Binding Strength of Nucleobases and Nucleosides on Silver Nanoparticles Probed by a Colorimetric Method

Because of their unique and tunable properties, oligonucleotide-functionalized noble metal nanoparticles have provided a versatile platform for various engineering and biomedical applications. The vast majority of such applications were demonstrated with gold nanoparticles (AuNPs) while only a few were demonstrated with sliver nanoparticles (AgNPs). This is largely due to the lack of robust protocols to functionalize AgNPs with thiol-modified oligonucleotides. Previous studies have revealed strong interactions between nucleobases and AgNPs. This could enable an alternative way to functionalize AgNPs with non-thiolated oligonucleotides. However, there is no quantitative study on the interaction strengths between AgNPs and oligonucleotides. Several methods have been used for quantitative evaluation of the interaction strengths between AuNPs and oligonucleotides. These methods often require specialized equipment that might not be widely accessible or rely on labor-intensive procedures to obtain the adsorption isotherms. Herein, we developed a colorimetric method, as a simple and high-throughput alternative of existing methods, to quantify the binding strength between AgNPs and nucleobases/nucleosides. In this colorimetric method, concentration-dependent destabilizing effects of nucleobase/nucleoside adsorption on AgNPs are utilized to indirectly quantify the amount of nucleobases/nucleosides adsorbed on AgNPs, thus deriving the binding strength between AgNPs and nucleobases/nucleosides. First, the concentration-dependent AgNP aggregation kinetics in the presence of nucleobases/nucleosides were systematically investigated. Then, this colorimetric method was used to determine the binding strengths between AgNPs and various DNA/RNA nucleobases/nucleosides. It was found that the ranking of interaction strengths between AgNPs and DNA/RNA nucleosides (dC < dT < dA, rC < rU < rA) is generally agreed with that between AgNPs and corresponding nucleobases (C < T < U < A). This suggests that DNA/RNA nucleosides interact with AgNPs mainly via the constituent nucleobases. It was also revealed that interactions of AgNPs with DNA/RNA nucleosides are significantly weaker than that with corresponding nucleobases. This implies that deoxyribose/ribose might sterically inhibit the interactions between nucleobases and AuNPs

Crystal Structures of Polymorphic Prion Protein β1 Peptides Reveal Variable Steric Zipper Conformations

The pathogenesis of prion diseases is associated with the conformational conversion of normal, predominantly α-helical prion protein (PrP^C) into a pathogenic form that is enriched with β-sheets (PrP^Sc). Several PrP^C crystal structures have revealed β1-mediated intermolecular sheets, suggesting that the β1 strand may contribute to a possible initiation site for β-sheet-mediated PrP^Sc propagation. This β1 strand contains the polymorphic residue 129 that influences disease susceptibility and phenotype. To investigate the effect of the residue 129 polymorphism on the conformation of amyloid-like continuous β-sheets formed by β1, crystal structures of β1 peptides containing each of the polymorphic residues were determined. To probe the conformational influence of the peptide construct design, four different lengths of β1 peptides were studied. From the 12 peptides studied, 11 yielded crystal structures ranging in resolution from 0.9 to 1.4 Å. This ensemble of β1 crystal structures reveals conformational differences that are influenced by both the nature of the polymorphic residue and the extent of the peptide construct, indicating that comprehensive studies in which peptide constructs vary are a more rigorous approach to surveying conformational possibilities

Accurate and Sensitive Peptide Identification with Mascot Percolator

Sound scoring methods for sequence database search algorithms such as Mascot and Sequest are essential for sensitive and accurate peptide and protein identifications from proteomic tandem mass spectrometry data. In this paper, we present a software package that interfaces Mascot with Percolator, a well performing machine learning method for rescoring database search results, and demonstrate it to be amenable for both low and high accuracy mass spectrometry data, outperforming all available Mascot scoring schemes as well as providing reliable significance measures. Mascot Percolator can be readily used as a stand alone tool or integrated into existing data analysis pipelines

S1 Dataset -

The use of online teaching mode has grown rapidly in recent years, particularly under the COVID-19 pandemic. To promote the learning motivation of students and teaching effectiveness, development of attractive online teaching material such as videos is important. In the present study, we developed 15 theory-related videos and 9 case-based videos in the context of a leadership course focusing on psychological well-being and psychosocial competence. Using a qualitative research methodology via focus groups (N = 48 students) to evaluate these videos, six themes emerged from the data, including video arrangement, design of videos, content of videos, benefits to students’ pre-lesson self-learning, benefits to students’ learning of course content, and contribution to students’ class participation. The findings suggest that the videos can elicit positive perceptions of the students in a flipped classroom arrangement. Students also benefit from the videos in terms of their understanding of course content and their participation in class discussion. Besides, the study suggests that the videos promote the learning efficiency of the students. The present qualitative findings concurred with the previous quantitative findings, suggesting the value of using virtual teaching and learning to promote psychosocial competence in university students.</div

Semi-structured interview guide.

