bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep-Disordered Breathing Profiles in Patients with Cardiovascular Diseases: Kurume SDB-CVD Study
Authors: Shimozono Koutatsu , Adachi Hisashi , Nohara Shoichiro , Shibata Tatsuhiro , Sugiyama Yoichi , Ioji Tetsuya , Fukumoto Yoshihiro 
Published: June 2024

AbstractBackgroundWhile evidence links sleep-disordered breathing (SDB) to various cardiovascular diseases (CVDs), comprehensive insights and detailed profiles of CVD patients with SDB remain scarce. This study aimed to examine the characteristics of CVD patients complicated by SDB.MethodsThis retrospective study enrolled all consecutive patients who underwent screening tests for SDB during hospitalization at Kurume University Hospital from January 2014 to December 2019. To explore the relationship between SDB severity and clinical data, we classified SDB severity into four groups and assessed its prevalence and severity across different CVDs, categorized by sex and age.ResultsA total of 5,765 patients were enrolled. Desaturation during sleep in SDB was significantly worse in terms of age, sex, daytime resting oxygen saturation (SpO2), systolic blood pressure (SBP), pulse pressure, body mass index (BMI), white blood cell count, hemoglobin A1c, serum creatinine, N-terminal Pro-B-type natriuretic peptide (NT-proBNP), cardiothoracic ratio on chest X-ray, and left ventricular ejection fraction (LVEF) on echocardiography (all p-values < 0.001, except for SBP p=0.002, and NT-proBNP p=0.004). Daytime SpO2and BMI strongly correlated across ages. Differences in renal function, diabetes control, and LVEF were notable between sex and ages. Analysis also showed the more prevalence and severity of SDB in coronary artery disease and heart failure, versus lower in pulmonary hypertension. Heatmaps of daytime SpO2 and BMI can effectively predict the severe SDB in patients with CVDs, suggesting the potential for efficient therapeutic interventions for SDB.ConclusionCoronary artery disease and heart failure were associated with a higher prevalence and a greater risk of moderate to severe SDB, typically in older patients. Notably, low SpO2during daytime and elevated BMI were indicative of SDB across all age categories for both sexes.
Convergent Acquisition of Glucomannan β-galactosyltransferases in Asterids and Rosids
Authors: Ishida Konan , Penner Matthew , Fukushima Kenji , Yoshimi Yoshihisa , Wilson Louis F.L. , Echevarría-Poza Alberto , Yu Li , Dupree Paul 
Published: June 2024

Abstractβ-Galactoglucomannan (β-GGM) is a primary cell wall polysaccharide in rosids and asterids. The β-GGM polymer has a backbone of repeating glucose and mannose, usually with mono- or di-galactosyl sidechains on the mannosyl residues. CELLULOSE SYNTHASE-LIKE 2 (CSLA2), MANNAN α-GALACTOSYLTRANSFERASE (MAGT), and MANNAN β-GALACTOSYLTRANSFERASE (MBGT) are required for β-GGM synthesis inArabidopsis thaliana. The single MBGT identified so far,AtMBGT1, lies in glycosyltransferase family 47A subclade VII, and was identified in Arabidopsis. However, despite the presence of β-GGM, an orthologous gene is absent in tomato (Solanum lycopersicum), a model asterid. In this study, we screened candidateMBGTgenes from the tomato genome, functionally tested the activities of encoded proteins, and identified the tomato MBGT (SlMBGT1) in GT47A-III. Interestingly therefore,AtMBGT1 andSlMBGT1 are located in different GT47A subclades. Further, phylogenetic and glucomannan structural analysis from different species raised the possibility that various asterids possess conserved MBGTs in GT47A-III, indicating that MBGT activity has been acquired convergently among asterids and rosids. Although functional convergence was observed, the acquired amino acid substitutions among the two MBGT groups were not shared, suggesting different evolutionary pathways to achieve the same biochemical outcome. The present study highlights the promiscuous emergence of donor and acceptor preference in GT47A enzymes, and suggests an adaptive advantage for eudicots to acquire β-GGM β-galactosylation.
Prenatal Exposure to the Genocide against the Tutsi in Rwanda is associated with DNA methylation at candidate genes in early adulthood: the role of trauma severity and postnatal adversity
Authors: Rivera Luisa Maria , Uwizeye Glorieuse , Stolrow Hannah , Christensen Brock , Rutherford Julienne , Thayer Zaneta 
Published: June 2024

