bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation
Authors: Dommann Julian , Keiser Jennifer , Garneau Julian , Gandelin Alison , Casanova Carlo , Keller Peter M. , Sayasone Somphou , Vonaesch Pascale , Schneeberger Pierre H. H. 
Published: January 2024

AbstractDue to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challengingin vitroresulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.
Characterization of a novel humanized heavy chain antibody targeting endogenous retroviruses with anti-lymphoma activity
Authors: Spriano Filippo , Cascione Luciano , Sgrignani Jacopo , Bendik Nikolai , Napoli Sara , Sartori Giulio , Cannas Eleonora , Gong Tao , Arribas Alberto J. , Pizzi Marco , Rossi Davide , Robbiani Davide F. , Cavalli Andrea , Bertoni Francesco 
Published: January 2024

AbstractLymphomas continue to pose therapeutic challenges, with a considerable portion of patients facing refractory disease. This study focuses on Diffuse Large B-cell Lymphoma (DLBCL), the most prevalent lymphoma type. Within the human genome, transposable elements (TEs), particularly Human Endogenous Retroviruses (HERVs), constitute a significant yet understudied portion. Among HERVs, the HERV-K family, specifically HERV-K113 and HERV-K115, has intact open reading frames. Epigenetic regulation tightly controls HERV expression, and aberrant expression has been observed in various cancers, including lymphomas.This research investigates the potential of HERV-K as a therapeutic target in DLBCL. The study encompasses comprehensive methods, including RNA extraction, PCR detection, flow cytometry, immunoblotting, peptide prediction, phage display, surface plasmon resonance, ELISA, antibody-dependent cell-mediated cytotoxicity, internalization assays, and bioinformatic analysis. Results reveal the presence and expression of HERVs in lymphoma patients and cell lines, with the HERV-K envelope protein identified as a crucial contributor to lymphoma cell growth. Moreover, the study identifies immunogenic regions of HERV-K, leading to the development of a humanized camelid nanobody (FF-01) with potential therapeutic applications. Furthermore, bioinformatic analysis differentiates DLBCL subgroups based on TE expression, providing insights into prognostic variations. Patients with high HERV-K113 expression show activation of pathways related to antiviral responses, suggesting a viral mimicry state.In conclusion, the study highlights the clinical relevance of HERVs in lymphomas, proposing them as novel therapeutic targets. The newly developed nanobody FF-01 demonstrates anti-lymphoma activity through antibody-dependent cellular cytotoxicity and internalization. This research opens avenues for exploring endogenous retroviruses as targets for immunotherapy in lymphomas, showcasing the potential of FF-01 as a promising candidate for further investigation.
A Bacteriophage Cocktail TargetingYersinia pestisProvides Strong Post-Exposure Protection in a Rat Pneumonic Plague Model
Authors: Kilgore Paul B. , Sha Jian , Hendrix Emily K. , Neil Blake H. , Lawrence William S. , Peel Jennifer E. , Hittle Lauren , Woolston Joelle , Sulakvelidze Alexander , Schwartz Jennifer A. , Chopra Ashok K. 
Published: January 2024

ABSTRACTYersinia pestis, one of the deadliest bacterial pathogens ever known, is responsible for three plague pandemics and several epidemics, with over 200 million deaths during recorded history. Due to high genomic plasticity,Y. pestisis amenable to genetic mutations as well as genetic engineering that can lead to the emergence or intentional development of pan-drug resistant strains. The dissemination of suchY. pestisstrains could be catastrophic, with public health consequences far more daunting than those caused by the recent COVID-19 pandemic. Thus, there is an urgent need to develop novel, safe, and effective treatment approaches for managingY. pestisinfections. This includes infections by antigenically distinct strains for which vaccines, none FDA approved yet, may not be effective, and those that cannot be controlled by approved antibiotics. Lytic bacteriophages provide one such alternative approach. In this study, we examined post-exposure efficacy of a bacteriophage cocktail, YPP-401, to combat pneumonic plague caused byY. pestisCO92. YPP-401 is a four-phage preparation with a 100% lytic activity against a panel of 68 genetically diverseY. pestisstrains. Using a pneumonic plague aerosol challenge model in gender-balanced Brown Norway rats, YPP-401 demonstrated ∼88% protection when delivered 18 hours post-exposure for each of two administration routes (i.e., intraperitoneal and intranasal) in a dose-dependent manner. Our studies suggest that YPP-401 could provide an innovative, safe, and effective approach for managingY. pestisinfections, including those caused by naturally occurring or intentionally developed strains that cannot be managed by vaccines in development and antibiotics.
Multiple Pathways Impact Swarming Motility ofPseudomonas fluorescensPf0-1
Authors: Pastora Alexander B. , Rzasa Kara M. , O’Toole George A. 
Published: January 2024

