In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics.

In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear.

Synergistic metabolism of salivary MUC5B in oral commensal bacteria during early biofilm formation.

The study of bacterial interactions and salivary-mediated regulation of early dental biofilm activity is of interest for understanding oral microbial adaptation to environmental cues and biofilm maturation. Findings in oral commensals can prove useful from the perspectives of both oral and systemic health of the host, as well as the understanding of general microbial biofilm physiology. The knowledge may provide a basis for the development of prognostic biomarkers, or development of new treatment strategies, related to oral health and disease and possibly also to other biofilm-induced conditions.

Metabolite Profiling of Conifer Needles: Tracing Pollution and Climate Effects.

In the face of escalating environmental challenges, understanding the intricate relationship between plant metabolites, pollution stress, and climatic conditions is of paramount importance. This study aimed to conduct a comprehensive analysis of metabolic variations generated through H and C NMR measurements in evergreen needles collected from different regions with varying pollution levels. Multivariate analyses were employed to identify specific metabolites responsive to pollution stress and climatic factors.

Polystyrene micro- and nanoplastics cause placental dysfunction in mice†.

Maternal exposure to microplastics and nanoplastics has been shown to result in fetal growth restriction in mice. In this study, we investigated the placental and fetal hemodynamic responses to plastics exposure in mice using high-frequency ultrasound. Healthy, pregnant CD-1 dams were given either 106 ng/L of 5 μm polystyrene microplastics or 106 ng/L of 50 nm polystyrene nanoplastics in drinking water throughout gestation and were compared with controls.

The Chemical Composition of Honey and Propolis Collected in Two Locations: Similarities and Differences.

The chemical composition of stingless bee honey and propolis depends on the plant sources they are derived from, and thus reflects the flora available in the vicinity of the hives, the preferences of the bee species, and the climate (altitude and temperature). To understand the relative influence of these factors, we studied the composition of honey and propolis of the stingless bee . Samples from 24 colonies were analyzed: 12 each from two meliponaries located in the state of Chiapas in southern Mexico, approximately 8.

A Screening Protocol for Exploring Loop Length Requirements for the Formation of a Three Cytosine-Cytosine Base-Paired i-Motif.

DNA sequences containing at least four runs of repetitive cytosines can fold into tetra-helical structures called i-Motifs (iMs). The interest in these DNA secondary structures is increasing due to their therapeutical and technological applications. Still, limited knowledge of their folding requirements is currently available.

Evidence for the formation of fused aromatic ring structures in an organic soil profile in the early diagenesis.

The presence of fused aromatic ring (FAR) structures in soil define the stability of the recalcitrant soil organic matter (RSOM). FAR are important skeletal features in RSOM that contribute to its extended residence time. During the early diagenesis, FAR structures are formed through condensation and polymerization of biomolecules produced during plant residue and microbial product decay.

Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction.

Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability.

Cytotoxicity and Antibacterial Efficacy of Betaine- and Choline-Substituted Polymers.

Cationic charge has been widely used to increase polymer adsorption and flocculation of dispersions or to provide antimicrobial activity. In this work, cationization of hydroxyethyl cellulose (HEC) and polyvinyl alcohol (PVA) was achieved by covalently coupling betaine hydrochloride and choline chloride to the polymer backbones through carbonyl diimidazole (CDI) activation. Two approaches for activation were investigated.

Exploring the Potential of Broadband Complementary Metal Oxide Semiconductor Micro-Coil Nuclear Magnetic Resonance for Environmental Research.

With sensitivity being the Achilles' heel of nuclear magnetic resonance (NMR), the superior mass sensitivity offered by micro-coils can be an excellent choice for tiny, mass limited samples such as eggs and small organisms. Recently, complementary metal oxide semiconductor (CMOS)-based micro-coil transceivers have been reported and demonstrate excellent mass sensitivity. However, the ability of broadband CMOS micro-coils to study heteronuclei has yet to be investigated, and here their potential is explored within the lens of environmental research.

Evolutionary conservation of the structure and function of meiotic Rec114-Mei4 and Mer2 complexes.

Meiosis-specific Rec114-Mei4 and Mer2 complexes are thought to enable Spo11-mediated DNA double-strand break (DSB) formation through a mechanism that involves DNA-dependent condensation. However, the structure, molecular properties, and evolutionary conservation of Rec114-Mei4 and Mer2 are unclear. Here, we present AlphaFold models of Rec114-Mei4 and Mer2 complexes supported by nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), and mutagenesis.

Affinity-enhanced RNA-binding domains as tools to understand RNA recognition.

Understanding how the RNA-binding domains of a protein regulator are used to recognize its RNA targets is a key problem in RNA biology, but RNA-binding domains with very low affinity do not perform well in the methods currently available to characterize protein-RNA interactions. Here, we propose to use conservative mutations that enhance the affinity of RNA-binding domains to overcome this limitation. As a proof of principle, we have designed and validated an affinity-enhanced K-homology (KH) domain mutant of the fragile X syndrome protein FMRP, a key regulator of neuronal development, and used this mutant to determine the domain's sequence preference and to explain FMRP recognition of specific RNA motifs in the cell.

