New automatic method for generating atomistic models of multi-branched and arbitrary-shaped seamless junctions of carbon nanostructures
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01.11.2020 |
Zhang G.
Glukhova O.E.
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Computational Materials Science |
10.1016/j.commatsci.2020.109943 |
0 |
Ссылка
© 2020 Elsevier B.V. This work proposes an original method for generating atomistic models of multi-branched and arbitrary-shaped seamless junctions of different nanostructures. Atomic frameworks of new hybrid systems with a wide variety of topological forms based on 1D and 2D structures can be obtained using this method. The topological diversity of generated hybrid systems is provided by the some features of the developed method. This method combines a triangulated nanomesh framework generation with a molecular dynamics (MD) method that allows us to generate dozens of topological configurations of the contact region of different objects. Energetically favorable junctions of carbon nanostructures, including Y- and X-shaped junctions of carbon nanotubes, a fullerene-nanotube junction, and a fullerene-graphene hybrid system are created using the developed original method.
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Electronic coupling between molybdenum disulfide and gold nanoparticles to enhance the peroxidase activity for the colorimetric immunoassays of hydrogen peroxide and cancer cells
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15.10.2020 |
Sun H.
Gao Y.
Hu N.
Zhang Y.
Guo C.
Gao G.
Ma Z.
Ivan Ivanovich K.
Qiu Y.
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Journal of Colloid and Interface Science |
10.1016/j.jcis.2020.06.001 |
0 |
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© 2020 Elsevier Inc. Peroxidase nanoenzymes exhibit a specific affinity toward substrates, thereby demonstrating application potential for realizing the colorimetric immunoassays of hydrogen peroxide (H2O2), which can be further used as a probe for imaging cancer cells. To enhance the intrinsic peroxidase activity of molybdenum sulfide (MoS2) nanomaterials, gold (Au) nanoparticles with an average diameter of approximately 2.1 nm were modified on a MoS2/carbon surface (denoted as MoS2/C-Au600) via ascorbic acid reduction. MoS2/C-Au600 can oxidize 3,3′,5,5′-tetramethylbenzidine (TMB) to generate a blue oxidation product in the presence of H2O2; this product exhibits peroxidase-like activities, superior to those of most existing MoS2-based nanoenzymes. Furthermore, MoS2/C-Au600 exhibits a high detection capability for H2O2 in the range of 1 × 10−5 to 2 × 10−4 mol/L (R2 = 0.99), and the lowest detection limit is 1.82 µmol/L in a sodium acetate and acetic acid buffer solution. Steady state kinetics studies indicate that the catalytic mechanism is consistent with the ping-pong mechanism. Given its strong absorption peak at 652 nm in the visible region, MoS2/C-Au600 can be used to image cancer cells due to the enhanced permeability and retention effect. Our findings demonstrate that the synergistic electronic coupling between multiple components can enhance the peroxidase activity, which can facilitate the development of an effective, facile, and reliable method to perform colorimetric immunoassays of H2O2 and cancer cells.
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Intracellular quality control of mitochondrial DNA: evidence and limitations
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20.01.2020 |
Knorre D.
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Philosophical transactions of the Royal Society of London. Series B, Biological sciences |
10.1098/rstb.2019.0176 |
0 |
Ссылка
Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent 'leakage' of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Intracellular quality control of mitochondrial DNA: evidence and limitations
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20.01.2020 |
Knorre D.
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Philosophical transactions of the Royal Society of London. Series B, Biological sciences |
10.1098/rstb.2019.0176 |
0 |
Ссылка
Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent 'leakage' of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Intracellular quality control of mitochondrial DNA: evidence and limitations
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20.01.2020 |
Knorre D.
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Philosophical transactions of the Royal Society of London. Series B, Biological sciences |
10.1098/rstb.2019.0176 |
0 |
Ссылка
Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent 'leakage' of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Intracellular quality control of mitochondrial DNA: evidence and limitations
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20.01.2020 |
Knorre D.
|
Philosophical transactions of the Royal Society of London. Series B, Biological sciences |
10.1098/rstb.2019.0176 |
0 |
Ссылка
Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent 'leakage' of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs
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01.01.2020 |
Zolotovskaia M.
Sorokin M.
Garazha A.
Borisov N.
Buzdin A.
