D. Dykhuizen | SUNY: Stony Brook University (original) (raw)
Papers by D. Dykhuizen
Molecular Biology and Evolution, 2009
Journal of Clinical Microbiology, 1998
In recent years, the utility of serum-based diagnostic testing for Lyme disease has improved subs... more In recent years, the utility of serum-based diagnostic testing for Lyme disease has improved substantially; however, recovery by culture of the bacterium from skin biopsies of suspected patients is still the only definitive laboratory test. Reinfection of patients has been assumed to occur but as yet has not been documented by serial isolates from the same person. We present a case of culture-confirmed reinfection of a patient in Menominee County, Michigan. Borrelia burgdorferi was isolated from the skin punch biopsy specimens during each episode of erythema migrans (EM) and was subjected to molecular strain typing, genetic analysis of two outer surface protein genes, protein profile analysis, and serum antibody response testing. Results show that these isolates are distinct strains of the bacterium and that the two episodes of EM were caused by independent infections. This report describes the documented, culture-confirmed reinfection of a human by two different strains of B. burgd...
Genetics, 1980
We have used gluconate-limited chemostats to study selective differences between isogenic strains... more We have used gluconate-limited chemostats to study selective differences between isogenic strains of Escherichia coli K12 into which four naturally occurring alleles coding for allozymes of 6-phosphogluconate dehydrogenase (6PGD) had been transferred. The limit of detectability of selection with our procedures is a selection coefficient of 0.5%. In the normal E. coli K12 genetic background, all alleles are selectively neutral or nearly neutral. The absence of detectable selection does, however, depend on genetic background and on such environmental factors as cell density. In a genetic background containing a mutation that cuts off the alternative metabolic route for 6-phosphogluconate, selection between allozymes can be detected, and the selection is in the direction expected from the measured apparent Km values of the allozymes. Even when the alternative metabolic route is not blocked by mutation, one of the 6PGD allozymes has a detrimental, but density-dependent, interaction with...
Genetics, 1980
We have used gluconate-limited chemostats to study selective differences between isogenic strains... more We have used gluconate-limited chemostats to study selective differences between isogenic strains of Escherichia coli K12 into which four naturally occurring alleles coding for allozymes of 6-phosphogluconate dehydrogenase (6PGD) had been transferred. The limit of detectability of selection with our procedures is a selection coefficient of 0.5%. In the normal E. coli K12 genetic background, all alleles are selectively neutral or nearly neutral. The absence of detectable selection does, however, depend on genetic background and on such environmental factors as cell density. In a genetic background containing a mutation that cuts off the alternative metabolic route for 6-phosphogluconate, selection between allozymes can be detected, and the selection is in the direction expected from the measured apparent Km values of the allozymes. Even when the alternative metabolic route is not blocked by mutation, one of the 6PGD allozymes has a detrimental, but density-dependent, interaction with...
Microbios, 1978
A lambda prophage increases the competitive ability of E. coli K12 in a glucose-limited chemostat... more A lambda prophage increases the competitive ability of E. coli K12 in a glucose-limited chemostat. This phenomenon does not involve the lambdarex gene. Expression of the lambdarex gene conditionally decreases fitness in two ways: (1) it causes malT- but not malT+ lysogens to be at a selective disadvantage in competition with non-lysogens. (2) During adaptation to slow, glucose-limited chemostat growth from rapid, glucose-excess flask growth, expression of the lambdarex gene transiently decreases the growth rate when compared to the non-lysogen.
Encyclopedia of Evolutionary Biology, 2016
Lyme borreliosis, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne ... more Lyme borreliosis, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne disease in North America and Western Europe. As the major delayed immune response in humans, a better understanding of the major outer surface lipoproteins OspA and OspB are of much interest. These proteins have been shown to exhibit three distinct phylogenetic genotypes based on their DNA sequences.
Genetics, 1987
A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been ... more A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS1, IS2, IS3, IS4, IS5 and IS30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with...
