Coloring the Mu transpososome

Isabel K. Darcy, Colin McKinney, Ram K. Medikonduri, and Travis Thompson are with the Mathematics Department, University of Iowa, Iowa City, IA 52242, USA, -- Jeff Chang, and Jesse Sweet are with the Mathematics Department, University of Texas at Austin, Austin, TX 78712, USA, -- Nathan Druivenga is with the Mathematics Department, Indiana University, Bloomington, IN 47405, USA, -- Stacy Mills is with the Mathematics Department, Florida State University, Tallahassee, FL 32306, USA, -- Junalyn Navarra-Madsen is with the Mathematics Department, Texas Woman's University, Denton, TX 76204, USA and -- Arun Ponnusamy is with Credit Suisse First, Boston, MA 02110, USABackground: Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis can be extended to model any stable protein-DNA complex. -- Results: We discuss a computational method for finding the topological conformation of DNA bound within a protein complex. We use an elementary invariant from knot theory called colorability to encode and search for possible DNA conformations. We apply this method to analyze the experimental results of Pathania, Jayaram, and Harshey (Cell 2002). We show that the only topological DNA conformation bound by Mu transposase which is biologically likely is the five crossing solution found by Pathania et al (although other possibilities are discussed). -- Conclusion: Our algorithm can be used to analyze the results of the experimental technique described in Pathania et al in order to determine the topological conformation of DNA bound within a stable protein-DNA [email protected]

Mathematics Tutoring and Course Completion Mathematics Tutoring and Course Completion

Abstract Given the completion-based shift in fundingformula for higher education, there is an ever-increasing pressure to improve graduation rate. Colleges and universities around the world are finding innovative student programs such as tutoring and counseling services, to increase student success. This preliminary study was designed to determine the relationship between tutoring and course completion rate of students. Specifically, this study would like to answer the following questions: 1) what is the course completion rate of students who took advantage of tutoring and students who did not?; 2) is there a significant difference on the rate of course completion between these two groups?; and 3) zooming in on the tutored students, what relationship exists between the total number of hours spent in the tutoring lab and the final grade in the course tutored