Biomarker testing, wherein the concentration of a biochemical marker is measured to predict the presence or absence of a certain binary characteristic (e.g., a disease) in a subject, is an essential component of public health screening. For many diseases, the concentration of disease-related biomarkers may exhibit a wide range, particularly among the disease positive subjects, in part due to variations caused by external and/or subject-specific factors. Further, a subject's actual biomarker concentration is not directly observable by the decision maker (e.g., the tester), who has access only to the test's measurement of the biomarker concentration, which can be noisy. In this setting, the decision maker needs to determine a classification scheme in order to classify each subject as test negative or test positive. However, the inherent variability in biomarker concentrations and the noisy test measurements can increase the likelihood of subject misclassification. We develop an optimal data-driven framework, which integrates optimization and data analytics methodologies, for subject classification in disease screening, with the aim of minimizing classification errors. In particular, our framework utilizes data analytics methodologies to estimate the posterior disease risk of each subject, based on both subject-specific and external factors, coupled with robust optimization methodologies to derive an optimal robust subject classification scheme, under uncertainty on actual biomarker concentrations. We establish various key structural properties of optimal classification schemes, show that they are easily implementable, and develop key insights and principles for classification schemes in disease screening. As one application of our framework, we study newborn screening for cystic fibrosis in the United States. Cystic fibrosis is one of the most common genetic diseases in the United States. Early diagnosis of cystic fibrosis can substantially improve health outcomes, while a delayed diagnosis can result in severe symptoms of the disease, including fatality. We demonstrate our framework on a five-year newborn screening data set from the North Carolina State Laboratory of Public Health. Our study underscores the value of optimization-based approaches to subject classification, and show that substantial reductions in classification error can be achieved through the use of the proposed framework over current practices. / Doctor of Philosophy / A biomarker is a measurable characteristic that is used as an indicator of a biological state or condition, such as a disease or disorder. Biomarker testing, where a biochemical marker is used to predict the presence or absence of a disease in a subject, is an essential tool in public health screening. For many diseases, related biomarkers may have a wide range of concentration among subjects, particularly among the disease positive subjects. Furthermore, biomarker levels may fluctuate based on external factors (e.g., temperature, humidity) or subject-specific characteristics (e.g., weight, race, gender). These sources of variability can increase the likelihood of subject misclassification based on a biomarker test. We develop an optimal data-driven framework, which integrates optimization and data analytics methodologies, for subject classification in disease screening, with the aim of minimizing classification errors. We establish various key structural properties of optimal classification schemes, show that they are easily implementable, and develop key insights and principles for classification schemes in disease screening. As one application of our framework, we study newborn screening for cystic fibrosis in the United States. Cystic fibrosis is one of the most common genetic diseases in the United States. Early diagnosis of cystic fibrosis can substantially improve health outcomes, while a delayed diagnosis can result in severe symptoms of the disease, including fatality. As a result, newborn screening for cystic fibrosis is conducted throughout the United States. We demonstrate our framework on a five-year newborn screening data set from the North Carolina State Laboratory of Public Health. Our study underscores the value of optimization-based approaches to subject classification, and show that substantial reductions in classification error can be achieved through the use of the proposed framework over current practices.

<p dir="ltr"><i>Stenotrophomonas maltophilia</i> is an emerging multidrug-resistant, Gram-negative opportunistic pathogen. It causes many hospital-acquired infections such as sepsis, endocarditis, meningitis, and catheter-related urinary tract infections. It also affects individuals with cystic fibrosis, exacerbating their lung condition. <i>S. maltophilia</i> often causes pathogenesis through the formation of biofilms. However, the molecular mechanisms <i>S. maltophilia</i> uses to carry out these pathogenic steps are unclear. The SMF-1 chaperone/usher pilus has been thought to mediate <i>S. maltophilia</i> attachment. To confirm this role, we created an isogenic deletion of the <i>smf-1</i> pilin gene and observed a defect in biofilm compared to wild type. We also discovered 2 additional chaperone/usher pilus operons, mutation of which also caused attenuation in biofilm levels. Analysis of <i>S. maltophilia</i> clinical strains and <i>S. maltophili</i><i>a</i> complete genomes listed in NCBI showed that these three pili are prevalent and highly conserved, suggesting a vital role in infection. Intriguingly, through TEM studies, we found that the mutation of one pilus is not phenotypically compensated by another. Infection of <i>Galleria mellonella</i> larvae revealed increased virulence of the pilus mutants. Additionally, we also demonstrated a relationship between pilus and flagella contributing to the overall biofilm development of <i>S. maltophilia</i>. Understanding their activity may help identify therapeutic targets for this pathogen.</p>

