bluuebunny/crossref_metadata_2025_split huggingface dataset:
Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection
Authors: Kerkhofs Kyra , Guydosh Nicholas R. , Bayfield Mark A. 
Published: August 2024

AbstractViral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5’-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5’-cap structures of host mRNAs and thus inhibition of cap-dependent translation initiation would likely also reduce viral translation. We confirmed that RSV limits widespread translation initiation inhibition and unexpectedly found that the fraction of ribosomes within polysomes increases during infection, indicating higher ribosome loading on mRNAs during infection. We found that AU-rich host transcripts that are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar to RSV transcripts. Viral transcripts are transcribed in cytoplasmic inclusion bodies, where the viral AU-rich binding protein M2-1 has been shown to bind viral transcripts and shuttle them into the cytoplasm. We further demonstrated that M2-1 is found on polysomes, and that M2-1 might deliver host AU-rich transcripts for translation.ImportanceViruses strongly rely on the host’s translational machinery to produce viral proteins required for replication. However, it is unknown how viruses that do not globally inhibit cap-dependent translation compete with abundant host transcripts for ribosomes. In this study, we found that respiratory syncytial virus (RSV) infection results in redistribution of 80S monosomes into the polysomes. High-throughput sequencing of translating transcripts revealed that low translation efficiency transcripts become more efficient at ribosome recruitment which are virus-resembling AU-rich host transcripts. Finally, we also uncover that AU-rich RNA binding protein RSV-M2-1 interacts with polysomes through contacts to mRNA. These findings revealed that RSV optimizes the translational landscape rather than inhibiting host translation.
Engineered prime editors with minimal genomic errors
Authors: Chauhan Vikash P. , Sharp Phillip A. , Langer Robert 
Published: August 2024

AbstractPrime editors make programmed genome modifications by writing new sequences into extensions of nicked DNA 3’ ends. These edited 3’ new strands must displace competing 5’ strands to install edits, yet a bias toward retaining the competing 5’ strands hinders efficiency and can cause indel errors. Using rational design of the constituent Cas9-nickase to reposition prime editor nicks, we discovered that competing 5’ strands are destabilized to favor the edited 3’ new strands. We exploit this mechanism to engineer efficient prime editors with strikingly low indel errors. Combining this error-suppressing strategy with the latest efficiency-boosting architecture, we design a next- generation prime editor (vPE). Compared with previous editors, vPE features comparable efficiency yet up to 60-fold lower indel errors, enabling edit:indel ratios as high as 465:1.One Sentence SummaryPrime editors designed with repositioned DNA breaks nearly eliminate undesired genome editing errors
Nascent flagellar basal bodies are immobilized by rod assembly inBacillus subtilis
Authors: Dunn Caroline M. , Foust Daniel , Gao Yongqiang , Biteen Julie S. , Shaw Sidney L. , Kearns Daniel B. 
Published: August 2024

ABSTRACTFlagella are complex, trans-envelope nanomachines that localize to species- specific cellular addresses. Here we study the localization dynamics of the earliest stage of basal body formation inBacillus subtilisusing a fluorescent fusion to the C-ring protein FliM. We find thatB. subtilisbasal bodies do not exhibit dynamic subunit exchange and are largely stationary at steady state, consistent with flagellar assembly through the peptidoglycan. Rare basal bodies were observed to be mobile however, and the frequency of basal body mobility is elevated both early in basal body assembly and when the rod is mutated. Thus, basal body mobility is a precursor to patterning and we propose that rod polymerization probes the peptidoglycan superstructure for pores of sufficient diameter that permit rod completion. Furthermore, mutation of the rod also disrupts basal body patterning in a way that phenocopies mutation of the cytoplasmic flagellar patterning protein FlhF. We infer that conformational changes in the basal body exchange information between rod synthesis and the cytoplasmic patterning proteins to restrict assembly at certain pores established by a grid-like pattern pre-existent in the peptidoglycan itself.IMPORTANCEBacteria insert flagella in a species-specific pattern on the cell body, but how patterns are achieved is poorly understood. In bacteria with a single polar flagellum, a marker protein localizes to the cell pole and nucleates the assembly of the flagellum at that site.Bacillus subtilisassembles ∼15 flagella over the length of the cell body in a grid-like pattern and lacks all proteins associated with targeted assembly in polarly flagellated bacteria. Here we show thatB. subtilisbasal bodies are mobile soon after assembly and become immobilized when the flagellar rod transits the peptidoglycan wall. Moreover, defects in the flagellar rod lead to an asymmetric distribution of flagella with respect to the midcell. We conclude that the patterning of flagella is different inB. subtilis, and we infer that theB. subtilisrod probes the peptidoglycan for holes that can accommodate the machine.
A general principle of neuronal evolution reveals a human-accelerated neuron type potentially underlying the high prevalence of autism in humans
Authors: Starr Alexander L. , Fraser Hunter B. 
Published: August 2024

