bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coliextra-intestinal population translocation in leukemia patients
Authors: Marin Julie , Walewski Violaine , Dziri Samira , Magnan Mélanie , Denamur Erick , Carbonnelle Etienne , Bridier-Nahmias Antoine 
Published: January 2024

AbstractEscherichia coli, a commensal species of the human gut, is an opportunistic pathogen which can reach extra-intestinal compartments, including the bloodstream and the bladder, among others. In non-immunosuppressed patients, purifying or neutral evolution ofE. colipopulations has been reported in the gut. Conversely, it has been suggested that when migrating to extra-intestinal compartments,E. coligenomes undergo diversifying selection as supported by strong evidence for adaptation. The level of genomic polymorphism and the size of the populations translocating from the gut to extra-intestinal compartments is largely unknown.To gain insights in the pathophysiology of these translocations, we investigated the level of polymorphism and the evolutionary forces acting on the genomes of 77E. coliisolated from various compartments in three immunosuppressed patients. We detected a unique strain for each patient across the blood, the urine and the gut. In one case, all isolates recovered were mutators i.e. isolates with a very high mutation rate. In all instances, we observed that translocation encompasses the majority of the genomic diversity present in the gut. The same signature of selection, whether purifying or diversifying, and as anticipated, neutral for mutator isolates, was observed in both the gut and bloodstream. Additionally, we found a limited number of non-specific mutations among compartments for non-mutator isolates. In all cases, urine isolates were dominated by neutral selection. These findings indicate that substantial proportions of populations are undergoing translocation and that they present a complex compartment-specific pattern of selection at the patient level.ImportanceIt has been suggested that intra and extra-intestinal compartments differentially constrain the evolution ofE. colistrains. Whether host particular conditions, such as immunosuppression, could affect the strain evolutionary trajectories remain understudied. We found that, in immunosuppressed patients, large fractions ofE. coligut populations are translocating with variable modifications of the signature of selection for commensal and pathogenic isolates according to the compartment and/or the patient. Such multiple site sampling should be performed in large cohorts of patients to get a better understanding ofE. coliextra-intestinal diseases.
Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction
Authors: Dupuis Sunnyjoy , Lingappa Usha F. , Mayali Xavier , Sindermann Eve S. , Chastain Jordan L. , Weber Peter K. , Stuart Rhona , Merchant Sabeeha S. 
Published: January 2024

ABSTRACTAlthough the green algaChlamydomonas reinhardtiihas long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigatedC. reinhardtii’scapacity to support a heterotrophic microbe using the established coculture system withMesorhizobium japonicum, a vitamin B12-producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more13C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga’s fermentative degradation of starch reserves during the night would boostM. japonicumheterotrophy.15NH4assimilation rates and changes in cell size revealed thatM. japonicumcells reduced new biomass synthesis in coculture with the alga but continued to divide – a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B12and supported the growth of a B12-dependentC. reinhardtiimutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B12exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
Impaired glycolysis in aged endothelial cells is associated with reduced neovascularisation upon tissue ischemia
Authors: Kiesworo Kevin , Agius Thomas , Lyon Arnaud , Macarthur Michael R , Zhang Jing , Déglise Sébastien , Markmann James F. , Uygun Korkut , Yeh Heidi , Bock Katrien De , Mitchell Sarah J. , Ocampo Alejandro , Allagnat Florent , Longchamp Alban 
Published: January 2024

ABSTRACTThe vascular system experiences an age-associated decline in tissue perfusion and response to ischemic diseases. The factors driving this age-associated neovascularization decline remain unclear. While old endothelial cells (ECs) adopt a pro-angiogenic gene expression profile, we observed a stark reduction in the proliferative capacity of old ECs, while migratory capabilities remain intact. This is paralleled by a drastic decline in glycolytic capacity and ATP production, which likely act as limiting factors to neovascularization. These findings may provide new strategies to restore EC function in aging, thereby improving organ resilience and extending health- and lifespan.
In silico λ-dynamics predicts protein binding specificities to modified RNAs
Authors: Angelo Murphy , Zhang Wen , Vilseck Jonah Z. , Aoki Scott T. 
Published: January 2024

AbstractRNA modifications shape gene expression through a smorgasbord of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.
Environmental and Population influences on Mummichog (Fundulus heteroclitus) Gut Microbiomes
Authors: Ma Lei , Hahn Mark E. , Karchner Sibel I. , Nacci Diane , Clark Bryan W. , Apprill Amy 
Published: January 2024

