1
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Miyazawa H, Muraoka M, Matsuda Y, Toma T, Morio T, Shigemura T, Haraguchi K, Matsubayashi T, Kawai T, Shirai Y, Wada T. Clinical and molecular significance of flow cytometric analysis for reactive oxygen species production and residual p67 phox expression in p67 phox-deficient chronic granulomatous disease. Scand J Immunol 2024; 100:e13372. [PMID: 38654426 DOI: 10.1111/sji.13372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/23/2024] [Accepted: 03/30/2024] [Indexed: 04/26/2024]
Abstract
Chronic granulomatous disease (CGD) is a primary immunodeficiency disease caused by molecular defects in nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. p67phox-CGD is an autosomal recessive CGD, which is caused by a defect in the cytosolic components of NADPH oxidase, p67phox, encoded by NCF2. We previously established a flow cytometric analysis for p67phox expression, which allows accurate assessment of residual protein expression in p67phox-CGD. We evaluated the correlation between oxidase function and p67phox expression, and assessed the relevancy to genotypes and clinical phenotypes in 11 patients with p67phox-CGD. Reactive oxygen species (ROS) production by granulocytes was evaluated using dihydrorhodamine-1,2,3 (DHR) assays. p67phox expression was evaluated in the monocyte population. DHR activity and p67phox expression were significantly correlated (r = 0.718, p < 0.0162). Additionally, DHR activity and p67phox expression were significantly higher in patients carrying one missense variant in combination with one nonsense or frameshift variant in the NCF2 gene than in patients with only null variants. The available clinical parameters of our patients (i.e., age at disease onset, number of infectious episodes, and each infection complication) were not linked with DHR activity or p67phox expression levels. In summary, our flow cytometric analysis revealed a significant correlation between residual ROS production and p67phox expression. More deleterious NCF2 genotypes were associated with lower levels of DHR activity and p67phox expression. DHR assays and protein expression analysis by using flow cytometry may be relevant strategies for predicting the genotypes of p67phox-CGD.
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Affiliation(s)
- Hanae Miyazawa
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Masahiro Muraoka
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Yusuke Matsuda
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Tomoko Toma
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Tokyo, Japan
| | - Tomonari Shigemura
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kohei Haraguchi
- Department of Pediatrics, Nagasaki University Hospital, Nagasaki, Japan
| | | | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Yuya Shirai
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Taizo Wada
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
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2
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Shiraishi T, Katayama Y, Nishiyama M, Shoji H, Miyakawa T, Mizoo T, Matsumoto A, Hijikata A, Shirai T, Mayanagi K, Nakayama KI. The complex etiology of autism spectrum disorder due to missense mutations of CHD8. Mol Psychiatry 2024:10.1038/s41380-024-02491-y. [PMID: 38438524 DOI: 10.1038/s41380-024-02491-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Abstract
CHD8 is an ATP-dependent chromatin-remodeling factor encoded by the most frequently mutated gene in individuals with autism spectrum disorder (ASD). Although many studies have examined the consequences of CHD8 haploinsufficiency in cells and mice, few have focused on missense mutations, the most common type of CHD8 alteration in ASD patients. We here characterized CHD8 missense mutations in ASD patients according to six prediction scores and experimentally examined the effects of such mutations on the biochemical activities of CHD8, neural differentiation of embryonic stem cells, and mouse behavior. Only mutations with high prediction scores gave rise to ASD-like phenotypes in mice, suggesting that not all CHD8 missense mutations detected in ASD patients are directly responsible for the development of ASD. Furthermore, we found that mutations with high scores cause ASD by mechanisms either dependent on or independent of loss of chromatin-remodeling function. Our results thus provide insight into the molecular underpinnings of ASD pathogenesis caused by missense mutations of CHD8.
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Affiliation(s)
- Taichi Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Yuta Katayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Masaaki Nishiyama
- Department of Histology and Cell Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Kouta Mayanagi
- Department of Drug Discovery Structural Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan.
