bluuebunny/crossref_metadata_2025 huggingface dataset:
Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing
Authors: Sagniez Mélanie , Budhraja Anshul , Paré Bastien , Simpson Shawn M. , Vinet-Ouellette Clément , Rozendaal Marieke , Smith Martin A.
Published: March 2024

Resolving the transcriptomes of higher eukaryotes is more tangible with the advent of long read sequencing, which greatly facilitates the identification of new transcripts and their splicing isoforms. However, the computational analysis of long read RNA sequencing data remains challenging as it is difficult to disentangle technical artifacts frombona fidebiological information. To address this, we evaluated the performance of multiple leading transcriptome assembly algorithms on their ability to accurately reconstruct RNA transcript isoforms. We specifically focused on deep nanopore sequencing of synthetic RNA spike-in controls (Sequins™ and SIRVs) across different chemistries, including cDNA and direct RNA protocols. Our systematic comparative benchmarking exposes the strengths and limitations of the different surveyed strategies. We also highlight conceptual and technical challenges with the annotation of transcriptomes and the formalization of assembly quality metrics. Our results complement similar recent endeavors, helping forge a path towards a gold standard analytical pipeline for long read transcriptome assembly.
Endogenous CD28 drives CAR T cell responses in multiple myeloma
Authors: Lieberman Mackenzie M. , Tong Jason H. , Odukwe Nkechi U. , Chavel Colin A. , Purdon Terence J. , Burchett Rebecca , Gillard Bryan M. , Brackett Craig M. , McGray A. J. Robert , Bramson Jonathan L. , Brentjens Renier J. , Lee Kelvin P. , Olejniczak Scott H.
Published: March 2024

Recent FDA approvals of chimeric antigen receptor (CAR) T cell therapy for multiple myeloma (MM) have reshaped the therapeutic landscape for this incurable cancer. In pivotal clinical trials B cell maturation antigen (BCMA) targeted, 4-1BB co-stimulated (BBζ) CAR T cells dramatically outperformed standard-of-care chemotherapy, yet most patients experienced MM relapse within two years of therapy, underscoring the need to improve CAR T cell efficacy in MM. We set out to determine if inhibition of MM bone marrow microenvironment (BME) survival signaling could increase sensitivity to CAR T cells. In contrast to expectations, blocking the CD28 MM survival signal with abatacept (CTLA4-Ig) accelerated disease relapse following CAR T therapy in preclinical models, potentially due to blocking CD28 signaling in CAR T cells. Knockout studies confirmed that endogenous CD28 expressed on BBζ CAR T cells drovein vivoanti-MM activity. Mechanistically, CD28 reprogrammed mitochondrial metabolism to maintain redox balance and CAR T cell proliferation in the MM BME. Transient CD28 inhibition with abatacept restrained rapid BBζ CAR T cell expansion and limited inflammatory cytokines in the MM BME without significantly affecting long-term survival of treated mice. Overall, data directly demonstrate a need for CD28 signaling for sustainedin vivofunction of CAR T cells and indicate that transient CD28 blockade could reduce cytokine release and associated toxicities.
Hypothalamic Sex-Specific Metabolic Shift by Canagliflozin during Aging
Authors: Jayarathne H.S.M. , Sullivan R. , Stilgenbauer L. , Debarba L.K. , Kuchumov A. , Koshko L. , Scofield S. , Liu W. , Ginsburg B.C. , Miller R.A. , Sadagurski M.
Published: March 2024

The hypothalamus undergoes significant changes with aging and plays crucial roles in age-related metabolic alterations. Sodium-glucose co-transporter 2 inhibitors (SGLT2i) are anti-diabetic agents that promote glucose excretion, and promote metabolic homeostasis. Recent studies have shown that SGLT2i, Canagliflozin (Cana), can extend the median survival of genetically heterogeneous UM-HET3 male mice and improve central metabolic control via increases in hypothalamic insulin responsiveness in aged males, as well as reduced age-associated hypothalamic inflammation. We studied the long- and short-term effects of Cana on hypothalamic metabolic control in UM-HET3 mice. We show that Cana treatment reduced body weight and fat mass in male mice that was associated with enhanced glucose tolerance and insulin sensitivity observed by 12 months. Indirect calorimetry showed that short-term Cana treatment (5 months) increased energy expenditure in male, but not female mice, at 12 months of age. Long-term Cana treatment (18 months) increased metabolic rates in both sexes, and markedly increasing formation of both orexigenic and anorexigenic projections to the paraventricular nucleus of the hypothalamus (PVH) mostly in females by 25 months. Hypothalamic RNA-sequencing analysis revealed sex-specific genes and signaling pathways related to insulin signaling, glycogen catabolic pathway, neuropeptide signaling, and mitochondrial function upregulated by Cana, with males showing a more pronounced and sustained effect on metabolic pathways at both age groups. Overall, our data provide critical evidence for sex-specific mechanisms that are impacted by Cana during aging suggesting key targets of hypothalamic Cana-induced neuroprotection for metabolic control.
Snapshots ofPseudomonas aeruginosaSOS response activation complex reveal structural prerequisites for LexA engagement and cleavage
Authors: Vascon Filippo , Felice Sofia De , Gasparotto Matteo , Huber Stefan T. , Catalano Claudio , Chinellato Monica , Grinzato Alessandro , Filippini Francesco , Maso Lorenzo , Jakobi Arjen J. , Cendron Laura
Published: March 2024

