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Tang G, Peng J, Huo L, Yin W. An N6-methyladenosine regulation- and mRNAsi-related prognostic index reveals the distinct immune microenvironment and immunotherapy responses in lower-grade glioma. BMC Bioinformatics 2023; 24:225. [PMID: 37264314 DOI: 10.1186/s12859-023-05328-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification is involved in tumorigenesis and progression as well as closely correlated with stem cell differentiation and pluripotency. Moreover, tumor progression includes the acquisition of stemness characteristics and accumulating loss of differentiation phenotype. Therefore, we integrated m6A modification and stemness indicator mRNAsi to classify patients and predict prognosis for LGG. METHODS We performed consensus clustering, weighted gene co-expression network analysis, and least absolute shrinkage and selection operator Cox regression analysis to identify an m6A regulation- and mRNAsi-related prognostic index (MRMRPI). Based on this prognostic index, we also explored the differences in immune microenvironments between high- and low-risk populations. Next, immunotherapy responses were also predicted. Moreover, single-cell RNA sequencing data was further used to verify the expression of these genes in MRMRPI. At last, the tumor-promoting and tumor-associated macrophage polarization roles of TIMP1 in LGG were validated by in vitro experiments. RESULTS Ten genes (DGCR10, CYP2E1, CSMD3, HOXB3, CABP4, AVIL, PTCRA, TIMP1, CLEC18A, and SAMD9) were identified to construct the MRMRPI, which was able to successfully classify patients into high- and low-risk group. Significant differences in prognosis, immune microenvironment, and immunotherapy responses were found between distinct groups. A nomogram integrating the MRMRPI and other prognostic factors were also developed to accurately predict prognosis. Moreover, in vitro experiments illustrated that inhibition of TIMP1 could inhibit the proliferation, migration, and invasion of LGG cells and also inhibit the polarization of tumor-associated macrophages. CONCLUSION These findings provide novel insights into understanding the interactions of m6A methylation regulation and tumor stemness on LGG development and contribute to guiding more precise immunotherapy strategies.
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Affiliation(s)
- Guihua Tang
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The first affiliated hospital of Hunan Normal University, The College of Clinical Medicine of Human Normal University), Changsha, 410005, Hunan Province, People's Republic of China.
| | - Jianqiao Peng
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The first affiliated hospital of Hunan Normal University, The College of Clinical Medicine of Human Normal University), Changsha, 410005, Hunan Province, People's Republic of China
| | - Longwei Huo
- Department of Neurosurgery, Yulin First Hospital Affiliated to Xi'an Jiao Tong University, Yulin, 719000, People's Republic of China
| | - Wen Yin
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, 410008, Hunan Province, People's Republic of China.
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Datkhile KD, Durgawale PP, Gudur RA, Gudur AK, Patil SR. CYP2D6 and CYP2E1 Gene Polymorphisms and their Association with Cervical Cancer Susceptibility: A Hospital Based Case-Control Study from South-Western Maharashtra. Asian Pac J Cancer Prev 2022; 23:2591-2597. [PMID: 36037111 PMCID: PMC9741880 DOI: 10.31557/apjcp.2022.23.8.2591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In last few years several studies all over the world discovered the genetic polymorphisms in different cytochrome P450 genes associated with risk of various cancers, but contradictory outcomes were evidenced in case of cervical cancer risk. In this case-control study we aimed to see whether the polymorphism of CYP2D6 or CYP2E1 genes may or may not be associated with cervical cancer risk in women of rural Maharashtra. METHODS In this case-control study, the association of CYP2D6 and CYP2E1 gene polymorphism with cervical cancer risk was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The study was conducted with 350 clinically confirmed cervical cancer patients and 350 healthy women in a population of South-Western Maharashtra. The Odds ratio (OR) with 95% confidence interval and p-value were evaluated, where p ≤0.005 was considered as statistically significant. RESULTS After the analysis of SNP (rs389209) of CYP2D6 and SNPs (rs2031920, rs6413432, rs6413420) of CYP2E1, we noticed that variant allele A of CYP2E1*6 showed significant increase in cervical cancer cases (OR=4.81; 95% CI: 1.57- 14.77; p=0.005). The genotypic distribution of heterozygote G/A genotype of CYP2D6*4 showed negative association with cervical cancer development when age of cancer occurrence (OR=0.41; 95% CI: 0.27- 0.61; p<0.0001) and tobacco history (OR=0.35; 95% CI: 0.20- 0.59; p=0.0001) was considered. CONCLUSION The findings from this study supported that rs6413432 SNP of CYP2E1*6 increased cervical cancer risk in the studied rural women population.
