bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis for condensin enrichment at pericentromeres
Authors: Wang Menglu , Zou Juan , Spanos Christos , Rappsilber Juri , Marston Adele L. 
Published: March 2024

SummaryFaithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces and ensure the bioriented attachment of kinetochores to microtubules in mitosis. Here we demonstrate that budding yeast condensin is recruited to pericentromeres through a direct interaction between its Ycg1 subunit and the pericentromeric adaptor protein, shugoshin (Sgo1). We identify a Short Linear Motif (SLiM), termed CR1, within the C-terminal region of Sgo1 which inserts into a conserved pocket on Ycg1. Disruption of this interface abolishes the Sgo1-condensin interaction, prevents condensin recruitment to pericentromeres and results in defective sister kinetochore biorientation in mitosis. Similar motifs to CR1 are found in known and potential condensin binding partners and the Ycg1 binding pocket is broadly conserved, including in the mammalian homolog CAP-G. Overall, we uncover the molecular mechanism that targets condensin to define a specialized chromosomal domain.
Membrane vesicles can contribute to cellulose degradation byTeredinibacter turnerae,a cultivable intracellular endosymbiont of shipworms
Authors: Gasser Mark T. , Liu Annie , Altamia Marvin , Brensinger Bryan R. , Brewer Sarah L. , Flatau Ron , Hancock Eric R. , Preheim Sarah P. , Filone Claire Marie , Distel Dan L. 
Published: March 2024

AbstractTeredinibacter turneraeis a cultivable cellulolytic Gammaproteobacterium (Cellvibrionaceae) that commonly occurs as an intracellular endosymbiont in the gills of wood-eating bivalves of the family Teredinidae (shipworms). The genome ofT. turneraeencodes a broad range of enzymes that deconstruct cellulose, hemicellulose, and pectin and contribute to wood (lignocellulose) digestion in the shipworm gut. However, the mechanisms by whichT. turneraesecretes lignocellulolytic enzymes are incompletely understood. Here, we show thatT. turneraecultures grown on carboxymethyl cellulose (CMC) produce membrane vesicles (MVs) that include a variety of proteins identified by LC-MS/MS as carbohydrate-active enzymes (CAZymes) with predicted activities against cellulose, hemicellulose, and pectin. Reducing sugar assays and zymography confirm that these MVs exhibit cellulolytic activity, as evidenced by the hydrolysis of CMC. Additionally, these MVs were enriched withTonB-dependent receptors, which are essential to carbohydrate and iron acquisition by free-living bacteria. These observations indicate a potential role for MVs in lignocellulose utilization byT. turneraein the free-living state, suggest possible mechanisms for host-symbiont interaction, and may be informative for commercial applications such as enzyme production and lignocellulosic biomass conversion.
Membrane curvature association of amphipathic helix 8 drives constitutive endocytosis of GPCRs
Authors: Schmidt Jan Hendrik , Herlo Rasmus , Rombach Joscha , Larsen Andreas Haahr , Stoklund Mikkel , Perslev Mathias , Nielsen Tommas Theiss Ehlers , Andersen Keenie Ayla , Herenbrink Carmen Klein , Lycas Matthew D. , Ejdrup Aske Lykke , Christensen Nikolaj Riis , Christensen Jan P. , Salman Mootaz , Herborg Freja , Gether Ulrik , Hauser Alexander Sebastian , Bassereau Patricia , Perrais David , Madsen Kenneth Lindegaard 
Published: March 2024

AbstractCellular signaling relies on the activity of transmembrane receptors and their presentation on the cellular surface. Their continuous insertion in the plasma membrane is balanced by constitutive and activity dependent internalization, which is orchestrated by adaptor proteins recognizing semi-specific motifs within the receptors’ intracellular regions. Here we describe a complementary and evolutionary conserved and refined trafficking mechanism for G-protein coupled receptors (GPCR). This mechanism relies on the insertion of their amphipathic helix 8 into the inner leaflet of lipid membranes, orthogonal to the transmembrane helices. These amphipathic helices dictate subcellular localization of the receptors and autonomously drive their endocytosis by cooperative assembly and association with areas of high membrane curvature. The strength of helix 8 membrane insertion propensity quantitatively predicts the rate of constitutive internalization of GPCRs. This discovery advances our understanding of membrane protein trafficking and highlights a new principle of receptor-lipid interactions that may have broader implications for cellular signaling and therapeutic targeting.One-Sentence SummaryReceptor proteins navigate cellular membranes by interacting with their curvature using an evolutionary conserved mechanism that relies on amphipathic helices and complements direct coupling to the endocytic protein machinery.
Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions
Authors: Qin Sanbo , Zhou Huan-Xiang 
Published: March 2024

