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Tolmacheva E, Bolshakova AS, Shubina J, Rogacheva MS, Ekimov AN, Podurovskaya JL, Burov AA, Rebrikov DV, Bychenko VG, Trofimov DY, Sukhikh GT. Expanding phenotype of MED13-associated syndrome presenting novel de novo missense variant in a patient with multiple congenital anomalies. BMC Med Genomics 2024; 17:130. [PMID: 38745205 PMCID: PMC11094910 DOI: 10.1186/s12920-024-01857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/29/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Whole exome sequencing allows rapid identification of causative single nucleotide variants and short insertions/deletions in children with congenital anomalies and/or intellectual disability, which aids in accurate diagnosis, prognosis, appropriate therapeutic interventions, and family counselling. Recently, de novo variants in the MED13 gene were described in patients with an intellectual developmental disorder that included global developmental delay, mild congenital heart anomalies, and hearing and vision problems in some patients. RESULTS Here we describe an infant who carried a de novo p.Pro835Ser missense variant in the MED13 gene, according to whole exome trio sequencing. He presented with congenital heart anomalies, dysmorphic features, hydrocephalic changes, hypoplastic corpus callosum, bilateral optic nerve atrophy, optic chiasm atrophy, brain stem atrophy, and overall a more severe condition compared to previously described patients. CONCLUSIONS Therefore, we propose to expand the MED13-associated phenotype to include severe complications that could end up with multiple organ failure and neonatal death.
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Affiliation(s)
- Ekaterina Tolmacheva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Anna S Bolshakova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Jekaterina Shubina
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia.
| | - Margarita S Rogacheva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Alexey N Ekimov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Julia L Podurovskaya
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Artem A Burov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Denis V Rebrikov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Vladimir G Bychenko
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Dmitry Yu Trofimov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Gennady T Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
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Kosykh AV, Ryumina II, Botkina AS, Evtushenko NA, Zhigmitova EB, Martynova AA, Gurskaya NG, Rebrikov DV. EBS in Children with De Novo Pathogenic Variants Disturbing Krt14. Int J Mol Sci 2024; 25:2989. [PMID: 38474236 DOI: 10.3390/ijms25052989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Epidermolysis bullosa simplex (EBS) is a dermatological condition marked by skin fragility and blister formation resulting from separation within the basal layer of the epidermis, which can be attributed to various genetic etiologies. This study presents three pathogenic de novo variants in young children, with clinical manifestations appearing as early as the neonatal period. The variants contribute to the EBS phenotype through two distinct mechanisms: direct keratin abnormalities due to pathogenic variants in the Krt14 gene, and indirect effects via pathogenic mutation in the KLHL24 gene, which interfere with the natural proteasome-mediated degradation pathway of KRT14. We report one severe case of EBS with mottled pigmentation arising from the Met119Thr pathogenic variant in KRT14, another case involving a pathogenic KLHL24 Met1Val variant, and a third case featuring the hot spot mutation Arg125His in KRT14, all manifesting within the first few weeks of life. This research underscores the complexity of genetic influences in EBS and highlights the importance of early genetic screening for accurate diagnosis and management.
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Affiliation(s)
- Anastasiya V Kosykh
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Irina I Ryumina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, ul Akademika Oparina, 4, Moscow 117997, Russia
| | - Alexandra S Botkina
- Department of Dermatovenereology, Russian Children's Clinical Hospital, Pirogov Russian National Research Medical University, Leninsky Prospekt, 117, k3, Moscow 119571, Russia
| | - Nadezhda A Evtushenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Elena B Zhigmitova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Aleksandra A Martynova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Nadya G Gurskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Denis V Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, ul Akademika Oparina, 4, Moscow 117997, Russia
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Buianova AA, Proskura MV, Cheranev VV, Belova VA, Shmitko AO, Pavlova AS, Vasiliadis IA, Suchalko ON, Rebrikov DV, Petrosyan EK, Korostin DO. Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study. Int J Mol Sci 2023; 24:15984. [PMID: 37958966 PMCID: PMC10647220 DOI: 10.3390/ijms242115984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
IgA nephropathy (IgAN) is an autoimmune disorder which is believed to be non-monogenic. We performed an exome-wide association study of 70 children with IgAN and 637 healthy donors. The HLA allele frequencies were compared between the patients and healthy donors from the bone marrow registry of the Pirogov University. We tested 78,020 gene markers for association and performed functional enrichment analysis and transcription factor binding preference detection. We identified 333 genetic variants, employing three inheritance models. The most significant association with the disorder was observed for rs143409664 (PRAG1) in the case of the additive and dominant models (PBONF = 1.808 × 10-15 and PBONF = 1.654 × 10-15, respectively), and for rs13028230 (UBR3) in the case of the recessive model (PBONF = 1.545 × 10-9). Enrichment analysis indicated the strongly overrepresented "immune system" and "kidney development" terms. The HLA-DQA1*01:01:01G allele (p = 0.0076; OR, 2.021 [95% CI, 1.322-3.048]) was significantly the most frequent among IgAN patients. Here, we characterized, for the first time, the genetic background of Russian IgAN patients, identifying the risk alleles typical of the population. The most important signals were detected in previously undescribed loci.
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Affiliation(s)
- Anastasiia A. Buianova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Mariia V. Proskura
- Nephrology Department, Russian Children’s Clinical Hospital, Leninsky Prospect 117, 119571 Moscow, Russia; (M.V.P.); (E.K.P.)
| | - Valery V. Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Anna O. Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Anna S. Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Iuliia A. Vasiliadis
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Oleg N. Suchalko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Edita K. Petrosyan
- Nephrology Department, Russian Children’s Clinical Hospital, Leninsky Prospect 117, 119571 Moscow, Russia; (M.V.P.); (E.K.P.)
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
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Tolmacheva ER, Shubina J, Kochetkova TO, Ushakova LV, Bokerija EL, Vasiliev GS, Mikhaylovskaya GV, Atapina EE, Zaretskaya NV, Sukhikh GT, Rebrikov DV, Trofimov DY. CAMK2D De Novo Missense Variant in Patient with Syndromic Neurodevelopmental Disorder: A Case Report. Genes (Basel) 2023; 14:1177. [PMID: 37372357 DOI: 10.3390/genes14061177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Intellectual disability with developmental delay is the most common developmental disorder. However, this diagnosis is rarely associated with congenital cardiomyopathy. In the current report, we present the case of a patient suffering from dilated cardiomyopathy and developmental delay. METHODS Neurological pathology in a newborn was diagnosed immediately after birth, and the acquisition of psychomotor skills lagged behind by 3-4 months during the first year of life. WES analysis of the proband did not reveal a causal variant, so the search was extended to trio. RESULTS Trio sequencing revealed a de novo missense variant in the CAMK2D gene (p.Arg275His), that is, according to the OMIM database and available literature, not currently associated with any specific inborn disease. The expression of Ca2+/calmodulin-dependent protein kinase II delta (CaMKIIδ) protein is known to be increased in the heart tissues from patients with dilated cardiomyopathy. The functional effect of the CaMKIIδ Arg275His mutant was recently reported; however, no specific mechanism of its pathogenicity was proposed. A structural analysis and comparison of available three-dimensional structures of CaMKIIδ confirmed the probable pathogenicity of the observed missense variant. CONCLUSIONS We suggest that the CaMKIIδ Arg275His variant is highly likely the cause of dilated cardiomyopathy and neurodevelopmental disorders.
