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Sviridov AV, Shushkova TV, Ermakova IT, Ivanova EV, Epiktetov DO, Leontievsky AA. Microbial degradation of glyphosate herbicides (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020209] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ivanova E, Hwang GS, Pan ZH. Characterization of transgenic mouse lines expressing Cre recombinase in the retina. Neuroscience 2009; 165:233-43. [PMID: 19837136 DOI: 10.1016/j.neuroscience.2009.10.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 10/09/2009] [Accepted: 10/13/2009] [Indexed: 11/25/2022]
Abstract
The mammalian retina consists of five major classes of neuronal cells, as well as glial cells, and it contains more than 50 cell types. The ability to manipulate gene expression in specific cell type(s) in the retina is important for understanding the molecular mechanisms of retinal function and diseases. The Cre/LoxP recombination system has become a powerful tool, allowing gene deletion, over-expression, and ectopic expression in vivo in a cell- and tissue-specific fashion. The key to this tool is the availability of Cre mouse lines with cell- or tissue-type specific expression of Cre recombinase. To date, a large number of Cre-transgenic mouse lines have been generated to target Cre recombinase expression to specific neuronal and glial cell populations in the central nervous system; however, information about the expression patterns of Cre recombinase lines in the retina is largely lacking. In this study, we examined and characterized the expression patterns of Cre recombinase in the retinas of 15 Cre-transgenic mouse lines. Significant Cre-induced recombination or expression of Cre recombinase was observed in the majority of these lines. In particular, we found several Cre lines in which the Cre-induced recombination was found to target exclusively or predominantly a single type or class of retinal cells, including bistratified retinal ganglion cells, starburst amacrine cells, rod bipolar cells, and Müller glial cells. In other lines, the Cre-induced recombination was found in several retinal cell types. These Cre lines provide a valuable resource for retinal research.
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Research Support, N.I.H., Extramural |
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63 |
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Bonora GM, Ivanova E, Zarytova V, Burcovich B, Veronese FM. Synthesis and characterization of high-molecular mass polyethylene glycol-conjugated oligonucleotides. Bioconjug Chem 1997; 8:793-7. [PMID: 9404651 DOI: 10.1021/bc970082p] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The use of synthetic oligonucleotides as possible drugs for human therapy is usually hampered by their low in vivo stability and capacity to achieve high concentrations at their cellular targets. To overcome this, it has been suggested that they be modified chemically. Among the various options, conjugation with short- and long-chain polyethylene glycols (PEGs) has several advantages: PEG is nontoxic and very soluble, reduces immunogenic reactions, and increases the stability of the conjugated molecules. PEG is generally joined to oligonucleotides while bound to the insoluble solid-phase supports, after their synthesis, which does not allow for their being easy scaled up. The use of the liquid-phase approach as an alternative synthetic process, utilizing the PEG polymer both as a soluble, inert synthetic support and a stabilizing agent of the oligonucleotide, is proposed. A new protocol has been set up, characterized by a stable phosphate bond between the support and the oligonucleotide. This method has been tested on a 12mer previously investigated as an antisense agent against HIV. The PEG-conjugated 12mer was efficiently synthesized and purified. It was found that the high-molecular mass PEG chain results in enzymatic stability and does not interfere with the formation of the duplex with its nucleic acid target.
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Puller C, Ivanova E, Euler T, Haverkamp S, Schubert T. OFF bipolar cells express distinct types of dendritic glutamate receptors in the mouse retina. Neuroscience 2013; 243:136-48. [PMID: 23567811 DOI: 10.1016/j.neuroscience.2013.03.054] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 12/22/2022]
Abstract
Parallel representations of the visual world are already established at the very first synapse of the visual system. Cone photoreceptors, which hyperpolarize in response to light, forward the visual signal onto distinct types of ON and OFF cone bipolar cells (BCs). In the case of OFF BCs, the glutamatergic cone input is integrated by ionotropic glutamate receptors, giving rise to a sign-preserving mode of synaptic transmission. The combination of glutamate receptor (GluR) subunits, i.e. AMPA or kainate subunits, importantly contributes to shaping the OFF bipolar cells' distinct response properties. The mouse is one of the few mammals in which the (most likely) complete set of (five) retinal OFF BC types is identified. However, it is not clear which GluR subtypes are expressed by the different mouse OFF BC types. We addressed this question by combining immunolabeling, electrical whole-cell recordings and pharmacology, and present evidence that the different types of OFF BCs express distinct types of glutamate receptors: Type 1 BCs exclusively expressed AMPA receptors, whereas type 2 and type 3a BCs expressed kainate receptors of different subunit compositions. Additionally, we found that two OFF BC types (3b and 4) very likely express both AMPA and kainate receptors but, interestingly, the two receptor subunits were not co-localized at the same dendritic site. The complex, BC type-specific expression pattern of GluRs we describe here supports their essential role in establishing parallel pathways at the first synapse of the mouse visual system.
