Superresolution Imaging Identifies That Conventional Trafficking Pathways Are Not Essential for Endoplasmic Reticulum to Outer Mitochondrial Membrane Protein Transport

Theoretical insight on the saturated stimulated emission intensity of a squaraine dye for STED nanoscopy

Stimulated emission depletion nanoscopy (STED) is increasingly applied for the insights into the ultra-structures of organelles in live cells because of the bypassing of the Abbe's optical diffraction limit. Theoretically, with the increase of excitation and depletion laser power, the imaging resolution can be accordingly enhanced and even close to the infinity. Unfortunately, powerful laser illuminations usually produce severe phototoxicity and photobleaching, which will lead to more extra-interference with biological events in live cells and accelerate the decomposition of the fluorescent probes. In view of the trade-off of cell viability and imaging resolution, excellent probes with superior photophysical properties are great in demand. For a qualified STED probes, the saturated stimulated emission intensity (I_sat) is considered as a key evaluating factor. According to the formula, I_sat is inversely proportional to the stimulated emission cross section (σ_sti) of the fluorescent probe. However, the relationship between the σ_sti and chemical structure of the STED probe remain to be unclear. In this work, we explore the influence factors by theoretical calculations on a squaraine dye (MitoEsq-635) and a commercial dye (Atto647N). The results indicate that the increase of transition dipole moment (μ) are beneficial for the increase of σ_sti, thereafter reducing I_sat. Furthermore, we firstly proposed that stimulated emission depletion was qualitatively interpreted by the investigation on the potential energy surfaces of ground states (S₀) and the first excited states (S₁) of the dyes.

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.

Ruminant fat intake improves gut microbiota, serum inflammatory parameter and fatty acid profile in tissues of Wistar rats

This study tested the hypothesis that naturally and industrially produced trans-fatty acids can exert distinct effects on metabolic parameters and on gut microbiota of rats. Wistar rats were randomized into three groups according to the diet: CONT-control, with 5% soybean oil and normal amount of fat; HVF-20% of hydrogenated vegetable fat (industrial); and RUM-20% of ruminant fat (natural). After 53 days of treatment, serum biochemical markers, fatty acid composition of liver, heart and adipose tissue, histology and hepatic oxidative parameters, as well as gut microbiota composition were evaluated. HVF diet intake reduced triglycerides (≈ 39.39%) and VLDL levels (≈ 39.49%). Trans-fatty acids levels in all tissue were higher in HVF group. However, RUM diet intake elevated amounts of anti-inflammatory cytokine IL-10 (≈ 14.7%) compared to CONT, but not to HVF. Furthermore, RUM intake led to higher concentrations of stearic acid and conjugated linoleic acid in all tissue; this particular diet was associated with a hepatoprotective effect. The microbial gut communities were significantly different among the groups. Our results show that ruminant fat reversed the hepatic steatosis normally caused by high fat diets, which may be related to the remodelling of the gut microbiota and its anti-inflammatory potential.

Cubic spline-based depth-dependent localization of mitochondria-endoplasmic reticulum contacts by three-dimensional light-sheet super-resolution microscopy

The contact distance between mitochondria (Mito) and endoplasmic reticulum (ER) has received considerable attention owing to their crucial function in maintaining lipid and calcium homeostasis. Herein, cubic spline algorithm-based depth-dependent fluorescence-free three-dimensional light-sheet super-resolution microscopy (3D LSRM) with dual-wavelength illumination sources was investigated to study the distance of Mito-ER contacts in various live cells. To detect wavelength-dependent scattering, 12 nm gold nanoparticles (AuNPs) and 20 nm silver nanoparticles (AgNPs) as fluorescence-free nanoprobes were conjugated with Mito and ER. The cubic spline algorithm-based method showed improved localization precision in lateral and axial directions compared with that for previously used least squares and least cubic algorithms. The cubic spline-based depth-dependent localization was applied to the spatial localization of nanoprobes in super-resolution images, in which the average distance of Mito and ER was 22.4 nm in HeLa cells, 22.2 nm in RAW264.7 macrophage cells, 21.9 nm in AGS cells, 21.4 nm in HT29 cells, and 21.3 nm in HEK293 cells. The distances were ∼12% larger than those previously determined by electron microscopy, which demonstrated that this method was accessible and reliable for studying the intracellular structures of various live cells at the subdiffraction limit resolution.

