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Scott RT, Su J, Tao X, Forman EJ, Hong KH, Taylor D, Treff NR. Trophectoderm DNA fingerprinting by quantitative real-time PCR successfully distinguishes sibling human embryos. J Assist Reprod Genet 2014; 31:1421-5. [PMID: 25129376 PMCID: PMC4389931 DOI: 10.1007/s10815-014-0315-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/06/2014] [Indexed: 01/31/2023] Open
Abstract
PURPOSE To validate a novel and more practical system for trophectoderm DNA fingerprinting which reliably distinguishes sibling embryos from each other. METHODS In this prospective and blinded study two-cell and 5-cell samples from commercially available sibling cell lines and excess DNA from trophectoderm biopsies of sibling human blastocysts were evaluated for accurate assignment of relationship using qPCR-based allelic discrimination from 40 single nucleotide polymorphisms (SNPs) with low allele frequency variation and high heterozygosity. RESULTS Cell samples with self relationships averaged 95.1 ± 5.9 % similarity. Sibling relationships averaged 57.2 ± 5.9 % similarity for all 40 SNPs, and 40.8 ± 8.2 % similarity for the 25 informative SNPs. Assignment of relationships was accomplished with 100 % accuracy for cell lines and embryos. CONCLUSIONS These data demonstrate the first trophectoderm qPCR-based DNA fingerprinting technology capable of unequivocal discrimination of sibling human embryos. This methodology will empower research and development of new markers of, and interventions that influence embryonic reproductive potential.
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Affiliation(s)
- Richard T. Scott
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
| | - Jing Su
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
| | - Xin Tao
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
| | - Eric J. Forman
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
- />Division of Reproductive Endocrinology, Department of Obstetrics Gynecology and Reproductive Science, Rutgers-Robert Wood Johnson Medical School, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
| | - Kathleen H. Hong
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
- />Division of Reproductive Endocrinology, Department of Obstetrics Gynecology and Reproductive Science, Rutgers-Robert Wood Johnson Medical School, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
| | - Deanne Taylor
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
- />Division of Reproductive Endocrinology, Department of Obstetrics Gynecology and Reproductive Science, Rutgers-Robert Wood Johnson Medical School, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
| | - Nathan R. Treff
- />Reproductive Medicine Associates of New Jersey, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
- />Division of Reproductive Endocrinology, Department of Obstetrics Gynecology and Reproductive Science, Rutgers-Robert Wood Johnson Medical School, 140 Allen Rd, Basking Ridge, Morristown, NJ 07960 USA
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Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
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Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen JPT, Hyvönen J. Advances in plant gene-targeted and functional markers: a review. Plant Methods 2013; 9:6. [PMID: 23406322 PMCID: PMC3583794 DOI: 10.1186/1746-4811-9-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 02/05/2013] [Indexed: 05/03/2023]
Abstract
Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.
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Affiliation(s)
- Péter Poczai
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
| | - Ildikó Varga
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
| | - Maarja Laos
- Institute of Biotechnology, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
| | - András Cseh
- Agricultural Institute, Centre of Agricultural Research, Hungarian Academy of Sciences, PO Box 19, H-2462, Martonvásár, Hungary
| | - Neil Bell
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
- Botanical Museum, University of Helsinki, PO Box 7, 00014, Helsinki, FIN, Finland
| | - Jari PT Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, 00014, Helsinki, FIN, Finland
| | - Jaakko Hyvönen
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, 00014, Helsinki, FIN, Finland
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Wu JH, Ferguson AR, Murray BG, Jia Y, Datson PM, Zhang J. Induced polyploidy dramatically increases the size and alters the shape of fruit in Actinidia chinensis. Ann Bot 2012; 109:169-79. [PMID: 21980192 PMCID: PMC3241580 DOI: 10.1093/aob/mcr256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Some otherwise promising selections of Actinidia chinensis (kiwifruit) have fruit that are too small for successful commercialization. We have therefore made the first detailed study in diploid kiwifruit of the effects of chromosome doubling induced by colchicine on fruit size, shape and crop loading. METHODS Flow cytometric analysis of young leaves and chromosome analysis of flower buds and root tips was used to confirm the stability of induced autotetraploids. Fruit weight, size and crop load were measured in the third year after planting in the field and for three consecutive years. DNA fingerprinting was used to confirm the origin of the material. KEY RESULTS There was a very significant increase in fruit size in induced autotetraploids of different genotypes of A. chinensis. With the commercially important diploid cultivar 'Hort16A', most regenerants, Type A plants, had fruit which were much the same shape as fruit of the diploid but, at the same fruit load, were much larger and heavier. Some regenerants, Type B plants, produced fruit similar to 'fasciated' fruit. Fruit of the autotetraploids induced from three female red-fleshed A. chinensis selections were also 50-60 % larger than fruit of their diploid progenitors. The main increase in fruit dimensions was in their diameters. These improved fruit characteristics were stable over several seasons. CONCLUSIONS Chromosome doubling has been shown to increase significantly fruit size in autotetraploid A. chinensis, highlighting the considerable potential of this technique to produce new cultivars with fruit of adequate size. Other variants with differently shaped fruit were also produced but the genetic basis of this variation remains to be elucidated. Autoploids of other Actinidia species with commercial potential may also show improved fruit characteristics, opening up many new possibilities for commercial development.
