Biology subjects

Pham, D. N.

Publications and source records attributed to Pham, D. N..

5 recordsLinked to original sources

bioRxiv2026

Heart rate of the blue mussel Mytilus edulis in a simulated intertidal environment

Despite being a topic of early experimental studies, the effects of immersion-emersion cycles and temperature on the heart rate of intertidal Mytilus mussels have not been fully characterized. Using a recently released intertidal chamber paired with our own software package, we conducted a multiday experiment and continuously monitored the heart rate of the blue mussel Mytilus edulis. Under normal conditions, we detected a subtle spike in heart rate upon emersion before the eventual decline, as well as an overshoot upon reimmersion. Additionally, heart rate was sensitive to temperature changes during immersion but less responsive during emersion. These patterns were markedly altered following an unintended prolonged emersion event, which led to the loss of the emersion spike, an extended reimmersion overshoot, and heightened thermal sensitivity on top of an overall elevation in heart rate. However, the heart rate gradually returned to the pre-event baseline over the following days, demonstrating the significant resilience of the mussels. Our study highlights the potential of high-resolution physiological data in assessing the effects of environmental stressors on coastal ecosystems.

physiology↗

bioRxiv2024

FRUCTOSE ACTIVATES A STRESS RESPONSE SHARED BY METHYLGLYOXAL AND HYDROGEN PEROXIDE IN STREPTOCOCCUS MUTANS

Fructose catabolism by Streptococcus mutans is initiated by three PTS transporters yielding fructose-1-phoshate (F-1-P) or fructose-6-phosphate. Deletion of one such F-1-P-generating PTS, fruI, was shown to reduce the cariogenicity of S. mutans in rats fed a high-sucrose diet. Moreover, a recent study linked fructose metabolism in S. mutans to a reactive electrophile species (RES) methylglyoxal. Here, we conducted a comparative transcriptomic analysis of S. mutans treated briefly with 50 mM fructose, 50 mM glucose, 5 mM methylglyoxal, or 0.5 mM hydrogen peroxide (H2O2). The results revealed a striking overlap between the fructose and methylglyoxal transcriptomes, totaling 176 genes, 61 of which were also shared with the H2O2 transcriptome. This core of 61 genes encompassed many of the same pathways affected by exposure to low pH or zinc intoxication. Consistent with these findings, fructose negatively impacted metal homeostasis of a mutant deficient in zinc expulsion and the growth of a mutant of the major oxidative stress regulator SpxA1. Importantly, fructose metabolism lowered culture pH at a faster pace, allowed better survival under acidic and nutrient-depleted conditions, and enhanced the competitiveness of S. mutans against Streptococcus sanguinis, although a moderated level of F-1-P might further boost some of these benefits. Conversely, several commensal streptococcal species displayed a greater sensitivity to fructose that may negatively affect their persistence and competitiveness in dental biofilm. In conclusion, fructose metabolism is integrated into the stress core of S. mutans and regulates critical functions required for survival and its ability to induce dysbiosis in the oral cavity. Importance.Fructose is a common monosaccharide in the biosphere, yet its overconsumption has been linked to various health problems in humans including insulin resistance, obesity, diabetes, non-alcoholic liver diseases, and even cancer. These effects are in large part attributable to the unique biochemical characteristics and metabolic responses associated with the degradation of fructose. Yet, an understanding of the effects of fructose on the physiology of bacteria and its implications to the human microbiome is severely lacking. Here we performed a series of analyses on the gene regulation of a dental pathogen Streptococcus mutans by exposing it to fructose and other important stress agents. Further supported by growth, persistence, and competition assays, our findings revealed the ability of fructose to activate a set of stress-related functions that may prove critical to the ability of the bacterium to persist and cause diseases both within and without of the oral cavity.

microbiology↗

bioRxiv2024

Systematic Analysis of the Glucose-PTS in Streptococcus sanguinis Highlighted its Importance in Central Metabolism and Bacterial Fitness

