bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlates of COVID-19 conspiracy theory beliefs in Japan: A nationally-representative cross-sectional survey
Authors: Sato Yukihiro , Kawachi Ichiro , Saijo Yasuaki , Yoshioka Eiji , Osaka Ken , Tabuchi Takahiro 
Published: September 2024

AbstractBackgroundThe COVID-19 pandemic was associated with an increase in conspiracy theories worldwide. However, the prevalence of COVID-19 conspiracy beliefs among Japanese has remained unclear. This study aimed to estimate the prevalence and correlates of COVID-19 conspiracy beliefs in Japan using a nationwide survey of 28,175 residents aged 16–81 years old.MethodsA nationally representative, cross-sectional self-administered survey was conducted from September to October 2021. To assess the number of COVID-19 conspiracy beliefs, we used three questions from the Oxford Coronavirus Explanations, Attitudes, and Narratives Survey. Independent variables included general vaccine conspiracy beliefs, sociodemographic variables, information sources for COVID-19, trust in authorities, and fear of COVID-19.ResultsAfter applying sampling weights and imputation, the estimated prevalence of holding at least one COVID-19 conspiracy belief was 24.4%. From a linear regression model, several factors were independently associated with conspiracy beliefs. Notably, people with the lowest level of education (lower secondary school) endorsed fewer COVID-19 conspiracy beliefs (B -0.089, vs. upper secondary school). Furthermore, higher socioeconomic backgrounds–such as higher income, higher wealth, and regular employment–were associated with endorsing conspiracy beliefs. Additionally, only 37.3% of respondents trusted the government of Japan, but paradoxically, trust in the government was positively associated with conspiracy beliefs (B 0.175, vs. distrust).ConclusionsConspiracy beliefs about COVID-19 were prevalent in about a quarter of the Japanese population. Certain groups are more likely to endorse conspiracy beliefs, and targeting interventions towards these groups might be efficient in stemming the spread of conspiracy beliefs.
Pangenome analysis ofClostridium scindens: a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains
Authors: Olivos-Caicedo Kelly Y. , Fernandez Francelys , Daniel Steven L. , Anantharaman Karthik , Ridlon Jason M. , Alves João M. P. 
Published: September 2024

ABSTRACTClostridium scindensis a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains,C. scindensATCC 35704 andC. scindensVPI 12708, have been characterizedin vitroandin vivoto any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention ofClostridium difficileinfection. We therefore wanted to determine the pangenome of 34 cultured strains ofC. scindensand a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains ofC. scindenshave an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes was identified among groups of strains. The analysis reveals thatC. scindensstrains are distributed into two clades, indicating the possible onset ofC. scindensseparation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of theC. scindenspangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.
Modulating NLRP3 splicing with antisense oligonucleotides to control pathological inflammation
Authors: Klein Roni , Onyuru Janset , Viera Estela M. , Putnam Christopher D. , Hoffman Hal M. , Hastings Michelle L. 
Published: September 2024

