Nup358 regulates remodelling of ER-mitochondrial contact sites and autophagy

The contact sites between ER and mitochondria regulate several cellular processes including inter-organelle lipid transport, calcium homeostasis and autophagy. However, the mechanisms that regulate the dynamics and functions of these contact sites remain unresolved. We show that annulate lamellae (AL), a relatively unexplored subcellular structure representing subdomains of ER enriched with a subset of nucleoporins, are present at ER-mitochondria contact sites (ERMCS). Depletion of one of the AL-resident nucleoporins, Nup358, results in increased contacts between ER and mitochondria. Mechanistically, Nup358 modulates ERMCS dynamics by restricting mTORC2/Akt signalling. Our results suggest that growth factor-mediated remodelling of ERMCS depends on a reciprocal binding of Nup358 and mTOR to the ERMCS tethering complex consisting of VAPB and PTPIP51. Furthermore, Nup358 also interacts with IP3R, an ERMCS-enriched Ca2+ channel, and controls Ca2+ release from the ER. Consequently, depletion of Nup358 leads to elevated cytoplasmic Ca2+ and autophagy via activation of Ca2+/CaMKK2/AMPK axis. Our study thus uncovers a novel role for AL, particularly for Nup358, in regulating mTORC2-mediated ERMCS remodelling and Ca2+-directed autophagy, possibly via independent mechanisms.

A cellular and molecular atlas reveals the basis of chytrid development.

The chytrids (phylum Chytridiomycota) are a major early-diverging fungal lineage of ecological and evolutionary importance. Despite their importance, many fundamental aspects of chytrid developmental and cell biology remain poorly understood. To address these knowledge gaps, we combined quantitative volume electron microscopy and comparative transcriptome profiling to create an "atlas" of the cellular and molecular basis of the chytrid life cycle, using the model chytrid Rhizoclosmatium globosum. From our developmental atlas, we show that zoospores exhibit a specialised biological repertoire dominated by inactive ribosome aggregates, and that lipid processing is complex and dynamic throughout the cell cycle. We demonstrate that the chytrid apophysis is a distinct subcellular structure characterised by high intracellular trafficking, providing evidence for division of labour in the chytrid cell plan, and show that zoosporogenesis includes "animal like" amoeboid cell morphologies resulting from endocytotic cargo transport from the interstitial maternal cytoplasm. Taken together, our results reveal insights into chytrid developmental biology and provide a basis for future investigations into early-diverging fungal cell biology.

Infrared Nanoscopy and Tomography of Intracellular Structures

The few microscopic techniques that simultaneously gather morphological and chemical data often rely on the use of specific markers. To eliminate this flaw, we have developed a method of examining cellular cross sections using the imaging power of scattering-type scanning near-field optical microscopy and Fourier-transform infrared spectroscopy at a spatial resolution far beyond the diffraction limit. Herewith, nanoscale surface and volumetric chemical imaging is performed using the intrinsic contrast generated by the characteristic absorption of mid-infrared radiation by the covalent bonds. We employ infrared nanoscopy to study the subcellular structures of eukaryotic (Chlamydomonas reinhardtii) and prokaryotic (Escherichia coli) species, revealing chemically distinct regions within each cell such as the microtubular structure of the flagellum. Serial 100 nm-thick cellular cross-sections were compiled into a tomogram yielding a three-dimensional infrared image of subcellular structure distribution at 20 nm resolution. The presented methodology is able to image biological samples competing current fluorescence nanoscopy but at less interference due to the low energy of infrared radiation and the absence of labeling.

