85 research outputs found

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

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    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 Ī²1 Peptides Reveal Variable Steric Zipper Conformations

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    The pathogenesis of prion diseases is associated with the conformational conversion of normal, predominantly Ī±-helical prion protein (PrP<sup>C</sup>) into a pathogenic form that is enriched with Ī²-sheets (PrP<sup>Sc</sup>). Several PrP<sup>C</sup> crystal structures have revealed Ī²1-mediated intermolecular sheets, suggesting that the Ī²1 strand may contribute to a possible initiation site for Ī²-sheet-mediated PrP<sup>Sc</sup> propagation. This Ī²1 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 Ī²-sheets formed by Ī²1, crystal structures of Ī²1 peptides containing each of the polymorphic residues were determined. To probe the conformational influence of the peptide construct design, four different lengths of Ī²1 peptides were studied. From the 12 peptides studied, 11 yielded crystal structures ranging in resolution from 0.9 to 1.4 ƅ. This ensemble of Ī²1 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

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    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 -

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    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 studentsā€™ pre-lesson self-learning, benefits to studentsā€™ learning of course content, and contribution to studentsā€™ 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.

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    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 studentsā€™ pre-lesson self-learning, benefits to studentsā€™ learning of course content, and contribution to studentsā€™ 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.

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    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.

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

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

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    The interaction of dyes with a sulfonated Gemini surfactant was investigated in aqueous solution using FoĢˆrster 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
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