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Polat S, Karaburgu S, Unluhizarci K, Dundar M, Ozkul Y, Arslan YK, Karaca Z, Kelestimur F. Unexpectedly high mutation rate of cyp11b1 compared to cyp21a2 in randomly-selected turkish women: a large screening study. J Endocrinol Invest 2023; 46:2367-2377. [PMID: 37055708 DOI: 10.1007/s40618-023-02093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
PURPOSE Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders resulting from enzyme deficiencies associated with steroidogenesis. The clinical presentation of non-classic CAH (NCAH) in females is often indistinguishable from other hyperandrogenic disorders like polycystic ovary syndrome (PCOS). The data on the prevalence of NCAH in unselected women in the literature is scanty. The research aimed to evaluate the prevalence of NCAH, carrier frequencies, and the correlation between clinical symptoms and genotype in Turkish women. METHODS The study group comprised two hundred and seventy randomly-selected unrelated asymptomatic women of reproductive age (18-45). Subjects were recruited from female blood donors. All volunteers underwent clinical examination and hormone measurements. The protein-encoding exons and exon-intron boundaries of the CYP21A2, CYP11B1, HSD3β2 and CYP21A2 promoter were sequenced by direct DNA sequencing. RESULTS After genotyping, seven (2.2%) individuals were diagnosed with NCAH. The heterozygous carrier frequencies of CYP21A2, CYP21A2 promoter, CYP11B1, and HSD3β2 genes with 34, 34, 41, and 1 pathologic mutation were determined at 12.6%, 12.6%, 15.2%, and 0.37% of volunteers, respectively. Gene-conversion (GC) frequencies between CYP21A2/CYP21A1P and CYP11B1/CYP11B2 were determined as 10.4% and 14.8%, respectively. CONCLUSION Despite GC-derived higher mutation frequency determined in the CYP11B1 gene, the reason for the low frequency of NCAH due to 11OHD compared to 21OHD might be that gene-conversion arises with active CYP11B2 rather than an inactive pseudogene. HSD3β1 exhibits high homology with HSD3β2 located on the same chromosome; remarkably, it demonstrates low heterozygosity and no GC, most probably the outcome of a tissue-specific expression pattern.
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Affiliation(s)
- S Polat
- Department of Medical Genetics, Medical Faculty, Erzincan Binali Yıldırım University, Basbaglar Mah., 24100, Erzincan, Merkez, Turkey.
| | - S Karaburgu
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - K Unluhizarci
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - M Dundar
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - Y Ozkul
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - Y K Arslan
- Department of Biostatistics, Medical Faculty, Çukurova University, Adana, Turkey
| | - Z Karaca
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
| | - F Kelestimur
- Department of Endocrinology, Medical Faculty, Erciyes University, Kayseri, Turkey
- Department of Endocrinology, Medical Faculty, Yeditepe University, Istanbul, Turkey
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Arriba M, Ezquieta B. Molecular Diagnosis of Steroid 21-Hydroxylase Deficiency: A Practical Approach. Front Endocrinol (Lausanne) 2022; 13:834549. [PMID: 35422767 PMCID: PMC9001848 DOI: 10.3389/fendo.2022.834549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Adrenal insufficiency in paediatric patients is mostly due to congenital adrenal hyperplasia (CAH), a severe monogenic disease caused by steroid 21-hydroxylase deficiency (21-OHD, encoded by the CYP21A2 gene) in 95% of cases. CYP21A2 genotyping requires careful analyses that guaranty gene-specific PCR, accurate definition of pseudogene-gene chimeras, gene duplications and allele dropout avoidance. A small panel of well-established disease-causing alterations enables a high diagnostic yield in confirming/discarding the disorder not only in symptomatic patients but also in those asymptomatic with borderline/positive results of 17-hydroxyprogesterone. Unfortunately, the complexity of this locus makes it today reluctant to high throughput techniques of massive sequencing. The strong relationship existing between the molecular alterations and the degree of enzymatic deficiency has allowed genetic studies to demonstrate its usefulness in predicting/classifying the clinical form of the disease. Other aspects of interest regarding molecular studies include its independence of physiological variations and analytical interferences, its usefulness in the diagnosis of simple virilizing forms in males and its inherent contribution to the genetic counseling, an aspect of great importance taking into account the high carrier frequency of CAH in the general population. Genetic testing of CYP21A2 constitutes an irreplaceable tool to detect severe alleles not just in family members of classical forms but also in mild late-onset forms of the disease and couples. It is also helpful in areas such as assisted reproduction and preimplantation diagnosis. Molecular diagnosis of 21-OHD under expert knowledge definitely contributes to a better management of the disease in every step of the clinical course.