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Methods in Molecular Biology |
10.1007/978-1-0716-0138-9_16 |
0 |
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© Springer Science+Business Media, LLC, part of Springer Nature 2020. DNA mutations govern cancer development. Cancer mutation profiles vary dramatically among the individuals. In some cases, they may serve as the predictors of disease progression and response to therapies. However, the biomarker potential of cancer mutations can be dramatically (several orders of magnitude) enhanced by applying molecular pathway-based approach. We developed Oncobox system for calculation of pathway instability (PI) values for the molecular pathways that are aggregated mutation frequencies of the pathway members normalized on gene lengths and on number of genes in the pathway. PI scores can be effective biomarkers in different types of comparisons, for example, as the cancer type biomarkers and as the predictors of tumor response to target therapies. The latter option is implemented using mutation drug score (MDS) values, which algorithmically rank the drugs capacity of interfering with the mutated molecular pathways. Here, describe the mathematical basis and algorithms for PI and MDS values calculation, validation and implementation. The example analysis is provided encompassing 5956 human tumor mutation profiles of 15 cancer types from The Cancer Genome Atlas (TCGA) project, that totally make 2,316,670 mutations in 19,872 genes and 1748 molecular pathways, thus enabling ranking of 128 clinically approved target drugs. Our results evidence that the Oncobox PI and MDS approaches are highly useful for basic and applied aspects of molecular oncology and pharmacology research.
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Interactions of the Rad51 inhibitor DIDS with human and bovine serum albumins: Optical spectroscopy and isothermal calorimetry approaches
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01.12.2019 |
Velic D.
Charlier C.
Popova M.
Jaunet-Lahary T.
Bouchouireb Z.
Henry S.
Weigel P.
Masson J.
Laurent A.
Nabiev I.
Fleury F.
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Biochimie |
10.1016/j.biochi.2019.09.016 |
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© 2019 Rad51 is a key protein in DNA repair by homologous recombination and an important target for development of drugs in cancer therapy. 4′-diisothiocyanostilbene-2,2′-disulfonic acid (DIDS) has been used in clinic during the past 30 years as an inhibitor of anion transporters and channels. Recently DIDS has been demonstrated to affect Rad51-mediated homologous pairing and strand exchange, key processes in homologous recombination. Consequently, DIDS has been considered as a potential revertant of radio- and chemo-resistance of cancer cells, the major causes of therapy failure. Here, we have investigated the behavior of DIDS towards serum albumins. The effects of environmental factors, primarily, solvent polarity, on DIDS stability were evaluated, and the mechanisms of interaction of DIDS with human or bovine serum albumin were analyzed using isothermal calorimetry, circular dichroism and fluorescence spectroscopies. DIDS interaction with both serum albumins have been demonstrated, and the interaction characteristics have been determined. By comparing these characteristics for several DIDS derivatives, we have identified the DIDS moiety essential for the interaction. Furthermore, site competition data indicate that human albumin has two DIDS-binding sites: a high-affinity site in the IIIA subdomain and a low-affinity one in the IB subdomain. Molecular docking has revealed the key molecular moieties of DIDS responsible for its interactions in each site and shown that the IB site can bind two ligands. These findings show that binding of DIDS to serum albumin may change the balance between the free and bound DIDS forms, thereby affecting its bioavailability and efficacy against Rad51.
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Role of anti-DNA auto-antibodies as biomarkers of response to treatment in systemic lupus erythematosus patients: hypes and hopes. Insights and implications from a comprehensive review of the literature
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02.11.2019 |
Bragazzi N.
Watad A.
Damiani G.
Adawi M.
Amital H.
Shoenfeld Y.
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Expert Review of Molecular Diagnostics |
10.1080/14737159.2019.1665511 |
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Ссылка
© 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group. Introduction: Due to the polymorphic clinical presentations and manifestations of systemic lupus erythematosus (SLE), biomarkers with enough diagnostic and prognostic value are of paramount importance. Recently, anti-double stranded DNA (anti-dsDNA) auto-antibodies have been proposed to monitor the response to different therapies. It has also been suggested that they should be employed as entry markers in trial studies. However, their clinical use remains still debated and, sometimes, controversial, due to conflicting findings reported. Areas covered: Through an extensive literature review, we evaluated changes in anti-dsDNA auto-antibodies levels before and after the administration of the treatment (either biological or non-biological). Expert opinion: Anti-dsDNA auto-antibodies related findings are still difficult to compare mainly because of the different detecting methods employed, even though in most studies included in this review a consistent decreasing pattern after the treatment seems to emerge. Hence, if properly standardized, anti-dsDNA auto-antibody profile may be a reliable biomarker to monitor the effectiveness of biologics as well as of non-biological drugs, especially if grouped in composite outcomes scores, such as the ‘Lupus Multivariable Outcome Score’ (LUMOS) or measured with other biomarkers, such as anti-nucleosome auto-antibodies. We recommend the assessment of anti-dsDNA auto-antibodies levels in both daily practice and research settings.
