This panel and audience will discuss the use of our experience and knowledge of data visualizatio... more This panel and audience will discuss the use of our experience and knowledge of data visualization methods, software, and hardware in presenting the rather abstract information contained in data bases, digital libraries, and other massive collections of data and information. The panelists and audience will examine and debate how to create effective information visualizations and how to use them effectively
Simultaneous label-free autofluorescence multi-harmonic (SLAM) microscopy images of treated and n... more Simultaneous label-free autofluorescence multi-harmonic (SLAM) microscopy images of treated and non-treated mice with xenografts derived from human pancreatic tumors were acquired and analyzed for evaluation of chemotherapeutic drug response.
American Journal of Physiology-regulatory Integrative and Comparative Physiology, Sep 1, 2021
Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating micr... more Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating microbiota remain unclear. Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain often with comorbid urinary dysfunction and anxiety/depression, and recent studies find fecal dysbiosis in patients with IC/BPS. We identified the locus encoding acyloxyacyl hydrolase, Aoah, as a modulator of pelvic pain severity in a murine IC/BPS model. AOAH-deficient mice spontaneously develop rodent correlates of pelvic pain, increased responses to induced pelvic pain models, voiding dysfunction, and anxious/depressive behaviors. Here, we report that AOAH-deficient mice exhibit dysbiosis of gastrointestinal (GI) microbiota. AOAH-deficient mice exhibit an enlarged cecum, a phenotype long associated with germ-free rodents, and a “leaky gut” phenotype. AOAH-deficient ceca showed altered gene expression consistent with inflammation, Wnt signaling, and urologic disease. 16S sequencing of stool revealed altered microbiota in AOAH-deficient mice, and GC-MS identified altered metabolomes. Cohousing AOAH-deficient mice with wild-type mice resulted in converged microbiota and altered predicted metagenomes. Cohousing also abrogated the pelvic pain phenotype of AOAH-deficient mice, which was corroborated by oral gavage of AOAH-deficient mice with stool slurry of wild-type mice. Converged microbiota also alleviated comorbid anxiety-like behavior in AOAH-deficient mice. Oral gavage of AOAH-deficient mice with anaerobes cultured from IC/BPS stool resulted in exacerbation of pelvic allodynia. Together, these data indicate that AOAH is a host determinant of normal gut microbiota, and dysbiosis associated with AOAH deficiency contributes to pelvic pain. These findings suggest that the gut microbiome is a potential therapeutic target for IC/BPS.
Supplementary data and figures for Rahman-Enyart et al., 2021. These files include 16S and metabo... more Supplementary data and figures for Rahman-Enyart et al., 2021. These files include 16S and metabolomics data comparing wild-type and AOAH-deficient mice ceca.
Urologic chronic pelvic pain syndrome patients include men chronic prostatitis/chronic pelvic pai... more Urologic chronic pelvic pain syndrome patients include men chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and patients, mainly women, with interstitial cystitis/bladder pain syndrome (IC/BPS or IC). CP/CPPS is marked by severe chronic pelvic pain of unknown etiology that is differentially associated with prostatic inflammation. Microbes are known to modulate sensory responses, and microbiota are increasingly understood to drive normal biological processes and pathogenesis, including inflammation. Recent studies have linked fecal dysbiosis with chronic pelvic pain in IC/BPS, suggesting a role for microbiota in modulating UCPPS pain. Similarly, dysbiosis has been reported in CP/CPPS patients, but the relationship between with the dysbiosis of IC/BPS patients is unclear. Here, we characterized the fecal microbiota of men with CP/CPPS and women and men with IC/BPS. Similar to recent reports, we identified fecal dysbiosis in men with CP/CPPS relative to healthy controls among...
