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The lower airways of patients with chronic airway diseases including cystic fibrosis (CF) are colonized by diverse communities of microorganisms. Over-time the airways of some 60% of CF patients become permanently colonized and dominated by Pseudomonas aeruginosa. Chronic infection of P. aeruginosa has been associated with a decline in pulmonary function, worse prognosis, and eventual patient mortality. Although P. aeruginosa evolves within the CF airways resulting in complex populations, the mechanism by which these complex populations contribute to disease progression is not well understood. Here we show diversity among isolates by observed changes in genome sequences of a strain of P. aeruginosa, known as Prairie Epidemic Strain (PES). Using whole genome sequencing and comparative genomics we identified a large core genome across 195 PES isolates from 57 CF patients of the Calgary Adult Cystic Fibrosis Clinic (CACFC) where 88% of the pangenome was categorized as core genes. Single nucleotide polymorphism (SNPs) mutations were shown to be the largest contributor of diversity at the nucleotide level compared to other polymorphism types consisting of 87% of the total polymorphisms present across the 195 PES isolates. CRISPR arrays and mobile elements such as prophage and plasmids demonstrate this strain of P. aeruginosa was stable over 30 years. In a second aim, I show variation in the populations of P. aeruginosa across an exacerbation event further highlighting the complexity of the lung bacterial community. Distinct populations of P. aeruginosa at the onset and resolution of an exacerbation within a single CF patient were identified by SNPs. These results a model where adaptive radiation as well as natural mutations contribute to the heterogeneity and diversification within populations of P. aeruginosa in CF patients. Understanding the evolution and population structure of PES through the identification of important genes and mutations through the clinical course of an exacerbation can aid in identifying new targets for patient treatment of P. aeruginosa in CF. / Thesis / Master of Science (MSc) / Cystic fibrosis is a life-threatening disease characterized by cycles of stability and respiratory illness. Bacterial species within the lungs of these patients are the main contributor to disease progression. I investigated a specific transmissible epidemic strain, Pseudomonas aeruginosa Prairie Epidemic Strain, using a unique collection of samples provided by collaborators at the adult cystic fibrosis clinic in Calgary. Using these samples, I first explored the differences between patients over a period of 34 years. I hypothesized that similar changes in genome sequences will be observed in multiple patients with a possible commonality in disease progression. Second, I explored the role this bacterial pathogen may play in cycles of respiratory illness. I hypothesize that a specific bacterial subpopulation could initiate these cycles and be identified by changes at the genome level. This research provides further knowledge of an epidemic strain of cystic fibrosis.

The cystic fibrosis transmembrane conductance regulator (CFTR) is one of the most studied membrane protein models because of its clear clinical significance. Mutations within the CFTR gene lead to cystic fibrosis, the most common autosomal recessive genetic disorder in the Caucasian population. CFTR, a large 160 kDa glycoprotein, is a chloride ion channel in the ABC superfamily of transporter proteins. Due to low natural abundance of CFTR and difficulties producing sufficient amounts in heterologous systems, the exact protein function/structure relationship is unknown. Expression of CFTR in E. coli is lethal and mammalian culture systems are expensive and low yielding. However, successful bioproduction of many complex human proteins has been shown in transgenic plants. Our research objective is to develop tobacco as a model system for expressing human CFTR. Constructs of full-length CFTR fused to the 35S double enhanced promoter could not be propagated in E. coli, suggesting that the CFTR product generated by "leaky" expression was detrimental to bacteria. Two strategies were undertaken to address the problem: 1) a plant intron was introduced into CFTR sequence and 2) a more tightly regulated wound-inducible promoter MeGATM was used. Tobacco was transformed with all constructs. CFTR presence was determined by polymerase chain reaction (PCR). Expression and intron splicing was analyzed by reverse transcriptase-PCR. Splicing did not occur presumably due to intron /exon contexts. In tobacco expressing MeGA:CFTR, however, novel high-molecular-weight membrane-associated proteins were immunodetected using anti-CFTR antibodies suggesting that tobacco may be capable of producing human CFTR. / Master of Science

Cystic fibrosis is an autosomal recessive disease caused by mutations in the CFTR gene. A significant number of mutations (~13%) alter the correct splicing of the CFTR gene, causing the transcription of aberrant transcripts resulting in the production of a non-functional CFTR channel. We focus our research on two intronic CF causing mutations, 3272-26A>G and 3849+10kbC>T that create a new acceptor and donor splice site, respectively, generating in the inclusion of intronic portions into the mRNA. We developed a new genome editing approach to permanently correct the abovementioned mutations by means of CRISPR nucleases. We exploited the use of either Streptococcus pyogenes Cas9, SpCas9, or Acidaminococcus sp. BV3L6, AsCas12a, to edit the aberrant splicing sites and restore the production of the correct transcript, avoiding modifications of the CFTR coding sequence. A comparative analysis between SpCas9 and AsCas12a revealed that the use of AsCas12a with a single crRNA efficiently edits the target loci, producing correctly spliced mRNAs in both 3272-26A>G and 3849+10kbC>T mutations. Furthermore, this genetic repair strategy proved to be highly specific, exhibiting a strong discrimination between the mutated and the wild-type allele and no detectable off-target activity with genome-wide analysis. The selected crRNAs were tested in patients derived primary airway cells and intestinal organoids compound heterozygous for the 3272-26A>G or 3849+10kbC>T mutations, that are considered relevant CF models for translational research. The efficient splicing repair and the complete recovery of CFTR channel activity observed confirmed the goodness of the proposed gene editing strategy. These results demonstrated that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases.

