Self-sustained Replication of an RNA Enzyme

Self-sustained Replication of an RNA Enzyme

Author: Tracey Ann Lincoln

Publisher: ProQuest

Published: 2009

Total Pages: 208

ISBN-13: 9781109124675

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RNA enzymes based on the R3C ligase ribozyme motif were previously shown to undergo both self- and cross-catalytic replication, albeit very inefficiently. In an attempt to develop efficient cross-replicating RNA enzymes that can undergo self-sustained exponential amplification in the absence of proteins, in vitro evolution was carried out to optimize their catalytic activity. Two enzymes, E and E, ́ were selected for their ability to catalyze each other's synthesis from a total of four component substrates (A, B and A, ́ B)́. The optimized cross-replicating RNA enzymes were able to undergo self-sustained exponential amplification at a constant temperature in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about one hour, and can be continued indefinitely, provided the system is replenished with substrates. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates. This was demonstrated through serial transfer experiments which employed 5 [muM of each type of A, A, ́ B, and B ́and initiated with 0.1 [muM of each type of E and E.́ After 5 h incubation, 5% of the reaction mixture was removed and transferred to a separate reaction vessel that contained a fresh supply of substrates. This process was repeated for up to 20 transfers, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.


The Science and Applications of Synthetic and Systems Biology

The Science and Applications of Synthetic and Systems Biology

Author: Institute of Medicine

Publisher: National Academies Press

Published: 2011-12-30

Total Pages: 570

ISBN-13: 0309219396

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Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.


Ribozymes

Ribozymes

Author: Sabine Müller

Publisher: John Wiley & Sons

Published: 2021-07-09

Total Pages: 81

ISBN-13: 3527814531

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Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.


Designing Nanostructures at the Interface between Biomedical and Physical Systems

Designing Nanostructures at the Interface between Biomedical and Physical Systems

Author: The National Academies

Publisher: National Academies Press

Published: 2005-06-01

Total Pages: 120

ISBN-13: 0309181542

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Last November, the National Academies Keck Futures Initiative held the Designing Nanostructures at the Interface Between Biomedical and Physical Systems conference at which researchers from science, engineering and medicine discussed recent developments in nanotechnology, directions for future research, and possible biomedical applications. The centerpiece of the conference was breakout sessions in which ten focus groups of researchers from different fields spent eight hours developing research plans to solve various problems in the field of nanotechnology. Among the challenges were: Building a nanosystem that can isolate, sequence and identify RNA or DNA Developing a system to detect disease in vivo Sequencing a single molecule of protein Creating a biological system that will create a local hydrogen fuel source, and Growing a biological in vivo power source. Representatives from public and private funding organizations, government, industry, and the science media also participated in the focus groups. This book provides a summary of the conference focus groups. For more information about the conference, visit Keck Futures Initiative. The National Academies Keck Futures Initiative was launched in 2003 to stimulate new modes of scientific inquiry and break down the conceptual and institutional barriers to interdisciplinary research. The National Academies and the W.M. Keck Foundation believe considerable scientific progress and social benefit will be achieved by providing a counterbalance to the tendency to isolate research within academic fields. The Futures Initiative is designed to enable researchers from different disciplines to focus on new questions upon which they can base entirely new research, and to encourage better communication between scientists as well as between the scientific community and the public. Funded by a $40 million grant from the W.M. Keck Foundation, the National Academies Keck Futures Initiative is a 15-year effort to catalyze interdisciplinary inquiry and to enhance communication among researchers, funding agencies, universities, and the general publicâ€"with the object of stimulating interdisciplinary research at the most exciting frontiers. The Futures Initiative builds on three pillars of vital and sustained research: interdisciplinary encounters that counterbalance specialization and isolation; the identification and exploration of new research topics; and communication that bridges languages, cultures, habits of thought, and institutions. Toward these goals, the National Academies Keck Futures Initiative incorporates three core activities each year: Futures conferences, Futures grants, and National Academies Communication Awards.


