339 research outputs found
Automating the diagnosis and rectification of deflection yoke production using hybrid knowledge acquisition and case-based reasoning
No full textDeflection yoke (DY) is one of the main components of the color display tube (CDT) that determines the image quality of a computer monitor. Once a DY anomaly is found during production, the remedy process is performed in two steps: identifying the type of anomaly from the observed problem pattern and adjusting manufacturing process parameters to rectify it. To support this process, we introduce a knowledge-based system using a hybrid knowledge acquisition technique and case-based reasoning. The initial phase of the knowledge acquisition employs a systematic and quantitative data processing including stepwise regression and an inductive learning algorithm. This automated expertise elicitation produces strategies, which are represented by decision trees or if-then rules, to specify DY anomalies from display patterns. The strategies are then refined by introducing human expertise. The knowledge acquisition process was designed to support for this cognitive cooperation. For coordinating the process parameters to remedy the specified anomalies, a case-based reasoning is utilized. The laboratory and field test proved that the developed knowledge-based system could produce highly effective decisions for the process control in DY production
Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
No full textSubmicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 mm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity.11Nsciescopu
Tension exerted on cells by magnetic nanoparticles regulates differentiation of human mesenchymal stem cells
No full textCells can ‘sense’ physical cues in the surrounding microenvironment and ‘react’ by changing their function. Previous studies have focused on regulating the physical properties of the matrix, such as stiffness and topography, thus changing the tension ‘felt’ by the cell as a result. In this study, by directly applying a quantified magnetic force to the cell, a correlation between differentiation and tension was shown. The magnetic force, quantified by magnetic tweezers, was applied by incorporating magnetotactic bacteria-isolated magnetic nanoparticles (MNPs) in human mesenchymal stem cells. As the applied tension increased, the expression levels of osteogenic differentiation marker genes and proteins were proportionally upregulated. Additionally, the translocation of YAP and RUNX2, deformation of nucleus, and activation of the MAPK signaling pathway were observed in tension-based osteogenic differentiation. Our findings provide a platform for the quantitative control of tension, a key factor in stem cell differentiation, between cells and the matrix using MNPs. Furthermore, these findings improve the understanding of osteogenic differentiation by mechanotransduction. © 2022 Elsevier B.V.11Nsciescopu
Trends of declining productivity and biodiversity in an Oregon estuarine reserve
No full textColleen Walker, Shon Schooler, Dan Bottom, and Bree Yednock.Title from PDF cover (viewed on January 23, 2023).This archived document is maintained by the State Library of Oregon as part of the Oregon Documents Depository Program. It is for informational purposes and may not be suitable for legal purposes.Includes bibliographical references (pages 13-14).Mode of access: Internet from the Oregon Government Publications Collection.Text in English
Observing Extremely Weak Protein-Protein Interactions with Conventional Single-Molecule Fluorescence Microscopy
No full textExtremely weak protein-protein interactions (PPIs), signified by micromolar or even millimolar dissociation constants, are one of the keys to understanding the rapid responses of cellular systems. Although single-molecule methods are particularly useful in determining kinetics of biological processes, their application is largely limited to rather strong interactions because of the diffraction-limited observation volume. In this study, we report a single-molecule method that allows the characterization of PPIs using a prey concentration 4 orders of magnitude lower than the dissociation constant. Instead of increasing the concentration of diffusing molecules, which is inevitably limited by the optical diffraction limit, we employed an increased density of surface bait protein. The low occupancy of the surface baits permitted determination of the kinetics with single-molecule resolution. We used this approach to study a PPI network consisting of Ras and its downstream proteins including full-length Rafs and catalytic subunits of phosphoinositide 3-kinase. © 2016 American Chemical Society1541sciescopu
Focused clamping of a single neuronal SNARE complex by complexin under high mechanical tension
No full textNeuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) catalyze synaptic vesicle fusion with presynaptic membranes through the formation of SNARE complexes. Complexin (Cpx) is the only presynaptic protein that tightly binds to SNAREs and regulates membrane fusion, but how it modulates the energy landscape of SNARE complex assembly, especially under mechanical tension on the complex, remains unclear. Here, using magnetic tweezers, we report how Cpx interacts with single SNARE complexes. The effects of Cpx manifest only under high mechanical tensions above 13 pN. Cpx stabilizes the central four-helix bundle of SNARE motifs and, at the same time, prevents the complete zippering of SNAREs by inhibiting linker-domain assembly. These results suggest that Cpx generates a focused clamp for the neuronal SNARE complex in a linker-open conformation. Our results provide a hint as to how Cpx cooperates with neuronal SNAREs to prime synaptic vesicles in preparation for synchronous neurotransmitter release.11Nsciescopu
Mapping the distributions of Pacific and western brook lampreys along the Oregon south coast using eDNA and community science : ... report
No full textShon Schooler, Jenni Schmitt, Deborah Rudd, Becky Flitcroft, and Ian Rodger.This archived document is maintained by the State Library of Oregon as part of the Oregon Documents Depository Program. It is for informational purposes and may not be suitable for legal purposes.Includes bibliographic references.USDA U.S. Forest Service provided funding for this projectMode of access: Internet from the Oregon Government Publications Collection.Text in English
Profiling protein-protein interactions of single cancer cells with in situ lysis and co-immunoprecipitation
No full textHeterogeneity in a tumor allows a small portion of cancer cells to survive and regrow upon targeted cancer therapy, eventually leading to cancer relapse. Such drug-resistant cells often exhibit dynamic adaptation of their signaling pathways at the level of protein- protein interactions (PPIs). To probe the rewiring of signaling pathways and the heterogeneity across individual cancer cells, we developed a single-cell version of the co-immunoprecipitation (co-IP) analysis that examines the amount and PPIs of target proteins immunoprecipitated from individual cells. The method captures cancer cells at predefined locations using a microfluidic chip, pulls down target proteins on the surface using antibodies, and lyses the captured cells in situ. Then, subsequent addition of eGFP-labeled downstream proteins enables the determination of the corresponding PPIs for the minimal amount of target proteins sampled from a single cell. We applied the technique to probe epidermal growth factor receptors (EGFRs) in PC9 lung adenocarcinoma cells. The results reveal that the strength of EGFR PPIs can be largely uncorrelated with the expression level of EGFRs in single cells. In addition, the individual PC9 cells showed markedly different patterns of PPIs, indicating a high heterogeneity in EGFR signaling within a genetically homogeneous population.11Nsciescopu
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