Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments.

In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).

Patients' Satisfaction With Physiotherapy Services of Red Cross Physical Rehabilitation Services and Related Factors: A Case Study of Afghanistan.

Patient satisfaction is essential to the patient-centered approach in health services delivery, but little is known about satisfaction with physiotherapy services in Afghanistan. This study evaluated patients' satisfaction with physiotherapy services and related factors in this country. This study was conducted on 420 recipients of a physiotherapy center in Afghanistan. A questionnaire was used to collect data that measured satisfaction in 4 dimensions: treatment process, logistics, organizational factors, and overall. The scale of the questionnaire was 5-point Likert. The highest possible score was 100. Statistics methods included Spearman's correlation coefficient, Mann-Whitney and Kruskal-Wallis tests for univariate analysis, and Linear Regression for multivariate analysis. The average overall satisfaction score was 84.82 ± 13.24. Among the demographic variables, the relationship between education level and overall satisfaction score was significant. The findings of the linear regression model showed that the 3 dimensions of satisfaction, including the treatment process, logistics, and organizational factors, had statistically significant relationships with overall satisfaction. The level of satisfaction was high in all dimensions. To maximize satisfaction, reducing waiting time and better communication with patients, as components of logistics and organizational factors, are suggested. Patients also need to receive feedback from physiotherapists that are an essential components of the treatment process dimension.

Outcomes of a novel algorithm for levator muscle plication surgery in congenital blepharoptosis.

AIM: to assess the outcomes of a novel algorithm for the calculation of the amount levator muscle plication in congenital blepharoptosis surgery. METHODS: this retrospective comparative study included 34 patients with congenital ptosis subjected to levator muscle plication surgery during the period from October 2021 to November 2022. They were divided into two groups. Group A: the amount of levator muscle plication was calculated by a traditional formula [(amount of ptosis x 3) + 9 mm in cases with good levator function or (amount of ptosis x 3) + 11 mm in cases with fair levator function]. Group B: the amount of levator muscle plication was calculated by a novel nomogram [the result of the traditional formula was modified by subtracting 4 mm if the calculated amount was ≥ 15 mm or subtracting 3 mm if the calculated amount was < 15 mm]. Demographic data, baseline ptosis characteristics and postoperative results at 1st week, 1st month, 3rd month and 6th month were compared between the groups. Primary outcome measure was postoperative Marginal Reflex Distance (MRD1). Secondary outcome measures were lid contour, lid crease and any reported complications. RESULTS: Group A included 20 eyes of 18 patients while Group B included 20 eyes of 16 patients. The mean amount of levator muscle plication was 16.98 ± 2.44 mm and 13.48 ± 2.42 mm in group A and group B respectively. The difference between the two groups was highly statistically significant (p < 0.001). Mean MRD1 at the 1st postoperative week was 4.95 ± 0.37 mm in group A and 4.08 ± 0.64 mm in group B. This difference was highly statistically significant (P < 0.001). Overcorrection was seen in 8 (40%) eyes in group A and 1 (5%) eye in group B. The difference was statistically significant between the two groups (p = 0.008). Undercorrection was seen in only 1 (5%) eye in group B. No other complications were reported. Surgical success was achieved in 12 (60%) eyes in group A versus 18 (90%) eyes in group B. The difference between the two groups was statistically significant (p = 0.03). CONCLUSION: our novel nomogram for the calculation of the amount levator muscle plication in congenital blepharoptosis surgery is effective in achieving a satisfactory postoperative MRD1.

Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages.

CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. A doublesex-targeting gene drive was able to suppress laboratory Anopheles mosquito populations in small and large cages, and it is considered for field application. Challenges related to the field-use of gene drives and the evolving regulatory framework suggest that systems able to modulate or revert the action of gene drives, could be part of post-release risk-mitigation plans. In this study, we challenge an AcrIIA4-based anti-drive to inhibit gene drive spread in age-structured Anopheles gambiae population under complex feeding and behavioural conditions. A stochastic model predicts the experimentally-observed genotype dynamics in age-structured populations in medium-sized cages and highlights the necessity of large-sized cage trials. These experiments and experimental-modelling framework demonstrate the effectiveness of the anti-drive in different scenarios, providing further corroboration for its use in controlling the spread of gene drive in Anopheles.

Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation.

A classical and well-established mechanism that enables cells to adapt to new and adverse conditions is the acquisition of beneficial genetic mutations. Much less is known about epigenetic mechanisms that allow cells to develop novel and adaptive phenotypes without altering their genetic blueprint. It has been recently proposed that histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), normally reserved to maintain genome integrity, can be redistributed across the genome to establish new and potentially adaptive phenotypes. To uncover the dynamics of this process, we developed a precision engineered genetic approach to trigger H3K9me redistribution on-demand in fission yeast. This enabled us to trace genome-scale RNA and chromatin changes over time prior to and during adaptation in long-term continuous cultures. Establishing adaptive H3K9me occurs over remarkably slow time-scales relative to the initiating stress. During this time, we captured dynamic H3K9me redistribution events ultimately leading to cells converging on an optimal adaptive solution. Upon removal of stress, cells relax to new transcriptional and chromatin states rather than revert to their initial (ground) state, establishing a tunable memory for a future adaptive epigenetic response. Collectively, our tools uncover the slow kinetics of epigenetic adaptation that allow cells to search for and heritably encode adaptive solutions, with implications for drug resistance and response to infection.

Assessment of the In Vivo Reprotoxicity of Isotretinoin in Sprague-Dawley Male Rat.

BACKGROUND: Isotretinoin (ISO) belongs to a family of drugs called retinoids. It is the most effective drug prescribed by dermatologists for the treatment of the inflammatory disease, acne vulgaris. A significant barrier to the use of ISO has worries regarding its adverse effect profile. Despite the well-recognized reproductive toxicity and teratogenicity in females, there is no warning related to the use by male patients in the medication prospectus. Current data on the effects on human male fertility is contradictory and inconclusive. OBJECTIVES: This study was undertaken to investigate the potential effects of ISO oral doses in the Sprague-Dawley male rat germ cells using the sperm morphology assay. Also, the serum levels of the follicle-stimulating hormone (FSH), luteinizing hormone (LH), and testosterone were measured. METHODS: The rat groups were given varying ISO doses via gastric gavage for seven consecutive days. The epididymis sperm specimens were microscopically examined for the following reproductive toxicity parameters: sperm concentration, examined viability, motility, and morphology. The serum FSH, LH, and testosterone levels were measured by using the corresponding enzyme-linked immunosorbent assay (ELISA) kit. The data were analyzed statistically by one-way analysis of variance (ANOVA) followed by the Tukey test at P ≤ 0.05 significance level. RESULTS: The results indicated that the drug did not significantly increase the sex hormone levels but notably affected both the sperm quantity and quality. CONCLUSION: These observations suggest that ISO was reprotoxic, and future therapies should be further reassessed.

Histotoxicity induced by copper oxide nanoparticles (CuO-NPs) on developing mice (Mus musculus).

The wide range of applications of nanoparticles (NPs) in various industries have led to serious consequences in terms of teratogenic toxicity. The aim of current work was to evaluate the teratogenic effects of copper oxide (CuO) nanoparticles in albino mice.In this experimental study, after mating, inseminated 40 female mice were divided randomly into 4 pools (1 control and 3 experimental), ten each. Doses were administered intravenously (We followed the protocol by Yaqub et al. (2018), intravenous application is faster route as compared to oral dosage)to all the experimental groups on the 6th day of gestation (GD), dose concentrations were 200, 133.3 and 100 mg/kg body weights respectively.The doses were prepared in sequence (1/2, 1/3, 1/4 0f LD50) according to already published work. The effects of CuO-NPs show linear relationship with the above sequence. The control group was administered only with distilled water.The gravid females were sacrificed through cervical disruption at the 18th day of gestation, fetuses were removed and divided into four sets (pools) for morphometric, morphological and histological studies. Data were subjected to statistical analysis by using Tukey's test in light of ANOVA at p < 0.05 level of significance. Findings of the present study showed that CuO-NPs various concentrations affect developmental abnormalities i.e.runt embryos, resorbed uteri, exencephaly, hygroma, macroglossia, micromelia, open eye, omphalocoel, scoliosis, kyphosis and kinked tail. It is concluded that exposure to CuO-NPs may potentially lead to the developmental deformities in mice.

