Publications by authors named "Dmitry Semenov"

38 Publications

Tissue optical properties combined with machine learning enables estimation of articular cartilage composition and functional integrity.

Biomed Opt Express 2020 Nov 19;11(11):6480-6494. Epub 2020 Oct 19.

University of Eastern Finland, Department of Applied Physics, Yliopistonranta 1, Kuopio 70120, Finland.

Absorption and reduced scattering coefficients ( ) of biological tissues have shown significant potential in biomedical applications. Thus, they are effective parameters for the characterization of tissue integrity and provide vital information on the health of biological tissues. This study investigates the potential of optical properties ( ) for estimating articular cartilage composition and biomechanical properties using multivariate and machine learning techniques. The results suggest that μ could optimally estimate cartilage proteoglycan content in the superficial zone, in addition to its equilibrium modulus. While could effectively estimate the proteoglycan content of the middle and deep zones in addition to the instantaneous and dynamic moduli of articular cartilage.
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http://dx.doi.org/10.1364/BOE.402929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687936PMC
November 2020

Diffusion processes modeling in magnetic resonance imaging.

Insights Imaging 2020 Apr 28;11(1):60. Epub 2020 Apr 28.

Central Institute of Traumatology and Orthopaedics named after N. N. Priorov, 10, ul. Priorova, Moscow, 127299, Russia.

Background: The paper covers modern approaches to the evaluation of neoplastic processes with diffusion-weighted imaging (DWI) and proposes a physical model for monitoring the primary quantitative parameters of DWI and quality assurance. Models of hindered and restricted diffusion are studied.

Material And Method: To simulate hindered diffusion, we used aqueous solutions of polyvinylpyrrolidone with concentrations of 0 to 70%. We created siloxane-based water-in-oil emulsions that simulate restricted diffusion in the intracellular space. To obtain a high signal on DWI in the broadest range of b values, we used silicon oil with high T: cyclomethicone and caprylyl methicone. For quantitative assessment of our phantom, we performed DWI on 1.5T magnetic resonance scanner with various fat suppression techniques. We assessed water-in-oil emulsion as an extracorporeal source signal by simultaneously scanning a patient in whole-body DWI sequence.

Results: We developed phantom with control substances for apparent diffusion coefficient (ADC) measurements ranging from normal tissue to benign and malignant lesions: from 2.29 to 0.28 mm/s. The ADC values of polymer solutions are well relevant to the mono-exponential equation with the mean relative difference of 0.91%.

Conclusion: The phantom can be used to assess the accuracy of the ADC measurements, as well as the effectiveness of fat suppression. The control substances (emulsions) can be used as a body marker for quality assurance in whole-body DWI with a wide range of b values.
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http://dx.doi.org/10.1186/s13244-020-00863-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188746PMC
April 2020

Are Small Nucleolar RNAs "CRISPRable"? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells.

Front Pharmacol 2019 4;10:1246. Epub 2019 Nov 4.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.

CRISPR technologies are nowadays widely used for targeted knockout of numerous protein-coding genes and for the study of various processes and metabolic pathways in human cells. Most attention in the genome editing field is now focused on the cleavage of protein-coding genes or genes encoding long non-coding RNAs (lncRNAs), while the studies on targeted knockout of intron-encoded regulatory RNAs are sparse. Small nucleolar RNAs (snoRNAs) present a class of non-coding RNAs encoded within the introns of various host genes and involved in post-transcriptional maturation of ribosomal RNAs (rRNAs) in eukaryotic cells. Box C/D snoRNAs direct 2'-O-methylation of rRNA nucleotides. These short RNAs have specific elements in their structure, namely, boxes C and D, and a target-recognizing region. Here, we present the study devoted to CRISPR/Cas9-mediated editing of box C/D snoRNA genes in . We obtained monoclonal cell lines carrying mutations in snoRNA genes and analyzed the levels of the mutant box C/D snoRNA as well as the 2'-O-methylation status of the target rRNA nucleotide in the obtained cells. Mutations in in the obtained monoclonal cell line were shown to result in aberrant splicing of with exclusion of exons 3 to 5, which was confirmed by RT-PCR and RNA-Seq. The obtained results suggest that contains an element for binding of some factors regulating maturation of Gas5 pre-lncRNA. We suggest that METTL3/METTL14 is among such factors, and mA-methylation pathways are involved in regulation of splicing. Our results shell light on the role of in regulating splicing of the host gene.
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http://dx.doi.org/10.3389/fphar.2019.01246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856654PMC
November 2019

Spin-optoelectronic devices based on hybrid organic-inorganic trihalide perovskites.

Nat Commun 2019 01 10;10(1):129. Epub 2019 Jan 10.

Department of Physics & Astronomy, University of Utah, Salt Lake City, UT, 84112, USA.