AbstractWe investigated associations between prenatal genocidal trauma, including maternal rape, and postnatal adverse childhood experiences (ACEs) on DNA methylation of genes associated with the stress response. In a comparative cross-sectional study of 91 Rwandan young adults, categorized by prenatal exposure to genocide and maternal rape, genocide without rape, and unexposed controls, we analyzed DNA methylation from dried blood spots and assessed ACEs and mental health at age 24. Prenatal exposure to maternal rape was associated with DNA methylation changes inBDNFandSLC6A4, with the association inBDNFattenuated by ACEs exposure. Genocide exposure without rape was associated with methylation changes inPRDM8after adjusting for early adversity. Methylation inBDNFandSLC6A4correlated with mental health scores. These findings underscore the impact of prenatal and postnatal trauma on DNA methylation and mental health, emphasizing the need for continued support for survivors in the decades after conflict.
Evaluation of a flow cytometry-based surrogate assay (FlowSA) for the detection of SARS-CoV-2 in clinical samples
Authors: Upasani Vinit , Knoester Marjolein , Pantano Daniele , Gard Lili , Smit Jolanda M. , van der Gun Bernardina T.F. , Tami Adriana , Rodenhuis-Zybert Izabela A. 
Published: June 2024

AbstractThe current diagnostic methods for SARS-CoV-2 rely on quantitative RT-PCR. However, the presence of viral RNA in samples does not necessarily reflect the presence of an infectious virus. Therefore, the reliable detection of infectious SARS-CoV-2 in clinical samples is necessary to limit viral transmission. Here, we developed a flow cytometry-based surrogate assay (FlowSA), wherein the presence of infectious SARS-CoV-2 was detected using virus nucleocapsid-specific antibodies. We showed that FlowSA allows the detection of a wide range of viral titers of multiple SARS-CoV-2 variants. Furthermore, the assay was successfully used to detect infectious SARS-CoV-2 in nasopharyngeal swabs from SARS-CoV-2 positive individuals, including those with high Ct values. Notably, FlowSA identified the presence of infectious SARS-CoV-2 in biological specimens that scored negative for cytopathic effect (CPE) in cell culture and would otherwise be considered negative. We propose that FlowSA can be adopted as an alternative to conventional CPE methods for viral diagnostics.
Suspected Adverse Drug Reactions Associated with Leukotriene Receptor Antagonists Versus First Line Asthma Medications: A National Registry-Pharmacology Approach
Authors: Khan Mohammed , Hirsch Christine , Jones Alan M. 
Published: June 2024

AbstractAimsTo determine the suspected adverse drug reaction (ADR) profile of leukotriene receptor antagonists (LTRAs: montelukast and zafirlukast) relative to first-line asthma medications short-acting beta agonists (SABA: salbutamol) and inhaled corticosteroid (ICH: beclomethasone) in the United Kingdom. To determine chemical and pharmacological rationale for the suspected ADR signals.MethodsProperties of the asthma medications (pharmacokinetics and pharmacology) were datamined from the chemical database of bioactive molecules with drug-like properties, European molecular Biology laboratory (ChEMBL). Suspected ADR profiles of the asthma medications was curated from the Medicines and Healthcare products Regulatory Authority (MHRA) Yellow Card interactive drug analysis profiles (iDAP) and concatenated to the standardised prescribing levels (Open Prescribing) between 2018-2023.ResultsTotal ADRs per 100,000Rx(P< .001) and psychiatric system organ class (SOC) ADRs (P< .001) reached statistical significance. Montelukast exhibited the greatest ADR rate at 15.64 per 100,000Rx. The low lipophilic ligand efficiency (LLE = 0.15) of montelukast relative to the controls may explain the promiscuity of interactions with off-target G-coupled protein receptors (GPCRs). This included the dopamine signalling axis, which in combination with bioaccumulation in the cerebrospinal fluid (CSF) to achieve Cmaxbeyond a typical dose can be ascribed to the psychiatric side effects observed. Cardiac ADRs did not reach statistical significance but inhibitory interaction of montelukast with the MAP kinase p38 alpha (a cardiac protective pathway) was identified as a potential rationale for montelukast withdrawal cardiac effects.ConclusionRelative to the controls, montelukast displays a range of suspected system organ class level ADRs. For psychiatric ADR, montelukast is statistically significant (P< .001). A mechanistic hypothesis is proposed based on polypharmacological interactions in combination with CSF levels attained. This work further supports the close monitoring of montelukast for neuropsychiatric side effects.
The GenoPred Pipeline: A Comprehensive and Scalable Pipeline for Polygenic Scoring
Authors: Pain Oliver , Al-Chalabi Ammar , Lewis Cathryn M. 
Published: June 2024

