Inability of Ogataea parapolymorpha pho91-Δ mutant to produce active methanol oxidase can be compensated by inactivation of the PHO87 gene.

Cells of the methylotrophic yeast Ogataea parapolymorpha have two genes encoding low-affinity phosphate transporters: PHO87, encoding the plasma membrane transporter, and PHO91, encoding a protein, which is homologous to the Saccharomyces cerevisiae vacuolar membrane transporter. Earlier, we reported that inactivation of PHO91 in O. parapolymorpha interferes with methanol utilization due to the lack of activity of methanol oxidase encoded by the MOX gene.

Ultrasensitive Lateral Flow Immunoassay of Fluoroquinolone Antibiotic Gatifloxacin Using Au@Ag Nanoparticles as a Signal-Enhancing Label.

Gatifloxacin (GAT), an antibiotic belonging to the fluoroquinolone (FQ) class, is a toxicant that may contaminate food products. In this study, a method of ultrasensitive immunochromatographic detection of GAT was developed for the first time. An indirect format of the lateral flow immunoassay (LFIA) was performed.

SERS Sensors with Bio-Derived Substrates Under the Way to Agricultural Monitoring of Pesticide Residues.

Uncontrolled use of pesticides in agriculture leads to negative consequences for the environment, as well as for human and animal health. Therefore, timely detection of pesticides will allow application of measures to eliminate the excess of maximum residue limits and reduce possible negative consequences in advance. Common methods of pesticide analysis suffer from high costs, and are time consuming, and labor intensive.

Conformational dynamics of the enzyme-substrate complex of protein kinase A with pseudosubstrate SP20 and adenosine triphosphate.

The phosphorylation reaction, catalyzed by the enzyme protein kinase A (PKA), plays one of the key roles in the work of the glutamatergic system, primarily involved in memory functioning. The analysis of the dynamic behavior of the enzyme-substrate complex allows one to learn the mechanism of the enzymatic reaction. According to the results of classical molecular dynamics calculations followed by hierarchical clustering, the most preferred proton acceptor during the phosphorylation reaction catalyzed by PKA is the carboxyl group of the amino acid residue Asp166; however, the γ-phosphate group of ATP can also act as an acceptor.

Near-atomic cryo-EM structure of the light-harvesting complex LH2 from the sulfur purple bacterium Ectothiorhodospira haloalkaliphila.

Bacteria with the simplest system for solar energy absorption and conversion use various types of light-harvesting complexes for these purposes. Light-harvesting complex 2 (LH2), an important component of the bacterial photosynthetic apparatus, has been structurally well characterized among purple non-sulfur bacteria. In contrast, so far only one high-resolution LH2 structure from sulfur bacteria is known.

Novel Mutation Lys30Glu in the Gene Leads to Pediatric Left Ventricular Non-Compaction and Dilated Cardiomyopathy via Impairment of Structural and Functional Properties of Cardiac Tropomyosin.

Pediatric dilated cardiomyopathy (DCM) is a rare heart muscle disorder leading to the enlargement of all chambers and systolic dysfunction. We identified a novel de novo variant, c.88A>G (p.

Effect of Dihydroquercetin During Long-Last Growth of Yeast: Anti-Aging Potential and Hormetic Properties.

Polyphenols are powerful natural antioxidants with numerous biological activities. They change cell membrane permeability, interact with receptors, intracellular enzymes, and cell membrane transporters, and quench reactive oxygen species (ROS). yeast, being similar to mammalian cells, can be used as a model to study their survival ability upon long-lasting cultivation, assaying the effect of dihydroquercetin polyphenol (DHQ).

Calcium Indicators with Fluorescence Lifetime-Based Signal Readout: A Structure-Function Study.

The calcium cation is a crucial signaling molecule involved in numerous cellular pathways. Beyond its role as a messenger or modulator in intracellular cascades, calcium's function in excitable cells, including nerve impulse transmission, is remarkable. The central role of calcium in nervous activity has driven the rapid development of fluorescent techniques for monitoring this cation in living cells.

Menthol-Induced Chirality in Semiconductor Nanostructures: Chiroptical Properties of Atomically Thin 2D CdSe Nanoplatelets Capped with Enantiomeric L-(-)/D-(+)-Menthyl Thioglycolates.

