@phdthesis{Numberger2019,
  author    = {Numberger, Daniela},
  title     = {Urban wastewater and lakes as habitats for bacteria and potential vectors for pathogens},
  doi       = {10.25932/publishup-43709},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437095},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VI, 130},
  year      = {2019},
  abstract  = {Wasser ist lebensnotwendig und somit eine essentielle Ressource. Jedoch sind unsere S{\"u}ßwasser-Ressourcen begrenzt und ihre Erhaltung daher besonders wichtig. Verschmutzungen mit Chemikalien und Krankheitserregern, die mit einer wachsenden Bev{\"o}lkerung und Urbanisierung einhergehen, verschlechtern die Qualit{\"a}t unseres S{\"u}ßwassers. Außerdem kann Wasser als {\"U}bertragungsvektor f{\"u}r Krankheitserreger dienen und daher wasserb{\"u}rtige Krankheiten verursachen. Der Leibniz-Forschungsverbund INFECTIONS'21 untersuchte innerhalb der interdisziplin{\"a}ren Forschungsgruppe III - „Wasser", Gew{\"a}sser als zentralen Mittelpunkt f{\"u}r Krankheiterreger. Dabei konzentrierte man sich auf Clostridioides difficile sowie avi{\"a}re Influenza A-Viren, von denen angenommen wird, dass sie in die Gew{\"a}sser ausgeschieden werden. Ein weiteres Ziel bestand darin, die bakterielle Gemeinschaften eines Kl{\"a}rwerkes der deutschen Hauptstadt Berlin zu charakterisieren, um anschließend eine Bewertung des potentiellen Gesundheitsrisikos geben zu k{\"o}nnen. Bakterielle Gemeinschaften des Roh- und Klarwassers aus dem Kl{\"a}rwerk unterschieden sich signifikant voneinander. Der Anteil an Darm-/F{\"a}kalbakterien war relativ niedrig und potentielle Darmpathogene wurden gr{\"o}ßtenteils aus dem Rohwasser entfernt. Ein potentielles Gesundheitsrisiko konnte allerdings von potentiell pathogenen Legionellen wie L. lytica festgestellt werden, deren relative Abundanz im Klarwasser h{\"o}her war als im Rohwasser. Es wurden außerdem drei C. difficile-Isolate aus den Kl{\"a}rwerk-Rohwasser und einem st{\"a}dtischen Badesee in Berlin (Weisser See) gewonnen und sequenziert. Die beiden Isolate aus dem Kl{\"a}rwerk tragen keine Toxin-Gene, wohingegen das Isolat aus dem See Toxin-Gene besitzt. Alle drei Isolate sind sehr nah mit humanen St{\"a}mmen verwandt. Dies deutet auf ein potentielles, wenn auch sporadisches Gesundheitsrisiko hin. (Avi{\"a}re) Influenza A-Viren wurden in 38.8\% der untersuchten Sedimentproben mittels PCR detektiert, aber die Virusisolierung schlug fehl. Ein Experiment mit beimpften Wasser- und Sedimentproben zeigte, dass f{\"u}r die Isolierung aus Sedimentproben eine relativ hohe Viruskonzentration n{\"o}tig ist. In Wasserproben ist jedoch ein niedriger Titer an Influenza A-Viren ausreichend, um eine Infektion auszul{\"o}sen. Es konnte zudem auch festgestellt werden, dass sich „Madin-Darby Canine Kidney (MDCK)―-Zellkulturen im Gegensatz zu embryonierten H{\"u}hnereiern besser eignen, um Influenza A-Viren aus Sediment zu isolieren. Zusammenfassend l{\"a}sst sich sagen, dass diese Arbeit m{\"o}gliche Gesundheitsrisiken aufgedeckt hat, wie etwa durch Legionellen im untersuchten Berliner Kl{\"a}rwerk, deren relative Abundanz in gekl{\"a}rtem Abwasser h{\"o}her ist als im Rohwasser. Desweiteren wird indiziert, dass Abwasser und Gew{\"a}sser als Reservoir und Vektor f{\"u}r pathogene Organismen dienen k{\"o}nnen, selbst f{\"u}r nicht-typische Wasser-Pathogene wie C. difficile.},
  language  = {en}
}
@phdthesis{Hintsche2018,
  author    = {Hintsche, Marius},
  title     = {Locomotion of a bacterium with a polar bundle of flagella},
  doi       = {10.25932/publishup-42697},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426972},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xi, 108},
  year      = {2018},
  abstract  = {Movement and navigation are essential for many organisms during some parts of their lives. This is also true for bacteria, which can move along surfaces and swim though liquid environments. They are able to sense their environment, and move towards environmental cues in a directed fashion. These abilities enable microbial lifecyles in biofilms, improved food uptake, host infection, and many more. In this thesis we study aspects of the swimming movement - or motility - of the soil bacterium (P. putida). Like most bacteria, P. putida swims by rotating its helical flagella, but their arrangement differs from the main model organism in bacterial motility research: (E. coli). P. putida is known for its intriguing motility strategy, where fast and slow episodes can occur after each other. Up until now, it was not known how these two speeds can be produced, and what advantages they might confer to this bacterium. Normally the flagella, the main component of thrust generation in bacteria, are not observable by ordinary light microscopy. In order to elucidate this behavior, we therefore used a fluorescent staining technique on a mutant strain of this species to specifically label the flagella, while leaving the cell body only faintly stained. This allowed us to image the flagella of the swimming bacteria with high spacial and temporal resolution with a customized high speed fluorescence microscopy setup. Our observations show that P. putida can swim in three different modes. First, It can swim with the flagella pushing the cell body, which is the main mode of swimming motility previously known from other bacteria. Second, it can swim with the flagella pulling the cell body, which was thought not to be possible in situations with multiple flagella. Lastly, it can wrap its flagellar bundle around the cell body, which results in a speed wich is slower by a factor of two. In this mode, the flagella are in a different physical conformation with a larger radius so