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You searched for: Publication Year 2009 Remove constraint Publication Year: 2009 Subject term DNA primers Remove constraint Subject term: DNA primers Text Availability Full Text Remove constraint Text Availability: Full Text
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1. Analysis of Two Gene Clusters Involved in the Degradation of 4-Fluorophenol by Arthrobacter sp. Strain IF1

Author:
Ferreira, Maria Isabel M.; Iida, Toshiya; Hasan, Syed A.; Nakamura, Kaoru; Fraaije, Marco W.; Janssen, Dick B.; Kudo, Toshiaki
Source:
Applied and environmental microbiology 2009 v.75 no.24 pp. 7767-7773
ISSN:
0099-2240
Subject:
Arthrobacter; DNA libraries; DNA primers; Escherichia coli; NAD (coenzyme); Northern blotting; adenine; carbon; clones; dehalogenation; energy; gene expression; hydroquinone; hydroxylation; multigene family; p-nitrophenol; reverse transcriptase polymerase chain reaction; screening
Abstract:
... Arthrobacter sp. strain IF1 is able to grow on 4-fluorophenol (4-FP) as a sole source of carbon and energy. To clone the 4-FP degradation genes, DNA libraries were constructed and screened with a probe obtained by PCR using primers designed on the basis of conserved regions of aromatic two-component monooxygenases. Sequencing of positive clones yielded two gene clusters, each harboring a gene enco ...
DOI:
10.1128/AEM.00171-09
PubMed:
19837837
PubMed Central:
PMC2794112

2. Biodiversity of Thermophilic Prokaryotes with Hydrolytic Activities in Hot Springs of Uzon Caldera, Kamchatka (Russia)

Author:
Kublanov, Ilya V.; Perevalova, Anna A.; Slobodkina, Galina B.; Lebedinsky, Aleksander V.; Bidzhieva, Salima K.; Kolganova, Tatyana V.; Kaliberda, Elena N.; Rumsh, Lev D.; Haertlé, Thomas; Bonch-Osmolovskaya, Elizaveta A.
Source:
Applied and environmental microbiology 2009 v.75 no.1 pp. 286-291
ISSN:
0099-2240
Subject:
denaturing gradient gel electrophoresis; prokaryotic cells; ribosomal RNA; DNA primers; springs (water); genes; sediments; clones; Crenarchaeota; bacterial communities; carboxymethylcellulose; Dictyoglomus; albumins; polymerase chain reaction; casein; enrichment culture; biodiversity; Caldicellulosiruptor; temperature; chitin; Thermotogales; pH; polymers; Russia
Abstract:
... Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87°C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or α- or β-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydro ...
DOI:
10.1128/AEM.00607-08
PubMed:
18978089
PubMed Central:
PMC2612224

3. Broadly Reactive Pan-Paramyxovirus Reverse Transcription Polymerase Chain Reaction and Sequence Analysis for the Detection of Canine Distemper Virus in a Case of Canine Meningoencephalitis of Unknown Etiology

Author:
Scott J. Schatzberg; Qiang Li; Brian F. Porter; Renee M. Barber; Mary Kate Claiborne; Jonathan M. Levine; Gwendolyn J. Levine; Sarah K. Israel; Benjamin D. Young; Matti Kiupel; Craig Greene; Susan Ruone; Larry Anderson; Suxiang Tong
Source:
Journal of veterinary diagnostic investigation v.21 no.6 pp. 844-849
ISSN:
1040-6387
Subject:
phosphoproteins; peripheral nervous system diseases; dogs; Canine morbillivirus; brain; reverse transcriptase polymerase chain reaction; DNA primers; pathogen identification; canine distemper; genes; necropsy; nucleotide sequences; vaccination; meningoencephalitis; case studies; signs and symptoms (animals and humans); disease diagnosis
Abstract:
... Despite the immunologic protection associated with routine vaccination protocols, Canine distemper virus (CDV) remains an important pathogen of dogs. Antemortem diagnosis of systemic CDV infection may be made by reverse transcription polymerase chain reaction (RT-PCR) and/or immunohistochemical testing for CDV antigen; central nervous system infection often requires postmortem confirmation via his ...
DOI:
10.1177/104063870902100613
PubMed:
19901287
PubMed Central:
PMC5052812

4. Characterization of a Dehalobacter Coculture That Dechlorinates 1,2-Dichloroethane to Ethene and Identification of the Putative Reductive Dehalogenase Gene

Author:
Grostern, Ariel; Edwards, Elizabeth A.
Source:
Applied and environmental microbiology 2009 v.75 no.9 pp. 2684-2693
ISSN:
0099-2240
Subject:
Acetobacterium; DNA primers; Dehalobacter; RNA-directed DNA polymerase; coculture; dechlorination; enrichment culture; ethylene; ethylene dichloride; genes; mixed culture; polymerase chain reaction; ribosomal RNA
Abstract:
... Dehalobacter and "Dehalococcoides" spp. were previously shown to be involved in the biotransformation of 1,1,2-trichloroethane (1,1,2-TCA) and 1,2-dichloroethane (1,2-DCA) to ethene in a mixed anaerobic enrichment culture. Here we report the further enrichment and characterization of a Dehalobacter sp. from this mixed culture in coculture with an Acetobacterium sp. Through a series of serial trans ...
DOI:
10.1128/AEM.02037-08
PubMed:
19270140
PubMed Central:
PMC2681677

5. Cloning and Characterization of an Intracellular Esterase from the Wine-Associated Lactic Acid Bacterium Oenococcus oeni

Author:
Sumby, Krista M.; Matthews, Angela H.; Grbin, Paul R.; Jiranek, Vladimir
Source:
Applied and environmental microbiology 2009 v.75 no.21 pp. 6729-6735
ISSN:
0099-2240
Subject:
DNA primers; Escherichia coli; Oenococcus oeni; amino acid sequences; clones; enzymes; ethanol; genes; lactic acid bacteria; open reading frames; pH; polymerase chain reaction; temperature; winemaking; wines
Abstract:
... We report the cloning and characterization of EstB28, the first esterase to be so characterized from the wine-associated lactic acid bacterium, Oenococcus oeni. The published sequence for O. oeni strain PSU-1 was used to identify putative esterase genes and design PCR primers in order to amplify the corresponding region from strain Ooeni28, an isolate intended for inoculation of wines. In this way ...
DOI:
10.1128/AEM.01563-09
PubMed:
19734337
PubMed Central:
PMC2772441

6. Combination of Chromogenic Differential Medium and estA-Specific PCR for Isolation and Detection of Phytopathogenic Xanthomonas spp