The scientific visualization group is a multidisciplinary team focused on creating high impact im... more The scientific visualization group is a multidisciplinary team focused on creating high impact images, movies, and interactive displays of scientific data (social data? economic?). The group is formed by physicists, computer scientists, graphic artists, and interaction designers. This mixture allows us, as a team, to produce beautiful and appealing, as well as scientifically correct and relevant visualizations. We work with data from a wide variety of fields, from climate data to molecular dynamics, social simulations, material sciences, or geophysics, among others
Introduction: Myxomatous mitral valve disease (MMVD) is a degenerative condition characterized by... more Introduction: Myxomatous mitral valve disease (MMVD) is a degenerative condition characterized by tissue fibrosis and matrix remodeling which ultimately progresses to leaflet prolapse. While recent work has shown that transforming growth factor beta (TGF-β) signaling contributes to the pathogenesis of MMVD, upstream regulators of this and other pathways remain poorly understood. Hypothesis: We sought to use high-throughput RNA sequencing coupled with microRNA (miRNA) sequencing to identify novel molecular targets as well as upstream regulators contributing to MMVD. Methods: We conducted mRNA and miRNA sequencing on normal (n = 10) and myxomatous human mitral valve samples (n = 10). Differential expression was identified using linear modeling and parallel random forest analyses. Canonical pathways were identified by Ingenuity Pathway Analyses (IPA). Predicted miRNA targets were identified using TargetScanHuman 6.2. Results: We found 2784 mRNAs that were differentially expressed betwe...
Accurate detection and risk stratification of latent tuberculosis infection (LTBI) remains a majo... more Accurate detection and risk stratification of latent tuberculosis infection (LTBI) remains a major clinical and public health problem. We hypothesize that multiparameter strategies that probe immune responses to Mycobacterium tuberculosis can provide new diagnostic insights into not only the status of LTBI infection, but also the risk of reactivation. After the initial proof-of-concept study, we developed a 13-plex immunoassay panel to profile cytokine release from peripheral blood mononuclear cells stimulated separately with Mtb-relevant and non-specific antigens to identify putative biomarker signatures. We sequentially enrolled 65 subjects with various risk of TB exposure, including 32 subjects with diagnosis of LTBI. Random Forest feature selection and statistical data reduction methods were applied to determine cytokine levels across different normalized stimulation conditions. Receiver Operator Characteristic (ROC) analysis for full and reduced feature sets revealed difference...
BackgroundA growing body of literature supports the ability of specific foods and nutrients to im... more BackgroundA growing body of literature supports the ability of specific foods and nutrients to impact the gastrointestinal microbiome. However, there is a dearth of knowledge on the interplay of di...
This panel and audience will discuss the use of our experience and knowledge of data visualizatio... more This panel and audience will discuss the use of our experience and knowledge of data visualization methods, software, and hardware in presenting the rather abstract information contained in data bases, digital libraries, and other massive collections of data and information. The panelists and audience will examine and debate how to create effective information visualizations and how to use them effectively
Simultaneous label-free autofluorescence multi-harmonic (SLAM) microscopy images of treated and n... more Simultaneous label-free autofluorescence multi-harmonic (SLAM) microscopy images of treated and non-treated mice with xenografts derived from human pancreatic tumors were acquired and analyzed for evaluation of chemotherapeutic drug response.
American Journal of Physiology-regulatory Integrative and Comparative Physiology, Sep 1, 2021
Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating micr... more Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating microbiota remain unclear. Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain often with comorbid urinary dysfunction and anxiety/depression, and recent studies find fecal dysbiosis in patients with IC/BPS. We identified the locus encoding acyloxyacyl hydrolase, Aoah, as a modulator of pelvic pain severity in a murine IC/BPS model. AOAH-deficient mice spontaneously develop rodent correlates of pelvic pain, increased responses to induced pelvic pain models, voiding dysfunction, and anxious/depressive behaviors. Here, we report that AOAH-deficient mice exhibit dysbiosis of gastrointestinal (GI) microbiota. AOAH-deficient mice exhibit an enlarged cecum, a phenotype long associated with germ-free rodents, and a “leaky gut” phenotype. AOAH-deficient ceca showed altered gene expression consistent with inflammation, Wnt signaling, and urologic disease. 16S sequencing of stool revealed altered microbiota in AOAH-deficient mice, and GC-MS identified altered metabolomes. Cohousing AOAH-deficient mice with wild-type mice resulted in converged microbiota and altered predicted metagenomes. Cohousing also abrogated the pelvic pain phenotype of AOAH-deficient mice, which was corroborated by oral gavage of AOAH-deficient mice with stool slurry of wild-type mice. Converged microbiota also alleviated comorbid anxiety-like behavior in AOAH-deficient mice. Oral gavage of AOAH-deficient mice with anaerobes cultured from IC/BPS stool resulted in exacerbation of pelvic allodynia. Together, these data indicate that AOAH is a host determinant of normal gut microbiota, and dysbiosis associated with AOAH deficiency contributes to pelvic pain. These findings suggest that the gut microbiome is a potential therapeutic target for IC/BPS.
