Functional Data Analytic Inference for Systems Governed By Differential Equations with Applications

The objective of this dissertation research is to develop formal statistical methodology for analyzing systems governed by ordinary differential equations (ODE). Ordinary differential equations are commonly used to describe a wide variety of biological and physiological phenomena. They arise in the description of gene regulatory networks, study of HIV dynamics and other infectious diseases and toxicology . This work is motivated by physiologically based pharmacokinetic (PBPK) models in toxicology which are deterministic models used to describe chemical kinetics in human or animal physiology. These models relate the concentration of chemicals in tissues and blood to their rates of change and physiological parameters, such as tissue volume and blood flow, and metabolic parameters among others, through a system of ODEs. Usual strategies of analyzing such models involve non-linear least squares methodology which can potentially be computationally intensive. Often, some of the existing procedures for modeling ODEs do not necessarily account for inter and intra-individual variability that are common in multi-subject experiments. Using functional data analytic methods, in this dissertation research, we provide a formal statistical framework for drawing statistical inferences regarding subject specific and population specific parameters in models governed by a system of ODE. One of the main features of the proposed methodology is to cast the problem in a constrained inferential framework and thus avoid solving the differential equations, which is often challenging and time consuming. Such a formulation allows for the possibility that all components of the ODE may not adequately describe the underlying biological phenomena. The proposed framework also allows the researcher to estimate both within and between subject variability, while drawing statistical inferences at the individual as well as the population level. We make as few assumptions as possible while taking into account the underlying structure in the data. The proposed framework allows researchers to compare parameters among several populations, such as different dose groups, while adjusting covariates, whether discrete or continuous. Such inferences were not possible until now. We illustrate the proposed methodology using some simulated data sets as well as a real data set on benzene concentration in exhaled breath

Amino acid changes in the repressor of bacteriophage lambda due to temperature-sensitive mutations in its cI gene and the structure of a highly temperature-sensitive mutant repressor

The mutant cIts genes from seven different λcIts phages carrying tsU50, tsU9, tsU46, ts1, tsU51, tsI-22 and ts2 mutations were cloned in plasmid. The positions of these mutations and the resulting changes of amino acids in the repressor were determined by DNA sequencing. The first four mutations mapping in the N-terminal domain show the following changes: I21S, G53S, A62T and V73A, respectively. Of the three remaining mutations mapping in the C-terminal domain, cItsI-22 and cIts2 show N207T and K224E substitutions respectively, while the mutant cItsU51 gene carries F141I and P153L substitutions. Among these ts repressors, CIts2 having the charge-reversal change K224E was overexpressed from tac promoter in a plasmid and purified, and its structure and function were studied. Operator-binding studies suggest that the ts2 repressor is somewhat defective in monomer-dimer equilibrium and/ or cooperativity even at permissive temperatures and loses its operator-binding ability very rapidly above 25°C. Comparative studies of fluorescence and CD spectra, sulfhydryl group reactivity and elution behaviour in size-exclusion HPLC of both wild-type and ts2-mutant repressors at permissive and non-permissive temperatures suggest that the C-terminal domain of the ts2 repressor carrying a K224E substitution has a structure that does not favor tetramer formation at non-permissive temperatures

Multiphasic denaturation of the λ repressor by urea and its implications for the repressor structure

Urea denaturation of the λ repressor has been studied by fluorescence and circular dichroic spectroscopies. Three phases of denaturation could be detected which we have assigned to part of the C-terminal domain, N-terminal domain and subunit dissociation coupled with further denaturation of the rest of the C-terminal domain at increasing urea concentrations. Acrylamide quenching suggests that at least one of the three tryptophan residues of the λ repressor is in a different environment and its emission maximum is considerably blue-shifted. The transition in low urea concentration (midpoint approximately 2 M) affects the environment of this tryptophan residue, which is located in the C-terminal domain. Removal of the hinge and the N-terminal domain shifts this transition towards even lower urea concentrations, indicating the presence of interaction between hinge on N-terminal and C-terminal domains in the intact repressor

