TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Chepurna, Oksana A1 - Grebinyk, Sergii A1 - Prylutskyy, Yuriy A1 - Ritter, Uwe A1 - Ohulchanskyy, Tymish Y. A1 - Matyshevska, Olga A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - Synergy of Chemo- and Photodynamic Therapies with C60 Fullerene-Doxorubicin Nanocomplex JF - Nanomaterials N2 - A nanosized drug complex was explored to improve the efficiency of cancer chemotherapy, complementing it with nanodelivery and photodynamic therapy. For this, nanomolar amounts of a non-covalent nanocomplex of Doxorubicin (Dox) with carbon nanoparticle C60 fullerene (C60) were applied in 1:1 and 2:1 molar ratio, exploiting C60 both as a drug-carrier and as a photosensitizer. The fluorescence microscopy analysis of human leukemic CCRF-CEM cells, in vitro cancer model, treated with nanocomplexes showed Dox’s nuclear and C60’s extranuclear localization. It gave an opportunity to realize a double hit strategy against cancer cells based on Dox’s antiproliferative activity and C60’s photoinduced pro-oxidant activity. When cells were treated with 2:1 C60-Dox and irradiated at 405 nm the high cytotoxicity of photo-irradiated C60-Dox enabled a nanomolar concentration of Dox and C60 to efficiently kill cancer cells in vitro. The high pro-oxidant and pro-apoptotic efficiency decreased IC50 16, 9 and 7 × 103-fold, if compared with the action of Dox, non-irradiated nanocomplex, and C60’s photodynamic effect, correspondingly. Hereafter, a strong synergy of therapy arising from the combination of C60-mediated Dox delivery and C60 photoexcitation was revealed. Our data indicate that a combination of chemo- and photodynamic therapies with C60-Dox nanoformulation provides a promising synergetic approach for cancer treatment. KW - photodynamic chemotherapy KW - synergistic effect KW - C60 fullerene KW - doxorubicin KW - nanocomplex KW - leukemic cell KW - apoptosis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12940 SN - 2079-4991 VL - 9 IS - 11 PB - MDPI ER - TY - JOUR A1 - Kober, Liane A1 - Hollert, Henner A1 - Frohme, Marcus T1 - Quantification of nitroaromatic explosives in contaminated soil using MALDI-TOF mass spectrometry JF - Analytical and Bioanalytical Chemistry N2 - Contamination from various sources is a global environmental and health threat, with mining and military activities in particular having spread nitroaromatic compounds, such as 2,4,6-trinitrotoluene and its degradation products and by-products, to the soil. The investigation and monitoring of large contaminated areas requires new detection methods since the established ones are expensive and time-consuming. Hence, we established a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) method using 1,5-diaminonaphthalene as the matrix substance and an internal standard for quantification. Analyzing standard substances, we found specific signals for radical and fragment ions of different nitrotoluenes and nitrobenzenes with good reproducibility and detection limits down to 0.25 ng/μL. The analysis of soil sample extracts from a former production site showed clear signals for 2,4,6-trinitrotoluene and the primary degradation products aminodinitrotoluenes. Furthermore, quantification gave results comparable to those obtained by conventional liquid chromatography--tandem mass spectrometry analysis. The MALDI-TOF MS method has a comparatively lower reproducibility, with relative standard deviations of 6% to 20% for multiple measurements of standard solutions and soil sample extracts. Nevertheless, a comparison of both methods revealed the advantages of MALDI-TOF MS analysis of explosive-contaminated areas with regard to costs, time, and handling. Finally, our MALDI-TOF MS method fulfills all the needs for high sample throughput and can therefore be a valuable screening tool for explosive-contaminated areas. KW - explosives KW - soil contamination KW - TNT KW - matrix-assisted laser desorption/ionization quantification Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12388 SN - 1618-2650 VL - 411 IS - 23 SP - 5993 EP - 6003 ER - TY - JOUR A1 - Gottschalk, Josefine Johanna A1 - Stollfuß, Carsten A1 - Lietzau, Kai-Henning A1 - Foitzik, Andreas A1 - Richetta, Maria T1 - Conceptual study for long-term monitoring of chemotherapeutic induced cell reactions by ESPI JF - tm - Technisches Messen N2 - 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). KW - interferometry KW - ESPI KW - anticancer drug KW - cellular displacement Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10676 SN - 2196-7113 VL - 85 IS - 2 SP - 111 EP - 118 ER - TY - JOUR A1 - Steglich, Patrick A1 - Hülsemann, Marcel A1 - Dietzel, Birgit A1 - Mai, Andreas T1 - Optical Biosensors Based on Silicon-On-Insulator Ring Resonators: A Review JF - Molecules N2 - Recent developments in optical biosensors based on integrated photonic devices are reviewed with a special emphasis on silicon-on-insulator ring resonators. The review is mainly devoted to the following aspects: (1) Principles of sensing mechanism, (2) sensor design, (3) biofunctionalization procedures for specific molecule detection and (4) system integration and measurement set-ups. The inherent challenges of implementing photonics-based biosensors to meet specific requirements of applications in medicine, food analysis, and environmental monitoring are discussed. KW - biosensor KW - biophotonics KW - integrated optical sensor KW - aptamer KW - biomaterial KW - optical sensor KW - silicon photonics KW - ring resonator KW - lab-on-a-chip Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10822 SN - 1420-3049 VL - 24 IS - 3 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grebinyk, Sergii A1 - Prylutskyy, Yuriy A1 - Ritter, Uwe A1 - Matyshevska, Olga A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - Complexation with C60 Fullerene Increases Doxorubicin Efficiency against Leukemic Cells In Vitro JF - Nanoscale Research Letters N2 - Conventional anticancer chemotherapy is limited because of severe side effects as well as a quickly evolving multidrug resistance of the tumor cells. To address this problem, we have explored a C60 fullerene-based nanosized system as a carrier for anticancer drugs for an optimized drug delivery to leukemic cells. Here, we studied the physicochemical properties and anticancer activity of C60 fullerene noncovalent complexes with the commonly used anticancer drug doxorubicin. C60-Doxorubicin complexes in a ratio 1:1 and 2:1 were characterized with UV/Vis spectrometry, dynamic light scattering, and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The obtained analytical data indicated that the 140-nm complexes were stable and could be used for biological applications. In leukemic cell lines (CCRF-CEM, Jurkat, THP1 and Molt-16), the nanocomplexes revealed ≤ 3.5 higher cytotoxic potential in comparison with the free drug in a range of nanomolar concentrations. Also, the intracellular drug’s level evidenced C60 fullerene considerable nanocarrier function. The results of this study indicated that C60 fullerene-based delivery nanocomplexes had a potential value for optimization of doxorubicin efficiency against leukemic cells. KW - C60 fullerene KW - doxorubicin KW - noncovalent complex KW - leukemic cell KW - cytotoxicity KW - accumulation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10966 SN - 1556-276X N1 - Das Dokument wurde zurückgezogen. Die korrigierte Version ist unter dem folgenden Link zu finden: https://nbn-resolving.org/urn:nbn:de:kobv:526-opus4-11415 VL - 14 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grebinyk, Sergii A1 - Prylutskyy, Yuriy A1 - Ritter, Uwe A1 - Matyshevska, Olga A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - Complexation with C60 Fullerene Increases Doxorubicin Efficiency against Leukemic Cells In Vitro JF - Nanoscale Research Letters N2 - Conventional anticancer chemotherapy is limited because of severe side effects as well as a quickly evolving multidrug resistance of the tumor cells. To address this problem, we have explored a C60 fullerene-based nanosized system as a carrier for anticancer drugs for an optimized drug delivery to leukemic cells. Here, we studied the physicochemical properties and anticancer activity of C60 fullerene noncovalent complexes with the commonly used anticancer drug doxorubicin. C60-Doxorubicin complexes in a ratio 1:1 and 2:1 were characterized with UV/Vis spectrometry, dynamic light scattering, and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The obtained analytical data indicated that the 140-nm complexes were stable and could be used for biological applications. In leukemic cell lines (CCRF-CEM, Jurkat, THP1 and Molt-16), the nanocomplexes revealed ≤ 3.5 higher cytotoxic potential in comparison with the free drug in a range of nanomolar concentrations. Also, the intracellular drug’s