Methods in enzymology, 1979
Evolution in Health and Disease, 2007
Trends in Ecology & Evolution, 1990
Philosophical Transactions of the Royal Society B: Biological Sciences, 1986
It is proposed that certain families of transposable elements originally evolved in plasmids and ... more It is proposed that certain families of transposable elements originally evolved in plasmids and functioned in forming replicon fusions to aid in the horizontal transmission of non-conjugational plasmids. This hypothesis is supported by the finding that the transposable elements Tn 3 and γδ are found almost exclusively in plasmids, and also by the distribution of the unrelated insertion sequences IS4 and IS 5 among a reference collection of 67 natural isolates of Escherichia coli. Each insertion sequence was found to be present in only about one-third of the strains. Among the ten strains found to contain both insertion sequences, the number of copies of the elements was negatively correlated. With respect to IS 5 , approximately half of the strains containing a chromosomal copy of the insertion element also contained copies within the plasmid complement of the strain.
Applied and Environmental Microbiology, 2012
ABSTRACTMultilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeepi... more ABSTRACTMultilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeeping loci in the bacterial chromosome and has provided detailed descriptions of the population structure of bacterial species important to human health. However, even strains with identical MLST profiles (known as sequence types or STs) may possess distinct genotypes, which enable different eco- or pathotypic lifestyles. Here we describe a two-locus, sequence-based typing scheme forEscherichia colithat utilizes a 489-nucleotide (nt) internal fragment offimH(encoding the type 1 fimbrial adhesin) and the 469-nt internalfumCfragment used in standard MLST. Based on sequence typing of 191 model commensal and pathogenic isolates plus 853 freshly isolated clinicalE. colistrains, this 2-locus approach—which we call CH (fumC/fimH) typing—consistently yielded more haplotypes than standard 7-locus MLST, splitting large STs into multiple clonal subgroups and often distinguishing different within-ST ec...
Trends in Ecology & Evolution, 1990
Proceedings of the Royal Society B: Biological Sciences, 2008
Molecular Biology and Evolution, 2009
Journal of Clinical Microbiology, 1998
In recent years, the utility of serum-based diagnostic testing for Lyme disease has improved subs... more In recent years, the utility of serum-based diagnostic testing for Lyme disease has improved substantially; however, recovery by culture of the bacterium from skin biopsies of suspected patients is still the only definitive laboratory test. Reinfection of patients has been assumed to occur but as yet has not been documented by serial isolates from the same person. We present a case of culture-confirmed reinfection of a patient in Menominee County, Michigan. Borrelia burgdorferi was isolated from the skin punch biopsy specimens during each episode of erythema migrans (EM) and was subjected to molecular strain typing, genetic analysis of two outer surface protein genes, protein profile analysis, and serum antibody response testing. Results show that these isolates are distinct strains of the bacterium and that the two episodes of EM were caused by independent infections. This report describes the documented, culture-confirmed reinfection of a human by two different strains of B. burgd...
Genetics, 1980
We have used gluconate-limited chemostats to study selective differences between isogenic strains... more We have used gluconate-limited chemostats to study selective differences between isogenic strains of Escherichia coli K12 into which four naturally occurring alleles coding for allozymes of 6-phosphogluconate dehydrogenase (6PGD) had been transferred. The limit of detectability of selection with our procedures is a selection coefficient of 0.5%. In the normal E. coli K12 genetic background, all alleles are selectively neutral or nearly neutral. The absence of detectable selection does, however, depend on genetic background and on such environmental factors as cell density. In a genetic background containing a mutation that cuts off the alternative metabolic route for 6-phosphogluconate, selection between allozymes can be detected, and the selection is in the direction expected from the measured apparent Km values of the allozymes. Even when the alternative metabolic route is not blocked by mutation, one of the 6PGD allozymes has a detrimental, but density-dependent, interaction with...
