bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of VIM-1 producing Klebsiella pneumoniae isolates from a hospital outbreak reveals the genetic bases of the loss of the urease-positive identification character
Authors: Cabanel Nicolas , Rosinski-Chupin Isabelle , Chiarelli Adriana , Botin Tatana , Tato Marta , Canton Rafael , Glaser Philippe 
Published: March 2021

ABSTRACTOutbreaks of carbapenemase producing Klebsiella pneumoniae (CPKp) represent a major threat for hospitals. We molecularly characterized the first outbreak of VIM-1 producing K. pneumoniae in Spain, that raised fears about the spread of this strain or of the plasmid carrying blaVIM-1. Through in-depth genomic analysis of 18 isolates recovered between October 2005 and September 2007, we show that 17 ST39 isolates were clonal, whereas the last isolate had acquired the VIM-1 plasmid from the epidemic clone. The index isolate carried 31 antibiotic resistance genes (ARGs) and was resistant to almost all antibiotics tested. Later isolates further gained mutations in efflux pumps regulators ramR and opxR, deletion of mgrB (colistin resistance) and frameshift mutations in ompK36 (ß-lactam resistance) likely selected by antibiotic usage. Comparison with publicly available genome sequences and literature review revealed no sign of dissemination of this CPKp strain. However, the VIM-1 plasmid was found in diverse Enterobacterales species, although restricted to Spain. One isolate became urease negative following IS5075 transposition into ureC. Analysis of 9755 K. pneumoniae genomes showed the same ureC::IS5075 insertion in 14.1% of the isolates and explained why urease activity is a variable identification trait for K pneumoniae. Transposition into ureC results from the similarity of its 3’-end and the terminal inverted repeats of Tn21 like transposons, the targets of IS5075 and related ISs. As these transposons frequently carry ARGs, this might explain the frequent chromosomal invasion by these ISs and ureC inactivation in multidrug resistant isolates.IMPORTANCEEvolution of multidrug resistant bacterial pathogens occurs at multiple scales, in the patient, locally in the hospital or more globally. Some mutations or gene acquisitions, for instance in response to antibiotic treatment, may be restricted to a single patient due to their high fitness cost. However, some events are more general. By analyzing the evolution of a hospital acquired multidrug resistant K. pneumoniae strain producing the carbapenemase VIM-1, we showed a likely environmental source in the hospital and identified mutations contributing to a further decrease in antibiotic susceptibility. By combining the genomic analysis of this outbreak with literature data and genome sequences available in databases, we showed that the VIM-1 plasmid has been acquired by different Enterobacterales but is only endemic in Spain. We also discovered that urease loss in K. pneumoniae results from the specific transposition of an IS element into the ureC gene and was more frequent in fluoroquinolone resistant isolates and carrying a carbapenemase gene.
Long-term effects of mass screening for latent and active tuberculosis in the Marshall Islands
Authors: Ragonnet Romain , Williams Bridget M , Largen Angela , Nasa Joaquin , Jack Tom , Langinlur Mailynn K , Ko Eunyoung , Rahevar Kalpeshsinh , Islam Tauhid , Denholm Justin , Marais Ben J , Marks Guy B , McBryde Emma S , Trauer James M 
Published: March 2021

AbstractRationaleThe Marshall Islands implemented ambitious population-based screening programs for latent and active tuberculosis in 2017 and 2018. These interventions’ long-term effects remain to be estimated.ObjectivesTo predict the long-term impact of the previous interventions and identify strategies to drive tuberculosis towards elimination.MethodsWe built a transmission model of tuberculosis informed by local data to capture the epidemic’s historical dynamics. We used the model to project the future epidemic trajectory following the screening interventions, as well as considering a counterfactual scenario with no intervention. We also simulated future scenarios including periodic interventions similar to those previously implemented, to assess the feasibility of reaching the End TB Strategy targets and tuberculosis pre-elimination.Measurements and Main ResultsThe 2017-2018 screening activities were estimated to have reduced tuberculosis incidence and mortality by more than one third in 2020, and are predicted to achieve the End TB Strategy milestone of 50% incidence reduction by 2025 compared to 2015. Interventions had a considerably greater impact when individuals were also screened for latent infection than active case finding alone. Such combined programs implemented at the national level could achieve tuberculosis pre-elimination by 2035 if repeated every two years, and around 2045 if repeated every five years.ConclusionsWe predict that it is possible to achieve tuberculosis pre-elimination by 2035 in the Marshall Islands through periodic repetition of the same ambitious interventions as those previously implemented. Including latent infection testing in active screening activities will be a critical pillar for achieving these ambitious goals.
Learning to Treat Hypotensive Episodes in Sepsis Patients Using a Counterfactual Reasoning Framework
Authors: Jeter Russell , Lehman Li-Wei , Josef Christopher , Shashikumar Supreeth , Nemati Shamim 
Published: March 2021