Recently the hybrid organic-inorganic trihalide perovskites have shown remarkable performance as active layers in photovoltaic and other optoelectronic devices. However, their spin characteristic properties have not been fully studied, although due to the relatively large spin-orbit coupling these materials may show great promise for spintronic applications. Here we demonstrate spin-polarized carrier injection into methylammonium lead bromide films from metallic ferromagnetic electrodes in two spintronic-based devices: a 'spin light emitting diode' that results in circularly polarized electroluminescence emission; and a 'vertical spin valve' that shows giant magnetoresistance. In addition, we also apply a magnetic field perpendicular to the injected spins orientation for measuring the 'Hanle effect', from which we obtain a relatively long spin lifetime for the electrically injected carriers. Our measurements initiate the field of hybrid perovskites spin-related optoelectronic applications.
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http://dx.doi.org/10.1038/s41467-018-07952-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328620PMC
January 2019

Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs.

Genes (Basel) 2018 Nov 2;9(11). Epub 2018 Nov 2.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.

Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m⁵C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.
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http://dx.doi.org/10.3390/genes9110531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266926PMC
November 2018

Characterization of primary normal and malignant breast cancer cell and their response to chemotherapy and immunostimulatory agents.

BMC Cancer 2018 Jul 9;18(1):728. Epub 2018 Jul 9.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue, 8, 630090, Novosibirsk, Russia.

Background: The phenomenon of chemotherapy-resistant cancers has necessitated the development of new therapeutics as well as the identification of specific prognostic markers to predict the response to novel drugs. Primary cancer cells provide a model to study the multiplicity of tumourigenic transformation, to investigate alterations of the cellular response to various molecular stimuli, and to test therapeutics for cancer treatment.

Methods: Here, we developed primary cultures of human breast tissue - normal cells (BN1), cancer cells (BC5), and cells from a chemotherapy-treated tumour (BrCCh1) to compare their response to conventional chemotherapeutics and to innate immunity stimulators with that of the immortalized breast cells MCF7, MDA-MB-231, and MCF10A. Expression of the progesterone receptor (PGR), oestrogen receptor (ER) α and β, human epidermal growth factor receptor (HER) 2 and 3 and aromatase CYP19, as well as expression of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) mRNA in human breast cells were characterized.

Results: We revealed that BC5 carcinoma cells were PGR/ERb/ERa/Cyp19, the BrCCh1 cells that originated from the recurrent tumour were PGR/ERb/ERa/Cyp19, and normal BN cells were PGR/ERb/ERa/Cyp19. The treatment of primary culture cells with antitumour therapeutics revealed that BrCCh1 cells were doxorubicine-resistant and sensitive to cisplatin. BC5 cells exhibited low sensitivity to tamoxifen and cisplatin. The innate immunity activators interferon-α and an artificial small nucleolar RNA analogue increased expression of IFIT3 at different levels in primary cells and in the immortalized breast cells MCF7, MDA-MB-231, and MCF10A. The relative level of activation of IFIT3 expression was inversely correlated with the baseline level of IFIT3 mRNA expression in breast cell lines.

Conclusion: Our data demonstrated that primary cancer cells are a useful model for the development of novel cancer treatments. Our findings suggest that expression of IFIT3 mRNA can be used as a prognostic marker of breast cancer cell sensitivity to immunostimulating therapeutics.
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http://dx.doi.org/10.1186/s12885-018-4635-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6038312PMC
July 2018

Origin of the RNA world: The fate of nucleobases in warm little ponds.

Proc Natl Acad Sci U S A 2017 10 2;114(43):11327-11332. Epub 2017 Oct 2.

Planet and Star Formation Department, Max Planck Institute for Astronomy, 69117 Heidelberg, Germany.

Before the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favorable environments on early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet-dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth's early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (less than a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean, but this increasing availability of "targets" for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods, mean that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet-dry cycles. Under these conditions, RNA polymers likely appeared before 4.17 billion years ago.
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http://dx.doi.org/10.1073/pnas.1710339114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664528PMC
October 2017

Variety of RNAs in Peripheral Blood Cells, Plasma, and Plasma Fractions.

Biomed Res Int 2017 3;2017:7404912. Epub 2017 Jan 3.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue 8, Novosibirsk 630090, Russia.