Yes / A dry powder inhaled liposomal azithromycin formulation was developed for the treatment of chronic respiratory diseases such as cystic fibrosis and bronchiectasis. Key properties including liposome size, charge and encapsulation efficiency powder size, shape, glass transition temperature (Tg), water content and in vitro respiratory deposition were determined. Antimicrobial activity against cystic fibrosis (CF) respiratory pathogens was determined by MIC, MBC and biofilm assays. Cytotoxicity and cellular uptake studies were performed using A549 cells. The average liposome size was 105 nm, charge was 55 mV and encapsulation efficiency was 75 %. The mean powder particle size d[v,50] of 4.54 µm and Mass Median Aerodynamic Diameter (MMAD) was 5.23 µm with a mean Tg of 76˚C and water content of 2.1 %. These excellent physicochemical characteristics were maintained over one year. Liposomal loaded azithromycin demonstrated enhanced activity against P. aeruginosa clinical isolates grown in biofilm. The formulation was rapidly delivered into bacterial cells with > 75 % uptake in 1 h. Rapid uptake into A549 cells via a cholesterol-dependent endocytosis pathway with no cytotoxic effects apparent. These data demonstrate that this formulation could offer benefits over current treatment regimens for people with chronic respiratory infection.

No description available.

INTRODUÇÃO: Com o aumento da longevidade dos portadores de fibrose cística, o Diabetes Mellitus surgiu como sua primeira co-morbidade. Visando ao diagnóstico precoce, buscou-se maior compreensão do mecanismo fisiopatológico do Diabetes Mellitus Relacionado à Fibrose Cística (DRFC) através do estudo da resposta endócrina do pâncreas após dois tipos de estímulo. MÉTODOS: Neste estudo transversal, prospectivo e controlado conduzido entre junho de 2004 a agosto de 2005, foram comparadas as respostas de glicose, insulina, peptídeo-C, proinsulina e glucagon aos testes de sobrecarga com glicose (OGTT) e com dieta líquida (TTDM) realizados num intervalo inferior a 10 semanas, num grupo de 52 crianças e adolescentes com fibrose cística, entre 5 e 19 anos, acompanhadas na Unidade de Pneumologia Pediátrica do Instituto da Criança. RESULTADOS: O TTDM provocou uma hiperglicemia de menor duração (p < 0,05) e uma resposta mais precoce no tempo 30 minutos de insulina (p < 0,05), peptídeo-C (p < 0,05) e glucagon (p < 0,05), enquanto que o OGTT produziu uma hiperglicemia mais prolongada e respostas de insulina (p < 0,001), peptídeo-C (p < 0,001) e proinsulina (p < 0,001) mais tardias e sustentadas nos tempos 120 e 180 minutos. Ao grupo portador de DRFC sem hiperglicemia de jejum associaram-se níveis médios elevados de insulina (p < 0,05), peptídeo-C (p < 0,01) e proinsulina (p < 0,05) no tempo 120 minutos, revelando resistência insulínica. Houve sobreposição das respostas hormonais dos grupos normal, pré-diabético e diabético com hiperglicemia de jejum no tempo 120 minutos, sugerindo disfunção de célula beta nos dois últimos grupos. CONCLUSÕES: O estímulo da dieta líquida revelou uma resposta hormonal mais rápida provavelmente mediada pelos nutrientes diferentes da glicose. A resistência insulínica, além da disfunção da célula beta, está associada à fisiopatologia dos distúrbios glicêmicos da fibrose cística. / INTRODUCTION: Cystic fibrosis-related diabetes is a common complication leading to clinical deterioration of these patients. Aiming at an earlier diagnosis, we investigated the kinetics of the glucose-metabolism abnormalities by evaluating glucose, insulin, pro-insulin, C-peptide and glucagon responses after oral glucose (OGTT) and a mixed meal tolerance (MMTT) tests. METHODS: In a cross-sectional and controlled study, conducted from july/2004 till august/2005, 52 children and adolescents with cystic fibrosis, from 5 to 19 years old, underwent both tests in an interval of less than 10 weeks. RESULTS: Plasma glucose values were significantly lower during MMTT after 60 minutes and insulin, C-peptide and glucagon were secreted earlier, being significantly higher at 30 minutes. During OGTT, patients showed a delayed but higher peak insulin, C-peptide and pro-insulin secretion at time 120 minutes. Patients with Cystic Fibrosis-Related Diabetes (CFRD) without fasting hyperglycemia presented insulin, C-peptide and proinsulin values significantly higher than those patients with normal glucose tolerance or pre-diabetes, at time 120 minutes, indicating increased peripheral insulin resistance. An overlap of insulin, C-peptide and pro-insulin levels was observed in normal and pre-diabetic patients as well as in people with CFRD with fasting hyperglycemia, at 120 minutes, suggesting beta cell dysfunction in the latter groups. Conclusion: Mixed meal ingestion caused an earlier hormone secretion stimulated probably by nutrients different from glucose. Insulin resistance besides beta cell dysfunction are involved in the pathogenesis of cystic fibrosis related glucose disturbances.

