Structural Driving Factors for the Coupled Electron and Proton Transfer Reactions in Mitochondrial Cytochrome BC1 Complex: Binding Geometries of Substrates and Protonation States of Ionizable Amino Acid Side Chains Near Qi and Qo Sites

Coupled electron and proton transfer (CEPT) events are fundamental for many bioenergetic conversions that involve redox reactions. Understanding the details underlying CEPT processes will advance our knowledge of (1) how nature regulates energy conversion; (2) our strategies for achieving renewable energy sources; (3) how to cope with CEPT dysfunction diseases. Studies of the detailed mechanism(s) of CEPT in biological systems is challenging due to their complex nature. Consequently, controversies between the concerted and sequential mechanism of CEPT for many systems remain. This dissertation focuses on the bovine mitochondrial cytochrome bc1 complex. CEPT in the bc1 complex operates by a modified Q-cycle (1) and catalyzes electron transfer from ubiquinol (QH2), to cyt c via an iron sulfur cluster (ISC) and to the low potential hemes of cyt b, where it reduces ubiquinone (UQ). The electron transfer is coupled to the translocation of protons across the mitochondrial inner membrane, generating a proton gradient that drives ATP synthesis. Although the Q-cycle is widely accepted as the model that best describes how electrons and protons flow in bc1, detailed binding geometries at the Qo site (QH2 oxidation site) and Qi site (UQ reduction site) remain controversial. The binding geometries play critical roles in the thermodynamic and/or kinetic control of the reaction and protonatable amino acid side chains can participate in the proton transfer. The central focuses of this dissertation are molecular dynamics simulations of cofactor binding geometries near the Qo and Qi sites, calculations of the pKa values of ionizable amino acid side chains implicated in cofactor binding, especially the ISC-coordinated histidines, and implications for the proposed mechanism(s) of CEPT. For the first time, pKa values of the ISC-coordinated histidines are differentiated. The computed pKa values of 7.8±0.5 for His141 and 9.1±0.6 for His161 agree well with experiment (7.63±0.15 and 9.16±0.28). Thus, His161 should be protonated at physiological pH and cannot be the first proton acceptor in the QH2 oxidation. Water mediated hydrogen bonds between substrate models and the protein and water accessibility to the Qo and Qi sites were maintained in simulations, implying that water molecules are likely the proton donors and acceptors

EDMODO USE IN ESP WRITING: STUDENTS’ PERCEPTIONS

A growing body of literature has examined the nature of blended learning and its effects on language teaching and learning, including the use of Edmodo to promote student writing. However, this type of integration of face-to-face instruction and online learning remains relatively new for EFL contexts. Also, teaching writing at the Vietnamese contexts, particularly in the ESP tertiary education, is still largely dependent on conventional way. This paper therefore reports students’ perceptions about Edmodo use in writing classes at a Vietnamese university. This paper draws on data collected as part of a larger mixed methods project including tests and interviews over a fifteen-week semester of an ESP writing class. In this paper, the focus is the data from interviews, which explored how students perceived the effects of Edmodo use in their writing learning process. The findings indicate students’ positive perceptions about this supportive learning delivery method in writing classes. Implications for teachers and school administrators with regard to practical applications of Edmodo as a potential tool are also discussed.  Article visualizations

Evaluating factors affecting attitudes of IT-intensive and non-IT-intensive students towards e-assessment

Despite the significant shift to distance computer-based test as an inevitable outcome of Industry 4.0 and the public lockdown of COVID-19, little effort has been made to research this new testing mode. To address this issue, this study targets two groups of information technology (IT)-intensive and non-IT-intensive students with an aim of investigating factors that effectively encourage each group to adopt online assessment and whether their majors cause any differences in the students’ attitudes. Based on the student perception of e-assessment questionnaire (SPEAQ) with some slight modifications, a final 28-item survey was formed and distributed to 400 students. Results have shown that the factors of security, and affective factors were the top factors to impact both groups of students, while the impact of validity and practicality varied among the two groups and reliability and teaching-learning were at the bottom. Besides, there were no noticeable differences in the attitudes of students coming from different majors

Differentiable Bayesian Structure Learning with Acyclicity Assurance

Score-based approaches in the structure learning task are thriving because of their scalability. Continuous relaxation has been the key reason for this advancement. Despite achieving promising outcomes, most of these methods are still struggling to ensure that the graphs generated from the latent space are acyclic by minimizing a defined score. There has also been another trend of permutation-based approaches, which concern the search for the topological ordering of the variables in the directed acyclic graph in order to limit the search space of the graph. In this study, we propose an alternative approach for strictly constraining the acyclicty of the graphs with an integration of the knowledge from the topological orderings. Our approach can reduce inference complexity while ensuring the structures of the generated graphs to be acyclic. Our empirical experiments with simulated and real-world data show that our approach can outperform related Bayesian score-based approaches.Comment: Accepted as a regular paper (9.37%) at the 23rd IEEE International Conference on Data Mining (ICDM 2023

Comparing the effectiveness of online and onsite learning in English proficiency classes: Learners’ perspectives

Online education has significantly gained popularity due to new technology and more importantly, the growing impact of the digitalization of the economy. Despite its prominent advantages such as accessibility, affordability and flexibility, the effectiveness of online education is still a constant debate and needs extensive investigations in different research contexts. This study aimed to evaluate the effectiveness of online learning in comparison to traditional learning in the context of English language teaching. This descriptive study was undertaken with learners of English as a foreign language (EFL) in English proficiency preparation classes, employing an online questionnaire together with final scores of proficiency tests. The results revealed that the participants had relatively positive perceptions towards online learning in all four aspects: course content, teachers, learning environment and course supports. The significant finding was that when comparing the final results of the VSTEP exams, the online learners generally were able to perform better than the learners in traditional classrooms, though the difference was not largely remarkable. Online education in the new normal will continue to excel and the effectiveness of this learning mode certainly needs further investigation from different perspectives