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Research Support, Non-U.S. Gov't |
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Lu Q, Ganjawala TH, Ivanova E, Cheng JG, Troilo D, Pan ZH. AAV-mediated transduction and targeting of retinal bipolar cells with improved mGluR6 promoters in rodents and primates. Gene Ther 2016; 23:680-9. [PMID: 27115727 PMCID: PMC4863234 DOI: 10.1038/gt.2016.42] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Adeno-associated virus (AAV) vectors have been a powerful gene delivery vehicle to the retina for basic research and gene therapy. For many of these applications, achieving cell type-specific targeting and high transduction efficiency is desired. Recently, there has been increasing interest in AAV-mediated gene targeting to specific retinal bipolar cell types. A 200-bp enhancer in combination with a basal SV40 promoter has been commonly used to target transgenes into ON-type bipolar cells. In the current study, we searched for additional cis-regulatory elements in the mGluR6 gene for improving AAV-mediated transduction efficiency into retinal bipolar cells. Our results showed that the combination of the endogenous mGluR6 promoter with additional enhancers in the introns of the mGluR6 gene markedly enhanced AAV transduction efficiency as well as made the targeting more selective for rod bipolar cells in mice. Furthermore, the AAV vectors with the improved promoter could target to ON bipolar cells with robust transduction efficiency in the parafovea and the far peripheral retina of marmoset monkeys. The improved mGluR6 promoter constructs could provide a valuable tool for genetic manipulation in rod bipolar cells in mice and facilitate clinical applications for ON bipolar cell-based gene therapies.
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Research Support, N.I.H., Extramural |
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Saenz-de-Juano MD, Ivanova E, Romero S, Lolicato F, Sánchez F, Van Ranst H, Krueger F, Segonds-Pichon A, De Vos M, Andrews S, Smitz J, Kelsey G, Anckaert E. DNA methylation and mRNA expression of imprinted genes in blastocysts derived from an improved in vitro maturation method for oocytes from small antral follicles in polycystic ovary syndrome patients. Hum Reprod 2019; 34:1640-1649. [PMID: 31398248 DOI: 10.1093/humrep/dez121] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/04/2019] [Accepted: 06/17/2019] [Indexed: 11/08/2023] Open
Abstract
STUDY QUESTION Does imprinted DNA methylation or imprinted gene expression differ between human blastocysts from conventional ovarian stimulation (COS) and an optimized two-step IVM method (CAPA-IVM) in age-matched polycystic ovary syndrome (PCOS) patients? SUMMARY ANSWER No significant differences in imprinted DNA methylation and gene expression were detected between COS and CAPA-IVM blastocysts. WHAT IS KNOWN ALREADY Animal models have revealed alterations in DNA methylation maintenance at imprinted germline differentially methylated regions (gDMRs) after use of ARTs. This effect increases as more ART interventions are applied to oocytes or embryos. IVM is a minimal-stimulation ART with reduced hormone-related side effects and risks for patients. CAPA-IVM is an improved IVM system that includes a pre-maturation step (CAPA), followed by an IVM step, both in the presence of physiological compounds that promote oocyte developmental capacity. STUDY DESIGN, SIZE, DURATION For DNA methylation analysis 20 CAPA-IVM blastocysts were compared to 12 COS blastocysts. For RNA-Seq analysis a separate set of 15 CAPA-IVM blastocysts were compared to 5 COS blastocysts. PARTICIPANTS/MATERIALS, SETTING, METHODS COS embryos originated from 12 patients with PCOS (according to Rotterdam criteria) who underwent conventional ovarian stimulation. For CAPA-IVM 23 women were treated for 3-5 days with highly purified hMG (HP-hMG) and no hCG trigger was given before oocyte retrieval. Oocytes