TY - JOUR A1 - Marcos-Zambrano, Laura Judith A1 - López-Molina, Víctor Manuel A1 - Bakir-Gungor, Burcu A1 - Frohme, Marcus A1 - Karaduzovic-Hadziabdic, Kanita A1 - Klammsteiner, Thomas A1 - Ibrahimi, Eliana A1 - Lahti, Leo A1 - Loncar-Turukalo, Tatjana A1 - Dhamo, Xhilda A1 - Simeon, Andrea A1 - Nechyporenko, Alina A1 - Pio, Gianvito A1 - Przymus, Piotr A1 - Sampri, Alexia A1 - Trajkovik, Vladimir A1 - Lacruz-Pleguezuelos, Blanca A1 - Aasmets, Oliver A1 - Araujo, Ricardo A1 - Anagnostopoulos, Ioannis A1 - Aydemir, Önder A1 - Berland, Magali A1 - Calle, M. Luz A1 - Ceci, Michelangelo A1 - Duman, Hatice A1 - Gündoğdu, Aycan A1 - Havulinna, Aki S. A1 - Kaka Bra, Kardokh Hama Najib A1 - Kalluci, Eglantina A1 - Karav, Sercan A1 - Lode, Daniel A1 - Lopes, Marta B. A1 - May, Patrick A1 - Nap, Bram A1 - Nedyalkova, Miroslava A1 - Paciência, Inês A1 - Pasic, Lejla A1 - Pujolassos, Meritxell A1 - Shigdel, Rajesh A1 - Susín, Antonio A1 - Thiele, Ines A1 - Truică, Ciprian-Octavian A1 - Wilmes, Paul A1 - Yilmaz, Ercument A1 - Yousef, Malik A1 - Claesson, Marcus Joakim A1 - Truu, Jaak A1 - Carrillo de Santa Pau, Enrique T1 - A toolbox of machine learning software to support microbiome analysis JF - Frontiers in Microbiology N2 - The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis. KW - microbiome KW - machine learning KW - software KW - feature generation KW - feature analysis KW - data integration KW - microbial gene prediction KW - microbial metabolic modeling Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18271 UR - https://www.frontiersin.org/articles/10.3389/fmicb.2023.1250806/ SN - 1664-302X VL - 14 PB - Frontiers 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 - 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 - GEN A1 - Tillich, Ulrich M. A1 - Grüber, Stefanie A1 - Frohme, Marcus T1 - Etablierung von Hochdurchsatz-Kultivierungs- und -Screeningmethoden für phototrophe Einzeller T2 - Wissenschaftliche Beiträge 2012 N2 - Mit Hochdurchsatz-Kultivierungs- und -Screeningmethoden können viele Proben parallel, miniaturisiert und kostengünstig bearbeitet werden. Für phototrophe Organismen wie Mikroalgen und Cyanobakterien sind Hochdurchsatz-Kultivierungsverfahren jedoch bis heute kaum etabliert. Im Rahmen dieser Arbeit wurden diese Verfahren beispielhaft für das Cyanobakterium Synechocystis sp. PCC 6803 etabliert. Die benötigte technische Automatisierung wurde hierbei durch den Einsatz eines Tecan Genesis RSP 150 Pipettierroboters erreicht. Die Kultivierung erfolgte in Deepwell-Mikrotiterplatten innerhalb einer speziell angefertigten Kammer mit programmierbaren Schüttlern, einstellbarer Belichtung und CO2-Atmosphäre. Die in diesem System erreichten Wachstumsraten sind vergleichbar mit publizierten Kultivierungsmethoden. Das Hochdurchsatz-Screening wurde mit Hilfe eines in den Roboter integrierten Tecan Genios Plus Plattenreaders durchgeführt. Es wurden beispielhaft Methoden zur Bestimmung von optischer Dichte und Chlorophyllgehalt etabliert. Die hier vorgestellte Plattform kann vielseitig zur Analyse phototropher Organismen eingesetzt werden und ist durch entsprechende Assays leicht zur Messung anderer Parameter erweiterbar. N2 - High-throughput cultivation and screening methods allow a parallel, miniaturized and cost efficient processing of many samples. These methods however, have not been generally established for phototrophic organisms such as microalgae or cyanobacteria. In this work we describe and test high-throughput methods with the model organism Synechocystis sp. PC6803. The required technical automation for these processes was archived with a Tecan Genesis RSP 150 pipetting robot. The cultivation was performed in deepwell microtiter plates within a specially constructed cultivation chamber. The chamber is outfitted with programmable shaking conditions, variable illumination and an adjustable CO2 atmosphere. The growth rates archived within this system are comparable to those achieved with established methods such as bioreactors. The high-throughput screening was achieved with a Tecan Genios Plus plate reader integrated within the pipetting robot. Methods for determination of optical density and amount of chlorophyll were established within the scope of this work. The presented platform can be used for a variety of analyses of phototrophic organisms and is easily expandable with further assays to screen for additional targets. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-1335 SN - 0949-8214 VL - 16 SP - 31 EP - 36 ER - TY - GEN A1 - Radke, Lars A1 - Lubitz, Annika A1 - Giese, Christoph A1 - Frohme, Marcus T1 - Einfluss der Kryokonservierung auf die Immunantwort von Leukozyten T2 - Wissenschaftliche Beiträge 2012 N2 - Die Messung von Zytokinen in Stimulationsexperimenten zur Bestimmung von Stärke und Umfang einer Immunreaktion werden in der Praxis häufig an kryokonserviertem Zellmaterial durchgeführt. Bisherige Untersuchungen zum Einfluss der Kryokonservierung auf die Zytokinexpression sind widersprüchlich. In den hier durchgeführten Experimenten wurden die Genexpression und/ oder Sekretion der Zytokine IL-2, IL-4, IL-5, IL-10, IL-12, IL-13, GM-CSF, IFN-γ und TNF-α in frisch isolierten und kryokonservierten Immunzellen aus Blut (PBMC) eines gesunden Spenders bestimmt. Diese wurden mit den Immunsystem-aktivierenden Stoffen OKT-3 und Concanavalin A (Con A) stimuliert und für 4 bzw. 24 h kultiviert. Ein Vergleich der frisch-isolierten und kryokonservierten PBMC in Stimulationsexperimenten zeigt, (1) dass die Messung der Genexpression genauere Einblicke zu Beginn der einsetzenden Immunreaktion verschafft, als die Messung der ausgeschütteten Zytokine, (2) dass durch Einfrieren die Immunreaktion insbesondere zu diesem Zeitpunkt beeinflusst wird und (3) dass zu späteren Zeitpunkten die Konzentrationsbestimmung der Zytokine im Zellkulturüberstand das Mittel der Wahl ist. N2 - The measurement of cytokines in stimulation experiments with the aim to determine the strength and the complexitiy of an immune reaction is commonly carried out on cryopreserved cells. Previous studies, investigating the impact of cryopreservation on the cytokine expression, are inconsistent in their findings. Experiments conducted in this study determine the gene expression and/or secretion of IL-2, IL-4, IL-5, IL-10, IL-12, IL-13, GM-CSF, IFN-γ and TNF-α in freshly isolated and cryopreserved PBMC of a healthy donor. The cells were stimulated with the substances OKT-3 and Concanavalin A (Con A) and cultured for 4h and 24h. The comparison of freshly isolated and cryopreserved cells in stimulation experiments showed (1) that the measurement of the gene expression offers a more accurate insight into the immune-reaction at early timepoints than the measurement of the secreted cytokines; (2) that freezing of the cells affect the immune response at this early stage and (3) that at later points the measurement of secreted proteins is the method of choice. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-1363 SN - 0949-8214 VL - 16 SP - 9 EP - 14 ER - TY - GEN A1 - Reich, Peggy A1 - Frohme, Marcus A1 - Rantala, Juha A1 - Nees, Matthias T1 - Implementation of a siRNA Screen for Prostate Tumour Cell Lines Using Living Cell Arrays T2 - Wissenschaftliche Beiträge 2008 N2 - Prostate cancer is one of the most common causes of death in men. In this work a siRNA screen of around 1500 cancer-relevant genes was performed using 3 different cell lines (VCaP, LAPC-4, RWPE-1). A novel technique, the living cell array, was initiated in order to obtain information about the biology of Androgeninduced growth in prostate tumour cell lines. This technique is based on the principal of reverse transfection [1] and genes are knocked down by siRNAs. The cells on the living cell array were set under stress by reduction of the androgens in the media while the proliferation and apoptosis were quantified. The statistical analysis of the data implicates the success of the screen and shows that this method is suitable for large-scale experiments. N2 - Prostatakrebs ist neben Lungenkrebs eine der häufigsten Todesursachen bei Männern. In dieser Arbeit wurden 1500 potenziell tumorrelevante Gene in drei Zelllinien (VCaP, LAPC-4, RWPE-1) gescreent. Dafür