Growth and Maintenance of Escherichia coli Laboratory Strains

High-complexity of DNA double-strand breaks is key for alternative end-joining choice

The repair of DNA double-strand breaks (DSBs) through alternative non-homologous end-joining (alt-NHEJ) pathway significantly contributes to genetic instability. However, the mechanism governing alt-NHEJ pathway choice, particularly its association with DSB complexity, remains elusive due to the absence of a suitable reporter system. In this study, we established a unique Escherichia coli reporter system for detecting complex DSB-initiated alternative end-joining (A-EJ), an alt-NHEJ-like pathway. By utilizing various types of ionizing radiation to generate DSBs with varying degrees of complexity, we discovered that high complexity of DSBs might be a determinant for A-EJ choice. To facilitate efficient repair of high-complexity DSBs, A-EJ employs distinct molecular patterns such as longer micro-homologous junctions and non-templated nucleotide addition. Furthermore, the A-EJ choice is modulated by the degree of homology near DSB loci, competing with homologous recombination machinery. These findings further enhance the understanding of A-EJ/alt-NHEJ pathway choice.

The phylogroups and antibiotic susceptibilities of Escherichia coli isolates from the feces of Anatolian Ground Squirrels (Spermophilus xanthoprymnus)

The current study was conducted to determine the phylogroups and antibiotic susceptibilities of Escherichia coli isolates recovered from fecal samples of Anatolian Ground Squirrels (Spermophilus xanthoprymnus) and to examine the relationship between them. Eighty-two E. coli isolates obtained from 150 fecal samples were investigated. The quadruplex polymerase chain reaction (PCR), phylogroup C-, and E-specific mPCR were subjected to phylogenetic typing of the isolates. The susceptibilities to fifteen antibiotics of the isolates were detected by the disk diffusion method. In the result of phylogenetic typing, phylogroup B2 was most predominant (58.6 %), followed by B1 (25.6 %), E (8.5 %), C (4.9 %), and D (2.4 %). The phylogroup A, F, and Escherichia clades were not detected. The antibiotic susceptibility test revealed that 59.8 % (49/82) and 19.5 % (16/82) of E. coli isolates were resistant to at least one antibiotic and multidrug-resistant (MDR), respectively. Twenty-six (31.7 %), 19 (23.2 %), 11 (13.4 %), and 10 (12.2 %) of the isolates were found to be resistant to gentamicin, tetracycline, amoxicillin-clavulanic acid, and cefoxitin. Of the 49 E. coli isolates that were found to be resistant to any antibiotic analyzed, 30, 13, 4, and 2 were located in phylogroup B2, B1, E, and D, respectively. MDR isolates were mostly located in both phylogroup B1 (31.3 %) and B2 (31.3 %). In conclusion, data from the current study suggest that the isolates may potentially have pathogenic properties, since the majority (69.5 %) of E. coli isolates from fecal samples of Spermophilus xanthoprymnus were located in the pathogenic phylogroup and resistance to various antibiotics was detected.

The 'Erlenmeter': a low-cost, open-source turbidimeter for no-sampling phenotyping of microorganism growth

This work presents a low-cost, open-source turbidimeter, the 'Erlenmeter', designed to monitor the growth of microorganisms in batch cultures. It is easy to build, based exclusively on inexpensive off-the-shelf electronic components and 3D-printed parts. The Erlenmeter allows measuring the optical density of cultures on standard Erlenmeyer flasks without the need to open the flasks to collect aliquots, ensuring speed, minimal use of consumables, and elimination of the risk of contamination. These features make it particularly well-suited not just for routine research assays but also for experimental teaching. Here we illustrate the use of the Erlenmeter turbidimeter to record the growth of the microalga Phaeodactylum tricornutum, of the bacterium Escherichia coli, and of the yeast Saccharomyces cerevisiae, model organisms that are widely used in research and teaching. The Erlenmeter allows a detailed characterization of the growth curves of all organisms, confirming its usefulness for studying microbial populations dynamics both for research purposes and in classroom settings.