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Affiliation(s)
- Jin-Hu Wu
- The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
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Hamilton MJ, Hadi AZ, Griffith JF, Ishii S, Sadowsky MJ. Large scale analysis of virulence genes in Escherichia coli strains isolated from Avalon Bay, CA. Water Res 2010; 44:5463-73. [PMID: 20643468 PMCID: PMC2952692 DOI: 10.1016/j.watres.2010.06.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 05/21/2023]
Abstract
Contamination of recreational waters with Escherichia coli and Enterococcus sp. is a widespread problem resulting in beach closures and loss of recreational activity. While E. coli is frequently used as an indicator of fecal contamination, and has been extensively measured in waterways, few studies have examined the presence of potentially pathogenic E. coli strains in beach waters. In this study, a combination of high-throughput, robot-assisted colony hybridization and PCR-based analyses were used to determine the genomic composition and frequency of virulence genes present in E. coli isolated from beach water in Avalon Bay, Santa Catalina Island, CA. A total of 24,493 E. coli isolates were collected from two sites at a popular swimming beach between August through September 2007 and from July through August 2008. All isolates were examined for the presence of shiga-like toxins (stx1/stx2), intimin (eaeA), and enterotoxins (ST/LT). Of the 24,493 isolates examined, 3.6% contained the eaeA gene, indicating that these isolates were potential EPEC strains. On five dates, however, greater than 10% of the strains were potential EPEC, suggesting that incidence of virulence genes at this beach has a strong temporal component. No STEC or ETEC isolates were detected, and only eight (<1.0%) of the potential EPEC isolates were found to carry the EAF plasmid. The potential EPEC isolates mainly belonged to E. coli phylogenetic groups B1 or B2, and carried the β intimin subtype. DNA fingerprint analyses of the potential EPEC strains indicated that the isolates belonged to several genetically diverse groups, although clonal isolates were frequently detected. While the presence of virulence genes alone cannot be used to determine the pathogenicity of strains, results from this study show that potential EPEC strains can be found in marine beach water and their presence needs to be considered as one of the factors used in decisions concerning beach closures.
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Affiliation(s)
- Matthew J. Hamilton
- Department of Microbiology, University of Minnesota, MMC 196, 420 Delaware Street, S.E., Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, 140 GorL, St. Paul, MN, 55108, USA
| | - Asbah Z. Hadi
- Department of Microbiology, University of Minnesota, MMC 196, 420 Delaware Street, S.E., Minneapolis, MN 55455, USA
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, 438 BorH, St. Paul, MN, 55108, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd., Suite 110, Costa Mesa, CA, USA
| | - Satoshi Ishii
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, 438 BorH, St. Paul, MN, 55108, USA
| | - Michael J. Sadowsky
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, 140 GorL, St. Paul, MN, 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, 438 BorH, St. Paul, MN, 55108, USA
- Corresponding author: Tel.: +1 (612) 624 2706; fax: +1 (612) 625 2208. (M. Sadowsky)
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Anssour S, Krügel T, Sharbel TF, Saluz HP, Bonaventure G, Baldwin IT. Phenotypic, genetic and genomic consequences of natural and synthetic polyploidization of Nicotiana attenuata and Nicotiana obtusifolia. Ann Bot 2009; 103:1207-17. [PMID: 19307190 PMCID: PMC2685307 DOI: 10.1093/aob/mcp058] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/19/2009] [Accepted: 02/02/2009] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND METHODS Polyploidy results in genetic turmoil, much of which is associated with new phenotypes that result in speciation. Five independent lines of synthetic allotetraploid N. x obtusiata (N x o) were created from crosses between the diploid N. attenuata (Na) (male) and N. obtusifolia (No) (female) and the autotetraploids of Na (NaT) and No (NoT) were synthesized. Their genetic, genomic and phenotypic changes were then compared with those of the parental diploid species (Na and No) as well as to the natural allotetraploids, N. quadrivalvis (Nq) and N. clevelandii (Nc), which formed 1 million years ago from crosses between ancient Na and No. KEY RESULTS DNA fingerprinting profiles (by UP-PCR) revealed that the five N x o lines shared similar but not identical profiles. Both synthetic and natural polyploidy showed a dosage effect on genome size (as measured in seeds); however, only Nq was associated with a genome upsizing. Phenotypic analysis revealed that at the cellular level, N x o lines had phenotypes intermediate of the parental phenotypes. Both allo- and autotetraploidization had a dosage effect on seed and dry biomass (except for NaT), but not on stalk height at first flower. Nc showed paternal (Na) cellular phenotypes but inherited maternal (No) biomass and seed mass, whereas Nq showed maternal (No) cellular phenotypes but inherited paternal (Na) biomass and seed mass patterns. Principal component analysis grouped Nq with N x o lines, due to similar seed mass, stalk height and genome size. These traits separated Nc, No and Na from Nq and N x o lines, whereas biomass distinguished Na from N x o and Nq lines, and NaT clustered closer to Nq and N x o lines than to Na. CONCLUSIONS Both allo- and autotetraploidy induce considerable morphological, genetic and genomic changes, many of which are retained by at least one of the natural polyploids. It is proposed that both natural and synthetic polyploids are well suited for studying the evolution of adaptive responses.
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Affiliation(s)
- S. Anssour
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - T. Krügel
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - T. F. Sharbel
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - H. P. Saluz
- Leibniz Institute for Natural Product Research and Infection Biology e.V, Hans-Knöll-Institute (HKI) Beutenbergstr. 11a, 07745 Jena, Germany
| | - G. Bonaventure
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - I. T. Baldwin
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
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Vieira P, Burgermeister W, Mota M, Metge K, Silva G. Lack of Genetic Variation of Bursaphelenchus xylophilus in Portugal Revealed by RAPD-PCR Analyses. J Nematol 2007; 39:118-126. [PMID: 19259480 PMCID: PMC2586491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Indexed: 05/27/2023] Open
Abstract
Random Amplified Polymorphic DNA (RAPD-PCR) technique was used to assess the level of genetic variability and genetic relationships among 24 Portuguese isolates of pinewood nematode, Bursaphelenchus xylophilus. The isolates represent the main infested areas of Portugal. Two additional isolates of B. xylophilus representing North America and East Asia were included, and B. mucronatus was used as out-group. Twenty-eight random primers generated a total of 640 DNA fragments. The Nei and Li similarity index revealed a high genetic similarity among the Portuguese isolates (above 90%). Hierarchical cluster analysis was performed to illustrate the relatedness among the isolates. No indication for separate groups among the Portuguese isolates was obtained, and the low level of genetic diversity strongly suggests that they were dispersed recently from a single introduction. The lack of apparent relationship between the genetic and the geographic matrices of the Portuguese isolates limits the use of this technique for following recent pathways of distribution. Genetic distance of the Portuguese isolates towards an isolate from China was much lower as compared to an isolate from the USA. This confirmed previous results suggesting an East Asian origin of the Portuguese B. xylophilus.