Human peripheral blood contains RNA in cells and in extracellular membrane vesicles, microvesicles and exosomes, as well as in cell-free ribonucleoproteins. Circulating mRNAs and noncoding RNAs, being internalized, possess the ability to modulate vital processes in recipient cells. In this study, with SOLiD sequencing technology, we performed identification, classification, and quantification of RNAs from blood fractions: cells, plasma, plasma vesicles pelleted at 16,000 and 160,000, and vesicle-depleted plasma supernatant of healthy donors and non-small cell lung cancer (NSCLC) patients. It was determined that 16,000 blood plasma vesicles were enriched with cell-free mitochondria and with a set of mitochondrial RNAs. The variable RNA set of blood plasma 160,000 pellets reflected the prominent contribution of U1, U5, and U6 small nuclear RNAs' fragments and at the same time was characterized by a remarkable depletion of small nucleolar RNAs. Besides microRNAs, the variety of fragments of mRNAs and snoRNAs dominated in the set of circulating RNAs differentially expressed in blood fractions of NSCLC patients. Taken together, our data emphasize that not only extracellular microRNAs but also circulating fragments of messenger and small nuclear/nucleolar RNAs represent prominent classes of circulating regulatory ncRNAs as well as promising circulating biomarkers for the development of disease diagnostic approaches.
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http://dx.doi.org/10.1155/2017/7404912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5239830PMC
February 2017

Surface modification of SOI-FET sensors for label-free and specific detection of short RNA analyte.

Nanomedicine (Lond) 2016 08 27;11(16):2073-82. Epub 2016 Jul 27.

SB RAS, Institute of Chemical Biology & Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.

Aim: A new type of surface modification of SOI-FET sensors with ultrathin sensor-probe transition layer and uncharged probes for highly specific detection of short RNA (saRNA) was suggested.

Materials & Methods: Carbonyldiimidazole (CDI) or glycidoxypropyltrimethoxysilane were used as precursors of sensor-probe interface layers, together with peptide nucleic acids and new NA analogues - phosphoryl guanidine oligo(2'-OMe)ribonucleotides (PGO) as probes for RNA hybridization. RNA sequences corresponding to mRNA NELFA (NM_005663) and microRNA-29a (cancer markers) were used as saRNA targets. Real-time saRNA detection by SOI-FET sensors and fluorescence analysis were applied.

Results: Highly specific response with femtomolar sensitivity to saRNA was demonstrated for CDI-PGO-modified sensors fabricated by optical lithography.

Conclusion: The proposed CDI-PGO protocol of modification of Si sensor surface is a promising procedure for biomedical applications.
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http://dx.doi.org/10.2217/nnm-2016-0071DOI Listing
August 2016

Optical identification based on time domain optical coherence tomography.

Appl Opt 2015 Sep;54(25):7514-9

We present a novel method for optical identification, i.e., authenticating valuable documents such as a passport, credit cards, and bank notes, using optical coherence tomography (OCT). An OCT system can capture three-dimensional (3D) images and visualize the internal structure of an object. In our work, as an object, we consider a multilayered optical identification tag composed of a limited number of thin layers (10-100 μm thick). The thickness, width, and location of the layers in the tag encode a unique identification information. Reading of the tag is done using a time domain OCT (TD-OCT) system. Typically, a TD-OCT system requires continuous mechanical scanning in one or more directions to get a 3D volume image of an object. The continuous scanning implies a complicated optical setup, which makes an OCT system fragile and expensive. We propose to avoid the conventional scanning by (1) not requiring 3D imaging, and (2) utilizing the motion of the optical tag itself. The motion is introduced to the tag reader, for example, by a user, which replaces the need for conventional scanning. The absence of a conventional scanning mechanism makes the proposed OCT method very simple and suited for identification purposes; however, it also puts some constraints to the construction of the optical tag, which we discuss in this paper in detail.
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http://dx.doi.org/10.1364/AO.54.007514DOI Listing
September 2015

Hypobaric Preconditioning Modifies Group I mGluRs Signaling in Brain Cortex.

Neurochem Res 2015 Nov 29;40(11):2200-10. Epub 2015 Aug 29.

Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106, Warsaw, Poland.

The study assessed involvement of Ca(2+) signaling mediated by the metabotropic glutamate receptors mGluR1/5 in brain tolerance induced by hypoxic preconditioning. Acute slices of rat piriform cortex were tested 1 day after exposure of adult rats to mild hypobaric hypoxia for 2 h at a pressure of 480 hPa once a day for three consecutive days. We detected 44.1 ± 11.6 % suppression of in vitro anoxia-induced increases of intracellular Ca(2+) levels and a fivefold increase in Ca(2+) transients evoked by selective mGluR1/5 agonist, DHPG. Western blot analysis of cortical homogenates demonstrated a 11 ± 4 % decrease in mGluR1 immunoreactivity (IR), and in the nuclei-enriched fraction a 12 ± 3 % increase in IR of phospholipase Cβ1 (PLCβ1), which is a major mediator of mGluR1/5 signaling. Immunocytochemical analysis of the cortex revealed increase in the mGluR1/5 and PLCβ1 IR in perikarya, and a decrease in IR of the neuronal inositol trisphosphate receptors (IP3Rs). We suggest that enhanced expression of mGluR5 and PLCβ1 and potentiation of Ca(2+) signaling may represent pro-survival upregulation of Ca(2+)-dependent genomic processes, while decrease in mGluR1 and IP3R IR may be attributed to a feedback mechanism preventing excessive intracellular Ca(2+) release.
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http://dx.doi.org/10.1007/s11064-015-1708-9DOI Listing
November 2015

Sensitivity of endometrial cancer cells from primary human tumor samples to new potential anticancer peptide lactaptin.