INTRODUÇÃO: Com o aumento da longevidade dos portadores de fibrose cística, o Diabetes Mellitus surgiu como sua primeira co-morbidade. Visando ao diagnóstico precoce, buscou-se maior compreensão do mecanismo fisiopatológico do Diabetes Mellitus Relacionado à Fibrose Cística (DRFC) através do estudo da resposta endócrina do pâncreas após dois tipos de estímulo. MÉTODOS: Neste estudo transversal, prospectivo e controlado conduzido entre junho de 2004 a agosto de 2005, foram comparadas as respostas de glicose, insulina, peptídeo-C, proinsulina e glucagon aos testes de sobrecarga com glicose (OGTT) e com dieta líquida (TTDM) realizados num intervalo inferior a 10 semanas, num grupo de 52 crianças e adolescentes com fibrose cística, entre 5 e 19 anos, acompanhadas na Unidade de Pneumologia Pediátrica do Instituto da Criança. RESULTADOS: O TTDM provocou uma hiperglicemia de menor duração (p < 0,05) e uma resposta mais precoce no tempo 30 minutos de insulina (p < 0,05), peptídeo-C (p < 0,05) e glucagon (p < 0,05), enquanto que o OGTT produziu uma hiperglicemia mais prolongada e respostas de insulina (p < 0,001), peptídeo-C (p < 0,001) e proinsulina (p < 0,001) mais tardias e sustentadas nos tempos 120 e 180 minutos. Ao grupo portador de DRFC sem hiperglicemia de jejum associaram-se níveis médios elevados de insulina (p < 0,05), peptídeo-C (p < 0,01) e proinsulina (p < 0,05) no tempo 120 minutos, revelando resistência insulínica. Houve sobreposição das respostas hormonais dos grupos normal, pré-diabético e diabético com hiperglicemia de jejum no tempo 120 minutos, sugerindo disfunção de célula beta nos dois últimos grupos. CONCLUSÕES: O estímulo da dieta líquida revelou uma resposta hormonal mais rápida provavelmente mediada pelos nutrientes diferentes da glicose. A resistência insulínica, além da disfunção da célula beta, está associada à fisiopatologia dos distúrbios glicêmicos da fibrose cística. / INTRODUCTION: Cystic fibrosis-related diabetes is a common complication leading to clinical deterioration of these patients. Aiming at an earlier diagnosis, we investigated the kinetics of the glucose-metabolism abnormalities by evaluating glucose, insulin, pro-insulin, C-peptide and glucagon responses after oral glucose (OGTT) and a mixed meal tolerance (MMTT) tests. METHODS: In a cross-sectional and controlled study, conducted from july/2004 till august/2005, 52 children and adolescents with cystic fibrosis, from 5 to 19 years old, underwent both tests in an interval of less than 10 weeks. RESULTS: Plasma glucose values were significantly lower during MMTT after 60 minutes and insulin, C-peptide and glucagon were secreted earlier, being significantly higher at 30 minutes. During OGTT, patients showed a delayed but higher peak insulin, C-peptide and pro-insulin secretion at time 120 minutes. Patients with Cystic Fibrosis-Related Diabetes (CFRD) without fasting hyperglycemia presented insulin, C-peptide and proinsulin values significantly higher than those patients with normal glucose tolerance or pre-diabetes, at time 120 minutes, indicating increased peripheral insulin resistance. An overlap of insulin, C-peptide and pro-insulin levels was observed in normal and pre-diabetic patients as well as in people with CFRD with fasting hyperglycemia, at 120 minutes, suggesting beta cell dysfunction in the latter groups. Conclusion: Mixed meal ingestion caused an earlier hormone secretion stimulated probably by nutrients different from glucose. Insulin resistance besides beta cell dysfunction are involved in the pathogenesis of cystic fibrosis related glucose disturbances.

