Plasmolipin and Its Role in Cell Processes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):883-896. doi: 10.31857/S0026898421060112.ABSTRACTThe mechanisms involved in the origin and development of malignant and neurodegenerative diseases are an important area of modern biomedicine. A crucial task is to identify new molecular markers that are associated with rearrangements of intracellular signaling and can be used for prognosis and the development of effective treatment approaches. The proteolipid plasmolipin (PLLP) is a possible marker. PLLP is a main component of the myelin sheath and plays an important role in the development and normal function of the nervous system. PLLP ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Shulgin T D Lebedev V S Prassolov P V Spirin Source Type: research

Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action
Mol Biol (Mosk). 2021 Nov-Dec;55(6):897-926. doi: 10.31857/S0026898421050104.ABSTRACTThe emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compound, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial, or antiprotozoal activity. Particular attention is paid to the mechanisms that...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Zenchenko M S Drenichev I A Ilyicheva S N Mikhailov Source Type: research

Whole-Genome Duplications in Evolution, Ontogeny, and Pathology: Complexity and Emergency Reserves
Mol Biol (Mosk). 2021 Nov-Dec;55(6):927-943. doi: 10.31857/S0026898421060021.ABSTRACTWhole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the cell. WGDs of whole organisms are found in all branches of eukaryotes and act as a driving force of speciation, complication, and adaptations. Somatic-cell WGDs are observed in all types of tissues and can result from normal or altered ontogenetic programs, regeneration, pathological conditions, aging, malignancy, and metastasis. Despite the versatility of WGDs, their functional significance, general properties, and causes of their higher adap...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O V Anatskaya A E Vinogradov Source Type: research

Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens
Mol Biol (Mosk). 2021 Nov-Dec;55(6):944-955. doi: 10.31857/S0026898421050062.ABSTRACTA prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, wh...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S A Lapa R A Miftakhov E S Klochikhina Yu I Ammur S A Blagodatskikh V E Shershov A S Zasedatelev A V Chudinov Source Type: research

Risk of Multiple Sclerosis: Analysis of Interactions Between Variants of Nuclear and Mitochondrial Genomes
This study expands the current understanding of the role of mitonuclear interactions and variance of nuclear genes, whose products function in mitochondria, and in risk of MS.PMID:34837699 | DOI:10.31857/S0026898421060070 (Source: Molekuliarnaia Biologiia)
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M S Kozin I S Kiselev N M Baulina G V Pavlova A N Boyko O G Kulakova O O Favorova Source Type: research

Possible Role of Prep 1 Homeodomain Transcription Factor in Cardiac Mesenchymal Stromal Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):965-971. doi: 10.31857/S0026898421060124.ABSTRACTHomeodomain transcription factors play a significant role in mesenchymal stromal cells (MSCs). Previously, the role of Meis1, Pbx1 and Prep1 proteins from the TALE (Three Amino acid Loop Extension) family in adipocytic and osteogenic differentiation of mouse mesenchymal stromal cells was established. In this work, using ChIP-seq and bioinformatic analysis we investigated the binding pattern of PREP1 with the genomic DNA of human heart MSCs, identified nearby genes, and analyzed their ontology. The target genes of the PREP1 factor in cardia...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: Y S Stafeev E K Shevchenko M A Boldireva D N Penkov Source Type: research

POU2F1 (Oct-1) Differently Autoregulates the Alternative Promoters of Its Own Gene by Binding to Different Regulatory Sites
Mol Biol (Mosk). 2021 Nov-Dec;55(6):972-981. doi: 10.31857/S0026898421060100.ABSTRACTThe POU2F1 gene, which plays an important role in regulating the mammalian genome and development, has both a ubiquitous (U) and a tissue-specific (L) promoter and is subject to intricate regulation. Regions of POU2F1 gene were found to contain multiple binding sites for its product POU2F1 (Oct-1), a transcription factor. Interspecies homology in these regions was found to exceed 90% among the human, mouse, rat, pig, and dog genomes, almost all of the Oct-1 binding sites being identical. Some of the sites cluster in the vicinity of each of...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: E V Pankratova T N Portseva A A Makarova В М Lyanova S G Georgieva A G Stepchenko Source Type: research