were first cultured in pre-maturation medium (CAPA for 24 h containing C-type natriuretic peptide), followed by an IVM step (30 h) in medium containing FSH and Amphiregulin. After ICSI, Day 5 or 6 embryos in both groups were vitrified and used for post-bisulphite adaptor tagging (PBAT) DNA methylation analysis or RNA-seq gene expression analysis of individual embryos. Data from specific genes and gDMRs were extracted from the PABT and RNA-seq datasets. MAIN RESULTS AND THE ROLE OF CHANCE CAPA-IVM blastocysts showed similar rates of methylation and gene expression at gDMRs compared to COS embryos. In addition, expression of major epigenetic regulators was similar between the groups. LIMITATIONS, REASONS FOR CAUTION The embryos from the COS group were generated in a range of culture media. The CAPA-IVM embryos were all generated using the same sperm donor. The DNA methylation level of gDMRs in purely in vivo-derived human blastocysts is not known. WIDER IMPLICATIONS OF THE FINDINGS A follow-up of children born after CAPA-IVM is important as it is for other new ARTs, which are generally introduced into clinical practice without prior epigenetic safety studies on human blastocysts. CAPA-IVM opens new perspectives for patient-friendly ART in PCOS. STUDY FUNDING/COMPETING INTEREST(S) IVM research at the Vrije Universiteit Brussel has been supported by grants from the Institute for the Promotion of Innovation by Science and Technology in Flanders (Agentschap voor Innovatie door Wetenschap en Technologie-IWT, project 110680), the Fund for Research Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen-FWO-AL 679 project, project G.0343.13), the Belgian Foundation Against Cancer (HOPE project, Dossier C69Ref Nr 2016-119) and the Vrije Universiteit Brussel (IOF Project 4R-ART Nr 2042). Work in G.K.'s laboratory is supported by the UK Biotechnology and Biological Sciences Research Council and Medical Research Council. The authors have no conflicts of interest.
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Mihaylov M, Ivanova E, Thibault-Starzyk F, Daturi M, Dimitrov L, Hadjiivanov K. New types of nonclassical iridium carbonyls formed in Ir-ZSM-5: a Fourier transform infrared spectroscopy investigation. J Phys Chem B 2007; 110:10383-9. [PMID: 16722743 DOI: 10.1021/jp057128t] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we report some new nonclassical carbonyls of iridium formed after CO adsorption on Ir-ZSM-5 (Ir-MFI). Mainly Ir+ cations were found on sample activated at 523 K and reduced by CO at the same temperature. With CO they formed Ir+(CO)2 gem-dicarbonyls (2104 and 2033 cm(-1)) that decomposed at 673 K without leaving a measurable fraction of monocarbonyls. The dicarbonyl structure was established by 12CO-13CO coadsortpion experiments. In the presence of CO in the gaseous phase and at ambient temperature the Ir+(CO)2 dicarbonyls were converted into Ir+(CO)3 species (2182, 2099, and 2074 cm(-1)). At 100 K these complexes are able to accommodate a fourth CO molecule thus producing tetracarbonyls (2155, 2145, 2125, and 2105 cm(-1)). The results are explained by the high coordinative unsaturation of the Ir+ cations in the ZSM-5 matrix. This is also the reason for the formation of mixed Ir+(H2O)(CO)2 species after CO-H2O coadsorption (2087 and 2015 cm(-1)). Evacuation of the sample at 673 K, followed by treatment with CO at 523 K, generates Ir2+ cations. With CO these cations form another kind of geminal complex, namely, Ir2+(CO)2 species (2173 and 2129 cm(-1)). Here again, the structure was confirmed by 12CO-13CO coadsortpion experiments. These dicarbonyls are decomposed at 573 K (again without producing monocarbonyls) and are able to accommodate additionally neither CO nor water molecules. The results are explained by the smaller cationic radius of Ir2+ (as compared to Ir+), which is associated with a decrease of the number of ligands required for coordinative saturation.
