The Experts below are selected from a list of 306 Experts worldwide ranked by ideXlab platform
Alan M Lambowitz - One of the best experts on this subject based on the ideXlab platform.
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targeted and random Bacterial Gene disruption using a group ii intron targetron vector containing a retrotransposition activated selectable marker
Nucleic Acids Research, 2003Co-Authors: Jin Zhong, Michael Karberg, Alan M LambowitzAbstract:Mobile group II introns have been used to develop a novel class of Gene targeting vectors, targetrons, which employ base pairing for DNA target recognition and can thus be programmed to insert into any desired target DNA. Here, we have developed a targetron containing a retrotransposition-activated selectable marker (RAM), which enables one-step Bacterial Gene disruption at near 100% efficiency after selection. The targetron can be Generated via PCR without cloning, and after intron integration, the marker Gene can be excised by recombination between flanking Flp recombinase sites, enabling multiple sequential disruptions. We also show that a RAM-targetron with randomized target site recognition sequences yields single insertions throughout the Escherichia coli genome, creating a Gene knockout library. Analysis of the randomly selected insertion sites provides further insight into group II intron target site recognition rules. It also suggests that a subset of retrohoming events may occur by using a primer Generated during DNA replication, and reveals a previously unsuspected bias for group II intron insertion near the chromosome replication origin. This insertional bias likely reflects at least in part the higher copy number of origin proximal Genes, but interaction with the replication machinery or other features of DNA structure or packaging may also contribute.
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targeted and random Bacterial Gene disruption using a group ii intron targetron vector containing a retrotransposition activated selectable marker
Nucleic Acids Research, 2003Co-Authors: Jin Zhong, Michael Karberg, Alan M LambowitzAbstract:Mobile group II introns have been used to develop a novel class of Gene targeting vectors, targetrons, which employ base pairing for DNA target recognition and can thus be programmed to insert into any desired target DNA. Here, we have developed a targetron containing a retrotransposition-activated selectable marker (RAM), which enables one-step Bacterial Gene disruption at near 100% efficiency after selection. The targetron can be Generated via PCR without cloning, and after intron integration, the marker Gene can be excised by recombination between flanking Flp recombinase sites, enabling multiple sequential disruptions. We also show that a RAM-targetron with randomized target site recognition sequences yields single insertions throughout the Escherichia coli genome, creating a Gene knockout library. Analysis of the randomly selected insertion sites provides further insight into group II intron target site recognition rules. It also suggests that a subset of retrohoming events may occur by using a primer Generated during DNA replication, and reveals a previously unsuspected bias for group II intron insertion near the chromosome replication origin. This insertional bias likely reflects at least in part the higher copy number of origin proximal Genes, but interaction with the replication machinery or other features of DNA structure or packaging may also contribute.
Julio Collado-vides - One of the best experts on this subject based on the ideXlab platform.
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Redefining fundamental concepts of transcription initiation in bacteria
Nature Reviews Genetics, 2020Co-Authors: Citlalli Mejía-almonte, Stephen J. W. Busby, Joseph T. Wade, Jacques Helden, Adam P. Arkin, Gary D. Stormo, Karen Eilbeck, Bernhard O. Palsson, James E. Galagan, Julio Collado-videsAbstract: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. In this Expert Recommendation, the authors review the definitions of classic concepts relating to Bacterial Gene regulation, with a focus on transcription initiation, and suggest up-to-date, precise definitions to provide a reference for knowledge representation, modelling and future research on Bacterial Gene regulation.
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Redefining fundamental concepts of transcription initiation in bacteria
Nature Reviews Genetics, 2020Co-Authors: Citlalli Mejía-almonte, Gary D. Stormo, Karen Eilbeck, James E. Galagan, Stephen Busby, Joseph Wade, Jacques Van Helden, Adam Arkin, Bernhard Palsson, Julio Collado-videsAbstract: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.
Ronald R Breaker - One of the best experts on this subject based on the ideXlab platform.
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regulation of Bacterial Gene expression by riboswitches
Annual Review of Microbiology, 2005Co-Authors: Wade C Winkler, Ronald R BreakerAbstract:AbstractRiboswitches are structured domains that usually reside in the noncoding regions of mRNAs, where they bind metabolites and control Gene expression. Like their protein counterparts, these RNA Gene control elements form highly specific binding pockets for the target metabolite and undergo allosteric changes in structure. Numerous classes of riboswitches are present in bacteria and they comprise a common and robust metabolite-sensing system.
