Clyde Phelix | University of Texas at San Antonio (original) (raw)

Papers by Clyde Phelix

ACS chemical neuroscience, Jan 11, 2018

Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating gl... more Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K and high V, specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free...

Biochemical and biophysical research communications, Dec 9, 2017

Glucose transporters (GLUTs), expressed in all types of human cells, are responsible for the upta... more Glucose transporters (GLUTs), expressed in all types of human cells, are responsible for the uptake of sugars as the primary energy source for the normal functions of good cells and for the abnormal growth of cancer cells. The E. coli xylose permease (XylE), a homologue of human GLUTs, has been investigated more thoroughly than other major facilitator proteins in the current literature. In this paper, we present a molecular dynamics (MD) study of an all-atom model system to elucidate the atomistic details and the free-energy landscape along the path of binding a xylopyranose (XYP) from the extracellular space to the inside of the transporter protein XylE. From the MD simulations, the Gibbs free energy of binding was found to be -4.4kcal/mol in agreement with the experimental value of -4.7kcal/mol. The accuracy of our study is further shown in the computed hydration energy of XYP of -14.6kcal/mol in comparison with the experimental data of -15.0kcal/mol. Along the binding path, the G...

International Journal of Clinical Medicine, 2016

Metabolically stressed kidney is in part characterized by infiltrating macrophages and macrophage... more Metabolically stressed kidney is in part characterized by infiltrating macrophages and macrophage-derived TGF-β1 that promote the synthesis of various ECM molecules. TGF-β1 strongly enhances the expression of the gene TGFBI that encodes a cell-adhesion class, proapoptotic ECM protein called BIGH3. We hypothesized that in a diabetic environment a relationship between infiltrating macrophages, macrophage-derived TGF-β1, and BIGH3 protein promotes renal cell death. To investigate this hypothesis, we used our mouse model of diabetic complications. Mice on a high-fat diet developed hypercholesterolemia, and exposure to streptozotocin rendered hypercholesterolemic mice diabetic. Immunohistochemical images show increased macrophage infiltration and BIGH3 protein in the kidney cortices of hypercholesterolemic and diabetic mice. Macrophages induced a twofold increase in BIGH3 expression and an 86% increase in renal proximal tubule epithelial cell apoptosis. TGF-β1 antibody and TGF-β1 receptor chemical antagonist blocked macrophage-induced apoptosis. BIGH3 antibody completely blocked apoptosis that was induced by TGF-β1, and blocked apoptosis induced by exogenous recombinant BIGH3. These results uncover a distinctive interplay of macrophage-derived TGF-β1, BIGH3 protein, and apoptosis, and indicate that BIGH3 is central in a novel pathway that promotes diabetic nephropathy. Macrophage TGF-β1 and BIGH3 are identified as prediabetic biomarkers, and potential therapeutic targets for intervention in prediabetic and diabetic individuals.

The Canadian Journal of Neurological Sciences, 2012

2014 IEEE Healthcare Innovation Conference (HIC), 2014

ABSTRACT Precision medicine requires the right drug at the right dose for the right patient at th... more ABSTRACT Precision medicine requires the right drug at the right dose for the right patient at the right time. This study used a computational biology model of 30 metabolic and transport pathways and multiple compartments to simulate oral dosing of pioglitazone that is currently in clinical trials to delay onset of Alzheimer's disease. The Transcriptome-To-Metabolome™ Method was used to simulate individual human subjects by using their gene expression profiles to determine parameters for the kinetic biosimulation. The in silico plasma profiles for multiple doses matched those for in vivo results from literature. Individual ED50 values were determined on each subject for the mitochondrial pyruvate carrier bound by pioglitazone as the target. This approach will allow determination of effective dosing for individual subjects in clinical trials and patients for treatments.

Advances in Intelligent and Soft Computing, 2012

ABSTRACT Integrated Systems Biology was used to study bone cancer via an iterative process of in ... more ABSTRACT Integrated Systems Biology was used to study bone cancer via an iterative process of in vitro testing for validation of an in silico computer simulation where the transcriptome was used to derive the parameters of a kinetic model. A computer simulation model of the transforming growth factor-beta (TGF-β1) signaling pathway was obtained from Reactome®. The transcriptome of MG-63 cells was accessed from NCBI GEO GSE11414. With this method the model is not trained to match the biological system. The in vitro study on osteosarcoma (MG-63) cells was used to compare with the results from the computer simulation. MG-63 cells were grown in culture and exposed to TGF-β1 to identify differences in expression of a target-gene, TGF-β -Induced 68kDa protein (TGFBI), at serial time intervals. Real-time PCR was used to measure TGFBI mRNA levels and the temporal profile was identical with that predicted by the in silico model. A sensitivities test was performed through the in silico model and a candidate target for gene-knock-down in the TGF-β signaling pathway, Smad3, was identified. An 80% reduction of this reactant in the model attenuated TGFBI expression by 64%, an effect that matched such knockdown of Smad3, in vitro, for other target genes reported in the literature. The assumption that the transcriptome drives the reactome is validated and substantiates a novel method for deriving parameters for kinetic deterministic models of biological systems.