Cadmium Uptake, In Vivo Metastasis and Subcellular Environmental Response of Five Wetland Plants Using DFT Method

The main purpose of this study is to analyze whether Cd2+ affects the absorption of Ca2+ and Fe2+ by the roots of five wetland plants and the toxic mechanism of cadmium on the subcellular structure. Five wetland plant samples were collected from the constructed wetland in the upper reaches of the Yangtze River. Based on the experiment and density function theory (DFT), we measured the Cd2+ content in the root, stem, and leaf, the morphological dimensions of plants, and in the subcellular structure the electronic activity of Cd compound was calculated to describe the stability and activity of the products. In general, Zephyranthes candida,Cynodon dactylon, Arundo donax, and Pontederia cordata have distinct cadmium uptake characteristics, while Phragmites communis does not. The results indicated tolerance to cadmium in all but Phragmites communis, which was due to cadmium distribution through the process of transpiration and a mechanical interception. The simulation results showed that Cd2+ imposed no obvious inhibition on the absorption of Ca2+ and Fe2+ in plants, as the energy barrier of the process is about 1–3 eV. Cd2+ could improve the amount of pyruvate and glucose by 30% via spd orbital hybridization, making them more chemically reactive. At the same time, Cd2+ could replace Mg2+ in chlorophyll through a copper substitution reaction, making the electron energy of chlorophyll more concentrated. As a result, the valence-band electron at −40 eV was vacant. In conclusion, we determined that Cd2+ has no obvious inhibitory effect on Ca2+ and Fe2+ in root absorption and that Cd2+ could affect the properties of compounds of the subcellular structure and thus produce physiological toxicity.

A deep generative model of 3D single-cell organization

We introduce a framework for end-to-end integrative modeling of 3D single-cell multi-channel fluorescent image data of diverse subcellular structures. We employ stacked conditional β-variational autoencoders to first learn a latent representation of cell morphology, and then learn a latent representation of subcellular structure localization which is conditioned on the learned cell morphology. Our model is flexible and can be trained on images of arbitrary subcellular structures and at varying degrees of sparsity and reconstruction fidelity. We train our full model on 3D cell image data and explore design trade-offs in the 2D setting. Once trained, our model can be used to impute structures in cells where they were not imaged and to quantify the variation in the location of all subcellular structures by generating plausible instantiations of each structure in arbitrary cell geometries. We apply our trained model to a small drug perturbation screen to demonstrate its applicability to new data. We show how the latent representations of drugged cells differ from unperturbed cells as expected by on-target effects of the drugs.

Structured illumination microscopy artefacts caused by illumination scattering

Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artefacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artefacts caused by scattering in thick samples. This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 1)'.

Mechanical Mechanisms of Chromosome Segregation

Chromosome segregation—the partitioning of genetic material into two daughter cells—is one of the most crucial processes in cell division. In all Eukaryotes, chromosome segregation is driven by the spindle, a microtubule-based, self-organizing subcellular structure. Extensive research performed over the past 150 years has identified numerous commonalities and contrasts between spindles in different systems. In this review, we use simple coarse-grained models to organize and integrate previous studies of chromosome segregation. We discuss sites of force generation in spindles and fundamental mechanical principles that any understanding of chromosome segregation must be based upon. We argue that conserved sites of force generation may interact differently in different spindles, leading to distinct mechanical mechanisms of chromosome segregation. We suggest experiments to determine which mechanical mechanism is operative in a particular spindle under study. Finally, we propose that combining biophysical experiments, coarse-grained theories, and evolutionary genetics will be a productive approach to enhance our understanding of chromosome segregation in the future.

Structured illumination microscopy artifacts caused by illumination scattering

Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artifacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index (RI) from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artifacts caused by scattering in thick samples.

Plant cell divisions: variations from the shortest symmetric path

In plants, the spatial arrangement of cells within tissues and organs is a direct consequence of the positioning of the new cell walls during cell division. Since the nineteenth century, scientists have proposed rules to explain the orientation of plant cell divisions. Most of these rules predict the new wall will follow the shortest path passing through the cell centroid halving the cell into two equal volumes. However, in some developmental contexts, divisions deviate significantly from this rule. In these situations, mechanical stress, hormonal signalling, or cell polarity have been described to influence the division path. Here we discuss the mechanism and subcellular structure required to define the cell division placement then we provide an overview of the situations where division deviates from the shortest symmetric path.