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Probing the effect of the disordered flank regions on amyloid fibril growth and proliferation

RSC advances 2025年第26期15卷 20668-20681页

作者： Jacob Aunstrup Larsen Juami H M van Gils Soumik Ray Marcel Dickmanns Shuangyan Wang Ahmed Sadek Hossein Mohammad-Beigi Masoumeh Zanganeh Sanne Abeln Alexander K Buell Department of Biotechnology and Biomedicine Technical University of Denmark Søltofts Plads 2800 Lyngby Denmark s.abeln@uu.nl alebu@dtu.dk. Bioinformatics Group Computer Science Department Vrije Universiteit Amsterdam de Boelelaan 1111 1081HV Amsterdam The Netherlands. Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany. Insitute of Bioengineering École Polytechnique Fédérale de Lausanne (EPFL) Rte Cantonale 1015 Lausanne Switzerland. AI Technology for Life AI & Data Science Utrecht University Princetonplein 5 3584CC Utrecht The Netherlands.

Amyloid fibrils typically consist of a dense core made up of β-strands, with disordered flanks on either side, and are sometimes interrupted by disordered loop regions (the fuzzy coat). α-Synuclein found in Lewy Bodies of Parkinson's Disease patients is mostly C-terminally truncated, meaning that a large fraction of the fuzzy coat of disease-related fibrils is enzymatically degraded in the amyloid state. We demonstrate that the proteolytic removal of the fuzzy coat leads to enhanced fibril-fibril interactions and flocculation, which renders the study of the role of the fuzzy coat in bulk solution very challenging. In order to overcome these challenges, here we use Quartz Crystal Microbalance with Dissipation (QCM-D), a surface based biosensing technique, to study the effects of proteolytic removal of the fuzzy coat of α-synuclein amyloids. We demonstrate that Dissipation-Frequency analysis can illuminate multiple simultaneous reactions and characterize the monomer-fibril interactions in detail. We find that removal of the fuzzy coat increases apparent fibril elongation rates permanently. Utilizing kinetic models, we demonstrate that our results cannot be rationalized by alterations of the elongation rate of fibrils alone, but indicate that proteolytic cleavage of the fuzzy coat of α-synuclein fibrils can lead to the formation of new growth-competent fibril ends. We propose that such phenomena may be highly relevant for understanding disease-related α-synuclein amyloid formation. Furthermore we suggest that the QCM-D is a particularly attractive platform for studying post-translational modifications in real-time and their effect on amyloid growth or molecular interactions.

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In-silico prediction of microRNA targets and finding genes suggesting significant involvement in the development of Glycine max seed

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Vegetos 2019年第4期32卷 450-463页

作者： Nivedita Yadav Kavita Goswami Budhayash Gautam Pramod Kumar Yadav Jacob Institute of Biotechnology and Bioengineering Department of Computational Biology and Bioinformatics Sam Higginbottom University of Agriculture Technology and Sciences Prayagraj 211007 Uttar Pradesh India

Glycine max is a worldwide leading economic crop and its seeds are deepening with proteins and oils which supply food and sustenance to all being. Various amounts of alimentary constituents are racked up in the G. max seed in the period of its ontogenesis. Thus, grasping the regulation of biological functions during seed enlargement belong to the basics for crop enhancement. The gene regulatory characteristics of miRNAs in G. max attracted us to focus on its target gene prediction, gene ontology (GO) analysis and expression pattern to their miRNA target genes, which suggest significant involvement in the development of G. max seed. Seven miRNAs have been found from the differential gene expression analysis of development stage 0–4 mm vs. 12–16 mm of G. max seed on the statistical parameter of p value ≤ 0.05 by computational-based microarray data analysis for miRNA target gene prediction. The miRNA target prediction analysis showed total 23 genes that were cleaved from 6 miRNAs, and computationally validated by identifying t-plots of miRNA targets using CleaveLand tool. GO results confirmed that the differentially expressed target genes could be classified into 20 molecular function categories, 73 biological process categories, and 10 cell components categories. On the basis of GO results, two genes were found to be significantly involved in the developmental process of *** seed. The first miRNA target gene Glyma.01g119500 was predicted to annotate for embryo development ending in seed dormancy, seed dormancy, seed maturation, and seed germination. The second miRNA target gene Glyma.15g005300 was found to be involved in the regulation of seed germination. The Soybean eFP browser analysis suggests that the gene Glyma.01g119500 and Glyma.15g005300 reaches its maximum expression level of 35.88 and 26.6 respectively in the Soybean data source. The present study provides an avenue to explore more genomic and proteomic information about G. max seed developmental stage-sp

