COMPUTATIONAL MODELING OF METABOLIC PATHWAYS TOWARD PREDICTING DYNAMIC PHENOTYPES

Metabolic systems are important to a wide variety of applications, including therapeutic development, agricultural crop production, and manufacturing of industrial chemicals. Developing metabolic models is one of the best approaches to study metabolism, as computational experiments are generally cheaper and faster to perform than experiments in a laboratory. While there are computational frameworks that can model large metabolic systems at steady state or the metabolite dynamics of a small number of key metabolic pathways, it is substantially more difficult to model the dynamics of metabolism at the genome scale. In this thesis dissertation, I present three computational platforms that address several of the challenges in developing dynamic genome-scale metabolic models. First, I devised a stepwise machine learning strategy for identifying the regulatory topology within metabolic systems, which can be used to construct more accurate metabolic models. I then developed a framework for inferring absolute concentrations from relative abundances in metabolomics data, which will allow metabolomics (the systems-scale study of metabolites) to be more easily used with metabolic modeling tools. Finally, I implemented new constraints within a linear programming dynamic modeling framework that increase its ability to model a wider variety of metabolic systems. Together, these three platforms create a cohesive workflow for modeling the dynamics of metabolism at any scale.Ph.D

Distribution of Abdominal Obesity and Fitness Level in Overweight and Obese Korean Adults

Background. Abdominal obesity and its relative distribution are known to differ in association with metabolic characteristics and cardiorespiratory fitness. This study aimed to determine an association between fitness level and abdominal adiposity in overweight and obese adults. Methods. 228 overweight and obese individuals were classified as either cardiorespiratory unfit or fit based on their recovery heart rate. Visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), the visceral-to-subcutaneous adipose tissue ratio (VAT/SAT ratio), and cardiometabolic characteristics were analyzed to examine the relationship between recovery heart rate and abdominal adiposity components. Results. After adjustments for age and sex, significant relationships of recovery heart rate and VAT, SAT, and VAT/SAT ratio were found; however, SAT was not significantly associated after further adjustment for body mass index (BMI) (r=0.045, P=0.499), whereas VAT (r=0.232, P<0.001) and VAT/SAT ratio (r=0.214, P=0.001) remained associated. Through stepwise multiple regression analyses after adjustment for age, sex, BMI, lifestyle factors, mean blood pressure, fasting glucose, HOMA-IR, lipid profiles, and hsCRP, recovery heart rate was identified as an independent variable associated with VAT (β=0.204, P<0.001) and VAT/SAT ratio (β=0.163, P=0.008) but not with SAT (β=0.097, P=0.111). Conclusions. Cardiorespiratory fitness level is independently associated with VAT and the VAT/SAT ratio but not with SAT in overweight and obese adults

An ANGPTL4-ceramide-protein kinase Cζ axis mediates chronic glucocorticoid exposure-induced hepatic steatosis and hypertriglyceridemia in mice.

Chronic or excess glucocorticoid exposure causes lipid disorders such as hypertriglyceridemia and hepatic steatosis. Angptl4 (angiopoietin-like 4), a primary target gene of the glucocorticoid receptor in hepatocytes and adipocytes, is required for hypertriglyceridemia and hepatic steatosis induced by the synthetic glucocorticoid dexamethasone. Angptl4 has also been shown to be required for dexamethasone-induced hepatic ceramide production. Here, we further examined the role of ceramide-mediated signaling in hepatic dyslipidemia caused by chronic glucocorticoid exposure. Using a stable isotope-labeling technique, we found that dexamethasone treatment induced the rate of hepatic de novo lipogenesis and triglyceride synthesis. These dexamethasone responses were compromised in Angptl4-null mice (Angptl4-/-). Treating mice with myriocin, an inhibitor of the rate-controlling enzyme of de novo ceramide synthesis, serine palmitoyltransferase long-chain base subunit 1 (SPTLC1)/SPTLC2, decreased dexamethasone-induced plasma and liver triglyceride levels in WT but not Angptl4-/- mice. We noted similar results in mice infected with adeno-associated virus-expressing small hairpin RNAs targeting Sptlc2. Protein phosphatase 2 phosphatase activator (PP2A) and protein kinase Cζ (PKCζ) are two known downstream effectors of ceramides. We found here that mice treated with an inhibitor of PKCζ, 2-acetyl-1,3-cyclopentanedione (ACPD), had lower levels of dexamethasone-induced triglyceride accumulation in plasma and liver. However, small hairpin RNA-mediated targeting of the catalytic PP2A subunit (Ppp2ca) had no effect on dexamethasone responses on plasma and liver triglyceride levels. Overall, our results indicate that chronic dexamethasone treatment induces an ANGPTL4-ceramide-PKCζ axis that activates hepatic de novo lipogenesis and triglyceride synthesis, resulting in lipid disorders