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Affiliation(s)
- Ekaterina R Tolmacheva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Jekaterina Shubina
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Taisiya O Kochetkova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Lubov' V Ushakova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Ekaterina L Bokerija
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Grigory S Vasiliev
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Galina V Mikhaylovskaya
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Ekaterina E Atapina
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Nadezhda V Zaretskaya
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Gennady T Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Denis V Rebrikov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Dmitriy Yu Trofimov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
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5
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Kochetkova TO, Maslennikov DN, Tolmacheva ER, Shubina J, Bolshakova AS, Suvorova DI, Degtyareva AV, Orlovskaya IV, Kuznetsova MV, Rachkova AA, Sukhikh GT, Rebrikov DV, Trofimov DY. De Novo Variant in the KCNJ9 Gene as a Possible Cause of Neonatal Seizures. Genes (Basel) 2023; 14:genes14020366. [PMID: 36833293 PMCID: PMC9956824 DOI: 10.3390/genes14020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The reduction in next-generation sequencing (NGS) costs allows for using this method for newborn screening for monogenic diseases (MDs). In this report, we describe a clinical case of a newborn participating in the EXAMEN project (ClinicalTrials.gov Identifier: NCT05325749). METHODS The child presented with convulsive syndrome on the third day of life. Generalized convulsive seizures were accompanied by electroencephalographic patterns corresponding to epileptiform activity. Proband WES expanded to trio sequencing was performed. RESULTS A differential diagnosis was made between symptomatic (dysmetabolic, structural, infectious) neonatal seizures and benign neonatal seizures. There were no data in favor of the dysmetabolic, structural, or infectious nature of seizures. Molecular karyotyping and whole exome sequencing were not informative. Trio WES revealed a de novo variant in the KCNJ9 gene (1:160087612T > C, p.Phe326Ser, NM_004983), for which, according to the OMIM database, no association with the disease has been described to date. Three-dimensional modeling was used to predict the structure of the KCNJ9 protein using the known structure of its homologs. According to the predictions, Phe326Ser change possibly disrupts the hydrophobic contacts with the valine side chain. Destabilization of the neighboring structures may undermine the formation of GIRK2/GIRK3 tetramers necessary for their proper functioning. CONCLUSIONS We believe that the identified variant may be the cause of the disease in this patient but further studies, including the search for other patients with the KCNJ9 variants, are needed.
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Shagin DA, Rebrikov DV. Molecular biology applications of the red king crab duplex-specific nuclease. BRSMU 2022. [DOI: 10.24075/brsmu.2022.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Duplex-specific nuclease (DSN) from hepatopancreas of the craboid Paralithodes camtschaticus (red king crab) has a unique combination of properties. Along with thermal stability and a high optimal temperature of catalysis, this enzyme exhibits high substrate selectivity, cleaving only DNA in duplexes (DNA-DNA or DNA-RNA). Accordingly, it digests neither single strands (nor single-stranded regions) of DNA, nor RNA strands with any secondary structure. Such properties make it possible to create unique protocols based on DSN, which is also an important object of fundamental research in the field of nuclease evolution. The review considers diverse applications of the red king crab DSN in modern methods of molecular biology.
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Chaplin AV, Shcherbakova VA, Pikina AP, Sokolova SR, Korzhanova M, Belova VA, Korostin DO, Rebrikov DV, Kardonsky DA, Urban AS, Zakharzhevskaya NB, Suzina NE, Podoprigora IV, Das MS, Kholopova DO, Efimov BA. Diplocloster agilis gen. nov., sp. nov. and Diplocloster modestus sp. nov., two novel anaerobic fermentative members of Lachnospiraceae isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H2 as the end metabolic products. Strains ASD3451 and ASD5720T were motile, fermented lactose and raffinose, and weakly fermented maltose. Strain ASD4241T was non-motile and did not ferment the carbohydrates listed above but fermented starch. Strains ASD3451 and ASD5720T shared average nucleotide identity higher than 98.5 % with each other, while ASD4241T had only 88.5-89 % identity to them. Based on phylogenetic and chemotaxonomic analyses, we propose Diplocloster agilis gen. nov., sp. nov. (ASD5720T=JCM 34353T=VKM B-3497T) and Diplocloster modestus sp. nov. (ASD4241T=JCM 34351T=VKM B-3498T) within the family
Lachnospiraceae
.
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Affiliation(s)
- Andrei V. Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoria A. Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Alla P. Pikina
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofia R. Sokolova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A. Kardonsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Anatoly S. Urban
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia B. Zakharzhevskaya
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Irina V. Podoprigora
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Milana S. Das
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Daria O. Kholopova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A. Efimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
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Usman NY, Rebrikov DV. Recombinant adeno-associated viruses as a gene delivery vehicle for the use in molecular medicine. BRSMU 2021. [DOI: 10.24075/brsmu.2021.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Viral mechanisms for the delivery of genetic material are widely used in molecular medicine. Recombinant adeno-associated viruses (rAAV) represent a promising tool for in vivo gene delivery. The review considers nosological spectrum, molecular mechanisms, the choice of drug administration route depending on target structures, the choice of serotype, and the methods of active ingredient manufacturing for rAAV-mediated gene therapy.
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Affiliation(s)
- NYu Usman
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - DV Rebrikov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
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Lolomadze EA, Degtyareva AV, Rebrikov DV. The newborns Torque teno virus dynamics depending on the term, feeding type and maternal viral load. Acta Virol 2021; 65:307-312. [PMID: 34565159 DOI: 10.4149/av_2021_306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The first weeks of life are extremely important for the development of the immunity-virome interaction that affects human health in adulthood. In this study we analyzed Torque teno virus (TTV) dynamics during the first weeks of life in the full-term/premature infants in relation with the maternal TTV load and the type of feeding. 152 infants aged 1-14 weeks (63 full-term and 89 premature) and 33 mother-child pairs were analyzed for the whole blood TTV load by qPCR with test sensitivity of 1000 viral copies/ml. 50 infants were retested (at 2-11 time points) for TTV dynamics data. All one-week babies (n = 71) from TTV-positive mothers were TTV-negative, consistently with the previous findings of the lack of transplacental transmission of the virus. TTV was not detectable in newborns under two weeks of age. Most infants are TTV-positive by 14 weeks of age. Whole blood TTV load does not show significant correlation with full-term/prematurity, maternal TTV load, or feeding type. Keywords: Torque teno virus; transfusion-transmitted virus; commensal virus; TTV; viral load dynamics; TORCH infections; full-term and premature babies; breastfeeding; virome.