A Multiplex MoClo Toolkit for Extensive and Flexible Engineering of Saccharomyces cerevisiae.

Synthetic biology toolkits are one of the core foundations on which the field has been built, facilitating and accelerating efforts to reprogram cells and organisms for diverse biotechnological applications. The yeast Saccharomyces cerevisiae, an important model and industrial organism, has benefited from a wide range of toolkits. In particular, the MoClo Yeast Toolkit (YTK) enables the fast and straightforward construction of multigene plasmids from a library of highly characterized parts for programming new cellular behavior in a more predictable manner. While YTK has cultivated a strong parts ecosystem and excels in plasmid construction, it is limited in the extent and flexibility with which it can create new strains of yeast. Here, we describe a new and improved toolkit, the Multiplex Yeast Toolkit (MYT), that extends the capabilities of YTK and addresses strain engineering limitations. MYT provides a set of new integration vectors and selectable markers usable across common laboratory strains, as well as additional assembly cassettes to increase the number of transcriptional units in multigene constructs, CRISPR-Cas9 tools for highly efficient multiplexed vector integration, and three orthogonal and inducible promoter systems for conditional programming of gene expression. With these tools, we provide yeast synthetic biologists with a powerful platform to take their engineering ambitions to exciting new levels.

Radiation-induced lattice relaxation in [Formula: see text]-Fe[Formula: see text]O[Formula: see text] nanorods.

We report radiation-induced lattice relaxation of the [Formula: see text]-Fe[Formula: see text]O[Formula: see text] and its associated alteration of particle morphology. The [Formula: see text]-Fe[Formula: see text]O[Formula: see text] was grown in solution by microwave hydrothermal synthesis technique in which more than half of the synthesized material was nanorods with axis along the (001) direction. Five sets of the synthesized [Formula: see text]-Fe[Formula: see text]O[Formula: see text] samples were irradiated using gamma-ray from [Formula: see text]Co cell with doses of 600 kGy, 700 kGy, 800 kGy, 900 kGy, and 1 MGy. The investigation of the pristine and gamma-irradiated samples was carried out using X-ray powder diffraction, transmission electron microscope, and electron paramagnetic resonance methods. Results showed that continuous alternation of radiation-induced lattice compression and expansion causes lattice relaxation. The morphology of the [Formula: see text]-Fe[Formula: see text]O[Formula: see text] nanorods was found to change with absorbed dose into buckyball-shaped particles in response to the alternation of the compression and expansion strain. The EPR results showed a correlation between distortion in the [Formula: see text]-[Formula: see text] octahedron structure and the relaxation of the lattice. The synthesis, growth, and relaxation are discussed in detail.

Prevalence of soil-transmitted helminths and associated risk factors among primary school children in Kandahar, Afghanistan: A cross-sectional analytical study.

BACKGROUND: Soil-transmitted helminth (STH) infections are global health problem, especially in low-income countries. Main objectives of this study were to estimate the prevalence and intensity of STH and its risk factors among school children in Kandahar city of Afghanistan. METHODOLOGY/PRINCIPAL FINDINGS: This was a school-based cross-sectional analytical study, with data collected during eight-month-period (May-December, 2022) from 6- and 12-years old school children in Kandahar city, Afghanistan. All the stool samples were examined by saline wet mount method and Kato-Katz technique. Data were analyzed by using descriptive statistics, Chi square test, and multivariate logistic regression. A total of 1275 children from eight schools of Kandahar city were included in this study. Mean age of these children was 8.3 years with 53.3% boys. The overall prevalence of any intestinal parasitic infection was 68.4%. The overall prevalence of STH infection was 39.1%, with Ascaris lumbricoides (29.4%) as the most prevalent STH species. Mean intensity of overall STH infection was 97.8. Multivariate logistic regression revealed playing barefoot (AOR 1.6, 95% CI 1.1-2.2), not washing hands after defecating and before eating (AOR 1.3, 95% CI 1.0-1.7), having untrimmed nails (AOR 1.4, 95% CI 1.1-1.8), and belonging to poor families (AOR 1.3, 95% CI 1.0-1.7) as the risk factors associated with the predisposition of school children for getting STH in Kandahar city of Afghanistan. CONCLUSIONS/SIGNIFICANCE: There is high prevalence of STH among school children of Kandahar city in Afghanistan. Most of the risk factors are related to poverty, decreased sanitation, and improper hygiene. Improvement of socioeconomic status, sanitation, and health education to promote public awareness about health and hygiene together with periodic mass deworming programs are better strategies for the control of STH infections in Afghanistan.

