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Biomicrofluidics Jul 2022Microfluidic tools are well suited for studying bacteria as they enable the analysis of small colonies or single cells. However, current techniques for studying...
Microfluidic tools are well suited for studying bacteria as they enable the analysis of small colonies or single cells. However, current techniques for studying bacterial response to antibiotics are largely limited to static dosing. Here, we describe a microfluidic device and a method for entrapping and cultivating bacteria in hydrogel plugs. Ring-shaped isolation valves are used to define the shape of the plugs and also to control exposure of the plugs to the surrounding medium. We demonstrate bacterial cultivation, determination of the minimum inhibitory concentration of an antibiotic, and transient dosing of an antibiotic at sub-1-h doses. The transient dosing experiments reveal that at dose durations on the order of minutes, ampicillin's bactericidal effect has both a time and concentration dependency.
PubMed: 35935120
DOI: 10.1063/5.0091704 -
MBio May 2020Different species exposed to a common stress may adapt by mutations in shared pathways or in unique systems, depending on how past environments have molded their...
Different species exposed to a common stress may adapt by mutations in shared pathways or in unique systems, depending on how past environments have molded their genomes. Understanding how diverse bacterial pathogens evolve in response to an antimicrobial treatment is a pressing example of this problem, where discovery of molecular parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in environments containing antibiotics, combined with periodic whole-population genome sequencing, can be used to identify many contending routes to antimicrobial resistance. We separately propagated two clinically relevant Gram-negative pathogens, and , in increasing concentrations of tobramycin in two different environments each: planktonic and biofilm. Independently of the pathogen, the populations adapted to tobramycin selection by parallel evolution of mutations in , encoding elongation factor G, and , encoding phosphoenolpyruvate phosphotransferase. As neither gene is a direct target of this aminoglycoside, mutations to either are unexpected and underreported causes of resistance. Additionally, both species acquired antibiotic resistance-associated mutations that were more prevalent in the biofilm lifestyle than in the planktonic lifestyle; these mutations were in electron transport chain components in and lipopolysaccharide biosynthesis enzymes in populations. Using existing databases, we discovered site-specific parallelism of mutations that extends across bacterial phyla and clinical isolates. This study suggests that strong selective pressures, such as antibiotic treatment, may result in high levels of predictability in molecular targets of evolution, despite differences between organisms' genetic backgrounds and environments. The rise of antimicrobial resistance is a leading medical threat, motivating efforts to forecast both its evolutionary dynamics and its genetic causes. Aminoglycosides are a major class of antibiotics that disrupt translation, but resistance may occur by a number of mechanisms. Here, we show the repeated evolution of resistance to the aminoglycoside tobramycin in both and via mutations in , encoding elongation factor G, and , encoding the nitrogen-specific phosphotransferase system. Laboratory evolution and whole-population genome sequencing were used to identify these targets, but mutations at identical amino acid positions were also found in published genomes of diverse bacterial species and clinical isolates. We also identified other resistance mechanisms associated with growth in biofilms that likely interfere with drug binding or uptake. Characterizing the evolution of multiple species in the presence of antibiotics can identify new, repeatable causes of resistance that may be predicted and counteracted by alternative treatment.
Topics: Acinetobacter baumannii; Anti-Bacterial Agents; Biofilms; Directed Molecular Evolution; Drug Resistance, Bacterial; Microbial Sensitivity Tests; Mutation; Peptide Elongation Factor G; Pseudomonas aeruginosa; Tobramycin; Whole Genome Sequencing
PubMed: 32457248
DOI: 10.1128/mBio.00932-20 -
Molecular Systems Biology Sep 2022Current strategies to improve the throughput of continuous directed evolution technologies often involve complex mechanical fluid-controlling system or robotic...
Current strategies to improve the throughput of continuous directed evolution technologies often involve complex mechanical fluid-controlling system or robotic platforms, which limits their popularization and application in general laboratories. Inspired by our previous study on bacterial range expansion, in this study, we report a system termed SPACE for rapid and extensively parallelizable evolution of biomolecules by introducing spatial dimensions into the landmark phage-assisted continuous evolution system. Specifically, M13 phages and chemotactic Escherichia coli cells were closely inoculated onto a semisolid agar. The phages came into contact with the expanding front of the bacterial range, and then comigrated with the bacteria. This system leverages competition over space, wherein evolutionary progress is closely associated with the production of spatial patterns, allowing the emergence of improved or new protein functions. In a prototypical problem, SPACE remarkably simplified the process and evolved the promoter recognition of T7 RNA polymerase (RNAP) to a library of 96 random sequences in parallel. These results establish SPACE as a simple, easy to implement, and massively parallelizable platform for continuous directed evolution in general laboratories.