Mitochondrial fragmentation enables localized signaling required for cell repair

Plasma membrane injury can cause lethal influx of calcium, but cells survive by mounting a polarized repair response targeted to the wound site. Mitochondrial signaling within seconds after injury enables this response. However, as mitochondria are distributed throughout the cell in an interconnected network, it is unclear how they generate a spatially restricted signal to repair the plasma membrane wound. Here we show that calcium influx and Drp1-mediated, rapid mitochondrial fission at the injury site help polarize the repair response. Fission of injury-proximal mitochondria allows for greater amplitude and duration of calcium increase in these mitochondria, allowing them to generate local redox signaling required for plasma membrane repair. Drp1 knockout cells and patient cells lacking the Drp1 adaptor protein MiD49 fail to undergo injury-triggered mitochondrial fission, preventing polarized mitochondrial calcium increase and plasma membrane repair. Although mitochondrial fission is considered to be an indicator of cell damage and death, our findings identify that mitochondrial fission generates localized signaling required for cell survival.

Mitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane

Mitochondrial enzymes involved in energy transformation are organized into multiprotein complexes that channel the reaction intermediates for efficient ATP production. Three of the mammalian urea cycle enzymes: N-acetylglutamate synthase (NAGS), carbamylphosphate synthetase 1 (CPS1), and ornithine transcarbamylase (OTC) reside in the mitochondria. Urea cycle is required to convert ammonia into urea and protect the brain from ammonia toxicity. Urea cycle intermediates are tightly channeled in and out of mitochondria, indicating that efficient activity of these enzymes relies upon their coordinated interaction with each other, perhaps in a cluster. This view is supported by mutations in surface residues of the urea cycle proteins that impair ureagenesis in the patients, but do not affect protein stability or catalytic activity. We find the NAGS, CPS1, and OTC proteins in liver mitochondria can associate with the inner mitochondrial membrane (IMM) and can be co-immunoprecipitated. Our in-silico analysis of vertebrate NAGS proteins, the least abundant of the urea cycle enzymes, identified a protein-protein interaction region present only in the mammalian NAGS protein—“variable segment,” which mediates the interaction of NAGS with CPS1. Use of super resolution microscopy showed that NAGS, CPS1 and OTC are organized into clusters in the hepatocyte mitochondria. These results indicate that mitochondrial urea cycle proteins cluster, instead of functioning either independently or in a rigid multienzyme complex.

Integrated mRNA and miRNA expression profile analysis of female and male gonads in Hyriopsis cumingii

Hyriopsis cumingii is an important species for freshwater pearl cultivation in China. In terms of pearl production, males have larger pearls and better glossiness than females, but there are few reports focusing on the sex of H. cumingii. In this study, six mRNA and six microRNA (miRNA) libraries were prepared from ovaries and testes. Additionally, 28,502 differentially expressed genes (DEGs) and 32 differentially expressed miRNAs (DEMs) were identified. Compared with testis, 14,360 mRNAs and 20 miRNAs were up-regulated in ovary, 14,142 mRNAs and 12 miRNAs were down-regulated. In DEGs, the known genes related to sex determinism and/or differentiation were also identified, such as DMRT1, SOX9, SF1 for males, FOXL2 for females, and other potentially significant candidate genes. Three sex-related pathways have also been identified, which are Wnt, Notch, and TGF-beta. In 32 DEMs, the three miRNAs (miR-9-5p, miR-92, miR-184) were paid more attention, they predicted 28 target genes, which may also be candidates for sex-related miRNAs and genes. Differential miRNAs target genes analysis reveals the pathway associated with oocyte meiosis and spermatogenesis. Overall, the findings of the study provide significant insights to enhance our understanding of sex differentiation and/or sex determination mechanisms for H. cumingii.

Lignocellulosic biomass supported metal nanoparticles for the catalytic reduction of organic pollutants

Lignocellulosic biomass waste is a cheap, eco-friendly, and sustainable raw material for a wide array of applications. In the present study, an easy, fast, and economically feasible route has been proposed for the preparation of different zero-valent metal nanoparticles (ZV-MNPs) based on Cu, Co, Ag, and Ni NPs using empty fruit bunch (EFB) biomass residue as support material. The catalytic efficiency of ZV-MNPs/EFB catalyst was investigated against five model pollutants, such as methyl orange (MO), congo red (CR), methylene blue (MB), acridine orange (AO), and 4-nitrophenol (4-NP) using NaBH₄ as a source of hydrogen and electron. Comparative study revealed that among as-prepared ZV-MNPs/EFB catalysts, Cu-NPs immobilized onto EFB (Cu/EFB) exhibited maximum catalytic efficiency towards pollutant abasement. Degradation reactions were highly efficient, and were completed within a short time (4 min) in case of MO, CR, and MB, whilst AO and 4-NP were reduced in less than 15 min. Kinetic investigation revealed that the degradation rate of model pollutants accorded with pseudo-first order model. Furthermore, supported catalysts were easily recovered after the completion of experiment by simply pulling the catalyst from reaction system. Recyclability tests performed on Cu/EFB revealed that more than 97% of the reduction was achieved in case of MO dye for four successive cycles of reuse. The as-prepared heterostructure showed multifunctional properties, such as enhanced uptake of contaminants, high catalytic efficiency, and easy recovery, hence, offers great prospects in wastewater purification.