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Affiliation(s)
- Paulo Vieira
- NemaLab-ICAM, Departamento de Biologia, Universidade de Evora, 7002-554 Evora, Portugal Institute for Plant Virology, Microbiology and Biosafety, Federal Biological Research Centre for Agriculture and Forestry (BBA), Messeweg 11-12, D-38104 Braunschweig, Germany
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Zhang D, Arevalo-Gardini E, Mischke S, Zúñiga-Cernades L, Barreto-Chavez A, Del Aguila JA. Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru. Ann Bot 2006; 98:647-55. [PMID: 16845139 PMCID: PMC3292056 DOI: 10.1093/aob/mcl146] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.
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Affiliation(s)
- Dapeng Zhang
- USDA ARS PSI SPCL, 10300 Baltimore Avenue, Bldg 050, Rm 100, BARC-W, Beltsville, MD 20705, USA.
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Johnson EL, Zhang D, Emche SD. Inter- and intra-specific variation among five Erythroxylum taxa assessed by AFLP. Ann Bot 2005; 95:601-8. [PMID: 15650009 PMCID: PMC4246853 DOI: 10.1093/aob/mci062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 09/23/2004] [Accepted: 11/15/2004] [Indexed: 05/24/2023]
Abstract
BACKGROUND and Aims The four cultivated Erythroxylum taxa (E. coca var. coca, E. novogranatense var. novogranatense, E. coca var. ipadu and E. novogranatense var. truxillense) are indigenous to the Andean region of South America and have been cultivated for folk-medicine and, within the last century, for illicit cocaine production. The objective of this research was to assess the structure of genetic diversity within and among the four cultivated alkaloid-bearing taxa of Erythroxylum in the living collection at Beltsville Agricultural Research Center. METHODS Amplified fragment length polymorphism (AFLP) fingerprinting was performed in 86 Erythroxylum accessions using a capillary genotyping system. Cluster analysis, multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) were used to assess the pattern and level of genetic variation among and within the taxa. KEY RESULTS A clear distinction was revealed between E. coca and E. novogranatense. At the intra-specific level, significant differentiation was observed between E. c. var. coca and E. c. var. ipadu, but the differentiation between E. n. var. novogranatense and E. n. var. truxillense was negligible. Erythroxylum c. var. ipadu had a significantly lower amount of diversity than the E. c. var. coca and is genetically different from the E. c. var. ipadu currently under cultivation in Colombia, South America. CONCLUSIONS There is a heterogeneous genetic structure among the cultivated Erythroxylum taxa where E. coca and E. novogranatense are two independent species. Erythroxylum coca var. coca is most likely the ancestral taxon of E. c. var. ipadu and a founder effect may have occurred as E. c. var. ipadu moved from the eastern Andes in Peru and Bolivia into the lowland Amazonian basin. There is an indication of artificial hybridization in coca grown in Colombia.
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Affiliation(s)
- Emanuel L Johnson
- USDA ARS PSI ACSL, 10300 Baltimore Avenue, BARC-W, Beltsville, MD 20705, USA.
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de León JH, Jones WA. Genetic differentiation among geographic populations of Gonatocerus ashmeadi, the predominant egg parasitoid of the glassy-winged sharpshooter, Homalodisca coagulata. J Insect Sci 2005; 5:2. [PMID: 16299592 PMCID: PMC1283883 DOI: 10.1093/jis/5.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2004] [Accepted: 09/13/2004] [Indexed: 05/05/2023]
Abstract
The aim of genetically comparing different populations of the same species of natural enemies is to identify the strain that is most adapted to the environment where it will be released. In the present study, Inter-Simple Sequence Repeat-Polymerase Chain Reaction (ISSR-PCR) was utilized to estimate the population genetic structure of Gonatocerus ashmeadi (Girault) (Hymenoptera: Mymaridae), the predominant egg parasitoid of Homalodisca coagulata (Say) (Homoptera:Cicadellidae), the glassy-winged sharpshooter. Six populations from throughout the U.S. and a population from Argentina identified as near G. ashmeadi were analyzed. Four populations (California; San Antonio, Texas; Weslaco, Texas [WTX-2]; and Florida) were field collected and two (Louisiana and Weslaco, Texas [WTX-1]) were reared. Three ISSR-PCR reactions were pooled to generate 41 polymorphic markers among the six U.S. populations. Nei's expected heterozygosity values (h), including the reared population from Louisiana, were high (9.01-14.3%) for all populations, except for a reared population from WTX-1 (2.9%). The total genetic diversity value (Ht) for the field populations was high (23%). Interestingly, the Florida population that was collected from one egg mass (siblings) generated the greatest number of polymorphic markers (20) and was observed with the highest gene diversity value (14.3%). All populations, except WTX-2 generated population-specific markers. Comparison of genetic differentiation estimates, which evaluate the degree of genetic subdivision, demonstrated good agreement between G(ST) and theta values, 0.38 and 0.50, respectively for field populations, and 0.44 and 0.50, respectively for all populations. Genetic divergence (D) indicated that the WTX-1 population was the most differentiated. Average D results from the Argentina population support the taxonomic data that it is a different species. The present results estimate the population genetic structure of G. ashmeadi, demonstrating genetic divergence and restricted gene flow (Nm = 0.83) among populations. These results are of interest to the Pierce's disease/glassy-winged sharpshooter biological control program because the key to successful biological control may not be in another species, but instead in different geographic races or biotypes.
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Affiliation(s)
- Jesse H de León
- United States Department of Agriculture, Agricultural Research Service, Subtropical Agricultural Research Center, Beneficial Insects Research Unit, 2413 E. Highway 83, Weslaco, Texas 78596, USA.