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Affiliation(s)
- Kailas D Datkhile
- Department of Molecular Biology & Genetics, Krishna Institute of Medical Sciences, “Deemed to be University”, Taluka-Karad, Dist- Satara, Pin-415 539, (Maharashtra) India. ,For Correspondence:
| | - Pratik P Durgawale
- Department of Molecular Biology & Genetics, Krishna Institute of Medical Sciences, “Deemed to be University”, Taluka-Karad, Dist- Satara, Pin-415 539, (Maharashtra) India.
| | - Rashmi A Gudur
- Department of Oncology Krishna Institute of Medical Sciences “Deemed to be University” Taluka-Karad, Dist- Satara, Pin-415 539, Maharashtra, India.
| | - Anand K Gudur
- Department of Oncology Krishna Institute of Medical Sciences “Deemed to be University” Taluka-Karad, Dist- Satara, Pin-415 539, Maharashtra, India.
| | - Satish R Patil
- Department of Molecular Biology & Genetics, Krishna Institute of Medical Sciences, “Deemed to be University”, Taluka-Karad, Dist- Satara, Pin-415 539, (Maharashtra) India.
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Wu C, Wu D, Liu Y, Zhong Y. Genetic polymorphism in cytochrome P450 2E1 and alcoholic pancreatitis sus-ceptibility: a meta-analysis. Hippokratia 2018; 22:60-67. [PMID: 31217677 PMCID: PMC6548521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND The association between cytochrome P450 2E1 (CYP2E1) polymorphism and the risk of alcoholic pancreatitis is contentious. This meta-analysis aimed to demonstrate the association between CYP2E1 RsaI/PstI, or DraI polymorphisms and the susceptibility of alcoholic pancreatitis. MATERIALS AND METHODS We searched for sources and background in Pubmed, Medline, Web of science and CNKI (Chinese national knowledge infrastructure), using the following keywords: "cytochrome P450 2E1" or "CYP2E1", "polymorphism" or "genotype", in combination with "alcoholic pancreatitis". All meta-analyses were performed with Stata 12.0. Subgroup analyses on ethnicity and type of alcoholic pancreatitis were conducted as well. Results: Eleven articles, which met the inclusion criteria, included 595 patients with alcoholic pancreatitis, and 1767 controls. For the general population, our analysis suggested no obvious association between CYP2E1 RsaI/PstI or DraI polymorphisms and the risk of alcoholic pancreatitis. However, in the non-Asian subgroup, significant associations were found between the risk for alcoholic pancreatitis and CYP2E1 RsaI/PstI polymorphism [dominant model: odds ratio (OR) =1.92, 95 % confidence interval (CI): 1.25-2.95, p =0.003; allelic contrast model: OR =1.99, 95 % CI: 1.35-2.92, p <0.001. There was not a significant association found within the Asian group. Meanwhile, the susceptibilities of chronic alcoholic pancreatitis were significantly increased for dominant and allelic contrast models of CYP2E1 RsaI/PstI polymorphism [OR =1.62, 95 % CI: 1.12-2.34; p =0.011; OR =1.62, 95 % CI: 1.17-2.24, p = 0.004, respectively] but not for acute alcoholic pancreatitis for all population. CONCLUSIONS CYP2E1 RsaI/PstI polymorphism may increase the risk of alcoholic pancreatitis in the non-Asian population. Additionally, the CYP2E1 RsaI/PstI polymorphism may increase the susceptibility for chronic alcoholic pancreatitis for all population. HIPPOKRATIA 2018, 22(2): 60-67.
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Affiliation(s)
- C Wu
- ICU Center of the Second Xiangya Hospital, Central South University, Changsha, China
| | - D Wu
- ICU Center of the Second Xiangya Hospital, Central South University, Changsha, China
| | - Y Liu
- Hematological department of the Third Xiangya Hospital, Central South University, Changsha, China
| | - Y Zhong
- ICU Center of the Second Xiangya Hospital, Central South University, Changsha, China
- Hematological department of the Third Xiangya Hospital, Central South University, Changsha, China
- Department of Surgery of University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Yahouédéhou SCMA, Carvalho MOS, Oliveira RM, Santiago RP, da Guarda CC, Carvalho SP, Ferreira JRD, Aleluia MM, Adorno EV, Gonçalves MDS. Sickle Cell Anemia Patients in Use of Hydroxyurea: Association between Polymorphisms in Genes Encoding Metabolizing Drug Enzymes and Laboratory Parameters. DISEASE MARKERS 2018; 2018:6105691. [PMID: 29619129 PMCID: PMC5829363 DOI: 10.1155/2018/6105691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 11/25/2017] [Accepted: 12/04/2017] [Indexed: 12/15/2022]
Abstract
This study investigated associations between SNPs in genes encoding metabolizing drug enzymes and laboratory parameters in sickle cell anemia patients under hydroxyurea (SCA-HU+). We evaluated hematologic and biochemical parameters by electronic methods and SNPs by PCR-RFLP and multiplex PCR in 35 SCA-HU+ patients and 67 SCA-HU- patients. The HbS, total cholesterol, lactate dehydrogenase, aspartate aminotransferase, total bilirubin and fractions levels, and leukocyte, eosinophil, monocyte, and erythroblast counts were reduced in SCA-HU+ patients (p < 0.05). Moreover, they presented higher HbF, C-reactive protein, and ferritin levels and elevated MCH and MCV values (p < 0.05). Genotype frequencies of variants GA + AA of MPO -463G>A and c1c2 + c2c2 of CYP2E1 -1293G>C/-1053C>T were higher in SCA-HU+ patients (p < 0.05). Independent associations were found between the variant A allele and lower total cholesterol, between c2 allele and low alpha-1 antitrypsin and between the null GSTT1 variant and high indirect and total bilirubin in SCA-HU+ patients. In SCA-HU- patients, independent associations were found between the variant A allele and high uric acid and between c2 allele and high urea. Our results suggest that SNPs MPO -463G>A, CYP2E1 -1293G>C/-1053C>T, and GSTT1 can be associated with alterations in lipid, inflammatory, renal, hemolytic, and hepatic profiles. However, further studies are needed to elucidate these associations.
