bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea
Authors: Lu Zhongyi , Zhang Siyu , Liu Yang , Xia Runyue , Li Meng 
Published: July 2023

AbstractFunctional interplay between the endosomal sorting complexes required for transport (ESCRT) and ubiquitin system underlies the ubiquitin-dependent sorting pathway, a specific trait of eukaryotic endomembrane system. Yet, its evolutionary origin remains unclear. Here, we show that a novel UEV-Vps23 family protein, that contains UEV and Vps23 domains, mediates an ancient ESCRT and ubiquitin system interplay in Asgard archaea. The UEV binds ubiquitin with high-affinity, making the UEV-Vps23 a sensor for sorting ubiquitinated cargo. A steadiness box in the Vps23 domain undergoes ubiquitination through a eukaryotic-like Asgard E1, E2, and RING E3 cascade. The UEV-Vps23 can switch between autoinhibited and active forms, by which likely regulates the ESCRT and ubiquitin system interplay. Furthermore, the shared sequence and structural homology among the UEV-Vps23, eukaryotic Vps23 and archaeal CdvA, implying that these proteins share a common evolutionary origin. Together, this work presents evidence that the ESCRT and ubiquitin system interplay had arisen early in Asgard evolution, antedating emergence of endomembrane system in eukaryogenesis.TeaserThe ESCRT and ubiquitin system interplay, a specific trait of eukaryotic endomembrane system, likely inherited from an Asgard archaeal ancestor.
Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex
Authors: Dubiez Etienne , Pellegrini Erika , Brask Maja Finderup , Garland William , Foucher Anne-Emmanuelle , Huard Karine , Jensen Torben Heick , Cusack Stephen , Kadlec Jan 
Published: July 2023

SummaryThe nuclear cap-binding complex (CBC) co-ordinates co-transcriptional maturation, transport, or degradation of nascent Pol II transcripts. CBC with its partner ARS2 form mutually exclusive complexes with diverse ‘effectors’ that promote either productive or destructive outcomes. Combining Alphafold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18 and other effectors compete for binding to ARS2. In ternary CBCA complexes with either PHAX, NCBP3 or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show thatin vivoZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for proper CTCF function
Authors: Iurlaro Mario , Masoni Francesca , Wirbelauer Christiane , Iskar Murat , Burger Lukas , Schübeler Dirk 
Published: July 2023

Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and DNA binding of transcription factors, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions, we derived a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to drastic reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. While this affects adjacent nucleosome occupancy, it only modestly impacts CTCF binding itself. In the absence of accessibility, the structural function of CTCF is nevertheless impaired resulting in lower occupancy of cohesin and cohesin release factor, and reduced physical insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function.These results separate local CTCF binding from insulator function in nuclear organization and reveal a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites. They designate local accessibility as critical for cohesin positioning and establishment of physical insulation.
A geminivirus AC5 protein interacts with plant hormonal signalling and impacts plant defence
Authors: Kumar Rohit , Dasgupta Indranil 
Published: July 2023

AbstractGeminiviruses are a large group of plant viruses responsible for yield loss in various crops, mainly in the tropical and sub-tropical regions. Geminiviruses encode six to nine multifunctional proteins, which interact with plant components to cause pathogenesis. One of the least studied geminiviral proteins is AC5. This study presents the first evidence of an AC5 protein interacting with a component of the abscisic acid signalling pathway, resulting in a depressed state. We show that the AC5 protein, encoded by Sri Lankan cassava mosaic virus is important for symptom development and virus accumulation in the experimental hostNicotiana benthamiana. The above interaction perturbs the abscisic acid signalling pathways, leading to compromised expression of defense-related genes and insensitivity to abscisic acid in transgenic Arabidopsis plants. This suggests a novel role of AC5 to facilitate virus propagation. Furthermore, we show that transiently suppressing the expression inN. benthamiana PP2Cwith which AC5 interacts, results in a reduction in viral titers possibly due to augmented ABA signaling and its defense-related roles. This research provides valuable insights into how geminiviral proteins manipulate ABA-mediated defence pathways, paving the way for further investigation into the underlying mechanisms and potential applications in plant protection against viral infections.
Novel centriolar defects underlie a primary ciliary dyskinesia phenotype in an adenylate kinase 7 deficient ciliated epithelium
Authors: Sheridan Jennifer , Grata Aline , Suva Eve E. , Bresteau Enzo , Mitchell Linus R. , Hassan Osama , Mitchell Brian 
Published: July 2023