Antimicrobial resistance represents a major threat to human health andPseudomonas aeruginosastands out among the pathogens responsible for this emergency. The SOS response to DNA damage plays a pivotal role in bacterial evolution, driving the development of resistance mechanisms and influencing the adaptability of bacterial populations to challenging environments, particularly in the context of antibiotic exposure. Recombinase A (RecA) and the transcriptional repressor LexA are the key players that orchestrate this process, determining either the silencing or the active transcription of the genes under their control. By integrating state-of-the-art structural approaches with binding and functional assaysin vitro, we elucidated the molecular events governing the SOS response activation inP. aeruginosa, focusing on the RecA-LexA interaction. Our findings identify the conserved determinants and strength of the interactions that let RecA trigger the autocleavage and inactivation of the LexA repressor. These results provide the groundwork for designing novel antimicrobial strategies and for exploring the potential translation ofEscherichia coli-derived approaches, to address the health-threatening implications of bacterial infections.

Graphical Abstract
FEVER: An interactive web-based resource for evolutionary transcriptomics across fishes
Authors: Montfort Jérôme , Hervas-Sotomayor Francisca , Cam Aurélie Le , Murat Florent
Published: March 2024

Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible athttps://fever.sk8.inrae.fr/.
Trait evolution linked to climatic shifts contributes to adaptive divergence in an alpine carnation (Dianthus sylvestris)
Authors: Paalsson Aksel , Fior Simone , Widmer Alex
Published: March 2024

Populations expanding to new habitats may encounter novel selection regimes which can lead to ecotype formation. In the Alps, elevation corresponds to steep ecological gradients, along which ecotype formation has occurred in many species. The majority of alpine plant species are perennial and little is known about how selection acts across different stages of their life-cycles and how fitness trade-offs shape adaptive processes in perennials. We investigated how selection at opposite ends of elevational gradients has driven ecotype formation inDianthus sylvestris, a perennial herb that expanded its ecological niche to low elevation habitats after the Last Glacial Maximum. Through a multi-year reciprocal transplant experiment including parental populations and recombinant crosses we assessed fitness under natural conditions and dissect how adaptation is mediated by different fitness components with inherent trade-offs, and pinpoint the contribution of growth and reproductive traits to this process. We show that the evolution of local adaptation proceeded by selection acting primarily through reproduction and survival at low and high elevation, respectively. At low elevation the primary contribution to adaptation was third year reproduction, concomitant with a left skewed age distribution. At high elevation the contribution to adaptation and the age distribution were more dispersed across the life cycle. We found that large, early flowering plants have a consistent fitness advantage. This was mediated by direct selection favoring large size through reproductive output at low elevation, and early flowering through the probability to produce seeds at high elevation. Our results indicate that the selection regime imposed by the warm low elevation habitat led to the evolution of an ecotype exhibiting a life-history strategy characterized by high investment in rapid growth and early reproduction. In contrast, the high elevation strategy favors high investment in self-maintenance. Our results suggest that weakening of a key fitness trade-off associated with resource allocation contributed to the evolution of distinct ecotypes in this perennial plant species.
Combining positive and negative regulation for modular and robust biomolecular control architectures
Authors: Sechkar Kirill , Steel Harrsion
Published: March 2024

Engineered biotechnologies are powered by synthetic gene regulation and control systems, known as genetic circuits, which must be modular and robust to disturbances if they are to perform reliably. An emerging family of regulatory mechanisms is mediated by clustered interspaced palindromic repeats (CRISPR) that can both interfere with (downregulate) or activate (upregulate) a given gene’s expression. However, all CRSIPR regulation relies on a shared resource pool of dCas9 proteins. Hence, a circuit’s components can indirectly affect one another via resource competition – even without any intended interactions between them – which compromises the modularity of synthetic biological designs. Using a resourceaware model of CRISPR regulation, we find that circuit modules which simultaneously subject a gene to CRISPR interference and activation are rendered robust to resource competition crosstalk. Evaluating this architecture’s simulated performance, we identify the scenarios where it can be advantageous over the extant resource competition mitigation strategies. We then consider different feedback architectures to demonstrate that combining opposite regulatory interactions overcomes the trade-off in robustness to perturbations of different nature. The motif of combined positive and negative regulation may therefore give rise to more robust and modular biomolecular controllers, as well as hint at the characteristics of natural systems that possess it.
Allele-specific CRISPR/Cas9 editing inactivates a single nucleotide variant associated with collagen VI muscular dystrophy
Authors: Bolduc Véronique , Sizov Katherine , Brull Astrid , Esposito Eric , Chen Grace S. , Uapinyoying Prech , Sarathy Apurva , Johnson Kory , Bönnemann Carsten G.
Published: March 2024