J Cancer Res Ther 2015 Apr-Jun;11(2):345-51

Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State University, Novosibirsk, Russia.

Purpose: Endometrial carcinoma is the most common gynecologic malignancy which is associated with a poor prognosis when diagnosed at an advanced stage; therefore, the discovery of efficacious new drugs is required to reinforce conventional chemotherapy. Short-term cultures of primary cells from endometrial tumors could be used for testing new anticancer therapeutics as well as for the development of personalized cancer therapy strategy. Here, the antitumor effect of a recombinant analogue of lactaptin (RL2), a new potential anticancer molecule, was examined against primary human endometrial cancer cells.

Materials And Methods: Primary cell cultures of malignant and normal human endometrium were performed by enzymatic digestion of endometrial tissue from biopsy material. Real-time quantitative reverse transcription polymerase chain reaction (RT-PCR) was performed to determine the messenger ribonucleic acid (mRNA) state of estrogen (ERs) and progesterone (PRs) hormone receptors and aromatase (Cyp 19) in cell cultures. Dynamic monitoring of cell adhesion and proliferation was made using the iCELLigence system (ASEA Biosciences). The sensitivity of cell cultures to conventional anticancer drugs and the lactaptin analog was estimated by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, flow cytometry, and the iCELLligence system.

Results: Established short-term primary cultures of endometrial cancer cells were ERα/ERβ/PR-positive and sensitive for RL2. The IC 50 values of doxorubicin and cisplatin were determined for all of the primary cultures designed. KE normal cells displaying low Cyp19 mRNA levels and high ERβ and PR mRNA levels were more resistant to RL2 treatment as well as to cisplatin and doxorubicin.

Conclusions: Our results indicate that the recombinant analog of lactaptin, RL2, exerts cytotoxic effects against primary hormone-dependent endometrial tumor cells in vitro with features of apoptosis.
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http://dx.doi.org/10.4103/0973-1482.157301DOI Listing
March 2016

Regulatory role of small nucleolar RNAs in human diseases.

Biomed Res Int 2015 28;2015:206849. Epub 2015 Apr 28.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, Novosibirsk 630090, Russia.

Small nucleolar RNAs (snoRNAs) are appreciable players in gene expression regulation in human cells. The canonical function of box C/D and box H/ACA snoRNAs is posttranscriptional modification of ribosomal RNAs (rRNAs), namely, 2'-O-methylation and pseudouridylation, respectively. A series of independent studies demonstrated that snoRNAs, as well as other noncoding RNAs, serve as the source of various short regulatory RNAs. Some snoRNAs and their fragments can also participate in the regulation of alternative splicing and posttranscriptional modification of mRNA. Alterations in snoRNA expression in human cells can affect numerous vital cellular processes. SnoRNA level in human cells, blood serum, and plasma presents a promising target for diagnostics and treatment of human pathologies. Here we discuss the relation between snoRNAs and oncological, neurodegenerative, and viral diseases and also describe changes in snoRNA level in response to artificial stress and some drugs.
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http://dx.doi.org/10.1155/2015/206849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427830PMC
April 2016

Lactaptin induces p53-independent cell death associated with features of apoptosis and autophagy and delays growth of breast cancer cells in mouse xenografts.

PLoS One 2014 7;9(4):e93921. Epub 2014 Apr 7.

Institute of Chemical Biology and Fundamental Medicine SB RUS, Novosibirsk, Russia.

Lactaptin, the proteolytic fragment of human milk kappa-casein, induces the death of various cultured cancer cells. The mechanisms leading to cell death after lactaptin treatment have not been well characterized. In this study the in vivo and in vitro effects of a recombinant analogue of lactaptin (RL2) were examined. Following treatment with the recombinant analogue of lactaptin strong caspase -3, -7 activation was detected. As a consequence of caspase activation we observed the appearance of a sub-G1 population of cells with subdiploid DNA content. Dynamic changes in the mRNA and protein levels of apoptosis-related genes were estimated. No statistically reliable differences in p53 mRNA level or protein level were found between control and RL2-treated cells. We observed that RL2 constitutively suppressed bcl-2 mRNA expression and down regulated Bcl-2 protein expression in MDA-MB-231 cells. We demonstrated that RL2 penetrates cancer and non-transformed cells. Identification of the cellular targets of the lactaptin analogue revealed that α/β-tubulin and α-actinin-1 were RL2-bound proteins. As the alteration in cellular viability in response to protein stimulus can be realized not only by way of apoptosis but also by autophagy, we examined the implications of autophagy in RL2-dependent cell death. We also found that RL2 treatment induces LC3-processing, which is a hallmark of autophagy. The autophagy inhibitor chloroquine enhanced RL2 cytotoxicity to MDA-MB-231 cells, indicating the pro-survival effect of RL2-dependent autophagy. The antitumour potential of RL2 was investigated in vivo in mouse xenografts bearing MDA-MB-231 cells. We demonstrated that the recombinant analogue of lactaptin significantly suppressed the growth of solid tumours. Our results indicate that lactaptin could be a new molecule for the development of anticancer drugs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093921PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978064PMC
January 2015

