@book{AlnemrPolyvyanyyAbuJarouretal.2010, author = {Alnemr, Rehab and Polyvyanyy, Artem and AbuJarour, Mohammed and Appeltauer, Malte and Hildebrandt, Dieter and Thomas, Ivonne and Overdick, Hagen and Sch{\"o}bel, Michael and Uflacker, Matthias and Kluth, Stephan and Menzel, Michael and Schmidt, Alexander and Hagedorn, Benjamin and Pascalau, Emilian and Perscheid, Michael and Vogel, Thomas and Hentschel, Uwe and Feinbube, Frank and Kowark, Thomas and Tr{\"u}mper, Jonas and Vogel, Tobias and Becker, Basil}, title = {Proceedings of the 4th Ph.D. Retreat of the HPI Research School on Service-oriented Systems Engineering}, editor = {Meinel, Christoph and Plattner, Hasso and D{\"o}llner, J{\"u}rgen Roland Friedrich and Weske, Mathias and Polze, Andreas and Hirschfeld, Robert and Naumann, Felix and Giese, Holger}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-036-6}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40838}, publisher = {Universit{\"a}t Potsdam}, pages = {Getr. Z{\"a}hlung}, year = {2010}, language = {en} } @article{AlbertiGonzalezPaijmansetal.2018, author = {Alberti, Federica and Gonzalez, Javier and Paijmans, Johanna L. A. and Basler, Nikolas and Preick, Michaela and Henneberger, Kirstin and Trinks, Alexandra and Rabeder, Gernot and Conard, Nicholas J. and Muenzel, Susanne C. and Joger, Ulrich and Fritsch, Guido and Hildebrandt, Thomas and Hofreiter, Michael and Barlow, Axel}, title = {Optimized DNA sampling of ancient bones using Computed Tomography scans}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12911}, pages = {1196 -- 1208}, year = {2018}, abstract = {The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99\% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.}, language = {en} } @article{FrascavonGrabergFengetal.2010, author = {Frasca, Stefano and von Graberg, Till and Feng, Jiu-Ju and Thomas, Arne and Smarsly, Bernd M. and Weidinger, Inez M. and Scheller, Frieder W. and Hildebrandt, Peter and Wollenberger, Ursula}, title = {Mesoporous indium tin oxide as a novel platform for bioelectronics}, issn = {1867-3880}, doi = {10.1002/cctc.201000047}, year = {2010}, abstract = {Stable immobilization and reversible electrochemistry of cytochrome c in a tranparent indium tin oxide film with a well-defined mesoporosity (mpITO) is demonstrated. the transparency and good conductivity, in combination with the large surface area of mpITO, allow the incorporation of a high amount of elelctroactive biomolecules and their electrochemical and spectroscopic investigation. UV/Vis and resonance Raman spectroscopy, in combination with direct protein voltammetry are employed for the characterization of cytochrome c immobilized in the mpITO and reveal no perturbant of the structural of the integrity of the redox protein. The potential of this modified material as a biosensor detection of superoxide anions is also demonstrated.}, language = {en} } @article{CywinskiMoroRitscheletal.2011, author = {Cywinski, Piotr J. and Moro, Artur J. and Ritschel, Thomas and Hildebrandt, Niko and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Sensitive and selective fluorescence detection of guanosine nucleotides by nanoparticles conjugated with a naphthyridine receptor}, series = {Analytical \& bioanalytical chemistry}, volume = {399}, journal = {Analytical \& bioanalytical chemistry}, number = {3}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-010-4420-2}, pages = {1215 -- 1222}, year = {2011}, abstract = {Novel fluorescent nanosensors, based on a naphthyridine receptor, have been developed for the detection of guanosine nucleotides, and both their sensitivity and selectivity to various nucleotides were evaluated. The nanosensors were constructed from polystyrene nanoparticles functionalized by (N-(7-((3-aminophenyl) ethynyl)-1,8-naphthyridin- 2-yl) acetamide) via carbodiimide ester activation. We show that this naphthyridine nanosensor binds guanosine nucleotides preferentially over adenine, cytosine, and thymidine nucleotides. Upon interaction with nucleotides, the fluorescence of the nanosensor is gradually quenched yielding Stern-Volmer constants in the range of 2.1 to 35.9mM(-1). For all the studied quenchers, limits of detection (LOD) and tolerance levels for the nanosensors were also determined. The lowest (3 sigma) LOD was found for guanosine 3',5'-cyclic monophosphate (cGMP) and it was as low as 150 ng/ml. In addition, we demonstrated that the spatial arrangement of bound analytes on the nanosensors' surfaces is what is responsible for their selectivity to different guanosine nucleotides. We found a correlation between the changes of the fluorescence signal and the number of phosphate groups of a nucleotide. Results of molecular modeling and zeta-potential measurements confirm that the arrangement of analytes on the surface provides for the selectivity of the nanosensors. These fluorescent nanosensors have the potential to be applied in multi-analyte, array-based detection platforms, as well as in multiplexed microfluidic systems.}, language = {en} } @article{JesusSchmidtFickeletal.2022, author = {Jesus, Sonia A. and Schmidt, Anke and Fickel, J{\"o}rns and Doherr, Marcus G. and Boonprasert, Khajohnpat and Thitaram, Chatchote and Sariya, Ladawan and Ratanakron, Parntep and Hildebrandt, Thomas Bernd}, title = {Assessing coagulation parameters in healthy Asian Elephants (Elephas maximus) from European and thai populations}, series = {Animals}, volume = {12}, journal = {Animals}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2076-2615}, doi = {10.3390/ani12030361}, pages = {16}, year = {2022}, abstract = {Simple Summary Asian elephants (Elephas maximus) are considered endangered and their population is in continuous decline. Understanding their social interactions, health, and welfare status has been a topic of intense research in recent decades. Coagulation assessments have been underutilized in wildlife but can give valuable information on individual health. This