The application of allele-specific gene editing tools can expand the therapeutic options for dominant genetic conditions, either via gene correction or via allelic gene inactivation in situations where haploinsufficiency is tolerated. Here, we used allele-targeted CRISPR/Cas9 guide RNAs (gRNAs) to introduce inactivating frameshifting indels at a single nucleotide variant in theCOL6A1gene (c.868G>A; G290R), a variant that acts as dominant negative and that is associated with a severe form of congenital muscular dystrophy. We expressed spCas9 along with allele-targeted gRNAs, without providing a repair template, in primary fibroblasts derived from four patients and one control subject. Amplicon deep-sequencing for two gRNAs tested showed that single nucleotide deletions accounted for the majority of indels introduced. While activity of the two gRNAs was greater at the G290R allele, both gRNAs were also active at the wild-type allele. To enhance allele-selectivity, we introduced deliberate additional mismatches to one gRNA. One of these optimized gRNAs showed minimal activity at the WT allele, while generating productive edits and improving collagen VI matrix in cultured patient fibroblasts. This study strengthens the potential of gene editing to treat dominant-negative disorders, but also underscores the challenges in achieving allele selectivity with gRNAs.
Microbial communities thriving in agave fermentations are locally influenced across diverse biogeographic regions
Authors: Jara-Servin Angélica , Alcaraz Luis D. , Juarez-Serrano Sabino I. , Espinosa-Jaime Aarón , Barajas Ivan , Morales Lucia , DeLuna Alexander , Hernández-López Antonio , Mancera Eugenio
Published: March 2024

The production of traditional agave spirits in Mexico is a deeply rooted traditional process that relies on environmental microorganisms to ferment the cooked must from agave plants. Analysis of these microorganisms provides the opportunity to understand the dynamics of the microbial communities in the interface of natural and human-associated environments in a biologically and culturally rich region of the world. Here, we performed 16S and ITS amplicon sequencing of close to 100 fermentation tanks from 42 distilleries throughout Mexico. TheAgavespecies used, production practices, climatic conditions, and biogeographic characteristics varied considerably among sites. Yet, we did find taxa present in most fermentations suggesting that there is a core of microorganisms that are hallmarks of these communities. These core taxa are represented by hundreds of OTUs showing large intra-specific variation. The only variable that was consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that microbial composition is determined by the local production practices and unique attributes of each site. Fermentation stage, climate and producing region were also associated with the community composition, but only for prokaryotes. Analysis of microbial composition in several tanks within three distilleries also revealed taxa that were enriched in specific fermentation stages or agave species. Our work provides a comprehensive analysis of the microbiome of agave fermentations, contributing key knowledge for its management and conservation.
Feather degradation inStenotrophomonas maltophiliarelies on conversion and internalization of keratin monomer
Authors: Cao ZhangJun , Song XiaoXiao , Xue Kai , Zhang Wei , Zhang YunLong , Chen Ting , Zhang XingQun
Published: March 2024

Feather keratin is the most abundant nitrogen source waste in nature. This insoluble material cannot be directly utilized as nutrition by most organisms, especially animals and plants. While feathers are naturally decomposed by some microorganisms through keratinase-based degradation which remains mechanistically not fully understood. In this study, we find that when feathers serve as the only nutrient source forStenotrophomonas maltophiliaculture, keratin monomer of about 10 kDa is present in the medium as a predominant hydrolyzed product. We further show that keratin monomers bind to cells and in turn enter cells via an undetermined pathway. The cell entry of keratin monomer elicits keratinase activity to promote the forward reaction in keratin hydrolysis. This study highlights the importance of keratin monomer production as the first step in feather biodegradation, in which the insoluble feather is converted into soluble intermediate to facilitate its internalization and complete hydrolysis.