AbstractThe optimal treatment strategy for volume resuscitation and vasopressor dosing to combat hypotensive episodes in septic patients remains a subject of ongoing controversy and can vary from clinician to clinician. We develop a machine learning approach to guide a fluid and vasopressor dosing strategy that adapts to patient-specific clinical states to improve the survival of septic patients. We adopt a model-free reinforcement learning (RL) framework in a continuous action space with a clinically significant reward function, and use a Switching Generalized Linear Model (SGLM) to characterize patient-specific clinical states. We use retrospective data from the MIMIC III database to train this model to learn volume resuscitation and vasopressor dosing strategies among the 5,366 patients (totalling 352,328 unique hourly measurements) with ICU-onset sepsis or septic shock, as diagnosed by the Sepsis-3 definition. The RL agent receives short- and long-term rewards associated with optimizing in-hospital survival and avoiding end-organ damage to learn volume resuscitation and vasopressor dosing strategies. On average, the RL agent learns to resuscitate patients earlier than clinicians with a fluid bolus (one hour vs. four hours after the diagnosis of sepsis), and improves the expected survival by ≈ 3%. Our preliminary results indicate that adherence to RL-based individualized fluid and vasopressor dosing recommendations is associated with a significant mortality reduction in septic patients, even after adjusting for severity of illness.
Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021
Authors: Wilton Thomas , Bujaki Erika , Klapsa Dimitra , Fritzsche Martin , Mate Ryan , Martin Javier 
Published: March 2021

AbstractSARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world raising concerns on their possible impact on human immune response to the virus and vaccine efficacy against them. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since November 2020. As surveillance for these SARS-CoV-2 variants of concern (VOCs) becomes critical, we have investigated the use of environmental surveillance (ES) for the rapid detection and quantification of B.1.1.7 viruses in sewage as a way of monitoring its expansion that is independent on the investigation of identified clinical cases. B.1.1.7 mutations in viral sequences from sewage were first identified in a sample collected in London on 10thNovember 2020 and shown to rapidly increase in frequency to >95% in January 2021, in agreement with clinical data over the same period. We show that ES can provide an early warning of VOCs becoming prevalent in the population and that, as well as B.1.1.7, our method can potentially detect VOCs B.1.351 and P.1, first identified in South Africa and Brazil, respectively, and other viruses also carrying critical spike mutation E484K, known to have an effect on virus antigenicity.
Dual oxic-anoxic co-culture enables direct study of host-anaerobe interactions at the airway epithelial interface
Authors: Moore Patrick J. , Wiggen Talia D. , Kent Leslie A. , Arif Sabrina J. , Lucas Sarah K. , Fletcher Joshua R. , Villareal Alex R. , Gilbertsen Adam , O’Grady Scott M. , Hunter Ryan C. 
Published: March 2021

SUMMARYStrict and facultative anaerobic bacteria are widely associated with both acute and chronic airway disease. However, their potential role(s) in disease pathophysiology remain poorly understood due to inherent limitations of existing models and conflicting oxygen demands between anaerobes and host cells. To overcome these limitations, we optimized a dual oxic-anoxic culture (DOAC) platform that maintains an oxygen-limited microenvironment at the epithelial interface while host cells are oxygenated basolaterally. This approach enables host-bacterial co-culture for ∼24h, and here we demonstrate its utility via two applications. First, we show that anaerobe challenge results in epithelial mucus degradation, inflammatory marker gene expression, and enhanced pathogen colonization. Second, we combine DOAC with single cell RNA sequencing (scRNAseq) to reveal a cell type-specific transcriptional response of the airway epithelium to anaerobe infection. Together, these data illustrate the versatility of DOAC while revealing new insights into anaerobe-host interactions and their mechanistic contributions to airway disease pathophysiology.
Cell competition removes segmental aneuploid cells fromDrosophilaimaginal disc-derived tissues based on ribosomal protein gene dose
Authors: Ji Zhejun , Chuen Jacky , Kiparaki Marianthi , Baker Nicholas E. 
Published: March 2021