A cognate tRNA specific conformational change in glutaminyl-tRNA synthetase and its implication for specificity

Conformational changes that occur upon substrate binding are known to play crucial roles in the recognition and specific aminoacylation of cognate tRNA by glutaminyl-tRNA synthetase. In a previous study we had shown that glutaminyl-tRNA synthetase labeled selectively in a nonessential sulfhydryl residue by an environment sensitive probe, acrylodan, monitors many of the conformational changes that occur upon substrate binding. In this article we have shown that the conformational change that occurs upon tRNAGln binding to glnRS/ATP complex is absent in a noncognate tRNA tRNAGlu-glnRS/ATP complex. CD spectroscopy indicates that this cognate tRNAGln-induced conformational change may involve only a small change in secondary structure. The Van't Hoff plot of cognate and noncognate tRNA binding in the presence of ATP is similar, suggesting similar modes of interaction. It was concluded that the cognate tRNA induces a local conformational change in the synthetase that may be one of the critical elements that causes enhanced aminoacylation of the cognate tRNA over the noncognate ones

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.

BACKGROUND:Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whether environmental toxicants in breastmilk affect the composition and function of the infant gut microbiome at 1 month. We measured environmental toxicants in breastmilk, fecal short-chain fatty acids (SCFAs), and gut microbial composition from 16S rRNA gene amplicon sequencing using samples from 267 mother-child pairs in the Norwegian Microbiota Cohort (NoMIC). We tested 28 chemical exposures: polychlorinated biphenyls (PCBs), polybrominated flame retardants (PBDEs), per- and polyfluoroalkyl substances (PFASs), and organochlorine pesticides. We assessed chemical exposure and alpha diversity/SCFAs using elastic net regression modeling and generalized linear models, adjusting for confounders, and variation in beta diversity (UniFrac), taxa abundance (ANCOM), and predicted metagenomes (PiCRUSt) in low, medium, and high exposed groups. RESULTS:PBDE-28 and the surfactant perfluorooctanesulfonic acid (PFOS) were associated with less microbiome diversity. Some sub-OTUs of Lactobacillus, an important genus in early life, were lower in abundance in samples from infants with relative "high" (> 80th percentile) vs. "low" (< 20th percentile) toxicant exposure in this cohort. Moreover, breast milk toxicants were associated with microbiome functionality, explaining up to 34% of variance in acetic and propionic SCFAs, essential signaling molecules. Per one standard deviation of exposure, PBDE-28 was associated with less propionic acid (- 24% [95% CI - 35% to - 14%] relative to the mean), and PCB-209 with less acetic acid (- 15% [95% CI - 29% to - 0.4%]). Conversely, PFOA and dioxin-like PCB-167 were associated with 61% (95% CI 35% to 87%) and 22% (95% CI 8% to 35%) more propionic and acetic acid, respectively. CONCLUSIONS:Environmental toxicant exposure may influence infant gut microbial function during a critical developmental window. Future studies are needed to replicate these novel findings and investigate whether this has any impact on child health

Comparative pharmacokinetics of ceftriaxone and tazobactam (8:1) between healthy and Escherichia coli induced diarrhoeic birds

Antibiotic-resistant Escherichia coli infection of poultry causes significant economic losses. Extended spectrum β lactamases (ESBL) producing E. coli was inoculated in a broiler, Rhode Island Red and Haringhata Black birds orally at 56×108 c.f.u. mL-1 for induction of diarrhoea. Pharmacokinetics of ceftriaxone-tazobactam combination (8:1) was studied following a single intramuscular injection at 28.125 mg kg-1 and the combination was administered twice daily to treat such infection. Plasma concentration of both ceftriaxone persisted up to 8 h in experimental birds and maintained an approximate ratio of 8:1 with tazobactam for a period of 2 h, 0.25 h and 0.75 h, respectively in a broiler, Rhode Island Red and Haringhata Black birds. The Kel was significantly lower in all experimental birds compared to healthy birds. Efficacy study was conducted in diarrhoeic birds by administration of ceftriaxone-tazobactam combination at 28.125 mg kg-1 body weight twice daily intramuscularly for three days which caused an increase in specific antibody titre in the broiler on 5th day and in Rhode Island Red birds 10th day. However, Haringhata black birds were inherently showed more resistance towards the infection. The combination of ceftriaxone and tazobactam in the ratio of 8:1 can be an effective treatment to combat ESBL producing E. coli infections