Importance

A large amount of feathers have been produced in poultry breeding, which could cause environmental pollution if not processed in time. On the other hand, amino acids degraded from feathers can be used in many fields, such as feed, fertilizer, daily chemicals and other fields. Biodegradable feathers have the advantages of low energy consumption, mild conditions and no destruction of the amino acids obtained from degradation. We previously isolated and identified a highly efficient feather-degrading bacterium, Stenotrophomonas maltophilia DHHJ, which can grow well on the medium with feathers as the only nutrient and completely degrade feathers. We know, feather particles are much larger than bacterial cells. In what form and how they are absorbed into cells by bacteria are interesting and critical questions for feather degradation. In our research, feathers had been first degraded extracellularly by basically expressed keratinase into keratin monomers. The keratin monomers bound to cells and enter across the membrane and can induce further expression of keratinase. The understanding of keratin monomers provides new clues for the study of feather degradation mechanisms.
Host cell-specific metabolism of linoleic acid controlsToxoplasma gondiigrowth in cell culture
Authors: Hryckowian Nicole D. , Zinda Caitlin , Park Sung Chul , Kelty Martin T. , Knoll Laura J.
Published: March 2024

The obligate intracellular parasiteToxoplasma gondiican infect and replicate in any warm-blooded cell tested to date, but much of our knowledge aboutT. gondiicell biology comes from just one host cell type: human foreskin fibroblasts (HFFs). To expand our knowledge of host-parasite lipid interactions, we studiedT. gondiiin intestinal epithelial cells, the first site of host-parasite contact following oral infection and the exclusive site of parasite sexual development in feline hosts. We found that highly metabolic Caco-2 cells are permissive toT. gondiigrowth even when treated with high levels of linoleic acid (LA), a polyunsaturated fatty acid (PUFA) that kills parasites in HFFs. Caco-2 cells appear to sequester LA away from the parasite, preventing membrane disruptions and lipotoxicity that characterize LA-induced parasite death in HFFs. Our work is an important step toward understanding host-parasite interactions in feline intestinal epithelial cells, an understudied but important cell type in theT. gondiilife cycle.
Novel oil-associated bacteria in Arctic seawater exposed to different nutrient biostimulation regimes
Authors: Davila Aleman Francisco Daniel , Bautista Maria A , McCalder Janine , Jobin Kaiden , Murphy Sean M.C. , Else Brent , Hubert Casey RJ
Published: March 2024

The Arctic Ocean is an oligotrophic ecosystem facing escalating threats of oil spills as ship traffic increases owing to climate change-induced sea ice retreat. Biostimulation is an oil spill mitigation strategy that involves introducing bioavailable nutrients to enhance crude oil biodegradation by endemic oil-degrading microbes. For bioremediation to offer a viable response for future oil spill mitigation in extreme Arctic conditions, a better understanding of the effects of nutrient addition on Arctic marine microorganisms is needed. Comprehensive population tracking of controlled oil-spill microcosms using cell counting and microbial biodiversity screening revealed a significant decline in community diversity together with changes in microbial community composition. These shifts were also indicative of changes in prevailing genomic traits as inferred from 16S rRNA taxonomy of resulting communities. In addition to well-recognized hydrocarbonoclastic bacteria, differential abundance analysis highlighted significant enrichment of unexpected genera Lacinutrix, Halarcobacter and Candidatus Pseudothioglobus. These groups have not been associated with hydrocarbon biodegradation until now, even though genomes from closely related isolates confirm the potential for hydrocarbon metabolism. These findings broaden understanding of marine oil spill bioremediation and how Arctic marine microbiomes and their novel lineages can respond to nutrient biostimulation as a strategy for oil spill mitigation.
Laboratory evolution inNovosphingobium aromaticivoransenables rapid catabolism of a model lignin-derived aromatic dimer
Authors: Allemann Marco N. , Kato Ryo , Alexander William G. , Giannone Richard J. , Kamimura Naofumi , Masai Eiji , Michener Joshua K.
Published: March 2024

Lignin contains a variety of interunit linkages, which leads to a range of potential decomposition products that can be used as carbon sources by microbes. β-O-4 linkages are the most common in native lignin and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from β-O-4 dimer cleavage has not been fully elucidated. Here, we used experimental evolution to identify mutant strains ofNovosphingobium aromaticivoranswith improved catabolism of a model aromatic dimer containing a β-O-4 linkage, guaiacylglycerol-β-guaiacyl ether (GGE). We identified several parallel causal mutations, including a single nucleotide mutation in the promoter of an uncharacterized gene that roughly doubled the growth yield with GGE. We characterized the associated enzyme and demonstrated that it oxidizes an intermediate in GGE catabolism, β-hydroxypropiovanillone, to vanilloyl acetaldehyde. Identification of this enzyme and its key role in GGE catabolism furthers our understanding of catabolic pathways for lignin-derived aromatic compounds.

