bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods for studying microbial acid stress responses: from molecules to populations
Authors: Atasoy Merve , Bartkova Simona , Çetecioğlu-Gürol Zeynep , P Mira Nuno , O'Byrne Conor , Pérez-Rodríguez Fernando , Possas Aricia , Scheler Ott , Sedláková-Kaduková Jana , Sinčák Mirka , Steiger Matthias , Ziv Carmit , Lund Peter A 
Published: May 2024

Abstract
The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.
Regulation of copper uptake by the SWI/SNF chromatin remodeling complex in Candida albicans affects susceptibility to antifungal and oxidative stresses under hypoxia
Authors: Khemiri Inès , Tebbji Faiza , Burgain Anaïs , Sellam Adnane 
Published: May 2024

Abstract
Candida albicans is a human colonizer and also an opportunistic yeast occupying different niches that are mostly hypoxic. While hypoxia is the prevalent condition within the host, the machinery that integrates oxygen status to tune the fitness of fungal pathogens remains poorly characterized. Here, we uncovered that Snf5, a subunit of the chromatin remodeling complex SWI/SNF, is required to tolerate antifungal stress particularly under hypoxia. RNA-seq profiling of snf5 mutant exposed to amphotericin B and fluconazole under hypoxic conditions uncovered a signature that is reminiscent of copper (Cu) starvation. We found that under hypoxic and Cu-starved environments, Snf5 is critical for preserving Cu homeostasis and the transcriptional modulation of the Cu regulon. Furthermore, snf5 exhibits elevated levels of reactive oxygen species and an increased sensitivity to oxidative stress principally under hypoxia. Supplementing growth medium with Cu or increasing gene dosage of the Cu transporter CTR1 alleviated snf5 growth defect and attenuated reactive oxygen species levels in response to antifungal challenge. Genetic interaction analysis suggests that Snf5 and the bona fide Cu homeostasis regulator Mac1 function in separate pathways. Together, our data underlined a unique role of SWI/SNF complex as a potent regulator of Cu metabolism and antifungal stress under hypoxia.
Support for Family Caregivers: Implications of Work Strain and Its Intersections With Formal and Informal Help
Authors: Svec Joseph , Nemmers Natasha , Lee Jeong Eun 
Published: May 2024

Abstract

Objectives
This study seeks to assess whether and to what extent caregiver work strain is ameliorated by the presence of additional family caregivers and formal service use. Building on the stress process model and stress-appraisal moderation, we examine how formal and informal support varies in associations with caregiver distress for men and women.

Methods
This study utilizes data provided by the National Study of Caregiving, which is linked with care-recipient information from the National Health and Aging Trends Study. Using panel methods for the pooled waves, we estimated caregiver outcomes of emotional well-being on the intersection of experiences of work strain and (a) the number of additional caregivers and (b) utilization of 6 different types of formal support.

Results
Additional informal caregivers for each respective care recipient are associated with lower levels of distress, although utilization of formal services (paid help and Medicaid funding) is positively associated with caregiver distress. Informal support can offset the impact of work strain, but interactions are only evident for women caregivers.

Discussion
The findings suggest that informal support, exemplified by the number of additional caregivers, corresponds with reduced emotional distress among employed caregivers and can mitigate the negative impacts of work strain. However, positive associations between formal support and male and female caregiver distress suggest that the context of formal services may offer limited or untimely support. This study is expected to broaden our understanding of informal caregiving in later life and provide practical implications on how to sustain informal care.
Intersectional Inequalities in the Transition to Grandparenthood and Cognitive Functioning: A Longitudinal Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy
Authors: Alonso-Perez Enrique , Heisig Jan Paul , Kreyenfeld Michaela , Gellert Paul , O’Sullivan Julie Lorraine 
Published: May 2024

Abstract

Objectives
In aging societies, more people become vulnerable to experiencing cognitive decline. Simultaneously, the role of grandparenthood is central for older adults and their families. Our study investigates inequalities in the level and trajectories of cognitive functioning among older adults, focusing on possible intersectional effects of social determinants and grandparenthood as a life course transition that may contribute to delaying cognitive decline.

Methods
Using longitudinal data from the Survey of Health, Aging, and Retirement in Europe, we analyzed a sample of 19,953 individuals aged 50–85 without grandchildren at baseline. We applied multilevel analysis of individual heterogeneity and discriminatory accuracy to investigate variation in cognitive functioning across 48 intersectional strata, defined by sex/gender, migration, education, and occupation. We allowed the impact of becoming a grandparent on cognitive functioning trajectories to vary across strata by including random slopes.