Intein-Mediated Protein trans-Splicing of the Recombinant Streptavidin on Magnetosomes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):982-986. doi: 10.31857/S0026898421060057.ABSTRACTWhen expressing streptavidin recombinant polypeptide on magnetosomes (called bacterial magnetic nanoparticles, or BMPs), the presence of endogenous bacterial biotin might be detrimental. In the study, the streptavidin monomer fragment (S1-116) was fused with the intein N-terminal (termed precursor S1-116-IN), and S1-116-IN was expressed in E. coli (BL21). Meanwhile, the SA117-160 fragment was fused with the C-terminal intein, and then this chimeric polypeptide was expressed on magnetosomes by fusion with magnetosome membrance protein MamF....
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S B Duan S S Wei H M Wang S H Ding Y Z Chen J J Tian Y J Wang W Chen J Chen Q L Meng Source Type: research

Immunogenic Properties of the DNA Construct Encoding the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein
Mol Biol (Mosk). 2021 Nov-Dec;55(6):987-998. doi: 10.31857/S0026898421060045.ABSTRACTThe development of preventive vaccines became the first order task in the COVID-19 pandemic caused by SARS-CoV-2. This paper reports the construction of the pVAX-RBD plasmid containing the Receptor-Binding Domain (RBD) of the S protein and a unique signal sequence 176 which promotes target protein secretion into the extracellular space thereby increasing the efficiency of humoral immune response activation. A polyglucine-spermidine conjugate (PGS) was used to deliver pVAX-RBD into the cells. The comparative immunogenicity study of the nake...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M B Borgoyakova L I Karpenko A P Rudometov D V Shanshin A A Isaeva V S Nesmeyanova N V Volkova S V Belenkaya D E Murashkin D N Shcherbakov E A Volosnikova E V Starostina L A Orlova N V Danilchenko A V Zaikovskaya O V Pyankov A A Ilyichev Source Type: research

Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus
Mol Biol (Mosk). 2021 Nov-Dec;55(6):999-1010. doi: 10.31857/S0026898421060082.ABSTRACTA fundamental difference between somatic nuclei (macronuclei) of ciliates and cell nuclei of higher eukaryotes is that the macronuclear genome is a huge number (up to tens or hundreds of thousands) of gene-sized (0.5-25 kb) or subchromosomal (up to 2000 kb) minichromosomes. Electron microscopy shows that macronuclear chromatin usually looks like chromatin bodies or fibrils 200-300 nm thick in the interphase. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. The organization of chro...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O G Leonova A A Potekhin I V Nekrasova B P Karajan B V Syomin V S Prassolov V I Popenko Source Type: research

Serum of Mice Immunized with Mt1-MMP Metalloproteinase Reduces Migration Potential of Pancreatic Cancer Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1011-1020. doi: 10.31857/S0026898421060094.ABSTRACTExpression levels of matrix metalloproteinases, in particular MT1-MMP, are elevated in pancreatic cancer (PC) cells, and this is associated with increased tumor proliferation, invasion, and migration. MT1-MMP is considered a promising target for drug therapy of PC, but the use of inhibitors and therapeutic antibodies to MT1-MMP is limited because maximal efficiency is only observed in a narrow time interval, at the early asymptomatic stages of the disease. This problem could be solved by immunization to MPs at the moment of detection of ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: N A Mitkin A S Ustiugova A N Uvarova K A Rumyantsev K V Korneev V V Pavshintsev Source Type: research

PHF10, a Subunit of the PBAF Chromatin Remodeling Complex, Changes Its Localization and Interacts with c-FOS during the Initiation of Long-Term Potentiation in Neuronal Culture
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1021-1029. doi: 10.31857/S0026898421060033.ABSTRACTThe PBAF chromatin remodeling complex interacts with many transcriptional activators and is recruited to target chromatin regions. PBAF plays an important role in maintaining and modifying the chromatin structure in mammalian cells. A subunit of the PBAF complex, the PHF10 transcription factor, is required for proliferation of neuronal precursors in the early stages of mouse brain development and gene expression in differentiated neurons. We showed that PHF10 interacts with the protein product of the early response gene c-FOS, the c-FOS ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A M Azieva A A Sheynov D A Kirillova E V Tatarskiy S G Georgieva N V Soshnikova Source Type: research

Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1030-1044. doi: 10.31857/S0026898421060069.ABSTRACTThe development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: V M Golyshev D V Pyshnyi A A Lomzov Source Type: research

miRNA-16 AS an Internal Control in Breast Cancer Studies: A Systematic Review and Meta-analysis
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1045-1056. doi: 10.31857/S0026898421060136.ABSTRACTReverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a method of choice for quantifying micro RNAs (miRNAs). Typically, RT-qPCR data are normalized to reference genes. While miRNAs are used for diagnosing and subtyping breast cancer, various studies show their deregulation in this condition, thus, undermining miRNAs' utility as a reference. This review examines the expression pattern of miR-16 and suggests normalization approaches for breast cancer. We analyzed the data from selected peer-reviewed studies to calculat...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: H N N Thu H T N Vy T N N Thanh D T N Giang T N Nhan N P Hoang T N Hue Source Type: research

Plasmolipin and Its Role in Cell Processes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):883-896. doi: 10.31857/S0026898421060112.ABSTRACTThe mechanisms involved in the origin and development of malignant and neurodegenerative diseases are an important area of modern biomedicine. A crucial task is to identify new molecular markers that are associated with rearrangements of intracellular signaling and can be used for prognosis and the development of effective treatment approaches. The proteolipid plasmolipin (PLLP) is a possible marker. PLLP is a main component of the myelin sheath and plays an important role in the development and normal function of the nervous system. PLLP ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Shulgin T D Lebedev V S Prassolov P V Spirin Source Type: research

Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action
Mol Biol (Mosk). 2021 Nov-Dec;55(6):897-926. doi: 10.31857/S0026898421050104.ABSTRACTThe emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compound, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial, or antiprotozoal activity. Particular attention is paid to the mechanisms that...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Zenchenko M S Drenichev I A Ilyicheva S N Mikhailov Source Type: research

Whole-Genome Duplications in Evolution, Ontogeny, and Pathology: Complexity and Emergency Reserves
Mol Biol (Mosk). 2021 Nov-Dec;55(6):927-943. doi: 10.31857/S0026898421060021.ABSTRACTWhole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the cell. WGDs of whole organisms are found in all branches of eukaryotes and act as a driving force of speciation, complication, and adaptations. Somatic-cell WGDs are observed in all types of tissues and can result from normal or altered ontogenetic programs, regeneration, pathological conditions, aging, malignancy, and metastasis. Despite the versatility of WGDs, their functional significance, general properties, and causes of their higher adap...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O V Anatskaya A E Vinogradov Source Type: research

Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens
Mol Biol (Mosk). 2021 Nov-Dec;55(6):944-955. doi: 10.31857/S0026898421050062.ABSTRACTA prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, wh...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S A Lapa R A Miftakhov E S Klochikhina Yu I Ammur S A Blagodatskikh V E Shershov A S Zasedatelev A V Chudinov Source Type: research

Risk of Multiple Sclerosis: Analysis of Interactions Between Variants of Nuclear and Mitochondrial Genomes
This study expands the current understanding of the role of mitonuclear interactions and variance of nuclear genes, whose products function in mitochondria, and in risk of MS.PMID:34837699 | DOI:10.31857/S0026898421060070 (Source: Molekuliarnaia Biologiia)
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M S Kozin I S Kiselev N M Baulina G V Pavlova A N Boyko O G Kulakova O O Favorova Source Type: research

Possible Role of Prep 1 Homeodomain Transcription Factor in Cardiac Mesenchymal Stromal Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):965-971. doi: 10.31857/S0026898421060124.ABSTRACTHomeodomain transcription factors play a significant role in mesenchymal stromal cells (MSCs). Previously, the role of Meis1, Pbx1 and Prep1 proteins from the TALE (Three Amino acid Loop Extension) family in adipocytic and osteogenic differentiation of mouse mesenchymal stromal cells was established. In this work, using ChIP-seq and bioinformatic analysis we investigated the binding pattern of PREP1 with the genomic DNA of human heart MSCs, identified nearby genes, and analyzed their ontology. The target genes of the PREP1 factor in cardia...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: Y S Stafeev E K Shevchenko M A Boldireva D N Penkov Source Type: research