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Affiliation(s)
- María Arriba
- Molecular Diagnostics Laboratory, Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
| | - Begoña Ezquieta
- Molecular Diagnostics Laboratory, Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
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EMQN best practice guidelines for molecular genetic testing and reporting of 21-hydroxylase deficiency. Eur J Hum Genet 2020; 28:1341-1367. [PMID: 32616876 PMCID: PMC7609334 DOI: 10.1038/s41431-020-0653-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 11/25/2022] Open
Abstract
Molecular genetic testing for congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD) is offered worldwide and is of importance for differential diagnosis, carrier detection and adequate genetic counseling, particularly for family planning. In 2008 the European Molecular Genetics Quality Network (EMQN) for the first time offered a European-wide external quality assessment scheme for CAH (due to 21-OH deficiency). The interest was great and over the last years at about 60 laboratories from Europe, USA and Australia regularly participated in that scheme. These best practice guidelines were drafted on the basis of the extensive knowledge and experience got from those annually organized CAH-schemes. In order to obtain the widest possible consultation with practicing laboratories the draft was therefore circulated twice by EMQN to all laboratories participating in the EQA-scheme for CAH genotyping and was updated by that input. The present guidelines address quality requirements for diagnostic molecular genetic laboratories, as well as criteria for CYP21A2 genotyping (including carrier-testing and prenatal diagnosis). A key aspect of that article is the use of appropriate methodologies (e.g., sequencing methods, MLPA (multiplex ligation dependent probe amplification), mutation specific assays) and respective limitations and analytical accuracy. Moreover, these guidelines focus on classification of variants, and the interpretation and standardization of the reporting of CYP21A2 genotyping results. In addition, the article provides a comprehensive list of common as well as so far unreported CYP21A2-variants.
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Karlsson L, de Paula Michelatto D, Lusa ALG, D'Almeida Mgnani Silva C, Östberg LJ, Persson B, Guerra-Júnior G, Valente de Lemos-Marini SH, Baldazzi L, Menabó S, Balsamo A, Greggio NA, Palandi de Mello M, Barbaro M, Lajic S. Novel non-classic CYP21A2 variants, including combined alleles, identified in patients with congenital adrenal hyperplasia. Clin Biochem 2019; 73:50-56. [PMID: 31344365 DOI: 10.1016/j.clinbiochem.2019.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Congenital adrenal hyperplasia (CAH) is an inborn error of metabolism and a common disorder of sex development where >90% of all cases are due to 21-hydroxylase deficiency. Novel and rare pathogenic variants account for 5% of all clinical cases. Here, we sought to investigate the functional and structural effects of four novel (p.Val358Ile, p.Arg369Gln, p.Asp377Tyr, and p.Leu461Pro) and three combinations of CYP21A2 variants (i.e. one allele containing two variants p.[Ile172Asn;Val358Ile], p.[Val281Leu;Arg369Gln], or p.[Asp377Tyr;Leu461Pro]) identified in patients with CAH. METHODS All variants were reconstructed by in vitro site-directed mutagenesis, the proteins were transiently expressed in COS-1 cells and enzyme activities directed toward the two natural substrates (17-hydroxyprogesterone and progesterone) were determined. In parallel, in silico prediction of the pathogenicity of the variants based on the human CYP21 X-ray structure was performed. RESULTS The novel variants, p.Val358Ile, p.Arg369Gln, p.Asp377Tyr, and p.Leu461Pro exhibited residual enzymatic activities within the range of non-classic (NC) CAH variants (40-82%). An additive effect on the reduction of enzymatic activity (1-17%) was observed when two variants were expressed together, as identified in several patients, resulting in either NC or more severe phenotypes. In silico predictions were in line with the in vitro data except for p.Leu461Pro. CONCLUSIONS Altogether, the combination of clinical data, in silico prediction, and data from in vitro studies are important for establishing a correct genotype and phenotype correlation in patients with CAH.
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Affiliation(s)
- Leif Karlsson
- Department of Women's and Children's Health, Karolinska Institutet, Pediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden
| | - Débora de Paula Michelatto
- Department of Women's and Children's Health, Karolinska Institutet, Pediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden; Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Ana Letícia Gori Lusa
- Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Linus J Östberg
- Science for Life Laboratory and eSSENCE, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Persson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Gil Guerra-Júnior
- Departamento de Pediatria, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Lilia Baldazzi
- Department of Woman, Child and Urological Diseases, Centre for Rare Endocrine Conditions (CARENDO BO; Endo-ERN), S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Soara Menabó
- Department of Woman, Child and Urological Diseases, Centre for Rare Endocrine Conditions (CARENDO BO; Endo-ERN), S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Antonio Balsamo
- Department of Woman, Child and Urological Diseases, Centre for Rare Endocrine Conditions (CARENDO BO; Endo-ERN), S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Nella Augusta Greggio
- Department of Women's and Children's Health of Padua, Pediatric Endocrinology Unit, Italy
| | - Maricilda Palandi de Mello
- Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Michela Barbaro
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Center for Inherited Metabolic Diseases (CMMS L7:05), Karolinska University Hospital, Stockholm, Sweden
| | - Svetlana Lajic
- Department of Women's and Children's Health, Karolinska Institutet, Pediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden.