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Replenishment of hepatitis B virus cccDNA pool is restricted by baseline expression of host restriction factors in vitro
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01.11.2019 |
Brezgin S.
Kostyusheva A.
Bayurova E.
Gordeychuk I.
Isaguliants M.
Goptar I.
Nikiforova A.
Smirnov V.
Volchkova E.
Glebe D.
Kostyushev D.
Chulanov V.
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Microorganisms |
10.3390/microorganisms7110533 |
0 |
Ссылка
© 2019 by the authors. Licensee MDPI, Basel, Switzerland. Background: Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is the major cause of viral persistence in patients with chronic HBV infection. Understanding the mechanisms underlying stability and persistence of HBV cccDNA in hepatocytes is critical for developing novel therapeutics and managing chronic hepatitis B. In this study, we observed an unexpected increase in HBV cccDNA levels upon suppression of transcription by de novo DNA methyltransferase DNMT3A and uncovered additional mechanisms potentially involved in HBV cccDNA maintenance. Methods: HBV-expressing cell lines were transfected with a DNMT3A-expressing plasmid. Real-time PCR and HBsAg assays were used to assess the HBV replication rate. Cell cycling was analyzed by fluorescent cell sorting. CRISPR/Cas9 was utilized to abrogate expression of APOBEC3A and APOBEC3B. Alterations in the expression of target genes were measured by real-time PCR. Results: Similar to previous studies, HBV replication induced DNMT3A expression, which in turn, led to reduced HBV transcription but elevated HBV cccDNA levels (4-to 6-fold increase). Increased levels of HBV cccDNA were not related to cell cycling, as DNMT3A accelerated proliferation of infected cells and could not contribute to HBV cccDNA expansion by arresting cells in a quiescent state. At the same time, DNMT3A suppressed transcription of innate immunity factors including cytidine deaminases APOBEC3A and APOBEC3B. CRISPR/Cas9-mediated silencing of APOBEC3A and APOBEC3B transcription had minor effects on HBV transcription, but significantly increased HBV cccDNA levels, similar to DNMT3A. In an attempt to further analyze the detrimental effects of HBV and DNMT3A on infected cells, we visualized γ-H2AX foci and demonstrated that HBV inflicts and DNMT3A aggravates DNA damage, possibly by downregulating DNA damage response factors. Additionally, suppression of HBV replication by DNMT3A may be related to reduced ATM/ATR expression. Conclusion: Formation and maintenance of HBV cccDNA pools may be partially suppressed by the baseline expression of host inhibitory factors including APOBEC3A and APOBEC3B. HBV inflicts DNA damage both directly and by inducing DNMT3A expression.
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ATM and ATR Expression Potentiates HBV Replication and Contributes to Reactivation of HBV Infection upon DNA Damage
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31.10.2019 |
Kostyusheva A.
Brezgin S.
Bayurova E.
Gordeychuk I.
Isaguliants M.
Goptar I.
Urusov F.
Nikiforova A.
Volchkova E.
Kostyushev D.
Chulanov V.
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Viruses |
10.3390/v11110997 |
1 |
Ссылка
Chronic hepatitis B virus infection (CHB) caused by the hepatitis B virus (HBV) is one of the most common viral infections in the world. Reactivation of HBV infection is a life-threatening condition observed in patients with CHB receiving chemotherapy or other medications. Although HBV reactivation is commonly attributed to immune suppression, other factors have long been suspected to play a role, including intracellular signaling activated in response to DNA damage. We investigated the effects of DNA-damaging factors (doxorubicin and hydrogen peroxide) on HBV reactivation/replication and the consequent DNA-damage response. Dose-dependent activation of HBV replication was observed in response to doxorubicin and hydrogen peroxide which was associated with a marked elevation in the mRNA levels of ataxia-telangiectasia mutated (ATM) and ATM- and RAD3-related (ATR) kinases. Downregulation of ATM or ATR expression by shRNAs substantially reduced the levels of HBV RNAs and DNA. In contrast, transcriptional activation of ATM or ATR using CRISPRa significantly increased HBV replication. We conclude that ATM and ATR are essential for HBV replication. Furthermore, DNA damage leading to the activation of ATM and ATR transcription, results in the reactivation of HBV replication.
