Metabolic engineering with multi-objective optimization of kinetic models

Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility.

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Hormonal, metabolic and nutritional alterations in smokers: emergency for smoking abstinence

OBJECTIVE: To evaluate the biochemical and nutritional status of smokers in treatment for smoking cessation and its association with anthropometric parameters. METHODS: This is a cross-sectional study with convenience sample. Adult smokers were assessed at the start of treatment in the Interdisciplinary Center for Tobacco Research and Intervention of the University Hospital of the Federal University of Juiz de Fora (CIPIT/HU-UFJF). We evaluated the body mass index (BMI), conicity index (CI); waist circumference (WC), percentage of body fat (%BF), fasting glycemia, cortisol, insulin, total cholesterol (TC), LDL-c, HDL-c, triglycerides (TG) and metabolic syndrome (MS). RESULTS: Most participants (52.2%) had MS and high cardiovascular risk. The fasting glycemia was abnormal in 30.4%. There was a significant positive correlation between BMI and WC (r = 0.90; p = 0.0001), %BF (r = 0.79; p = 0.0001), CI (r = 0.65; p = 0.0001), glycemia (r = 0.42; p = 0.04) and TG (r = 0.47; p = 0.002). The CI presented positive correction with insulin (r = 0.60; p = 0.001), glycemia (r = 0.55; p = 0.007), TG (r = 0.54; p = 0.008) and %BF (r = 0.43; p = 0.004). Patients with longer duration of smoking had a higher risk of developing MS (OR = 9.6, p = 0.016). CONCLUSION: The smokers evaluated had increased risk for developing MS, especially those with longer duration of smoking, requiring urgent smoking cessation.

Evaluation of the heart rate and arrhythmias following the Maze procedure for chronic atrial fibrillation

PURPOSE: To assess the presence and the prevalence of arrhythmias and the variability of the heart rate in the medium-term postoperative period following the maze procedure for chronic atrial fibrillation (AF). METHODS: Seventeen patients with a mean age of 51.7±12.9 years, who previously underwent the maze procedure without cryoablation for chronic atrial fibrillation, were evaluated with the 24 hour electrocardiogram (ECG) - Holter monitoring from the 6th month after the operation. Valvular and coronary procedures were concomitantly performed. RESULTS: The mean heart rate during Holter monitoring was 82±8bpm; the maximal heart rate was 126 ± 23bpm and the minimal heart rate 57±7bpm. Sinus rhythm was found in 10 (59%) patients and atrial rhythm was found in 7 (41%). Supraventricular extrasystoles had a rate of 2.3±5.5% of the total number of heartbeats and occurred in 16 (94%) patients. Six (35%) patients showed nonsustained atrial tachycardia. Ventricular extrasystoles, with a rate of 0.8±0.5% of the total heartbeats, occurred in 14 (82%) patients. The chronotropic competence was normal in 9 (53%) patients and attenuated in 8 (47%). The atrioventricular conduction (AV) was unchanged in 13 (76%) patients and there were 4 (24%) cases of first degree atrioventricular block (AVB). CONCLUSION: After the maze procedure, the values for the mean heart rate, AV conduction and chronotropic competence approach the normal range, although some cases show attenuation of the chronotropic response, first degree AV block or benign arrhythmias.

Assessment of functional capacity through oxygen consumption in patients with asymptomatic probable heart disease

PURPOSE: To compare peak exercise oxygen consumption (VO2peak) of healthy individuals with asymptomatic individuals with probable heart disease. METHODS: Ninety-eight men were evaluated. They were divided into two groups: 1) 39 healthy individuals (group N) with an age range of 50±4.6 years; and 2) 59 asymptomatic individuals with signs of atherosclerotic and/or hypertensive heart disease (group C) with an age range of 51.9±10.4 years. In regard to age, height, body surface area, percentage of fat, lean body mass, and daily physical activity, both groups were statistically similar. Environmental conditions during the ergometric test were also controlled. RESULTS: Maximal aerobic power (watts), VO2peak, maximal heart rate, and maximal pulmonary ventilation were lower in group C (p<0.01) than in group N; weight, however, was lower in group N (p=0.031) than in group C. Differences in the respiratory gas exchange index, heart rate at rest, and the maximal double product of the two groups were not statistically significant. CONCLUSION: Signs of probable heart disease, even though asymptomatic, may reduce the functional capacity, perhaps due to the lower maximal cardiac output and/or muscle metabolic changes.

Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Candida tropicalis biofilms: biomass, metabolic activity and secreted aspartyl proteinase production

According to epidemiological data, Candida tropicalis has been related to urinary tract infections and haematological malignancy. Several virulence factors seem to be responsible for C. tropicalis infections, for example: their ability to adhere and to form biofilms onto different indwelling medical devices; their capacity to adhere, invade and damage host human tissues due to enzymes production such as proteinases. The main aim of this work was to study the behaviour of C. tropicalis biofilms of different ages (24120 h) formed in artificial urine (AU) and their ability to express aspartyl proteinase (SAPT) genes. The reference strain C. tropicalis ATCC 750 and two C. tropicalis isolates from urine were used. Biofilms were evaluated in terms of culturable cells by colony-forming units enumeration; total biofilm biomass was evaluated using the crystal violet staining method; metabolic activity was evaluated by XTT assay; and SAPT gene expression was determined by real-time PCR. All strains of C. tropicalis were able to form biofilms in AU, although with differences between strains. Candida tropicalis biofilms showed a decrease in terms of the number of culturable cells from 48 to 72 h. Generally, SAPT3 was highly expressed. C. tropicalis strains assayed were able to form biofilms in the presence of AU although in a strain- and time-dependent way, and SAPT genes are expressed during C. tropicalis biofilm formation.

Sex differences in the fetal heart rate variability indices of twins

Aims: To evaluate the differences in linear and complex heart rate dynamics in twin pairs according to fetal sex combination [male-female (MF), male-male (MM), and female-female (FF)]. Methods: Fourteen twin pairs (6 MF, 3 MM, and 5 FF) were monitored between 31 and 36.4 weeks of gestation. Twenty-six fetal heart rate (FHR) recordings of both twins were simultaneously acquired and analyzed with a system for computerized analysis of cardiotocograms. Linear and nonlinear FHR indices were calculated. Results: Overall, MM twins presented higher intrapair average in linear indices than the other pairs, whereas FF twins showed higher sympathetic-vagal balance. MF twins exhibited higher intrapair average in entropy indices and MM twins presented lower entropy values than FF twins considering the (automatically selected) threshold rLu. MM twin pairs showed higher intrapair differences in linear heart rate indices than MF and FF twins, whereas FF twins exhibited lower intrapair differences in entropy indices. Conclusions: The results of this exploratory study suggest that twins have sex-specific differences in linear and nonlinear indices of FHR. MM twins expressed signs of a more active autonomic nervous system and MF twins showed the most active complexity control system. These results suggest that fetal sex combination should be taken into consideration when performing detailed evaluation of the FHR in twins.

Fetal behavior and heart rate in twin pregnancy: a review

Fetal movements and fetal heart rate (FHR) are well-established markers of fetal well-being and maturation of the fetal central nervous system. The purpose of this paper is to review and discuss the available knowledge on fetal movements and heart rate patterns in twin pregnancies. There is some evidence for an association or similarity in fetal movement incidences or FHR patterns between both members of twin pairs. However, the temporal occurrence of these patterns seems to be for the most part asynchronous, especially when stricter criteria are used to define synchrony. The available data suggest that fetal behavior is largely independent of sex combination, fetal position, and presentation. Conversely, chorionicity appears to have some influence on fetal behavior, mainly before 30 weeks of gestation. There is preliminary evidence for the continuity of inter-individual differences in fetal activity and FHR patterns over pregnancy. Comparisons between studies are limited by large methodological differences and absence of uniform concepts and definitions. Future studies with high methodological quality are needed to provide a more comprehensive knowledge of normal fetal behavior in twin pregnancy.

Can the Cardiopulmonary 6-Minute Walk Test Reproduce the Usual Activities of Patients with Heart Failure?