- Anticancer Strategies Laboratory, TMDU Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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3
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Nakajima K, Suzuki H, Yamamoto M, Yamamoto T, Kawai T, Nakabayashi K, Hata K, Kosaki K, Nakajima H, Sano S, Kubo A. A familial case of periodontal Ehlers-Danlos syndrome lacking skin extensibility and joint hypermobility with a missense mutation in C1R. J Dermatol 2022; 49:714-718. [PMID: 35365885 DOI: 10.1111/1346-8138.16372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/09/2022] [Accepted: 03/03/2022] [Indexed: 12/26/2022]
Abstract
Periodontal Ehlers-Danlos syndrome (pEDS) is an autosomal-dominant disorder first described by Stewart in 1977 that is characterized by severe gingival recession and periodontitis that triggers premature loss of permanent teeth and alveolar bone absorption. It was recently shown that pEDS is caused by a heterozygous missense mutation in C1R or C1S, which encode complement 1 proteases. Here, we report a familial case of pEDS with a novel heterozygous missense mutation, c.674G>C (p.R225P), in C1R (NM_001733.4). The case exhibited pretibial hyperpigmentation and extended periodontitis but neither skin extensibility nor joint hypermobility, suggesting that this mutation will expand the definition of pEDS.
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Affiliation(s)
- Kimiko Nakajima
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Mayuko Yamamoto
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, Japan
| | - Tetsuya Yamamoto
- Department of Oral and Maxillofacial Surgery, Kochi Medical School, Kochi University, Kochi, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Reseasch Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Reseasch Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Reseasch Institute for Child Health and Development, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hideki Nakajima
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, Japan
| | - Shigetoshi Sano
- Department of Dermatology, Kochi Medical School, Kochi University, Kochi, Japan
| | - Akiharu Kubo
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
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4
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Ibrahim IH, Abd El-Aziz HG, Amer NNL, Abd El-Sameea HS. Mutational pattern of PIK3CA exon 20 in circulating DNA in breast cancer. Saudi J Biol Sci 2022; 29:2828-2835. [PMID: 35531214 PMCID: PMC9073026 DOI: 10.1016/j.sjbs.2022.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/28/2021] [Accepted: 01/02/2022] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is one of the most common cancers with diverse mutations, etiology and causes. Mutational signature of the driver genes could allow for better understanding disease etiology and progression. This study aims to assess PIK3CA Exon 20 somatic mutational signature in relation to potential underlying etiology. Circulating DNA of 71 Egyptian BC patients was isolated, amplified for PIK3CA Exon 20, and sequenced. Mutational signature was determined according to COSMIC v2 signature. Public BC dataset was analysed to assess PIK3CA mutations effect on the transcriptomic profile. Somatic mutations of PIK3CA exon 20 were found in 66.2% of the study cohort. Nucleotide substitution patterns were similar to general nucleotide substitution patterns in BC. Signature 3 and 9 were the most common signatures in the studied BC patients. Signature of Aristolochic acid exposure was found in some cases. The most common nucleotide substitution was T > A transversion, but substitutions T > G and T > C were correlated to each other and to the total mutation number. PIK3CA mutations were found to disrupt several pathways including RAC1, PDGF, Wnt, and integrin signalling. PIK3CA exon 20 mutational signatures in Egyptian BC patients could suggest a disease etiology involving homologous recombination deficiency (HRD) and polymerase eta (Pol η). Nucleotide substitution patterns could indicate the role of exposure to oxidative stress and some carcinogens such as 4-aminobiphenyl and Aristolochic acid.
