SRI of Physical Chemical Medicine

Moscow, Russia

SRI of Physical Chemical Medicine

Moscow, Russia
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Radchenko V.V.,Kuban State University | Ilnitskaya E.V.,Kuban State University | Rodionova A.S.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Shuvaeva T.M.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | And 5 more authors.
Russian Journal of Biopharmaceuticals | Year: 2016

Comparative analysis of the differential distribution of members of the autochthonous microflora in distinct compartments of the gastrointestinal tract of the Japanese quail (Coturnix japonica) was carried out using the method of quantitative real-time PCR. The study of the culture characteristics and morphology of mixed cultures and individual clones of species-associated microorganisms was conducted. The isolated cultures of the strains of the most abundant genera Lactobacillus, Bifidobacterium and Bacillus were obtained. According to the data of the analysis of the nucleotide sequence of 16S rRNA gene, the isolated strains were attributed to the species L. agilis, L. salivarius, L. intermedius, Bifidobacterium spp., Bacillus spp., B. Subtilis, and B.megaterium. The intraspecific genetic differences between seven isolated strains of bacteria were elucidated using the molecular typing methods. The new approaches for an optimization of the existing domestic probiotics and the development of the new highly efficient ones were suggested on the basis of the identified evolutionary established microbial associations that are natural for those species. © 2016, Folium Ltd. All rights reserved.


Boyko K.,RAS A.N. Bach Institute of Biochemistry | Gorbacheva M.,RAS A.N. Bach Institute of Biochemistry | Rakitina T.,RAS Research Center Kurchatov Institute | Korzhenevskiy D.,RAS Research Center Kurchatov Institute | And 4 more authors.
Acta Crystallographica Section F:Structural Biology Communications | Year: 2015

HU proteins belong to the nucleoid-associated proteins (NAPs) that are involved in vital processes such as DNA compaction and reparation, gene transcription etc. No data are available on the structures of HU proteins from mycoplasmas. To this end, the HU protein from the parasitic mycoplasma Spiroplasma melliferum KC3 was cloned, overexpressed in Escherichia coli and purified to homogeneity. Prismatic crystals of the protein were obtained by the vapour-diffusion technique at 4°C. The crystals diffracted to 1.36Å resolution (the best resolution ever obtained for a HU protein). The diffraction data were indexed in space group C2 and the structure of the protein was solved by the molecular-replacement method with one monomer per asymmetric unit. © 2015 International Union of Crystallography.


PubMed | RAS A.N. Bach Institute of Biochemistry, SRI of Physical Chemical Medicine and National Research Center `Kurchatov Institute
Type: Journal Article | Journal: Acta crystallographica. Section F, Structural biology communications | Year: 2015

HU proteins belong to the nucleoid-associated proteins (NAPs) that are involved in vital processes such as DNA compaction and reparation, gene transcription etc. No data are available on the structures of HU proteins from mycoplasmas. To this end, the HU protein from the parasitic mycoplasma Spiroplasma melliferum KC3 was cloned, overexpressed in Escherichia coli and purified to homogeneity. Prismatic crystals of the protein were obtained by the vapour-diffusion technique at 4C. The crystals diffracted to 1.36 resolution (the best resolution ever obtained for a HU protein). The diffraction data were indexed in space group C2 and the structure of the protein was solved by the molecular-replacement method with one monomer per asymmetric unit.


Kirillova Y.,Moscow State University | Boyarskaya N.,Moscow State University | Dezhenkov A.,Moscow State University | Tankevich M.,Moscow State University | And 6 more authors.
PLoS ONE | Year: 2015

New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA. © 2015 Kirillova et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in anymedium, provided the original author and source are credited.


Tsvetkov V.,RAS Topchiev Institute of Petrochemical Synthesis | Pozmogova G.,SRI of Physical Chemical Medicine | Varizhuk A.,RAS Engelhardt Institute of Molecular Biology
Journal of Biomolecular Structure and Dynamics | Year: 2016

Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe GQ geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed. © 2015 The Author(s).


PubMed | Moscow State University, SRI of Physical Chemical Medicine and RAS Engelhardt Institute of Molecular Biology
Type: Journal Article | Journal: PloS one | Year: 2015

New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral - and -monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified -S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA.


