Genomic fragments of the HN and L genes from Brazilian bovine parainfluenza 3 virus (bPIV-3) isolated as contaminants from cell cultures and clinical specimens were amplified by reverse transcription-polymerase chain reaction (RT-PCR), sequenced using specific degenerate primers and analyzed by phylogenetic comparison with reference strains of bPI3V. The Brazilian isolates revealed a high degre...

INTRODUCTION Nucleus pulposus (NP) cells have a phenotype similar to articular cartilage (AC) cells. However, the matrix of the NP is clearly different to that of AC suggesting that specific cell phenotypes exist. The aim of this study was to identify novel genes that could be used to distinguish bovine NP cells from AC and annulus fibrosus (AF) cells, and to further determine their expression ...

A polymerase chain reaction (PCR) primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur, for example, when studying a f...

Ž . A cw degenerate phase conjugate resonator PCR with intracavity aero-optic turbulent flow is demonstrated using sodium vapor pumped with a low intensity cw laser. A turbulent helium jet at a high flow velocity of 250 mrs and forcing frequency of 18 kHz generated the spatio-temporal aberrations. The intracavity normalized peak-to-peak intensity fluctuations at 18 kHz measured with a pinhole-d...

To gain information on retrotransposons in the genome of Paragonimus westermani, PCR was carried out with degenerate primers, specific to protease and reverse transcriptase (rt) genes of long-terminal-repeat (LTR) retrotransposons. The PCR products were cloned and sequenced, after which 12 different retrotransposon-related sequences were isolated from the trematode genome. These showed various ...

DNA that encodes elements for degenerate replication events by use of artificial nucleobases offers a versatile approach to manipulating sequences for applications in biotechnology. We have designed a family of artificial nucleobases that are capable of assuming multiple hydrogen bonding orientations through internal bond rotations to provide a means for degenerate molecular recognition. Incorp...

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoreti...

Rodent herpesviruses such as murine cytomegalovirus (host, Mus musculus), rat cytomegalovirus (host, Rattus norvegicus), and murine gammaherpesvirus 68 (hosts, Apodemus species) are important tools for the experimental study of human herpesvirus diseases. However, alphaherpesviruses, roseoloviruses, and lymphocryptoviruses, as well as rhadinoviruses, that naturally infect Mus musculus (house mo...

background: potyviruses are accounted for 40% of viral diseases of various crops including vegetables and legumes. potyviruses can be transmitted through plant sap, seeds and many aphid species. due to ease of spread of these viruses detection of such viruses are crucial as to the control of the incited diseases. objectives: this study compared the efficiencies of two couples of primers in thei...