Chemistry in protoplanetary disks.

Chem Rev 2013 Dec 5;113(12):9016-42. Epub 2013 Nov 5.

Max Planck Institute for Astronomy , Königstuhl 17, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1021/cr400128pDOI Listing
December 2013

Artificial box C/D RNAs affect pre-mRNA maturation in human cells.

Biomed Res Int 2013 31;2013:656158. Epub 2013 Mar 31.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue 8, Novosibirsk 630090, Russia.

Box C/D small nucleolar RNAs (snoRNAs) are known to guide the 2'-O-ribose methylation of nucleotides in eukaryotic ribosomal RNAs and small nuclear RNAs. Recently snoRNAs are predicted to regulate posttranscriptional modifications of pre-mRNA. To expand understanding of the role of snoRNAs in control of gene expression, in this study we tested the ability of artificial box C/D RNAs to affect the maturation of target pre-mRNA. We found that transfection of artificial box C/D snoRNA analogues directed to HSPA8 pre-mRNAs into human cells induced suppression of the target mRNA expression in a time- and dose-dependent manner. The artificial box C/D RNA directed to the branch point adenosine of the second intron, as well as the analogue directed to the last nucleotide of the second exon of the HSPA8 pre-mRNA caused the most prominent influence on the level of HSPA8 mRNAs. Neither box D nor the ability to direct 2'-O-methylation of nucleotides in target RNA was essential for the knockdown activity of artificial snoRNAs. Inasmuch as artificial box C/D RNAs decreased viability of transfected human cells, we propose that natural snoRNAs as well as their artificial analogues can influence the maturation of complementary pre-mRNA and can be effective regulators of vital cellular processes.
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http://dx.doi.org/10.1155/2013/656158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626359PMC
September 2013

A novel pro-apoptotic effector lactaptin inhibits tumor growth in mice models.

Biochimie 2012 Dec 30;94(12):2467-74. Epub 2012 Aug 30.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, Novosibirsk 630090, Russia.

Lactaptin, a human milk-derived protein, induces apoptosis in cultured tumor cells. We designed a recombinant analog of lactaptin (RL2) and tested its antitumor activity. The sensitivity of hepatocarcinoma A-1 (HA-1), Lewis lung carcinoma, and Ehrlich carcinoma to RL2 were tested to determine the most reliable in vitro animal model. HA-1 cells, which had the highest sensitivity to RL2, were transplanted into A/Sn mice to investigate RL2 antitumor activity in vivo. Investigation of the molecular effects of RL2 shows that RL2 induces apoptotic transformation of HA-1 cells in vitro: phosphatidylserine translocation from inner side of the lipid bilayer to the outer one and dissipation of the mitochondrial membrane potential. Repetitive injections of RL2 (5-50 mg/kg) for 3-5 days effectively inhibited ascites and solid tumor transplant growth when administered intravenously or intraperitoneally, without obvious side effects. The solid tumor inhibitory effect of RL2 (5 i.v. injections, cumulative dose 125 mg/kg) was comparable with that of cyclophosphamide at a therapeutic dose (5 i.v. injections, cumulative dose 150 mg/kg). In combination therapy with cyclophosphamide, RL2 had an additive antitumor effect for ascites-producing tumors. Histomorphometric analysis indicated a three-fold reduction of spontaneous metastases in the liver of RL2-treated mice with solid tumor transplants in comparison with control animals. Repeated RL2 treatment substantially prolonged the lifespan of mice with intravenously injected tumor cells. Recombinant analog of lactaptin effectively induced apoptosis of tumor cells in vitro and suppressed the growth of sensitive tumors and metastases in vivo.
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http://dx.doi.org/10.1016/j.biochi.2012.08.017DOI Listing
December 2012

Unbiased approach to profile the variety of small non-coding RNA of human blood plasma with massively parallel sequencing technology.

Expert Opin Biol Ther 2012 Jun 18;12 Suppl 1:S43-51. Epub 2012 Apr 18.

Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia.