POU2F1 (Oct-1) Differently Autoregulates the Alternative Promoters of Its Own Gene by Binding to Different Regulatory Sites
Mol Biol (Mosk). 2021 Nov-Dec;55(6):972-981. doi: 10.31857/S0026898421060100.ABSTRACTThe POU2F1 gene, which plays an important role in regulating the mammalian genome and development, has both a ubiquitous (U) and a tissue-specific (L) promoter and is subject to intricate regulation. Regions of POU2F1 gene were found to contain multiple binding sites for its product POU2F1 (Oct-1), a transcription factor. Interspecies homology in these regions was found to exceed 90% among the human, mouse, rat, pig, and dog genomes, almost all of the Oct-1 binding sites being identical. Some of the sites cluster in the vicinity of each of...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: E V Pankratova T N Portseva A A Makarova В М Lyanova S G Georgieva A G Stepchenko Source Type: research

Intein-Mediated Protein trans-Splicing of the Recombinant Streptavidin on Magnetosomes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):982-986. doi: 10.31857/S0026898421060057.ABSTRACTWhen expressing streptavidin recombinant polypeptide on magnetosomes (called bacterial magnetic nanoparticles, or BMPs), the presence of endogenous bacterial biotin might be detrimental. In the study, the streptavidin monomer fragment (S1-116) was fused with the intein N-terminal (termed precursor S1-116-IN), and S1-116-IN was expressed in E. coli (BL21). Meanwhile, the SA117-160 fragment was fused with the C-terminal intein, and then this chimeric polypeptide was expressed on magnetosomes by fusion with magnetosome membrance protein MamF....
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S B Duan S S Wei H M Wang S H Ding Y Z Chen J J Tian Y J Wang W Chen J Chen Q L Meng Source Type: research

Immunogenic Properties of the DNA Construct Encoding the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein
Mol Biol (Mosk). 2021 Nov-Dec;55(6):987-998. doi: 10.31857/S0026898421060045.ABSTRACTThe development of preventive vaccines became the first order task in the COVID-19 pandemic caused by SARS-CoV-2. This paper reports the construction of the pVAX-RBD plasmid containing the Receptor-Binding Domain (RBD) of the S protein and a unique signal sequence 176 which promotes target protein secretion into the extracellular space thereby increasing the efficiency of humoral immune response activation. A polyglucine-spermidine conjugate (PGS) was used to deliver pVAX-RBD into the cells. The comparative immunogenicity study of the nake...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M B Borgoyakova L I Karpenko A P Rudometov D V Shanshin A A Isaeva V S Nesmeyanova N V Volkova S V Belenkaya D E Murashkin D N Shcherbakov E A Volosnikova E V Starostina L A Orlova N V Danilchenko A V Zaikovskaya O V Pyankov A A Ilyichev Source Type: research

Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus
Mol Biol (Mosk). 2021 Nov-Dec;55(6):999-1010. doi: 10.31857/S0026898421060082.ABSTRACTA fundamental difference between somatic nuclei (macronuclei) of ciliates and cell nuclei of higher eukaryotes is that the macronuclear genome is a huge number (up to tens or hundreds of thousands) of gene-sized (0.5-25 kb) or subchromosomal (up to 2000 kb) minichromosomes. Electron microscopy shows that macronuclear chromatin usually looks like chromatin bodies or fibrils 200-300 nm thick in the interphase. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. The organization of chro...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O G Leonova A A Potekhin I V Nekrasova B P Karajan B V Syomin V S Prassolov V I Popenko Source Type: research

Serum of Mice Immunized with Mt1-MMP Metalloproteinase Reduces Migration Potential of Pancreatic Cancer Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1011-1020. doi: 10.31857/S0026898421060094.ABSTRACTExpression levels of matrix metalloproteinases, in particular MT1-MMP, are elevated in pancreatic cancer (PC) cells, and this is associated with increased tumor proliferation, invasion, and migration. MT1-MMP is considered a promising target for drug therapy of PC, but the use of inhibitors and therapeutic antibodies to MT1-MMP is limited because maximal efficiency is only observed in a narrow time interval, at the early asymptomatic stages of the disease. This problem could be solved by immunization to MPs at the moment of detection of ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: N A Mitkin A S Ustiugova A N Uvarova K A Rumyantsev K V Korneev V V Pavshintsev Source Type: research