AbstractInflammation has an essential role in healing. However, over-active inflammation disrupts normal cellular functions and can be life-threatening when not resolved. The NLRP3 inflammasome, a component of the innate immune system, is an intracellular multiprotein complex that senses stress-associated signals, and, for this reason is a promising therapeutic target for treating unresolved, pathogenic inflammation. Alternative splicing ofNLRP3RNA has been suggested as a regulatory mechanism for inflammasome activation, as some spliced isoforms encode NLRP3 proteins with compromised function. Here, we take advantage of this natural regulatory mechanism and devise a way to control pathogenic inflammation using splice-switching antisense oligonucleotides (ASOs). To identify and induce NLRP3 spliced isoforms lacking inflammatory activity, we tested a series of ASOs, each targeting a different exon, to determine the most effective strategy for down-regulating NLRP3. We identify several ASOs that modulateNLRP3splicing, reduce NLRP3 protein, and decrease inflammasome signalingin vitro. The most effective ASO suppresses systemic inflammationin vivoin mouse models of acute inflammation and cryopyrin-associated periodic syndrome (CAPS). Our results demonstrate a systematic approach to protein engineering using splice-switching ASOs to generate isoforms with altered activity, and identify an ASO that can treat pathological inflammation in mice by reducing functional NLRP3.
USP24 is an ISG15 cross-reactive deubiquitinase that mediates IFN-I production by de-ISGylating the RNA helicase MOV10
Authors: Mukhopadhyay Rishov , Draganov Simeon D. , Akkermans Jimmy J. L. L. , Kikkert Marjolein , Knobeloch Klaus-Peter , Fritz Günter , Guzmán María , Zuñiga Sonia , Kim Robbert. Q. , Kessler Benedikt M. , Pinto-Fernández Adán , Geurink Paul P. , Sapmaz Aysegul 
Published: September 2024

ABSTRACTThe interferon-stimulated gene 15 (ISG15) is a ubiquitin-like modifier induced by type I Interferon (IFN-I) and plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade through a process called ISGylation. While ubiquitin-specific protease 18 (USP18) is a well-defined deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Our study reports USP24 as a novel ISG15 cross-reactive DUB identified through activity-based protein profiling (ABPP). We demonstrate that recombinant USP24 processed pro-ISG15 and ISG15-linked synthetic substratesin vitro. Moreover, the depletion of USP24 significantly increased the accumulation of ISG15 conjugates upon IFN-β stimulation. An extensive proteomic analysis of the USP24-dependent ISGylome, integrating total proteome, GG-peptidome, and ISG15 interactome data, identified the helicase Moloney leukemia virus 10 (MOV10) as a specific target of USP24 for deISGylation. Further validation in cells revealed that ISGylated MOV10 enhances IFN-β production/secretion, whereas USP24 deISGylates MOV10 to negatively regulate the innate immune response. This study showcases USP24’s novel roles in modulating ISGylation and modulation of the IFN-I-dependent immune responses, with potential therapeutic implications in infectious diseases, cancer, autoimmunity, and neuroinflammation.
GelGenie: an AI-powered framework for gel electrophoresis image analysis
Authors: Aquilina Matthew , Wu Nathan J.W. , Kwan Kiros , Bušić Filip , Dodd James , Nicolás-Sáenz Laura , O’Callaghan Alan , Bankhead Peter , Dunn Katherine E. 
Published: September 2024

AbstractGel electrophoresis is a ubiquitous laboratory method for the separation and semi-quantitative analysis of biomolecules. However, gel image analysis principles have barely advanced for decades, in stark contrast to other fields where AI has revolutionised data processing. Here, we show that an AI-based system can automatically identify gel bands in seconds for a wide range of experimental conditions, far surpassing the capabilities of current software. We used a dataset containing 500+ images of manually-labelled gels to train various U-Nets to accurately identify bands through segmentation, i.e. classifying pixels as ‘band’ or ‘background’. When applied to gel electrophoresis data from other laboratories, our system generated results that quantitatively matched those of the original authors. We have publicly released our models through GelGenie, an open-source application that allows users to extract bands from gel images on their own devices, with no expert knowledge or experience required.
The penta-EF-hand protein Pef1 ofCandida albicansfunctions at sites of membrane perturbation to support polarized growth and membrane integrity
Authors: Weichert Martin , Schumann Marcel René , Brandt Ulrike , Brand Alexandra C. , Fleißner André 
Published: September 2024