Competing mechanisms in bacterial invasion of human colon mucus probed with agent-based modeling

The gastrointestinal tract is inhabited by a vast community of microorganisms, termed the gut microbiota. Large colonies can pose a health threat, but the gastrointestinal mucus system protects epithelial cells from microbiota invasion. The human colon features a bilayer of mucus lining. Due to imbalances in intestinal homeostasis, bacteria may successfully penetrate the inner mucus layer, which can lead to severe gut diseases. However, it is hard to tease apart the competing mechanisms that lead to this penetration. To probe the conditions that permit bacteria penetration into the inner mucus layer, we develop an agent-based model consisting of bacteria and an inner mucus layer subject to a constant flux of nutrient fields feeding the bacteria. We find that there are three important variables that determine bacterial invasion: the bacterial reproduction rate, the contact energy between bacteria and mucus, and the rate of bacteria degrading the mucus. Under healthy conditions, all bacteria are naturally eliminated by the constant removal of mucus. In diseased states, imbalances between the rates of bacterial degradation and mucus secretion lead to bacterial invasion at certain junctures. We conduct uncertainty quantification and sensitivity analysis to compare the relative impact between these parameters. The contact energy has the strongest influence on bacterial penetration, which, in combination with bacterial degradation rate and growth rate, greatly accelerates bacterial invasion of the human gut mucus lining. Our findings will serve as predictive indicators for the etiology of intestinal diseases and highlight important considerations when developing gut therapeutics.

Critical steps in an environmental metaproteomics workflow

Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

Mechanisms of Pathogenic Escherichia coli Attachment to Meat

Escherichia coli are present in the human and animal microbiome as facultative anaerobes and are viewed as an integral part of the whole gastrointestinal environment. In certain circumstances, some species can also become opportunistic pathogens responsible for severe infections in humans. These infections are caused by the enterotoxinogenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli and the enterohemorrhagic E. coli species, frequently present in food products and on food matrices. Severe human infections can be caused by consumption of meat contaminated upon exposure to animal feces, and as such, farm animals are considered to be a natural reservoir. The mechanisms by which these four major species of E. coli adhere and persist in meat postslaughter are of major interest to public health and food processors given their frequent involvement in foodborne outbreaks. This review aims to structure and provide an update on the mechanistic roles of environmental factors, curli, type I and type IV pili on E. coli adherence/interaction with meat postslaughter. Furthermore, we emphasize on the importance of bacterial surface structures, which can be used in designing interventions to enhance food safety and protect public health by reducing the burden of foodborne illnesses.

A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli

The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.

Cell pleomorphism and changes in the enzymatic profile of selected Candida albicans strains in interaction with Escherichia coli - pilot study

Interactions between C. albicans and the microbiota play an important role in maintaining the balance between commensal and pathogenic organisms. Although the exact role of bacteria in reducing the pathogenicity of yeast remains poorly understood, a few examples have been documented so far: probiotics administration effectively reduces the formation of biofilm and bacterial metabolites inhibit the formation of hyphae. The aim of the study was to analyze C. albicans virulence levels based on the changes in the morphological structure and enzymatic profile in experimental cultures mixed with Escherichia coli. Viable cell abundance, cell pleomorphism and enzymatic profile were analyzed in single and mixed cultures (C. albicans + E. coli). The microscope analysis showed a large decrease in the number of viable C. albicans cells in mixed cultures with E. coli from 485.3±132.1 immediately after the establishment of the culture to 238.1±71.2 after an hour of incubation and 24.4±5.4 after 24 h. The length of C. albicans cells differed significantly between the single-species cultures and the mixed cultures for 24 h. Our present findings indicate a significant reduction in the secretion of several enzymes by fungi following contact with E. coli, including acid phosphatase, N-acetyl-β-glucosaminidase, naphthol-AS-BI-phosphohydrolase and leucine arylamidase. The interactions between fungi and bacteria appear to be extremely complex. On the one hand, during C. albicans with E. coli co-incubation, the bacteria stimulated the elongation of yeast cells, leading to the formation of a filamentous form; however, the number of yeast cells and their enzymatic activity decreased significantly. Therefore, it can be concluded that while E. coli stimulates some pathogenic properties, e.g. cell elongation, it also inhibits other virulence features, e.g. enzymatic activity of C. albicans.

