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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [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: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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David A, Deepa Arul Priya J, Gautam A. DNA Sequencing Technologies and DNA Barcoding. Methods Mol Biol 2024; 2744:139-154. [PMID: 38683316 DOI: 10.1007/978-1-0716-3581-0_8] [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: 05/01/2024]
Abstract
DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.
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Affiliation(s)
- Anisha David
- Department of Botany, School of Life Sciences, St Joseph's University, Bengaluru, India
| | | | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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Povkhova LV, Pushkova EN, Rozhmina TA, Zhuchenko AA, Frykin RI, Novakovskiy RO, Dvorianinova EM, Gryzunov AA, Borkhert EV, Sigova EA, Vladimirov GN, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA, Melnikova NV. Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil. PLANTS (BASEL, SWITZERLAND) 2022; 12:95. [PMID: 36616223 PMCID: PMC9824437 DOI: 10.3390/plants12010095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Roman I. Frykin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Aleksey A. Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry—Branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 127422 Moscow, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | | | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Akhmetshina AO, Strygina KV, Khlestkina EK, Porokhovinova EA, Brutch NB. High-throughput sequencing techniques to flax genetics and breeding. ECOLOGICAL GENETICS 2020. [PMID: 0 DOI: 10.17816/ecogen16126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatissimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.
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Bolsheva NL, Melnikova NV, Kirov IV, Dmitriev AA, Krasnov GS, Amosova АV, Samatadze TE, Yurkevich OY, Zoshchuk SA, Kudryavtseva AV, Muravenko OV. Characterization of repeated DNA sequences in genomes of blue-flowered flax. BMC Evol Biol 2019; 19:49. [PMID: 30813893 PMCID: PMC6391757 DOI: 10.1186/s12862-019-1375-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Members of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Since such variability is determined mainly by the amount and composition of repeated sequences, we conducted a comparative study of the repeatomes of species from four sections forming a clade of blue-flowered flax. Based on the results of high-throughput genome sequencing performed in this study as well as available WGS data, bioinformatic analyses of repeated sequences from 12 flax samples were carried out using a graph-based clustering method. RESULTS It was found that the genomes of closely related species, which have a similar karyotype structure, are also similar in the repeatome composition. In contrast, the repeatomes of karyologically distinct species differed significantly, and no similar tandem-organized repeats have been identified in their genomes. At the same time, many common mobile element families have been identified in genomes of all species, among them, Athila Ty3/gypsy LTR retrotransposon was the most abundant. The 30-chromosome members of the sect. Linum (including the cultivated species L. usitatissimum) differed significantly from other studied species by a great number of satellite DNA families as well as their relative content in genomes. CONCLUSIONS The evolution of studied flax species was accompanied by waves of amplification of satellite DNAs and LTR retrotransposons. The observed inverse correlation between the total contents of dispersed repeats and satellite DNAs allowed to suggest a relationship between both classes of repeating sequences. Significant interspecific differences in satellite DNA sets indicated a high rate of evolution of this genomic fraction. The phylogenetic relationships between the investigated flax species, obtained by comparison of the repeatomes, agreed with the results of previous molecular phylogenetic studies.
