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Kim R, Witelski TP. Uncovering the dynamics of a circadian-dopamine model influenced by the light-dark cycle. Math Biosci 2021; 344:108764. [PMID: 34952036 DOI: 10.1016/j.mbs.2021.108764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The neurotransmitter dopamine (DA) is known to be influenced by the circadian timekeeping system in the mammalian brain. We have previously created a single-cell differential equations model to understand the mechanisms behind circadian rhythms of extracellular DA. In this paper, we investigate the dynamics in our model and study different behaviors such as entrainment to the 24-hour light-dark cycle and robust periodicity versus decoupling, quasiperiodicity, and chaos. Imbalances in DA are often accompanied by disrupted circadian rhythms, such as in Parkinson's disease, hyperactivity, and mood disorders. Our model provides new insights into the links between the circadian clock and DA. We show that the daily rhythmicity of DA can be disrupted by decoupling between interlocked loops of the clock circuitry or by quasiperiodic clock behaviors caused by misalignment with the light-dark cycle. The model can be used to further study how the circadian clock affects the dopaminergic system, and to help develop therapeutic strategies for disrupted DA rhythms. .
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Affiliation(s)
- Ruby Kim
- Department of Mathematics, Duke University, Durham, NC, USA.
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Kim R, Nijhout HF, Reed MC. One-carbon metabolism during the menstrual cycle and pregnancy. PLoS Comput Biol 2021; 17:e1009708. [PMID: 34914693 PMCID: PMC8741061 DOI: 10.1371/journal.pcbi.1009708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/07/2022] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
Many enzymes in one-carbon metabolism (OCM) are up- or down-regulated by the sex hormones which vary diurnally and throughout the menstrual cycle. During pregnancy, estradiol and progesterone levels increase tremendously to modulate physiological changes in the reproductive system. In this work, we extend and improve an existing mathematical model of hepatic OCM to understand the dynamic metabolic changes that happen during the menstrual cycle and pregnancy due to estradiol variation. In particular, we add the polyamine drain on S-adenosyl methionine and the direct effects of estradiol on the enzymes cystathionine β-synthase (CBS), thymidylate synthase (TS), and dihydrofolate reductase (DHFR). We show that the homocysteine concentration varies inversely with estradiol concentration, discuss the fluctuations in 14 other one-carbon metabolites and velocities throughout the menstrual cycle, and draw comparisons with the literature. We then use the model to study the effects of vitamin B12, vitamin B6, and folate deficiencies and explain why homocysteine is not a good biomarker for vitamin deficiencies. Additionally, we compute homocysteine throughout pregnancy, and compare the results with experimental data. Our mathematical model explains how numerous homeostatic mechanisms in OCM function and provides new insights into how homocysteine and its deleterious effects are influenced by estradiol. The mathematical model can be used by others for further in silico experiments on changes in one-carbon metabolism during the menstrual cycle and pregnancy.
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Affiliation(s)
- Ruby Kim
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - H. Frederik Nijhout
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Michael C. Reed
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
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Kim R, Reed MC. A mathematical model of circadian rhythms and dopamine. Theor Biol Med Model 2021; 18:8. [PMID: 33596936 PMCID: PMC7891144 DOI: 10.1186/s12976-021-00139-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 02/03/2021] [Indexed: 11/21/2022] Open
Abstract
Background The superchiasmatic nucleus (SCN) serves as the primary circadian (24hr) clock in mammals and is known to control important physiological functions such as the sleep-wake cycle, hormonal rhythms, and neurotransmitter regulation. Experimental results suggest that some of these functions reciprocally influence circadian rhythms, creating a highly complex network. Among the clock’s downstream products, orphan nuclear receptors REV-ERB and ROR are particularly interesting because they coordinately modulate the core clock circuitry. Recent experimental evidence shows that REV-ERB and ROR are not only crucial for lipid metabolism but are also involved in dopamine (DA) synthesis and degradation, which could have meaningful clinical implications for conditions such as Parkinson’s disease and mood disorders. Methods We create a mathematical model consisting of differential equations that express how the circadian variables are influenced by light, how REV-ERB and ROR feedback to the clock, and how REV-ERB, ROR, and BMAL1-CLOCK affect the dopaminergic system. The structure of the model is based on the findings of experimentalists. Results We compare our model predictions to experimental data on clock components in different light-dark conditions and in the presence of genetic perturbations. Our model results are consistent with experimental results on REV-ERB and ROR and allow us to predict the circadian variations in tyrosine hydroxylase and monoamine oxidase seen in experiments. By connecting our model to an extant model of dopamine synthesis, release, and reuptake, we are able to predict circadian oscillations in extracellular DA and homovanillic acid that correspond well with experimental observations. Conclusions The predictions of the mathematical model are consistent with a wide variety of experimental observations. Our calculations show that the mechanisms proposed by experimentalists by which REV-ERB, ROR, and BMAL1-CLOCK influence the DA system are sufficient to explain the circadian oscillations observed in dopaminergic variables. Our mathematical model can be used for further investigations of the effects of the mammalian circadian clock on the dopaminergic system. The model can also be used to predict how perturbations in the circadian clock disrupt the dopaminergic system and could potentially be used to find drug targets that ameliorate these disruptions.