the cell body can fit inside. These three swimming modes explain the previous observation of two speeds, as well as the non strict alternation of the different speeds. Because most bacterial swimming in nature does not occur in smoothly walled glass enclosures under a microscope, we used an artificial, microfluidic, structured system of obstacles to study the motion of our model organism in a structured environment. Bacteria were observed in microchannels with cylindrical obstacles of different sizes and with different distances with video microscopy and cell tracking. We analyzed turning angles, run times, and run length, which we compared to a minimal model for movement in structured geometries. Our findings show that hydrodynamic interactions with the walls lead to a guiding of the bacteria along obstacles. When comparing the observed behavior with the statics of a particle that is deflected with every obstacle contact, we find that cells run for longer distances than that model. Navigation in chemical gradients is one of the main applications of motility in bacteria. We studied the swimming response of P. putida cells to chemical stimuli (chemotaxis) of the common food preservative sodium benzoate. Using a microfluidic gradient generation device, we created gradients of varying strength, and observed the motion of cells with a video microscope and subsequent cell tracking. Analysis of different motility parameters like run lengths and times, shows that P. putida employs the classical chemotaxis strategy of E. coli: runs up the gradient are biased to be longer than those down the gradient. Using the two different run speeds we observed due to the different swimming modes, we classify runs into `fast' and `slow' modes with a Gaussian mixture model (GMM). We find no evidence that P. putida's uses its swimming modes to perform chemotaxis. In most studies of bacterial motility, cell tracking is used to gather trajectories of individual swimming cells. These trajectories then have to be decomposed into run sections and tumble sections. Several algorithms have been developed to this end, but most require manual tuning of a number of parameters, or extensive measurements with chemotaxis mutant strains. Together with our collaborators, we developed a novel motility analysis scheme, based on generalized Kramers-Moyal-coefficients. From the underlying stochastic model, many parameters like run length etc., can be inferred by an optimization procedure without the need for explicit run and tumble classification. The method can, however, be extended to a fully fledged tumble classifier. Using this method, we analyze E. coli chemotaxis measurements in an aspartate analog, and find evidence for a chemotactic bias in the tumble angles.},
  language  = {en}
}
@phdthesis{Codutti2018,
  author    = {Codutti, Agnese},
  title     = {Behavior of magnetic microswimmers},
  doi       = {10.25932/publishup-42297},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-422976},
  school      = {Universit{\"a}t Potsdam},
  pages     = {iv, 142},
  year      = {2018},
  abstract  = {Microswimmers, i.e. swimmers of micron size experiencing low Reynolds numbers, have received a great deal of attention in the last years, since many applications are envisioned in medicine and bioremediation. A promising field is the one of magnetic swimmers, since magnetism is biocom-patible and could be used to direct or actuate the swimmers. This thesis studies two examples of magnetic microswimmers from a physics point of view. The first system to be studied are magnetic cells, which can be magnetic biohybrids (a swimming cell coupled with a magnetic synthetic component) or magnetotactic bacteria (naturally occurring bacteria that produce an intracellular chain of magnetic crystals). A magnetic cell can passively interact with external magnetic fields, which can be used for direction. The aim of the thesis is to understand how magnetic cells couple this magnetic interaction to their swimming strategies, mainly how they combine it with chemotaxis (the ability to sense external gradient of chemical species and to bias their walk on these gradients). In particular, one open question addresses the advantage given by these magnetic interactions for the magnetotactic bacteria in a natural environment, such as porous sediments. In the thesis, a modified Active Brownian Particle model is used to perform simulations and to reproduce experimental data for different systems such as bacteria swimming in the bulk, in a capillary or in confined geometries. I will show that magnetic fields speed up chemotaxis under special conditions, depending on parameters such as their swimming strategy (run-and-tumble or run-and-reverse), aerotactic strategy (axial or polar), and magnetic fields (intensities and orientations), but it can also hinder bacterial chemotaxis depending on the system. The second example of magnetic microswimmer are rigid magnetic propellers such as helices or random-shaped propellers. These propellers are actuated and directed by an external rotating magnetic field. One open question is how shape and magnetic properties influence the propeller behavior; the goal of this research field is to design the best propeller for a given situation. The aim of the thesis is to propose a simulation method to reproduce the behavior of experimentally-realized propellers and to determine their magnetic properties. The hydrodynamic simulations are based on the use of the mobility matrix. As main result, I propose a method to match the experimental data, while showing that not only shape but also the magnetic properties influence the propellers swimming characteristics.},
  language  = {en}
}