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Uzun M, Alekseeva L, Krutkina M, Koziaeva V, Grouzdev D. Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases. Sci Data 2020; 7:252. [PMID: 32737307 PMCID: PMC7449369 DOI: 10.1038/s41597-020-00593-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.
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Affiliation(s)
- Maria Uzun
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia. .,Lomonosov Moscow State University, Moscow, Russia.
| | - Lolita Alekseeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Maria Krutkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Veronika Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
| | - Denis Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Moscow, Russia
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Abstract
Quantification of endogenous hormonal steroids and their precursors is essential for diagnosing a wide range of endocrine disorders. Historically, these analyses have been carried out using immunoassay, but such methods are problematic, especially for low-concentration analytes, due to assay interference by other endogenous steroids. MS offers improved specificity over immunoassay and can be highly sensitive. GC–MS, with use of stable isotopically labeled internal standards, is considered the ‘gold standard’ method for serum steroid analysis. GC–MS is the method of choice for profiling steroid metabolites in urine, but these techniques are not appropriate for routine use in clinical laboratories owing to a need for extensive sample preparation, as well as analytical expertise. LC–MS/MS compares well to GC–MS in terms of accuracy, precision and sensitivity, but allows simplified sample preparation. While most publications have featured only one or a limited number of steroids, we consider that steroid paneling (which we propose as the preferred term for multitargeted steroid analysis) has great potential to enable clinicians to make a definitive diagnosis. It is adaptable for use in a number of matrices, including serum, saliva and dried blood spots. However, LC–MS/MS-based steroid analysis is not straightforward, and understanding the chemical and analytical processes involved is essential for implementation of a robust clinical service. This article discusses specific challenges in the measurement of endogenous steroids using LC–MS/MS, and provides examples of the benefits it offers.
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Abstract
Most steroid disorders of the adrenal cortex come to clinical attention in childhood and in order to investigate these problems, there are many challenges to the laboratory which need to be appreciated to a certain extent by clinicians. The analysis of sex steroids in biological fluids from neonates, over adrenarche and puberty present challenges of specificities and concentrations often in small sample sizes. Different reference ranges are also needed for interpretations. For around 40 years, quantitative assays for the steroids and their regulatory peptide hormones have been possible using immunoassay techniques. Problems are recognised and this review aims to summarise the benefits and failings of immunoassays and introduce where tandem mass spectrometry is anticipated to meet the clinical needs for steroid analysis in paediatric endocrine investigations. It is important to keep a dialogue between clinicians and the laboratory, especially when any laboratory result does not make sense in the clinical investigation.
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Affiliation(s)
- John W Honour
- Clinical Biochemistry, University College London Hospitals, London, England.
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Loi V, Vertzoni M, Vryonidou A, Phenekos C. Development and validation of a simple reversed-phase high-performance liquid chromatography method for the determination of testosterone in serum of males. J Pharm Biomed Anal 2006; 41:527-32. [PMID: 16406451 DOI: 10.1016/j.jpba.2005.11.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 11/09/2005] [Accepted: 11/17/2005] [Indexed: 11/19/2022]
Abstract
An isocratic high-performance liquid chromatographic method with detection at 234 nm was developed, optimized and validated for the determination of testosterone in human serum. Propylparaben was used as internal standard. A Hypersil BDS RP-C18 column (150 mmx4.6 mm, 5 microm), was equilibrated with a mobile phase composed of acetonitrile and water (35:65, v/v) and having a flow rate of 1 ml/min. The elution time for testosterone and internal standard was approximately 11.6 and 9.9 min, respectively. Calibration curves of testosterone in serum were linear in the concentration range of 1-20 ng/ml. Limits of detection and quantification in serum were 0.4 and 1.1 ng/ml, respectively. Recovery was greater than 92%. Intra- and inter-day relative standard deviation for testosterone in serum was less than 2.1 and 3.9%, respectively. This method was applied to the determination of testosterone serum levels of 12 healthy males and data were correlated with data obtained using a radioimmunoassay method.
