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1. Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

Author:
Kuan-Liang Liu; Andrea Porras-Alfaro; Cheryl R. Kuske; Stephanie A. Eichorst; Gary Xie
Source:
Applied and environmental microbiology 2012 v.78 no.5 pp. 1523-1533
ISSN:
0099-2240
Subject:
DNA primers; databases; educational materials; fungi; genes; internal transcribed spacers; polymerase chain reaction; ribosomal RNA; surveys
Abstract:
... Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxon ...
DOI:
10.1128/AEM.06826-11
PubMed:
22194300
PubMed Central:
PMC3294464

2. Allele-specific qRT-PCR demonstrates superior detection of single nucleotide polymorphisms as genetic markers for West Nile virus compared to Luminex® and quantitative sequencing

Author:
Gabriella Worwa; Christy C. Andrade; Tara C. Thiemann; Bborie Park; Payal D. Maharaj; Michael Anishchenko; Aaron C. Brault; William K. Reisen
Source:
Journal of virological methods 2014 v.195 pp. 76-85
ISSN:
0166-0934
Subject:
DNA primers; RNA; West Nile virus; cell culture; genes; genetic markers; genetic stability; mutants; phenotype; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; single nucleotide polymorphism; site-directed mutagenesis; viral load; viruses
Abstract:
... To enable in vivo and in vitro competitive fitness comparisons among West Nile viruses (WNV), three reference viruses were marked genetically by site-directed mutagenesis with five synonymous nucleotide substitutions in the envelope gene region of the genome. Phenotypic neutrality of the mutants was assessed experimentally by competitive replication in cell culture and genetic stability of the sub ...
DOI:
10.1016/j.jviromet.2013.09.014
PubMed:
24121135
PubMed Central:
PMC3856659

3. Allelic variation of gene expression in maize hybrids

Author:
Guo, M.; Rupe, M.A.; Zinselmeier, C.; Habben, J.; Bowen, B.A.; Smith, O.S.
Source:
plant cell 2004 v.16 no.7 pp. 1707-1716
ISSN:
1040-4651
Subject:
Zea mays; hybrids; alleles; messenger RNA; DNA primers; corn; drought; transcription (genetics); gene expression; water stress; plant density; reverse transcriptase polymerase chain reaction; nucleotide sequences; genotype-environment interaction; genetic variation; reciprocal crosses
Abstract:
... Allelic expression variation of nonimprinted autosomal genes has recently been uncovered in mouse hybrids and humans. The allelic expression variation is attributed to differences in noncoding DNA sequences and does not involve epigenetic regulation or gene imprinting. This expression variation is suggested to play important roles in determining phenotypic diversity. Virtually nothing is known abo ...
DOI:
10.1105/tpc.022087
PubMed:
15194819
PubMed Central:
PMC514155

4. Amplified Intergenic Locus Polymorphism as a Basis for Bacterial Typing of Listeria spp. and Escherichia coli

Author:
Somer, Lilach; Danin-Poleg, Yael; Diamant, Eran; Gur-Arie, Riva; Palti, Yniv; Kashi, Yechezkel
Source:
Applied and environmental microbiology 2005 v.71 no.6 pp. 3144-3152
ISSN:
0099-2240
Subject:
loci; open reading frames; DNA primers; polymerase chain reaction; pathogen identification; food pathogens; genotype; Listeria monocytogenes; genetic polymorphism; Escherichia coli
Abstract:
... DNA-based methods are increasingly important for bacterial typing. The high number of polymorphic sites present among closely related bacterial genomes is the basis for the presented method. The method identifies multilocus genomic polymorphisms in intergenic regions termed AILP (amplified intergenic locus polymorphism). For each locus, a pair of unique PCR primers was designed to amplify an inter ...
DOI:
10.1128/AEM.71.6.3144-3152.2005
PubMed:
15933014
PubMed Central:
PMC1151823