ABSTRACTWe present a method, FMAPS(q), for calculating the structure factor,S(q), of a protein solution, by extending ourfast Fourier transform-basedmodeling ofatomisticprotein-protein interactions (FMAP) approach. The interaction energy consists of steric, nonpolar attractive, and electrostatic terms that are additive among all pairs of atoms between two protein molecules. In the present version, we invoke the free-rotation approximation, such that the structure factor is given by the Fourier transform of the protein center-center distribution functiongC(R). At low protein concentrations,gC(R) can be approximated ase−βW(R), whereW(R) is the potential of mean force along the center-center distanceR. We calculateW(R) using FMAPB2, a member of the FMAP class of methods that is specialized for the second virial coefficient [Qin and Zhou, J Phys Chem B 123 (2019) 8203-8215]. For higher protein concentrations, we obtainS(q) by a modified random-phase approximation, which is a perturbation around the steric-only energy function. Without adjusting any parameters, the calculated structure factors for lysozyme and bovine serum albumin at various ionic strengths, temperatures, and protein concentrations are all in reasonable agreement with those measured by small-angle X-ray or neutron scattering. This initial success motivates further developments, including removing approximations and parameterizing the interaction energy function.
Molecular Basis for RNA Cytidine Acetylation by NAT10
Authors: Zhou Mingyang , Gamage Supuni Thalalla , Tran Khoa A. , Bartee David , Wei Xuepeng , Yin Boyu , Berger Shelley , Meier Jordan L. , Marmorstein Ronen 
Published: March 2024

ABSTRACTHuman NAT10 acetylates the N4 position of cytidine in RNA, predominantly on rRNA and tRNA, to facilitate ribosome biogenesis and protein translation. NAT10 has been proposed as a therapeutic target in cancers as well as aging-associated pathologies such as Hutchinson-Gilford Progeria Syndrome (HGPS). The ∼120 kDa NAT10 protein uses its acetyl-CoA-dependent acetyltransferase, ATP-dependent helicase, and RNA binding domains in concert to mediate RNA-specific N4-cytidine acetylation. While the biochemical activity of NAT10 is well known, the molecular basis for catalysis of eukaryotic RNA acetylation remains relatively undefined. To provide molecular insights into the RNA-specific acetylation by NAT10, we determined the single particle cryo-EM structures ofChaetomium thermophilumNAT10 (CtNAT10) bound to a bisubstrate cytidine-CoA probe with and without ADP. The structures reveal that NAT10 forms a symmetrical heart-shaped dimer with conserved functional domains surrounding the acetyltransferase active sites harboring the cytidine-CoA probe. Structure-based mutagenesis with analysis of mutantsin vitrosupports the catalytic role of two conserved active site residues (His548 and Tyr549 inCtNAT10), and two basic patches, both proximal and distal to the active site for RNA-specific acetylation. Yeast complementation analyses and senescence assays in human cells also implicates NAT10 catalytic activity in yeast thermoadaptation and cellular senescence. Comparison of the NAT10 structure to protein lysine and N-terminal acetyltransferase enzymes reveals an unusually open active site suggesting that these enzymes have been evolutionarily tailored for RNA recognition and cytidine-specific acetylation.
Extracellular biosynthesis of silver nanoparticles using cell suspension ofRhodococcus fascians
Authors: Ghadamgahi Farideh , Konakalla Naga Charan , Sang Atash Masome Mehraban , Ortiz Rodomiro , Vetukuri Ramesh 
Published: March 2024

