bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acinetobacter baumannii and cefiderocol between cidality and adaptability
Authors: Stracquadanio Stefano , Bonomo Carmelo , Marino Andrea , Bongiorno Dafne , Privitera Grete Francesca , Bivona Dalida Angela , Mirabile Alessia , Bonacci Paolo Giuseppe , Stefani Stefania 
Published: May 2022

ABSTRACTAmong the bacterial species included in the ESKAPE group, Acinetobacter baumannii is of great interest due to its intrinsic and acquired resistance to many antibiotic classes and its ability to infect different body districts. Cefiderocol is a novel cephalosporin active against Gram-negative bacteria with promising efficacy on A. baumannii infections, but some studies have reported therapeutic failures even in the presence of susceptible A. baumannii strains.This study aims to investigate the interactions between cefiderocol and ten A. baumannii strains with different susceptibility profiles to this drug. We confirmed diverse susceptibility profiles in the strains, with resistance values close to the EUCAST-proposed breakpoints. MBC/MIC (minimal bactericidal concentration/minimal inhibitory concentration) ratios, demonstrated bactericidal activity of the drug; on the other hand, bacterial regrowth was evident after exposition to cefiderocol, as were changes in the shape of colonies and bacterial cells. A switch to a non-susceptible phenotype in the presence of high cefiderocol concentrations was found as adaptation mechanisms implemented by these A. baumannii strains to overcome the cidal activity of this antibiotic, also confirmed by the presence of heteroresistant, unstable subpopulations. As our isolates harbored numerous β-lactamase genes, β-lactamase inhibitors showed the ability to restore the antimicrobial activity of cefiderocol regardless of the different non-susceptibility levels of the tested strains.These in vitro results, can sustain the concept of using combination therapy to eliminate drug-adapted subpopulations and regain full cefiderocol activity in this difficult-to-treat species.
Bacterial association with metals enables in vivo tracking of microbiota using magnetic resonance imaging
Authors: Donnelly Sarah C. , Gelman Neil , Thompson R. Terry , Prato Frank S. , Burton Jeremy P. , Goldhawk Donna E. 
Published: May 2022

AbstractBacteria constitute a significant part of the biomass of the human microbiota, but their interactions are complex and difficult to replicate outside the host. Exploiting the superior resolution of magnetic resonance imaging (MRI) to examine signal parameters of selected human isolates may allow tracking of their dispersion throughout the body. We investigated longitudinal and transverse MRI relaxation rates and found significant differences between several bacterial strains. Common commensal strains of lactobacilli display notably high MRI relaxation rates, partially explained by outstanding cellular manganese content, while other species contain more iron than manganese. Lactobacillus crispatus show particularly high values, 4-fold greater than any other species; over 10-fold greater signal than relevant tissue background; and a linear relationship between relaxation rate and fraction of live cells. Different bacterial strains have detectable, repeatable MRI relaxation rates that in future may enable tracking of their persistence in the human body for enhanced molecular imaging.IMPORTANCETo understand how spatial and temporal distribution of microbiota impact human health, dynamic tools for monitoring microbiota landscapes inside the host are needed. Particularly when considering the complexity of the gastrointestinal tract and the microbiota that dwell within, tools for monitoring deep segments of the gut non-invasively are required. Medical imaging provides solutions that enable the study of microorganisms in their preferred niche regardless of health status. To bootstrap this technology, we investigated the magnetic resonance imaging (MRI) properties of bacterial isolates and showed that outstanding signal detection is an inherent property of several strains. Among these, we showed that bacteria relying on manganese metabolism have an MRI characteristic that is distinct from mammalian cells. Our findings will lead to direct and safe imaging of bacteria; influence how we monitor both infection and gut health; and help direct the use of antibiotics to curtail the growing threat of antibiotic resistance.
Enterobacteralesplasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK
Authors: Matlock William , Lipworth Samuel , Chau Kevin K. , Abu Oun Manal , Barker Leanne , Kavanagh James , Andersson Monique , Oakley Sarah , Morgan Marcus , Crook Derrick W. , Read Daniel S. , Anjum Muna , Shaw Liam P. , Stoesser Nicole ,   REHAB Consortium
Published: May 2022