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Ibrahim IH, Abdel-Aziz HG, Hassan FE, El-Sameea HS. Role of GATA3 exon 6 germline mutations in breast cancer progression in Egyptian female patients. Exp Biol Med (Maywood) 2020; 246:40-47. [PMID: 32938228 DOI: 10.1177/1535370220958610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IMPACT STATEMENT GATA3 mutations are known to play an important role in breast cancer progression. The exact role and mechanisms of these mutations remain controversial as some studies suggest a relation to breast tumor growth, while others suggest a relation to longer survival. GATA3 germline mutations are not well studied in breast cancer. In this study, it was hypothesized that different types of GATA3 mutations could contribute to the breast cancer progression in different ways. GATA3 exon 6, which is important for GATA3 protein functions, was reported to have hotspots, and hence it was selected for study. Intronic GATA3 germline mutations were found to be related to favorable prognosis, while protein coding mutations were found to be related to unfavorable prognosis. Bioinformatics study of large publically available datasets showed that GATA3 mutations lead to dysregulation of pathways related to T-cells activation, inflammation, and breast cancer development.
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Affiliation(s)
- Iman H Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls) Al-Azhar University, Cairo 11765, Egypt
| | - Heba G Abdel-Aziz
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls) Al-Azhar University, Cairo 11765, Egypt
| | - Fatema Em Hassan
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls) Al-Azhar University, Cairo 11765, Egypt
| | - Hesham Sa El-Sameea
- Department of Clinical Pathology, Faculty of Medicine (New Damietta) Al-Azhar University, Damietta 34711, Egypt
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6
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Abumsimir B, Mrabti M, Laraqui A, Ameur A, Koraishi SI, Mzibrie M, Benchekroun MN, Bessi H, Tiabi I, Almahasneh I, Ennaji MM. Most frequent mutational events of home box 13 gene in prostatic adenocarcinoma and correlation with tumor characteristics. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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7
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Shafaat M, Hashemi M, Majd A, Abiri M, Zeinali S. Genetic testing of Mucopolysaccharidoses disease using multiplex PCR- based panels of STR markers: in silico analysis of novel mutations. Metab Brain Dis 2019; 34:1447-1455. [PMID: 31236806 DOI: 10.1007/s11011-019-00434-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/13/2019] [Indexed: 12/22/2022]
Abstract
The Mucopolysaccharidoses (MPS) are group of inherited metabolic diseases caused by the deficiency of enzymes required to degrade glycosaminoglycans (GAGs) in the lysosomes. GAGs are sulfated polysaccharides involving repeating disaccharides, uronic acid and hexosamines including chondroitin sulfate (CS), dermatan sulfate (DS), heparan sulfate (HS) and keratan sulfate (KS). Hyaluronan is excluded in terms of being non-sulfated in the GAG family. Different types of mutations have been identified as the causative agent in all types of MPS. Herein, we planned to investigate the pathogenic mutations in different types of MPS including type I (IDUA gene), IIIA (SGSH) and IIIB (NAGLU) in the eight Iranian patients. Autozygosity mapping was performed to identify the potential pathogenic variants in these 8 patients indirectly with the clinical diagnosis of MPSs. so three panels of STR (Short Tandem Repeat) markres flanking IDUA, SGSH and NAGLU genes were selected for multiplex PCR amplification. Then in each family candidate gene was sequenced to identify the pathogenic mutation. Our study showed two novel mutations c.469 T > C and c.903C > G in the IDUA gene, four recurrent mutations: c.1A > C in IDUA, c.220C > T, c.1298G > A in SGSH gene and c.457G > A in the NAGLU gene. The c.1A > C in IDUA was the most common mutation in our study. In silico analysis were performed as well to predict the pathogenicity of the novel variants.
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Affiliation(s)
- Mehdi Shafaat
- Department of Biology, Faculty of Science, North Tehran Branch of Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ahmad Majd
- Department of Biology, Faculty of Science, North Tehran Branch of Islamic Azad University, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics and Molecular biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St, Tehran, Iran.
- Dr. Zeinali's Medical Genetics Lab, Kawsar Human Genetics Center, No. 41 Majlesi St., Vali Asr St., Postal Code, Tehran, 1595645513, Iran.
