Developing and applying computational resources for biochemistry education.
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ABSTRACT:
SUBMITTER: Craig PA
PROVIDER: S-EPMC7508772 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:While it is essential for life science students to be trained in modern techniques and approaches, rapidly developing, interdisciplinary fields such as bioinformatics present distinct challenges to undergraduate educators. In particular, many educators lack training in new fields, and high-quality teaching and learning materials may be sparse. To address this challenge with respect to bioinformatics, the Network for the Integration of Bioinformatics into Life Science Education (NIBLSE), in partnership with Quantitative Undergraduate Biology Education and Synthesis (QUBES), developed incubators, a novel collaborative process for the development of open educational resources (OER). Incubators are short-term, online communities that refine unpublished teaching lessons into more polished and widely usable learning resources. The resulting products are published and made freely available in the NIBLSE Resource Collection, providing recognition of scholarly work by incubator participants. In addition to producing accessible, high-quality resources, incubators also provide opportunities for faculty development. Because participants are intentionally chosen to represent a range of expertise in bioinformatics and pedagogy, incubators also build professional connections among educators with diverse backgrounds and perspectives and promote the discussion of practical issues involved in deploying a resource in the classroom. Here we describe the incubator process and provide examples of beneficial outcomes. Our experience indicates that incubators are a low cost, short-term, flexible method for the development of OERs and professional community that could be adapted to a variety of disciplinary and pedagogical contexts.
| S-EPMC7496352 | biostudies-literature
Project description:BACKGROUND: E-learning resources (e-resources) have been widely used to facilitate self-directed learning among medical students. The Department of Biochemistry at Christian Medical College (CMC), Vellore, India, has made available e-resources to first-year medical students to supplement conventional lecture-based teaching in the subject. This study was designed to assess students' perceptions of the impact of these e-resources on various aspects of their learning in biochemistry. METHODS: Sixty first-year medical students were the subjects of this study. At the end of the one-year course in biochemistry, the students were administered a questionnaire that asked them to assess the impact of the e-resources on various aspects of their learning in biochemistry. RESULTS: Ninety-eight percent of students had used the e-resources provided to varying extents. Most of them found the e-resources provided useful and of a high quality. The majority of them used these resources to prepare for periodic formative and final summative assessments in the course. The use of these resources increased steadily as the academic year progressed. Students said that the extent to which they understood the subject (83%) and their ability to answer questions in assessments (86%) had improved as a result of using these resources. They also said that they found biochemistry interesting (73%) and felt motivated to study the subject (59%). CONCLUSIONS: We found that first-year medical students extensively used the e-resources in biochemistry that were provided. They perceived that these resources had made a positive impact on various aspects of their learning in biochemistry. We conclude that e-resources are a useful supplement to conventional lecture-based teaching in the medical curriculum.
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Project description:Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate 's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate 's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART.
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Project description:Biochemistry is a core component of medical education as it contributes to the fundamental basis and understanding of molecular mechanisms in pathophysiological processes. The convergence of nutritional factors also gives insight to many chronic diseases. Topics of nutrition are often incorporated into biochemistry coursework and must be integrated in a way that makes sense within the overall curriculum. An important issue raised by this structure is determining which topics are most important to a student's understanding and what topics are most relevant to future clinical practice. Previous surveys show medical undergraduates feel that much of current medical biochemistry coursework lacks clinical relevance and pays too much attention to small details. Here we report the results of a survey that aims to determine the biochemical and nutritional topics that physicians and educators feel are most important to teach in medical school. This information is important for medical schools to better prepare their students for what they will see and apply in their future clinical practice. Physicians and medical educators were surveyed, asked demographic questions, and then requested to provide a prioritized list of the top 10 biochemistry and nutrition topics that they believed should be focused on in undergraduate medical education. Topics suggested by participants were normalized for spelling, acronyms, and abbreviations and given a weight from 10 to 1. A prioritized list was then created based on the suggested topics. This list provides insight into the topics that medical educators and physicians consider important to cover in undergraduate medical education.
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Project description:Obtaining continuing education can be difficult in countries with limited resources. Members of the Pediatric Orthopaedic Society of North America (POSNA) have developed a program for providing outreach continuing education courses in pediatric orthopaedics. POSNA members provide their own transportation to the host country, while the orthopaedic physicians along with the educational institutions in the host country in turn provide the support needed to carry out the courses. They also provide lodging, meals, and local transportation. Since its inception in 1998, 30 courses have been conducted in 19 countries with limited resources. The program has expanded to develop a partnership with the European Pediatric Orthopaedic Society. The protocol for organizing the courses is discussed.