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Affiliation(s)
- Ruby Kim
- Department of Mathematics, Duke University, 120 Science Drive, Box 90320, Durham, 27708, NC, USA
| | - Michael C Reed
- Department of Mathematics, Duke University, 120 Science Drive, Box 90320, Durham, 27708, NC, USA.
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Best J, Duncan W, Sadre-Marandi F, Hashemi P, Nijhout HF, Reed M. Autoreceptor control of serotonin dynamics. BMC Neurosci 2020; 21:40. [PMID: 32967609 PMCID: PMC7509944 DOI: 10.1186/s12868-020-00587-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/29/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Serotonin is a neurotransmitter that has been linked to a wide variety of behaviors including feeding and body-weight regulation, social hierarchies, aggression and suicidality, obsessive compulsive disorder, alcoholism, anxiety, and affective disorders. Full understanding involves genomics, neurochemistry, electrophysiology, and behavior. The scientific issues are daunting but important for human health because of the use of selective serotonin reuptake inhibitors and other pharmacological agents to treat disorders. This paper presents a new deterministic model of serotonin metabolism and a new systems population model that takes into account the large variation in enzyme and transporter expression levels, tryptophan input, and autoreceptor function. RESULTS We discuss the steady state of the model and the steady state distribution of extracellular serotonin under different hypotheses on the autoreceptors and we show the effect of tryptophan input on the steady state and the effect of meals. We use the deterministic model to interpret experimental data on the responses in the hippocampus of male and female mice, and to illustrate the short-time dynamics of the autoreceptors. We show there are likely two reuptake mechanisms for serotonin and that the autoreceptors have long-lasting influence and compare our results to measurements of serotonin dynamics in the substantia nigra pars reticulata. We also show how histamine affects serotonin dynamics. We examine experimental data that show very variable response curves in populations of mice and ask how much variation in parameters in the model is necessary to produce the observed variation in the data. Finally, we show how the systems population model can potentially be used to investigate specific biological and clinical questions. CONCLUSIONS We have shown that our new models can be used to investigate the effects of tryptophan input and meals and the behavior of experimental response curves in different brain nuclei. The systems population model incorporates individual variation and can be used to investigate clinical questions and the variation in drug efficacy. The codes for both the deterministic model and the systems population model are available from the authors and can be used by other researchers to investigate the serotonergic system.