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Dundar A, Bayramov R, Onal MG, Akkus M, Dogan ME, Kenanoglu S, Cerrah Gunes M, Kazimli U, Ozbek MN, Ercan O, Yildirim R, Celmeli G, Parlak M, Dundar I, Hatipoglu N, Unluhizarci K, Akalin H, Ozkul Y, Saatci C, Dundar M. The molecular basis and genotype–phenotype correlations of congenital adrenal hyperplasia (CAH) in Anatolian population. Mol Biol Rep 2019; 46:3677-3690. [DOI: 10.1007/s11033-019-04809-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/10/2019] [Indexed: 11/29/2022]
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Congenital Adrenal Hyperplasia (CAH) due to 21-Hydroxylase Deficiency: A Comprehensive Focus on 233 Pathogenic Variants of CYP21A2 Gene. Mol Diagn Ther 2018; 22:261-280. [DOI: 10.1007/s40291-018-0319-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Simonetti L, Bruque CD, Fernández CS, Benavides-Mori B, Delea M, Kolomenski JE, Espeche LD, Buzzalino ND, Nadra AD, Dain L. CYP21A2 mutation update: Comprehensive analysis of databases and published genetic variants. Hum Mutat 2017; 39:5-22. [PMID: 29035424 DOI: 10.1002/humu.23351] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/20/2017] [Accepted: 10/02/2017] [Indexed: 12/31/2022]
Abstract
Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders of adrenal steroidogenesis. Disorders in steroid 21-hydroxylation account for over 95% of patients with CAH. Clinically, the 21-hydroxylase deficiency has been classified in a broad spectrum of clinical forms, ranging from severe or classical, to mild late onset or non-classical. Known allelic variants in the disease causing CYP21A2 gene are spread among different sources. Until recently, most variants reported have been identified in the clinical setting, which presumably bias described variants to pathogenic ones, as those found in the CYPAlleles database. Nevertheless, a large number of variants are being described in massive genome projects, many of which are found in dbSNP, but lack functional implications and/or their phenotypic effect. In this work, we gathered a total of 1,340 GVs in the CYP21A2 gene, from which 899 variants were unique and 230 have an effect on human health, and compiled all this information in an integrated database. We also connected CYP21A2 sequence information to phenotypic effects for all available mutations, including double mutants in cis. Data compiled in the present work could help physicians in the genetic counseling of families affected with 21-hydroxylase deficiency.
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Affiliation(s)
| | - Carlos D Bruque
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina.,Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | | | | | - Marisol Delea
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Jorge E Kolomenski
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - Lucía D Espeche
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | | | - Alejandro D Nadra
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Dain
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina.,Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Bruque CD, Delea M, Fernández CS, Orza JV, Taboas M, Buzzalino N, Espeche LD, Solari A, Luccerini V, Alba L, Nadra AD, Dain L. Structure-based activity prediction of CYP21A2 stability variants: A survey of available gene variations. Sci Rep 2016; 6:39082. [PMID: 27966633 PMCID: PMC5155424 DOI: 10.1038/srep39082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/16/2016] [Indexed: 01/14/2023] Open
Abstract
Congenital adrenal hyperplasia due to 21-hydroxylase deficiency accounts for 90-95% of CAH cases. In this work we performed an extensive survey of mutations and SNPs modifying the coding sequence of the CYP21A2 gene. Using bioinformatic tools and two plausible CYP21A2 structures as templates, we initially classified all known mutants (n = 343) according to their putative functional impacts, which were either reported in the literature or inferred from structural models. We then performed a detailed analysis on the subset of mutations believed to exclusively impact protein stability. For those mutants, the predicted stability was calculated and correlated with the variant's expected activity. A high concordance was obtained when comparing our predictions with available in vitro residual activities and/or the patient's phenotype. The predicted stability and derived activity of all reported mutations and SNPs lacking functional assays (n = 108) were assessed. As expected, most of the SNPs (52/76) showed no biological implications. Moreover, this approach was applied to evaluate the putative synergy that could emerge when two mutations occurred in cis. In addition, we propose a putative pathogenic effect of five novel mutations, p.L107Q, p.L122R, p.R132H, p.P335L and p.H466fs, found in 21-hydroxylase deficient patients of our cohort.
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Affiliation(s)
- Carlos D Bruque
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina.,Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - Marisol Delea
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | | | - Juan V Orza
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Melisa Taboas
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Noemí Buzzalino
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Lucía D Espeche
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Andrea Solari
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | | | - Liliana Alba
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Alejandro D Nadra
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Liliana Dain
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina.,Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
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Hao W, Ji F, Wang J, Zhang Y, Wang T, Bao Y. Biochemical characterization of unusual meso-2,3-butanediol dehydrogenase from a strain of Bacillus subtilis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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