Structural insights into semicrystalline states of electrospun nanofibers: a multiscale analytical approach

A dedicated nanofiber design for applications in the biomedical domain is based on the understanding of nanofiber structures. The structure of electrospun nanofibers strongly influences their properties and functionalities. In polymeric nanofibers X-ray scattering and diffraction methods, i.e. SAXS and WAXD, are capable of decoding their structural insights from about 100 nm down to the Angström scale. Here, we present a comprehensive X-ray scattering and diffraction based study and introduce new data analysis approaches to unveil detailed structural features in electrospun poly(vinylidene fluoride-co-hexafluoropropylene) (PVDFhfp) nanofiber membranes. Particular emphasis was placed on anisotropic morphologies being developed during the nanofiber fabrication process. Global analysis was performed on SAXS data to derive the nanofibrillar structure of repeating lamella crystalline domains with average dimensions of 12.5 nm thickness and 7.8 nm spacing along with associated tie-molecules. The varying surface roughness of the nanofiber was evaluated by extracting the Porod exponent in parallel and perpendicular direction to the nanofiber axis, which was further validated by Atomic Force Microscopy. Additionally, the presence of a mixture of the monoclinic alpha and the orthorhombic beta PVDFhfp phases both exhibiting about 6% larger unit cells compared to the corresponding pure PVDF phases was derived from WAXD. The current study shows a generic approach in detailed understanding of internal structures and surface morphology for nanofibers. This forms the basis for targeted structure and morphology steering and the respective controlling during the fabrication process with the aim to engineer nanofibers for different biomedical applications with specific requirements.

Rituximab effectively reverses Tyrosine kinase inhibitors (TKIs) resistance through inhibiting the accumulation of rictor on mitochondria-associated ER-membrane (MAM)

Tyrosine kinase inhibitors (TKIs), a novel group of target-specific anti lung cancer drugs, have recently been found to resistant to some NSCLC cells which have the T790M EGFR mutation. However, recent investigations on the therapies of resistance to EGFR-TKIs are very limited. Therefore, it is important to develop more effective therapies to reverse EGFR-TKIs resistance. In our present study, erlotinib was used as the TKIs drug and the effects of the erlotinib on cell growth were evaluated. Cell viability and concentration dependent studies were performed using HCI-H1975 and HCI-H1299 cells alone with erlotinib, respectively. Further combined with rituximab, the results showed that erlotinib and rituximab were significantly inhibited the cell growth. Furthermore, the combination of erlotinib and rituximab greatly decreased the expression of p-mTOR and p-EGFR. Additional results from western blotting and immunofluorescence assays demonstrated that the accumulation of rictor was also decreased on MAM. Thus, all these results suggested that EGFR-TKIs combined with CD20 mono-antibody significantly decrease the cell growth of H1975 cells and H1299, with T790M EGFR mutation, and inhibit the localization of the key mTOR pathway proteins to MAM. So, it may be a promising strategy for overcoming EGFR TKI resistance in NSCLC patients.

Caught in the act - protein adaptation and the expanding roles of the PACS proteins in tissue homeostasis and disease

Vertebrate proteins that fulfill multiple and seemingly disparate functions are increasingly recognized as vital solutions to maintaining homeostasis in the face of the complex cell and tissue physiology of higher metazoans. However, the molecular adaptations that underpin this increased functionality remain elusive. In this Commentary, we review the PACS proteins - which first appeared in lower metazoans as protein traffic modulators and evolved in vertebrates to integrate cytoplasmic protein traffic and interorganellar communication with nuclear gene expression - as examples of protein adaptation 'caught in the act'. Vertebrate PACS-1 and PACS-2 increased their functional density and roles as metabolic switches by acquiring phosphorylation sites and nuclear trafficking signals within disordered regions of the proteins. These findings illustrate one mechanism by which vertebrates accommodate their complex cell physiology with a limited set of proteins. We will also highlight how pathogenic viruses exploit the PACS sorting pathways as well as recent studies on PACS genes with mutations or altered expression that result in diverse diseases. These discoveries suggest that investigation of the evolving PACS protein family provides a rich opportunity for insight into vertebrate cell and organ homeostasis.