The authors had validated a proprietary method, Transcriptome-To-Metabolome™ (TTM™) Biosimulation... more The authors had validated a proprietary method, Transcriptome-To-Metabolome™ (TTM™) Biosimulation, for using the transcriptome to determine parameters for kinetic biosimulation of 16 core metabolic pathways. In vivo and in silico evidence confirmed that hippocampal cholesterol metabolism decreases with aging and increases with Alzheimer's disease (AD). The molecular studies on aging primate and human hippocampus, including AD samples, provided internal validations on the biosimulations, while evidence from the literature, bibliome, provided external validations. This study extends the investigations with the TTM™ Biosimulations into the changes in these 16 metabolic pathways in aging male human hippocampus and for stages of AD. The authors report robust hippocampal hypometabolism in the fifth to tenth decade of life involving glucose and lipid metabolism in male humans. These findings are validated externally from the bibliome. Several changes in AD are demonstrated to be exaggerations or deviations of very late stage changes of normal aging among these pathways.

2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2014

We validated a model of the TGF-β signaling pathway using reactions from Reactome. Using a patent... more We validated a model of the TGF-β signaling pathway using reactions from Reactome. Using a patentpending technique, gene expression profiles from individual patients are used to determine model parameters. Gene expression profiles from 45 women, normal, or benign tumor and malignant breast cancer were used as training and validating sets for assessing clinical sensitivity and specificity. Biomarkers were identified from the biosimulation results using sensitivity analyses and derivative properties from the model. A membrane signaling marker had sensitivity of 80% and specificity of 60%; while a nuclear transcription factor marker had sensitivity of 80% and specificity of 90% to predict malignancy. Use of Fagan's nomogram increased probability from 7.5% for positive mammogram to 39% with positive results of the biosimulation for the nuclear marker. Our technology will allow researchers to identify and develop biomarkers and assist clinicians in diagnostic and treatment decision making.

Cancer Research, 2013

Genome-wide gene-expression profiles, transcriptomes, from microarray tests are used for clinical... more Genome-wide gene-expression profiles, transcriptomes, from microarray tests are used for clinical decision-making; novel uses of transcriptomes will continue to emerge. We are commercializing a patent-pending technology using transcriptomes to determine parameters for deterministic-kinetic models of biological pathways, Transcriptome-To-Reactome:Transforming Growth Factor Beta Signaling. We demonstrate how biosimulation results for proteomics, flux, and a derivative property of the network system can be utilized as biomarkers for breast cancer. The TGFbeta Signaling Model was accessed from Reactome.org; manual curation was performed to add beta-induced-gene-human-clone-3 as a target gene for Smad transcription factors. Biosimulations were run with COPASI. Transcriptomes were accessed from NCBI GEO archives, where peripheral blood mononuclear cells (PBMC) were collected from women with suspect initial mammograms, prior to undergoing diagnostic biopsy to differentiate benign from mali...

2013 6th International IEEE/EMBS Conference on Neural Engineering (NER), 2013

ABSTRACT A multi-compartmental molecular model has been developed for rodent basal forebrain chol... more ABSTRACT A multi-compartmental molecular model has been developed for rodent basal forebrain cholinergic neurons with established gene expression levels. Reconstruction of neurons and network function were acquired using the Transcriptome-To-Physiome™ (TTP™) NeurobioSimulation. Gene expression values [NCBI GEO GSE 13379] were used to derive protein level and kinetic parameters for ligand and voltage gated ion channels in the TTP™ NeurobioSimulator Model using COPASI® software. Global parameters for membrane potential used permeability and ion concentrations inside and outside of the membrane in the Goldman-Hodgkin-Katz equation. Four compartments of the model neuron are included: glutamate synapse, distal dendrite, proximal dendrite, and axon hillock. The simulation of a voltage-gated sodium channel activation, and inactivated states of distal dendrites of cholinergic modeled neurons depends on the excitatory postsynaptic potential (EPSP) event. This distally activated event yielded temporally relevant proximal dendritic activation and inactivation of voltage-gated sodium and potassium channels in the reconstructed neuron. Graded potentials showed temporal summation and a classic action potential occurs at the axon hillock with sodium and potassium fluxes as expected. In future studies, we will reconstruct the electrophysiology of vulnerable neuronal populations in the diseased brain and compare them to controls thus lending substantial insight into molecular and network function corollary to neuropathogenesis.

