine , Forrister Dale , Gargallo‐Garriga Albert , Jassey Vincent E. J. , Marr Sue , Neumann Steffen , Pellissier Loïc , Peñuelas Josep , Peters Kristian , Rasmann Sergio , Roessner Ute , Sardans Jordi , Schrodt Franziska , Schuman Meredith C. , Soule Abrianna , Uthe Henriette , Weckwerth Wolfram , Wolfender Jean‐Luc , van Dam Nicole M. , Salguero‐Gómez Roberto 
Published: January 2022

Abstract

A major aim of ecology is to upscale attributes of individuals to understand processes at population, community and ecosystem scales. Such attributes are typically described using functional traits, that is, standardised characteristics that impact fitness via effects on survival, growth and/or reproduction. However, commonly used functional traits (e.g. wood density, SLA) are becoming increasingly criticised for not being truly mechanistic and for being questionable predictors of ecological processes.

This Special Feature reviews and studies how the metabolome (i.e. the thousands of unique metabolites that underpin physiology) can enhance trait‐based ecology and our understanding of plant and ecosystem functioning.

In this Editorial, we explore how the metabolome relates to plant functional traits, with reference to life‐history trade‐offs governing fitness between generations and plasticity shaping fitness within generations. We also identify solutions to challenges of acquiring, interpreting and contextualising metabolome data, and propose a roadmap for integrating the metabolome into ecology.

We next summarise the seven studies composing the Special Feature, which use the metabolome to examine mechanisms behind plant community assembly, plant‐organismal interactions and effects of plants and soil micro‐organisms on ecosystem processes.

Synthesis. We demonstrate the potential of the metabolome to improve mechanistic and predictive power in ecology by providing a high‐resolution coupling between physiology and fitness. However, applying metabolomics to ecological questions is currently limited by a lack of conceptual, technical and data frameworks, which needs to be overcome to realise the full potential of the metabolome for ecology.
Atmospheric resonance: sonic motion and the question of religious mediation
Authors: Eisenlohr Patrick 
Published: January 2022

AbstractBecause of its material characteristics, the sonic poses a challenge to the influential paradigm of religion as mediation. This article makes a case for a neo‐phenomenological analytic of atmospheres in order to do justice to the sonic in anthropological approaches to religion. Approaching the sonic as atmospheric half‐things, I propose a different understanding of religious mediation from the one developed in contexts where images, objects, and technical media dominate. Based on research on the recitation of Urdu devotional poetry among Mauritian Muslims, it is suggested that sonic religion does not function as a stable in‐between connecting humans and the divine. Instead, it operates through processes of resonant bundling, intertwining different strands of lived experience, including religious traditions.
Institutional trust and emergency preparedness: Perceptions of Covid 19 crisis management in Sweden
Authors: Bengtsson Rikard , Brommesson Douglas 
Published: January 2022

AbstractThe Covid 19 pandemic has put the issue of public trust at the centre of political analysis. This article inquires into the level of public trust in Sweden concerning current crisis management as well as preparedness for future crises. The empirical basis for this study consists of unique data generated through two surveys on the Covid 19 virus conducted during 2020 in Sweden. Respondents were asked to assess their trust in different actors' crisis management. In addition, the first survey asked about how the actions of different actors impact on the forward‐oriented trust held in Swedish emergency preparedness for a future severe crisis. Four key findings stand out. First, the results display rather weak levels of interpersonal trust. Second, a surprisingly high level of institutional trust can be found during the initial phase of the pandemic. Simultaneously we see somewhat decreasing levels of trust later during the pandemic. The results include interesting variations across age, gender and education. Third, relating the results to earlier research on trust in Sweden, the results contain indications of stable trust levels despite the all but stable contextual conditions. Fourth, the analysis shows important variations in trust levels among different institutions and layers of government.
Changes in the free amino acid profile of pickling cucumber during lactic acid fermentation
Authors: Moore Jennifer Fideler , DuVivier Rachel , Johanningsmeier Suzanne D. 
Published: January 2022