ABSTRACTAneuploidy causes birth defects and miscarriages, occurs in nearly all cancers, and is a hallmark of aging. Individual aneuploid cells can be eliminated from developing tissues by unknown mechanisms. Cells with ribosomal protein (Rp) gene mutations are also eliminated, by cell competition with normal cells. BecauseRpgenes are spread across the genome, their copy number is a marker for chromosome aberrations. Elimination of imaginal disc cells with irradiation-induced genome damage often required cell competition genes. When defined chromosome regions were deleted, segmentally-aneuploid cells were eliminated by the RpS12-Xrp1 cell competition pathway in an apoptosis- dependent manner when they differed from neighboring cells inRpgene dose. Cells with normal doses of theRp(andeIF2γ) genes survived and differentiated adult tissues. Thus, cell competition, triggered by differences inRpgene dose between cells, is a significant mechanism for the elimination of aneuploid somatic cells, likely to contribute to preventing cancer.
Benzofuran sulfonates and small self-lipid antigens activate type II NKT cells via CD1d
Authors: Almeida CF , Smith D , Cheng T-Y , Harpur C , Batleska E , Nguyen T , Hilmenyuk T , Nguyen-Robertson CV , Reddiex SJJ , Van Rhijn I , Rossjohn J , Uldrich AP , Moody DB , Williams SJ , Pellicci DG , Godfrey DI 
Published: March 2021

AbstractNatural Killer T (NKT) cells detect lipids presented by CD1d. Most studies focus on type I NKT cells that express semi-invariant αβ T cell receptors (TCR) and recognise α-galactosylceramides. However, CD1d also presents structurally distinct lipids to NKT cells expressing diverse TCRs (type II NKT cells) but our knowledge of the antigens for type II NKT cells is limited. An early study identified an NKT cell agonist, phenyl pentamethyldihydrobenzofuransulfonate (PPBF), which is notable for its similarity to common sulfa-drugs, but its mechanism of NKT-cell activation remained unknown. Here we demonstrate that a range of pentamethylbenzofuransulfonate (PBFs), including PPBF, activate polyclonal type II NKT cells from human donors. Whereas these sulfa drug-like molecules might have acted pharmacologically on cells, here we demonstrate direct contact between TCRs and PBF-treated CD1d complexes. Further, PBF-treated CD1d-tetramers identified type II NKT cell populations cells expressing αβ and γδTCRs, including those with variable and joining region gene usage (TRAV12-1–TRAJ6) that was conserved across donors. By trapping a CD1d-type II NKT TCR complex for direct mass spectrometric analysis, we detected molecules that allow binding of CD1d to TCRs, finding that both PBF and short-chain sphingomyelin lipids are present in these complexes. Furthermore, the combination of PPBF and short-chain sphingomyelin enhances CD1d tetramer staining of PPBF-reactive T cell lines over either molecule alone. This study demonstrates that non-lipidic small molecules, that resemble sulfa-drugs implicated in systemic hypersensitivity and drug allergy reactions, activate a polyclonal population of type II NKT cells in a CD1d-restricted manner.Significance StatementWhereas T cells are known to recognize peptide, vitamin B metabolite or lipid antigens, we identify several non-lipidic small molecules, pentamethylbenzofuransulfonates (PBFs), that activate a population of CD1d-restricted NKT cells. This represents a breakthrough in the field of NKT cell biology. This study also reveals a previously unknown population of PBF-reactive NKT cells in healthy individuals with stereotyped receptors that paves the way for future studies of the role of these cells in immunity, including sulfa-drug hypersensitivity.
A genetically encoded fluorescent biosensor for extracellular L-lactate
Authors: Nasu Yusuke , Murphy-Royal Ciaran , Wen Yurong , Haidey Jordan , Molina M. Rosana S. , Aggarwal Abhi , Zhang Shuce , Kamijo Yuki , Paquet Marie-Eve , Podgorski Kaspar , Drobizhev Mikhail , Bains Jaideep S. , Joanne Lemieux M. , Gordon Grant R. , Campbell Robert E. 
Published: March 2021

