bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drinking water chlorination impact on fecal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae in Bangladeshi children in a double-blind, cluster-randomized controlled trial
Authors: Montealegre Maria Camila , Greenwood Esther E. , Teichmann Lisa , Nadimpalli Maya L. , Caduff Lea , Swarthout Jenna M. , Nydegger Tabea , Sultana Sonia , Islam Mohammad Aminul , Lanza Val F. , Luby Stephen P. , Pickering Amy J. , Julian Timothy R. 
Published: April 2022

SUMMARYBackgroundWater, sanitation, and hygiene (WASH) services have the potential to interrupt transmission of antimicrobial-resistant bacteria and reduce the need for antibiotics, thereby reducing selection for resistance. However, evidence of WASH impacts on antimicrobial resistance (AMR) is lacking.MethodsWe evaluated extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and ESBL-KESC (Klebsiella spp., Enterobacter spp., Serratia spp., and Citrobacter spp.) carriage in the feces of 479 Bangladeshi children under 5 years of age enrolled in a double-blind, cluster-randomized controlled trial of in-line drinking water chlorination in two low-income urban communities in Bangladesh. We additionally assessed the intervention’s impact on circulating beta-lactamase genes in fecal metagenomes and in genomes of fecal ESBL-E. coli isolates.FindingsWe detected ESBL-E. coli in 65% (n = 309) and ESBL-KESC in 12% (n = 56) of enrolled children. We observed no effect of the intervention on the prevalence of ESBL-E. coli (relative risk [95% confidence interval] = 0.98 [0.78, 1.23]) when controlling for study site and age. Although ESBL-KESC (0.76 [0.44, 1.29]) was lower among children in the intervention group, the relative risk was not significant. Concentrations of ESBL-E. coli (log10 CFU/g-wet) were on average [95% confidence interval] 0.13 [-0.16, 0.42] higher in the intervention group and ESBL-KESC (log10 CFU/g-wet) were 0.10 [-0.22, 0.02], lower in the intervention group, when controlling for study site and age. Furthermore, the distribution of ESBL-E.coli sequence types, type of beta-lactamase-encoding genes in ESBL-E. coli isolates, and the presence and relative abundance of beta-lactamase-encoding genes in children’s fecal metagenomes did not differ significantly between the intervention and control children.InterpretationOne year of in-line drinking water chlorination in communities did not meaningfully impact the carriage of ESBL-E. coli among children in an area of high ESBL-E. coli carriage. While ESBL-KESC was at lower prevalence than ESBL-E. coli, in the intervention group, limited study power prevented a clear interpretation of treatment effect. Development and evaluation of effective interventions to reduce AMR carriage are needed to support calls for WASH embedded in current National and Global AMR Action Plans.
Protist diversity and metabolic strategy in freshwater lakes are shaped by trophic state and watershed land use at a continental scale
Authors: Garner Rebecca E. , Kraemer Susanne A. , Onana Vera E. , Huot Yannick , Gregory-Eaves Irene , Walsh David A. 
Published: April 2022

AbstractProtists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. Yet, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic extent covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high- nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies at smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information in further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors.ImportanceFreshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
Evidence of attack deflection suggests adaptive evolution of wing tails in butterflies
Authors: Chotard Ariane , Ledamoisel Joséphine , Decamps Thierry , Herrel Anthony , Chaine Alexis , Llaurens Violaine , Debat Vincent 
Published: April 2022

AbstractPredation is a powerful selective force shaping many behavioural and morphological traits in prey species. The deflection of predator attacks from vital parts of the prey usually involves the coordinated evolution of prey body shape and colour. Here, we test the deflection effect of hindwing tails in the swallowtail butterflyIphiclides podalirius. In this species, hindwings display long tails associated with a conspicuous colour pattern. By surveying the wings within a wild population ofI. podalirius, we observed that wing damage was much more frequent on the tails. We then used a standardised behavioural assay employing dummy butterflies with realI. podaliriuswings to study the location of attacks by great titsParus major. Wing tails and conspicuous coloration of the hindwings were struck more often than the rest of the body by birds. Finally, we characterised the mechanical properties of fresh wings and found that the tail vein was more fragile than the others, suggesting facilitated escape ability of butterflies attacked at this location. Our results clearly support the deflective effect of hindwing tails and suggest that predation is an important selective driver of the evolution of wing tails and colour pattern in butterflies.
Overexpression of TopBP1 leads to transformation with a TP53 mutation of non-tumorigenic breast epithelial cells
Authors: Umesh Rintu M , Lahiri Mayurika 
Published: April 2022