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Mitsai E, Kuchmizhak A, Pustovalov E, Sergeev A, Mironenko A, Bratskaya S, Linklater DP, Balčytis A, Ivanova E, Juodkazis S. Chemically non-perturbing SERS detection of a catalytic reaction with black silicon. NANOSCALE 2018; 10:9780-9787. [PMID: 29767209 DOI: 10.1039/c8nr02123f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
All-dielectric resonant micro- and nano-structures made of high-index dielectrics have recently emerged as a promising surface-enhanced Raman scattering (SERS) platform which can complement or potentially replace the metal-based counterparts in routine sensing measurements. These unique structures combine the highly-tunable optical response and high field enhancement with the non-invasiveness, i.e. chemically non-perturbing the analyte, simple chemical modification and recyclability. Meanwhile, commercially competitive fabrication technologies for mass production of such structures are still missing. Here, we attest a chemically inert black silicon (b-Si) substrate consisting of randomly-arranged spiky Mie resonators for a true non-invasive (chemically non-perturbing) SERS identification of the molecular fingerprints at low concentrations. Based on the comparative in situ SERS tracking of the para-aminothiophenol (PATP)-to-4,4'-dimercaptoazobenzene (DMAB) catalytic conversion on the bare and metal-coated b-Si, we justify the applicability of the metal-free b-Si for ultra-sensitive non-invasive SERS detection at a concentration level as low as 10-6 M. We performed supporting finite-difference time-domain (FDTD) calculations to reveal the electromagnetic enhancement provided by an isolated spiky Si resonator in the visible spectral range. Additional comparative SERS studies of the PATP-to-DMAB conversion performed with a chemically active bare black copper oxide (b-CuO) substrate as well as SERS detection of the slow daylight-driven PATP-to-DMAB catalytic conversion in the aqueous methanol solution loaded with colloidal silver nanoparticles (Ag NPs) confirm the non-invasive SERS performance of the all-dielectric crystalline b-Si substrate. A proposed SERS substrate can be fabricated using the easy-to-implement scalable technology of plasma etching amenable on substrate areas over 10 × 10 cm2 making such inexpensive all-dielectric substrates promising for routine SERS applications, where the non-invasiveness is of high importance.
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Djondjurov L, Ivanova E, Tsanev R. Two chromatin fractions with different metabolic properties of non-histone proteins and of newly synthesized RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 97:133-9. [PMID: 289497 DOI: 10.1111/j.1432-1033.1979.tb13094.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Digestion of chromatin with micrococcal nuclease under mild conditions results in the release of a minor chromatin fraction showing an increased RNA and non-histone protein content, a fast turnover of the non-histone proteins and the presence of rapidly labelled heterogeneous nuclear RNA (hnRNA) with half-life of about 20 min. Further digestion of the chromatin leads to the elimination of about 19% of the initial chromosomal DNA, thus leaving a second chromatin fraction relatively resistant to nuclease attack. This fraction has a low protein and RNA content and contains only metabolically stable non-histone proteins. No differences in the histone complement of the two fractions was found except for a 40% deficiency of H1 in the minor fraction.