Cooperative assembly confers regulatory specificity and long-term genetic circuit stability.

A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.

Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways.

Aggregation of TAR DNA-binding protein 43 kDa (TDP-43) is thought to drive the pathophysiology of amyotrophic lateral sclerosis and some frontotemporal dementias. TDP-43 is normally a nuclear protein that in neurons translocates to the cytoplasm and can form insoluble aggregates upon activation of the integrated stress response (ISR). Viruses evolved to control the ISR. In the case of Herpesvirus 8, the protein ORF57 acts to bind protein kinase R, inhibit phosphorylation of eIF2α and reduce activation of the ISR. We hypothesized that ORF57 might also possess the ability to inhibit aggregation of TDP-43. ORF57 was expressed in the neuronal SH-SY5Y line and its effects on TDP-43 aggregation characterized. We report that ORF57 inhibits TDP-43 aggregation by 55% and elicits a 2.45-fold increase in the rate of dispersion of existing TDP-43 granules. These changes were associated with a 50% decrease in cell death. Proteomic studies were carried out to identify the protein interaction network of ORF57. We observed that ORF57 directly binds to TDP-43 as well as interacts with many components of the ISR, including elements of the proteostasis machinery known to reduce TDP-43 aggregation. We propose that viral proteins designed to inhibit a chronic ISR can be engineered to remove aggregated proteins and dampen a chronic ISR.

Long-term evolution of proliferating cells using the eVOLVER platform.

Experimental evolution using fast-growing unicellular organisms is a unique strategy for deciphering the principles and mechanisms underlying evolutionary processes as well as the architecture and wiring of basic biological functions. Over the past decade, this approach has benefited from the development of powerful systems for the continuous control of the growth of independently evolving cultures. While the first devices compatible with multiplexed experimental evolution remained challenging to implement and required constant user intervention, the recently developed eVOLVER framework represents a fully automated closed-loop system for laboratory evolution assays. However, it remained difficult to maintain and compare parallel evolving cultures in tightly controlled environments over long periods of time using eVOLVER. Furthermore, a number of tools were lacking to cope with the various issues that inevitably occur when conducting such long-term assays. Here we present a significant upgrade of the eVOLVER framework, providing major modifications of the experimental methodology, hardware and software as well as a new stand-alone protocol. Altogether, these adaptations and improvements make the eVOLVER a versatile and unparalleled set-up for long-term experimental evolution.

Pediatric glaucoma in aniridia in a population of Egyptian children.

PURPOSE: To report on the incidence, characteristics, and treatment of glaucoma in association with aniridia in a population of Egyptian children. METHODS: A retrospective chart review was conducted of children (<18 years of age) presenting with aniridia between 2007 and 2022. Diagnosis of glaucoma was based on cup:disk ratio (>0.3) and IOP (>16 mm Hg). Success of glaucoma surgery was defined as IOP ≤16 mm Hg and stable or regressing cup:disk ratio. RESULTS: A total of 93 eyes of 47 children were included. The mean patient age at presentation was 41.2 ± 44.7 months. The mean intraocular pressure (IOP), corneal diameter, cup:disk ratio, and axial length on presentation were 16.4 ± 10.3 mm Hg, 11.4 ± 1.3 mm, 0.4 ± 0.3, and 22.43 ± 2.6 mm Hg. Of eyes with IOP and cup:disk ratio data at presentation, 23 (30%) were diagnosed with glaucoma. Fourteen eyes underwent surgery after presentation; follow-up data were available for half the remaining eyes. At the final follow-up, glaucoma was present in 20 eyes (49%). Glaucoma surgery was performed in 17 eyes, with a complete or qualified success rate of 82.4% at final follow-up, with 15 eyes having at least 12 months' follow-up. CONCLUSIONS: In this study cohort, children with aniridia presented at around 3 years of age, with glaucoma at presentation in almost one-third of the cases.