关键词： Degradome analysis Expression pattern GO analysis miRNA target prediction miRNAs

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Antibiotics-Induced Transfer of Resistance Genes and Emergence of New Resistant Bacteria in Red Swamp Crayfish Guts and Culture Sediments

SSRN

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SSRN 2022年

作者： Jin, Xuexia Liu, Sizhen Zhang, Zhenting Liu, Tong Liang, Yunxiang Zheng, Jinshui Peng, Nan State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University of Science and Technology Hubei Wuhan430070 China Hubei Hongshan Laboratory College of Life Science and Technology Hubei Wuhan430070 China Runge College of Bioengineering Mianzhu Sichuan Deyang618200 China Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics Huazhong Agricultural University Wuhan430070 China

Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, which could lead to treatment failure of bacterial infections. The aquaculture, which is polluted by over-used antibiotics, is considered as a notorious reservoir of ARGs. However, the fact on the mobilization of ARGs in aquaculture systems, and their contributions to the emergence and dissemination of antibiotic resistant bacteria (ARB) remain elusive. In this study, we used crayfish as an aquatic animal model to analyze longitudinal changes of bacterial communities, ARGs and mobile gene elements (MGEs) in the gut and sediment samples in response to enrofloxacin administration. Our metagenomic analysis revealed significant perturbations of the microbiota and ARGs compositions in the gut compared to those in sediments, which is characterized by an obviously delayed recovery after antibiotic administration. MGEs facilitated the diffuse of ARGs through horizontal gene transfer mainly in the bacteria from Enterobacteriaceae family in gut and sediment environments. Especially, the transposase-mediated recombination was the major driver of the transfer for ARGs in the pressure of antibiotics. Simultaneously, the changes in community composition as the emerged and proliferating of the multiple resistant pathogenic bacteria played a crucial role in the augment of various ARGs . © 2022, The Authors. All rights reserved.

关键词： Antibiotics

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Exact probability landscapes of stochastic phenotype switching in feed-forward loops: Phase diagrams of multimodality

arXiv

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arXiv 2021年

作者： Terebus, Anna Manuchehrfar, Farid Cao, Youfang Liang, Jie Center for Bioinformatics and Quantitative Biology Richard and Loan Hill Department of Bioengineering University of Illinois at Chicago ChicagoIL60607 United States Constellation BaltimoreMD United States Merck & Co. Inc. KenilworthNJ United States

Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we provide full characterizations of the properties of stochastic multimodality of FFLs, and how switching between different network phenotypes are controlled. We have computed the exact steady state probability landscapes of all eight types of coherent and incoherent FFLs using the finite-butter ACME algorithm, and quantified the exact topological features of their high-dimensional probability landscapes using persistent homology. Through analysis of the degree of multimodality for each of a set of 10,812 probability landscapes, where each landscape resides over 105-106 microstates, we have constructed comprehensive phase diagrams of all relevant behavior of FFL multimodality over broad ranges of input and regulation intensities, as well as different regimes of promoter binding dynamics. In addition, we have quantified the topological sensitivity of the multimodality of the landscapes to regulation intensities. Our results show that with slow binding and unbinding dynamics of transcription factor to promoter, FFLs exhibit strong stochastic behavior that is very different from what would be inferred from deterministic models. In addition, input intensity play major roles in the phenotypes of FFLs: At weak input intensity, FFL exhibit monomodality, but strong input intensity may result in up to 6 stable phenotypes. Furthermore, we found that gene duplication can enlarge stable regions of specific multimodalities and enrich the phenotypic diversity of FFL networks, providing means for cells towards better adaptation to changing environment. Our results are directly applicable to analysis of behavior of FFLs in biological processes such as stem cell differentiation and for design of synthetic networks when certain phenotypic behavior is desir

