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Biochemistry and Molecular Biology... Nov 2020Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I...
Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process.
Topics: Biochemistry; Computer Simulation; Humans; Software; Students
PubMed: 32203640
DOI: 10.1002/bmb.21347 -
Current Biology : CB Oct 2007
Topics: Biochemistry; Germany; History, 20th Century; History, 21st Century; Molecular Biology; Protein Transport
PubMed: 17990367
DOI: 10.1016/j.cub.2007.07.017 -
Biochemistry and Molecular Biology... 2015Qualitative questions are proposed to assess the understanding of solubility and some of its applications. To improve those results, a simple quantitative problem on the...
Qualitative questions are proposed to assess the understanding of solubility and some of its applications. To improve those results, a simple quantitative problem on the precipitation of proteins is proposed.
Topics: Biochemistry; Curriculum; Education, Medical, Undergraduate; Humans; Problem-Based Learning; Solubility
PubMed: 25395353
DOI: 10.1002/bmb.20839 -
Proceedings of the National Academy of... Aug 2015
Topics: Animals; Biochemistry; History, 20th Century; History, 21st Century; Humans; United States
PubMed: 26209653
DOI: 10.1073/pnas.1512413112 -
ELife Feb 2019Most efforts to estimate the reproducibility of published findings have focused on specific areas of research, even though science is usually assessed and funded on a...
Most efforts to estimate the reproducibility of published findings have focused on specific areas of research, even though science is usually assessed and funded on a regional or national basis. Here we describe a project to assess the reproducibility of findings in biomedical science published by researchers based in Brazil. The Brazilian Reproducibility Initiative is a systematic, multicenter effort to repeat between 60 and 100 experiments: the project will focus on a set of common methods, repeating each experiment in three different laboratories from a countrywide network. The results, due in 2021, will allow us to estimate the level of reproducibility of biomedical science in Brazil, and to investigate what aspects of the published literature might help to predict whether a finding is reproducible.
Topics: Biochemistry; Biomedical Research; Brazil; Reproducibility of Results
PubMed: 30720433
DOI: 10.7554/eLife.41602 -
Biochemistry and Molecular Biology... 2014Encouraging undergraduate students to access, read, and analyze current primary literature can positively impact learning, especially in advanced courses. The... (Review)
Review
Encouraging undergraduate students to access, read, and analyze current primary literature can positively impact learning, especially in advanced courses. The incorporation of literature into coursework typically involves reading and responding to full research reports. Such exercises have clear value as students make connections between experiments and are able to probe and critique scientific logic. The exclusive use of full papers, though, may reinforce certain students' tendencies to rely on textual clues rather than a critical analysis of the actual data presented. I propose that structured activities requiring students to focus on individual parts of research papers, even on a single figure, are beneficial in a literature-centered advanced undergraduate course, because they promote the deep reading that is critical to scientific discourse. In addition, I describe how one such focused assignment boosted learning and was well received by students in a second-semester biochemistry course.
Topics: Animals; Biochemistry; Education, Professional
PubMed: 24243802
DOI: 10.1002/bmb.20744 -
Biochemistry Nov 2021Since the establishment of site-specific mutagenesis of single amino acids to interrogate protein function in the 1970s, biochemists have sought to tailor protein... (Review)
Review
Since the establishment of site-specific mutagenesis of single amino acids to interrogate protein function in the 1970s, biochemists have sought to tailor protein structure in the native cell environment. Fine-tuning the chemical properties of proteins is an indispensable way to address fundamental mechanistic questions. Unnatural amino acids (UAAs) offer the possibility to expand beyond the 20 naturally occurring amino acids in most species and install new and useful chemical functions. Here, we review the literature about advances in UAA incorporation technology from chemoenzymatic aminoacylation of modified tRNAs to translation systems to genetic encoding of UAAs in the native cell environment and whole organisms. We discuss innovative applications of the UAA technology to challenges in bioengineering and medicine.
Topics: Amino Acids; Biochemistry; Genetic Code; History, 20th Century; History, 21st Century; Mutagenesis, Site-Directed; RNA, Transfer
PubMed: 34196546
DOI: 10.1021/acs.biochem.1c00286 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Feb 2023Biochemistry and Molecular Biology are the cornerstone courses of talent training in the field of life science. Taking these course as an example, this study explored...
Biochemistry and Molecular Biology are the cornerstone courses of talent training in the field of life science. Taking these course as an example, this study explored reconstructing the knowledge framework, developing teaching cases, sharing teaching resources, innovating teaching means and establishing ideological education patterns. Supported by the scientific research achievements with discipline characteristics and online teaching platform, this research explored and practiced an integrated curriculum reform mode. This mode is guided by scientific research and education, based on the course development, and driven by communication and cooperation. A shared space of "exchange, practice, openness and informatization" was developed to achieve free and independent integration of undergraduate and graduate teaching motivated by learning knowledge, resulting in an effective student training.
Topics: Humans; Curriculum; Students; Learning; Molecular Biology; Biochemistry
PubMed: 36847105
DOI: 10.13345/j.cjb.220502 -
Biochemistry and Molecular Biology... 2015Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that... (Comparative Study)
Comparative Study
Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices.
Topics: Biochemistry; Educational Measurement; Humans; Learning; Molecular Biology; Students; Surveys and Questionnaires
PubMed: 26172264
DOI: 10.1002/bmb.20869 -
CBE Life Sciences Education Jun 2021With support from the American Society for Biochemistry and Molecular Biology (ASBMB), a community of biochemistry and molecular biology (BMB) scientist-educators has...
With support from the American Society for Biochemistry and Molecular Biology (ASBMB), a community of biochemistry and molecular biology (BMB) scientist-educators has developed and administered an assessment instrument designed to evaluate student competence across four core concept and skill areas fundamental to BMB. The four areas encompass energy and metabolism; information storage and transfer; macromolecular structure, function, and assembly; and skills including analytical and quantitative reasoning. First offered in 2014, the exam has now been administered to nearly 4000 students in ASBMB-accredited programs at more than 70 colleges and universities. Here, we describe the development and continued maturation of the exam program, including the organic role of faculty volunteers as drivers and stewards of all facets: content and format selection, question development, and scoring.
Topics: Biochemistry; Certification; Humans; Molecular Biology; Students; Universities
PubMed: 33900121
DOI: 10.1187/cbe.19-12-0265