wurde eine neue Technik, die Lebendzellarrays, genutzt, um Informationen über die Biologie Androgen-unabhängiger Prostatazellen zu gewinnen. Die Lebendzellarrays basieren auf dem Prinzip der reversen Transfektion [1], und in Folge werden die mRNAs der gewünschten Gene durch spezifische »silencer RNAs« (siRNAs) ausgeschaltet. Die Zellen wurden parallel sowohl in normalem Medium untersucht als auch mit androgen-reduziertem Medium unter Stress gesetzt. Das Wachstum der Prostatazellen wurde mittels Markern für Proliferation und Apoptose beobachtet. Die Daten der Screens wurden mit Hilfe statistischer Verfahren evaluiert. Die Lebendzellarrays konnten erfolgreich für einen umfangreichen SiRNA-screen angewendet werden. Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-635 SN - 0949-8214 VL - 13 SP - 19 EP - 24 ER - TY - GEN A1 - Mali, Brahim A1 - Grohme, Markus A1 - Wełnicz, Weronika A1 - Dandekar, Thomas A1 - Schnölzer, Martina A1 - Reuter, Dirk A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Genomic Analyses of Cryptobiotic Tardigrades T2 - Wissenschaftliche Beiträge 2008 N2 - Genomics technologies, especially transcriptional profiling, allows comparisons of gene expression within and across different organisms. By the use of the model group Tardigrada, also known as water bear, we try to understand the phenomenon of cryptobiosis. The dry organisms can survive for years without water. When re-exposed to water, the animals rehydrate and come back to life. The expression of genes in response to dehydratation and rehydratation is being examined in our laboratory through the generation of expressed sequence tags (ESTs), representational difference analysis (RDA) and subsequent microarray analysis. Molecular dissection of this complex phenomenom, including gene regulation, will allow the development of techniques for preservation and stabilisation of biological materials in a dried state. N2 - Techniken der Genomanalyse, speziell das transkriptionelle Profiling, erlauben uns, Genexpression innerhalb eines und zwischen verschiedenen Organismen zu untersuchen. Wir nutzen als Modell Tardigraden, auch bekannt als Bärtierchen, um das Phänomen der Kryptobiose besser zu verstehen. Die ausgetrockneten Tiere können Jahre überdauern. Wenn man Wasser hinzugibt, rehydrieren die Tiere und werden wieder zum Leben erweckt. In unserem Labor untersuchen wir die Genexpression als Antwort auf das Austrockenen und Rehydrieren mittels Bibliotheken Exprimierter Sequenz Tags (ESTs), Repräsentativer Differenz Analyse und Mikroarray-Untersuchungen. Die molekulare Analyse des komplexen Phänomens und seiner Regulation auf Ebene der Gene wird es ermöglichen, Techniken für die Konservierung und Stabilisierung von biologischem Material in trockenem Zustand zu entwickeln. Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-672 SN - 0949-8214 VL - 13 SP - 35 EP - 39 ER - TY - GEN A1 - Radke, Lars A1 - López-Hemmerling, Diana A1 - Lubitz, Annika A1 - Giese, Christoph A1 - Wildenauer, Franz-Xaver A1 - Frohme, Marcus T1 - Etablierung verschiedener Bead-basierter Multiplexmethoden mit einem Suspensions Array-System für molekulardiagnostische Zwecke T2 - Wissenschaftliche Beiträge 2009/2010 N2 - Die simultane Bestimmung mehrerer Analyten und die Erstellung komplexer Parameterprofi e erlangt immer größere Bedeutung in der heutigen Labordiagnostik. Die Bead-basierte Multiplexanalytik bietet hier eine flexible, schnelle und einfache Methode zur Erstellung individueller Analysen. Aufgrund der Vielzahl von Anwendungsmöglichkeiten, die diese moderne Nachweismethode im Bereich molekularbiologischer Fragestellungen bietet, ist die Etablierung der Beadbasierten Multiplexanalytik im Labor für Molekularbiologie und funktionelle Genomik der Technischen Hochschule Wildau von großem Nutzen. Zur Einarbeitung in das Testsystem wurden die Konzentrationen der Zytokine IL-2, IL-4, IFN-γ und TNF-α in Zellkulturüberständen mit kommerziellen Fertigsystemen gemessen und mit mRNA-Expressionsraten der gleichen Proben verglichen. Des Weiteren wurde ein Testsystem zum Nachweis von humanen Antikörpern