Ablation of ventricular tachycardia from coronary sinus in congenitally corrected transposition of great arteries.

Congenitally corrected transposition of the great arteries (ccTGA) compromises less than 1% of all congenital heart diseases, where the RV is the systemic ventricle. It can be associated with heart block, twin AV nodes and accessory pathway connections. Idiopathic Ventricular tachycardia (VT) is not common, with only few reported cases, and they were scar related. Previously reported cases of VT ablation from coronary venous sinus (CVS) are in structurally normal hearts. We performed a VT ablation in ccTGA patient from the CVS, resulting in symptomatic improvement and a decrease in PVC burden from 35% to less than 1%. CVS should be considered as a potential site in ccTGA patients especially when PVCs have RBBB morphology and superior axis.

Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes.

Engineering biology relies on the accurate prediction of cell responses. However, making these predictions is challenging for a variety of reasons, including the stochasticity of biochemical reactions, variability between cells, and incomplete information about underlying biological processes. Machine learning methods, which can model diverse input-output relationships without requiring a priori mechanistic knowledge, are an ideal tool for this task. For example, such approaches can be used to predict gene expression dynamics given time-series data of past expression history. To explore this application, we computationally simulated single-cell responses, incorporating different sources of noise and alternative genetic circuit designs. We showed that deep neural networks trained on these simulated data were able to correctly infer the underlying dynamics of a cell response even in the presence of measurement noise and stochasticity in the biochemical reactions. The training set size and the amount of past data provided as inputs both affected prediction quality, with cascaded genetic circuits that introduce delays requiring more past data. We also tested prediction performance on a bistable auto-activation circuit, finding that our initial method for predicting a single trajectory was fundamentally ill-suited for multimodal dynamics. To address this, we updated the network architecture to predict the entire distribution of future states, showing it could accurately predict bimodal expression distributions. Overall, these methods can be readily applied to the diverse prediction tasks necessary to predict and control a variety of biological circuits, a key aspect of many synthetic biology applications.

The Effects of Self-Polymerized Polydopamine Coating on Mechanical Properties of Polylactic Acid (PLA)-Kenaf Fiber (KF) in Fused Deposition Modeling (FDM).

This research examines the impact of self-polymerized polydopamine (PDA) coating on the mechanical properties and microstructural behavior of polylactic acid (PLA)/kenaf fiber (KF) composites in fused deposition modeling (FDM). A biodegradable FDM model of natural fiber-reinforced composite (NFRC) filaments, coated with dopamine and reinforced with 5 to 20 wt.% bast kenaf fibers, was developed for 3D printing applications. Tensile, compression, and flexural test specimens were 3D printed, and the influence of kenaf fiber content on their mechanical properties was assessed. A comprehensive characterization of the blended pellets and printed composite materials was performed, encompassing chemical, physical, and microscopic analyses. The results demonstrate that the self-polymerized polydopamine coating acted as a coupling agent, enhancing the interfacial adhesion between kenaf fibers and the PLA matrix and leading to improved mechanical properties. An increase in density and porosity was observed in the FDM specimens of the PLA-PDA-KF composites, proportional to their kenaf fiber content. The enhanced bonding between kenaf fiber particles and the PLA matrix contributed to an increase of up to 13.4% for tensile and 15.3% for flexural in the Young's modulus of PLA-PDA-KF composites and an increase of up to 30% in compressive stress. The incorporation of polydopamine as a coupling agent in the FDM filament composite led to an improvement in tensile, compressive, and flexural stresses and strain at break, surpassing that of pure PLA, while the reinforcement provided by kenaf fibers was enhanced more by delayed crack growth, resulting in a higher strain at break. The self-polymerized polydopamine coatings exhibit remarkable mechanical properties, suggesting their potential as a sustainable material for diverse applications in FDM.

