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Optimal spectral coordination of subantennae in natural antennae as an efficient strategy for light harvesting in photosynthesis

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Journal of bioinformatics and Computational Biology 2006年第4期4卷 887-909页

作者： Novikov, A.A. Taisova, A.S. Fetisova, Z.G. Bioengineering and Bioinformatics Faculty M. V. Lomonosov Moscow State University Moscow 119992 Russian Federation A. N. Belozersky Institute of Physico-Chemical Biology M. V. Lomonosov Moscow State University Moscow 119992 Russian Federation

This work continues a series of our investigations on efficient strategies of functioning of natural light-harvesting antennae, initiated by a concept of rigorous optimization of photosynthetic apparatus by functional criterion, and deals with the problem of an optimal spectral coordination of subantennae in photosynthetic superantenna of the green bacterium Oscillochloris trichoides from a new family of green bacteria Oscillochloridaceae based in 2000. At present, two subantennae were identified surely: chlorosomal BChl c subantenna B750 and membrane BChl a subantennae B805-860. Some indirect experiments indicated on the presence of minor amounts of BChl a in isolated chlorosomes which allowed us to propose on the existence of an intermediate-energy subantenna which can connect the chlorosomal BChl c and the membrane BChl a ones. However, in the absorption spectra of isolated chlorosomes, this BChl a subantenna was not visually identified. This promoted us to perform a theoretical analysis of the optimality of spectral coordination of Oscillochloris trichoides subantennae. Using mathematical modeling for the functioning of the natural superantenna, we showed that an intermediate-energy subantenna, connecting B750 and B805-860 ones, allows one to control superantenna efficiency, i.e. to optimize the excitation energy transfer from B750 to B805 by functional criterion, and hence, the existence of such intermediate-energy subantenna is biologically expedient. © 2006 Imperial College Press.

关键词： Green bacteria Light-harvesting antenna Model calculations Photosynthesis

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Quantification of Mitochondrial Morphology in situ

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Cell and Tissue Biology 2017年第1期11卷 51-58页

作者： Popkov, V.A. Plotnikov, E. Yu. Zorova, L.D. Pevzner, I.B. Silachev, D.N. Babenko, V.A. Jankauskas, S.S. Zorov, S.D. Zorov, D.B. Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow 119991 Russian Federation Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow 119991 Russian Federation International Laser Center Lomonosov Moscow State University Moscow 119991 Russian Federation

The structural organization of mitochondria reflects their functional status and largely is an index of cell viability. The indirect parameter to assess the functional state of mitochondria in cells is the degree of their fragmentation, i.e., the ratio of long or branched mitochondrial structures to round mitochondria. Such evaluations requires an approach that allows to create an integral pattern of the three-dimensional organization of mitochondrial reticulum using confocal images of mitochondria stained with a fluorescent probe. In the present study, we tested three approaches to analyzing the structural architecture of mitochondria under normal conditions and fission induced by oxidative stress. We revealed that, while the most informative is a three-dimensional reconstruction based on series of confocal images taken along the Z-dimension, with some restrictions it is plausible to use more simple algorithms of analysis, including one that uses unitary twodimensional images. Further improvement of these methods of image analysis will allow more comprehensive study of mitochondrial architecture under normal conditions and different pathological states. It may also provide quantification of a number of mitochondrial parameters determining the morphofunctional state of mitochondria—primarily, their absolute and relative volumes—and give additional information on threedimensional organization of the mitochondrion. © 2017, Pleiades Publishing, Ltd. All Right Reserved.

