@article{GottschalkStollfussLietzauetal.2017, author = {Gottschalk, Josefine Johanna and Stollfuß, Carsten and Lietzau, Kai-Henning and Foitzik, Andreas and Richetta, Maria}, title = {Conceptual study for long-term monitoring of chemotherapeutic induced cell reactions by ESPI}, series = {tm - Technisches Messen}, volume = {85}, journal = {tm - Technisches Messen}, number = {2}, issn = {2196-7113}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10676}, pages = {111 -- 118}, year = {2017}, abstract = {During the last years, various approaches on an individualized drug therapy for benign cells have been researched. However, due to the complex topic a universal approach has not been found up until this point. Commonly, the effect of cytotoxic drugs on benign cells is in most cases the same compared to regular cells while the actual effect on patient still can't be predicted. In order to reduce unwanted side effects or unspecific drug reactions a test system for patients which allows to analyse the interaction between cytotoxic agents and the targeted cells is needed. Furthermore, this should also include an adequate measurement system which is capable to work in a natural environment and without any additional preparation. In terms of this work, a first proof of concept with different benign cells and cytotoxic agents is presented while monitoring the obtained displacement using electronic speckle pattern interferometry (ESPI).}, language = {en} } @article{GrebinykYashchukBashmakovaetal.2019, author = {Grebinyk, Anna and Yashchuk, Valeriy and Bashmakova, Nataliya and Gryn, Dmytro and Hagemann, Tobias and Naumenko, Antonina and Kutsevol, Nataliya and Dandekar, Thomas and Frohme, Marcus}, title = {A New Triple System DNA-Nanosilver-Berberine for Cancer Therapy}, series = {Applied Nanoscience}, journal = {Applied Nanoscience}, issn = {2190-5517}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10628}, year = {2019}, abstract = {The isoquinoline quaternary alkaloid Berberine possesses a variety of pharmacological properties that suggests its promising application for an anticancer delivery system design utilizing its ability to intercalate DNA.In the current work we have investigated the effects of Berberine on the human T-cell leukemia cell line in vitro.Fluorescent microscopy of leukemic cells revealed Berberine nuclear localization. The results showed that Berberine inhibited leukemic cell growth in a time-and dose-dependent manner, that was associated with reactive oxygen species production intensification and caspase 3/7 activity increase with followed apoptosis induction.Berberine was used as a toxic and phototoxic agent for triple system synthesis along with DNA as a carrier and nanosilver as a plasmonic accelerator of Berberine electronic transitions and high energy emission absorbent centers.The proposed method allows to obtain the complex of DNA with Berberine molecules and silver nanopoarticles. The optical properties of free components as well as their various combinations, including the final triple system DNA-Nanosilver-Berberine, were investigated. Obtained results support the possibility to use the triple system DNA-Nanosilver-Berberine as an alternative therapeutic agent for cancer treatment.}, language = {en} } @article{GrebinykGrebinykPrylutskaetal.2018, author = {Grebinyk, Anna and Grebinyk, Sergii and Prylutska, Svitlana and Ritter, Uwe and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {C60 fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy}, series = {Free Radical Biology and Medicine}, volume = {124}, journal = {Free Radical Biology and Medicine}, issn = {1873-4596}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10588}, pages = {319 -- 327}, year = {2018}, abstract = {Recent progress in nanobiotechnology has attracted interest to a biomedical application of the carbon nanostructure C60 fullerene since it possesses a unique structure and versatile biological activity. C60 fullerene potential application in the frame of cancer photodynamic therapy (PDT) relies on rapid development of new light sources as well as on better understanding of the fullerene interaction with cells. The aim of this study was to analyze C60 fullerene effects on human leukemic cells (CCRF-CEM) in combination with high power single chip light-emitting diodes (LEDs) light irradiation of different wavelengths: ultraviolet (UV, 365 nm), violet (405 nm), green (515 nm) and red (632 nm). The time-dependent accumulation of fullerene C60 in CCRF-CEM cells up to 250 ng/106 cells at 24 h with predominant localization within mitochondria was demonstrated with immunocytochemical staining and liquid chromatography mass spectrometry. In a cell viability assay we studied photoexcitation of the accumulated C60 nanostructures with ultraviolet or violet LEDs and could prove that significant phototoxic effects did arise. A less pronounced C60 fullerene phototoxic effect was observed after irradiation with green, and no effect was detected with red light. A C60 fullerene photoactivation with violet light induced substantial ROS generation and apoptotic cell death, confirmed by caspase3/7 activation and plasma membrane phosphatidylserine externalization. Our work proved C60 fullerene ability to induce apoptosis of leukemic cells after photoexcitation with high power single chip 405 nm LED as a light source. This underlined the potential for application of C60 nanostructure as a photosensitizer for anticancer therapy.}, language = {en} } @article{GerhardStappenbeck2018, author = {Gerhard, Christoph and Stappenbeck, Marco}, title = {Impact of the Polishing Suspension Concentration on Laser Damage of Classically Manufactured and Plasma Post-Processed Zinc Crown Glass Surfaces}, series = {Applied Sciences}, volume = {8}, journal = {Applied Sciences}, number = {9}, publisher = {MDPI}, issn = {2076-3417}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10556}, pages = {1 -- 15}, year = {2018}, abstract = {The laser-induced damage threshold of optics is an issue of essential importance in high-power laser applications. However, the complex and partially interacting mechanisms as well as the underlying reasons for laser damage of glass surfaces are not yet fully understood. The aim of the present work is to contribute to a better understanding of such damage mechanisms by providing original results on the impact of classical glass surface machining on the laser-induced damage threshold. For this purpose, glass samples were prepared with well-defined process conditions in terms of the used lapping and polishing agents and suspensions. Further, the samples were post-processed by atmospheric pressure plasma for precision cleaning. The laser-induced damage threshold and surface contamination by residues from the manufacturing process were determined before and after plasma post-processing. It is shown that the polishing suspension concentration has a certain impact on the laser-induced damage threshold and surface contamination by residues from used working materials. The highest damage threshold of 15.2 J/cm² is found for the lowest surface contamination by carbon which occurs in the case of the highest polishing suspension concentration. After plasma treatment for merely 60 s, this value was increased to 20.3 J/cm² due to the removal of surface-adherent carbon. The results thus imply that the laser-induced damage threshold can notably be increased by first choosing appropriate process parameters during classical manufacturing and second plasma post-processing for surface finishing.}, language = {en} } @article{DevulapallyBuergerMielkeetal.2018, author = {Devulapally, Praneeth Reddy and B{\"u}rger, J{\"o}rg and Mielke, Thorsten and Konthur, Zolt{\´a}n and Lehrach, Hans and Yaspo, Marie-Laure and Gl{\"o}kler, J{\"o}rn and Warnatz, Hans-J{\"o}rg}, title = {Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes}, series = {Genome Medicine}, volume = {10}, journal = {Genome Medicine}, issn = {1756-994X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10538}, pages = {1 -- 12}, year = {2018}, abstract = {Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.}, language = {en} } @article{GerhardGimpelTascheetal.2018, author = {Gerhard, Christoph and Gimpel, Thomas and Tasche, Daniel and Koch, Jennifer and Br{\"u}ckner, Stephan and Flachenecker, G{\"u}nter and Wieneke, Stephan and Schade, Wolfgang and Vi{\"o}l, Wolfgang}, title = {Atmospheric pressure plasma-assisted femtosecond laser engraving of aluminium}, series = {Journal of Physics D: Applied Physics}, volume = {51}, journal = {Journal of Physics D: Applied Physics}, issn = {1361-6463}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10521}, pages = {1 -- 7}, year = {2018}, abstract = {In this contribution, we report on the impact of direct dielectric barrier discharge argon plasma at atmospheric pressure on femtosecond laser engraving of aluminium. It is shown that the assisting plasma strongly affects the surface geometry and formation of spikes of both laser-engraved single lines and patterns of adjacent lines with an appropriate overlap. Further, it was observed that the overall ablation depth is significantly increased in case of large-scale patterning whereas no notable differences in ablation depth are found for single lines. Several possible mechanisms and underlying effects of this behaviour are suggested. The increase in ablation depth is supposed to be due to a plasma-induced removal of debris particles from the cutting point via charging and oxidation as supported by EDX analysis of the re-solidified debris. Furthermore, the impact of a higher degree of surface wrinkling as well as direct interactions of plasma species with the aluminium surface on the ablation process are discussed.