Correlative montage parallel array cryo-tomography for in situ structural cell biology.

Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here we present robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens. The combination of correlative cryo-fluorescence microscopy, focused-ion-beam milling, substrate micropatterning, and MPACT supports studies that contextually define the three-dimensional architecture of cells. To further extend the flexibility of MPACT, tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.

Publisher Correction: IGF1R is an entry receptor for respiratory syncytial virus.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

IGF1R is an entry receptor for respiratory syncytial virus.

Pneumonia resulting from infection is one of the leading causes of death worldwide. Pulmonary infection by the respiratory syncytial virus (RSV) is a large burden on human health, for which there are few therapeutic options1. RSV targets ciliated epithelial cells in the airways, but how viruses such as RSV interact with receptors on these cells is not understood. Nucleolin is an entry coreceptor for RSV2 and also mediates the cellular entry of influenza, the parainfluenza virus, some enteroviruses and the bacterium that causes tularaemia3,4. Here we show a mechanism of RSV entry into cells in which outside-in signalling, involving binding of the prefusion RSV-F glycoprotein with the insulin-like growth factor-1 receptor, triggers the activation of protein kinase C zeta (PKCζ). This cellular signalling cascade recruits nucleolin from the nuclei of cells to the plasma membrane, where it also binds to RSV-F on virions. We find that inhibiting PKCζ activation prevents the trafficking of nucleolin to RSV particles on airway organoid cultures, and reduces viral replication and pathology in RSV-infected mice. These findings reveal a mechanism of virus entry in which receptor engagement and signal transduction bring the coreceptor to viral particles at the cell surface, and could form the basis of new therapeutics to treat RSV infection.

Butyrophilin 3A1 binds phosphorylated antigens and stimulates human γδ T cells.

Human T cells that express a T cell antigen receptor (TCR) containing γ-chain variable region 9 and δ-chain variable region 2 (Vγ9Vδ2) recognize phosphorylated prenyl metabolites as antigens in the presence of antigen-presenting cells but independently of major histocompatibility complex (MHC), the MHC class I-related molecule MR1 and antigen-presenting CD1 molecules. Here we used genetic approaches to identify the molecule that binds and presents phosphorylated antigens. We found that the butyrophilin BTN3A1 bound phosphorylated antigens with low affinity, at a stoichiometry of 1:1, and stimulated mouse T cells with transgenic expression of a human Vγ9Vδ2 TCR. The structures of the BTN3A1 distal domain in complex with host- or microbe-derived phosphorylated antigens had an immunoglobulin-like fold in which the antigens bound in a shallow pocket. Soluble Vγ9Vδ2 TCR interacted specifically with BTN3A1-antigen complexes. Accordingly, BTN3A1 represents an antigen-presenting molecule required for the activation of Vγ9Vδ2 T cells.

Harnessing Natural Polymers for Nano-Scaffolds in Bone Tissue Engineering: A Comprehensive Overview of Bone Disease Treatment.

Numerous surgeries are carried out to replace tissues that have been harmed by an illness or an accident. Due to various surgical interventions and the requirement of bone substitutes, the emerging field of bone tissue engineering attempts to repair damaged tissues with the help of scaffolds. These scaffolds act as template for bone regeneration by controlling the development of new cells. For the creation of functional tissues and organs, there are three elements of bone tissue engineering that play very crucial role: cells, signals and scaffolds. For the achievement of these aims, various types of natural polymers, like chitosan, chitin, cellulose, albumin and silk fibroin, have been used for the preparation of scaffolds. Scaffolds produced from natural polymers have many advantages: they are less immunogenic as well as being biodegradable, biocompatible, non-toxic and cost effective. The hierarchal structure of bone, from microscale to nanoscale, is mostly made up of organic and inorganic components like nanohydroxyapatite and collagen components. This review paper summarizes the knowledge and updates the information about the use of natural polymers for the preparation of scaffolds, with their application in recent research trends and development in the area of bone tissue engineering (BTE). The article extensively explores the related research to analyze the advancement of nanotechnology for the treatment of bone-related diseases and bone repair.

Novel TMPRSS6 variants and their impact on iron-refractory iron deficiency anaemia in pregnancy: A North Indian genotype phenotype study.

