No description available.

No description available.

Thesis advisor: Kenneth Williams / Due to overuse and misuse of antibiotics, the global threat of antibiotic resistance is a growing crisis. Three critical issues surrounding antibiotic resistance are the lack of rapid testing, treatment failure, and evolution of resistance. However, with new technology facilitating data collection and powerful statistical learning advances, our understanding of the bacterial stress response to antibiotics is rapidly expanding. With a recent influx of omics data, it has become possible to develop powerful computational methods that make the best use of growing systems-level datasets. In this work, I present several such approaches that address the three challenges around resistance. While this body of work was motivated by the antibiotic resistance crisis, the approaches presented here favor generalization, that is, applicability beyond just one context. First, I present ShinyOmics, a web-based application that allow visualization, sharing, exploration and comparison of systems-level data. An overview of transcriptomics data in the bacterial pathogen Streptococcus pneumoniae led to the hypothesis that stress-susceptible strains have more chaotic gene expression patterns than stress-resistant ones. This hypothesis was supported by data from multiple strains, species, antibiotics and non-antibiotic stress factors, leading to the development of a transcriptomic entropy based, general predictor for bacterial fitness. I show the potential utility of this predictor in predicting antibiotic susceptibility phenotype, and drug minimum inhibitory concentrations, which can be applied to bacterial isolates from patients in the near future. Predictors for antibiotic susceptibility are of great value when there is large phenotypic variability across isolates from the same species. Phenotypic variability is accompanied by genomic diversity harbored within a species. I address the genomic diversity by developing BFClust, a software package that for the first time enables pan-genome analysis with confidence scores. Using pan-genome level information, I then develop predictors of essential genes unique to certain strains and predictors for genes that acquire adaptive mutations under prolonged stress exposure. Genes that are essential offer attractive drug targets, and those that are essential only in certain strains would make great targets for very narrow-spectrum antibiotics, potentially leading the way to personalized therapies in infectious disease. Finally, the prediction of adaptive outcome can lead to predictions of future cross-resistance or collateral sensitivities. Overall, this body of work exemplifies how computational methods can complement the increasingly rapid data generation in the lab, and pave the way to the development of more effective antibiotic stewardship practices. / Thesis (PhD) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Selective serotonin reuptake inhibitors (SSRIs), like fluoxetine, are widely used to treat depressive disorders during pregnancy. These antidepressants reach water reservoirs through sewage treatment facilities and expose the aquatic vertebrates, including fish. It has been shown that early-life exposure to fluoxetine could disrupt the normal function of the stress axis by decreasing the level of circulating glucocorticoids in humans, rodents, and teleosts. Our lab recently showed that early life exposure to fluoxetine resulted in transgenerational hyporcortisolism and altered exploratory behaviour in adult male zebrafish and their descendant male adults for at least three generations. In the current study, we used a stress-responsive transgenic zebrafish line (SR4G) that expresses green fluorescence protein (eGFP) under the control of six consecutive glucocorticoid response elements. The effects of developmental exposure to fluoxetine on the transcriptional profiles of genes in the larval head and male adult telencephalon and hypothalamus were analysed using high throughput RNA sequencing. We also assessed the potential of eGFP mRNA to evaluate blunted stress response as an alternative to cortisol immunoassay measurements. The effects of bisphenol A, vinclozolin and fluoxetine were ytested in the SR4G line. Developmental exposure to fluoxetine resulted in a life-long dysregulation of pathways involved in nervous system development, stress response, and lipid metabolism in both larvae and adult zebrafish. Numerous differentially expressed genes in zebrafish are orthologous to genes in Homo sapiens linked the development of the major depressive disorder and epigenetics regulation and include bdnf, trkb, npas4, per1, per2, dnmt3a, adarb1, adaeb2, hdac4, hdac5, hdac8, and atf2. It is suggested that the dysregulation of the primary transcription regulators of circadian rhythm (clocka) and stress response (nr3c1), amongst others, were the potential drivers of the observed life-long effects. Furthermore, we report on a significant positive linear correlation between cortisol levels and eGFP mRNA levels in SR4G transgenic zebrafish larvae (R2> 0.9). Random forest and logistic regression models trained by eGFP mRNA levels both correctly predicted the blunted stress response. The negative predictive value (NPV) for both models was 100%. Models based on the mRNA levels of 11 genes associated with neurogenesis, stress response and depression resulted in a similar 100% NPV. These findings provide evidence for a life-long effect of developmental exposure to fluoxetine. This study also provides a proof-of-concept for an in vivo biomonitoring assay to screen chemicals for their stress-disrupting potential.