AbstractThe mummichog,Fundulus heteroclitus, an abundant estuarine fish broadly distributed along the eastern coast of North America, has repeatedly evolved tolerance to otherwise lethal levels of aromatic hydrocarbon exposure. This tolerance is linked to reduced activation of the aryl hydrocarbon receptor (AHR) signaling pathway. In other animals, the AHR has been shown to influence the gastrointestinal-associated microbial community, or gut microbiome, particularly when activated by the model toxic pollutant 3,3’,4,4’,5-pentachlorobiphenyl (PCB-126) and other dioxin-like compounds. In order to understand host population and PCB-126 exposure effects on mummichog gut microbiota, we sampled two populations of wild fish, one from a PCB-contaminated environment (New Bedford Harbor, MA) and the other from a non-polluted location (Scorton Creek, MA), as well as laboratory-reared F2 generation fish originating from each of these populations. We examined the bacteria and archaea associated with the gut of these fish using amplicon sequencing of small subunit ribosomal RNA genes. Fish living in the PCB-polluted site had high microbial alpha and beta diversity and an altered microbial network structure compared to fish from the non-polluted site. These differences between wild fish were not present in laboratory-reared F2 fish that originated from the same populations. Microbial compositional differences existed between the wild and lab-reared fish, with the wild fish dominated by Vibrionaceae and the lab-reared fish by Enterococceae. These results suggest that mummichog habitat and/or environmental conditions has a stronger influence on the mummichog gut microbiome compared to population or hereditary-based influences. Mummichog are important eco-evolutionary model organisms; this work reveals their importance for exploring host-environmental-microbiome dynamics.
Acid-treatedStaphylococcus aureusinduces acute silkworm hemolymph melanization
Authors: Matsumoto Yasuhiko , Sato Eri , Sugita Takashi 
Published: January 2024

AbstractThe skin microbiome maintains healthy human skin, and disruption of the microbiome balance leads to inflammatory skin diseases such as folliculitis and atopic dermatitis.Staphylococcus aureusandCutibacterium acnesare pathogenic bacteria that simultaneously inhabit the skin and cause inflammatory diseases of the skin through the activation of innate immune responses. Silkworms are useful invertebrate animal models for evaluating innate immune responses. In silkworms, phenoloxidase generates melanin as an indicator of innate immune activation upon the recognition of bacterial or fungal components. We hypothesized thatS. aureusandC. acnesinteract to increase the innate immunity-activating properties ofS. aureus. In the present study, we showed that acidification is involved in the activation of silkworm hemolymph melanization byS. aureus. Autoclaved-killedS. aureus(S. aureus[AC]) alone does not greatly activate silkworm hemolymph melanization. On the other hand, applyingS. aureus[AC] treated withC. acnesculture supernatant increased the silkworm hemolymph melanization. AddingC. acnesculture supernatant to the medium decreased the pH.S. aureus[AC] treated with propionic acid, acetic acid, or lactic acid induced higher silkworm hemolymph melanization activity than untreatedS. aureus[AC].S. aureus[AC] treated with hydrochloric acid also induced silkworm hemolymph melanization. The silkworm hemolymph melanization activity ofS. aureus[AC] treated with hydrochloric acid was inhibited by protease treatment ofS. aureus[AC]. These results suggest that acid treatment ofS. aureusinduces innate immune activation in silkworms and thatS. aureusproteins are involved in the induction of innate immunity in silkworms.
A critical role for Pol II CTD phosphorylation in heterochromatic gene activation
Authors: Kainth Amoldeep S. , Zhang Hesheng , Gross David S. 
Published: January 2024

AbstractHow gene activation works in heterochromatin, and how the mechanism might differ from the one used in euchromatin, has been largely unexplored. Previous work has shown that inSIR-regulated heterochromatin ofSaccharomyces cerevisiae, gene activation occurs in the absence of covalent histone modifications and other alterations of chromatin commonly associated with transcription. Here we demonstrate that such activation occurs in a substantial fraction of cells, and this raises the possibility that an alternative activation pathway might be used. We address one such possibility, Pol II CTD phosphorylation, and explore this idea using a natural telomere-linked gene,YFR057w, as a model. Unlike covalent histone modifications, CTD phosphorylation at Ser2, Ser5 and Ser7 is abundant at the drug-induced heterochromatic gene. Particularly enriched relative to the euchromatic state is Ser2 phosphorylation. Consistent with a functional role for Ser2P,YFR057wis negligibly activated in cells deficient in the Ser2 CTD kinases Ctk1 and Bur1 even though the gene is strongly stimulated inctk1Δ bur1cells when it is placed in a euchromatic context. Collectively, our results are consistent with a critical role for Ser2 CTD phosphorylation in driving Pol II recruitment and transcription of a natural heterochromatic gene – an activity that may help supplant the need for histone epigenetic modifications.
Analyzing the implications of protein folding delay caused by translation
Authors: Houben Bert , Duran-Romaña Ramon , Migens Paula Fernández , Rousseau Frederic , Schymkowitz Joost 
Published: January 2024