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Lebedin Y, Lyang OV, Galstyan AG, Panteleeva AV, Belousov VV, Rebrikov DV. The importance of determining SARS-CoV-2 N-Ag serodiagnostics for the management of COVID-19 pneumonia in hospital settings. BRSMU 2021. [DOI: 10.24075/brsmu.2021.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new coronavirus infection caused by the SARS-CoV-2 virus, which appeared in December 2019, has claimed the lives of 2.5 million people in almost a year. The high contagiousness of this virus has led to its wide and rapid spread around the world. As of February 2021, the total number of cases is 111 million people; more than 4 million cases of SARS-CoV-2 infection have been registered in the Russian Federation. To successfully combat the emerging pandemic, it is necessary to quickly diagnose the disease at an early stage, which will prevent the further spread of this virus and prescribe the necessary treatment on time. The aim of the work was to evaluate the use of the SARS-CoV-2 nucleocapsid antigen (N-Ag) and respective antibodies as diagnostic markers in pneumonia patients. The study was conducted at the height of COVID-19 pandemic in Moscow, Russia. It included 425 emergency patients with clinical signs of COVID-19 pneumonia, of which 280 (66%) were positive for either serum N-Ag and/or its respective antibodies. We demonstrate the total prevalence of N-Ag seroconversion in SARS-CoV-2associated pneumonia patients within 3–5 days after hospital admission. The results indicate high feasibility of SARS-CoV-2 serodiagnostics in emergency patients.
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Affiliation(s)
| | - OV Lyang
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - AG Galstyan
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | | | - VV Belousov
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - DV Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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Averina OV, Kovtun AS, Polyakova SI, Savilova AM, Rebrikov DV, Danilenko VN. The bacterial neurometabolic signature of the gut microbiota of young children with autism spectrum disorders. J Med Microbiol 2020; 69:558-571. [DOI: 10.1099/jmm.0.001178] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. The human gut microbiota is currently seen as an important factor that can promote autism spectrum disorder (ASD) development in children.
Aim. This study aimed to detect differences in the taxonomic composition and content of bacterial genes encoding key enzymes involved in the metabolism of neuroactive biomarker compounds in the metagenomes of gut microbiota of children with ASD and neurotypical children.
Methodology. A whole metagenome sequencing approach was used to obtain metagenomic data on faecal specimens of 36 children with ASD and 21 healthy neurotypical children of 3–5 years old. Taxonomic analysis was conducted using MetaPhlAn2. The developed bioinformatics algorithm and created catalogue of the orthologues were applied to identify bacterial genes of neuroactive compounds in the metagenomes. For the identification of metagenomic signatures of children with ASD, Wilcoxon's test and adjustment for multiple comparisons were used.
Results. Statistically significant differences with decreases in average abundance in the microbiota of ASD children were found for the genera
Barnesiella
and
Parabacteroides
and species
Alistipes putredinis
,
B. caccae
, Bacteroides intestinihominis,
Eubacterium rectale
,
Parabacteroides distasonis
and
Ruminococcus lactaris
. Average relative abundances of the detected genes and neurometabolic signature approach did not reveal many significant differences in the metagenomes of the groups that were compared. We noted decreases in the abundance of genes linked to production of GABA, melatonine and butyric acid in the ASD metagenomes.
Conclusion. For the first time, the neurometabolic signature of the gut microbiota of young children with ASD is presented. The data can help to provide a comparative assessment of the transcriptional and metabolomic activity of the identified genes.
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Affiliation(s)
- Olga V. Averina
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey S. Kovtun
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast 141701, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | | | | | - Denis V. Rebrikov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Valery N. Danilenko
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast 141701, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
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12
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Degtyareva AV, Proshlyakova TY, Gautier MS, Degtyarev DN, Kamenets EA, Baydakova GV, Rebrikov DV, Zakharova EY. Oxysterol/chitotriosidase based selective screening for Niemann-Pick type C in infantile cholestasis syndrome patients. BMC Med Genet 2019; 20:123. [PMID: 31296176 PMCID: PMC6625024 DOI: 10.1186/s12881-019-0857-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/02/2019] [Indexed: 01/11/2023]
Abstract
Background Niemann-Pick disease type C (NP-C) is an inherited neurodegenerative disease (1 per 100 000 newborns) caused by NPC proteins impairment that leads to unesterified cholesterol accumulation in late endosomal/lysosomal compartments. To date the NP-C diagnostics is usually based on cholesterol detection in fibroblasts using an invasive and time-consuming Filipin staining and we need more arguments to widely introduce oxysterols as a biomarkers in NP-C. Methods Insofar as NP-C represents about 8% of all infant cholestases, in this prospective observational study we tried to re-assess the specificity plasma oxysterol and chitotriosidase as a biochemical screening markers of NP-C in children with cholestasis syndrome of unknown origin. For 108 patients (aged from 2 weeks to 7 years) the levels of cholestane-3β,5α,6β-triol (C-triol) and chitotriosidase (ChT) were measured. For patients with elevated C-triol and/or ChT the NPC1 and NPC2 genes were Sanger-sequenced and 47 additional genes (from the custom liver damage panel) were NGS-sequenced. Results Increased C-triol level (> 50 ng/ml) was detected in 4 (of 108) infants with cholestasis syndrome of unknown origin, with following molecular genetic NP-C diagnosis for one patient. Plasma cholesterol significantly correlates with C-triol (p < 0.05). NGS of high C-triol infants identified three patients with mutations in JAG1 (Alagille syndrome) and ABCB11 (Byler disease) genes. Increased ChT activity was detected in 8 (of 108) patients with various aetiologies, including NP-C, Byler disease and biliary atresia. Conclusion Combined analysis of ChT activity and C-triol levels is an effective method for identifying NP-C.
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Affiliation(s)
- Anna V Degtyareva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia.,Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Marina S Gautier
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Dmitry N Degtyarev
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia.,Sechenov First Moscow State Medical University, Moscow, Russia
| | | | | | - Denis V Rebrikov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia.
