Biology subjects

Bren, A.

Publications and source records attributed to Bren, A..

6 recordsLinked to original sources

bioRxiv2025

Dynamic growth trajectories distinguish bacteriostatic and bactericidal antibiotics at subinhibitory concentrations

Subinhibitory antibiotic exposures are common in clinical and environmental contexts, yet their effects on bacterial growth dynamics remain incompletely understood. We studied the temporal response of Escherichia coli to a panel of bactericidal ("cidal") and bacteriostatic ("static") antibiotics at sub-minimum inhibitory concentrations (sub-MIC). We uncover a sharp dynamical distinction between the two classes. Bacteriostatic antibiotics reduce the initial growth rate in a dose-dependent manner, similar to a nutrient starvation response. In contrast, bactericidal antibiotics do not alter initial growth rates - cells continue to grow as fast as untreated cells - until an abrupt slowdown in growth rate. The onset of slowdown occurs earlier with increasing dose, suggesting a damage accumulation mechanism leading to a lethal threshold. Cidals also show a steeper dose-response curve. We propose that bacteria respond to cidal antibiotics with a "grow-fast-then-crash" strategy that is adaptive for transient lethal threats, whereas static antibiotics trigger stress adaptation and slower growth. While clinical outcomes of statics and cidals may be similar at full inhibitory doses, these sub-MIC dynamical signatures could influence resistance evolution and treatment outcomes in biofilms or partially resistant strains. Our findings offer a dynamic framework for antibiotic classification and raise new questions about how bacteria respond to sublethal antibiotic stress.

systems biology↗

bioRxiv2024

Preventing plasmid multimer formation in commonly used synthetic biology plasmids

Plasmids are an essential tool for basic research and biotechnology applications. To optimize plasmid-based circuits, it is crucial to control plasmid integrity, including the formation of plasmid multimers. Multimers are tandem repeats of entire plasmids formed during replication by failed dimer resolution. Multimers can affect the behavior of synthetic circuits, especially ones that include DNA-editing enzymes. However, occurrence of multimers is not commonly assayed. Here we survey four commonly used plasmid backbones for occurrence of multimers in cloning (JM109) and wild-type (MG1655) strains. We find that multimers occur appreciably only in MG1655, with the fraction of plasmids existing as multimers increasing with both plasmid copy number and culture passaging. In contrast, introduction of multimers into JM109 can produce strains containing only multimers. We present an MG1655{Delta} recA single-locus knockout that avoids multimer production. These results can aid synthetic biologists in improving design and reliability of plasmid-based circuits.

synthetic biology↗

bioRxiv2023

Longitudinal hair cortisol in bipolar disorder and a mechanism based on HPA dynamics

Bipolar disorder (BD) is a dynamic disease in which mania, depression and mixed states vary on a timescale of months to years. BD patients characteristically exhibit elevated levels of the hormone cortisol. Persistently elevated cortisol can also cause mood episodes in a substantial fraction of the general population. Although BD is a dynamic disease that is related to cortisol, longitudinal cortisol dynamics in BD have rarely been studied. Here we use hair to measure past cortisol where each cm of hair corresponds to a month of growth. Cortisol was measured in 12 cm hair samples from people with BD (n=26) and controls (n=59), corresponding to one year of cortisol data. We found that hair cortisol exhibited a frequency spectrum with enhanced year-scale fluctuations whose amplitude was about 4-fold higher on average in BD compared to controls. Cortisol in the proximal 2 cm hair segment correlated with mood scales that report on mood in the past two months. In line with the notion that cortisol correlates with mood, we find that the mean frequency spectrum of depression (n=266) and mania (n=273) scores from a large longitudinal study of BD is similar to the hair cortisol spectrum from the present cohort. Taken together, these results suggest a mechanism for BD as the intersection of two neuropsychological traits: cortisol-induced mood episodes (CIM) and high emotional reactivity (ER). High ER causes fluctuations in which cortisol is elevated for months, as shown by a mathematical model of the hypothalamic-pituitary-adrenal (HPA) axis that regulates cortisol. In individuals with CIM, the magnitude of these persistent cortisol fluctuations can be high enough to trigger mood episodes. Thus, this study combines longitudinal cortisol measurements and mathematical modeling to provide a potential mechanistic link between the timescales of cortisol and moods in BD.

systems biology↗

bioRxiv2023

Robust differentiation in a synthetic stem-cell circuit

Differentiation is a process fundamental to multicellularity. In its simplest form, differentiation converts self-renewing stem cells into non-proliferative cells with specified function. This process is inherently susceptible to mutant takeover -- mutant stem cells that never differentiate produce excess proliferative daughter cells, driving cancer-like expansion and decreasing the availability of differentiated cells to the organism. It has been proposed that coupling differentiation to an essential trait can select against these mutants by producing a biphasic fitness curve. This would provide mutant stem cells that do not differentiate with a selective disadvantage. However, this theory has yet to be tested experimentally. Here we use "fitness landscape engineering" to design and construct a synthetic biological model of stem cell differentiation in Escherichia coli with biphasic fitness. We find that this circuit is robust to mutations as predicted. Surprisingly, its optimal differentiation rate is robust to a wide range of environmental pressures. This environmental robustness is driven by transit-amplifying cells that differentiate and proliferate irrespective of environment. These results provide new interpretations for natural differentiation mechanisms and suggest strategies for engineering robust, complex multicellular consortia.

synthetic biology↗

bioRxiv2022

Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing

Antibiotics can kill or stop the growth of bacteria, and their effectiveness depends on many factors. It is important to understand the relation between bacterial physiology, the environment and antibiotic action. While many of the mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. Death rate in antibiotics has often been shown to rise linearly with growth rate; however, it remains unclear how environmental factors, in concert with whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated bacterial death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Specifically, stressors lower the death rate compared to a non-stressed environment with the same growth rate. To understand the role of stress, we developed a mathematical model of bacterial death based on resource allocation that takes into account a newly defined stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the death rate and minimal inhibitory concentration of antibiotics across a wide range of conditions, including a previously unknown increase in the stress response and protection from death at very low levels of cAMP. The present death-growth model suggests conditions that may improve antibiotic efficacy.

systems biology↗

bioRxiv2018

A bacterial growth law out of steady-state

Bacterial growth depends on numerous reactions, and yet follows surprisingly simple laws that inspired biologists for decades. Growth laws until now primarily dealt with steady-state exponential growth in constant conditions. However, bacteria in nature often face fluctuating environments, with nutritional upshifts and downshifts. We therefore ask whether there are growth laws that apply to changing environments. We derive a law for strong upshifts using an optimal resource-allocation model that was previously calibrated at steady-state growth: the post-shift growth rate equals the geometrical mean of the pre-shift growth rate and the growth rate on saturating carbon. We test this using chemostat and robotic batch culture experiments, as well as previous data from several species, and find good agreement with the model predictions. The increase in growth rate after an upshift indicates that ribosomes have spare capacity. We demonstrate theoretically that spare ribosomal capacity has the cost of slow steady-state growth, but is beneficial in fluctuating environments because it prevents large overshoots in intracellular metabolites after an upshift and allows rapid response to change. We also provide predictions for downshifts for future experimental tests. Spare capacity appears in diverse biological systems, and the present study quantifies the optimal degree of spare capacity, which rises the slower the growth rate, and suggests that it can be precisely regulated.

systems biology↗