AbstractThe fungal plasma membrane is the target of fungicidal compounds, such as polyenes and saponins, that directly interact with fungus-specific ergosterol to cause deleterious membrane disruption. To counter membrane attack, diverse eukaryotic cells employ Ca2+-binding penta-EF (PEF)-hand proteins, including the human ortholog, ALG-2, to maintain membrane integrity.Candida albicansis a major fungal pathogen in humans, where increasing resistance to current antifungal drugs that target the plasma membrane is a serious cause of concern. Combinatorial treatments that additionally compromise the plasma membrane offer a way forward, but our mechanistic understanding of how fungi respond to direct membrane disruption remains limited. Here, we characterized the PEF-hand ortholog, Pef1, in this polymorphic species. GFP-tagged Pef1 localized at sites of polarized growth in yeast and hyphal cells ofC. albicans. On treatment of cells with the polyene drug, amphotericin B, or the saponin, tomatine, GFP-Pef1 appeared as punctate spots at the membrane. In a similar manner, loss of calcineurin, but not of its transcription factor, Crz1, caused a punctate localization pattern of GFP-Pef1, which correlated with the serum sensitivity of thecna1Δ mutant. While deletion ofPEF1impaired yeast cell separation, filamentation was not affected. Strikingly,pef1Δ hyphae could not maintain plasma membrane integrity in serum. Consistent with this, the mutant exhibited attenuated virulence in an insect larvae infection model. Taken together, these observations suggest that Pef1 localizes to sites of membrane perturbation in order to maintain cell integrity, including sites of dynamic polarized growth and fungicide-induced membrane disruption.
Macrophage-intrinsic MDA5-IRF5 axis drives HIV-1 icRNA-induced inflammatory responses
Authors: Ramaswamy Sita , Akiyama Hisashi , Berrigan Jacob , Quiñones Andrés , Olson Alex , Chen Yunhan , Liang Yan Mei , Henderson Andrew J. , Asundi Archana , Sagar Manish , Gummuluru Suryaram 
Published: September 2024

AbstractDespite effective antiretroviral therapy (ART), transcriptionally competent HIV-1 reservoirs persist and contribute to persistent immune activation in people living with HIV (PWH). HIV-1-infected macrophages are important mediators of chronic innate immune activation, though mechanisms remain unclear. We previously reported that nuclear export and cytoplasmic expression of HIV-1 intron-containing RNA (icRNA) activates mitochondrial antiviral signaling protein (MAVS)-mediated type I interferon (IFN) responses in macrophages. In this study, we demonstrate an essential role of melanoma differentiation-associated protein 5 (MDA5) in sensing HIV-1 icRNA and promoting MAVS-dependent IRF5 activation in macrophages. Suppression of MDA5, but not RIG-I expression nor disruption of endosomal TLR pathway, abrogated HIV-1 icRNA-induced type I IFN responses and IP-10 expression in macrophages. Furthermore, induction of IP-10 in macrophages upon HIV-1 icRNA sensing by MDA5 was uniquely dependent on IRF5. Additionally, monocytes and MDMs from older (>50 years) individuals exhibit constitutively higher levels of IRF5 expression compared to younger (<35 years) individuals, and HIV-1 icRNA induced IP-10 expression was significantly enhanced in older macrophages, which was attenuated upon ablation of IRF5 expression suggesting that IRF5 functions as a major mediator of pro-inflammatory response downstream of MDA5-dependent HIV-1 icRNA sensing, dysregulation of which might contribute to chronic inflammation in older PWH.
CRISPRi with barcoded expression reporters dissects regulatory networks in human cells
Authors: Kim Jinyoung , Muller Ryan Y. , Bondra Eliana R. , Ingolia Nicholas T. 
Published: September 2024

AbstractGenome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.
Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth ofCampylobacterotaisolates
Authors: Heo Hokwan , Nguyen-Dinh Thanh , Jung Man-Young , Greening Chris , Yoon Sukhwan 
Published: September 2024