关键词： 3D modeling confocal microscopy fragmentation mitochondria

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Simulating the long-timescale structural behavior of bacterial and influenza neuraminidases with different HPC resources

Supercomputing Frontiers and Innovations

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Supercomputing Frontiers and Innovations 2018年第3期5卷 30-33页

作者： Sharapova, Yana A. Suplatov, Dmitry A. Švedas, Vytas K. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Moscow Russia

Understanding the conformational dynamics which affects ligand binding by Neuraminidases is needed to improve the in silico selection of novel drug candidates targeting these pathogenicity factors and to adequately estimate the efficacy of potential drugs. Conventional molecular dynamics (MD) is a powerful tool to study conformational sampling, drug-target recognition and binding, but requires significant computational effort to reach timescales relevant for biology. In this work the advances in a computer power and specialized architectures were evaluated at simulating long MD trajectories of the structural behavior of Neuraminidases. We conclude that modern GPU accelerators enable calculations at the timescales that would previously have been intractable, providing routine access to microsecond-long trajectories in a daily laboratory practice. This opens an opportunity to move away from the "static" affinity-driven strategies in drug design towards a deeper understanding of ligand-specific conformational adaptation of target sites in protein structures, leading to a better selection of efficient drug candidates in silico. However, the performance of modern GPUs is yet far behind the deeply-specialized supercomputers co-designed for MD. Further development of affordable specialized architectures is needed to move towards the much-desired millisecond timescale to simulate large proteins at a daily routine. © The Authors 2018.

关键词： Molecular dynamics

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An Event-Driven Closed-Loop Ultrasound Stimulator Composed of a Micro-Transducer and Multi-Site Electrodes in Vitro

An Event-Driven Closed-Loop Ultrasound Stimulator Composed o...

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17th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2024

作者： Furukawa, Ryo Murakami, Shuichi Tateno, Takashi Bioengineering and Bioinformatics Graduate School of Information Science and Technology Hokkaido University Kita 14 Nishi 9 Kita-ku Hokkaido Sapporo060-0814 Japan Osaka Research Institute of Industrial Science and Technology 2-7-1 Ayumino Izumi Osaka594-1157 Japan Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Kita 14 Nishi 9 Kita-ku Hokkaido Sapporo060-0814 Japan

Ultrasound neuromodulation, in which local and deep brain areas are stimulated, holds promise for clinical applications. However, the mechanisms of action underlying the stimulation effects are still unknown. In vitro experiments are helpful for investigating the stimulation mechanisms because they allow easy control of extracellular conditions. Compared with closed-loop systems, conventional open-loop systems do not permit monitoring of neural activity, and thus can lead to excessive neural stimulation. In this study, we developed a piezoelectric micromachined ultrasound transducer (PMUT) combined with monitoring microelectrodes. To examine the potential of our device as a neuromodulation tool, we measured the cellular responses to generated ultrasound stimulation. Subsequently, we constructed a closed-loop system that combined our PMUT with monitoring electrodes, and applied event-related ultrasound stimulation to brain slices in vitro. We discuss future applications of a closed-loop ultrasound stimulation system. © 2024 by SCITEPRESS–Science and Technology Publications, Lda.

关键词： Microelectrodes

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High-Speed Observations of Acoustic Droplet Ejection of a Shear-Thinning Polymer Solution in an External High-Voltage Electric Field

High-Speed Observations of Acoustic Droplet Ejection of a Sh...

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IEEE International Symposium on Applications of Ferroelectrics (ISAF)

作者： Joni Mäkinen Nobuki Kudo Jere Hyvönen Mamoru Hashimoto Edward Hæggström Ari Salmi Department of Physics Faculty of Science University of Helsinki Helsinki Finland Division of Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Sapporo Japan

ISBN: (数字)9798350371901

ISBN: (纸本)9798350371918

High-speed observations of ultrasonic ejection of a viscoelastic, shear-thinning, polymer solution, 1 wt% PEO dissolved in water, for the purpose of electrospinning initiation are presented. A focused ultrasound source at 2.68 MHz is used for the ejection. A high-voltage electric field is applied between the solution and a conducting plate above. With a suitable ultrasonic ejection of the solution, electrospinning is initiatied as the electric field pulls a thinning jet from the solution, eventually producing a *** ultrasonic pulse regimes are investigated for the ejection: short (≤ 100 cycles) but high-amplitude (≈ 4.4 MPa), and long (≥ 5000 cycles) but low-amplitude (≈ 0.8 MPa) pulsing. Three different types of ejections leading to the electric field being able to pull a jet from the solution are observed. Most notably, we observed an unstable drop-chain formation which lead to the jetting of liquid from the drop-chain, which was further pulled by the electric field into a thinning jet.