level evidenced C60 fullerene considerable nanocarrier function. The results of this study indicated that C60 fullerene-based delivery nanocomplexes had a potential value for optimization of doxorubicin efficiency against leukemic cells. KW - C60 fullerene KW - doxorubicin KW - noncovalent complex KW - leukemic cell KW - cytotoxicity KW - accumulation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-11415 SN - 1556-276X VL - 14 ER - TY - JOUR A1 - Hornemann, Andrea A1 - Sinning, Denise A1 - Cortes, Sofia A1 - Campino, Lenea A1 - Emmer, Peggy A1 - Kuhls, Katrin A1 - Ulm, Gerhard A1 - Frohme, Marcus A1 - Beckhoff, Burkhard T1 - A pilot study on fingerprinting Leishmania species from the Old World using Fourier transform infrared spectroscopy JF - Analytical and Bioanalytical Chemistry N2 - 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. KW - Fourier transform infrared spectroscopy KW - hierarchical cluster analysis (HCA) KW - principal components analysis (PCA) KW - Leishmania KW - DNA KW - multivariate differentiation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10080 SN - 1432-1130 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Grebinyk, Sergii A1 - Prylutska, Svitlana A1 - Ritter, Uwe A1 - Matyshevska, Olga A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - HPLC-ESI-MS method for C60 fullerene mitochondrial content quantification JF - Data in Brief N2 - 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. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10368 SN - 2352-3409 VL - 19 SP - 2047 EP - 2052 ER - TY - JOUR A1 - Fischbach, Jens A1 - Frohme, Marcus A1 - Glökler, Jörn T1 - Hinge-initiated Primer-dependent Amplification of Nucleic Acids (HIP) – A New Versatile Isothermal Amplification Method JF - Scientific Reports N2 - 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. KW - DNA synthesis KW - pathogen Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9824 SN - 2045-2322 VL - 7 ER - TY - JOUR A1 - Karakuş, Mehmet A1 - Nasereddin, Abed A1 - Onay, Hüseyin A1 - Karaca, Emin A1 - Özkeklikçi, Ahmet A1 - Jaffe, Charles L. A1 - Kuhls, Katrin A1 - Özbilgin, Ahmet A1 - Ertabaklar, Hatice A1 - Demir, Samiye A1 - Özbel, Yusuf A1 - Töz, Seray T1 - Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT) JF - PLoS Neglected Tropical Diseases N2 - 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 Şanlıurfa 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 Şanlıurfa 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. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9313 SN - 1935-2735 VL - 11 IS - 4 ER - TY - JOUR A1 - Pfeil, Juliane A1 - Frohme, Marcus A1 - Schulze, Katja T1 - Mobile microscopy for the examination of blood samples JF - EMBnet.journal N2 - 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. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10509 SN - 2226-6089 VL - 23 SP - e904 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Grebinyk, Sergii A1 - Prylutska, Svitlana A1 - Ritter, Uwe A1 - Matyshevska, Olga A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - C60 fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy JF - Free Radical Biology and Medicine N2 - 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. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10588 SN - 1873-4596 VL - 124 SP - 319 EP - 327 ER - TY - JOUR A1 - Kinuthia, Chuaga A1 - Frohme, Marcus A1 - Brödel, Oliver A1 - Mugendi, Beatrice T1 - LCMS Analysis of Biochemical Composition in Different Kenyan Coffee Classifications JF - Food Science and Quality Management N2 - 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. KW - biochemical composition KW - coffee classification KW - LCMS Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10185 UR - https://iiste.org/Journals/index.php/FSQM/article/view/39645/40765 SN - 2225-0557 VL - 69 SP - 44 EP - 52 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grebinyk, Sergii A1 - Evstigneev, Maxim A1 - Krysiuk, Iryna A1 - Skaterna, Tetiana A1 - Horak, Iryna A1 - Sun, Yanfang A1 - Drobot, Liudmyla A1 - Matyshevska, Olga A1 - Prylutskyy, Yuriy A1 - Ritter, Uwe A1 - Frohme, Marcus T1 - Antitumor efficiency of the natural alkaloid berberine complexed with C60 fullerene in Lewis lung carcinoma in vitro and in vivo JF - Cancer Nanotechnology N2 - Background Berberine (Ber) is a herbal alkaloid with pharmacological activity in general and a high anticancer potency in particular. However, due to its low bioavailability, the difficulty in reaching a target and choosing the right dose, there is a need to improve approaches of Ber use in anticancer therapy. In this study, Ber, noncovalently bound to a carbon nanostructure C60 fullerene (C60) at various molar ratios of the components, was explored against Lewis lung carcinoma (LLC). Methods C60–Ber noncovalent nanocomplexes were synthesized in 1:2, 1:1 and 2:1 molar ratios. Ber release from the nanocomplexes was studied after prolonged incubation at different pH with the liquid chromatography–mass spectrometry analysis of free Ber content. Biological effects of the free and C60-complaxated Ber were studied in vitro towards LLC cells with phase-contrast and fluorescence microscopy, flow cytometry, MTT reduction, caspase activity and wound closure assays. The treatment with C60–Ber nanocomplex was evaluated in vivo with the LLC-tumored C57Bl mice. The mice body weight, tumor size, tumor weight and tumor weight index were assessed for four groups, treated with saline, 15 mg C60/kg, 7.5 mg Ber/kg or 2:1 C60-Ber nanocomplex (15 mg C60/kg, 7.5 mg Ber/kg). Results Ber release from C60–Ber nanocomplexes was promoted with medium acidification. LLC cells treatment with C60–Ber nanocomplexes was followed by enhanced Ber intracellular uptake as compared to free Ber. The cytotoxicity of the studied agents followed the order: free Ber < 1:2 < 1:1 < 2:1 C60–Ber nanocomplex. The potency of cytotoxic effect of 2:1 C60–Ber nanocomplex was confirmed by 21.3-fold decrease of IC50 value (0.8 ± 0.3 µM) compared to IC50 for free Ber (17 ± 2 µM). C60–Ber nanocomplexes induced caspase 3/7 activation and suppressed the migration activity of LLC cells. The therapeutic potency of 2:1 C60–Ber nanocomplex was confirmed in a mouse model of LLC. The tumor growth in the group treated with 2:1 C60–Ber nanocomplex is suppressed by approximately 50% at the end of experiment, while in the tumor-bearing group treated with free Ber no therapeutic effect was detected. Conclusions This study indicates that complexation of natural alkaloid Ber with C60 may be a novel therapeutic strategy against lung carcinoma. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14749 SN - 1868-6966 VL - 12 SP - 24 PB - BioMed Central ER - TY - THES A1 - Grebinyk, Anna T1 - Synergistic Chemo- and Photodynamic Treatment of Cancer Cells with C60 Fullerene Nanocomplexes N2 - Recent progress in nanotechnology has attracted interest to a biomedical application of the carbon nanoparticle C60 fullerene (C60) due to its unique structure and versatile biological activity. In the current study the dual functionality of C60 as a photosensitizer and a drug nanocarrier was exploited to improve the efficiency of chemotherapeutic drugs towards human leukemic cells. Pristine C60 demonstrated time-dependent accumulation with predominant mitochondrial localization in leukemic cells. C60’s effects on leukemic cells irradiated with high power single chip LEDs of different wavelengths were assessed to find out the most effective photoexcitation conditions. A C60-based noncovalent nanosized system as a carrier for an optimized drug delivery to the cells was evaluated in accordance to its physicochemical properties and toxic effects. Finally, nanomolar amounts of C60-drug nanocomplexes in 1:1 and 2:1 molar ratios were explored to improve the efficiency of cell treatment, complementing it with photodynamic approach. A proposed treatment strategy was developed for C60 nanocomplexes with the common chemotherapeutic drug Doxorubicin, whose intracellular accumulation and localization, cytotoxicity and mechanism of action were investigated. The developed strategy was revealed to be transferable to an alternative potent anticancer drug – the herbal alkaloid Berberine. Hereafter, a strong synergy of treatments arising from the combination of C60-mediated drug delivery and C60 photoexcitation was revealed. Presented data indicate that a combination of chemo- and photodynamic treatments with C60-drug nanoformulations could provide a promising synergetic approach for cancer treatment. KW - cancer KW - drug delivery KW - photodynamic therapy KW - fullerene Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14137 ER - TY - JOUR A1 - Pajčin, Ivana A1 - Vlajkov, Vanja A1 - Frohme, Marcus A1 - Grebinyk, Sergii A1 - Grahovac, Mila A1 - Mojićević, Marija A1 - Grahovac, Jovana T1 - Pepper