}, language = {en} } @article{GrebinykPrylutskaGrynyuketal.2018, author = {Grebinyk, Anna and Prylutska, Svitlana and Grynyuk, I. and Kolp, Benjamin and Hurmach, V. and Sliva, T. and Amirkhanov, Volodymyr and Trush, V. and Matyshevska, Olga and Slobodyanik, M. and Prylutskyy, Yuriy and Frohme, Marcus and Ritter, Uwe}, title = {C60 Fullerene Effects on Diphenyl-N-(trichloroacetyl)-amidophosphate Interaction with DNA In Silico and Its Cytotoxic Activity Against Human Leukemic Cell Line In Vitro}, series = {Nanoscale Research Letters}, volume = {2018}, journal = {Nanoscale Research Letters}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10515}, pages = {1 -- 9}, year = {2018}, abstract = {New representative of carbacylamidophosphates - diphenyl-N-(trichloroacetyl)-amidophosphate (HL), which contains two phenoxy substituents near the phosphoryl group, was synthesized, identified by elemental analysis and IR and NMR spectroscopy, and tested as a cytotoxic agent itself and in combination with C60 fullerene. According to molecular simulation results, C60 fullerene and HL could interact with DNA and form a rigid complex stabilized by stacking interactions of HL phenyl groups with C60 fullerene and DNA G nucleotide, as well as by interactions of HL CCl3 group by ion-π bonds with C60 molecule and by electrostatic bonds with DNA G nucleotide. With the use of MTT test, the cytotoxic activity of HL against human leukemic CCRF-CM cells with IC50 value detected at 10 μM concentration at 72 h of cells treatment was shown. Under combined action of 16 μM C60 fullerene and HL, the value of IC50 was detected at lower 5 μM HL concentration and at earlier 48 h period of incubation, besides the cytotoxic effect of HL was observed at a low 2.5 μM concentration at which HL by itself had no influence on cell viability. Binding of C60 fullerene and HL with minor DNA groove with formation of a stable complex is assumed to be one of the possible reasons of their synergistic inhibition of CCRF-CЕM cells proliferation. Application of C60 fullerene in combination with 2.5 μM HL was shown to have no harmful effect on structural stability of blood erythrocytes membrane. Thus, combined action of C60 fullerene and HL in a low concentration potentiated HL cytotoxic effect against human leukemic cells and was not followed by hemolytic effect.}, language = {en} } @article{PfeilFrohmeSchulze2018, author = {Pfeil, Juliane and Frohme, Marcus and Schulze, Katja}, title = {Mobile microscopy for the examination of blood samples}, series = {EMBnet.journal}, volume = {23}, journal = {EMBnet.journal}, issn = {2226-6089}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10509}, pages = {e904}, year = {2018}, abstract = {The analysis of blood is one of the best possibilities to diagnose and control diseases and deficiency symptoms. Common blood tests that are performed in medical laboratories are time-consuming and work-intensive. In under-developed areas, there is often also a lack of specialised staff and facilities. The development of a mobile microscopic system that contains an automated image analysis and that can be used via a smartphone, could represent a valuable help to improve the diagnostic care, especially in those areas. it aims to enable a very fast, cheap, location- and knowledge-independent application for many use cases.}, language = {en} } @article{RoeschTolkiehn2018, author = {R{\"o}sch, Olga and Tolkiehn, G{\"u}nter-Ulrich}, title = {Zum Diskurs {\"u}ber die Sprache in der Wissenschaftskommunikation}, series = {Die neue Hochschule : DNH}, journal = {Die neue Hochschule : DNH}, number = {4}, issn = {0340-448X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10465}, pages = {26 -- 29}, year = {2018}, abstract = {Der Diskurs {\"u}ber die Wissenschaftssprache darf nicht von außerwissenschaftlichen Interessen bestimmt werden. Er muss in den Bereich der Wissenschaft zur{\"u}ckgeholt und dort freiheitlich mit wissenschaftlicher Rationalit{\"a}t gef{\"u}hrt werden.}, language = {de} } @article{GrebinykGrebinykPrylutskaetal.2018, author = {Grebinyk, Anna and Grebinyk, Sergii and Prylutska, Svitlana and Ritter, Uwe and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {HPLC-ESI-MS method for C60 fullerene mitochondrial content quantification}, series = {Data in Brief}, volume = {19}, journal = {Data in Brief}, issn = {2352-3409}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10368}, pages = {2047 -- 2052}, year = {2018}, abstract = {The presented dataset describes the quantification of carbon nanoparticle C60 fullerene accumulated in mitochondria of human leukemic cells treated with nanostructure. Firstly, the high performance liquid chromatography-electro spray ionization-mass spectrometry (HPLC-ESI-MS) method was developed for quantitative analysis of pristine C60 fullerene. Then, human leukemic cells were incubated with C60 fullerene, homogenized and subjected to the differential centrifugation to retrieve mitochondrial fraction. The C60 fullerene content was quantified by HPLC-ESI-MS in extracts of cellular fractions. This data article refers to the research article "C60 Fullerene Accumulation in Human Leukemic Cells and Perspectives of LED-mediated Photodynamic Therapy" by Grebinyk et al.}, language = {en} } @article{LuxEdlingSiemrothetal.2018, author = {Lux, Helge and Edling, Matthias and Siemroth, Peter and Schrader, Sigurd}, title = {Fast and Cost-Effective Synthesis of High-Quality Graphene on Copper Foils Using High-Current Arc Evaporation}, series = {Materials}, volume = {11}, journal = {Materials}, number = {5}, issn = {1996-1944}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10359}, pages = {1 -- 10}, year = {2018}, abstract = {In this paper, we present an innovative and ultra-fast process for the deposition of high-quality graphene on different metal foils and thin metal films. The graphene layer can be homogeneously deposited in only 30 s process time. Due to the weak adhesion to the substrate material, the monolayer graphene is easy to transfer using the established processes. For the production, we use magnetic filtered high-current arc evaporation (Φ-HCA) with a solid, graphitic carbon source. This ultra-fast growth process can pave the way towards a cost-effective graphene synthesis for the mass production e.g., in a roll-to-roll process, avoiding time consuming established processes.}, language = {en} } @article{KinuthiaFrohmeBroedeletal.2017, author = {Kinuthia, Chuaga and Frohme, Marcus and Br{\"o}del, Oliver and Mugendi, Beatrice}, title = {LCMS Analysis of Biochemical Composition in Different Kenyan Coffee Classifications}, series = {Food Science and Quality Management}, volume = {69}, journal = {Food Science and Quality Management}, issn = {2225-0557}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10185}, pages = {44 -- 52}, year = {2017}, abstract = {Kenyan coffee is classified by defects after grading by the 'Devonshire method.' The method involves classification of the coffee beans into different classes based on the raw and roasted coffees and cup quality, with class one being the best and ten the poorest. In this study, the relationship between classification of the coffee and the content of sucrose, trigonelline, caffeine and chlorogenic acids was determined by simultaneous LC-MS analysis. By using the sensory variables the class 3 coffee portrayed the best quality, followed by class 4 and 5 which were placed further distinctively from the other classes (6, 7, 8 and 9). The class 3 coffee had a high percent of non-defective beans with 94.31\% and class 9 had a high defect count at 79.53\% hence the defective beans increased with decrease in coffee class. The caffeine concentration in green coffee for class 3 coffee was significantly different from the rest of the coffees at 1.23 ± 0.00g/100g. A higher content of trigonelline levels was observed as the quality of the green coffee decreased in classes 6, 7 and 8. The highest level of sucrose in green coffee beans was observed in class 3 coffee and the lowest in the class 9. Lower content of chlorogenic acids were observed among the high quality coffees i.e. class 3, 4 and 5 with class 3 having the lowest while a higher content was observed among the lower quality coffees i.e. classes 6, 7 and 9 with class 6 having a higher content was it significantly different in class 6 compared to 7 and 9?. Quantities of different chemical components among the classes are clear indicators that the classification method used on the Kenyan coffees brings out the differences in coffee quality based on the analysis of the green and the roasted coffees.}, language = {en} } @article{RoggeZinnProspositoetal.2017, author = {Rogge, Christian and Zinn, Steffen and Prosposito, Paolo and Francini, Roberto and Foitzik, Andreas}, title = {Transmitted light pH optode for small sample volumes}, series = {Journal of Sensors and Sensor Systems}, volume = {6}, journal = {Journal of Sensors and Sensor Systems}, number = {2}, issn = {2194-878X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10093}, pages = {351 -- 359}, year = {2017}, abstract = {An innovative concept of a low-cost pH optode with working volumes of less than 150 µL is presented. The pH monitoring is based on the color changing effect of pH indicators. The optode includes an RGB color sensor patch TCS34725 from Adafruit, a controllable LED and reactor slides and is addressed by a self-written LabVIEW© software. Utilizing the hue value of the HSV color model, it is possible to analyze the color change of the indicator and estimate the pH value of the analyzed samples by exploiting sigmoidal fit models. Measurements carried out with phenol red and DMEM (Dulbecco's Modified Eagle's Medium) reported a standard error of calibration in the physiologic pH range (6.5-7.5) of ±0.04 pH units.