Iron-refractory iron deficiency anaemia (IRIDA) is a rare autosomal recessive disorder, distinguished by hypochromic microcytic anaemia, low transferrin levels and inappropriately elevated hepcidin (HEPC) levels. It is caused by mutations in TMPRSS6 gene. Systematic screening of 500 pregnant women with iron deficiency anaemia having moderate to severe microcytosis with no other causes of anaemia were enrolled to rule out oral iron refractoriness. It identified a final cohort of 10 (2.15% prevalence) individuals with IRIDA phenotype. Haematological and biochemical analysis revealed significant differences between iron responders and iron non-responders, with iron non-responders showing lower haemoglobin, red blood cell count, serum iron and serum ferritin levels, along with elevated HEPC (9.47 ± 2.75 ng/mL, p = 0.0009) and erythropoietin (4.58 ± 4.07 µ/mL, p = 0.0196) levels. Genetic sequencing of the TMPRSS6 gene in this final cohort identified 10 novel variants, including seven missense and three frame-shift mutations, with four missense variants showing high functional impact defining the IRIDA phenotype. Structural analysis revealed significant damage caused by two variants (p.L83R and p.S235R). This study provides valuable insights into IRIDA among pregnant women in the Indian subcontinent, unveiling its underlying causes of unresponsiveness, genetic mechanisms and prevalence. Furthermore, research collaboration is essential to validate these findings and develop effective treatments.

Cutaneous infection due to Mycobacterium marinum: A series of four cases from Kerala, India.

Mycobacterium marinum is a non-tuberculous mycobacterium which can be found in naturally occurring, non-chlorinated water sources and is a known pathogen that affects fish. In humans, M. marinum typically results in cutaneous lesions, it can occasionally lead to more invasive disorders. We discuss four cases of M. marinum-related cutaneous infections examined in a tertiary care facility. We want to draw attention to the challenges of accurately diagnosing this infection, stress the significance of having a high level of clinical suspicion in order to identify it, and discuss the available treatment choices.

The role of TMPRSS6 gene polymorphism in iron resistance iron deficiency anaemia (IRIDA): a systematic review.

Iron resistance iron deficiency anaemia is a rare autosomal recessive disorder characterized by hypochromic microcytic anaemia, low transferrin saturation and inappropriately high hepcidin levels. The aetiology of this condition is rooted in genetic variations within the transmembrane serine protease 6 (TMPRSS6) genes, responsible for encoding matriptase-2, a pivotal negative regulator of hepcidin. We conducted a systematic search across four electronic databases, yielding 538 articles in total out of which 25 were finally included and were preceded further, aiming to prognosticate prevalent single nucleotide polymorphisms (SNPs) and detrimental genetic alterations. This review aims to elucidate the effects of various SNPs and pathogenic mutations on both haematological and biochemical parameters, as well as their potential interethnic correlation. Employing bioinformatics tools, we subjected over 100 SNPs to scrutiny, discerning their potential functional ramifications. We found rs1373272804, rs1430692214 and rs855791 variants to be most frequent and were having a significant impact on haematological and biochemical profile. We found that individuals of European ancestry were more prone to have these variants compared to other ethnic groups. In conclusion, this review not only sheds light on the association of TMPRSS6 polymorphism in iron resistance iron deficiency anaemia (IRIDA), but also highlights the critical need for further investigations involving larger sample size and more diverse ethnic groups around the globe. These future studies will be vital for gaining a stronger and more reliable understanding of how these genetic differences are linked to the development of IRIDA.

Exosome-like nanoparticles from Mulberry bark prevent DSS-induced colitis via the AhR/COPS8 pathway.

Bark protects the tree against environmental insults. Here, we analyzed whether this defensive strategy could be utilized to broadly enhance protection against colitis. As a proof of concept, we show that exosome-like nanoparticles (MBELNs) derived from edible mulberry bark confer protection against colitis in a mouse model by promoting heat shock protein family A (Hsp70) member 8 (HSPA8)-mediated activation of the AhR signaling pathway. Activation of this pathway in intestinal epithelial cells leads to the induction of COP9 Constitutive Photomorphogenic Homolog Subunit 8 (COPS8). Utilizing a gut epithelium-specific knockout of COPS8, we demonstrate that COPS8 acts downstream of the AhR pathway and is required for the protective effect of MBELNs by inducing an array of anti-microbial peptides. Our results indicate that MBELNs represent an undescribed mode of inter-kingdom communication in the mammalian intestine through an AhR-COPS8-mediated anti-inflammatory pathway. These data suggest that inflammatory pathways in a microbiota-enriched intestinal environment are regulated by COPS8 and that edible plant-derived ELNs may hold the potential as new agents for the prevention and treatment of gut-related inflammatory disease.

Ru(II)-Catalyzed [4 + 2]-Annulation of 2-Alkenyl/Arylimidazoles with N-Substituted Maleimides and 1,4-Naphthoquinones: Access to Imidazo-Fused Polyheterocycles.

