Subcellular structure, heterogeneity, and plasticity of senescent cells

Cellular senescence is a state of permanent growth arrest. It can be triggered by telomere shortening (replicative senescence) or prematurely induced by stresses such as DNA damage, oncogene overactivation, loss of tumor suppressor genes, oxidative stress, tissue factors, and others. Advances in techniques and experimental designs have provided new evidence about the biology of senescent cells (SnCs) and their importance in human health and disease. This review aims to describe the main aspects of SnCs phenotype focusing on alterations in subcellular compartments like plasma membrane, cytoskeleton, organelles, and nuclei. We also discuss the heterogeneity, dynamics, and plasticity of SnCs' phenotype, including the SASP, and pro-survival mechanisms. We advance on the multiple layers of phenotypic heterogeneity of SnCs, such as the heterogeneity between inducers, tissues and within a population of SnCs, discussing the relevance of these aspects to human health and disease. We also raise the main challenges as well alternatives to overcome them. Ultimately, we present open questions and perspectives in understanding the phenotype of SnCs from the perspective of basic and applied questions.

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures

The possibility to replicate and reproduce published research results is one of the biggest challenges in all areas of science. In computational neuroscience, there are thousands of models available. However, it is rarely possible to reimplement the models based on the information in the original publication, let alone rerun the models just because the model implementations have not been made publicly available. We evaluate and discuss the comparability of a versatile choice of simulation tools: tools for biochemical reactions and spiking neuronal networks, and relatively new tools for growth in cell cultures. The replicability and reproducibility issues are considered for computational models that are equally diverse, including the models for intracellular signal transduction of neurons and glial cells, in addition to single glial cells, neuron-glia interactions, and selected examples of spiking neuronal networks. We also address the comparability of the simulation results with one another to comprehend if the studied models can be used to answer similar research questions. In addition to presenting the challenges in reproducibility and replicability of published results in computational neuroscience, we highlight the need for developing recommendations and good practices for publishing simulation tools and computational models. Model validation and flexible model description must be an integral part of the tool used to simulate and develop computational models. Constant improvement on experimental techniques and recording protocols leads to increasing knowledge about the biophysical mechanisms in neural systems. This poses new challenges for computational neuroscience: extended or completely new computational methods and models may be required. Careful evaluation and categorization of the existing models and tools provide a foundation for these future needs, for constructing multiscale models or extending the models to incorporate additional or more detailed biophysical mechanisms. Improving the quality of publications in computational neuroscience, enabling progressive building of advanced computational models and tools, can be achieved only through adopting publishing standards which underline replicability and reproducibility of research results.

Nucleus preservation in early Ediacaran Weng'an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record

The challenge of identifying fossilized organelles has long hampered attempts to interpret the fossil record of early eukaryote evolution. We explore this challenge through experimental taphonomy of nuclei in a living eukaryote and microscale physical and chemical characterization of putative nuclei in embryo-like fossils from the early Ediacaran Weng'an Biota. The fossil nuclei exhibit diverse preservational modes that differ in shape, presence or absence of an inner body and the chemistry of the associated mineralization. The nuclei are not directly fossilized; rather, they manifest as external moulds. Experimental taphonomy of epidermal cells from the common onion (Allium cepa) demonstrates that nuclei are more decay resistant than their host cells, generally maintaining their physical dimensions for weeks to months post-mortem, though under some experimental conditions they exhibit shrinkage and/or become shrouded in microbial biofilms. The fossil and experimental evidence may be rationalized in a single taphonomic pathway of selective mineralization of the cell cytoplasm, preserving an external mould of the nucleus that is itself resistant to both decay and mineral replication. Combined, our results provide both a secure identification of the Weng'an nuclei as well as the potential of a fossil record of organelles that might help arbitrate in long-standing debates over the relative and absolute timing of the evolutionary assembly of eukaryote-grade cells.

Characterizing the Xenoma of Vairimorpha necatrix Provides Insights Into the Most Efficient Mode of Microsporidian Proliferation

Microsporidia are a group of obligated intracellular parasites that can infect nearly all vertebrates and invertebrates, including humans and economic animals. Microsporidian Vairimorpha necatrix is a natural pathogen of multiple insects and can massively proliferate by making tumor-like xenoma in host tissue. However, little is known about the subcellular structures of this xenoma and the proliferation features of the pathogens inside. Here, we characterized the V. necatrix xenoma produced in muscle cells of silkworm midgut. In result, the whitish xenoma was initially observed on the 12^th day post infection on the outer surface of the midgut and later became larger and numerous. The observation by scanning electronic microscopy showed that the xenoma is mostly elliptical and spindle with dense pathogen-containing protrusions and spores on the surface, which were likely shedding off the xenoma through exocytosis and could be an infection source of other tissues. Demonstrated with transmission electron microscopy and fluorescent staining, the xenoma was enveloped by a monolayer membrane, and full of vesicle structures, mitochondria, and endoplasmic reticulum around parasites in development, suggesting that high level of energy and nutrients were produced to support the massive proliferation of the parasites. Multiple hypertrophic nuclei were found in one single xenoma, indicating that the cyst was probably formed by fusion of multiple muscle cells. Observed by fluorescence in situ hybridization, pathogens in the xenoma were in merongony, sporogony, and octosporogony, and mature stages. And mature spores were pushed to the center while vegetative pathogens were in the surface layer of the xenoma. The V. necatrix meront usually contained two to three nuclei, and sporont contained two nuclei and was wrapped by a thick membrane with high electron density. The V. necatrix sporogony produces two types of spores, the ordinary dikaryotic spore and unicellular octospores, the latter of which were smaller in size and packed in a sporophorous vesicle. In summary, V. necatrix xenoma is a specialized cyst likely formed by fusion of multiple muscle cells and provides high concentration of energy and nutrients with increased number of mitochondria and endoplasmic reticulum for the massive proliferation of pathogens inside.

