@phdthesis{Wutke2016,
  author    = {Wutke, Saskia},
  title     = {Tracing Changes in Space and Time},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 84},
  year      = {2016},
  abstract  = {The horse is a fascinating animal symbolizing power, beauty, strength and grace. Among all the animal species domesticated the horse had the largest impact on the course of human history due to its importance for warfare and transportation. Studying the process of horse domestication contributes to the knowledge about the history of horses and even of our own species. Research based on molecular methods has increasingly focused on the genetic basis of horse domestication. Mitochondrial DNA (mtDNA) analyses of modern and ancient horses detected immense maternal diversity, probably due to many mares that contributed to the domestic population. However, mtDNA does not provide an informative phylogeographic structure. In contrast, Y chromosome analyses displayed almost complete uniformity in modern stallions but relatively high diversity in a few ancient horses. Further molecular markers that seem to be well suited to infer the domestication history of horses or genetic and phenotypic changes during this process are loci associated with phenotypic traits. This doctoral thesis consists of three different parts for which I analyzed various single nucleotide polymorphisms (SNPs) associated with coat color, locomotion or Y chromosomal variation of horses. These SNPs were genotyped in 350 ancient horses from the Chalcolithic (5,000 BC) to the Middle Ages (11th century). The distribution of the samples ranges from China to the Iberian Peninsula and Iceland. By applying multiplexed next-generation sequencing (NGS) I sequenced short amplicons covering the relevant positions: i) eight coat-color-associated mutations in six genes to deduce the coat color phenotype; ii) the so-called 'Gait-keeper' SNP in the DMRT3 gene to screen for the ability to amble; iii) 16 SNPs previously detected in ancient horses to infer the corresponding haplotype. Based on these data I investigated the occurrence and frequencies of alleles underlying the respective phenotypes as well as Y chromosome haplotypes at different times and regions. Also, selection coefficients for several Y chromosome lineages or phenotypes were estimated. Concerning coat color differences in ancient horses my work constitutes the most comprehensive study to date. I detected an increase of chestnut horses in the Middle Ages as well as differential selection for spotted and solid phenotypes over time which reflects changing human preferences. With regard to ambling horses, the corresponding allele was present in medieval English and Icelandic horses. Based on these results I argue that Norse settlers, who frequently invaded parts of Britain, brought ambling individuals to Iceland from the British Isles which can be regarded the origin of this trait. Moreover, these settlers appear to have selected for ambling in Icelandic horses. Relating to the third trait, the paternal diversity, these findings represent the largest ancient dataset of Y chromosome variation in non-humans. I proved the existence of several Y chromosome haplotypes in early domestic horses. The decline of Y chromosome variation coincides with the movement of nomadic peoples from the Eurasian steppes and later with different breeding practices in the Roman period. In conclusion, positive selection was estimated for several phenotypes/lineages in different regions or times which indicates that these were preferred by humans. Furthermore, I could successfully infer the distribution and dispersal of horses in association with human movements and actions. Thereby, a better understanding of the influence of people on the changing appearance and genetic diversity of domestic horses could be gained. My results also emphasize the close relationship of ancient genetics and archeology or history and that only in combination well-founded conclusions can be reached.},
  language  = {en}
}
@phdthesis{Hofferek2016,
  author    = {Hofferek, Vinzenz},
  title     = {Starvation response of Drosophila melanogaster},
  school      = {Universit{\"a}t Potsdam},
  pages     = {105},
  year      = {2016},
  language  = {en}
}
@phdthesis{AvcilarKucukgoze2016,
  author    = {Avcilar-Kucukgoze, Irem},
  title     = {Effect of tRNA Aminoacylation and Cellular Resources Allocation on the Dynamics of Translation in Escherichia coli},
  school      = {Universit{\"a}t Potsdam},
  pages     = {131},
  year      = {2016},
  language  = {en}
}
@phdthesis{Reil2016,
  author    = {Reil, Daniela},
  title     = {Puumala hantavirus dynamics in bank voles: identification of environmental correlates to predict human infection risk},
  school      = {Universit{\"a}t Potsdam},
  pages     = {85},
  year      = {2016},
  language  = {en}
}
@phdthesis{Bolger2016,
  author    = {Bolger, Anthony},
  title     = {Sequencing the Genome of the stress-tolerant wild tomato Solanum pennellii and Novel Algorithms motivated thereby},
  school      = {Universit{\"a}t Potsdam},
  pages     = {143},
  year      = {2016},
  language  = {en}
}
@phdthesis{Zhu2016,
  author    = {Zhu, Fangjun},
  title     = {Gene evolution and expression patterns in the all-female fish Amazon molly: Poecilia formosa},
  school      = {Universit{\"a}t Potsdam},
  pages     = {113},
  year      = {2016},
  language  = {en}
}
@phdthesis{Dotzek2016,
  author    = {Dotzek, Jana},
  title     = {Mitochondria in the genus Oenothera - Non-Mendelian inheritance patterns, in vitro structure and evolutionary dynamics},
  school      = {Universit{\"a}t Potsdam},
  pages     = {134},
  year      = {2016},
  language  = {en}
}
@phdthesis{Sas2016,
  author    = {Sas, Claudia},
  title     = {Evolution of the selfing syndrome in the genus capsella},
  school      = {Universit{\"a}t Potsdam},
  pages     = {94},
  year      = {2016},
  language  = {en}
}
@phdthesis{Kloss2016,
  author    = {Kloß, Lena},
  title     = {The link between genetic diversity and species diversity},
  school      = {Universit{\"a}t Potsdam},
  pages     = {109},
  year      = {2016},
  language  = {en}
}
@phdthesis{Hoffmann2016,
  author    = {Hoffmann, Stefan},
  title     = {In vivo Selection of Switchable DNA-Binding Proteins},
  school      = {Universit{\"a}t Potsdam},
  pages     = {97},
  year      = {2016},
  language  = {en}
}
@phdthesis{Prokopović2016,
  author    = {Prokopović, Vladimir Z.},
