Proteomics Impact on Cell Biology to Resolve Cell Structure and Function.

The acceleration of advances in proteomics has enabled integration with imaging at the EM and light microscopy levels, cryo-EM of protein structures, and artificial intelligence with proteins comprehensively and accurately resolved for cell structures at nanometer to subnanometer resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path toward the goal of a compendium of all proteins to understand mechanistically cell structure and function.

Art and Science of the Cellular Mesoscale.

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

Soft X-ray tomograms provide a structural basis for whole-cell modeling.

Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.

Improvement of the viability of Tetragenococcus halophilus under acidic stress by forming the biofilm cell structure based on RNA-Seq and iTRAQ analyses.

BACKGROUND: Tetragenococcus halophilus is a halophilic lactic acid bacterium (LAB) isolated from soya sauce moromi. During the production of these fermented foods, acid stress is an inevitable environmental stress. In our previous study, T. halophilus could form biofilms and the cells in the biofilms exhibited higher cell viability under multiple environmental stresses, including acid stress. RESULTS: In this study, the effect of preformed T. halophilus biofilms on cell survival, cellular structure, intracellular environment, and the expression of genes and proteins under acid stress was investigated. The result showed that acid stress with pH 4.30 for 1.5 h reduced the live T. halophilus cell count and caused cellular structure damage. However, T. halophilus biofilm cells exhibited greater cell survival under acid stress than the planktonic cells, and biofilm formation reduced the damage of acid stress to the cell membrane and cell wall. The biofilm cells maintained a higher level of H+ -ATPase activity and intracellular ammonia concentration after acid stress. The RNA-Seq and iTRAQ technologies revealed that the genes and proteins associated with ATP production, the uptake of trehalose and N-acetylmuramic acid, the assembly of H+ -ATPase, amino acid biosynthesis and metabolism, ammonia production, fatty acid biosynthesis, CoA biosynthesis, thiamine production, and acetoin biosynthesis might be responsible for the stronger acid tolerance of T. halophilus biofilm cells together. CONCLUSION: These findings further explained the mechanisms that allowed LAB biofilm cells to resist environmental stress. © 2023 Society of Chemical Industry.

Comparative analysis of thioflavin T and other fluorescent dyes for fluorescent staining of Bacillus subtilis vegetative cell, sporulating cell, and mature spore.

Thioflavin T, a cationic benzothiazole dye, is typically used to detect amyloid fibrils. In this study, we analyzed the staining properties of Bacillus subtilis cells using several fluorescent dyes, including thioflavin T analogs, 2-(4'-methylaminophenyl) benzothiazole (BTA-1), and 2-(4-aminophenyl) benzothiazole (APBT). Thioflavin T stained vegetative cells in the early log phase and outer layer structures of forespores and mature spores. The inner parts of forespores and heat-killed mature spores were also stained with thioflavin T. Congo red, auramine O, and rhodamine B stained forespores and mature spores similar to thioflavin T. In contrast, APBT and BTA-1 fluorescence was detected in the outer layers of vegetative cells, mother cells, forespores, and mature spores, indicating that they bind to the cell membrane and/or cell wall. The combination of the fluorescent dyes used in this study will help analyze morphogenetic processes during the sporulation and the damage mechanisms of vegetative cells and spores.

Combined treatment of ε-polylysine and heat damages protective structures and spore inner membranes to inactivate Bacillus subtilis spores.

The sterilizing effect of a combination of heat (80, 90, and 100 °C) and ε-polylysine (ε-PL, 0.25 and 1 g/L) treatments on Bacillus subtilis spores was investigated and compared with that of conventional heat sterilization. The inactivation rate of spores and changes in their protective structure were evaluated using different methods and techniques. Changes in cell membrane's fatty acids, cell walls, proteins and nucleic acids were also analyzed. The results showed that the combined heat and ε-PL treatments significantly (p < 0.05) inactivated the Bacillus subtilis spores compared with the single heat treatment. Besides, the inactivation of spores was enhanced as the temperature and ε-PL concentration of combined treatments increased. The inactivation rate was found to be 2.18 log after heating at 90 °C for 60 min combined with the addition of 1 g/L ε-PL. Additionally, the electrical conductivity of spores' suspension and the positive region of flow cytometry significantly (p < 0.05) increased depending on temperature and ε-PL concentration of a combination treatment, indicating significant damage in the cell membranes and increased permeability. Significant changes in the spore morphology were also observed by the microscopy analysis after a combination treatment. Furthermore, the Fourier transform infrared spectra indicated a phase change in the inner membrane and alteration in the structure of peptidoglycan layer, as well as protein and nucleic acids denaturation after combined treatments. Therefore, the combined heat and ε-PL treatments can be suggested as sterilizing alternative to conventional heat sterilization in the food industry.