关键词： Stochastic systems

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Toward a Universal Model for Spatially Structured Populations

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Physical Review Letters 2021年第21期127卷 218102-218102页

作者： Loïc Marrec Irene Lamberti Anne-Florence Bitbol Sorbonne Université CNRS Institut de Biologie Paris-Seine Laboratoire Jean Perrin (UMR 8237) F-75005 Paris France Institute of Bioengineering School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland SIB Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland

A key question in evolution is how likely a mutant is to take over. This depends on natural selection and on stochastic fluctuations. Population spatial structure can impact mutant fixation probabilities. We introduce a model for structured populations on graphs that generalizes previous ones by making migrations independent of birth and death. We demonstrate that by tuning migration asymmetry, the star graph transitions from amplifying to suppressing natural selection. The results from our model are universal in the sense that they do not hinge on a modeling choice of microscopic dynamics or update rules. Instead, they depend on migration asymmetry, which can be experimentally tuned and measured.

关键词： Ecology & evolution Evolutionary dynamics Population genetics

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Translating from Na to Ca : Na/Ca-exchanger exerts Na -dependent control over astrocytic Ca oscillations

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The European Physical Journal Plus 2021年第7期136卷 1-16页

作者： Verisokin, Andrey Yu. Verveyko, Darya V. Kucherenko, Varvara V. Postnov, Dmitry E. Brazhe, Alexey R. Department of Theoretical Physics Kursk State University Kursk Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia Saratov State National Research University Saratov Russia Biological Faculty Lomonosov Moscow State University Moscow Russia Department of Molecular Neurobiology Institute of Bioorganic Chemistry RAS Moscow Russia

Recently accumulated evidences suggest that astrocyte signaling is in touch link with extracellular volume regulation and interstitial fluid drainage from the brain. Classical understanding of astrocyte activity is based on IP $$_3$$ -dependent calcium exchange with intracellular stores. Recent evidence shifts focus to calcium entry from extracellular space via multiple mechanisms and widens it to taking other ions into account. It has been hypothesized that Na/Ca-exchanger can translate activity-dependent Na $$^+$$ transients into modulation of Ca $$^{2+}$$ dynamics. We combine a model of IP $$_3$$ -based Ca $$^{2+}$$ dynamics with a model of Ca $$^{2+}$$ flow through Na/Ca-exchanger to provide theoretical insights into the possible effects of such modulation. We find that the exchanger can provide for bidirectional Na $$^+$$ -dependent modulation of the sensitivity to extracellular glutamate, oscillation amplitude and frequency modulation, as well as extending the available set of dynamical regimes. The extent of the emergent Na $$^+$$ sensitivity is predicted to be scaled by a morphology-dependent balance between the maximal flow through the exchanger and the rate of entry from intracellular stores.

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Exploring the anticancer potential of fluoro flavone analogues: insights from molecular docking and dynamics studies with Aurora Kinase B

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In silico pharmacology 2024年第1期12卷 26页

作者： Ipsa A Singh Kiran Bharat Lokhande K Venkateswara Swamy Bioinformatics Research Laboratory Dr. D. Y. Patil Biotechnology and Bioinformatics Institute Dr. D. Y. Patil Vidyapeeth Pune India. Present Address: Translational Bioinformatics and Computational Genomics Research Lab Department of Life Sciences Shiv Nadar Institution of Eminence Gautam Buddha Nagar Greater Noida UP India. Drug Discovery Group MIT School of Bioengineering Sciences & Research MIT Art Design and Technology University Pune 412201 India.