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Thiamine derivatives bind messenger RNAs directly to regulate Bacterial Gene expression
Nature, 2002Co-Authors: Wade Winkler, Ali Nahvi, Ronald R BreakerAbstract:Although proteins fulfil most of the requirements that biology has for structural and functional components such as enzymes and receptors, RNA can also serve in these capacities. For example, RNA has sufficient structural plasticity to form ribozyme and receptor elements that exhibit considerable enzymatic power and binding specificity. Moreover, these activities can be combined to create allosteric ribozymes that are modulated by effector molecules. It has also been proposed that certain messenger RNAs might use allosteric mechanisms to mediate regulatory responses depending on specific metabolites. We report here that mRNAs encoding enzymes involved in thiamine (vitamin B(1)) biosynthesis in Escherichia coli can bind thiamine or its pyrophosphate derivative without the need for protein cofactors. The mRNA-effector complex adopts a distinct structure that sequesters the ribosome-binding site and leads to a reduction in Gene expression. This metabolite-sensing regulatory system provides an example of a 'riboswitch' whose evolutionary origin might pre-date the emergence of proteins.
Jin Zhong - One of the best experts on this subject based on the ideXlab platform.
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targeted and random Bacterial Gene disruption using a group ii intron targetron vector containing a retrotransposition activated selectable marker
Nucleic Acids Research, 2003Co-Authors: Jin Zhong, Michael Karberg, Alan M LambowitzAbstract:Mobile group II introns have been used to develop a novel class of Gene targeting vectors, targetrons, which employ base pairing for DNA target recognition and can thus be programmed to insert into any desired target DNA. Here, we have developed a targetron containing a retrotransposition-activated selectable marker (RAM), which enables one-step Bacterial Gene disruption at near 100% efficiency after selection. The targetron can be Generated via PCR without cloning, and after intron integration, the marker Gene can be excised by recombination between flanking Flp recombinase sites, enabling multiple sequential disruptions. We also show that a RAM-targetron with randomized target site recognition sequences yields single insertions throughout the Escherichia coli genome, creating a Gene knockout library. Analysis of the randomly selected insertion sites provides further insight into group II intron target site recognition rules. It also suggests that a subset of retrohoming events may occur by using a primer Generated during DNA replication, and reveals a previously unsuspected bias for group II intron insertion near the chromosome replication origin. This insertional bias likely reflects at least in part the higher copy number of origin proximal Genes, but interaction with the replication machinery or other features of DNA structure or packaging may also contribute.
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targeted and random Bacterial Gene disruption using a group ii intron targetron vector containing a retrotransposition activated selectable marker
Nucleic Acids Research, 2003Co-Authors: Jin Zhong, Michael Karberg, Alan M LambowitzAbstract:Mobile group II introns have been used to develop a novel class of Gene targeting vectors, targetrons, which employ base pairing for DNA target recognition and can thus be programmed to insert into any desired target DNA. Here, we have developed a targetron containing a retrotransposition-activated selectable marker (RAM), which enables one-step Bacterial Gene disruption at near 100% efficiency after selection. The targetron can be Generated via PCR without cloning, and after intron integration, the marker Gene can be excised by recombination between flanking Flp recombinase sites, enabling multiple sequential disruptions. We also show that a RAM-targetron with randomized target site recognition sequences yields single insertions throughout the Escherichia coli genome, creating a Gene knockout library. Analysis of the randomly selected insertion sites provides further insight into group II intron target site recognition rules. It also suggests that a subset of retrohoming events may occur by using a primer Generated during DNA replication, and reveals a previously unsuspected bias for group II intron insertion near the chromosome replication origin. This insertional bias likely reflects at least in part the higher copy number of origin proximal Genes, but interaction with the replication machinery or other features of DNA structure or packaging may also contribute.
Citlalli Mejía-almonte - One of the best experts on this subject based on the ideXlab platform.
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Redefining fundamental concepts of transcription initiation in bacteria
Nature Reviews Genetics, 2020Co-Authors: Citlalli Mejía-almonte, Stephen J. W. Busby, Joseph T. Wade, Jacques Helden, Adam P. Arkin, Gary D. Stormo, Karen Eilbeck, Bernhard O. Palsson, James E. Galagan, Julio Collado-videsAbstract: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. In this Expert Recommendation, the authors review the definitions of classic concepts relating to Bacterial Gene regulation, with a focus on transcription initiation, and suggest up-to-date, precise definitions to provide a reference for knowledge representation, modelling and future research on Bacterial Gene regulation.
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Redefining fundamental concepts of transcription initiation in bacteria
Nature Reviews Genetics, 2020Co-Authors: Citlalli Mejía-almonte, Gary D. Stormo, Karen Eilbeck, James E. Galagan, Stephen Busby, Joseph Wade, Jacques Van Helden, Adam Arkin, Bernhard Palsson, Julio Collado-videsAbstract: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.