Author:
Lee, Yung-An; Sung, Ai-Ning; Liu, Tzu-Fen; Lee, Yung-Shan
Source:
Applied and environmental microbiology 2009 v.75 no.21 pp. 6831-6838
ISSN:
0099-2240
Subject:
DNA; DNA primers; Escherichia coli; Stenotrophomonas maltophilia; Xanthomonas campestris pv. campestris; antibiotics; bacteria; cabbage; color; genes; hydrolysis; isolation techniques; nucleotide sequences; polymerase chain reaction; seeds
Abstract:
... A xanthomonad differential medium (designated Xan-D medium) was developed, on which streaks and colonies of xanthomonads, including 13 species of the genus Xanthomonas, turned wet-shining yellow-green and were surrounded with a smaller milky zone and a bigger clear zone in 3 to 4 days. The characteristics could easily be differentiated from those of yellow nonxanthomonads and other bacteria. The m ...
DOI:
10.1128/AEM.01653-09
PubMed:
19749062
PubMed Central:
PMC2772435

7. ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery

Author:
You, Frank M.; Huo, Naxin; Lazo, Gerard R.; Dvorak, Jan; Anderson, Olin D.
Source:
BMC bioinformatics 2009 v.10 no.331 pp. -
ISSN:
1471-2105
Subject:
DNA primers; polymerase chain reaction; wheat; expressed sequence tags; Triticum aestivum; introns; single nucleotide polymorphism
Abstract:
... Background: In some genomic applications it is necessary to design large numbers of PCR primers in exons flanking one or several introns on the basis of orthologous gene sequences in related species. The primer pairs designed by this target gene approach are called "intron-flanking primers" or because they are located in exonic sequences which are usually conserved between related species, "conser ...
Handle:
10113/40810
DOI:
10.1186/1471-2105-10-33
PubMed:
19171029
PubMed Central:
PMC2656475

8. DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton

Author:
Yingzhi Lu; Jessica Curtiss; R. G. Percy; S. E. Hughs; Shuxun Yu; Jinfa Zhang
Source:
Crop science 2009 v.49 no.5 pp. 1695-1704
ISSN:
0011-183X
Subject:
cotton; plant development; Gossypium hirsutum; DNA primers; polymerase chain reaction; Gossypium barbadense; genes; genetic markers; single nucleotide polymorphism
Abstract:
... The lack of genetic diversity within cultivated upland cotton (Gossypium hirsutum L.) has hindered the construction of genomewide linkage maps and their applications in genetics and breeding. The objective of this investigation was to develop candidate gene markers for fiber quality and yield on the basis of approximately 90 genes implicated in fiber development. Polymorphisms using sequence-tagge ...
Handle:
10113/35036
DOI:
10.2135/cropsci2008.12.0693

9. Detection and Quantification of Dehalogenimonas and "Dehalococcoides" Populations via PCR-Based Protocols Targeting 16S rRNA Genes

Author:
Yan, Jun; Rash, Brian A.; Rainey, Fred A.; Moe, William M.
Source:
Applied and environmental microbiology 2009 v.75 no.23 pp. 7560-7564
ISSN:
0099-2240
Subject:
DNA primers; Dehalococcoides; genes; nucleotide sequences; polymerase chain reaction; ribosomal RNA
Abstract:
... Members of the haloalkane dechlorinating genus Dehalogenimonas are distantly related to "Dehalococcoides" but share high homology in some variable regions of their 16S rRNA gene sequences. In this study, primers and PCR protocols intended to uniquely target Dehalococcoides were reevaluated, and primers and PCR protocols intended to uniquely target Dehalogenimonas were developed and tested. Use of ...
DOI:
10.1128/AEM.01938-09
PubMed:
19820163
PubMed Central:
PMC2786429

10. Development and characterization of 15 polymorphic microsatellite loci isolated from Rafinesque's big-eared bat, Corynorhinus rafinesquii

Author:
PIAGGIO, ANTOINETTE J.; FIGUEROA, JULIA A.; PERKINS, SUSAN L.
Source:
Molecular ecology notes 2009 v.9 no.4 pp. 1191-1193
ISSN:
1755-0998
Subject:
Chiroptera; loci; microsatellite repeats; genetic markers; genetic polymorphism; alleles; heterozygosity; DNA primers; polymerase chain reaction
Abstract:
... We developed and characterized 15 microsatellite markers for Rafinesque's big-eared bat, Corynorhinus rafinesquii. In a population from Tennessee, the number of alleles per locus ranged from three to 13 and observed heterozygosities were 0.35 to 0.97 per locus. These loci will provide appropriate variability for estimation of population connectivity, demographic parameters, and genetic diversity f ...
Handle:
10113/32230
DOI:
10.1111/j.1755-0998.2009.02625.x
PubMed:
21564872

11. Development of 10 polymorphic microsatellite loci isolated from the mountain beaver, Aplodontia rufa rufa (Rafinesque)

Author:
Piaggio, Antoinette J.; Neubaum, Melissa A.; Yueh, Hesther; Ritland, Carol E.; Johnston, John J.; Perkins, Susan L.
Source:
Molecular ecology notes 2009 v.9 no.1 pp. 323-325
ISSN:
1755-0998
Subject:
sequence analysis; microsatellite repeats; endangered species; loci; DNA primers; polymerase chain reaction; Castoridae; genetic polymorphism
Abstract:
... We developed 10 microsatellite markers for the mountain beaver, Aplodontia rufa rufa. In three populations of A. r. rufa, the number of alleles for these loci ranged from monomorphic to nine. Average observed heterozygosities in these populations ranged from 0.29 to 0.60. We also tested previously published markers from the endangered subspecies A. r. nigra in A. r. rufa populations. ...
Handle:
10113/23139
DOI:
10.1111/j.1755-0998.2008.02382.x
PubMed:
21564639

12. Development of a Cell Culture Method To Isolate and Enrich Salmonella enterica Serotype Enteritidis from Shell Eggs for Subsequent Detection by Real-Time PCR

Author:
Day, J.B.; Basavanna, U.; Sharma, S.K.
Source:
Applied and environmental microbiology 2009 v.75 no.16 pp. 5321-5327
ISSN:
0099-2240
Subject:
feeds; DNA primers; genes; ingestion; Salmonella Enteritidis; xylose; DNA; macrophages; food microbiology; international organizations; lysine; cell culture; hosts; polymerase chain reaction; eukaryotic cells; raw eggs; serotypes; mice; eggs; egg shell; salmonellosis; reference standards; bacteria
Abstract:
... Salmonella enterica serotype Enteritidis is a major cause of nontyphoidal salmonellosis from ingestion of contaminated raw or undercooked shell eggs. Current techniques used to identify Salmonella serotype Enteritidis in eggs are extremely laborious and time-consuming. In this study, a novel eukaryotic cell culture system was combined with real-time PCR analysis to rapidly identify Salmonella sero ...
DOI:
10.1128/AEM.02422-08
PubMed:
19561188
PubMed Central:
PMC2725483

