Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy.

We propose symmetrical cationic trimethine cyanine dyes with β-substituents in the polymethine chain based on modified benzothiazole and benzoxazole heterocycles as probes for the detection and visualization of live and fixed cells by fluorescence microscopy. The spectral-luminescent properties of trimethine cyanines have been characterized for free dyes and in the presence of nucleic acids (NA) and globular proteins. The studied cyanines are low to moderate fluorescent when free, but in the presence of NA, they show an increase in emission intensity up to 111 times; the most pronounced emission increase was observed for the dyes in the presence of dsDNA and with RNA.

Advances in Optical Tools to Study Taste Sensation.

Taste sensation is the process of converting chemical identities in food into a neural code of the brain. Taste information is initially formed in the taste buds on the tongue, travels through the afferent gustatory nerves to the sensory ganglion neurons, and finally reaches the multiple taste centers of the brain. In the taste field, optical tools to observe cellular-level functions play a pivotal role in understanding how taste information is processed along a pathway.

Structure-guided isoform identification for the human transcriptome.

Recently developed methods to predict three-dimensional protein structure with high accuracy have opened new avenues for genome and proteome research. We explore a new hypothesis in genome annotation, namely whether computationally predicted structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by protein structure predictions, we evaluated over 230,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues.

VLDL-VLDLR axis facilitates brown fat thermogenesis through replenishment of lipid fuels and PPARβ/δ activation.

In mammals, brown adipose tissue (BAT) is specialized to conduct non-shivering thermogenesis for survival under cold acclimation. Although emerging evidence suggests that lipid metabolites are essential for heat generation in cold-activated BAT, the underlying mechanisms of lipid uptake in BAT have not been thoroughly understood. Here, we show that very-low-density lipoprotein (VLDL) uptaken by VLDL receptor (VLDLR) plays important roles in thermogenic execution in BAT.

eDNA, Amyloid Fibers and Membrane Vesicles Identified in SBW25 Biofilms.

SBW25 is a model soil- and plant-associated bacterium capable of forming a variety of air-liquid interface biofilms in experimental microcosms and on plant surfaces. Previous investigations have shown that cellulose is the primary structural matrix component in the robust and well-attached Wrinkly Spreader biofilm, as well as in the fragile Viscous Mass biofilm. Here, we demonstrate that both biofilms include extracellular DNA (eDNA) which can be visualized using confocal laser scanning microscopy (CLSM), quantified by absorbance measurements, and degraded by DNase I treatment.

Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT.

The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure.

Dual action of a tyrosinase-mesoporous silica nanoparticle complex for synergistic tissue adhesion.

Bridging biological tissues for immediate adhesion and long-term sustainability was accomplished using a combination of mesoporous silica nanoparticles (MSNs) and tyrosinase. Tyrosinase-loaded MSNs provided rapid physical adsorption, while tyrosinase within MSNs induced enzymatic chemical bond gluing of tissues. This synergistic strategy has robust potential in tissue adhesives for clinical settings.

Analysis of Relative Average Length of Telomeres in Leukocytes of Women with COVID-19.

Coronavirus disease (COVID-19) is an acute infectious disease of the respiratory tract caused by a new SARS-CoV-2 coronavirus. A global vaccination program against SARS-CoV-2 continues, and the incidence of COVID-19 worldwide is significantly decreasing. However, among millions of those who survived COVID-19, numerous groups will need assistance due to increased clinical consequences after COVID-19.

LambdaPP: Fast and accessible protein-specific phenotype predictions.

The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first internet server making AI protein predictions available in 1992. Given a protein sequence as input, LambdaPP provides easily accessible visualizations of protein 3D structure, along with predictions at the protein level (GeneOntology, subcellular location), and the residue level (binding to metal ions, small molecules, and nucleotides; conservation; intrinsic disorder; secondary structure; alpha-helical and beta-barrel transmembrane segments; signal-peptides; variant effect) in seconds.

Necroptosis-dependent Immunogenicity of Cisplatin: Implications for Enhancing the Radiation-induced Abscopal Effect.

Purpose: Cisplatin is increasingly used in chemoimmunotherapy and may enhance the T cell-dependent radiation-induced abscopal effect, but how it promotes antitumor immunity is poorly understood. We investigated whether and why cisplatin is immunogenic, and the implications for the cisplatin-enhanced abscopal effect.

Experimental Design: Cisplatin, carboplatin, and the well-known immunogenic cell death (ICD) inducer oxaliplatin were compared for their potency to enhance the abscopal effect and induce type I IFN (IFN-I) and extracellular ATP, danger signals of ICD.

Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells.

Exhausted CD8 T cells during chronic inflammatory responses against viral infections and cancer are phenotypically and functionally heterogeneous. In particular, CD8 T cells with cytolytic effector function have been recently identified among the exhausted CD8 T cell subsets. However, the regulation of their differentiation and function remains largely unknown.