}, language = {en} } @article{HornemannSinningCortesetal.2017, author = {Hornemann, Andrea and Sinning, Denise and Cortes, Sofia and Campino, Lenea and Emmer, Peggy and Kuhls, Katrin and Ulm, Gerhard and Frohme, Marcus and Beckhoff, Burkhard}, title = {A pilot study on fingerprinting Leishmania species from the Old World using Fourier transform infrared spectroscopy}, series = {Analytical and Bioanalytical Chemistry}, journal = {Analytical and Bioanalytical Chemistry}, issn = {1432-1130}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10080}, year = {2017}, abstract = {Leishmania species are protozoan parasites and the causative agents of leishmaniasis, a vector borne disease that imposes a large health burden on individuals living mainly in tropical and subtropical regions. Different Leishmania species are responsible for the distinct clinical patterns, such as cutaneous, mucocutaneous, and visceral leishmaniasis, with the latter being potentially fatal if left untreated. For this reason, it is important to perform correct species identification and differentiation. Fourier transform infrared spectroscopy (FTIR) is an analytical spectroscopic technique increasingly being used as a potential tool for identification of microorganisms for diagnostic purposes. By employing mid-infrared (MIR) spectral data, it is not only possible to assess the chemical structures but also to achieve differentiation supported by multivariate statistic analysis. This work comprises a pilot study on differentiation of Leishmania species of the Old World (L. major, L. tropica, L. infantum, and L. donovani) as well as hybrids of distinct species by using vibrational spectroscopic fingerprints. Films of intact Leishmania parasites and their deoxyribonucleic acid (DNA) were characterized comparatively with respect to their biochemical nature and MIR spectral patterns. The strains' hyperspectral datasets were multivariately examined by means of variance-based principal components analysis (PCA) and distance-based hierarchical cluster analysis (HCA). With the implementation of MIR spectral datasets we show that a phenotypic differentiation of Leishmania at species and intra-species level is feasible. Thus, FTIR spectroscopy can be further exploited for building up spectral databases of Leishmania parasites in view of high-throughput analysis of clinical specimens.}, language = {en} } @article{AmroAlDwibeGashoutetal.2017, author = {Amro, Ahmad and Al-Dwibe, Hamida and Gashout, Aisha and Moskalenko, Olga and Galafin, Marlena and Hamarsheh, Omar and Frohme, Marcus and Jaeschke, Anja and Sch{\"o}nian, Gabriele and Kuhls, Katrin}, title = {Spatiotemporal and molecular epidemiology of cutaneous leishmaniasis in Libya}, series = {PLoS Neglected Tropical Diseases}, volume = {11}, journal = {PLoS Neglected Tropical Diseases}, number = {9}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10054}, year = {2017}, abstract = {Cutaneous leishmaniasis (CL) is a skin infection caused by a single-celled parasite that is transmitted by the bite of a phlebotomine sandfly. CL is the most common form of leishmaniasis characterized by localized lesions in the skin and mucous membranes. The disease is prevalent in all countries around the Mediterranean Basin. In this paper, we describe spatiotemporal and eco-epidemiological parameters of CL in Libya. Moreover, we explored current spatiotemporal distributions of CL cases and explored the future projection of the disease. Our study indicates the presence of higher risk of CL in the coastal regions of Libya. Future projection until 2060 showed a trend of increasing incidence of CL in the north-western part of Libya, a spread along the coastal region and a possible emergence of new endemics in the north-eastern districts of Libya. These scenarios should be considered by health authorities in order to develop appropriate intervention strategies and plan effective control programs.}, language = {en} } @article{AkhoundiDowningVotypkaetal.2017, author = {Akhoundi, Mohammad and Downing, Tim and Vot{\´y}pka, Jan and Kuhls, Katrin and Lukeš, Julius and Cannet, Arnaud and Ravel, Christophe and Marty, Pierre and Delaunay, Pascal and Kasbari, Mohamed and Granouillac, Bruno and Gradoni, Luigi and Sereno, Denis}, title = {Leishmania infections: Molecular targets and diagnosis}, series = {Molecular Aspects of Medicine}, volume = {57}, journal = {Molecular Aspects of Medicine}, issn = {0098-2997}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9908}, pages = {1 -- 29}, year = {2017}, abstract = {Progress in the diagnosis of leishmaniases depends on the development of effective methods and the discovery of suitable biomarkers. We propose firstly an update classification of Leishmania species and their synonymies. We demonstrate a global map highlighting the geography of known endemic Leishmania species pathogenic to humans. We summarize a complete list of techniques currently in use and discuss their advantages and limitations. The available data highlights the benefits of molecular markers in terms of their sensitivity and specificity to quantify variation from the subgeneric level to species complexes, (sub) species within complexes, and individual populations and infection foci. Each DNA-based detection method is supplied with a comprehensive description of markers and primers and proposal for a classification based on the role of each target and primer in the detection, identification and quantification of leishmaniasis infection. We outline a genome-wide map of genes informative for diagnosis that have been used for Leishmania genotyping. Furthermore, we propose a classification method based on the suitability of well-studied molecular markers for typing the 21 known Leishmania species pathogenic to humans. This can be applied to newly discovered species and to hybrid strains originating from inter-species crosses. Developing more effective and sensitive diagnostic methods and biomarkers is vital for enhancing Leishmania infection control programs.}, language = {en} } @article{RadkeSandigLubitzetal.2017, author = {Radke, Lars and Sandig, Grit and Lubitz, Annika and Schließer, Ulrike and von Horsten, Hans Henning and Blanchard, V{\´e}ronique and Keil, Karolin and Sandig, Volker and Giese, Christoph and Hummel, Michael and Hinderlich, Stephan and Frohme, Marcus}, title = {In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor}, series = {Bioengineering}, volume = {4}, journal = {Bioengineering}, number = {3}, issn = {2306-5354}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9831}, year = {2017}, abstract = {Subunit vaccines often require adjuvants to elicit sustained immune activity. Here, a method is described to evaluate the efficacy of single vaccine candidates in the preclinical stage based on cytokine and gene expression analysis. As a model, the recombinant human respiratory syncytial virus (RSV) fusion protein (RSV-F) was produced in CHO cells. For comparison, wild-type and glycoengineered, afucosylated RSV-F were established. Both glycoprotein vaccines were tested in a commercial Human Artificial Lymph Node in vitro model (HuALN®). The analysis of six key cytokines in cell culture supernatants showed well-balanced immune responses for the afucosylated RSV-F, while immune response of wild-type RSV-F was more Th1 accentuated. In particular, stronger and specific secretion of interleukin-4 after each round of re-stimulation underlined higher potency and efficacy of the afucosylated vaccine candidate. Comprehensive gene expression analysis by nCounter gene expression assay confirmed the stronger onset of the immunologic reaction in stimulation experiments with the afucosylated vaccine in comparison to wild-type RSV-F and particularly revealed prominent activation of Th17 related genes, innate immunity, and comprehensive activation of humoral immunity. We, therefore, show that our method is suited to distinguish the potency of two vaccine candidates with minor structural differences.}, language = {en} } @article{FischbachFrohmeGloekler2017, author = {Fischbach, Jens and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Hinge-initiated Primer-dependent Amplification of Nucleic Acids (HIP) - A New Versatile Isothermal Amplification Method}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9824}, year = {2017}, abstract = {The growing demand for cost-effective nucleic acid detection assays leads to an increasing number of different isothermal amplification reaction methods. However, all of the most efficient methods suffer from highly complex assay conditions due to the use of complicated primer sets and/or auxiliary enzymes. The present study describes the application of a new linker moiety that can be incorporated between a primer and a secondary target binding site which can act both as a block to polymerase extension as well as a hinge for refolding. This novel "hinge-primer" approach results in an efficient regeneration of the primer binding site and thus improves the strand-displacement and amplification process under isothermal conditions. Our investigations revealed that the reaction with forward and reverse hinge-primer including an abasic site is very efficient. The assay complexity can be reduced by combining the hinge-primer with a corresponding linear primer. Furthermore, the reaction speed can be increased by reducing the length of the amplified target sequence. We tested the sensitivity down to 104 copies and found a linear correlation between reaction time and input copy number. Our approach overcomes the usually cumbersome primer-design and extends the range of isothermal amplification methods using a polymerase with strand-displacement activity.