Objective: Understanding structures of circulating RNA expands fundamental knowledge of cell communications and signaling pathways as well as allows developing new molecular diagnostic approaches. The aim of this study was to deploy a new approach to sequencing cDNA library construction which expands the capabilities of high-throughput sequencing analysis of small non-coding RNAs. With the approach, we performed massively parallel sequencing of human blood plasma RNA to document profile of common and peculiar RNA species normally circulating in blood of healthy individuals.

Methods: Total RNA was extracted from blood plasma samples of eight apparently healthy individuals. To obtain comprehensive cDNA libraries RNA was dephosphorylated and then 5'-phosphorylated. 5'-Phosphorylated total plasma RNA was ligated with adapters, reverse transcribed and eight personalized cDNA libraries were constructed. Libraries were sequenced with SOLiD(™) technology.

Results/conclusion: Fragments of rRNA, mitochondrial transcripts, microRNAs, fragments of scRNAs, snRNA and snoRNA, fragments of several mRNAs as well as the set of newly discovered transcripts were found to be permanent representatives of human blood plasma RNAs. Advanced mapping allowed to identify circulating herpes virus and enterobacterial transcripts. Documented profile of circulating RNA of healthy individuals provides basis for development of new approaches in research and diagnosis of human pathology.
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http://dx.doi.org/10.1517/14712598.2012.679653DOI Listing
June 2012

Pleural effusion as a result of chronic renal ischemia.

J Thorac Dis 2011 Sep;3(3):205-6

Department of Surgery No1, Pavlov' State Medical University, Saint-Petersburg, Russia;

We would like to present a case of patient with a transudative pleural effusion as a result of atherosclerotic occlusion of renal arteries. About 50 liters of fluid were drained from the right pleural cavity during 10 months period of observation. Successful revascularization of kidneys improved left ventricular function, stabilized hemodynamic of the pulmonary circulation and thus led to elimination of pleural effusion.
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http://dx.doi.org/10.3978/j.issn.2072-1439.2010.12.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256528PMC
September 2011

Radionuclide transfer to reptiles.

Radiat Environ Biophys 2010 Nov 20;49(4):509-30. Epub 2010 Aug 20.

School of Environmental Sciences, University of Liverpool, Liverpool, Merseyside, UK.

Reptiles are an important, and often protected, component of many ecosystems but have rarely been fully considered within ecological risk assessments (ERA) due to a paucity of data on contaminant uptake and effects. This paper presents a meta-analysis of literature-derived environmental media (soil and water) to whole-body concentration ratios (CRs) for predicting the transfer of 35 elements (Am, As, B, Ba, Ca, Cd, Ce, Cm, Co, Cr, Cs, Cu, Fe, Hg, K, La, Mg, Mn, Mo, Na, Ni, Pb, Po, Pu, Ra, Rb, Sb, Se, Sr, Th, U, V, Y, Zn, Zr) to reptiles in freshwater ecosystems and 15 elements (Am, C, Cs, Cu, K, Mn, Ni, Pb, Po, Pu, Sr, Tc, Th, U, Zn) to reptiles in terrestrial ecosystems. These reptile CRs are compared with CRs for other vertebrate groups. Tissue distribution data are also presented along with data on the fractional mass of bone, kidney, liver and muscle in reptiles. Although the data were originally collected for use in radiation dose assessments, many of the CR data presented in this paper will also be useful for chemical ERA and for the assessments of dietary transfer in humans for whom reptiles constitute an important component of the diet, such as in Australian aboriginal communities.
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http://dx.doi.org/10.1007/s00411-010-0321-1DOI Listing
November 2010

Recombinant analogs of a novel milk pro-apoptotic peptide, lactaptin, and their effect on cultured human cells.

Protein J 2010 Apr;29(3):174-80

Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, 630090, Novosibirsk, Russia.

We recently isolated and characterized a human milk peptide, lactaptin, which induced apoptosis of cultured human MCF-7 cells. Lactaptin was identified as a proteolytic fragment of human kappa-casein. Here, we generated two recombinant analogs of the peptide, RL1 and RL2, containing truncated and complete amino acid sequences of lactaptin, respectively. Analogs were produced in E.coli, purified and assayed for biological activity on cultured human MCF-7 cells. RL1 was shown to induce only a small decrease in cell viability, whereas RL2 lowered the viability of MCF-7 cells by 60%. This reduction in MCF-7 cell viability was associated with apoptosis, which was indicated by phosphatidilserine externalization and caspase-7 activation. The viability of A549 and Hep-2 cells was also reduced by RL2, albeit to a lesser degree than seen with MCF-7 cells; this reduced viability was not accompanied by apoptosis. Non-malignant human mesenchymal stem cells (MSC) were completely resistant to RL2 action.
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http://dx.doi.org/10.1007/s10930-010-9237-5DOI Listing
April 2010

Distance sensing to rough semitransparent and multiscattering materials using dynamic speckles.