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Bonartsev AP, Zharkova II, Yakovlev SG, Myshkina VL, Makhina TK, Zernov AL, Kudryashova KS, Feofanov AV, Akulina EA, Ivanova EV, Zhuikov VA, Andreeva NV, Voinova VV, Bessonov IV, Kopitsyna MV, Morozov AS, Bonartseva GA, Shaitan KV, Kirpichnikov MP. 3D-Scaffolds from Poly(3-hydroxybutyrate)Poly(ethylene glycol) Copolymer for Tissue Engineering. J BIOMATER TISS ENG 2016; 6:42-52. [DOI: 10.1166/jbt.2016.1414] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
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Berger A, Ivanova E, Gareau C, Scherrer A, Mazroui R, Strub K. Direct binding of the Alu binding protein dimer SRP9/14 to 40S ribosomal subunits promotes stress granule formation and is regulated by Alu RNA. Nucleic Acids Res 2014; 42:11203-17. [PMID: 25200073 PMCID: PMC4176187 DOI: 10.1093/nar/gku822] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Stress granules (SGs) are formed in response to stress, contain mRNAs, 40S ribosomal subunits, initiation factors, RNA-binding and signaling proteins, and promote cell survival. Our study describes a novel function of the protein heterodimer SRP9/14 and Alu RNA in SG formation and disassembly. In human cells, SRP9/14 exists assembled into SRP, bound to Alu RNA and as a free protein. SRP9/14, but not SRP, localizes to SGs following arsenite or hippuristanol treatment. Depletion of the protein decreases SG size and the number of SG-positive cells. Localization and function of SRP9/14 in SGs depend primarily on its ability to bind directly to the 40S subunit. Binding of SRP9/14 to 40S and Alu RNA is mutually exclusive indicating that the protein alone is bound to 40S in SGs and that Alu RNA might competitively regulate 40S binding. Indeed, by changing the effective Alu RNA concentration in the cell or by expressing an Alu RNA binding-defective protein we were able to influence SG formation and disassembly. Our findings suggest a model in which SRP9/14 binding to 40S promotes SG formation whereas the increase in cytoplasmic Alu RNA following stress promotes disassembly of SGs by disengaging SRP9/14 from 40S.
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Research Support, Non-U.S. Gov't |
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Fraikin GY, Strakhovskaya MG, Ivanova EV, Rubin AB. Near-UV activation of enzymatic conversion of 5-hydroxytryptophan to serotonin. Photochem Photobiol 1989; 49:475-7. [PMID: 2786220 DOI: 10.1111/j.1751-1097.1989.tb09197.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Near-UV (337 nm) photoactivation of the 5-hydroxytryptophan decarboxylation reaction producing serotonin has been observed. The photoactivation effect was investigated as a function of fluence rate and fluence, and pH. Photoactivation of decarboxylase activity was found to occur at nearly neutral pH values (low activity of the enzyme in the dark). The findings indicate that the effect of light is similar to a pH shift toward the acid region, which causes the enzyme conversion from the inactive to active form. Pyridoxal phosphate, the decarboxylase cofactor, in the form of an adduct absorbing at 330-340 nm, is suggested as a candidate for the role of the photoactive chromophore of decarboxylase.
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Mihaylov M, Andonova S, Chakarova K, Vimont A, Ivanova E, Drenchev N, Hadjiivanov K. An advanced approach for measuring acidity of hydroxyls in confined space: a FTIR study of low-temperature CO and (15)N2 adsorption on MOF samples from the MIL-53(Al) series. Phys Chem Chem Phys 2015; 17:24304-14. [PMID: 26325096 DOI: 10.1039/c5cp04139b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acidity of solids is decisive for their interaction with guest molecules. One of the most used methods for measuring the acidity of surface hydroxyl groups is the hydrogen bond method based on the spectral shift of the OH stretching modes induced by the adsorption of weak bases. However, many materials of practical interest (e.g. metal organic frameworks, zeolites, etc.) are porous and the OH groups are involved in H-bonding with framework basic sites. Here we show that MIL-53(Al) and NH2-MIL-53(Al) samples are characterized by one type of structural hydroxyl but three IR bands are detected at 100 K with these materials (at 3721, 3711 and 3683 cm(-1)). These bands are assigned to structural hydroxyls involved in H-bonding with different strengths. There is no correlation between the acidities of the hydroxyls, as measured by low-temperature CO or (15)N2 adsorption, and the main reason for this is the pre-existing H-bond. A method for the estimation of the intrinsic frequency of the OH groups (i.e. if not participating in H-bonds), based on the analysis of the spectral data obtained with two molecular probes, is proposed. According to this method, the OH stretching frequency of the structural hydroxyls of MIL-53(Al) samples is determined to be 3727 cm(-1). The formation of 1 : 1 adducts between the hydroxyls and strong bases leads to breaking of the pre-existing H-bonds. When the base is weak, bifurcated complexes are formed which slightly affects the spectral shift. The conclusions derived here considerably broaden the applicability of the H-bond method for assessing protonic acidity of materials and systems where the OH groups are preliminarily involved in H-bonding.