AbstractDNA topoisomerase IIβ - binding protein 1 (TopBP1) is a mediator protein that regulates the cell cycle checkpoint signaling pathway. A plethora of studies suggests high TopBP1 levels are positively associated with various cancers. Although TopBP1 transcript, as well as protein expression levels, are high in breast cancers, its role in breast tumorigenesis is not yet explored. In our studies, we observed that TopBP1 levels are high in premalignant and malignant cells of the MCF10A cancer progression series compared to the non-tumorigenic MCF10A cells. In order to establish the role of TopBP1 in tumorigenesis, TopBP1 overexpression in non-tumorigenic MCF10A, and stable knock-down in malignant MCF10CA1a cells were performed and grown in Matrigel™ as breast spheroids.Overexpression of TopBP1 in MCF10A spheroids induced hyperproliferation, disruption of polarity and cell-cell junctions. Moreover, TopBP1 overexpressing 3D dissociated cells exhibited EMT-like phenotype and tumorigenic properties such as increased cell migration, invasion, colony formation capabilitiy and anchorage-independent growth, indicating acquisition of cellular transformation. Finally, we demonstrated TopBP1 overexpressing cells to form tumors in athymic mice thereby confirming their tumorigenic potential. We also confirmed that overexpression of TopBP1 led to a mutation in TP53 and other genomic insults. To summarise, we observed that ectopic expression of TopBP1 transforms MCF10A breast epithelial cells. These transformed cells harbour phenotypic and genotypic characteristics similar to that of malignant cells.
Flagellar Motility During E. Coli Biofilm Formation Provides a Competitive Disadvantage Which Recedes in the Presence of Co-Colonizers
Authors: Ben Youssef Wafa , Deforet Maxime , Monmeyran Amaury , Henry Nelly 
Published: April 2022

AbstractIn nature, bacteria form biofilms in very diverse environments, involving a range of specific properties and exhibiting competitive advantages for surface colonization. However, the underlying mechanisms are difficult to decipher. In particular, the contribution of cell flagellar motility to biofilm formation remains unclear. Here, we examined the ability of motile and nonmotile E. coli cells to form a biofilm in a well-controlled geometry, both in a simple situation involving a single-species biofilm and in the presence of co-colonizers. Using a millifluidic channel, we determined that motile cells have a clear disadvantage in forming a biofilm, exhibiting a long delay as compared to nonmotile cells. By monitoring biofilm development in real time, we observed that the decisive impact of flagellar motility on biofilm formation consists in the alteration of surface access time. Implementing a simple mathematical model to calculate surface access velocity for both motile (diffusion) and nonmotile (settling) cells, we discovered that the competitive advantage strongly depends on the geometry of the environment to be colonized. Interestingly, this advantage reverts for the smallest geometries, with a crossover at a height of 100 μm. We also report that the difference between and nonmotile cells in the ability to form a biofilm diminishes in the presence of cocolonizers, which could be due to motility inhibition through the consumption of key resources by the co-colonizers. We conclude that the impact of flagellar motility on surface colonization closely depends on the environment geometry and the population features, suggesting a unifying vision of the role of cell motility in surface colonization and biofilm formation.
Myosin Heavy Chain Converter Domain Mutations Drive Early-Stage Changes in Extracellular Matrix Dynamics in Hypertrophic Cardiomyopathy
Authors: Hsieh Jeanne , Becklin Kelsie , Givens Sophie , Komosa Elizabeth R. , Abrahante Lloréns Juan E. , Kamdar Forum , Moriarity Branden S. , Webber Beau R. , Singh Bhairab N. , Ogle Brenda M. 
Published: April 2022

