Molecular techniques are useful tools for solving taxonomic confusion among species. Polymerase chain reaction (PCR) and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methods were applied for the identification of barnyardgrass, early watergrass, and late watergrass. Total DNA was extracted from 266 accessions, which were collected from different rice growing areas of Turkey. The two primer sets (trn-a and trn-b1, and trn-c and trn-d) specific to a target region of the intergenic spacer between trnT (UGU) and trnL (UAA) and the entire intron region of trnL (UAA), respectively, were used in PCR amplifications. Of the 266 accessions of Echinochloa spp., only eight accessions gave a similar fragment size, which was slightly shorter than 495 bp. The PCR product obtained with the primers trn-a and trn-b1 gave two fragments when EcoRI restriction enzyme was used in barnyardgrass and early watergrass. However, not all accessions of late watergrass were digested with this enzyme. In contrast to EcoRI, the PCR product obtained using the trn-c and trn-d primer set was digested into two fragments by using AluI restriction enzyme in all accessions of late watergrass; whereas, it was not digested in barnyardgrass and early watergrass. This molecular differentiation among barnyardgrass, early watergrass, and late watergrass supports the hypothesis that late watergrass is not a synonym of early watergrass in Turkish accessions.

Restriction enzyme fragmentation pattern (REFP) analysis was used to recognise Staphylococcus aureus strain variation in naturally occurring bovine subclinical mastitis. Multiple colony REFP analysis identified eight distinct strains of S. aureus in addition to the original strains A and B that were infused via the intramammary route, indicating that individual quarters of the udder may be colonised simultaneously by more than one strain of S. aureus. Examination of multiple colonies per milk sample may benefit bacterial strain recognition as an epidemiological tool in mastitis investigations. The dynamics of intramammary infection were determined using a novel double crossover experimental challenge. Quarters remained persistently infected for several weeks following challenge in all four cows, irrespective of the challenge strain. This indicated that no alteration of the original subclinical infection, including the possible induction of clearance of the quarters infected with S. aureus, or replacement of the original strain by the infused strain was induced by challenge. The persistent subclinical infection in all four animals supports previous reports on the chronicity of S. aureus intramammary infection in dairy cows.