D Revie - Academia.edu (original) (raw)

Papers by D Revie

Research paper thumbnail of Kinetic analysis for optimization of DNA ligation reactions

Nucleic acids research, 1988

Kinetic equations describing ligation of DNA to circular recombinant forms were developed and sol... more Kinetic equations describing ligation of DNA to circular recombinant forms were developed and solved for four types of reactions: (a) a homogeneous population of singly restricted DNA fragments, (b) insertion of singly restricted insert into vector, (c) forced directional insertion of doubly restricted insert into vector, and (d) insertion of singly restricted insert into phosphatased vector. The effects of varying vector and insert sizes, starting concentrations, and phosphatase treatment on the yield of circular 1:1 recombinants were analyzed. Selected theoretical predictions were experimentally tested and verified. Our suggestions on optimizing ligation reactions in several cases are at variance with common practice. For example, optimum conditions in case (b) and (d) ligations are best specified as individual insert and vector concentrations rather than as insert/vector molar ratios, except in case (d) ligations involving very small insert size. In case (c) ligations, highest efficiencies are obtained when both vector and insert are at relatively low concentration.

Research paper thumbnail of Covalent association of protein with replicative form DNA of parvovirus H-1

Proceedings of the National Academy of Sciences, 1979

The double-stranded replicative form (RF) DNA of the autonomous parvovirus H-1 can be isolated fr... more The double-stranded replicative form (RF) DNA of the autonomous parvovirus H-1 can be isolated from infected cells in a covalent complex with protein. The protein is present on most or all of the RF DNA, including actively replicating molecules, and is associated with the 5'-terminal endonuclease Hae III fragments of both the viral and complementary strands of RF. The size of the protein is estimated to be 60,000-70,000 daltons from its effect on buoyant density of DNA. DNA with covalently bound protein has not been found in H-1 virions.

Research paper thumbnail of P.185 Analysis of the 5′UTR of in vitro replicated human hepatitis C virus

Journal of Clinical Virology, 2006

Research paper thumbnail of Research Analysis of the 5'UTR of HCV genotype 3 grown in vitro in human B cells, T cells, and macrophages

Background: Previously, we have reported the isolation and molecular characterization of human He... more Background: Previously, we have reported the isolation and molecular characterization of human Hepatitis C virus genotype 1 (HCV-1) from infected patients. We are now reporting an analysis of HCV obtained from patients infected with HCV genotype ...

Research paper thumbnail of Analysis of in vitro replicated human hepatitis C virus (HCV) for the determination of genotypes and quasispecies

Virol J, 2006

Isolation and self-replication of infectious HCV has been a difficult task. However, this is need... more Isolation and self-replication of infectious HCV has been a difficult task. However, this is needed for the purposes of developing rational drugs and for the analysis of the natural virus. Our recent report of an in vitro system for the isolation of human HCV from ...

Research paper thumbnail of Discovery of significant variants containing large deletions in the 5'UTR of human hepatitis C virus (HCV)

Virol J, 2006

We recently reported the isolation and in vitro replication of hepatitis C virus. These isolates ... more We recently reported the isolation and in vitro replication of hepatitis C virus. These isolates were termed CIMM-HCV and analyzed to establish genotypes and subtypes, which are reported elsewhere. During this analysis, an HCV isolated from a patient was ...

Research paper thumbnail of Transmission of human hepatitis C virus from patients in secondary cells for long term culture

Virology …, 2005

Infection by human hepatitis C virus (HCV) is the principal cause of post-transfusion hepatitis a... more Infection by human hepatitis C virus (HCV) is the principal cause of post-transfusion hepatitis and chronic liver diseases worldwide. A reliable in vitro culture system for the isolation and analysis of this virus is not currently available, and, as a consequence, HCV pathogenesis is ...

Research paper thumbnail of Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

G3 (Bethesda, Md.), Jan 4, 2015

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila mela... more The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have higher transposon density (25%-50%) than euchromatic reference regions (3%-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% versus 11%-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density ...

