scholarly journals PCR-Based Identification of Pandemic GroupVibrio parahaemolyticuswith a Novel Group-Specific Primer Pair

2004 ◽  
Vol 48 (10) ◽  
pp. 787-790 ◽  
Author(s):  
Masatoshi Okura ◽  
Ro Osawa ◽  
Atsushi Iguchi ◽  
Michihiro Takagi ◽  
Eiji Arakawa ◽  
...  
Keyword(s):  
Specific Primer ◽  
Group Specific Primer

Analysis of community structures in anaerobic processes using a quantitative real-time PCR method

2005 ◽  
Vol 52 (1-2) ◽  
pp. 85-91 ◽  
Author(s):  
Y. Yu ◽  
C. Lee ◽  
S. Hwang
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Rrna Gene ◽  
Quantitative Real Time Pcr ◽  
Community Structures ◽  
Specific Primer ◽  
Anaerobic Processes ◽  
Promising Tool ◽  
Pcr Method ◽  
Group Specific Primer

The methanogenic community structures of four different anaerobic processes were characterized using a quantitative real-time PCR with group-specific primer and probe sets targeting the 16S rRNA gene (rDNA). The group specific primer and probe sets were developed and used to detect the orders Methanosarcinales, and the families Methanosarcinaceae and Methanosaetaceae. Two separate sets targeting the domains Archaea and Bacteria were also used. Each microbial population in different anaerobic processes was determined and the relative abundance in the system was compared with each other. Dominant methanogenic populations and the community structures in the processes were varied by hydraulic retention time and acetate concentration. This indicates that the real-time PCR method with the primer and probe sets is a promising tool to analyze community structures in anaerobic processes.

scholarly journals Rapid PCR-based Detection of Phytoplasmas from Infected Plants

HortScience ◽  
2003 ◽  
Vol 38 (6) ◽  
pp. 1134-1136 ◽  
Author(s):  
Yonghong Guo ◽  
Zong-Ming Cheng ◽  
James A. Walla
Keyword(s):  
Sodium Hydroxide ◽  
Cross Sections ◽  
Infected Plant ◽  
Pcr Amplification ◽  
Green Ash ◽  
Specific Primer ◽  
Plant Materials ◽  
Dna Preparation ◽  
Group Specific Primer ◽  
Triton X

Five simplified DNA preparation procedures for polymerase chain reaction (PCR) amplification were tested for detection of phytoplasmas from infected herbaceous and woody plants. Thin freehand cross-sections made from infected plant tissues and stored in acetone were used as sources for DNA preparation. The tissue sections were treated by: 1) grinding in sodium hydroxide; 2) sonicating in water; 3) microwaving in water; 4) boiling in sodium hydroxide; or 5) placing directly in PCR tube. PCR amplification was performed with a universal phytoplasma-specific primer pair in a reaction buffer containing 0.5% (v/v) Triton X-100, 1.5 mm magnesium chloride, and 10 mm Tris-HCl. All five procedures provided phytoplasmal template DNA for successful PCR amplification from infected herbaceous plants {periwinkle [Catharanthus roseus (L.) G. Don (periwinkle)], carrot (Daucus carota L.), maize (Zea mays L.)}, while the grinding, microwaving, and boiling procedures also allowed positive amplification from a woody plant [green ash (Fraxinus pennsylvanica Marsh.)]. The quality of the resulting DNA was adequate for subsequent identification of the aster yellows and ash yellows phytoplasmas through nested-PCR using phytoplasma group-specific primer pairs. These methods provide remarkable savings in labor and materials, making disease testing and indexing of plant materials much more attractive.

scholarly journals First Report of Streptocarpus flower break virus in Streptocarpus in the United States

Plant Disease ◽  
2007 ◽  
Vol 91 (10) ◽  
pp. 1361-1361 ◽  
Author(s):  
H. R. Pappu ◽  
K. B. Druffel
Keyword(s):  
United States ◽  
Genomic Sequence ◽  
The United States ◽  
Genomic Region ◽  
Rt Pcr ◽  
Specific Primer ◽  
Sequence Comparisons ◽  
First Report ◽  
Group Specific Primer ◽  
Free Material

Streptocarpus flower break virus (SFBV) belongs to the genus Tobamovirus and was described from naturally infected streptocarpus plants in 1995 (2). The complete genomic sequence was recently reported (1). Prominent symptoms include flower breaking while foliar symptoms are often lacking. In March 2007, four streptocarpus plants (cv. Indigo Dream) from San Diego County, CA were tested for the presence of SFBV by ELISA and reverse transcription (RT)-PCR. Symptoms suggestive of a virus infection were not present on these mother plants at the time of sampling. ELISA with SFBV-specific antiserum showed that all samples were infected with SFBV. The ELISA results were verified by RT-PCR followed by cloning and sequencing. Two sets of primer pairs were used in separate RT-PCR tests. One was a degenerate tobamovirus group-specific primer pair and the second primer pair was specific to SFBV (1). The tobamovirus group-specific primer pair consisted of Tob Uni1, 5′-ATT TAA GTG GAG GGA AAA CCA CT-3′ and Tob Uni2, 5′-GTY GTT GAT GAG TTC GTG GA-3′. The SFBV-specific primers were SFBVcpF: 5′-AAA ATG TCG TAC GTG GTG GT and SFBVcpR: 5′-ACC CAC AGA ACT TCC TTC AA-3′ (1). PCR amplicons of the expected size (686 bp for the tobamovirus group-specific primer pair and 562 bp for the SFBV-specific primer pair) were obtained for each primer pair. The positive PCR test using the SFBV-specific primer pair confirmed the presence of SFBV. To further verify the identity of the virus, the amplicons obtained with each primer pair were separately cloned and sequenced. At least two clones for each amplicon were sequenced in both directions. Sequence comparisons with those available in GenBank showed 98% sequence identity with the corresponding genomic region (GenBank Accession No. NC_008365) of SFBV (1). To our knowledge, this is the first report of SFBV in the United States and it highlights the need for testing for this virus to ensure propagation and distribution of virus-free material. References: (1) C. Heinze et al. Arch. Virol. 151:763, 2006. (2) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 101:311, 1995.

Search of optimal locations for species- or group-specific primer design in DNA sequences: Non-dominated Sorting Genetic Algorithm II (NSGA-II)

2015 ◽  
Vol 29 ◽  
pp. 214-220 ◽  
Author(s):  
Kwang-Seuk Jeong ◽  
MinHyeok Kim ◽  
Hyunbin Jo ◽  
Jeong-An Gim ◽  
Dong-Kyun Kim ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
Dna Sequences ◽  
Primer Design ◽  
Specific Primer ◽  
Nsga Ii ◽  
Group Specific Primer

Design of specific primer sets for SARS-CoV-2 variants using evolutionary algorithms

2021 ◽  
Author(s):  
Alejandro Lopez Rincon ◽  
Carmina A. Perez Romero ◽  
Lucero Mendoza Maldonado ◽  
Eric Claassen ◽  
Johan Garssen ◽  
...  
Keyword(s):  
Evolutionary Algorithms ◽  
Specific Primer ◽  
Primer Sets

Combining tag-specific primer extension and magneto-DNA system for Cas14a-based universal bacterial diagnostic platform

2021 ◽  
Vol 185 ◽  
pp. 113262
Author(s):  
Fengge Song ◽  
Yangdao Wei ◽  
Peng Wang ◽  
Xiaolin Ge ◽  
Chaoyang Li ◽  
...  
Keyword(s):  
Primer Extension ◽  
Specific Primer

scholarly journals Circular Double-Stranded Forms of TT Virus DNA in the Liver

2000 ◽  
Vol 74 (11) ◽  
pp. 5161-5167 ◽  
Author(s):  
Hiroaki Okamoto ◽  
Masato Ukita ◽  
Tsutomu Nishizawa ◽  
Junichi Kishimoto ◽  
Yuji Hoshi ◽  
...  
Keyword(s):  
Human Beings ◽  
Specific Primer ◽  
Dna Virus ◽  
S1 Nuclease ◽  
Tt Virus ◽  
Double Stranded Dna ◽  
Replicative Intermediates ◽  
Paired Serum ◽  
Genomic Length ◽  
Liver Tissues

ABSTRACT TT virus (TTV) is an unenveloped, circular, and single-stranded DNA virus commonly infecting human beings worldwide. TTV DNAs in paired serum and liver tissues from three viremic individuals were separated by gel electrophoresis and characterized biophysically. TTV DNAs in sera migrated in sizes ranging from 2.0 to 2.5 kb. TTV DNAs in liver tissues, however, migrated at 2.0 to 2.5 kb as well as at 3.5 to 6.1 kb. Both faster- and slower-migrating forms of TTV DNAs in the liver were found to be circular and of the full genomic length of 3.8 kb. TTV DNAs migrating at 2.0 to 2.5 kb, from either serum or liver tissues, were sensitive to S1 nuclease but resistant to restriction endonucleases, and therefore, they were single-stranded. By contrast, TTV DNAs in liver tissues that migrated at 3.5 to 6.1 kb were resistant to S1 nuclease. They migrated at 3.7 to 4.0 kb after digestion with EcoRI, which suggests that they represent circular, double-stranded replicative intermediates of TTV. When TTV DNAs were subjected to strand-specific primer extension and then amplified by PCR with internal primers, those in serum were found to be minus-stranded DNAs while those in liver tissues were found to be a mixture of plus- and minus-stranded DNAs. These results suggest that TTV replicates in the liver via a circular double-stranded DNA.

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