AbstractMotivationPolygenic scoring is a commonly used approach for estimating an individual’s likelihood of a given outcome. Polygenic scores are typically calculated using genetic effects derived from genome-wide association study (GWAS) summary statistics and individual-level genotype data for the target sample. Using a reference-standardised framework ensures the polygenic score can be reliably interpreted. Going from genotype to interpretable polygenic scores involves many steps and there are many methods available, limiting the accessibility of polygenic scores for research and clinical application. Additional challenges exist for studies in ancestrally diverse populations. We have implemented the leading polygenic scoring methodologies within an easy-to-use pipeline called GenoPred.ResultsHere we present the GenoPred pipeline, an easy-to-use, high-performance, reference-standardised and reproducible workflow for polygenic scoring. The pipeline requires just a few readily available inputs to get started, with configuration options available to cater for a range of use-cases. GenoPred implements a comprehensive set of analyses, including genotype and GWAS quality control, target sample ancestry inference, polygenic score file generation using a range of leading methods, and target sample scoring. GenoPred standardises the polygenic scoring process using reference genetic data, providing interpretable polygenic scores, and improving the transferability of results to external datasets. The pipeline is applicable to GWAS and target data from any population within the reference, facilitating studies of diverse ancestry. GenoPred is a Snakemake pipeline with associated Conda software environments, ensuring reproducibility. We apply the pipeline to UK Biobank data demonstrating the pipeline’s simplicity, efficiency, and performance. GenoPred is open-source software, that will continue to develop as polygenic scoring methodology develops.ConclusionsThe GenoPred pipeline provides a novel resource for polygenic scoring, integrating a range of complex processes within an easy-to-use framework. GenoPred widens access of the leading polygenic scoring methodology and their application to studies of diverse ancestry.
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication
Authors: Sanchez-Londono Mariana , Rust Selina , Hernández-Tamayo Rogelio , Gomes-Filho José Vicente , Thanbichler Martin , Randau Lennart 
Published: June 2024

ABSTRACTType IV CRISPR-Cas effector complexes are often encoded on plasmids and are proposed to prevent the replication of competing plasmids. The Type IV-A1 CRISPR-Cas system ofPseudomonas oleovoransadditionally harbors a CRISPR RNA (crRNA) that tightly regulates the transcript levels of a chromosomal target and represents a natural CRISPR interference (CRISPRi) tool. This study investigates CRISPRi effects of this system using synthetic crRNAs against genome and plasmid sequences. Targeting of reporter genes revealed extended interference inP. oleovoransandEscherichia colicells producing recombinant CRISPR ribonucleoprotein (crRNP) complexes. RNA-Seq analyses of Type IV-A1 CRISPRi-induced transcriptome alterations demonstrated highly effective long-range down-regulation of histidine operon expression, whereas CRISPRi effects of dCas9 remained limited to the vicinity of its binding site. Single-molecule microscopy uncovered the localization dynamics of crRNP complexes. The tracks of fluorescently labeled crRNPs co-localized with regions of increased plasmid replication, supporting efficient plasmid targeting. These results identify mechanistic principles that facilitate the application of Type IV-A1 CRISPRi for the regulation of gene expression and plasmid replication.
In-host evolution ofYersinia enterocoliticaduring a chronic human infection
Authors: Cyril Savin , Pierre Lê-Bury , Julien Guglielmini , Thibaut Douché , Rodolphe Buzelé , Cécile Le Brun , Frédéric Bastides , Maud François , Béatrice Birmelé , Laura Guichard , Nicolas Cabanel , Laurent Dortet , Mariette Matondo , Olivier Dussurget , Elisabeth Carniel , Philippe Lanotte , Javier Pizarro-Cerdá 
Published: June 2024