AbstractSwarming motility in pseudomonads typically requires both a functional flagellum and production/secretion of a biosurfactant. Published work has shown that the wild-typePseudomonas fluorescensPf0-1 is swarming-deficient due to a point mutation in thegacAgene, which until recently, was thought to inactivate rather than attenuate the Gac/Rsm pathway. As a result, little is known about the underlying mechanisms that regulate swarming motility byP. fluorescensPf0-1. Here, we demonstrate that a ΔrsmAΔrsmEΔrsmImutant, which phenotypically mimics Gac/Rsm pathway overstimulation, is proficient at swarming motility. RsmA and RsmE appear to play a key role in this regulation. Transposon mutagenesis of the ΔrsmAΔrsmEΔrsmImutant identified multiple factors that impact swarming motility, including pathways involved in flagellar synthesis and biosurfactant production/secretion. We find that loss of genes linked to biosurfactant Gacamide A biosynthesis or secretion impact swarming motility, as does loss of the alternative sigma factor FliA, which results in a defect in flagellar function. Collectively, these findings provide evidence thatP. fluorescensPf0-1 can swarm if the Gac/Rsm pathway is activated, highlight the regulatory complexity of swarming motility in this strain, and demonstrate that the cyclic lipopeptide Gacamide A is utilized as a biosurfactant for swarming motility.ImportanceSwarming motility is a coordinated process that allows communities of bacteria to collectively move across a surface. ForP. fluorescensPf0-1, this phenotype is notably absent in the parental strain and to date little is known about the regulation of swarming in this strain. Here, we identify RsmA and RsmE as key repressors of swarming motility via modulating the levels of biosurfactant production/secretion. Via transposon mutagenesis and subsequent genetic analyses, we further identify potential regulatory mechanisms of swarming motility and link Gacamide A biosynthesis and transport machinery to swarming motility.
TheBacillus subtiliscell envelope stress-inducibleytpABoperon modulates membrane properties and contributes to bacitracin resistance
Authors: Willdigg Jessica R. , Patel Yesha , Arquilevich Briana E. , Subramanian Chitra , Frank Matthew W. , Rock Charles O. , Helmann John D. 
Published: January 2024

AbstractAntibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σMresponds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependentytpABoperon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35terpenoids. Using targeted lipidomics we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless,ytpAwas critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression ofytpAincreased membrane fluidity as monitored by fluorescence anisotropy. TheytpAgene contributes to bacitracin resistance in mutants additionally lacking thebceABorbcrCgenes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of theytpABoperon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl-phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes proteins involved in cell wall homeostasis.ImportancePeptidoglycan synthesis inhibitors include some of our most important antibiotics. InBacillus subtilis, peptidoglycan synthesis inhibitors induce the σMregulon, which is critical for intrinsic antibiotic resistance. The σM-dependentytpABoperon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Further, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the UPP lipid carrier that sustains peptidoglycan synthesis.
Neisseria gonorrhoeaescavenges host sialic acid for Siglec-mediated, complement-independent suppression of neutrophil activation
Authors: Cardenas Amaris J , Thomas Keena S. , Broden Mary W. , Ferraro Noel J. , John Constance M. , Pires Marcos M. , Jarvis Gary A. , Criss Alison K. 
Published: January 2024

ABSTRACTGonorrhea, caused by the bacteriumNeisseria gonorrhoeae(Gc), is characterized by neutrophil influx to infection sites. Gc has developed mechanisms to resist killing by neutrophils that include modifications to its surface lipooligosaccharide (LOS). One such LOS modification is sialylation: Gc sialylates its terminal LOS sugars with cytidine-5’-monophosphate-N-acetylneuraminic acid (CMP-NANA) scavenged from the host using LOS sialyltransferase (Lst), since Gc cannot make its own sialic acid. Sialylation enables sensitive strains of Gc to resist complement-mediated killing in a serum-dependent manner. However, little is known about the contribution of sialylation to complement-independent, direct Gc-neutrophil interactions. In the absence of complement, we found sialylated Gc expressing opacity-associated (Opa) proteins decreased the oxidative burst and granule exocytosis from primary human neutrophils. In addition, sialylated Opa+ Gc survived better than vehicle treated or ΔlstGc when challenged with neutrophils. However, Gc sialylation did not significantly affect Opa-dependent association with or internalization of Gc by neutrophils. Previous studies have implicated sialic acid-binding immunoglobulin-type lectins (Siglecs) in modulating neutrophil interactions with sialylated Gc. Blocking neutrophil Siglecs with antibodies that bind to their extracellular domains eliminated the ability of sialylated Opa+ Gc to suppress oxidative burst and resist neutrophil killing. These findings highlight a new role for sialylation in Gc evasion of human innate immunity, with implications for the development of vaccines and therapeutics for gonorrhea.IMPORTANCENeisseria gonorrhoeae,the bacterium that causes gonorrhea, is an urgent global health concern due to increasing infection rates, widespread antibiotic resistance, and its ability to thwart protective immune responses. The mechanisms by which Gc subvert protective immune responses remain poorly characterized. One wayN. gonorrhoeaeevades human immunity is by adding sialic acid that is scavenged from the host onto its lipooligosaccharide, using the sialyltransferase Lst. Here, we found that sialylation enhancesN. gonorrhoeaesurvival from neutrophil assault and inhibits neutrophil activation, independently of the complement system. Our results implicate bacterial binding of sialic acid-binding lectins (Siglecs) on the neutrophil surface, which dampen neutrophil antimicrobial responses. This work identifies a new role for sialylation in protectingN. gonorrhoeaefrom cellular innate immunity, which can be targeted to enhance the human immune response in gonorrhea.
Neutralizing gut-derived lipopolysaccharide as a novel therapeutic strategy for severe leptospirosis
Authors: Xie Xufeng , Chen Xi , Zhang Shilei , Liu Jiuxi , Zhang Wenlong , Cao Yongguo 
Published: January 2024