AbstractMore than 60% of hypertrophic cardiomyopathy (HCM)-causing mutations are found in the gene loci encoding cardiac myosin-associated proteins including myosin heavy chain (MHC) and myosin binding protein C (MyBP-C). Moreover, patients with more than one independent HCM mutation may be at increased risk for more severe disease expression and adverse outcomes. However detailed mechanistic understanding, especially at early stages of disease progression, is limited. To identify early-stage HCM triggers, we generated single (MYH7 c.2167C>T [R723C] with a known pathogenic significance in the MHC converter domain) and double (MYH7 c.2167C>T [R723C]; MYH6 c.2173C>T [R725C] with unknown significance) myosin gene mutations in human induced pluripotent stem cells (hiPSCs) using a base-editing strategy. Cardiomyocytes (CMs) derived from hiPSCs with either single or double mutation exhibited phenotypic characteristics consistent with later-stage HCM including hypertrophy, multinucleation, altered calcium handling, metabolism and arrhythmia. We then probed mutant CMs at time points prior to the detection of known HCM characteristics. We found MYH7/MYH6 dual mutation dysregulated extracellular matrix (ECM) remodeling, altered integrin expression, and interrupted cell-ECM adhesion by limiting the formation of focal adhesions. These results point to a new phenotypic feature of early-stage HCM and reveal novel therapeutic avenues aimed to delay or prohibit disease onset.
Extracellular Vesicle Antibody Microarray for Multiplexed Inner and Outer Protein Analysis
Authors: Martel Rosalie , Shen Molly L. , DeCorwin-Martin Philippe , de Araujo Lorenna Oliveira Fernandes , Juncker David 
Published: April 2022

AbstractProteins are found both outside and inside of extracellular vesicles (EVs) and govern the properties and functions of EVs, while also constituting a signature of the cell of origin and of biological function and disease. Outer proteins on EVs can be directly bound by antibodies to either enrich EVs, or probe the expression of a protein on EVs, including in a combinatorial manner. However, co-profiling of inner proteins remains challenging. Here, we present the high-throughput, multiplexed analysis of extracellular vesicle inner and outer proteins (EVPio). We describe the optimization of fixation and heat-induced protein epitope retrieval for EVs, along with oligo-barcoded antibodies and branched DNA signal amplification for sensitive, multiplexed and high-throughput assays. We captured 4 subpopulations of EVs from colorectal cancer cell lines HT29 and SW403 based on EpCAM, CD9, CD63 and CD81 expression, and quantified the co-expression of 8 outer (integrins and tetraspanins) and 4 inner (heat shock, endosomal and inner leaflet) proteins. The differences in co-expression patterns were consistent with the literature and known biological function. In conclusion, EVPio analysis can simultaneously detect multiple inner and outer proteins in EVs immobilized on a surface, opening the way to extensive combinatorial protein profiles for both discovery and clinical translation.
Barcoding genetically distinctPlasmodium falciparumstrains for comparative assessment of fitness and antimalarial drug resistance
Authors: Carrasquilla Manuela , Drammeh Ndey Fatou , Rawat Mukul , Sanderson Theo , Zenonos Zenon , Rayner Julian C , Lee Marcus CS 
Published: April 2022

AbstractThe repeated emergence of antimalarial drug resistance inPlasmodium falciparum, including to the current frontline antimalarial artemisinin, is a perennial problem for malaria control. Nextgeneration sequencing has greatly accelerated the identification of polymorphisms in resistance-associated genes, but has also highlighted the need for more sensitive and accurate laboratory tools to profile current and future antimalarials, and to quantify the impact of drug resistance acquisition on parasite fitness. The interplay of fitness and drug response is of fundamental importance in understanding why particular genetic backgrounds are better at driving the evolution of drug resistance in natural populations, but the impact of parasite fitness landscapes on the epidemiology of drug resistance has typically been laborious to accurately quantify in the lab, with assays being limited in accuracy and throughput. Here we present a scalable method to profile fitness and drug response of genetically distinctP. falciparumstrains with well-described sensitivities to several antimalarials. We leverage CRISPR/Cas9 genome-editing and barcode sequencing to track unique barcodes integrated into a non-essential gene (pfrh3). We validate this approach in multiplex competitive growth assays of three strains with distinct geographical origins. Furthermore, we demonstrate that this method can be a powerful approach for tracking artemisinin response as it can identify an artemisinin resistant strain within a mix of multiple parasite lines, suggesting an approach for scaling the laborious ring-stage survival assay (RSA) across libraries of barcoded parasite lines. Overall, we present a novel high-throughput method for multiplexed competitive growth assays to evaluate parasite fitness and drug response
RNA decay defines the response to transcriptional perturbation in leukaemia
Authors: Todorovski Izabela , Feran Breon , Fan Zheng , Gadipally Sreeja , Yoannidis David , Kong Isabella Y , Bjelosevic Stefan , Zethoven Magnus , Hawkins Edwin D , Simpson Kaylene J , Arnau Gisela Mir , Papenfuss Anthony T , Johnstone Ricky W , Vervoort Stephin J 
Published: April 2022