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Affiliation(s)
- Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Аlexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Bolsheva NL, Melnikova NV, Kirov IV, Speranskaya AS, Krinitsina AA, Dmitriev AA, Belenikin MS, Krasnov GS, Lakunina VA, Snezhkina AV, Rozhmina TA, Samatadze TE, Yurkevich OY, Zoshchuk SA, Amosova АV, Kudryavtseva AV, Muravenko OV. Evolution of blue-flowered species of genus Linum based on high-throughput sequencing of ribosomal RNA genes. BMC Evol Biol 2017; 17:253. [PMID: 29297314 PMCID: PMC5751768 DOI: 10.1186/s12862-017-1105-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The species relationships within the genus Linum have already been studied several times by means of different molecular and phylogenetic approaches. Nevertheless, a number of ambiguities in phylogeny of Linum still remain unresolved. In particular, the species relationships within the sections Stellerolinum and Dasylinum need further clarification. Also, the question of independence of the species of the section Adenolinum still remains unanswered. Moreover, the relationships of L. narbonense and other species of the section Linum require further clarification. Additionally, the origin of tetraploid species of the section Linum (2n = 30) including the cultivated species L. usitatissimum has not been explored. The present study examines the phylogeny of blue-flowered species of Linum by comparisons of 5S rRNA gene sequences as well as ITS1 and ITS2 sequences of 35S rRNA genes. RESULTS High-throughput sequencing has been used for analysis of multicopy rRNA gene families. In addition to the molecular phylogenetic analysis, the number and chromosomal localization of 5S and 35S rDNA sites has been determined by FISH. Our findings confirm that L. stelleroides forms a basal branch from the clade of blue-flowered flaxes which is independent of the branch formed by species of the sect. Dasylinum. The current molecular phylogenetic approaches, the cytogenetic analysis as well as different genomic DNA fingerprinting methods applied previously did not discriminate certain species within the sect. Adenolinum. The allotetraploid cultivated species L. usitatissimum and its wild ancestor L. angustifolium (2n = 30) could originate either as the result of hybridization of two diploid species (2n = 16) related to the modern L. gandiflorum and L. decumbens, or hybridization of a diploid species (2n = 16) and a diploid ancestor of modern L. narbonense (2n = 14). CONCLUSIONS High-throughput sequencing of multicopy rRNA gene families allowed us to make several adjustments to the phylogeny of blue-flowered flax species and also reveal intra- and interspecific divergence of the rRNA gene sequences.
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Affiliation(s)
- Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maxim S Belenikin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina A Lakunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana A Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,All-Russian Research Institute for Flax, Torzhok, Russia
| | - Tatiana E Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Yu Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Аlexandra V Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Kringel D, Ultsch A, Zimmermann M, Jansen JP, Ilias W, Freynhagen R, Griessinger N, Kopf A, Stein C, Doehring A, Resch E, Lötsch J. Emergent biomarker derived from next-generation sequencing to identify pain patients requiring uncommonly high opioid doses. THE PHARMACOGENOMICS JOURNAL 2017; 17:419-426. [PMID: 27139154 PMCID: PMC5637232 DOI: 10.1038/tpj.2016.28] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/05/2015] [Accepted: 11/13/2015] [Indexed: 12/14/2022]
Abstract
Next-generation sequencing (NGS) provides unrestricted access to the genome, but it produces 'big data' exceeding in amount and complexity the classical analytical approaches. We introduce a bioinformatics-based classifying biomarker that uses emergent properties in genetics to separate pain patients requiring extremely high opioid doses from controls. Following precisely calculated selection of the 34 most informative markers in the OPRM1, OPRK1, OPRD1 and SIGMAR1 genes, pattern of genotypes belonging to either patient group could be derived using a k-nearest neighbor (kNN) classifier that provided a diagnostic accuracy of 80.6±4%. This outperformed alternative classifiers such as reportedly functional opioid receptor gene variants or complex biomarkers obtained via multiple regression or decision tree analysis. The accumulation of several genetic variants with only minor functional influences may result in a qualitative consequence affecting complex phenotypes, pointing at emergent properties in genetics.
