Biology subjects

Batra, A.

Publications and source records attributed to Batra, A..

11 recordsLinked to original sources

bioRxiv2026

Antibiotic tolerance due to filamentation shapes β-lactam pharmacodynamics in Escherichia coli

Pharmacodynamic curves describe how changes in drug concentration affect pathogen growth. They are essential for designing treatments that promote pathogen eradication and minimize the evolution of antibiotic resistance. The classical function for modelling pharmacodynamics is a phenomenological, S-shaped curve with stable growth and death rates separated by a single drop. In this study, we characterized the pharmacodynamic curve of the {beta}-lactam antibiotic cefotaxime (CTX) acting against Escherichia coli. We found that the relationship between CTX concentration and net growth rate diverged from classical model predictions, instead yielding a two-step curve defined by distinct phases of growth, population maintenance, and killing. We hypothesized that the intermediate phase arose from antibiotic tolerance conferred by bacterial filaments. Microscopic assessment of treated cells indeed showed a difference in degree of filamentation with concentration. We further sought to explain this with a semi-mechanistic pharmacodynamic function, modelling the binding of CTX to its cellular targets, penicillin binding proteins (PBP) 1 and 3. By incorporating the preferential concentration-dependent binding of CTX to PBP3 and then PBP1, yielding filaments or lysed cells respectively, we replicated the two-step curve in silico. We also assessed the pharmacodynamics of CTX against mutants conferring resistance; these displayed further altered curves, in line with their fitness costs. Altogether, our results show that CTX has a two-step pharmacodynamic curve against E. coli arising from multiple targets separated in their affinity for the antibiotic. We present a model offering a mechanistically grounded framework for capturing such dynamics. These pharmacodynamic curves deserve careful consideration when defining optimal dosing.

microbiology↗

bioRxiv2026

Experimental evolution of collective β-lactam resistance in Escherichia coli via activation of a dormant outermembrane porin

Understanding the mechanisms that drive antibiotic resistance is relevant for both evolutionary theory and the design of effective drug therapies. A specific challenge are collective resistance mechanisms, where bacterial populations survive drug concentrations that kill individual bacteria. Here, we explore the evolvability of collective resistance mechanisms in bacterial strains expressing antibiotic-degrading {beta}-lactamases with different levels of privatization. Four strains of Escherichia coli, with or without outermembrane porin OmpF to affect drug permeability and expressing either a low or high-activity periplasmic {beta}-lactamase, were subjected to lineage selection in a gradient of the drug cefotaxime. Strains with a low-activity enzyme increased cell-level resistance, while strains with low permeability, and hence a more private {beta}-lactamase function, increased collective resistance. Remarkably, increased collective resistance in the strain with a private high-activity {beta}-lactamase came with decreased cell-level resistance. This tradeoff was primarily caused by the activation of a dormant outermembrane porin, NmpC, via the excision of an insertion sequence. Increased drug permeability through NmpC explained both its lower cell-level resistance and its greater collective resistance through faster drug removal and growth recovery via enhanced filamentation at high cell density. The recovery advantage of the NmpC mutant also explained its initial invasion within the ancestral population, suggesting that drug permeability is a readily evolvable collective-resistance mechanism in bacteria with high-activity {beta}-lactamases. Our findings highlight the role of filamentation and drug permeability in {beta}-lactamase-mediated collective resistance to these widely used drugs.

evolutionary biology↗

bioRxiv2025

Robust antibiotic sensitization of pathogenic Pseudomonas aeruginosa via negative hysteresis in the cell envelope

Antibiotic combination in time and space is a key strategy to combat antimicrobial resistance. The success of such treatment designs requires their robust efficacy across treatment conditions and a pathogens genomic diversity. This study found that an initial treatment with a {beta}-lactam antibiotic causes robust cellular sensitization towards an aminoglycoside antibiotic across the high-risk human pathogen Pseudomonas aeruginosa, including resistant strains. This phenomenon of cellular sensitization, termed negative hysteresis, is modulated by the Cpx envelope stress response system and linked to membrane stress during growth. The increase in efficacy is achieved through a {beta}-lactam induced elevated cellular uptake of the subsequently administered aminoglycoside. Negative hysteresis and the Cpx system are linked in several cases to the expression of synergistic drug interactions, thus enhancing efficacy of antibiotic combinations. Overall, our study identifies the phenomenon of negative hysteresis as a robustly inducible phenotype and thus a unique focus for optimizing antimicrobial therapy.

evolutionary biology↗

bioRxiv2025

Insulin modulates mPFC gene expression and emotional behavior in a sex-specific manner following fetal growth restriction