PHF10, a Subunit of the PBAF Chromatin Remodeling Complex, Changes Its Localization and Interacts with c-FOS during the Initiation of Long-Term Potentiation in Neuronal Culture
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1021-1029. doi: 10.31857/S0026898421060033.ABSTRACTThe PBAF chromatin remodeling complex interacts with many transcriptional activators and is recruited to target chromatin regions. PBAF plays an important role in maintaining and modifying the chromatin structure in mammalian cells. A subunit of the PBAF complex, the PHF10 transcription factor, is required for proliferation of neuronal precursors in the early stages of mouse brain development and gene expression in differentiated neurons. We showed that PHF10 interacts with the protein product of the early response gene c-FOS, the c-FOS ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A M Azieva A A Sheynov D A Kirillova E V Tatarskiy S G Georgieva N V Soshnikova Source Type: research

Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1030-1044. doi: 10.31857/S0026898421060069.ABSTRACTThe development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: V M Golyshev D V Pyshnyi A A Lomzov Source Type: research

miRNA-16 AS an Internal Control in Breast Cancer Studies: A Systematic Review and Meta-analysis
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1045-1056. doi: 10.31857/S0026898421060136.ABSTRACTReverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a method of choice for quantifying micro RNAs (miRNAs). Typically, RT-qPCR data are normalized to reference genes. While miRNAs are used for diagnosing and subtyping breast cancer, various studies show their deregulation in this condition, thus, undermining miRNAs' utility as a reference. This review examines the expression pattern of miR-16 and suggests normalization approaches for breast cancer. We analyzed the data from selected peer-reviewed studies to calculat...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: H N N Thu H T N Vy T N N Thanh D T N Giang T N Nhan N P Hoang T N Hue Source Type: research

Plasmolipin and Its Role in Cell Processes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):883-896. doi: 10.31857/S0026898421060112.ABSTRACTThe mechanisms involved in the origin and development of malignant and neurodegenerative diseases are an important area of modern biomedicine. A crucial task is to identify new molecular markers that are associated with rearrangements of intracellular signaling and can be used for prognosis and the development of effective treatment approaches. The proteolipid plasmolipin (PLLP) is a possible marker. PLLP is a main component of the myelin sheath and plays an important role in the development and normal function of the nervous system. PLLP ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Shulgin T D Lebedev V S Prassolov P V Spirin Source Type: research

Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action
Mol Biol (Mosk). 2021 Nov-Dec;55(6):897-926. doi: 10.31857/S0026898421050104.ABSTRACTThe emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compound, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial, or antiprotozoal activity. Particular attention is paid to the mechanisms that...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Zenchenko M S Drenichev I A Ilyicheva S N Mikhailov Source Type: research

Whole-Genome Duplications in Evolution, Ontogeny, and Pathology: Complexity and Emergency Reserves
Mol Biol (Mosk). 2021 Nov-Dec;55(6):927-943. doi: 10.31857/S0026898421060021.ABSTRACTWhole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the cell. WGDs of whole organisms are found in all branches of eukaryotes and act as a driving force of speciation, complication, and adaptations. Somatic-cell WGDs are observed in all types of tissues and can result from normal or altered ontogenetic programs, regeneration, pathological conditions, aging, malignancy, and metastasis. Despite the versatility of WGDs, their functional significance, general properties, and causes of their higher adap...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O V Anatskaya A E Vinogradov Source Type: research

Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens
Mol Biol (Mosk). 2021 Nov-Dec;55(6):944-955. doi: 10.31857/S0026898421050062.ABSTRACTA prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, wh...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S A Lapa R A Miftakhov E S Klochikhina Yu I Ammur S A Blagodatskikh V E Shershov A S Zasedatelev A V Chudinov Source Type: research

Risk of Multiple Sclerosis: Analysis of Interactions Between Variants of Nuclear and Mitochondrial Genomes
This study expands the current understanding of the role of mitonuclear interactions and variance of nuclear genes, whose products function in mitochondria, and in risk of MS.PMID:34837699 | DOI:10.31857/S0026898421060070 (Source: Molekuliarnaia Biologiia)
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M S Kozin I S Kiselev N M Baulina G V Pavlova A N Boyko O G Kulakova O O Favorova Source Type: research