Results
Intersectional strata accounted for 17.43% of the overall variance in cognitive functioning, with most of the stratum-level variation explained by additive effects of the stratum-defining characteristics. Transition to grandparenthood was associated with higher cognitive functioning, showing a stronger effect for women. Stratum-level variation in the grandparenthood effect was modest, especially after accounting for interactions between grandparenthood and the stratum-defining variables.

Discussion
This study highlights the importance of social determinants for understanding heterogeneities in older adults’ level of cognitive functioning and its association with the transition to grandparenthood. Cumulative disadvantages negatively affect cognitive functioning, hence adopting an intersectional lens is useful to decompose inequalities and derive tailored interventions to promote equal healthy aging.
Validation of the Perceived Community Support Questionnaire for Older Chinese
Authors: Che Run-Ping , Cheung Mei-Chun , Herrero Juan 
Published: May 2024

Abstract

Background and Objectives
Community support has a profound positive impact on older people’s health and plays a crucial role in facilitating aging in place. This impact is particularly significant in the Chinese context, where community support can alleviate the pressure on traditional family caregiving. This study translated, adapted, and validated the perceived community support questionnaire (PCSQ) for use with older Chinese.

Research Design and Methods
Data for this validation study were collected from a cross-sectional survey of 1,064 Chinese aged 65 years and above. Following the cultural adaptation of the PCSQ-14, confirmatory factor analysis (CFA) was conducted to examine its factor structure. Criterion validity, convergent and discriminant validity, internal consistency reliability, and test–retest reliability of the scale were also assessed.

Results
Based on the CFA results, the adapted PCSQ-14 was found to have a 3-factor solution for community integration, community participation, and community organizations. The criterion-related validity was supported by its significant correlation with depression. Convergent and discriminant validity were established, with the internal consistency of the scale being 0.90. The test–retest reliability intraclass correlation coefficient for the scale was 0.78.

Discussion and Implications
The adapted version of the PCSQ-14 demonstrated promising psychometric properties in assessing perceived community support in older Chinese. The adapted PCSQ-14 could assist researchers in determining older Chinese adults’ perceptions of community support, and could also assist practitioners and policymakers in developing targeted services for older people and allocating resources more effectively.
A generalized curvilinear solver for spherical shell Rayleigh–Bénard convection
Authors: Naskar Souvik , Chongsiripinyo Karu , Mishra Siddhant , Pal Anikesh , Jananan Akshay 
Published: May 2024

SUMMARY
A 3-D finite-difference solver has been developed and implemented for Boussinesq convection in a spherical shell. The solver transforms any complex curvilinear domain into an equivalent Cartesian domain using Jacobi transformation and solves the governing equations in the latter. This feature enables the solver to account for the effects of the non-spherical shape of the convective regions of planets and stars. Apart from parallelization using MPI, implicit treatment of the viscous terms using a pipeline alternating direction implicit scheme and HYPRE multigrid accelerator for pressure correction makes the solver efficient for high-fidelity direct numerical simulations. We have performed simulations of Rayleigh–Bénard convection at two Rayleigh numbers Ra = 105 and 107 while keeping the Prandtl number fixed at unity (Pr = 1). The average radial temperature profile and the Nusselt number match very well, both qualitatively and quantitatively, with the existing literature. Closure of the turbulent kinetic energy budget, apart from the relative magnitude of the grid spacing compared to the local Kolmogorov scales, ensures sufficient spatial resolution.
Inhibitors of dermatan sulfate epimerase 1 decreased accumulation of glycosaminoglycans in mucopolysaccharidosis type I fibroblasts
Authors: Maccarana Marco , Li Binjie , Li Honglian , Fang Jianping , Yu Mingjia , Li Jin-ping 
Published: May 2024