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MESH Headings
- Analgesics, Opioid/administration & dosage
- Analgesics, Opioid/therapeutic use
- Biomarkers, Pharmacological/analysis
- Chronic Pain/drug therapy
- Chronic Pain/genetics
- Dose-Response Relationship, Drug
- Genotype
- High-Throughput Nucleotide Sequencing
- Humans
- Pharmacogenomic Testing
- Pharmacogenomic Variants
- Receptors, Opioid/genetics
- Receptors, Opioid, delta/genetics
- Receptors, Opioid, kappa/genetics
- Receptors, Opioid, mu/genetics
- Receptors, sigma/genetics
- Sigma-1 Receptor
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Affiliation(s)
- D Kringel
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany
| | - A Ultsch
- DataBionics Research Group, University of Marburg, Marburg, Germany
| | - M Zimmermann
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | | | - W Ilias
- Department of Anaesthesiology and Intensive Care Medicine, Vienna, Austria
| | - R Freynhagen
- Zentrum für Anästhesiologie, Intensivmedizin, Schmerztherapie & Palliativmedizin, Benedictus Krankenhaus Tutzing, Tutzing, Germany
- Klinik für Anästhesiologie, Technische Universität München, München, Germany
| | - N Griessinger
- Department of Anesthesiology, University Hospital Erlangen, Erlangen, Germany
| | - A Kopf
- Department of Anesthesiology and Critical Care Medicine, Freie Universität Berlin–Charité, Berlin, Germany
| | - C Stein
- Department of Anesthesiology and Critical Care Medicine, Freie Universität Berlin–Charité, Berlin, Germany
| | - A Doehring
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany
| | - E Resch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - J Lötsch
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
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Fofana B, Ghose K, Somalraju A, McCallum J, Main D, Deyholos MK, Rowland GG, Cloutier S. Induced Mutagenesis in UGT74S1 Gene Leads to Stable New Flax Lines with Altered Secoisolariciresinol Diglucoside (SDG) Profiles. FRONTIERS IN PLANT SCIENCE 2017; 8:1638. [PMID: 28983308 PMCID: PMC5613138 DOI: 10.3389/fpls.2017.01638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
Flax secoisolariciresinol (SECO) diglucoside (SDG) lignan is an emerging natural product purported to prevent chronic diseases in humans. SECO, the aglycone form of SDG, has shown higher intestinal cell absorption but it is not accumulated naturally in planta. Recently, we have identified and characterized a UDP-glucosyltransferase gene, UGT74S1, that glucosylates SECO into its monoglucoside (SMG) and SDG forms when expressed in yeast. However, whether this gene is unique in controlling SECO glucosylation into SDG in planta is unclear. Here, we report on the use of UGT74S1 in reverse and forward genetics to characterize an ethyl methane sulfonate (EMS) mutagenized flax population from cultivar CDC Bethune and consisting of 1996 M2 families. EMS mutagenesis generated 73 SNP variants causing 79 mutational events in the UGT74S1 exonic regions of 93 M2 families. The mutation frequency in the exonic regions was determined to be one per 28 Kb. Of these mutations, 13 homozygous missense mutations and two homozygous nonsense mutations were observed and all were transmitted into the M3 and M4 generations. Forward genetics screening of the population showed homozygous nonsense mutants completely lacking SDG biosynthesis while the production of SMG was observed only in a subset of the M4 lines. Heterozygous or homozygous M4 missense mutants displayed a wide range of SDG levels, some being greater than those of CDC Bethune. No additional deleterious mutations were detected in these mutant lines using a panel of 10 other genes potentially involved in the lignan biosynthesis. This study provides further evidence that UGT74S1 is unique in controlling SDG formation from SECO and this is the first report of non-transgenic flax germplasm with simultaneous knockout of SDG and presence of SMG in planta.
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Affiliation(s)
- Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food CanadaCharlottetown, PE, Canada
| | - Kaushik Ghose
- Charlottetown Research and Development Centre, Agriculture and Agri-Food CanadaCharlottetown, PE, Canada
| | - Ashok Somalraju
- Charlottetown Research and Development Centre, Agriculture and Agri-Food CanadaCharlottetown, PE, Canada
| | - Jason McCallum
- Charlottetown Research and Development Centre, Agriculture and Agri-Food CanadaCharlottetown, PE, Canada
| | - David Main
- Charlottetown Research and Development Centre, Agriculture and Agri-Food CanadaCharlottetown, PE, Canada
| | | | - Gordon G. Rowland
- Department of Plant Science, Crop Development Centre, University of SaskatchewanSaskatoon, SK, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food CanadaOttawa, ON, Canada
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Ohnami S, Nagashima T, Urakami K, Shimoda Y, Kamada F, Saito J, Naruoka A, Serizawa M, Masuda Y, Ohnami S, Kusuhara M, Yamaguchi K. Whole exome sequencing detects variants of genes that mediate response to anticancer drugs. J Toxicol Sci 2017; 42:137-144. [PMID: 28321040 DOI: 10.2131/jts.42.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Certain interindividual differences affecting the efficacy of drug treatment and adverse drug reactions are caused by genetic variants, and their phenotypic effects differ among ethnic groups. In this study, we used whole exome sequencing (WES) systematically to identify germline mutations that influence the activities of drug-metabolizing enzymes, as well as that of a transporter. We analyzed DNA isolated from blood samples from 2,042 Japanese patients with diverse cancers. We identified sequence variants of CYP2B6 (rs3745274), CYP2C9 (rs1057910), CYP2C19 (rs4986893), CYP2C19 (rs4244285), TPMT (rs1142345), NAT2 (rs1799930), NAT2 (rs1799931), UGT1A1 (rs4148323), COMT (rs4680), ABCB1 (rs1045642), and CDA (rs60369023). Wider application of WES will help to determine the effects of mutations on the activities of proteins encoded by drug response genes, and the information gained will accelerate the development of personalized therapies for patients with cancer. Moreover, this knowledge may provide clues for preventing cancer before the onset of symptoms.
