3% (Pei et al., 2010). This could see more lead to product pool with a range of Tm from one strain, posing an additional challenge to DGGE analysis. Some have attempted new strategies to avoid the problem by choosing a gene that carries a single copy per cell (Dahllof et al., 2000; Adekambi et al., 2009). A further challenge to DGGE entails heteroduplex formation during the PCR process (Jensen & Straus, 1993; Ferris & Ward, 1997), occurring when two highly similar sequences anneal together during PCR rather than the normal complementary sequence

(Muyzer & Smalla, 1998). This causes a change in the melting activity of the PCR product in DGGE (Muyzer & Smalla, 1998). Heteroduplex formation between two PCR products leads to four bands occurring on the gel. Yet, the formation of heteroduplexes does not have a significant impact Adriamycin in vitro on the analysis of DGGE patterns for complex communities (Murray et al., 1996). This is supported by the observation that heteroduplex formation appears to occur only between closely related species (Ferris & Ward, 1997). Use of a standardized PCR protocol should lead to a fixed proportion of heteroduplex formation, and thus not adversely affect the DGGE result. We recommend procuring an oligonucleotide batch large enough to conduct an entire project, to avoid the

need for further syntheses. In this way, any oligonucleotide-specific variations can be avoided. Secondly,

we reiterate previous suggestions to choose GC clamps that are C-rich, avoiding two or more consecutive G residues. This should decrease the degree of GC-clamp error. This research was funded by SD00H296-081HG from the South Dakota Agricultural Experiment Station to V.S.B. E.A.R. was supported by a scholarship from the NASA South Dakota Space Grant Consortium. We acknowledge use of the SDSU-Functional Genomics Core Facility, supported by NSF/EPSCoR Grant No. 0091948, the South Dakota 2010 Drought Initiative, Ceramide glucosyltransferase and the South Dakota Agricultural Experiment Station. “
“Some of the staphylococcal superantigen-like (SSL) proteins SSL5, SSL7, SSL9, and SSL11 act as immunomodulatory proteins in Staphylococcus aureus. However, little is known about their regulatory mechanisms. We determined the expression levels of ssl5 and ssl8 in seven clinically important S. aureus strains and their regulatory mechanisms in the Newman strain, which had the highest ssl5 and ssl8 expression. Independent comparisons of ssl5 or ssl8 coding and upstream sequences in these strains identified multiple haplotypes that did not correlate with the differential expression of ssl5 and ssl8, suggesting the role of additional regulatory elements. Using knockout mutant strains of known S.