Synthesis of imidazo-fused polyheterocyclic molecular frameworks, viz. imidazo[1,2-a]pyrrolo[3,4-e]pyridines, imidazo[2,1-a]pyrrolo[3,4-c]isoquinolines, and benzo[g]imidazo[1,2-a]quinoline-6,11-diones, has been achieved by the ruthenium(II)-catalyzed [4 + 2] C-H/N-H annulation of 2-alkenyl/2-arylimidazoles with N-substituted maleimides and 1,4-naphthoquinones. The developed protocol is operationally simple, exhibits broad substrate scope with excellent functional group tolerance, and provides the desired products in moderate to good yields. The mechanistic studies suggest that the reaction involves the formation of a C-C bond through Ru-catalyzed C(sp2)-H bond activation followed by intramolecular cyclization.

Temperature Effect on Fluorescence Intensity and Dipole Moment Using Thermochromic Shift Method of 7DA3MHBI-2HChromen-2-one Laser Dye in Highly Viscous Glycerol Solvent.

The steady-state method is used to study the effect of temperature on the fluorescence characteristics of 7-(diethylamino)-3-(1-methyl-1H-benzo[d]imidazol-2-yl)-2H-chromen-2-one (7DA3MHBI-2HChromen-2-one) laser dye in glycerol solvent for the temperature range 293-343 K. Absorption and emission characteristics are affected by varying temperatures due to induced thermal effects. Transition probabilities mechanism of non-radiative and radiative are studied and frequency dependent parameters are estimated. Dipole moments in the ground and excited state are estimated using the thermochromic shift method over general solvatochromic methods.

Achieving White Light Emission with High Luminescence Efficiency via Combustion Produced Sr3Y(PO4)3: Dy3+ Nanophosphors for Photonic Applications.

Extensive investigations were conducted on the structural and photoluminescence characteristics of the present nanosamples, encompassing PL, TEM, PXRD, EDAX, CCT, and CIE research. PXRD studies established a single phase, and TEM instruments were used to examine the dimensions and topographical behavior. The EDAX analysis examined the magnitude of the different components that were present. Decay lifetimes, radiative and non-radiative energy transfer rates, and a number of intensity limitations have all been found using PL spectra. Two significant peaks were visible in the blue (B) and yellow (Y) regions of the photoluminescence (PL) spectra upon NUV excitation, at 486 nm and 577 nm. At 7 mol% Dy3+ ions, the PL intensity peaked. After that, it began to decline as a result of the concentration quenching process brought on by multipolar exchanges (s = 4.1445). The values of 0.86423 ms, 81%, and 226 s-1 were discovered to be the decay life time, non radiative rates, and quantum efficiency of the ideal powder, respectively. Further analysis of Sr3Y0.93Dy0.07(PO4)3 nanocrystals revealed that their chromaticity coordinates (0.305, 0.321), and CCT value (6902 K) matched those of NTSE and commercial LEDs, certifying their use in innovative optoelectronic appliances, particularly single phased WLEDs.

Experimental and Theoretical Rotational Diffusion Studies of 7DM4M1M1,8, N-2(1H)-one and 7A4T2H1B-2-one in Series of Alcohol Solvents: Stoke's-Einstein-Debye and Alavi-Waldeck Models.

Rotational diffusion studies of two solutes 7-(dimethylamino)-4-methoxy-1-methyl-1,8-naphthyridin-2(1H)-one (7DM4M1M1,8, N-2(1H)-one) and 7-amino-4-(trifluoromethyl)-2H-1-benzopyran-2-one (7A4T2H1B-2-one) having equal volumes but different chemical natures are studied in series of alcohol solvents at 303 K using steady-state methods. HOMO-LUMO, Electron density, Molecular electrostatic potential (MEP), etc., are obtained from computational calculations using Gaussian 09 software. Rotational reorientation times of 7DM4M1M1,8, N-2(1H)-one solute molecule is found to be less than 7A4T2H1B-2-one solute molecule indicates it rotates slowly in chosen solvents. Stoke's-Einstein-Debye (SED) model with stick boundary conditions for the 7A4T2H1B-2-one solute molecule is modeled to describe mechanical friction. Polar solutes along with mechanical friction also experience dielectric friction. Both these frictions being non-separable, the Alavi-Waldeck (AW) model is studied for dielectric friction contribution to the total friction solute experiences in solvents. AW model effectively explains the observed dielectric friction in alcohol solvents.

Influence of Temperature on Rotational Dynamics of 3B7D2HC-2-one Molecule in Non-polar, Polar, and Polar Aprotic Solvents.

Rotational dynamics of 3-(3H-2l4-benzo[c]isothiazol-2-yl)-7-(diethylamino)-2H-chromen-2-one (3B7D2HC-2-one) is studied using steady-state fluorescence depolarization and time-resolved fluorescence techniques in non-polar, polar and polar aprotic solvents by varying temperatures. Computational calculations are performed using Gaussian 09 software. Over the general solvatochromic method, an advanced thermochromic shift method is used to estimate dipole moments. Experiment rotational diffusion of 3B7D2HC-2-one in methanol indicates slow rotation over the other two solvents. Further, experiment rotational diffusion is analyzed using hydrodynamic and Quasi-hydrodynamic theories. The observed reorientation time follows the trend as predicted by quasi-hydrodynamic models.