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de León JH, Jones WA, Morgan DJW. Molecular distinction between populations of Gonatocerus morrilli, egg parasitoids of the glassy-winged sharpshooter from Texas and California: do cryptic species exist? J Insect Sci 2004; 4:39. [PMID: 15861254 PMCID: PMC1081561 DOI: 10.1093/jis/4.1.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2004] [Accepted: 08/23/2004] [Indexed: 05/24/2023]
Abstract
Two molecular methods were utilized to distinguish geographic populations of Gonatocerus morrilli (Howard) from Texas and California and to test the possibility that this species could exist as a species-complex. Inter-Simple Sequence Repeat-Polymerase Chain Reactions (ISSR-PCR) were performed with a 5'-anchored ISSR primer. Twenty-five markers were generated with four populations (40 individuals) of G. morrilli. Twenty-three were polymorphic and the percentage of polymorphic loci was 92%. Most markers could be considered diagnostic since there was no band sharing between the Texas and California populations. Such differences typically are not found unless the populations are reproductively isolated. Exact tests for population differentiation indicated significant differences in marker frequencies among the populations. Comparison of other genetic differentiation estimates, which evaluate the degree of genetic subdivision, demonstrated excellent agreement between GST and theta values, 0.92 and 0.94, respectively, indicating that about 92 to 94% of the variance was distributed among populations. The average genetic divergence (D), as measured by genetic distance, was extremely high (Nei = 0.82 and Reynolds = 2.79). A dendrogram based on Nei's genetic distance separated the Texas and California populations into two clusters, respectively. Amplification of the Internal Transcribed Spacer-1 (ITS-1) region showed no size differences, whereas the ITS-2 DNA fragment varied in size between the two geographic populations. The ITS-2 fragment sizes were about 865 and 1099 base pairs for the California and Texas populations, respectively. The present study using the two molecular methods provides novel data critical to the glassy-winged sharpshooter/Pierce's disease biological control program in California.
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Affiliation(s)
- Jesse H de León
- United States Department of Agriculture, Agricultural Research Service, Subtropical Agricultural Research Center, Beneficial Insects Research Unit, 2413 E. Highway 83, Weslaco, Texas 78596, USA.
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13
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Abstract
BACKGROUND Although the rate of multiple drug resistance is high, there is no published data on the transmission rate of drug-resistant strains of Mycobacterium tuberculosis in the Aegean region of western Turkey that are based on molecular methods. METHODS IS6110 and pTBN12 restriction fragment length polymorphism (RFLP) methods were used for typing M. tuberculosis strains isolated from 26 sputum samples from 26 patients. RESULTS Nineteen of the rifampin-resistant isolates (73.1%) contained 6 to 11 copies of IS6110. Eighteen different IS6110 DNA fingerprint patterns were observed in the 26 rifampin-resistant isolates. Twenty-three of the 26 rifampin-resistant isolates were also resistant to isoniazid. When evaluated together, both methods yielded 21 (80.9%) different banding patterns and the level of clustering was 34.6%. The average number per pattern was 1.23 (26/21). CONCLUSIONS IS6110 fingerprinting suggests that the rifampin-resistant isolates obtained from the Aegean region had a relatively high clustering rate and were clonally related. These findings showed that the rifampin-resistant isolates are actively transmitted between patients. Urgent measures should be taken to prevent the spread of these resistant strains.
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Affiliation(s)
- Cengiz Cavusoglu
- Ege University Medical Faculty, Department of Microbiology and Clinical Microbiology, Bornova, Izmir, Turkey.
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14
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Blackwood KS, Al-Azem A, Elliott LJ, Hershfield ES, Kabani AM. Conventional and molecular epidemiology of tuberculosis in Manitoba. BMC Infect Dis 2003; 3:18. [PMID: 12917019 PMCID: PMC194617 DOI: 10.1186/1471-2334-3-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Accepted: 08/13/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To describe the demographic and geographic distribution of tuberculosis (TB) in Manitoba, thus determining risk factors associated with clustering and higher incidence rates in distinct subpopulations. METHODS Data from the Manitoba TB Registry was compiled to generate a database on 855 patients with tuberculosis and their contacts from 1992-1999. Recovered isolates of M. tuberculosis were typed by IS6110 restriction fragment length polymorphisms. Bivariate and multivariate logistic regression models were used to identify risk factors involved in clustering. RESULTS A trend to clustering was observed among the Canadian-born treaty Aboriginal subgroup in contrast to the foreign-born. The dominant type, designated fingerprint type 1, accounts for 25.8% of total cases and 75.3% of treaty Aboriginal cases. Among type 1 patients residing in urban areas, 98.9% lived in Winnipeg. In rural areas, 92.8% lived on Aboriginal reserves. Statistical models revealed that significant risk factors for acquiring clustered tuberculosis are gender, age, ethnic origin and residence. Those at increased risk are: males (p < 0.05); those under age 65 (p < 0.01 for each age subgroup); treaty Aboriginals (p < 0.001), and those living on reserve land (p < 0.001). CONCLUSION Molecular typing of isolates in conjunction with contact tracing data supports the notion of the largest ongoing transmission of a single strain of TB within the treaty-status population of Canada recorded to date. This data demonstrates the necessity of continued surveillance of countries with low prevalence of the disease in order to determine and target high-risk populations for concentrated prevention and control measures.
