@misc{WestburyBalekaBarlowetal.2017, author = {Westbury, Michael V. and Baleka, Sina Isabelle and Barlow, Axel and Hartmann, Stefanie and Paijmans, Johanna L. A. and Kramarz, Alejandro and Forasiepi, Anal{\´i}a M. and Bond, Mariano and Gelfo, Javier N. and Reguero, Marcelo A. and L{\´o}pez-Mendoza, Patricio and Taglioretti, Matias and Scaglia, Fernando and Rinderknecht, Andr{\´e}s and Jones, Washington and Mena, Francisco and Billet, Guillaume and de Muizon, Christian and Aguilar, Jos{\´e} Luis and MacPhee, Ross D.E. and Hofreiter, Michael}, title = {A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {793}, issn = {1866-8372}, doi = {10.25932/publishup-44080}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-440801}, pages = {8}, year = {2017}, abstract = {The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95\% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.}, language = {en} } @misc{SchaalRutlohWeidenfeldetal.2018, author = {Schaal, Frederik and Rutloh, Michael and Weidenfeld, Susanne and Stumpe, Joachim and Michler, Peter and Pruss, Christof and Osten, Wolfgang}, title = {Optically addressed modulator for tunable spatial polarization control}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1001}, issn = {1866-8372}, doi = {10.25932/publishup-44626}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-446263}, pages = {28119 -- 28130}, year = {2018}, abstract = {We present an optically addressed non-pixelated spatial light modulator. The system is based on reversible photoalignment of a LC cell using a red light sensitive novel azobenzene photoalignment layer. It is an electrode-free device that manipulates the liquid crystal orientation and consequently the polarization via light without artifacts caused by electrodes. The capability to miniaturize the spatial light modulator allows the integration into a microscope objective. This includes a miniaturized 200 channel optical addressing system based on a VCSEL array and hybrid refractive-diffractive beam shapers. As an application example, the utilization as a microscope objective integrated analog phase contrast modulator is shown. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement}, language = {en} } @misc{SammlerBleidornTiedemann2017, author = {Sammler, Svenja and Bleidorn, Christoph and Tiedemann, Ralph}, title = {Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400889}, pages = {10}, year = {2017}, abstract = {Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.}, language = {en} } @misc{MeyerPalkopoulouBalekaetal.2017, author = {Meyer, Matthias and Palkopoulou, Eleftheria and Baleka, Sina Isabelle and Stiller, Mathias and Penkman, Kirsty E. H. and Alt, Kurt W. and Ishida, Yasuko and Mania, Dietrich and Mallick, Swapan and Meijer, Tom and Meller, Harald and Nagel, Sarah and Nickel, Birgit and Ostritz, Sven and Rohland, Nadin and Schauer, Karol and Sch{\"u}ler, Tim and Roca, Alfred L. and Reich, David and Shapiro, Beth and Hofreiter, Michael}, title = {Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {790}, issn = {1866-8372}, doi = {10.25932/publishup-44013}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-440139}, pages = {14}, year = {2017}, abstract = {The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods similar to 120 and similar to 244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.}, language = {en} } @phdthesis{Laux2016, author = {Laux, Eva-Maria}, title = {Electric field-assisted immobilization and alignment of biomolecules}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-90271}, school = {Universit{\"a}t Potsdam}, pages = {IX, 120}, year = {2016}, abstract = {In this dissertation, an electric field-assisted method was developed and applied to achieve immobilization and alignment of biomolecules on metal electrodes in a simple one-step experiment. Neither modifications of the biomolecule nor of the electrodes were needed. The two major electrokinetic effects that lead to molecule motion in the chosen electrode configurations used were identified as dielectrophoresis and AC electroosmotic flow. To minimize AC electroosmotic flow, a new 3D electrode configuration was designed. Thus, the influence of experimental parameters on the dielectrophoretic force and the associated molecule movement could be studied. Permanent immobilization of proteins was examined and quantified absolutely using an atomic force microscope. By measuring the volumes of the immobilized protein deposits, a maximal number of proteins contained therein was calculated. This was possible since the proteins adhered to the tungsten electrodes even after switching off the electric field. The permanent immobilization of functional proteins on surfaces or electrodes is one crucial prerequisite for the fabrication of biosensors. Furthermore, the biofunctionality of the proteins must be retained after immobilization. Due to the chemical or physical modifications on the proteins caused by immobilization, their biofunctionality is sometimes hampered. The activity of dielectrophoretically immobilized proteins, however, was proven here for an enzyme for the first time. The enzyme horseradish peroxidase was used exemplarily, and its activity was demonstrated with the oxidation of dihydrorhodamine 123, a non-fluorescent precursor of the fluorescence dye rhodamine 123. Molecular alignment and immobilization - reversible and permanent - was achieved under the influence of inhomogeneous AC electric fields. For orientational investigations, a fluorescence microscope setup, a reliable experimental procedure and an evaluation protocol were developed and validated using self-made control samples of aligned acridine orange molecules in a liquid crystal. Lambda-DNA strands were stretched and aligned temporarily between adjacent interdigitated electrodes, and the orientation of PicoGreen molecules, which intercalate into the DNA strands, was determined. Similarly, the aligned immobilization of enhanced Green Fluorescent Protein was demonstrated exploiting the protein's fluorescence and structural properties. For this protein, the angle of the chromophore with respect to the protein's geometrical axis was determined in good agreement with X-ray crystallographic data. Permanent immobilization with simultaneous alignment of the proteins was achieved along the edges, tips and on the surface of interdigitated electrodes. This was the first demonstration of aligned immobilization of proteins by electric fields. Thus, the presented electric field-assisted immobilization method is promising with regard to enhanced antibody binding capacities and enzymatic activities, which is a requirement for industrial biosensor production, as well as for general interaction studies of proteins.}, language = {en} } @misc{DiFlorioBruendermannYadavallietal.2013, author = {Di Florio, Giuseppe and Br{\"u}ndermann, Erik and Yadavalli, Nataraja Sekhar and Santer, Svetlana and Havenith, Martina}, title = {Polarized 3D Raman and nanoscale near-field optical microscopy of optically inscribed surface relief gratings}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-95233}, pages = {1544 -- 1554}, year = {2013}, abstract = {We have used polarized confocal Raman microspectroscopy and scanning near-field optical microscopy with a resolution of 60 nm to characterize photoinscribed grating structures of azobenzene doped polymer films on a glass support. Polarized Raman microscopy allowed determining the reorientation of the chromophores as a function of the grating phase and penetration depth of the inscribing laser in three dimensions. We found periodic patterns, which are not restricted to the surface alone, but appear also well below the surface in the bulk of the material. Near-field optical microscopy with nanoscale resolution revealed lateral two-dimensional optical contrast, which is not observable by atomic force and Raman microscopy.}, language = {en} }