Possible Role of Prep 1 Homeodomain Transcription Factor in Cardiac Mesenchymal Stromal Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):965-971. doi: 10.31857/S0026898421060124.ABSTRACTHomeodomain transcription factors play a significant role in mesenchymal stromal cells (MSCs). Previously, the role of Meis1, Pbx1 and Prep1 proteins from the TALE (Three Amino acid Loop Extension) family in adipocytic and osteogenic differentiation of mouse mesenchymal stromal cells was established. In this work, using ChIP-seq and bioinformatic analysis we investigated the binding pattern of PREP1 with the genomic DNA of human heart MSCs, identified nearby genes, and analyzed their ontology. The target genes of the PREP1 factor in cardia...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: Y S Stafeev E K Shevchenko M A Boldireva D N Penkov Source Type: research

POU2F1 (Oct-1) Differently Autoregulates the Alternative Promoters of Its Own Gene by Binding to Different Regulatory Sites
Mol Biol (Mosk). 2021 Nov-Dec;55(6):972-981. doi: 10.31857/S0026898421060100.ABSTRACTThe POU2F1 gene, which plays an important role in regulating the mammalian genome and development, has both a ubiquitous (U) and a tissue-specific (L) promoter and is subject to intricate regulation. Regions of POU2F1 gene were found to contain multiple binding sites for its product POU2F1 (Oct-1), a transcription factor. Interspecies homology in these regions was found to exceed 90% among the human, mouse, rat, pig, and dog genomes, almost all of the Oct-1 binding sites being identical. Some of the sites cluster in the vicinity of each of...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: E V Pankratova T N Portseva A A Makarova В М Lyanova S G Georgieva A G Stepchenko Source Type: research

Intein-Mediated Protein trans-Splicing of the Recombinant Streptavidin on Magnetosomes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):982-986. doi: 10.31857/S0026898421060057.ABSTRACTWhen expressing streptavidin recombinant polypeptide on magnetosomes (called bacterial magnetic nanoparticles, or BMPs), the presence of endogenous bacterial biotin might be detrimental. In the study, the streptavidin monomer fragment (S1-116) was fused with the intein N-terminal (termed precursor S1-116-IN), and S1-116-IN was expressed in E. coli (BL21). Meanwhile, the SA117-160 fragment was fused with the C-terminal intein, and then this chimeric polypeptide was expressed on magnetosomes by fusion with magnetosome membrance protein MamF....
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S B Duan S S Wei H M Wang S H Ding Y Z Chen J J Tian Y J Wang W Chen J Chen Q L Meng Source Type: research

Immunogenic Properties of the DNA Construct Encoding the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein
Mol Biol (Mosk). 2021 Nov-Dec;55(6):987-998. doi: 10.31857/S0026898421060045.ABSTRACTThe development of preventive vaccines became the first order task in the COVID-19 pandemic caused by SARS-CoV-2. This paper reports the construction of the pVAX-RBD plasmid containing the Receptor-Binding Domain (RBD) of the S protein and a unique signal sequence 176 which promotes target protein secretion into the extracellular space thereby increasing the efficiency of humoral immune response activation. A polyglucine-spermidine conjugate (PGS) was used to deliver pVAX-RBD into the cells. The comparative immunogenicity study of the nake...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M B Borgoyakova L I Karpenko A P Rudometov D V Shanshin A A Isaeva V S Nesmeyanova N V Volkova S V Belenkaya D E Murashkin D N Shcherbakov E A Volosnikova E V Starostina L A Orlova N V Danilchenko A V Zaikovskaya O V Pyankov A A Ilyichev Source Type: research

Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus
Mol Biol (Mosk). 2021 Nov-Dec;55(6):999-1010. doi: 10.31857/S0026898421060082.ABSTRACTA fundamental difference between somatic nuclei (macronuclei) of ciliates and cell nuclei of higher eukaryotes is that the macronuclear genome is a huge number (up to tens or hundreds of thousands) of gene-sized (0.5-25 kb) or subchromosomal (up to 2000 kb) minichromosomes. Electron microscopy shows that macronuclear chromatin usually looks like chromatin bodies or fibrils 200-300 nm thick in the interphase. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. The organization of chro...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O G Leonova A A Potekhin I V Nekrasova B P Karajan B V Syomin V S Prassolov V I Popenko Source Type: research