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Affiliation(s)
- Kym S Blackwood
- National Reference Center for Mycobacteriology, National Microbiology Laboratory, Health, Canada, Winnipeg, MB, Canada
| | - Assaad Al-Azem
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Lawrence J Elliott
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Earl S Hershfield
- Department of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Amin M Kabani
- National Reference Center for Mycobacteriology, National Microbiology Laboratory, Health, Canada, Winnipeg, MB, Canada
- Department of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Clinical Microbiology, Health Sciences Center, Winnipeg, MB, Canada
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15
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Driscoll JR, Bifani PJ, Mathema B, McGarry MA, Zickas GM, Kreiswirth BN, Taber HW. Spoligologos: a bioinformatic approach to displaying and analyzing Mycobacterium tuberculosis data. Emerg Infect Dis 2002; 8:1306-9. [PMID: 12453361 PMCID: PMC2738554 DOI: 10.3201/eid0811.020174] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Spacer oligonucleotide (spoligotyping) analysis is a rapid polymerase chain reaction-based method of DNA fingerprinting the Mycobacterium tuberculosis complex. We examined spoligotype data using a bioinformatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. Logo analysis of spoligotyping data provides a simple way to describe a fingerprint signature and may be useful in categorizing unique spoligotypes patterns as they are discovered. Large databases of DNA fingerprint information, such as those from the U.S. National Tuberculosis Genotyping and Surveillance Network and the European Concerted Action on Tuberculosis, contain information on thousands of strains from diverse regions. The description of related spoligotypes has depended on exhaustive listings of the individual spoligotyping patterns. Logo analysis may become another useful graphic method of visualizing and presenting spoligotyping clusters from these databases.
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16
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Cronin WA, Golub JE, Lathan MJ, Mukasa LN, Hooper N, Razeq JH, Baruch NG, Mulcahy D, Benjamin WH, Magder LS, Strickland GT, Bishai WR. Molecular epidemiology of tuberculosis in a low- to moderate-incidence state: are contact investigations enough? Emerg Infect Dis 2002; 8:1271-9. [PMID: 12453355 PMCID: PMC2738531 DOI: 10.3201/eid0811.020261] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To assess the circumstances of recent transmission of tuberculosis (TB) (progression to active disease <2 years after infection), we obtained DNA fingerprints for 1172 (99%) of 1179 Mycobacterium tuberculosis isolates collected from Maryland TB patients from 1996 to 2000. We also reviewed medical records and interviewed patients with genetically matching M. tuberculosis strains to identify epidemiologic links (cluster investigation). Traditional settings for transmission were defined as households or close relatives and friends; all other settings were considered nontraditional. Of 436 clustered patients, 115 had recently acquired TB. Cluster investigations were significantly more likely than contact investigations to identify patients who recently acquired TB in nontraditional settings (33/42 vs. 23/72, respectively; p<0.001). Transmission from a foreign-born person to a U.S.-born person was rare and occurred mainly in public settings. The time from symptom onset to diagnosis was twice as long for transmitters as for nontransmitters (16.8 vs. 8.5 weeks, respectively; p<0.01). Molecular epidemiologic studies showed that reducing diagnostic delays can prevent TB transmission in nontraditional settings, which elude contact investigations.
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Affiliation(s)
- Wendy A Cronin
- Maryland Department of Health and Mental Hygiene, Baltimore, Maryland 21201, USA.
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17
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Miller AC, Sharnprapai S, Suruki R, Corkren E, Nardell EA, Driscoll JR, McGarry M, Taber H, Etkind S. Impact of genotyping of Mycobacterium tuberculosis on public health practice in Massachusetts. Emerg Infect Dis 2002; 8:1285-9. [PMID: 12453357 PMCID: PMC2738536 DOI: 10.3201/eid0811.020316] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Massachusetts was one of seven sentinel surveillance sites in the National Tuberculosis Genotyping and Surveillance Network. From 1996 through 2000, isolates from new patients with tuberculosis (TB) underwent genotyping. We describe the impact that genotyping had on public health practice in Massachusetts and some limitations of the technique. Through genotyping, we explored the dynamics of TB outbreaks, investigated laboratory cross-contamination, and identified Mycobacterium tuberculosis strains, transmission sites, and accurate epidemiologic links. Genotyping should be used with epidemiologic follow-up to identify how resources can best be allocated to investigate genotypic findings.
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Affiliation(s)
- Ann C. Miller
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sharon Sharnprapai
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Robert Suruki
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Edward Corkren
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Edward A. Nardell
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
- Harvard University, Boston, Massachusetts, USA
| | | | | | - Harry Taber
- New York State Department of Health, Albany, New York, USA
| | - Sue Etkind
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
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18
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Abstract
DNA fingerprinting of Mycobacterium tuberculosis--a relatively new laboratory technique--offers promise as a powerful aid in the prevention and control of tuberculosis (TB). Established in 1996 by the Centers for Disease Control and Prevention (CDC), the National Tuberculosis Genotyping and Surveillance Network was a 5-year prospective, population-based study of DNA fingerprinting conducted from 1996 to 2000. The data from this study suggest multiple molecular epidemiologic and program management uses for DNA fingerprinting in TB public health practice. From these data, we also gain a clearer understanding of the overall diversity of M. tuberculosis strains as well as the presence of endemic strains in the United States. We summarize the key findings and the impact that DNA fingerprinting may have on future approaches to TB control. Although challenges and limitations to the use of DNA fingerprinting exist, the widespread implementation of the technique into routine TB prevention and control practices appears scientifically justified.
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Affiliation(s)
- Scott J N McNabb
- Centers for Disesase Control and Prevention, Atlanta, GA 30333, USA.
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19
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Northrup JM, Miller AC, Nardell E, Sharnprapai S, Etkind S, Driscoll J, McGarry M, Taber HW, Elvin P, Qualls NL, Braden CR. Estimated costs of false laboratory diagnoses of tuberculosis in three patients. Emerg Infect Dis 2002. [PMID: 12453354 PMCID: PMC2738552 DOI: 10.3201/eid0811020387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We estimated direct medical and nonmedical costs associated with a false diagnosis of tuberculosis (TB) caused by laboratory cross-contamination of Mycobacterium tuberculosis cultures in Massachusetts in 1998 and 1999. For three patients who received misdiagnoses of active TB disease on the basis of laboratory cross-contamination, the costs totaled U.S. dollars 32618. Of the total, 97% was attributed to the public sector (local and state health departments, public health hospital and laboratory, and county and state correctional facilities); 3% to the private sector (physicians, hospitals, and laboratories); and <1% to the patient. Hospitalizations and inpatient tests, procedures, and TB medications accounted for 69% of costs, and outpatient TB medications accounted for 18%. The average cost per patient was dollars 10873 (range, dollars 1033-dollars 21306). Reducing laboratory cross-contamination and quickly identifying patients with cross-contaminated cultures can prevent unnecessary and potentially dangerous treatment regimens and anguish for the patient and financial burden to the health-care system.
