检索结果-内蒙古大学图书馆

2024 International Conference Laser Optics, ICLO 2024

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

ISBN: (纸本)9798350390674

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. © 2024 IEEE.

关键词： Gene expression

来源：评论

学校读者我要写书评

暂无评论

Effect of 4-(Trifluoromethoxy)phenylhydrazone Carbonyl Cyanide (FCCP) on FcεRI-Dependent Cytokine Production by RBL-2H3 Cells

引用

Moscow University Biological Sciences Bulletin 2023年第2期78卷 66-73页

作者： Pavlyuchenkova, A.N. Smirnov, M.S. Chelombitko, M.A. Belozersky Institute of Physicochemical Biology Moscow State University Moscow 119992 Russian Federation Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119992 Russian Federation

Abstract: Mast cells (MCs) play a key role in the development of allergic diseases. The interaction of antigens with immunoglobulin E and the subsequent binding of these complexes to the FcεRI receptor, which ultimately leads to rapid exocytosis of granules and subsequent production of cytokines, play a major role in MC activation in an allergy. There are data on the role of the mitochondrial membrane potential in the FcεRI-dependent activation of MCs. Thus, the use of classical uncouplers of oxidative phosphorylation reduces the level of MC degranulation. However, their effect on the production of MC cytokines has not been studied. In this work, it was demonstrated that pretreatment of RBL-2H3 MC with the uncoupler carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP) leads to a decrease not only in the level of FcεRI-dependent degranulation but also in the production of TNFα and IL-4 cytokines. At the same time, FCCP prevents the phosphorylation of the LAT adapter molecule, as well as the Erk1/2 kinase, which may underlie the inhibitory effect of the uncoupler on the FcεRI-dependent activation of RBL-2H3 cell line. The data obtained indicate that the mitochondrial membrane potential plays an important role in the FcεRI-dependent activation of MCs, and the uncoupling of oxidative phosphorylation and respiration of mitochondria with the help of uncouplers can be used to regulate this process. © 2023, Allerton Press, Inc.

关键词： allergy FCCP FcεRI-dependent activation mast cells mitochondria uncouplers

来源：评论

学校读者我要写书评

暂无评论

Exploring The Interplay Between Scoring Functions and Physico-chemical Properties in Antibody-antigen Docking

引用

IPSJ Transactions on bioinformatics 2024年 17卷 10-17页

作者： Ratnayake, Sangeetha Martinelli, Axel Endo, Toshinori Osada, Naoki Division of Bioinformatics and Bioengineering Graduate School of Information Science and Technology Hokkaido University Hokkaido Sapporo060–0814 Japan BigOmics Analytics Via Serafino Balestra 12 Lugano6900 Switzerland Faculty of Information Science and Technology Hokkaido University Hokkaido Sapporo060–0814 Japan

The advent of antibody therapy has brought about a change in the treatment of diseases. The efficacy of antibody modeling relies on the intricate atomic interactions between antibodies and antigens. Traditional methods for determining antibody structures, such as X-ray crystallography, are costly and time-consuming. Computational docking offers a faster and more cost-effective approach to obtaining complex antibody and antigen complexes even in challenging scenarios. Rosetta, a widely employed software for protein structure modeling, incorporates a scoring function specifically tailored for modeling antibody-antigen interactions. The unique characteristics of the antibody-antigen interface can result in inaccurate predictions. Therefore, it is essential to understand the existing scoring function and the behavior of the antibody-antigen interface. In this study, we evaluated specific parameters within Rosetta-derived scoring functions, with a particular focus on the energy landscape of the structures they generated. We found that performance in antibody-antigen docking simulations could be enhanced by omitting parameters related to solvation. Also, we delved into the physico-chemical properties of antibody-antigen interfaces, paying special attention to the complementarity-determining regions and epitopes. Our exploration helped identify certain parameters that significantly influence docking simulation performance. These insights pave the way for the creation of more accurate scoring functions tailored for specific antibody-antigen interactions. © 2024 Information Processing Society of Japan.