Hippocampus, 2010

Changes in brain cholesterol homeostasis are associated with multiple diseases, such as Alzheimer... more Changes in brain cholesterol homeostasis are associated with multiple diseases, such as Alzheimer's and Huntington's; however, controversy persists as to whether adult neurons produce their own cholesterol, or if it is outsourced to astrocytes. To address this issue, we analyzed 25 genes most immediately involved in cholesterol homeostasis from in situ data provided by the Allen Brain Mouse Atlas. We compared the relative mRNA expression in the pyramidal and granule layers, populated with neurons, with the rest of the hippocampus which is populated with neuronal processes and glia. Comparing the expression of the individual genes to markers for neurons and astrocytes, we found that cholesterol homeostasis genes are preferentially targeted to neuronal layers.…

Journal of Health Care for the Poor and Underserved, 2014

Apolipoprotein E 4 (ApoE 4) has been linked to pathogenesis of Alzheimer's disease and has been s... more Apolipoprotein E 4 (ApoE 4) has been linked to pathogenesis of Alzheimer's disease and has been suggested to be maintained through evolutionary pressure via a protective role in malaria infection. We evaluated Plasmodium falciparum viability at the intraerythrocyte stage by exposure to plasma from human subjects with ApoE 4/4 or ApoE 3/3. Plasma samples from ApoE 4/4 but not ApoE 3/3 donors inhibited growth and disrupted morphology of P. falciparum. Evolutionary history is characterized by war between pathogenic microorganisms and defense mechanisms countering their pathogenicities. ApoE 4 frequency is highest in sub-Saharan Africa and other isolated populations (e.g., Papua New Guinea) that exhibit endemic malaria. High ApoE frequency may offer selective advantage protecting against some infectious diseases (e.g., Plasmodium falciparum). These results implicate evolutionary pressure by malaria selecting humans with ApoE 4/4, even considering lower survival in late life. These selective advantages may be relevant in the exploration of possible disparities between Black and Whites in the incidence of Alzheimer's Disease.

Molecular bioSystems, 2011

An important part of the challenge of building models of biochemical reactions is determining rea... more An important part of the challenge of building models of biochemical reactions is determining reaction rate constants that transform substrates into products. We present a method to derive enzymatic kinetic values from mRNA expression levels for modeling biological networks without requiring further tuning. The core metabolic reactions of cholesterol in the brain, particularly in the hippocampus, were simulated. To build the model the baseline mRNA expression levels of genes involved in cholesterol metabolism were obtained from the Allen Mouse Brain Atlas. The model is capable of replicating the trends of relative cholesterol levels in Alzheimer's and Huntington's diseases; and reliably simulated SLOS, desmosterolosis, and Dhcr14/Lbr knockout studies. A sensitivity analysis correctly…

Alzheimer's & Dementia, 2012

Background: Oxidative stress is linked to the pathogenesis of neurodegeneration. 1) Beta-amyloid ... more Background: Oxidative stress is linked to the pathogenesis of neurodegeneration. 1) Beta-amyloid oligomers cause cognitive dysfunction and synaptotoxicity in AD. However, the relationship between oxidative stress, oligomer, and their localization during AD progression is not fully understood. Our group previously reported that mice deficient in cytoplasmic superoxide dismutase (CuZn-SOD, SOD1) have typical phenotypes of geriatric diseases, such as drusen in age-related macular degeneration, fatty liver, skin thinning and osteoporosis. 2) On the other hand, even though mitochondrial oxidative stress has been hitherto believed to be the main contributors to AD, the recent report revealed that mitochondrial SOD (Mn-SOD, SOD2) did not affect Ab oligomerization in vivo. 3) To evaluate the potential of cytoplasmic oxidative stress in AD, we generated an AD-model mouse lacking Sod 1 (h APP/Sod1-/-), and analyzed it for AD-like pathology. Methods: Memory and behavioral abnormalities were estimated by Morris water maze and Y-maze. Ab oligomerization was tested on dot blotting and Western blotting. Senile plaque and neuroinflammation were evaluated using immunohistochemistry. The levels of tau, synaptophysin, each SOD were examined by Western blotting. hAPP processing was estimated on ELISA. Conclusions: These findings suggest that cytoplasmic oxidative stress could be involved in Ab aggregation (oligomerization), as well as production, and imply the role of intracellular Ab oligomerization. Activation of Sod1 may be a therapeutic strategy to delay AD progression. References:

Alzheimer's & Dementia, 2012

Alzheimer's & Dementia, 2013

International Journal of Knowledge Discovery in Bioinformatics, 2015

Anesthetics are a widely used class of drugs with a fast onset and comparatively slow offset, whi... more Anesthetics are a widely used class of drugs with a fast onset and comparatively slow offset, which consequently equates to a low therapeutic index. Unfortunately, the mechanism of action for this class of drugs is considered unknown. For that reason, there is great medical need to study effects of anesthetics on the brain. In this study transcriptomes, generated 6 hours after a 15 minute exposure to isoflurane, from the rat cortex and basolateral amygdala were used to determine parameters for a deterministic biosimulation model of metabolic pathways. Metabolomic results indicated involvement of lipid pathways known for anesthetic effects on membrane function and alternate energy sources due to reduced glucose utilization. Key insights are revealed for potential mechanisms by which anesthetics block memory of the medical procedures.