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Affiliation(s)
- Jill M. Northrup
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Ann C. Miller
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Edward Nardell
- Massachusetts Department of Public Health, Boston, Massachusetts, USA,Harvard Medical School, Boston, Massachusetts, USA
| | | | - Sue Etkind
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Jeffrey Driscoll
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | - Michael McGarry
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | - Harry W. Taber
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | - Paul Elvin
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Noreen L. Qualls
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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20
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Abstract
Quality assessment exercises were conducted to evaluate the reproducibility of IS6110 DNA fingerprinting performed by eight laboratories in the National Tuberculosis Genotyping and Surveillance Network. Three panels, each with 8 to 16 isolates, were typed at all laboratories, resulting in 280 images. When the pattern obtained by the majority for each isolate was used as the standard, exact matches were obtained for 73% of patterns; 90% and 97% of patterns matched within one- and two-band differences, respectively. A second approach involved retyping of randomly selected isolates at the Centers for Disease Control and Prevention. Retyping was done for 8-19 isolates per laboratory (76 total). Paired images matched exactly for 54% of isolates and within one and two band differences, 78% and 93%, respectively. We evaluated reasons for mismatching. We also evaluated the reproducibility of spoligotyping using a test panel of 13 isolates; a discrepancy of 1 in 91 results was noted.
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21
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Bennett DE, Onorato IM, Ellis BA, Crawford JT, Schable B, Byers R, Kammerer JS, Braden CR. DNA fingerprinting of Mycobacterium tuberculosis isolates from epidemiologically linked case pairs. Emerg Infect Dis 2002; 8:1224-9. [PMID: 12453346 PMCID: PMC2738550 DOI: 10.3201/eid0811.020420] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
DNA fingerprinting was used to evaluate epidemiologically linked case pairs found during routine tuberculosis (TB) contact investigations in seven sentinel sites from 1996 to 2000. Transmission was confirmed when the DNA fingerprints of source and secondary cases matched. Of 538 case pairs identified, 156 (29%) did not have matching fingerprints. Case pairs from the same household were no more likely to have confirmed transmission than those linked elsewhere. Case pairs with unconfirmed transmission were more likely to include a smear-negative source case (odds ratio [OR] 2.0) or a foreign-born secondary case (OR 3.4) and less likely to include a secondary case <15 years old (OR 0.3). Our study suggests that contact investigations should focus not only on the household but also on all settings frequented by an index case. Foreign-born persons with TB may have been infected previously in high-prevalence countries; screening and preventive measures recommended by the Institute of Medicine could prevent TB reactivation in these cases.
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Affiliation(s)
- Diane E Bennett
- Centers for Disease control and Prevention, Atlanta, GA 30333, USA.
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22
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Sharnprapai S, Miller AC, Suruki R, Corkren E, Etkind S, Driscoll J, McGarry M, Nardell E. Genotyping analyses of tuberculosis cases in U.S.- and foreign-born Massachusetts residents. Emerg Infect Dis 2002; 8:1239-45. [PMID: 12453348 PMCID: PMC2738545 DOI: 10.3201/eid0811.020370] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We used molecular genotyping to further understand the epidemiology and transmission patterns of tuberculosis (TB) in Massachusetts. The study population included 983 TB patients whose cases were verified by the Massachusetts Department of Public Health between July 1, 1996, and December 31, 2000, and for whom genotyping results and information on country of origin were available. Two hundred seventy-two (28%) of TB patients were in genetic clusters, and isolates from U.S-born were twice as likely to cluster as those of foreign-born (odds ratio [OR] 2.29, 95% confidence interval [CI] 1.69 to 3.12). Our results suggest that restriction fragment length polymorphism analysis has limited capacity to differentiate TB strains when the isolate contains six or fewer copies of IS6110, even with spoligotyping. Clusters of TB patients with more than six copies of IS6110 were more likely to have epidemiologic connections than were clusters of TB patients with isolates with few copies of IS6110 (OR 8.01, 95%; CI 3.45 to 18.93).
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Affiliation(s)
- Sharon Sharnprapai
- Massahusetts Department of Public Health, Boston, Massahusetts 02130, USA.
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23
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Dillaha JA, Yang Z, Ijaz K, Eisenach KD, Cave MD, Wilson FJ, Stead WW, Bates JH. Transmission of Mycobacterium tuberculosis in a rural community, Arkansas, 1945-2000. Emerg Infect Dis 2002; 8:1246-8. [PMID: 12453349 PMCID: PMC2738561 DOI: 10.3201/eid0811.020299] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A cluster of tuberculosis cases in a rural community in Arkansas persisted from 1991 to 1999. The cluster had 13 members, 11 linked epidemiologically. Old records identified 24 additional patients for 40 linked cases during a 54-year period. Residents of this neighborhood represent a population at high risk who should be considered for tuberculin testing and treatment for latent tuberculosis infection.