13. Development of a Multiplex Real-Time PCR for Detection and Differentiation of Malignant Catarrhal Fever Viruses in Clinical Samples

Author:
Cunha, Cristina W.; Otto, Lisa; Taus, Naomi S.; Knowles, Donald P.; Li, Hong
Source:
Journal of clinical microbiology JCM 2009 v.47 no.8 pp. 2586-2589
ISSN:
0095-1137
Subject:
DNA primers; fluorescence; polymerase chain reaction; microbial detection; Alcelaphine gammaherpesvirus 1
Abstract:
... A multiplex real-time PCR was developed using a single pair of primers and fluorescent probes specific for five malignant catarrhal fever viruses and an internal positive control. The assay was able to simultaneously detect and differentiate the viruses in clinical samples with high sensitivity (97.2%) and specificity (100%). ...
Handle:
10113/35869
DOI:
10.1128/JCM.00997-09
PubMed:
19494077
PubMed Central:
PMC2725674

14. Discovery and characterization of a molecular marker for Sclerotinia minor (Jagger) resistance in peanut

Author:
Chenault, Kelly D.; Maas, Andrea L.; Damicone, John P.; Payton, Mark E.; Melouk, Hassan A.
Source:
Euphytica 2009 v.166 no.3 pp. 357-365
ISSN:
0014-2336
Subject:
Arachis hypogaea; peanuts; disease resistance; Sclerotinia minor; blight; fungal diseases of plants; genetic markers; microsatellite repeats; polymerase chain reaction; DNA primers; genotype
Abstract:
... The production of cultivated peanut, an important agronomic crop throughout the United States and the world, is consistently threatened by various diseases and pests. Sclerotinia minor Jagger (S. minor), the causal agent of Sclerotinia blight, is a major threat to peanut production in the Southwestern US, Virginia and North Carolina. Although information on the variability of morphological traits ...
Handle:
10113/27152
DOI:
10.1007/s10681-008-9816-0

15. Diversity among mainland USA sugarcane cultivars examined by SSR genotyping

Author:
Glynn, Neil C.; McCorkle, Kay; Comstock, Jack C.
Source:
Journal of the American Society of Sugar Cane Technologists 2009 v.29 pp. 36-52
Subject:
Saccharum officinarum; Saccharum spontaneum; sugarcane; plant breeding; interspecific hybridization; hybrids; genetic variation; cultivars; DNA fingerprinting; microsatellite repeats; simple sequence length polymorphism; alleles; gene frequency; DNA primers; geographical variation; pedigree; cluster analysis; Florida; Louisiana; Texas
Abstract:
... The analysis of variations in SSR fragments provides an effective tool for examining diversity to improve plant breeding strategies. Identifying useful SSRs is critical but in sugarcane this can be a lengthy and difficult process due to their abundance and the complexity of the sugarcane genome. The amplification characteristics of 181 previously designed SSRs were evaluated. DNA from one clone of ...
Handle:
10113/37130

16. Diversity and Stratification of Archaea in a Hypersaline Microbial Mat

Author:
Robertson, Charles E.; Spear, John R.; Harris, J. Kirk; Pace, Norman R.
Source:
Applied and environmental microbiology 2009 v.75 no.7 pp. 1801-1810
ISSN:
0099-2240
Subject:
Crenarchaeota; DNA libraries; DNA primers; bacteria; genes; nucleotide sequences; polymerase chain reaction; ponds; pumps; ribosomal RNA; salinity; seawater; surveys; Mexico; Pacific Ocean
Abstract:
... The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial ...
DOI:
10.1128/AEM.01811-08
PubMed:
19114531
PubMed Central:
PMC2663194

17. Eight polymorphic microsatellite loci developed and characterized from Townsend's big-eared bat, Corynorhinus townsendii

Author:
Piaggio, Antoinette J.; Miller, Katie Erin G.; Matocq, Marjorie D.; Perkins, Susan L.
Source:
Molecular ecology notes 2009 v.9 no.1 pp. 258-260
ISSN:
1755-0998
Subject:
sequence analysis; microsatellite repeats; endangered species; loci; DNA primers; polymerase chain reaction; Chiroptera; gene frequency
Abstract:
... Two of the five subspecies of the western big-eared bat, Corynorhinus townsendii, are listed as federally endangered with the remaining three being of conservation concern. Knowing the degree of connectivity among populations would aid in the establishment of sound conservation and management plans for this taxon. For this purpose, we have developed and characterized eight polymorphic microsatelli ...
Handle:
10113/23138
DOI:
10.1111/j.1755-0998.2008.02243.x
PubMed:
21564620

18. Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis

Author:
Morales, Sergio E.; Holben, William E.
Source:
Applied and environmental microbiology 2009 v.75 no.9 pp. 2677-2683
ISSN:
0099-2240
Subject:
DNA libraries; DNA primers; genes; libraries; microbial ecology; nucleotide sequences; phylogeny; polymerase chain reaction; population dynamics; prokaryotic cells; ribosomal RNA; soil bacteria; soil sampling; variance
Abstract:
... Phylogenetic and "fingerprinting" analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of ...
DOI:
10.1128/AEM.02166-08
PubMed:
19251890
PubMed Central:
PMC2681686

19. Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice

Author:
Fukao, Takeshi; Harris, Tristan; Bailey-Serres, Julia
Source:
Annals of botany 2009 v.103 no.2 pp. 143-150
ISSN:
0305-7364
Subject:
DNA primers; Oryza sativa; alleles; domestication; gene duplication; genetic variation; loci; multigene family; phylogeny; sequence analysis; submergence; wild relatives; wild rice
Abstract:
... BACKGROUND AND AIMS: Tolerance of complete submergence is recognized in a small number of accessions of domesticated Asian rice (Oryza sativa) and can be conferred by the Sub1A-1 gene of the polygenic Submergence-1 (Sub1) locus. In all O. sativa varieties, the Sub1 locus encodes the ethylene-responsive factor (ERF) genes Sub1B and Sub1C. A third paralogous ERF gene, Sub1A, is limited to a subset o ...
DOI:
10.1093/aob/mcn172
PubMed:
18824474
PubMed Central:
PMC2707309

20. Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans

Author:
Liu, Hui; Probert, Ian; Uitz, Julia; Claustre, Hervé; Aris-Brosou, Stéphane; Frada, Miguel; Not, Fabrice; de Vargas, Colomban
Source:
Proceedings of the National Academy of Sciences of the United States of America 2009 v.106 no.31 pp. 12803-12808
ISSN:
0027-8424
Subject:
Cyanobacteria; DNA primers; Haptophyta; biodiversity; biosphere; carbon; chlorophyll; chloroplasts; eukaryotic cells; euphotic zone; genome; oceans; photosynthesis; phylogeny; phytoplankton; polymerase chain reaction; primary productivity
Abstract:
... The current paradigm holds that cyanobacteria, which evolved oxygenic photosynthesis more than 2 billion years ago, are still the major light harvesters driving primary productivity in open oceans. Here we show that tiny unicellular eukaryotes belonging to the photosynthetic lineage of the Haptophyta are dramatically diverse and ecologically dominant in the planktonic photic realm. The use of Hapt ...
DOI:
10.1073/pnas.0905841106
PubMed:
19622724
PubMed Central:
PMC2722306

21. Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein

Author:
Post, Klara; Kankia, Besik; Gopalakrishnan, Swathi; Yang, Victoria; Cramer, Elizabeth; Saladores, Pilar; Gorelick, Robert J.; Guo, Jianhui; Musier-Forsyth, Karin; Levin, Judith G.
Source:
Nucleic acids research 2009 v.37 no.6 pp. 1755-1766
ISSN:
0305-1048
Subject:
RNA-directed DNA polymerase; thermal stability; DNA replication; Human immunodeficiency virus 1; zinc; DNA primers; DNA; models; reverse transcription; nucleotide sequences; ribonucleases; RNA; binding capacity; nucleocapsid proteins
Abstract:
... During minus-strand DNA synthesis, RNase H degrades viral RNA sequences, generating potential plus-strand DNA primers. However, selection of the 3' polypurine tract (PPT) as the exclusive primer is required for formation of viral DNA with the correct 5'-end and for subsequent integration. Here we show a new function for the nucleic acid chaperone activity of HIV-1 nucleocapsid protein (NC) in reve ...
DOI:
10.1093/nar/gkn1045
PubMed:
19158189
PubMed Central:
PMC2665208

22. Genetic Diversity and Host Range Variation of Ralstonia solanacearum Strains Entering North America

Author:
Norman, David J.; Zapata, Mildred; Gabriel, Dean W.; Duan, Y.P.; Yuen, Jeanne M.F.; Mangravita-Novo, Arianna; Donahoo, Ryan S.
Source:
Phytopathology 2009 v.99 no.9 pp. 1070-1077
ISSN:
0031-949X
Subject:
Pelargonium; ornamental plants; bacterial diseases of plants; Ralstonia solanacearum; plant pathogenic bacteria; pathogenicity; signs and symptoms (plants); pathotypes; genetic variation; strain differences; host range; Solanum lycopersicum var. lycopersicum; tomatoes; Nicotiana tabacum; tobacco; Solanum tuberosum; potatoes; Anthurium; Epipremnum pinnatum; pathogen identification; DNA primers; cytochrome b; genes; nucleotide sequences; polymerase chain reaction; provenance; United States
Abstract:
... Each year, large volumes of ornamental and food plant propagative stock are imported into the North America; occasionally, Ralstonia solanacearum is found systemically infecting this plant material. In this study, 107 new R. solanacearum strains were collected over a 10-year period from imported propagative stock and compared with 32 previously characterized R. solanacearum strains using repetitiv ...
Handle:
10113/35167
DOI:
10.1094/PHYTO-99-9-1070
PubMed:
19671009

23. Genomic Regions Conserved in Lineage II Escherichia coli O157:H7 Strains

Author:
Steele, Marina; Ziebell, Kim; Zhang, Yongxiang; Benson, Andrew; Johnson, Roger; Laing, Chad; Taboada, Eduardo; Gannon, Victor
Source:
Applied and environmental microbiology 2009 v.75 no.10 pp. 3271-3280
ISSN:
0099-2240
Subject:
DNA primers; Escherichia coli O157; bacteriophages; genotype; genotyping; human diseases; humans; loci; nucleotide sequences; pathogens; polymerase chain reaction; sequence analysis; suppression subtractive hybridization; virulence
Abstract:
... Populations of the food- and waterborne pathogen Escherichia coli O157:H7 are comprised of two major lineages. Recent studies have shown that specific genotypes within these lineages differ substantially in the frequencies with which they are associated with human clinical disease. While the nucleotide sequences of the genomes of lineage I strains E. coli O157 Sakai and EDL9333 have been determine ...
DOI:
10.1128/AEM.02123-08
PubMed:
19329668
PubMed Central:
PMC2681618

24. Hierarchical Oligonucleotide Primer Extension as a Time- and Cost-Effective Approach for Quantitative Determination of Bifidobacterium spp. in Infant Feces

Author:
Hong, Pei-Ying; Yap, Gaik Chin; Lee, Bee Wah; Chua, Kaw Yan; Liu, Wen-Tso
Source:
Applied and environmental microbiology 2009 v.75 no.8 pp. 2573-2576
ISSN:
0099-2240
Subject:
Bifidobacterium longum; DNA primers; eczema; feces; fluorescence; genes; hybridization; infants; ribosomal RNA
Abstract:
... The Bifidobacterium spp. present in 10 infant fecal samples (4 from infants with eczema and 6 from healthy infants) were quantified with both hierarchical oligonucleotide primer extension (HOPE) and fluorescence in situ hybridization-flow cytometry. The relative abundances of Bifidobacterium longum and B. catenulatum with respect to the total bifidobacteria had a poor correlation (ρ, <0.600; P val ...
DOI:
10.1128/AEM.02576-08
PubMed:
19218419
PubMed Central:
PMC2675208

25. High-Throughput Molecular Determination of Salmonella enterica Serovars by Use of Multiplex PCR and Capillary Electrophoresis Analysis

Author:
Leader, Brandon T.; Frye, Jonathan G.; Hu, Jinxin; Fedorka-Cray, Paula J.; Boyle, David S.
Source:
Journal of clinical microbiology JCM 2009 v.47 no.5 pp. 1290-1299
ISSN:
0095-1137
Subject:
Salmonella enterica; serotypes; polymerase chain reaction; capillary electrophoresis; DNA primers; fluorescent dyes; fluorescent labeling; microbial genetics; pathogen identification
Abstract:
... Salmonella enterica is a leading cause of food-borne illness worldwide and is also a major cause of morbidity and mortality in domestic and wild animals. In the current study, a high-throughput molecular assay was developed to determine the most common clinical and nonhuman serovars of S. enterica in the United States. Sixteen genomic targets were identified based on their differential distributio ...
Handle:
10113/37270
DOI:
10.1128/JCM.02095-08
PubMed:
19261787
PubMed Central:
PMC2681873

