MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.

Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at nucleotide resolution along single DNA strands. Probing with cytosine DNA methyltransferases followed by bisulfite sequencing (MAPit) is an effective technique for mapping protein-DNA interactions. Here, MAPit methylation footprinting with M.CviPI, a GC methyltransferase we previously cloned and characterized, was used to probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells. Because M.CviPI-probed samples contain both CG and GC methylation, we developed a versatile, visually-intuitive program, called MethylViewer, for evaluating the bisulfite sequencing results. Uniquely, MethylViewer can simultaneously query cytosine methylation status in bisulfite-converted sequences at as many as four different user-defined motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data can also be exported for statistical analysis and as publication-quality images. Analysis of hMLH1 MAPit data with MethylViewer showed that endogenous CG methylation and accessible GC sites were both mapped on single molecules at high resolution. Disruption of positioned nucleosomes on single molecules of the PHO5 promoter was detected in budding yeast using M.CviPII, increasing the number of enzymes available for probing protein-DNA interactions. MethylViewer provides an integrated solution for primer design and rapid, accurate and detailed analysis of bisulfite sequencing or MAPit datasets from virtually any biological or biochemical system.

The distinct and secondary harmful effect of pelvic and extremity injury on the outcome of laparotomy for trauma.

HYPOTHESIS: Extra-abdominal injury negatively affects the outcome of abdominal injury following trauma laparotomy. DESIGN: Retrospective review of 920 consecutive patients receiving laparotomy for trauma who survived more than 24 h between January 1989 and May 1998 at a Level 1 trauma center. Major abdominal complications (MAC) were defined as: abdominal compartment syndrome (ACS), abscess/peritonitis, enterocutaneous fistula, necrotizing fasciitis, and necrotizing pancreatitis. METHODS: Univariant and multivariant logistic regression were used to identify predictors of MAC. RESULTS: Sixty-nine patients (7.5%) developed one or more MAC. Patients who developed MAC had higher injury severity scores (ISS), abdominal trauma indices (ATI), and blood transfusions in the first 24 h (PRCs) than patients who did not develop MAC. Patients with MAC were more likely to have suffered a thoracic or pelvic injury with an abbreviated injury scale (AIS) > or =3 and were more likely to have received an extremity injury (AIS > or =3) operation than patients without MAC. Independent predictors of MAC in multivariant analysis included colon injury (AIS > or =3) [odds ratio (OR) = 3.1, 95% confidence interval (CI) 1.5- 6.3)], pelvic injury (AIS > or =3) or operation for extremity injury (AIS > or =3) [OR 2.9, 95% CI 1.5-5.3], and ATI (OR = 1.03 for each 10 unit increase in ATI, 95% CI 1.02-1.05). PRCs did not independently predict MAC. CONCLUSION: The outcome of laparotomy for trauma (both blunt and penetrating) is negatively affected by a severe pelvic injury or a severe extremity injury operation independent of initial hemorrhage and abdominal injury severity.