The use of online teaching mode has grown rapidly in recent years, particularly under the COVID-19 pandemic. To promote the learning motivation of students and teaching effectiveness, development of attractive online teaching material such as videos is important. In the present study, we developed 15 theory-related videos and 9 case-based videos in the context of a leadership course focusing on psychological well-being and psychosocial competence. Using a qualitative research methodology via focus groups (N = 48 students) to evaluate these videos, six themes emerged from the data, including video arrangement, design of videos, content of videos, benefits to students’ pre-lesson self-learning, benefits to students’ learning of course content, and contribution to students’ class participation. The findings suggest that the videos can elicit positive perceptions of the students in a flipped classroom arrangement. Students also benefit from the videos in terms of their understanding of course content and their participation in class discussion. Besides, the study suggests that the videos promote the learning efficiency of the students. The present qualitative findings concurred with the previous quantitative findings, suggesting the value of using virtual teaching and learning to promote psychosocial competence in university students.</div

Duration of the interview, number of participants, and language used in each focus group interview.

Duration of the interview, number of participants, and language used in each focus group interview.</p

Side-by-side comparison of quantitative and qualitative research findings.

Side-by-side comparison of quantitative and qualitative research findings.</p

Self-Assembly of Anionic Gemini Surfactant: Fluorescence Resonance Energy Transfer and Simulation Study

The interaction of dyes with a sulfonated Gemini surfactant was investigated in aqueous solution using Förster resonance energy transfer with acridine orange (AO) as a donor and rhodamine B (RhB) as an acceptor. Surface tension results showed that AO and RhB have different effects on the self-assembly of the Gemini surfactant, with AO giving a higher critical micelle concentration (cmc) and lower surface tension, while the opposite was observed for RhB. Energy transfer from AO to RhB was observed in the presence of the surfactant, and the energy transfer efficiency initially improved with increased surfactant concentration but then decreased significantly when the surfactant reached a higher concentration due to the formation of larger aggregates, which increased the average distance between AO and RhB. Dynamic light scattering demonstrated the existence of these large aggregates. Moreover, simulations using dissipative particle dynamics supported the experimental results

Novel <i>trans</i>-Ferulic Acid Derivatives Containing a Chalcone Moiety as Potential Activator for Plant Resistance Induction

A series of novel <i>trans</i>-ferulic acid derivatives containing a chalcone moiety were designed and synthesized to induce plant resistance. Antiviral activities of the compounds were evaluated. Bioassay results demonstrated that compounds <b>F3</b>, <b>F6</b>, <b>F17</b>, and <b>F27</b> showed remarkable curative, protective, and inactivating activities against tobacco mosaic virus (TMV). With a 50% effective concentration (EC₅₀) value of 98.78 μg mL^–1, compound <b>F27</b> exhibited the best protective activity compared with <i>trans</i>-ferulic acid (328.6 μg mL^–1), dufulin (385.6 μg mL^–1), and ningnanmycin (241.3 μg mL^–1). This protective ability was associated with potentiation of defense-related enzyme activity and activation of photosynthesis of tobacco at an early stage. This notion was confirmed by up-regulated expression of stress responses and photosynthesis regulating proteins. This work revealed that <b>F27</b> can induce resistance and enhance plant tolerance to TMV infection. Hence, <b>F27</b> can be considered as a novel activator for inducing plant resistance

Visible-Light-Induced Regioselective Cyanomethylation of Imidazopyridines and Its Application in Drug Synthesis

3-Cyanomethylated imidazopyridines were synthesized via a visible light-promoted reaction of imidazopyridines with bromoacetonitrile or iodoacetonitrile catalyzed by <i>fac</i>-Ir­(ppy)₃ under mild conditions. For the substrates with various substituents on benzene or pyridine ring, the reaction proceeded smoothly to give the corresponding products in moderate to good yields. The synthetic utility of this visible-light-induced reaction has been illustrated in the efficient synthesis of zolpidem and alpidem