bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among theCoronaviridae
Authors: Waller Stephanie J. , Tortosa Pablo , Thurley Tertia , O’Donnell Colin , Jackson Rebecca , Dennis Gillian , Grimwood Rebecca M. , Holmes Edward C. , McInnes Kate , Geoghegan Jemma L. 
Published: June 2023

1.AbstractThe lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand’s only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world.Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand we aimed to characterise the viromes of New Zealand’s bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary– and environmental-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what is possibly the shortest genome within theCoronaviridaeidentified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand’s only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.
The association of neutralizing antibodies with protection against symptomatic dengue virus infection varies by serotype, prior infection history, and assay condition
Authors: Bos Sandra , Graber Aaron L. , Cardona-Ospina Jaime A. , Duarte Elias M. , Zambrana Jose Victor , Ruíz Salinas Jorge A. , Mercado-Hernandez Reinaldo , Singh Tulika , Katzelnick Leah C. , de Silva Aravinda , Kuan Guillermina , Balmaseda Angel , Harris Eva 
Published: June 2023

AbstractThe four dengue virus serotypes (DENV1–4) are the most prevalent arboviruses in humans and a major public health concern worldwide. Understanding immune mechanisms that modulate DENV infection outcome is critical for epidemic preparedness and development of a safe and effective vaccine. Neutralizing antibodies (nAbs) are an essential component of the protective response, yet their measurement often relies on a single cellular substrate and partially mature virions, which do not capture the full breadth of neutralizing activity and may lead to biased estimations of nAb potency. Here, we investigated the characteristics of nAbs associated with protection against dengue cases using samples collected after one or more DENV infections but prior to subsequent symptomatic or inapparent DENV1, DENV2, or DENV3 infections from a long- standing pediatric cohort study in Nicaragua. By assessing nAb responses using Vero cells with or without the attachment factor DC-SIGN and with mature or partially mature virions, we found that nAb potency and the protective NT50cutoff were greatly influenced by cell substrate and virion maturation state. Additionally, the correlation between nAb titer and protection from disease depended on an individual’s prior infection history and the subsequent infecting DENV serotype. Finally, we uncovered variations in nAbs composition that contributed to protection from symptomatic DENV infection differently after primary and secondary prior infection. These findings have important implications for identifying antibody correlates of protection in the context of vaccines and natural infections.
Magnetogenetic cell activation using endogenous ferritin
Authors: Pomeranz Lisa , Li Rosemary , Yu Xiaofei , Kelly Leah , Hassanzadeh Gholamreza , Molina Henrik , Gross Daniel , Brier Matthew , Vaisey George , Wang Putianqi , Jimenez-Gonzalez Maria , Garcia-Ocana Adolfo , Dordick Jonathan , Friedman Jeffrey , Stanley Sarah 
Published: June 2023

AbstractThe ability to precisely control the activity of defined cell populations enables studies of their physiological roles and may provide therapeutic applications. While prior studies have shown that magnetic activation of ferritin-tagged ion channels allows cell-specific modulation of cellular activity, the large size of the constructs made the use of adeno-associated virus, AAV, the vector of choice for gene therapy, impractical. In addition, simple means for generating magnetic fields of sufficient strength have been lacking. Toward these ends, we first generated a novel anti-ferritin nanobody that when fused to transient receptor potential cation channel subfamily V member 1, TRPV1, enables direct binding of the channel to endogenous ferritin in mouse and human cells. This smaller construct can be delivered in a single AAV and we validated that it robustly enables magnetically induced cell activationin vitro. In parallel, we developed a simple benchtop electromagnet capable of gating the nanobody-tagged channelin vivo. Finally, we showed that delivering these new constructs by AAV to pancreatic beta cells in combination with the benchtop magnetic field delivery stimulates glucose-stimulated insulin release to improve glucose tolerance in micein vivo. Together, the novel anti-ferritin nanobody, nanobody-TRPV1 construct and new hardware advance the utility of magnetogenetics in animals and potentially humans.
An aptamer-mediated base editing platform for simultaneous knock-in and multiple gene knockout for allogeneic CAR-T cells generation
Authors: Porreca Immacolata , Blassberg Robert , Harbottle Jennifer , Joubert Bronwyn , Mielczarek Olga , Stombaugh Jesse , Hemphill Kevin , Sumner Jonathan , Pazeraitis Deividas , Touza Julia Liz , Francesatto Margherita , Selmi Tommaso , Collantes Juan Carlos , Strezoska Zaklina , Taylor Benjamin , Jin Shengkan , Wiggins Ceri M , van Brabant Smith Anja , Lambourne John J. 
Published: June 2023