Exposure to prenatal adversity (e.g., stress, malnutrition) is a major risk factor for lifelong vulnerability to neuropsychiatric and metabolic disorders, and alterations in the function of peripheral hormones in the brain are suggested as a possible and unexplored mechanism. Although insulin is well known for its peripheral metabolic functions, it also influences brain development and emotional regulation, particularly within the medial prefrontal cortex (mPFC). Here, we identify insulin signaling as a key mechanistic link between prenatal stress and long-term alterations in brain function and behavior. Using a validated rat model of prenatal adversity (prenatal food restriction, FR), we found that insulin administration selectively modulates gene expression in FR animals at P0, P21 and P90, affecting pathways involved in neurodevelopment and stress regulation, such as Wnt/{beta}-catenin signaling. Targeted insulin infusion into the mPFC of adult animals reversed behavioral phenotypes induced by FR in a sex- and context-dependent manner, decreasing emotional reactivity to environmental cues. These findings offer novel insight into the neurodevelopmental role of insulin and suggest that insulin signaling may serve as a therapeutic target to mitigate the long-term brain and behavioral consequences of prenatal adversity.

genomics↗

bioRxiv2025

Guanylyl cyclase signaling in AFD neurons regulates systemic stress resilience in Caenorhabditis elegans

Thermal fluctuations in the environment, particularly high temperatures, pose a major challenge to organisms and require robust mechanisms for survival under heat stress. Although the molecular basis of cellular heat shock responses is well understood, how thermosensory neurons contribute to systemic stress adaptation remains unclear. Here, using Caenorhabditis elegans as a model, we examine whether ther-mosensory receptor guanylyl cyclases (rGCs) in AFD neurons regulate organism-wide stress responses under noxious temperatures and how individual rGCs contribute to this coordination. Among the AFD-expressed rGCs, we identify gcy-18 and gcy-23 as key regulators of the physiological response to thermal stress, acting through modulation of canonical heat shock response (HSR) genes. Our findings indicate that rGC signaling is crucial for activation of heat shock chaperones and maintenance of proteostasis under high temperatures (35{degrees}C). Supporting this, quantitative analysis of HSP-16.2 revealed that rGC activity in AFD neurons modulates the HSR magnitude in distal tissues, such as the intestine. Together, our findings uncover an important role for thermosensory rGCs in maintaining cellular proteostasis through selective modulation of the HSR.

physiology↗

bioRxiv2025

Resistance variation and bacterial interactions shape the adaptation of a genetically diverse bacterial population to antimicrobial treatment

Bacterial infections are often polymicrobial and subject to the evolution of antimicrobial resistance (AMR). Existing knowledge on AMR in such polymicrobial infections usually relies on observational patient data, for which cause-effect relationships are difficult to infer, or on studying interactions between different bacterial species, ignoring the commonly encountered variation within species. Here, we therefore asked how mixed populations with strains from the same species evolve under antibiotic treatment. We used a genetically diverse population of the high-risk human pathogen Pseudomonas aeruginosa, and first identified strain variation in both AMR and pairwise bacteria-bacteria interactions, the latter ranging from beneficial, neutral, to competitive. Using experimental evolution, we subsequently demonstrate that the response to selection by different antibiotic treatments is significantly influenced by AMR strain variation, bacterial interactions, and also spatial population structure. Moreover, de novo AMR evolution was additionally impacted by variation in resistance rates towards the two considered antibiotics. A second evolution experiment emphasized the central role of strain variation and bacterial interactions in determining the evolutionary outcome. We conclude that ecological dynamics in genetically diverse pathogen populations are key for our general understanding of infection characteristics and AMR evolution, and, therefore, deserve particular attention during treatment of polymicrobial infections.

evolutionary biology↗

bioRxiv2025

Neuronal Decoding of Temperature Signals in Caenorhabditis elegans

Neural processing in animals facilitate sensory adaptation by eliciting appropriate responses to changing environmental stimuli. Although sensory adaptation is well recognized, the specific role of individual neurons in these adaptive mechanisms remains poorly understood from a theoretical standpoint. Specifically, it is unclear how single neurons influence the processing of sensory information and modulate their responses to environmental changes. In Caenorhabditis elegans (C. elegans), the primary AFD thermosensory neurons respond to external thermal stimuli incorporating experience-dependent temperature response thresholds. While extensive experimental studies have highlighted the functional features of the AFD neurons, mathematical understanding of their responses is still not well established. In this study, we develop a theoretical framework that captures how a single pair of AFD neurons encodes sensory information and regulates their responses to thermal warming signals, with a focus on how prior environmental experiences influence these responses. Through this framework we find that the interaction between two key entities i.e. cGMP and calcium, plays a crucial role in processing sensory information and fine-tuning neuronal responses to thermal changes. In addition to reproducing experimentally known trends, our results show that growth conditions such as cultivation temperature of the worms significantly shape the neurons functional properties, including their operating range, activation thresholds and response start time and duration. The findings in this work, therefore, enhance the overall understanding of how environmental experiences by single neuron shape sensory systems and provide a deeper connection between experimental data and quantitative models.