Diabetes and mortality in patients with prostate cancer: a meta-analysis

Background: There are conflicting results as to the association between pre-existing diabetes and the risk of mortality in patients with prostate cancer. The purpose of this study is to estimate the influence of pre-existing diabetes on prostate cancer-specific mortality and all-cause mortality. Methods: We searched PubMed and Embase to identify studies that investigated the association between pre-existing diabetes and risk of death among men with prostate cancer. Pooled risk estimates and 95 % confidence intervals were calculated using fixed-effects models or random-effects models. Heterogeneity tests were conducted between studies. Publication bias was analyzed by using the Egger’s test, Begg’s test, and the trim and fill method. Results: Of the 733 articles identified, 17 cohort studies that had 274,677 male patients were included in this meta-analysis. Pre-existing diabetes was associated with a 29 % increase in prostate cancer-specific mortality [relative risk (RR) 1.29, 95 % CI 1.22–1.38, I2 = 66.68 %], and with a 37 % increase in all-cause mortality (RR 1.37, 95 % CI 1.29–1.45, p < 0.01, I2 = 90.26 %). Additionally, in a subgroup analysis that was a type specific analysis focusing on type 2 diabetes and was conducted only with three cohort studies, pre-existing type 2 diabetes was associated with all-cause mortality (RR 2.01, 95 % CI 1.37–2.96, I2 = 95.55 %) and no significant association with prostate cancer-specific mortality was detected (RR 1.17, 95 % CI 0.96–1.42, I2 = 75.59 %). There was significant heterogeneity between studies and no publication bias was found. Conclusions: This meta-analysis suggests diabetes may result in a worse prognosis for men with prostate cancer. Considering heterogeneity between studies, additional studies should be conducted to confirm these findings, and to allow generalization regarding the influence that each type of diabetes has on prostate cancer mortality

Field theoretical representation of the Hohenberg-Kohn free energy for fluids

To go beyond Gaussian approximation to the Hohenberg-Kohn free energy playing the key role in the density functional theory (DFT), the density functional \textit{integral} representation would be relevant, because field theoretical approach to perturbative calculations becomes available. Then the present letter first derives the associated Hamiltonian of density functional, explicitly including logarithmic entropy term, from the grand partition function expressed by configurational integrals. Moreover, two things are done so that the efficiency of the obtained form may be revealed: to demonstrate that this representation facilitates the field theoretical treatment of the perturbative calculation, and further to compare our perturbative formulation with that of the DFT.Comment: 5 pages, revtex, modified on 13 April 2000 [see eqs. (3), (6), and (13)

BRST-antifield-treatment of metric-affine gravity

The metric-affine gauge theory of gravity provides a broad framework in which gauge theories of gravity can be formulated. In this article we fit metric-affine gravity into the covariant BRST--antifield formalism in order to obtain gauge fixed quantum actions. As an example the gauge fixing of a general two-dimensional model of metric-affine gravity is worked out explicitly. The result is shown to contain the gauge fixed action of the bosonic string in conformal gauge as a special case.Comment: 19 pages LATEX, to appear in Phys. Rev.

DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation

Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and progression by the replicative DNA polymerase δ/proliferating cell nuclear antigen/replication factor C complex on telomeric templates that mimic the leading C-rich and lagging G-rich strands. Increased polymerase stalling occurred on the G-rich template, compared with the C-rich and nontelomeric templates. Suppression of G4 formation by substituting Li(+) for K(+) as the cation, or by using templates with 7-deaza-G residues, did not alleviate Pol δ pause sites within the G residues. Furthermore, we provide evidence that G4 folding is less stable on single-stranded circular TTAGGG templates where ends are constrained, compared with linear oligonucleotides. Artificially stabilizing G4 structures on the circular templates with the G4 ligand BRACO-19 inhibited Pol δ progression into the G-rich repeats. Similar results were obtained for yeast and human Pol δ complexes. Our data indicate that G4 formation is not required for polymerase stalling on telomeric lagging strands and suggest that an alternative mechanism, in addition to stable G4s, contributes to replication stalling at telomeres

Distribution of Abdominal Obesity and Fitness Level in Overweight and Obese Korean Adults

Background. Abdominal obesity and its relative distribution are known to differ in association with metabolic characteristics and cardiorespiratory fitness. This study aimed to determine an association between fitness level and abdominal adiposity in overweight and obese adults. Methods. 228 overweight and obese individuals were classified as either cardiorespiratory unfit or fit based on their recovery heart rate. Visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), the visceral-to-subcutaneous adipose tissue ratio (VAT/SAT ratio), and cardiometabolic characteristics were analyzed to examine the relationship between recovery heart rate and abdominal adiposity components. Results. After adjustments for age and sex, significant relationships of recovery heart rate and VAT, SAT, and VAT/SAT ratio were found; however, SAT was not significantly associated after further adjustment for body mass index (BMI) ( = 0.045, = 0.499), whereas VAT ( = 0.232, &lt; 0.001) and VAT/SAT ratio ( = 0.214, = 0.001) remained associated. Through stepwise multiple regression analyses after adjustment for age, sex, BMI, lifestyle factors, mean blood pressure, fasting glucose, HOMA-IR, lipid profiles, and hsCRP, recovery heart rate was identified as an independent variable associated with VAT ( = 0.204, &lt; 0.001) and VAT/SAT ratio ( = 0.163, = 0.008) but not with SAT ( = 0.097, = 0.111). Conclusions. Cardiorespiratory fitness level is independently associated with VAT and the VAT/SAT ratio but not with SAT in overweight and obese adults