der Klassen IgG und IgM sowie deren antigen-spezifischer Anteil in Zellkulturüberständen entwickelt. Außerdem konnte durch die erfolgreiche Detektion von DNA-gekoppelten Beads mittels markierter Oligonukleotidsequenz die Kopplung und die Anwendbarkeit der Methode auf Bindungsexperimente mit Nukleotidsequenzen gezeigt werden N2 - The simultaneous determination of multiple analytes and the generation of complex parameter profi les gains increasing importance in today’s laboratory diagnostics. The bead-based multiplex assay is offering a flexible, rapid and easy to handle method for the creation of individual analyses. Because of the multitude of applications this modern detection system offers, the establishment of the bead-based multiplex technique is of great benefit for the Laboratory for Molecular Biology and Functional Genomics of the Technical University of Applied Sciences Wildau. To familiarize with the testing system the concentrations of the cytokines IL-2, IL-4, IFN-γ and TNF-α in cell culture supernatant were analysed with commercially available assays and compared with mRNA expression ratios of the same samples. Furthermore a custom testing system was developed for the detection of human IgG and IgM antibodies and also antigen specific antibodies in cell culture supernatants. The assignability of the method to binding experiments with nucleotide sequences could be shown by the successful detection of DNA-modified beads by conjugated oligonucleotides Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-802 SN - 0949-8214 VL - 14 SP - 6 EP - 12 ER - TY - GEN A1 - Weinert, Stefan A1 - Wohlfahrt, Ingolf A1 - Schmid, Andrea A1 - Frohme, Marcus T1 - Einführung eines Qualitätsmanagement-Systems in einem molekularbiologischen Labor einer Hochschule T2 - Wissenschaftliche Beiträge 2009/2010 N2 - Zertifizierte Qualitätsmanagementsysteme (QM-Systeme) sind in akademischen Forschungslaboren bisher kaum vertreten. Hier ist vor allem die Bedeutung eines zertifizierten Labors vor dem Hintergrund der Veröffentlichung wissenschaftlicher Publikationen scheinbar bedeutungslos. Im industriellen Bereich hingegen sind QM-Systeme weitaus häufiger eingeführt. Labore im akademischen Bereich stehen jedoch grundsätzlich in der Verantwortung, schonend mit den Ressourcen des Staates umzugehen, und haben darüber hinaus das Bestreben, Forschungs-/Industrieaufträge einzuwerben. Mit dieser Publikation wird gezeigt, wie durch die Einrichtung eines QM-Systems und der Einhaltung der normativen Vorgabe ein verbesserter schonender Umgang mit staatlichen Ressourcen möglich ist, die Ergebnissicherheit erhöht, Betriebsabläufe optimiert, die Chancen für Studenten auf dem Arbeitsmarkt verbessert werden und mehr Forschungs-/Industrieaufträge akquiriert werden können. Es wird dargestellt, wie ein QM-System in einem Labor eingerichtet werden kann. Dabei wird erläutert, welche QM-Regelwerke für ein Labor im Hochschulbereich in Betracht kommen. Zudem wird eine Methodik in Form eines Projektplans vorgestellt, mit dem die Anforderungen der Norm strukturiert umgesetzt werden können. Das QM-System wurde im Labor für Molekularbiologie und Funktionelle Genomik an der Technischen Hochschule Wildau [FH] eingeführt und im Rahmen der Zertifizierung der Hochschule in das Audit einbezogen. N2 - Up to now certified Quality-Management-Systems(QM-system) are hardly prevalent in university research laboratories. Even if a laboratory is certified, it seems to have no meaning for a scientific publication originating from this laboratory. In the industrial sector QM-systems are a lot more common. Basically, academic laboratories have to use their rescources, provided primarily by govermental funding, very sparingly and responsible. Furthermore universities have a strong endeavour to accquire funding for further research. We demonstrate here, how the establishment of a QM-system, and compliance to normative requirements, can improve the economic use of governmental funding. Furthermore a QM-system can ensure result reliability and work routines can be optimized. In addition the job perspectives for graduates