AbstractGene editing technologies hold promise for enabling the next generation of adoptive cellular therapies. Conventional gene editing platforms that rely on nuclease activity, such as Clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9), allow efficient introduction of genetic modifications; however, these modifications occur via the generation of DNA double-strand breaks (DSBs) and can lead to unwanted genomic alterations and genotoxicity. Here, we apply the novel modular RNA aptamer-mediated Pin-point™ base editing platform to simultaneously introduce multiple gene knockouts and site-specific integration of a transgene in human primary T cells. We demonstrate high editing efficiency and purity at all target sites and significantly reduced frequency of chromosomal translocations compared to the conventional CRISPR-Cas9 system. Site-specific knock-in of a chimeric antigen receptor (CAR) and multiplex gene knockout are achieved within a single intervention and without the requirement for additional sequence-targeting components. The ability to perform complex genome editing efficiently and precisely highlights the potential of the Pin-point platform for application in a range of advanced cell therapies.
Sexual dimorphism in the social behaviour ofCntnap2KO mice correlates with disrupted synaptic connectivity and increased microglial activity in the anterior cingulate cortex of males
Authors: Dawson Matt S. , Gordon-Fleet Kevin , Yan Lingxin , Tardos Vera , He Huanying , Mui Kwong , Nawani Smriti , Asgarian Zeinab , Catani Marco , Fernandes Cathy , Drescher Uwe 
Published: June 2023

AbstractA biological understanding of the apparent sex bias in autism is lacking. We have identifiedCntnap2KO mice as a model system to help better understand this dimorphism. Using this model, we observed social deficits in juvenile male KO mice only. These male-specific social deficits correlated with reduced spine densities of Layer 2/3 and Layer 5 pyramidal neurons in the Anterior Cingulate Cortex, a forebrain region prominently associated with the control of social behaviour. Furthermore, in male KO mice, microglia showed an increased activated morphology and phagocytosis of synaptic structures compared to WT mice, whereas no differences were seen in female KO and WT mice. Our data suggest that sexually dimorphic microglial activity may be involved in the aetiology of ASD, disrupting the development of neural circuits that control social behaviour by overpruning synapses at a developmentally critical period.
The Cystic Fibrosis treatment, Trikafta, affects growth, viability, and cell wall ofAspergillus fumigatusbiofilms
Authors: Jones Jane T. , Morelli Kaesi A. , Vesely Elisa M. , Puerner Charles T.S. , Pavuluri Chetan K. , Ross Brandon S. , van Rhijn Norman , Bromley Michael J. , Cramer Robert A. 
Published: June 2023

ABSTRACTPeople with Cystic Fibrosis (pwCF) commonly test positive for the pathogenic fungus,Aspergillus fumigatus,which is associated with a decline in lung function. Trikafta is a recently approved therapy for pwCF that improves quantity and function of the CFTR protein, however, it is not known how Trikafta affects microbial communities in the lung. Therefore, the aim of this study was to determine whether Trikafta directly affectsA. fumigatusgrowth and biology. While Trikafta did not impact the viability ofA. fumigatusconidia, treatment ofA. fumigatusbiofilms with Trikafta reduced overall biofilm biomass. This finding was associated with increased membrane permeability, decreased viability, and reduced metabolic activity following long-term treatment of biofilms. Trikafta-induced membrane permeability and biomass reduction was partially blocked with the calcium channel inhibitor Verapamil and fully blocked by the mammalian CFTR inhibitor GlyH-101. Trikafta-induced biomass reduction and metabolic activity was shown to be regulated by the High Osmolarity Glycerol (HOG) pathway genesakA. Trikafta treatment also induced resistance to the cell wall stressor calcofluor white, susceptibility to the antifungal caspofungin, and decreased inflammatory responses from murine bone marrow cells. Collectively, these results reveal that Trikafta affects infection-relevantA. fumigatusbiology and host-microbial interactions.IMPORTANCEPeople with Cystic Fibrosis (pwCF) commonly test positive for the pathogenic fungus,Aspergillus fumigatus, which is associated with a decline in lung function. Trikafta is a recently approved therapy for pwCF that improves quantity and function of the CFTR protein, however, it is not known how Trikafta affects microbial communities in the CF lung. Here we report that Trikafta has anti-fungal activity against the infection relevant form ofA. fumigatus, termed biofilms. When exposed to TrikaftaA. fumigatusbiofilms lose their viability. In addition, exposure to Trikafta enhances the susceptibility ofA. fumigatusbiofilms to the clinically utilized anti-fungal drug caspofungin. These data suggest Trikafta impacts the cell wall of A. fumigatus and suggests the potential for using Trikafta to augment existing anti-fungal therapy.
Chemical inhibition of histidine biosynthesis curtailsM. tuberculosisinfection
Authors: Tiwari Satish , Ahmad Mohammed , Kumar Varun , Kar Deepsikha , Kumari Swati , Dwivedy Abhisek , Pal Ravi Kant , Mohapatra Amit Kumar , Nain Vaibhav Kumar , Barik Vishawjeet , Pal Rahul , Nanda Ranjan Kumar , Pandey Amit Kumar , Biswal Bichitra Kumar 
Published: June 2023

