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SDSU
Pavel
Pevzner Wednesday,
May 2nd, 2007 Shotgun Protein Sequencing Despite significant advances in the identification of known proteins, the analysis of unknown proteins by tandem mass spectrometry (MS/MS) still remains a challenging open problem. Although Klaus Biemann recognized the potential of tandem mass spectrometry for sequencing of unknown proteins in the 1980s, low-throughput Edman degradation still remains the main method to sequence unknown proteins. The automated interpretation of MS/MS spectra has been limited by a focus on individual spectra and has not capitalized on the information contained in spectra of overlapping peptides. Indeed, the powerful Shotgun DNA Sequencing strategies have not been extended to automated protein sequencing. We demonstrate, for the first time, the feasibility of automated Shotgun Protein Sequencing of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities. We validate this approach by generating highly accurate de novo reconstructions of multiple regions of various proteins in western diamondback rattlesnake venom. We further argue that Shotgun Protein Sequencing has the potential to overcome the limitations of Edman degradation and eventually replace it in studies of unknown proteins. This is a joint work with Nuno Bandeira (UCSD) and Karl Clauser (Broad). The Colloquium ...ends the year with a bang, with Martin
Bohner
speaking on Logistic differential, difference, and dynamic equations Thursday,
May 3, 2007 Abstract: We give a brief introduction to the theory of dynamic equations on time scales. Then we proceed to present and verify the Cushing-Henson conjectures on time scales. The central part of these conjectures asserts that based on a model using the dynamic Beverton-Holt equation, a periodic environment is deleterious for the population. The proof technique is as follows: First, the Beverton-Holt equation is identified as a logistic dynamic equation. The usual substitution transforms this equation into a linear equation. Then the proof is completed using a recently established dynamic version of the generalized Jensen inequality. If time permits, we also will consider the case of harvesting with constant effort and will maximize the seasonal sustainable yield to find the optimal harvesting policy and the optimal population level. The main objects in this talk are logistic differential equations, logistic difference equations, and their unified counterparts, logistic dynamic equations on time scales. This
talk's on the topic of time,
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