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Affiliation(s)
- Sètondji Cocou Modeste Alexandre Yahouédéhou
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
- Laboratório de Pesquisa em Anemia (LPA), Departamento de Análises Clínicas, Faculdade de Farmácia, Universidade Federal da Bahia, Rua Barão do Jeremoabo 147, Ondina, 40170-115 Salvador, BA, Brazil
| | - Magda Oliveira Seixas Carvalho
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Rodrigo Mota Oliveira
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Rayra Pereira Santiago
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Caroline Conceição da Guarda
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Suellen Pinheiro Carvalho
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Júnia Raquel Dutra Ferreira
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Milena Magalhães Aleluia
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
| | - Elisângela Vitória Adorno
- Laboratório de Pesquisa em Anemia (LPA), Departamento de Análises Clínicas, Faculdade de Farmácia, Universidade Federal da Bahia, Rua Barão do Jeremoabo 147, Ondina, 40170-115 Salvador, BA, Brazil
| | - Marilda de Souza Gonçalves
- Laboratório de Hematologia, Genética e Biologia Computacional (LHGB), Fiocruz Bahia-Instituto Gonçalo Moniz (IGM), Rua Waldemar Falcão 121, Candeal, 40296-710 Salvador, BA, Brazil
- Laboratório de Pesquisa em Anemia (LPA), Departamento de Análises Clínicas, Faculdade de Farmácia, Universidade Federal da Bahia, Rua Barão do Jeremoabo 147, Ondina, 40170-115 Salvador, BA, Brazil
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Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
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Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
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López-Cortés A, Guerrero S, Redal MA, Alvarado AT, Quiñones LA. State of Art of Cancer Pharmacogenomics in Latin American Populations. Int J Mol Sci 2017; 18:E639. [PMID: 28545225 PMCID: PMC5485925 DOI: 10.3390/ijms18060639] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 12/22/2022] Open
Abstract
Over the past decades, several studies have shown that tumor-related somatic and germline alterations predicts tumor prognosis, drug response and toxicity. Latin American populations present a vast geno-phenotypic diversity due to the great interethnic and interracial mixing. This genetic flow leads to the appearance of complex characteristics that allow individuals to adapt to endemic environments, such as high altitude or extreme tropical weather. These genetic changes, most of them subtle and unexplored, could establish a mutational profile to develop new pharmacogenomic therapies specific for Latin American populations. In this review, we present the current status of research on somatic and germline alterations in Latin America compared to those found in Caucasian and Asian populations.
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Affiliation(s)
- Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad Tecnológica Equinoccial, Quito 170527, Ecuador.
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
| | - María Ana Redal
- Instituto de Fisiopatología y Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Centro de Diagnóstico Molecular, MEDgenomica, Buenos Aires 1000-1499, Argentina.
| | - Angel Tito Alvarado
- Unidad de Bioequivalencia y Medicina Personalizada, Facultad de Medicina, Universidad de San Martín de Porres, Lima 12, Peru.
| | - Luis Abel Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago 70111, Chile.
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Hartman JH, Miller GP, Meyer JN. Toxicological Implications of Mitochondrial Localization of CYP2E1. Toxicol Res (Camb) 2017; 6:273-289. [PMID: 28989700 DOI: 10.1039/c7tx00020k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cytochrome P450 2E1 (CYP2E1) metabolizes an extensive array of pollutants, drugs, and other small molecules, often resulting in bioactivation to reactive metabolites. Therefore, it is unsurprising that it has been the subject of decades of research publications and reviews. However, while CYP2E1 has historically been studied in the endoplasmic reticulum (erCYP2E1), active CYP2E1 is also present in mitochondria (mtCYP2E1). Relatively few studies have specifically focused on mtCYP2E1, but there is growing interest in this form of the enzyme as a driver in toxicological mechanisms given its activity and location. Many previous studies have linked total CYP2E1 to conditions that involve mitochondrial dysfunction (fasting, diabetes, non-alcoholic steatohepatitis, and obesity). Furthermore, a large number of reactive metabolites that are formed by CYP2E1 through metabolism of drugs and pollutants have been demonstrated to cause mitochondrial dysfunction. Finally, there appears to be significant inter-individual variability in targeting to the mitochondria, which could constitute a source of variability in individual response to exposures. This review discusses those outcomes, the biochemical properties and toxicological consequences of mtCYP2E1, and highlights important knowledge gaps and future directions. Overall, we feel that this exciting area of research is rich with new and important questions about the relationship between mtCYP2E1, mitochondrial dysfunction, and pathology.
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Affiliation(s)
| | - Grover P Miller
- Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC
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