Aurora Kinase B belongs to the serine kinase family. It plays an essential role in cell division and participates in mitosis and chromatid segregation. Overexpression, polymorphism, and splicing variants in the protein lead to tumorigenesis, leading to cancer. Flavones belong to the class of flavonoids and are derived from plants and show anti-cancer activities. Fluoro flavones and their analogs are taken from the PubChem database, resulting in 3882 compounds which is 90% similar to the fluoro flavones. Lipinski's rule of five, REOS and PAINS drug-like filters were applied which resulted 2448 compounds. These compounds are docked with Aurora Kinase B using SP and XP modules of Glide software. The best binding scores for SP docking were − 9.153 kcal/mol for the compound with CID: 44298667, and XP docking was − 10.287 kcal/mol with CID: 101664315. Enrichment calculations were done using Aurora Kinase B's decoys to validate the docking result. The resulting R2 = 0.96 from enrichment calculations suggests that the docking protocol is valid. The SP and XP docking lead compounds and the Fluoro flavone were subjected to 100 ns MD simulation to probe the protein–ligand complex stability. Also, the binding free energies between the Aurora kinase B and lead compounds were computed by Prime MM/GBSA module. The result suggests that the lead compounds bind more strongly with Aurora Kinase B than the Fluoro flavone. These lead compounds can be further evaluated in vitro and in vivo and can be used as future novel drugs for the curation of cancer.

关键词： Aurora kinase B Cancer Fluoro flavones MD simulation Molecular docking

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Comparison of Analgesia Methods Through a Web Platform in Patients Undergoing Thoracic Surgery: Pilot Design, Implementation, and Validation Study

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JMIR Formative Research 2024年 8卷 e56674页

作者： Trò, Rosella Orecchia, Angelica Disma, Nicola Uva, Paolo Cavanna, Roberto Zanardi, Nicolò Torre, Michele Fato, Marco Massimo Department of Informatics Bioengineering Robotics and System Engineering University of Genoa Genoa Italy Unit for Research in Anaesthesia Istituto di Ricovero e Cura a Carattere Scientifico Giannina Gaslini Genoa Italy Clinical Bioinformatics Istituto di Ricovero e Cura a Carattere Scientifico Giannina Gaslini Genoa Italy Pediatric Thoracic and Airway Surgery Unit Istituto di Ricovero e Cura a Carattere Scientifico Giannina Gaslini Genoa Italy Department of Neuroscience Rehabilitation Ophthalmology Genetics Maternal and Child Health University of Genoa Genoa Italy

Background: Pain management is a vital and essential part of postoperative pectus excavatum (PE) care. Given the lack of an international consensus on guidelines for postoperative handling and evaluation, further research is necessary to compare the efficacy of existing pain management methods regarding pain relief, side effects, and long-term outcomes. In this context, the use of eHealth solutions for data mining can enhance data collection efficiency, reduce errors, and improve patient engagement. However, these digital health care frameworks are currently underused in the context of pain management for PE. Objective: This research is part of the broader Cryoanalgesia for Pain Management After Pectus Excavatum Repair (COPPER) study conducted by Giannina Gaslini Children’s Hospital to address postoperative pain and recovery in PE patients treated with either standard thoracic epidural analgesia or cryoanalgesia, which is considered its innovative alternative approach. Specifically, this work is aimed at introducing a valuable tool for a comprehensive and quantitative comparison of the 2 analgesia strategies. The tool is a web and mobile app designed to facilitate data collection, management, and analysis of clinical data for pain assessment. Methods: The adopted approach involves a careful design based on clinician input, resulting in an intuitive app structure with 3 main screens. Digital surveys are borrowed from paper surveys, including medical history and preoperative, postoperative, and follow-up evaluations. XTENS 2.0 was used to manage the data, and Ionic facilitated cross-platform app development, ensuring secure and adaptable data handling. Results: Preliminary analysis on a pilot cohort of 72 patients (36 treated with standard therapy and 36 treated with cryoanalgesia) indicated successful patient enrollment and balanced representation across treatment groups and genders. Notably, hospital stay was significantly shorter with cryoanalgesia than with standa