Apart from CFRD, low cognitive skill index (CSI) was also found in CF patients and was attributed the lacking of vitamin E. Since it is known that insulin plays a role in the learning and memory, decreased plasma insulin level in CF patients is an alternative mechanism for impaired cognitive function. Although numerous studies have found that insulin can improve learning and memory, the mechanism of it is not well understood. In this study, we investigated the effect of insulin on the expression of hippocampal early-phase long-term potentiation (E-LTP) in the immature rats. Hippocampal brain slices were acutely prepared from 10-12 days and 2 months old rats and field excitatory postsynaptic potentials (tEPSCs) were recorded from CA1 region by a multi-electrode in vitro recording system. In the control group, the hippocampal slices of neonatal rats showed no increase in the magnitude of fEPSC after conventional high frequency stimulation (HFS). After pretreatment of the slices with 0.08ng/ml insulin for over one hour, there was no significant change in the magnitude of E-LTP. However, when the insulin concentration increased to 0.8ng/ml, a significant increase in the magnitude of E-LTP was observed. On the contrary, any doses of insulin failed to affect the magnitude of E-LTP of mature rats. These results suggested that insulin could dose-dependently facilitate the production of E-LTP in the hippocampus of infant rats. Application of AG-1024, an inhibitor of insulin receptor, largely abolished the insulin-dependent E-LTP in immature rats rather than adult rats, indicating the involvement of insulin signaling pathway in the insulin effect. On the other hand, increasing the concentration of glucose from 11mM to 22 or 33 mM did not facilitate the E-LTP and application of indinavir, a blocker of insulin-sensitive glucose transporter-4, did not inhibit the effect of insulin. Therefore, it is unlikely that the facilitory action of insulin on E-LTP is via an indirect effect on glucose homeostasis or utilization. Pretreatment with the MAPK pathway inhibitor PD98059 blocked insulin-mediated E-LTP facilitation. Furthermore, the tetanic stimulation induced a significant increase in the level of phosphorylated p42MAPK in the insulin-treated hippocampus than that in the control group. In conclusion, our results suggested that insulin could facilitate the production of hippocampal E-LTP in infant rats, which may play an important role in modulating the expression of LTP in the developing brain and perhaps is an underlying mechanism for the improving effect of insulin on learning and memory. Since insulin plays an important role in the developing brain, perhaps the deficiency of insulin effect resulted from CF patients induces the impairment of cognitive function. / Cystic fibrosis (CF), which is caused by the deficiency of cystic fibrosis transmembrne conductance regulator (CFTR), is the most common autosomal recessive systemic disease with an incidence of 1: 2500 in Caucasians. Cystic fibrosis-related diabetes (CFRD), as one of the complications of CF patients, is regarded as one of the leading co-morbidity in CF patients. The mechanism ofCFRD is attributed to the reduced number of islets due to pancreatic fibrosis caused by the loss of CFTR in pancreatic duct. However, the above mechanism failed to explain the dynamics of insulin secretion induced by glucose tolerance test (GTT) in some CF patients and therefore, we were forced to re-consider the mechanism for the pathogenesis of CFRD. Interestingly, the following facts imply that perhaps there is another mechanism for the onset of CFRD: decreased insulin secretion and decreased plasma HCO3 - concentration was observed in the metabolic acidosis disease, plasma HCO3- level increased accompanied by the elevation of plasma insulin after food intake and CFTR accounted for HCO3 - transport in many epithelial cells. These facts promoted us to hypothesize that the loss of HCO3--induced insulin secretion resulting from the deficiency of CFTR is an alternative mechanism for the onset of CFRD. Our results showed that HCO3- could induce insulin secretion of isolated islets from rats. Ca2+ imaging revealed that HCO3- dose-dependently induced an increase in intracellular Ca2+ ([Ca2+] i) in RIN-5F cells, an insulin-secreting cell line. Removal of extracellular Ca2+ or addition of nifedipine, the blocker of L-type Ca 2+ channel, decreased the effect of HCO3- significantly, indicating the activation of L-type Ca2+ channel during HCO3- stimulation. The inhibitory effect of BaCl2 implied the involvement of K+ channel. The results that HCO3--induced increase in [Ca 2+]i was reduced by PKA inhibitor and sAC blocker demonstrated that the pathway of sAC-cAMP-PKA-ATP-sentitive K+ channel (K ATP