DNA sequence analysis of the regions adjacent to the hlyA gene, which encodes listeriolysin O, an essential virulence factor of Listeria monocytogenes, revealed the presence of two open reading frames (ORFs): ORF D located 304 base pairs downstream from hlyA, and ORF U located 224 base pairs upstream from and in opposite direction to hlyA. Promoter mapping performed with RNAs extracted from cel...

Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as...

BACKGROUND Orf virus, the prototype of parapoxvirus, is the main causative agent of contagious ecthyma. Little is known about the status of the disease in Ethiopia and this study was aimed at determining its status using PCR as a confirmatory tool. METHODS a total of 400 randomly selected sheep and goat was screened for the identification of the virus using amplification of B2L gene and trans...

Substrate identification is the key to defining molecular pathways or cellular processes regulated by proteases. Although phage display with random peptide libraries has been used to analyze substrate specificity of proteases, it is difficult to deduce endogenous substrates from mapped peptide motifs. Phage display with conventional cDNA libraries identifies high percentage of non-open reading ...

The nucleotide sequence of the genomic RNA of barley yellow dwarf virus, PAV serotype was determined, except for the 5'-terminal base, and its genome organization deduced. The 5,677 nucleotide genome contains five large open reading frames (ORFs). The genes for the coat protein (1) and the putative viral RNA-dependent RNA polymerase were identified. The latter shows a striking degree of similar...

We had previously identified a new family of human endogenous retrovirus-like elements, the HERV-L elements (human endogenous retrovirus with leucine tRNA primer), whose pol gene was most closely related to that of the foamy viruses. HERV-L pol-related sequences were also detected in other mammalian species. The recent cloning of the mouse Fv1 gene (S. Best, P. Le Tissier, G. Towers, and J. P. ...

Abbreviations: Adeno-associated virus, (AAV); bacilli Calmette-Guerin, (BCG); base pairs, (bp); cottontail rabbit papilloma virus, (CRPV); E6-associated protein, (E6-AP); epidermal growth factor receptor, (EGFR); histone deacetylases, (HDAC); human papillomavirus, (HPV); inverted terminal repeats, (ITRs); listerolysin O, (LLO); of lysosome-associated membrane protein, (LAMP); open reading frame...

An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated ge...

Borna disease virus (BDV) is a nonsegmented, negative-strand RNA virus that employs several unique strategies for gene expression. The shortest transcript of BDV, X/P mRNA, encodes at least three open reading frames (ORFs): upstream ORF (uORF), X, and P in the 5' to 3' direction. The X is a negative regulator of viral polymerase activity, while the P phosphoprotein is a necessary cofactor of th...

The causative agent of myonecrosis affecting cultured Penaeus vannamei in Brazil was demonstrated to be a virus after purification of the agent from infected shrimp tissues. Purified viral particles were injected into specific pathogen-free P. vannamei, resulting in a disease that displayed the same characteristics as those found in the original shrimp used for purification. The virus was named...