AbstractThe skin ofXenopusembryos contains numerous multiciliated cells (MCCs), which collectively generate a directed fluid flow across the epithelial surface essential for distributing the overlaying mucous. MCCs develop into highly specialized cells to generate this flow, containing approximately 150 evenly spaced centrioles that give rise to motile cilia. MCC-driven fluid flow can be impaired when ciliary dysfunction occurs, resulting in primary ciliary dyskinesia (PCD) in humans. Mutations in a large number of genes (∼50) have been found to be causative to PCD. Recently, studies have linked low levels of Adenylate Kinase 7 (AK7) gene expression to patients with PCD; however, the mechanism for this link remains unclear. Additionally, AK7 mutations have been linked to multiple PCD patients. Adenylate kinases modulate ATP production and consumption, with AK7 explicitly associated with motile cilia. Here we reproduce an AK7 PCD-like phenotype inXenopusand describe the cellular consequences that occur with manipulation of AK7 levels. We show that AK7 localizes throughout the cilia in a DPY30 domain-dependent manner, suggesting a ciliary function. Additionally, we find that AK7 overexpression increases centriole number, suggesting a role in regulating centriole biogenesis. We find that in AK7-depleted embryos, cilia number, length, and beat frequency are all reduced, which in turn, significantly decreases the tissue-wide mucociliary flow. Additionally, we find a decrease in centriole number and an increase in sub-apical centrioles, implying that AK7 influences both centriole biogenesis and docking, which we propose underlie its defect in ciliogenesis. We propose that AK7 plays a role in PCD by impacting centriole biogenesis and apical docking, ultimately leading to ciliogenesis defects that impair mucociliary clearance.
UropathogenicEscherichia coliwield enterobactin-derived catabolites as siderophores
Authors: Zou Zongsen , Robinson John I. , Steinberg Lindsey K. , Henderson Jeffrey P. 
Published: July 2023

ABSTRACTUropathogenicE. coli(UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here we find the siderophore enterobactin and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined enterobactin biosynthesis and import mutants, we identify lower molecular weight, dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. InE. coli,iron acquisition from iron(III)-enterobactin complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed enterobactin, we find that enterobactin and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
Stress-induced vascular remodeling: novel insight into the role of omega-3 fatty acid metabolite, 4-oxoDHA
Authors: Nishimori Makoto , Hayasaka Naomi , Otsui Kazunori , Inoue Nobutaka , Nagao Manabu , Toh Ryuji , Ishida Tatsuro , Hirata Ken-ichi , Furuyashiki Tomoyuki , Shinohara Masakazu 
Published: July 2023

AbstractBackgroundStress has garnered significant attention as a prominent risk factor for inflammation-related diseases, particularly cardiovascular diseases (CVDs). However, the precise mechanisms underlying stress-driven CVDs remain elusive, thereby impeding the development of effective preventive and therapeutic strategies.MethodsTo explore the correlation between plasma lipid metabolites and depressive states, we conducted a study involving healthy volunteers (n=408). Liquid chromatography (LC)/mass spectrometry (MS)/MS-based lipidomics and the self-rating depression (SDS) scale questionnaire were employed for data collection. In addition, we utilized a mouse model by subjecting mice to restraint stress and investigating the impact of stress on plasma lipid metabolites and vascular remodeling following carotid ligation. In vitro functional and mechanistic studies were performed using macrophages, endothelial cells, and neutrophil cells.ResultsOur findings revealed a significant association between depressive state and reduced plasma levels of 4-oxoDHA, a specific omega-3 fatty acid metabolite regulated by 5-lipoxygenase (LO) in neutrophils in healthy volunteers. In mice, restraint stress led to decreased plasma 4-oxoDHA levels and exacerbated vascular remodeling. Moreover, 4-oxoDHA demonstrated the ability to enhance Nrf2-HO-1 pathways, exerting anti-inflammatory effects on endothelial cells and macrophages. Mechanistically, stress-induced noradrenaline triggered the degradation of 5-LO in neutrophils through the proteasome system, facilitated by dopamine D2-like receptor activation. The reduction in circulating 4-oxoDHA resulted in the downregulation of the Nrf2-HO-1 anti-inflammatory axis and an increase in ICAM-1 expression, vascular permeability, and remodeling.ConclusionsOur study unveiled a novel stress-induced pathway of vascular inflammation, mediated through the regulation of omega-3 fatty acid metabolites. Reduced levels of circulating 4-oxoDHA under stress conditions may serve as a promising biomarker for stress. This understanding of the interplay between neurobiology and lipid metabolism provides a potential avenue for the development of treatments aimed at preventing stress-induced systemic neuroinflammation.Highlights– Our study reveals that stress-induced reduction in circulating levels of a specific omega-3 fatty acid metabolite, 4-oxoDHA, contributes to vascular inflammation.– We have identified a novel pathway that explains how stress promotes systemic vascular inflammation by regulating omega-3 fatty acid metabolites in the circulation.– Our findings provide new evidence for the role of 4-oxoDHA in maintaining Nrf2-ARE-related anti-inflammatory functions in endothelial cells and macrophages.
Russulasubgen.Cremeoochraceaesubgen. nov.: a very small and ancient lineage sharing withMultifurca(Russulaceae) an identical, largely circum-Pacific distribution pattern
Authors: Buyck B , Horak E. , Cooper J.A. , Wang X.H 
Published: July 2023

AbstractThe application of DNA data on a worldwide sampling has revolutionized the infrageneric classification of the highly diverse ectomycorrhizal genusRussula. Based on collections made in New Zealand, East Asia and North America, this study describes the new subgenusCremeoochraceae, the ninth subgenus inRussula. Even though BLASTn of the ITS sequences suggested affinities with species of subgeneraRussulaandHeterophyllidiae, the phylogenetic analysis based on a five-locus DNA dataset placed the target samples in an independent major clade that is systematically equivalent to subgenus. The new subgenus shares with subgen.Brevipedumsubsect.Pallidosporinaethe general field habit, the unequal lamellae and the relatively small spores with inamyloid suprahilar spot and similar spore ornamentation. It differs from the latter subsection principally in the poor contents of all types of cystidioid cells and the often areolate-scurfy pileus surface composed of slender, undulating hyphal terminations with frequent subcapitate apices. Biogeographically, subgen.Cremeoochraceaeshares withMultifurca, the sister genus ofLactarius, a circum-Pacific distribution pattern with the exception of South America. Both lineages lack representatives in Europe and Africa. The hypothesis proposing an African origin for the genus is considered unlikely.
Histone variant H2A.Z is required for plant salt response by regulating gene transcription
Authors: Miao Rongqing , Zhang Yue , Liu Xinxin , Yuan Yue , Zang Wei , Li Zhiqi , Yan Xiufeng , Pang Qiuying , Zhang Aiqin 
Published: July 2023

AbstractAs a well-conserved histone variant, H2A.Z epigenetically regulates plant growth and development as well as the interaction with environmental factors. However, the role of H2A.Z in response to salt stress remains unclear, and whether nucleosomal H2A.Z occupancy work on the gene responsiveness upon salinity is obscure. Here, we elucidate the involvement of H2A.Z in salt response by analyzing H2A.Z disorder plants with impaired or overloaded H2A.Z deposition. The salt tolerance is dramatically accompanied by H2A.Z deficiency and reacquired in H2A.Z OE lines. H2A.Z disorder changes the expression profiles of large-scale of salt responsive genes, announcing that H2A.Z is required for plant salt response. Genome-wide H2A.Z mapping shows that H2A.Z level is induced by salt condition across promoter, TSS and TES (−1 kb to +1kb), the peaks preferentially enrich at promoter regions near TSS. We further show that H2A.Z deposition within TSS provides a direct role on transcriptional control, which has both repressive and activating effects, while it is found generally H2A.Z enrichment negatively correlate with gene expression level response to salt stress. This study shed light on the H2A.Z function in salt tolerance, highlighting the complex regulatory mechanisms of H2A.Z on transcriptional activity for yielding appropriate responses to particularly environmental stress.
The effect of perceived social support on postpartum depression in immigrant and Turkish women
Authors: Karadeniz Benli Cansu , Kulakaç Özen 
Published: July 2023

Purpose
The purpose of this study was to examine the effect of perceived social support on postpartum depression (PPD) in Arab immigrant mothers and Turkish mothers.

Design/methodology/approach
This descriptive study was conducted with 140 mothers between September 2017 and January 2018. The data was collected via the Turkish and Arabic versions of the sociodemographic questionnaire, the Edinburgh Postnatal Depression Scale (EPDS) and the Multidimensional Scale of Perceived Social Support. Percentage and arithmetic mean calculations, independent samples t-test, Mann–Whitney U test, paired logistic regression analysis backward elimination method and Pearson and Spearman correlation analyses were conducted to analyze the data.

Findings
The data revealed that the risk of PPD was twice as high in Arab immigrant mothers (56.3%) compared to Turkish mothers (29%). The EPDS mean score was 12.37 ± 6.28 for Arab immigrant mothers and 8.81 ± 5.48 for Turkish mothers. The social support mean score was found to be 50.70 ± 19.27 for Arab immigrant mothers and 61.41 ± 16.51 for Turkish mothers. The independent risk factors for Turkish mothers included mother’s age, monthly income level and infant’s age, while the independent risk factors for Arab immigrant mothers included number of children, husband’s status of employment and access to regular medical care during pregnancy. The negative correlation between EPDS and social support overall scores and subscale scores was found to be significant for both groups.