Ultra-centrifugation force in adaptive evolution changes the cell structure of oleaginous yeast Trichosporon cutaneum into a favorable space for lipid accumulation.

Microbial lipid production from lignocellulose biomass provides an essential option for sustainable and carbon-neutral supply of future aviation fuels, biodiesel, as well as various food and nutrition products. Oleaginous yeast is the major microbial cell factory but its lipid-producing performance is far below the requirements of industrial application. Here we show an ultra-centrifugation fractionation in adaptive evolution (UCF) of Trichosporon cutaneum based on the minor cell density difference. The lightest cells with the maximum intracellular lipid content were isolated by ultra-centrifugation fractionation in the long-term adaptive evolution. Significant changes occurred in the cell morphology with a fragile cell wall wrapping and enlarged intracellular space (two orders of magnitude increase in cell size). Complete and coordinate assimilations of all nonglucose sugars derived from lignocellulose were triggered and fluxed into lipid synthesis. Genome mutations and significant transcriptional regulations of the genes responsible for cell structure were identified and experimentally confirmed. The obtained T. cutaneum MP11 cells achieved a high lipid production of wheat straw, approximately five-fold greater than that of the parental cells. The study provided an effective method for screening the high lipid-containing oleaginous yeast cells as well as the intracellular products accumulating cells in general.

Microstructural evolution during short heat treatment of constrained groove pressed Cu-5%Zn alloy.

Severe plastic deformation (SPD) is a widely used technique to obtain superior material properties specially mechanical properties. Constrained groove pressing (CGP) is found to be the most attractive SPD technique for the deformation of sheets and plates. However, this technique results in microstructural inhomogeneity during processing. The microstructural inhomogeneity can be alleviated by employing a thermal cycle, which assists in controlled recovery and recrystallisation. The current work focuses on, the microstructure evolution of one pass as-deform CGP sample followed by a short heat-treated (SHT). A correlative imaging technique of transmission Kikuchi diffraction (TKD) and transmission electron microscopy (TEM) showed the presence of dislocation cell structure in an as-deformed condition. The short heat treatment resulted in the transformation of the dislocation cell wall to high-angle boundaries, with a further increase in heat-treatment time resulting in grain growth.

Survey of Molecular Mechanisms of Hyperbaric Oxygen in Tissue Repair.

For more than six decades, hyperbaric oxygen (HBO) has been used for a variety of indications involving tissue repair. These indications comprise a wide range of diseases ranging from intoxications to ischemia-reperfusion injury, crush syndrome, central nervous injury, radiation-induced tissue damage, burn injury and chronic wounds. In a systematic review, the molecular mechanisms triggered by HBO described within the last two decades were compiled. They cover a wide range of pathways, including transcription, cell-to-cell contacts, structure, adhesion and transmigration, vascular signaling and response to oxidative stress, apoptosis, autophagy and cell death, as well as inflammatory processes. By analyzing 71 predominantly experimental publications, we established an overview of the current concepts regarding the molecular mechanisms underlying the effects of HBO. We considered both the abovementioned pathways and their role in various applications and indications.

Effect of the order of incorporation of cake ingredients on the formation of batter and the final properties: contribution of the addition of pea flour.

The investigation dealt with the effect of the replacement of a part of wheat flour by pea flour on the properties of batters and cakes. As the protein composition of pea flour differs from that of wheat, the effect of its incorporation on batter formation and cake properties was monitored throughout the different steps of cake processing. The incorporation of air, which influences the cell structure and density of the cake, was the subject of particular attention. Four orders of incorporation were first investigated to identify their effects on a standard recipe made with 100% wheat flour. Mixing first egg and sugar together allows introducing air, but most of it is lost after oil and flour introduction. Whatever the order of incorporation, the density of the batter ends around 1.1 ± 0.2 g.cm-1. However, batter consistencies are significantly different and resulting cakes show different crumb structures. These results are discussed in terms of physicochemical mechanisms, and a schematic representation of the phenomena occurring at the different steps of mixing depending on the order of ingredient incorporation is proposed. When 20 and 40% of the wheat flour was replaced by pea flour using the two most energy-efficient orders of incorporation, more air was incorporated into the batter. However, the resulting cakes were denser, but surprisingly softer. Differences in cell structure explain this apparent contradiction.

Determining mechanical features of modulated epithelial monolayers using subnuclear particle tracking.