AbstractBiosynthesis of metallic nanoparticles using biological systems such as bacteria has become an important nanobiotechnology area. In this report, we present the first extracellular biosynthesis of silver nanoparticles (AgNPs) using the gram-positive bacteriumRhodococcus fascians. The AgNPs underwent characterization through various analytical techniques, encompassing UV–visible spectroscopy, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Transmission electron microscopy (TEM) and Scanning electron microscopy (SEM). UV-visible spectroscopy revealed the emergence of an absorbance peak at 430 nm due to the synthesis of AgNPs.R. fasciansstarted producing AgNPs after 12 h of incubation, with the highest yield after 48 h. The extent of synthesis was higher when cultures were grown in the dark than in the light. According to TEM and SEM, the AgNPs had a uniform spherical morphology of diameter 10–80 nm. The AgNPs exhibited antifungal efficacy against the virulent filamentous fungiRhizoctonia solani, Botrytis cinerea, andFusarium graminearum, which cause root rot, soft rot and head blight on plants, respectively. This research provides evidence on the ability ofR. fasciansto generate AgNPs from silver nitrate, as well as their subsequent assembly and potential for controlling vascular wilt disease.
Assembling bacterial puzzles: piecing together functions into microbial pathways
Authors: Chung Henri , Friedberg Iddo , Bromberg Yana 
Published: March 2024

AbstractFunctional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in KEGG. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.
Effects of iron on cardiovascular, kidney and safety outcomes in patients with chronic kidney disease: a systematic review and meta-analysis
Authors: Chan Bernard , Varghese Amanda , Badve Sunil V , Pecoits-Filho Roberto , Guedes Murilo , Arnott Clare , Kozor Rebecca , O’Lone Emma , Jun Min , Kotwal Sradha , Block Geoffrey A , Chertow Glenn M. , Solomon Scott D , Vaduganathan Muthiah , Neuen Brendon L. 
Published: March 2024

ABSTRACTBackground and aimsHeart failure and chronic kidney disease (CKD) are closely linked, with iron deficiency being highly prevalent in both conditions. Yet, major cardiovascular and nephrology guidelines offer contrasting recommendations on the use of iron. We evaluated the effects of iron versus usual care/placebo on clinical outcomes in patients with CKD.MethodsWe conducted a systematic review and meta-analysis of randomised trials of intravenous or oral iron in CKD (PROSPERO CRD42023453468). We searched Medline, Embase and the Cochrane Register from database inception until February 1, 2024 to identify eligible trials. We determined results overall and stratified by dialysis- and non-dialysis-requiring CKD using random effects models, with certainty of evidence assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. The primary composite endpoint was heart failure hospitalisation or cardiovascular death.ResultsWe identified 45 trials that met our inclusion criteria. Compared to usual care/placebo, iron reduced the risk of the primary composite endpoint (1659 events; RR 0.84, 95% CI 0.75-0.94; moderate certainty) an effect consistent across dialysis and non-dialysis requiring CKD (P-heterogeneity=0.70). The effect on the primary endpoint appeared driven by both components of hospitalisation for heart failure (RR 0.77; 95% CI 0.61-0.96; moderate certainty) and cardiovascular death (RR 0.81; 95% CI 0.65-1.02; low certainty). The incidence of serious adverse events was lower for iron compared to usual care/placebo (RR 0.90, 95% CI 0.82-0.98; moderate certainty; P-heterogeneity=0.09).ConclusionIron therapies may reduce the risk of heart failure or cardiovascular death in patients with CKD. Randomised rials evaluating effects of iron on clinical outcomes are needed, especially in non-dialysis CKD, with or without anaemia.
Associations of employment status, working time and job satisfaction with sleep duration and sleep quality among the Japanese 50+ population
Authors: Wels Jacques , Fu Rong 
Published: March 2024