5. Anaerobic Ammonia-Oxidizing Bacteria and Related Activity in Baltimore Inner Harbor Sediment

Author:
Tal, Yossi; Watts, Joy E. M.; Schreier, Harold J.
Source:
Applied and environmental microbiology 2005 v.71 no.4 pp. 1816-1821
ISSN:
0099-2240
Subject:
DNA; DNA primers; ammonia; bacteria; basins; biogeochemical cycles; denaturing gradient gel electrophoresis; fluorescence in situ hybridization; nucleotide sequences; oxidation; ribosomal RNA; sediments; Chesapeake Bay
Abstract:
... The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by ¹⁵N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Pl ...
DOI:
10.1128/AEM.71.4.1816-1821.2005
PubMed:
15812006
PubMed Central:
PMC1082547

6. An Anaerobic Methane-Oxidizing Community of ANME-1b Archaea in Hypersaline Gulf of Mexico Sediments

Author:
Lloyd, Karen G.; Lapham, Laura; Teske, Andreas
Source:
Applied and environmental microbiology 2006 v.72 no.11 pp. 7218-7230
ISSN:
0099-2240
Subject:
Archaea; DNA libraries; DNA primers; canyons; clones; community structure; electrons; genes; methane; microbial communities; molecular cloning; oxidation; polymerase chain reaction; ribosomal RNA; sediments; sulfates; Gulf of Mexico
Abstract:
... Sediments overlying a brine pool methane seep in the Gulf of Mexico (Green Canyon 205) were analyzed using molecular and geochemical approaches to identify geochemical controls on microbial community composition and stratification. 16S rRNA gene and rRNA clone libraries, as well as mcrA gene clone libraries, showed that the archaeal community consists predominantly of ANME-1b methane oxidizers; no ...
DOI:
10.1128/AEM.00886-06
PubMed:
16980428
PubMed Central:
PMC1636178

7. Analysis of BAC-end sequences in rainbow trout:Content characterization and assessment of synteny between trout and other fish genomes

Author:
Carine Genet
Source:
BMC genomics 2011 v.12 no. pp. -
ISSN:
1471-2164
Subject:
DNA primers; Danio rerio; Gasterosteidae; Oncorhynchus mykiss; ancestry; bacterial artificial chromosomes; chromosome mapping; databases; evolution; genes; genomics; microsatellite repeats; models; molecular cloning; polymerase chain reaction; proteins; quantitative trait loci; sequence analysis; single nucleotide polymorphism; transcriptome; trout
Abstract:
... Background: Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-dip ...
Handle:
10113/55358
DOI:
10.1186/1471-2164-12-314
PubMed:
21672188
PubMed Central:
PMC3125269

8. 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

9. Analysis of genetic structure and interrelationships in lentil species using morphological and SSR markers

Author:
Priyanka Mohan Koul; Vikas Sharma; Maneet Rana; Rakesh K. Chahota; Shiv Kumar; Tilak R. Sharma
Source:
3 Biotech 2017 v.7 no.1 pp. 83
ISSN:
2190-572X
Subject:
DNA primers; Lens; alleles; breeding; cluster analysis; genetic background; genetic markers; genetic variance; genetic variation; lentils; microsatellite repeats; variance
Abstract:
... Genetic structure and relationships of 130 lentil accessions belonging to six taxa were analysed. For this purpose, seven morphological traits and 31 polymorphic simple sequence repeat (SSR) primers were used for this purpose. Morphological traits grouped lentil accessions into five main clusters. SSR primers collectively amplified 139 polymorphic alleles in a range of 2–10 with an average of 4.48 ...
DOI:
10.1007/s13205-017-0683-z
PubMed:
28500404
PubMed Central:
PMC5429312