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13
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Tsukanov KY, Krasnenko AY, Plakhina DA, Korostin DO, Churov AV, Druzhilovskaya OS, Rebrikov DV, Ilinsky VV. [A bioinformatic pipeline for NGS data analysis and mutation calling in human solid tumors]. Biomed Khim 2019; 63:413-417. [PMID: 29080873 DOI: 10.18097/pbmc20176305413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM. The effect of SNV on the protein function was estimated by SIFT and PolyPhen2. Mutation frequencies were obtained from 1000 Genomes and ExAC projects, as well as from our own databases with frequency data. In order to evaluate the pipeline we used 18 breast cancer tumor biopsies. The MYbaits Onconome KL v1.5 Panel ("MYcroarray") was used for targeted enrichment. NGS was performed on the Illumina HiSeq 2500 platform. As a result, we identified alterations in BRCA1, BRCA2, ATM, CDH1, CHEK2, TP53 genes that affected the sequence of encoded proteins. Our pipeline can be used for effective search and annotation of tumor SNVs. In this study, for the first time, we have tested this pipeline for NGS data analysis of samples from patients of the Russian population. However, further confirmation of efficiency and accuracy of the pipeline is required on NGS data from larger datasets as well as data from several types of solid tumors.
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Affiliation(s)
| | | | | | - D O Korostin
- Vavilov Institute of General Genetics, Moscow, Russia
| | - A V Churov
- Institute of Biology of Karelian Research Centre, Petrozavodsk, Russia
| | | | - D V Rebrikov
- Vavilov Institute of General Genetics, Moscow, Russia
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14
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Smirnov GP, Malyshev PP, Rozhkova TA, Zubareva MY, Shuvalova YA, Rebrikov DV, Titov VN. [The effect of ABCA1 rs2230806 common gene variant on plasma lipid levels in patients with dyslipidemia.]. Klin Lab Diagn 2019; 63:410-413. [PMID: 30720955 DOI: 10.18821/0869-2084 -2018-63-7-410-413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/01/2018] [Indexed: 11/17/2022]
Abstract
The aim of this work was to assess the relationship of rs2230806 SNP of ABCA1 with lipid profile in patients with severe dyslipidemia. The study included 363 patients (42.8% of males), the average age was 48.7 years, 35.5% of patients received hypolipidemic drugs (mainly statins). Quantitative determination of total cholesterol (ТС) and triglycerides (TG) in fasting serum was carried out by a unified enzymatic method, and high density lipoproteins (HDL) - by a direct homogeneous method. Genotype according to the rs2230806 position in the ABCA1 gene was determined by polymerase chain reaction (PCR) «in real time» using adjacent samples and melting reaction products after PCR. The frequencies of alleles and genotypes of variant rs2230806 of ABCA1 gene in patients with dyslipidemia did not differ from those in the control group of healthy individuals (athletes). The levels of plasma lipids - TC, TG and HDL cholesterol, on average, in patients with dyslipidemia were 7.8±3,4, 3,4±6,5 and 1.29±0.4 mmol/l, respectively. Compared to different genotypes, the plasma lipid concentrations did not differ significantly, but the analysis of different inheritance models of the allelic variant studied showed a significant association with the level of TG in the additive model, in which each minor allele (a) further enhanced the effect on the level of plasma TG at 1.02 mmol/l (p=0.044). The results of this study demonstrate the effect of a common variant rs2230806 of the ABCA1 gene on the plasma TG level in patients with severe dyslipidemia.
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Affiliation(s)
- G P Smirnov
- City Polyclinic № 212 of the Moscow Healthcare Department, Moscow, 119620
| | - P P Malyshev
- National Medical Research Center of Cardiology, Moscow, 121552
| | - T A Rozhkova
- National Medical Research Center of Cardiology, Moscow, 121552
| | - M Y Zubareva
- National Medical Research Center of Cardiology, Moscow, 121552
| | - Y A Shuvalova
- National Medical Research Center of Cardiology, Moscow, 121552
| | - D V Rebrikov
- Pirogov Russian National Research Medical University, Moscow, 117997.,National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997
| | - V N Titov
- National Medical Research Center of Cardiology, Moscow, 121552
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15
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Tyschik EA, Rasskazova AS, Degtyareva AV, Rebrikov DV, Sukhikh GT. Torque teno virus dynamics during the first year of life. Virol J 2018; 15:96. [PMID: 29843750 PMCID: PMC5975406 DOI: 10.1186/s12985-018-1007-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/21/2018] [Indexed: 01/03/2023] Open
Abstract
Background Torque teno virus is a small chronically persisting circular negative ssDNA virus reaching near 100% prevalence. It is reported to be a marker for immune function in immunocompromised patients. The possibility of vertical maternal-fetal transmission remains controversial but incidence rate of TTV DNA in children increased with age. TTV dynamics well studied for allogeneic hematopoietic stem cell transplantation as a predictor of post-transplant complications but there is no viral proliferation kinetics data for other patient groups or healthy individuals. The aim of this study was to determine TTV dynamics during the first year of life of healthy infants. Methods Ninety eight clinically healthy breastfeeding infants (1–12 months of age) were analyzed by quantitative PCR for the whole blood TTV load with the test sensitivity of about 1000 viral copies per milliliter of blood (total number of samples including repeatedly tested infants was 109). Results 67% of all analyzed samples were TTV-positive demonstrating significant positive correlation between age and TTV load (r = 0.81, p < 0.01). Conclusions This is the first study to suggest that viral load increases during the first year of life reaching a plateau after 6 months with strong proliferation for the first 60 days. Our data well correlates with TTV dynamics in patients following allogeneic hematopoietic stem cell transplantation.
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Affiliation(s)
- Elena A Tyschik
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Oparina 4, Moscow, 117513, Russia
| | - Anastasiya S Rasskazova
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, 117997, Russia
| | - Anna V Degtyareva
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Oparina 4, Moscow, 117513, Russia
| | - Denis V Rebrikov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Oparina 4, Moscow, 117513, Russia. .,Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, 117997, Russia.
| | - Gennady T Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Oparina 4, Moscow, 117513, Russia
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16
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Komech EA, Pogorelyy MV, Egorov ES, Britanova OV, Rebrikov DV, Bochkova AG, Shmidt EI, Shostak NA, Shugay M, Lukyanov S, Mamedov IZ, Lebedev YB, Chudakov DM, Zvyagin IV. CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. Rheumatology (Oxford) 2018; 57:1097-1104. [DOI: 10.1093/rheumatology/kex517] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- Ekaterina A Komech
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail V Pogorelyy
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Evgeniy S Egorov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga V Britanova
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Denis V Rebrikov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Gynecology and Perinatology, Kulakov Research Center for Obstetrics, Moscow, Russia
| | - Anna G Bochkova
- V.A. Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Evgeniya I Shmidt
- City Clinical Hospital #1, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadejda A Shostak
- City Clinical Hospital #1, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail Shugay
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sergey Lukyanov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z Mamedov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Gynecology and Perinatology, Kulakov Research Center for Obstetrics, Moscow, Russia
| | - Yuriy B Lebedev
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Biological Department, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy M Chudakov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Ivan V Zvyagin
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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17
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Abstract
Background TTV has been detected in almost every human tissue type or body fluid reaching near 100% prevalence. Several studies report mother-to-child postnatal transmission of TTV in infancy but the risk of transplacental transmission of TTV is still unclear. Methods The blood and plasma collected postpartum from 100 mother-child pairs were analyzed using TTV-specific qPCR. Samples were collected from the peripheral vein of the mother and the umbilical cord. Results Eighty four percent of pregnant women were TTV positive (median titers: 8 × 104 copies/mL; range: 103 – 3 × 107). The TTV load in plasma was approximately 100 times lower than in whole blood. TTV was not detected in any of cord blood samples. Conclusions Our data demonstrate the lack of transplacental transmission of TTV (or effective prenatal inhibition of viral proliferation). The presence of the virus in infants may be associated with mother-to-child transmission through breast feeding or other routes of transmission.