Semiconductor colloidal nanostructures capped with chiral organic molecules are a research hotspot due to their wide range of important implications for photonic and spintronic applications. However, to date, the study of chiral ligands has been limited almost exclusively to naturally occurring chiral amino and hydroxy acids, which typically contain only one stereocenter. Here, we show the pronounced induction of chirality in atomically thin CdSe nanoplatelets (NPLs) by capping them with enantiopure menthol derivatives as multi-stereocenter molecules.

Potential of photodynamic therapy using polycationic photosensitizers in the treatment of lung cancer patients with SARS-CoV-2 infection and bacterial complications: Our recent experience.

The problem of treating cancer patients with lung cancer has become more difficult due to the SARS-CoV-2 viral infection and concomitant bacterial lesions. The analysis shows that the photodynamic effect of long-wavelength polycationic photosensitizers suppresses the tumor process (including the destruction of cancer stem cells), SARS-CoV-2 coronavirus infection, Gram-positive and Gram-negative bacteria, including those that can cause pneumonia. Therefore, the photodynamic approach using such photosensitizers is promising for the development of an effective treatment method for patients with lung cancer, including those with SARS-CoV-2 infection and bacterial complications.

Fate of cultured populations when exposed to moxifloxacin.

Given the current need for predictive persisting model for , we adopted a classical assay to study drug-tolerant bacterial persisters, focusing on the behavior of a small antibiotic-insensitive subpopulation during prolonged exposure to moxifloxacin. Our study showed a wide-ranging response of , depending on antibiotic concentration, growth stage of mycobacterial cultures, and the availability of potassium ions in the medium. Mid-logarithmic cultures, initially grown in either balanced or K-free medium, contained small sup-populations capable of prolonged and stable survival in the presence of moxifloxacin.

Kinetic Profiling of Oxidoreductase-Mimicking Nanozymes: Impact of Multiple Activities, Chemical Transformations, and Colloidal Stability.

In contrast to homogeneous enzyme catalysis, nanozymes are nanosized heterogeneous catalysts that perform reactions on a rigid surface. This fundamental difference between enzymes and nanozymes is often overlooked in kinetic studies and practical applications. In this article, using 14 nanozymes of various compositions (core@shell, metal-organic frameworks, metal, and metal oxide nanoparticles), we systematically demonstrate that nontypical features of nanozymes, such as multiple catalytic activities, chemical transformations, and aggregation, need to be considered in nanozyme catalysis.

Co-culture of postnatal mouse spinal cord and skeletal muscle explants as an experimental model of neuromuscular interactions.

The intercommunication between nerves and muscles plays an important role in the functioning of our body, and its failure leads to severe neuromuscular disorders such as spinal muscular atrophy and amyotrophic lateral sclerosis. Understanding the cellular and molecular mechanisms underlying nerve-muscle interactions and mediating their mutual influence is an integral part of strategies aimed at curing neuromuscular diseases. Here, we propose a novel ex vivo experimental model for the spinal cord (SC) and skeletal muscle interactions which for the first time utilizes only fully formed (but not yet quite functional) postnatal tissues.

Matrikines of Sea Cucumbers: Structure, Biological Activity and Mechanisms of Action.

Matrikines (MKs), the products of enzymatic fragmentation of various extracellular matrix (ECM) proteins, regulate cellular activity by interacting with specific receptors. MKs affect cell growth, proliferation, and migration, can induce apoptosis and autophagy, and are also effectively used in biomedicine and functional nutrition. Recently, there has been great interest in the structural features and biological activity of MKs from various sources.

Oestrogen Detoxification Ability of White Rot Fungus LE-BIN 072: Exoproteome and Transformation Product Profiling.

White rot fungi, especially representatives of the genus spp. (Polyporaceae), are effective destructors of various xenobiotics, including oestrogens (phenol-like steroids), which are now widespread in the environment and pose a serious threat to the health of humans, animals and aquatic organisms. In this work, the ability of the white rot fungus LE-BIN 072 to transform oestrone (E1) and 17β-oestradiol (E2), the main endocrine disruptors, was shown.

The Key Enzymes of Carbon Metabolism and the Glutathione Antioxidant System Protect Yeast Against pH-Induced Stress.

In this study, we first thoroughly assayed the response of the key enzymes of energy metabolism and the antioxidant system in yeast at extreme pH. The activity of the tricarboxylic acid cycle enzymes, namely NAD-dependent isocitrate dehydrogenase, aconitate hydratase, NAD-dependent malate dehydrogenase, and fumarate hydratase, NADPH-producing enzymes of glucose-6-P dehydrogenase and NADP-dependent isocitrate dehydrogenase, and the enzymes of the glutathione system was assessed. All the enzymes that were tested showed a significant induction contrary to some decrease in the aconitate hydratase activity with acidic and alkaline stress.