Aging and kinase kinetics of Y77E11.A and Y17G7B.10 in C. Elegans Jacob Goodlaxson, Department of Biomedical Sciences, College of Medicine, East Tennessee State University, Johnson City, TN. The free radical theory of aging suggests that free radical induced oxidative damage may play a role in the pathogenesis of age-related neurological diseases. The reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) protects against redox stress by providing reducing equivalents to antioxidants such as glutathione and thioredoxin. A measurement of the kinase kinetics of nicotinamide adenine dinucleotide demonstrated a decline in the rate of conversion from NAD into NADP. A homeostatic relationship of NADPH and NADP+ in mitochondria and cytosol may prevent the progression of aging due to the amelioration of the reactive oxygen species (ROS), and other charged particles. The NAPD+ cation is the chief acceptor of negatively charged particles which ionize and create free radical ions. Two previously uncharacterized proteins, Y77E11.A (NADK1) and Y17G7B.10 (NADK2), were studied for their possible kinetic role in producing and maintaining NADPH levels. The roles of NADK1 and NADK2 were determined by taking whole worm lysates of Caenorhabditis elegans deficient of these proteins, followed by supplementation with NAD, then monitoring of NADP levels. These two proteins were statistically important in the conversion of NAD to NADP+. These NADK’s displayed statistically significant reduction in NADP production which could lead to more redox stress. This research indicates that pro-longevity therapies should aim to maintain elevated levels of NADPH and NADP+ to hinder the aging process.

Chlamydia trachomatis, the most common bacterial sexually transmitted disease agent worldwide, enters a viable, non-dividing and non-infectious state (historically termed persistence and more recently referred to as the chlamydial stress response) when exposed to penicillin G in culture. Notably, penicillin G-exposed chlamydiae can reenter the normal developmental cycle upon drug removal and are resistant to azithromycin-mediated killing. Because penicillin G is less frequently prescribed than other ß-lactams, the clinical relevance of penicillin G-induced chlamydial persistence/stress has been questioned. The goal of this study was to determine whether more commonly used penicillins also induce C. trachomatis serovar E persistence/stress. All penicillins tested, as well as clavulanic acid, induced formation of aberrant, enlarged reticulate bodies (RB) (called aberrant bodies or AB) characteristic of persistent/stressed chlamydiae. Exposure to the penicillins and clavulanic acid also reduced chlamydial infectivity by >95%. None of the drugs tested significantly reduced chlamydial unprocessed 16S rRNA or genomic DNA accumulation, indicating that the organisms were viable, though non-infectious. Finally, recovery assays demonstrated that chlamydiae rendered essentially non-infectious by exposure to ampicillin, amoxicillin, carbenicillin, piperacillin, penicillin V, and clavulanic acid recovered infectivity after antibiotic removal. These data definitively demonstrate that several commonly used penicillins induce C. trachomatis persistence/stress at clinically relevant concentrations.

In our study, we analyzed four stress markers (cortisol, cortisone, DHEA and DHEAS) in blood serum in young sows using minimally invasive heart catheterisation as the stress factor. The marker levels were assessed in four defined periods of the experiment, beginning with the baseline level on the day before intervention (1), the second period was after the introduction of anaesthesia (2), the third was after conducting tissue stimulation or ablation (3), and the final period was after the end of the catheterisation (4). Cortisol and cortisone were detected using HPLC method, DHEA(S) by commercial kits. For statistical analyses non-parametric tests were used (due to non standard Gaussian data distribution). In our study we arranged these experiments: 1. Diurnal variability in these markers concentration during heart catheterisation was tested. 2. Are there differences between stress markers concentration the day before experiment (sampling 1) and in the day of the catheterisation (samplings 2, 3, 4)? 3. Are there differences between these markers concentration during operation (the first sampling was excluded)? 4. The cortisol/cortisone ratio was calculated. We found only minimal statistical differences in studied markers between the morning and afternoon group (p > 0.05) in experiment 1. For tested...

Thesis advisor: Tim van Opijnen / Thesis advisor: Welkin Johnson / Pathogenic bacteria can experience various stress factors during an infection including antibiotics and the host immune system. Whether a pathogen will establish an infection largely depends on its survival-success while enduring these stress factors. We reasoned that the ability to predict whether a pathogen will survive under and/or adapt to a stressful condition will provide great diagnostic and prognostic value. However, it is unknown what information is needed to enable such predictions. We hypothesized that under a stressful condition, a bacterium triggers responses that indicate how the stress is experienced in the genome, thereby correctly identifying a stress response holds the key to enabling such predictions. Bacterial stress responses have long been studied by determining how small groups of individual genes or pathways respond to certain environmental triggers. However, the conservation of these genes and the manner in which they respond to a stress can vary widely across species. Thus, this thesis sought to achieve a genome-wide and systems-level understanding of a bacterial stress response with the goal to identify signatures that enable predictions of survival and adaptation outcomes in a pathogen- and stress-independent manner. Here, we first set up a multi-omics framework that maps out a stress response on a genome-wide level using the human respiratory pathogen Streptococcus pneumoniae as a model organism. Under an environmental stress, gene fitness changes are determined by transposon insertion sequencing (Tn-Seq) which represents the phenotypic response. Differential expression is profiled by RNA-Seq which represents as the transcriptional response. Much to our surprise, the phenotypic response and transcriptional response are separated on different genes, meaning that differentially expressed genes are poor indicators of genes that contribute to the fitness of the bacterium. By devising and performing topological network analysis, we show that phenotypic and transcriptional responses are coordinated under evolutionary familiar stress, such as nutrient depletion and host infection, in both Gram-positive and -negative pathogens. However, such coordination is lost under the relatively unfamiliar stress of antibiotic treatment. We reasoned that this could mean that a generalizable stress response signature might exist that indicates the level to which a bacterium is adapted to a stress. By extending stress response profiling to 9 antibiotics and 3 nutrient depletion conditions, we found that such a signature indeed exists and can be captured by the level of transcriptomic disruption, defined by us as transcriptomic entropy. Centered on entropy, we constructed predictive models that perform with high accuracy for both survival outcomes and antibiotic sensitivity across 7 species. To further develop these models with the goal to eventually enable predictions on disease progression, we developed a dual RNA-Seq technique that maps out the transcriptomic responses of both S. pneumoniae and its murine host during lung infection. Preliminary data show that a high entropy is observed in the pathogen’s transcriptome during clearance (a failed infection) compared to a successful/severe infection, while the host transcriptome exhibits a pro-inflammatory and active immune response under the severe infection. Lastly, we characterized evolutionary trajectories that lead to long-term survival success of S. pneumoniae, for instance this means that the bacterium successfully adapts to the presence of an antibiotic and becomes resistant or can grow successfully in the absence of a formerly critical nutrient. These trajectories show that adaptive mutations tend to occur in genes closely related to the adapted stress. Additionally, independent of the stress, adaptation triggers rewiring of transcriptional responses resulting in a change in entropy from high to low. Most importantly, we demonstrate that by combining multi-omics profiles with additional genomic data including gene conservation and expression plasticity, and feeding this into machine learning models, that adaptive evolution can become (at least partially) predictable. Additionally, the genetic diversity in bacterial genomes across different strains and species can indeed influence a bacterium’s adaptation trajectory. In conclusion, this thesis presents a substantial collection of multi-omics stress response profiles of S. pneumoniae and other pathogenic bacteria under various environmental and clinically-relevant stresses. By demonstrating the feasibility of predictions on bacterial survival and adaptive outcomes, this thesis paves the way towards future improvements on infectious disease prognostics and forecasting the emergence of antibiotic resistance. / Thesis (PhD) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Mechanical ventilation (MV) is widely used in spinal injury patients to compensate for respiratory muscle failure. MV is known to induce lung inflammation, while spinal cord injury (SCI) is known to contribute to local inflammatory response. Interaction between MV and SCI was evaluated in order to assess the impact it may have on the pulmonary inflammatory profile. Sprague Dawley rats were anesthetized for 24 h and randomized to receive either MV or not. The MV group included C4–C5 SCI, T10 SCI and uninjured animals. The nonventilated (NV) group included T10 SCI and uninjured animals. Inflammatory cytokine profile, inflammation related to the SCI level, and oxidative stress mediators were measured in the bronchoalveolar lavage (BAL). The cytokine profile in BAL of MV animals showed increased levels of TNF-α, IL-1β, IL-6 and a decrease in IL-10 (P = 0.007) compared to the NV group. SCI did not modify IL-6 and IL-10 levels either in the MV or the NV groups, but cervical injury induced a decrease in IL-1β levels in MV animals. Cervical injury also reduced MV-induced pulmonary oxidative stress responses by decreasing isoprostane levels while increasing heme oxygenase-1 level. The thoracic SCI in NV animals increased M-CSF expression and promoted antioxidant pulmonary responses with low isoprostane and high heme oxygenase-1 levels. SCI shows a positive impact on MV-induced pulmonary inflammation, modulating specific lung immune and oxidative stress responses. Inflammation induced by MV and SCI interact closely and may have strong clinical implications since effective treatment of ventilated SCI patients may amplify pulmonary biotrauma.