Bio-response of copper-magnesium co-substituted mesoporous bioactive glass for bone tissue regeneration

Mesoporous bioactive glass (MBG) is widely acknowledged in bone tissue engineering due to its mesoporous structure, large surface area, and bioactivity. Recent research indicates that introduction of metallic ions has beneficial impacts on bone metabolism and angiogenesis. Thus, the features of MBG can be modified by incorporating combinations of ions, such as magnesium (Mg) and copper (Cu), which can play a considerable role in bone formation, influencing angiogenesis, osteogenesis, as well as antibacterial properties. In this study, Mg and Cu were co-doped for the first time (in a ratio of 1 : 1) in 80SiO2-5P2O5-(15 - 2x)CaO-xMgO-xCuO glass composition with x = 0, 0.5, 1, and 2 mol%, synthesized using the sol-gel and evaporation-induced self-assembly method. X-ray diffraction analysis confirmed the amorphous nature of the powders, while inductively coupled plasma-optical emission spectrometry verified the existence of dopant ions in the respective amounts. The nitrogen sorption method indicated the formation of uniform cylindrical mesopores which are open at both ends and a high surface area of the powders. TEM images show fringes, indicating an ordered mesoporous structure in all MgCu co-doped systems. In vitro bioactivity was observed in all MBG powders, confirmed by the formation of an apatite phase when placed in simulated body fluid (SBF). Flake-like microstructure characteristics of HAp crystals found on the surface of MBG powders were visualized using FESEM. Cytotoxicity tests at lower concentrations (0.1 and 1 wt/vol%) of co-doped 2MC MBG (co-doping up to 2 mol%) showed cell proliferation and viability of osteoblast-like MG-63 cells and normal human dermal fibroblast (NHDF) cells similar to the basic glass 80S. Antibacterial study of MBG pellets showed an increment in the zone of inhibition with the sequential addition of doping ions. The turbidity measurement of bacterial cultures revealed that the optimal concentration for effectively inhibiting bacterial growth was 1 wt/vol% (i.e., 10 mg mL-1) concentration of MBG extracts. The result suggested that the incorporation of Mg and Cu ions in MBG in lower concentrations of up to 2 mol% can be useful in bone regeneration owing to bioactivity, cell proliferation, and antibacterial characteristics.

Enhancing circuit stability under growth feedback with supplementary repressive regulation

The field of synthetic biology and biosystems engineering increasingly acknowledges the need for a holistic design approach that incorporates circuit-host interactions into the design process. Engineered circuits are not isolated entities but inherently entwined with the dynamic host environment. One such circuit-host interaction, 'growth feedback', results when modifications in host growth patterns influence the operation of gene circuits. The growth-mediated effects can range from growth-dependent elevation in protein/mRNA dilution rate to changes in resource reallocation within the cell, which can lead to complete functional collapse in complex circuits. To achieve robust circuit performance, synthetic biologists employ a variety of control mechanisms to stabilize and insulate circuit behavior against growth changes. Here we propose a simple strategy by incorporating one repressive edge in a growth-sensitive bistable circuit. Through both simulation and in vitro experimentation, we demonstrate how this additional repressive node stabilizes protein levels and increases the robustness of a bistable circuit in response to growth feedback. We propose the incorporation of repressive links in gene circuits as a control strategy for desensitizing gene circuits against growth fluctuations.

Multiple Rounds of In Vivo Random Mutagenesis and Selection in Vibrio natriegens Result in Substantial Increases in REE Binding Capacity

Rare earth elements (REE) are essential ingredients in many modern technologies, yet their purification remains either environmentally harmful or economically unviable. Adsorption, or biosorption, of REE onto bacterial cell membranes offers a sustainable alternative to traditional solvent extraction methods. But in order for biosorption-based REE purification to compete economically, the capacity and specificity of biosorption sites must be enhanced. Although there have been some recent advances in characterizing the genetics of REE-biosorption, the variety and complexity of bacterial membrane surface sites make targeted genetic engineering difficult. Here, we propose using multiple rounds of in vivo random mutagenesis induced by the MP6 plasmid combined with plate-throughput REE-biosorption screening to improve a microbe's capacity and selectivity for biosorbing REE. We engineered a strain of Vibrio natriegens capable of biosorbing 210% more dysprosium compared to the wild-type and produced selectivity improvements of up to 50% between the lightest (lanthanum) and heaviest (lutetium) REE. We believe that mutations we observed in ABC transporters as well as a nonessential protein in the BAM outer membrane β-barrel protein insertion complex likely contribute to some─but almost certainly not all─of the biosorption changes we observed. Given the ease of finding significant biosorption mutants, these results highlight just how many genes likely contribute to biosorption as well as the power of random mutagenesis in identifying genes of interest and optimizing a biological system for a task.