}, language = {en} } @article{BayBuschLisdatetal.2017, author = {Bay, Daniyah H. and Busch, Annika and Lisdat, Fred and Iida, Keisuke and Ikebukuro, Kazunori and Nagasawa, Kazuo and Karube, Isao and Yoshida, Wataru}, title = {Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands}, series = {BMC Molecular Biology}, volume = {18}, journal = {BMC Molecular Biology}, number = {17}, issn = {1471-2199}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9811}, year = {2017}, abstract = {G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay.}, language = {en} } @article{LuxSiemrothSgarlataetal.2015, author = {Lux, Helge and Siemroth, Peter and Sgarlata, Anna and Prosposito, Paolo and Schubert, Markus Andreas and Casalboni, Mauro and Schrader, Sigurd}, title = {Synthesis of graphene-like transparent conductive films on dielectric substrates using a modified filtered vacuum arc system}, series = {Journal of Applied Physics}, volume = {117}, journal = {Journal of Applied Physics}, number = {19}, issn = {1089-7550}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9738}, year = {2015}, abstract = {Here, we present a reliable process to deposit transparent conductive films on silicon oxide, quartz, and sapphire using a solid carbon source. This layer consists of partially ordered graphene flakes with a lateral dimension of about 5 nm. The process does not require any catalytic metal and exploits a high current arc evaporation (Φ-HCA) to homogeneously deposit a layer of carbon on heated substrates. A gas atmosphere consisting of Argon or Argon/Hydrogen blend acting as a buffer influences the morphology of the growing film. scanning tunneling microscopy, transmission electron microscopy, and Raman spectra were used for a thorough characterization of the samples in order to optimize the growth parameters. The best carbon layers have a surface resistance of 5.7 × 103 Ω◻ whereas the optical transparency of the coatings is 88\% with an excellent homogeneity over areas of several cm2. Such results are compatible with most semiconductor fabrication processes and make this method very promising for various industrial applications.}, language = {en} } @article{KlingspornKirnerVillringeretal.2016, author = {Klingsporn, M. and Kirner, S. and Villringer, Claus and Abou-Ras, D. and Costina, Ioan and Lehmann, M. and Stannowski, Bernd}, title = {Resolving the nanostructure of plasma-enhanced chemical vapor deposited nanocrystalline SiOx layers for application in solar cells}, series = {Journal of Applied Physics}, volume = {119}, journal = {Journal of Applied Physics}, number = {22}, issn = {1089-7550}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9727}, year = {2016}, abstract = {Nanocrystalline silicon suboxides (nc-SiOx) have attracted attention during the past years for the use in thin-film silicon solar cells. We investigated the relationships between the nanostructure as well as the chemical, electrical, and optical properties of phosphorous, doped, nc-SiO0.8:H fabricated by plasma-enhanced chemical vapor deposition. The nanostructure was varied through the sample series by changing the deposition pressure from 533 to 1067 Pa. The samples were then characterized by X-ray photoelectron spectroscopy, spectroscopic ellipsometry, Raman spectroscopy, aberration-corrected high-resolution transmission electron microscopy, selected-area electron diffraction, and a specialized plasmon imaging method. We found that the material changed with increasing pressure from predominantly amorphous silicon monoxide to silicon dioxide containing nanocrystalline silicon. The nanostructure changed from amorphous silicon filaments to nanocrystalline silicon filaments, which were found to cause anisotropic electron transport.}, language = {en} } @article{OuAnwandKoegleretal.2014, author = {Ou, Xin and Anwand, Wolfgang and K{\"o}gler, Reinhard and Zhou, Hong-Bo and Richter, Asta}, title = {The role of helium implantation induced vacancy defect on hardening of tungsten}, series = {Journal of Applied Physics}, volume = {115}, journal = {Journal of Applied Physics}, number = {12}, issn = {1089-7550}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5623}, year = {2014}, abstract = {Vacancy-type defects created by helium implantation in tungsten and their impact on the nano-hardness characteristics were investigated by correlating the results from the positron annihilation spectroscopy and the nano-indentation technique. Helium implantation was performed at room temperature (RT) and at an elevated temperate of 600 °C. Also, the effect of post-annealing of the RT implanted sample was studied. The S parameter characterizing the open volume in the material was found to increase after helium irradiation and is significantly enhanced for the samples thermally treated at 600 °C either by irradiation at high temperature or by post-annealing. Two types of helium-vacancy defects were detected after helium irradiation; small defects with high helium-to-vacancy ratio (low S parameter) for RT irradiation and large defects with low helium-to-vacancy ratio (high S parameter) for thermally treated tungsten. The hardness of the heat treated tungsten coincides with the S parameter, and hence is controlled by the large helium-vacancy defects. The hardness of tungsten irradiated at RT without thermal treatment is dominated by manufacturing related defects such as dislocation loops and impurity clusters and additionally by trapped He atoms from irradiation effects, which enhance hardness. He-stabilized dislocation loops mainly cause the very high hardness values in RT irradiated samples without post-annealing.}, language = {en} } @article{MeierGrawBeyerleinetal.2017, author = {Meier, Richard and Graw, Stefan and Beyerlein, Peter and Koestler, Devin and Molina, Julian R. and Chien, Jeremy}, title = {digit—a tool for detection and identification of genomic interchromosomal translocations}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {9}, issn = {1362-4962}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9697}, pages = {e72}, year = {2017}, abstract = {Structural variations (SVs) in genomic DNA can have profound effects on the evolution of living organisms, on phenotypic variations and on disease processes. A critical step in discovering the full extent of structural variations is the development of tools to characterize these variations accurately in next generation sequencing data. Toward this goal, we developed a software pipeline named digit that implements a novel measure of mapping ambiguity to discover interchromosomal SVs from mate-pair and pair-end sequencing data. The workflow robustly handles the high numbers of artifacts present in mate-pair sequencing and reduces the false positive rate while maintaining sensitivity. In the simulated data set, our workflow recovered 96\% of simulated SVs. It generates a self-updating library of common translocations and allows for the investigation of patient- or group-specific events, making it suitable for discovering and cataloging chromosomal translocations associated with specific groups, traits, diseases or population structures.}, language = {en} } @article{SandigvonHorstenRadkeetal.2017, author = {Sandig, Grit and von Horsten, Hans Henning and Radke, Lars and Blanchard, V{\´e}ronique and Frohme, Marcus and Giese, Christoph and Sandig, Volker and Hinderlich, Stephan}, title = {Engineering of CHO Cells for the Production of Recombinant Glycoprotein Vaccines with Xylosylated N-glycans}, series = {Bioengineering}, volume = {4}, journal = {Bioengineering}, number = {2}, issn = {2306-5354}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9620}, year = {2017}, abstract = {Xylose is a general component of O-glycans in mammals. Core-xylosylation of N-glycans is only found in plants and helminth. Consequently, xylosylated N-glycans cause immunological response in humans. We have used the F-protein of the human respiratory syncytial virus (RSV), one of the main causes of respiratory tract infection in infants and elderly, as a model protein for vaccination. The RSV-F protein was expressed in CHO-DG44 cells, which were further modified by co-expression of β1,2-xylosyltransferase from Nicotiana tabacum. Xylosylation of RSV-F N-glycans was shown by monosaccharide analysis and MALDI-TOF mass spectrometry. In immunogenic studies with a human artificial lymph node model, the engineered RSV-F protein revealed improved vaccination efficacy.}, language = {en} } @article{KarakuşNasereddinOnayetal.2017, author = {Karaku{\c{s}}, Mehmet and Nasereddin, Abed and Onay, H{\"u}seyin and Karaca, Emin and {\"O}zkeklik{\c{c}}i, Ahmet and Jaffe, Charles L. and Kuhls, Katrin and {\"O}zbilgin, Ahmet and Ertabaklar, Hatice and Demir, Samiye and {\"O}zbel, Yusuf and T{\"o}z, Seray}, title = {Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT)}, series = {PLoS Neglected Tropical Diseases}, volume = {11}, journal = {PLoS Neglected Tropical Diseases}, number = {4}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9313}, pages = {12}, year = {2017}, abstract = {Turkey is located in an important geographical location, in terms of the epidemiology of vector-borne diseases, linking Asia and Europe. Cutaneous leishmaniasis (CL) is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey, 45\% of CL patients originate from Şanl{\i}urfa province located in southeastern Turkey. Herein, the epidemiological status of CL, caused by L. tropica, in Turkey was examined using multilocus microsatellite typing (MLMT) of strains obtained from Turkish and Syrian patients. A total of 38 cryopreserved strains and 20 Giemsa-stained smears were included in the present study. MLMT was performed using 12 highly specific microsatellite markers. Delta K (ΔK) calculation and Bayesian statistics were used to determine the population structure. Three main populations (POP A, B and C) were identified and further examination revealed the presence of three subpopulations for POP B and C. Combined analysis was performed using the data of previously typed L. tropica strains and Mediterranean and Şanl{\i}urfa populations were identified. This finding suggests that the epidemiological status of L. tropica is more complicated than expected when compared to previous studies. A new population, comprised of Syrian L. tropica samples, was reported for the first time in Turkey, and the data presented here will provide new epidemiological information for further studies.