关键词： Antibodies

来源：评论

学校读者我要写书评

暂无评论

Advancing Antibody-antigen Interface Analysis in Docking Scoring Functions for Precision Docking Analysis

引用

IPSJ Transactions on bioinformatics 2024年 17卷 40-47页

Molecular docking simulations utilizing scoring functions are pivotal for assessing the stability of complex formations. The unique biochemical characteristics of antibody-antigen interfaces, however, present challenges in applying general parameter sets of scoring functions to these molecules, necessitating the customization of the scoring function to enhance prediction accuracy for structural configurations and binding affinities. In response to this, we have developed models within the Rosetta software framework, widely recognized for its utility in predicting antigen-antibody docking, to optimize the parameters of its scoring function. Through a quantitative evaluation of the shape of decoy distribution generated by Rosetta, we have been able to refine the parameters for each antibody-antigen complex, yielding a notable improvement in the prediction accuracy of the software for a given dataset. Furthermore, we have identified a distinct parameter set that is effective for the majority of complexes in our dataset, though not universally applicable. This study introduces a novel approach to customizing scoring functions, potentially contributing to advancements in drug discovery and deepening our understanding of the complexities inherent in antibody-antigen interactions at a molecular level. © 2024 Information Processing Society of Japan.

关键词： Antibodies

来源：评论

学校读者我要写书评

暂无评论

Developing a Head-Attached Interface Device for Closed-Loop Transcranial Ultrasound Stimulation in the Mouse Brain

Developing a Head-Attached Interface Device for Closed-Loop ...

引用

18th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2025

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

Transcranial ultrasound stimulation (TUS), which can be used to noninvasively stimulate local and deep brain areas, holds significant promise for clinical applications. However, TUS apparatus is typically constructed with several components, including a relatively large single-element ultrasound (US) transducer, a waveguide, and a driving source. These components pose challenges when conducting experiments with freely moving small animals, especially in the context of wearable devices. Additionally, conventional open-loop stimulation systems do not allow for the simultaneous monitoring of neural activity, which can sometimes result in the overactivation of neural responses. In this study, we developed a head-mounted piezoelectric micromachined ultrasound transducer (PMUT) array with integrated monitoring electrodes to serve as a TUS interface for mice. To determine effective array patterns for optimal US beam profiles, we first conducted beamforming simulations. We then microfabricated the PMUT arrays according to the results of these simulations. Subsequently, we performed electroencephalographic (EEG) recordings to evaluate the potential of TUS in mice while simultaneously monitoring neural activities. Finally, we discuss future applications of a closed loop TUS system in the treatment of brain diseases. © 2025 by SCITEPRESS– Science and Technology Publications, Lda.

关键词： Closed loop systems

来源：评论

学校读者我要写书评

暂无评论

De Novo Gene Birth

引用

Molecular Biology 2025年第1期59卷 17-25页

作者： Aristova, E.O. Volkhin, I.A. Denisova, A.A. Nikitin, P.A. Petrukhin, E.R. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119234 Russian Federation Life Sciences Research Center Moscow Institute of Physics and Technology (National Research University) Moscow oblast Dolgoprudny 141700 Russian Federation Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow 119071 Russian Federation

Abstract: According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately. © Pleiades Publishing, Ltd. 2025.

关键词： de novo gene orphan gene pervasive transcription pervasive translation

来源：评论

学校读者我要写书评

暂无评论

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...

引用

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

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

来源：评论

学校读者我要写书评

暂无评论

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...

引用

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

来源：评论

学校读者我要写书评

暂无评论

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

Fluorescently controlled investigation of super-enhancers wi...

引用

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

关键词： Lasers Genomics Interference Fluorescence Gene expression bioinformatics

来源：评论

学校读者我要写书评

暂无评论

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：