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Bogomolov A, Filonov S, Chadaeva I, Rasskazov D, Khandaev B, Zolotareva K, Kazachek A, Oshchepkov D, Ivanisenko VA, Demenkov P, Podkolodnyy N, Kondratyuk E, Ponomarenko P, Podkolodnaya O, Mustafin Z, Savinkova L, Kolchanov N, Tverdokhleb N, Ponomarenko M. Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection. Int J Mol Sci 2023; 24:ijms24109010. [PMID: 37240358 DOI: 10.3390/ijms24109010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Atherosclerosis is a systemic disease in which focal lesions in arteries promote the build-up of lipoproteins and cholesterol they are transporting. The development of atheroma (atherogenesis) narrows blood vessels, reduces the blood supply and leads to cardiovascular diseases. According to the World Health Organization (WHO), cardiovascular diseases are the leading cause of death, which has been especially boosted since the COVID-19 pandemic. There is a variety of contributors to atherosclerosis, including lifestyle factors and genetic predisposition. Antioxidant diets and recreational exercises act as atheroprotectors and can retard atherogenesis. The search for molecular markers of atherogenesis and atheroprotection for predictive, preventive and personalized medicine appears to be the most promising direction for the study of atherosclerosis. In this work, we have analyzed 1068 human genes associated with atherogenesis, atherosclerosis and atheroprotection. The hub genes regulating these processes have been found to be the most ancient. In silico analysis of all 5112 SNPs in their promoters has revealed 330 candidate SNP markers, which statistically significantly change the affinity of the TATA-binding protein (TBP) for these promoters. These molecular markers have made us confident that natural selection acts against underexpression of the hub genes for atherogenesis, atherosclerosis and atheroprotection. At the same time, upregulation of the one for atheroprotection promotes human health.
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Affiliation(s)
- Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Sergey Filonov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Natalya Tverdokhleb
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2020; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. Video Abstract
A catalog of 47 million genes was generated from 370 globally distributed metagenomes Meta-omics data integration disentangled the mechanisms of changes in transcript pools Transcript pool changes of metabolic marker genes show distinct mechanistic patterns Community turnover as a response to ocean warming may be strongest in polar regions
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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Cheng GC, Chen DT, Chen JJ, Soong SJ, Lamartiniere C, Barnes S. A chain reaction approach to modelling gene pathways. Transl Cancer Res 2012; 1:61-73. [PMID: 22943042 PMCID: PMC3431024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND: Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. RESULTS: In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By applying it to microarray data, the chain reaction model computed a set of reaction rates to examine the effects of three polyphenols (EGCG, genistein, and resveratrol) on gene expression in this pathway during puberty. We first performed statistical analysis to test the time factor on the estrogen synthesis pathway. Global tests were used to evaluate an overall gene expression change during puberty for each experimental group. Then, a chain reaction model was employed to simulate the estrogen synthesis pathway. Specifically, the model computed the reaction rates in a set of ordinary differential equations to describe interactions between genes in the pathway (A reaction rate K of A to B represents gene A will induce gene B per unit at a rate of K; we give details in the "method" section). Since disparate changes of gene expression may cause numerical error problems in solving these differential equations, we used an implicit scheme to address this issue. We first applied the chain reaction model to obtain the reaction rates for the control group. A sensitivity study was conducted to evaluate how well the model fits to the control group data at Day 50. Results showed a small bias and mean square error. These observations indicated the model is robust to low random noises and has a good fit for the control group. Then the chain reaction model derived from the control group data was used to predict gene expression at Day 50 for the three polyphenol groups. If these nutrients affect the estrogen synthesis pathways during puberty, we expect discrepancy between observed and expected expressions. Results indicated some genes had large differences in the EGCG (e.g., Hsd3b and Sts) and the resveratrol (e.g., Hsd3b and Hrmt12) groups. CONCLUSIONS: In the present study, we have presented (I) experimental studies of the effect of nutrient diets on the gene expression changes in a selected estrogen synthesis pathway. This experiment is valuable because it allows us to examine how the nutrient-containing diets regulate gene expression in the estrogen synthesis pathway during puberty; (II) global tests to assess an overall association of this particular pathway with time factor by utilizing generalized linear models to analyze microarray data; and (III) a chain reaction model to simulate the pathway. This is a novel application because we are able to translate the gene pathway into the chemical reactions in which each reaction channel describes gene-gene relationship in the pathway. In the chain reaction model, the implicit scheme is employed to efficiently solve the differential equations. Data analysis results show the proposed model is capable of predicting gene expression changes and demonstrating the effect of nutrient-containing diets on gene expression changes in the pathway. One of the objectives of this study is to explore and develop a numerical approach for simulating the gene expression change so that it can be applied and calibrated when the data of more time slices are available, and thus can be used to interpolate the expression change at a desired time point without conducting expensive experiments for a large amount of time points. Hence, we are not claiming this is either essential or the most efficient way for simulating this problem, rather a mathematical/numerical approach that can model the expression change of a large set of genes of a complex pathway. In addition, we understand the limitation of this experiment and realize that it is still far from being a complete model of predicting nutrient-gene interactions. The reason is that in the present model, the reaction rates were estimated based on available data at two time points; hence, the gene expression change is dependent upon the reaction rates and a linear function of the gene expressions. More data sets containing gene expression at various time slices are needed in order to improve the present model so that a non-linear variation of gene expression changes at different time can be predicted.
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Affiliation(s)
- Gary C. Cheng
- Department of Mechanical Engineering, University of Alabama at Birmingham, HOEN 320A, 1530 3rd Ave. S., Birmingham, AL 35294-4461, USA
| | - Dung-Tsa Chen
- Department of Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - James J. Chen
- Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
| | - Seng-jaw Soong
- Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, University of Alabama at Birmingham, 153 Wallace Tumour Institute, 1824 6th Avenue South, Birmingham, AL 35294, USA
| | - Coral Lamartiniere
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, VH 124, 1670 University Boulevard, Birmingham, AL 35294, USA
| | - Stephen Barnes
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, MCLM 452, 1918 University Boulevard, Birmingham, AL 35294, USA
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