}, language = {en} } @article{HollandMoritzVandenhouten2013, author = {Holland-Moritz, Ralph and Vandenhouten, Ralf}, title = {Detection of Movement Profiles in Facility Management Using Complex Event Processing}, series = {International Journal of Information Science}, volume = {3}, journal = {International Journal of Information Science}, number = {1}, issn = {2163-193X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9495}, pages = {7 -- 12}, year = {2013}, abstract = {This paper presents a solution for detecting movement and spreading profiles by analyzing sensor data in the facility management. First of all, a scenario is defined and described. On the basis of this scenario an approach is made using integration of events over time and location. For making the integration possible the required information, which the data objects have to provide, is identified. At the end a solution is presented using Complex Event Processing to implement the integration of events.}, language = {en} } @article{VandenhoutenWendlandt2015, author = {Vandenhouten, Ralf and Wendlandt, Ole}, title = {High-precision Optical Position Measurement in Indoor Environments}, series = {Optik \& Photonik}, volume = {10}, journal = {Optik \& Photonik}, number = {3}, issn = {1863-1460}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9305}, pages = {24 -- 27}, year = {2015}, abstract = {Indoor localization is still a challenge today. Conventional methods based on satellite navigation, like GPS, can only be used outdoors. On the other hand, radio signal architectures, like WiFi or NFC, require high cost infrastructure to be installed inside the building. In collaboration with Ixellence GmbH, the research group for telematics of the University of Applied Science Wildau is developing a new inexpensive solution based on the camera of a mobile device. This approach only requires the availability of multiple identifiable landmarks that can be installed cost-efficiently in an indoor environment. Our investigations show that this method is very accurate and can produce repeatable, robust results.}, language = {en} } @article{PrylutskaGrynyukGrebinyketal.2017, author = {Prylutska, Svitlana and Grynyuk, I. and Grebinyk, Anna and Hurmach, V. and Shatrava, Iu. and Sliva, T. and Amirkhanov, Volodymyr and Prylutskyy, Yuriy and Matyshevska, Olga and Slobodyanik, M. and Frohme, Marcus and Ritter, Uwe}, title = {Cytotoxic Effects of Dimorfolido-N-Trichloroacetylphosphorylamide and Dimorfolido-N-Benzoylphosphorylamide in Combination with C60 Fullerene on Leukemic Cells and Docking Study of Their Interaction with DNA}, series = {Nanoscale Research Letters}, volume = {12}, journal = {Nanoscale Research Letters}, number = {124}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9273}, year = {2017}, abstract = {Dimorfolido-N-trichloroacetylphosphorylamide (HL1) and dimorfolido-N-benzoylphosphorylamide (HL2) as representatives of carbacylamidophosphates were synthesized and identified by the methods of IR, 1H, and 31P NMR spectroscopy. In vitro HL1 and HL2 at 1 mM concentration caused cell specific and time-dependent decrease of leukemic cell viability. Compounds caused the similar gradual decrease of Jurkat cells viability at 72 h (by 35\%). HL1 had earlier and more profound toxic effect as compared to HL2 regardless on leukemic cell line. Viability of Molt-16 and CCRF-CEM cells under the action of HL1 was decreased at 24 h (by 32 and 45\%, respectively) with no substantial further reducing up to 72 h. Toxic effect of HL2 was detected only at 72 h of incubation of Jurkat and Molt-16 cells (cell viability was decreased by 40 and 45\%, respectively). It was shown that C60 fullerene enhanced the toxic effect of HL2 on leukemic cells. Viability of Jurkat and CCRF-CEM cells at combined action of C60 fullerene and HL2 was decreased at 72 h (by 20 and 24\%, respectively) in comparison with the effect of HL2 taken separately. In silico study showed that HL1 and HL2 can interact with DNA and form complexes with DNA both separately and in combination with C60 fullerene. More stable complexes are formed when DNA interacts with HL1 or C60 + HL2 structure. Strong stacking interactions can be formed between HL2 and C60 fullerene. Differences in the types of identified bonds and ways of binding can determine distinction in cytotoxic effects of studied compounds.}, language = {en} } @article{FischbachLohBieretal.2017, author = {Fischbach, Jens and Loh, Qiuting and Bier, Frank Fabian and Lim, Theam Soon and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9248}, year = {2017}, abstract = {We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.}, language = {en} } @article{KaltdorfSchulzeHelmprobstetal.2017, author = {Kaltdorf, Kristin Verena and Schulze, Katja and Helmprobst, Frederik and Kollmannsberger, Philip and Dandekar, Thomas and Stigloher, Christian}, title = {FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms}, series = {PLoS Computational Biology}, volume = {13}, journal = {PLoS Computational Biology}, number = {1}, issn = {1553-7358}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9218}, year = {2017}, abstract = {Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.}, language = {en} } @article{AzmitiaMohnkeWiechers2016, author = {Azmitia, Alfredo and Mohnke, Janett and Wiechers, Henning}, title = {Wo bin ich? iBeacons im Einsatz in der Bibliothek der TH Wildau}, series = {Bibliothek : Forschung und Praxis}, volume = {40}, journal = {Bibliothek : Forschung und Praxis}, number = {3}, issn = {1865-7648}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9186}, pages = {395 -- 404}, year = {2016}, abstract = {Mit diesem Beitrag soll der Einsatz von iBeacons als Basis eines Indoor-Ortungssystems in der Hochschulbibliothek der Technischen Hochschule Wildau vorgestellt werden. F{\"u}r die Ortung innerhalb von Geb{\"a}uden sind bisher unterschiedliche Strategien zum Einsatz gekommen. Die von Apple Inc. entwickelte iBeacon-Technologie kommuniziert {\"u}ber Bluetooth Low Energy (BLE) und setzt somit eine Technologie ein, die einen großen Kreis von Nutzern erreicht. Als wesentlicher Teil der Campus-App Unidos Wildau operiert das Ortungssystem auf der Basis des Kartendienstes iCampus Wildau Maps. Gemachte Erfahrungen mit der iBeacon-Technologie werden ebenso im Fokus dieses Beitrags stehen wie Ergebnisse der Implementierung unseres Ortungssystems sowie Pl{\"a}ne f{\"u}r die Weiterentwicklung.}, language = {de} } @article{JanowskiGrossSauerGuerthetal.2016, author = {Janowski, Susann and Gross, Ina and Sauer-G{\"u}rth, Hedwig and Tietze, Dieter Thomas and Grohme, Markus and Frohme, Marcus and Becker, Peter and Wink, Michael}, title = {New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing}, series = {The Open Ornithology Journal}, volume = {9}, journal = {The Open Ornithology Journal}, issn = {1874-4532}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6789}, pages = {50 -- 59}, year = {2016}, abstract = {Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern, Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns, e.g. in the aforementioned colony monitored for decades.}, language = {en} } @article{FeifelStiegerKappetal.2016, author = {Feifel, Sven Christian and Stieger, Kai Ralf and Kapp, Andreas and Weber, Dennis and Allegrozzi, Marco and Piccioli, Mario and Turano, Paola and Lisdat, Fred}, title = {Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix}, series = {ACS Omega}, volume = {1}, journal = {ACS Omega}, number = {6}, issn = {2470-1343}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6753}, pages = {1058 -- 1066}, year = {2016}, abstract = {The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.}, language = {en} } @article{EndrullatGloeklerFrankeetal.2016, author = {Endrullat, Christoph and Gl{\"o}kler, J{\"o}rn and Franke, Philipp and Frohme, Marcus}, title = {Standardization and quality management in next-generation sequencing}, series = {Applied \& Translational Genomics}, volume = {10}, journal = {Applied \& Translational Genomics}, issn = {2212-0661}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6637}, pages = {2 -- 9}, year = {2016}, abstract = {DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.}, language = {en} } @article{RistićFurboMoseretal.2016, author = {Ristić, Alenka and Furbo, Simon and Moser, Christoph and Schranzhofer, Hermann and Lazaro, Ana and Delgado, Monica and Pe{\~n}alosa, Conchita and Zalewski, Laurent and Diarce, Gonzalo and Alkan, Cemil and Gunasekara, Saman N. and Haussmann, Thomas and Gschwander, Stefan and Rathgeber, Christoph and Schmit, Henri and Barreneche, Camila and Cabeza, Luiza and Ferrer, Gerard and Konuklu, Yeliz and Paksoy, Halime and Rammelberg, Holger and Munz, Gunther and Herzog, Thomas H. and J{\"a}nchen, Jochen and del Barrio, Elena Palomo}, title = {IEA SHC Task 42 / ECES Annex 29 WG A1: Engineering and Processing of PCMs, TCMs and Sorption Materials}, series = {Energy Procedia}, volume = {91}, journal = {Energy Procedia}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6629}, pages = {207 -- 217}, year = {2016}, abstract = {An overview on the recent results on the engineering and characterization of sorption materials, PCMs and TCMs investigated in the working group WG A1 "Engineering and processing of TES materials" of IEA SHC Task 42 / ECES Annex 29 (Task 4229) entitled "Compact Thermal Energy Storage" is presented.