26. Improved DNA Barcoding Method for Bemisia tabaci and Related Aleyrodidae: Development of Universal and Bemisia tabaci Biotype-Specific Mitochondrial Cytochrome c Oxidase I Polymerase Chain Reaction Primers

Author:
Shatters, Robert G. Jr.; Powell, Charles A.; Boykin, Laura M.; Liansheng, He; McKenzie, C.L.
Source:
Journal of economic entomology 2009 v.102 no.2 pp. 750-758
ISSN:
0022-0493
Subject:
sequence analysis; Bemisia tabaci; mitochondrial DNA; DNA primers; polymerase chain reaction; rapid methods; biotypes; cytochrome-c oxidase; molecular systematics; pest identification
Abstract:
... Whiteflies, heteropterans in the family Aleyrodidae, are globally distributed and severe agricultural pests. The mitochondrial cytochrome c oxidase I (mtCOI) sequence has been used extensively in whitefly phylogenetic comparisons and in biotype identification of the agriculturally important Bemisia tabaci (Gennadius) whitefly. Because of the economic importance of several whitefly genera, and the ...
Handle:
10113/29041
DOI:
10.1603/029.102.0236
PubMed:
19449657

27. Integrative placement and orientation of non-redundant SSR loci in cotton linkage groups by deficiency analysis

Author:
Gutiérrez, Osman A.; Stelly, David M.; Saha, Sukumar; Jenkins, Johnie N.; McCarty, Jack C. Jr; Raska, Dwaine A.; Scheffler, Brian E.
Source:
Molecular breeding 2009 v.23 no.4 pp. 693-707
ISSN:
1380-3743
Subject:
plant genetics; Gossypium hirsutum; Gossypium barbadense; Gossypium tomentosum; cotton; microsatellite repeats; chromosome mapping; linkage (genetics); aneuploidy; DNA primers; genetic polymorphism; gene duplication; gene deletion; centromeres
Abstract:
... A combination of previously mapped and unmapped non-redundant SSR loci, using 381 primer pairs were chromosomally and sub-chromosomally localized by deficiency analysis of two sets of quasi-isogenic interspecific Gossypium hirsutum L. hypoaneuploid F₁ hybrids involving Gossypium barbadense L. and Gossypium tomentosum (Nuttall ex Seemann). Polymorphisms were detected for 369 SSR primer pairs. A tot ...
Handle:
10113/44255
DOI:
10.1007/s11032-009-9266-y

28. Interaction of fish aryl hydrocarbon receptor paralogs (AHR1 and AHR2) with the retinoblastoma protein

Author:
Merson, Rebeka R.; Karchner, Sibel I.; Hahn, Mark E.
Source:
Aquatic toxicology 2009 v.94 no.1 pp. 47-55
ISSN:
0166-445X
Subject:
Fundulus heteroclitus; tetrachlorodibenzo-p-dioxin; water pollution; receptors; cytotoxicity; in vitro studies; messenger RNA; gene expression; complementary DNA; molecular cloning; polymerase chain reaction; neoplasms; DNA primers; nucleotide sequences
Abstract:
... The aryl hydrocarbon receptor (AHR) mediates the toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds. In some mammalian cell lines, TCDD induces G1 cell cycle arrest, which depends on an interaction between the AHR and the retinoblastoma tumor suppressor (RB). Mammals possess one AHR, whereas fishes possess two or more AHR paralogs that differ in the domains important ...
DOI:
10.1016/j.aquatox.2009.05.015
PubMed:
19539383
PubMed Central:
PMC2833323

29. Molecular Diagnostic for Boll Weevil (Coleoptera: Curculionidae) Based on Amplification of Three Species-Specific Microsatellites

Author:
Kim, Kyung Seok; Szendrei, Zsofia; Rodriguez-Saona, Cesar; Mulder, Phillip G. Jr.; Sappington, Thomas W.
Source:
Journal of economic entomology 2009 v.102 no.2 pp. 759-766
ISSN:
0022-0493
Subject:
Anthonomus grandis grandis; pest identification; insect taxonomy; molecular systematics; microsatellite repeats; genetic markers; internal transcribed spacers; DNA primers; polymerase chain reaction
Abstract:
... The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a serious pest of cultivated cotton, Gossypium hirsutum L., in the Americas, and reinfestation of zones from which they have been eradicated is of perpetual concern. Extensive arrays of pheromone traps monitor for reintroductions, but occasionally the traps collect nontarget weevils that can be misidentified by sco ...
Handle:
10113/28705
DOI:
10.1603/029.102.0237
PubMed:
19449658

30. Molecular and morpho-physiological characterization of sea, ruderal and cultivated beets

Author:
Saccomani, Massimo; Stevanato, Piergiorgio; Trebbi, Daniele; McGrath, J. Mitchell; Biancardi, Enrico
Source:
Euphytica 2009 v.169 no.1 pp. 19-29
ISSN:
0014-2336
Subject:
DNA primers; roots; sulfates; glucose; fructose; Beta vulgaris subsp. maritima; wild relatives; cultivars; sugar beet; genetic improvement; nutrient deficiencies; Beta vulgaris subsp. vulgaris; nutrient requirements; plant genetic resources; abiotic stress; plant physiology; stress tolerance; genetic variation; agronomic traits; gene amplification; plant morphology; chemical constituents of plants; germplasm screening; Italy
Abstract:
... Beta vulgaris genetic resources are essential for broadening genetic base of sugar beet and developing cultivars adapted to adverse environmental conditions. Wild beets (sea beets, B. vulgaris spp. maritima and their naturalized introgressions with cultivated beets known as ruderal beets) harbor substantial genetic diversity that could be useful for beet improvement. Here, we compared molecular an ...
Handle:
10113/33587
DOI:
10.1007/s10681-009-9888-5

31. Molecular characterization of swine leucocyte antigen class I genes in outbred pig populations

Author:
Ho, C.-S.; Lunney, J.K.; Franzo-Romain, M.H.; Martens, G.W.; Lee, Y.-J.; Lee, J.-H.; Wysocki, M.; Rowland, R.R.R.; Smith, D.M.
Source:
Animal genetics 2009 v.40 no.4 pp. 468-478
ISSN:
0268-9146
Subject:
outbred lines; alleles; loci; haplotypes; DNA primers; polymerase chain reaction; major histocompatibility complex; swine
Abstract:
... The highly polymorphic swine leucocyte antigen (SLA) genes are one of the most important determinants in swine immune responses to infectious diseases, vaccines, and in transplantation success. Study of SLA influence requires accurate and effective typing methods. We developed a simple and rapid method to type alleles at the three classical SLA class I loci (SLA-1, SLA-3 and SLA-2) using the PCR-s ...
Handle:
10113/41899
DOI:
10.1111/j.1365-2052.2009.01860.x
PubMed:
19392823