AbstractPlasmids enable the dissemination of antimicrobial resistance (AMR) in commonEnterobacteralespathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution betweenEnterobacteralescausing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is highly relevant to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets)Enterobacterales. Isolates were collected between 2008-2020 from sites <60km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared “backbones”, with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid “backbones” were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.FundingThis study was funded by the Antimicrobial Resistance Cross-council Initiative supported by the seven research councils and the NIHR, UK.
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
Authors: Lycksell Marie , Rovšnik Urška , Hanke Anton , Martel Anne , Howard Rebecca J , Lindahl Erik 
Published: May 2022

AbstractPentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging from bacteria to humans. Among the prokaryotic pLGICs there is architectural diversity involving N-terminal domains (NTDs) not found in eukaryotic relatives, exemplified by the calcium-sensitive channel (DeCLIC) from a Desulfofustis deltaproteobacterium, which has an NTD in addition to the canonical pLGIC structure. Here we have characterized the structure and dynamics of DeCLIC through cryo-electron microscopy (cryo-EM), small-angle neutron scattering (SANS), and molecular dynamics (MD) simulations. In the presence and absence of calcium, cryo-EM yielded structures with alternative conformations of the calcium binding site. SANS profiles further revealed conformational diversity at room temperature beyond that observed in static structures, shown through MD to be largely attributable to rigid body motions of the NTD relative to the protein core, with expanded and asymmetric conformations improving the fit of the SANS data. This work reveals the range of motion available to the DeCLIC NTD and calcium binding site, expanding the conformational landscape of the pLGIC family. Further, these findings demonstrate the power of combining low-resolution scattering, high-resolution structural, and MD-simulation data to elucidate interfacial interactions that are highly conserved in the pLGIC family.
Vertical gradients in photosynthetic physiology diverge at the latitudinal range extremes of white spruce
Authors: Schmiege Stephanie C. , Griffin Kevin L. , Boelman Natalie T. , Vierling Lee A. , Bruner Sarah G. , Min Elizabeth , Maguire Andrew J. , Jensen Johanna , Eitel Jan U. H. 
Published: May 2022

ABSTRACTLight availability drives vertical canopy gradients in photosynthetic functioning and carbon (C) balance, yet patterns of variability in these gradients remain unclear. We measured light availability, photosynthetic CO2 and light response curves, foliar C, nitrogen (N) and pigment concentrations, and the photochemical reflectance index (PRI) on upper and lower canopy needles of white spruce trees (Picea glauca) at the species’ northern and southern range extremes. We combined our photosynthetic data with previously published respiratory data to compare and contrast canopy C balance between latitudinal extremes. We found steep canopy gradients in irradiance, photosynthesis, and leaf traits at the southern range limit, but a lack of variation across canopy positions at the northern range limit. Thus, unlike many tree species from tropical to mid-latitude forests, high latitude trees may not require vertical gradients of metabolic activity to optimize photosynthetic C gain. Consequently, accounting for self-shading is less critical for predicting gross primary productivity at northern relative to southern latitudes. Northern trees also had a significantly smaller net positive leaf C balance than southern trees suggesting that, regardless of canopy position, low photosynthetic rates coupled with high respiratory costs may ultimately constrain the northern range limit of this widely distributed boreal species.SUMMARY STATEMENTCanopy gradients in photosynthetic capacity of white spruce diminish at high compared to low latitudes. Low carbon balance in high latitude trees may determine the extent of northern treeline.
Crystal structure and biochemical analysis suggest that YjoB ATPase is a substrate-specific molecular chaperone
Authors: Kwon Eunju , Dahal Pawan , Kim Dong Young 
Published: May 2022