OBJECTIVE: The 6-minute walk test is an way of assessing exercise capacity and predicting survival in heart failure. The 6-minute walk test was suggested to be similar to that of daily activities. We investigated the effect of motivation during the 6-minute walk test in heart failure. METHODS: We studied 12 males, age 45±12 years, ejection fraction 23±7%, and functional class III. Patients underwent the following tests: maximal cardiopulmonary exercise test on the treadmill (max), cardiopulmonary 6-minute walk test with the walking rhythm maintained between relatively easy and slightly tiring (levels 11 and 13 on the Borg scale) (6EB), and cardiopulmonary 6-minute walk test using the usual recommendations (6RU). The 6EB and 6RU tests were performed on a treadmill with zero inclination and control of the velocity by the patient. RESULTS: The values obtained in the max, 6EB, and 6RU tests were, respectively, as follows: O2 consumption (ml.kg-1.min-1) 15.4±1.8, 9.8±1.9 (60±10%), and 13.3±2.2 (90±10%); heart rate (bpm) 142±12, 110±13 (77±9%), and 126±11 (89±7%); distance walked (m) 733±147, 332±66, and 470±48; and respiratory exchange ratio (R) 1.13±0.06, 0.9±0.06, and 1.06±0.12. Significant differences were observed in the values of the variables cited between the max and 6EB tests, the max and 6RU tests, and the 6EB and 6RU tests (p<0.05). CONCLUSION: Patients, who undergo the cardiopulmonary 6-minute walk test and are motivated to walk as much as they possibly can, usually walk almost to their maximum capacity, which may not correspond to that of their daily activities. The use of the Borg scale during the cardiopulmonary 6-minute walk test seems to better correspond to the metabolic demand of the usual activities in this group of patients.

Female alcoholics: electrocardiographic changes and associated metabolic and electrolytic disorders

OBJECTIVE: To identify the electrocardiographic changes and their associations with metabolic and electrolytic changes in female alcoholics. METHODS: The study comprised 44 female alcoholics with no apparent physical disorder. They underwent the following examinations: conventional electrocardiography; serologic tests for syphilis, Chagas' disease, and hepatitis B and C viruses; urinary pregnancy testing; hematimetric analysis; biochemical measurements of albumin, fibrinogen, fasting and postprandial glycemias, lipids, hepatic enzymes, and markers for tissue necrosis and inflammation. RESULTS: Some type of electrocardiographic change was identified in 33 (75%) patients. In 17 (38.6%) patients, more than one of the following changes were present: prolonged QTc interval in 24 (54.5%), change in ventricular repolarization in 11(25%), left ventricular hypertrophy in 6 (13.6%), sinus bradycardia in 4 (9.1%), sinus tachycardia in 3 (6.8%), and conduction disorder in 3 (6.8%). The patients had elevated mean serum levels of creatine phosphokinase, aspartate aminotransferases, and gamma glutamyl transferase, as well as hypocalcemia and low levels of total cholesterol and LDL-cholesterol. The patients with altered electrocardiograms had a more elevated age, a lower alcohol consumption, hypopotassemia, and significantly elevated levels of triglycerides, postprandial glucose, sodium and gamma glutamyl transferase than those with normal electrocardiograms. The opposite occurred with fasting glycemia, magnesium, and alanine aminotransferase. CONCLUSION: The electrocardiographic changes found were prolonged QTc interval, change in ventricular repolarization, and left ventricular hypertrophy. Patients with normal and abnormal electrocardiograms had different metabolic and electrolytic changes.

"Differential metabolic recruitment of cognitive, emotional and modulatory brain regions in infant and adolescent rats undergoing two-way active avoidance training"

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2011

Methodenoptimierung für multifokale Simultanableitungen von Muster-Elektroretinogramm und visuell evozierten Potentialen : Einfluss von Reiz-Rate und Reiz-Typ

Magdeburg, Univ., Diss., Med. Fak., 2011

Proposal Intensity Adequacy of Expiratory Effort and Heart Rate Behavior During the Valsalva Maneuver in Preadolescents

Background: When performing the Valsalva maneuver (VM), adults and preadolescents produce the same expiratory resistance values. Objective: To analyze heart rate (HR) in preadolescents performing VM, and propose a new method for selecting expiratory resistance. Method: The maximal expiratory pressure (MEP) was measured in 45 sedentary children aged 9-12 years who subsequently performed VM for 20 s using an expiratory pressure of 60%, 70%, or 80% of MEP. HR was measured before, during, and after VM. These procedures were repeated 30 days later, and the data collected in the sessions (E1, E2) were analyzed and compared in periods before, during (0-10 and 10-20 s), and after VM using nonparametric tests. Results: All 45 participants adequately performed VM in E1 and E2 at 60% of MEP. However, only 38 (84.4%) and 25 (55.5%) of the participants performed the maneuver at 70% and 80% of MEP, respectively. The HR delta measured during 0-10 s and 10-20 s significantly increased as the expiratory effort increased, indicating an effective cardiac autonomic response during VM. However, our findings suggest the VM should not be performed at these intensities. Conclusion: HR increased with all effort intensities tested during VM. However, 60% of MEP was the only level of expiratory resistance that all participants could use to perform VM. Therefore, 60% of MEP may be the optimal expiratory resistance that should be used in clinical practice.