AbstractLeptospirosis is an emerging infectious disease caused by pathogenicLeptospiraspp. Humans and some mammals can develop severe forms of leptospirosis accompanied by a dysregulated inflammatory response, which often results in death. The gut microbiota has been increasingly recognized as a vital element in systemic health. However, the precise role of the gut microbiota in severe leptospirosis is still unknown. Here, we aimed to explore the function and potential mechanisms of the gut microbiota in a hamster model of severe leptospirosis. Our study showed that leptospires were able to multiply in the intestine, cause pathological injury, and induce intestinal and systemic inflammatory responses. 16S rRNA gene sequencing analysis revealed thatLeptospirainfection changed the composition of the gut microbiota of hamsters with an expansion of Proteobacteria. In addition, gut barrier permeability was increased after infection, as reflected by a decrease in the expression of tight junctions. Translocated Proteobacteria were found in the intestinal epithelium of moribund hamsters, as determined by fluorescence in situ hybridization, with elevated LPS levels in the serum. Moreover, gut microbiota depletion reduced the survival time, increased the leptospiral load, and promoted the expression of proinflammatory cytokines afterLeptospirainfection. Intriguingly, fecal filtration and serum from moribund hamsters both increased the transcription ofTNF-α,IL-1β,IL-10, andTLR4in macrophages compared with those from uninfected hamsters. These stimulating activities were inhibited by LPS neutralization using polymyxin B. Based on our findings, we identified an LPS neutralization therapy that significantly improved the survival rates in severe leptospirosis when used in combination with antibiotic therapy or polyclonal antibody therapy. In conclusion, our study not only uncovers the role of the gut microbiota in severe leptospirosis but also provides a therapeutic strategy for severe leptospirosis.
Analysis of dietary vitamin C intake levels and the risk of hyperuricemia and gout based on cross-sectional studies and bi-directional Mendelian randomisation
Authors: Peng Zi-Ning , Wang Xing-Qiang , Deng Qian , Yan Wei-Tian , Zhao Wei-Qing , Pu Yong-Bin , Liu Nian , Gu Ling-Li , Peng Jiang-Yun 
Published: January 2024

AbstractBackgroundVitamin C, a common antioxidant, may be useful for treating hyperuricemia and gout. The aim of this study was to investigate the risk association between dietary vitamin C intake and hyperuricemia/gout and to test for causality using the bi-directional Mendelian randomisation method.MethodsCross-sectional studies were selected from the National Health and Nutrition Examination Survey from 2007–2018 to assess the association between dietary vitamin C intake and the risk of hyperuricemia/gout, according to multivariate logistic regression modelling. Bi-directional Mendelian randomisation studies were conducted using genetic data from large-scale genome-wide association surveys of supplemental vitamin C, pharmacological vitamin C, and ascorbic acid intake and hyperuricemia/gout; these aimed to infer causal relationships between vitamin C and hyperuricemia/gout. Inverse variance weighting was used as the primary method of Mendelian randomisation analysis. A series of sensitivity analyses were used to assess multiplicity.ResultsThe cross-sectional study included 17.52% and 82.48% patients with and without hyperuricemia, respectively, as well as 2.67% and 97.33% patients with and without gout, respectively. In the model correcting for all covariates, the association between vitamin C intake and the risk of hyperuricemia/gout was stable, and the risk of hyperuricemia was generally lower in patients who consumed >111.75 mg vitamin C than in other patients when comparing three models with different moderators. Restricted cubic spline scores indicated that vitamin C intake recommendations of 75–525 mg and 75–225 mg were effective for targeting hyperuricemia and gout, respectively. In inverse variance weighting in the Mendelian randomisation analysis, the amount of vitamin C absorbed was negatively associated with hyperuricemia (OR = 0.985, 95% CI = 0.973–0.997, p = 0.015), and supplemental vitamin C was negatively associated with gout (OR = 0.857, 95% CI = 0.797–0.921, p < 0.001); sensitivity analysis yielded consistent results. Reverse Mendelian randomisation analysis showed that vitamin C had no reverse causal relationship with hyperuricemia and gout.ConclusionWe hypothesise that a dietary vitamin C intake of 75–525 mg or 75–225 mg may reduce the risk of hyperuricemia and gout, respectively. Further research with larger samples is required to confirm this.
Leveraging co-evolutionary insights and AI-based structural modeling to unravel receptor-peptide ligand-binding mechanisms
Authors: Snoeck Simon , Lee Hyun Kyung , Schmid Marc W. , Bender Kyle W. , Neeracher Matthias J. , Fernández-Fernández Alvaro D. , Santiago Julia , Zipfel Cyril 
Published: January 2024