Genetics, 1980
We have used gluconate-limited chemostats to study selective differences between isogenic strains... more We have used gluconate-limited chemostats to study selective differences between isogenic strains of Escherichia coli K12 into which four naturally occurring alleles coding for allozymes of 6-phosphogluconate dehydrogenase (6PGD) had been transferred. The limit of detectability of selection with our procedures is a selection coefficient of 0.5%. In the normal E. coli K12 genetic background, all alleles are selectively neutral or nearly neutral. The absence of detectable selection does, however, depend on genetic background and on such environmental factors as cell density. In a genetic background containing a mutation that cuts off the alternative metabolic route for 6-phosphogluconate, selection between allozymes can be detected, and the selection is in the direction expected from the measured apparent Km values of the allozymes. Even when the alternative metabolic route is not blocked by mutation, one of the 6PGD allozymes has a detrimental, but density-dependent, interaction with...
Microbios, 1978
A lambda prophage increases the competitive ability of E. coli K12 in a glucose-limited chemostat... more A lambda prophage increases the competitive ability of E. coli K12 in a glucose-limited chemostat. This phenomenon does not involve the lambdarex gene. Expression of the lambdarex gene conditionally decreases fitness in two ways: (1) it causes malT- but not malT+ lysogens to be at a selective disadvantage in competition with non-lysogens. (2) During adaptation to slow, glucose-limited chemostat growth from rapid, glucose-excess flask growth, expression of the lambdarex gene transiently decreases the growth rate when compared to the non-lysogen.
Encyclopedia of Evolutionary Biology, 2016
Lyme borreliosis, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne ... more Lyme borreliosis, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne disease in North America and Western Europe. As the major delayed immune response in humans, a better understanding of the major outer surface lipoproteins OspA and OspB are of much interest. These proteins have been shown to exhibit three distinct phylogenetic genotypes based on their DNA sequences.
Genetics, 1987
A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been ... more A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS1, IS2, IS3, IS4, IS5 and IS30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with...
Methods in enzymology, 1979
Evolution in Health and Disease, 2007
Trends in Ecology & Evolution, 1990
Philosophical Transactions of the Royal Society B: Biological Sciences, 1986
It is proposed that certain families of transposable elements originally evolved in plasmids and ... more It is proposed that certain families of transposable elements originally evolved in plasmids and functioned in forming replicon fusions to aid in the horizontal transmission of non-conjugational plasmids. This hypothesis is supported by the finding that the transposable elements Tn 3 and γδ are found almost exclusively in plasmids, and also by the distribution of the unrelated insertion sequences IS4 and IS 5 among a reference collection of 67 natural isolates of Escherichia coli. Each insertion sequence was found to be present in only about one-third of the strains. Among the ten strains found to contain both insertion sequences, the number of copies of the elements was negatively correlated. With respect to IS 5 , approximately half of the strains containing a chromosomal copy of the insertion element also contained copies within the plasmid complement of the strain.
Applied and Environmental Microbiology, 2012
ABSTRACTMultilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeepi... more ABSTRACTMultilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeeping loci in the bacterial chromosome and has provided detailed descriptions of the population structure of bacterial species important to human health. However, even strains with identical MLST profiles (known as sequence types or STs) may possess distinct genotypes, which enable different eco- or pathotypic lifestyles. Here we describe a two-locus, sequence-based typing scheme forEscherichia colithat utilizes a 489-nucleotide (nt) internal fragment offimH(encoding the type 1 fimbrial adhesin) and the 469-nt internalfumCfragment used in standard MLST. Based on sequence typing of 191 model commensal and pathogenic isolates plus 853 freshly isolated clinicalE. colistrains, this 2-locus approach—which we call CH (fumC/fimH) typing—consistently yielded more haplotypes than standard 7-locus MLST, splitting large STs into multiple clonal subgroups and often distinguishing different within-ST ec...
Trends in Ecology & Evolution, 1990
Proceedings of the Royal Society B: Biological Sciences, 2008