as well as the possibilities to aquire funding will be improved. We present how a QM-system can be established in a lifescience- laboratory. Thereby it will be outlined which regulations are applicable to an academic research lab. Following that, a method to implement a QM-system will be presented. This method is shown as a project schedule and explains the requirements that are necessary to establish quality standards. The QM-system was implemented in the Laboratory for Molecular Biology and Functional Genomics of the Technical University of Applied Sciences Wildau and was included within the scope of the certification of the university in the audit. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-859 SN - 0949-8214 VL - 14 SP - 49 EP - 56 ER - TY - GEN A1 - Schulze, Katja A1 - Glökler, Jörn A1 - Kadolsky, Marianne A1 - Frohme, Marcus T1 - Detektion des Kartoffelspindelknollen Viroids mit Hilfe der Loop Mediated Isothermal Amplification T2 - Wissenschaftliche Beiträge 2011 N2 - PSTV ist ein hoch infektiöses Viroid, das in Kartoffeln verkleinerte und spindelähnliche Knollen verursacht. Um Ernteverlusten vorzubeugen, ist eine Detektion in frühen Infektionsstadien von großer Bedeutung. Aufgrund ihrer hohen Sensitivität und Spezifität wird die PCR als Standardnachweisverfahren für PSTV verwendet. Nachteilig an dieser Methode sind der apparative Aufwand und die zeitaufwändige Durchführung. Als viel versprechende Alternative konnte der Nachweis von PSTV mit Hilfe der Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) gezeigt werden. Hierbei handelt es sich um eine einfache und schnelle Methode, für die wenig aufwändige Laborausrüstung benötigt wird. Dabei ermöglichte eine an den Amplifikationsprozess gekoppelte Fluoreszenzreaktion die Detektion von Produkten direkt nach der Nachweisreaktion mit dem bloßen Auge (bzw. unter UV-Licht). Die Ergebnisse konnten mit Hilfe einer Real Time Detektion des auftretenden Fluoreszenzsignals bestätigt werden. N2 - PSTV is a highly infectious viroid which leads to small and spindle shaped tubers in potatoes. The detection at an early stage of infection is important to minimize loss of harvest. Normally PCR is used for the detection of PSTV, because of its high sensitivity and specificity. Disadvantages of this method are the requirement of sophisticated equipment and the time consuming process. As a promising alternative, the detection of PSTV with the reverse transcription loop mediated isothermal amplification (RT-LAMP) was shown. LAMP is a very fast and simple detection method requiring only standard laboratory equipment. A fluorescence reaction, coupled to the amplification process, allowed the detection of amplification products directly after the reaction with the naked eye (or under UV light, respectively). Real time detection of the occurring fluorescence signal was possible and confirmed the obtained results. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-1025 SN - 0949-8214 VL - 15 SP - 7 EP - 12 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 - 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 - Tillich, Ulrich M. A1 - Wolter, Nick A1 - Franke, Philipp A1 - Dühring, Ulf A1 - Frohme, Marcus T1 - Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution JF - BMC Biotechnology N2 - Temperature tolerance is an important aspect for commercial scale outdoor cultivation of microalgae and cyanobacteria. While various genes are known to be related to Synechocystis sp. PCC6803's heat shock response, there is very limited published data concerning the specific genes involved in long term thermal tolerance. We have previously used random mutagenesis and adaptive evolution to generate a mixture of strains of Synechocystis sp. PCC6803 with significantly increased thermal tolerance. The genetic modifications leading to the phenotypes of the newly generated strains are the focus of this work. KW - cyanobacteria KW - synechocystis KW - thermal tolerance KW - HTS KW - NGS KW - adaptive evolution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6014 SN - 1472-6750 VL - 14 IS - 66 