study aims to increase the knowledge of the coagulation status in healthy Asian elephants from different backgrounds and age groups, using a fast point-of-care analyzer. This tool can be further used in either routine health check-ups performed by caretakers or in a clinical emergency, such as in cases of elephant endotheliotropic herpesvirus hemorrhagic disease outbreaks. We have also investigated the presence of genomic mutations in one coagulation factor-factor VII-where a disorder was previously reported in an Asian elephant. Hereby, we report new reference values for coagulation parameters, such as coagulation times and fibrinogen concentration of Asian elephants assessed in Thailand and in Europe, as well as several single point mutations found in the exons of Elephas maximus coagulation F7 gene. We found the point-of-care analyzer used in this study to be very practical and user friendly for a zoo and field environment and hope that this project will incentivize further coagulation studies in Asian elephants and in other wildlife species. The Asian elephant population is continuously declining due to several extrinsic reasons in their range countries, but also due to diseases in captive populations worldwide. One of these diseases, the elephant endotheliotropic herpesvirus (EEHV) hemorrhagic disease, is very impactful because it particularly affects Asian elephant calves. It is commonly fatal and presents as an acute and generalized hemorrhagic syndrome. Therefore, having reference values of coagulation parameters, and obtaining such values for diseased animals in a very short time, is of great importance. We analyzed prothrombin time (PT), activated partial thromboplastin time (aPTT), and fibrinogen concentrations using a portable and fast point-of-care analyzer (VetScan Pro) in 127 Asian elephants from Thai camps and European captive herds. We found significantly different PT and aPTT coagulation times between elephants from the two regions, as well as clear differences in fibrinogen concentration. Nevertheless, these alterations were not expected to have biological or clinical implications. We have also sequenced the coagulation factor VII gene of 141 animals to assess the presence of a previously reported hereditary coagulation disorder in Asian elephants and to investigate the presence of other mutations. We did not find the previously reported mutation in our study population. Instead, we discovered the presence of several new single nucleotide polymorphisms, two of them being considered as deleterious by effect prediction software.}, language = {en} } @article{MuellervanSchaikBlumeetal.2014, author = {M{\"u}ller, Eva Nora and van Schaik, Loes and Blume, Theresa and Bronstert, Axel and Carus, Jana and Fleckenstein, Jan H. and Fohrer, Nicola and Geissler, Katja and Gerke, Horst H. and Gr{\"a}ff, Thomas and Hesse, Cornelia and Hildebrandt, Anke and H{\"o}lker, Franz and Hunke, Philip and K{\"o}rner, Katrin and Lewandowski, J{\"o}rg and Lohmann, Dirk and Meinikmann, Karin and Schibalski, Anett and Schmalz, Britta and Schr{\"o}der-Esselbach, Boris and Tietjen, Britta}, title = {Scales, key aspects, feedbacks and challenges of ecohydrological research in Germany}, series = {Hydrologie und Wasserbewirtschaftung}, volume = {58}, journal = {Hydrologie und Wasserbewirtschaftung}, number = {4}, publisher = {Bundesanst. f{\"u}r Gew{\"a}sserkunde}, address = {Koblenz}, issn = {1439-1783}, doi = {10.5675/HyWa_2014,4_2}, pages = {221 -- 240}, year = {2014}, abstract = {Ecohydrology analyses the interactions of biotic and abiotic aspects of our ecosystems and landscapes. It is a highly diverse discipline in terms of its thematic and methodical research foci. This article gives an overview of current German ecohydrological research approaches within plant-animal-soil-systems, meso-scale catchments and their river networks, lake systems, coastal areas and tidal rivers. It discusses their relevant spatial and temporal process scales and different types of interactions and feedback dynamics between hydrological and biotic processes and patterns. The following topics are considered key challenges: innovative analysis of the interdisciplinary scale continuum, development of dynamically coupled model systems, integrated monitoring of coupled processes at the interface and transition from basic to applied ecohydrological science to develop sustainable water and land resource management strategies under regional and global change.}, language = {de} } @article{LangeReiterKniepertetal.2015, author = {Lange, Ilja and Reiter, Sina and Kniepert, Juliane and Piersimoni, Fortunato and Paetzel, Michael and Hildebrandt, Jana and Brenner, Thomas J. K. and Hecht, Stefan and Neher, Dieter}, title = {Zinc oxide modified with benzylphosphonic acids as transparent electrodes in regular and inverted organic solar cell structures}, series = {Applied physics letters}, volume = {106}, journal = {Applied physics letters}, number = {11}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0003-6951}, doi = {10.1063/1.4916182}, pages = {5}, year = {2015}, abstract = {An approach is presented to modify the work function of solution-processed sol-gel derived zinc oxide (ZnO) over an exceptionally wide range of more than 2.3 eV. This approach relies on the formation of dense and homogeneous self-assembled monolayers based on phosphonic acids with different dipole moments. This allows us to apply ZnO as charge selective bottom electrodes in either regular or inverted solar cell structures, using poly(3-hexylthiophene): phenyl-C71-butyric acid methyl ester as the active layer. These devices compete with or even surpass the performance of the reference on indium tin oxide/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate. Our findings highlight the potential of properly modified ZnO as electron or hole extracting electrodes in hybrid optoelectronic devices. (C) 2015 AIP Publishing LLC.}, language = {en} }