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Bimodular antiparallel G-quadruplex nanoconstruct with antiproliferative activity
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08.10.2019 |
Antipova O.
Samoylenkova N.
Savchenko E.
Zavyalova E.
Revishchin A.
Pavlova G.
Kopylov A.
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Molecules |
10.3390/molecules24193625 |
0 |
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© 2019 by the authors. Oligonucleotides with an antiproliferative activity for human cancer cells have attracted attention over the past decades; many of them have a G-quadruplex structure (GQ), and a cryptic target. In particular, DNA oligonucleotide HD1, a minimal GQ, could inhibit proliferation of some cancer cell lines. The HD1 is a 15-nucleotide DNA oligonucleotide that folds into a minimal chair-like monomolecular antiparallel GQ structure. In this study, for eight human cancer cell lines, we have analyzed the antiproliferative activities of minimal bimodular DNA oligonucleotide, biHD1, which has two HD1 modules covalently linked via single T-nucleotide residue. Oligonucleotide biHD1 exhibits a dose-dependent antiproliferative activity for lung cancer cell line RL-67 and cell line of central nervous system cancer U87 by MTT-test and Ki-67 immunoassay. The study of derivatives of biHD1 for the RL-67 and U87 cell lines revealed a structure-activity correlation of GQ folding and antiproliferative activity. Therefore, a covalent joining of two putative GQ modules within biHD1 molecule provides the antiproliferative activity of initial HD1, opening a possibility to design further GQ multimodular nanoconstructs with antiproliferative activity—either as themselves or as carriers.
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Association of DNMT3B and DNMN3L Gene Polymorphisms with Early Pregnancy Loss
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01.08.2019 |
Azova M.
Ahmed A.
Ait Aissa A.
Blagonravov M.
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Bulletin of Experimental Biology and Medicine |
10.1007/s10517-019-04553-6 |
0 |
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© 2019, Springer Science+Business Media, LLC, part of Springer Nature. A total of 100 women with early pregnancy loss were recruited and further classified into two subgroups: sporadic pregnancy loss and recurrent pregnancy loss; each subgroup consisted of 50 women. The control group included 56 women with normal pregnancies. Genotyping was performed by PCR with restriction fragment length polymorphism analysis. A statistically significant increase in the frequencies of TT genotype and T allele for DNMT3B rs2424913 polymorphism was found in the total patient group and in both patient subgroups in comparison with the control. Moreover, homozygous TT genotype was associated with increased risk of early pregnancy loss (both sporadic and recurrent). DNMT3B rs2424913 gene polymorphism in women can be used a marker of predisposition to early pregnancy loss and recurrent pregnancy loss.
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Recombinant allergens for immunotherapy: State of the art
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01.08.2019 |
Zhernov Y.
Curin M.
Khaitov M.
Karaulov A.
Valenta R.
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Current Opinion in Allergy and Clinical Immunology |
10.1097/ACI.0000000000000536 |
1 |
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Copyright © 2019 Wolters Kluwer Health, Inc. All rights reserved. Purpose of review More than 30 years ago, the first molecular structures of allergens were elucidated and defined recombinant allergens became available. We review the state of the art regarding molecular AIT with the goal to understand why progress in this field has been slow, although there is huge potential for treatment and allergen-specific prevention. Recent findings On the basis of allergen structures, several AIT strategies have been developed and were advanced into clinical evaluation. In clinical AIT trials, promising results were obtained with recombinant and synthetic allergen derivatives inducing allergen-specific IgG antibodies, which interfered with allergen recognition by IgE whereas clinical efficacy could not yet be demonstrated for approaches targeting only allergen-specific T-cell responses. Available data suggest that molecular AIT strategies have many advantages over allergen extract-based AIT. Summary Clinical studies indicate that recombinant allergen-based AIT vaccines, which are superior to existing allergen extract-based AIT can be developed for respiratory, food and venom allergy. Allergen-specific preventive strategies based on recombinant allergen-based vaccine approaches and induction of T-cell tolerance are on the horizon and hold promise that allergy can be prevented. However, progress is limited by lack of resources needed for clinical studies, which are necessary for the development of these innovative strategies.
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Clinical implications of hepatitis b virus rna and covalently closed circular dna in monitoring patients with chronic hepatitis b today with a gaze into the future: The field is unprepared for a sterilizing cure
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05.10.2018 |
Kostyusheva A.
Kostyushev D.
Brezgin S.
Volchkova E.
Chulanov V.