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Affiliation(s)
- Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute
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10
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Li W, Guo H, Wang Y, Xie Y, Zhao L, Gu J, Zhao S, Zhao B, Wang G, Liu L. Identification of novel alleles induced by EMS-mutagenesis in key genes of kernel hardness and starch biosynthesis in wheat by TILLING. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0504-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Dmitriev AA, Krasnov GS, Rozhmina TA, Kishlyan NV, Zyablitsin AV, Sadritdinova AF, Snezhkina AV, Fedorova MS, Yurkevich OY, Muravenko OV, Bolsheva NL, Kudryavtseva AV, Melnikova NV. Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax. FRONTIERS IN PLANT SCIENCE 2016; 7:1920. [PMID: 28066475 PMCID: PMC5174120 DOI: 10.3389/fpls.2016.01920] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/02/2016] [Indexed: 05/19/2023]
Abstract
About 30% of the world's ice-free land area is occupied by acid soils. In soils with pH below 5, aluminum (Al) releases to the soil solution, and becomes highly toxic for plants. Therefore, breeding of varieties that are resistant to Al is needed. Flax (Linum usitatissimum L.) is grown worldwide for fiber and seed production. Al toxicity in acid soils is a serious problem for flax cultivation. However, very little is known about mechanisms of flax resistance to Al and the genetics of this resistance. In the present work, we sequenced 16 transcriptomes of flax cultivars resistant (Hermes and TMP1919) and sensitive (Lira and Orshanskiy) to Al, which were exposed to control conditions and aluminum treatment for 4, 12, and 24 h. In total, 44.9-63.3 million paired-end 100-nucleotide reads were generated for each sequencing library. Based on the obtained high-throughput sequencing data, genes with differential expression under aluminum exposure were revealed in flax. The majority of the top 50 up-regulated genes were involved in transmembrane transport and transporter activity in both the Al-resistant and Al-sensitive cultivars. However, genes encoding proteins with glutathione transferase and UDP-glycosyltransferase activity were in the top 50 up-regulated genes only in the flax cultivars resistant to aluminum. For qPCR analysis in extended sampling, two UDP-glycosyltransferases (UGTs), and three glutathione S-transferases (GSTs) were selected. The general trend of alterations in the expression of the examined genes was the up-regulation under Al stress, especially after 4 h of Al exposure. Moreover, in the flax cultivars resistant to aluminum, the increase in expression was more pronounced than that in the sensitive cultivars. We speculate that the defense against the Al toxicity via GST antioxidant activity is the probable mechanism of the response of flax plants to aluminum stress. We also suggest that UGTs could be involved in cell wall modification and protection from reactive oxygen species (ROS) in response to Al stress in L. usitatissimum. Thus, GSTs and UGTs, probably, play an important role in the response of flax to Al via detoxification of ROS and cell wall modification.