Studies on Fluorescence Quenching, Decay Rate Parameters, Dipole Moment, Rotational Diffusion of 3-(benzo[d]thiazol-2-yl)-7-(diethylamino)-2H-chromen-2-one Laser Dye in Excited Singlet State: Temperature Effect.

The effect of temperature on the absorption and emission characteristics of 3-(benzo[d]thiazol-2-yl)-7-(diethylamino)-2H-chromen-2-one (3BT7D2H-one) laser dye in glycerol solvent has been studied by the steady-state method. Fluorescence intensity decreases with an increase in temperature and shifts towards a shorter wavelength. Parameters like fluorescence lifetime, rate constants, activation energy, and dipole moment (using the thermochromic method) are determined experimentally. Also, the temperature effect on rotational diffusion of 3BT7D2H-one laser dye is studied and also estimated theoretical and experimental hydrodynamic volumes.

Anthocyanins of Delonix Regia Floral Petals: A Novel Approach on Fluorescence Enhancement, Forster Resonance Energy Transfer Mechanism and Photostability Studies for Optoelectronic Applications.

In this work, we focused on extracting the anthocyanin dye in acetone, butanol, ethanol, and water solvents from Delonix regia flowers by a simple maceration extraction process. The identification of functional group analysis, vibrational studies, energy transfer mechanisms, optoelectronic properties, photostability studies, FRET-assisted potential light emissions and photometric properties of the anthocyanin dyes are successively investigated. FTIR spectroscopy and vibrational studies have confirmed the existence of polyphenolic groups in 2-phenyl chromenylium (anthocyanin) dyes. The optoelectronic results show the least direct bandgap (2.04 eV), indirect bandgap (1.55 eV), Urbach energy (0.380 eV), high refractive index (1.20), dielectric constant (2.794), and high optical conductivity (1.954 × 103 S/m) for the anthocyanin dye extracted found in water solvent. The photoluminescence properties such as Stoke's shift, high quantum yield, and lifetime results show that anthocyanin dyes are promising candidates for red-LEDs and optical materials. The absorption and emission spectra of the anthocyanin dyes follow the mirror image rule and the Franck-Condon factor exists between vibrational energy levels corresponding to all the electronic transitions. The excellent correspondence between the absorption and emission spectra reinforces that the anthocyanins are efficient (46%) FRET probes. Further, photometric properties such as CIE, CRI, CCT and colour purity results of anthocyanins in all studied solvents revealed that this material exhibits orange to red shades (x = 0.48 → 0.54 and y = 0.36 →0.45) and is well suitable for have great potential in the manufacturing of Organic-LEDs and other optoelectronic device applications.

Shedding light on evolution of Raman line shape with probing laser power: Light-induced perturbation in electron-phonon coupling.

The laser power mediated changes in the Raman line shape have been considered in terms of interference between discrete phonon states ρ and the electronic continuum states Ï° contributed by Urbach tail states. The laser-induced effects are treated in terms of the increase in the surface temperature and thereby the scaling of electronic disorder, i.e., Urbach energy, which can further contribute to the electron-phonon interactions. Therefore, the visualization of this effect is attempted analytically as a perturbation term in the Hamiltonian, which clearly accounts for the observed changes with laser power. This has been investigated based on the experimental results of laser power dependent Raman spectra of bulk EuFeO3 and silicon nanowires, which are found to provide convincing interpretations.

Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology.

The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.

A novel method for enrichment of Morganella morganii in fecal samples using designed culture medium.

Morganella morganii is a gram negative, facultative anaerobic rod-shaped bacterium, commonly found in environment and in the intestine of human, mammals, and reptiles as a part of their gut microbiome. M. morganii can cause Gram-negative folliculitis, black nail infection, acute retiform purpura, fetal demise, and subdural empyema. The increasing frequency of M. morganii infections generate the need for efficient methods to enrich the presence of M. morganii in clinical samples to make its detection easier. Culturomics aims to grow and maximize the number of culturable bacteria. Different methods are followed to maximize the growth of minority population of bacteria by disrupting the growth of bacteria which are present in higher concentration. This article presents a method for selective enriching the M. morganii in human fecal samples. This method includes prior incubation of fecal microbiota in an anaerobic environment, adding supplement like fecal water to give dormant bacteria a break to become active to grow to threshold concentration, and an enrichment stage which provides the additional opportunity of growing to M. morganii on the selective medium. This method also provides an ingenuous way for augmenting the growth of fecal M. morganii species.

Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T.

Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.