关键词： health care informatics pain assessment pectus excavatum web platform

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Modulatory effect of NCX on IP3-dependent Ca2+oscillations in astrocytes

Modulatory effect of NCX on IP3-dependent Ca2+oscillations i...

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Saratov Fall Meeting 2020 - Computations and Data Analysis: From Molecular Processes to Brain Functions

作者： Verisokin, Andrey Yu. Verveyko, Darya V. Kucherenko, Varvara V. Postnov, Dmitry E. Brazhe, Alexey R. Department of Theoretical Physics Kursk State University Radishcheva st. 33 Kursk305000 Russia Saratov State National Research University Astrakhanskaya st. 83 Saratov Russia Biological Faculty Lomonosov Moscow State University Leninskie Gory 1/24 Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Leninskie Gory 1/73 Moscow Russia Department of Molecular Neurobiology Institute of Bioorganic Chemistry RAS Miklukho-Maklay str 16/10 Moscow Russia

ISBN: (纸本)9781510645325

Most of the existing models of calcium dynamics of astrocytes do not take into account the effect of the Na/Ca- exchanger on the formation of calcium oscillations and their properties. However, recent experimental studies show that at an increased sodium concentration, the Na/Ca-exchanger works in the reverse mode, providing an additional calcium entry into the cell cytosol. In this work we study a model that simultaneously takes into account the IP3-mediated exchange with intracellular [Ca2+] stores and bidirectional [Ca2+] flow through Na/Ca-exchanger. We analyze the behavior of the system under stimulation with external glutamate- of the cell, explore the possible behavior regimes and reveal the effect of the cytosolic sodium concentration, the maximum current through the Na/Ca-exchanger, and the stimulus amplitude on the astrocytic calcium dynamics. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.

关键词： Sodium

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Improving the joint centre location of a markerless motion analysis system through a functional calibration method: A pilot study

Improving the joint centre location of a markerless motion a...

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作者： Sganga, Magalí Nuñez, Marcos Alfredo Ritacco, Lucas Eduardo Crespo, Marcos José Ravera, Emiliano Pablo CONICET - Universidad Maimónides Buenos Aires Argentina Departamento de Informática en Salud Hospital Italiano Buenos Aires Argentina Laboratorio de análisis de marcha y movimiento LAMM y Tecnología en rehabilitación Clínica de tecnología asistiva TA. FLENI Escobar Argentina Group of Analysis Modeling Processing and Clinician Implementation of Biomechanical Signals and Systems Bioengineering and Bioinformatics Institute CONICET-UNER Oro Verde Argentina Oro Verde Argentina

Biomechanical analysis is a tool to evaluate pathological movements and their rehabilitation. This paper examines the feasibility of improvements to the hip joint centre location in a Markerless Motion Capture System through the application of a functional calibration method. The movement of a young female with no physical impairments was analysed. Data taken from a gold standard system (Motion Capture System, MOCAP) and a low-cost alternative (Microsoft Kinect) were acquired simultaneously. Static and dynamic acquisitions were recorded. Five virtual markers for each leg were created from Kinect and introduced into the optimal common shape technique and in the symmetrical centre of rotation estimation method to determine both hip joint centres. Results showed an improvement in joint centre location when compared to MOCAP information. In conclusion, this approach would improve the data obtained with Kinect and is shown to be a feasible method to apply in the rehabilitation field. © 2021, The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Calibration

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