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 - tardigrade 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 - 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 - 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 - 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 - Silbermann, Jascha A1 - Wernicke, Catrin A1 - Pospisil, Heike A1 - Frohme, Marcus T1 - RefPrimeCouch—a reference gene primer CouchApp JF - Database: The Journal of Biological Databases and Curation N2 - To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6330 SN - 1758-0463 VL - 2013 ER - TY - JOUR A1 - Falckenhayn, Cassandra A1 - Boerjan, Bart A1 - Raddatz, Günter A1 - Frohme, Marcus A1 - Schoofs, Liliane A1 - Lyko, Frank T1 - Characterization of genome methylation patterns in the desert locust Schistocerca gregaria JF - The Journal of Experimental Biology N2 - DNA methylation is a widely conserved epigenetic modification. The analysis of genome-scale DNA methylation patterns in various organisms suggests that major features of animal methylomes are widely conserved. However, based on the variation of DNA methyltransferase genes in invertebrates, it has also been proposed that DNA methylation could provide a molecular mechanism for ecological adaptation. We have now analyzed the methylome of the desert locust, Schistocerca gregaria, which represents an organism with a high degree of phenotypic plasticity. Using genome-scale bisulfite sequencing, we show here that the S. gregaria methylome is characterized by CpG- and exon-specific methylation and thus shares two major features with other animal methylomes. In contrast to other invertebrates, however, overall methylation levels were substantially higher and a significant fraction of transposons was methylated. Additionally, genic sequences were densely methylated in a pronounced bimodal pattern, suggesting a role for DNA methylation in the regulation of locust gene expression. Our results thus uncover a unique pattern of genome methylation in locusts and provide an important foundation for investigating the role of DNA methylation in locust phase polyphenism. KW - DNA methylation KW - Schistocerca gregaria KW - locust KW - methylome Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6350 SN - 0022-0949 VL - 216 SP - 1423 EP - 1429 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 - 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 - López, Diana A. A1 - Tillich, Ulrich M. A1 - Frohme, Marcus T1 - A simple viability analysis for unicellular cyanobacteria using a new autofluorescence assay, automated microscopy, and ImageJ JF - BMC Biotechnology N2 - Currently established methods to identify viable and non-viable cells of cyanobacteria are either time-consuming (eg. plating) or preparation-intensive (eg. fluorescent staining). In this paper we present a new and fast viability assay for unicellular cyanobacteria, which uses red chlorophyll fluorescence and an unspecific green autofluorescence for the differentiation of viable and non-viable cells without the need of sample preparation. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6192 SN - 1472-6750 VL - 11 IS - 118 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 - 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 - CHAP A1 - Chepurna, Oksana A1 - Grebinyk, Anna A1 - Petrushko, Yulia A1 - Prylutska, Svitlana A1 - Grebinyk, Sergii A1 - Yashchuk, Valeriy A1 - Matyshevska, Olga A1 - Ritter, Uwe A1 - Dandekar, Thomas A1 - Frohme, Marcus A1 - Qu, Junle A1 - Ohulchanskyy, Tymish Y. T1 - LED-based portable light source for photodynamic therapy N2 - Photodynamic therapy (PDT) employs light activation of tissue-localized photosensitizer in an oxygen-dependent process which initiates oxidative stress, inflammation, and cell death. Laser systems, which are mostly used in PDT as light sources can be costly and oversized. light-emitting diodes (LEDs) equipment has a high potential to simplify technical part of phototriggered therapies and to reduce its costs. We develop the LED-based system that includes the control and irradiation units. The system provides the same power