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Affiliation(s)
- Janet Best
- Department of Mathematics, The Ohio State University, 231 W 18th Ave., Columbus, OH 43210 USA
| | - William Duncan
- Department of Mathematics, Duke University, Durham, NC 27708 USA
| | | | - Parastoo Hashemi
- Department of Bioengineering, Imperial College, London, SW7 2AZ UK
| | | | - Michael Reed
- Department of Mathematics, Duke University, Durham, NC 27708 USA
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Nijhout HF, Best JA, Reed MC. Systems biology of robustness and homeostatic mechanisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1440. [DOI: 10.1002/wsbm.1440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/30/2018] [Accepted: 09/21/2018] [Indexed: 12/30/2022]
Affiliation(s)
| | - Janet A. Best
- Department of Mathematics Ohio State University Columbus Ohio
| | - Michael C. Reed
- Department of Mathematics Duke University Durham North Carolina
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Galmozzi A, Sonne SB, Altshuler-Keylin S, Hasegawa Y, Shinoda K, Luijten IHN, Chang JW, Sharp LZ, Cravatt BF, Saez E, Kajimura S. ThermoMouse: an in vivo model to identify modulators of UCP1 expression in brown adipose tissue. Cell Rep 2014; 9:1584-1593. [PMID: 25466254 DOI: 10.1016/j.celrep.2014.10.066] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 10/13/2014] [Accepted: 10/24/2014] [Indexed: 12/25/2022] Open
Abstract
Obesity develops when energy intake chronically exceeds energy expenditure. Because brown adipose tissue (BAT) dissipates energy in the form of heat, increasing energy expenditure by augmenting BAT-mediated thermogenesis may represent an approach to counter obesity and its complications. The ability of BAT to dissipate energy is dependent on expression of mitochondrial uncoupling protein 1 (UCP1). To facilitate the identification of pharmacological modulators of BAT UCP1 levels, which may have potential as antiobesity medications, we developed a transgenic model in which luciferase activity faithfully mimics endogenous UCP1 expression and its response to physiologic stimuli. Phenotypic screening of a library using cells derived from this model yielded a small molecule that increases UCP1 expression in brown fat cells and mice. Upon adrenergic stimulation, compound-treated mice showed increased energy expenditure. These tools offer an opportunity to identify pharmacologic modulators of UCP1 expression and uncover regulatory pathways that impact BAT-mediated thermogenesis.
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Affiliation(s)
- Andrea Galmozzi
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Si B Sonne
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Svetlana Altshuler-Keylin
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Yutaka Hasegawa
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Kosaku Shinoda
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Ineke H N Luijten
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Jae Won Chang
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Louis Z Sharp
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Benjamin F Cravatt
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Enrique Saez
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Shingo Kajimura
- UCSF Diabetes Center, Department of Cell and Tissue Biology, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA.
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Zhang Y, Bossé Y, Marceau P, Biron S, Lebel S, Richard D, Vohl MC, Tchernof A. Gene expression variability in subcutaneous and omental adipose tissue of obese men. Gene Expr 2007; 14:35-46. [PMID: 17933217 PMCID: PMC6042019 DOI: 10.3727/000000007783991772] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We investigated interindividual variability in gene expression in abdominal subcutaneous (SC) and omental (OM) adipose tissue of 10 massively obese men. Affymetrix human U133A microarrays were used to measure gene expression levels. A total of 6811 probesets generated significant signal in both depots in all samples. Interindividual variability in gene expression was rather low, with more than 90% of transcripts showing a coefficient of variation (CV) lower than 23.6% and 21.7% in OM and SC adipose tissues, respectively. The distributions of CV were similar between the two fat depots. A set of highly variable genes was identified for both tissues on the basis of a high CV and elevated gene expression level. Among the set of highly regulated genes, 18 transcripts were involved in lipid metabolism and 28 transcripts were involved in cell death for SC and OM samples, respectively. In conclusion, gene expression interindividual variability was rather low and globally similar between fat compartments, and the adipose tissue transcriptome appeared as relatively stable, although specific pathways were found to be highly variable in SC and OM depots.