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Affiliation(s)
- V Loi
- Department of Endocrinology, Diabetes and Metabolism, Red Cross Hospital, Athens, Greece
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Vieira JGH, Nakamura OH, Noguti KO. Aplicação da Cromatografia Líquida de Alta Performance Como Método Preparativo Para a Dosagem de Esteróides Hormonais Por RIE: Dosagens de 17OH-Progesterona e Diidrotestosterona. ACTA ACUST UNITED AC 2002. [DOI: 10.1590/s0004-27302002000100013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A dosagem dos esteróides hormonais tem apresentado evolução técnica significativa, sendo os principais esteróides de interesse clínico dosados, atualmente, por métodos simples, rápidos e automatizados. Existe, no entanto, um compromisso em detrimento da exatidão, que é mais evidente na determinação de esteróides de menor concentração relativa e maior número de interferentes potenciais, como a 17-hidroxiprogesterona (17OHP), a diidrotestosterona (DHT) e outros. Nestes casos, um processo preparativo versátil e robusto é fundamental para garantir resultados com alto grau de exatidão. Apresentamos a padronização de um processo preparativo baseado em cromatografia líquida de alta performance (HPLC) comparado à cromatografia em coluna de celite para a dosagem de 17OHP e DHT. Os anticorpos empregados nos respectivos radioimunoensaios apresentam especificidade semelhante aos descritos na literatura. As amostras foram inicialmente extraídas em éter etílico e em seguida submetidas ao processo cromatográfico. Amostras de soro provenientes da rotina foram dosadas em paralelo pelos dois métodos, sendo 57 amostras para 17OHP e 84 para DHT. Não houve diferença significativa entre os resultados, e os índices de correlação foram elevados (R= 0,95 e 0,97). Os resultados comprovam que a aplicação do HPLC é válida, além de ser mais reprodutível, versátil e menos operador-dependente. Sua aplicação mais ampla permitirá uma melhora de exatidão na dosagem de esteróides de baixa concentração relativa, onde os métodos mais simples resultam em valores falsamente elevados.
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Marwah A, Marwah P, Lardy H. High-performance liquid chromatographic analysis of dehydroepiandrosterone. J Chromatogr A 2001; 935:279-96. [PMID: 11762780 DOI: 10.1016/s0021-9673(01)01268-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Qualitative and quantitative analysis of dehydroepiandrosterone and its conjugates in biological matrices and establishment of their relationships with physiological functions is a very active field. This review article discusses methods of separation and quantification of dehydroepiandrosterone and its conjugates using high-performance liquid chromatographic techniques.
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Affiliation(s)
- A Marwah
- Institute for Enzyme Research, Department of Biochemistry University of Wisconsin at Madison, 53705, USA
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Wong JY, Lee EJ, Ang SB. Liquid chromatographic assay with ultraviolet detection for the study of microsomal steroid metabolism. J Pharm Biomed Anal 1991; 9:91-5. [PMID: 2043728 DOI: 10.1016/0731-7085(91)80243-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J Y Wong
- Department of Pharmacology, Faculty of Medicine, National University of Singapore
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Robards K, Towers P. Chromatography as a reference technique for the determination of clinically important steroids. Biomed Chromatogr 1990; 4:1-19. [PMID: 2178705 DOI: 10.1002/bmc.1130040102] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chromatographic methods (paper chromatography, thin layer chromatography, high performance liquid chromatography, gas chromatography and gas chromatography-mass spectrometry) for the determination of clinically important steroids in biological specimens are reviewed. The emphasis is on the use of gas chromatography, gas chromatography-mass spectrometry and high performance liquid chromatography as reference rather than routine techniques. Chromatographic methods are compared with colorimetric, fluorimetric and radioimmunoassay procedures in terms of simplicity of operation, cost and ability to analyse large numbers of specimens. The importance of correct specimen collection and storage are discussed. Sample preparation techniques for the various analytical methods are described. These include extraction of free and conjugated steroids from serum, plasma, urine and saliva by solvent partition, with polymer-based resins such as Amberlite XAD-2, DEAE-Sephadex and Sephadex resins bonded with various other function groups and, more recently, with chemically bonded reversed-phase silicas.
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Affiliation(s)
- K Robards
- School of Science and Technology, Charles Sturt University-Riverina, Wagga Wagga, Australia
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Orlowski J, Clark AF. An Isocratic Reversed-Phase High Performance Liquid Chromatographic Analysis of 5α-Reduced Androgen Metabolites Formed by Rat Ventral Prostate Cells in Culture. ACTA ACUST UNITED AC 1989. [DOI: 10.1080/01483918908049536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Makin HL, Heftmann E. High-performance liquid chromatography of steroid hormones. MONOGRAPHS ON ENDOCRINOLOGY 1988; 30:183-234. [PMID: 3068525 DOI: 10.1007/978-3-642-83467-7_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although a considerable amount of work has been carried out in the last ten years in developing methods for the separation of steroids by HPLC, it is still not widespread for the reasons discussed above. There is however no doubt that further developments in HPLC technology, in increasing sensitivity and/or specificity of detection systems, perhaps with microbore columns, may lead to an increase in the use of this powerful analytical procedure as an additional separation method to improve specificity of assay. Solution of the problem of simple interfacing of HPLC systems with mass spectrometers (discussed in another chapter by Games) should further increase the application of HPLC. HPLC is of particular value in providing a means of separating unstable compounds prior to assay by relatively nonspecific quantitation methods. Most steroids do not fall into this category, but the steroid vitamin D and its metabolites do and HPLC has proved in this area to be invaluable (see chapter by Jones & DeLuca). There are a multiplicity of different HPLC systems for the separation of steroids, varying in column type (and manufacturer), solvent composition and method of elution, temperature of elution, etc., and only a few attempts have been made to rationalise these data. It would therefore seem that a fruitful area of future study would be the investigation of computerised systems for the selection and optimisation of HPLC systems for particular steroid separations.
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