32. Multiplex primer prediction software for divergent targets

Author:
Gardner, Shea N.; Hiddessen, Amy L.; Williams, Peter L.; Hara, Christine; Wagner, Mark C.; Colston, Bill W. Jr.
Source:
Nucleic acids research 2009 v.37 no.19 pp. 6291-6304
ISSN:
0305-1048
Subject:
DNA primers; Foot-and-mouth disease virus; Human immunodeficiency virus 1; Influenza A virus; Norwalk virus; Vaccinia virus; algorithms; computer software; hemagglutinins; nucleic acids; prediction; sequence alignment; sialidase; viruses
Abstract:
... We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are ...
DOI:
10.1093/nar/gkp659
PubMed:
19759213
PubMed Central:
PMC2770652

33. New Design Strategy for Development of Specific Primer Sets for PCR-Based Detection of Chlorophyceae and Bacillariophyceae in Environmental Samples

Author:
Valiente Moro, Claire; Crouzet, Olivier; Rasconi, Séréna; Thouvenot, Antoine; Coffe, Gérard; Batisson, Isabelle; Bohatier, Jacques
Source:
Applied and environmental microbiology 2009 v.75 no.17 pp. 5729-5733
ISSN:
0099-2240
Subject:
Bacillariophyceae; Chlorophyceae; DNA primers; aquatic environment; biodiversity; computer software; fungi; genes; health status; limnology; microalgae; polymerase chain reaction; ribosomal RNA; water quality
Abstract:
... Studying aquatic microalgae is essential for monitoring biodiversity and water quality. We designed new sets of 18S rRNA PCR primers for Chlorophyceae and Bacillariophyceae by using the ARB software and implementing a virtual PCR program. The results of specificity analysis showed that most of the targeted algal families were identified and nontargeted organisms, such as fungi or ciliates, were ex ...
DOI:
10.1128/AEM.00509-09
PubMed:
19592531
PubMed Central:
PMC2737940

34. New SSR Markers for Use in Cotton (Gossypium spp.) Improvement

Author:
Xiao, J.; Wu, K.; Fang, David D.; Stelly, David M.; Yu, John; Cantrell, Roy G.
Source:
Journal of cotton science 2009 v.13 no.2 pp. 75-157
ISSN:
1524-3303
Subject:
Gossypium hirsutum; microsatellite repeats; genetic markers; DNA libraries; expressed sequence tags; DNA primers; linkage groups; chromosome mapping; genetic polymorphism; genetic improvement; plant genetic resources
Abstract:
... SSR markers, also known as microsatellite DNA markers, are very useful for saturation of the large and complex upland cotton (Gossypium hirsutum L.) genetic linkage map. Monsanto has invested heavily in development of cotton SSRs and has implemented molecular breeding technologies for the genetic improvement of cotton globally and the acceleration of the integration of biotechnology traits into th ...
Handle:
10113/32314

35. Nineteen Novel Microsatellite Markers for the Olympia Oyster, Ostrea conchaphila/lurida

Author:
David A. Stick; Chris J. Langdon; Michael A. Banks; Mark D. Camara
Source:
Molecular ecology notes 2009 v.9 pp. 153-155
ISSN:
1755-0998
Subject:
DNA primers; Ostrea; chromosome mapping; clones; genetic markers; genomic libraries; heterozygosity; loci; microsatellite repeats; oysters; pedigree; polymerase chain reaction; population structure
Abstract:
... Accurate evaluation of remnant Ostrea conchaphila/lurida population structure is critical for developing appropriate restoration efforts. Here we report 19 polymorphic microsatellites suitable for analyses of population differentiation, pedigree reconstruction and linkage map construction. We screened clones from four enriched genomic libraries, identified 73 microsatellite-containing sequences an ...
Handle:
10113/55640
DOI:
10.1111/j.1755-0998.2008.02413.x
PubMed:
21564588

36. Pathway Analysis of Ceratitis capitata (Diptera: Tephritidae) Using Mitochondrial DNA

Author:
Barr, Norman B.
Source:
Journal of economic entomology 2009 v.102 no.1 pp. 401-411
ISSN:
0022-0493
Subject:
restriction fragment length polymorphism; sequence analysis; haplotypes; mitochondrial DNA; DNA primers; polymerase chain reaction; fruit flies; genetic variation; Ceratitis capitata; population structure; genetic markers
Abstract:
... The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method described in a previous publication to document worldwide population structure of Mediterranean fruit flies and analyze probable sources of fly introductions is re-evaluated. Analysis of representatives of the RFLP-based markers using the ND5-tRNA-ND4 mitochondrial locus through DNA sequencing shows that the o ...
Handle:
10113/29070
DOI:
10.1603/029.102.0153
PubMed:
19253662

37. Phylogenetic Analysis Indicates Evolutionary Diversity and Environmental Segregation of Marine Podovirus DNA Polymerase Gene Sequences

Author:
Labonté, Jessica M.; Reid, Karen E.; Suttle, Curtis A.
Source:
Applied and environmental microbiology 2009 v.75 no.11 pp. 3634-3640
ISSN:
0099-2240
Subject:
DNA; DNA primers; DNA-directed DNA polymerase; bacteriophages; cameras; coastal water; databases; genes; genetic variation; genotype; marine environment; metagenomics; nucleotide sequences; oceans; phylogeny; polymerase chain reaction; restriction fragment length polymorphism; British Columbia; Gulf of Mexico
Abstract:
... The distribution of viral genotypes in the ocean and their evolutionary relatedness remain poorly constrained. This paper presents data on the genetic diversity and evolutionary relationships of 1.2-kb DNA polymerase (pol) gene fragments from podoviruses. A newly designed set of PCR primers was used to amplify DNA directly from coastal sediment and water samples collected from inlets adjacent to t ...
DOI:
10.1128/AEM.02317-08
PubMed:
19363063
PubMed Central:
PMC2687296

38. A Phytoplasma Related to 'Candidatus Phytoplasma asteri' Detected in Citrus Showing Huanglongbing (Yellow Shoot Disease) Symptoms in Guangdong, P. R. China