AbstractThe remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons—layer 2/3 intratelencephalic excitatory neurons—has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In sum, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.
An engineered prodrug selectively suppresses β-lactam resistant bacteria in a mixed microbial setting
Authors: Duda Addison M. , Ma Helena R. , Villalobos César A. , Kuhn Sophia A. , He Katherine , Seay Sarah R. , Jackson Abigail C. , Suh Christine M. , Puccio Elena A. , Anderson Deverick J. , Fowler Vance G. , You Lingchong , Franz Katherine J. 
Published: August 2024

AbstractThe rise of β-lactam resistance necessitates new strategies to combat bacterial infections. We purposefully engineered the β-lactam prodrug AcephPT to exploit β-lactamase activity to selectively suppress resistant bacteria producing extended-spectrum-β-lactamases (ESBLs). Selective targeting of resistant bacteria requires avoiding interaction with penicillin-binding proteins, the conventional targets of β-lactam antibiotics, while maintaining recognition by ESBLs to activate AcephPT only in resistant cells. Computational approaches provide a rationale for structural modifications to the prodrug to achieve this biased activity. We show AcephPT selectively suppresses gram-negative ESBL-producing bacteria in clonal populations and in mixed microbial cultures, with effective selectivity for both lab strains and clinical isolates expressing ESBLs. Time-course NMR experiments confirm hydrolytic activation of AcephPT exclusively by ESBL-producing bacteria. In mixed microbial cultures, AcephPT suppresses proliferation of ESBL-producing strains while sustaining growth of β-lactamase-non-producing bacteria, highlighting its potential to combat β-lactam resistance while promoting antimicrobial stewardship.Abstract Figure
Isolation and characterization of mollicute symbionts from a fungus-growing ant reveals genome reduction and host specialization
Authors: Green Emily A. , Klepacki Ian , Klassen Jonathan L. 
Published: August 2024

ABSTRACTTwo mollicute species belonging to theMesoplasmaandSpiroplasmagenera have been detected in several species of fungus-growing ants using molecular methods. However, their ecological roles remain largely only inferred from metagenomic data. To better understand their diversity and specialization, we cultured both of theseMesoplasmaandSpiroplasmasymbionts from the fungus-growing antTrachymyrmex septentrionalis, providing the first isolated mollicutes from any fungus-growing ant species. The genomes of our isolates and related metagenome-assembled genomes (MAGs) fromT. septentrionalisfungus gardens comprise two unique phylogenetic lineages compared to previously describedMesoplasmaandSpiroplasmaspecies, and from related MAGs previously sequenced from the leaf-cutting antAcromyrmex echinatior. This suggests that theT. septentrionalissymbionts comprise undescribed species with distinct host specificities.Mesoplasmagenomes and MAGs also demonstrate regional specificity with theirT. septentrionalisant hosts. BothMesoplasmaandSpiroplasmastrains fromT. septentrionaliscan catabolize glucose and fructose; both sugars are common in the ant’s diet. Similarly, both theseMesoplasmaandSpiroplasmacan catabolize arginine but onlyMesoplasmacan catabolizeN-acetylglucosamine, which could both produce ammonia for the ants or fungus garden. Based on our genomic and phenotypic analyses, we describe theseT. septentrionalissymbionts asMesoplasma whartonense sp. nov.andSpiroplasma attinicola sp. nov., providing insight into their genomic and phenotypic diversity, and cultures to facilitate future studies of these common but poorly understood members of the fungus-growing ant symbiosis.
CaMKII induces an autophagy-dependent anabolic response in Articular Chondrocytes
Authors: Day Nicholas James , Dutta Angshumi , Heluany Cintia Scucuglia , Asopa Vipin , Sochart David , Fielding Barbara , Nalesso Giovanna 
Published: August 2024

