The detection of NO-forming nitrite reductase genes (nir) has become the standard when studying denitrifying communities in the environment, despite well-known amplification biases in available primers. We review the performance of 35 published and 121 newly designed primers targeting the nirS and nirK genes, against sequences from complete genomes and 47 metagenomes from three major habitats w...

HIV type 1 (HIV-1) specifically uses host cell tRNALys-3 as a primer for reverse transcription. The 3' 18 nucleotides of this tRNA are complementary to a region on the HIV RNA genome known as the primer binding site (PBS). HIV-1 has a strong preference for maintaining a lysine-specific PBS in vivo, and viral genomes with mutated PBS sequences quickly revert to be complementary to tRNALys-3. To ...

DNA replication is a semiconservative process in which a DNA polymerase uses one DNA strand as a template for the synthesis of a second, complementary, DNA strand. However, in contrast to RNA polymerases, which can initiate RNA synthesis on a DNA template de novo, all DNA polymerases require a preexisting primer on which to initiate DNA synthesis (Kornberg and Baker 1992). One apparent exceptio...

Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental...

Background: The present study aimed to investigate the presence of leptin mRNA transcript in epididymal spermatozoa of Holstein cattle by RT-PCR analysis. Materials and Methods: To collect sperm from epididymis, the whole testes of three adult Holstein bulls were quickly removed after slaughtering. Samples were transferred to the laboratory on ice and subsequently the epididymal contents were c...

Chlamydophila abortus (C. abortus) is one of the most important infectious agents causing abortion in ruminants. The bacterium is obligately intracellular, cannot grow on agar, but it needs cell culture or embryonated eggs for growth. Therefore, culture-independent detection methods such as the polymerase chain reaction are increasingly important and needed. The aim of this study was to develop...

A unique oligonucleotide pair, GOCC56:GOCC427, was designed that correctly primed specific amplification of a approximately 370-bp sequence spanning the ITS and 5.8S rDNA regions of Glomus occultum and Glomus brasilianum. In addition, this primer pair successfully detected G. occultum and G. brasilianum DNA in nested PCR using a primary PCR product amplified from highly diluted extracts of colo...

We report the development of a method for the simultaneous genotyping of several distinct nucleotide positions by means of fluorescence-coupled competitive primer extension. We demonstrate the application of this method for the simultaneous detection of three point mutations in the human mitochondrial genome, at nucleotide positions 3460, 11778 and 14484, which account for about 90% of cases wi...

DNA microarray technology offers potential for future high-throughput variation genotyping. Allele-specific primer extension procedure on microarray has been considered as an efficient method for single nucleotide polymorphism(SNP) genotyping. However, the high cost of the fluorescent-labeled dNTP used for signal detection in this method limits its application. In the present study, we evaluate...