Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity.

Non-coding RNAs are regarded as promising targets for the discovery of innovative drugs due to their abundance in the genome and their involvement in many biological processes. Phytochemicals (PCs) are the primary source of ligand-based drugs due to their broad spectrum of biological activities. Since many PCs are heterocyclic and have chemical groups potentially involved in the interaction with nucleic acids, detailed interaction analysis between PCs and RNA is crucial to explore the effect of PCs on RNA functions.

Backbone chemical shift spectral assignments of SARS coronavirus-2 non-structural protein nsp9.

As part of an International consortium aiming at the characterization by NMR of the proteins of the SARS-CoV-2 virus, we have obtained the virtually complete assignment of the backbone atoms of the non-structural protein nsp9. This small (12 kDa) protein is encoded by ORF1a, binds to RNA and seems to be essential for viral RNA synthesis. The crystal structures of the SARS-CoV-2 protein and other homologues suggest that the protein is dimeric as also confirmed by analytical ultracentrifugation and dynamic light scattering.

Reorientational dynamics of highly asymmetric binary non-polymeric mixtures - a dielectric spectroscopy study.

We present an analysis of dielectric spectra measured for a specially designed non-polymeric asymmetric binary glass former characterized by a large difference of the component's T (ΔT = 216 K). We cover the whole additive concentration range from 4% up to 90% (by mass). Two main relaxations α and α are identified, which are characterized by well separated time scales and are attributed to the dynamics associated with the high-T component (α) and the low-T component (α).

Structural Basis of Activation of Fast Skeletal Muscle.

Troponin regulates the calcium-mediated activation of skeletal muscle. Muscle weakness in diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy occurs from diminished neuromuscular output. The first direct fast skeletal troponin activator, , amplifies the response of muscle to neuromuscular input.

Serum metabolomic profiling correlated with ISS and clinical outcome for multiple myeloma patients treated with high-dose melphalan and autologous stem cell transplantation.

The metabolome, which is the final down-stream global product of metabolic processes in organisms, is not sufficiently described in multiple myeloma (MM) patients. The aim of this study was, therefore, to study the serum metabolomic profile using proton nuclear magnetic resonance (H-NMR) spectroscopy, and its relationship to clinical characteristics and patient outcome. Serum samples, which were taken at diagnosis, from 201 MM patients who underwent high-dose melphalan followed by autologous stem cell transplantation as the first-line therapy, were analyzed.

Targeted Metabolomic Assessment of the Sub-Lethal Toxicity of Halogenated Acetic Acids (HAAs) to .

Halogenated acetic acids (HAAs) are amongst the most frequently detected disinfection by-products in aquatic environments. Despite this, little is known about their toxicity, especially at the molecular level. The model organism , which is an indicator species for freshwater ecosystems, was exposed to sub-lethal concentrations of dichloroacetic acid (DCAA), trichloroacetic acid (TCAA) and dibromoacetic acid (DBAA) for 48 h.

Insight into formation propensity of pseudocircular DNA G-hairpins.

We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their function in vivo and their applications in biotechnology, has not been elucidated. Here, we show that despite its 'circular' nature, PGHs tolerate single-stranded (ss) protrusions.

Off-line multidimensional high performance thin-layer chromatography for fractionation of Japanese knotweed rhizome bark extract and isolation of flavan-3-ols, proanthocyanidins and anthraquinones.

A methodology based on off-line multidimensional thin-layer chromatography was developed for isolation of several secondary metabolites from bark of Japanese knotweed (Fallopia japonica Houtt.) rhizomes. Successive fractionation steps using PLC silica gel and HPTLC silica gel or HPTLC cellulose plates in combination with various developing solvents enabled isolation of (+)-catechin, (-)-epicatechin, (-)-epicatechin gallate, procyanidin B1, procyanidin B2, procyanidin B3, proanthocyanidin B dimer gallate, emodin, emodin-8-O-glucoside and emodin-8-O-malonyl-glucoside.

Structure, self-assembly, and properties of a truncated reflectin variant.

Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation.

Unravelling the pathways of air plasma induced aflatoxin B degradation and detoxification.

Aflatoxins are considered to be a critical dietary risk factor for humans, with aflatoxin B (AFB) identified by the WHO as one of the most potent natural group 1 carcinogen. Despite this, more than half of the world's population is chronically exposed, resulting in up to 170,000 annual cases of human hepatocellular carcinoma cancer. Here we report an easily implemented approach using non-equilibrium plasma for targeted degradation of AFB.

On the interaction of an anticancer trisubstituted naphthalene diimide with G-quadruplexes of different topologies: a structural insight.

Naphthalene diimides showed significant anticancer activity in animal models, with therapeutic potential related to their ability to strongly interact with G-quadruplexes. Recently, a trifunctionalized naphthalene diimide, named NDI-5, was identified as the best analogue of a mini-library of novel naphthalene diimides for its high G-quadruplex binding affinity along with marked, selective anticancer activity, emerging as promising candidate drug for in vivo studies. Here we used NMR, dynamic light scattering, circular dichroism and fluorescence analyses to investigate the interactions of NDI-5 with G-quadruplexes featuring either parallel or hybrid topology.

Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming a .

Bone remodeling is a fine-tuned process principally regulated by a cascade triggered by interaction of receptor activator of NF-κB (RANK) and RANK ligand (RANKL). Excessive activity of the gene leads to increased bone resorption and can influence the incidence of osteoporosis. Although much has been learned about the intracellular signals activated by RANKL/RANK complex, significantly less is known about the molecular mechanisms of regulation of expression.