AbstractTo enable investigations of the emerging roles of cell-to-cell shuttling of L-lactate, we have developed an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. We demonstrate that this biosensor, designated eLACCO1.1, enables minimally invasive cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.
Reciprocal recombination reflects sexual reproduction in symbiotic arbuscular mycorrhizal fungi
Authors: Mateus Ivan D. , Auxier Ben , Ndiaye Mam M. S. , Cruz Joaquim , Lee Soon-Jae , Sanders Ian R. 
Published: March 2021

AbstractArbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and contain either one or two haploid nuclear genotypes (monokaryon and dikaryon) identified by the alleles at a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite identification of a putative mating-type locus and functional activation of genes related to mating when two isolates co-exist, it remains unknown if AMF take part in a mainly sexual life cycle.We used publicly available genome sequences to test if dikaryon genomes display signatures of sexual reproduction in the form of reciprocal recombination patterns, or if they display signatures of parasexual reproduction involving gene conversion.We used short-read and long-read sequence data to identify nucleus genotype-specific haplotypes within dikaryons and then compared them to orthologous gene sequences from related monokaryon isolates displaying the same putative MAT-types. We observed that these genotype-specific haplotypes display reciprocal recombination and not gene conversion.These results are consistent with a sexual origin of the dikaryon rather than a parasexual origin and provides an important step to understand the life cycle of these globally important symbiotic fungi.
Genomic structure and diversity of oak populations in British Parklands
Authors: Nocchi Gabriele , Brown Nathan , Coker Tim , Plumb William , Stocks Jonathan , Denman Sandra , Buggs Richard 
Published: March 2021

AbstractThe two predominant oak species in Britain areQuercus robur(English or pedunculate oak) andQ. petraea(sessile oak). We sequenced the whole genomes of 386 oak trees from four British parkland sites and found over 50 million nuclear single nucleotide polymorphisms (SNPs), allowing us to identify 360Q. robur, tenQ. petraeaand 16 hybrid individuals using clustering methods. ComparingQ. roburandQ. petraeatrees from Attingham Park, we found that the nuclear genomes of the two species are largely undifferentiated but identified 81 coding regions exhibiting strong interspecific differentiation. The nuclear genomes of our 360Q. roburindividuals showed no clear differentiation among the four parkland sites. Scans for selective sweeps inQ. roburhighlighted regions containing genes with putative involvement in stress tolerance, one of which was moderately differentiated fromQ. petraea. Reconstructions of past effective population sizes suggested a long population size decline in bothQ. roburandQ. petraeaover the Pleistocene, but population growth after the last glacial maximum. We assembled the whole chloroplast genomes of 287Q. robur, 8Q. petraeaand 14 hybrid trees. In a phylogenetic network, these fell into five major haplotypes, which were shared among species but differed in frequency among parkland sites. We matched our chloroplast genome haplotypes to restriction enzyme fragment haplotypes identified in older studies that had surveyed ancient woodlands in Britain and much of Europe. This suggested that the parkland populations in our study derive from local seed sources.
3D Cell Neighbour Dynamics in Growing Pseudostratified Epithelia
Authors: Gómez Harold F. , Dumont Mathilde S. , Hodel Leonie , Vetter Roman , Iber Dagmar 
Published: March 2021

ABSTRACTDuring morphogenesis, epithelial sheets remodel into complex geometries. How cells dynamically organize their contact with neighbouring cells in these tightly packed tissues is poorly understood. We have used light-sheet microscopy of growing mouse embryonic lung explants, three-dimensional cell segmentation, and physical theory to unravel the principles behind 3D cell organization in growing pseudostratified epithelia. We find that cells have highly irregular 3D shapes and exhibit numerous neighbour intercalations along the apical-basal axis as well as over time. Despite the fluidic nature, the cell packing configurations follow fundamental relationships previously described for apical epithelial layers, i.e., Euler’s formula, Lewis’ law, and Aboav-Weaire’s law, at all times and across the entire tissue thickness. This arrangement minimizes the lateral cell-cell surface energy for a given cross-sectional area variability, generated primarily by the distribution and movement of nuclei. We conclude that the complex 3D cell organization in growing epithelia emerges from simple physical principles.
TheMycobacterium tuberculosistransposon sequencing database (MtbTnDB): a large-scale guide to genetic conditional essentiality
Authors: Jinich Adrian , Zaveri Anisha , DeJesus Michael A. , Flores-Bautista Emanuel , Almada-Monter Ricardo , Smith Clare M. , Sassetti Christopher M. , Rock Jeremy M. , Ehrt Sabine , Schnappinger Dirk , Ioerger Thomas R. , Rhee Kyu Y. 
Published: March 2021