ABSTRACTDissimilatory nitrate reduction to ammonium (DNRA) is a key process in global nitrogen cycling, supporting the energy conservation of diverse microbes. For a long time, DNRA has been thought to primarily depend on organic electron donors, and thus to be governed by carbon-to-nitrogen (C:N) ratios. However, recent studies suggest that inorganic electron donors, such as sulfur compounds and iron, may also facilitate DNRA. The coupling of DNRA with molecular hydrogen (H2) oxidation is theoretically feasible, but largely unexplored microbial process. Here, we report the isolation of twoCampylobacterotastrains,Aliarcobacter butzlerihDNRA1 andSulfurospirillumsp. hDNRA2, that grow by using H2as an electron donor for DNRA. In both batch and continuous cultures, DNRAsensu stricto, i.e., NO2−-to-NH+reduction, depended on the presence of H2and was stoichiometric with H2oxidation. The electrons for NO−reduction were clearly derived from H, and hydrogenotrophic DNRA was largely unaffected by the ratio of either carbon or electron donor to NO−/NO−. Genomic and transcriptomic analyses indicate that group 1b [NiFe]-hydrogenase and cytochromec552nitrite reductase are the key enzymes catalyzing hydrogenotrophic DNRA. These findings reveal novel physiological mechanisms enabling anaerobic bacterial growth, challenge the traditional C:N ratio paradigm, and uncover new biogeochemical processes and mediators controlling the global nitrogen and hydrogen cycles.
Genome scale identification of new genes using saturated reporter transposon mutagenesis
Authors: Goodall Emily C. A. , Hodges Freya , Kok Weine , Permana Budi , Cuddihy Thom , Yang Zihao , Kahler Nicole , Shires Kenneth , Pullela Karthik , Torres Von Vergel L. , Rooke Jessica L. , Delhaye Antoine , Collet Jean-François , Bryant Jack A. , Forde Brian M. , Hemm Matthew , Henderson Ian R. 
Published: September 2024

AbstractSmall or overlapping genes are prevalent across all domains of life but are often overlooked for annotation and function because of challenges in their detection. The advent of high-density mutagenesis and data-mining studies suggest the existence of further coding potential within bacterial genomes. To overcome limitations in existing protein detection methods, we applied a genetics-based approach. We combined transposon insertion sequencing with a translation reporter to identify translated open reading frames throughout the genome at scale, independent of genome annotation. We applied our method to the well-characterised speciesEscherichia coliand identified ∼200 putative novel protein coding sequences (CDS). These are mostly short CDSs (<50 amino acids) and in some cases highly conserved. We validated the expression of selected CDSs demonstrating the utility of this approach. Despite the extensive study ofE. coli, this method revealed proteins that have not been described previously, including proteins that are conserved and neighbour functionally important genes, suggesting significant functional roles of these small proteins. We present this as a complementary method to whole cell proteomics and ribosome trapping for condition-dependent identification of protein CDSs, and as a high-throughput method for testing conditional gene expression. We anticipate this technique will be a starting point for future high-throughput genetics investigations to determine the existence of unannotated genes in multiple bacterial species.
Integrative Multi-Omics Analysis of IFNγ-induced Macrophages and Atherosclerotic Plaques Reveals Macrophage-dependent STAT1-Driven Transcription in Atherosclerosis
Authors: Boroujeni Mahdi Eskandarian , Lopacinska Natalia , Antonczyk Aleksandra , Kluzek Katarzyna , Wesoly Joanna , Bluyssen Hans AR 
Published: September 2024