Importance

Lignin degradation is a key step for both carbon cycling in nature and biomass conversion to fuels and chemicals. Bacteria can catabolize lignin-derived aromatic compounds, but the complexity of lignin means that full mineralization requires numerous catabolic pathways and often results in slow growth. Using experimental evolution, we identified a new enzyme for catabolism of a lignin-derived aromatic monomer, β-hydroxypropiovanillone. A single mutation in the promoter of the associated gene significantly increased bacterial growth with either β-hydroxypropiovanillone or a related lignin-derived aromatic dimer. This work expands the repertoire of known aromatic catabolic genes and demonstrates that slow catabolism of lignin-derived aromatic compounds may be due to misregulation under laboratory conditions rather than inherent catabolic challenges.
Genetic elements and defense systems drive diversification and evolution in Asgard archaea
Authors: Valentin-Alvarado Luis E. , Shi Ling-Dong , Appler Kathryn E. , Crits-Christoph Alexander , Cui Michael , De Anda Valerie , Leão Pedro , Adler Benjamin A. , Roberts Richard J. , Sachdeva Rohan , Baker Brett J. , Savage David F. , Banfield Jillian F.
Published: March 2024

Asgard Archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, wetland Asgard archaea phylum represented by two complete genomes. We used soil depth-resolved population metagenomic datasets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kilobase pair (kbp) circular plasmid (the first reported for Asgard archaea) and two groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp circularizable plasmid-like MGE integrates genomically into an Atabeyarchaeia chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp MGE encodes a highly expressed methylase with a sequence specificity matching an active methylation motif identified by PacBio sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea Freyarchaeia which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.
Transcription factor EB (TFEB) interaction with RagC is disrupted during Enterovirus D68 Infection
Authors: Jassey Alagie , Pollack Noah , Wagner Michael A. , Wu Jiapeng , Benton Ashley , Jackson William T.
Published: March 2024

Enterovirus D68 (EV-D68) is a picornavirus associated with severe respiratory illness and a paralytic disease called acute flaccid myelitis in infants. Currently, no protective vaccines or antivirals are available to combat this virus. Like other enteroviruses, EV-D68 uses components of the cellular autophagy pathway to rewire membranes for its replication. Here, we show that transcription factor EB (TFEB), the master transcriptional regulator of autophagy and lysosomal biogenesis, is essential for EV-D68 infection. Knockdown of TFEB attenuated EV-D68 genomic RNA replication but did not impact viral binding or entry into host cells. The 3C protease of EV-D68 cleaves TFEB at the N-terminus immediately post-peak viral RNA replication, disrupting TFEB-RagC interaction and restricting TFEB transport to the surface of the lysosome. Despite this, TFEB remained mostly cytosolic during EV-D68 infection. Overexpression of a TFEB mutant construct lacking the RagC binding domain, but not the wild-type construct, blocks autophagy and increases EV-D68 nonlytic release in H1HeLa cells, but not in autophagy defective ATG7 KO H1HeLa cells. Our results identify TFEB as a vital host factor regulating multiple stages of the EV-D68 lifecycle and suggest that TFEB could be a promising target for antiviral development against EV-D68.

Importance

Enteroviruses are among the most significant causes of human disease. Some enteroviruses are responsible for severe paralytic diseases such as poliomyelitis or acute flaccid myelitis (AFM). The latter disease is associated with multiple non-polio enterovirus species, including Enterovirus D68 (EV-D68), Enterovirus 71 (EV-71), and coxsackievirus B3 (CVB3). Here we demonstrate that EV-D68 interacts with a host transcription factor, TFEB, to promote vRNA replication and regulate egress of virions from cells. TFEB was previously implicated in viral egress of CVB3, and the viral protease 3C cleaves TFEB during infection. Here we show EV-D68 3C protease also cleaves TFEB after the peak of vRNA replication. This cleavage disrupts TFEB interaction with the host protein RagC, which changes the localization and regulation of TFEB. TFEB lacking a RagC-binding domain inhibits autophagic flux and promotes virus egress. These mechanistic insights highlight how common host factors affect closely related, medically-important viruses differently.
Bacteria adapt nutrient deprivation by reducing vacant 70S ribosomes via the silencing factor RsfS
Authors: Zhang Hong , Nikolay Rainer , Jiang Liang , Brotman Yariv , Zhang Gong , Qin Bo
Published: March 2024

Bacteria downregulate protein synthesis to conserve energy during nutrient deprivation stress. The stringent response is a widely recognized strategy employed by bacteria to counter this stress by suppressingde novoribosome synthesis, while leaving the pre-existing ribosomes unaffected. The conserved bacterial ribosome silencing factor (RsfS) has been identified as the sole factor affecting the equilibrium between pre-existing 70S ribosomes and their subunits; however, the detailed mechanism remains elusive. Here we demonstrate how bacteria adapt to nutrient deprivation through RsfS-mediated processes. During nutrient downshift, vacant 70S ribosomes (without translating mRNAs and tRNAs) tend to accumulate in the cells, causing a devastating energy drain by stimulating the activity of GTPase proteins such as EF-G. RsfS exclusively dissociates the vacant 70S ribosomes, leaving those involved in translation with tRNAs intact, thus conserving cellular energy and resources. This process facilitates the expression of enzymes essential for biosynthetic pathways and energy production. These observations reveal the translational regulatory role of RsfS in efficiently utilizing cellular resources during starvation conditions.
Homeless people’s experiences of the illicit drug supply during COVID-19
Authors: James Susanna , Maguire Nick
Published: March 2024

