@misc{AstSchmaelzlinLoehmannsroebenetal.2012,
  author    = {Ast, Cindy and Schm{\"a}lzlin, Elmar and L{\"o}hmannsr{\"o}ben, Hans-Gerd and van Dongen, Joost T.},
  title     = {Optical oxygen micro- and nanosensors for plant applications},
  series = {Sensors},
  volume    = {12},
  journal   = {Sensors},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1424-8220},
  doi       = {10.3390/s120607015},
  pages     = {7015 -- 7032},
  year      = {2012},
  abstract  = {Pioneered by Clark's microelectrode more than half a century ago, there has been substantial interest in developing new, miniaturized optical methods to detect molecular oxygen inside cells. While extensively used for animal tissue measurements, applications of intracellular optical oxygen biosensors are still scarce in plant science. A critical aspect is the strong autofluorescence of the green plant tissue that interferes with optical signals of commonly used oxygen probes. A recently developed dual-frequency phase modulation technique can overcome this limitation, offering new perspectives for plant research. This review gives an overview on the latest optical sensing techniques and methods based on phosphorescence quenching in diverse tissues and discusses the potential pitfalls for applications in plants. The most promising oxygen sensitive probes are reviewed plus different oxygen sensing structures ranging from micro-optodes to soluble nanoparticles. Moreover, the applicability of using heterologously expressed oxygen binding proteins and fluorescent proteins to determine changes in the cellular oxygen concentration are discussed as potential non-invasive cellular oxygen reporters.},
  language  = {en}
}
@phdthesis{Breuer2016,
  author    = {Breuer, David},
  title     = {The plant cytoskeleton as a transportation network},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93583},
  school      = {Universit{\"a}t Potsdam},
  pages     = {164},
  year      = {2016},
  abstract  = {The cytoskeleton is an essential component of living cells. It is composed of different types of protein filaments that form complex, dynamically rearranging, and interconnected networks. The cytoskeleton serves a multitude of cellular functions which further depend on the cell context. In animal cells, the cytoskeleton prominently shapes the cell's mechanical properties and movement. In plant cells, in contrast, the presence of a rigid cell wall as well as their larger sizes highlight the role of the cytoskeleton in long-distance intracellular transport. As it provides the basis for cell growth and biomass production, cytoskeletal transport in plant cells is of direct environmental and economical relevance. However, while knowledge about the molecular details of the cytoskeletal transport is growing rapidly, the organizational principles that shape these processes on a whole-cell level remain elusive. This thesis is devoted to the following question: How does the complex architecture of the plant cytoskeleton relate to its transport functionality? The answer requires a systems level perspective of plant cytoskeletal structure and transport. To this end, I combined state-of-the-art confocal microscopy, quantitative digital image analysis, and mathematically powerful, intuitively accessible graph-theoretical approaches. This thesis summarizes five of my publications that shed light on the plant cytoskeleton as a transportation network: (1) I developed network-based frameworks for accurate, automated quantification of cytoskeletal structures, applicable in, e.g., genetic or chemical screens; (2) I showed that the actin cytoskeleton displays properties of efficient transport networks, hinting at its biological design principles; (3) Using multi-objective optimization, I demonstrated that different plant cell types sustain cytoskeletal networks with cell-type specific and near-optimal organization; (4) By investigating actual transport of organelles through the cell, I showed that properties of the actin cytoskeleton are predictive of organelle flow and provided quantitative evidence for a coordination of transport at a cellular level; (5) I devised a robust, optimization-based method to identify individual cytoskeletal filaments from a given network representation, allowing the investigation of single filament properties in the network context. The developed methods were made publicly available as open-source software tools. Altogether, my findings and proposed frameworks provide quantitative, system-level insights into intracellular transport in living cells. Despite my focus on the plant cytoskeleton, the established combination of experimental and theoretical approaches is readily applicable to different organisms. Despite the necessity of detailed molecular studies, only a complementary, systemic perspective, as presented here, enables both understanding of cytoskeletal function in its evolutionary context as well as its future technological control and utilization.},
  language  = {en}
}
@phdthesis{Kolk2019,
  author    = {Kolk, Jens},
  title     = {The long-term legacy of historical land cover changes},
  doi       = {10.25932/publishup-43939},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439398},
  school      = {Universit{\"a}t Potsdam},
  pages     = {196},
  year      = {2019},
  abstract  = {Over the last years there is an increasing awareness that historical land cover changes and associated land use legacies may be important drivers for present-day species richness and biodiversity due to time-delayed extinctions or colonizations in response to historical environmental changes. Historically altered habitat patches may therefore exhibit an extinction debt or colonization credit and can be expected to lose or gain species in the future. However, extinction debts and colonization credits are difficult to detect and their actual magnitudes or payments have rarely been quantified because species richness patterns and dynamics are also shaped by recent environmental conditions and recent environmental changes. In this thesis we aimed to determine patterns of herb-layer species richness and recent species richness dynamics of forest herb layer plants and link those patterns and dynamics to historical land cover changes and associated land use legacies. The study was conducted in the Prignitz, NE-Germany, where the forest distribution remained stable for the last ca. 100 years but where a) the deciduous forest area had declined by more than 90 per cent (leaving only remnants of "ancient forests"), b) small new forests had been established on former agricultural land ("post-agricultural forests"). Here, we analyzed the relative importance of land use history and associated historical land cover changes for herb layer species richness compared to recent environmental factors and determined magnitudes of extinction debt and colonization credit and their payment in ancient and post-agricultural forests, respectively. We showed that present-day species richness patterns were still shaped by historical land cover changes that ranged back to more than a century. Although recent environmental conditions were largely comparable we found significantly more forest specialists, species with short-distance dispersal capabilities and clonals in ancient forests than in post-agricultural forests. Those species richness differences were largely contingent to a colonization credit in post-agricultural forests that ranged up to 9 species (average 4.7), while the extinction debt in ancient forests had almost completely been paid. Environmental legacies from historical agricultural land use played a minor role for species richness differences. Instead, patch connectivity was most important. Species richness in ancient forests was still dependent on historical connectivity, indicating a last glimpse of an extinction debt, and the colonization credit was highest in isolated post-agricultural forests. In post-agricultural forests that were better connected or directly adjacent to ancient forest patches the colonization credit was way smaller and we were able to verify a gradual payment of the colonization credit from 2.7 species to 1.5 species over the last six decades.},
  language  = {en}
}