Author:
Chen, J.; Pu, X.; Deng, X.; Liu, S.; Li, H.; Civerolo, E.
Source:
Phytopathology 2009 v.99 no.3 pp. 236-242
ISSN:
0031-949X
Subject:
Phytoplasma; greening disease; phytoplasmal diseases; Candidatus Liberibacter; strains; signs and symptoms (plants); polymerase chain reaction; nucleotide sequences; DNA primers; sequence analysis; disease detection; Catharanthus roseus; Citrus reticulata; Citrus sinensis; Citrus maxima; correlation; China
Abstract:
... Citrus huanglongbing (HLB) or yellow shoot disease (i.e., greening disease) is highly destructive to citrus production worldwide. Understanding the etiology of HLB is critical for managing the disease. HLB is currently associated with infection by 'Candidatus Liberibacter spp.' around the world, including China. However, Koch's postulates have not been fulfilled. In addition, other plant pathogens ...
Handle:
10113/29150
DOI:
10.1094/PHYTO-99-3-0236
PubMed:
19203275

39. Promoter anchored amplified polymorphism based on random amplified polymorphic DNA (PAAP-RAPD) in cotton

Author:
Pang, Mingxiong; Percy, R. G.; Hughs, Ed.; Zhang, Jinfa
Source:
Euphytica 2009 v.167 no.3 pp. 281-291
ISSN:
0014-2336
Subject:
Gossypium hirsutum; Gossypium barbadense; cotton; promoter regions; random amplified polymorphic DNA technique; DNA primers; genetic markers
Abstract:
... Non-coding sequences account for a majority of the higher plant genome, some of which have important effects in gene regulation and plant development. In an effort to develop molecular marker systems to search for polymorphisms associated with high fiber yield and quality in cotton, we have developed a methodology that could specifically target the regulatory regions of the cotton genome. In this ...
Handle:
10113/29078
DOI:
10.1007/s10681-008-9850-y

40. Quantitative evaluation of DNA methylation by optimization of a differential-high resolution melt analysis protocol

Author:
Malentacchi, Francesca; Forni, Giulia; Vinci, Serena; Orlando, Claudio
Source:
Nucleic acids research 2009 v.37 no.12 pp. e86
ISSN:
0305-1048
Subject:
DNA; DNA methylation; DNA primers; body fluids; carcinogenesis; drugs; fluorescence; genes; melting; melting point; nucleotide sequences; patients; polymerase chain reaction; quantitative analysis; transcription (genetics); urinary bladder neoplasms
Abstract:
... DNA methylation is a key regulator of gene transcription. Alterations in DNA methylation patterns are common in most cancers, occur early in carcinogenesis and can be detected in body fluids. Reliable and sensitive quantitative assays are required to improve the diagnostic role of methylation in the management of cancer patients. Here we present an optimized procedure, based on differential-high r ...
DOI:
10.1093/nar/gkp383
PubMed:
19454604
PubMed Central:
PMC2709587

41. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

Author:
Wanjugi, Humphrey; Coleman-Derr, Devin; Huo, Naxin; Kianian, Shahryar F.; Luo, Ming-Cheng; Wu, Jiajie; Anderson, Olin; Gu, Yong Qiang
Source:
Genome = 2009 v.52 no.6 pp. 576-587
ISSN:
0831-2796
Subject:
retrotransposons; genome; DNA primers; polymerase chain reaction; wheat; Triticum aestivum; physical chromosome mapping; genetic markers
Abstract:
... In hexaploid wheat (Triticum aestivum L.) (AABBDD, C = 17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we expl ...
Handle:
10113/32670
DOI:
10.1139/g09-033
PubMed:
19483776

42. An Rrf2-Type Transcriptional Regulator Is Required for Expression of psaAB Genes in the Cyanobacterium Synechocystis sp. PCC 6803

Author:
Midorikawa, Takafumi; Matsumoto, Koji; Narikawa, Rei; Ikeuchi, Masahiko
Source:
Plant physiology 2009 v.151 no.2 pp. 882-892
ISSN:
0032-0889
Subject:
protein binding; phenotype; Synechocystis; DNA primers; gene expression regulation; gene expression; photosystem II; mutants; photosystem I; chlorophyll; autotrophs; promoter regions
Abstract:
... Photosynthetic organisms must regulate photosystem stoichiometry (photosystem I-to-photosystem II ratio) under various light conditions. Transcriptional regulation of the psaAB genes is a critical process for this photoacclimation in cyanobacteria. In the course of our screening of transcriptional regulators in the cyanobacterium Synechocystis sp. PCC 6803, we found that chlorophyll accumulation w ...
DOI:
10.1104/pp.109.141390
PubMed:
19692537
PubMed Central:
PMC2754614

43. Seasonal Dynamics and Metagenomic Characterization of Estuarine Viriobenthos Assemblages by Randomly Amplified Polymorphic DNA PCR

Author:
Helton, Rebekah R.; Wommack, K. Eric
Source:
Applied and environmental microbiology 2009 v.75 no.8 pp. 2259-2265
ISSN:
0099-2240
Subject:
DNA primers; Myoviridae; Podoviridae; amino acid sequences; bacteriophages; cluster analysis; databases; estuarine sediments; genetic variation; metagenomics; proteins; random amplified polymorphic DNA technique; sequence homology; Chesapeake Bay
Abstract:
... Direct enumeration and genetic analyses indicate that aquatic sediments harbor abundant and diverse viral communities. Thus far, synecological analysis of estuarine sediment viral diversity over an annual cycle has not been reported. This oversight is due in large part to a lack of molecular genetic approaches for assessing viral diversity within a large collection of environmental samples. Here, ...
DOI:
10.1128/AEM.02551-08
PubMed:
19218408
PubMed Central:
PMC2675235

44. Sequencing and Analysis of Fungal rRNA Operons for Development of Broad-Range Fungal PCR Assays

Author:
Khot, Prasanna D.; Ko, Daisy L.; Fredricks, David N.
Source:
Applied and environmental microbiology 2009 v.75 no.6 pp. 1559-1565
ISSN:
0099-2240
Subject:
DNA; DNA primers; databases; fungi; gene targeting; internal transcribed spacers; operon; pathogen identification; pathogens; phylogeny; polymerase chain reaction; ribosomal RNA; sequence homology; taxonomy
Abstract:
... rRNA genes are attractive targets for developing PCR assays targeting human fungal pathogens. Most studies have focused on the 18S rRNA gene, internal transcribed spacers, and the 5' end of the 28S rRNA gene. An approximately 2,900-bp region of the 28S rRNA gene remains largely unexplored because sequences of many medically relevant fungi are either unavailable or undefined in genomic databases. T ...
DOI:
10.1128/AEM.02383-08
PubMed:
19139223
PubMed Central:
PMC2655463