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Tsanev R, Djondjurov L, Ivanova E. Cell cycle dependent turnover of non-histone proteins in chromatin. Exp Cell Res 1974; 84:137-42. [PMID: 4856333 DOI: 10.1016/0014-4827(74)90389-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Kondakova IV, Spirina LV, Koval VD, Shashova EE, Choinzonov EL, Ivanova EV, Kolomiets LA, Chernyshova AL, Slonimskaya EM, Usynin EA, Afanas’ev SG. Chymotrypsin-like activity and subunit composition of proteasomes in human cancers. Mol Biol 2014. [DOI: 10.1134/s002689331403011x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Djondjurov L, Ivanova E, Markov D, Bardarov S, Sachsenmaier W. Is the nuclear matrix the site of DNA replication in eukaryotic cells? Exp Cell Res 1986; 164:79-96. [PMID: 3956599 DOI: 10.1016/0014-4827(86)90456-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Four types of experiment were carried out to test the recently proposed model of matrix-bound replication in eukaryotic cells. In experiments with pulse-labelling we found preferential association of newly replicated DNA with the matrix only when the procedure for isolation includes first high-salt treatment of isolated nuclei and then digestion with nucleases, or when prior to digestion the nuclei have been stored for a prolonged time. In both cases, however, evidence was found that this preferential association is due to a secondary, artifactual binding of the newly replicated chromatin region to the matrix elements. Pulse-chase experiments and experiments with continuous labelling were carried out to answer the question whether during replication the DNA is reeled through the replication complexes, i.e., whether newly replicated DNA is temporarily or permanently associated with the matrix. The results showed that at that time the matrix DNA does not move from its site of attachment. Since, according to the model of matrix-bound replication, the forks are assumed to be firmly anchored to high-salt resistant proteinaceous matrix structures, the chromatin fragments isolated with endonuclease not recognizing newly replicated DNA and purified by sucrose gradient centrifugation should be free of replication intermediates. The electronmicroscopic analysis of such fragments revealed the existence of intact replication micro-bubbles. Moreover, the fragments with replication configurations appeared as smooth chromatin fibres not attached to elements characteristic for the matrix. All these experiments suggest that the nuclear skeleton is not a native site of DNA replication in eukaryotic cells.
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Miroshnichenko DV, Drozdnik ID, Kaftan YS, Ivanova EV, Sirokotyaga KN, Desna NA. Kinetic characteristics of coal oxidation. COKE AND CHEMISTRY 2012. [DOI: 10.3103/s1068364x12030039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sviridov AV, Shushkova TV, Ermakova IT, Ivanova EV, Epiktetov DO, Leont'evskii AA. [Microbial degradation of glyphosate herbicides (review)]. PRIKLADNAIA BIOKHIMIIA I MIKROBIOLOGIIA 2015; 51:183-90. [PMID: 26027353 DOI: 10.7868/s0555109915020221] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review analyzes the issues associated with biodegradation of glyphosate (N-(phosphonomethyl)glycine), one of the most widespread herbicides. Glyphosate can accumulate in natural environments and can be toxic not only for plants but also for animals and bacteria. Microbial transformation and mineralization ofglyphosate, as the only means of its rapid degradation, are discussed in detail. The different pathways of glyphosate catabolism employed by the known destructing bacteria representing different taxonomic groups are described. The potential existence of alternative glyphosate degradation pathways, apart from those mediated by C-P lyase and glyphosate oxidoreductase, is considered. Since the problem of purifying glyphosate-contaminated soils and water bodies is a topical issue, the possibilities of applying glyphosate-degrading bacteria for their bioremediation are discussed.