AbstractBackgroundFew studies have captured the relationship between employment status, working time and job satisfaction and sleep duration and quality in Japan where poor sleep quality and low sleep duration are major public health concerns.MethodsWe use four waves from the Japan Study of Aging and Retirement (JSTAR) to assess the relationship between employment status and self-reported job satisfaction and sleep duration and self-reported sleep quality. We control for socio-demographic characteristics, working time and self-reported measures of health. The initial sample includes 7,082 respondents. We use mixed effects modified Poisson regression for binary outcomes for sleep quality and linear mixed effects for sleep duration and multiple imputations to correct for sample attrition.ResultsNo major difference is observed between employment status and poor sleep quality except for housekeepers (0.123 [ 95%CI: 0.041; 0.205]) in comparison with full-time employed workers. All categories of workers tend to report sleeping longer than full-time employees with higher hours among those who retired (0.339 [95%CI: 0.218; 0.460]). Poor job satisfaction is associated with higher risks of self-reported poor sleep quality (0.230 [95%CI: 0.040, 0.421]) and waking up at night (0.362 [95%CI: 0.025, 0.699]) but the associations fade away when controlling for other health measurements (respectively, −0.137 [95%CI: −0.328, 0.054] and 0.092 [95%CI: −0.248; 0.432]).ConclusionRetirement increases sleep duration without improving sleep quality and housekeepers sleep longer but with poorer sleep quality. Job satisfaction is a major cofounder of sleep quality among the workforce but the effect is mediated by physical and mental health levels.
Mitochondrial genome variation affects humoral and cell-mediated innate immune responses and infection outcomes
Authors: Salminen Tiina S. , Vesala Laura , Basikhina Yuliya , Kutzer Megan , Tuomela Tea , Lucas Ryan , Monteith Katy , Prakash Arun , Tietz Tilman , Vale Pedro F. 
Published: March 2024

AbstractThe role of mitochondria in both adaptive and innate immune responses is increasingly recognized, but the role of mitochondrial DNA (mtDNA) variation as an immunomodulatory factor has received less attention. One reason for this is the difficulty of separating the effect of mtDNA from that of the nuclear genome. By utilizing the fruit flyDrosophila melanogaster, a powerful model system, we created cytoplasmic hybrids, aka. cybrid lines, where unique mtDNAs (mitotypes) were introgressed into a controlled isogenic nuclear background. We harnessed a panel of cybrid lines to study the effect of mtDNA variation on humoral and cell-mediated innate immune responses. Mitotypes exhibited heterogeneity in infection outcomes upon bacterial, viral and parasitoid infections. One mitotype of note (mtKSA2) was more immunocompetent when compared to other mitotypes. We performed transcriptomic profiling of uninfected and infected flies to find the mechanistic basis of the immunocompetence of the mtKSA2 line. We found that in uninfected flies mtKSA2 caused an upregulation of oxidative phosphorylation (OXPHOS) and tricarboxylic acid cycle (TCA) related genes and a downregulation of a set of antimicrobial peptides (AMPs). Upon infection, mtKSA2 flies produced transcriptomic changes that were infection type and duration specific. When we examined immune cells (hemocytes) in mtKSA2 larvae, we noted an increase in hemocyte numbers. These hemocytes were activated in the absence of infection, increased their production of ROS, and showed evidence of increased encapsulation efficiency upon parasitoid wasp infection. Overall, our results show that mtDNA variation acts as an immunomodulatory factor in both humoral and cell-mediated innate immunity and that specific mitotypes can provide enhanced protection against various infections.
Effect of micro-particles on cavitation erosion behavior of 2Cr3WMoV steel
Authors: Zhao Han , Ding Qingmiao , Li Yaozhi , Cui Yanyu , Luo Junjie 
Published: March 2024

Purpose
This paper aims to study the influence of microparticles on the surface cavitation behavior of 2Cr3WMoV steel; microparticle suspensions of different concentration, particle size, material and shape were prepared based on ultrasonic vibration cavitation experimental device.

Design/methodology/approach
2Cr3WMoV steel was taken as the research object for ultrasonic cavitation experiment. The morphology, quantity and distribution of cavitation pits were observed and analyzed by metallographic microscope and scanning electron microscope.

Findings
The study findings showed that the surface cavitation process produced pinhole cavitation pits on the surface of 2Cr3WMoV steel. High temperature in the process led to oxidation and carbon precipitation on the material surface, resulting in the “rainbow ring” cavitation morphology. Both the concentration and size of microparticles affected the number of pits on the material surface. When the concentration of microparticles was 1 g/L, the number of pits reached the maximum, and when the size of microparticles was 20 µm, the number of pits reached the minimum. The microparticles of Fe3O4, Al2O3, SiC and SiO2 all increased the number of pits on the surface of 2Cr3WMoV steel. In addition, the distribution of pits of spherical microparticles was more concentrated than that of irregularly shaped microparticles in turbidity.