AbstractFree amino acid (FAA) profiles of fresh, acidified, naturally fermented, and starter culture fermented cucumbers were analyzed by liquid chromatography triple quadrupole mass spectrometry. Fermented cucumbers contained more total FAA than acidified cucumbers (1,302 ± 102 mg/kg and 635 ± 35 mg/kg, respectively). Total FAA content of fermented cucumber was similar regardless of brine salt levels (2–6% NaCl) and starter culture addition. Glutamine (1491.4 ± 69.3 mg/kg), γ‐aminobutyric acid (GABA, 269.6 ± 21.4 mg/kg), asparagine (113.0 ± 6.4 mg/kg), and citrulline (110.3 ± 8.5 mg/kg) were the most abundant FAA in fresh pickling cucumber, whereas GABA (181.3 ± 21.5 mg/kg), isoleucine (165.2 ± 11.2 mg/kg), leucine (129.8 ± 10.9 mg/kg), and lysine (110.9 ± 5.0 mg/kg) were the most abundant in fermented cucumber. GABA and ornithine were produced during fermentation, indicating glutamate decarboxylase and arginine deiminase activities. Notably, ornithine was significantly higher in natural (63.3 ± 31.5 mg/kg) versus starter culture fermented cucumbers (3.0 ± 0.7 mg/kg). This new information on FAA composition of fresh and fermented pickling cucumbers shows the impact of fermentation conditions on cucumber amino acid profiles while providing insight for manipulating fermentations for health promotion and consumer acceptance.Practical ApplicationThis study reports changes in the free amino acid profiles of raw, fermented and acidified cucumbers, which may be valuable for understanding the impact of these foods on human health and nutrition. This information is useful for food microbiologists studying the metabolism of lactic acid bacteria during fermentation and/or designing starter cultures and could contribute to the development of novel fermented cucumber pickle products with enhanced nutritional value.
Remotely sensed vegetation productivity predicts breeding activity and drought refuges for a threatened bird in semi‐arid Australia
Authors: Young A. R. , Selwood K. E. , Benshemesh J. , Wright J. , Southwell D. 
Published: January 2022

AbstractRefuges play a critical role protecting species against the effects of climate change. Managing high priority refuges could improve species resilience and facilitate dispersal during periods of environmental change. In this study, we identified drought refuges in semi‐arid Australia for a threatened bird, the malleefowl Leipoa ocellata. Using a Poisson regression model, we quantified the effect of remotely sensed vegetation indices, rainfall, soil moisture and site characteristics on malleefowl breeding activity at 144 sites surveyed from 2000 to 2017 during and after drought. We tested the effect of two vegetation productivity indices on malleefowl breeding activity – the Normalized Difference Vegetation Index (NDVI) and the Enhanced Vegetation Index (EVI) – averaged across three temporal and three spatial scales during the mound building and incubation stage of the breeding cycle. We found that NDVI and EVI were better predictors of malleefowl breeding activity than soil moisture and winter rainfall. The model with the lowest Akaike information criterion value contained NDVI averaged over 3 months (June–August) and a 1‐km radius. Malleefowl breeding activity had a strong positive association with NDVI (0.42 ± se 0.03) and a negative association with slope (−0.34 ± se 0.03) and vegetation patch size (−0.23 ± se 0.02). We found the proportion of refugia (top 20% of predicted breeding activity) in protected areas was highly variable, decreasing from 42% in an extreme wet year (2011) to 14% in an extreme drought year (2007). Expanding the reserve network to include refugia predicted to occur in the south of semi‐arid Victoria could improve resilience of malleefowl to climate change. We demonstrate how remotely sensed vegetation indices combined with citizen science data can identify where to protect native vegetation with high, stable productivity. Our approach could be applied to a broad range of species in semi‐arid regions vulnerable to climate change.