10. Analysis of hybrids of durum wheat with Thinopyrum junceiforme using RAPD markers

Author:
Bommineni, V.R.; Jauhar, P.P.; Peterson, T.S.; Chibbar, R.N.; Almouslem, A.B.
Source:
Theoretical and applied genetics 1997 v.95 no.5/6 pp. 757-763
ISSN:
0040-5752
Subject:
Triticum turgidum; Southern blotting; Elytrigia; cultivars; hybrids; restriction fragment length polymorphism; intergeneric hybridization; random amplified polymorphic DNA technique; backcrossing; Thinopyrum pycnanthum; DNA primers; Leymus; DNA; genomics; Elymus; Thinopyrum elongatum; Thinopyrum bessarabicum; genetic markers
Abstract:
... The objective of this study was to detect the presence of alien chromatin in intergeneric hybrids of durum wheat (Triticum turgidum, 2n = 4x = 28; AABB genomes) with the perennial grass Thinopyrum junceiforme (2n = 4x = 28; J1J1J2J2) using RAPD markers. The first step was to identify amplification of species-specific DNA markers in the parental grass species and durum wheat cultivars. Initially, t ...
Handle:
10113/16398
DOI:
10.1007/s001220050622

11. Analysis of microsatellites in the vulnerable orchid Gastrodia flavilabella: the development of microsatellite markers, and cross-species amplification in Gastrodia

Author:
Chi-Chu Tsai; Pei-Yin Wu; Chia-Chi Kuo; Min-Chun Huang; Sheng-Kun Yu; Tsai-Wen Hsu; Tzen-Yuh Chiang; Yu-Chung Chiang
Source:
Botanical studies 2014 v.55 no.1 pp. 72
ISSN:
1999-3110
Subject:
microsatellite repeats; vascular plants; alleles; amplified fragment length polymorphism; loci; mycorrhizal fungi; herbaria; DNA primers; symbiosis; carbohydrates; coniferous forests; heterozygosity; vulnerable species; Gastrodia; phylogeography; genetic variation; nutrients; genetic markers; Taiwan
Abstract:
... BACKGROUND: Gastrodia flabilabella is a mycoheterotrophic orchid that obtains carbohydrates and nutrients from its symbiotic mycorrhizal fungi. The species is an endemic and vulnerable species enlisted in the “A Preliminary Red List of Taiwanese Vascular Plants” according to the IUCN Red List Categories and Criteria Version 3.1. G. flabilabella dwells the underground of broadleaf and coniferous fo ...
DOI:
10.1186/s40529-014-0072-4
PubMed:
28510952
PubMed Central:
PMC5430336

12. Analysis of the Fine-Scale Population Structure of "Candidatus Accumulibacter phosphatis" in Enhanced Biological Phosphorus Removal Sludge, Using Fluorescence In Situ Hybridization and Flow Cytometric Sorting

Author:
Kim, Jeong Myeong; Lee, Hyo Jung; Kim, Sun Young; Song, Jae Jun; Park, Woojun; Jeon, Che Ok
Source:
Applied and environmental microbiology 2010 v.76 no.12 pp. 3825-3835
ISSN:
0099-2240
Subject:
DNA primers; activated sludge; flow cytometry; fluorescence; fluorescence in situ hybridization; genes; nucleotide sequences; phosphorus; phylogeny; polymerase chain reaction; population structure; ribosomal RNA; sodium acetate; sorting; species diversity
Abstract:
... To investigate the fine-scale diversity of the polyphosphate-accumulating organisms (PAO) "Candidatus Accumulibacter phosphatis" (henceforth referred to as "Ca. Accumulibacter"), two laboratory-scale sequencing batch reactors (SBRs) for enhanced biological phosphorus removal (EBPR) were operated with sodium acetate as the sole carbon source. During SBR operations, activated sludge always contained ...
DOI:
10.1128/AEM.00260-10
PubMed:
20418432
PubMed Central:
PMC2893498

13. Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones

Author:
Conn, V.M.; Franco, C.M.M.
Source:
Applied and environmental microbiology 2004 v.70 no.3 pp. 1787-1794
ISSN:
0099-2240
Subject:
restriction fragment length polymorphism; endophytes; sandy soils; Mycobacterium; ribosomal RNA; loam soils; DNA primers; wheat; Triticum aestivum; species diversity; Kitasatospora; Streptomyces; genes; nucleotide sequences; roots; sandy loam soils; South Australia
Abstract:
... The endophytic actinobacterial population in the roots of wheat grown in three different soils obtained from the southeast part of South Australia was investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of the amplified 16S rRNA genes. A new, validated approach was applied to the T-RFLP analysis in order to estimate, to the genus level, the actinobacterial populatio ...
DOI:
10.1128/AEM.70.3.1787-1794.2004
PubMed:
15006805
PubMed Central:
PMC368409

14. Analysis of the type IV fimbrial-subunit gene fimA of Xanthomonas hyacinthi: application in PCR-mediated detection of yellow disease in hyacinths

Author:
Doorn, J. van.; Hollinger, T.C.; Oudega, B.
Source:
Applied and environmental microbiology 2001 v.67 no.2 pp. 598-607
ISSN:
0099-2240
Subject:
disease diagnosis; Xanthomonas; plant pathogenic bacteria; genes; fimbriae; bacterial proteins; nucleotide sequences; amino acid sequences; polymerase chain reaction; plant diseases and disorders; DNA; Hyacinthus; DNA primers
Abstract:
... A sensitive and specific detection method was developed for Xanthomonas hyacinthi; this method was based on amplification of a subsequence of the type IV fimbrial-subunit gene fimA from strain S148. The fimA gene was amplified by PCR with degenerate DNA primers designed by using the N-terminal and C-terminal amino acid sequences of trypsin fragments of FimA. The nucleotide sequence of fimA was det ...
DOI:
10.1128/AEM.67.2.598-607.2001
PubMed:
11157222
PubMed Central:
PMC92626

15. Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification

Author:
Ventura, M.; Canchaya, C.; Meylan, V.; Klaenhammer, T.R.; Zink, R.
Source:
Applied and environmental microbiology 2003 v.69 no.11 pp. 6908-6922
ISSN:
0099-2240
Subject:
Lactobacillus; Bifidobacterium; loci; genes; binding proteins; nucleotide sequences; sequence alignment; phylogeny; polymerase chain reaction; DNA primers; chemotaxonomy
DOI:
10.1128/AEM.69.11.6908-6922.2003
PubMed:
14602655
PubMed Central:
PMC262312

16. Annotation and Re-Sequencing of Genes from De Novo Transcriptome Assembly of Abies alba (Pinaceae)

Author:
Roschanski Anna M.; Fady Bruno; Ziegenhagen Birgit; Liepelt Sascha
Source:
Applications in plant sciences 2013 v.1 no.1 pp. -
ISSN:
2168-0450
Subject:
Abies alba; DNA primers; cDNA libraries; complementary DNA; conifers; genes; proteins; seedlings; single nucleotide polymorphism; transcriptome
Abstract:
... Premise of the study: We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba. Methods and Results: A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25 149 contigs. T ...
DOI:
10.3732/apps.1200179
PubMed:
25202477
PubMed Central:
PMC4105350

17. Antagonistic potential of Pseudomonas graminis 49M against Erwinia amylovora, the causal agent of fire blight

Author:
Artur Mikiciński; Piotr Sobiczewski; Joanna Puławska; Eligio Malusa
Source:
Archives of microbiology 2016 v.198 no.6 pp. 531-539
ISSN:
0302-8933
Subject:
DNA primers; Erwinia amylovora; Malus domestica; Pseudomonas graminis; agar; antibiotics; biofilm; drought tolerance; ferric chloride; glycerol; growth retardation; homoserine; host plants; lactones; pathogens; phyllosphere; poly(vinyl chloride); polymerase chain reaction; polystyrenes; regulator genes; secondary metabolites; siderophores; sucrose; Poland
Abstract:
... In a previous study (Mikiciński et al. in Eur J Plant Pathol, doi: 10.1007/s10658-015-0837-y , 2015), we described the characterization of novel strain 49M of Pseudomonas graminis, isolated from the phyllosphere of apple trees in Poland showing a good protective activity against fire blight on different organs of host plants. We now report investigations to clarify the basis for this activity. Str ...
DOI:
10.1007/s00203-016-1207-7
PubMed:
27002332
PubMed Central:
PMC4930463

18. Antibiotic Resistances of Starter and Probiotic Strains of Lactic Acid Bacteria

Author:
Hummel, Anja S.; Hertel, Christian; Holzapfel, Wilhelm H.; Franz, Charles M.A.P.
Source:
Applied and environmental microbiology 2007 v.73 no.3 pp. 730-739
ISSN:
0099-2240
Subject:
DNA primers; Lactobacillus salivarius; Lactococcus; Leuconostoc; Pediococcus; Streptococcus; ampicillin; antibiotic resistance; chloramphenicol; chromosomes; ciprofloxacin; erythromycin; genes; genetic resistance; gentamicin; lactic acid bacteria; mutation; resistance mechanisms; reverse transcriptase polymerase chain reaction; ribosomal proteins; starter cultures; streptomycin; tetracycline
Abstract:
... The antibiotic resistances of 45 lactic acid bacteria strains belonging to the genera Lactobacillus, Streptococcus, Lactococcus, Pediococcus, and Leuconostoc were investigated. The objective was to determine antibiotic resistances and to verify these at the genetic level, as is currently suggested by the European "qualified presumption of safety" safety evaluation system for industrial starter str ...
DOI:
10.1128/AEM.02105-06
PubMed:
17122388
PubMed Central:
PMC1800751

19. Application of Bacillus velezensis NJAU-Z9 Enhanced Plant Growth Associated with Efficient Rhizospheric Colonization Monitored by qPCR with Primers Designed from the Whole Genome Sequence

Author:
Yang Zhang; Xu Gao; Shuai Wang; Chengzhi Zhu; Rong Li; Qirong Shen
Source:
Current microbiology 2018 v.75 no.12 pp. 1574-1583
ISSN:
0343-8651
Subject:
DNA primers; biomass; colonizing ability; genome; monitoring; nutrient uptake; pepper; plant growth; plant growth-promoting rhizobacteria; quantitative polymerase chain reaction; rhizosphere; seedlings; soil
Abstract:
... Plant growth-promoting rhizobacteria (PGPR) have been reported to influence plant growth, yield, and nutrient uptake by an array of mechanisms. Uncovering the behavioral dynamics of PGPR is one of the most important issues necessary for understanding their functional performances. In this study, strain NJAU-Z9 which was found to possess complex functions and efficient rhizospheric colonization abi ...
DOI:
10.1007/s00284-018-1563-4
PubMed:
30194479
PubMed Central:
PMC6208667

20. Application of Fluorescent Amplified Fragment Length Polymorphism for Comparison of Human and Animal Isolates of Yersinia enterocolitica

Author:
Fearnley, Catherine; On, Stephen L. W.; Kokotovic, Branko; Manning, Georgina; Cheasty, Tom; Newell, Diane G.
Source:
Applied and environmental microbiology 2005 v.71 no.9 pp. 4960-4965
ISSN:
0099-2240
Subject:
yersiniosis; human diseases; amplified fragment length polymorphism; sheep; cattle; fluorescence; DNA primers; biotypes; swine; strains; Yersinia enterocolitica; animal diseases
Abstract:
... An amplified fragment length polymorphism (AFLP) method, developed to genotype Yersinia enterocolitica, has been used to investigate 70 representative strains isolated from humans, pigs, sheep, and cattle in the United Kingdom. AFLP primarily distinguished Y. enterocolitica strains according to their biotype, with strains dividing into two distinct clusters: cluster A, comprising largely the putat ...
DOI:
10.1128/AEM.71.9.4960-4965.2005
PubMed:
16151073
PubMed Central:
PMC1214646