Originality/value
Most of the current studies have not systematically focused on the effect of each factor of microparticles on the cavitation behavior when they act separately, and the results of the studies are more scattered and varied. At the same time, it has not been found to carry out the study of microparticle cavitation with 2Cr3WMoV steel as the research material, and there is a lack of relevant cavitation morphology and experimental data.
Assessing the asymmetric cost behavior in China
Authors: Shan Yuxin , Richardson Vernon J. , Cheng Peng 
Published: March 2024

PurposeA country’s institutional environment influences every facet of its business. This paper aims to identify institutional factors (state ownership, government attention on employment and employees’ educational background) that affect the asymmetric cost behavior in China.Design/methodology/approachUsing 2,570 listed firms’ data between 2002 and 2015, we use empirical models to explore the effects of state ownership, government attention on employment and employees’ educational background on the asymmetric cost behavior in China.FindingsThis study found that the asymmetric cost behavior of central state-owned enterprises (CSOEs) is greater than local state-owned enterprises (LSOEs). Meanwhile, the empirical results show that government attention on employment is reflected in five-year government plans, and employees’ educational backgrounds are positively associated with asymmetric cost behavior.Originality/valueThis study contributes to the economic theory of sticky costs, institutional theory and asymmetric cost behavior literature by providing evidence that shows how government intervention and employee educational background limit the flexibility of corporate cost adjustments. Additionally, this study provides guidance to policymakers by showing how government long-term plans affect firm-level resource adjustment decisions.
Investigating the effect of augmented reality packaging on behavioral intentions in traditional Iranian nougat GAZ packaging
Authors: Tabaeeian Reihaneh Alsadat , Hossieni Farzaneh Alsadat , Fatehi Maedeh , Forghani Tehrani Alireza 
Published: March 2024

PurposeThe purpose of the study is to investigate the effect of augmented reality (AR) characteristics in packaging on perceived value and consumer behavioral intentions such as purchase intention and pay more in traditional Iranian nougat GAZ packaging.Design/methodology/approachThe statistical population was the 550 customers bought traditional Iranian nougat GAZ. Sampling method was simple random sampling. Questionnaire had been chosen for collecting data. In total, 236 customers filled in questionnaires. Research model tested by structural equation modeling method and by using SPSS and PLS software.FindingsThe finding considered the characteristics of AR packaging which include interactivity, informativeness, enjoyment and usefulness have a positive effect on the dimensions of the perceived value, hedonic and utilitarian value. In the same way hedonic and utilitarian value had positive effects on the consumer behavior, purchase intention and willingness to pay more.Originality/valueThese results help managers to use AR characteristics to improve the interaction between customers and product and sell their products.
Mixed ownership reform and non-state-owned enterprise innovation: Evidence from China
Authors: Ling Runze , Pan Ailing , Xu Lei 
Published: March 2024

PurposeThis study examines the impact of China’s mixed-ownership reform on the innovation of non-state-owned acquirers, with a particular focus on the impact on firms with high financing constraints, low-quality accounting information or less tangible assets.Design/methodology/approachWe use a proprietary dataset of firms listed on the Shanghai and Shenzhen Stock Exchanges to investigate the impact of mixed ownership reform on non-state-owned enterprise (non-SOE) innovation. We employ regression analysis to examine the association between mixed ownership reform and firm innovation.FindingsThe study finds that non-state-owned firms can improve innovation by acquiring equity in state-owned enterprises (SOEs) under the reform. Eased financing constraints, lowered financing costs, better access to tax incentives or government subsidies, lowered agency costs, better accounting information quality and more credit loans are underlying the impact. Additionally, cross-ownership connections amongst non-SOE executives and government intervention strengthen the impact, whilst regional marketisation weakens it.Originality/valueThis study adds to the literature on the association between mixed ownership reform and firm innovation by focussing on the conditions under which this impact is stronger. It also sheds light on the policy implications for SOE reforms in emerging economies.