AbstractTherapeutic targeting of dysregulated transcriptional programs has arisen as a promising strategy for the treatment of leukaemias. The therapeutic response to small molecule inhibitors of Bromodomain-Containing Proteins (BRD), such as BRD2 and BRD4, P300/cAMP-response element binding protein (CBP) and Cyclin Dependent Kinases (CDKs), is generally attributed to the selective disruption of oncogenic gene expression networks driven by enhancers, super-enhancers (SEs) and lineage-specific transcription factors (TFs), including thec-MYConcogene. Using technologies such as thiol (SH)-linked alkylation for the metabolic sequencing of RNA sequencing (SLAM-seq) to profile messenger RNA (mRNA) decay and production rates, we demonstrate that gene intrinsic properties largely govern the selectivity associated with transcriptional inhibition, where total mRNA response signatures are dominated with genes that have short transcript half-lives, including those regulated by SEs and oncogenic TFs. Further highlighting that gene sensitivities only occur in the context of short transcript half-lives, stabilisation of thec-MYCtranscript through changes in the 3’ UTR rendered it insensitive to transcriptional targeting. However, this was not sufficient to rescuec-MYCtarget gene transcription and anti-leukaemia effects following transcriptional inhibition. Importantly, long-lived mRNAs encoding essential genes that evade transcriptional targeting can be rendered sensitive via modulation of mRNA decay kinetics through inhibition of the RNA Binding Protein (RBP), ELAV Like RNA binding protein 1 (ELAVL1)/ Human Antigen R (HuR). Taken together, these data demonstrate that mRNA decay shapes the therapeutic response to transcriptional perturbation and can be modulated for novel therapeutic outcomes using transcriptional agents in leukaemia.
Functional plasticity and recurrent cell states of malignant B cells in follicular lymphoma
Authors: Attaf Noudjoud , Dong Chuang , Gil Laurine , Cervera-Marzal Inãki , Gharsalli Tarek , Navarro Jean-Marc , Mboumba Diana-Laure , Chasson Lionel , Lemonnier François , Gaulard Philippe , Roulland Sandrine , Spinelli Lionel , Nadel Bertrand , Milpied Pierre 
Published: April 2022

ABSTRACTFollicular lymphoma (FL) derives from malignant transformation of germinal center (GC) B cells. FL malignant B cells are heterogeneous and diverge from their GC B cell-of-origin, but the diversity, function, and location of malignant B cell states remain to be addressed. Based on integrative single-cell RNA-seq, we identified and studied recurrent FL malignant B cell states and dynamics. Most FL B cells spanned a continuum of states from proliferating GC-like to quiescent memory (Mem)-like cell states. That GC-to-Mem axis was the main source of intra-tumor transcriptional heterogeneity. While FL B cell states were independent from subclonal B cell receptor genetics divergence, T follicular helper (TFH) cell-derived signals controlled the transition from Mem-like to GC-like states. GC-like, TFH-activated and Mem-like FL B cells tended to occupy distinct niches within and around tumor follicles. Our study characterizes novel malignant cell states recurrent in B cell lymphomas, and highlights the functional plasticity of malignant B cells.
SOX9 binds TCFs to mediate Wnt/β-catenin target gene activation
Authors: Ramakrishnan Aravinda-Bharathi , Burby Peter E. , Adiga Kavya , Cadigan Ken M. 
Published: April 2022

AbstractActivation of the Wnt/β-catenin pathway regulates gene expression by promoting the formation of a β-catenin-TCF complex on target gene chromatin. The transcription factor SOX9 antagonises Wnt signalling in many contexts through its ability to down-regulate β-catenin protein levels. Here, we find that SOX9 promotes the proliferation of Wnt-driven colorectal cancer (CRC) cells. We identify multiple enhancers activated by SOX9 working in concert with the Wnt pathway. These enhancers are co-occupied by TCFs and SOX9 and contain TCF and SOX9 binding sites that are necessary for transcriptional activation. In addition, we identify a physical interaction between the DNA-binding domains of TCFs and SOX9 and show that TCF-SOX9 interactions are important for target gene regulation and CRC cell growth. Our work demonstrates a highly context-dependent effect of SOX9 on Wnt targets, with activation or repression being dependent on the presence or absence of SOX9 binding sites on Wnt-regulated enhancers respectively.