Reduced branched-chain aminotransferase activity alleviates metabolic vulnerability caused by dim light exposure at night in .

The rhythmic pattern of biological processes controlled by light over 24 h is termed the circadian rhythm. Disturbance of circadian rhythm due to exposure to light at night (LAN) disrupts the sleep-wake cycle and can promote cardiovascular disease, diabetes, cancer, and metabolic disorders in humans. We studied how dim LAN affects the circadian rhythm and metabolism using male .

Three-dimensional imaging and analysis of pathological tissue samples with de novo generation of citrate-based fluorophores.

Two-dimensional (2D) histopathology based on the observation of thin tissue slides is the current paradigm in diagnosis and prognosis. However, labeling strategies in conventional histopathology are limited in compatibility with 3D imaging combined with tissue clearing techniques. Here, we present a rapid and efficient volumetric imaging technique of pathological tissues called 3D tissue imaging through de novo formation of fluorophores, or 3DNFC, which is the integration of citrate-based fluorogenic reaction DNFC and tissue clearing techniques.

Application of zeolites and zeolitic imidazolate frameworks in the biosensor development.

Biosensors are advanced devices for analysis of composition of blood, urine, environmental samples, and many other media. Their current development is tightly linked with nanomaterials, such as zeolites and zeolitic imidazolate framework (ZIFs). The present review describes electrochemical (amperometric, conductometric, ISFET) and optical (fluorescent and colorimetric) biosensors that incorporate zeolites and ZIFs in their biorecognition elements.

Collagen Obtained from Leather Production Waste Provides Suitable Gels for Biomedical Applications.

Collagen and its derivates are typically obtained by extracting them from fresh animal tissues. Lately, however, there has been an increased interest in obtaining collagen from other sources, such as waste material, because of the growing trend to replace synthetic materials with sustainable, natural counterparts in various industries, as well as to ensure a rational waste revalorization. In this paper, collagen was obtained from non-tanned waste of leather production, taken at different stages of the production process: limed pelt, delimed pelt, and fleshings.

Manifestations of intramolecular H-bonds of CH… O and OH… C type in quercetin molecule: Analysis of IR spectra by mean of density functional theory.

The IR spectra of 48 conformers of quercetin which represent full conformation space of its tautomers have been modeled at B3LYP/6-311++G(d,p) level of the density functional theory. The presence of intramolecular H-bonds C2'H/C6'H…O3 and O3H…C2'/C6' was characterized by their spectral manifestations. The C2'H/C6'H…O3 contacts were found to have a spectral blue-shift.

A conserved function of Human DLC3 and Cv-c in testis development.

The identification of genes affecting gonad development is essential to understand the mechanisms causing Variations/Differences in Sex Development (DSD). Recently, a DLC3 mutation was associated with male gonadal dysgenesis in 46,XY DSD patients. We have studied the requirement of Cv-c, the ortholog of DLC3, in gonad development, as well as the functional capacity of DLC3 human variants to rescue gonad defects.

Perinatal derivatives application: Identifying possibilities for clinical use.

Perinatal derivatives are drawing growing interest among the scientific community as an unrestricted source of multipotent stromal cells, stem cells, cellular soluble mediators, and biological matrices. They are useful for the treatment of diseases that currently have limited or no effective therapeutic options by means of developing regenerative approaches. In this paper, to generate a complete view of the state of the art, a comprehensive 10-years compilation of clinical-trial data with the common denominator of PnD usage has been discussed, including commercialized products.

A history of the MetaSUB consortium: Tracking urban microbes around the globe.

The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic.

Cytotoxic Potential of the Marine Diatom : Insights into Bioactivity of 24-Methylene Cholesterol.

Marine microalgae are receiving great interest as sustainable sources of bioactive metabolites for health, nutrition and personal care. In the present study, a bioassay-guided screening allowed identifying an enriched fraction from SPE separation of the methanolic extract of the marine diatom with a chemically heterogeneous composition of cytotoxic molecules, including PUFAs, the terpene phytol, the carotenoid fucoxanthin and the phytosterol 24-methylene cholesterol (24-MChol). In particular, this latter was the object of deep investigation aimed to gain insight into the mechanisms of action activated in two tumour cell models recognised as resistant to chemical treatments, the breast MCF7 and the lung A549 cell lines.

UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi.

In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade.

Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial.

Background/aims: We aim to evaluate the differences in the microbiome of responders and non-responders, as well as predict the response to probiotic therapy, based on fecal microbiome data in patients with diarrhea-predominant irritable bowel syndrome (IBS-D).

Methods: A multi-strain probiotics that contains (KCTC 11906BP), (KCTC11867BP), (KCTC 11868BP), (KCTC 11858BP), (KCTC 11903BP), (KCTC 11860BP), and (KCTC 11870BP) were used. Patients were categorized into probiotic and placebo groups, and fecal samples were collected from all patients before and at the end of 8 weeks of treatment.