TY - JOUR A1 - Gong, Chen Chris A1 - Klumpp, Stefan T1 - Modeling sRNA-Regulated Plasmid Maintenance JF - PLoS one N2 - We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid. Key to their function is the tight regulation of expression of a protein toxin by an sRNA antitoxin. Here, we focus on the nonlinear nature of the regulatory circuit dynamics of the toxin-antitoxin mechanism. The mechanism relies on a transient increase in protein concentration rather than on the steady state of the genetic circuit. Through a systematic analysis of the parameter dependence of this transient increase, we confirm some known design features of this system and identify new ones: for an efficient toxin-antitoxin mechanism, the synthesis rate of the toxin’s mRNA template should be lower that of the sRNA antitoxin, the mRNA template should be more stable than the sRNA antitoxin, and the mRNA-sRNA complex should be more stable than the sRNA antitoxin. Moreover, a short half-life of the protein toxin is also beneficial to the function of the toxin-antitoxin system. In addition, we study a therapeutic scenario in which a competitor mRNA is introduced to sequester the sRNA antitoxin, causing the toxic protein to be expressed. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0169703 SN - 1932-6203 VL - 12 PB - PLoS CY - San Fransisco ER - TY - THES A1 - Klumpp, Stefan T1 - Movements of molecular motors : diffusion and directed walks N2 - Bewegungen von prozessiven molekularen Motoren des Zytoskeletts sind durch ein Wechselspiel von gerichteter Bewegung entlang von Filamenten und Diffusion in der umgebenden Lösung gekennzeichnet. Diese eigentümlichen Bewegungen werden in der vorliegenden Arbeit untersucht, indem sie als Random Walks auf einem Gitter modelliert werden. Ein weiterer Gegenstand der Untersuchung sind Effekte von Wechselwirkungen zwischen den Motoren auf diese Bewegungen. Im einzelnen werden vier Transportphänomene untersucht: (i) Random Walks von einzelnen Motoren in Kompartimenten verschiedener Geometrien, (ii) stationäre Konzentrationsprofile, die sich in geschlossenen Kompartimenten infolge dieser Bewegungen einstellen, (iii) randinduzierte Phasenübergänge in offenen röhrenartigen Kompartimenten, die an Motorenreservoirs gekoppelt sind, und (iv) der Einfluß von kooperativen Effekten bei der Motor-Filament-Bindung auf die Bewegung. Alle diese Phänomene sind experimentell zugänglich, und mögliche experimentelle Realisierungen werden diskutiert. N2 - Movements of processive cytoskeletal motors are characterized by an interplay between directed motion along filament and diffusion in the surrounding solution. In the present work, these peculiar movements are studied by modeling them as random walks on a lattice. An additional subject of our studies is the effect of motor-motor interactions on these movements. In detail, four transport phenomena are studied: (i) Random walks of single motors in compartments of various geometries, (ii) stationary concentration profiles which build up as a result of these movements in closed compartments, (iii) boundary-induced phase transitions in open tube-like compartments coupled to reservoirs of motors, and (iv) the influence of cooperative effects in motor-filament binding on the movements. All these phenomena are experimentally accessible and possible experimental realizations are discussed. KW - molekulare Motoren KW - aktive Prozesse KW - Diffusion KW - Random Walks KW - Gittermodelle KW - Phasenübergänge KW - Staus KW - kooperative Phänomene KW - molecular motors KW - active processes KW - diffusion KW - random walks KW - lattice models KW - phase transitions KW - traffic jams KW - cooperative phenomena Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-0000806 ER -