关键词： Ultrasonic imaging Liquids High-voltage techniques Acoustics Polymers Electric fields Frequency control

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PERFECTOS-APE: Predicting regulatory functional effect of SNPs by approximate P-value estimation 6

PERFECTOS-APE: Predicting regulatory functional effect of SN...

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6th International Conference on bioinformatics Models, Methods and Algorithms, bioinformatics 2015

作者： Vorontsov, Ilya E. Kulakovskiy, Ivan V. Khimulya, Grigory Nikolaeva, Daria D. Makeev, Vsevolod J. Department of Computational Systems Biology Vavilov Institute of General Genetics Gubkina Str. 3 Moscow Russia Laboratory of Bioinformatics and Systems Biology Engelhardt Institute of Molecular Biology Vavilova Str. 32 Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia Department of Medical and Biological Physics Moscow Institute of Physics and Technology Moscow Region Russia

ISBN: (纸本)9789897580703

Single nucleotide polymorphisms (SNPs) and variants (SNVs) are often found in regulatory regions of human genome. Nucleotide substitutions in promoter and enhancer regions may affect transcription factor (TF) binding and alter gene expression regulation. Nowadays binding patterns are known for hundreds of human TFs. Thus one can assess possible functional effects of allele variations or mutations in TF binding sites using sequence analysis. We present PERFECTOS-APE, the software to PrEdict Regulatory Functional Effect of SNPs by Approximate P-value Estimation. Using a predefined collection of position weight matrices (PWMs) representing TF binding patterns, PERFECTOS-APE identifies transcription factors whose binding sites can be significantly affected by given nucleotide substitutions. PERFECTOS-APE supports both classic PWMs under the position independency assumption, and dinucleotide PWMs accounting for the dinucleotide composition and correlations between nucleotides in adjacent positions within binding sites. PERFECTOS-APE uses dynamic programming to calculate PWM score distribution and convert the scores to P-values with an optional binary search mode using a precomputed P-value list to speed-up the computations. Software is written in Java and is freely available as standalone program and online tool: http://***/perfectosape/. We have tested our algorithm on several disease associated SNVs as well as on a set of cancer somatic mutations occurring in intronic regions of the human genome.

关键词： Binding sites

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Fluorescently controlled investigation of super-enhancers with CRISPR interference and CRISPR prime editing systems

Fluorescently controlled investigation of super-enhancers wi...

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International Conference on Laser Optics

作者： N.N. Orlova M.G. Gladkova G.A Ashniev A.V. Orlov Prokhorov General Physics Institute of the Russian Academy of Sciences Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia

ISBN: (数字)9798350390674

ISBN: (纸本)9798350390681

In the evolving landscape of genomic research, our study delves into the intricate exploration of super-enhancers, pivotal and controversial elements exerting profound influence over gene expression. Utilizing CRISPR interference and CRISPR prime editing systems, our work yields promising results and opens avenues for future research to refine and expand these approaches across diverse cell types.