density at any irradiation point. Among the advantages of the device is a possibility to change the irradiation area and tune the irradiation dose. PDT experiments with cancer cells in vitro treated with two different photosensitizers demonstrated a possibility to use the developed LED-based system as a low-cost light source in PDT. KW - light source KW - high power single chip LED KW - photodynamic therapy Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14778 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 - Kagel, Heike A1 - Bier, Frank Fabian A1 - Frohme, Marcus A1 - Glökler, Jörn T1 - A Novel Optical Method To Reversibly Control Enzymatic Activity Based On Photoacids JF - Scientific Reports N2 - Most biochemical reactions depend on the pH value of the aqueous environment and some are strongly favoured to occur in an acidic environment. A non-invasive control of pH to tightly regulate such reactions with defined start and end points is a highly desirable feature in certain applications, but has proven difficult to achieve so far. We report a novel optical approach to reversibly control a typical biochemical reaction by changing the pH and using acid phosphatase as a model enzyme. The reversible photoacid G-acid functions as a proton donor, changing the pH rapidly and reversibly by using high power UV LEDs as an illumination source in our experimental setup. The reaction can be tightly controlled by simply switching the light on and off and should be applicable to a wide range of other enzymatic reactions, thus enabling miniaturization and parallelization through non-invasive optical means. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12685 SN - 2045-2322 VL - 9 ER - TY - JOUR A1 - Kagel, Heike A1 - Jacobs, Hannes A1 - Bier, Frank Fabian A1 - Glökler, Jörn A1 - Frohme, Marcus T1 - A Novel Microtiter Plate Format High Power Open Source LED Array JF - Photonics N2 - Many photochemical or photobiological applications require the use of high power ultraviolet light sources, such as high-pressure mercury arc lamps. In addition, many photo-induced chemical, biochemical and biological applications require either a combinatorial setting or a parallel assay of multiple samples under the same environmental conditions to ensure reproducibility. To achieve this, alternative, controllable light sources, such as ultraviolet light emitting diodes (UV LEDs) with high power and spatial control are required. Preferably, LEDs are arranged in a suitable standardized 96-well microtiter plate format. We designed such an array and established the methods required for heat management and enabling stable, controllable illumination over time. KW - optics KW - photonics KW - light KW - LED array KW - High-power LED KW - 365 nm KW - microtiter plate Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-11307 SN - 2304-6732 VL - 6 IS - 1 ER - TY - CHAP A1 - Li, X.-K. A1 - Amirkhanyan, Z. A1 - Aftab, N. A1 - Boonpornprasert, Prach A1 - Dmytriiev, D. A1 - Frohme, Marcus A1 - Georgiev, G. A1 - Grebinyk, Anna A1 - Gross, M. A1 - Hoffmann, A. A1 - Komar, Yuliia A1 - Krasilnikov, M. A1 - Loisch, G. A1 - Oppelt, A. A1 - Richard, C. A1 - Riemer, F. A1 - Philipp, S. A1 - Schmitz, M. A1 - Müller, F. A1 - Obier, F. A1 - Vashchenko, Grygorii A1 - Worm, S. A1 - Stephan, F. T1 - Overview of FLASHlab@PITZ: the new R&D platform for FLASH radiation therapy and radiation biology T2 - Journal of Physics: Conference Series, Volume 2687, Applications of Accelerators, Technology Transfer and Industrial Relations and Outreach N2 - An R&D platform for electron FLASH radiation therapy and radiation biology is being prepared at the Photo Injector Test facility at DESY in Zeuthen (FLASHlab@PITZ). This platform is based on the unique beam parameters available at PITZ: ps scale electron bunches of up to 22 MeV with up to 5 nC bunch charge at MHz bunch repetition rate in bunch trains of up to 1 ms in length repeating at 1 to 10 Hz. It works together with the Technical University of Applied Sciences Wildau (TH Wildau) as partner in close vicinity for the biological resources. A startup beamline