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Genes |
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2 |
Ссылка
© 2018, MDPI AG. All rights reserved. Chronic hepatitis B virus (HBV) infection has long remained a critical global health issue. Covalently closed circular DNA (cccDNA) is a persistent form of the HBV genome that maintains HBV chronicity. Decades of extensive research resulted in the two therapeutic options currently available: nucleot(s)ide analogs and interferon (IFN) therapy. A plethora of reliable markers to monitor HBV patients has been established, including the recently discovered encapsidated pregenomic RNA in serum, which can be used to determine treatment end-points and to predict the susceptibility of patients to IFN. Additionally, HBV RNA splice variants and cccDNA and its epigenetic modifications are associated with the clinical course and risks of hepatocellular carcinoma (HCC) and liver fibrosis. However, new antivirals, including CRISPR/Cas9, APOBEC-mediated degradation of cccDNA, and T-cell therapies aim at completely eliminating HBV, and it is clear that the diagnostic arsenal for defining the long-awaited sterilizing cure is missing. In this review, we discuss the currently available tools for detecting and measuring HBV RNAs and cccDNA, as well as the state-of-the-art in clinical implications of these markers, and debate needs and goals within the context of the sterilizing cure that is soon to come.
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Study of Genetic Diversity and Population Structure of the Yak (Bos grunniens) in the Sayan-Altai Region
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01.10.2018 |
Oyun N.
Konorov E.
Urum A.
Artyushin I.
Svishcheva G.
Cendsuren C.
Stolpovsky Y.
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Russian Journal of Genetics |
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0 |
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© 2018, Pleiades Publishing, Inc. Abstract: The paper reports the first study of genetic diversity of the domestic yak in the Sayan-Altai region of Russia (Altai and Tuva) and Mongolia (Khuvsgul and Gobi) on the basis of the polymorphism analysis of the mtDNA D-loop hypervariable region. It has been demonstrated that, among all the studied populations, Tuva yaks are characterized by the highest haplotype diversity. Four new haplotypes, A4, A13, D9, and E3, have been described for the first time. The analysis of the contribution of maternal genetic component to the yak intrabreed and interbreed mtDNA diversity revealed two large clades. For the first time, comparative analysis of genetic structure of the Russian yak populations was carried out using 15 microsatellite loci. Low genetic difference between the populations was revealed, which may apparently be accounted for by the specific features of farm breeding, in particular, by animal exchange between the adjacent territories of the Sayan-Altai region.
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DNA Barcoding of Celyphidae (Diptera) from Vietnam
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01.08.2018 |
Galinskaya T.
Oyun N.
Nartschuk E.
Shatalkin A.
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Russian Journal of Genetics |
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0 |
Ссылка
© 2018, Pleiades Publishing, Inc. The COI gene fragment was first examined in representatives of the family Celyphidae. The presence of a considerable hiatus between interspecific and intraspecific distances was demonstrated, which enabled using the barcoding method to distinguish species of the family Celyphidae. The results of the analysis showed that different species of Celyphidae clustered together. Within the Celyphus (Hemiglobus) porosus cluster, some haplotype heterogeneity, which was, however, within the limits of intraspecific variability, was observed.
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Comparison of Some Plant DNA Extraction Methods
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01.05.2018 |
Scobeyeva V.
Omelchenko D.
Dyakov L.
Konovalov A.
Speranskaya A.
Krinitsina A.
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Russian Journal of Genetics |
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1 |
Ссылка
© 2018, Pleiades Publishing, Inc. DNA isolation is a routine procedure when performed in laboratory environment, yet in the field it may still remain problematic. This is especially true of some crop species bred for useful metabolites that may also hinder DNA extraction. Here we compare the efficiency of DNA extraction protocols and commercial DNA isolation kits when used on samples from Helianthus and Allium. Since extraction of DNA is known to be compromised by co-extraction of PCR-inhibiting metabolites, the isolation of DNA was followed by PCR as a testing procedure for the isolation step. The MagnoPrime Fact and MagnoPrime Uni DNA isolation kits were better suited for field work due to faster processing times and smaller required amount of starting material (20 mg fresh/0.5 mg dry). In all cases the subsequent PCR managed to amplify the DNA fragments of interest well enough to be useful in further research.
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Synthesis, DNA and BSA binding of Pd(II) and Pt(II) complexes featuring tetrazolylacetic acids and their esters
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24.03.2018 |
Protas A.
Popova E.
Mikolaichuk O.
Porozov Y.
Mehtiev A.
Ott I.
Alekseev G.
Kasyanenko N.
Trifonov R.