AbstractSecreted signaling peptides are central regulators of growth, development, and stress responses, but specific steps in the evolution of these peptides and their receptors are not well understood. In addition, the molecular mechanisms of peptide-receptor binding are only known for a few examples, primarily owing to the limited availability of structural capabilities to few laboratories worldwide. Plants have evolved a multitude of secreted signaling peptides and corresponding transmembrane receptors. Stress-responsive SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs) were recently identified. Bioactive SCOOPs are proteolytically processed by subtilases and are perceived by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) in the model plantArabidopsis thaliana. How SCOOPs and MIK2 have (co-)evolved, and how SCOOPs bind to MIK2 are however still unknown. Usingin silicoanalysis of 350 plant genomes and subsequent functional testing, we revealed the conservation of MIK2 as SCOOP receptor within the plant order Brassicales. We then leveraged AlphaFold-Multimer and comparative genomics to identify two conserved putative SCOOP-MIK2 binding pockets across Brassicales MIK2 homologues predicted to interact with the ‘SxS’ motif of otherwise sequence-divergent SCOOPs. Notably, mutagenesis of both predicted binding pockets compromised SCOOP binding to MIK2, SCOOP-induced complex formation between MIK2 and its co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1), and SCOOP-induced reactive oxygen species production; thus, confirming ourin silicopredictions. Collectively, in addition to revealing the elusive SCOOP-MIK2 binding mechanisms, our analytic pipeline combining phylogenomics, AI-based structural predictions, and experimental biochemical and physiological validation provides a blueprint for the elucidation of peptide ligand-receptor perception mechanisms.Significance statementThis study presents a rapid and inexpensive alternative to classical structure-based approaches for resolving ligand-receptor binding mechanisms. It relies on a multilayered bioinformatic approach that leverages genomic data across diverse species in combination with AI-based structural modeling to identify true ligand and receptor homologues, and subsequently predict their binding mechanisms.In silicofindings were validated by multiple experimental approaches, which investigated the effect of amino acid changes in the proposed binding pockets on ligand-binding, complex formation with a co-receptor essential for downstream signaling, and activation of downstream signaling. Our analysis combining evolutionary insights,in silicomodeling and functional validation provides a framework for structure-function analysis of other peptide-receptor pairs, which could be easily implemented by most laboratories.
Localising elements in single-particle reconstructions by REEL-EM: Reconstructed Electron Energy-Loss - Elemental Mapping
Authors: Pfeil-Gardiner Olivia , Rosa Higor Vinícius Dias , Riedel Dietmar , Chen Yu Seby , Lörks Dominique , Kükelhan Pirmin , Linck Martin , Müller Heiko , Van Petegem Filip , Murphy Bonnie J. 
Published: January 2024

AbstractFor structures determined by single particle cryo-EM, no technique currently exists for mapping elements to defined locations, leading to errors in the assignment of metals and other ions, cofactors, substrates, inhibitors, and lipids that play essential roles in activity and regulation. Elemental mapping in the electron microscope is well established for dose-tolerant samples but is challenging for biological samples, especially in a cryo-preserved state. Here, we combine electron energy-loss spectroscopy (EELS) with single-particle image processing to allow elemental mapping in cryo-preserved macromolecular complexes. Proof-of-principle data show that our method, REEL-EM, allows 3D reconstruction of EELS data, such that a high total electron dose is accumulated across many copies of a complex. Working with two test samples, we demonstrate that we can reliably localise abundant elements. We discuss the current limitations of the method and potential future developments.