Neuroscience and Biobehavioral Reviews, 1997

Light microscopic immunocytochemical studies, using a sensitive silver intensification procedure,... more Light microscopic immunocytochemical studies, using a sensitive silver intensification procedure, show that dopamine (DA) and serotonin (5-HT) axons terminate on neurons in the nucleus accumbens (NAcc) (A10) terminals and also in dorsal striatum (DSTr) (A9) terminals. The data demonstrate a prominent endogenous anatomic interaction at these distal presynaptic sites between the neurotransmitters 5-HT and DA; the pattern of the 5-HT-DA interaction differs between A10 and A9 terminals. Moreover, in distinction to the variance shown anatomically between 5-HT--DA interactions at distal A9 and A10 sites, the 5-HT--DA interactions at the level of DA somatodendrites, the proximal site, are similar, i.e. 5-HT terminals in the midbrain tegmentum are profuse and have a massive overlap with DA neurons in both ventral tegmental area (VTA) and substantia nigra pars compacta (SNpc). We suggest with reference to the DA neurons of A10 and A9 pathways, inclusive of somatodendrites (sites of proximal presynaptic interactions in the midbrain) and axons (sites of distal presynaptic interactions), that 5-HT--DA interactions in A10 terminals are more likely to exceed those in the DStr arrangement. Furthermore, our neuroanatomic data show that axonally released DA at A10 terminals may originate from proximal 5-HT somatodendrites, i.e. dorsal raphe (DR) or the proximal DA somatodendrites, VTA. In vivo microvoltammetric studies were done with highly sensitive temporal and spatial resolution; the studies demonstrate basal (endogenous) real time 5-HT release at distal A10 and distal A9 terminal fields and real time 5-HT release at proximal A10 VTA somatodendrites. In vivo microvoltammetric studies were performed concurrently and on line with studies of DA release, also at distal A10 and distal A9 terminal fields and at proximal A10 somatodendrites. Serotonin release was detected in a separate voltammetric peak from the DA voltammetric peak. The electrochemical signal for 5-HT release was detected within 10-12 s and that for DA release within 12-15 s, after each biogenic amine diffused through the synaptic environment onto the microelectrode surface. The electrochemical signal for 5-HT and a separate electrochemical signal for DA are detected on the same voltammogram within 22-27 s; each electrochemical signal represents current changes in picoamperes, within seconds of detection time. The amplitude of each electrochemical signal reflects the changes in diffusion of each biogenic amine to the microelectrode surface. Each neurotransmitter has a distinct potential at which oxidation occurs; this results in a recording which has a distinct peak for a specific neurotransmitter. The concentration of each neurotransmitter within the synaptic environment is directly related to the electrochemical signal detected via the Cottrell equation. Voltammograms were recorded every 5 min. At the time that basal 5-HT release and basal DA release were recorded within same animal control, open-field behavioral studies were performed, also concurrently, by infrared photocell beams. The frequency of each behavioral parameter was monitored every 100 ms; the number of behavioral events, were summated every 5 min during the time course of study. Thus, the detection of neurotransmitters occurs in real time, while simultaneously monitoring the animal's behavior by infrared photocell beams. The results from the in vivo microvoltammetric and behavioral data from this study show that basal 5-HT release at distal A10 and A9 terminals dramatically increased with DA release. Moreover, each increase in basal 5-HT release, at both A10 and at A9 terminal fields occurred consistently and at the same time as each increase in open-field locomotion and stereotypy occurred naturally during the animal's exploration in a novel chamber. Thus, the terminology 'synchronous and simultaneous' describes aptly the correlation between 5-HT release at distal A10 and A9 terminal fields and open-field locomo

Brain Research Bulletin, 1995

The mesencephalic tegmentum contains monoaminergic neurons that project to the nucleus accumbens ... more The mesencephalic tegmentum contains monoaminergic neurons that project to the nucleus accumbens (NAcc). These monoaminergic neurons consist of the serotonergic (5-HT) neurons of the dorsal and median raphe and the dopaminergic (DA) neurons of the ventral tegmental area (VTA). Recent neurochemical reports describe cocaine-induced alterations in dopamine and serotonin release in NAcc that has coincidental occurrence both spatially and temporally, as shown by in vivo voltammetry. There is a functional role for 5-HT-DA interactions within the NAcc in the underlying mechanism of action of cocaine as well as for 5-HT in A10 DA neurons in the basal or endogenous state whether or not cocaine-relevant reward circuits are involved. Our objective was to study the neuroanatomic localization of tyrosine hydroxylase-containing (TH) and 5-HT-containing axons in the ventrolateral region of the rat NAcc, where codetection of monoamines had been assessed. The significance of this vINAcc is its reciprocal connectivity with VTA, which contains the somatodendritic portions of the mesoacumbens DA neurons. The results showed that, in the vINAcc, the core contained a dense terminal field of TH axons that had an extensive overlap with 5-HT axons in the periphery within the core. Because the in vivo electrochemical codetection of DA and 5-HT assessed in the ventral-most aspect of this overlap zone can be correlated with terminal release, a functional interaction of 5-HT and DA at postsynaptic sites in vINAcc is possible.