Topics: Agar; Bacteria; Bacteriophages; Escherichia coli; Promoter Regions, Genetic
PubMed: 36129229
DOI: 10.15252/msb.202210934 -
Journal of Evolutionary Biology Jan 2021Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide... (Comparative Study)
Comparative Study
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxF > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
Topics: Animals; Biological Evolution; Bivalvia; Gene Flow; Genetic Introgression; Introduced Species; RNA, Long Noncoding; Transcriptome
PubMed: 33251632
DOI: 10.1111/jeb.13746 -
JMIR Research Protocols Aug 2022Predictive theoretical models suggest that health knowledge works in conjunction with motivation and behavioral skills to influence adolescents' obesogenic behavior....
A Web-Based Intervention to Improve Health Literacy and Obesogenic Behaviors Among Adolescents: Protocol of a Randomized Pilot Feasibility Study for a Parallel Randomized Controlled Trial.
BACKGROUND
Predictive theoretical models suggest that health knowledge works in conjunction with motivation and behavioral skills to influence adolescents' obesogenic behavior. However, most of the existing adolescent interventions target these variables in isolation. Furthermore, health literacy (HL), a precursor to health knowledge, is necessary for translating health knowledge into behavior and is negatively related to adolescents' obesity status. However, HL has not been included in obesity interventions targeting adolescents.
OBJECTIVE
This study aims to pilot the feasibility of a 2-armed web-based obesity prevention intervention in school settings and assess the preliminary effectiveness of adding an HL module to an obesity prevention intervention for adolescents.
METHODS
This web-based pilot feasibility study will take place in the Northeastern United States. Participants will be adolescents (aged 13-16 years) attending school, and recruitment will be conducted through flyers to parents and adolescents in participating classes or advisory groups at the school. The intervention includes 2 arms: an experimental arm that will receive an HL module and 3 obesity prevention modules and a comparison arm that will receive a vaping module and 3 obesity prevention modules. A blinded randomized procedure will be used to allocate classrooms and advisory groups to the experimental and comparison arms. The intervention will be fully web-based. Participants will complete measures of their HL and obesogenic behavior-related health knowledge, motivation, and behaviors at 3 time points (baseline, 1 month after the intervention, and 3 months after the intervention) via web-based surveys. The primary outcomes will be the measures of study feasibility (recruitment, retention, completion, and treatment fidelity rates). Secondary outcomes will be preliminary efficacy, as measured by logistic and linear regressions and calculation of effect sizes. Descriptive statistics will be calculated for all measures at each time point.
RESULTS
This study was approved by the City University of New York Institutional Review Board in August 2020. As of June 2022, the web-based intervention design is complete and ready for use. Recruitment, data collection, and intervention implementation are scheduled to begin in September 2022. These results are expected to be published in 2023.
CONCLUSIONS
This study's feasibility findings will inform changes to the intervention content and randomized controlled trial design. The study's efficacy findings will inform the sample size for the full-scale randomized controlled trial and the preliminary utility of the intervention.
TRIAL REGISTRATION
ClinicalTrials.gov NCT04252677; https://clinicaltrials.gov/ct2/show/NCT04252677.
INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)
PRR1-10.2196/40191.
PubMed: 35972787
DOI: 10.2196/40191 -
Frontiers in Computational Neuroscience 2023Over the past decade a body of work has emerged and shown the disruptive potential of neuromorphic systems across a broad range of studies, often combining novel machine...
Over the past decade a body of work has emerged and shown the disruptive potential of neuromorphic systems across a broad range of studies, often combining novel machine learning models and nanotechnologies. Still, the scope of investigations often remains limited to simple problems since the process of building, training, and evaluating mixed-signal neural models is slow and laborious. In this paper, we introduce an open-source framework, called EBANA, that provides a unified, modularized, and extensible infrastructure, similar to conventional machine learning pipelines, for building and validating analog neural networks (ANNs). It uses Python as interface language with a syntax similar to Keras, while hiding the complexity of the underlying analog simulations. It already includes the most common building blocks and maintains sufficient modularity and extensibility to easily incorporate new concepts, electrical, and technological models. These features make EBANA suitable for researchers and practitioners to experiment with different design topologies and explore the various tradeoffs that exist in the design space. We illustrate the framework capabilities by elaborating on the increasingly popular Energy-Based Models (EBMs), used in conjunction with the local Equilibrium Propagation (EP) training algorithm. Our experiments cover 3 datasets having up to 60,000 entries and explore network topologies generating circuits in excess of 1,000 electrical nodes that can be extensively benchmarked with ease and in reasonable time thanks to the native EBANA parallelization capability.