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month

Iszatt N, Janssen S, Lenters V, et al. Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month. Microbiome. 2019;7(1): 34

Leveraging Existing Cohorts to Study Health Effects of Air Pollution on Cardiometabolic Disorders:India Global Environmental and Occupational Health Hub

Air pollution is a growing public health concern in developing countries and poses a huge epidemiological burden. Despite the growing awareness of ill effects of air pollution, the evidence linking air pollution and health effects is sparse. This requires environmental exposure scientist and public health researchers to work more cohesively to generate evidence on health impacts of air pollution in developing countries for policy advocacy. In the Global Environmental and Occupational Health (GEOHealth) Program, we aim to build exposure assessment model to estimate ambient air pollution exposure at a very fine resolution which can be linked with health outcomes leveraging well-phenotyped cohorts which have information on geolocation of households of study participants. We aim to address how air pollution interacts with meteorological and weather parameters and other aspects of the urban environment, occupational classification, and socioeconomic status, to affect cardiometabolic risk factors and disease outcomes. This will help us generate evidence for cardiovascular health impacts of ambient air pollution in India needed for necessary policy advocacy. The other exploratory aims are to explore mediatory role of the epigenetic mechanisms (DNA methylation) and vitamin D exposure in determining the association between air pollution exposure and cardiovascular health outcomes. Other components of the GEOHealth program include building capacity and strengthening the skills of public health researchers in India through variety of training programs and international collaborations. This will help generate research capacity to address environmental and occupational health research questions in India. The expertise that we bring together in GEOHealth hub are public health, clinical epidemiology, environmental exposure science, statistical modeling, and policy advocacy

The effect of cumulative early life adversities, and their differential mediation through hair cortisol levels, on childhood growth and cognition: Three-year follow-up of a birth cohort in rural India.

Background: Early adversities negatively impact children's growth and development, putatively mediated by chronic physiological stress resulting from these adverse experiences. We aimed to estimate the associations between prospectively measured cumulative early adversities with growth and cognition outcomes in rural Indian preschool children and to explore if hair cortisol concentration (HCC), a measure of chronic physiological stress, mediated the above association. Methods: Participants were recruited from the SPRING cRCT in rural Haryana, India. Adversities experienced through pregnancy and the first year of life were measured in 1304 children at 12-months. HCC was measured at 12-months in 845 of them. Outcome measures were height-for-age-z-score (HAZ), weight-for-age-z-score (WAZ) and cognition, measured in 1124 children followed up at 3-years. Cognition was measured using a validated tablet-based gamified tool named DEEP. Results: Cumulative adversities at 12-months were inversely associated with all outcomes measures at 3-years. Each unit increase in adversity score led to a decrease of 0·08 units [95% confidence interval (CI):-0·11,-0·06] in DEEP-z-score; 0·12 units [-0·14,-0·09] in HAZ and 0·11 units [-0·13,-0·09] in WAZ. 12-month HCC was inversely associated with DEEP-z-score (-0·09 [-0·16,-0·01]) and HAZ (-0·12 [-0·20,-0·04]), but the association with WAZ was not significant (p = 0·142). HCC marginally mediated the association between cumulative adversities and HAZ (proportion mediated = 0·06, p = 0·014). No evidence of mediation was found for the cognition outcome. Conclusions: Cumulative early adversities and HCC measured at 12-months have persistent negative effects on child growth and cognition at 3-years. The association between adversities and these two child outcomes were differentially mediated by HCC, with no evidence of mediation observed for the cognitive outcome. Future studies should focus on other stress biomarkers, and alternate pathways such as the immune, inflammation and cellular ageing pathways, to unpack key mechanisms underlying the established relationship between early adversities and poor child outcomes