Enhancement of Repeat-Mediated Deletion Rearrangement Induced by Particle Irradiation in a RecA-Dependent Manner in Escherichia coli

Repeat-mediated deletion (RMD) rearrangement is a major source of genome instability and can be deleterious to the organism, whereby the intervening sequence between two repeats is deleted along with one of the repeats. RMD rearrangement is likely induced by DNA double-strand breaks (DSBs); however, it is unclear how the complexity of DSBs influences RMD rearrangement. Here, a transgenic Escherichia coli strain K12 MG1655 with a lacI repeat-controlled amp activation was used while taking advantage of particle irradiation, such as proton and carbon irradiation, to generate different complexities of DSBs. Our research confirmed the enhancement of RMD under proton and carbon irradiation and revealed a positive correlation between RMD enhancement and LET. In addition, RMD enhancement could be suppressed by an intermolecular homologous sequence, which was regulated by its composition and length. Meanwhile, RMD enhancement was significantly stimulated by exogenous λ-Red recombinase. Further results investigating its mechanisms showed that the enhancement of RMD, induced by particle irradiation, occurred in a RecA-dependent manner. Our finding has a significant impact on the understanding of RMD rearrangement and provides some clues for elucidating the repair process and possible outcomes of complex DNA damage.

Sterility testing of germ-free mouse colonies

In biomedical research, germ-free and gnotobiotic mouse models enable the mechanistic investigation of microbiota-host interactions and their role on (patho)physiology. Throughout any gnotobiotic experiment, standardized and periodic microbiological testing of defined gnotobiotic housing conditions is a key requirement. Here, we review basic principles of germ-free isolator technology, the suitability of various sterilization methods, and the use of sterility testing methods to monitor germ-free mouse colonies. We also discuss their effectiveness and limitations, and share the experience with protocols used in our facility. In addition, possible sources of isolator contamination are discussed and an overview of reported contaminants is provided.

Expression of His-tagged NADPH-dependent acetoacetyl-CoA reductase in recombinant Escherichia coli BL-21(DE3)

Poly-3-hydroxybutyrate (P(3HB)), a member of the polyhydroxyalkanoate (PHA) family, is a biodegradable polyester with diverse industrial applications. NADPH-dependent acetoacetyl-CoA reductase (phaB) is the enzyme which plays an essential role in P(3HB) synthesis by catalyzing the conversion of the intermediates. The expression of phaB enzyme using the recombinant Escherichia coli BL-21(DE3) and the purification of the synthesized enzyme were studied. The pET-B3 plasmid harbouring the phaB gene derived from Ralstonia eutropha H16, was driven by the lac promoter in E. coli BL-21(DE3). The enzyme was expressed with different induction time, temperatures and cell age. Results showed that the cell age of 4 h, induction time of 12 h at 37°C were identified as the optimal conditions for the enzyme reductase expression. A specific activity of 0.151 U mg-1 protein and total protein concentration of 0.518 mg mg-1 of dry cell weight (DCW) were attained. Affinity chromatography was performed to purify the His-tagged phaB enzyme, in which enhanced the specific activity (14.44 U mg-1) and purification fold (38-fold), despite relative low yield (44.6%) of the enzyme was obtained. The purified phaB showed an optimal enzyme activity at 30°C and pH 8.0. The findings provide an alternative for the synthesis of the reductase enzyme which can be used in the industrial-scale production of the biodegradable polymers.