AbstractObjectiveThe objective of this study was to elucidate the role of Calcium calmodulin-dependent Kinase II (CaMKII) in articular chondrocytes and its involvement in osteoarthritis (OA) pathogenesis. By performing gain and loss of function experiments, the research aimed to determine how CaMKII modulates chondrocyte metabolism, anabolic and catabolic processes, hypertrophic differentiation, and autophagy within the articular cartilage.DesignArticular cartilage was harvested from patients undergoing joint replacement surgery for OA, and adult human articular chondrocytes (AHACs) were isolated and cultured. Recombinant adenoviruses were used to overexpress a constitutively active form of CaMKIIγ (AdCaMKII) or inhibit CaMKII activity (AdAIP). Various assays, including RT-PCR analysis, alcian blue staining of Micromass cultures, immunofluorescence, and Western blotting, were performed to assess the effects of CaMKII modulation on chondrocyte function.ResultsOverexpression of activated CaMKIIγ promoted anabolism, evidenced by increased expression of SOX9, COL2A1, and ACAN, and decreased MMP-13 levels. It also enhanced proteoglycan content in AHAC micromass cultures. Furthermore, CaMKII counteracted the catabolic effects of IL-1β and preserved proteoglycan content. We also observed decreased chondrocyte proliferation and increased synthesis of hypertrophic marker Type X Collagen. CaMKII activation was found to induce autophagy, as indicated by increased phosphorylation of Beclin1 and decreased p62 expression. The anabolic effects of CaMKII were dependent on autophagy, as inhibition of autophagy with Bafilomycin prevented the CaMKII-induced increase in glycosaminoglycan content.ConclusionsCaMKII plays a significant role in modulating chondrocyte metabolism and maintaining cartilage homeostasis. It promotes anabolic processes, counteracts catabolic stimuli, and induces autophagy in articular chondrocytes. However, it also promotes hypertrophic differentiation, highlighting the complexity of CaMKII-mediated signalling in cartilage. Understanding these pathways could lead to new therapeutic strategies that leverage CaMKII’s anabolic potential while mitigating its pro-degenerative effects.
Social isolation in mid-life: associations with psychological distress, life satisfaction and self-rated health in two successive British birth cohorts
Authors: Mansfield Rosie , Richards Marcus , Ploubidis George B. , Henderson Morag , Patalay Praveetha 
Published: August 2024

AbstractLittle is known about the way in which different forms of isolation differentially impact mental health, whether they produce a ‘dose-response’ effect, and whether different forms of isolation interact in an additive or multiplicative way. The current study focuses on social isolation in mid-life (ages 42-26) – a life stage often neglected by the field. Data (N=32,391) were analysed from two successive British birth cohort studies: 1970 British Cohort Study N=16,585 and the 1958 National Child Development Study N=15,806. Linear multivariable regressions were run to investigate the independent, ‘dose-response’ and interactive associations of social isolation indicators with psychological distress, life satisfaction and self-rated health. Subsequently, all models were stratified to examine sex differences, and cohort effects were tested. Independent associations varied by isolation type and specific mental health outcomes, for instance, being out of employment was associated with all outcomes, living alone with only lower life satisfaction and a lack of frequent contact with friends and relatives, no labour market participation and limited community engagement were associated with lower life satisfaction and self-rated health. There was a ‘dose-response’ relationship with more social isolation associated with greater psychological distress, lower life satisfaction, and poorer self-reported health. The effects of different combinations of isolation on mental health appears to be additive, with no consistent sex and cohort differences observed. Results provide justification for investigating the separate and combined effects of different forms of social isolation; and the relevance of researching social isolation in relation to the complete mental health state. Isolation in its various forms was found to be detrimental for mental health, in mid-life, and over time in Great Britain. Social isolation was associated most consistently with lower levels of life satisfaction. Efforts to reduce isolation and its negative mental health impacts must recognise the complexity of experience across contexts and populations.
Chromatin-dependent motif syntax defines differentiation trajectories
Authors: Durdu Sevi , Iskar Murat , Isbel Luke , Hoerner Leslie , Wirbelauer Christiane , Burger Lukas , Hess Daniel , Iesmantavicius Vytautas , Schübeler Dirk 
Published: August 2024

ABSTRACTTranscription factors recognizing short DNA sequences within gene regulatory regions are crucial drivers of cell identity. Despite recent advances, their specificity remains incompletely understood. Here, we address this by contrasting two TFs, NGN2 and MyoD1, which recognize ubiquitous E-box motifs yet instigate distinct cell fates—neurons and muscles, respectively. Following controlled induction in embryonic stem cells, we monitor binding across differentiation trajectories, employing an interpretable machine-learning approach integrating pre-existing DNA accessibility data. This reveals a chromatin-dependent motif syntax, delineating both common and factor-specific binding and predicting genome engagement with high precision. Shared binding sites reside in open chromatin, locally influenced by nucleosomes. In contrast, factor-specific binding in closed chromatin involves NGN2 and MyoD1 acting as pioneer-factors, influenced by multi-motifs, rotational spacing, flanking sequences, and specific interaction partners, accounting for subsequent lineage divergence. Extending our methodology to other models demonstrates how such combination of opportunistic-binding and context-specific chromatin opening underpin transcription factor specificity driving differentiation trajectories.
Pitting behavior of austenitic stainless-steel welded joints with dense inclusions and methods to enhance pitting resistance
Authors: Zhou QingYuan , Sun Yangting , Wang Xiangyu , Tan Xin , Jiang Yiming , Li Jin 
Published: August 2024

Purpose
This study aims to assess the pitting resistance of austenitic stainless steel welded joints fusion zone (FZ) with high density of inclusions before and after surface treatment, including potentiostatic pulse technique (PPT) and pickling.

