bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTTeleost 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/.
Combining positive and negative regulation for modular and robust biomolecular control architectures
Authors: Sechkar Kirill , Steel Harrsion 
Published: March 2024

AbstractEngineered 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

AbstractThe 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

ABSTRACTThe 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

AbstractFeather 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.ImportanceA 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

AbstractThe 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.
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

AbstractLignin 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.ImportanceLignin 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

AbstractAsgard 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

AbstractEnterovirus 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.ImportanceEnteroviruses 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

AbstractBacteria 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.