ACS chemical neuroscience, Jan 11, 2018

Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating gl... more Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K and high V, specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free...

Biochemical and biophysical research communications, Dec 9, 2017

Glucose transporters (GLUTs), expressed in all types of human cells, are responsible for the upta... more Glucose transporters (GLUTs), expressed in all types of human cells, are responsible for the uptake of sugars as the primary energy source for the normal functions of good cells and for the abnormal growth of cancer cells. The E. coli xylose permease (XylE), a homologue of human GLUTs, has been investigated more thoroughly than other major facilitator proteins in the current literature. In this paper, we present a molecular dynamics (MD) study of an all-atom model system to elucidate the atomistic details and the free-energy landscape along the path of binding a xylopyranose (XYP) from the extracellular space to the inside of the transporter protein XylE. From the MD simulations, the Gibbs free energy of binding was found to be -4.4kcal/mol in agreement with the experimental value of -4.7kcal/mol. The accuracy of our study is further shown in the computed hydration energy of XYP of -14.6kcal/mol in comparison with the experimental data of -15.0kcal/mol. Along the binding path, the G...

International Journal of Clinical Medicine, 2016

Metabolically stressed kidney is in part characterized by infiltrating macrophages and macrophage... more Metabolically stressed kidney is in part characterized by infiltrating macrophages and macrophage-derived TGF-β1 that promote the synthesis of various ECM molecules. TGF-β1 strongly enhances the expression of the gene TGFBI that encodes a cell-adhesion class, proapoptotic ECM protein called BIGH3. We hypothesized that in a diabetic environment a relationship between infiltrating macrophages, macrophage-derived TGF-β1, and BIGH3 protein promotes renal cell death. To investigate this hypothesis, we used our mouse model of diabetic complications. Mice on a high-fat diet developed hypercholesterolemia, and exposure to streptozotocin rendered hypercholesterolemic mice diabetic. Immunohistochemical images show increased macrophage infiltration and BIGH3 protein in the kidney cortices of hypercholesterolemic and diabetic mice. Macrophages induced a twofold increase in BIGH3 expression and an 86% increase in renal proximal tubule epithelial cell apoptosis. TGF-β1 antibody and TGF-β1 receptor chemical antagonist blocked macrophage-induced apoptosis. BIGH3 antibody completely blocked apoptosis that was induced by TGF-β1, and blocked apoptosis induced by exogenous recombinant BIGH3. These results uncover a distinctive interplay of macrophage-derived TGF-β1, BIGH3 protein, and apoptosis, and indicate that BIGH3 is central in a novel pathway that promotes diabetic nephropathy. Macrophage TGF-β1 and BIGH3 are identified as prediabetic biomarkers, and potential therapeutic targets for intervention in prediabetic and diabetic individuals.

The Canadian Journal of Neurological Sciences, 2012

2014 IEEE Healthcare Innovation Conference (HIC), 2014

ABSTRACT Precision medicine requires the right drug at the right dose for the right patient at th... more ABSTRACT Precision medicine requires the right drug at the right dose for the right patient at the right time. This study used a computational biology model of 30 metabolic and transport pathways and multiple compartments to simulate oral dosing of pioglitazone that is currently in clinical trials to delay onset of Alzheimer's disease. The Transcriptome-To-Metabolome™ Method was used to simulate individual human subjects by using their gene expression profiles to determine parameters for the kinetic biosimulation. The in silico plasma profiles for multiple doses matched those for in vivo results from literature. Individual ED50 values were determined on each subject for the mitochondrial pyruvate carrier bound by pioglitazone as the target. This approach will allow determination of effective dosing for individual subjects in clinical trials and patients for treatments.

Advances in Intelligent and Soft Computing, 2012

ABSTRACT Integrated Systems Biology was used to study bone cancer via an iterative process of in ... more ABSTRACT Integrated Systems Biology was used to study bone cancer via an iterative process of in vitro testing for validation of an in silico computer simulation where the transcriptome was used to derive the parameters of a kinetic model. A computer simulation model of the transforming growth factor-beta (TGF-β1) signaling pathway was obtained from Reactome®. The transcriptome of MG-63 cells was accessed from NCBI GEO GSE11414. With this method the model is not trained to match the biological system. The in vitro study on osteosarcoma (MG-63) cells was used to compare with the results from the computer simulation. MG-63 cells were grown in culture and exposed to TGF-β1 to identify differences in expression of a target-gene, TGF-β -Induced 68kDa protein (TGFBI), at serial time intervals. Real-time PCR was used to measure TGFBI mRNA levels and the temporal profile was identical with that predicted by the in silico model. A sensitivities test was performed through the in silico model and a candidate target for gene-knock-down in the TGF-β signaling pathway, Smad3, was identified. An 80% reduction of this reactant in the model attenuated TGFBI expression by 64%, an effect that matched such knockdown of Smad3, in vitro, for other target genes reported in the literature. The assumption that the transcriptome drives the reactome is validated and substantiates a novel method for deriving parameters for kinetic deterministic models of biological systems.