Nanopatterning and Nanoscale Devices for Biological Applications

Nanopatterning and Nanoscale Devices for Biological Applications

Author: Seila Šelimović

Publisher: CRC Press

Published: 2017-12-19

Total Pages: 417

ISBN-13: 146658632X

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Nanoscale techniques and devices have had an explosive influence on research in life sciences and bioengineering. Reflecting this influence, Nanopatterning and Nanoscale Devices for Biological Applications provides valuable insight into the latest developments in nanoscale technologies for the study of biological systems. Written and edited by experts in the field, this first-of-its-kind collection of topics: Covers device fabrication methods targeting the substrate on the nanoscale through surface modification Explores the generation of nanostructured biointerfaces and bioelectronics elements Examines microfluidically generated droplets as reactors enabling nanoscale sample preparation and analysis Gives an overview of key biosensors and integrated devices with nanoscale functionalities Discusses the biological applications of nanoscale devices, including a review of nanotechnology in tissue engineering Readers gain a deep understanding of the cutting-edge applications of nanotechnologies in biological engineering, and learn how to apply the relevant scientific concepts to their own research. Nanopatterning and Nanoscale Devices for Biological Applications is the definitive reference for researchers in engineering, biology, and biomedicine, and for anyone exploring the newest trends in this innovative field.


Riboswitches as Targets and Tools

Riboswitches as Targets and Tools

Author:

Publisher: Academic Press

Published: 2015-01-12

Total Pages: 468

ISBN-13: 0128013362

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This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in riboswitches as targets and tools and contains sections on such topics as constructing and optimizing artificial riboswitches, live cell imaging and intracellular sensors with artificial riboswitches, conditional control of gene expression with artificial riboswitches, using artificial riboswitches for protein evolution and pathway optimization, and anti-riboswitch drug screens. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in riboswitches as targets and tools - Contains sections on such topics as constructing and optimizing artificial riboswitches, synthetic biology: live cell imaging and intracellular sensors with artificial riboswitches, synthetic biology: conditional control of gene expression with artificial riboswitches, synthetic biology: using artificial riboswitches for protein evolution and pathway optimization, anti-riboswitches drug screens


Polytope Projects

Polytope Projects

Author: Octavian Iordache

Publisher: CRC Press

Published: 2013-10-15

Total Pages: 233

ISBN-13: 1482204657

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How do you know what works and what doesn't? This book contains case studies highlighting the power of polytope projects for complex problem solving. Any sort of combinational problem characterized by a large variety of possibly complex constructions and deconstructions based on simple building blocks can be studied in a similar way. Although the m


Chaos Theory

Chaos Theory

Author: Mykhaylo Andriychuk

Publisher: BoD – Books on Demand

Published: 2024-05-22

Total Pages: 92

ISBN-13: 1837681228

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Chaos Theory – Recent Advances, New Perspectives and Applications provides a comprehensive overview of chaos theory. It includes five chapters that discuss the history and development of chaos theory, the effectiveness of a chaos auto-associated model based on the Chebyshev-type activation function, neurite morphology, chemical self-replication, and the use of chaotic small particles to create materials with specific refractive index and magnetic permeability.


Targeting Functional Centers of the Ribosome

Targeting Functional Centers of the Ribosome

Author: Chen Davidovich

Publisher: Springer Science & Business Media

Published: 2011-02-02

Total Pages: 85

ISBN-13: 3642169317

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This thesis describes research into the mode of function, inhibition, and evolution of the ribosomal catalytic center, the Peptidyl Transferase Center (PTC)--research that has already led to attempts at improving PTC antibiotics. The PhD candidate carried out two parallel studies. One using a combination of X-ray crystallography, biochemistry, molecular biology, and theoretical studies to obtain crystal structures of ribosomal particles with antibiotics that target the PTC, revealing the modes of action, resistance, cross-resistance and discrimination between ribosomes of eubacterial pathogens and eukaryotic hosts. In the second parallel study, the candidate synthesized a ribosomal substructure--one that may represent the minimal entity capable of catalyzing peptide bond formation--shedding light on the origin of the ribosome itself.


Live Long and Evolve

Live Long and Evolve

Author: Mohamed A. F. Noor

Publisher: Princeton University Press

Published: 2020-02-25

Total Pages: 210

ISBN-13: 0691203938

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"In Star Trek, crew members travel to unusual planets, meet diverse beings, and encounter unique civilizations. In these remarkable space adventures, does Star Trek reflect biology and evolution as we know it? What can the science in the science fiction of Star Trek teach us?"--Back cover