Abstract
Genetic deficiency of alpha-L-iduronidase causes mucopolysaccharidosis type I (MPS-I) disease, due to accumulation of glycosaminoglycans (GAGs) including chondroitin/dermatan sulfate (CS/DS) and heparan sulfate (HS) in cells. Currently, patients are treated by infusion of recombinant iduronidase or by hematopoietic stem cell transplantation. An alternative approach is to reduce the L-iduronidase substrate, through limiting the biosynthesis of iduronic acid. Our earlier study demonstrated that ebselen attenuated GAGs accumulation in MPS-I cells, through inhibiting iduronic acid producing enzymes. However, ebselen has multiple pharmacological effects, which prevents its application for MPS-I. Thus, we continued the study by looking for novel inhibitors of dermatan sulfate epimerase 1 (DS-epi1), the main responsible enzyme for production of iduronic acid in CS/DS chains. Based on virtual screening of chemicals towards chondroitinase AC, we constructed a library with 1,064 compounds that were tested for DS-epi1 inhibition. Seventeen compounds were identified to be able to inhibit 27%–86% of DS-epi1 activity at 10 μM. Two compounds were selected for further investigation based on the structure properties. The results show that both inhibitors had a comparable level in inhibition of DS-epi1while they had negligible effect on HS epimerase. The two inhibitors were able to reduce iduronic acid biosynthesis in CS/DS and GAG accumulation in WT and MPS-I fibroblasts. Docking of the inhibitors into DS-epi1 structure shows high affinity binding of both compounds to the active site. The collected data indicate that these hit compounds may be further elaborated to a potential lead drug used for attenuation of GAGs accumulation in MPS-I patients.
Combining Computational Fluid Dynamics and Experimental Data to Understand Fish Schooling Behavior
Authors: Pan Yu , Lauder George V 
Published: May 2024

Synopsis
Understanding the flow physics behind fish schooling poses significant challenges due to the difficulties in directly measuring hydrodynamic performance and the three-dimensional, chaotic, and complex flow structures generated by collective moving organisms. Numerous previous simulations and experiments have utilized computational, mechanical, or robotic models to represent live fish. And existing studies of live fish schools have contributed significantly to dissecting the complexities of fish schooling. But the scarcity of combined approaches that include both computational and experimental studies, ideally of the same fish schools, has limited our ability to understand the physical factors that are involved in fish collective behavior. This underscores the necessity of developing new approaches to working directly with live fish schools. An integrated method that combines experiments on live fish schools with computational fluid dynamics (CFD) simulations represents an innovative method of studying the hydrodynamics of fish schooling. CFD techniques can deliver accurate performance measurements and high-fidelity flow characteristics for comprehensive analysis. Concurrently, experimental approaches can capture the precise locomotor kinematics of fish and offer additional flow information through particle image velocimetry (PIV) measurements, potentially enhancing the accuracy and efficiency of CFD studies via advanced data assimilation techniques. The flow patterns observed in PIV experiments with fish schools and the complex hydrodynamic interactions revealed by integrated analyses highlight the complexity of fish schooling, prompting a reevaluation of the classic Weihs model of school dynamics. The synergy between CFD models and experimental data grants us comprehensive insights into the flow dynamics of fish schools, facilitating the evaluation of their functional significance and enabling comparative studies of schooling behavior. In addition, we consider the challenges in developing integrated analytical methods and suggest promising directions for future research.
Synthetic antimicrobial peptides: activity against vancomycin-resistant Enterococcus faecalis and modulation of chloramphenicol antibacterial activity
Authors: Gomes Lima Patrícia , Filho Noronha Souza Pedro , Pantoja Mesquita Felipe , Larré Oliveira Thaís , Drawanz Hartwig Daiane 
Published: May 2024

Abstract

Aims
Enterococcus faecalis (E. faecalis) is a leading cause of nosocomial infection and presents a wide spectrum of antibiotic resistance, being vancomycin-resistant Enterococcus (VRE) one of the most relevant. Synthetic antimicrobial peptides (SAMPs) are currently a promising option to overcome antimicrobial resistance. Thus, the purpose of this study was to assess the effect of eight SAMPs against vancomycin-resistant E. faecalis, as well as to investigate their mechanism of action and synergy with conventional antibiotics.

Methods and results
Here, eight SAMPs, Mo-CBP3-PepI, Mo-CBP3-PepII, Mo-CBP3-PepIII, RcAlb-PepI, RcAlb-PepII, RcAlb-PepIII, PepGAT, and PepKAA, were tested for antibacterial activity in vitro against E. faecalis (ATCC® 51299) through broth microdilution. A maximum of 48% of E. faecalis growth inhibition was achieved by treatment with SAMPs alone. However, when these peptides were combined with the antibiotic chloramphenicol, assessed by checkerboard method, the inhibition increased to 55%–76% of inhibition, two to three-folds of increase if compared to the effects of the compounds alone. Microscopic analysis showed that E. faecalis cells treated with a combination of SAMPs and chloramphenicol resulted in bacterial membrane damage. The biofilm inhibition maximum was 22% for SAMPs alone, when combined with chloramphenicol, the maximum increased to 33%.