Appl Opt 2009 Oct;48(28):5266-73

Department of Physics, University of Kuopio, P.O.B. 1627, FI-70211 Kuopio, Finland.

Noncontact methods of distance measurements to a moving surface using laser light are relevant for many industrial applications, such as surface profile and position monitoring, thickness measurements, and wear estimation. Application of existing methods (e.g., triangulation) is limited especially for nonhomogeneous, semitransparent and rough materials (paper, wood, plastic). The task is even more challenging for fast moving objects. We present a novel online method of distance sensing to semitransparent and multiscattering surfaces (papers, woods, polymers) based on spatial filtering of dynamic speckles. We validated a proposed method at the speed of the test surface as high as 35 m/s.
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http://dx.doi.org/10.1364/AO.48.005266DOI Listing
October 2009

Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform.

Clin Chim Acta 2009 Nov 20;409(1-2):21-7. Epub 2009 Aug 20.

Biochemistry Division, School for Physical and Chemical Sciences, North-West University, Potchefstroom Campus, South Africa.

Background: Fragments of genomic DNA that can be isolated from the blood and body fluids of vertebrates are also known as circulating DNA. This DNA has widely been investigated as a biomarker for cancer and other diseases but the origin and significance of circulating DNA have not been elucidated to date.

Methods: We used a parallel tagged sequencing method to sequence circulating DNA obtained from control individuals as well as cancer patients on the GSFLX sequencer (454 life sciences).

Results: Circulating DNA sequenced on one 16th of a picotiter plate produced approximately 3600 unique circulating DNA sequences which were distributed over the human genome and a higher frequency of mutations was observed in cancer patients compared to healthy controls.

Conclusion: Circulating DNA represents genomic DNA in the blood of an individual, some sequence related differences might be evident between circulating DNA from cancer individuals and controls but distribution over the genome is similar.
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http://dx.doi.org/10.1016/j.cca.2009.08.011DOI Listing
November 2009

Fragments of noncoding RNA in plasma of human blood.

Ann N Y Acad Sci 2008 Aug;1137:130-4

Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.

Mammalian extracellular fluids, such as plasma of blood or plasma of milk, contain cell-free RNAs. Fragments of ubiquitously expressed mRNAs as well as tumor-specific and viral RNAs have been previously revealed in human plasmas by template-defined RT-PCR. In the present work we aimed to detect major forms of human blood plasma RNAs or to reveal new forms by using two approaches which were independent of context of RNA templates. The first approach was based on ligation of total plasma RNAs with adapter-oligoribonucleotides, reverse transcription of RNA-constructs, and amplification and cloning of cDNA. The second EST-like approach involved reverse transcription of RNAs with 3'-N6 degenerate primer, ligation of cDNA with dsDNA-adapter, amplification and cloning. Using these approaches we determined tens of tiny RNAs of human plasma and identified several long (>100 nt) RNAs. Most of tiny RNAs could be attributed to the fragments of rRNAs, whereas longer forms are representatives of noncoding RNAs.
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http://dx.doi.org/10.1196/annals.1448.030DOI Listing
August 2008

Splicing by exon exclusion impaired by artificial box c/d RNA targeted to branch-point adenosine.

Ann N Y Acad Sci 2008 Aug;1137:119-24

Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia.

Box C/D small nucleolar RNAs guide the site-specific 2'-O-ribose methylation of nucleotides in target rRNAs and snRNAs. In this study we used the ability of C/D box snoRNAs to guide modification of target RNAs with the aim of affecting the expression of predetermined human genes. We constructed an analogue of the human U24 box C/D RNA, the first antisense element of which was directed to induce 2'-O-ribose methylation of branch-point adenosine in the intron of the human heat-shock cognate protein (HSC8) pre-mRNA. The second antisense element was directed to induce methylation of G1702 in human 18S rRNA. Constructed artificial box C/D RNA was obtained by in vitro transcription by T7 RNA polymerase from a synthetic DNA template. It was shown that passive transfection of human adenocarcinoma MCF-7 cells with the artificial box C/D RNA, accompanied by heat shock, induced 2'-O-ribose methylation of targeted 18S rRNA guanosine G1702 and impaired splicing of the HSC8 pre-mRNA. Derangement of HSC8 splicing was the result of exclusion of the exon downstream to the targeted intron branch point. The total efficacy of pre-mRNA splicing impairment induced by artificial C/D box RNA was estimated as 6 to 10%.
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http://dx.doi.org/10.1196/annals.1448.037DOI Listing
August 2008

Deamination of adenosines in extracellular RNA spontaneously internalized by human cells.

Ann N Y Acad Sci 2008 Aug;1137:51-7

Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia.