ABSTRACTAAA+ ATPases are ubiquitous proteins associated with most cellular processes, including DNA unwinding and protein unfolding. Their functional and structural properties are typically determined by domains and motifs added to the conserved ATPases domain. Currently, the molecular function and structure of many ATPases remain elusive. Here, we report the crystal structure and biochemical analyses of YjoB, a Bacillus subtilis AAA+ protein. The crystal structure revealed that the YjoB hexamer forms a bucket hat-shaped structure with a porous chamber. Biochemical analyses showed that YjoB prevents the aggregation of vegetative catalase KatA and gluconeogenesis-specific glyceraldehyde-3 phosphate dehydrogenase GapB, but not citrate synthase, a conventional substrate. Structural and biochemical analyses further showed that the internal chamber of YjoB is necessary for the chaperone activity. Our results suggest that YjoB, conserved in the class Bacilli, is a molecular chaperone acting in the starvation/stationary phases of B. subtilis growth.
Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin
Authors: Belyy Alexander , Lindemann Florian , Roderer Daniel , Funk Johanna , Bardiaux Benjamin , Protze Jonas , Bieling Peter , Oschkinat Hartmut , Raunser Stefan 
Published: May 2022

AbstractTc toxins deliver toxic enzymes into host cells by a unique injection mechanism. One of these enzymes is TccC3, an ADP-ribosyltransferase from Photorhabdus luminescens. Once TccC3 is translocated into the target cell, the enzyme ADP-ribosylates actin, resulting in clustering of the actin cytoskeleton and ultimately cell death. Here, we combine biochemistry, solution and solid-state NMR spectroscopy and cryo-EM to show in atomic detail how TccC3 modifies actin. We find that the ADP-ribosyltransferase does not bind to G-actin but interacts with two consecutive actin subunits of F-actin. The binding of TccC3 to F-actin occurs via an induced-fit mechanism that facilitates access of NAD+ to the nucleotide binding pocket. The following nucleophilic substitution reaction results in the transfer of ADP-ribose to threonine-148 of F-actin. We demonstrate that this site-specific modification of F-actin prevents its interaction with depolymerization factors, such as cofilin, which impairs actin network turnover and leads to steady actin polymerization. Our findings reveal in atomic detail a new mechanism of action of a bacterial toxin through specific targeting and modification of F-actin.
Urine-derived exosomes from individuals with IPF carry pro-fibrotic cargo
Authors: Elliot Sharon J. , Catanuto Paola , Pereira-Simon Simone , Xia Xiaomei , Shahzeidi Shahriar , Roberts Evan R. , Ludlow John W. , Hamdan Suzana , Daunert Sylvia , Parra Jennifer , Stone Rivka , Pastar Irena , Tomic-Canic Marjana , Glassberg Marilyn K. 
Published: May 2022

BackgroundMicroRNAs (miRNA) and other components contained in extracellular vesicles may reflect the presence of a disease. Lung tissue, sputum and sera of individuals with idiopathic pulmonary fibrosis (IPF) show alterations in miRNA expression. We designed this study to test whether urine and/or tissue derived exosomal miRNAs from individuals with IPF carry cargo that can promote fibrosis.MethodsExosomes were isolated from urine (U-IPFexo), lung tissue myofibroblasts (MF-IPFexo), serum from individuals with IPF (n=16) and age/sex-matched controls without lung disease (n=10). We analyzed microRNA expression of isolated exosomes and their in vivo bio-distribution. We investigated the effect on ex vivo skin wound healing and in in vivo mouse lung models.ResultsU-IPFexo or MF-IPFexo expressed miR let-7d, miR-29a-5p, miR 181b-3p and miR-199a-3p consistent with previous reports of miRNA expression obtained from lung tissue/sera from patients with IPF. In vivo bio-distribution experiments detected bioluminescent exosomes in the lung of normal C57Bl6 mice within 5 minutes after intravenous infusion, followed by distribution to other organs irrespective of exosome source. Exosomes labeled with gold nanoparticles and imaged by transmission electron microscopy were visualized in alveolar epithelial type I and type II cells. Treatment of human and mouse lung punches obtained from control, non-fibrotic lungs with either U-IPFexo or MF-IPFexo produced a fibrotic phenotype. A fibrotic phenotype was also induced in a human ex vivo skin model and in in vivo lung models.ConclusionsOur results provide evidence of a systemic feature of IPF whereby exosomes contain pro-fibrotic miRNAs when obtained from a fibrotic source and interfere with response to tissue injury as measured in skin and lung models.FundingThis work was supported in part by Lester and Sue Smith Foundation and The Samrick Family Foundation and NIH grants R21 AG060338 (SE and MKG), U01 DK119085 (IP, RS, MTC).
Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells
Authors: Govindaraj Vinodhini , Sarma Subrot , Karulkar Atharva , Purwar Rahul , Kar Sandip 
Published: May 2022