AbstractFollowing a pacemaker implantation, a 75-years-old patient suffered from five successive bacteremia episodes between in 1999 and 2013 despite long-term antibiotic treatment, with intermittent vegetation apparition on the device atrial lead. Four blood isolates, identified asYersinia enterocoliticabioserotype 4/O:3, were further genetically and phenotypically characterized. Phylogenetic reconstruction showed that the patient was chronically infected by the same strain, which evolved within the host for 14 years. Single-nucleotide polymorphism (SNP) analysis indicates that the last two isolates evolved in parallel and formed two independent lineages within the host. Pan-genome analysis and genome comparison showed that their common evolution was characterized by 41 small insertion/deletion events, loss of three large DNA fragments and mutations in 140 genes. A phylogenetic analysis by maximum likelihood identified two genes presenting a positive selection signal, suggesting that these mutations provided a survival advantage to bacteria during chronic infection. Quinolone resistance in the last two isolates was acquired through a so far undescribed deletion in thegyrAgene.Mass-spectrometry analysis revealed a strong proteome remodeling in the last two isolates which was correlated with a truncation in the stringent response regulator DksA. A reduced carbon, energy and purine metabolism supports their severe growth defectsin vitro. 3rd-generation cephalosporin resistance of the last isolate was correlated with a truncation of OmpF, the main porin translocating antibiotics through the outer-membrane, as well as an increased production of BlaA and AmpC β-lactamases.This is the first report of genetic and phenotypic changes associated to within-host adaptation of a pathogenicYersiniaspecies under antibiotic pressure.
Activation of NF-κB signaling by optogenetic clustering of IKKα and β
Authors: Fischer Alexandra A.M. , Grimm Merlin M. , Fliegauf Manfred , Grimbacher Bodo , Rahmann Sven , Weber Wilfried 
Published: June 2024

AbstractA large percentage of proteins form higher-order structures in order to fulfill their function. These structures are crucial for the precise spatial and temporal regulation of the cellular signaling network. Investigation of this network requires sophisticated research tools, such as optogenetic tools, that allow dynamic control over the signaling molecules. Cryptochrome 2 and its variations are the best-characterized oligomerizing photoreceptors the optogenetics toolbox has to offer. Therefore, we utilized this switch and combined it with an eGFP-binding nanobody, to build a toolbox of optogenetic constructs that enables the oligomerization of any eGFP-tagged protein of interest. We further introduced the higher clustering variant Cry2oligand an intrinsically disordered region to create higher-order oligomers or phase-separated assemblies to investigate the impact of different oligomerization states on eGFP-tagged signaling molecules. We apply these constructs to cluster IKKα and IKKβ, which resemble the central signaling integrator of the NF-κB pathway, thereby engineer a potent, blue-light-inducible activator of NF-κB signaling.
Ankyrin-B is required for the establishment and maintenance of lens cytoarchitecture, mechanics, and clarity
Authors: Maddala Rupalatha , Allen Ariana , Skiba Nikolai P. , Rao Ponugoti Vasantha 
Published: June 2024

ABSTRACTSummary StatementThis study illustrates a vital role for ankyrin-B in lens architecture, growth and function through its involvement in membrane protein and spectrin-actin cytoskeletal organization and stabilityThe transparent ocular lens is essential for vision by focusing light onto the retina. Despite recognizing the importance of its unique cellular architecture and mechanical properties, the molecular mechanisms governing these attributes remain elusive. This study aims to elucidate the role of ankyrin-B (AnkB), a membrane scaffolding protein, in lens cytoarchitecture, growth and function using a conditional knockout (cKO) mouse model. AnkB cKO mouse has no defects in lens morphogenesis, but exhibited changes that supported a global role for AnkB in maintenance of lens clarity, size, cytoarchitecture, and stiffness. Notably, absence of AnkB led to nuclear cataract formation, evident from P16. AnkB cKO lens fibers exhibit progressive disruption in membrane organization of the spectrin-actin cytoskeleton, channel proteins, cell-cell adhesion, shape change, loss and degradation of several membrane proteins (e.g., NrCAM. N-cadherin and aquaporin-0) along with a disorganized plasma membrane and impaired ball-and-socket membrane interdigitations. Furthermore, absence of AnkB led to decreased lens stiffness. Collectively, these results illustrate the essential role for AnkB in lens architecture, growth and function through its involvement in membrane protein and cytoskeletal organization.
Development of inducible promoter and CRISPRi plasmids functional inRickettsia rickettsii
Authors: Nock Adam M. , Clark Tina R. , Hackstadt Ted 
Published: June 2024