Advancing 2D fluorescence online monitoring in microtiter plates by separating scattered light and fluorescence measurement, using a tunable emission monochromator

Online fluorescence monitoring has become a key technology in modern bioprocess development, as it provides in-depth process knowledge at comparably low costs. In particular, the technology is widely established for high-throughput microbioreactor cultivation systems, due to its noninvasive character. For microtiter plates, previously also multi-wavelength 2D fluorescence monitoring was developed. To overcome an observed limitation of fluorescence sensitivity, this study presents a modified spectroscopic setup, including a tunable emission monochromator. The new optical component enables the separation of the scattered and fluorescent light measurements, which allows for the adjustment of integration times of the charge-coupled device detector. The resulting increased fluorescence sensitivity positively affected the performance of principal component analysis for spectral data of Escherichia coli batch cultivation experiments with varying sorbitol concentration supplementation. In direct comparison with spectral data recorded at short integration times, more biologically consistent signal dynamics were calculated. Furthermore, during partial least square regression for E. coli cultivation experiments with varying glucose concentrations, improved modeling performance was observed. Especially, for the growth-uncoupled acetate concentration, a considerable improvement of the root-mean-square error from 0.25 to 0.17 g/L was achieved. In conclusion, the modified setup represents another important step in advancing 2D fluorescence monitoring in microtiter plates.

Enhanced Growth of Bacterial Cells in a Smart 3D Printed Bioreactor

In the last decade, there has been a notable advancement in diverse bioreactor types catering to various applications. However, conventional bioreactors often exhibit bulkiness and high costs, making them less accessible to many researchers and laboratory facilities. In light of these challenges, this article aims to introduce and evaluate the development of a do-it-yourself (DIY) 3D printed smart bioreactor, offering a cost-effective and user-friendly solution for the proliferation of various bioentities, including bacteria and human organoids, among others. The customized bioreactor was fabricated under an ergonomic design and assembled with 3D printed mechanical parts combined with electronic components, under 3D printed housing. The 3D printed parts were designed using SOLIDWORKS® CAD Software (2022 SP2.0 Professional version) and fabricated via the fused filament fabrication (FFF) technique. All parts were 3D printed with acrylonitrile butadiene styrene (ABS) in order for the bioreactor to be used under sterile conditions. The printed low-cost bioreactor integrates Internet-of-things (IoT) functionalities, since it provides the operator with the ability to change its operational parameters (sampling frequency, rotor speed, and duty cycle) remotely, via a user-friendly developed mobile application and to save the user history locally on the device. Using this bioreactor, which is adjusted to a standard commercial 12-well plate, proof of concept of a successful operation of the bioreactor during a 2-day culture of Escherichia coli bacteria (Mach1 strain) is presented. This study paves the way for more in-depth investigation of bacterial and various biological-entity growth cultures, utilizing 3D printing technology to create customized low-cost bioreactors.

Development of a pumpless acoustofluidic device for rapid food pathogen detection

Mixing, homogenization, separation, and filtration are crucial processes in miniaturized analytical systems employed for in-vitro biological, environmental, and food analysis. However, in microfluidic systems achieving homogenization becomes more challenging due to the laminar flow conditions, which lack the turbulent flows typically used for mixing in traditional analytical systems. Here, we introduce an acoustofluidic platform that leverages an acoustic transducer to generate microvortex streaming, enabling effective homogenizing of food samples. To reduce reliance on external equipment, tubing, and pump, which is desirable for Point-of-Need testing, our pumpless platform employs a hydrophilic yarn capable of continuous wicking for sample perfusion. Following the homogenization process, the platform incorporates an array of micropillars for filtering out large particles from the samples. Additionally, the porous structure of the yarn provides a secondary screening mechanism. The resulting system is compact, and reliable, and was successfully applied to the detection of Escherichia coli (E. coli) in two different types of berries using quantitative polymerase chain reaction (qPCR). The platform demonstrated a detection limit of 5 CFU g^-1, showcasing its effectiveness in rapid and sensitive pathogen detection.

A Multi-Layer-Controlled Strategy for Cloning and Expression of Toxin Genes in Escherichia coli

Molecular cloning and controlled expression remain challenging when the target gene encodes a protein that is toxic to the host. We developed a set of multi-layer control systems to enable cloning of genes encoding proteins known to be highly toxic in Escherichia coli and other bacteria. The different multi-layer control systems combine a promoter-operator system on a transcriptional level with a riboswitch for translational control. Additionally, replicational control is ensured by using a strain that reduces the plasmid copy number. The use of weaker promoters (such as PBAD or PfdeA) in combination with the effective theophylline riboswitch is essential for cloning genes that encode notoriously toxic proteins that directly target translation and transcription. Controlled overexpression is possible, allowing the system to be used for evaluating in vivo effects of the toxin. Systems with a stronger promoter can be used for successful overexpression and purification of the desired protein but are limited to toxins that are more moderate and do not interfere with their own production.

Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)

The fluctuation assay remains an important tool for analyzing the levels of mutagenesis in microbial populations. The mutant counts originating from some average number of mutations are usually assumed to obey the Luria-Delbrück distribution. While several tools for estimating mutation rates are available, they sometimes lack accuracy or versatility under non-standard conditions. In this work, extensions to the Luria-Delbrück protocol to account for phenotypic lag and cellular death with either perfect or partial plating were developed. Hence, the novel MLE MUtation Rate calculator, or mlemur, is the first tool that provides a user-friendly graphical interface allowing the researchers to model their data with consideration for partial plating, differential growth of mutants and non-mutants, phenotypic lag, cellular death, variability of the final number of cells, post-exponential-phase mutations, and the size of the inoculum. Additionally, mlemur allows the users to incorporate most of these special conditions at the same time to obtain highly accurate estimates of mutation rates and P values, confidence intervals for an arbitrary function of data (such as fold), and perform power analysis and sample size determination for the likelihood ratio test. The accuracy of point and interval estimates produced by mlemur against historical and simulated fluctuation experiments are assessed. Both mlemur and the analyses in this work might be of great help when evaluating fluctuation experiments and increase the awareness of the limitations of the widely-used Lea-Coulson formulation of the Luria-Delbrück distribution in the more realistic biological contexts.

Interplay between strain fitness and transmission frequency determines prevalence of antimicrobial resistance

The steep rise of infections caused by bacteria that are resistant to antimicrobial agents threatens global health. However, the association between antimicrobial use and the prevalence of resistance is not straightforward. Therefore, it is necessary to quantify the importance of additional factors that affect this relationship. We theoretically explore how the prevalence of resistance is affected by the combination of three factors: antimicrobial use, bacterial transmission, and fitness cost of resistance. We present a model that combines within-host, between-hosts and between-populations dynamics, built upon the competitive Lotka-Volterra equations. We developed the model in a manner that allows future experimental validation of the findings with single isolates in the laboratory. Each host may carry two strains (susceptible and resistant) that represent the host’s commensal microbiome and are not the target of the antimicrobial treatment. The model simulates a population of hosts who are treated periodically with antibiotics and transmit bacteria to each other. We show that bacterial transmission results in strain co-existence. Transmission disseminates resistant bacteria in the population, increasing the levels of resistance. Counterintuitively, when the cost of resistance is low, high transmission frequencies reduce resistance prevalence. Transmission between host populations leads to more similar resistance levels, increasing the susceptibility of the population with higher antimicrobial use. Overall, our results indicate that the interplay between bacterial transmission and strain fitness affects the prevalence of resistance in a non-linear way. We then place our results within the context of ecological theory, particularly on temporal niche partitioning and metapopulation rescue, and we formulate testable experimental predictions for future research.

Preparation and Use of Cellular Reagents: A Low-resource Molecular Biology Reagent Platform

Protein reagents are indispensable for most molecular and synthetic biology procedures. Most conventional protocols rely on highly purified protein reagents that require considerable expertise, time, and infrastructure to produce. In consequence, most proteins are acquired from commercial sources, reagent expense is often high, and accessibility may be hampered by shipping delays, customs barriers, geopolitical constraints, and the need for a constant cold chain. Such limitations to the widespread availability of protein reagents, in turn, limit the expansion and adoption of molecular biology methods in research, education, and technology development and application. Here, we describe protocols for producing a low-resource and locally sustainable reagent delivery system, termed "cellular reagents," in which bacteria engineered to overexpress proteins of interest are dried and can then be used directly as reagent packets in numerous molecular biology reactions, without the need for protein purification or a constant cold chain. As an example of their application, we describe the execution of polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) using cellular reagents, detailing how to replace pure protein reagents with optimal amounts of rehydrated cellular reagents. We additionally describe a do-it-yourself fluorescence visualization device for using these cellular reagents in common molecular biology applications. The methods presented in this article can be used for low-cost, on-site production of commonly used molecular biology reagents (including DNA and RNA polymerases, reverse transcriptases, and ligases) with minimal instrumentation and expertise, and without the need for protein purification. Consequently, these methods should generally make molecular biology reagents more affordable and accessible. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of cellular reagents Alternate Protocol 1: Preparation of lyophilized cellular reagents Alternate Protocol 2: Evaluation of bacterial culture growth via comparison to McFarland turbidity standards Support Protocol 1: SDS-PAGE for protein expression analysis of cellular reagents Basic Protocol 2: Using Taq DNA polymerase cellular reagents for PCR Basic Protocol 3: Using Br512 DNA polymerase cellular reagents for loop-mediated isothermal amplification (LAMP) Support Protocol 2: Building a fluorescence visualization device.