AbstractTo overcome the drug resistance crisis and shorten the current duration of human tuberculosis (TB) therapy, new anti-TB molecules is required. In an earlier study, we have shown thatMycobacterium tuberculosis(Mtb), the causative agent of TB, with a fractured de novo histidine biosynthesis fails to mount TB infection in mouse model, emboldening that disrupting the function of this pathway may constitute a novel strategy to curtailing TB infection. In this study, through a target based approach we have designed a number of triazole scaffold molecules specific to imidazole glycerol phosphate dehydratase (IGPD; HisB) of this pathway and have delineated atomic level interactions between the enzyme and inhibitors which pinpointed the specificity and the inhibitory mechanism. Importantly, these molecules exhibited significant potency against free as well as macrophage-internalized wild-type and drug-resistant clinical isolates in culture medium. Notably, a couple of these compounds showed efficacy in reducing the bacterial burden inMtb-infected mouse model. The chemical inhibition of IGPD induces histidine auxotrophy inMtband brings in new prospects to the area of anti-TB drug discovery.
Resistance towards and biotransformation ofPseudomonas-produced secondary metabolites during community invasion
Authors: Hansen Morten L. , Dénes Zsófia , Jarmusch Scott A. , Wibowo Mario , Lozano-Andrade Carlos N. , Kovács Ákos T. , Strube Mikael L. , Andersen Aaron J. C. , Jelsbak Lars 
Published: June 2023

AbstractThe role of antagonistic secondary metabolites produced byPseudomonas protegensin suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability ofP. protegensto establish in soil and rhizosphere microbiomes remains ambiguous. Here, we use a four-species synthetic community to determine how antibiotic production contributes toP. protegenscommunity invasion and identify community traits that alter the abundance of keyP. protegensantimicrobial metabolites (DAPG, pyoluteorin and orfamide A). Surprisingly, mutants deficient in antimicrobial production caused similar perturbations in community composition compared to invasion by wildtypeP. protegens. Intriguingly, while pyoluteorin and orfamide A are secreted at levels toxic to individual bacterial strains, community-level resistance circumvents toxicity. Here, we identify the underlying mechanism by which the cyclic lipopeptide, orfamide A, is inactivated and degraded byRhodococcus globerulusD757 andStenotrophomonas indicatrixD763. Altogether, the demonstration that the synthetic community constrainsP. protegensinvasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectivenessin situ.
Divergence of TORC1-mediated Stress Response Leads to Novel Acquired Stress Resistance in a Pathogenic Yeast
Authors: Liang Jinye , Tang Hanxi , Snyder Lindsey F. , Youngstrom Christopher E. , He Bin Z. 
Published: June 2023

AbstractAcquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeastC. glabrataand protects it against a severe H2O2stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative,S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of- Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1’s response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.
Ultrastructural details of resistance factors of the bacterial spore revealed by in situ cryo-electron tomography
Authors: Bauda Elda , Gallet Benoit , Moravcova Jana , Effantin Gregory , Chan Helena , Novacek Jiri , Jouneau Pierre-Henri , Rodrigues Christopher D.A. , Schoehn Guy , Moriscot Christine , Morlot Cecile 
Published: June 2023