关键词： Lasers Genomics Interference Fluorescence Gene expression bioinformatics

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Urban Dust Nanoparticles Induce Pro-inflammatory Activation of Neutrophils and Macrophages

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Moscow University Biological Sciences Bulletin 2024年第3期79卷 154-161页

作者： Pavlyuchenkova, A.N. Vorobjeva, N.V. Dashkevich, A.A. Zinovkina, L.A. Ivaneev, A.I. Ermolin, M.S. Fedotov, P.S. Zinovkin, R.A. Chelombitko, M.A. Chernyak, B.V. Belozersky Institute of Physico-Chemical Biology Moscow State University Moscow 119992 Russian Federation Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119234 Russian Federation Evolutionary Cytogerontology Sector Faculty of Biology Moscow State University Moscow 119234 Russian Federation Department of Immunology Faculty of Biology Moscow State University Moscow 119234 Russian Federation Vernadsky Institute of Geochemistry and Analytical Chemistry Russian Academy of Sciences Moscow 119334 Russian Federation

Abstract: Urban dust particles are a major pathogenic factor in respiratory diseases such as asthma and chronic obstructive pulmonary disease, and also increase the risk of cardiovascular diseases, and lung cancer. Nanoparticles (NPs) of various origins are an important component of urban dust, but their effects on the human body are barely studied. In the present work, the effect of urban dust NPs on innate immune cells, neutrophils and macrophages was investigated in vitro. The study used urban dust NPs isolated from urban dust samples using the coiled tube field-flow fractionation technique. Urban dust NPs were shown to induce a significant increase in the production of reactive oxygen species in human neutrophils. Preincubation of neutrophils with dust NPs resulted in a fourfold increase in production of reactive oxygen species in response to the chemoattractant peptide N-formyl-methionyl-leucyl-phenylalanine (fMLP), which indicates an effect of neutrophil priming with nanoparticles. On macrophages differentiated from the monocytic line THP-1, urban dust NPs stimulated the secretion of pro-inflammatory cytokines, tumor necrosis factor, and interleukin-6. The inflammatory activation of neutrophils and macrophages was reduced by antibiotic polymyxin B, which is able to bind bacterial wall lipopolysaccharide. The results suggest that the pro-inflammatory effect of urban dust NPs on neutrophils and macrophages is, at least in part, due to the presence of bacterial wall lipopolysaccharide. © Allerton Press, Inc. 2024.

关键词： inflammatory activation innate immune cells macrophages nanoparticles neutrophils urban dust

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Using operonic gene pairs to set the threshold correlation coefficient for differently expressed genes

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Biophysics 2011年第6期56卷 1041-1042页

作者： Hedge, Sh Klimova, E. Yu Mande, Sh Medvedeva, Yu A. Makeev, V. Yu Permina, E.A. Centre for DNA Fingerprinting and Diagnostics Hyderabad-500 001 India Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119991 Russian Federation Scientific Center GosNIIgenetika Moscow 117545 Russian Federation Vavilov Insitute for General Genetics Moscow 119991 Russian Federation Engelhardt Institute of Molecular Biology Moscow 119991 Russian Federation

We have developed an approach to estimating the correlations in the noise component of gene expression data. An efficient noise reduction technique has been suggested. The resulting methods have been applied to E. col... 详细信息

关键词： correlation tables E. coli microarrays noise reduction

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Exclusive sequences of different genomes

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Journal of bioinformatics and Computational Biology 2010年第3期8卷 519-534页

作者： Mitrofanov, Sergey I. Panchin, Alexander Y. Spirin, Sergei A. Alexeevski, Andrei V. Panchin, Yuri V. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russian Federation Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russian Federation A.N. Belozersky Institute of Physical-Chemical Biology Moscow State University Moscow Russian Federation Scientific Research Institute for System Studies (NIISI RAN) Moscow Russian Federation

We studied the distribution of 1-7 bp words in a dataset that includes 139 complete eukaryotic genomes, 33 masked eukaryotic genomes and coding regions from 35 genomes. We tested different statistical models to determine over- and under-represented words. The method described by Karlin et al. has the strongest predictive power compared to other methods. Using this method we identified over- and under-represented words consistent within a large array of taxonomic groups. Some of those words have not yet been described as exclusive. For example, CGCG is over-represented in CG-deficient organisms. We also describe exceptions for widely known exclusive words, such as CG and TA. © 2010 Imperial College Press.

关键词： Complete genomes Content CpG TpA Words

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