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Project description:Pseudokinases regulate diverse cellular processes associated with normal cellular functions and disease. They are defined bioinformatically based on the absence of one or more catalytic residues that are required for canonical protein kinase functions. The ability to define pseudokinases based on primary sequence comparison has enabled the systematic mapping and cataloging of pseudokinase orthologs across the tree of life. While these sequences contain critical information regarding pseudokinase evolution and functional specialization, extracting this information and generating testable hypotheses based on integrative mining of sequence and structural data requires specialized computational tools and resources. In this chapter, we review recent advances in the development and application of open-source tools and resources for pseudokinase research. Specifically, we describe the application of an interactive data analytics framework, KinView, for visualizing the patterns of conservation and variation in the catalytic domain motifs of pseudokinases and evolutionarily related canonical kinases using a consistent set of curated alignments organized based on the widely used kinome evolutionary hierarchy. We also demonstrate the application of an integrated Protein Kinase Ontology (ProKinO) and an interactive viewer, ProtVista, for mapping and analyzing primary sequence motifs and annotations in the context of 3D structures and AlphaFold2 models. We provide examples and protocols for generating testable hypotheses on pseudokinase functions both for bench biologists and advanced users.
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Project description:Prevalence rates for mental health problems are higher when an individual's socioeconomic status (SES) is low, but the underlying mechanisms are not clearly understood. We investigated associations between education as indicator for SES and depressive symptoms as well as positive mental health (PMH). Moreover, we hypothesized that low education is associated with a lack of psychosocial resources and more daily hassles, which in turn mediate the relationships between education and mental health. In a German representative sample (N?=?7937), we cross-sectionally first examined whether a person's educational level was associated with depressive symptoms and PMH. Educational level was defined as the highest academic qualification achieved. Second, we investigated whether also sense of control, resilience, delay of gratification, cultural activity and daily hassles followed gradients along the educational level. Third, we investigated whether they mediated the relationship between education and mental health. Results showed that depressive symptoms measured by items from the DASS-42 depression subscale were more prevalent for persons with a low educational level, PMH operationalized by the Positive Mental Health Scale was equally distributed, and all psychosocial characteristics followed the gradient of educational level. In addition, the group with a high school diploma was particularly burdened. Structural equation modeling indicated that the associations between education and mental health were mediated by all psychosocial characteristics and daily hassles, apart from the delay of gratification. In the group with the lowest educational level the model fit indices for depressive symptoms and PMH were acceptable (?2?=?10007.243 (627), CFI?=?0.869, RMSEA?=?0.04 (90% CI [0.04, 0.04], SRMR?=?0.05; and ?2?=?12779.968 (741), CFI?=?0.86, RMSEA?=?0.05 (90% CI [0.05, 0.05], SRMR?=?0.05), respectively). The effect size Pm refers to the proportion of the total effect that is mediated by one or more variables ("M"), and the effect size of all indirect effects in the model for depressive symptoms was Pm?=?.80 and for PMH it was Pm?=?.68. The results support our hypotheses that low education is associated with less psychosocial resources, which in turn serve together with daily hassles as pathways between education and depressive symptoms as well as PMH. Building on these findings, longitudinal studies are necessary to investigate causality.
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Project description:Leadership could refer to holding official leadership positions or advocating for patients and the profession. Different pharmacy organizations recommend the inclusion of leadership development in pharmacy education and as such some pharmacy schools have introduced courses or various initiatives which support the development of leadership skills. In this commentary, we discuss means by which various pharmacy schools incorporate ways to develop leadership skills. This commentary also addresses the competencies used to assess leadership skills in pharmacy education.Supplementary informationThe online version contains supplementary material available at 10.1007/s40670-022-01532-x.
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Project description:Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.
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Project description:The CRISPR-Cas system has become a cutting-edge technology that revolutionized genome engineering. The use of Cas9 nuclease is currently the method of choice in most tasks requiring a specific DNA modification. The rapid development in the field of CRISPR-Cas is reflected by the constantly expanding ecosystem of computational tools aimed at facilitating experimental design and result analysis. The first group of CRISPR-Cas-related tools that we review is dedicated to aid in guide RNA design by prediction of their efficiency and specificity. The second, relatively new group of tools exploits the observed biases in repair outcomes to predict the results of CRISPR-Cas edits. The third class of tools is developed to assist in the evaluation of the editing outcomes by analysis of the sequencing data. These utilities are accompanied by relevant repositories and databases. Here we present a comprehensive and updated overview of the currently available CRISPR-Cas-related tools, from the perspective of a user who needs a convenient and reliable means to facilitate genome editing experiments at every step, from the guide RNA design to analysis of editing outcomes. Moreover, we discuss the current limitations and challenges that the field must overcome for further improvement in the CRISPR-Cas endeavor.
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