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Inorganica Chimica Acta |
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13 |
Ссылка
© 2017 Elsevier B.V. Two series of palladium(II) and platinum(II) complexes featuring esters of tetrazol-1-yl and tetrazol-5-ylacetic acids {trans-[PdCl2L2] and trans-[PtCl2L2], L = 5-methyl-1H-tetrazol-1-ylacetic acid and its ethyl, butyl, isobutyl esters (1–5); 2-R-2H-tetrazol-5-ylacetic acid and its ethyl esters, R = tBu, CH2CH2OH (6–10)} were synthesized and their binding to calf-thymus DNA (CT DNA) and bovine serum albumin (BSA) were studied by means of experimental (CD, UV, viscometry, fluorometric and electrophoretic techniques) and theoretical methods. According to the spectrophotometric data, the interaction of the metal complexes with CT DNA is observed. The significant increase of melting point of CT DNA in the presence of the metal complexes (ΔTm = 8–13 °C) indicates strong stabilization of the DNA helix. Electrophoretic studies demonstrate the ability of the metal complexes to interact with pBR322 plasmid DNA and to change its mobility. According to the data of the fluorescence quenching technique, binding with constants (Kbin) of Pd(II) complexes with BSA are in the range 0.83–4.12 × 105 L M−1. The molecular docking studies show the minor groove binding behavior of tetrazole-containing palladium(II) and platinum(II) complexes to DNA (ΔGbinding. −5.56 − −6.12 kcal/mol) and effective binding to BSA via the favored binding site Trp213 (ΔGbinding −7.2 − −7.56 kcal/mol). The complex trans-[PtCl2(2-tert-butyl-tetrazol-5-ylacetic acid)2] exhibited noticeable antiproliferative activity in two human cancer cell lines with IC50 values of 11.40 µM in HT-29 cells and 11.02 µM in MDA-MB-231 cell line.
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Role of mycoplasma infection in acute bronchial asthma in children
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01.01.2018 |
Gorina L.
Krylova N.
Goncharova S.
Rakovskaya I.
Barkhatova O.
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Infektsionnye Bolezni |
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© 2018, Dynasty Publishing House. All rights reserved. The objective. To specify the duration of persistence of antigens and DNA of Mycoplasma pneumoniae (M. pneumoniae) and Mycoplasma hominis (M. hominis) cells in the free state and as part of circulating immune complexes in blood of children suffering from bronchial asthma. Patients and methods. In the University Children’s Clinical Hospital of the Sechenov University, 161 children aged 1 to 14 years were observed. Group 1 (treatment group) included 126 children with bronchial asthma. 55 children (43.7%) had a mild course of disease, 52 children – moderate (42.1%) and 19 children (15.1%) – severe. All children were in the exacerbation period. Group 2 (control) consisted of 35 children with ARVI. The mean age of children in group 1 – 5.4 ± 1.8 years (79 boys (62.7%) and 47 girls (37.3%)); in group 2 – 5.7 ± 1.9 years (20 boys (57.1%) and 15 girls (42.9%). Diagnostic methods used: cultivation of mycoplasmas, preparation of immune serums, aggregate-haemagglutination assays (AHAA), polymerase chain reaction (PCR), direct immunofluorescence (DIF), methods of detection of circulating immune complexes (CIC). Results. AHAA examination of 126 serum samples of children from group 1 with BA, M. pneumoniae and M. hominis antigens in the free state were found in 73 and 50% of cases, respectively. In children of group 2 AHAA detected M. pneumoniae and M. hominis significantly more rarely: M. pneumoniae was found in 3 (8.6%) children (p = 95.3), M. hominis – in 2 (5.7%) children (p = 97.1). Further examination of serum samples of children with BA found M. pneumoniae and M. hominis cell DNA in 7.14 and 16.6% of cases, respectively. The work has shown that M. pneumoniae antigens are found in the composition of CIC in 55.5% of cases, M. hominis antigens – in 46.8% of cases, DNA – in 26.98 and 46.8%, respectively. For treatment of mycoplasma infection, children with BA received three azitromicin courses in the dose 10 mg/kg for 3 days with a 4-day interval. Conclusion. These data are indicative of long-term persistence of mycoplasma cell antigens and DNA in the free state and in CIC in blood of children with BA. Mycoplasmas can be regarded as one of the factors of inducing BA exacerbations in children. Tests for mycoplasma infection are indicated in patients with BA. Addition of macrolides to standard BA therapy in children with mycoplasma infection, as a rule, yields positive results.
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