}, language = {en} } @article{HerzogJaenchen2016, author = {Herzog, Thomas H. and J{\"a}nchen, Jochen}, title = {Adsorption Properties of Modified Zeolites for Operating Range Enhancement of Adsorption Heat Pumps through the Use of Organic Adsorptive Agents}, series = {Energy Procedia}, volume = {91}, journal = {Energy Procedia}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6614}, pages = {155 -- 160}, year = {2016}, abstract = {Faujasite zeolites with the highest possible Al-content and different cations as well as a dealuminated zeolite Y have been chosen to study the impact on the adsorption behavior in view of differed adsorptive agents for heat pumps or thermochemical storages. Our results show advantages and disadvantages for water, methanol or ethanol adsorption due to the structure of the anion skeleton, kind of cations and size of the adsorbat molecule.}, language = {en} } @article{MarczokBortzWangetal.2016, author = {Marczok, Stefanie and Bortz, Birgit and Wang, Chong and Pospisil, Heike}, title = {Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {7}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6607}, pages = {18}, year = {2016}, abstract = {Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15\% of samples for each tumor entity while BPRs were maximal in 12\% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed 'common BPRs') exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression.}, language = {en} } @article{HooglandBoettcherVerhoefetal.2016, author = {Hoogland, A. Marije and B{\"o}ttcher, Ren{\´e} and Verhoef, Esther and Jenster, Guido and van Leenders, Geert J.L.H.}, title = {Gene-expression analysis of gleason grade 3 tumor glands embedded in low- and high-risk prostate cancer}, series = {Oncotarget}, volume = {7}, journal = {Oncotarget}, number = {25}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6573}, pages = {37846 -- 37856}, year = {2016}, abstract = {The Gleason score (GS) of prostate cancer on diagnostic biopsies is an important parameter for therapeutic decision-making. Biopsy GS under-estimates the actual GS at radical prostatectomy in a significant number of patients due to samplingartifact. The aim of this study was to identify markers that are differentially expressed in Gleason grade 3 (GG3) tumor glands embedded in GS 4 + 3 = 7 and GS 3 + 3 = 6 prostate cancer using laser capture microdissection and RNA sequencing. GG3 tumor glands embedded in nine GS 3 + 3 = 6 and nine GS 4 + 3 = 7 prostate cancers were isolated by laser capture microdissection of frozen radical prostatectomy specimens. After RNA amplification and RNA sequencing, differentially expressed genes in both GG3 components were identified by a 2log fold change > 1.0 and p-value < 0.05. We applied immunohistochemistry on a tissue micro-array representing 481 radical prostatectomy samples for further validation on protein level. A total of 501 genes were up-regulated and 421 down-regulated in GG3 glands embedded in GS 4 + 3 = 7 as compared to GS 3 + 3 = 6 prostate cancer. We selected HELLS, ZIC2 and ZIC5 genes for further validation. ZIC5 mRNA was up-regulated 17 fold (p = 8.4E-07), ZIC2 8 fold (p = 1.3E-05) and HELLS 2 fold (p = 0.006) in GG3 glands derived from GS 4 + 3 = 7. HELLS expression of ≥ 1\% occurred in 10\% GS < 7, 17\% GS 7 and 43\% GS >7 prostate cancer (p < 0.001). Using a cut-off of ≥ 1\%, protein expression of ZIC5 was present in 28\% GS < 7, 43\% GS 7 and 57\% GS > 7 cancer (p < 0.001). ZIC2 was neither associated with GS nor outcome in our validation set. HELLS was independently predictive for biochemical-recurrence after radical prostatectomy (HR 2.3; CI 1.5-3.6; p < 0.01). In conclusion, HELLS and ZIC5 might be promising candidate markers for selection of biopsy GS 6 prostate cancer being at risk for up-grading at prostatectomy.}, language = {en} } @article{HaiderAschauerSchmidt2014, author = {Haider, Christian and Aschauer, Gerald J. and Schmidt, Conrad}, title = {IT Based Attempt to Evaluate and Promote Intermodal Transport Solutions in Central and Southeast Europe}, series = {Transportation Research Procedia}, volume = {3}, journal = {Transportation Research Procedia}, issn = {2352-1465}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6535}, pages = {641 -- 650}, year = {2014}, abstract = {The transport sector is one of the main emitters of greenhouse gas emissions. The awareness about this is increasing because of heightened environmental sensitivity among customers, politicians and the media. Studies dealing with sustainability in logistics have been inducted to show that companies around the world are keen to promote "green solutions" through the management of logistics. From now, it is difficult to gauge how far these efforts reflect true desire to help the environment as opposed to enhance public relations. The paper addresses an IT based attempt to evaluate and promote intermodal transport procedures in the corridor of Central and Southeast Europe. Through the assessment of the relative importance of intermodal transport nodes the described tool is a useful instrument to demonstrate the most important advantages for environmental friendly transport solutions. In combination with accessibility as well as network scenario attempts stakeholders have full information available when preparing several transport plans due to transparent strengths of rail and inland waterway transports.}, language = {en} } @article{KipkorirMuhohoMuliroetal.2015, author = {Kipkorir, R. and Muhoho, S. and Muliro, P. and Mugendi, Beatrice and Frohme, Marcus and Br{\"o}del, Oliver}, title = {Effects of Coffee Processing Technologies on Aroma Profiles and Sensory Quality of Ruiru 11 and SL 28 Kenyan Coffee Varieties}, series = {Asian Journal of Agriculture and Food Sciences}, volume = {3}, journal = {Asian Journal of Agriculture and Food Sciences}, number = {2}, issn = {2321-1571}, doi = {10.15771/2321-1571_2015_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6482}, pages = {178 -- 188}, year = {2015}, abstract = {The study aimed at comparing the effects of three coffee processing methods on aroma profiles and sensory quality of Ruiru 11 and SL 28 coffee varieties. The processing methods varied on stages of processing and method of mucilage removal. The green coffee beans obtained from the three processing methods were graded and roasted, ground and analyzed for the aroma profiles and sensory quality. Headspace Solid phase Microextraction fibre (SPME) technique were used for the extraction of aroma compounds from coffee samples and characterization of the compounds with use of gas chromatography mass spectrometry (GC-MS). Sensory quality were analyzed by an expert panelist. Various volatile aroma compounds were identified in roasted coffee and classified into their chemical classes involving furans, ketones, pyrazines ketones pyridines, pyrroles and acids. The intensity of aroma compounds were compared in terms of their peak areas and variations were noted between the processing methods with the ecopulper showing higher levels of pyrazines such as 2-methylpyrazine, 2-ethyl-6-methylpyrazine, and wet pulper showing higher levels of furans such as furfuryl formate and furfuryl alcohol, acetate. The hand pulper was high in the level of acids and esters such as acetic acid and propanoic acid, ethyl ester. Similar aroma compounds were identified in headspace of Ruiru 11 and SL 28 and there were variations in the intensities of aroma groups such as pyrroles and pyridines. It was concluded that the eco-pulper and hand pulper methods gives better aroma quality than the wet pulper while SL 28 variety gives higher sensory quality than Ruiru 11.}, language = {en} } @article{BoettcherHooglandDitsetal.2015, author = {B{\"o}ttcher, Ren{\´e} and Hoogland, A. Marije and Dits, Natasja and Verhoef, Esther and Kweldam, Charlotte and Waranecki, Piotr and Bangma, Chris H. and van Leenders, Geert J.L.H. and Jenster, Guido}, title = {Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer}, series = {Oncotarget}, volume = {6}, journal = {Oncotarget}, number = {6}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6329}, pages = {4036 -- 4050}, year = {2015}, abstract = {Current prostate cancer (PCa) biomarkers such as PSA are not optimal in distinguishing cancer from benign prostate diseases and predicting disease outcome. To discover additional biomarkers, we investigated PCa-specific expression of novel unannotated transcripts. Using the unique probe design of Affymetrix Human Exon Arrays, we identified 334 candidates (EPCATs), of which 15 were validated by RT-PCR. Combined into a diagnostic panel, 11 EPCATs classified 80\% of PCa samples correctly, while maintaining 100\% specificity. High specificity was confirmed by in situ hybridization for EPCAT4R966 and EPCAT2F176 (SChLAP1) on extensive tissue microarrays. Besides being diagnostic, EPCAT2F176 and EPCAT4R966 showed significant association with pT-stage and were present in PIN lesions. We also found EPCAT2F176 and EPCAT2R709 to be associated with development of metastases and PCa-related death, and EPCAT2F176 to be enriched in lymph node metastases. Functional significance of expression of 9 EPCATs was investigated by siRNA transfection, revealing that knockdown of 5 different EPCATs impaired growth of LNCaP and 22RV1 PCa cells. Only the minority of EPCATs appear to be controlled by androgen receptor or ERG. Although the underlying transcriptional regulation is not fully understood, the novel PCa-associated transcripts are new diagnostic and prognostic markers with functional relevance to prostate cancer growth.