Conclusions
SAMPs and their combination with chloramphenicol demonstrate antibacterial activity against E. faecalis, possibly by inducing bacterial membrane damage.
Genetic response of a perennial grass to warm and wet environments interacts and is associated with trait means as well as plasticity
Authors: Münzbergová Zuzana , Šurinová Maria , Biscarini Filippo , Níčová Eva 
Published: May 2024

Abstract
The potential for rapid evolution is an important mechanism allowing species to adapt to changing climatic conditions. Although such potential has been largely studied in various short-lived organisms, to what extent we can observe similar patterns in long-lived plant species, which often dominate natural systems, is largely unexplored. We explored the potential for rapid evolution in Festuca rubra, a long-lived grass with extensive clonal growth dominating in alpine grasslands. We used a field sowing experiment simulating expected climate change in our model region. Specifically, we exposed seeds from five independent seed sources to novel climatic conditions by shifting them along a natural climatic grid and explored the genetic profiles of established seedlings after 3 years. Data on genetic profiles of plants selected under different novel conditions indicate that different climate shifts select significantly different pools of genotypes from common seed pools. Increasing soil moisture was more important than increasing temperature or the interaction of the two climatic factors in selecting pressure. This can indicate negative genetic interaction in response to the combined effects or that the effects of different climates are interactive rather than additive. The selected alleles were found in genomic regions, likely affecting the function of specific genes or their expression. Many of these were also linked to morphological traits (mainly to trait plasticity), suggesting these changes may have a consequence on plant performance. Overall, these data indicate that even long-lived plant species may experience strong selection by climate, and their populations thus have the potential to rapidly adapt to these novel conditions.
Range of trait variation in prey determines evolutionary contributions to predator growth rates
Authors: Hermann Ruben J , Pantel Jelena H , Réveillon Tom , Becks Lutz 
Published: May 2024

Abstract
Evolutionary and ecological dynamics can occur on similar timescales and thus influence each other. While it has been shown that the relative contribution of ecological and evolutionary change to population dynamics can vary, it still remains unknown what influences these differences. Here, we test whether prey populations with increased variation in their defence and competitiveness traits will have a stronger impact on evolution for predator growth rates. We controlled trait variation by pairing distinct clonal lineages of the green alga Chlamydomonas reinhardtii with known traits as prey with the rotifer Brachionus calyciforus as predator and compared those results with a mechanistic model matching the empirical system. We measured the impact of evolution (shift in prey clonal frequency) and ecology (shift in prey population density) for predator growth rate and its dependency on trait variation using an approach based on a 2-way ANOVA. Our experimental results indicated that higher trait variation, i.e., a greater distance in trait space, increased the relative contribution of prey evolution to predator growth rate over 3–4 predator generations, which was also observed in model simulations spanning longer time periods. In our model, we also observed clone-specific results, where a more competitive undefended prey resulted in a higher evolutionary contribution, independent of the trait distance. Our results suggest that trait combinations and total prey trait variation combine to influence the contribution of evolution to predator population dynamics, and that trait variation can be used to identify and better predict the role of eco-evolutionary dynamics in predator–prey systems.
Plant protein–lipid interfaces studied by molecular dynamics simulations
Authors: Neubergerová Michaela , Pleskot Roman 
Published: May 2024

Abstract
The delineation of protein–lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid–protein interactions by experimental techniques is challenging. Molecular dynamics simulations provide a powerful computational alternative with a spatial–temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to molecular dynamics simulations. We describe different steps of performing molecular dynamics simulations and provide a broad survey of molecular dynamics studies investigating plant protein–lipid interfaces. Our aim is also to illustrate that combining molecular dynamics simulations with artificial intelligence-based protein structure determination opens up unprecedented possibilities for future investigations of dynamic plant protein–lipid interfaces.
Decoding the functionality of plant transcription factors
Authors: Dhatterwal Pinky , Sharma Namisha , Prasad Manoj 
Published: May 2024

Abstract
Transcription factors (TFs) intricately govern cellular processes and responses to external stimuli by modulating gene expression. TFs help plants to balance the trade-off between stress tolerance and growth, thus ensuring their long-term survival in challenging environments. Understanding the factors and mechanisms that define the functionality of plant TFs is of paramount importance for unravelling the intricate regulatory networks governing development, growth, and responses to environmental stimuli in plants. This review provides a comprehensive understanding of these factors and mechanisms defining the activity of TFs. Understanding the dynamic nature of TFs has practical implications for modern molecular breeding programmes, as it provides insights into how to manipulate gene expression to optimize desired traits in crops. Moreover, recent studies also report the functional duality of TFs, highlighting their ability to switch between activation and repression modes; this represents an important mechanism for attuning gene expression. Here we discuss what the possible reasons for the dual nature of TFs are and how this duality instructs the cell fate decision during development, and fine-tunes stress responses in plants, enabling them to adapt to various environmental challenges.