The authors had validated a proprietary method, Transcriptome-To-Metabolome™ (TTM™) Biosimulation... more The authors had validated a proprietary method, Transcriptome-To-Metabolome™ (TTM™) Biosimulation, for using the transcriptome to determine parameters for kinetic biosimulation of 16 core metabolic pathways. In vivo and in silico evidence confirmed that hippocampal cholesterol metabolism decreases with aging and increases with Alzheimer's disease (AD). The molecular studies on aging primate and human hippocampus, including AD samples, provided internal validations on the biosimulations, while evidence from the literature, bibliome, provided external validations. This study extends the investigations with the TTM™ Biosimulations into the changes in these 16 metabolic pathways in aging male human hippocampus and for stages of AD. The authors report robust hippocampal hypometabolism in the fifth to tenth decade of life involving glucose and lipid metabolism in male humans. These findings are validated externally from the bibliome. Several changes in AD are demonstrated to be exaggerations or deviations of very late stage changes of normal aging among these pathways.

2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2014

We validated a model of the TGF-β signaling pathway using reactions from Reactome. Using a patent... more We validated a model of the TGF-β signaling pathway using reactions from Reactome. Using a patentpending technique, gene expression profiles from individual patients are used to determine model parameters. Gene expression profiles from 45 women, normal, or benign tumor and malignant breast cancer were used as training and validating sets for assessing clinical sensitivity and specificity. Biomarkers were identified from the biosimulation results using sensitivity analyses and derivative properties from the model. A membrane signaling marker had sensitivity of 80% and specificity of 60%; while a nuclear transcription factor marker had sensitivity of 80% and specificity of 90% to predict malignancy. Use of Fagan's nomogram increased probability from 7.5% for positive mammogram to 39% with positive results of the biosimulation for the nuclear marker. Our technology will allow researchers to identify and develop biomarkers and assist clinicians in diagnostic and treatment decision making.

Cancer Research, 2013

Genome-wide gene-expression profiles, transcriptomes, from microarray tests are used for clinical... more Genome-wide gene-expression profiles, transcriptomes, from microarray tests are used for clinical decision-making; novel uses of transcriptomes will continue to emerge. We are commercializing a patent-pending technology using transcriptomes to determine parameters for deterministic-kinetic models of biological pathways, Transcriptome-To-Reactome:Transforming Growth Factor Beta Signaling. We demonstrate how biosimulation results for proteomics, flux, and a derivative property of the network system can be utilized as biomarkers for breast cancer. The TGFbeta Signaling Model was accessed from Reactome.org; manual curation was performed to add beta-induced-gene-human-clone-3 as a target gene for Smad transcription factors. Biosimulations were run with COPASI. Transcriptomes were accessed from NCBI GEO archives, where peripheral blood mononuclear cells (PBMC) were collected from women with suspect initial mammograms, prior to undergoing diagnostic biopsy to differentiate benign from mali...

2013 6th International IEEE/EMBS Conference on Neural Engineering (NER), 2013

ABSTRACT A multi-compartmental molecular model has been developed for rodent basal forebrain chol... more ABSTRACT A multi-compartmental molecular model has been developed for rodent basal forebrain cholinergic neurons with established gene expression levels. Reconstruction of neurons and network function were acquired using the Transcriptome-To-Physiome™ (TTP™) NeurobioSimulation. Gene expression values [NCBI GEO GSE 13379] were used to derive protein level and kinetic parameters for ligand and voltage gated ion channels in the TTP™ NeurobioSimulator Model using COPASI® software. Global parameters for membrane potential used permeability and ion concentrations inside and outside of the membrane in the Goldman-Hodgkin-Katz equation. Four compartments of the model neuron are included: glutamate synapse, distal dendrite, proximal dendrite, and axon hillock. The simulation of a voltage-gated sodium channel activation, and inactivated states of distal dendrites of cholinergic modeled neurons depends on the excitatory postsynaptic potential (EPSP) event. This distally activated event yielded temporally relevant proximal dendritic activation and inactivation of voltage-gated sodium and potassium channels in the reconstructed neuron. Graded potentials showed temporal summation and a classic action potential occurs at the axon hillock with sodium and potassium fluxes as expected. In future studies, we will reconstruct the electrophysiology of vulnerable neuronal populations in the diseased brain and compare them to controls thus lending substantial insight into molecular and network function corollary to neuropathogenesis.