Originality/value
To the best of the authors’ knowledge, this is the first study on the impact of social support on PPD in Arab immigrant and Turkish women in the national and international literature. The study helped reveal the correlation between perceived social support and PPD, the PPD risk rates and risk factors according to citizenship status for the first time.
Can crowdfunding creators learn from previous experiences to have a better future financing performance?
Authors: Fang Xing 
Published: July 2023

PurposeThis paper aims to explore whether crowdfunding creators can learn from previous experiences to have a better financing performance of future crowdfunding projects.Design/methodology/approachThis paper uses Python to capture the data of 6,267 crowdfunding projects from one of the largest crowdfunding platforms in China (JingDong Crowdfunding) and the author use the negative binomial regression model and the OLS model in this empirical study.FindingsThe empirical results show that both the early-stage experience of creating a crowdfunding project and the early-stage experience of supporting projects of other crowdfunding creators can improve the financing performance of their newly launched projects. The social network of the previous projects and the “Blockbuster” projects initiated before can also make the newly initiated projects obtain better financing performance.Originality/valueCurrent research on entrepreneurial experience shows that serial entrepreneurs have significantly different success rates than novice or inexperienced entrepreneurs but there is limited literature on the learning effect of crowdfunding creators. This study adds to the literature on entrepreneurial learning and provides suggestions to crowdfunding creators.
Case series analysis validation of the ERICSO: a new assessment tool for internet child abuse material offenders
Authors: Garrington Catherine , Kelty Sally Fiona , Rickwood Debra , Boer Douglas 
Published: July 2023

Purpose
There are limited risk assessment tools validated for use with the internet child abuse material (I/CAM) offender cohort. Developed through a multi-stage process, the purpose of this paper is to present the “Estimated Risk for Internet Child Sexual Offending” (ERICSO), a new tool for I/CAM offender assessment, including demographic, collection, nature of engagement and social domains, plus a structured professional judgement section. Validation studies remain ongoing.

Design/methodology/approach
This paper presents a case series analysis of six Australian men, including two Aboriginal men, convicted of I/CAM offences to pilot proposed ERICSO domains and commence validation against the short self-esteem scale, University of California Los Angles loneliness scale, internet sex screening test and the sexual violence risk-20 V2.

Findings
Participants of all ages generally reported histories of mental health diagnosis and/or treatment and substance abuse. Two participants reported prior sexual offending, one for I/CAM offences. Participants expressed sexual preferences for female child victims and were convicted of possessing thousands of I/CAM files. Two participants reported accessing I/CAM for over six and 10 years, respectively, before detection by law enforcement.

Practical implications
Preliminary implications indicate ERICSO higher scores are consistent with I/CAM offenders having more online sexual behaviour diversity and more areas of risk/treatment need. For example, participants with problematic self-esteem and loneliness in our data set have higher ERICSO scores. Social connectedness may be a relevant factor though definitive conclusions cannot be drawn from the small sample size.

Originality/value
The ERICSO presents novel assessment of factors in considering treatment targets in addressing both illegal I/CAM and problematic legal sexual behaviours.
Progressive deterioration of reinforced concrete structures: effect on dynamic properties of flexural members
Authors: Khan Qaiser Uz Zaman , Farhan Muhammad , Raza Ali 
Published: July 2023

PurposeThe main purpose of this study is to examine the damage behavior of flexural members under different loading conditions. The finite element model is proposed for the prediction of modal parameters, damage assessment and damage detection of flexural members. Moreover, the analysis of flexural members has been done for the sensor arrangement to accurately predict the damage parameters without the laborious work of experimentation in the laboratory.Design/methodology/approachBeam-like structures are structures that are subjected to flexural loadings that are involved in almost every type of civil engineering construction like buildings, bridges, etc. Experimental Modal Analysis (EMA) is a popular technique to detect damages in structures without requiring tough and complex methods. Experimental work conducted in this study concludes that a structure experiences high changes in modal properties once when cracking occurs and then at the stage where cracks start at the critical neutral axis. Moreover, among the various modal parameters of the flexural members, natural frequency and mode shapes are the viable parameters for the damage detection.FindingsFor torsional mode, drop in natural frequency is high for higher damages as compared to low levels. This is because of the opening and closing of cracks in modal testing. When damage occurs in the structure, there is a reduction in the magnitude of the FRF plot. The measure of this drop can also lead to damage assessment in addition to damage detection. The natural frequency of the system is the most reliable modal parameter in detecting damages. However, for damage localization, the next step after damage assessment, mode shapes can be more helpful as compared to all other parameters.Originality/valueEffect on Dynamic Properties of Flexural Members during the Progressive Deterioration of Reinforced Concrete Structures is studied.