ABSTRACTBecause of vectorial protein production, residues that interact in the native protein structure but are distantly separated in the primary sequence are unavailable simultaneously. Instead, there is a temporal delay during which the N-terminal interaction partner is vulnerable to off-pathway, non-native interactions. In this analysis, we introduce “FoldDelay” (FD), a metric that integrates the topological pattern of atomic interactions of the native structure with translation kinetics to quantify such time delays. The FD metric reveals that many proteins, particularly at eukaryotic translation rates, exhibit residues with FDs in the range of tens of seconds. These residues, predominantly in well-structured, buried regions, often coincide with predicted aggregation-prone regions. We show a correlation between FD and co-translational engagement by the yeast Hsp70 chaperone Ssb, suggesting that fold-delayed regions have a propensity to misfold. In support of this, we show that proteins with high FDs are more frequently co-translationally ubiquitinated and prone to aggregate upon Ssb deletion. Finally, we find that FD cannot be adequately reduced through codon optimization, highlighting the importance of co-translational chaperones to shield these vulnerable regions. This work offers insights into co-translational proteostasis and the delicate balance between efficient folding and potential misfolding and aggregation during translation.
Coral reef fish resilience and recovery following major environmental disturbances caused by cyclones and coral bleaching: A case study at Lizard Island
Authors: Lévy Simon A. , Pessina Letizia , Bshary Redouan , Triki Zegni 
Published: January 2024

AbstractCoral reef fish communities can be affected by natural disturbances such as cyclones and coral bleaching. It is not yet understood how long it takes these communities to recover from such extreme events, particularly when they occur repeatedly. To investigate this, we conducted fish surveys repeatedly between 2011 and 2022 at Lizard Island on the Great Barrier Reef in Australia. We focused on two reef sites, Mermaid Cove and Northern Horseshoe, both of which were damaged by a large-scale coral bleaching event in 2016 and 2017, as well as two cyclones that occurred in 2014 and 2015 (the cyclones hit Mermaid Cove but not Northern Horseshoe). Between 2016 and 2017, both reef sites saw a decrease in the total fish abundance of about 68 % and across most functional groups (carnivores, corallivores, herbivores, and omnivores). Despite the two sites showing different decline and recovery patterns, they both showed an improvement in fish abundance and across the majority of functional groups at both sites by 2022. The recovery reached similar numbers as those documented in the fish census data collected before the disturbances occurred. Our findings provide a case study highlighting how fish community resilience can vary on small local scales, with potential recovery if conditions are favourable over several years.
Combined benefits of active and passive social media during the COVID-19 pandemic: a health perspective
Authors: So Bohee , Kwon Ki Han 
Published: January 2024

Purpose
This study, a narrative literature review, aims to examine the combined benefits of the active and passive use of social media (SM) for well-being (WB), physical and mental health during the COVID-19 pandemic.

Design/methodology/approach
A search strategy has been carried out in the databases: Riss, PubMed, Medline, Scopus and Google Scholar, including all the articles published until 19 October 2023.

Findings
SM offers various benefits, including global risk awareness, health information, social connections and support. With the natural increase in physical inactivity due to COVID-19 social restrictions, SM has been identified as an appropriate tool for promoting physical activity (PA) at home to improve health.

Research limitations/implications
It suggests that the combined use of active and passive benefits of SM could potentially play an important role in public health by increasing individuals’ health behaviours. In addition, dissemination, sharing and social interaction of information provided by YouTube can encourage healthy behaviours, contribute to WB, physical and mental health and raise public health awareness.