Design/methodology/approach
The potentiodynamic polarization tests and critical pitting temperature tests were carried out for estimating pitting resistance. The PPT and pickling were performed as surface treatment. Scanning electron microscope (SEM) and energy dispersive spectrometer were used for characterize the microstructure and elemental distribution. Electron back-scattered diffraction (EBSD) was used to assess the portion of phases and morphology of grains.

Findings
The weld metal exhibits a higher degree of alloying compared to the base metal, and it contains d-phase and sulfur-containing inclusions. Sulfur-containing inclusions serve as initiation sites for pitting, and they diminish the pitting resistance of weld metal. Both PPT and pickling can remove sulfur-containing inclusions, but PPT causes localized dissolution of the weld metal matrix around the inclusions, while pickling does not. Because of the high density of inclusions, certain pits initiated by PPT are significantly deeper, which makes the formation of stable pitting easier. Because of the high density of inclusions, certain pits initiated by the PPT are deeper. This characteristic facilitates the progression of these initial defects into fully developed, stable pits.

Originality/value
Analysis of pitting initiation in shielded metal arc welding FZ with PPT and ex situ SEM tracking observation. Explanation of why the PPT surface treatment is not able to enhance the pitting resistance of stainless steel with a high inclusion density.
The effect of investor protection on forced CEO turnover
Authors: D’Alauro Gabriele , Quagli Alberto , Nicoliello Mario 
Published: August 2024

Purpose
This paper aims to analyze the direct and indirect effects of investor protection on forced CEO turnover.

Design/methodology/approach
The authors investigate 5,175 firm-year observations from 16 European countries over 2012–2018, collect data on four national investor protection indicators, identify 196 forced CEO turnovers and use multiple logistic regression models.

Findings
The results show that a reduction in the degree of investor protection significantly increases the probability of a forced change of the company’s CEO. Furthermore, when the degree of investor protection increases, directors are attributed a lower degree of responsibility in the event of a decline in earnings performance. Therefore, the relation between a decrease in profitability and a forced change of CEO is reduced.

Research limitations/implications
The research is focused on countries belonging to the European Economic Area and most of the investor protection indicators are derived from surveys. Concerning policy implications, the findings suggest that regulators should focus on the effective enforcement of investor protection mechanisms.

Social implications
The results confirm that characteristics at the country level have an impact on corporate decisions, highlighting the importance of increasing the degree of investor protection as a means of mitigating agency conflicts and improving stewardship.

Originality/value
To the best of the authors’ knowledge, this study explores a relatively underinvestigated topic as it uses investor protection indicators to jointly evaluate both direct and indirect effects on forced changes of CEO through cross-national research.
Critical factors affecting workplace well-being at construction sites across countries with different income levels
Authors: Omer Mazen M. , Moyo Tirivavi , Al-Otaibi Ali , Alawag Aawag Mohsen , Rizal Alias Ahmad , Rahman Rahimi A. 
Published: August 2024

Purpose
This study aims to analyze the critical factors affecting workplace well-being at construction sites across countries with different income levels. Accordingly, this study’s objectives are to identify: critical factors affecting workplace well-being at construction sites in low-, lower-middle-, upper-middle- and high-income countries, overlapping critical factors across countries with different income levels and agreements on the critical factors across countries with different income levels.

Design/methodology/approach
This study identified 19 factors affecting workplace well-being using a systematic literature review and interviews with construction industry professionals. Subsequently, the factors were inserted into a questionnaire survey and distributed among construction industry professionals across Yemen, Zimbabwe, Malaysia and Saudi Arabia, receiving 110, 169, 335 and 193 responses. The collected data were analyzed using descriptive and inferential statistics, including mean, normalized value, overlap analysis and agreement analysis.

Findings
This study identified 16 critical factors across all income levels. From those, 3 critical factors overlap across all countries (communication between workers, general safety and health monitoring and timeline of salary payment). Also, 3 critical factors (salary package, working environment and working hours) overlap across low-, low-middle and upper-middle-income countries, and 1 critical factor (project leadership) overlaps across low-middle, upper-middle and high-income countries. The agreements are inclined to be compatible between low- and low-middle-income, and between low- and high-income countries. However, agreements are incompatible across the remaining countries.

Practical implications
This study can serve as a standard for maintaining satisfactory workplace well-being at construction sites.

Originality/value
To the best of the authors’ knowledge, this study is the first attempt to analyze factors affecting workplace well-being at construction sites across countries with different income levels.