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Affiliation(s)
- Jennifer A Dillaha
- University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
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24
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Northrup JM, Miller AC, Nardell E, Sharnprapai S, Etkind S, Driscoll J, McGarry M, Taber HW, Elvin P, Qualls NL, Braden CR. Estimated costs of false laboratory diagnoses of tuberculosis in three patients. Emerg Infect Dis 2002; 8:1264-70. [PMID: 12453354 PMCID: PMC2738552 DOI: 10.3201/eid0811.020387] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We estimated direct medical and nonmedical costs associated with a false diagnosis of tuberculosis (TB) caused by laboratory cross-contamination of Mycobacterium tuberculosis cultures in Massachusetts in 1998 and 1999. For three patients who received misdiagnoses of active TB disease on the basis of laboratory cross-contamination, the costs totaled U.S. dollars 32618. Of the total, 97% was attributed to the public sector (local and state health departments, public health hospital and laboratory, and county and state correctional facilities); 3% to the private sector (physicians, hospitals, and laboratories); and <1% to the patient. Hospitalizations and inpatient tests, procedures, and TB medications accounted for 69% of costs, and outpatient TB medications accounted for 18%. The average cost per patient was dollars 10873 (range, dollars 1033-dollars 21306). Reducing laboratory cross-contamination and quickly identifying patients with cross-contaminated cultures can prevent unnecessary and potentially dangerous treatment regimens and anguish for the patient and financial burden to the health-care system.
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Affiliation(s)
- Jill M Northrup
- Massachusetts Department of Public Health, Boston, Massachusetts, USA.
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25
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McElroy PD, Sterling TR, Driver CR, Kreiswirth B, Woodley CL, Cronin WA, Hardge DX, Shilkret KL, Ridzon R. Use of DNA fingerprinting to investigate a multiyear, multistate tuberculosis outbreak. Emerg Infect Dis 2002; 8:1252-6. [PMID: 12453351 PMCID: PMC2738549 DOI: 10.3201/eid0811.020424] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 1998-1999, the Baltimore TB control program detected a cluster of 21 tuberculosis (TB) cases. Patients reported frequent travel to various East Coast cities. An investigation was conducted to determine whether transmission of the same Mycobacterium tuberculosis strain was occurring in these other localities. A collaborative investigation among federal, state, and local TB controllers included TB record reviews, interviews of patients, and restriction fragment length polymorphism (RFLP) analysis of selected M. tuberculosis isolates from diagnosed TB patients in several cities in 1996-2001. A national TB genotyping database was searched for RFLP patterns that matched the outbreak pattern. Eighteen additional outbreak-related cases were detected outside of Baltimore-the earliest diagnosed in New Jersey in 1996, and the most recent in New York City in late 2001. The outbreak demonstrates the need for strategies to detect links among patients diagnosed with TB across multiple TB control jurisdictions.
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Affiliation(s)
- Peter D McElroy
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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26
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Jasmer RM, Roemer M, Hamilton J, Bunter J, Braden CR, Shinnick TM, Desmond EP. A prospective, multicenter study of laboratory cross-contamination of Mycobacterium tuberculosis cultures. Emerg Infect Dis 2002; 8:1260-3. [PMID: 12453353 PMCID: PMC2738534 DOI: 10.3201/eid0811.020298] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A prospective study of false-positive cultures of Mycobacterium tuberculosis that resulted from laboratory cross-contamination was conducted at three laboratories in California. Laboratory cross-contamination accounted for 2% of the positive cultures. Cross-contamination should be a concern when an isolate matches the genotype of another sample processed during the same period.
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Affiliation(s)
- Robert M Jasmer
- San francisco General Hospital Medical Center and University of California, San Francisco, California 94110, USA.
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27
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Abstract
We describe the implementation of a mandatory tuberculosis (TB) screening program that uses symptom screening and tuberculin skin testing in homeless shelters. We used the results of DNA fingerprinting of Mycobacterium tuberculosis isolates to evaluate the effect of the program on TB incidence and transmission. After the program was implemented, the proportion of cases among homeless persons detected by screening activities increased, and the estimated TB incidence decreased from 510 to 121 cases per 100000 population per year. Recent transmission, defined by DNA fingerprinting analysis as clustered patterns occurring within 2 years, decreased from 49% to 14% (p=0.03). Our results suggest that the shelter-based screening program decreased the incidence of TB by decreasing its transmission among the homeless.
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28
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WONG CAROL, KIEW RUTH, ARGENT GEORGE, SET OHN, LEE SINGKONG, GAN YIKYUEN. Assessment of the validity of the sections in Musa (musaceae) using AFLP. Ann Bot 2002; 90:231-8. [PMID: 12197520 PMCID: PMC4240415 DOI: 10.1093/aob/mcf170] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Musa L. (Musaceae) is currently separated into five sections (Musa. Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on chromosome numbers and morphological characters. However, the validation of this classification system is questioned due to the common occurrence of hybridizations across sections and the system not accommodating anomalous species. This study employed amplified fragment length polymorphism (AFLP) in a phenetic examination of the relationships among four sections (material of sect. Ingentimusa was not available) to evaluate whether their genetic differences justify distinction into separate groups. Using eight primer combinations, a total of 276 bands was scored, of which 275 were polymorphic. Among the monomorphic bands, 11 unique markers were identified that revealed the distinct separation of the 11-chromosome species from the 10-chromosome species. AFLP results suggest that species of sect. Rhodochlamys should be combined into a single section with species of sect. Musa, and likewise for species of sect. Australimnusa to be merged with those of sect. Callimusa.
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Affiliation(s)
- CAROL WONG
- Natural Sciences Academic Group, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, 637616 Singapore
| | - RUTH KIEW
- Singapore Botanic Gardens, 1 Cluny Road, 259569 Singapore
| | | | - OHN SET
- Singapore Botanic Gardens, 1 Cluny Road, 259569 Singapore
| | - SING KONG LEE
- Natural Sciences Academic Group, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, 637616 Singapore
| | - YIK YUEN GAN
- Natural Sciences Academic Group, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, 637616 Singapore
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29
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Abstract
Among the goals of the molecular epidemiology of infectious disease are to quantify the extent of ongoing transmission of infectious agents and to identify host- and strain-specific risk factors for disease spread. I demonstrate the potential bias in estimates of recent transmission and the impact of risk factors for clustering by using computer simulations to reconstruct populations of tuberculosis patients and sample from them. The bias consistently results in underestimating recent transmission and the impact of risk factors for recent transmission.