Originality/value
The findings presented in this study highlight the combined benefits of differentiating the features of SM use. Compared to other SM platforms, YouTube can be used as a useful tool for home-based PA that promotes health by enabling people to remain active and avoid barriers to PA due to social restrictions during the global crisis. In addition, some recommendations from the findings may help protect against potential risks and improve public health outcomes during global crises, such as the COVID-19 pandemic, among the general public using SM.
Is B Corp certification sufficiently attractive to emerging markets? A conceptual study of B Corps in China
Authors: Xiang Guangming , He Zheng , Feng Tianli , Feng Zhenzhen 
Published: January 2024

PurposeThis paper aims to explore how firms enter or exit B Corp certification faced with the tension between local and B Corp institutions, providing a better understanding of the unique impact of institutional complexity on B Corps' decision-making.Design/methodology/approachThis paper applies multi-case analysis to 20 Chinese firms in various stages of B Corp certification, including eight certified B Corps, six decertified firms and six candidates. The qualitative data was used to code separately for two research questions.FindingsThe study findings reveal that: (1) Participants who can obtain expected social and economic benefits by innovating their operational mode to efficiently deal with this tension attempt to continuously pursue B Corp certification. A self-renewal model was developed to show how firms hybridize the two institutional logics; (2) Participants who find it hard to mitigate this tension tend to compromise with the local institution and conform less with the B Corp institution due to high opportunity and accounting costs, low short-term benefits and collective culture.Originality/valueBy highlighting the different responses of firms to institutional complexity, this study contributes to B Corp research, social identity theory and institutional complexity, providing practical implications for B Lab strategies in China.
Acceptance of ChatGPT by undergraduates in Sri Lanka: a hybrid approach of SEM-ANN
Authors: Sabraz Nawaz Samsudeen , Fathima Sanjeetha Mohamed Buhary , Al Murshidi Ghadah , Mohamed Riyath Mohamed Ismail , Mat Yamin Fadhilah Bt , Mohamed Rusith 
Published: January 2024

Purpose
This study aims to investigate Sri Lankan Government university students’ acceptance of Chat Generative Pretrained Transformer (ChatGPT) for educational purposes. Using the unified theory of acceptance and use of technology 2 (UTAUT2) model as the primary theoretical lens, this study incorporated personal innovativeness as both a dependent and moderating variable to understand students’ ChatGPT use behaviour.

Design/methodology/approach
This quantitative study used a questionnaire survey to collect data. A total of 500 legitimate undergraduates from 17 government universities in Sri Lanka were selected for this study. Items for the variables were adopted from previously validated instruments. Partial least squares structural equation modelling (PLS-SEM) using SmartPLS 4 was used to investigate latent constructs’ relationships. Furthermore, the variables’ relative relevance was ranked using a two-stage artificial neural network analysis with the SPSS 27 application.

Findings
The results of the analysis revealed that eight of the nine proposed hypotheses were confirmed. The most significant determinants of behavioural intention were habit and performance expectancy, closely followed by hedonic motivation and perceived ease of use. Use behaviour was highly influenced by both behavioural intention and personal inventiveness. Though personal innovativeness (PI) was suggested as a moderator, the relationship was not significant.

Research limitations/implications
The research highlights the impact of habit, performance expectancy and perceived ease of use on students’ acceptance of AI applications such as ChatGPT, emphasising the need for efficient implementation techniques, individual variations in technology adoption and continuous support and training to improve students’ proficiency.

Originality/value
This study enhances the comprehension of how undergraduate students adopt ChatGPT in an educational setting. The study emphasises the significance of certain variables in the UTAUT2 model and the importance of PI in influencing the adoption of ChatGPT in educational environments.
Songs of the self: the importance of authentic leadership and core self-evaluations for LGBT managers
Authors: Fletcher Luke , Pichler Shaun , Chandrasekaran Lakshmi 
Published: January 2024

PurposeBased on authentic leadership (AL) theory and research on lesbian, gay, bisexual and transgender (LGBT) workplace experiences, this study proposes that AL explains variance beyond transformational leadership (TL) in attitudinal outcomes for LGBT managers compared to non-LGBT managers. It is further predicted that core self-evaluations (CSEs) bound relationships between AL, LGBT status and outcomes.Design/methodology/approachA time-lagged survey of 193 LGBT and 218 non-LGBT (i.e. heterosexual and cisgender) managers was conducted. The first survey assessed respondents' evaluations of their leadership behavior and CSEs whereas the second survey, conducted one month later, assessed role engagement and career satisfaction.FindingsRegression and moderation analyses revealed support for the hypotheses. AL seems especially relevant for LGBT leaders, particularly at low levels of CSEs.Practical implicationsLeadership development programmes emphasizing AL could be particularly beneficial for LGBT managers, especially those low in CSEs. Harnessing a leader’s sense of identity could help those who have been marginalized.Originality/value The current study proposes, explains and demonstrates that relationships between AL and leader outcomes will likely be different between managers with and without stigmatized identities, in this case those who are (not) LGBT.