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Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
- All-Russian Research Institute for FlaxTorzhok, Russia
| | | | | | - Asiya F. Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | | | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga Y. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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Cunha KS, Oliveira NS, Fausto AK, de Souza CC, Gros A, Bandres T, Idrissi Y, Merlio JP, de Moura Neto RS, Silva R, Geller M, Cappellen D. Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene. Genes (Basel) 2016; 7:genes7120133. [PMID: 27999334 PMCID: PMC5192509 DOI: 10.3390/genes7120133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
Neurofibromatosis 1 (NF1) is one of the most common genetic disorders and is caused by mutations in the NF1 gene. NF1 gene mutational analysis presents a considerable challenge because of its large size, existence of highly homologous pseudogenes located throughout the human genome, absence of mutational hotspots, and diversity of mutations types, including deep intronic splicing mutations. We aimed to evaluate the use of hybridization capture-based next-generation sequencing to screen coding and noncoding NF1 regions. Hybridization capture-based next-generation sequencing, with genomic DNA as starting material, was used to sequence the whole NF1 gene (exons and introns) from 11 unrelated individuals and 1 relative, who all had NF1. All of them met the NF1 clinical diagnostic criteria. We showed a mutation detection rate of 91% (10 out of 11). We identified eight recurrent and two novel mutations, which were all confirmed by Sanger methodology. In the Sanger sequencing confirmation, we also included another three relatives with NF1. Splicing alterations accounted for 50% of the mutations. One of them was caused by a deep intronic mutation (c.1260 + 1604A > G). Frameshift truncation and missense mutations corresponded to 30% and 20% of the pathogenic variants, respectively. In conclusion, we show the use of a simple and fast approach to screen, at once, the entire NF1 gene (exons and introns) for different types of pathogenic variations, including the deep intronic splicing mutations.
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Affiliation(s)
- Karin Soares Cunha
- Graduate Program in Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
- Department of Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
- Neurofibromatosis National Center (Centro Nacional de Neurofibromatose), Rio de Janeiro 20011-330, Brazil.
| | - Nathalia Silva Oliveira
- Anatomy Pathology Service, Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
| | - Anna Karoline Fausto
- Anatomy Pathology Service, Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
| | | | - Audrey Gros
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
| | - Thomas Bandres
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
| | - Yamina Idrissi
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
| | - Jean-Philippe Merlio
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
| | | | - Rosane Silva
- Carlos Chagas Filho Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Mauro Geller
- Department of Immunology and Microbiology, School of Medicine, Centro Universitário Serra dos Órgãos, Teresópolis 25964-004, Brazil.
- Martagão Gesteira Child Care and Pediatrics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil.
| | - David Cappellen
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
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Kazemi S, Hatam I, Lanoil B. Bacterial community succession in a high-altitude subarctic glacier foreland is a three-stage process. Mol Ecol 2016; 25:5557-5567. [DOI: 10.1111/mec.13835] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 08/16/2016] [Accepted: 08/22/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Sina Kazemi
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
| | - Ido Hatam
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
| | - Brian Lanoil
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
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Krannich CT, Maletzki L, Kurowsky C, Horn R. Network Candidate Genes in Breeding for Drought Tolerant Crops. Int J Mol Sci 2015; 16:16378-400. [PMID: 26193269 PMCID: PMC4519955 DOI: 10.3390/ijms160716378] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 01/09/2023] Open
Abstract
Climate change leading to increased periods of low water availability as well as increasing demands for food in the coming years makes breeding for drought tolerant crops a high priority. Plants have developed diverse strategies and mechanisms to survive drought stress. However, most of these represent drought escape or avoidance strategies like early flowering or low stomatal conductance that are not applicable in breeding for crops with high yields under drought conditions. Even though a great deal of research is ongoing, especially in cereals, in this regard, not all mechanisms involved in drought tolerance are yet understood. The identification of candidate genes for drought tolerance that have a high potential to be used for breeding drought tolerant crops represents a challenge. Breeding for drought tolerant crops has to focus on acceptable yields under water-limited conditions and not on survival. However, as more and more knowledge about the complex networks and the cross talk during drought is available, more options are revealed. In addition, it has to be considered that conditioning a crop for drought tolerance might require the production of metabolites and might cost the plants energy and resources that cannot be used in terms of yield. Recent research indicates that yield penalty exists and efficient breeding for drought tolerant crops with acceptable yields under well-watered and drought conditions might require uncoupling yield penalty from drought tolerance.
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Affiliation(s)
- Christoph Tim Krannich
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
| | - Lisa Maletzki
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
| | - Christina Kurowsky
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
| | - Renate Horn
- Institute of Biological Sciences, Department of Plant Genetics, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany.
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