SEISMICgraph: a web-based tool for RNA structure data visualization.

In recent years, RNA has been increasingly recognized for its essential roles in biology, functioning not only as a carrier of genetic information but also as a dynamic regulator of gene expression through its interactions with other RNAs, proteins, and itself. Advances in chemical probing techniques have significantly enhanced our ability to identify RNA secondary structures and understand their regulatory roles. These developments, alongside improvements in experimental design and data processing, have greatly increased the resolution and throughput of structural analyses.

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures.

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures.

Baked sweetpotato textures and sweetness: An investigation into relationships between physicochemical and cooked attributes.

Sweetpotato varieties vary greatly in perceived textures and sweetness. This study identified physicochemical factors that influence these attributes in cooked sweetpotatoes. Fifteen genotypes grown on three plots were baked and evaluated by a trained descriptive sensory analysis panel for sweetness and 13 texture attributes.

RNA levers and switches controlling viral gene expression.

RNA viruses are diverse and abundant pathogens that are responsible for numerous human diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often by encoding overlapping reading frames. These reading frames are then decoded by mechanisms such as alternative splicing and ribosomal frameshifting to produce multiple distinct proteins.

3D RNA-scaffolded wireframe origami.

Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds.

Nutritional stress exacerbates impact of a novel insecticide on solitary bees' behaviour, reproduction and survival.

Pesticide exposure and food stress are major threats to bees, but their potential synergistic impacts under field-realistic conditions remain poorly understood and are not considered in current pesticide risk assessments. We conducted a semi-field experiment to examine the single and interactive effects of the novel insecticide flupyradifurone (FPF) and nutritional stress on fitness proxies in the solitary bee . Individually marked bees were released into flight cages with monocultures of buckwheat, wild mustard or purple tansy, which were assigned to an insecticide treatment (FPF or control) in a crossed design.

Variable Effects of Twenty Sugars and Sugar Alcohols on the Retrogradation of Wheat Starch Gels.

Starch retrogradation is desirable for some food textures and nutritional traits but detrimental to sensory and storage qualities of other foods. The objective of this study was to determine the impact of sweetener structure and concentration on the retrogradation of wheat starch gels. The effects of 20 sweeteners selected based on common food usage and stereochemical structures of interest, and ranging in concentration from 10 to 50%/, on the retrogradation of wheat starch gels were monitored spectrophotometrically over time.

Sweetpotato chip texture and fat content: Effects of enzymatic modification of cell wall polymers.

Impacts of cell wall polymers on sweetpotato chip texture and fat content were investigated through enzymatic modification. Covington sweetpotato slices were treated with cellulase, hemicellulase, pectinase, pectin methyl esterase, protease, the enzyme blend Viscozyme, or no enzymes (control) at 40-45°C for 0.5-2 h.

Indirect COVID-19 health effects and potential mitigating interventions: Cost-effectiveness framework.

Background: The COVID-19 pandemic led to important indirect health and social harms in addition to deaths and morbidity due to SARS-CoV-2 infection. These indirect impacts, such as increased depression and substance abuse, can have persistent effects over the life course. Estimated health and cost outcomes of such conditions and mitigation strategies may guide public health responses.

Results of Ring-Testing of a Semifield Study Design to Investigate Potential Impacts of Crop Protection Products on Bumblebees (Hymenoptera, Apidae) and a Proposal of a Potential Test Design.

In Europe, the risk assessment for bees at the European Union or national level has always focussed on potential impacts on honeybees. During the revision of the European Food Safety Authority bee guidance it was explicitly stated that bumblebees and solitary bees should be considered as well and consequently concerns were raised regarding the representativeness of honeybees for these other bee species. These concerns originate from differences in size as well as differences in behavioral and life history traits of other bee species.

Drug Interactions Affecting Kidney Function: Beware of Health Threats from Triple Whammy.

Triple whammy (TW) is a potentially dangerous drug combination that can lead to acute kidney injury (AKI). This drug interaction (DI) occurs when angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) are used together with diuretics and non-steroidal anti-inflammatory drugs (NSAIDs). One of the most serious consequences of TW DI is an increased risk of developing pre-renal acute kidney injury (pr-AKI).

Fungicide and insecticide exposure adversely impacts bumblebees and pollination services under semi-field conditions.

Sulfoximines, the next generation systemic insecticides developed to replace neonicotinoids, have been shown to negatively impact pollinator development and reproduction. However, field-realistic studies on sulfoximines are few and consequences on pollination services unexplored. Moreover, the impacts of other agrochemicals such as fungicides, and their combined effects with insecticides remain poorly investigated.