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Affiliation(s)
- Elena A Tyschik
- Kulakov Research Center for Obstetrics, Gynecology and Perinatology, 117997, Oparina 4, Moscow, Russia
| | - Sophia M Shcherbakova
- Pirogov Russian National Research Medical University, 117997, Ostrovityanova 1, Moscow, Russia
| | - Ruslan R Ibragimov
- Kulakov Research Center for Obstetrics, Gynecology and Perinatology, 117997, Oparina 4, Moscow, Russia
| | - Denis V Rebrikov
- Kulakov Research Center for Obstetrics, Gynecology and Perinatology, 117997, Oparina 4, Moscow, Russia. .,Pirogov Russian National Research Medical University, 117997, Ostrovityanova 1, Moscow, Russia.
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18
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Zorina OA, Aymadinova NK, Basovа АА, Shibaeva AV, Rebrikov DV. [Gender-related marker pathogens of periodontal disease in chronic periodontitis]. Stomatologiia (Mosk) 2016; 95:10-16. [PMID: 27367192 DOI: 10.17116/stomat201695310-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
By using qPCR system, women as well as men were found to have an equal periodontal pathogen colonization. However, the women are subjected to have a higher risk of chronic periodontitis onsets. Women with the chronic periodontitis usually expose an evident hypercolonization with a single pathogen. P. gingivalis is the most prevalent causative agent of the chronic periodontitis in women but not in men. In health as well as in the chronic periodontitis a complex of periodontal pathogens forms such as P. gingivalis, P. intermedia, T. forsythensis and T. denticola. T. forsythensis demonstrates the highest correlation with the chronic periodontitis onset in men. Our data allow us to prove T. forsythensis playing the key role in the forming of periodontal pathogen complex.
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Affiliation(s)
- O A Zorina
- Central Research Institute of Dentistry and Maxillofacial Surgery of Ministry of Health of the Russian Federation, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow
| | - N K Aymadinova
- Central Research Institute of Dentistry and Maxillofacial Surgery of Ministry of Health of the Russian Federation, Moscow, Russia
| | - А А Basovа
- Central Research Institute of Dentistry and Maxillofacial Surgery of Ministry of Health of the Russian Federation, Moscow, Russia
| | - A V Shibaeva
- Emanuel Biochemical Physics institute RAS, Moscow; Vavilov Institute of General Genetics, Moscow
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19
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Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J Immunol 2016; 196:5005-13. [PMID: 27183615 DOI: 10.4049/jimmunol.1600005] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/16/2016] [Indexed: 01/29/2023]
Abstract
The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.
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Affiliation(s)
- Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Denis V Rebrikov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; Vavilov Institute of General Genetics of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
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20
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Zorina OA, Aimadinova NK, Basova AA, Rebrikov DV. [The relationship of molecular genetic markers with clinical signs and risk factors of periodontitis]. Stomatologiia (Mosk) 2016; 95:12-18. [PMID: 27876716 DOI: 10.17116/stomat201695512-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The study revealed positive correlation between bleeding on probing and teeth loss risk with periodontal hypercolonization by Porphyromonas gingivalis, Prevotella intermedia and Treponema denticola. Pathological tooth mobility was associated with hypercolonization by P. intermedia and Tannerella forsythensis. Expression of IL8, TNF-α, MMP8 and MMP9 genes was also assessed in patient groups divided according to the depth of periodontal pockets and-the severity of chronic periodontitis revealing IL8 as positive diagnostic marker.
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Affiliation(s)
- O A Zorina
- Sechenov First Moscow State Medical University, Moscow, Russia; Central Research Institute of Dentistry and Maxillofacial Surgery of Ministry of Health of Russian Federation, Moscow, Russia
| | - N K Aimadinova
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - A A Basova
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - D V Rebrikov
- Pirogov Russian National Research Medical University, Moscow, Russia
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21
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Shibaeva AV, Ayvazova RA, Rebrikov DV, Trubnikova EV, Kudykina YK, Belyakova AV, Zaripova RS, Shevelev AB. [USE OF THE REAL-TIME PCR FOR STUDY OF THE PERIODONTAL MICROBIOME IN PATIENTS WITH COMBINED PATHOLOGY OF GASTRODUODENAL ZONE AND CHRONIC PERIODONTITIS]. Mol Gen Mikrobiol Virusol 2016; 34:26-30. [PMID: 27183718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The total of 54 patients with chronic periodontitis of different severity was tested using real-time PCR (Dentoflor kit). The group included 38 patients with chronic gastritis. For the first time, a higher prevalence of Treponema denticola in periodontium of males in comparison with females was demonstrated. The patients with chronic gastritis had more human genome DNA at their periodontium than healthy individuals. Non-parametric statistical analysis demonstrated high association of periodontium colonization with. T. forsythensis and T. denticola (but not Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia) with the severity of the chronic periodontitis.
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Borinskaya SA, Gureev AS, Orlova AA, Sanina ED, Kim AA, Gasemianrodsari F, Shirmanov VI, Balanovsky OP, Rebrikov DV, Koshechkin AV, Yankovsky NK. [Allele frequency distributions of -174G/C polymorphism in regulatory region of interleukin 6 gene (IL6) in Russian and worldwide populations]. Genetika 2013; 49:113-124. [PMID: 23662429 DOI: 10.7868/s0016675813010037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Allele and genotype frequencies of the -174G/C polymorphism (rs1800795) in the regulatory region of the IL6 gene, which encode anti-inflammatory cytokine interleukin 6, were determined in seven populations representing five ethnic groups from the European part of Russia (440 individuals), as well as in small cohorts that represent populations from 24 countries of Africa and Eurasia (365 individuals). The maps of the geographic distribution of the -174G/C allele frequencies were constructed based on personal (22 populations) and the literature data (66 populations), and the data from dbSNP database obtained by the HapMap project (10 populations). The frequency of the -174G allele varied from 45 to 100% and was characterized by nonrandom geographic distribution. These data could reflect the adaptive load of the alleles examined, which was different in different regions of the world. It is suggested that the level of pathogen prevalence is one of the environmental factors that determine different adaptive values of the IL6*--174G/C alleles. This suggestion is supported by a positive correlation between the -174G allele frequency and level of pathogen prevalence calculated based on historical data (R = 0.768; p < 0.0001).
