Spatial chaos and complexity in the intracellular space of cancer and normal cells

BACKGROUND: One of the most challenging problems in biological image analysis is the quantification of the dynamical mechanism and complexity of the intracellular space. This paper investigates potential spatial chaos and complex behavior of the intracellular space of typical cancer and normal cell images whose structural details are revealed by the combination of scanning electron microscopy and focused ion beam systems. Such numerical quantifications have important implications for computer modeling and simulation of diseases. METHODS: Cancer cell lines derived from a human head and neck squamous cell carcinoma (SCC-61) and normal mouse embryonic fibroblast (MEF) cells produced by focused ion beam scanning electron microscopes were used in this study. Spatial distributions of the organelles of cancer and normal cells can be analyzed at both short range and long range of the bounded dynamical system of the image space, depending on the orientations of the spatial cell. A procedure was designed for calculating the largest Lyapunov exponent, which is an indicator of the potential chaotic behavior in intracellular images. Furthermore, the sample entropy and regularity dimension were applied to measure the complexity of the intracellular images. RESULTS: Positive values of the largest Lyapunov exponents (LLEs) of the intracellular space of the SCC-61 were obtained in different spatial orientations for both long-range and short-range models, suggesting the chaotic behavior of the cell. The MEF has smaller positive values of LLEs in the long range than those of the SCC-61, and zero vales of the LLEs in the short range analysis, suggesting a non-chaotic behavior. The intracellular space of the SCC-61 is found to be more complex than that of the MEF. The degree of complexity measured in the spatial distribution of the intracellular space in the diagonal direction was found to be approximately twice larger than the complexity measured in the horizontal and vertical directions. CONCLUSION: Initial findings are promising for characterizing different types of cells and therefore useful for studying cancer cells in the spatial domain using state-of-the-art imaging technology. The measures of the chaotic behavior and complexity of the spatial cell will help computational biologists gain insights into identifying associations between the oscillation patterns and spatial parameters of cells, and appropriate model for simulating cancer cell signaling networks for cancer treatment and new drug discovery

Microstructure and Solute Segregation around the Melt-Pool Boundary of Orientation-Controlled 316L Austenitic Stainless Steel Produced by Laser Powder Bed Fusion

For this article, we studied the microstructure and solute segregation seen around the melt pool boundary of orientation-controlled 316L austenitic stainless steel produced by laser powder bed fusion, using transmission electron microscopy and energy-dispersive x-ray spectroscopy. We found that the solidification cellular microstructures could be visualized with the aid of solute segregation (Cr and Mo) during solidification. Mn–Si–O inclusions (10–15 nm in diameter) were distributed along the lamellar boundaries, as well as in the dislocation cell walls. It is believed that the grain growth of the inclusions can be effectively suppressed by rapid quenching during the laser powder-bed fusion process. A thin region without cellular microstructures was observed at the melt-pool boundary. The cellular spacing widened near the bottom of the melt-pool boundary, owing to the decrease in the cooling rate. Atomic-structure analysis at the lamellar boundary by high-resolution transmission electron microscopy revealed a local interfacial structure, which is complementary to the results of electron back-scatter diffraction.Sato K., Takagi S., Ichikawa S., et al. Microstructure and Solute Segregation around the Melt-Pool Boundary of Orientation-Controlled 316L Austenitic Stainless Steel Produced by Laser Powder Bed Fusion. Materials 16, 218 (2023); https://doi.org/10.3390/ma16010218

Local valence analysis of 316L austenitic stainless steel produced by laser powder bed fusion

Sato K., Takagi S., Ichikawa S., et al. Local valence analysis of 316L austenitic stainless steel produced by laser powder bed fusion. Materials Letters 372, 136978 (2024); https://doi.org/10.1016/j.matlet.2024.136978.Ultra-rapid cooling of laser powder bed fusion (LPBF) generates a cellular solidification microstructure with submicron-sized periodicity accompanied by non-negligible segregation. In 316L austenitic stainless steel, an important corrosion-resistant alloy, the effect of segregation, particularly variations in Cr concentration, on the corrosion resistance of the LPBF product is unknown. Local valence analysis of the LPBF-produced 316L by electron energy-loss spectroscopy revealed no obvious changes in the energy-loss near-edge structures of Cr and Fe measured within the solidification cellular microstructure, at the cell boundary, or at the melt-pool boundary. This result indicates that solidification segregation in the LPBF-produced 316L is unlikely to affect the corrosion resistance of the material

Electrophoresis and electro-affinity transfer with specific antibodies to alpha-fetoprotein for detection of circulating immune complexes of alpha-fetoprotein.