biophysics↗

bioRxiv2024

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, it is ranked by the World Health Organization among the top 3 high priority pathogens, for which new treatment options are urgently required. An evaluation of new treatments is usually performed experimentally with one of the canonical laboratory strains (e.g., PAO1 or PA14). However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the genomic diversity of the species, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses towards antibiotics and general growth characteristics. Only few of the measured traits are related, and if so, only for specific antibiotics. Moreover, high levels of resistance were only identified for clinical mPact isolates and could be linked to known AMR (antimicrobial resistance) genes in the sequenced genomes. One strain also produced highly unstable AMR, indicating an evolutionary cost to resistance expression. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains towards either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species genomic diversity. ImportanceNew treatment strategies are urgently needed for high risk pathogens such as the opportunistic and often multidrug resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics, (ii) related traits associated with the response to antibiotics, and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.

microbiology↗

bioRxiv2021

High potency of sequential therapy with only beta-lactam antibiotics

Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution- informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only {beta}-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross- resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.

evolutionary biology↗

bioRxiv2020

Inferring intestinal mucosal immune cell associated microbiome species and microbiota-derived metabolites in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a complex, chronic inflammatory disease of the gastrointestinal tract with subtypes Crohns disease (CD) and ulcerative colitis (UC). While evidence indicates IBD is characterized by alterations in the composition and abundance of the intestinal microbiome, the challenge remains to specify bacterial species and their metabolites associated with IBD pathogenesis. By the integration of microbiome multi-omics data and computational methods, we provide analyses and methods for the first time to identify microbiome species and their metabolites that are associated with the human intestine mucosal immune response in patients with CD and UC at a systems level. First, we identified seven gut bacterial species and seventeen metabolites that are significantly associated with Th17 cellular differentiation and immunity in patients with active CD by comparing with those obtained in inactive CD and non-IBD controls. The seven species are Ruminococcus gnavus, Escherichia coli, Lachnospiraceae bacterium, Clostridium hathewayi, Bacteroides faecis, Bacteroides vulgatus, and Akkermansia muciniphila, and a few associated metabolites include the secondary bile acid lithocholate and three short-chain fatty acids (SCFAs): propionate, butyrate, and caproate. We next systematically characterized potential mechanistic relationships between the Th17-involved metabolites and bacterial species and further performed differential abundance analysis for both microbiome species and their metabolites in CD and UC relative to non-IBD controls with their metagenomic and metabolomic data. Based on the deconvolution of immune cell compositions from host intestinal bulk RNA-seq, we investigated changes in immune cell composition and abundance in CD and UC in comparison to non-IBD controls. Finally, we further extended our species and metabolite associations with immune cells from Th17 and Th2 cells to B cells, plasma B cells, plasmablasts, CD4+ T cells, and CD8+ T cells. While a set of associations of immune cells with bacterial species and metabolites was supported by published evidence, the new findings in this work will help to furthering our understanding of immune responses and pathogenesis in IBD.

bioinformatics↗

bioRxiv2020

Maladaptive myelination promotes epileptogenesis in absence epilepsy

Neuronal activity can influence the generation of new oligodendrocytes (oligodendrogenesis) and myelination. In health, this is an adaptive process that can increase synchrony within distributed neuronal networks and contribute to cognitive function. We hypothesized that in seizure disorders, aberrant neuronal activity may promote maladaptive myelination that contributes to pathogenesis. Absence epilepsy is a disease defined by increasingly frequent behavioral arrest seizures over time, thought to be due to thalamocortical network hypersynchrony. We tested the hypothesis that activity-dependent myelination resulting from absence seizures promotes epileptogenesis. Using two distinct models of absence epilepsy, Wag/Rij rats and Scn8a+/mut mice, we found increased oligodendrogenesis and myelination specifically within the absence seizure network. These changes are evident only after seizure onset in both models and are prevented with pharmacological inhibition of seizures. Genetic blockade of activity-dependent myelination during epileptogenesis markedly decreased seizure frequency in the Scn8a+/mut mouse model of absence epilepsy. Taken together, these findings indicate that activity-dependent myelination driven by absence seizures contributes to seizure kindling during epileptogenesis.

neuroscience↗