Hippocampus, 2010

Changes in brain cholesterol homeostasis are associated with multiple diseases, such as Alzheimer... more Changes in brain cholesterol homeostasis are associated with multiple diseases, such as Alzheimer's and Huntington's; however, controversy persists as to whether adult neurons produce their own cholesterol, or if it is outsourced to astrocytes. To address this issue, we analyzed 25 genes most immediately involved in cholesterol homeostasis from in situ data provided by the Allen Brain Mouse Atlas. We compared the relative mRNA expression in the pyramidal and granule layers, populated with neurons, with the rest of the hippocampus which is populated with neuronal processes and glia. Comparing the expression of the individual genes to markers for neurons and astrocytes, we found that cholesterol homeostasis genes are preferentially targeted to neuronal layers.…

Journal of Health Care for the Poor and Underserved, 2014

Apolipoprotein E 4 (ApoE 4) has been linked to pathogenesis of Alzheimer's disease and has been s... more Apolipoprotein E 4 (ApoE 4) has been linked to pathogenesis of Alzheimer's disease and has been suggested to be maintained through evolutionary pressure via a protective role in malaria infection. We evaluated Plasmodium falciparum viability at the intraerythrocyte stage by exposure to plasma from human subjects with ApoE 4/4 or ApoE 3/3. Plasma samples from ApoE 4/4 but not ApoE 3/3 donors inhibited growth and disrupted morphology of P. falciparum. Evolutionary history is characterized by war between pathogenic microorganisms and defense mechanisms countering their pathogenicities. ApoE 4 frequency is highest in sub-Saharan Africa and other isolated populations (e.g., Papua New Guinea) that exhibit endemic malaria. High ApoE frequency may offer selective advantage protecting against some infectious diseases (e.g., Plasmodium falciparum). These results implicate evolutionary pressure by malaria selecting humans with ApoE 4/4, even considering lower survival in late life. These selective advantages may be relevant in the exploration of possible disparities between Black and Whites in the incidence of Alzheimer's Disease.

Molecular bioSystems, 2011

An important part of the challenge of building models of biochemical reactions is determining rea... more An important part of the challenge of building models of biochemical reactions is determining reaction rate constants that transform substrates into products. We present a method to derive enzymatic kinetic values from mRNA expression levels for modeling biological networks without requiring further tuning. The core metabolic reactions of cholesterol in the brain, particularly in the hippocampus, were simulated. To build the model the baseline mRNA expression levels of genes involved in cholesterol metabolism were obtained from the Allen Mouse Brain Atlas. The model is capable of replicating the trends of relative cholesterol levels in Alzheimer's and Huntington's diseases; and reliably simulated SLOS, desmosterolosis, and Dhcr14/Lbr knockout studies. A sensitivity analysis correctly…

Alzheimer's & Dementia, 2012

Background: Oxidative stress is linked to the pathogenesis of neurodegeneration. 1) Beta-amyloid ... more Background: Oxidative stress is linked to the pathogenesis of neurodegeneration. 1) Beta-amyloid oligomers cause cognitive dysfunction and synaptotoxicity in AD. However, the relationship between oxidative stress, oligomer, and their localization during AD progression is not fully understood. Our group previously reported that mice deficient in cytoplasmic superoxide dismutase (CuZn-SOD, SOD1) have typical phenotypes of geriatric diseases, such as drusen in age-related macular degeneration, fatty liver, skin thinning and osteoporosis. 2) On the other hand, even though mitochondrial oxidative stress has been hitherto believed to be the main contributors to AD, the recent report revealed that mitochondrial SOD (Mn-SOD, SOD2) did not affect Ab oligomerization in vivo. 3) To evaluate the potential of cytoplasmic oxidative stress in AD, we generated an AD-model mouse lacking Sod 1 (h APP/Sod1-/-), and analyzed it for AD-like pathology. Methods: Memory and behavioral abnormalities were estimated by Morris water maze and Y-maze. Ab oligomerization was tested on dot blotting and Western blotting. Senile plaque and neuroinflammation were evaluated using immunohistochemistry. The levels of tau, synaptophysin, each SOD were examined by Western blotting. hAPP processing was estimated on ELISA. Conclusions: These findings suggest that cytoplasmic oxidative stress could be involved in Ab aggregation (oligomerization), as well as production, and imply the role of intracellular Ab oligomerization. Activation of Sod1 may be a therapeutic strategy to delay AD progression. References:

Alzheimer's & Dementia, 2012

Alzheimer's & Dementia, 2013

International Journal of Knowledge Discovery in Bioinformatics, 2015

Anesthetics are a widely used class of drugs with a fast onset and comparatively slow offset, whi... more Anesthetics are a widely used class of drugs with a fast onset and comparatively slow offset, which consequently equates to a low therapeutic index. Unfortunately, the mechanism of action for this class of drugs is considered unknown. For that reason, there is great medical need to study effects of anesthetics on the brain. In this study transcriptomes, generated 6 hours after a 15 minute exposure to isoflurane, from the rat cortex and basolateral amygdala were used to determine parameters for a deterministic biosimulation model of metabolic pathways. Metabolomic results indicated involvement of lipid pathways known for anesthetic effects on membrane function and alternate energy sources due to reduced glucose utilization. Key insights are revealed for potential mechanisms by which anesthetics block memory of the medical procedures.