AbstractCharacterizing genetic essentiality across various conditions is fundamental for understanding gene function. Transposon sequencing (TnSeq) is a powerful technique to generate genome-wide essentiality profiles in bacteria and has been extensively applied toMycobacterium tuberculosis(Mtb). Dozens of TnSeq screens have yielded valuable insights into the biology of Mtb in vitro, inside macrophages, and in model host organisms. Despite their value, these Mtb TnSeq profiles have not been standardized or collated into a single, easily searchable database. This results in significant challenges when attempting to query and compare these resources, limiting our ability to obtain a comprehensive and consistent understanding of genetic conditional essentiality in Mtb. We address this problem by building a central repository of publicly available Mtb TnSeq screens, the Mtb transposon sequencing database (MtbTnDB). The MtbTnDB is a living resource that encompasses to date ≈150 standardized TnSeq screens, enabling open access to data, visualizations, and functional predictions through an interactive web app (www.mtbtndb.app). We conduct several statistical analyses on the complete database, such as demonstrating that (i) genes in the same genomic neighborhood have similar TnSeq profiles, and (ii) clusters of genes with similar TnSeq profiles are enriched for genes from similar functional categories. We further analyze the performance of machine learning models trained on TnSeq profiles to predict functional annotation of orphan genes in Mtb. By facilitating the comparison of TnSeq screens across conditions, the MtbTnDB will accelerate the exploration of conditional genetic essentiality, provide insights into the functional organization of Mtb genes, and help predict gene function in this important human pathogen.
A Biosensor for Detection of Indole Metabolites
Authors: Wang Jiefei , Zhang Chao , Childers W. Seth 
Published: March 2021

ABSTRACTThe lack of diverse health-related biosensors limits the progress towards our understanding of how the microbiome metabolism impacts health. Microbially produced indole-3-aldehyde (I3A) has been associated with reducing inflammation in diseases such as ulcerative colitis by stimulating the aryl hydrocarbon receptor (AhR) pathway. We mined the protein database for gut microbiome metabolites’ sensors and developed a biosensor for I3A. We engineeredE. coliembedded with a single plasmid carrying a chimeric two-component system that detects I3A. Our I3A receptor characterization identified residues that contribute to the sensor’s high specificity in a range of 0.1-10 µM. The I3A biosensor opens the door to sensing indole metabolites produced at the host-microbe interface and provides new parts for synthetic biology applications.
Long-read sequencing of SARS-CoV-2 reveals novel transcripts and a diverse complex transcriptome landscape
Authors: Li-Pook-Than Jennifer , Banuelos Selene , Honkala Alexander , Sahoo Malaya K. , Pinsky Benjamin A. , Snyder Michael P. 
Published: March 2021

AbstractSevere Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2 (COVID-19), is a positive single-stranded RNA virus with a 30 kb genome that is responsible for the current pandemic. To date, the genomes of global COVID-19 variants have been primarily characterized via short-read sequencing methods. Here, we devised a long-read RNA (IsoSeq) sequencing approach to characterize the COVID-19 transcript landscape and expression of its ∼27 coding regions. Our analysis identified novel COVID-19 transcripts including a) a short ∼65-70 nt 5’-UTR fused to various downstream ORFs encoding accessory proteins such as the envelope, ORF 8, and ORF 9 (nucleocapsid) proteins, that are relatively highly expressed, b) novel SNVs that are differentially expressed, whereby a subset are suggestive of partial RNA editing events, and c) SNVs at functional sites, whereby at least one is associated with a differentially expressed spike protein isoform. These previously uncharacterized COVID-19 isoforms, expressed genes, and gene variants were corroborated using ddPCR. Understanding this transcriptional complexity may help provide insight into the biology and pathogenicity of SARS-CoV-2 compared to other coronaviruses.