Force generation within cells, mediated by motor proteins along cytoskeletal networks, maintains the function of multicellular structures during homeostasis and when generating collective forces. Here, we describe the use of chromatin dynamics to detect cellular force propagation [a technique termed SINK (sensors from intranuclear kinetics)] and investigate the force response of cells to disruption of the monolayer and changes in substrate stiffness. We find that chromatin dynamics change in a substrate stiffness-dependent manner within epithelial monolayers. We also investigate point defects within monolayers to map the impact on the strain field of a heterogeneous monolayer. We find that cell monolayers behave as a colloidal assembly rather than as a continuum since the data fit an exponential decay; the lateral characteristic length of recovery from the mechanical defect is ∼50 µm for cells with a 10 µm spacing. At distances greater than this characteristic length, cells behave similarly to those in a fully intact monolayer. This work demonstrates the power of SINK to investigate diseases including cancer and atherosclerosis that result from single cells or heterogeneities in monolayers.This article has an associated First Person interview with the first author of the paper.

Dendritic Cell-Inspired Designed Architectures toward Highly Efficient Electrocatalysts for Nitrate Reduction Reaction.

Electrocatalysis for nitrate reduction reaction (NRR) has recently been recognized as a promising technology to convert nitrate to nitrogen. Catalyst support plays an important role in electrocatalytic process. Although porous carbon and metal oxides are considered as common supports for metal-based catalysts, fabrication of such architecture with high electric conductivity, uniform dispersion of nanoparticles, and long-term catalytic stability through a simple and feasible approach still remains a significant challenge. Herein, inspired by the signal transfer mode of dendritic cell, an all-carbon dendritic cell-like (DCL) architecture comprising mesoporous carbon spheres (MCS) connected by tethered carbon nanotubes (CNTs) with CuPd nanoparticles dispersed throughout (CuPd@DCL-MCS/CNTs) is reported. An impressive removal capacity as high as 22 500 mg N g-1 CuPd (≈12 times superior to Fe-based catalysts), high nitrate conversion (>95%) and nitrogen selectivity (>95%) are achieved under a low initial concentration of nitrate (100 mg L-1 ) when using an optimized-NRR electrocatalyst (4CuPd@DCL-MCS/CNTs). Remarkably, nitrate conversion and nitrogen selectivity are both close to 100% in an ultralow concentration of 10 mg L-1 , meeting drinking water standard. The present work not only provides high electrocatalytic performance for NRR but also introduces new inspiration for the preparation of other DCL-based architectures.

Fast and cost-effective preparation of plant cells for scanning electron microscopy (SEM) analysis.

The analysis of plant cell structure provides valuable information about its morphological, physiological, and biochemical characteristics. Nowadays, scanning electron microscope (SEM) is widely used to provide high-resolution images at the surface of biological samples. However, biological specimens require preparation, including dehydration and coating with conductive materials for imaging by SEM. There are several techniques for providing images with maximum maintenance of cell structure and minimum cellular damage, but each requires the use of expensive and hazardous materials, which can be damaging to the cell in many cases. Therefore, the provision of new and effective preparation methods based on maintaining cell structure for imaging can be very practical. In the present study, a fast and cost-effective protocol was first performed for chemical fixation and preparation of the plant cells for imaging by SEM. Taxus baccata and Zhumeria majdae cells were chemically fixed using glutaraldehyde and then successfully dried with different percentages of ethanol including 70, 80, 90, and 100%. In addition, SEM was performed for imaging the cell surface in different micro-scales. This protocol can be used by plant cell biologists and biotechnologists who are interested in studying structural and biochemical responses of treated or stressed plant cells by SEM.

Microtubules: From understanding their dynamics to using them as potential therapeutic targets.

Microtubules (MT) and actin microfilaments are dynamic cytoskeleton components involved in a range of intracellular processes. MTs play a role in cell division, beating of cilia and flagella, and intracellular transport. Over the past decades, much knowledge has been gained regarding MT function and structure, and its role in underlying disease progression. This makes MT potential therapeutic targets for various disorders. Disturbances in MT and their associated proteins are the underlying cause of diseases such as Alzheimer's disease, cancer, and several genetic diseases. Some of the advances in the field of MT research, as well as the potenti G beta gamma, is needed al uses of MT-targeting agents in various conditions have been reviewed here.

A generative model of realistic brain cells with application to numerical simulation of the diffusion-weighted MR signal.