}, language = {en} } @article{GrawMeierMinnetal.2015, author = {Graw, Stefan and Meier, Richard and Minn, Kay and Bloomer, Clark and Godwin, Andrew K. and Fridley, Brooke and Vlad, Anda and Beyerlein, Peter and Chien, Jeremy}, title = {Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples}, series = {Scientific Reports}, volume = {5}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6319}, pages = {11}, year = {2015}, abstract = {Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67\% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.}, language = {en} } @article{MunchelHoangYueetal.2015, author = {Munchel, Sarah and Hoang, Yen and Yue, Zhao and Cottrell, Joseph and Klotzle, Brandy and Godwin, Andrew K. and Koestler, Devin and Beyerlein, Peter and Fan, Jian-Bing and Bibikova, Marina and Chien, Jeremy}, title = {Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics}, series = {Oncotarget}, volume = {6}, journal = {Oncotarget}, number = {28}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6307}, pages = {25943 -- 25961}, year = {2015}, abstract = {Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G > T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26\%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.}, language = {en} } @article{BelinskyRinkCaietal.2015, author = {Belinsky, Martin G. and Rink, Lori and Cai, Kathy Q. and Capuzzi, Stephen J. and Hoang, Yen and Chien, Jeremy and Godwin, Andrew K. and von Mehren, Margaret}, title = {Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case}, series = {BMC Cancer}, volume = {15}, journal = {BMC Cancer}, number = {887}, issn = {1471-2407}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6292}, year = {2015}, abstract = {Approximately 10-15 \% of gastrointestinal stromal tumors (GISTs) lack gain of function mutations in the KIT and platelet-derived growth factor receptor alpha (PDGFRA) genes. An alternate mechanism of oncogenesis through loss of function of the succinate-dehydrogenase (SDH) enzyme complex has been identified for a subset of these "wild type" GISTs.}, language = {en} } @article{Enders2016, author = {Enders, Peter}, title = {Historical Prospective: Boltzmann's versus Planck's State Counting—Why Boltzmann Did Not Arrive at Planck's Distribution Law}, series = {Journal of Thermodynamics}, volume = {2016}, journal = {Journal of Thermodynamics}, issn = {1687-9252}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6281}, pages = {13}, year = {2016}, abstract = {Why does Planck (1900), referring to Boltzmann's 1877 probabilistic treatment, obtain his quantum distribution function while Boltzmann did not? To answer this question, both treatments are compared on the basis of Boltzmann's 1868 three-level scheme (configuration—occupation—occupancy). Some calculations by Planck (1900, 1901, and 1913) and Einstein (1907) are also sketched. For obtaining a quantum distribution, it is crucial to stick with a discrete energy spectrum and to make the limit transitions to infinity at the right place. For correct state counting, the concept of interchangeability of particles is superior to that of indistinguishability.}, language = {en} } @article{Michalk2013, author = {Michalk, Philip}, title = {Optimizing sales areas of combined transport chains}, series = {LogForum}, volume = {9}, journal = {LogForum}, number = {4}, issn = {1734-459X}, doi = {10.15771/1734-459X_2013_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6252}, pages = {247 -- 253}, year = {2013}, abstract = {Background: Combined transport chains (such as intermodal transport), have certain advantages. The main advantage from customer points of view is the possibility to bundle freight and thereby decrease transport costs. On the other hand, a combined transport chain can cause longer transport times, due to the necessary transshipment processes. Methods: The area around a terminal, in which a combined service has favourable properties to a customer in comparison to a direct transport, can be understood as a sales-area, in which a combined transport product is marketable. The aim of this paper was to find a method to determine the best shape and size of this area. Results and conclusions: The paper at hand lined out a method in order to calculate such a sales area and determine which geographical points around a terminal have an advantage in comparison to a direct transport service.}, language = {en} } @article{TillichWolterSchulzeetal.2014, author = {Tillich, Ulrich M. and Wolter, Nick and Schulze, Katja and Kramer, Dan and Br{\"o}del, Oliver and Frohme, Marcus}, title = {High-throughput cultivation and screening platform for unicellular phototrophs}, series = {BMC Microbiology}, volume = {14}, journal = {BMC Microbiology}, number = {239}, issn = {1471-2180}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6007}, pages = {13}, year = {2014}, abstract = {In this work we describe and test high-throughput methods with the model organism Synechocystis sp. PCC6803. The required technical automation for these processes was achieved with a Tecan Freedom Evo 200 pipetting robot. The cultivation was performed in 2.2 ml deepwell microtiter plates within a cultivation chamber outfitted with programmable shaking conditions, variable illumination, variable temperature, and an adjustable CO2 atmosphere. Each microtiter-well within the chamber functions as a separate cultivation vessel with reproducible conditions. The automated measurement of various parameters such as growth, full absorption spectrum, chlorophyll concentration, MALDI-TOF-MS, as well as a novel vitality measurement protocol, have already been established and can be monitored during cultivation. Measurement of growth parameters can be used as inputs for the system to allow for periodic automatic dilutions and therefore a semi-continuous cultivation of hundreds of cultures in parallel. The system also allows the automatic generation of mid and long term backups of cultures to repeat experiments or to retrieve strains of interest.}, language = {en} } @article{BaleelaLlewellynFitzpatricketal.2014, author = {Baleela, Rania and Llewellyn, Martin S. and Fitzpatrick, Sinead and Kuhls, Katrin and Sch{\"o}nian, Gabriele and Miles, Michael A. and Mauricio, Isabel L.}, title = {Leishmania donovani populations in Eastern Sudan: temporal structuring and a link between human and canine transmission}, series = {Parasites \& Vectors}, volume = {7}, journal = {Parasites \& Vectors}, number = {496}, issn = {1756-3305}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5921}, pages = {9}, year = {2014}, abstract = {Visceral leishmaniasis (VL), caused by the members of the Leishmania donovani complex, has been responsible for devastating VL epidemics in the Sudan. Multilocus microsatellite and sequence typing studies can provide valuable insights into the molecular epidemiology of leishmaniasis, when applied at local scales. Here we present population genetic data for a large panel of strains and clones collected in endemic Sudan between 1993 and 2001.}, language = {en} } @article{SchulzeLangEnkeetal.2015, author = {Schulze, Katja and Lang, Imke and Enke, Heike and Grohme, Diana and Frohme, Marcus}, title = {The use of fluorescence microscopy and image analysis for rapid detection of non-producing revertant cells of Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002}, series = {BMC Research Notes}, volume = {8}, journal = {BMC Research Notes}, number = {160}, issn = {1756-0500}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5911}, pages = {11}, year = {2015}, abstract = {Ethanol production via genetically engineered cyanobacteria is a promising solution for the production of biofuels. Through the introduction of a pyruvate decarboxylase and alcohol dehydrogenase direct ethanol production becomes possible within the cells. However, during cultivation genetic instability can lead to mutations and thus loss of ethanol production. Cells then revert back to the wild type phenotype. A method for a rapid and simple detection of these non-producing revertant cells in an ethanol producing cell population is an important quality control measure in order to predict genetic stability and the longevity of a producing culture. Several comparable cultivation experiments revealed a difference in the pigmentation for non-producing and producing cells: the accessory pigment phycocyanin (PC) is reduced in case of the ethanol producer, resulting in a yellowish appearance of the culture. Microarray and western blot studies of Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002 confirmed this PC reduction on the level of RNA and protein.}, language = {en} } @article{KoberMeyerAlertGrienitzetal.2015, author = {Kober, Liane and Meyer-Alert, Henriette and Grienitz, Desir{\´e}e and Hollert, Henner and Frohme, Marcus}, title = {Intact cell mass spectrometry as a rapid and specific tool for the differentiation of toxic effects in cell-based ecotoxicological test systems}, series = {Analytical and Bioanalytical Chemistry}, volume = {407}, journal = {Analytical and Bioanalytical Chemistry}, number = {25}, issn = {1618-2650}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5900}, pages = {7721 -- 7731}, year = {2015}, abstract = {In the last few decades, MALDI-TOF MS has become a useful technique not only in proteomics, but also as a fast and specific tool for whole cell analysis through intact cell mass spectrometry (IC-MS). The present study evaluated IC-MS as a novel tool for the detection of distinct patterns that can be observed after exposure to a certain toxin or concentration by utilizing the eukaryotic fish cell line RTL-W1. Two different viability assays were performed to define the range for IC-MS investigations, each of which employing copper sulfate, acridine, and β-naphthoflavone (BNF) as model compounds for several classes of environmental toxins. The IC-MS of RTL-W1 cells revealed not only specific spectral patterns for the various toxins, but also that the concentration used had an effect on RTL-W1 profiles. After the exposure with copper sulfate and acridine, the spectra of RTL-W1 showed a significant increase of certain peaks in the higher mass range (m/z >7000), which is probably attributed to the apoptosis of RTL-W1. On the contrary, exposure to BNF showed a distinct change of ion abundances only in the lower mass range (m/z <7000). Furthermore, a set of mass peaks could be identified as a specific biomarker for a single toxin treatment, so IC-MS demonstrates a new method for the distinction of toxic effects in fish cells. Due to fast sample preparation and high throughput, IC-MS offers great potential for ecotoxicological studies to investigate cellular effects of different substances and complex environmental samples.