TY - JOUR A1 - Schokraie, Elham A1 - Hotz-Wagenblatt, Agnes A1 - Warnken, Uwe A1 - Mali, Brahim A1 - Frohme, Marcus A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Hengherr, Steffen A1 - Schill, Ralph O. A1 - Schnölzer, Martina T1 - Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms JF - PLoS ONE N2 - Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6214 SN - 1932-6203 VL - 5 IS - 3 ER - TY - JOUR A1 - Schokraie, Elham A1 - Warnken, Uwe A1 - Hotz-Wagenblatt, Agnes A1 - Grohme, Markus A1 - Hengherr, Steffen A1 - Förster, Frank A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas A1 - Schnölzer, Martina T1 - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state JF - PLoS ONE N2 - Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6392 SN - 1932-6203 VL - 7 IS - 9 ER - TY - JOUR A1 - Förster, Frank A1 - Beisser, Daniela A1 - Grohme, Markus A1 - Liang, Chunguang A1 - Mali, Brahim A1 - Siegl, Alexander Matthias A1 - Engelmann, Julia C. A1 - Shkumatov, Alexander A1 - Schokraie, Elham A1 - Müller, Tobias A1 - Schnölzer, Martina A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas T1 - Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations JF - Bioinformatics and Biology Insights N2 - Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. KW - RNA KW - expressed sequence tag KW - cluster KW - protein family KW - adaptation KW - tardigrada KW - transcriptome Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6153 SN - 1177-9322 VL - 2012 IS - 6 SP - 69 EP - 96 ER - TY - JOUR A1 - Förster, Frank A1 - Liang, Chunguang A1 - Shkumatov, Alexander A1 - Beisser, Daniela A1 - Engelmann, Julia C. A1 - Schnölzer, Martina A1 - Frohme, Marcus A1 - Müller, Tobias A1 - Schill, Ralph O. A1 - Dandekar, Thomas T1 - Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades JF - BMC Genomics N2 - Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences. Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6461 SN - 1471-2164 VL - 10 IS - 469 ER - TY - JOUR A1 - Mali, Brahim A1 - Grohme, Markus A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Schnölzer, Martina A1 - Reuter, Dirk A1 - Wełnicz, Weronika A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer JF - BMC Genomics N2 - The phenomenon of desiccation tolerance, also called anhydrobiosis, involves the ability of an organism to survive the loss of almost all cellular water without sustaining irreversible damage. Although there are several physiological, morphological and ecological studies on tardigrades, only limited DNA sequence information is available. Therefore, we explored the transcriptome in the active and anhydrobiotic state of the tardigrade Milnesium tardigradum which has extraordinary tolerance to desiccation and freezing. In this study, we present the first overview of the transcriptome of M. tardigradum and its response to desiccation and discuss potential parallels to stress responses in other organisms. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6207 SN - 1471-2164 VL - 11 IS - 168 ER - TY - JOUR A1 - Janowski, Susann A1 - Gross, Ina A1 - Sauer-Gürth, Hedwig A1 - Tietze, Dieter Thomas A1 - Grohme, Markus A1 - Frohme, Marcus A1 - Becker, Peter A1 - Wink, Michael T1 - New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing JF - The Open Ornithology Journal N2 - Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern, Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns, e.g. in the aforementioned colony monitored for decades. KW - common tern KW - COLONY software KW - genotyping KW - microsatellite KW - multiplex PCR KW - next-generation sequencing KW - parentage analysis KW - Sterna hirundo Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6789 SN - 1874-4532 VL - 9 SP - 50 EP - 59 ER - TY - JOUR A1 - Nitsche, Andreas A1 - Kurth, Andreas A1 - Dunkhorst, Anna A1 - Pänke, Oliver A1 - Sielaff, Hendrik A1 - Junge, Wolfgang A1 - Muth, Doreen A1 - Scheller, Frieder W. A1 - Stöcklein, Walter A1 - Dahmen, Claudia A1 - Pauli, Georg A1 - Kage, Andreas T1 - One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX JF - BMC Biotechnology N2 - As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6246 SN - 1472-6750 VL - 7 IS - 48 ER - TY - JOUR A1 - Wang, Chong A1 - Grohme, Markus A1 - Mali, Brahim A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing JF - PLoS ONE N2 - Many tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6029 SN - 1932-6203 VL - 9 IS - 3 ER - TY - JOUR A1 - Grohme, Markus A1 - Mali, Brahim A1 - Wełnicz, Weronika A1 - Michel, Stephanie A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum JF - Bioinformatics and Biology Insights N2 - Limno-terrestrial tardigrades are small invertebrates that are subjected to periodic drought of their micro-environment. They have evolved to cope with these unfavorable conditions by anhydrobiosis, an ametabolic state of low cellular water. During drying and rehydration, tardigrades go through drastic changes in cellular water content. By our transcriptome sequencing effort of the limno-terrestrial tardigrade Milnesium tardigradum and by a combination of cloning and targeted sequence assembly, we identified transcripts encoding eleven putative aquaporins. Analysis of these sequences proposed 2 classical aquaporins, 8 aquaglyceroporins and a single potentially intracellular unorthodox aquaporin. Using quantitative real-time PCR we analyzed aquaporin transcript expression in the anhydrobiotic context. We have identified additional unorthodox aquaporins in various insect genomes and have identified a novel common conserved structural feature in these proteins. Analysis of the genomic organization of insect aquaporin genes revealed several conserved gene clusters. KW - unorthodox aquaporin KW - anhydrobiosis KW - tardigrada Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6092 SN - 1177-9322 VL - 2013 IS - 7 SP - 153 EP - 165 ER - TY - JOUR A1 - Beisser, Daniela A1 - Grohme, Markus A1 - Kopka, Joachim A1 - Frohme, Marcus A1 - Schill, Ralph O. A1 - Hengherr, Steffen A1 - Dandekar, Thomas A1 - Klau, Gunnar W. A1 - Dittrich, Marcus A1 - Müller, Tobias T1 - Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum JF - BMC Systems Biology N2 - Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. KW - integrated network analysis KW - functional module KW - metabolic profile KW - metabolic pathway KW - trend test Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6146 SN - 1752-0509 VL - 6 IS - 72 ER - TY - JOUR A1 - Janowski, Susann A1 - Grohme, Markus A1 - Frohme, Marcus A1 - Wink, Michael T1 - Development of New Microsatellite (STR) Markers for Montagu’s Harrier (Circus pygargus) via 454 Shot-Gun Pyrosequencing JF - The Open Ornithology Journal N2 - During the last decades the ground-breeding Montagu’s harrier ( Circus pygargus , Linnaeus, 1758) has changed its breeding habitats in Europe to agricultural areas in which many local populations would be close to extinction without a special nest protection regime. Although Montagu’s harrier is a well-studied species in terms of ecology and breeding biology, its genetic structure and population genetics are almost unknown. As there is a lack of good genetic markers we developed a set of 19 microsatellite markers comprising 16 new STR markers which were identified by next-generation sequencing (NGS) using 454 shot-gun pyrosequencing of genomic DNA. The STR markers were arranged into three multiplex PCR sets for high throughput genotyping and characterised. The marker set provides a powerful tool for kinship analysis. The combined non-exclusion probability for parent pairs was 1.13* 10-11. Only three loci showed PIC values < 0.50. In total, 121 known family relationships were compared with genetically calculated ones to test the markers suitability for parentage analysis. In 97.5% of all cases full-sibships were accurately determined and 97.6% of all mothers were assigned correctly to their chicks. The present multiplex PCR panels can be used to investigate several hypotheses concerning breeding behaviour, kinship, exchange rates between populations and phylogeography. KW - Circus pygargus KW - Dipetalogaster maxima KW - genotyping KW - microsatellite KW - Montagu’s harrier KW - multiplex PCR KW - next-generation sequencing KW - parentage analysis Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5966 SN - 1874-4532 VL - 7 SP - 11 EP - 18 ER - TY - JOUR A1 - Petrillo, Mauro A1 - Fabbri, Marco A1 - Kagkli, Dafni Maria A1 - Querci, Maddalena A1 - Van den Eede, Guy A1 - Alm, Erik A1 - Aytan-Aktug, Derya A1 - Capella-Gutierrez, Salvador A1 - Carrillo, Catherine A1 - Cestaro, Alessandro A1 - Chan, Kok-Gan A1 - Coque, Teresa A1 - Endrullat, Christoph A1 - Gut, Ivo A1 - Hammer, Paul A1 - Kay, Gemma L. A1 - Madec, Jean-Yves A1 - Mather, Alison E. A1 - McHardy, Alice Carolyn A1 - Naas, Thierry A1 - Paracchini, Valentina A1 - Peter, Silke A1 - Pightling, Arthur A1 - Raffael, Barbara A1 - Rossen, John A1 - Ruppé, Etienne A1 - Schlaberg, Robert A1 - Vanneste, Kevin A1 - Weber, Lukas M. A1 - Westh, Henrik A1 - Angers-Loustau, Alexandre T1 - A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 1; peer review: 2 approved with reservations] JF - F1000Research N2 - Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community. KW - antimicrobial resistance KW - bioinformatics KW - next-generation sequencing KW - benchmarking Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15699 ER - TY - JOUR A1 - Endrullat, Christoph A1 - Glökler, Jörn A1 - Franke, Philipp A1 - Frohme, Marcus T1 - Standardization and quality management in next-generation sequencing JF - Applied & Translational Genomics N2 - DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data. KW - next-generation sequencing KW - quality management KW - data quality KW - standardization KW - validation KW - guideline Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6637 SN - 2212-0661 VL - 10 SP - 2 EP - 9 ER - TY - JOUR A1 - Mohr, Gunther A1 - Nowakowski, Susanna A1 - Altenburg, Simon J. A1 - Maierhofer, Christiane A1 - Hilgenberg, Kai T1 - Experimental Determination of the Emissivity of Powder Layers and Bulk Material in Laser Powder Bed Fusion Using Infrared Thermography and Thermocouples JF - Metals N2 - Recording the temperature distribution of the layer under construction during laser powder bed fusion (L-PBF) is of utmost interest for a deep process understanding as well as for quality assurance and in situ monitoring means. While having a notable number of thermal monitoring approaches in additive manufacturing (AM), attempts at temperature calibration and emissivity determination are relatively rare. This study aims for the experimental temperature adjustment of an off-axis infrared (IR) thermography setup used for in situ thermal data acquisition in L-PBF processes. The temperature adjustment was conducted by means of the so-called contact method using thermocouples at two different surface conditions and two different materials: AISI 316L L-PBF bulk surface, AISI 316L powder surface, and IN718 powder surface. The apparent emissivity values for the particular setup were determined. For the first time, also corrected, closer to real emissivity values of the bulk or powder surface condition are published. In the temperature region from approximately 150 °C to 580 °C, the corrected emissivity was determined in a range from 0.2 to 0.25 for a 316L L-PBF bulk surface, in a range from 0.37 to 0.45 for 316L powder layer, and in a range from 0.37 to 0.4 for IN718 powder layer. KW - laser powder bed fusion (L-PBF) KW - selective laser melting (SLM) KW - laser beam melting (LBM) KW - thermography KW - emissivity KW - calibration KW - thermocouples KW - 316L KW - IN718 KW - process monitoring Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13564 SN - 2075-4701 VL - 10 IS - 11 PB - MDPI ER - TY - JOUR A1 - Ristić, Alenka A1 - Furbo, Simon A1 - Moser, Christoph A1 - Schranzhofer, Hermann A1 - Lazaro, Ana A1 - Delgado, Monica A1 - Peñalosa, Conchita A1 - Zalewski, Laurent A1 - Diarce, Gonzalo A1 - Alkan, Cemil A1 - Gunasekara, Saman N. A1 - Haussmann, Thomas A1 - Gschwander, Stefan A1 - Rathgeber, Christoph A1 - Schmit, Henri A1 - Barreneche, Camila A1 - Cabeza, Luiza A1 - Ferrer, Gerard A1 - Konuklu, Yeliz A1 - Paksoy, Halime A1 - Rammelberg, Holger A1 - Munz, Gunther A1 - Herzog, Thomas H. A1 - Jänchen, Jochen A1 - del Barrio, Elena Palomo T1 - IEA SHC Task 42 / ECES Annex 29 WG A1: Engineering and Processing of PCMs, TCMs and Sorption Materials JF - Energy Procedia N2 - An overview on the recent results on the engineering and characterization of sorption materials, PCMs and TCMs investigated in the working group WG A1 “Engineering and processing of TES materials” of IEA SHC Task 42 / ECES Annex 29 (Task 4229) entitled “Compact Thermal Energy Storage” is presented. KW - engineering KW - processing KW - PCM KW - TCM KW - sorption material Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6629 