Serum of Mice Immunized with Mt1-MMP Metalloproteinase Reduces Migration Potential of Pancreatic Cancer Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1011-1020. doi: 10.31857/S0026898421060094.ABSTRACTExpression levels of matrix metalloproteinases, in particular MT1-MMP, are elevated in pancreatic cancer (PC) cells, and this is associated with increased tumor proliferation, invasion, and migration. MT1-MMP is considered a promising target for drug therapy of PC, but the use of inhibitors and therapeutic antibodies to MT1-MMP is limited because maximal efficiency is only observed in a narrow time interval, at the early asymptomatic stages of the disease. This problem could be solved by immunization to MPs at the moment of detection of ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: N A Mitkin A S Ustiugova A N Uvarova K A Rumyantsev K V Korneev V V Pavshintsev Source Type: research

PHF10, a Subunit of the PBAF Chromatin Remodeling Complex, Changes Its Localization and Interacts with c-FOS during the Initiation of Long-Term Potentiation in Neuronal Culture
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1021-1029. doi: 10.31857/S0026898421060033.ABSTRACTThe PBAF chromatin remodeling complex interacts with many transcriptional activators and is recruited to target chromatin regions. PBAF plays an important role in maintaining and modifying the chromatin structure in mammalian cells. A subunit of the PBAF complex, the PHF10 transcription factor, is required for proliferation of neuronal precursors in the early stages of mouse brain development and gene expression in differentiated neurons. We showed that PHF10 interacts with the protein product of the early response gene c-FOS, the c-FOS ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A M Azieva A A Sheynov D A Kirillova E V Tatarskiy S G Georgieva N V Soshnikova Source Type: research

Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1030-1044. doi: 10.31857/S0026898421060069.ABSTRACTThe development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: V M Golyshev D V Pyshnyi A A Lomzov Source Type: research

miRNA-16 AS an Internal Control in Breast Cancer Studies: A Systematic Review and Meta-analysis
Mol Biol (Mosk). 2021 Nov-Dec;55(6):1045-1056. doi: 10.31857/S0026898421060136.ABSTRACTReverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a method of choice for quantifying micro RNAs (miRNAs). Typically, RT-qPCR data are normalized to reference genes. While miRNAs are used for diagnosing and subtyping breast cancer, various studies show their deregulation in this condition, thus, undermining miRNAs' utility as a reference. This review examines the expression pattern of miR-16 and suggests normalization approaches for breast cancer. We analyzed the data from selected peer-reviewed studies to calculat...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: H N N Thu H T N Vy T N N Thanh D T N Giang T N Nhan N P Hoang T N Hue Source Type: research

Plasmolipin and Its Role in Cell Processes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):883-896. doi: 10.31857/S0026898421060112.ABSTRACTThe mechanisms involved in the origin and development of malignant and neurodegenerative diseases are an important area of modern biomedicine. A crucial task is to identify new molecular markers that are associated with rearrangements of intracellular signaling and can be used for prognosis and the development of effective treatment approaches. The proteolipid plasmolipin (PLLP) is a possible marker. PLLP is a main component of the myelin sheath and plays an important role in the development and normal function of the nervous system. PLLP ...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Shulgin T D Lebedev V S Prassolov P V Spirin Source Type: research

Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action
Mol Biol (Mosk). 2021 Nov-Dec;55(6):897-926. doi: 10.31857/S0026898421050104.ABSTRACTThe emergence of new viruses and resistant strains of pathogenic microorganisms has become a powerful stimulus in the search for new drugs. Nucleosides are a promising class of natural compound, and more than a hundred drugs have already been created based on them, including antiviral, antibacterial and antitumor agents. The review considers the structural and functional features and mechanisms of action of known nucleoside analogs with antiviral, antibacterial, or antiprotozoal activity. Particular attention is paid to the mechanisms that...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: A A Zenchenko M S Drenichev I A Ilyicheva S N Mikhailov Source Type: research