Ribonucleic acids circulating in mammalian extracellular fluids as well as RNAs accumulating in culture medium condensed by mammalian cells are internalized by acceptor cells and distributed among cellular compartments. The internalized RNA can be involved in the induction and regulation of cellular processes as guide or signaling molecules. The internalization of RNA may be accompanied by covalent modifications influencing the stability and functionality of this RNA. To analyze nucleotide modifications introduced by human cells in internalized extracellular RNA, 5.8S rRNA of S. cerevisiae was used. It was shown that 5.8S rRNA of S. cerevisiae is captured by human adenocarcinoma MCF-7 cells from culture medium and delivered to cytoplasm and nuclei. Most of the internalized RNA was hydrolyzed to mono- and oligonucleotides. Full-length RNA uptake was detected by RT-PCR in the cytoplasm and in nuclei after the pulse addition of RNA to the culture medium. 5'-Inosine was the only detectable modified nucleotide in the hydrolysate of cell-internalized RNAs. Consequently, extracellular RNAs entering human cells were subjected to partial adenosine deamination. Sequencing of cDNA confirmed that full-length extracellular RNA that accumulated in the nucleus, but not in the cytoplasm, was partially edited by adenosine deaminases. The deamination revealed in nuclear-stored, full-length RNA was site-specific. Adenosines edited in S. cerevisiae 5.8S rRNA are stack-closing A-U pairs A53 and A96, as well as unpaired A44 and A65. Our data emphasize the participation of adenosine deaminases in capturing and intracellular trafficking of internalized RNAs.
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http://dx.doi.org/10.1196/annals.1448.036DOI Listing
August 2008

Preconditioning reduces hypoxia-evoked alterations in glutamatergic Ca2+ signaling in rat cortex.

Acta Neurobiol Exp (Wars) 2008 ;68(2):169-79

Department of Neurochemistry, Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland.

The aims of this study were (1) to characterize calcium signaling in rat cortex induced by repeated in vitro application of the glutamatergic agonists L-glutamate, NMDA, AMPA and DHPG, (2) to analyze the influence of transient severe hypobaric hypoxia (180 Torr) administered in vivo on calcium responses to stimulation of glutamate receptors by their agonists, and (3) to evaluate the effects of preconditioning with intermittent mild hypobaric hypoxia (360 Torr) 24 h before the severe hypoxia, on these Ca2+ responses. Intracellular Ca2+ dynamics was studied using the fluorescent probes fura-2 and chlortetracycline to monitor free and bound calcium (Cai and Cab) respectively. In control cortical slices, application of L-glutamate, NMDA and AMPA induced concomitant increases in Cai and Cab, reflecting Ca2+ influx and its intracellular accumulation in neurons. DHPG, an agonist of group I mGlu receptors induced a decrease in Cab accompanied by a rise in Cai levels, indicating Ca2+ mobilization. In cortical slices collected 24 h after severe hypoxia, the responses of Cab to glutamate administration were increased, DHPG-induced shifts were reversed, the increase in Cab after the first application of AMPA was reduced, while after the second, Cab rises were potentiated, and the increases in Cab evoked by NMDA application were slightly suppressed. The alterations of responses in Cab to the selective agonists were completely prevented by preconditioning with mild hypoxia. Our results suggest that protection of normal glutamatergic calcium signaling contributes to tolerance to hypoxia induced by preconditioning.
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December 2008

Accuracy and resolution of a dynamic-speckle profilometer.

Appl Opt 2006 Jan;45(3):411-8

Department of Applied Physics, University of Kuopio, Finland.

We propose and demonstrate a new technique for fast noncontact and continuous profile measurement of a rough surface. The technique is based on frequency tracking of the power modulation of spatially filtered scattered light. A dynamic speckle pattern is created when the laser beam scans the surface under study. The main advantage of the proposed technique is high scanning speed, which provides an extremely short response time of the distance sensor (<0.1 micros). Parameters that affect accuracy and resolution of the system are analyzed. Possible ways for further improvement of the measurements accuracy are discussed.
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http://dx.doi.org/10.1364/ao.45.000411DOI Listing
January 2006

Dynamic speckle effect induced by an acousto-optic deflector for fast range sensing.

Opt Lett 2005 Dec;30(23):3147-9

Department of Applied Physics, University of Kuopio, Finland.

A technique for fast distance measurements based on continuous frequency measurements of the power modulation of spatially filtered scattered light is proposed. For what is to our knowledge the first time, it is shown that the technique works when laser beam scanning is performed with an acousto-optic deflector. The most impressive feature of the proposed technique is that it works at very high scanning speed, providing an extremely fast response time. Experimental verification of the technique is demonstrated at a scanning speed as as high as 130 m/s. The proposed method of range sensing allows the design of a distance sensor possessing a response time as fast as 80 ns.
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http://dx.doi.org/10.1364/ol.30.003147DOI Listing
December 2005
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