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8
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Newborn screening for Pompe disease in Japan: report and literature review of mutations in the GAA gene in Japanese and Asian patients. J Hum Genet 2019; 64:741-755. [DOI: 10.1038/s10038-019-0603-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 11/08/2022]
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9
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Azimi A, Nejati P, Tahmasebi S, Alimoradi S, Alibakhshi R. Characterization of the IVS-II-821 (A>C) ( HBB: c.316-30A>C) Mutation in a β-Thalassemia Phenotype in Iran. Hemoglobin 2019; 43:23-26. [DOI: 10.1080/03630269.2019.1592760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Azam Azimi
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parham Nejati
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soosan Tahmasebi
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sasan Alimoradi
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Alibakhshi
- Department of Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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GJB2 mutations causing autosomal recessive non-syndromic hearing loss (ARNSHL) in two Iranian populations: Report of two novel variants. Int J Pediatr Otorhinolaryngol 2018; 107:121-126. [PMID: 29501291 DOI: 10.1016/j.ijporl.2018.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Hereditary hearing loss (HL) is a noticeable concern in medicine all over the world. On average, 1 in 166 babies born are diagnosed with HL in Iran, which makes it a major public health issue. Autosomal recessive non-syndromic HL (ARNSHL) is the most prevalent form of HL. Although over 60 genes have been identified for ARNSHL, GJB2 mutations are the most prevalent causes of ARNSHL in many populations. Previous studies have estimated the average frequency of GJB2 mutations to be between 16 and 18% in Iran, but would vary among different ethnic groups. In the present study, we aimed to determine the frequency and mutation profile of 70 deaf patients from two different provinces (center and west) of Iran. METHODS We enrolled 70 Iranian deaf patients with ARNSHL from Isfahan (40 family) and Hamedan (30 family) provinces. After extraction of genomic DNA, the entire coding region of GJB2 was directly sequenced in all patients. Multiplex PCR was used for detection of del(GJB6-D13S1830) and del(GJB6-D13S1854) in the GJB6 gene. In silico analyses were also performed by available software tools. RESULTS A total of eleven different mutations were detected, nine of which were previously reported and the other two (c.130T > G and c.178T > G) were novel. Homozygous GJB2 mutations were observed in 22.5% and 20% of all the subjects from Isfahan and Hamedan provinces, respectively. c.35delG was the most frequent mutation. One compound heterozygous genotype (c.358_360delGAG/c.35delG) was observed for c.35delG. Screening for the two GJB6 deletions did not reveal any positive sample among heterozygous or GJB2 negative samples. CONCLUSIONS The present study suggests that mutations in the GJB2 gene specially c.35delG are important causes of ARNSHL in the center and west of Iran. Totally, 15% of the patients were heterozygous carriers. Further investigation is needed to detect the genetic cause of HL in the patients with monoallelic GJB2 mutations.
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Hijikata A, Tsuji T, Shionyu M, Shirai T. Decoding disease-causing mechanisms of missense mutations from supramolecular structures. Sci Rep 2017; 7:8541. [PMID: 28819267 PMCID: PMC5561164 DOI: 10.1038/s41598-017-08902-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/14/2017] [Indexed: 11/10/2022] Open
Abstract
The inheritance modes of pathogenic missense mutations are known to be highly associated with protein structures; recessive mutations are mainly observed in the buried region of protein structures, whereas dominant mutations are significantly enriched in the interfaces of molecular interactions. However, the differences in phenotypic impacts among various dominant mutations observed in individuals are not fully understood. In the present study, the functional effects of pathogenic missense mutations on three-dimensional macromolecular complex structures were explored in terms of dominant mutation types, namely, haploinsufficiency, dominant-negative, or toxic gain-of-function. The major types of dominant mutation were significantly associated with the different types of molecular interactions, such as protein-DNA, homo-oligomerization, or intramolecular domain-domain interactions, affected by mutations. The dominant-negative mutations were biased toward molecular interfaces for cognate protein or DNA. The haploinsufficiency mutations were enriched on the DNA interfaces. The gain-of-function mutations were localized to domain-domain interfaces. Our results demonstrate a novel use of macromolecular complex structures for predicting the disease-causing mechanisms through inheritance modes.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Toshiyuki Tsuji
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.,MITA International School, Yoga, Setagaya, Tokyo, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.