  title     = {Light-triggered release of bioactive compounds from HA/PLL multilayer films for stimulation of cells},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97927},
  school      = {Universit{\"a}t Potsdam},
  pages     = {91},
  year      = {2016},
  abstract  = {The concept of targeting cells and tissues by controlled delivery of molecules is essential in the field of biomedicine. The layer-by-layer (LbL) technology for the fabrication of polymer multilayer films is widely implemented as a powerful tool to assemble tailor-made materials for controlled drug delivery. The LbL films can as well be engineered to act as mimics of the natural cellular microenvironment. Thus, due to the myriad possibilities such as controlled cellular adhesion and drug delivery offered by LbL films, it becomes easily achievable to direct the fate of cells by growing them on the films. The aim of this work was to develop an approach for non-invasive and precise control of the presentation of bioactive molecules to cells. The strategy is based on employment of the LbL films, which function as support for cells and at the same time as reservoirs for bioactive molecules to be released in a controlled manner. UV light is used to trigger the release of the stored ATP with high spatio-temporal resolution. Both physico-chemical (competitive intermolecular interactions in the film) and biological aspects (cellular response and viability) are addressed in this study. Biopolymers hyaluronic acid (HA) and poly-L-lysine (PLL) were chosen as the building blocks for the LbL film assembly. Poor cellular adhesion to native HA/PLL films as well as significant degradation by cells within a few days were shown. However, coating the films with gold nanoparticles not only improved cellular adhesion and protected the films from degradation, but also formed a size-exclusion barrier with adjustable cut-off in the size range of a few tens of kDa. The films were shown to have high reservoir capacity for small charged molecules (reaching mM levels in the film). Furthermore, they were able to release the stored molecules in a sustained manner. The loading and release are explained by a mechanism based on interactions between charges of the stored molecules and uncompensated charges of the biopolymers in the film. Charge balance and polymer dynamics in the film play the pivotal role. Finally, the concept of light-triggered release from the films has been proven using caged ATP loaded into the films from which ATP was released on demand. ATP induces a fast cellular response, i.e. increase in intracellular [Ca2+], which was monitored in real-time. Limitations of the cellular stimulation by the proposed approach are highlighted by studying the stimulation as a function of irradiation parameters (time, distance, light power). Moreover, caging molecules bind to the film stronger than ATP does, which opens new perspectives for the use of the most diverse chemical compounds as caging molecules. Employment of HA/PLL films as a nouvelle support for cellular growth and hosting of bioactive molecules, along with the possibility to stimulate individual cells using focused light renders this approach highly efficient and unique in terms of precision and spatio-temporal resolution among those previously described. With its high potential, the concept presented herein provides the foundation for the design of new intelligent materials for single cell studies, with the focus on tissue engineering, diagnostics, and other cell-based applications.},
  language  = {en}
}
@phdthesis{Zhang2016,
  author    = {Zhang, Youjun},
  title     = {Investigation of the TCA cycle and glycolytic metabolons and their physiological impacts in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {175},
  year      = {2016},
  language  = {en}
}
@phdthesis{Loewenberg2016,
  author    = {L{\"o}wenberg, Candy},
  title     = {Shape-memory effect of gelatin-based hydrogels},
  school      = {Universit{\"a}t Potsdam},
  pages     = {122},
  year      = {2016},
  language  = {en}
}
@phdthesis{Klauschies2016,
  author    = {Klauschies, Toni},
  title     = {Revealing causes and consequences of functional diversity using trait-based models},
  school      = {Universit{\"a}t Potsdam},
  pages     = {231},
  year      = {2016},
  language  = {en}
}
@phdthesis{Stief2016,
  author    = {Stief, Anna},
  title     = {Genetics and ecology of plant heat stress memory},
  school      = {Universit{\"a}t Potsdam},
  pages     = {175},
  year      = {2016},
  language  = {en}
}
@phdthesis{Beltran2016,
  author    = {Beltran, Juan Camilo Moreno},
  title     = {Characterization of the Clp protease complex and identification of putative substrates in N. tabacum},
  school      = {Universit{\"a}t Potsdam},
  year      = {2016},
  language  = {en}
}
@misc{ZhuSchluppTiedemann2016,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97119},
  pages     = {19},
  year      = {2016},
  abstract  = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.},
  language  = {en}
}
@article{ZhuSchluppTiedemann2016,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors},
  series = {PLoS one},
  volume    = {11},
  journal   = {PLoS one},
  number    = {6},
  publisher = {PLoS},
  address   = {Lawrence, Kan.},
  issn      = {1932-6203},
  doi       = {10.1371/JOURNAL.PONE.0156209},
  pages     = {19},
  year      = {2016},
  abstract  = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.},
  language  = {en}
}
@misc{BatsiosRenBaumannetal.2016,
  author    = {Batsios, Petros and Ren, Xiang and Baumann, Otto and Larochelle, Denis A. and Gr{\"a}f, Ralph},
  title     = {Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97033},
  pages     = {15},
  year      = {2016},
  abstract  = {The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11-646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.},
  language  = {en}
}
@article{BatsiosRenBaumannetal.2016,
  author    = {Batsios, Petros and Ren, Xiang and Baumann, Otto and Larochelle, Denis A. and Gr{\"a}f, Ralph},
  title     = {Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81},
  series = {Cells},
  volume    = {5},
  journal   = {Cells},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4409},
  doi       = {10.3390/cells5010013},
  year      = {2016},
  abstract  = {The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11-646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.},
  language  = {en}
}