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Affiliation(s)
- Yonghua Zhang
- *Molecular Endocrinology and Oncology Research Center, Laval University Medical Research Center, Québec, Canada
| | - Yohan Bossé
- †McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Picard Marceau
- §Department of Surgery, Laval University, Québec, Canada
| | - Simon Biron
- §Department of Surgery, Laval University, Québec, Canada
| | - Stephan Lebel
- §Department of Surgery, Laval University, Québec, Canada
| | - Denis Richard
- ¶Cardiology Institute, Lava Hospital, Québec, Canada
| | - Marie-Claude Vohl
- *Molecular Endocrinology and Oncology Research Center, Laval University Medical Research Center, Québec, Canada
- ‡Department of Food Science and Nutrition, Laval University, Québec, Canada
| | - André Tchernof
- *Molecular Endocrinology and Oncology Research Center, Laval University Medical Research Center, Québec, Canada
- ‡Department of Food Science and Nutrition, Laval University, Québec, Canada
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Kim S, Sohn I, Ahn JI, Lee KH, Lee YS, Lee YS. Hepatic gene expression profiles in a long-term high-fat diet-induced obesity mouse model. Gene 2004; 340:99-109. [PMID: 15556298 DOI: 10.1016/j.gene.2004.06.015] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Revised: 05/17/2004] [Accepted: 06/01/2004] [Indexed: 10/26/2022]
Abstract
To understand the molecular mechanisms underlying alterations in the pathophysiologic status of dietary obesity, we examined hepatic genes differentially expressed in a long-term high-fat intake-induced obesity mouse model. C57BL/6J male mice were fed with two kinds of diets for 12 weeks; a low-fat diet (LFD), a high-fat diet (HFD; n=8), and the expression levels of approximately 10,000 transcripts in liver tissues from the two groups were assessed using cDNA microarray analysis. Twelve-week feeding with the HFD resulted in significant increase in body weight, visceral fat accumulation and circulating cholesterol concentration, compared with the LFD group. The cDNA microarray analysis revealed marked differences in the expressions of 97 hepatic genes. These genes were categorized into seven groups:metabolism; defense, stress, and inflammation responses; signal transduction, apoptosis, and cell cycle; transcription regulation; protein synthesis and modification; transport; and cellular adhesion, cytoskeleton and trafficking. The expression of genes involved in fatty acid catabolism and ketone body synthesis, such as acyl-CoA oxidase1 (Acox1) and HMG-CoA lyase (Hmgcl), was significantly increased, and expression of genes involved in lipogenesis and cholesterol synthesis, such as acetyl-CoA synthetase2 (Acs2), fatty acid synthase (Fasn), and squalene epoxidase (Sqle), was drastically decreased in the HFD group. Interestingly, the genes implicated in defense and stress responses, such as glutathione S-transferases (GSTs) and heat shock proteins (Hsps), were also highly represented in the HFD group. Besides, a number of previously unappreciated regulatory molecules were changed by the HFD. These results revealed a transcriptional adaptation to long-term HFD and provided interesting information about the molecules involved in the development and maintenance of the obesity phenotype in vivo.
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Affiliation(s)
- Sujong Kim
- Department of Biochemistry, College of Medicine, Hanyang University, 17, Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea.
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Burton GR, McGehee RE. Identification of candidate genes involved in the regulation of adipocyte differentiation using microarray-based gene expression profiling. Nutrition 2004; 20:109-14. [PMID: 14698024 DOI: 10.1016/j.nut.2003.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Gregory R Burton
- University of Arkansas for Medical Sciences, Department of Pediatrics/Division of Neonatology, Arkansas Cancer Research Center and Arkansas Children's Hospital, Little Rock, Arkansas 72205, USA
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Abstract
The function of brown adipose tissue is to transfer energy from food into heat; physiologically, both the heat produced and the resulting decrease in metabolic efficiency can be of significance. Both the acute activity of the tissue, i.e., the heat production, and the recruitment process in the tissue (that results in a higher thermogenic capacity) are under the control of norepinephrine released from sympathetic nerves. In thermoregulatory thermogenesis, brown adipose tissue is essential for classical nonshivering thermogenesis (this phenomenon does not exist in the absence of functional brown adipose tissue), as well as for the cold acclimation-recruited norepinephrine-induced thermogenesis. Heat production from brown adipose tissue is activated whenever the organism is in need of extra heat, e.g., postnatally, during entry into a febrile state, and during arousal from hibernation, and the rate of thermogenesis is centrally controlled via a pathway initiated in the hypothalamus. Feeding as such also results in activation of brown adipose tissue; a series of diets, apparently all characterized by being low in protein, result in a leptin-dependent recruitment of the tissue; this metaboloregulatory thermogenesis is also under hypothalamic control. When the tissue is active, high amounts of lipids and glucose are combusted in the tissue. The development of brown adipose tissue with its characteristic protein, uncoupling protein-1 (UCP1), was probably determinative for the evolutionary success of mammals, as its thermogenesis enhances neonatal survival and allows for active life even in cold surroundings.
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Affiliation(s)
- Barbara Cannon
- The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, Stockholm, Sweden
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Affiliation(s)
- Susanne Klaus
- German Institute of Human Nutrition in Potsdam, Bergholz-Rehbrücke, Germany.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003; 4:277-84. [PMID: 18629117 PMCID: PMC2447404 DOI: 10.1002/cfg.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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