Research paper thumbnail of The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Cell Biology Education, 2010

Genomics is not only essential for students to understand biology but also provides unprecedented... more Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre-and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Research paper thumbnail of Kinetic analysis for optimization of DNA ligation reactions

Nucleic acids research, 1988

Kinetic equations describing ligation of DNA to circular recombinant forms were developed and sol... more Kinetic equations describing ligation of DNA to circular recombinant forms were developed and solved for four types of reactions: (a) a homogeneous population of singly restricted DNA fragments, (b) insertion of singly restricted insert into vector, (c) forced directional insertion of doubly restricted insert into vector, and (d) insertion of singly restricted insert into phosphatased vector. The effects of varying vector and insert sizes, starting concentrations, and phosphatase treatment on the yield of circular 1:1 recombinants were analyzed. Selected theoretical predictions were experimentally tested and verified. Our suggestions on optimizing ligation reactions in several cases are at variance with common practice. For example, optimum conditions in case (b) and (d) ligations are best specified as individual insert and vector concentrations rather than as insert/vector molar ratios, except in case (d) ligations involving very small insert size. In case (c) ligations, highest efficiencies are obtained when both vector and insert are at relatively low concentration.

Research paper thumbnail of Covalent association of protein with replicative form DNA of parvovirus H-1

Proceedings of the National Academy of Sciences, 1979

The double-stranded replicative form (RF) DNA of the autonomous parvovirus H-1 can be isolated fr... more The double-stranded replicative form (RF) DNA of the autonomous parvovirus H-1 can be isolated from infected cells in a covalent complex with protein. The protein is present on most or all of the RF DNA, including actively replicating molecules, and is associated with the 5'-terminal endonuclease Hae III fragments of both the viral and complementary strands of RF. The size of the protein is estimated to be 60,000-70,000 daltons from its effect on buoyant density of DNA. DNA with covalently bound protein has not been found in H-1 virions.

Research paper thumbnail of P.185 Analysis of the 5′UTR of in vitro replicated human hepatitis C virus

Journal of Clinical Virology, 2006

Research paper thumbnail of Research Analysis of the 5'UTR of HCV genotype 3 grown in vitro in human B cells, T cells, and macrophages

Background: Previously, we have reported the isolation and molecular characterization of human He... more Background: Previously, we have reported the isolation and molecular characterization of human Hepatitis C virus genotype 1 (HCV-1) from infected patients. We are now reporting an analysis of HCV obtained from patients infected with HCV genotype ...

Research paper thumbnail of Analysis of in vitro replicated human hepatitis C virus (HCV) for the determination of genotypes and quasispecies

Virol J, 2006

Isolation and self-replication of infectious HCV has been a difficult task. However, this is need... more Isolation and self-replication of infectious HCV has been a difficult task. However, this is needed for the purposes of developing rational drugs and for the analysis of the natural virus. Our recent report of an in vitro system for the isolation of human HCV from ...

Research paper thumbnail of Discovery of significant variants containing large deletions in the 5'UTR of human hepatitis C virus (HCV)

Virol J, 2006

We recently reported the isolation and in vitro replication of hepatitis C virus. These isolates ... more We recently reported the isolation and in vitro replication of hepatitis C virus. These isolates were termed CIMM-HCV and analyzed to establish genotypes and subtypes, which are reported elsewhere. During this analysis, an HCV isolated from a patient was ...

Research paper thumbnail of Transmission of human hepatitis C virus from patients in secondary cells for long term culture

Virology …, 2005

Infection by human hepatitis C virus (HCV) is the principal cause of post-transfusion hepatitis a... more Infection by human hepatitis C virus (HCV) is the principal cause of post-transfusion hepatitis and chronic liver diseases worldwide. A reliable in vitro culture system for the isolation and analysis of this virus is not currently available, and, as a consequence, HCV pathogenesis is ...

Research paper thumbnail of Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

G3 (Bethesda, Md.), Jan 4, 2015

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila mela... more The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have higher transposon density (25%-50%) than euchromatic reference regions (3%-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% versus 11%-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density ...

Research paper thumbnail of The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Cell Biology Education, 2010

Genomics is not only essential for students to understand biology but also provides unprecedented... more Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre-and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.