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Tsvetkov S, Ivanova E, Djondjurov L. Metabolic behaviors of the core histones in proliferating Friend cells. Exp Cell Res 1989; 180:94-105. [PMID: 2909397 DOI: 10.1016/0014-4827(89)90215-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This study examines the turnover of the core histones in proliferating Friend cells. It was calculated that these proteins turn over with half-lives of 21.6 days for H2A, 13.8 days for H2B, 43.3 days for H3, and 138.6 days for H4. The significant differences in the half-lives of the four core histones indicate that the protein moiety of the nucleosome is not replaced as one entire unit but as a "mosaic" in which each component follows its own rate of replacement. In some experiments the turnover rates of the variants of H2A, H2B, and H3 were compared. The results did not indicate any differences among these histone variants, suggesting that they are not excluded from the mechanisms controlling histone turnover. Metabolic heterogeneity was discovered, however, when the turnover rates of the acetylated and nonacetylated molecules of histone H4 were followed: it appeared that the acetylated molecules are replaced 2.5 times faster. The comparison of the rate of replacement of the histones in proliferating and differentiated cells from one site and their level of acetylation from another suggests that this postsynthetic modification might be involved in the control of histone metabolism. Such a conclusion is supported also by a number of model experiments.
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Bonartsev AP, Zharkova II, Yakovlev SG, Myshkina VL, Mahina TK, Voinova VV, Zernov AL, Zhuikov VA, Akoulina EA, Ivanova EV, Kuznetsova ES, Shaitan KV, Bonartseva GA. Biosynthesis of poly(3-hydroxybutyrate) copolymers by Azotobacter chroococcum 7B: A precursor feeding strategy. Prep Biochem Biotechnol 2017; 47:173-184. [PMID: 27215309 DOI: 10.1080/10826068.2016.1188317] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A precursor feeding strategy for effective biopolymer producer strain Azotobacter chroococcum 7B was used to synthesize various poly(3-hydroxybutyrate) (PHB) copolymers. We performed experiments on biosynthesis of PHB copolymers by A. chroococcum 7B using various precursors: sucrose as the primary carbon source, various carboxylic acids and ethylene glycol (EG) derivatives [diethylene glycol (DEG), triethylene glycol (TEG), poly(ethylene glycol) (PEG) 300, PEG 400, PEG 1000] as additional carbon sources. We analyzed strain growth parameters including biomass and polymer yields as well as molecular weight and monomer composition of produced copolymers. We demonstrated that A. chroococcum 7B was able to synthesize copolymers using carboxylic acids with the length less than linear 6C, including poly(3-hydroxybutyrate-co-3-hydroxy-4-methylvalerate) (PHB-4MHV) using Y-shaped 6C 3-methylvaleric acid as precursor as well as EG-containing copolymers: PHB-DEG, PHB-TEG, PHB-PEG, and PHB-HV-PEG copolymers using short-chain PEGs (with n ≤ 9) as precursors. It was shown that use of the additional carbon sources caused inhibition of cell growth, decrease in polymer yields, fall in polymer molecular weight, decrease in 3-hydroxyvalerate content in produced PHB-HV-PEG copolymer, and change in bacterial cells morphology that were depended on the nature of the precursors (carboxylic acids or EG derivatives) and the timing of its addition to the growth medium.
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Pyshnyi DV, Pyshnaya I, Levina A, Goldberg E, Zarytova V, Knorre D, Ivanova E. Thermodynamic analysis of stacking hybridization of oligonucleotides with DNA template. J Biomol Struct Dyn 2001; 19:555-70. [PMID: 11790153 DOI: 10.1080/07391102.2001.10506763] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Contiguous stacking hybridization of oligodeoxyribonucleotides with DNA as template was investigated using three types of complexes: oligonucleotide contiguously stacked with the stem of the preformed minihairpin (complexes I), oligonucleotide tandems containing two (complexes II) or three (complexes III) short oligomers with a common DNA template. Enthalpy Delta H degrees and entropy Delta S degrees of the coaxial stacking of adjacent duplexes were determined for GC/G*pC, GT/A*pC, AC/G*pT, AT/A*pT, CT/A*pG, AG/C*pT, AA/T*pT and TT/A*pA nicked (*) dinucleotide base pairs. The maximal efficiency of co-operative interaction was found for the GC/G*pC interface (Delta G degrees(NN/N*pN)=-2.7 kcal/mol) and the minimal one for the AA/T*pT interface (Delta G degrees(NN/N*pN)=-1.2 kcal/mol) at 37 degrees C. As a whole, the efficiency of the base pairs interaction Delta G degrees(NN/N*pN) in the nick is not lower than that within the intact DNA helix (Delta G degrees(NN/NN)). These observed Delta G degrees(NN/N*pN) values are proposed may include the effect of the partial removal of fraying at the adjacent helix ends additionally to the effect of the direct stacking of the terminal base pairs in the duplex junction (Delta G degrees(NN/NN). The thermodynamic parameters have been found to describe adequately the formation of all tandem complexes of the II and III types with oligonucleotides of various length and hybridization properties. The performed thermodynamic analysis reveals features of stacking oligonucleotide hybridization which allow one to predict the temperature dependence of association of oligonucleotides and the DNA template within tandem complexes as well as to determine optimal concentration for formation of these complexes characterized by high co-operativity level.