AbstractMammalian cells exhibit a high degree of intercellular variability in cell cycle period and phase durations. However, the factors orchestrating the cell cycle duration heterogeneities remain unclear. Herein, by combining cell cycle network-based mathematical models with live single-cell imaging studies under varied serum conditions, we demonstrate that fluctuating transcription rates of cell cycle regulatory genes across cell lineages and during cell cycle progression in mammalian cells majorly govern the robust correlation patterns of cell cycle period and phase durations among sister, cousin, and mother-daughter lineage pairs. However, for the overall cellular population, alteration in serum level modulates the fluctuation and correlation patterns of cell cycle period and phase durations in a correlated manner. These heterogeneities at the population level can be finetuned under limited serum conditions by perturbing the cell cycle network using a p38-signaling inhibitor without affecting the robust lineage level correlations. Overall, our approach identifies transcriptional fluctuations as the key controlling factor for the cell cycle duration heterogeneities, and predicts ways to reduce cell-to-cell variabilities by perturbing the cell cycle network regulations.Significance statementIn malignant tumors, cells display a diverse pattern in cell division time. This cell-to-cell variability in cell cycle duration had been observed even under culture conditions for various mammalian cells. Here we used live-cell imaging studies to monitor FUCCI-HeLa cells and quantified the cell cycle period and time spent in different phases under varied serum conditions. We proposed a set of stochastic cell cycle network-based mathematical models to investigate the live-cell imaging data and unraveled that the transcription rate variation across cell lineages and during cell cycle phases explains every aspect of the cell cycle duration variabilities. Our models identified how different deterministic effects and stochastic fluctuations control these variabilities and predicted ways to alter these cell cycle duration variabilities.
Phasing of de novo mutations using a scaled-up multiple amplicon long-read sequencing approach
Authors: Holt G.S. , Batty L. , Alobaidi B. , Smith H. , Oud M.S. , Ramos L. , Xavier M.J. , Veltman J.A. 
Published: May 2022

AbstractDe novo mutations (DNMs) play an important role in severe genetic disorders that reduce fitness. To better understand the role of DNMs in disease, it is important to determine the parent-of-origin and timing of the mutational events that give rise to the mutations, especially in sex-specific developmental disorders such as male infertility. However, currently available short-read sequencing approaches are not ideally suited for phasing as this requires long continuous DNA strands that span both the DNM and one or more informative SNPs. To overcome these challenges, we optimised and implemented a multiplexed long-read sequencing approach using the Oxford Nanopore technologies MinION platform. We specifically focused on improving target amplification, integrating long-read sequenced data with high-quality short-read sequence data, and developing an anchored phasing computational method. This approach was able to handle the inherent phasing challenges that arise from long-range target amplification and the normal accumulation of sequencing error associated with long-read sequencing. In total, 77 out of 109 DNMs (71%) were successfully phased and parent-of-origin identified. The majority of phased DNMs were prezygotic (90%), the accuracy of which is highlighted by the average mutant allele frequency of 49.6% and a standard error margin of 0.84%. This study demonstrates the benefits of using an integrated short-read and long-read sequencing approach for large-scale DNM phasing.
SimBu: Bias-aware simulation of bulk RNA-seq data with variable cell type composition
Authors: Dietrich Alexander , Sturm Gregor , Merotto Lorenzo , Marini Federico , Finotello Francesca , List Markus 
Published: May 2022

