@article {789,
	title = {Animal propagation and genomic survey of a genotype 1 isolate of Cryptosporidium parvum.},
	journal = {Mol Biochem Parasitol},
	volume = {108},
	year = {2000},
	month = {2000 May},
	pages = {187-97},
	abstract = {Human cryptosporidiosis is attributed to two major Cryptosporidium parvum genotypes of which type 1 appears to be the predominant. Most laboratory investigations however are performed using genotype 2 isolates, the only type which readily infects laboratory animals. So far type 1 has only been identified in humans and primates. A type 1 isolate, obtained from an individual with HIV and cryptosporidiosis, was successfully adapted to propagate in gnotobiotic piglets. Genotypic characterization of oocyst DNA from this isolate using multiple restriction fragment length polymorphisms, a genotype-specific PCR marker, and direct sequence analysis of two polymorphic loci confirmed that this isolate, designated NEMC1, is indeed type 1. No changes in the genetic profile were identified during multiple passages in piglets. In contrast, the time period between infection and onset of fecal oocyst shedding, an indicator of adaptation, decreased with increasing number of passages. Consistent with other type 1 isolates, NEMC1 failed to infect mice. A preliminary survey of the NEMC1 genome covering approximately 2\% of the genome and encompassing 200 kb of unique sequence showed an average similarity of approximately 95\% between type 1 and 2 sequences. Twenty-four percent of the NEMC1 sequences were homologous to previously determined genotype 2 C. parvum sequences. To our knowledge, this is the first successful serial propagation of genotype 1 in animals, which should facilitate characterization of the unique features of this human pathogen.},
	keywords = {Animals, Cryptosporidiosis, Cryptosporidium parvum, Genome, Protozoan, Genotype, Germ-Free Life, Humans, Mice, Mice, Knockout, Molecular Sequence Data, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Sequence Analysis, DNA, Swine},
	issn = {0166-6851},
	author = {Widmer, G and Akiyoshi, D and Buckholt, M A and Feng, X and Rich, S M and Deary, K M and Bowman, C A and Xu, P and Wang, Y and Wang, X and Buck, G A and Tzipori, S}
}
@article {787,
	title = {Extensive polymorphism in Cryptosporidium parvum identified by multilocus microsatellite analysis.},
	journal = {Appl Environ Microbiol},
	volume = {66},
	year = {2000},
	month = {2000 Aug},
	pages = {3344-9},
	abstract = {Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.},
	keywords = {Animals, Base Sequence, Cattle, Cryptosporidiosis, Cryptosporidium parvum, DNA, Protozoan, Humans, Karyotyping, Mice, Mice, Knockout, Microsatellite Repeats, Molecular Sequence Data, Polymerase Chain Reaction, Polymorphism, Genetic, Sequence Analysis, DNA},
	issn = {0099-2240},
	author = {Feng, X and Rich, S M and Akiyoshi, D and Tumwine, J K and Kekitiinwa, A and Nabukeera, N and Tzipori, S and Widmer, G}
}
@article {784,
	title = {Genetic variation and the recent worldwide expansion of Plasmodium falciparum.},
	journal = {Gene},
	volume = {261},
	year = {2000},
	month = {2000 Dec 30},
	pages = {161-70},
	abstract = {Plasmodium falciparum, the agent of human malignant malaria, diverged from Plasmodium reichenowi, the chimpanzee parasite, about the time the human and chimpanzee lineages diverged from each other. The absence of synonymous nucleotide variation at ten loci indicates that the world populations of P. falciparum derive most recently from one single strain, or {\textquoteright}cenancestor,{\textquoteright} which lived a few thousand years ago. Antigenic genes of P. falciparum (such as Csp, Msp-1, and Msp-2) exhibit numerous polymorphisms that have been estimated to be millions of years old. We have discovered in these antigenic genes short repetitive sequences that distort the alignment of alleles and account for the apparent old age of the polymorphisms. The processes of intragenic recombination that generate the repeats occur at rates about 10(-3) to 10(-2), several orders of magnitude greater than the typical mutational process of nucleotide substitutions. We conclude that the antigenic polymorphisms of P. falciparum are consistent with a recent expansion of the world populations of the parasite from a cenancestor that lived in tropical Africa a few thousand years ago.},
	keywords = {Animals, Antigens, Protozoan, Base Sequence, Genetic Variation, Merozoite Surface Protein 1, Molecular Sequence Data, Phylogeny, Plasmodium, Plasmodium falciparum, Polymorphism, Genetic, Protozoan Proteins, Repetitive Sequences, Nucleic Acid, RNA, Ribosomal, Sequence Homology, Nucleic Acid, Species Specificity},
