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ELife Mar 2021Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an... (Review)
Review
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
Topics: Fluorescence Resonance Energy Transfer; Molecular Biology; Single Molecule Imaging
PubMed: 33779550
DOI: 10.7554/eLife.60416 -
Current Opinion in Structural Biology Dec 2020The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based... (Review)
Review
The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based experiments. However, there is a large range of macromolecular systems where the biological interest is predominantly in the slower dynamics (μs-s), that produce well diffracting microcrystals, and for which synchrotron-based experiments are extremely well suited. The combination of microfocus X-ray beams and the development of a range of sample delivery platforms has now made routine millisecond time-resolved experiments at microfocus macromolecular crystallography beamlines a real possibility and is driving development of dedicated endstations for time-resolved serial synchrotron crystallography.
Topics: Crystallography, X-Ray; Macromolecular Substances; Molecular Biology; Synchrotrons
PubMed: 32846363
DOI: 10.1016/j.sbi.2020.06.019 -
Essays in Biochemistry 2011Protist parasites cause important human and animal diseases, and because of their early divergence from other eukaryotes they possess structural and biochemical... (Review)
Review
Protist parasites cause important human and animal diseases, and because of their early divergence from other eukaryotes they possess structural and biochemical characteristics not found in other cells. The completion of the genome projects of most human protist parasites and the development of novel molecular tools for their study guarantee a rapid progress in understanding how they invade, modify and survive within their hosts. The ultimate goal of these studies will be the identification of targets for the design of drugs, diagnostics and vaccines. In addition, the accessibility of some of these parasites to multiple genetic manipulations has converted them into model systems in cell and molecular biology studies that could lead to the understanding of basic biological processes, as well as their evolution and pathogenesis. In the present chapter we discuss the biochemical and molecular peculiarities of these parasites and the molecular tools available for their study.
Topics: Animals; Genome; History, 21st Century; Host-Parasite Interactions; Humans; Molecular Biology; Parasites; Parasitology
PubMed: 22023438
DOI: 10.1042/bse0510001 -
Biochemistry and Molecular Biology... Jul 2019We describe an advanced, inquiry driven undergraduate course in Cancer Biology that combines faculty lectures typical of undergraduate courses with literature-driven...
We describe an advanced, inquiry driven undergraduate course in Cancer Biology that combines faculty lectures typical of undergraduate courses with literature-driven discussions typical of graduate courses. As a capstone course, one goal of this course is to integrate knowledge from previous coursework in physiology, cell and molecular biology, genetics, and chemistry, so that students acquire a state-of-the-art understanding of cancer and cancer treatment. A related goal is for students to learn, from the primary literature, how science is performed and how new scientific knowledge is used to improve cancer treatment. We report on the development of this course and the methods used to accomplish the course goals. We present the results of a 5-year survey that provides a detailed picture of the demographics of the class and demonstrates that the course results in improved understanding of both cancer biology and how science is performed. Student responses to our survey strongly support the use of original literature as a teaching tool. We suggest that incorporation of primary literature into advanced undergraduate science courses is an effective approach for improving scientific literacy. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):408-416, 2019.
Topics: Curriculum; Humans; Molecular Biology; Neoplasms; Students; Universities
PubMed: 30985963
DOI: 10.1002/bmb.21247 -
History and Philosophy of the Life... Feb 2021This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in...
This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries to biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science.
Topics: Cultural Diversity; Historiography; History, 20th Century; Molecular Biology
PubMed: 33538910
DOI: 10.1007/s40656-020-00364-5 -
Cold Spring Harbor Perspectives in... Jul 2009David Baltimore recalls the experiments that led to the discovery of the NF-kappaB transcription factor more than 20 years ago.
David Baltimore recalls the experiments that led to the discovery of the NF-kappaB transcription factor more than 20 years ago.
Topics: Animals; History, 20th Century; Humans; Inflammation; Models, Biological; Molecular Biology; NF-kappa B
PubMed: 20066072
DOI: 10.1101/cshperspect.a000026 -
Journal of Molecular Biology Oct 2018Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative... (Review)
Review
Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.
Topics: Animals; Cell Biology; Cytological Techniques; Humans; Models, Biological; Models, Molecular; Molecular Biology
PubMed: 29885327
DOI: 10.1016/j.jmb.2018.06.009 -
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 -
Biochemistry and Molecular Biology... 2013
Topics: Biochemistry; Humans; Molecular Biology; Students; Teaching
PubMed: 24078355
DOI: 10.1002/bmb.20726 -
Journal of Pediatric Hematology/oncology May 2016Great progress has been made in many areas of pediatric oncology. However, tumors of the central nervous system (CNS) remain a significant challenge. A recent explosion... (Review)
Review
Great progress has been made in many areas of pediatric oncology. However, tumors of the central nervous system (CNS) remain a significant challenge. A recent explosion of data has led to an opportunity to understand better the molecular basis of these diseases and is already providing a foundation for the pursuit of rationally chosen therapeutics targeting relevant molecular pathways. The molecular biology of pediatric brain tumors is shifting from a singular focus on basic scientific discovery to a platform upon which insights are being translated into therapies.
Topics: Brain Neoplasms; Central Nervous System Neoplasms; Child; Glioma; Humans; Medulloblastoma; Molecular Biology
PubMed: 26989915
DOI: 10.1097/MPH.0000000000000551