Effects of arbuscular mycorrhizal fungi on root architecture and ultrastructure of Hordeum jubatum under the interactive impact of nitrogen deposition and cold stress

Hordeum jubatum L. is a perennial herb with high ornamental value and strong stress tolerance. Nitrogen deposition and cold stress are key environmental factors that affect stability of ecosystems in cold regions of northeast China. These factors significantly affect plant growth and development. Arbuscular mycorrhizal fungi (AMF) are symbiotic soil fungi that can increase plant resistance and growth. However, research on impacts of nitrogen deposition and cold stress on roots of H. jubatum-AM symbionts remains limited. Root biomass (dry and fresh weight), architecture (length, surface area, volume, forks, number of fourth-order roots, and root fractal dimension), and ultrastructure of H. jubatum were assessed, both in the presence and absence of AMF, under conditions of nitrogen deposition and cold stress. Cold stress inhibited all indicators of root architecture and disrupted root ultrastructure, with greater inhibition shown in the N2 (NH4 +/NO3 - = 1:1) treatment under cold stress, indicating nitrogen deposition increased sensitivity of H. jubatum to cold stress. Inoculation with AMF significantly reduced damage caused by nitrogen deposition and cold stress on H. jubatum roots compared with the non-inoculation treatment. Our results demonstrate different effects of the interaction of nitrogen deposition and cold stress versus single stress (nitrogen deposition or cold stress) on plant root development and provide a scientific basis for the use of mycorrhizal technology to improve resistance and productivity of cold-tolerant plants in cold regions under stress conditions.

[Effects of increased O3 concentration on growth, subcellular structure and reactive oxygen metabolism of turf-type Festuca arundinace]

Taking ambient environmental O₃(40 nmol·mol^-1) as control, the study was conducted to assess the impact of elevated O₃(80 and 160 nmol·mol^-1) on the growth, subcellular structure and reactive oxygen metabolism of turf-type Festuca arundinace in open top-chambers (OTCs). The results showed that under 14-day fumigation, the height and leaf width of F. arundinace decreased significantly, and the total biomass decreased by 43.7%, and some fully expanded leaves yellowed under 80 nmol·mol^-1 O₃. Some visible injury symptoms, brown spots and necrosis appeared in the leaves, the total biomass decreased by 46.2%, and plasma membrane became loose from the cell wall and convoluted, chloroplast and mitochondria were damaged under 160 nmol·mol^-1 O₃. The rate of superoxide anion (O₂^-·) production, hydrogen peroxide (H₂O₂) content, malonaldehyde (MDA) content and the activities of antioxidant enzymes were higher under the increasing O₃ concentrations (80 and 160 nmol·mol^-1) compared with control. Total phenolics and the antioxidant capacity increased at first and then decreased with the rise of O₃ concentration. It indicated that O₃ has already affected F. arundinace growth and antioxidative metabolism before visible injury symptom appeared. F. arundinace had an adaptive response to elevated O₃, but it could not protect itself from excessive O₃ or long-term O₃ exposure.

An inducible tricolor reporter mouse for simultaneous imaging of lysosomes, mitochondria and microtubules

Cell-type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues, and their connection to cellular diversity, remain limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "kaleidoscope", for simultaneous imaging of lysosomes, mitochondria and microtubules in any cell type and at a single cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell-type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.

Organelle Interaction and Drug Discovery: Towards Correlative Nanoscopy and Molecular Dynamics Simulation

The inter-organelle interactions, including the cytomembrane, endoplasmic reticulum, mitochondrion, lysosome, dictyosome, and nucleus, play the important roles in maintaining the normal function and homeostasis of cells. Organelle dysfunction can lead to a range of diseases (e.g., Alzheimer's disease (AD), Parkinson's disease (PD), and cancer), and provide a new perspective for drug discovery. With the development of imaging techniques and functional fluorescent probes, a variety of algorithms and strategies have been developed for the ever-improving estimation of subcellular structures, organelle interaction, and organelle-related drug discovery with accounting for the dynamic structures of organelles, such as the nanoscopy technology and molecular dynamics (MD) simulations. Accordingly, this work summarizes a series of state-of-the-art examples of the recent progress in this rapidly changing field and uncovering the drug screening based on the structures and interactions of organelles. Finally, we propose the future outlook for exciting applications of organelle-related drug discovery, with the cooperation of nanoscopy and MD simulations.