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12
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Gojobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, Kinoshita K, Kwon Y, Migita O, Mizutani H, Muraoka M, Nagata K, Omori S, Sugawara H, Yamada D, Yura K. VaProS: a database-integration approach for protein/genome information retrieval. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2016; 17:69-81. [PMID: 28012137 PMCID: PMC5274651 DOI: 10.1007/s10969-016-9211-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023]
Abstract
Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts' knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/ .
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Affiliation(s)
- Takashi Gojobori
- Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan
| | - Kazuho Ikeo
- National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan
| | - Yukie Katayama
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Akira R Kinjo
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, Miyagi, Sendai, 980-8597, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Sendai, 980-8573, Japan
| | - Yeondae Kwon
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Ohsuke Migita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan
- Department of Pediatrics, St. Marianna University School of Medicine, Miyamae, Kawasaki, 216-8511, Japan
| | - Hisashi Mizutani
- National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan
| | - Masafumi Muraoka
- National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan
| | - Koji Nagata
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Satoshi Omori
- Graduate School of Information Sciences, Tohoku University, Miyagi, Sendai, 980-8597, Japan
| | - Hideaki Sugawara
- National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan
| | - Daichi Yamada
- Center for Informational Biology, Ochanomizu University, 2-1-1, Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Kei Yura
- National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.
- Center for Informational Biology, Ochanomizu University, 2-1-1, Otsuka, Bunkyo, Tokyo, 112-8610, Japan.
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13
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Mahdieh N, Rabbani B. Beta thalassemia in 31,734 cases with HBB gene mutations: Pathogenic and structural analysis of the common mutations; Iran as the crossroads of the Middle East. Blood Rev 2016; 30:493-508. [DOI: 10.1016/j.blre.2016.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 06/13/2016] [Accepted: 07/08/2016] [Indexed: 12/16/2022]
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14
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Neurogenetics in Argentina: diagnostic yield in a personalized research based clinic. Genet Res (Camb) 2016; 97:e10. [PMID: 25989649 DOI: 10.1017/s0016672315000087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As a whole neurogenetic diseases are a common group of neurological disorders. However, the recognitionand molecular diagnosis of these disorders is not always straightforward. Besides, there is a paucity of informationregarding the diagnostic yield that specialized neurogenetic clinics could obtain. We performed a prospective,observational, analytical study of the patients seen in a neurogenetic clinic at a tertiary medicalcentre to assess the diagnostic yield of a comprehensive diagnostic evaluation that included a personalizedclinical assessment along with traditional and next-generation sequencing diagnostic tests. We included a cohortof 387 patients from May 2008 to June 2014. For sub-group analysis we selected a sample of patientswhose main complaint was the presence of progressive ataxia, to whom we applied a systematic moleculardiagnostic algorithm. Overall, a diagnostic mutation was identified in 27·4% of our cohort. However, if weonly considered those patients where a molecular test could be performed, the success rate rises to 45%. Weobtained diagnostic yields of 23·5 and 57·5% in the global group of ataxic patients and in the subset of ataxicpatients with a positive family history, respectively. Thus, about a third of patients evaluated in a neurogeneticclinic could be successfully diagnosed.
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Sherman WA, Kuchibhatla DB, Limviphuvadh V, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes. J Bioinform Comput Biol 2015; 13:1550028. [PMID: 26503432 DOI: 10.1142/s0219720015500286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .
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Affiliation(s)
- Westley Arthur Sherman
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore
| | - Durga Bhavani Kuchibhatla
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore
| | - Vachiranee Limviphuvadh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive 4, Singapore 117597, Singapore
- School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Singapore
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GJB2 mutations in deaf population of Ilam (Western Iran): a different pattern of mutation distribution. Eur Arch Otorhinolaryngol 2015; 273:1161-5. [DOI: 10.1007/s00405-015-3684-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/03/2015] [Indexed: 11/26/2022]
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17
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Wada T, Sakakibara Y, Nishimura R, Toma T, Ueno Y, Horita S, Tanaka T, Nishi M, Kato K, Yasumi T, Ohara O, Yachie A. Down-regulation of CD5 expression on activated CD8+ T cells in familial hemophagocytic lymphohistiocytosis with perforin gene mutations. Hum Immunol 2013; 74:1579-85. [PMID: 24051121 DOI: 10.1016/j.humimm.2013.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Indexed: 12/24/2022]
Abstract
Hemophagocytic lymphohistiocytosis (HLH) is characterized by uncontrolled activation of T cells and macrophages with overproduction of cytokines. Familial HLH type 2 (FHL2) is the most common form of primary HLH and is caused by mutations in PRF1. We have recently described a significant increase in the subpopulation of CD8(+) T cells with clonal expansion and CD5 down-regulation in Epstein-Barr virus associated-HLH, which represented a valuable tool for its diagnosis. However, this unusual phenotype of CD8(+) T cells has not been investigated fully in patients with FHL2. We performed immunophenotypic analysis of peripheral blood and measured serum pro-inflammatory cytokines in five patients with FHL2. All patients showed significantly increased subpopulations of activated CD8(+) T cells with down-regulation of CD5, which were negligible among normal controls. Analysis of T-cell receptor Vβ repertoire suggested the reactive and oligoclonal expansion of these cells. The proportion of the subset declined after successful treatment concomitant with reduction in the serum levels of cytokines in all patients except one who continued to have a high proportion of the subset and died. These findings suggest that down-regulation of CD5 on activated CD8(+) T cells may serve as a useful marker of dysregulated T cell activation and proliferation in FHL2.
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Affiliation(s)
- Taizo Wada
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
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Athanasiadis P, Malousi A, Kouidou S, Maglaveras N. GREMET: an integrative tool for the prediction of mutation effects on gene regulation. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2013; 111:214-219. [PMID: 23648050 DOI: 10.1016/j.cmpb.2013.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 12/19/2012] [Accepted: 04/02/2013] [Indexed: 06/02/2023]
Abstract
The identification of thousands of mutations yearly has put new challenges to researchers who are interested in fast and effective annotation as well as the prediction of potential implications to the gene regulation mechanisms. This work presents an integrative tool, called GREMET, for the prediction of alterations in gene splicing regulation inferred by mutations of the human genome. GREMET supports the characterization of mutations either single-point or indels with respect to their effect on the splicing potential of the neighboring sequences and the binding strength of auxiliary cis-acting splicing enhancers. In addition, GREMET identifies possible consequences of mutations on the DNA methylation through the disruption or creation of CpG sequences. Besides locus-specific mutations, GREMET performs the analyses on newly identified mutations and provides an easy-to-use Web interface helping researchers to save time in routine mutation analyses. GREMET is freely accessible at: http://kedip.med.auth.gr/biotools/gremet/.
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Affiliation(s)
- Polykarpos Athanasiadis
- Laboratory of Medical Informatics, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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19
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Abstract
Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest possible causal links. A fair amount of this evidence comes from high-throughput experimentation. Thus, well-developed methods are necessary to reliably deal with the quantity of information at hand. Existing gene prioritization techniques already significantly improve the outcomes of targeted experimental studies. Faster and more reliable techniques that account for novel data types are necessary for the development of new diagnostics, treatments, and cure for many diseases.
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Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA.