SN - 1876-6102 VL - 91 SP - 207 EP - 217 ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grynyuk, I. A1 - Kolp, Benjamin A1 - Hurmach, V. A1 - Sliva, T. A1 - Amirkhanov, Volodymyr A1 - Trush, V. A1 - Matyshevska, Olga A1 - Slobodyanik, M. A1 - Prylutskyy, Yuriy A1 - Frohme, Marcus A1 - Ritter, Uwe T1 - C60 Fullerene Effects on Diphenyl-N-(trichloroacetyl)-amidophosphate Interaction with DNA In Silico and Its Cytotoxic Activity Against Human Leukemic Cell Line In Vitro JF - Nanoscale Research Letters N2 - New representative of carbacylamidophosphates - diphenyl-N-(trichloroacetyl)-amidophosphate (HL), which contains two phenoxy substituents near the phosphoryl group, was synthesized, identified by elemental analysis and IR and NMR spectroscopy, and tested as a cytotoxic agent itself and in combination with C60 fullerene. According to molecular simulation results, C60 fullerene and HL could interact with DNA and form a rigid complex stabilized by stacking interactions of HL phenyl groups with C60 fullerene and DNA G nucleotide, as well as by interactions of HL CCl3 group by ion-π bonds with C60 molecule and by electrostatic bonds with DNA G nucleotide. With the use of MTT test, the cytotoxic activity of HL against human leukemic CCRF-CM cells with IC50 value detected at 10 μM concentration at 72 h of cells treatment was shown. Under combined action of 16 μM C60 fullerene and HL, the value of IC50 was detected at lower 5 μM HL concentration and at earlier 48 h period of incubation, besides the cytotoxic effect of HL was observed at a low 2.5 μM concentration at which HL by itself had no influence on cell viability. Binding of C60 fullerene and HL with minor DNA groove with formation of a stable complex is assumed to be one of the possible reasons of their synergistic inhibition of CCRF-CЕM cells proliferation. Application of C60 fullerene in combination with 2.5 μM HL was shown to have no harmful effect on structural stability of blood erythrocytes membrane. Thus, combined action of C60 fullerene and HL in a low concentration potentiated HL cytotoxic effect against human leukemic cells and was not followed by hemolytic effect. KW - diphenyl-N-(trichloroacetyl)-amidophosphate (HL) KW - C60 fullerene KW - leukemic CCRF-CEM cell KW - DNA KW - molecular simulation Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10515 SN - 1556-276X VL - 2018 SP - 1 EP - 9 ER - TY - JOUR A1 - Hollmann, Susanne A1 - Frohme, Marcus A1 - Endrullat, Christoph A1 - Kremer, Andreas A1 - D'Elia, Domenica A1 - Regierer, Babette A1 - Nechyporenko, Alina T1 - Ten simple rules on how to write a standard operating procedure JF - PLoS Computational Biology N2 - Research publications and data nowadays should be publicly available on the internet and, theoretically, usable for everyone to develop further research, products, or services. The long-term accessibility of research data is, therefore, fundamental in the economy of the research production process. However, the availability of data is not sufficient by itself, but also their quality must be verifiable. Measures to ensure reuse and reproducibility need to include the entire research life cycle, from the experimental design to the generation of data, quality control, statistical analysis, interpretation, and validation of the results. Hence, high-quality records, particularly for providing a string of documents for the verifiable origin of data, are essential elements that can act as a certificate for potential users (customers). These records also improve the traceability and transparency of data and processes, therefore, improving the reliability of results. Standards for data acquisition, analysis, and documentation have been fostered in the last decade driven by grassroot initiatives of researchers and organizations such as the Research Data Alliance (RDA). Nevertheless, what is still largely missing in the life science academic research are agreed procedures for complex routine research workflows. Here, well-crafted documentation like standard operating procedures (SOPs) offer clear direction and instructions specifically designed to avoid deviations as an absolute necessity for reproducibility. Therefore, this paper provides a standardized workflow that explains step by step how to write an SOP to be used as a starting point for appropriate research documentation. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13598 SN - 1553-7358 VL - 16 IS - 9 SP - e1008095 ER - TY - JOUR A1 - Prylutska, Svitlana A1 - Grynyuk, I. A1 - Grebinyk, Anna A1 - Hurmach, V. A1 - Shatrava, Iu. A1 - Sliva, T. A1 - Amirkhanov, Volodymyr A1 - Prylutskyy, Yuriy A1 - Matyshevska, Olga A1 - Slobodyanik, M. A1 - Frohme, Marcus A1 - Ritter, Uwe T1 - Cytotoxic Effects of Dimorfolido-N-Trichloroacetylphosphorylamide and Dimorfolido-N-Benzoylphosphorylamide in Combination with C60 Fullerene on Leukemic Cells and Docking Study of Their Interaction with DNA JF - Nanoscale Research Letters N2 - Dimorfolido-N-trichloroacetylphosphorylamide (HL1) and dimorfolido-N-benzoylphosphorylamide (HL2) as representatives of carbacylamidophosphates were synthesized and identified by the methods of IR, 1H, and 31P NMR spectroscopy. In vitro HL1 and HL2 at 1 mM concentration caused cell specific and time-dependent decrease of leukemic cell viability. Compounds caused the similar gradual decrease of Jurkat cells viability at 72 h (by 35%). HL1 had earlier and more profound toxic effect as compared to HL2 regardless on leukemic cell line. Viability of Molt-16 and CCRF-CEM cells under the action of HL1 was decreased at 24 h (by 32 and 45%, respectively) with no substantial further reducing up to 72 h. Toxic effect of HL2 was detected only at 72 h of incubation of Jurkat and Molt-16 cells (cell viability was decreased by 40 and 45%, respectively). It was shown that C60 fullerene enhanced the toxic effect of HL2 on leukemic cells. Viability of Jurkat and CCRF-CEM cells at combined action of C60 fullerene and HL2 was decreased at 72 h (by 20 and 24%, respectively) in comparison with the effect of HL2 taken separately. In silico study showed that HL1 and HL2 can interact with DNA and form complexes with DNA both separately and in combination with C60 fullerene. More stable complexes are formed when DNA interacts with HL1 or C60 + HL2 structure. Strong stacking interactions can be formed between HL2 and C60 fullerene. Differences in the types of identified bonds and ways of binding can determine distinction in cytotoxic effects of studied compounds. KW - dimorfolido-N-trichloroacetylphosphorylamide KW - dimorfolido-N-benzoylphosphorylamide KW - C60 fullerene KW - leukemic cell KW - DNA KW - computer modeling Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9273 SN - 1556-276X VL - 12 IS - 124 ER - TY - JOUR A1 - Akhoundi, Mohammad A1 - Kuhls, Katrin A1 - Cannet, Arnaud A1 - Votýpka, Jan A1 - Marty, Pierre A1 - Delaunay, Pascal A1 - Sereno, Denis T1 - A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies JF - PLoS Neglected Tropical Diseases N2 - The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5853 SN - 1935-2735 VL - 10 IS - 3 ER - TY - JOUR A1 - Amro, Ahmad A1 - Al-Dwibe, Hamida A1 - Gashout, Aisha A1 - Moskalenko, Olga A1 - Galafin, Marlena A1 - Hamarsheh, Omar A1 - Frohme, Marcus A1 - Jaeschke, Anja A1 - Schönian, Gabriele A1 - Kuhls, Katrin T1 - Spatiotemporal and molecular epidemiology of cutaneous leishmaniasis in Libya JF - PLoS Neglected Tropical Diseases N2 - Cutaneous leishmaniasis (CL) is a skin infection caused by a single-celled parasite that is transmitted by the bite of a phlebotomine sandfly. CL is the most common form of leishmaniasis characterized by localized lesions in the skin and mucous membranes. The disease is prevalent in all countries around the Mediterranean Basin. In this paper, we describe spatiotemporal and eco-epidemiological parameters of CL in Libya. Moreover, we explored current spatiotemporal distributions of CL cases and explored the future projection of the disease. Our study indicates the presence of higher risk of CL in the coastal regions of Libya. Future projection until 2060 showed a trend of increasing incidence of CL in the north-western part of Libya, a spread along the coastal region and a possible emergence of new endemics in the north-eastern districts of Libya. These scenarios should be considered by health authorities in order to develop appropriate intervention strategies and plan effective control programs. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10054 SN - 1935-2735 VL - 11 IS - 9 ER -