	issn = {0378-1119},
	author = {Ayala, F J and Rich, S M}
}
@article {786,
	title = {The origin of antigenic diversity in Plasmodium falciparum.},
	journal = {Parasitol Today},
	volume = {16},
	year = {2000},
	month = {2000 Sep},
	pages = {390-6},
	abstract = {Most studies of genetic variability of Plasmodium falciparum have focused on protein antigens and the genes that encode them. The consensus is that populations exhibit high levels of genetic polymorphism, most notably the genes encoding surface proteins of the merozoite (Msp1, Msp2) and the sporozoite (Csp). The age and derivation of this variation is a subject that warrants further careful consideration, as discussed here by Stephen Rich, Marcelo Ferreira and Francisco Ayala.},
	keywords = {Amino Acid Sequence, Animals, Antigens, Protozoan, Base Sequence, Genes, Protozoan, Genetic Variation, Merozoite Surface Protein 1, Molecular Sequence Data, Plasmodium falciparum, Protozoan Proteins, Sequence Homology},
	issn = {0169-4758},
	author = {Rich, S M and Ferreira, M U and Ayala, F J}
}
@article {788,
	title = {Population structure and recent evolution of Plasmodium falciparum.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {97},
	year = {2000},
	month = {2000 Jun 20},
	pages = {6994-7001},
	abstract = {Plasmodium falciparum is the agent of malignant malaria, one of mankind{\textquoteright}s most severe maladies. The parasite exhibits antigenic polymorphisms that have been postulated to be ancient. We have proposed that the extant world populations of P. falciparum have derived from one single parasite, a cenancestor, within the last 5, 000-50,000 years. This inference derives from the virtual or complete absence of synonymous nucleotide polymorphisms at genes not involved in immune or drug responses. Seeking to conciliate this claim with extensive antigenic polymorphism, we first note that allele substitutions or polymorphisms can arise very rapidly, even in a single generation, in large populations subject to strong natural selection. Second, new alleles can arise not only by single-nucleotide mutations, but also by duplication/deletion of short simple-repeat DNA sequences, a process several orders of magnitude faster than single-nucleotide mutation. We analyze three antigenic genes known to be extremely polymorphic: Csp, Msp-1, and Msp-2. We identify regions consisting of tandem or proximally repetitive short DNA sequences, including some previously unnoticed. We conclude that the antigenic polymorphisms are consistent with the recent origin of the world populations of P. falciparum inferred from the analysis of nonantigenic genes.},
	keywords = {Amino Acid Sequence, Animals, Base Sequence, Biological Evolution, Genes, Protozoan, Genetics, Population, Molecular Sequence Data, Plasmodium falciparum},
	issn = {0027-8424},
	author = {Rich, S M and Ayala, F J}
}
@article {790,
	title = {Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum.},
	journal = {Parassitologia},
	volume = {41},
	year = {1999},
	month = {1999 Sep},
	pages = {55-68},
	abstract = {We have investigated the evolution of Plasmodium parasites by analyzing DNA sequences of several genes. We reach the following conclusions: (1) The four human parasites, P. falciparum, P. malariae, P. ovale, and P. vivax are very remotely related to each other, so that their evolutionary divergence predates the origin of the hominids; several of these parasites became associated with the human lineage by lateral transfer from other hosts. (2) P. falciparum diverged from P. reichenowi about 8 million years ago, consistently with the time of divergence of the human lineage from the apes; a parsimonious inference is that falciparum has been associated with humans since the origin of the hominids. (3) P. malariae is genetically indistinguishable from P. brasilianum, a parasite of New World monkeys; and, similarly. (4) P. vivax is genetically indistinguishable from the New World monkey parasite P. simium. We infer in each of these two cases a very recent lateral transfer between the human and monkey hosts, and explore alternative hypotheses about the direction of the transfer. We have also investigated the population structure of P. falciparum by analyzing 10 genes and conclude that the extant world populations of this parasite have evolved from a single strain within the last several thousand years. The extensive polymorphisms observed in the highly repetitive central region of the Csp gene, as well as the apparently very divergent two classes of alleles at the Msa-1 gene, are consistent with this conclusion.},