Relationships between isolated sweetpotato starch properties and textural attributes of sweetpotato French fries.

Sweetpotato French fry (SPFF) textures have been associated with dry matter and starch contents, but these do not fully account for all textural differences. This study investigated the relationships between the physicochemical properties of sweetpotato starch and textural attributes of sweetpotato fries. Starches from 16 sweetpotato genotypes that varied in dry matter content were isolated and analyzed.

Sulfoxaflor insecticide and azoxystrobin fungicide have no major impact on honeybees in a realistic-exposure semi-field experiment.

Exposure to pesticides is considered a major threat to bees and several neonicotinoid insecticides were recently banned in cropland within the European Union in light of evidence of their potential detrimental effects. Nonetheless, bees remain exposed to many pesticides whose effects are poorly understood. Recent evidence suggests that one of the most prominent replacements of the banned neonicotinoids - the insecticide sulfoxaflor - harms bees and that fungicides may have been overlooked as a driver of bee declines.

Effects of Sugars and Sugar Alcohols on the Gelatinization Temperatures of Wheat, Potato, and Corn Starches.

The gelatinization temperature (T) of starch increases in the presence of sweeteners due to sweetener-starch intermolecular interactions in the amorphous regions of starch. Different starch botanical sources contain different starch architectures, which may alter sweetener-starch interactions and the effects of sweeteners on Ts. To document these effects, the Ts of wheat, potato, waxy corn, dent corn, and 50% and 70% high amylose corn starches were determined in the presence of eleven different sweeteners and varying sweetener concentrations.

Relative humidity-temperature transition boundaries for anhydrous β-caffeine and caffeine hydrate crystalline forms.

Caffeine is a hydrate-forming polymorphic crystalline compound that can exist in α, β, and hydrate forms. Phase transitions between hydrate and anhydrous forms of a crystalline ingredient, and related water migration, can create product quality challenges. The objective of this study was to determine the relative humidity (RH)-temperature phase boundary between anhydrous β-caffeine and caffeine hydrate.

RH-temperature stability diagram of α- and β-anhydrous and monohydrate lactose crystalline forms.

Lactose crystals exhibit polymorphic, deliquescent, and hydrate-forming traits and can exist in monohydrate, β-anhydrate, stable α-anhydrate, and hygroscopic α-anhydrate (isomorphic desolvate) forms. The objective of this study was to identify the relative humidity (RH) and temperature boundaries at which anhydrate-hydrate transitions and deliquescence occur for these lactose crystal forms. The deliquescence point (RH) of lactose monohydrate was determined by measuring the water activity (a) of a saturated solution, and the RHs of the anhydrates were determined using dynamic vapor sorption measurement techniques.

RH-Temperature Stability Diagram of the Dihydrate, β-Anhydrate, and α-Anhydrate Forms of Crystalline Trehalose.

Trehalose crystals exhibit polymorphic, deliquescent, and hydrate-forming traits and can exist in dihydrate, β-anhydrate, or α-anhydrate (isomorphic desolvate) forms. The objective of this study was to identify the relative humidity (RH) and temperature boundaries for phase changes of these different trehalose crystal forms. The deliquescence points (RH s) of the anhydrate and dihydrate trehalose crystals were determined from 20 to 50 °C using a combination of water activity and dynamic vapor sorption measurement techniques.

Rotational Atherectomy Combined with Drug Coated-Balloons for in-Stent Restenosis.

Background: Refractory coronary in-stent restenosis remains a clinically relevant problem in interventional cardiology despite the use of drug coated balloon angioplasty and further drug eluting stent deployment. In this study, we investigated whether the novel approach of lesion debulking with rotational atherectomy prior to drug coated balloon angioplasty for challenging coronary in-stent restenosis is safe and effective.

Methods: Procedural and registry data was retrospectively analysed for 26 patients who underwent rotational atherectomy immediately followed by drug coated balloon angioplasty to 43 coronary in-stent restenosis lesions with mean follow up of 19 months.

OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes.

Monoclonal antibodies are becoming increasingly important therapeutic agents for the treatment of cancers, infectious diseases, and autoimmune disorders. However, laboratory-based methods of developing therapeutic monoclonal antibodies (e.g.

Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation.

Engineering high chemo-, regio-, and stereoselectivity is a prerequisite for enzyme usage in organic synthesis. Cytochromes P450 can oxidize a broad range of substrates, including macrocycles, which are becoming popular scaffolds for therapeutic agents. However, a large conformational space explored by macrocycles not only reduces the selectivity of oxidation but also impairs computational enzyme design strategies based on docking and molecular dynamics (MD) simulations.

Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.

Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants.