PCR-amplified

This SRM contains human cells from two cell culture lines from which DNA can be extracted, genomic DNA from those two cell lines plus eight individuals, PCR-amplified DNA from the two cell lines plus four of the eight individuals, a D1S80 allelic ladder for characterization of amplified DNA, and a DNA size marker to assure proper electrophoretic separations. 

The STR data generated at NIST were based on amplifying i.o ng of the genomic DNA with fluorescent labelled primers. The PCR amplified products were analyzed by slab gel electrophoresis followed by imaging with a Molecular Dynamics Fluorl-mager 595 or by capUlary electrophoresis using a PE-ABI 310 Genetic Analyzer. 

S. Jen.sen, L. Ovreas, F. L. Daae, and V. Torsvik, Diversity in methane enrichments from agricultural soil revealed by DGGE separation of PCR amplified 16S rDNA fragments. FEMS Microbiol. Ecol. 26 17 (1998). 

These DNA markers have been successfully employed to track specific strain-associated loci in endo- and ectomycorrhizal populations from agricultural land, forest nurseries, plantations, and natural ecosystems. The simplest strategy (digesting PCR-amplified ITS with selected endonucleases) has identified their symbionts in various ecosystems (18,36-38). Species discrimination by ITS-RFLP matching can be improved by comparing data for the targeted DNA with those on sequence databases (37). 

G. A. Kowalchuk, J. R. Stephen, W. DeBoer, J. 1. Prosser, T. M. Embley, and J. W. Woldendorp, Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified I6S ribosomal DNA fragments. Appl. Environ. Microbiol. 6.1 1489 (1997). 

Figure 5.3. Systematic mating ofyeast two-hybrid bait and prey pools. Each yeast ORF was cloned individually into both as a DNA binding domain fusion (bait) and activation domain fusion (prey). The bait fusions were introduced into a MATa strain and the prey fusions were introduced into a MATa strain. The bait and prey fusions were pooled in sets of 96 clones to generate a total of 62 pools of each. The pools were systematically mated (62 x 62) in a total of 3844 crosses. Interacting clones were selected and the bait and prey inserts were PCR amplified and sequenced to determine their identify. Figure adapted from Ito et al. (2001).

Most often proteins are the bacterial biopolymers studied using MALDI MS either from fractions or whole cells. They are not the only isolated cellular biopolymers studied by MALDI, nor the first. Very soon after the introduction of MALDI there were a few reports of the analysis of bacterial RNA or DNA from bacterial fractions. One of the first applications of MALDI to bacteria fractions involved analysis of RNA isolated from E. coli,4 Other studies included analysis of PCR-amplified DNA,5 6 DNA related to repair mechanisms7 and posttranscriptional modification of bacterial RNA.8 While most MALDI studies involve the use of UV lasers, IR MALDI has been reported for the analysis of double stranded DNA from restriction enzyme digested DNA plasmids, also isolated from E. coli.9... 

Table 2.1. Filarial nematodes infected with intracellular bacteria. The method of detection is shown. Neither electron microscopy nor the immuno-histochemical staining techniques used are to be regarded as Wolbachia specific (see note). Positive identification of intracellular bacteria as Wolbachia is shown only where PCR amplified products of rRNA or ftsZ genes have been sequenced. ...

Gasser, R.B., Zhu, X.Q. and McManus, D.P. (1998c) Display of sequence variation in PCR-amplified mitochondrial DNA regions of Echinococcus by single-strand conformation polymorphism. Acta Tropica 71, 107-115. 

Clark AG. Inference ofhaplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 1990 7 111-122. 

PCR amplifies DNA sequences that lie between specific 5 and 3 sequences. 

Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of Bacterial Communities in the Rhizosphere of Chrysanthemum via Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA as Well as DNA Fragments Coding for 16S rRNA. Appl Environ Micrbiol 67 172-178... 

Early PCR experiments were performed by manual or robotic transfer of reaction vials between water baths or heating blocks. These have been superseded by several generations of programmable thermal cyclers. Successful PCR amplifies a single or a few copies of a target sequence of DNA by many orders of magnitude. The process is described schematically in Figure 2.9. 

PCR-amplified DNA sequences tested for ( ) length difference (electrophoresis) and (2) sequence difference (allele-specific probes, ASOs)... 

Length and base composition of pcr-amplified nucleic adds using mass measurements from electrospray ionization mass spectrometry. Anal Chem 1997, 69, 1543-1549. 

In the DCC SELEX screen, aldehydes, the TAR RNA target, and a random library of 2 -amino RNAs were allowed to equilibrate. Next, the TAR RNA target and bound ligands were separated from the aptamer library. The selected 2 -amino RNAs that bound the TAR RNA target were then reverse transcribed into DNA and PCR amplified. These double-stranded... 

A disposable electrochemical enzyme-amplified genosensor was described for specific detection of Salmonella (Del Giallo et al., 2005). A DNA probe specific for Salmonella was immobilized onto screen-printed carbon electrodes and allowed to hybridize with a biotinylated PCR-amplified product of Salmonella. The hybridization reaction was detected using streptavidin conjugated-AP where the enzyme catalyzed the conversion of electroinactive a-naphthyl phosphate to electroactive a-naphthol, which was detected by differential pulse voltammetry. 

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