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Affiliation(s)
- Megan Murray
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachussetts 02115, USA.
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30
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Rosselló JA, Carmencebrián M, Mayol M. Testing taxonomic and biogeographical relationships in a narrow Mediterranean endemic complex (Hippocrepis balearica) using RAPD markers. Ann Bot 2002; 89:321-7. [PMID: 12096744 PMCID: PMC4233823 DOI: 10.1093/aob/mcf044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Analyses of RAPD profiles from 17 populations of the Hippocrepis balearica complex revealed a highly structured geographic pattern, not only among continental-insular areas but also within the eastern Balearic islands. In marked contrast to previous morphometric results, a clear separation between continental and insular samples was found, and intermediates between H. balearica and H. valentina samples were not detected. Molecular data indicated that western and eastern Balearic populations of the complex (H. grosii and H. balearica) were more closely related to each other than to continental populations (H. valentina). Multivariate analyses of the RAPD data clearly indicated that the similarities between continental and eastern Balearic samples of the H. balearica complex recovered by morphometric methods are due either to parallel evolution or to retention of plesiomorphic features.
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31
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Abstract
The Swedish moose was analysed for genetic variability at major histocompatibility complex (MHC) class I and class II DQA, DQB and DRB loci using restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP) techniques. Both methods revealed limited amounts of polymorphism. Since the SSCP analysis concerned an expressed DRB gene it can be concluded that the level of functional MHC class II polymorphism, at least at the DRB locus, is low in Swedish moose. DNA fingerprinting was used to determine if the unusual pattern of low MHC variability could be explained by a low degree of genome-wide genetic diversity. Hybridizations with two minisatellite probes gave similarity indices somewhat higher than the average for other natural population, but the data suggest that the low MHC variability cannot be explained by a recent population bottleneck. However, since minisatellite sequences evolve more rapidly than MHC sequences, the low levels of MHC diversity may be attributed to a bottleneck of more ancient origin. The selection pressure for MHC variability in moose may also be reduced and we discuss the possibility that its solitary life style may reduce lateral transmission of pathogens in the population.
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Affiliation(s)
- H Ellegren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Biomedical Centre, Uppsala
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32
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Abstract
The arbitrary primer polymerase chain reaction (AP-PCR) and Southern blot restriction fragment length polymorphism (RFLP) were used to genotype the periodontal pathogen A. actinomycetemcomitans. Total genomic DNA from 73 strains was extracted by conventional methods. Three random-sequence 10-base oligonucleotide primers were chosen for AP-PCR. The amplified DNA products were separated electrophoretically in a 1% agarose gel containing ethidium bromide and the banding patterns were compared among different strains. For RFLP analysis, DNA was digested with EcoRI, separated on a 0.8% agarose gel and transferred to a nylon membrane. The membrane was probed with a previously characterized 5.2 kilobases (kb) DNA fragment cloned from A. actinomycetemcomitans strain Y4. The probe was labeled with digoxigenin, and hybridized fragments were detected with anti-digoxigenin antibody. AP-PCR produced 4-10 DNA bands in the 0.5-5 kb regions and distinguished 9, 13 or 17 genotypes, depending on the specific primer used. Southern blot RFLP analysis revealed 12 hybridization patterns consisting of 1 or 2 DNA fragments (2-23 kb). The addition of the Southern blot analysis to the AP-PCR analysis gave rise to a total of 30 DNA profiles among the 73 A. actinomycetemcomitans study strains. The results indicate that both AP-PCR and Southern blot analysis are useful in clonal analysis of A. actinomycetemcomitans.
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Affiliation(s)
- J Slots
- Department of Periodontology, University of Southern California, School of Dentistry, Los Angeles
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Takada T, Suzuki S, Sugawara Y, Kominami R, Arakawa M, Niwa O, Yokoro K. Somatic mutation during metastasis of a mouse fibrosarcoma line detected by DNA fingerprint analysis. Jpn J Cancer Res 1992; 83:165-70. [PMID: 1555998 PMCID: PMC5918783 DOI: 10.1111/j.1349-7006.1992.tb00082.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metastatic nodules were examined by DNA fingerprint analysis. The probes used, Pc-1 and Pc-2, detect mutations as shifts in bands of the minisatellite loci which are dispersed among chromosomes. Four clonal lines of a fibrosarcoma from an F1 mouse (C57BL/Ka x C3H/He) were selected for various metastatic potentials upon inoculation into syngeneic mice. These four lines exhibited many extra bands resulting from recombination and/or DNA slippage, indicating accumulation of mutations during the successive passages in mice. One of the four, a 505 cell line which had been passaged extensively in vitro and consisted of a heterogenous population, was inoculated into thirteen syngeneic mice, and gave rise to six lung metastatic nodules in two mice. All the nodules showed band-patterns distinct from one another, although nodules within a given mouse tended to show similar patterns. When a genetically tagged 505-05-01 clone was analyzed, three of nine metastatic nodules obtained also revealed new bands. These results strongly suggest that somatic mutations occur at a high frequency during metastasis, providing direct evidence of genetic instability of the tumor cells.
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Affiliation(s)
- T Takada
- First Department of Biochemistry, Niigata University School of Medicine
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Abstract
Quercetin, a flavonoid, is found in many fruits and vegetables. This drug was previously shown to affect the metastatic potential of mouse tumor cells. Mutagenicity of quercetin was examined by means of DNA fingerprint analysis using the Pc-1 probe that efficiently detects mutations due to recombination. Treatment of BMT-11 and FM3A tumor cells with 55 microM quercetin resulted in gain and loss of bands in the fingerprints in both cell lines. The frequencies of the clones having undergone mutation were 3/11 and 6/26, respectively. This suggests that quercetin is mutagenic and induces recombination. This result seems to provide a molecular basis for the phenotypic variations of BMT-11 tumor cells induced by quercetin.
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Affiliation(s)
- S Suzuki
- First Department of Biochemistry, Niigata University School of Medicine
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