&lt;p&gt;A combination of agarose gel electrophoresis and a newly developed technique of electro-affinity transfer was applied to the detection of circulating immune complexes of human alpha-fetoprotein (AFP) and anti-AFP. After electrophoretic transfer to nitrocellulose membrane, to which affinity-purified polyclonal horse antibodies to human AFP were bound, the membranes were treated with or without rabbit immunoglobulins to human AFP, followed by overlaying with horseradish peroxidase-labeled goat anti-rabbit IgG for color development. Artificial complexes formed in vitro from human AFP and rabbit anti-AFP were clearly separated from free AFP by the agarose electrophoresis. The complexes were stained 20-40% as dark as the equivalent amount of free AFP by treatment with rabbit anti-AFP, and 10-20% as dark without the antibody treatment over a wide range of antigen-antibody ratios.&lt;/p&gt;</p

Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies

MT1-MMP is a potent invasion-promoting membrane protease employed by aggressive cancer cells. MT1-MMP localizes preferentially at membrane protrusions called invadopodia where it plays a central role in degradation of the surrounding extracellular matrix (ECM). Previous reports suggested a role for a continuous supply of MT1-MMP in ECM degradation. However, the turnover rate of MT1-MMP and the extent to which the turnover contributes to the ECM degradation at invadopodia have not been clarified. To approach this problem, we first performed FRAP (Fluorescence Recovery after Photobleaching) experiments with fluorescence-tagged MT1-MMP focusing on a single invadopodium and found very rapid recovery in FRAP signals, approximated by double-exponential plots with time constants of 26 s and 259 s. The recovery depended primarily on vesicle transport, but negligibly on lateral diffusion. Next we constructed a computational model employing the observed kinetics of the FRAP experiments. The simulations successfully reproduced our FRAP experiments. Next we inhibited the vesicle transport both experimentally, and in simulation. Addition of drugs inhibiting vesicle transport blocked ECM degradation experimentally, and the simulation showed no appreciable ECM degradation under conditions inhibiting vesicle transport. In addition, the degree of the reduction in ECM degradation depended on the degree of the reduction in the MT1-MMP turnover. Thus, our experiments and simulations have established the role of the rapid turnover of MT1-MMP in ECM degradation at invadopodia. Furthermore, our simulations suggested synergetic contributions of proteolytic activity and the MT1-MMP turnover to ECM degradation because there was a nonlinear and marked reduction in ECM degradation if both factors were reduced simultaneously. Thus our computational model provides a new in silico tool to design and evaluate intervention strategies in cancer cell invasion

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

Calculation method of reflectance distributions for computer-generated holograms using the finite-difference time-domain method

The research on reflectance distributions in computer-generated holograms (CGHs) is particularly sparse, and the textures of materials are not expressed. Thus, we propose a method for calculating reflectance distributions in CGHs that uses the finite-difference time-domain method. In this method, reflected light from an uneven surface made on a computer is analyzed by finite-difference time-domain simulation, and the reflected light distribution is applied to the CGH as an object light. We report the relations between the surface roughness of the objects and the reflectance distributions, and show that the reflectance distributions are given to CGHs by imaging simulation. (C) 2011 Optical Society of Americ

Regulation of nuclear NF-κB oscillation by a diffusion coefficient and its biological implications.

The transcription factor NF-κB shuttles between the cytoplasm and the nucleus, and nuclear NF-κB is known to oscillate with a cycle of 1.5-2.5 h following the application of external stimuli. Oscillation pattern of NF-κB is implicated in regulation of the gene expression profile. In a previous report, we found that the oscillation pattern of nuclear NF-κB in a computational 3D spherical cell was regulated by spatial parameters such as nuclear to cytoplasmic volume ratio, nuclear transport, locus of protein synthesis, and diffusion coefficient. Here we report analyses and a biological implication for the regulation of oscillation pattern by diffusion coefficient. Our analyses show that the "reset" of nuclear NF-κB, defined as the return of nuclear NF-κB to the initial level or lower, was crucial for the oscillation; this was confirmed by the flux analysis. In addition, we found that the distant cytoplasmic location from the nucleus acted as a "reservoir" for storing newly synthesized IκBα. When the diffusion coefficient of proteins was large (≥ 10-11 m2/s), a larger amount of IκBα was stored in the "reservoir" with a large flux by diffusion. Subsequently, stored IκBα diffused back to the nucleus, where nuclear NF-κB was "reset" to the initial state. This initiated the next oscillation cycle. When the diffusion coefficient was small (≤ 10-13 m2/s), oscillation of nuclear NF-κB was not observed because a smaller amount of IκBα was stored in the "reservoir" and there was incomplete "reset" of nuclear NF-κB. If the diffusion coefficient for IκBα was increased to 10-11 m2/s keeping other proteins at 10-13 m2/s, the oscillation was rescued confirming the "reset" and "reservoir" hypothesis. Finally, we showed altered effective value of diffusion coefficient by diffusion obstacles. Thus, organelle crowding seen in stressed cells possibly changes the oscillation pattern by controlling the effective diffusion coefficient