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Redefining fundamental concepts of transcription initiation in bacteria.

ABSTRACT: Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.

SUBMITTER: Mejia-Almonte C

PROVIDER: S-EPMC7990032 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Redefining fundamental concepts of transcription initiation in bacteria.

Mejía-Almonte Citlalli C Busby Stephen J W SJW Wade Joseph T JT van Helden Jacques J Arkin Adam P AP Stormo Gary D GD Eilbeck Karen K Palsson Bernhard O BO Galagan James E JE Collado-Vides Julio J

Nature reviews. Genetics 20200714 11

Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles ...[more]

PMID: 32665585

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Project description:BACKGROUND:Psychomotor skills related to the use of medical ultrasound are a fundamental, but often overlooked component of this ubiquitous medical imaging technology. Although discussions of image production/orientation, sonographic planes, and imaging/scanning techniques are common in existing literature, these discussions rarely address practical skills related to these basic concepts. The cognitive load of transducer movements and machine operation, in conjunction with learning the ultrasound representation of anatomy, may overwhelm a novice learner. Our goal was to develop and evaluate a set of ultrasound puzzle phantoms for students to use as they learn isolated, specific transducer movements and sonographic concepts. We intentionally created phantoms that contain objects that are likely familiar to students to reduce the cognitive load associated with simultaneously learning the ultrasound interpretation of anatomy. METHODS:This preliminary evaluation of our novel, homemade, gelatin ultrasound puzzle phantoms was performed using pretests and posttests obtained by scanning an assessment phantom, and student questionnaires. Two phases of training and testing occurred with feedback from Phase 1 allowing for refinement of the puzzles and techniques for testing. Skills taught and evaluated included probe rotation, depth assessment, sliding, and tilting. RESULTS:Twenty-eight students attended the Phase 1 training session with positive trends in students' abilities to use rotation, sliding, and tilting to answer questions, while only depth showed statistically significant improvements (p = 0.021). Overall students agreed the experience a productive use of time (86%), was beneficial (93%), and would recommend to others (93%). Fifteen (54%) students returned 3 months later. There was no significant decay in skills obtained from the prior training session. In Phase 2, 134 medical students participated, and 76 (57%) completed an online questionnaire. A majority of students agreed they had a better understanding of rotation (83%), depth (80%), sliding (88%) and tilting (55%). Similar to Phase 1, many students (75%) felt the experience was beneficial. CONCLUSIONS:This preliminary study gave us insight into student opinions, as well as information to guide future scalability and development of additional ultrasound puzzle phantoms to aid in medical student education of isolated transducer movements and sonographic concepts prior to imaging human anatomy.

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Redefining fundamental concepts of transcription initiation in bacteria.

Publications

Redefining fundamental concepts of transcription initiation in bacteria.

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