PubMed: 36936192
DOI: 10.3389/fncom.2023.1114651 -
Gastroenterology Report 2024Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice... (Review)
Review
Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice are frequently employed due to their practicality and genetic manipulability. However, for studies aiming to closely mimic human pathology, non-human primates such as monkeys and dogs offer valuable physiological parallels. Guinea pigs, while less commonly used, present unique advantages for investigating the intricate interplay between neurological and immunological factors in IBD. Additionally, New Zealand rabbits excel in endoscopic biopsy techniques, providing insights into mucosal inflammation and healing processes. Pigs, with their physiological similarities to humans, serve as ideal models for exploring the complex relationships between nutrition, metabolism, and immunity in IBD. Beyond mammals, non-mammalian organisms including zebrafish, , and nematodes offer specialized insights into specific aspects of IBD pathology, highlighting the diverse array of model systems available for advancing our understanding of this multifaceted disease. In this review, we conduct a thorough analysis of various animal models employed in IBD research, detailing their applications and essential experimental parameters. These include clinical observation, Disease Activity Index score, pathological assessment, intestinal barrier integrity, fibrosis, inflammatory markers, intestinal microbiome, and other critical parameters that are crucial for evaluating modeling success and drug efficacy in experimental mammalian studies. Overall, this review will serve as a valuable resource for researchers in the field of IBD, offering insights into the diverse array of animal models available and their respective applications in studying IBD.
PubMed: 38634007
DOI: 10.1093/gastro/goae021 -
Heliyon Jul 2022This paper proposes an approach to the real time simulation of photovoltaic (PV) arrays that are subjected to mismatching conditions, e.g. partial shadowing. The method,...
This paper proposes an approach to the real time simulation of photovoltaic (PV) arrays that are subjected to mismatching conditions, e.g. partial shadowing. The method, which has been named Model by Zone (MbZ), adopts the best PV model depending on the operating conditions of the cells in the module: it switches among single-diode model (SDM), linear model and constant voltage model. An optimized digital hardware architecture exploiting parallelism of operations over a FPGA system is exploited to effectively implement the proposed model. It reduces the computation time and the use of hardware resources. The good trade-off between accuracy and computation time of the proposed technique has been demonstrated in two cases of study: by evaluating the long-term PV power production of a PV field subjected to dynamic shadowing conditions and by analyzing the model performance in a maximum power point tracking (MPPT) application. In the former case, the proposed approach improves the computation time by with respect to methods that are available in recent literature, with a Relative Error (RE) at the Global Maximum Power Point (GMPP) lower than . In the MPPT application, the proposed technique allows to achieve a MAPE of and in the string voltage and power calculation, respectively.
PubMed: 35898607
DOI: 10.1016/j.heliyon.2022.e09969 -
BMJ Open Apr 2022Glaucoma is a progressive, chronic condition that can have a significant impact on a patient's health-related quality of life (HRQoL). Validated, disease-specific HRQoL...
INTRODUCTION
Glaucoma is a progressive, chronic condition that can have a significant impact on a patient's health-related quality of life (HRQoL). Validated, disease-specific HRQoL tools such as the Health Utility for Glaucoma (HUG-5) tool and the Glaucoma Quality of Life Questionnaire (GlauQoL-17) can be used to monitor a patient's quality of life. However, the utility of these tools in outpatient clinic practice is not well established. The primary objective of this study is to characterise the feasibility of administering periodic HRQoL questionnaires in glaucoma using a semi-automated workflow.
METHODS AND ANALYSIS
This study will be a single-centre, unblinded, randomised, parallel-group study with an exploratory data analysis framework. We aim to determine the feasibility of administering the HUG-5 in an outpatient clinic using a semi-automated workflow and determine patient engagement through email and telephone contact methods. We will also be investigating the association of the HUG-5 and GlauQoL-17 with patient visual field testing and visual acuity. Mean differences between groups will be tested with analysis of variance to determine if the frequency of calls affects burden, satisfaction and perceived value of information.
ETHICS AND DISSEMINATION
This study has been approved by the Hamilton Integrated Research Ethics board (ID: 13046) and will be conducted within Canadian Tri-Council Statement policy. Personal information of the study's participants will be anonymised with identification codes and data will be kept on an encrypted server. Results of this study will be disseminated through peer-reviewed journals, conferences and internal meetings.
Topics: Ambulatory Care Facilities; Canada; Feasibility Studies; Glaucoma; Humans; Quality of Life
PubMed: 35414566
DOI: 10.1136/bmjopen-2022-061057 -
Nature Communications Aug 2022Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two...
Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene, which have repeatedly and independently adapted to montane habitats on either side of the Andes. We sequenced 518 whole genomes from altitudinal transects and found many regions differentiated between highland (~ 1200 m) and lowland (~ 200 m) populations. We show repeated genetic differentiation across replicate populations within species, including allopatric comparisons. In contrast, there is little molecular parallelism between the two species. By sampling five close relatives, we find that a large proportion of divergent regions identified within species have arisen from standing variation and putative adaptive introgression from high-altitude specialist species. Taken together our study supports a role for both standing genetic variation and gene flow from independently adapted species in promoting parallel local adaptation to the environment.
Topics: Adaptation, Physiological; Altitude; Animals; Butterflies; Phenotype; Phylogeny
PubMed: 35945236
DOI: 10.1038/s41467-022-32316-x