Comparison of Conjugates Obtained Using DMSO and DMF as Solvents in the Production of Polyclonal Antibodies and ELISA Development: A Case Study on Bisphenol A.

When developing immunochemical test systems, it is necessary to obtain specific antibodies. Their quality depends, among other things, on the immunogen used. When preparing hapten-protein conjugates to obtain antibodies for low-molecular-weight compounds, the key factors are the structure of the hapten itself, the presence of a spacer, the size of the carrier protein and the degree of its modification by hapten molecules.

Evaluation of amplicons by AF4 as assistant for deep comprehension of loop-mediated isothermal amplification combined with lateral flow assay.

Loop-mediated isothermal amplification (LAMP) is a rapid and efficient method for DNA amplification, producing concatemers of varying lengths (amplicons). This study explores the characterization of LAMP amplicons using asymmetric flow field-flow fractionation (AF4) and their realization in LAMP - lateral flow assay (LFA) for point-of-care diagnostics. We examined LAMP products from the invA gene of Salmonella enterica using two specific primer sets and three methods: fluorescent staining with SYBR Green, electrophoretic detection, and AF4.

Structural insight into recognition of Clostridioides difficile toxin A by novel neutralizing nanobodies targeting QTIN-like motifs within its receptor-binding domain.

Clostridioides difficile causes a large proportion of nosocomial colon infections by producing toxins TcdA and TcdB as key virulence factors. TcdA and TcdB have analogous domain structures with a receptor-binding domain containing C-terminal combined repetitive oligopeptides (CROPs), an attractive target for the development of therapeutic antibodies. Here, we identify and characterize two potent neutralizing single-domain camelid anti-CROPsA antibodies, C4.

Removal of terpenes in the presence of easily degradable compounds during biofiltration of gas emissions from composting of municipal solid waste.

Composting of the organic fraction of municipal solid waste (OFMSW) is accompanied by the emission of large volumes of harmful, hazardous and foul-smelling volatile organic compounds (VOCs). To improve the efficiency of terpenes removal, which constitute a significant part of VOCs, pure cultures of microorganisms dominating in its microbiota were isolated from the microbial community of the biofilter, which has been cleaning such emissions for a long time. Seven pure cultures were isolated and then tested for being able to grow on a mineral medium in the presence of terpene vapor as the only source of carbon and energy.

A systematic overview of strategies for photosensitizer and light delivery in antibacterial photodynamic therapy for lung infections.

Antimicrobial photodynamic therapy (aPDT) emerges as a viable treatment strategy for infections resistant to conventional antibiotics. A complex interplay of factors, including intracellular photosensitizer (PS) accumulation, photochemical reaction type, and oxygen levels, determines the efficacy of aPDT. Recent progress includes the development of modified PSs with enhanced lipophilicity and target-specific strategies to improve bacterial cell wall penetration and targeting.

Re-engineering of a carotenoid-binding protein based on NMR structure.

Recently, a number of message passing neural network (MPNN)-based methods have been introduced that, based on backbone atom coordinates, efficiently recover native amino acid sequences of proteins and predict modifications that result in better expressing, more soluble, and stable variants. However, usually, X-ray structures, or artificial structures generated by algorithms trained on X-ray structures, were employed to define target backbone conformations. Here, we show that commonly used algorithms ProteinMPNN and SolubleMPNN display low sequence recovery on structures determined using NMR.

Insights into the Functioning of the D-amino Acid Transaminase from Haliscomenobacter Hydrossis via a Structural and Spectral Analysis of its Complex with 3-Aminooxypropionic Acid.

Pyridoxal 5'-phosphate-dependent enzymes play a crucial role in nitrogen metabolism. Carbonyl compounds, such as O-substituted hydroxylamines, stand out among numerous specific inhibitors of these enzymes, including those of practical importance, because they react with pyridoxal 5'-phosphate in the active site of the enzymes to form stable oximes. O-substituted hydroxylamines mimic the side group of amino acid substrates, thus providing highly potent and specific inhibition of the corresponding enzymes.

Link Between Individual Codon Frequencies and Protein Expression: Going Beyond Codon Adaptation Index.

An important role of a particular synonymous codon composition of a gene in its expression level is well known. There are a number of algorithms optimizing codon usage of recombinant genes to maximize their expression in host cells. Nevertheless, the underlying mechanism remains unsolved and is of significant relevance.