NMR Profiling of North Macedonian and Bulgarian Honeys for Detection of Botanical and Geographical Origin.

Bulgaria and North Macedonia have a long history of the production and use of honey; however, there is an obvious lack of systematic and in-depth research on honey from both countries. The oak honeydew honey is of particular interest, as it is highly valued by consumers because of its health benefits. The aim of this study was to characterize honeydew and floral honeys from Bulgaria and North Macedonia based on their NMR profiles.

Increased yield of enzymatic synthesis by chromatographic selection of different N-glycoforms of yeast invertase.

Invertases are glycosidases applied for synthesis of alkyl glycosides that are important and effective surfactants. Stability of invertases in the environment with increased content of organic solvent is crucial for increase of productivity of glycosidases. Their stability is significantly influenced by N-glycosylation.

Preparation and Biophysical Characterization of Quercetin Inclusion Complexes with β-Cyclodextrin Derivatives to be Formulated as Possible Nose-to-Brain Quercetin Delivery Systems.

Quercetin (Que) is a flavonoid associated with high oxygen radical scavenging activity and potential neuroprotective activity against Alzheimer's disease. Que's oral bioavailability is limited by its low water solubility and extended peripheral metabolism; thus, nasal administration may be a promising alternative to achieve effective Que concentrations in the brain. The formation of Que-2-hydroxypropylated-β-cyclodextrin (Que/HP-β-CD) complexes was previously found to increase the molecule's solubility and stability in aqueous media.

Chlorination of soil-derived dissolved organic matter: Long term nitrogen deposition does not increase terrestrial precursors of toxic disinfection byproducts.

Terrestrial dissolved organic matter (DOM) in forested watersheds is a known precursor of disinfection byproducts (DBPs) in drinking water. Although the characteristics of terrestrial DOM may change with increasing nitrogen (N) deposition in forests, how these changes alter formation potential and toxicity of DBPs remains unexplored. We analyzed the speciation and toxicity of DBPs from chlorination of DOM derived from soils (O, A, and B horizons) in an experimental temperate forest with 22 years of N addition.

Toxicity prediction and effect characterization of 90 pharmaceuticals and illicit drugs measured in plasma of fish from a major European river (Sava, Croatia).

Chemical analysis of plasma samples of wild fish from the Sava River (Croatia) revealed the presence of 90 different pharmaceuticals/illicit drugs and their metabolites (PhACs/IDrgs). The concentrations of these PhACs/IDrgs in plasma were 10 to 1000 times higher than their concentrations in river water. Antibiotics, allergy/cold medications and analgesics were categories with the highest plasma concentrations.

Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy.

Cell-free protein synthesis (CFPS) is an established method to produce recombinant proteins and has been used in a wide variety of applications. The use of CFPS has almost from the onset been favorably linked to the production of isotopically labelled proteins for NMR spectroscopy as the resulting labelling of the produced protein is defined by the chosen amino acids during reaction setup. Here we describe how to set up production and isotopic labelling of small intrinsically disordered proteins (IDPs) for NMR spectroscopy applications using an E.

Chlorines Are Not Evenly Substituted in Chlorinated Paraffins: A Predicted NMR Pattern Matching Framework for Isomeric Discrimination in Complex Contaminant Mixtures.

Chlorinated paraffins (CPs) can be mixtures of nearly a half-million possible isomers. Despite the extensive use of CPs, their isomer composition and effects on the environment remain poorly understood. Here, we reveal the isomeric distributions of nine CP mixtures with single-chain lengths (C) and varying degrees of chlorination.

Radiolabelled CCK R Antagonists Containing PEG Linkers: Design, Synthesis and Evaluation.

The cholecystokinin-2/gastrin receptor (CCK R) is considered a suitable target for the development of radiolabelled antagonists, due to its overexpression in various tumours, but no such compounds are available in clinical use. Therefore, we designed novel 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid-conjugated ligands based on CCK R antagonist Z360/nastorazepide. As a proof of concept that CCK R antagonistic activity can be retained by extending the Z360/nastorazepide structure using suitable linker, we present herein three compounds containing various PEG linkers synthesised on solid phase and in solution.

Paramagnetic Cobalt(II) Complexes with Cyclam Derivatives: Toward F MRI Contrast Agents.

In order to develop novel, more efficient, and/or selective contrast agents for magnetic resonance imaging (MRI), different are explored as alternatives to water-relaxation enhancement. In this work, cobalt(II/III) complexes of bis(-trifluoroethyl)cyclam derivatives with two acetate or two phosphonate pendant arms, H and H, were prepared and investigated. X-ray diffraction structures confirmed octahedral coordination with a very stable - cyclam conformation and with fluorine atoms located about 5.

Serum choline in extremely preterm infants declines with increasing parenteral nutrition.

Purpose: Choline is an essential nutrient for fetal and infant growth and development. Parenteral nutrition used in neonatal care lack free choline but contain small amounts of lipid-bound choline in the form of phosphatidylcholine (PC). Here, we examined the longitudinal development of serum free choline and metabolically related compounds betaine and methionine in extremely preterm infants and how the concentrations were affected by the proportion of parenteral fluids the infants received during the first 28 postnatal days (PNDs).