AbstractThis study investigates the role of STAT1-mediated IFNγ signaling in atherosclerosis progression through multi-omics integration and analysis of human and mouse models of atherosclerotic lesions. By integrating ATAC-seq, ChIP-seq, and RNA-seq data from IFNγ-treated bone marrow-derived macrophages, we identified 1139 STAT1-dependent integrative genes that show chromatin accessibility, differential epigenetic marks (H3K27ac, H3K4me1, H3K4me3), prominent transcription factor binding patterns (STAT1 and PU.1), and active transcription. These genes were also enriched for lipid metabolism and atherosclerosis-related pathways. We then validated our findings by tracing the expression of these genes in human atherosclerotic lesions and in ApoE-/- and LDLr-/-mouse models, revealing significant correlations with LDL cholesterol and diseased vessel traits. Single-cell RNA-seq of human and mouse atherosclerotic samples showed dynamic changes in macrophage subtypes, with foamy and tissue-resident macrophages displaying increased STAT1 activity. This comprehensive multi-omics approach provides new insights into the transcriptional regulation of atherosclerosis progression mediated by STAT1-PU.1 co-binding and IFNγ signaling. Moreover, our data delineates a STAT1-dependent gene signature, highlighting the potential of these integrative genes as biomarkers and therapeutic targets in atherosclerosis.
ER stress relief drives ß-cell proliferation
Authors: Bourgeois Stephanie , Van Mulders Annelore , Heremans Yves , Leuckx Gunter , Willems Lien , Coenen Sophie , Degroote Laure , Pierreux Julie , Kancheva Daliya , Scheyltjens Isabelle , Movahedi Kiavash , Carlotti Françoise , de Koning Eelco , Yi Xiaoyan , Vinci Chiara , Tong Yue , Cnop Miriam , Heimberg Harry , Leu Nico De , Staels Willem 
Published: September 2024

AbstractRegenerating endogenous pancreatic ß-cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote ß-cell regeneration. We aimed to investigate whether recovery from experimental hypovascularization of the endocrine pancreas, achieved by modulating the transgenic production of a VEGF-A blocker in ß-cells, could trigger mouse ß-cell proliferation. Serendipitously, we found that transgene overexpression in ß-cells induces endoplasmic reticulum (ER) stress and that subsequent relief from this stress stimulates ß-cell proliferation independent of vessel recovery. TransientGFPoverexpressionin vivoand chemical induction of ER stressin vitroreplicated this ß-cell cycling response. Our findings highlight the potential side effects of ER stress due to transgene overexpression in ß-cells and assert that ER stress relief serves as a potent regenerative stimulus.
Uukuniemi virus infection causes a pervasive remodelling of the RNA-binding proteome in tick cells
Authors: Wilson Alexandra , Kamel Wael , Davies Kelsey , De Laurent Zaydah R. , Arif Rozeena , Bell-Sakyi Lesley , Lamont Douglas , Demyanenko Yana , Noerenberg Marko , Kohl Alain , Mohammed Shabaz , Castello Alfredo , Brennan Benjamin 
Published: September 2024

AbstractCellular RNA-binding proteins (RBPs) are pivotal for the viral lifecycle, mediating key host-virus interactions that promote or repress virus infection. While these interactions have been largely studied in the vertebrate host, no comprehensive analyses of protein-RNA interactions occurring in cells of arbovirus vectors, in particular ticks, have been performed to date. Here we systematically identified the responses of the RNA-binding proteome (RBPome) to infection with a prototype bunyavirus (Uukuniemi virus; UUKV) in tick cells and discovered changes in RNA-binding activity for 283 proteins. In an orthogonal approach, we analysed the composition of the viral ribonucleoprotein by immunoprecipitation of UUKV nucleocapsid protein (N) in infected cells. We found many tick RBPs that are regulated by UUKV infection and associate with viral nucleocapsid protein complexes. We confirmed experimentally that these RBPs impact UUKV infection. This includes the tick homolog of topoisomerase 3B (TOP3B), a protein able to manipulate the topology of RNA, which showed an effect on viral particle production. Our data thus reveals the first protein-RNA interaction map for infected tick cells.Research highlightsUUKV RNAs interact with nearly three hundred tick cell RBPs.Demonstrated an enrichment of N protein interactors within the upregulated RIC data suggesting a direct involvement in viral RNA metabolism and translation.Developed a robust methodology to silence gene expression in tick cell cultures.The TOP3B complex facilitates efficient packaging of UUKV virions.