Kalinina N.,Moscow State University | Kharlampieva D.,SRI of Physical Chemical Medicine | Loguinova M.,SRI of Physical Chemical Medicine | Butenko I.,SRI of Physical Chemical Medicine | And 11 more authors.
Stem Cell Research and Therapy | Year: 2015

Introduction: This study was aimed at deciphering the secretome of adipose-derived mesenchymal stromal cells (ADSCs) cultured in standard and hypoxic conditions to reveal proteins, which may be responsible for regenerative action of these cells. Methods: Human ADSCs were isolated from 10 healthy donors and cultured for 3-4 passages. Cells were serum deprived and cell purity was assessed using multiple cell surface markers. Conditioned media was collected and analyzed using LC-MS with a focus on characterizing secreted proteins. Results: Purity of the ADSC assessed as CD90+/CD73+/CD105+/CD45-/CD31- cells was greater than 99 % and viability was greater than 97 %. More than 600 secreted proteins were detected in conditioned media of ADSCs. Of these 100 proteins were common to all cultures and included key molecules involved in tissue regeneration such as collagens and collagen maturation enzymes, matrix metalloproteases, matricellular proteins, macrophage-colony stimulating factor and pigment epithelium derived factor. Common set of proteins also included molecules, which contribute to regenerative processes but were not previously associated with ADSCs. These included olfactomedin-like 3, follistatin-like 1 and prosaposin. In addition, ADSCs from the different subjects secreted proteins, which were variable between different cultures. These included proteins with neurotrophic activities, which were not previously associated with ADSCs, such as mesencephalic astrocyte-derived neurotrophic factor, meteorin and neuron derived neurotrophic factor. Hypoxia resulted in secretion of 6 proteins, the most prominent included EGF-like repeats and discoidin I-like domains 3, adrenomedullin and ribonuclease 4 of RNase A family. It also caused the disappearance of 8 proteins, including regulator of osteogenic differentiation cartilage-associated protein. Conclusions: Human ADSCs with CD90+/CD73+/CD105+/CD45-/CD31-/PDGFRβ+/NG2+/CD146+(-) immunophenotype secrete a large array of proteins, the most represented group is comprised of extracellular matrix components. Number of secreted proteins is largely unaffected by prolonged hypoxia. Variability in the secretion of several proteins from cultured ADSCs of individual subjects suggests that these cells exist as a heterogeneous population containing functionally distinct subtypes, which differ in numbers between donors. © 2015 Kalinina et al.


PubMed | Moscow State University and SRI of Physical Chemical Medicine
Type: | Journal: Stem cell research & therapy | Year: 2015

This study was aimed at deciphering the secretome of adipose-derived mesenchymal stromal cells (ADSCs) cultured in standard and hypoxic conditions to reveal proteins, which may be responsible for regenerative action of these cells.Human ADSCs were isolated from 10 healthy donors and cultured for 3-4 passages. Cells were serum deprived and cell purity was assessed using multiple cell surface markers. Conditioned media was collected and analyzed using LC-MS with a focus on characterizing secreted proteins.Purity of the ADSC assessed as CD90+/CD73+/CD105+/CD45-/CD31- cells was greater than 99 % and viability was greater than 97 %. More than 600 secreted proteins were detected in conditioned media of ADSCs. Of these 100 proteins were common to all cultures and included key molecules involved in tissue regeneration such as collagens and collagen maturation enzymes, matrix metalloproteases, matricellular proteins, macrophage-colony stimulating factor and pigment epithelium derived factor. Common set of proteins also included molecules, which contribute to regenerative processes but were not previously associated with ADSCs. These included olfactomedin-like 3, follistatin-like 1 and prosaposin. In addition, ADSCs from the different subjects secreted proteins, which were variable between different cultures. These included proteins with neurotrophic activities, which were not previously associated with ADSCs, such as mesencephalic astrocyte-derived neurotrophic factor, meteorin and neuron derived neurotrophic factor. Hypoxia resulted in secretion of 6 proteins, the most prominent included EGF-like repeats and discoidin I-like domains 3, adrenomedullin and ribonuclease 4 of RNase A family. It also caused the disappearance of 8 proteins, including regulator of osteogenic differentiation cartilage-associated protein.Human ADSCs with CD90+/CD73+/CD105+/CD45-/CD31-/PDGFR+/NG2+/CD146+(-) immunophenotype secrete a large array of proteins, the most represented group is comprised of extracellular matrix components. Number of secreted proteins is largely unaffected by prolonged hypoxia. Variability in the secretion of several proteins from cultured ADSCs of individual subjects suggests that these cells exist as a heterogeneous population containing functionally distinct subtypes, which differ in numbers between donors.


PubMed | SRI of Physical Chemical Medicine
Type: Journal Article | Journal: Journal of biomolecular structure & dynamics | Year: 2016

Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe GQ geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed.

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