Bacterial Spot Control by Bacillus velezensis: Bioprocess Solution JF - Microorganisms N2 - Pepper bacterial spot is one of the most severe plant diseases in terms of infection persistence and economic losses when it comes to fresh pepper fruits used in nutrition and industrial processing. In this study, Bacillus velezensis IP22 isolated from fresh cheese was used as a biocontrol agent of pepper bacterial spot, whose main causal agent is the cosmopolitan pathogen Xanthomonas euvesicatoria. After optimization of the cultivation medium composition aimed at maximizing of the antimicrobial activity against X. euvesicatoria and validation of the optimized medium at the scale of a laboratory bioreactor, in planta tests were performed. The results have showed significant suppression of bacterial spot symptoms in pepper plants by the produced biocontrol agent, as well as reduction of disease spreading on the healthy (uninoculated) pepper leaves. Furthermore, HPLC-MS (high pressure liquid chromatography–mass spectrometry) analysis was employed to examine antimicrobial metabolites produced by B. velezensis IP22, where lipopeptides were found with similar m/z values compared to lipopeptides from fengycin and locillomycin families. The bioprocess solution developed at the laboratory scale investigated in this study represents a promising strategy for production of pepper bacterial spot biocontrol agent based on B. velezensis IP22, a food isolate with a great perspective for application in plant protection. KW - Xanthomonas euvesicatoria KW - biological control KW - biocontrol agent KW - medium optimization KW - lipopeptide KW - fengycin KW - locillomycin KW - HPLC-MS KW - bioreactor KW - laboratory scale Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13510 SN - 2076-2607 VL - 8 IS - 10 PB - MDPI ER - TY - GEN A1 - Balkenhohl, Thomas A1 - Beutler, Falko A1 - Schäfer, Daniel A1 - Lisdat, Fred T1 - Entwicklung eines impedimetrischen Biosensors für den Nachweis von Antigliadin Autoantikörpern T2 - Wissenschaftliche Beiträge 2007 N2 - In der vorliegenden Arbeit wurde ein Biosensor für den Nachweis von Antikörpern gegen Gliadin entwickelt. Gliadine sind Bestandteile der Getreideglutene und verantwortlich für die Manifestation der Zöliakie (Gluten-Unverträglichkeit). Der Biosensor basiert auf der Immobilisierung von Gliadin auf Goldelektroden, die zuvor mit Polystyrensulfonsäure beschichtet worden waren. Die erfolgreiche Immobilisierung wurde mit Hilfe der Quarzmikrowaage dokumentiert. Die Antigen-Antikörper-Bindung konnte durch die Inkubation mit einem Peroxidase-markierten Zweitantikörper und der enzymatischen Oxidation von 3-Amino-9- Ethylcarbazol (AEC) verstärkt werden. Die Zunahme in der Elektrodenisolierung durch die Bindungs- und Ablagerungsreaktion konnte durch elektrochemische Impedanzspektroskopie (EIS) in Anwesenheit des Hexacyanoferrat- Redoxsystems gemessen werden. Die Spektren wurden mit Hilfe eines Randles-Ersatzschaltbildes ausgewertet. Hierbei konnte eine Zunahme im Ladungstransferwiderstand festgestellt werden, die pro portional zur Antigliadin-Antikörperkonzentration, im Bereich von 10-8 M bis 10-6 M, war. Mit Hilfe dieses Sensors wurden schließlich humane Seren hinsichtlich ihrer Konzentration an Gliadinantikörpern, sowohl für Immunglobuline vom Typ IgG als auch IgA, untersucht. N2 - In this study an immunosensor was developed for the analysis of anti-gliadin antibodies. These antibodies can serve as an early diagnostic marker for celiac disease. The sensor is based on polystyrenesulfonic acid modifi ed gold electrodes on which gliadin was immobilized. The anti-gliadin antibody recognition was amplifi ed by a second binding step with a peroxidase- labeled antibody and subsequent peroxidase-catalyzed oxidation of 3-amino-9-ethylcarbazole (AEC) resulting in a precipitate formation on the electrode. The change of the electrode surface properties was followed by impedance spectroscopy in the presence of ferri-/ferrocyanide. By evaluating the impedance spectra the charge transfer resistance was found to be a suitable sensor parameter. A calibration curve for the detection of anti-gliadin antibodies was established for antibody concentrations between 10-8 M and 10-6 M and the sensor was also applied for the analysis of serum samples. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-522 SN - 0949-8214 VL - 12 SP - 48 EP - 57 ER - TY - GEN A1 - Hellmann, Michél A1 - Offermann, Judith A1 - Wildenauer, Franz-Xaver T1 - Cyanobakterienkultivierung zur Extraktion toxischer Metabolite T2 - Wissenschaftliche Beiträge 2007 N2 - Im Rahmen des Projektes »CyToTest« soll, in Kooperation mit der Firma BioTeZ Berlin-Buch GmbH, ein System entwickelt werden, mit dem direkt am Gewässer auf einfache Art und Weise die Cyanobakterientoxinkonzentration ermittelt werden kann. Dazu ist es nötig Cyanobakterien zu kultivieren und die Toxine zu isolieren. Beides wird gebraucht, um einerseits das Messsystem entwickeln zu können und andererseits an der TFH Wildau ein Verfahren zu entwickeln, mit dem die Cyanobakterien direkt am Gewässer aufgeschlossen und die Toxine extrahiert werden können. Im Rahmen dessen wurden sechs Gattungen Cyanobakterien kultiviert und ein Verfahren etabliert, um die Biomasse kalkulieren zu können. Weiterhin wurde mit der Kalibration der HPLC mit Toxinen begonnen, um die Extrakte später prüfen zu können. N2 - Within the project (in cooperation with BioTeZ Berlin- Buch GmbH) »CyToTest« a system shall be developed which allows to detect the concentration of cyanotoxins directly at the waterbody in a simple way. Therefore it is necessary to cultivate cyanobacteria and to isolate their toxins. This is essential for developing the measuring system and a procedure for digest the cyanobacteria and for extract the toxins directly at the waterbody. Therefore six species of cyanobacteria were cultivated and a method was developed for calculating the biomass. Furthermore the calibration of the HPLC with the toxins was begun for checking the extracts. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-518 SN - 0949-8214 VL - 12 SP - 41 EP - 47 ER - TY - JOUR A1 - Stern, Daniel A1 - Pauly, Diana A1 - Zydek, Martin A1 - Miller, Lilija A1 - Piesker, Janett A1 - Laue, Michael A1 - Lisdat, Fred A1 - Dorner, Martin B. A1 - Dorner, Brigitte G. A1 - Nitsche, Andreas T1 - Development of a Genus-Specific Antigen Capture ELISA for Orthopoxviruses – Target Selection and Optimized Screening JF - PLoS ONE N2 - 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. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5830 SN - 1932-6203 VL - 11 IS - 3 ER - TY - JOUR A1 - Schulze, Katja A1 - Lang, Imke A1 - Enke, Heike A1 - Grohme, Diana A1 - Frohme, Marcus T1 - The use of fluorescence microscopy and image analysis for rapid detection of non-producing revertant cells of Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002 JF - BMC Research Notes N2 - 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. KW - PCC6803 KW - PCC7002 KW - genetic instability KW - ethanol producer KW - 3D fluorescence scan KW - phycocyanin KW - absorption spectra KW - fluorescence microscopy KW - image analysis Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5911 SN - 1756-0500 VL - 8 IS - 160 ER - TY - JOUR A1 - Bilous, Nataliya A1 - Malko, Vladyslav A1 - Frohme, Marcus A1 - Nechyporenko, Alina T1 - Comparison of CNN-Based Architectures for Detection of Different Object Classes JF - AI N2 - (1) Background: Detecting people and technical objects in various situations, such as natural disasters and warfare, is critical to search and rescue operations and the safety of civilians. A fast and accurate detection of people and equipment can significantly increase the effectiveness of search and rescue missions and provide timely assistance to people. Computer vision and deep learning technologies play a key role in detecting the required objects due to their ability to analyze big volumes of visual data in real-time. (2) Methods: The performance of the neural networks such as You Only Look Once (YOLO) v4-v8, Faster R-CNN, Single Shot MultiBox Detector (SSD), and EfficientDet has been analyzed using COCO2017, SARD, SeaDronesSee, and VisDrone2019 datasets. The main metrics for comparison were mAP, Precision, Recall, F1-Score, and the ability of the neural network to work in real-time. (3) Results: The most important metrics for evaluating the efficiency and performance of models for a given task are accuracy (mAP), F1-Score, and processing speed (FPS). These metrics allow us to evaluate both the accuracy of object recognition and the ability to use the models in real-world environments where high processing speed is important. (4) Conclusion: Although different neural networks perform better on certain types of metrics, YOLO outperforms them on all metrics, showing the best results