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Benkhedda K, Infante HG, Ivanova E, Adams F. Electrothermal atomic absorption spectrometric determination of cobalt in biological samples and natural waters using a flow injection system with on-line preconcentration by ion-pair adsorption in a knotted reactor. FRESENIUS' JOURNAL OF ANALYTICAL CHEMISTRY 2000; 368:288-92. [PMID: 11220594 DOI: 10.1007/s002160000419] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An on-line flow injection preconcentration-ETAAS method is developed for trace determination of cobalt in biological materials and natural samples by ion-pair sorption on the inner walls of a PTFE knotted reactor. The ion-pair is formed between the negatively charged cobalt-nitroso-R-salt complex and the tetrabutylammonium counter-ion. An enhancement factor of 15, a sampling frequency of 17 and a concentration efficiency of 4 are obtained for a preconcentration time of 60 s and a sample loading flow rate of 5 mL min(-1). The detection limit (3sigma) is 5 ng L(-1). The relative standard deviation at the 0.2 microg L(-1) level is 2.3%. The analytical results obtained for standard reference materials are in good agreement with the certified or indicated values and satisfactory recoveries of spiked cobalt in tap water are obtained.
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Malinina L, Tereshko V, Ivanova E, Subirana JA, Zarytova V, Nekrasov Y. Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG). Biophys J 1998; 74:2482-90. [PMID: 9591674 PMCID: PMC1299590 DOI: 10.1016/s0006-3495(98)77956-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C222(1) with a = 69.73, b = 52.63, and c = 26.21 A, and to the space group P2(1) with a = 49.87, b = 41.26, c = 21.91 A, and gamma = 97.12 degrees. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base-phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes.
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Lu Q, Ivanova E, Pan ZH. Characterization of green fluorescent protein-expressing retinal cone bipolar cells in a 5-hydroxytryptamine receptor 2a transgenic mouse line. Neuroscience 2009; 163:662-8. [PMID: 19589372 PMCID: PMC2769501 DOI: 10.1016/j.neuroscience.2009.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 07/01/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
Retinal bipolar cells relay visual information from photoreceptors to third-order retinal neurons. Bipolar cells, comprising multiple types, play an essential role in segregating visual information into multiple parallel pathways in the retina. The identification of molecular markers that can label specific retinal bipolar cells could facilitate the investigation of bipolar cell functions in the retina. Transgenic mice with specific cell type(s) labeled with green fluorescent protein (GFP) have become a powerful tool for morphological and functional studies of neurons in the CNS, including the retina. In this study, we report a 5-hydroxytryptamine receptor 2a (5-HTR2a) transgenic mouse line in which expression of GFP was observed in two populations of bipolar cells in the retina. Based on the terminal stratification and immunostaining, all the strongly GFP-labeled bipolar cells were found to be type 4 cone bipolar cells. A small population of weakly labeled bipolar cells was also observed, which may represent type 8 or 9 cone bipolar cells. GFP expression in retinal cone bipolar cells was seen as early as postnatal day 5. In addition, despite severe retinal degeneration due to the presence of the rd1 mutation in this transgenic line, the density of GFP-labeled cone bipolar cells remained stable up to at least 6 months of age. This transgenic mouse line will be a useful tool for the study of type 4 cone bipolar cells in the retina under both normal and disease conditions.
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Zinurova EG, Kabal"nova NN, Shereshovets VV, Ivanova EV, Shults EE, Tolstikov GA, Yunusov MS. Russ Chem Bull 2001; 50:720-723. [DOI: 10.1023/a:1011385500970] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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