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Affiliation(s)
- S A Borinskaya
- Vavilov Institute of General Genetics, RAS, Moscow, Russia
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Zorina OA, Boriskina OA, Leonovich OA, Rebrikov DV. [Genetic factors of aggressive periodontitis risk(matrix proteins, matrix proteases and their regulators]. Stomatologiia (Mosk) 2013; 92:76-83. [PMID: 23814880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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24
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Zorina OA, Boriskina OA, Rebrikov DV. [Correlation of gene polymorphism and risk of aggressive periodontal disease]. Stomatologiia (Mosk) 2013; 92:28-30. [PMID: 23994852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The study included 179 patients aged 18-45 years (56 with aggressive periodontal disease and 123 with no clinical signs of periodontitis). Gene polymorphism was analyzed by means of real-time PCR and kissing probes in order to reveal marker panel for aggressive periodontal disease predisposition. Significant difference was found for gene MMP9 in rs17576 position for A allele (55.2% in aggressive periodontal disease patients and 69.5% in control group) and in rs3918242 position for C allele (67.7 and 81.7%, respectively).
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Turchaninova MA, Meshcheriakov AA, Rakhmankulova ZP, Rebrikov DV. [Characterization of circulating RNA in plasma as potential tool for breast cancer diagnostics]. Bioorg Khim 2011; 37:393-8. [PMID: 21899055 DOI: 10.1134/s1068162011030186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The representation patterns of 15 cytokines RNA in blood plasma and blood cells of patients with breast cancer and apparently healthy women were investigated. Relative levels of RNA IL-8 and IL-18 in plasma of breast cancer patients are significantly increased compared with control group. At the same time no obvious differences were found in relative concentrations of these transcripts in blood cells of patients and control groups. Relative concentration of IL-8 RNA was higher in blood plasma of locally advanced compared with early breast cancer patients.
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Zorina OA, Kulakov AA, Boriskina OA, Rebrikov DV. Relationship between the Pathogenic Representatives of Periodontal Pockets Microbiocenosis in Patients with Periodontitis with Varying Degrees of Severity. Acta Naturae 2011. [DOI: 10.32607/20758251-2011-3-2-99-102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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27
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Safonova AV, Petrin AN, Arutyunov SD, Tsarev VN, Akulenko LA, Zorina AO, Rebrikov DV, Rubanovich AV, Borinskaya SA, Yankovsky NK. Association of Cytokine Gene Alleles with the Inflammation of Human Periodontal Tissue. Acta Naturae 2011. [DOI: 10.32607/20758251-2011-3-1-116-122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Zorina OA, Kulakov AA, Boriskina OA, Rebrikov DV. [PCR "real time" to analyze the quantitative and qualitative relations microbiota of periodontal pockets]. Stomatologiia (Mosk) 2011; 90:31-33. [PMID: 21716234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The introduction of a broad medical practice PCR "real time" is just beginning and dentistry is no exception. Modern molecular genetic methods provide numerous opportunities for diagnosis, assessment and prediction in patients with inflammatory periodontal diseases. Early and accurate diagnosis can allow in the future reduce the incidence of periodontitis and the progression of its course.
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Zorina OA, Kulakov AA, Rebrikov DV. [Quantitative detection of periodontopatogenic microflora in periodontosis and healthy control]. Stomatologiia (Mosk) 2011; 90:40-42. [PMID: 21716237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mouth human populated set of microorganisms that are in dynamic equilibrium and forming microbiocaenosis. In a situation where this balance is disturbed, there is a "activation" of pathogens, including those that lead to the development of inflammatory periodontal diseases. Quantifying the relation parodontopatogenov in this material may be an important diagnostic tool, but data on the profile of individual microbiota subbiotopov mouth so far very little. In this study, we quantified the six pathogenic representatives of the periodontal pocket microbiota in health and periodontitis. Found that when disease development relationship pathogenic representatives of periodontal pocket microbiota varies considerably.
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Zvyagin IV, Dorodnykh VY, Mamedov IZ, Staroverov DB, Bochkova AG, Rebrikov DV, Lebedev YB. Association of ERAP1 Allelic Variants with Risk of Ankylosing Spondylitis. Acta Naturae 2010. [DOI: 10.32607/20758251-2010-2-3-72-77] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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Vasilyev EV, Trofimov DY, Tonevitsky AG, Ilinsky VV, Korostin DO, Rebrikov DV. Torque Teno Virus (TTV) distribution in healthy Russian population. Virol J 2009; 6:134. [PMID: 19735552 PMCID: PMC2745379 DOI: 10.1186/1743-422x-6-134] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 09/07/2009] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Torque teno virus (TTV) is a circular, single-stranded DNA virus that chronically infects healthy individuals of all ages worldwide. There is a lot of data on the prevalence and genetic heterogeneity of TTV in healthy populations and in patients with various diseases now available. However, little is known about TTV load among healthy human population. In this study we analyzed TTV load in the group of 512 Russian elite athletes, who are supposed to be, by some standards, the healthiest part of the human population. RESULTS The prevalence rate of TTV among the Russian Olympic Reserve members was 94% (for test sensitivity about 1000 genome equivalents per 1 ml of blood). Quantities varied from 103 (which corresponded to detection limit) to 1010 copies per 1 ml of blood, with median at 2.7 x 106 copies. CONCLUSION About 94% of healthy individuals in Russian population have more than 1000 TTV genome copies per 1 ml of blood. This result exceeds the previously published data, and can be explained by either more sensitive PCR test system or by higher TTV distribution in Russian population or both. TTV viral load neither depends on gender, nor age.
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Affiliation(s)
- Evgeny V Vasilyev
- DNA-Technology JSC, Kashirskoe shosse, 23-5-16, Moscow, 115478, Russia.
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32
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Turchaninova MA, Rebrikov DV. [Profile of RNA cytokines in blood plasma under conditions of normal physiological state of human body]. Mol Gen Mikrobiol Virusol 2009:22-24. [PMID: 19517806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The level of representation of extracellular RNA 14 cytokines in blood plasma in a group of apparently healthy subjects was analyzed. The level of representation of the transcripts of these cytokines in extracellular medium is characterized by specific profile different from the profile of expression of the genes in blood cells.