Purpose

The COVID-19 pandemic has affected many industries, and reports indicate that this includes the illicit drug market. Recent research suggests that the homeless are particularly vulnerable during the pandemic, and the UK Government has acted to house rough sleepers. Research is scarce regarding homeless people’s experiences of the illicit drug market. This study aims to explore homeless people’s experiences of the drug supply in the UK during COVID-19.

Design/methodology/approach

Eight homeless people who use illicit drugs, residing in hostels for homeless people in Southampton, participated in semi-structured one-on-one telephone-based interviews.

Findings

A thematic analysis revealed five themes: availability of drugs, presence of dealers, quality of drugs, finances and personal experiences. Participants reported varying experiences of the drug supply, with lockdown measures expressed as the main reason for reduced supplies, as users found it difficult to find dealers and generate income for purchasing drugs.

Research limitations/implications

The results may lack generalisability to the wider population, such as rough sleepers and drug dealers, suggesting a need for further research into people’s experiences of the drug supply during COVID-19. Research on this topic could be more in-depth through the use of research methods that are convenient for the homeless population.

Practical implications

Services should invest in harm reduction services and encourage homeless people who use drugs to engage in substitution treatment. Homeless services should provide psychological support for homeless people who use drugs.

Social implications

The changes in homeless people’s behaviour following the pandemic may have implications for their interactions with the rest of society (e.g. begging in town centres may reduce). These changes in behaviour may also change the way society can best support homeless people.

Originality/value

The results are partially consistent with other research findings about the illicit drug supply; however, they also suggest that some individuals experienced minimal change in the illicit drug supply.
Real in virtual: the influence mechanism of virtual reality on tourists’ perceptions of presence and authenticity in museum tourism
Authors: Li Minglong , Sun Xiaoyang , Zhu Yu , Qiu Hailian
Published: March 2024

Purpose

An increasing number of immersive technologies have been adopted in museum tourism in response to shifting consumer habits in the digital era. In contrast, the authenticity experience of museum tourists relies on genuine relics, the environment and activities, which are ancient or traditional. This raises the question of whether tourists can perceive authenticity in immersive technology-based museum tourism. To address this question, this study aims to explore the impact of virtual reality (VR) attributes on tourists’ presence, tourism authenticity and subsequent behavioral intentions in virtual museums.

Design/methodology/approach

Data were collected via scenario-based surveys of participants who had taken virtual museum tours based on VR. A total of 174 effective questionnaires were collected for exploratory factor analysis via SPSS 25. Afterward, 597 questionnaires were obtained for confirmatory factor analysis and path analysis via Mplus 7.4.

Findings

A conceptual model of how VR attributes influence presence, authenticity and visit intention was developed. There is a chain intermediary between presence and visit intentions, from original authenticity to interactive authenticity and then to emotional authenticity. Technology readiness and museum familiarity moderate some relationships between VR attributes and presence.

Practical implications

The findings can guide museums in improving the use of VR. For example, managers can improve the quality of virtual systems and adopt various interactive forms to enhance tourists’ participation experiences.

Originality/value

These research findings contribute to the research area of immersive technology adoption, enhance the understanding of tourism authenticity in the new context of technology application and extend the presence-emotion-intention theory.
From power asymmetry to collective action: Brazilian developers in the digital games ecosystem
Authors: Kirschbaum Charles , Sakuda Luiz Ojima
Published: March 2024

Purpose

The purpose of the article is to explore the perceptions of Brazilian game developers about the power relations between them and the sponsors of digital game platforms. It also aims to identify forms of collective action that developers can use to counteract the asymmetry of power.

Design/methodology/approach

The research employed an abductive approach, seeking empirical evidence that would challenge consolidated theory. To achieve this, semi-structured interviews were conducted with 25 Brazilian developers. The data were analyzed qualitatively using NVivo software. The aim was to resolve theoretical ambiguities identified in the literature review and to explore unexpected findings.

Findings

The study explores Brazilian game developers' perceptions through interviews, revealing their experiences within the industry’s concentrated structure and their use of collective action to navigate power dynamics.

Research limitations/implications

The study's focus on Brazil limits the generalizability of its findings to the broader game development industry.

Practical implications

The study suggests Brazilian game devs can leverage collective action to counteract power imbalance with platforms, collaborate through events and projects and facilitate internationalization of their games.

Social implications

The study suggests collective action could empower developers to challenge platform dominance and foster a stronger community among Brazilian game developers.