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20
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Wada T, Muraoka M, Toma T, Imai T, Shigemura T, Agematsu K, Haraguchi K, Moriuchi H, Oh-Ishi T, Kitoh T, Ohara O, Morio T, Yachie A. Rapid detection of intracellular p47phox and p67phox by flow cytometry; useful screening tests for chronic granulomatous disease. J Clin Immunol 2013; 33:857-64. [PMID: 23306776 DOI: 10.1007/s10875-012-9859-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/20/2012] [Indexed: 11/24/2022]
Abstract
Chronic granulomatous disease (CGD) is caused by defects of NADPH oxidase. The diagnosis of CGD can be made by analysis of NADPH oxidase activity, however, identification of the CGD subgroups is required before performing mutation analysis. The membrane-bound subunits, gp91phox and p22phox, can be quickly analyzed by flow cytometry, unlike the cytosolic components, p47phox and p67phox. We evaluated the feasibility of flow cytometric detection of p47phox and p67phox with specific monoclonal antibodies in two patients with p47phox deficiency and 7 patients with p67phox deficiency. Consistent with previous observations, p47phox and p67phox were expressed in phagocytes and B cells, but not in T or natural killer cells, from normal controls. In contrast, patients with p47phox and p67phox deficiency showed markedly reduced levels of p47phox and p67phox, respectively. These techniques will be useful to rapidly assess the expression of the cytosolic components, p47phox and p67phox, and represents important secondary screening tests for CGD.
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Affiliation(s)
- Taizo Wada
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, 920-8641, Japan.
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21
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Levy R, Sobolev V, Edelman M. First- and second-shell metal binding residues in human proteins are disproportionately associated with disease-related SNPs. Hum Mutat 2011; 32:1309-18. [DOI: 10.1002/humu.21573] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 07/06/2011] [Indexed: 11/10/2022]
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Goel R, Muthusamy B, Pandey A, Prasad TSK. Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol 2011; 48:87-95. [PMID: 20927658 DOI: 10.1007/s12033-010-9336-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the recent years, research in molecular biotechnology has transformed from being small scale studies targeted at a single or a small set of molecule(s) into a combination of high throughput discovery platforms and extensive validations. Such a discovery platform provided an unbiased approach which resulted in the identification of several novel genetic and protein biomarkers. High throughput nature of these investigations coupled with higher sensitivity and specificity of Next Generation technologies provided qualitatively and quantitatively richer biological data. These developments have also revolutionized biological research and speed of data generation. However, it is becoming difficult for individual investigators to directly benefit from this data because they are not easily accessible. Data resources became necessary to assimilate, store and disseminate information that could allow future discoveries. We have developed two resources--Human Protein Reference Database (HPRD) and Human Proteinpedia, which integrate knowledge relevant to human proteins. A number of protein features including protein-protein interactions, post-translational modifications, subcellular localization, and tissue expression, which have been studied using different strategies were incorporated in these databases. Human Proteinpedia also provides a portal for community participation to annotate and share proteomic data and uses HPRD as the scaffold for data processing. Proteomic investigators can even share unpublished data in Human Proteinpedia, which provides a meaningful platform for data sharing. As proteomic information reflects a direct view of cellular systems, proteomics is expected to complement other areas of biology such as genomics, transcriptomics, molecular biology, cloning, and classical genetics in understanding the relationships among multiple facets of biological systems.
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Affiliation(s)
- Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
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23
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Asai E, Wada T, Sakakibara Y, Toga A, Toma T, Shimizu T, Nampoothiri S, Imai K, Nonoyama S, Morio T, Muramatsu H, Kamachi Y, Ohara O, Yachie A. Analysis of mutations and recombination activity in RAG-deficient patients. Clin Immunol 2011; 138:172-7. [DOI: 10.1016/j.clim.2010.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/26/2010] [Accepted: 11/03/2010] [Indexed: 10/18/2022]
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