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Komarov AL, Shakhmatova OO, Stambol'skiĭ DV, Rebrikov DV, Kofiadi IA, Sirotkina OV, Panchenko EP. [Risk factors of thrombotic complications and prognosis of patients with chronic form of ischemic heart disease]. Kardiologiia 2009; 49:4-10. [PMID: 20001975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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34
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Trofimov DY, Rebrikov DV, Samatov GA, Semenov PA, Baluev AB, Goncharova EV, Alexeev LP, Khaitov RM. The delta-TF method for real-time PCR data standardization. Dokl Biol Sci 2008; 419:118-21. [PMID: 18536278 DOI: 10.1134/s0012496608020142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- D Yu Trofimov
- DNA-Technology, JSC, Kashirskoe shosse 23/5, Moscow, 115478, Russia
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Rebrikov DV. Identification of differential genes by suppression subtractive hybridization: I. Preparation of subtracted cDNA or genomic DNA library. Cold Spring Harb Protoc 2008; 2008:pdb.prot4855. [PMID: 21356860 DOI: 10.1101/pdb.prot4855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes the preparation of a subtracted cDNA or genomic DNA library, and includes methods for cDNA synthesis, tester and driver DNA digestion, and adapter ligation.
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36
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Rebrikov DV. Identification of Differential Genes by Suppression Subtractive Hybridization: V. PCR-Based DNA Dot Blot. Cold Spring Harb Protoc 2008; 2008:pdb.prot4859. [PMID: 21356864 DOI: 10.1101/pdb.prot4859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes a method for the use of PCR-based DNA dot blots in the differential screening of arrayed subtracted DNA clones. For high-throughput screening, a 96-well or 384-well format PCR from one of several thermal cycler manufacturers is recommended. Alternatively, single tubes can be used.
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37
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Rebrikov DV. Identification of Differential Genes by Suppression Subtractive Hybridization: IV. Mirror Orientation Selection (MOS). Cold Spring Harb Protoc 2008; 2008:pdb.prot4858. [PMID: 21356863 DOI: 10.1101/pdb.prot4858] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. The major drawback of SSH is the presence of background clones that represent nondifferentially expressed DNA species in the subtracted libraries. In some cases, the number of background clones may considerably exceed the number of target clones. This protocol describes mirror orientation selection (MOS)--a simple procedure that substantially decreases the number of background clones in libraries generated by SSH. The MOS technique is based on the rationale that after PCR amplification, during SSH, background molecules will be present in one orientation only, relative to the adapter sequences. Genuine SSH clones will be present in both sequence orientations.
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38
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Rebrikov DV. Identification of Differential Genes by Suppression Subtractive Hybridization: VI. Differential Hybridization with Tester and Driver DNA Probes. Cold Spring Harb Protoc 2008; 2008:pdb.prot4860. [PMID: 21356865 DOI: 10.1101/pdb.prot4860] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes a method for screening a subtracted cDNA library by differential hybridization using (1) a tester-specific subtracted probe (forward-subtracted probe), (2) a driver-specific subtracted probe (reverse-subtracted probe), (3) a cDNA probe synthesized directly from tester mRNA (or tester genomic DNA), and (4) a cDNA probe synthesized directly from driver mRNA (or driver genomic DNA).
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39
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Rebrikov DV. Identification of differential genes by suppression subtractive hybridization: an overview. Cold Spring Harb Protoc 2008; 2008:pdb.top21. [PMID: 21356875 DOI: 10.1101/pdb.top21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. We have used SSH in studies of regeneration and development on various types of model organisms (including freshwater planaria regeneration, Xenopus laevis development, and mammalian brain cortex development). We also use SSH for the analysis of strain-specific genes in bacteria with different characteristics. During these studies, a large number of differentially regulated and differentially presented genes have been identified, including transcriptional regulation factors and restriction modification enzymes. This article describes the SSH method and considerations for its use.
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40
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Rebrikov DV. Identification of Differential Genes by Suppression Subtractive Hybridization: II. Subtractive Hybridization. Cold Spring Harb Protoc 2008; 2008:pdb.prot4856. [PMID: 21356861 DOI: 10.1101/pdb.prot4856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. This protocol describes a method for subtractive hybridization using adapter-ligated tester and RsaI-digested driver DNA samples.
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41
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Rebrikov DV. Identification of Differential Genes by Suppression Subtractive Hybridization: III. PCR Amplification of Differentially Presented DNAs. Cold Spring Harb Protoc 2008; 2008:pdb.prot4857. [PMID: 21356862 DOI: 10.1101/pdb.prot4857] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTIONSuppression subtractive hybridization (SSH) is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. This technique can be used to compare two mRNA populations and obtain cDNAs representing genes that are either overexpressed or exclusively expressed in one population as compared to another. It can also be used for comparison of genomic DNA populations. In this protocol, differentially presented DNAs are selectively amplified using PCR. It is strongly recommended that subtractions be performed in both directions for each tester/driver DNA pair. Forward subtraction is designed to enrich for differentially presented molecules present in the tester but not in the driver; reverse subtraction is designed to enrich for differentially presented sequences present in the driver but not in the tester. Therefore, each experiment should have at least four reactions: (1) subtracted tester DNAs, (2) unsubtracted tester control, (3) reverse-subtracted tester DNAs, and (4) unsubtracted control for the reverse subtraction.
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42
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Stakhov VL, Gubin SV, Maksimovich SV, Rebrikov DV, Savilova AM, Kochkina GA, Ozerskaia SM, Ivanushkina NE, Vorob'eva EA. [Microbial communities of ancient seeds derived from permanently frozen Pleistocene deposits]. Mikrobiologiia 2008; 77:396-403. [PMID: 18683658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microbial communities from the surface of ancient seeds of higher plants and embedding frozen material dated to the late Pleistocene (formed about 30 thousand years ago) were studied by various methods: scanning electron microscopy, epifluorescence microscopy, and inoculation of nutrient media, followed by identification of isolated cultures. Both prokaryotic and eukaryotic microorganisms were found on the surface of ancient seeds. The total quantity of bacterial cells determined by direct counting and dilution plating (CFU) for the samples of ancient seeds exceeded the value in the embedding frozen material by one to two orders of magnitude. This pattern was not maintained for mycelial fungi; their quantity in the embedding material was also rather high. A significant difference was revealed between the microbial communities of ancient seeds and embedding frozen material. These findings suggest that ancient plant seeds are a particular ecological niche for microorganisms existing in permafrost and require individual detailed study.