No description available.

The three dimensional structure of the human genome is known to play a critical role in gene function and expression. I used chromosome conformation capture (3C) and 3C-carbon copy (5C) techniques to investigate the three-dimensional structure of the cystic fibrosis transmembrane conductance regulator (CFTR) locus. This is an important disease gene that, when mutated, causes cystic fibrosis. 3C experiments identified four distinct looping elements that contact the CFTR gene promoter only in CFTR-expressing cells. Using 5C, I expanded the region of study to a 2.8 Mb region surrounding the CFTR gene. The 5C study shows 7 clear topologically associating domains (TADs) present at the locus, identical in all five cell lines tested, regardless of gene expression status. CFTR and all its known regulatory elements are contained within one TAD, suggesting TADs play a role in constraining promoters to a local search space. The four looping elements identified in the 3C experiment and confirmed in the 5C experiment were then tested for enhancer activity using a luciferase assay, which showed that elements III and IV could act as enhancers. These elements were tested against a library of human transcription factors in a yeast one-hybrid assay to identify potential binding proteins. Element III gave two strong candidates, TCF4 and LEF1. A literature search supported these transcription factors as playing a role in CFTR gene expression. Overall, this work represents a model locus that can be used to test important questions regarding the role of three dimensional looping on gene expression.

No description available.

Cystic fibrosis (CF) is the most common genetic disease affecting Canadian newborns (1 in 3,850) and is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. This gene encodes for CFTR, a phosphorylation-dependent ion channel localized at the apical membrane. Phosphorylation of CFTR by the cyclic adenosine monophosphate (cAMP)-dependent enzyme protein kinase A activates its activity, facilitating the transport of chloride and bicarbonate ions across the epithelial membrane. CFTR contributes to ion and airway surface liquid regulation, crucial for maintaining host defenses. The inheritance of CFTR mutations leads to a variety of respiratory complications, including impaired mucociliary clearance, excessive mucus production, persistent airway infections, and heightened inflammation, ultimately causing lung damage. While there is currently no cure for CF, the development of CFTR modulators, targeting the defective CFTR protein directly, has significantly improved the quality of life for many CF patients. Despite these advancements, many patients remain unresponsive to current treatment options. It has been well-established that combination therapies outperform monotherapies, emphasizing the need for alternative or complementary therapeutic strategies for CF management. Furthermore, CFTR dysfunction extends beyond CF and has been implicated in other respiratory diseases, such as chronic obstructive pulmonary disease, which is primarily linked to tobacco smoke exposure. This Ph.D. thesis explores a complementary therapeutic approach, targeting proteins within the CFTR-containing macromolecular signaling complex to elevate intracellular cAMP levels, thereby enhancing CFTR function. We hypothesized that synergistic use of cAMP modulators, alongside CFTR modulators, will serve as an effective therapeutic strategy for CF and other respiratory diseases. Collectively, our studies highlight the potential of cAMP and CFTR modulation as a therapeutic strategy for improving the treatment of CF and other respiratory diseases, warranting further investigation, offering insights for future studies, and contributes to the ongoing pursuit of improved combination treatments. / Dissertation / Doctor of Philosophy (PhD) / Cystic fibrosis (CF) is the most common genetic condition affecting Canadian newborns, caused by inheritance of mutations in the CF transmembrane conductance regulator (CFTR) gene. These mutations result in respiratory issues, including breathlessness, excess mucus, and susceptibility to infections, causing lung damage and premature death. Despite progress in CF drug development, some patients remain unresponsive to existing drug combinations, highlighting the need for new combinations to improve the quality of life for all CF patients. CFTR function is also compromised in other respiratory diseases like chronic obstructive pulmonary disease, a lung disease that shares many characteristics with CF and is mainly caused by tobacco smoke exposure. This Ph.D. thesis explores the effectiveness of a new drug strategy targeting proteins interacting with CFTR. By investigating drugs to complement existing treatments, we aim to improve CFTR function. This research offers a promising strategy to improve treatment for CF and other respiratory diseases.