CD36 is a pleiotropic receptor involved in several pathophysiological conditions, including cerebral ischemia, neurovascular dysfunction and atherosclerosis, and recent reports implicate its involvement in the endoplasmic reticulum stress response (ERSR). We hypothesized that CD36 signaling contributes to the inflammation and microvascular dysfunction following spinal cord injury. Following contusive injury, CD36-/- mice demonstrated improved hindlimb functional recovery and greater white matter sparing than CD36+/+ mice. CD36-/- mice exhibited a reduced macrophage, but not neutrophil, infiltration into the injury epicenter. Fewer infiltrating macrophages were either apoptotic or positive for the ERSR marker, phospho-ATF4. CD36-/- mice also exhibited significant improvements in injury heterodomain vascularity and function. These microvessels accumulated less of the oxidized lipid product 4-hydroxy-trans-2-nonenal (4HNE) and exhibited a reduced ERSR, as detected by vascular phospho-ATF4, CHOP and CHAC-1 expression. In cultured primary endothelial cells, deletion of CD36 diminished 4HNE-induced phospho-ATF4 and CHOP expression. A reduction in phospho-eIF2α and subsequent increase in KDEL-positive, ER-localized proteins suggest that 4HNE-CD36 signaling facilitates the detection of misfolded proteins upstream of eIF2α phosphorylation, ultimately leading to CHOP-induced apoptosis. We conclude that CD36 deletion modestly, but significantly, improves functional recovery from spinal cord injury by enhancing vascular function and reducing macrophage infiltration. These phenotypes may, in part, stem from reduced ER stress-induced cell death within endothelial and macrophage cells following injury.