}, language = {en} } @article{DuscharlaBhumireddyLakshettietal.2016, author = {Duscharla, Divya and Bhumireddy, Sudarshana Reddy and Lakshetti, Sridhar and Pospisil, Heike and Murthy, P. V. L. N. and Walther, Reinhard and Sripadi, Prabhakar and Ummanni, Ramesh}, title = {Prostate Cancer Associated Lipid Signatures in Serum Studied by ESI-Tandem Mass Spectrometryas Potential New Biomarkers}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5863}, pages = {21}, year = {2016}, abstract = {Prostate cancer (PCa) is one amongst the most common cancersin western men. Incidence rate ofPCa is on the rise worldwide. The present study deals with theserum lipidome profiling of patients diagnosed with PCa to identify potential new biomarkers. We employed ESI-MS/MS and GC-MS for identification of significantly altered lipids in cancer patient's serum compared to controls. Lipidomic data revealed 24 lipids are significantly altered in cancer patinet's serum (n = 18) compared to normal (n = 18) with no history of PCa. By using hierarchical clustering and principal component analysis (PCA) we could clearly separate cancer patients from control group. Correlation and partition analysis along with Formal Concept Analysis (FCA) have identified that PC (39:6) and FA (22:3) could classify samples with higher certainty. Both the lipids, PC (39:6) and FA (22:3) could influence the cataloging of patients with 100\% sensitivity (all 18 control samples are classified correctly) and 77.7\% specificity (of 18 tumor samples 4 samples are misclassified) with p-value of 1.612×10-6 in Fischer's exact test. Further, we performed GC-MS to denote fatty acids altered in PCa patients and found that alpha-linolenic acid (ALA) levels are altered in PCa. We also performed an in vitro proliferation assay to determine the effect of ALA in survival of classical human PCa cell lines LNCaP and PC3. We hereby report that the altered lipids PC (39:6) and FA (22:3) offer a new set of biomarkers in addition to the existing diagnostic tests that could significantly improve sensitivity and specificity in PCa diagnosis.}, language = {en} } @article{AkhoundiKuhlsCannetetal.2016, author = {Akhoundi, Mohammad and Kuhls, Katrin and Cannet, Arnaud and Vot{\´y}pka, Jan and Marty, Pierre and Delaunay, Pascal and Sereno, Denis}, title = {A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies}, series = {PLoS Neglected Tropical Diseases}, volume = {10}, journal = {PLoS Neglected Tropical Diseases}, number = {3}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5853}, pages = {40}, year = {2016}, abstract = {The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale.}, language = {en} } @article{GladischSarauliSchaeferetal.2016, author = {Gladisch, Johannes and Sarauli, David and Sch{\"a}fer, Daniel and Dietzel, Birgit and Schulz, Burkhard and Lisdat, Fred}, title = {Towards a novel bioelectrocatalytic platform based on "wiring" of pyrroloquinoline quinone-dependent glucose dehydrogenase with an electrospun conductive polymeric fiber architecture}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5846}, pages = {10}, year = {2016}, abstract = {Electrospinning is known as a fabrication technique for electrode architectures that serve as immobilization matrices for biomolecules. The current work demonstrates a novel approach to construct a conductive polymeric platform, capable not only of immobilization, but also of electrical connection of the biomolecule with the electrode. It is produced upon electrospinning from mixtures of three different highly conductive sulfonated polyanilines and polyacrylonitrile on ITO electrodes. The resulting fiber mats are with a well-retained conductivity. After coupling the enzyme pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) to polymeric structures and addition of the substrate glucose an efficient bioelectrocatalysis is demonstrated. Depending on the choice of the sulfonated polyanilline mediatorless bioelectrocatalysis starts at low potentials; no large overpotential is needed to drive the reaction. Thus, the electrospun conductive immobilization matrix acts here as a transducing element, representing a promising strategy to use 3D polymeric scaffolds as wiring agents for active enzymes. In addition, the mild and well reproducible fabrication process and the active role of the polymer film in withdrawing electrons from the reduced PQQ-GDH lead to a system with high stability. This could provide access to a larger group of enzymes for bioelectrochemical applications including biosensors and biofuel cells.}, language = {en} } @article{SternPaulyZydeketal.2016, author = {Stern, Daniel and Pauly, Diana and Zydek, Martin and Miller, Lilija and Piesker, Janett and Laue, Michael and Lisdat, Fred and Dorner, Martin B. and Dorner, Brigitte G. and Nitsche, Andreas}, title = {Development of a Genus-Specific Antigen Capture ELISA for Orthopoxviruses - Target Selection and Optimized Screening}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5830}, pages = {22}, year = {2016}, abstract = {Orthopoxvirus species like cowpox, vaccinia and monkeypox virus cause zoonotic infections in humans worldwide. Infections often occur in rural areas lacking proper diagnostic infrastructure as exemplified by monkeypox, which is endemic in Western and Central Africa. While PCR detection requires demanding equipment and is restricted to genome detection, the evidence of virus particles can complement or replace PCR. Therefore, an easily distributable and manageable antigen capture enzyme-linked immunosorbent assay (ELISA) for the detection of orthopoxviruses was developed to facilitate particle detection. By comparing the virus particle binding properties of polyclonal antibodies developed against surface-exposed attachment or fusion proteins, the surface protein A27 was found to be a well-bound, highly immunogenic and exposed target for antibodies aiming at virus particle detection. Subsequently, eight monoclonal anti-A27 antibodies were generated and characterized by peptide epitope mapping and surface plasmon resonance measurements. All antibodies were found to bind with high affinity to two epitopes at the heparin binding site of A27, toward either the N- or C-terminal of the crucial KKEP-segment of A27. Two antibodies recognizing different epitopes were implemented in an antigen capture ELISA. Validation showed robust detection of virus particles from 11 different orthopoxvirus isolates pathogenic to humans, with the exception of MVA, which is apathogenic to humans. Most orthopoxviruses could be detected reliably for viral loads above 1 × 103 PFU/mL. To our knowledge, this is the first solely monoclonal and therefore reproducible antibody-based antigen capture ELISA able to detect all human pathogenic orthopoxviruses including monkeypox virus, except variola virus which was not included. Therefore, the newly developed antibody-based assay represents important progress towards feasible particle detection of this important genus of viruses.}, language = {en} } @article{TanneKracherDietzeletal.2014, author = {Tanne, Johannes and Kracher, Daniel and Dietzel, Birgit and Schulz, Burkhard and Ludwig, Roland and Lisdat, Fred and Scheller, Frieder W. and Bier, Frank Fabian}, title = {Carboxylated or Aminated Polyaniline—Multiwalled Carbon Nanotubes Nanohybrids for Immobilization of Cellobiose Dehydrogenase on Gold Electrodes}, series = {Biosensors}, volume = {4}, journal = {Biosensors}, number = {4}, issn = {2079-6374}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5826}, pages = {370 -- 386}, year = {2014}, abstract = {Polymer-multiwalled carbon nanotube (MWCNT) nanohybrids, which differ in surface charge have been synthesized to study the bioelectrocatalysis of adsorbed cellobiose dehydrogenase (CDH) from Phanerochaete sordida on gold electrodes. To obtain negatively charged nanohybrids, poly(3-amino-4-methoxybenzoic acid-co-aniline) (P(AMB-A)) was covalently linked to the surface of MWCNTs while modification with p-phenylenediamine (PDA) converted the COOH-groups to positively charged amino groups. Fourier transform infrared spectroscopy (FTIR) measurements verified the p-phenylenediamine (PDA) modification of the polymer-CNT nanohybrids. The positively charged nanohybrid MWCNT-P(AMB-A)-PDA promoted direct electron transfer (DET) of CDH to the electrode and bioelectrocatalysis of lactose was observed. Amperometric measurements gave an electrochemical response with KMapp = 8.89 mM and a current density of 410 nA/cm2 (15 mM lactose). The catalytic response was tested at pH 3.5 and 4.5. Interference by ascorbic acid was not observed. The study proves that DET between the MWCNT-P(AMB-A)-PDA nanohybrids and CDH is efficient and allows the sensorial detection of lactose.}, language = {en} }