Whole-Genome Duplications in Evolution, Ontogeny, and Pathology: Complexity and Emergency Reserves
Mol Biol (Mosk). 2021 Nov-Dec;55(6):927-943. doi: 10.31857/S0026898421060021.ABSTRACTWhole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the cell. WGDs of whole organisms are found in all branches of eukaryotes and act as a driving force of speciation, complication, and adaptations. Somatic-cell WGDs are observed in all types of tissues and can result from normal or altered ontogenetic programs, regeneration, pathological conditions, aging, malignancy, and metastasis. Despite the versatility of WGDs, their functional significance, general properties, and causes of their higher adap...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: O V Anatskaya A E Vinogradov Source Type: research

Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens
Mol Biol (Mosk). 2021 Nov-Dec;55(6):944-955. doi: 10.31857/S0026898421050062.ABSTRACTA prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, wh...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S A Lapa R A Miftakhov E S Klochikhina Yu I Ammur S A Blagodatskikh V E Shershov A S Zasedatelev A V Chudinov Source Type: research

Risk of Multiple Sclerosis: Analysis of Interactions Between Variants of Nuclear and Mitochondrial Genomes
This study expands the current understanding of the role of mitonuclear interactions and variance of nuclear genes, whose products function in mitochondria, and in risk of MS.PMID:34837699 | DOI:10.31857/S0026898421060070 (Source: Molekuliarnaia Biologiia)
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: M S Kozin I S Kiselev N M Baulina G V Pavlova A N Boyko O G Kulakova O O Favorova Source Type: research

Possible Role of Prep 1 Homeodomain Transcription Factor in Cardiac Mesenchymal Stromal Cells
Mol Biol (Mosk). 2021 Nov-Dec;55(6):965-971. doi: 10.31857/S0026898421060124.ABSTRACTHomeodomain transcription factors play a significant role in mesenchymal stromal cells (MSCs). Previously, the role of Meis1, Pbx1 and Prep1 proteins from the TALE (Three Amino acid Loop Extension) family in adipocytic and osteogenic differentiation of mouse mesenchymal stromal cells was established. In this work, using ChIP-seq and bioinformatic analysis we investigated the binding pattern of PREP1 with the genomic DNA of human heart MSCs, identified nearby genes, and analyzed their ontology. The target genes of the PREP1 factor in cardia...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: Y S Stafeev E K Shevchenko M A Boldireva D N Penkov Source Type: research

POU2F1 (Oct-1) Differently Autoregulates the Alternative Promoters of Its Own Gene by Binding to Different Regulatory Sites
Mol Biol (Mosk). 2021 Nov-Dec;55(6):972-981. doi: 10.31857/S0026898421060100.ABSTRACTThe POU2F1 gene, which plays an important role in regulating the mammalian genome and development, has both a ubiquitous (U) and a tissue-specific (L) promoter and is subject to intricate regulation. Regions of POU2F1 gene were found to contain multiple binding sites for its product POU2F1 (Oct-1), a transcription factor. Interspecies homology in these regions was found to exceed 90% among the human, mouse, rat, pig, and dog genomes, almost all of the Oct-1 binding sites being identical. Some of the sites cluster in the vicinity of each of...
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: E V Pankratova T N Portseva A A Makarova В М Lyanova S G Georgieva A G Stepchenko Source Type: research

Intein-Mediated Protein trans-Splicing of the Recombinant Streptavidin on Magnetosomes
Mol Biol (Mosk). 2021 Nov-Dec;55(6):982-986. doi: 10.31857/S0026898421060057.ABSTRACTWhen expressing streptavidin recombinant polypeptide on magnetosomes (called bacterial magnetic nanoparticles, or BMPs), the presence of endogenous bacterial biotin might be detrimental. In the study, the streptavidin monomer fragment (S1-116) was fused with the intein N-terminal (termed precursor S1-116-IN), and S1-116-IN was expressed in E. coli (BL21). Meanwhile, the SA117-160 fragment was fused with the C-terminal intein, and then this chimeric polypeptide was expressed on magnetosomes by fusion with magnetosome membrance protein MamF....
Source: Molekuliarnaia Biologiia - November 27, 2021 Category: Molecular Biology Authors: S B Duan S S Wei H M Wang S H Ding Y Z Chen J J Tian Y J Wang W Chen J Chen Q L Meng Source Type: research