Previous work reported that deletion of the Enzyme IIAB subunits (EIIABMan, manL) of the glucose phosphotransferase system (glucose-PTS, manLMNO) in Streptococcus sanguinis impacted carbon catabolite repression (CCR) and bacterial fitness. Here, a single nucleotide polymorphism in ManN, ManNA91E, produced the unusual phenotype of increased excretion of organic acids and H2O2, yet elevated PTS activities. To characterize the contributions of each component of the glucose-PTS to bacterial fitness, we performed genetic analyses by deleting from S. sanguinis SK36 the entire operon and each EIIMan subunit individually; and genes encoding the catabolite control protein CcpA ({Delta}ccpA) and the redox regulator Rex ({Delta}rex) for comparison. Deletion of each subunit incurred a growth defect on glucose partly due to elevated excretion of H2O2; when supplemented with catalase this defect was rescued, instead resulting in a significantly higher yield than the parent. All glucose-PTS deletion mutants presented an increased antagonism against the oral pathobiont Streptococcus mutans, a phenotype absent in {Delta}ccpA despite increased H2O2 output. A shift in the pyruvate node towards mixed acid fermentation and increased arginine deiminase activity enhanced pH homeostasis in glucose-PTS mutants, but not {Delta}ccpA. Despite the purported ability of Rex to regulate central carbon metabolism, deletion of rex had no significant impact on most of the phenotypes discussed here. These findings place glucose-PTS in the pivotal position of controlling central carbon flux in streptococci, with critical outcomes impacting acidogenicity, aciduricity, pH homeostasis, and antagonism, highlighting its potential as a therapeutic target for treating diseases with a dysbiotic microbiome. ImportanceManagement of carbohydrate metabolism and environmental stress is key to the survival of oral commensal species such as S. sanguinis. Antagonism of oral pathobionts and modulation of the environmental pH and oxidative potential by commensals are crucial to the maintenance of microbial homeostasis and prevention of oral diseases including dental caries. It is therefore vital to understand how these species regulate sugar fermentation, production of acids and ammonia, and stress management in an environment known for a feast-and-famine cycle of carbohydrates and similar fluctuations in pH and oxygen tension. Here, we detail that genetic alterations of the glucose-PTS transporter in S. sanguinis can significantly affect the regulation of factors required for bacterial fitness and homeostatic ability independent of known catabolic regulators, it is then discussed how these changes may impact the survival of streptococcal species and affect caries onset.

microbiology↗

bioRxiv2024

Glycerol Metabolism Contributes to Competition by Oral Streptococci through Production of Hydrogen Peroxide

As a biological byproduct from both humans and microbes, glycerols contribution to microbial homeostasis in the oral cavity remains understudied. Here we examined glycerol metabolism by Streptococcus sanguinis, a commensal associated with oral health. Genetic mutants of glucose-PTS enzyme II (manL), glycerol metabolism (glp and dha pathways), and transcriptional regulators were characterized with regard to glycerol catabolism, growth, production of hydrogen peroxide (H2O2), transcription, and competition with Streptococcus mutans. Biochemical assays identified the glp pathway as a novel source of H2O2 production by S. sanguinis that is independent of pyruvate oxidase (SpxB). Genetic analysis indicated that the glp pathway requires glycerol and a transcriptional regulator, GlpR, for expression and is negatively regulated by PTS, but not the catabolite control protein, CcpA. Conversely, deletion of either manL or ccpA increased expression of spxB and a second, H2O2-non-producing glycerol metabolic pathway (dha), indicative of a mode of regulation consistent with conventional carbon catabolite repression (CCR). In a plate-based antagonism assay and competition assays performed with planktonic and biofilm-grown cells, glycerol greatly benefited the competitive fitness of S. sanguinis against S. mutans. The glp pathway appears to be conserved in several commensal streptococci and actively expressed in caries-free plaque samples. Our study suggests that glycerol metabolism plays a more significant role in the ecology of the oral cavity than previously understood. Commensal streptococci, though not able to use glycerol as a sole carbohydrate for growth, benefit from catabolism of glycerol through production of both ATP and H2O2. ImportanceGlycerol is an abundant carbohydrate found in oral cavity, both due to biological activities of humans and microbes, and as a common ingredient of foods and health care products. However, very little is understood regarding the metabolism of glycerol by some of the most abundant oral bacteria, commensal streptococci. This was in part because most streptococci cannot grow on glycerol as the sole carbon source. Here we show that Streptococcus sanguinis, an oral commensal associated with dental health, can degrade glycerol for persistence and competition through two independent pathways, one of which generates hydrogen peroxide at levels capable of inhibiting a dental pathobiont, Streptococcus mutans. Preliminary studies suggest that several other commensal streptococci are also able to catabolize glycerol, and glycerol-related genes are being actively expressed in human dental plaque samples. Our findings reveal the potential of glycerol to significantly impact microbial homeostasis which warrants further exploration.

microbiology↗

bioRxiv2019

Software Toolkit for Fast High-Resolution TMS Modeling

Computational modeling of Transcranial Magnetic Stimulation (TMS) is a tradeoff between computational speed vs. spatial precision. In this study, we introduce a software toolkit for high-resolution TMS modeling, which may offer the best of both. The toolkit employs the recently developed boundary element fast multipole method (BEM-FMM) with accurate solution computations close to tissue interfaces. It operates within the MATLAB platform and is designed for a broad, medically-oriented computational research community. To enable easy, subject-specific operation, the package is compatible with human head models generated with automated tools such as SimNIBS and FreeSurfer.\n\nBoth coil design in free space as well as efficacy and focality of TMS for a specific subject could be modeled by the package, including optional user-defined parametric loops. Detailed and widely used coil models, generated in both CAD and wire formats, may include several hundred thousand elementary current elements and observation spaces with approximately 1 M field points; the corresponding computational times are on the order of 1 sec. Detailed head models with approximately 1 M triangular facets and a mesh resolution of 0.6 points per mm2 are simulated in approximately 1.5 min which is arguably the fastest time to date. Further reduction of computational times is foreseen. The toolkit is augmented with a population of 16 ready-to-use head models for performing simulations for computational studies that do not involve MRI data collection. The toolkit is also augmented with a coil geometry generator capable of creating accurate coil models.

neuroscience↗