	keywords = {Amino Acid Sequence, Animals, Base Sequence, DNA, Protozoan, Evolution, Molecular, Hominidae, Humans, Merozoite Surface Protein 1, Molecular Sequence Data, Plasmodium, Plasmodium falciparum, Polymorphism, Genetic, Sequence Alignment},
	issn = {0048-2951},
	author = {Ayala, F J and Escalante, A A and Rich, S M}
}
@article {795,
	title = {Heterogeneity of the internal transcribed spacer (ITS-2) region within individual deer ticks.},
	journal = {Insect Mol Biol},
	volume = {6},
	year = {1997},
	month = {1997 May},
	pages = {123-9},
	abstract = {To determine whether nuclear rDNA sequences provide a useful means for assessing the structure of populations of Ixodes ticks, we compared variability among copies of an internal transcribed spacer (ITS-2) sequence within individual ticks to the variability between ticks. At least 4\% of the nucleotides comprising this sequence vary among the copies present within individual ticks. ITS-2 diversity in each of two ticks is nearly half as great as that reported between ticks from geographically disparate populations. Because individual ticks retain ancestral polymorphism, ITS-2 variation does not accurately reflect descent relationships among these ticks. Sequencing single copies of PCR-amplified ITS-2 therefore does not permit assessment of the phylogenetic relationships among the I. ricinus-like ticks in eastern North America. We recommend caution in future analyses, and emphasize the importance of procedures designed to ensure that the many paralogous copies of the rDNA cistron have been sufficiently homogenized by concerted evolutionary processes. Such precautionary measures will make certain that phylogenetic trees based on these gene sequences reflect the phyletic relatedness of the biological species.},
	keywords = {Animals, Base Sequence, Deer, DNA, DNA, Ribosomal, Genetic Heterogeneity, Ixodes, Molecular Sequence Data},
	issn = {0962-1075},
	author = {Rich, S M and Rosenthal, B M and Telford, S R and Spielman, A and Hartl, D L and Ayala, F J}
}
@article {794,
	title = {Plasmodium falciparum antigenic diversity: evidence of clonal population structure.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {94},
	year = {1997},
	month = {1997 Nov 25},
	pages = {13040-5},
	abstract = {Plasmodium falciparum, the agent of malignant malaria, is one of mankind{\textquoteright}s most severe scourges. Efforts to develop preventive vaccines or remedial drugs are handicapped by the parasite{\textquoteright}s rapid evolution of drug resistance and protective antigens. We examine 25 DNA sequences of the gene coding for the highly polymorphic antigenic circumsporozoite protein. We observe total absence of silent nucleotide variation in the two nonrepeated regions of the gene. We propose that this absence reflects a recent origin (within several thousand years) of the world populations of P. falciparum from a single individual; the amino acid polymorphisms observed in these nonrepeat regions would result from strong natural selection. Analysis of these polymorphisms indicates that: (i) the incidence of recombination events does not increase with nucleotide distance; (ii) the strength of linkage disequilibrium between nucleotides is also independent of distance; and (iii) haplotypes in the two nonrepeat regions are correlated with one another, but not with the central repeat region they span. We propose two hypotheses: (i) variation in the highly polymorphic central repeat region arises by mitotic intragenic recombination, and (ii) the population structure of P. falciparum is clonal--a state of affairs that persists in spite of the necessary stage of physiological sexuality that the parasite must sustain in the mosquito vector to complete its life cycle.},
	keywords = {Amino Acid Sequence, Animals, Antigens, Protozoan, Molecular Sequence Data, Phylogeny, Plasmodium falciparum, Polymorphism, Genetic, Protozoan Proteins, Recombination, Genetic, Sequence Homology, Amino Acid},
	issn = {0027-8424},
	author = {Rich, S M and Hudson, R R and Ayala, F J}
}
@article {796,
	title = {Mosaic structure of plasmids from natural populations of Escherichia coli.},
	journal = {Genetics},
	volume = {143},
	year = {1996},
	month = {1996 Jul},
	pages = {1091-100},