Neuroscience and Biobehavioral Reviews, 1997

Light microscopic immunocytochemical studies, using a sensitive silver intensification procedure,... more Light microscopic immunocytochemical studies, using a sensitive silver intensification procedure, show that dopamine (DA) and serotonin (5-HT) axons terminate on neurons in the nucleus accumbens (NAcc) (A10) terminals and also in dorsal striatum (DSTr) (A9) terminals. The data demonstrate a prominent endogenous anatomic interaction at these distal presynaptic sites between the neurotransmitters 5-HT and DA; the pattern of the 5-HT-DA interaction differs between A10 and A9 terminals. Moreover, in distinction to the variance shown anatomically between 5-HT--DA interactions at distal A9 and A10 sites, the 5-HT--DA interactions at the level of DA somatodendrites, the proximal site, are similar, i.e. 5-HT terminals in the midbrain tegmentum are profuse and have a massive overlap with DA neurons in both ventral tegmental area (VTA) and substantia nigra pars compacta (SNpc). We suggest with reference to the DA neurons of A10 and A9 pathways, inclusive of somatodendrites (sites of proximal presynaptic interactions in the midbrain) and axons (sites of distal presynaptic interactions), that 5-HT--DA interactions in A10 terminals are more likely to exceed those in the DStr arrangement. Furthermore, our neuroanatomic data show that axonally released DA at A10 terminals may originate from proximal 5-HT somatodendrites, i.e. dorsal raphe (DR) or the proximal DA somatodendrites, VTA. In vivo microvoltammetric studies were done with highly sensitive temporal and spatial resolution; the studies demonstrate basal (endogenous) real time 5-HT release at distal A10 and distal A9 terminal fields and real time 5-HT release at proximal A10 VTA somatodendrites. In vivo microvoltammetric studies were performed concurrently and on line with studies of DA release, also at distal A10 and distal A9 terminal fields and at proximal A10 somatodendrites. Serotonin release was detected in a separate voltammetric peak from the DA voltammetric peak. The electrochemical signal for 5-HT release was detected within 10-12 s and that for DA release within 12-15 s, after each biogenic amine diffused through the synaptic environment onto the microelectrode surface. The electrochemical signal for 5-HT and a separate electrochemical signal for DA are detected on the same voltammogram within 22-27 s; each electrochemical signal represents current changes in picoamperes, within seconds of detection time. The amplitude of each electrochemical signal reflects the changes in diffusion of each biogenic amine to the microelectrode surface. Each neurotransmitter has a distinct potential at which oxidation occurs; this results in a recording which has a distinct peak for a specific neurotransmitter. The concentration of each neurotransmitter within the synaptic environment is directly related to the electrochemical signal detected via the Cottrell equation. Voltammograms were recorded every 5 min. At the time that basal 5-HT release and basal DA release were recorded within same animal control, open-field behavioral studies were performed, also concurrently, by infrared photocell beams. The frequency of each behavioral parameter was monitored every 100 ms; the number of behavioral events, were summated every 5 min during the time course of study. Thus, the detection of neurotransmitters occurs in real time, while simultaneously monitoring the animal's behavior by infrared photocell beams. The results from the in vivo microvoltammetric and behavioral data from this study show that basal 5-HT release at distal A10 and A9 terminals dramatically increased with DA release. Moreover, each increase in basal 5-HT release, at both A10 and at A9 terminal fields occurred consistently and at the same time as each increase in open-field locomotion and stereotypy occurred naturally during the animal's exploration in a novel chamber. Thus, the terminology 'synchronous and simultaneous' describes aptly the correlation between 5-HT release at distal A10 and A9 terminal fields and open-field locomo

Brain Research Bulletin, 1995

The mesencephalic tegmentum contains monoaminergic neurons that project to the nucleus accumbens ... more The mesencephalic tegmentum contains monoaminergic neurons that project to the nucleus accumbens (NAcc). These monoaminergic neurons consist of the serotonergic (5-HT) neurons of the dorsal and median raphe and the dopaminergic (DA) neurons of the ventral tegmental area (VTA). Recent neurochemical reports describe cocaine-induced alterations in dopamine and serotonin release in NAcc that has coincidental occurrence both spatially and temporally, as shown by in vivo voltammetry. There is a functional role for 5-HT-DA interactions within the NAcc in the underlying mechanism of action of cocaine as well as for 5-HT in A10 DA neurons in the basal or endogenous state whether or not cocaine-relevant reward circuits are involved. Our objective was to study the neuroanatomic localization of tyrosine hydroxylase-containing (TH) and 5-HT-containing axons in the ventrolateral region of the rat NAcc, where codetection of monoamines had been assessed. The significance of this vINAcc is its reciprocal connectivity with VTA, which contains the somatodendritic portions of the mesoacumbens DA neurons. The results showed that, in the vINAcc, the core contained a dense terminal field of TH axons that had an extensive overlap with 5-HT axons in the periphery within the core. Because the in vivo electrochemical codetection of DA and 5-HT assessed in the ventral-most aspect of this overlap zone can be correlated with terminal release, a functional interaction of 5-HT and DA at postsynaptic sites in vINAcc is possible.