AbstractMotivationAs complex tissues are typically composed of various cell types, deconvolution tools have been developed to computationally infer their cellular composition from bulk RNA sequencing (RNA-seq) data. To comprehensively assess deconvolution performance, gold-standard datasets are indispensable. Gold-standard, experimental techniques like flow cytometry or immunohistochemistry are resource-intensive and cannot be systematically applied to the numerous cell types and tissues profiled with high-throughput transcriptomics. The simulation of ‘pseudo-bulk’ data, generated by aggregating single-cell RNA-seq (scRNA-seq) expression profiles in pre-defined proportions, offers a scalable and cost-effective alternative. This makes it feasible to create in silico gold standards that allow fine-grained control of cell-type fractions not conceivable in an experimental setup. However, at present, no simulation software for generating pseudo-bulk RNA-seq data exists.ResultsWe developed SimBu, an R package capable of simulating pseudo-bulk samples based on various simulation scenarios, designed to test specific features of deconvolution methods. A unique feature of SimBu is the modelling of cell-type-specific mRNA bias using experimentally-derived or data-driven scaling factors. Here, we show that SimBu can generate realistic pseudo-bulk data, recapitulating the biological and statistical features of real RNA-seq data. Finally, we illustrate the impact of mRNA bias on the evaluation of deconvolution tools and provide recommendations for the selection of suitable methods for estimating mRNA content.ConclusionSimBu is a user-friendly and flexible tool for simulating realistic pseudo-bulk RNA-seq datasets serving as in silico gold-standard for assessing cell-type deconvolution methods.AvailabilitySimBu is freely available at https://github.com/omnideconv/SimBu as an R package under the GPL-3 license.Contactalex.dietrich@tum.de and markus.list@tum.deSupplementary informationSupplementary data are available at Bioinformatics online.
A Saccharomyces cerevisiae Model for Overexpression of Ntg1 a Base Excision DNA Repair Protein Reveals Novel Genetic Interactions
Authors: McPherson Annie J. , Jowhar Ziad M. , Doetsch Paul W. , Corbett Anita H. 
Published: May 2022

ABSTRACTThe Base Excision Repair (BER) pathway repairs oxidative DNA damage, a common and detrimental form of damage to the genome. Although biochemical steps in BER have been well define, little is understood about how the pathway is regulated. Such regulation is critical, as cells must respond rapidly to DNA damage while avoiding aberrant activation of repair proteins that can produce DNA damage as intermediates in the repair pathway. Indeed, overexpression of the human BER protein, NTHL1, a DNA N-glycosylase, can cause genomic instability and early cellular hallmarks of cancer. We developed a Saccharomyces cerevisiae model to explore how overexpression of NTHL1 may impair cellular function. Overexpression of Ntg1, the budding yeast orthologue of NTHL1, impairs cell growth. To dissect mechanisms underlying this growth defect, we overexpressed either wild-type Ntg1 or a catalytically inactive variant of Ntg1 (ntg1catdead). Consistent with results obtained for NTHL1, both variants of Ntg1 impair cell growth, but only the wild-type protein causes accumulation of double-strand breaks and chromosome loss. We screened a panel of DNA repair mutants for resistance/sensitivity to overexpression of wild-type Ntg1 or ntg1catdead. This analysis identified several cellular pathways that protect cells from Ntg1-induced damage, providing insight into interplay between DNA repair pathways. Finally, we identified a link to sumoylation and probed how this post-translational modification could contribute to regulation of Ntg1 function. This study describes a budding yeast system to understand how cells regulate and respond to dysregulation of the BER pathway.Take AwayOverexpression of a base excision DNA repair protein impairs cell growthOverexpression of a base excision DNA repair protein can cause DNA damageMultiple mechanisms cause DNA damage from overexpression of a repair proteinDNA repair pathways functionally interact to protect cells from DNA damagePrecise regulation of the activity of DNA repair proteins is critical