	abstract = {The distribution of plasmids related to the fertility factor F was examined in the ECOR reference collection of Escherichia coli. Probes specific for four F-related genes were isolated and used to survey the collection by DNA hybridization. To estimate the genetic diversity of genes in F-like plasmids, DNA sequences were obtained for four plasmid genes. The phylogenetic relationships among the plasmids in the ECOR strains is very different from that of the strains themselves. This finding supports the view that plasmid transfer has been frequent within and between the major groups of ECOR. Furthermore, the sequences indicate that recombination between genes in plasmids takes place at a considerably higher frequency than that observed for chromosomal genes. The plasmid genes, and by inference the plasmids themselves, are mosaic in structure with different regions acquired from different sources. Comparison of gene sequences from a variety of naturally occurring plasmids suggested a plausible donor of some of the recombinant regions as well as implicating a chi site in the mechanism of genetic exchange. The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Helicases, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Evolution, Molecular, Membrane Proteins, Molecular Sequence Data, Mosaicism, Nucleic Acid Hybridization, Phylogeny, Plasmids, Polymorphism, Genetic, Proteins, Recombination, Genetic, Repressor Proteins, RNA-Binding Proteins, Trans-Activators},
	issn = {0016-6731},
	author = {Boyd, E F and Hill, C W and Rich, S M and Hartl, D L}
}
@article {797,
	title = {A new Borrelia infecting Lone Star ticks.},
	journal = {Lancet},
	volume = {347},
	year = {1996},
	month = {1996 Jan 6},
	pages = {67-8},
	keywords = {Animals, Base Sequence, Borrelia, Borrelia Infections, Deer, Disease Vectors, DNA Primers, Maryland, Molecular Sequence Data, Ticks},
	issn = {0140-6736},
	author = {Armstrong, P M and Rich, S M and Smith, R D and Hartl, D L and Spielman, A and Telford, S R}
}
@article {798,
	title = {Discriminating between Ixodes ticks by means of mitochondrial DNA sequences.},
	journal = {Mol Phylogenet Evol},
	volume = {4},
	year = {1995},
	month = {1995 Dec},
	pages = {361-5},
	abstract = {Ticks of the genus Ixodes have recently assumed prominence because they frequently serve as vectors of important zoonoses, including Lyme disease and babesiosis. The morphological characteristics that have been used in their identification often are ambiguous and are useful solely at a particular stage of development. Here we report the DNA sequence of the mitochondrially encoded 16S rRNA gene of nine different Ixodes ticks and an outgroup from another genus, Dermacentor. The sequences readily discriminate between these ticks. Samples of I. dammini from the northeastern and upper midwestern United States differ from southeastern I. scapularis at about 2\% of the nucleotides. This difference is about half that separating other members of the I. ricinus group of species, but exceeds typical levels of intraspecific variation. Two major clades exist within the I. ricinus complex. One includes I. cookei, I. hexagonus, and I. angustus. The other includes I. persulcatus, I. pacificus, I. muris, I. ricinus, I. scapularis, and I. dammini. We conclude that mtDNA sequences are useful for unravelling the systematics of these important vectors of human disease.},
	keywords = {Animals, Arachnid Vectors, Base Sequence, Dermacentor, DNA Primers, DNA, Mitochondrial, Genes, Humans, Ixodes, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Species Specificity},
	issn = {1055-7903},
	doi = {10.1006/mpev.1995.1033},
	author = {Caporale, D A and Rich, S M and Spielman, A and Telford, S R and Kocher, T D}
}
@article {799,
	title = {Distribution of the Ixodes ricinus-like ticks of eastern North America.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {92},
	year = {1995},
	month = {1995 Jul 3},
	pages = {6284-8},
	abstract = {We analyzed the geographic distribution of the Ixodes ricinus-like ticks in eastern North America by comparing the mitochondrial 16S rDNA sequences of specimens sampled directly from the field during the 1990s. Two distinct lineages are evident. The southern clade includes ticks from the southeastern and middle-eastern regions of the United States. The range of the northern clade, which appears to have been restricted to the northeastern region until the mid-1900s, now extends throughout the northeastern and middle-eastern regions. These phyletic units correspond to northern and southern taxa that have previously been assigned specific status as Ixodes dammini and Ixodes scapularis, respectively. The expanding range of I. dammini appears to drive the present outbreaks of zoonotic disease in eastern North America that include Lyme disease and human babesiosis.},
	keywords = {Animals, Base Sequence, Demography, DNA Primers, DNA, Mitochondrial, DNA, Ribosomal, Geography, Mitochondria, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Population, RNA, Ribosomal, 16S, Ticks, United States},
	issn = {0027-8424},
	author = {Rich, S M and Caporale, D A and Telford, S R and Kocher, T D and Hartl, D L and Spielman, A}
}