Environmental metabolomics uncovers oxidative stress, amino acid dysregulation, and energy impairment in Daphnia magna with exposure to industrial effluents.

Anthropogenic activities are regarded as point sources of pollution entering freshwater bodies worldwide. With over 350,000 chemicals used in manufacturing, wastewater treatment and industrial effluents are comprised of complex mixtures of organic and inorganic pollutants of known and unknown origins. Consequently, their combined toxicity and mode of action are not well understood in aquatic organisms such as Daphnia magna.

Disorder to order: how halide mixing in MAPbIBr perovskites restricts MA dynamics.

Mixed-halide lead perovskites are of particular interest for the design of tandem solar cells currently reaching record efficiencies. While halide phase segregation upon illumination of mixed perovskites is extensively studied, the effect of halide disorder on A cation dynamics is not well understood, despite its importance for charge carrier diffusion and lifetime. Here, we study the methylammonium (MA) reorientational dynamics in mixed halide MAPbIBr perovskites by a combined approach of experimental solid-state NMR spectroscopy and molecular dynamics (MD) simulations based on machine-learning force-fields (MLFF).

Spatial arrangement of functional domains in OxyS stress response sRNA.

Small noncoding RNAs are an important class of regulatory RNAs in bacteria, often regulating responses to changes in environmental conditions. OxyS is a 110 nt, stable, -encoded small RNA found in and is induced by an increased concentration of hydrogen peroxide. OxyS has an important regulatory role in cell stress response, affecting the expression of multiple genes.

Attenuation of reverse transcriptase facilitates SAMHD1 restriction of HIV-1 in cycling cells.

Background: SAMHD1 is a deoxynucleotide triphosphohydrolase that restricts replication of HIV-1 in differentiated leucocytes. HIV-1 is not restricted in cycling cells and it has been proposed that this is due to phosphorylation of SAMHD1 at T592 in these cells inactivating the enzymatic activity. To distinguish between theories for how SAMHD1 restricts HIV-1 in differentiated but not cycling cells, we analysed the effects of substitutions at T592 on restriction and dNTP levels in both cycling and differentiated cells as well as tetramer stability and enzymatic activity in vitro.

Porous Salts Containing Cationic Al -Hydroxide-Acetate Clusters from Scalable, Green and Aqueous Synthesis Routes.

The solution chemistry of aluminum is highly complex and various polyoxocations are known. Here we report on the facile synthesis of a cationic Al cluster that forms porous salts of composition [Al (OH) (CH COO) ]X , denoted CAU-55-X, with X=Cl , Br , I , HSO . Three-dimensional electron diffraction was employed to determine the crystal structures.

Nitroreductase-sensitive fluorescent covalent organic framework for tumor hypoxia imaging in cells.

Covalent organic frameworks (COFs) have been used in cell imaging, but very rarely for imaging specific cell conditions. Herein, a β-ketoenamine-based fluorescent COF was post-synthetically modified to incorporate a hypoxia-targeting molecule. Fluorescence microscopy imaging shows that the material discriminates between HeLa cells grown under hypoxia and those cultured under normoxia.

Resolution enhancement of NMR by decoupling with the low-rank Hankel model.

Nuclear magnetic resonance (NMR) spectroscopy has become a formidable tool for biochemistry and medicine. Although -coupling carries essential structural information it may also limit the spectral resolution. Homonuclear decoupling remains a challenging problem.

Targeted Compound Selection with Increased Sensitivity in C-Enriched Biological and Environmental Samples Using C-DREAMTIME in Both High-Field and Low-Field NMR.

Chemical characterization of complex mixtures by Nuclear Magnetic Resonance (NMR) spectroscopy is challenging due to a high degree of spectral overlap and inherently low sensitivity. Therefore, NMR experiments that reduce overlap and increase signal intensity hold immense potential for the analysis of mixtures such as biological and environmental media. Here, we introduce a C version of DREAMTIME (Designed Refocused Excitation And Mixing for Targets In Vivo and Mixture Elucidation) NMR, which, when analyzing C-enriched materials, allows the user to selectively detect only the compound(s) of interest and remove all other peaks in a C spectrum.

Thiocarbohydrazone and Chalcone-Derived 3,4-Dihydropyrimidinethione as Lipid Peroxidation and Soybean Lipoxygenase Inhibitors.

The potential of the 4,6-diphenyl-3,4-dihydropyrimidine-2(1)-thione (abbreviated as ) and ()-'-benzylidenehydrazinecarbothiohydrazide (abbreviated as ) compounds as possible drug leads is investigated. and are synthesized in high yield of up to 97%. Their structure, binding in the active site of the LOX-1 enzyme, and their toxicity are studied via joint experimental and computational methodologies.

Structure and synthesis of a vaccine and diagnostic target for Enterocloster bolteae, an autism-associated gut pathogen - Part II.

Enterocloster bolteae (formerly known as Clostridium bolteae) is a gastro-intestinal pathogenic bacterium often detected in the fecal microbiome of children in the autism spectrum. E. bolteae excretes metabolites that are thought to act as neurotoxins.