channel) was responsible for the effect of HCO3 -. The reduction of extracellular Cl- or the inhibitor of anion exchanger (AE) inhibited the [Ca2+]i increase induced by HCO3- significantly but the omission of external Na+ failed. The facts that CFTR blocker decreased the effect of HCO3- markedly and the expression of CFTR in RIN-5F cells revealed by western blotting suggested the CFTR-mediated HCO3- transport. These results suggested that HCO 3- could induce insulin secretion in a CFTR-dependent manner, which provided a new insight into the understanding of pathogenesis of CFRD and paved the way for the therapy of CFRD. / Zhao, Wenchao. / "November 2010." / Advisers: Chang Chan; Wing Ho Yung. / Source: Dissertation Abstracts International, Volume: 73-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 115-138). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Background: Measurements of lung function are routinely used in patients with cystic fibrosis (CF) to provide information that may be clinically relevant. Spirometry is the conventional lung function measurement used, however young children find spirometry difficult to perform and often cannot achieve the strict acceptability criteria for the test. The forced oscillation technique (FOT) is a lung function measurement that only requires tidal breathing and is easy for young children to perform. However, there is limited information about the utility of this technique in the clinical assessment of young children with CF who are unable to perform spirometry. Aims: The aim of this project was to evaluate the FOT for clinical assessment in 2 to 7 year old children with CF. Specifically this involved: 1. Technical assessment of the FOT in children with CF; 2. Comparisons of lung function using the FOT in children with CF and healthy children; 3. Evaluation of associations with factors known to be associated with lung disease including: i) inflammation ii) infection and iii) structural damage. Methods Lung function was measured in a cohort of 59 children between the ages of 2 and 7 years with CF at the time of quarterly clinic visits. Resistance and reactance at 6, 8 and 10Hz (Rrs6, Rrs8, Rrs10, Xrs6, Xrs8, Xrs10, respectively) were reported and expressed as Z scores. Children were classified as asymptomatic or symptomatic based on a respiratory questionnaire and physical examination at the time of testing. Bronchoalveolar lavage and high resolution computed tomography (HRCT) were performed annually under general anaesthesia annually. BAL fluid was assessed for the presence of micro-organisms and quantification of a range of inflammatory markers and HRCT used to determine the extent of structural abnormalities. Results: The between test repeatability (n=25) for lung function was within limits previously described in healthy children. No systematic bias was observed and repeatability was not affected by the presence of respiratory symptoms. Children with CF (n=57) had significantly increased Rrs6-10 (p<0.0001) and decreased Xrs6-10 (p<0.004) compared to healthy children. Rrs6 and Xrs6-10 were significantly worse in the presence of respiratory symptoms, and Rrs6-10 progressively worsened from an asymptomatic to a symptomatic clinic visit. Children with CF (n=48) had no greater bronchodilator response (BDR) compared to healthy children. BDR was not influenced by the presence of an infection or respiratory symptoms. No relationships between inflammatory markers and lung function (n=39) were identified when the presence of an infection was adjusted for. Children with a current infection (n=20) had increased Rrs6-10 (p<0.01) and decreased Xrs6-10 (p<0.04) compared to children who were uninfected (n=23). These relationships were most marked for children infected with Pseudomonas aeruginosa, with children having a reduced lung function between 0.95 and 1.47 of a Z score. No relationships with the presence or absence of mild structural abnormalities (bronchiectasis, bronchial wall thickening and air trapping) and lung function at the time of HRCT were identified (n=34). Conclusion: The FOT is a repeatable measurement of lung function in children with CF and reliable results can be obtained in children as young as 2 years old. Young children with CF exhibit altered respiratory function which was affected by the presence of factors known to be associated with lung disease. The FOT has the potential to provide useful information about changes in clinical status in young children with CF and may be used to direct management of patient lung disease.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 150-153).

Thesis (Ph. D.)--University of Missouri--Columbia, 2001. / "May 2001." Typescript. Vita. Includes bibliographical references (leaves 168-199). Also available on the Internet.