Novel Biocompatible with Animal Cells Composite Material Based on Organosilicon Polymers and Fullerenes with Light-Induced Bacteriostatic Properties

A technology for producing a nanocomposite based on the borsiloxane polymer and chemically unmodified fullerenes has been developed. Nanocomposites containing 0.001, 0.01, and 0.1 wt% fullerene molecules have been created. It has been shown that the nanocomposite with any content of fullerene molecules did not lose the main rheological properties of borsiloxane and is capable of structural self-healing. The resulting nanomaterial is capable of generating reactive oxygen species (ROS) such as hydrogen peroxide and hydroxyl radicals in light. The rate of ROS generation increases with an increase in the concentration of fullerene molecules. In the absence of light, the nanocomposite exhibits antioxidant properties. The severity of antioxidant properties is also associated with the concentration of fullerene molecules in the polymer. It has been shown that the nanocomposite upon exposure to visible light leads to the formation of long-lived reactive protein species, and is also the reason for the appearance of such a key biomarker of oxidative stress as 8-oxoguanine in DNA. The intensity of the process increases with an increase in the concentration of fullerene molecules. In the dark, the polymer exhibits weak protective properties. It was found that under the action of light, the nanocomposite exhibits significant bacteriostatic properties, and the severity of these properties depends on the concentration of fullerene molecules. Moreover, it was found that bacterial cells adhere to the surfaces of the nanocomposite, and the nanocomposite can detach bacterial cells not only from the surfaces, but also from wetted substrates. The ability to capture bacterial cells is primarily associated with the properties of the polymer; they are weakly affected by both visible light and fullerene molecules. The nanocomposite is non-toxic to eukaryotic cells, the surface of the nanocomposite is suitable for eukaryotic cells for colonization. Due to the combination of self-healing properties, low cytotoxicity, and the presence of bacteriostatic properties, the nanocomposite can be used as a reusable dry disinfectant, as well as a material used in prosthetics.

Escherichia coli Cultivation Process Modelling Using ABC-GA Hybrid Algorithm

In this paper, the artificial bee colony (ABC) algorithm is hybridized with the genetic algorithm (GA) for a model parameter identification problem. When dealing with real-world and large-scale problems, it becomes evident that concentrating on a sole metaheuristic algorithm is somewhat restrictive. A skilled combination between metaheuristics or other optimization techniques, a so-called hybrid metaheuristic, can provide more efficient behavior and greater flexibility. Hybrid metaheuristics combine the advantages of one algorithm with the strengths of another. ABC, based on the foraging behavior of honey bees, and GA, based on the mechanics of nature selection, are among the most efficient biologically inspired population-based algorithms. The performance of the proposed ABC-GA hybrid algorithm is examined, including classic benchmark test functions. To demonstrate the effectiveness of ABC-GA for a real-world problem, parameter identification of an Escherichia coli MC4110 fed-batch cultivation process model is considered. The computational results of the designed algorithm are compared to the results of different hybridized biologically inspired techniques (ant colony optimization (ACO) and firefly algorithm (FA))—hybrid algorithms as ACO-GA, GA-ACO and ACO-FA. The algorithms are applied to the same problems—a set of benchmark test functions and the real nonlinear optimization problem. Taking into account the overall searchability and computational efficiency, the results clearly show that the proposed ABC–GA algorithm outperforms the considered hybrid algorithms.