Supplementary data and figures for Rahman-Enyart et al., 2021. These files include 16S and metabo... more Supplementary data and figures for Rahman-Enyart et al., 2021. These files include 16S and metabolomics data comparing wild-type and AOAH-deficient mice ceca.
Urologic chronic pelvic pain syndrome patients include men chronic prostatitis/chronic pelvic pai... more Urologic chronic pelvic pain syndrome patients include men chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and patients, mainly women, with interstitial cystitis/bladder pain syndrome (IC/BPS or IC). CP/CPPS is marked by severe chronic pelvic pain of unknown etiology that is differentially associated with prostatic inflammation. Microbes are known to modulate sensory responses, and microbiota are increasingly understood to drive normal biological processes and pathogenesis, including inflammation. Recent studies have linked fecal dysbiosis with chronic pelvic pain in IC/BPS, suggesting a role for microbiota in modulating UCPPS pain. Similarly, dysbiosis has been reported in CP/CPPS patients, but the relationship between with the dysbiosis of IC/BPS patients is unclear. Here, we characterized the fecal microbiota of men with CP/CPPS and women and men with IC/BPS. Similar to recent reports, we identified fecal dysbiosis in men with CP/CPPS relative to healthy controls among...
The scientific visualization group is a multidisciplinary team focused on creating high impact im... more The scientific visualization group is a multidisciplinary team focused on creating high impact images, movies, and interactive displays of scientific data (social data? economic?). The group is formed by physicists, computer scientists, graphic artists, and interaction designers. This mixture allows us, as a team, to produce beautiful and appealing, as well as scientifically correct and relevant visualizations. We work with data from a wide variety of fields, from climate data to molecular dynamics, social simulations, material sciences, or geophysics, among others
Introduction: Myxomatous mitral valve disease (MMVD) is a degenerative condition characterized by... more Introduction: Myxomatous mitral valve disease (MMVD) is a degenerative condition characterized by tissue fibrosis and matrix remodeling which ultimately progresses to leaflet prolapse. While recent work has shown that transforming growth factor beta (TGF-β) signaling contributes to the pathogenesis of MMVD, upstream regulators of this and other pathways remain poorly understood. Hypothesis: We sought to use high-throughput RNA sequencing coupled with microRNA (miRNA) sequencing to identify novel molecular targets as well as upstream regulators contributing to MMVD. Methods: We conducted mRNA and miRNA sequencing on normal (n = 10) and myxomatous human mitral valve samples (n = 10). Differential expression was identified using linear modeling and parallel random forest analyses. Canonical pathways were identified by Ingenuity Pathway Analyses (IPA). Predicted miRNA targets were identified using TargetScanHuman 6.2. Results: We found 2784 mRNAs that were differentially expressed betwe...
Accurate detection and risk stratification of latent tuberculosis infection (LTBI) remains a majo... more Accurate detection and risk stratification of latent tuberculosis infection (LTBI) remains a major clinical and public health problem. We hypothesize that multiparameter strategies that probe immune responses to Mycobacterium tuberculosis can provide new diagnostic insights into not only the status of LTBI infection, but also the risk of reactivation. After the initial proof-of-concept study, we developed a 13-plex immunoassay panel to profile cytokine release from peripheral blood mononuclear cells stimulated separately with Mtb-relevant and non-specific antigens to identify putative biomarker signatures. We sequentially enrolled 65 subjects with various risk of TB exposure, including 32 subjects with diagnosis of LTBI. Random Forest feature selection and statistical data reduction methods were applied to determine cytokine levels across different normalized stimulation conditions. Receiver Operator Characteristic (ROC) analysis for full and reduced feature sets revealed difference...
BackgroundA growing body of literature supports the ability of specific foods and nutrients to im... more BackgroundA growing body of literature supports the ability of specific foods and nutrients to impact the gastrointestinal microbiome. However, there is a dearth of knowledge on the interplay of di...
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Papers by Colleen Bushell