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Anisimova VE, Shcheglov AS, Bogdanova EA, Rebrikov DV, Nekrasov AN, Barsova EV, Shagin DA, Lukyanov SA. Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases? Gene 2008; 418:41-8. [PMID: 18514436 DOI: 10.1016/j.gene.2008.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 03/03/2008] [Accepted: 04/06/2008] [Indexed: 11/24/2022]
Abstract
Kamchatka crab duplex-specific nuclease (Par_DSN) has been classified as a member of the family of DNA/RNA non-specific beta-beta-alpha metal finger (bba-Me-finger) nucleases, the archetype of which is the nuclease from Serratia marcescens. Although the enzyme under investigation seems to belong to the family of S. marcescens nucleases, Par_DSN exhibits a marked preference for double-stranded DNA as a substrate and this property is unusual for other members of this family. We have searched other Arthropod species and identified a number of novel Par_DSN homologs. A phylogenetic analysis demonstrates that the Par_DSN-like enzymes constitute a separate branch in the evolutionary tree of bba-Me-finger nucleases. Combining sequence analysis and site-directed mutagenesis, we found that Par_DSN and its homologs possess the nuclease domain that is slightly longer than that of classic Serratia relatives. The active site composition of Par_DSN is similar but not identical to that of classic Serratia nucleases. Based on these findings, we proposed a new classification of Par_DSN-like nucleases.
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Affiliation(s)
- Veronika E Anisimova
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117871 Moscow, Russia
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Kofiadi IA, Rebrikov DV, Trofimov DY, Alexeev LP, Khaitov RM. Allelic distribution of the CCR5, CCR2, and SDF1 gene polymorphisms associated with HIV-1/AIDS resistance in Russian populations. Dokl Biol Sci 2007; 415:320-323. [PMID: 17929678 DOI: 10.1134/s0012496607040217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- I A Kofiadi
- State Research Center Institute of Immunology, Kashirskoe sh. 24, korp. 2, Moscow, 115478 Russia
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45
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Rebrikov DV, Rebrikov DN, Stepanova EV, Koroleva OV, Budarina ZI, Zakharova MV, Iurkova TV, Solonin AS, Belova OV, Pozhidaeva ZA, Leont'evskiĭ AA. [Laccase of the lignolytic fungus Trametes hirsuta: purification and characterization of the enzyme, and cloning and primary structure of the gene]. Prikl Biokhim Mikrobiol 2006; 42:645-53. [PMID: 17168293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The main physicochemical characteristics of the major isoform of the laccase secreted by the fungu, Trametes hirsuta 072 were studied. The enzyme belongs to the group of high redox potential laccases (E(T1) = 790 +/- 5), and it oxidizes with high efficiency various substrates of phenolic nature. The gene of this isoform was cloned, and its nucleotide sequence was determined. The length of the complete gene is 2134 bp. It comprises 11 exons and 10 introns. Analysis of the amino acid sequence of T. hirsuta 072 laccase demonstrated a high homology (to 96.9%) to the other laccases secreted by fungi of the genus Trametes.
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46
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Borinskaia SA, Rebrikov DV, Nefedova VV, Kofiadi IA, Sokolova MV, Kolchina EV, Kulikova EA, Chernyshov VN, Kutsev SI, Polonikov AV, Ivanov VP, Kozlov AI, Iankovskiĭ NK. [Molecular diagnosis and frequencies of primary hypolactasia in populations of RUSSIA and neighboring countries]. Mol Biol (Mosk) 2006; 40:1031-6. [PMID: 17209431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The digestion of the milk sugar (lactose) is observed every normal child but not in every adult. The decreased lactase synthesis in some adults results in problems with digestion of the whole milk (primary hypolactasy). An association of lactase activity in adults with carrying of the allele T within the polymorphism C/T-13910 located upstream of the lactase gene and 100% association of hypolactasy with the genotype C/C has recently been shown for a Finnish sample. In the present work we determined the LCT* C/T_13910 genotypes and allele frequencies in populations from Russia. The genotype C/C frequencies varied from 36.6% for Russians to 88.2% for Chukchi and were close to the published medical and epidemiological data on hypolactasy frequencies in respective populations. Genotyping was performed by three different methods to identify the optimal one. Our results have shown that the studied locus is the key determinant for the primary hypolactasy development in various human populations. Consequently, the DNA diagnostics of the C/C genotype carrying is a promising predictive test to detect the primary hypolactasy long before its clinical development. Practical application of this type of diagnostics would be a step towards the individual-oriented medicine.
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Rebrikov DV, Trofimov DI. [Real-time PCR: approaches to data analysis (a review)]. Prikl Biokhim Mikrobiol 2006; 42:520-8. [PMID: 17066950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The registration of the accumulation of polymerase chain reaction (PCR) products in the course of amplification (real-time PCR) requires specific equipment, i.e., detecting amplifiers capable of recording the level of fluorescence in the reaction tube during amplicon formation. By the time the reaction is completed, researchers obtain DNA accumulation graphs. The review discusses the most promising algorithms of analysis of real-time PCR curves and possible errors, whether caused by the software used or the operators' mistakes. The data included will assist researchers in understanding the features of the method to obtain more reliable results.
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Anisimova VE, Rebrikov DV, Zhulidov PA, Staroverov DB, Lukyanov SA, Shcheglov AS. Renaturation, activation, and practical use of recombinant duplex-specific nuclease from Kamchatka crab. Biochemistry (Mosc) 2006; 71:513-9. [PMID: 16732729 DOI: 10.1134/s0006297906050075] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We overexpressed duplex-specific nuclease (DSN) from Kamchatka crab in Escherichia coli cells and developed procedures for purification, renaturation, and activation of this protein. We demonstrated identity of the properties of the native and recombinant DSN. We also successfully applied the recombinant DSN for full-length cDNA library normalization.
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Affiliation(s)
- V E Anisimova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Abramov DD, Trofimov DI, Rebrikov DV. [Accuracy of a real-time polymerase-chain-reaction assay for a quantitative estimation of genetically modified sources in food products]. Prikl Biokhim Mikrobiol 2006; 42:485-8. [PMID: 17022461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The accuracy of a real-time polymerase-chain-reaction assay for genetically modified sources in food products was determined using two official test systems (kits) of primers and samples. These kits were recommended by the Federal Center of State Sanitary and Epidemiological Surveillance (Russian Ministry of Health) and the European Commission. We used the following three models of thermocyclers: iCycler iQ (BioRad, United States), Rotor-Gene 3000 (Corbett Research, Australia), and DT-322 (DNA-Technology, Russia). Studies of samples that contained 1% genetically modified sources showed that the error of a quantitative assay for genetically modified sources in food products corresponds to 20-30% and does not depend on the kit type and the thermocycler model used.
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Abstract
Hepatopancreas of king crab Paralithodes camtschatica produces a metalloprotease, which belongs to the astacin family, as cDNA cloning and sequencing showed. The metalloprotease has been purified chromatographically to apparent homogeneity. The purification factor was 16 and activity recovery was 20%. pH and temperature optimum have been determined. In its properties (molecular weight, pI, metal content) the metalloprotease is close to crayfish astacin. However, analysis of the enzyme sequences revealed differences, which account for differences in substrate specificities and imply a different activation mechanism.
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Affiliation(s)
- Svetlana A Semenova
- Chemistry Department of Moscow State University, Leninskie Gory, GSP-3, Moscow, 119899, Russia
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