Originality/value

The article’s value lies in examining Brazilian devs' experiences within their specific industry context and highlighting collective action as a potential strategy for developers.
The art of jieyuan: ethical affinity and the cultivation of Chinese Buddhist spirituality in Tanzania
Authors: Qiu Yu
Published: March 2024

Ethical encounters in cross‐cultural contexts have been a major concern in the anthropology of morality and religion, yet the dominant view assumes that processes of ethical transformation and conversion emphasize the centrality of texts and beliefs. These discussions are influenced by epistemological frameworks associated with Christian theology and practice. Yet studies of other religions have brought about challenges by either doubting whether ‘belief’ still serves as a fruitful analytical tool or stressing the diversity of non‐text‐driven and multimedia forms of conversion. Based on fieldwork in a Chinese Buddhist monastery in Tanzania, this essay examines how Buddhist monks from China seek to cultivate Buddhist spirituality among Tanzanian locals in an embodied and allegorical way. By ethnographically teasing out the Chinese Buddhist notion of jieyuan, it provides a way of understanding religious suasion not just as a rational and intellectual conversation, but also as a process of embodied illumination that induces gradual, inductive, sympathetic changes in others.
Concentration units used to report blood‐ and breath‐alcohol concentration for legal purposes differ between countries which is important to consider when blood/breath ratios of alcohol are compared and contrasted
Authors: Jones Alan Wayne
Published: March 2024

This technical note reviews the plethora of concentration units used to report blood‐alcohol concentration (BAC) and breath‐alcohol concentrations (BrAC) for legal purposes in different countries. The choice of units sometimes causes confusion when scientific papers originating from a certain country might be introduced into evidence via expert testimony, such as when alcohol‐related crimes are prosecuted. The concentration units are also important to consider when blood/breath ratios (BBRs) of alcohol are calculated and compared between countries. Statutory BAC limits for driving in most nations are reported in mass/volume (m/v) units, such as g/100 mL (g%) in the United States, mg/100 mL (mg%) in the United Kingdom and Republic of Ireland, or g/L (mg/mL) in many EU nations. By contrast, Germany and the Nordic countries report BAC as mass/mass (m/m) units, hence g/kg or mg/g, which are ~5.5% lower than m/v units, because whole blood has an average density of 1.055 g/mL. There are historical reasons for reporting BAC in mass/mass units because the aliquots of blood analyzed were measured by weight rather than volume. The difference between m/m and m/v is also important in postmortem toxicology, such as when distribution ratios of ethanol between blood and other biological specimens, such as urine, vitreous humor, and cerebrospinal fluid, are reported.
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries
Authors: Macko Patrik , Derka Tomáš , Čiamporová‐Zaťovičová Zuzana , Grabowski Michal , Čiampor Fedor
Published: March 2024

Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long‐term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second‐most species‐rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non‐existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum‐likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
Comparison of characteristics of muscle magnetic resonance imaging findings in patients with antineutrophilic cytoplasmic antibody‐associated vasculitis and polyarteritis nodosa
Authors: Ito Haruyasu , Yoshida Ken , Fukuda Takeshi , Noda Kentaro , Ukichi Taro , Kurosaka Daitaro
Published: March 2024

Aim

This study aimed to analyze the muscle magnetic resonance imaging (MRI) findings of patients with antineutrophilic cytoplasmic antibody‐associated vasculitis (AAV) and polyarteritis nodosa (PAN) presenting with clinical symptoms in the extremities.

Methods

Retrospective analysis was conducted on short tau inversion recovery MRI findings, with a focus on intramuscular vessels displaying abnormal perivascular signals, in 22 and eight patients with AAV and PAN, respectively. The number per unit area (4 cm2) and diameter of abnormal vessels on muscle MRI were compared between patients with AAV and those with PAN. Cut‐off values, clinical sensitivity, and specificity for these indices were calculated from the receiver operating characteristic curves to distinguish between AAV and PAN, and the relationship between the indices and clinical findings in AAV was analyzed.

Results

The number of abnormal vessels per unit area was significantly higher in AAV compared to PAN (p < .05). Additionally, the diameter of the abnormal vessels was significantly higher in PAN than in AAV (p < .05). The presence of >6.44 abnormal vessels per unit area or ≤3.61 mm diameter of abnormal vessels was able to predict AAV (sensitivity, 0.955; specificity, 0.625). AAV patients with peripheral neuropathy exhibited a significantly higher number of abnormal vessels per unit area than those without peripheral neuropathy (p < .05).