Synthesis, characterization and evaluation of anti-arthritic and anti-inflammatory potential of curcumin loaded chitosan nanoparticles.

Curcumin is a phytochemical isolated from the dried rhizome of Curcuma longa L. family Zingiberaceae which possesses versatile biological activities and has hydrophobic properties. The current study was conducted to fabricate, and optimize curcumin loaded chitosan and Sodium tripolyphosphate (STPP) nanoparticles (NPs) to improve the bioavailability of curcumin. NPs were fabricated employing the Ionic gelation method. Four formulations were developed based on the selected variables like STPP and chitosan concentration, rotations per minute (rpm), temperature, and pH of chitosan solution. NPs were characterized for morphology, drug-polymer compatibility, yield, particle size, encapsulation efficiency, release behavior, anti-inflammatory and anti-arthritic activity compared to curcumin and standard drug. Fourier transform infrared spectroscopy (FTIR) shows nanoparticle compatibility. The maximum yield was 60%. Entrapment efficiency ranged from 45 to 65%. Curcumin NPs and standard drug 600 µg/ml shows 59% and 70% anti-inflammatory activity by HRB membrane stabilization method respectively which are greater than curcumin alone whereas anti-arthritic activity by protein denaturation method which is also comparable to standard drug and greater than curcumin was 66 and 70% respectively. Statistical analysis shows the mean significant difference at p ≤ 0.05. The study concluded that curcumin-loaded chitosan and STPP NPs formulated successfully by the Ionic gelation method, which increased curcumin absorption leading to a reduced dosing rate and improved patient compliance.

Effects of antibiotic interaction on antimicrobial resistance development in wastewater.

While wastewater is understood to be a critically important reservoir of antimicrobial resistance due to the presence of multiple antibiotic residues from industrial and agricultural runoff, there is little known about the effects of antibiotic interactions in the wastewater on the development of resistance. We worked to fill this gap in quantitative understanding of antibiotic interaction in constant flow environments by experimentally monitoring E. coli populations under subinhibitory concentrations of combinations of antibiotics with synergistic, antagonistic, and additive interactions. We then used these results to expand our previously developed computational model to account for the effects of antibiotic interaction. We found that populations grown under synergistic and antagonistic antibiotic conditions exhibited significant differences from predicted behavior. E. coli populations grown with synergistically interacting antibiotics developed less resistance than predicted, indicating that synergistic antibiotics may have a suppressive effect on resistance development. Furthermore E. coli populations grown with antagonistically interacting antibiotics showed an antibiotic ratio-dependent development of resistance, suggesting that not only antibiotic interaction, but relative concentration is important in predicting resistance development. These results provide critical insight for quantitatively understanding the effects of antibiotic interactions in wastewater and provide a basis for future studies in modelling resistance in these environments.

Long-term evolution of proliferating cells using the eVOLVER platform.

Experimental evolution using fast-growing unicellular organisms is a unique strategy for deciphering the principles and mechanisms underlying evolutionary processes as well as the architecture and wiring of basic biological functions. Over the past decade, this approach has benefited from the development of powerful systems for the continuous control of the growth of independently evolving cultures. While the first devices compatible with multiplexed experimental evolution remained challenging to implement and required constant user intervention, the recently-developed eVOLVER framework represents a fully automated closed-loop system for laboratory evolution assays. However, it remained difficult to maintain and compare parallel evolving cultures in tightly controlled environments over long periods of time using eVOLVER. Furthermore, a number of tools were lacking to cope with the various issues that inevitably occur when conducting such long-term assays. Here we present a significant upgrade of the eVOLVER framework, providing major modifications of the experimental methodology, hardware and software as well as a new standalone protocol. Altogether, these adaptations and improvements make the eVOLVER a versatile and unparalleled setup for long-term experimental evolution.