ABSTRACTRickettsia rickettsiiis an obligate intracellular, tick-borne bacterium that causes Rocky Mountain spotted fever. The demanding nature of cultivating these bacteria within host cells and the labor involved in obtaining clonal isolates has severely limited progress regarding the development of compatible genetic tools to study this pathogen. Conditional expression of genes which might be toxic or have an otherwise undesirable effect is the next logical goal to expand upon the constitutive expression plasmids generated thus far. We describe the construction of an inducible promoter system based on the tet-On system, leveraging design elements from the anhydrotetracycline inducible promoter system used forBorrelia burgdorferiand one of the few characterized rickettsial promoters for the outer membrane gene,rompB(sca5). The functionality of this promoter is demonstrated via fluorescence of induced mScarlet production and was then used to construct a generalized inducible expression vector forR. rickettsii. The development of a functional inducible promoter was then applied to the construction of a CRISPR interference plasmid as a means to reduce or essentially silence the transcription of targeted genes. We demonstrate the viability of a simplified, single vector CRISPRi system to disrupt gene expression inR. rickettsiitargeting the type IV secreted effectorrarP2and autotransporter peptidaserapLas examples.IMPORTANCEThis work expands upon the genetic toolbox available forR. rickettsii. This is the first report of both an inducible promoter and CRISPRi system compatible withRickettsia, which may provide key instruments for the development of further tools. The development of an inducible promoter system allows for the overexpression of genes which might be toxic when expressed constitutively. The CRISPRi system enables the ability to knockdown genes with specificity, and critically, genes which may be essential and could not otherwise be knocked out. These developments may provide the foundation for unlocking genetic tools for other pathogens of the order Rickettsiales, such as theAnaplasma,Orientia, andEhrlichiafor which there are currently no inducible promoters or CRISPRi platforms.
DNA Nicks Drive Massive Expansions of (GAA)nRepeats
Authors: Li Liangzi , Scott W. Shem , Khristich Alexandra N. , Armenia Jillian F. , Mirkin Sergei M. 
Published: June 2024

AbstractOver 50 hereditary degenerative disorders are caused by expansions of short tandem DNA repeats (STRs). (GAA)nrepeat expansions are responsible for Friedreich’s ataxia as well as late-onset cerebellar ataxias (LOCAs). Thus, the mechanisms of (GAA)nrepeat expansions attract broad scientific attention. To investigate the role of DNA nicks in this process, we utilized a CRISPR-Cas9 nickase system to introduce targeted nicks adjacent to the (GAA)nrepeat tract. We found that DNA nicks 5’ of the (GAA)100run led to a dramatic increase in both the rate and scale of its expansion in dividing cells. Strikingly, they also promoted large-scale expansions of carrier- and large normal-size (GAA)nrepeats, recreating, for the first time in a model system, the expansion events that occur in human pedigrees. DNA nicks 3’ of the (GAA)100repeat led to a smaller but significant increase in the expansion rate as well. Our genetic analysis implies that in dividing cells, conversion of nicks into double-strand breaks (DSBs) during DNA replication followed by DSB or fork repair leads to repeat expansions. Finally, we showed that 5’ strand nicks increase expansion frequency in non-dividing yeast cells, albeit to a lesser extent that in dividing cells.
Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors ofChikungunyansP2 Cysteine Protease with Anti-alphavirus Activity
Authors: Ghoshal Anirban , Asressu Kesatebrhan Haile , Hossain Mohammad Anwar , Brown Peter J. , Merten Eric M. , Sears John D. , Perveen Sumera , Pearce Kenneth H. , Popov Konstantin I. , Moorman Nathaniel J. , Heise Mark T. , Willson Timothy M. 
Published: June 2024

AbstractDespite their widespread impact on human health there are no approved drugs for combating alphavirus infections. The heterocyclic β-aminomethyl vinyl sulfone RA-0002034 (1a) is a potent irreversible covalent inhibitor of the alphavirus nsP2 cysteine protease with broad spectrum antiviral activity. Analogs of1athat varied each of three regions of the molecule were synthesized to establish structure-activity relationships for inhibition ofChikungunya(CHIKV) nsP2 protease and viral replication. The covalent warhead was highly sensitive to modifications of the sulfone or vinyl substituents. However, numerous alterations to the core 5-membered heterocycle and its aryl substituent were well tolerated and several analogs were identified that enhanced CHIKV nsP2 binding. For example, the 4-cyanopyrazole analog8dexhibited akinact/Kiratio >10,000 M-1s-1. 3-Arylisoxazole was identified an isosteric replacement for the 5-membered heterocycle, which circumvented the intramolecular cyclization that complicated the synthesis of pyrazole-based inhibitors like1a. The accumulated structure-activity data was used to build a ligand-based model of the enzyme active site, which can be used to guide the design of covalent nsP2 protease inhibitors as potential therapeutics against alphaviruses.