of mAP-0.88, F1-0.88, and FPS-48, so the focus was on these models. KW - EfficientDet KW - SSD KW - YOLO KW - deep learning KW - neural network KW - object detection Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19634 VL - 5 IS - 4 SP - 2300 EP - 2320 PB - MDPI ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Lehmann, Sandra A1 - Schulze, Katja A1 - Dühring, Ulf A1 - Frohme, Marcus T1 - The Optimal Mutagen Dosage to Induce Point-Mutations in Synechocystis sp. PCC6803 and Its Application to Promote Temperature Tolerance JF - PLoS ONE N2 - Random mutagenesis is a useful tool to genetically modify organisms for various purposes, such as adaptation to cultivation conditions, the induction of tolerances, or increased yield of valuable substances. This is especially attractive for systems where it is not obvious which genes require modifications. Random mutagenesis has been extensively used to modify crop plants, but even with the renewed interest in microalgae and cyanobacteria for biofuel applications, there is relatively limited current research available on the application of random mutagenesis for these organisms, especially for cyanobacteria. In the presented work we characterized the lethality and rate of non-lethal point mutations for ultraviolet radiation and methyl methanesulphonate on the model cyanobacteria Synechocystis sp. PCC6803. Based on these results an optimal dosage of 10–50 J/m2 for UV and either 0.1 or 1 v% for MMS was determined. A Synechocystis wildtype culture was then mutagenized and selected for increased temperature tolerance in vivo. During the second round of mutagenesis the viability of the culture was monitored on a cell by cell level from the treatment of the cells up to the growth at an increased temperature. After four distinct rounds of treatment (two with each mutagen) the temperature tolerance of the strain was effectively raised by about 2°C. Coupled with an appropriate in vivo screening, the described methods should be applicable to induce a variety of desirable characteristics in various strains. Coupling random mutagenesis with high-throughput screening methods would additionally allow to select for important characteristics for biofuel production, which do not yield a higher fitness and can not be selected for in vivo, such as fatty acid concentration. In a combined approach with full genome sequencing random mutagenesis could be used to determine suitable target-genes for more focused methods. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6186 SN - 1932-6203 VL - 7 IS - 11 ER - TY - JOUR A1 - Schulze, Katja A1 - Tillich, Ulrich M. A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - PlanktoVision - an automated analysis system for the identification of phytoplankton JF - BMC Bioinformatics N2 - Phytoplankton communities are often used as a marker for the determination of fresh water quality. The routine analysis, however, is very time consuming and expensive as it is carried out manually by trained personnel. The goal of this work is to develop a system for an automated analysis. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6364 SN - 1471-2105 VL - 14 IS - 115 ER - TY - JOUR A1 - Böttcher, René A1 - Amberg, Ronny A1 - Ruzius, F. P. A1 - Guryev, V. A1 - Verhaegh, Wim F. J. A1 - Beyerlein, Peter A1 - van der Zaag, P. J. T1 - Using a priori knowledge to align sequencing reads to their exact genomic position JF - Nucleic Acids Research N2 - The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman–Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (∼92%). Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6407 SN - 1362-4962 VL - 40 IS - 16 ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Wolter, Nick A1 - Schulze, Katja A1 - Kramer, Dan A1 - Brödel, Oliver A1 - Frohme, Marcus T1 - High-throughput cultivation and screening platform for unicellular phototrophs JF - BMC Microbiology N2 - 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. KW - cyanobacteria KW - synechocystis KW - HTS KW - high throughput KW - automated cultivation Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6007 SN - 1471-2180 VL - 14 IS - 239 ER - TY - JOUR A1 - Omar, Noorsharmimi A1 - Loh, Qiuting A1 - Tye, Gee Jun A1 - Choong, Yee Siew A1 - Noordin, Rahmah A1 - Glökler, Jörn A1 - Lim, Theam Soon T1 - Development of an Antigen-DNAzyme Based Probe for a Direct Antibody-Antigen Assay Using the Intrinsic DNAzyme Activity of a Daunomycin Aptamer JF - Sensors N2 - G-Quadruplex (G-4) structures are formed when G-rich DNA sequences fold into intra- or intermolecular four-stranded structures in the presence of metal ions. G-4-hemin complexes are often effective peroxidase-mimicking DNAzymes that are applied in many detection systems. This work reports the application of a G-rich daunomycin-specific aptamer for the development of an antibody-antigen detection assay. We investigated the ability of the daunomycin aptamer to efficiently catalyze the hemin-dependent peroxidase activity independent of daunomycin. A reporter probe consisting of biotinylated antigen and daunomycin aptamer coupled to streptavidin gold nanoparticles was successfully used to generate a colorimetric readout. In conclusion, the daunomycin aptamer can function as a robust alternative DNAzyme for the development of colorimetric assays. KW - G-quadruplex KW - DNAzyme KW - gold nanoparticle KW - antibody Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6267 SN - 1424-8220 VL - 14 IS - 1 SP - 346 EP - 355 ER - TY - JOUR A1 - Graw, Stefan A1 - Meier, Richard A1 - Minn, Kay A1 - Bloomer, Clark A1 - Godwin, Andrew K. A1 - Fridley, Brooke A1 - Vlad, Anda A1 - Beyerlein, Peter A1 - Chien, Jeremy T1 - Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples JF - Scientific Reports N2 - 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. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6319 SN - 2045-2322 VL - 5 ER - TY - JOUR A1 - Hammer, Paul A1 - Banck, Michaela S. A1 - Amberg, Ronny A1 - Wang, Cheng A1 - Petznick, Gabriele A1 - Luo, Shujun A1 - Khrebtukova, Irina A1 - Schroth, Gary P. A1 - Beyerlein, Peter A1 - Beutler, Andreas S. T1 - mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain JF - Genome Research N2 - mRNA-seq is a paradigm-shifting technology because of its superior sensitivity and dynamic range and its potential to capture transcriptomes in an agnostic fashion, i.e., independently of existing genome annotations. Implementation of the agnostic approach, however, has not yet been fully achieved. In particular, agnostic mapping of pre-mRNA splice sites has not been demonstrated. The present study pursued dual goals: (1) to advance mRNA-seq bioinformatics toward unbiased transcriptome capture and (2) to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We have performed mRNA-seq on the L4 dorsal root ganglion (DRG) of rats with chronic neuropathic pain induced by spinal nerve ligation (SNL) of the neighboring (L5) spinal nerve. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 DRG 2 wk after SNL. These alterations persisted chronically (2 mo). Using a read cluster classifier with strong test characteristics (ROC area 97%), we discovered 10,464 novel exons. A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJs) achieved a precision of 97%. Integration of information from all mRNA-seq read classes including SJs led to genome reannotations specifically relevant for the species used (rat), the anatomical site studied (DRG), and the neurological disease considered (pain); for example, a 64-exon coreceptor for the nociceptive transmitter substance P was identified, and 21.9% of newly discovered exons were shown to be dysregulated. Thus, mRNA-seq with agnostic analysis methods appears to provide a highly productive approach for in vivo transcriptomics in the nervous system. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6446 SN - 1549-5469 VL - 20 IS - 6 ER - TY - JOUR A1 - Kipkorir, R. A1 - Muhoho, S. A1 - Muliro, P. A1 - Mugendi, Beatrice A1 - Frohme, Marcus A1 - Brödel, Oliver T1 - Effects of Coffee Processing Technologies on Aroma Profiles and Sensory Quality of Ruiru 11 and SL 28 Kenyan Coffee Varieties JF - Asian Journal of Agriculture and Food Sciences N2 - 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. KW - coffee KW - processing KW - aroma KW - sensory quality Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6482 UR - https://ajouronline.com/index.php/AJAFS/article/view/2551 SN - 2321-1571 VL - 3 IS - 2 SP - 178 EP - 188 ER - TY - JOUR A1 - Kaltdorf, Kristin Verena A1 - Schulze, Katja A1 - Helmprobst, Frederik A1 - Kollmannsberger, Philip A1 - Dandekar, Thomas A1 - Stigloher, Christian T1 - FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms JF - PLoS Computational Biology N2 - 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. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9218 SN - 1553-7358 VL - 13 IS - 1 ER - TY - JOUR A1 - Zhang, Youjun A1 - Sampathkumar, Arun A1 - Kerber, Sandra Mae-Lin A1 - Swart, Corné A1 - Hille, Carsten A1 - Seerangan, Kumar A1 - Graf, Alexander A1 - Sweetlove, Lee A1 - Fernie, Alisdair R. T1 - A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts JF - Nature Communications N2 - Glycolysis is one of the primordial pathways of metabolism, playing a pivotal role in energy metabolism and biosynthesis. Glycolytic enzymes are known to form transient multi-enzyme assemblies. Here we examine the wider protein-protein interactions of plant glycolytic enzymes and reveal a moonlighting role for specific glycolytic enzymes in mediating the co-localization of mitochondria and chloroplasts. Knockout mutation of phosphoglycerate mutase or enolase resulted in a significantly reduced association of the two organelles. We provide evidence that phosphoglycerate mutase and enolase form a substrate-channelling metabolon which is part of a larger complex of proteins including pyruvate kinase. These results alongside a range of genetic complementation experiments are discussed in the context of our current understanding of chloroplast-mitochondrial interactions within photosynthetic eukaryotes. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14812 SN - 2041-1723 VL - 11 SP - 4509 ER - TY - JOUR A1 - Bruun, Kristina A1 - Hille, Carsten T1 - Study on intracellular delivery of liposome encapsulated quantum dots using advanced fluorescence microscopy JF - Scientific Reports N2 - Quantum dots increasingly gain popularity for in vivo applications. However, their delivery and accumulation into cells can be challenging and there is still lack of detailed information. Thereby, the application of advanced fluorescence techniques can expand the portfolio of useful parameters for a more comprehensive evaluation. Here, we encapsulated hydrophilic quantum dots into liposomes for studying cellular uptake of these so-called lipodots into living cells. First, we investigated photophysical properties of free quantum dots and lipodots observing changes in the fluorescence decay time and translational diffusion behaviour. In comparison to empty liposomes, lipodots exhibited an altered zeta potential, whereas their hydrodynamic size did not change. Fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), both combined with two-photon excitation (2P), were used to investigate the interaction behaviour of lipodots with an insect epithelial tissue. In contrast to the application of free quantum dots, their successful delivery into the cytosol of salivary gland duct cells could be observed when applying lipodots. Lipodots with different lipid compositions and surface charges did not result in considerable differences in the intracellular labelling pattern, luminescence decay time and diffusion behaviour. However, quantum dot degradation after intracellular accumulation could be assumed from reduced luminescence decay times and blue-shifted luminescence signals. In addition to single diffusing quantum dots, possible intracellular clustering of quantum dots could be assumed from increased diffusion times. Thus, by using a simple and manageable liposome carrier system, 2P-FLIM and 2P-FCS recording protocols could be tested, which are promising for investigating the fate of quantum dots during cellular interaction. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12476 SN - 2045-2322 VL - 9 SP - 10504 ER - TY - JOUR A1 - Günther, Erika A1 - Klauß, André A1 - Toro-Nahuelpan, Mauricio A1 - Schüler, Dirk A1 - Hille, Carsten A1 - Faivre, Damien T1 - The in vivo mechanics of the magnetotactic backbone as revealed by correlative FLIM-FRET and STED microscopy JF - Scientific Reports N2 - Protein interaction and protein imaging strongly benefit from the advancements in time-resolved and superresolution fluorescence microscopic techniques. However, the techniques were typically applied separately and ex vivo because of technical challenges and the absence of suitable fluorescent protein pairs. Here, we show correlative in vivo fluorescence lifetime imaging microscopy Förster resonance energy transfer (FLIM-FRET) and stimulated emission depletion (STED) microscopy to unravel protein mechanics and structure in living cells. We use magnetotactic bacteria as a model system where two proteins, MamJ and MamK, are used to assemble magnetic particles called magnetosomes. The filament polymerizes out of MamK and the magnetosomes are connected via the linker MamJ. Our system reveals that bacterial filamentous structures are more fragile than the connection of biomineralized particles to this filament. More importantly, we anticipate the technique to find wide applicability for the study and quantification of biological processes in living cells and at high resolution. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14802 SN - 2045-2322 VL - 9 ER - TY - GEN A1 - Hunger, Hans-Dieter A1 - Vaskova, Katerina T1 - Präparation und Charakterisierung von biologisch aktiven Magnetit-Protein-Nanopartikeln T2 - Wissenschaftliche Beiträge 2006 N2 - Magnetische Nanopartikel besitzen Anwendungspotenzial in vielen biologischen und medizinischen Anwendungsgebieten. Superparamagnetische Magnetit-Nanopartikel werden klinisch verwendet als Kontrastmittel im Magnet-Resonanz-Imaging (MRI)und intensiv untersucht für Anwendungen wie Drug-Delivery-Systeme, Zell-Bewegungs-und Trenn-Systeme und Hyperthermie (1-5). Dabei sind Eisenoxid (Magnetit)-Nanopartikel besonders interessant, da sie größenabhängigen superparamagnetismus besitzen, nicht toxisch sind und im Organismus etabolisiert werden. Deshalb werden unterdessen Magnetit-Nanopartikel in vielen biomedizinischen und diagnostischen Anwendungen eingesetzt. Die Stabilität und Biokompatibilität der Magnetit-Nanopartikel sind von der Größe der Partikel und von der Oberflächenbeschichtung der Partikel in der Lösung abhängig. Die häufigste Methode zur Herstellung von superparamagnetischen Magnetit-Nanopartikeln ist die Kopräzipitation von Eisensalzen in der Gegenwart einer Base, meist Ammoniumhydroxid. Für biomedizinische Anwendungen sollte die Oberfläche der Magnetit-Partikel komplett mit einer Polymerschicht überzogen sein, um den Eisenoxidkern gegen die Blutproteine und Phagocytose-Rezeptoren abzuschirmen. Die üblichsten Beschichtungsmoleküle für biokompatible, auf Magnetit basierende Kolloide sind Derivate von Dextran und Polyethylenglycol. In dieser Arbeit beschreiben wir eine neue Präparationsmethode von Magnetit-Protein-Partikeln durch direkte Kopräzipitation von Eisensalzen und Proteinen. Als Modellprotein wird Humanserumalbumin (HSA) verwendet, das als Hauptprotein des humanen Blutserums an der Oberfläche von Partikeln zur Verwendung in medizinischen Diagnostik- und Therapieverfahren sehr gute Voraussetzungen für die Biokompatibilität der Magnetit-Partikel besitzt. Dabei wurde gefunden, dass die meisten der primären Präzipitationsprodukte zunächst biologisch inaktiv (z. B. nicht von HSA-spezifischen Antikörpern erkennbar) sind und erst durch weitere chemische Aktivierungsschritte biologisch aktiviert werden können. Das Verfahren der chemische Aktivierung und dessen Optimierung wird beschrieben und eine Modellvorstellung für diesen Aktivierungsschritt präsentiert. Magnetit-Nanopartikel-Kopplungsprodukte mit unterschiedlichen Biomolekülen (z.B. Antikörpern, Protein A) gehören zu den für eine Verwendung in humanmedizinischen Strategien favorisierten Transportvehikeln für bioaktive Moleküle. Deshalb wurden die von uns erhaltenen Magnetit-HSA-Komplexe in einem zweistufigen Glutaraldehyd Verfahren chemisch aktiviert und kovalent mit Protein A und Antikörpern (IgG) gekoppelt. KW - Nanopartikel Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-261 SN - 0949-8214 VL - 11 SP - 47 EP - 50 ER - TY - JOUR A1 - Praia, Ana Beatriz A1 - Herkenhoff, Marcos Edgar A1 - Brödel, Oliver A1 - Frohme, Marcus A1 - Saad, Susana Marta Isay T1 - Sour Beer with Lacticaseibacillus paracasei subsp. paracasei F19: Feasibility and Influence of Supplementation with Spondias mombin L. Juice and/or By-Product JF - Foods N2 - This study aimed to evaluate the probiotic strain Lacticaseibacillus (L.) paracasei subsp. paracasei F19 (F19) with the yeast Saccharomyces cerevisiae US-05 (US-05), using Spondias mombin L. (‘taperebá’ or ‘cajá’) juice and by-product, in four sour-type beer formulations: control, with bagasse, juice, and juice and bagasse. The viability of F19 was evaluated by pour-plating and PMA-qPCR. Fermentability, in addition to physicochemical and sensory parameters, and aroma and flavor, were evaluated during brewery by using Headspace Solid-Phase Microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC–MS). F19 was successful in fermenting bagasse in a MRS medium (9.28 log CFU/mL in 24 h) but had a low