Conclusions

Muscle MRI can detect small‐ to medium‐vessel vasculitis and be a valuable tool for distinguishing between patients with AAV and PAN experiencing clinical symptoms in the extremities.
“Everybody needs to find the best path for them”: Insights into recovery strategies of people who have not used specialty treatment for alcohol use disorder
Authors: Soweid Loulwa , Gilbert Paul A. , Maharjan Gaurab , Holdefer Paul J. , Evans Sydney , Mulia Nina
Published: March 2024

Background

Most people with alcohol use disorder (AUD) do not use treatment services, yet the majority ultimately resolve their AUD. As the phenomenon of untreated recovery remains poorly understood, we investigated the strategies used for recovery without treatment.

Methods

We conducted semi‐structured interviews with 65 adults (27 women, 37 White) with resolved AUD and no history of using specialty services (e.g., inpatient or outpatient rehabilitation, medication‐assisted treatment). Using both inductive and deductive coding, we identified and elaborated themes and meanings. We verified our findings through nine member‐check sessions with interviewers and interview participants.

Results

Majorities of interview participants met criteria for severe lifetime AUD (84.6%), were in long‐term recovery (>5 years; 81.5%), and indicated abstinence was their recovery goal (56.9%). Close to half (41.5%) had attended mutual‐help groups (e.g., Alcoholics Anonymous). We identified five active strategies (Changing Contexts, Social Connections. Activities, Substitution, and Other Strategies) and four additional factors (Mutual‐help Groups, Self‐Reliance, Spirituality, and Aging/Maturing) that contributed to their recovery. Most participants employed multiple strategies and were intentional in adopting the ones that best suited them. By far, the two most common strategies were Changing Contexts (reported by 69.2% of participants) whereby people reduced their alcohol exposure by modifying social networks or physical settings and relying on Social Connections (reported by 67.7%), especially connections to people with similar lived experiences and struggles. Notably, Social Connections and Mutual‐Help groups were the themes most often discussed jointly. Among other contributing factors mentioned, Spirituality appeared to play an important, but not universal, role as it was invoked by approximately half (49.2%) of participants.

Conclusions

Our study confirms that recovery without specialty treatment is possible, and that multiple strategies and contributing factors help to achieve it. These findings may inform novel interventions to support recovery among people unwilling or unable to obtain treatment for AUD.
Transcription factor KLF9 inhibits the proliferation, invasion, and migration of pancreatic cancer cells by repressing KIAA1522
Authors: Guo Yuting , Tian She , Li Haiyang , Zuo Shi , Yu Chao , Sun Chengyi
Published: March 2024

Aim

Pancreatic cancer (PC) has a poor prognosis and high mortality. Kruppel‐like factor 9 (KLF9), a transcription factor, is aberrantly expressed in various neoplasms. The current study sought to analyze the functional role of KLF9 in the proliferation, invasion, and migration of PC cells.

Methods

The expression patterns of KLF9 and KIAA1522 in normal pancreatic cells (HPDE‐C7) and PC cells (Panc 03.27, BxPc3, SW1990) were determined by real‐time quantitative polymerase chain reaction and Western blot assay. After treatment of KLF9 overexpression, proliferation, invasion, and migration were evaluated by cell counting kit‐8, 5‐ethynyl‐2′‐deoxyuridine staining, and Transwell assays. The binding of KLF9 to the KIAA1522 promoter was analyzed by dual‐luciferase assay and chromatin immunoprecipitation. The rescue experiment was conducted to analyze the role of KIAA1522.

Results

KLF9 was downregulated, while KIAA1522 was upregulated in PC cells. KLF9 overexpression mitigated the proliferation, invasion, and migration of PC cells. Enrichment of KLF9 led to inhibition of the KIAA1522 promoter and repressed KIAA1522 expression. KIAA1522 overexpression neutralized the inhibitory role of KLF9 in PC cell functions.

Conclusion

KLF9 is enriched in the KIAA1522 promoter and negatively regulates KIAA1522 expression, thereby mitigating the proliferation, invasion, and migration of PC cells.
Banker, pastor, teef: Christian financial elites and vernaculars of accountability in Ghana
Authors: Kauppinen Anna‐Riikka , Daswani Girish
Published: March 2024

When nine Ghanaian banks collapsed during the country's 2017–2019 financial crisis, a Charismatic Pentecostal pastor was at the center of public accusations as the board chairman of one of the failed banks. His role put a spotlight on the growing influence of Charismatic Pentecostal institutions and elites in Ghana's financial market. Shifting the perspective between diverse actors who reckoned with the bank's collapse, from ordinary Christians to artist‐activists, this article explores how Ghanaians evaluated the culpability of the pastor and in so doing problematized who Christian elites involved in banking and business are accountable to: God, their congregants, or the public at large? We argue that global financial liberalization has generated new types of financial elites, Pentecostal pastors among them, who become subject to new lines of accountability. Holding someone accountable comes with stakes expressed through vernacular registers that demonstrate how financial markets are engulfed in broader social relations and regimes of ethical evaluation.