AbstractThe bacterial spore owes its incredible resistance capacities to various molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography (cryo-ET) on bacteria lamellae generated by cryo-focused ion beam micromachining (cryo-FIBM) provides insights into the ultrastructural organization ofBacillus subtilissporangia, including that of the DNA and nascent coat layers. Analysis of the reconstructed tomograms reveal that rather early during sporulation, the chromosome in the developing spore (the forespore) adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a complex stack of amorphous or structured layers with distinct electron density, dimensions and organization. We investigated the nature of the nascent coat layers in various mutant strains using cryo-FIBM/ET and transmission electron microscopy on resin sections of freeze-substituted bacteria. Combining these two cellular electron microscopy approaches, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of the morphogenetic proteins SpoIVA, SpoVID, SafA and/or CotE.Significance statementBacterial spores are dormant cells that can resist to multiple stresses, including antibiotics, detergents, irradiation and high temperatures. Such resilience is an asset when spores are used for the benefit of humans, as in the case of probiotics, or a major problem for public health, food safety or biowarfare when it comes to spores of pathogenic bacteria. In this study, we combined state-of-the-art cryo-electron tomography and conventional cellular electron microscopy to provide insights into intermediate stages of spore development. Our data reveal the intracellular reorganization of the chromosome into a toroidal fibrillar structure and the complex assembly of the multi-protein, multilayered extracellular coat, shedding light on the mechanisms by which the spore acquires its incredible resistance capacities.
Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone allosterically mediates substrate binding to the active site
Authors: Bimaï Ornella , Banerjee Ipsita , Grinberg Inna Rozman , Huang Ping , Hultgren Lucas , Ekström Simon , Lundin Daniel , Sjöberg Britt-Marie , Logan Derek T. 
Published: June 2023

AbstractA small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerization and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical and structural information on the effects of ATP and dATP binding to the anaerobic RNR fromPrevotella copri. The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP,P. copriNrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it can not be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.
Mutational analysis of LtgC, a lytic transglycosylase required for cell separation inNeisseria gonorrhoeae
Authors: Schaub Ryan E. , Perez-Medina Krizia , Tomberg Joshua , Nicholas Robert A. , Dillard Joseph P. 
Published: June 2023

AbstractLytic transglycosylases function to degrade peptidoglycan strands that comprise the bacterial cell wall. Degradation of peptidoglycan at the septum following cell division is necessary for cell separation, and a deletion ofltgCinNeisseria gonorrhoeaeresults in growth in clusters of around 6-20 cells rather than as normal diplococci or monococci.N. gonorrhoeaeLtgC is a homolog ofEscherichia coliMltA, and comparison of the two proteins shows that LtgC has an extra domain not found in MltA, referred to as domain 3. To better understand the function of LtgC, we characterizedN. gonorrhoeaemutants with substitutions in amino acids predicted to be necessary for enzymatic activity or amino acids predicted to be on the surface of domain 3, and we characterized a mutant lacking domain 3. All the mutants showed defects in cell separation, and the bacteria failed to release peptidoglycan-derived disaccharides into the medium. Purified LtgC proteins with the amino acid substitutions had reduced peptidoglycan degradation activity. LtgC was found to bind AmiC in bacterial 2-hybrid assays, and domain 3 mutations reduced binding. In human blood, anltgCmutant showed decreased survival, suggesting the cell wall defects in the mutant make the bacteria more sensitive to innate immune system components.ImportanceNeisseria gonorrhoeaeuses a smaller set of proteins for peptidoglycan breakdown compared toEscherichia colior other model systems. The peptidoglycan breakdown that occurs at the septum following cell division inN. gonorrhoeaerequires three proteins, amidase AmiC, amidase activator NlpD, and lytic transglycosylase LtgC. LtgC has an unusual structure that includes a third domain not found in related proteins. Using mutants that lacked LtgC activity or had amino acid changes in the third domain, we found that the extra domain is involved in interaction of LtgC with AmiC and that it is required for LtgC function for cell separation. All of theltgCmutants examined showed reduced survival in blood, indicating the importance of LtgC activity for infection.