viability in hopped wort, growing better in formulations without bagasse or juice. No difference between formulations was observed regarding sensory acceptability, and the HS-SPME/GC-MS revealed different flavors and aroma compounds. In conclusion, the production of a potential probiotic sour beer with F19 and US-05 is feasible regarding probiotic viability. However, S. mombin, as juice or bagasse, threatened probiotic survival. Different flavors and aroma compounds were detected, whereas no difference between formulations was found regarding sensory acceptability. The moderate alcohol content achieved is important for bacterial survival and for the development of a probiotic beer with health claims. KW - sour beer KW - probiotics KW - co-fermentation KW - fruit by-product Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16852 SN - 2304-8158 VL - 11 IS - 24 PB - MDPI ER - TY - JOUR A1 - Radivoievych, Aleksandar A1 - Kolp, Benjamin A1 - Grebinyk, Sergii A1 - Prylutska, Svitlana A1 - Ritter, Uwe A1 - Zolk, Oliver A1 - Glökler, Jörn A1 - Frohme, Marcus A1 - Grebinyk, Anna T1 - Silent Death by Sound: C60 Fullerene Sonodynamic Treatment of Cancer Cells JF - International Journal of Molecular Sciences N2 - The acoustic pressure waves of ultrasound (US) not only penetrate biological tissues deeper than light, but they also generate light emission, termed sonoluminescence. This promoted the idea of its use as an alternative energy source for photosensitizer excitation. Pristine C60 fullerene (C60), an excellent photosensitizer, was explored in the frame of cancer sonodynamic therapy (SDT). For that purpose, we analyzed C60 effects on human cervix carcinoma HeLa cells in combination with a low-intensity US treatment. The time-dependent accumulation of C60 in HeLa cells reached its maximum at 24 h (800 ± 66 ng/106 cells). Half of extranuclear C60 is localized within mitochondria. The efficiency of the C60 nanostructure’s sonoexcitation with 1 MHz US was tested with cell-based assays. A significant proapoptotic sonotoxic effect of C60 was found for HeLa cells. C60′s ability to induce apoptosis of carcinoma cells after sonoexcitation with US provides a promising novel approach for cancer treatment. KW - ultrasound KW - C60 fullerene KW - sonodynamic therapy KW - HeLa cells KW - apoptosis Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16877 SN - 1422-0067 VL - 24 IS - 2 PB - MDPI ER - TY - JOUR A1 - Chumachenko, Dmytro A1 - Butkevych, Mykola A1 - Lode, Daniel A1 - Frohme, Marcus A1 - Schmailzl, Kurt J. G. A1 - Nechyporenko, Alina T1 - Machine Learning Methods in Predicting Patients with Suspected Myocardial Infarction Based on Short-Time HRV Data JF - Sensors N2 - Diagnosis of cardiovascular diseases is an urgent task because they are the main cause of death for 32% of the world’s population. Particularly relevant are automated diagnostics using machine learning methods in the digitalization of healthcare and introduction of personalized medicine in healthcare institutions, including at the individual level when designing smart houses. Therefore, this study aims to analyze short 10-s electrocardiogram measurements taken from 12 leads. In addition, the task is to classify patients with suspected myocardial infarction using machine learning methods. We have developed four models based on the k-nearest neighbor classifier, radial basis function, decision tree, and random forest to do this. An analysis of time parameters showed that the most significant parameters for diagnosing myocardial infraction are SDNN, BPM, and IBI. An experimental investigation was conducted on the data of the open PTB-XL dataset for patients with suspected myocardial infarction. The results showed that, according to the parameters of the short ECG, it is possible to classify patients with a suspected myocardial infraction as sick and healthy with high accuracy. The optimized Random Forest model showed the best performance with an accuracy of 99.63%, and a root mean absolute error is less than 0.004. The proposed novel approach can be used for patients who do not have other indicators of heart attacks. KW - myocardial infraction KW - heart rate variability KW - 10-second heart rate variability KW - diagnostics KW - machine learning KW - k-nearest neighbor classifier KW - radial basis function KW - decision tree KW - random forest Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16521 SN - 1424-8220 VL - 22 IS - 18 PB - MDPI ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grebinyk, Sergii A1 - Ponomarenko, Stanislav A1 - Virych, Pavlo A1 - Chumachenko, Vasyl A1 - Kutsevol, Nataliya A1 - Prylutskyy, Yuriy A1 - Ritter, Uwe A1 - Frohme, Marcus T1 - Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer JF - Nanoscale Advances N2 - The development of precision cancer medicine relies on novel formulation strategies for targeted drug delivery to increase the therapeutic outcome. Biocompatible polymer nanoparticles, namely dextran-graft-polyacrylamide (D-g-PAA) copolymers, represent one of the innovative non-invasive approaches for drug delivery applications in cancer therapy. In this study, the star-like D-g-PAA copolymer in anionic form (D-g-PAAan) was developed for pH-triggered targeted drug delivery of the common chemotherapeutic drugs – doxorubicin (Dox) and cisplatin (Cis). The initial D-g-PAA copolymer was synthesized by the radical graft polymerization method, and then alkaline-hydrolyzed to get this polymer in anionic form for further use for drug encapsulation. The acidification of the buffer promoted the release of loaded drugs. D-g-PAAan nanoparticles increased the toxic potential of the drugs against human and mouse lung carcinoma cells (A549 and LLC), but not against normal human lung cells (HEL299). The drug-loaded D-g-PAAan-nanoparticles promoted further oxidative stress and apoptosis induction in LLC cells. D-g-PAAan-nanoparticles improved Dox accumulation and drugs’ toxicity in a 3D LLC multi-cellular spheroid model. The data obtained indicate that the strategy of chemotherapeutic drug encapsulation within the branched D-g-PAAan nanoparticle allows not only to realize pH-triggered drug release but also to potentiate its cytotoxic, prooxidant and proapoptotic effects against lung carcinoma cells. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16749 VL - 4 IS - 23 SP - 5077 EP - 5088 PB - Royal Society of Chemistry (RSC) ER - TY - JOUR A1 - Kober, Liane A1 - Schaefer, Paul A1 - Hollert, Henner A1 - Frohme, Marcus T1 - A novel strategy for high-throughput sample collection, analysis and visualization of explosives' concentrations for contaminated areas JF - International Journal of Environmental Science and Technology N2 - The use of explosives has led to a widespread distribution of 2,4,6-trinitrotoluene (TNT) and its by- and degradation products in the soil on former production and testing sites. The investigation of those large contaminated sites is so far based on a few selected soil samples, due to high costs of conventional HPLC and GC analysis, although huge differences in concentrations can already be found in small areas and different collection depths. We introduce a novel high-throughput screening system for those areas, which combines a smartphone-based collection of GPS data and soil characteristics with a fast MALDI-TOF MS quantification of explosives in soil sample extracts and finally a heatmap visualization of the explosives’ spread in soil and an analysis of correlation between concentrations and soil characteristics. The analysis of a 400 m2 area presented an extensive contamination with TNT and lower concentrations of the degradation and by-products aminodinitrotoluenes (ADNT) and dinitrotoluenes (DNT) next to a former production facility for TNT. The contamination decreased in deeper soil levels and depended on the soil type. Pure humus samples showed significantly lower contaminations compared to sand and humus/sand mixtures, which is likely to be caused by an increased binding potential of the humic material. No correlation was found between the vegetation and the concentration of explosives. Since the results were obtained and visualized within several hours, the MALDI-TOF MS based comprehensive screening and heatmap analysis might be valuable for a fast and high-throughput characterization of contaminated areas. KW - 2,4,6-trinitrotoluene KW - explosives KW - heatmap KW - MALDI-TOF MS KW - risk analysis KW - smartphone Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15981 SN - 1735-2630 VL - 20 IS - 2 SP - 1399 EP - 1410 PB - Springer Nature ER - TY - JOUR A1 - Pfeil, Juliane A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Hufert, Frank T. A1 - Schulze, Katja T1 - Examination of blood samples using deep learning and mobile microscopy JF - BMC Bioinformatics N2 - Microscopic examination of human blood samples is an excellent opportunity to assess general health status and diagnose diseases. Conventional blood tests are performed in medical laboratories by specialized professionals and are time and labor intensive. The development of a point-of-care system based on a mobile microscope and powerful algorithms would be beneficial for providing care directly at the patient's bedside. For this purpose human blood samples were visualized using a low-cost mobile microscope, an ocular camera and a smartphone. Training and optimisation of different deep learning methods for instance segmentation are used to detect and count the different blood cells. The accuracy of the results is assessed using quantitative and qualitative evaluation standards. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15802 SN - 1471-2105 VL - 23 PB - BioMed Central ER - TY - JOUR A1 - Herkenhoff, Marcos Edgar A1 - Bovolenta, Luiz A. A1 - Brödel, Oliver A1 - dos Santos, Lucilene Delazari A1 - de Oliveira, Arthur C. A1 - Chuffa, Luiz G.A. A1 - Ribeiro, Amanda O. A1 - Lupi, Luiz A. A1 - Dias, Marco A.D. A1 - Hilsdorf, Alexandre W.S. A1 - Frohme, Marcus A1 - Pinhal, Danillo T1 - Variant expression signatures of microRNAs and protein related to growth in a crossbreed between two strains of Nile tilapia (Oreochromis niloticus) JF - Genomics N2 - Nile tilapia (Oreochromis niloticus) is a species of worldwide importance for aquaculture. A crossbred lineage was developed through introgressive backcross breeding techniques and combines the high growth performance of the Chitralada (CHIT) lwith attractive reddish color of the Red Stirling (REDS) strains. Since the crossbreed has an unknown genetically improved background, the objective of this work was to characterize expression signatures that portray the advantageous phenotype of the crossbreeds. We characterized the microRNA transcriptome by high throughput sequencing (RNA-seq) and the proteome through mass spectrometry (ESI-Q-TOF-MS) and applied bioinformatics for the comparative analysis of such molecular data on the three strains. Crossbreed expressed a distinct set of miRNAs and proteins compared to the parents. They comprised several microRNAs regulate traits of economic interest. Proteomic profiles revealed differences between parental and crossbreed in expression of proteins associated with glycolisis. Distinctive miRNA and protein signatures contribute to the phenotype of crossbreed. KW - Nile tilapia KW - growth KW - RNA-seq KW - miRNA KW - ESI-Q-TOF KW - proteome Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15571 SN - 0888-7543 VL - 113 IS - 6 SP - 4303 EP - 4312 PB - Elsevier ER - TY - JOUR A1 - Wieland, Ralf A1 - Kuhls, Katrin A1 - Lentz, Hartmut H.K. A1 - Conraths, Franz A1 - Kampen, Helge A1 - Werner, Doreen T1 - Combined climate and regional mosquito habitat model based on machine learning JF - Ecological Modelling N2 - Besides invasive mosquito species also several native species are proven or suspected vectors of arboviruses as West Nile or Usutu virus in Western Europe. Habitat models of these native vectors can be a helpful tool for assessing the risk of autochthonous occurrence, outbreaks and spread of diseases caused by such arboviruses. Modelling native mosquitoes is complicated because of the perfect adaptation to the climatic and landscape conditions and their high abundance in contrast to invasive species. Here we present a new approach for such a habitat model for native mosquito species in Germany, which are considered as vectors of West Nile virus (WNV). Epizootic emergence of WNV was registered in Germany since 2018. The models are based on surveillance data of mosquitoes from the German citizen science project “Mückenatlas” complemented by data from systematic trap monitoring in Germany, and on data freely available from the Deutscher Wetterdienst (DWD) and OpenStreetMap (OSM). While climatic factors still play an important role, we could show that habitat suitability is predictable only by the combination of the climate model with a regional model. Both models were based on a machine-learning approach using XGBoost. Evaluation of the accuracy of the models was done by statistical analysis, determining among others feature importances using the SHAP-Library. Final output of the combined climatic and regional models are maps showing the superposed habitat suitability which are generated through a number of steps described in detail. These maps also include the registered cases of WNV infections in the selected region of Germany. KW - citizen science data KW - mosquito habitat modelling KW - machine learning KW - XGBoost KW - West Nile virus KW - vector borne disease Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15649 SN - 0304-3800 VL - 452 CY - Elsevier ER - TY - JOUR A1 - Heinsohn, Natascha Katharina A1 - Niedl, Robert Raimund A1 - Anielski, Alexander A1 - Lisdat, Fred A1 - Beta, Carsten T1 - Electrophoretic µPAD for Purification and Analysis of DNA Samples JF - Biosensors N2 - In this work, the fabrication and characterization of a simple, inexpensive, and effective microfluidic paper analytic device (µPAD) for monitoring DNA samples is reported. The glass microfiber-based chip has been fabricated by a new wax-based transfer-printing technique and an electrode printing process. It is capable of moving DNA effectively in a time-dependent fashion. The nucleic acid sample is not damaged by this process and is accumulated in front of the anode, but not directly on the electrode. Thus, further DNA processing is feasible. The system allows the DNA to be purified by separating it from other components in sample mixtures such as proteins. Furthermore, it is demonstrated that DNA can be moved through several layers of the glass fiber material. This proof of concept will provide the basis for the development of rapid test systems, e.g., for the detection of pathogens in water samples. KW - microfluidic paper analytic device (µPAD) KW - patterning glass microfiber KW - fiber-electrophoresis chip KW - DNA KW - imprinted electrodes KW - cross layer chip KW - polymerase chain reaction (PCR) KW - purification Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15763 SN - 2079-6374 VL - 12 IS - 2 PB - MDPI ER - TY - JOUR A1 - Strelkova, Margarita V. A1 - Baranova, Alla M. A1 - Kuhls, Katrin T1 - History of the E.I. Martsinovsky Institute of Medical Parasitology and Tropical Medicine: research on malaria and leishmaniasis JF - História, Ciências, Saúde – Manguinhos N2 - This review presents the 100-year history of the Martsinovsky Institute of Medical Parasitology and Tropical Medicine in Moscow, Russia, starting with its foundation and early activities, and also describes the impact of its leading scientists, some of whom became internationally known. The institute headed a network of nine tropical institutes in the various Soviet republics from the 1920s to 1990. The extensive body of literature on the history and research accomplishments of this institute has mainly been published in Russian; our goal here is to introduce these achievements and this expertise to the international scientific and medical community, focusing on malaria and leishmaniasis and the development of measures to control and monitor these diseases in the USSR. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13675 SN - 1678-4758 VL - 27 IS - 4 SP - 1097 EP - 1124 PB - Casa de Oswaldo Cruz, Fundação Oswaldo Cruz ER - TY - JOUR A1 - Glökler, Jörn A1 - Lim, Theam Soon A1 - Ida, Jeunice A1 - Frohme, Marcus T1 - Isothermal amplifications – a comprehensive review on current methods JF - Critical Reviews in Biochemistry and Molecular Biology N2 - AbstractThe introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15154 SP - 1 EP - 44 PB - Taylor & Francis ER - TY - JOUR A1 - D'Elia, Domenica A1 - Truu, Jaak A1 - Lahti, Leo A1 - Berland, Magali A1 - Papoutsoglou, Georgios A1 - Ceci, Michelangelo A1 - Zomer, Aldert A1 - Lopes, Marta B. A1 - Ibrahimi, Eliana A1 - Gruca, Aleksandra A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Klammsteiner, Thomas A1 - Carrillo de Santa Pau, Enrique A1 - Marcos-Zambrano, Laura Judith A1 - Hron, Karel A1 - Pio, Gianvito A1 - Simeon, Andrea A1 - Suharoschi, Ramona A1 - Moreno-Indias, Isabel A1 - Temko, Andriy A1 - Nedyalkova, Miroslava A1 - Apostol, Elena-Simona A1 - Truică, Ciprian-Octavian A1 - Shigdel, Rajesh A1 - Telalović, Jasminka Hasić A1 - Bongcam-Rudloff, Erik A1 - Przymus, Piotr A1 - Jordamović, Naida Babić A1 - Falquet, Laurent A1 - Tarazona, Sonia A1 - Sampri, Alexia A1 - Isola, Gaetano A1 - Pérez-Serrano, David A1 - Trajkovik, Vladimir A1 - Klucar, Lubos A1 - Loncar-Turukalo, Tatjana A1 - Havulinna, Aki S. A1 - Jansen, Christian A1 - Bertelsen, Randi J. A1 - Claesson, Marcus Joakim T1 - Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action JF - Frontiers in Microbiology