To date, numerical simulations of the brain tissue have been limited by their lack of realism and flexibility. The purpose of this work is to propose a controlled and flexible generative model for brain cell morphology and an efficient computational pipeline for the reliable and robust simulation of realistic cellular structures with application to numerical simulation of intra-cellular diffusion-weighted MR (DW-MR) signal features. Inspired by the advances in computational neuroscience for modelling brain cells, we propose a generative model that enables users to simulate molecular diffusion within realistic digital brain cells, such as neurons, in a completely controlled and flexible fashion. We validate our new approach by showing an excellent match between the morphology (no statistically different 3D Sholl metrics, P > 0.05) and simulated intra-cellular DW-MR signal (mean relative difference < 2%) of the generated digital model of brain cells and those of digital reconstruction of real brain cells from available open-access databases. We demonstrate the versatility and potential of the framework by showing a select set of examples of relevance for the DW-MR community. The computational models introduced here are useful for synthesizing intra-cellular DW-MR signals, similar to those one might measure from brain metabolites DW-MRS experiments. They also provide the foundation for a more complete simulation system that will potentially include signals from extra-cellular compartments and exchange processes, necessary for synthesizing DW-MR signals of relevance for DW-MRI experiments.

Imaging cell morphology and physiology using X-rays.

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.

Dynamic Protein Allosteric Regulation and Disease.

Allostery is largely associated with conformational and functional transitions in individual proteins. All dynamic proteins are allosteric. This concept can be extended to consider the impact of conformational perturbations on cellular function and disease states. In this section, we will illuminate how allostery can control physiological activities and cause disease, aiming to increase the awareness of the linkage between disease symptoms on the cellular level and specific aberrant allosteric actions on the molecular level.

Toxic effects of tetracycline and its degradation products on freshwater green algae.

Tetracycline antibiotics are the most widely used antibiotics in the world and the most common veterinary drugs and feed additives used in livestock, poultry and aquaculture operations. Because antibiotics cannot be completely removed by currently existing sewage treatment facilities, these materials enter the environment directly via sewage treatment plant discharge, where they degrade. Accordingly, the metabolism and the ecological toxicity of tetracycline degradation products are worthy of attention. Herein, we investigated the effects of tetracycline and its degradation products (anhydrotetracycline and epitetracycline hydrochloride) on the growth, cell structure and algal cell oxidative stress of common Chlorella vulgaris. The results showed that the 96h-EC50 values of tetracycline (TC), anhydrotetracycline (ATC) and epitetracycline (ETC) on algal cells were 7.73, 5.96 and 8.42 mg/L, respectively. Moreover, the permeability of algal cells exposed to high concentrations of these three drugs was significantly enhanced. In addition, there were structural changes in the cells such as plasmolysis and starch granule deposition appeared, the thylakoid lamellae in the chloroplasts became blurred and deformed, and the vacuoles became larger. Exposure to higher concentrations (>5 mg/L) of TC and its degradation products ATC and ETC significantly upregulated the activity of ROS, as well as the antioxidants SOD and CAT. The levels of the lipid peroxidation product MDA also showed the same trend. Finally, ATC had the strongest toxicity toward algal cells, followed by TC and then ETC.

Protein Expression Landscape Defines the Differentiation Potential Specificity of Adipogenic and Myogenic Precursors in the Skeletal Muscle.

The balance of adipogenic and myogenic differentiation of skeletal muscle-derived mesenchymal stem cells is particularly important in muscle development and intramuscular fat deposition. This study aimed to explore the differential regulation between adipogenic and myogenic precursors by comparative analysis of their global proteome expression profile. Adipogenic and myogenic precursors isolated from neonatal porcine longissimus dorsi muscle by the preplate method were verified for their unique and distinct differentiation potential under myogenic or adipogenic induction. A total of 433 differentially expressed proteins (DEP) ( P < 0.05 and FC > 1.20 or <0.83) between adipogenic and myogenic precursors were detected via a tandem mass tag (TMT)-coupled LC-MS/MS approach, including 339 up-regulated and 94 down-regulated proteins in myogenic precursors compared with adipogenic precursors. On the basis of functional annotation and enrichment analysis of 433 DEP, adipogenic and myogenic precursors showed significantly different metabolic pattern of energy substances and differential regulations of gene expression, cell structure and development, ion homeostasis, and cell motility and migration. Three pathways including PPAR signaling pathway, phosphatidylinositol signaling system, and autophagy signaling pathway, which was differentially regulated between adipogenic and myogenic precursors, was also discovered to play crucial roles in cell differentiation. In conclusion, these differentiated regulation patterns between the two cell subsets of mesenchymal precursors together defines their differentiation potential specificity.