45. Simultaneous detection and identification of four sugarcane viruses by one-step RT-PCR

Author:
Xie, Yujia; Wang, Mingqiang; Xu, Donglin; Li, Ruhui; Zhou, Guohui
Source:
Journal of virological methods 2009 v.162 no.1-2 pp. 64-68
Subject:
Sugarcane mosaic virus; Sorghum mosaic virus; Sugarcane yellow leaf virus; reverse transcriptase polymerase chain reaction; DNA primers; microbial detection; Saccharum; sugarcane
Abstract:
... Sugarcane mosaic disease (SMD) caused by the Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV) and Sugarcane streak mosaic virus (SCSMV) and sugarcane yellow leaf disease (SYLD) caused by the Sugarcane yellow leaf virus (SCYLV) are the two most prevalent and economically important viral diseases of sugarcane. In this study, a one-step quadruplex reverse transcription (RT)-PCR method that ...
Handle:
10113/36395
DOI:
10.1016/j.jviromet.2009.07.015

46. Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode

Author:
Geibel, Sebastian; Banchenko, Sofia; Engel, Michael; Lanka, Erich; Saenger, Wolfram
Source:
Proceedings of the National Academy of Sciences of the United States of America 2009 v.106 no.19 pp. 7810-7815
ISSN:
0027-8424
Subject:
DNA primers; DNA replication; active sites; amino acids; crystal structure; models; plasmids; sequence analysis
Abstract:
... For the initiation of DNA replication, dsDNA is unwound by helicases. Primases then recognize specific sequences on the template DNA strands and synthesize complementary oligonucleotide primers that are elongated by DNA polymerases in leading- and lagging-strand mode. The bacterial plasmid RSF1010 provides a model for the initiation of DNA replication, because it encodes the smallest known primase ...
DOI:
10.1073/pnas.0902910106
PubMed:
19416864
PubMed Central:
PMC2683140

47. Universal primers suitable to assess population dynamics reveal apparent mutually exclusive transcription of the Babesia bovis ves1α gene

Author:
Żupańska, Agata K.; Drummond, Paul B.; Swetnam, Daniele M.; Al-Khedery, Basima; Allred, David R.
Source:
Molecular and biochemical parasitology 2009 v.166 no.1 pp. 47-53
ISSN:
0166-6851
Subject:
parasites; Babesia bovis; complementary DNA; antigens; livestock production; DNA primers; monitoring; polymerase chain reaction; antigenic variation; exons; population dynamics; Mexico
Abstract:
... Babesia bovis is an intraerythrocytic hemoparasite of widespread distribution, which adversely affects livestock production in many regions of the world. This parasite establishes persistent infections of long duration, at least in part through rapid antigenic variation of the VESA1 protein on the infected-erythrocyte surface. To understand the dynamics of in vivo antigenic variation among the par ...
DOI:
10.1016/j.molbiopara.2009.02.008
PubMed:
19428672
PubMed Central:
PMC2681252

48. Use of Chimeric DNA-RNA Primers in Quantitative PCR for Detection of Ehrlichia canis and Babesia canis

Author:
Peleg, Ofer; Baneth, Gad; Eyal, Osnat; Inbar, Jacob; Harrus, Shimon
Source:
Applied and environmental microbiology 2009 v.75 no.19 pp. 6393-6398
ISSN:
0099-2240
Subject:
Babesia canis; DNA primers; Ehrlichia canis; byproducts; dogs; genes; polymerase chain reaction; ribosomal RNA
Abstract:
... To overcome the problem of nonspecific by-products in quantitative PCR (qPCR) assays, we constructed DNA-RNA chimeric primers and evaluated their use in the detection and quantification of the Ehrlichia canis 16S rRNA, Babesia canis Hsp70, and canine β-actin genes. Several RNA bases were incorporated into specific positions in the DNA primers, while no RNA stretches were allowed. qPCR reactions we ...
DOI:
10.1128/AEM.00720-09
PubMed:
19633128
PubMed Central:
PMC2753072

49. Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachiswild species

Author:
Xuanqiang Liang; Xiaoping Chen; Yanbin Hong; Haiyan Liu; Guiyuan Zhou; Shaoxiong Li; Baozhu Guo
Source:
BMC plant biology 2009 v.9 no.1 pp. 35
ISSN:
1471-2229
Subject:
sequence analysis; microsatellite repeats; peanuts; alleles; point mutation; DNA primers; expressed sequence tags; genotype; genetic variation; Arachis hypogaea; wild relatives; genetic polymorphism; genetic markers
Abstract:
... BACKGROUND: Lack of sufficient molecular markers hinders current genetic research in peanuts (Arachis hypogaea L.). It is necessary to develop more molecular markers for potential use in peanut genetic research. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining. RESU ...
Handle:
10113/40304
DOI:
10.1186/1471-2229-9-35
PubMed:
19309524
PubMed Central:
PMC2678122

50. A Y genome specific STS marker in Pseudoroegneria and Elymus species (Triticeae: Gramineae)

Author:
Okito, Pungu; Mott, Ivan W.; Wu, Yajun; Wang, Richard R.C.
Source:
Genome = 2009 v.52 no.4 pp. 391-400
ISSN:
0831-2796
Subject:
random amplified polymorphic DNA technique; sequence alignment; genome; DNA primers; Pseudoroegneria; Elymus; repetitive sequences; genetic markers
Abstract:
... The tribe Triticeae Dumortier in the grass family (Poaceae) includes the most important cereal crops (e.g., wheat, barley, and rye) and some economically important forage grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 species occurring worldwide. The genomic constitutions of approximately 40% of Elymus species are unknown and some have unveri ...
Handle:
10113/30449
DOI:
10.1139/g09-015
PubMed:
19370094

51. [FeFe] Hydrogenase Genetic Diversity Provides Insight into Molecular Adaptation in a Saline Microbial Mat Community

Author:
Boyd, Eric S.; Spear, John R.; Peters, John W.
Source:
Applied and environmental microbiology 2009 v.75 no.13 pp. 4620-4623
ISSN:
0099-2240
Subject:
ferredoxin hydrogenase; salt tolerance; biofilm; DNA primers; ponds; polymerase chain reaction; environmental factors; genes; saline water; genetic variation; salt stress; Mexico
Abstract:
... Degenerate primers for the [FeFe] hydrogenase (hydA) were developed and used in PCRs to examine hydA in microbial mats that inhabit saltern evaporative ponds in Guerrero Negro (GN), Mexico. A diversity of deduced HydA was discovered that revealed unique variants, which may reflect adaptation to the environmental conditions present in GN. ...
DOI:
10.1128/AEM.00582-09
PubMed:
19429563
PubMed Central:
PMC2704818