N2 - The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices. KW - microbiome KW - machine learning KW - artificial intelligence KW - standard KW - best practice Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18004 SN - 1664-302X VL - 14 PB - Frontiers ER - TY - JOUR A1 - Radivoievych, Aleksandar A1 - Prylutska, Svitlana A1 - Zolk, Oliver A1 - Ritter, Uwe A1 - Frohme, Marcus A1 - Grebinyk, Anna T1 - Comparison of Sonodynamic Treatment Set-Ups for Cancer Cells with Organic Sonosensitizers and Nanosonosensitizers JF - Pharmaceutics N2 - Cancer sonodynamic therapy (SDT) is the therapeutic strategy of a high-frequency ultrasound (US) combined with a special sonosensitizer that becomes cytotoxic upon US exposure. The growing number of newly discovered sonosensitizers and custom US in vitro treatment solutions push the SDT field into a need for systemic studies and reproducible in vitro experimental set-ups. In the current research, we aimed to compare two of the most used and suitable SDT in vitro set-ups—“sealed well” and “transducer in well”—in one systematic study. We assessed US pressure, intensity, and temperature distribution in wells under US irradiation. Treatment efficacy was evaluated for both set-ups towards cancer cell lines of different origins, treated with two promising sonosensitizer candidates—carbon nanoparticle C60 fullerene (C60) and herbal alkaloid berberine. C60 was found to exhibit higher sonotoxicity toward cancer cells than berberine. The higher efficacy of sonodynamic treatment with a “transducer in well” set-up than a “sealed well” set-up underlined its promising application for SDT in vitro studies. The “transducer in well” set-up is recommended for in vitro US treatment investigations based on its US-field homogeneity and pronounced cellular effects. Moreover, SDT with C60 and berberine could be exploited as a promising combinative approach for cancer treatment. KW - ultrasound KW - C60 fullerene KW - berberine KW - sonodynamic therapy KW - apoptosis Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18223 SN - 1999-4923 VL - 15 IS - 11 PB - MDPI ER - TY - JOUR A1 - Shchotkina, Nataliia A1 - Palamarchuk, Y. A1 - Skorokhod, Iryna A1 - Dolinchuk, Liudmyla A1 - Sokol, Anatoliy A1 - Motronenko, Valentina A1 - Besarab, A. A1 - Gorchakova, N. A1 - Frohme, Marcus A1 - Herzog, Michael T1 - Features of technological regulation for cardiac bioimplants JF - Cell and Organ Transplantology N2 - Patients with congenital heart defects and cardiovascular diseases are required new approaches to surgical intervention. The use of biological cardiac implants, which are made from the extracellular matrix, is a promising trend in modern regenerative medicine. These bioimplants can completely replace defective tissue or organs, and when manufactured with strict protocols and quality control measures, can be safe and effective for therapeutic applications. The process of manufacturing bioimplants involves various risks that need to be assessed and mitigated with ongoing monitoring and evaluation necessary to ensure the highest standards of quality. Overall, this study was successfully evaluated the requirements for introducing a new medical device into practice and created a technical file that meets all necessary documentation for certification. KW - cardiac bioimplant KW - quality system KW - manufacturing risk management KW - technical regulation KW - medical device Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18248 SN - 2311-021X VL - 11 IS - 1 SP - 26 EP - 33 PB - Institute of Cell Therapy CY - Kiev ER - TY - THES A1 - Tillich, Ulrich M. T1 - Adaptive Evolution und Screening bei Cyanobakterien - Erzeugung und Untersuchung von Thermotoleranz in Synechocystis sp. PCC 6803 N2 - Ziel dieser Arbeit war die Erhöhung der Temperaturtoleranz des Cyanobakteriums Synechocystis sp. PCC 6803 mittels ungerichteter Mutagenese und adaptiver Evolution. Trotz des erneuten Interesses an Cyanobakterien und Mikroalgen in den letzten Jahren, gibt es nur relativ wenige aktuelle Studien zum Einsatz dieser Methoden an Cyanobakterien. Zur Analyse eines mittels Mutagenese erzeugten Gemischs an Stämmen, ist es von großem Vorteil Hochdurchsatz-Methoden zur Kultivierung und zum Screening einsetzen zu können. Auf Basis eines Pipettierroboters wurde solch eine Plattform für phototrophe Mikroorganismen neu entwickelt und folgend stetig verbessert. Die Kultivierung erfolgt in 2,2ml Deepwell-Mikrotiterplatten innerhalb einer speziell angefertigten Kultivierungskammer. Schüttelbedingungen, Beleuchtung, Temperatur und CO2-Atmosphäre sind hierbei vollständig einstellbar.Die Plattform erlaubt semi-kontinuierliche Kultivierungen mit automatisierten Verdünnungen von hunderten Kulturen gleichzeitig. Automatisierte Messungen des Wachstums, des Absorptionsspektrums, der Chlorophyllkonzentration, MALDI-TOF-MS sowie eines neu entwickelten Vitalitätsassays wurden etabliert. Für die Mutagenese wurden die Letalität- und die nicht-letale Punktmutationsrate von ultravioletter Strahlung und Methylmethansulfonat für Synechocystis charakterisiert. Synechocystis wurde mit den so ermittelten optimalen Dosen mehrfach behandelt und anschließend einer in vivo Selektion unterzogen. Somit wurde dessen Temperaturtoleranz um bis zu 3°C erhöht. Über die Screeningplattform wurden die thermotolerantesten monoklonalen Stämme identifiziert. Nach einer Validierung wurde das vollständige Genom der Stämme sequenziert. Hierdurch wurden erstmals Mutationen in verschiedenen Genen mit der Langzeittemperaturtoleranz von Synechocystis in Verbindung gebracht. Bei einigen dieser Gene ist es sehr unwahrscheinlich, dass sie mittels anderer Verfahren hätten identifiziert werden können. N2 - The goal of this work was the increase of the thermal tolerance of the cyanobacteria Synechocystis sp. PCC 6803 via random mutagenesis and adaptive evolution. Even with the renewed interest in cyanobacteria in the recent years, there is relatively limited current research available on the application of these methods on cyanobacteria. To analyse a mixture of various strains typically obtained through random mutagenesis, a method allowing high-throughput miniaturized cultivation and screening is of great advantage. Based on a pipetting robot a novel high-throughput screening system suitable for phototrophic microorganisms was developed and then constantly improved. 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. The platform allows semi-continuous cultivation of hundreds of cultures in parallel. Automated measurements of growth, full absorption spectrum, chlorophyll concentration, MALDI-TOF-MS, as well as a novel vitality measurement protocol, have been established. Prior to the mutagenesis, the lethality and rate of non-lethal point mutations of ultraviolet radiation and methyl-methanesulphonate were characterized for Synechocystis. The thus determined optimal dosages were applied to Synechocystis followed by in vivo selection in four rounds of mutagenesis, thereby raising its temperature tolerance by 3°C. The screening platform was used to identify the most thermotolerant monoclonal strains. After validation, their whole genomes were sequenced. Thus mutations in various genes were identified which promote the strains'' thermal tolerance. For some of the genes it is very unlikely that their link to high thermal tolerance could have been identified by other approaches. KW - liquid handling KW - Cyanobakterien KW - Thermotoleranz KW - Adaptive Evolution Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18307 ER - TY - JOUR A1 - Schilling, Vincent A1 - Beyerlein, Peter A1 - Chien, Jeremy T1 - A Bioinformatics Analysis of Ovarian Cancer Data Using Machine Learning JF - Algorithms N2 - The identification of biomarkers is crucial for cancer diagnosis, understanding the underlying biological mechanisms, and developing targeted therapies. In this study, we propose a machine learning approach to predict ovarian cancer patients’ outcomes and platinum resistance status using publicly available gene expression data. Six classical machine-learning algorithms are compared on their predictive performance. Those with the highest score are analyzed by their feature importance using the SHAP algorithm. We were able to select multiple genes that correlated with the outcome and platinum resistance status of the patients and validated those using Kaplan–Meier plots. In comparison to similar approaches, the performance of the models was higher, and different genes using feature importance analysis were identified. The most promising identified genes that could be used as biomarkers are TMEFF2, ACSM3, SLC4A1, and ALDH4A1. KW - ovarian cancer KW - machine learning KW - SHAP KW - diagnostic biomarker KW - platinum resistance Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17751 VL - 16 IS - 7 PB - MDPI ER -