has been installed to allow dosimetry studies and irradiation experiments on chemical, biochemical and biological samples after a 60-degree dispersive arm. The measured dose and dose rates under different beam conditions and first experimental results will be reported in this paper. In addition, a dedicated beamline for FLASHlab@PITZhas been designed for better control of the high brightness electron beams. This includes a dogleg to translate the beam and a 2D kicker system to scan the tiny beam focused by quadrupoles across the samples within less than 1 ms. Simulation studies will be presented to demonstrate the extremely flexible dose parameters with various irradiation options for electron FLASH radiation therapy and radiation biology studies. Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18474 VL - 2687 PB - Institute of Physics Publishing (IOP) ER - TY - JOUR A1 - Amro, Ahmad A1 - Moskalenko, Olga A1 - Hamarsheh, Omar A1 - Frohme, Marcus T1 - Spatiotemporal analysis of cutaneous leishmaniasis in Palestine and foresight study by projections modelling until 2060 based on climate change prediction JF - PLoS ONE N2 - Background Cutaneous leishmaniasis (CL) is a vector-borne parasitic diseases of public health importance that is prevalent in the West Bank but not in the Gaza Strip. The disease caused by parasitic protozoans from the genus Leishmania and it is transmitted by infected phlebotomine sand flies. The aim of our study is to investigate the eco-epidemiological parameters and spatiotemporal projections of CL in Palestine over a 30-years period from 1990 through 2020 and to explore future projections until 2060. Methodology/Principal findings This long-term descriptive epidemiological study includes investigation of demographic characteristics of reported patients by the Palestinian Ministry of Health (PMoH). Moreover, we explored spatiotemporal distribution of CL including future projection based on climate change scenarios. The number of CL patients reported during this period was 5855 cases, and the average annual incidence rate (AAIR) was 18.5 cases/105 population. The male to female ratio was 1.25:1. Patients-age ranged from 2 months to 89 years (mean = 22.5, std 18.67, and the median was 18 years). More than 65% of the cases came from three governates in the West Bank; Jenin 29% (1617 cases), Jericho 25% (1403), and Tubas 12% (658) with no cases reported in the Gaza Strip. Seasonal occurrence of CL starts to increase in December and peaked during March and April of the following year. Current distribution of CL indicate that Jericho, Tubas, Jenin and Nablus have the most suitable climatic settings for the sandfly vectors. Future projections until 2060 suggest an increasing incidence from northwest of Jenin down to the southwest of Ramallah, disappearance of the foci in Jericho and Tubas throughout the Jordan Vally, and possible emergence of new foci in Gaza Strip. Conclusions/Significance The future projection of CL in Palestine until 2060 show a tendency of increasing incidence in the north western parts of the West Bank, disappearance from Jericho and Tubas throughout the Jordan Vally, and emergence of new CL endemic foci in the Gaza Strip. These results should be considered to implement effective control and surveillance systems to counteract spatial expansion of CL vectors. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16166 SN - 1932-6203 VL - 17 IS - 6 PB - Public Library of Science (PLoS) ER - TY - JOUR A1 - Grebinyk, Anna A1 - Yashchuk, Valeriy A1 - Bashmakova, Nataliya A1 - Gryn, Dmytro A1 - Hagemann, Tobias A1 - Naumenko, Antonina A1 - Kutsevol, Nataliya A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - A new triple system DNA-Nanosilver-Berberine for cancer therapy JF - Applied Nanoscience N2 - The isoquinoline quaternary alkaloid Berberine possesses a variety of pharmacological properties that suggests its promising application for an anticancer delivery system design utilizing its ability to intercalate DNA. In the current work, we have investigated the effects of Berberine on the human T cell leukemia cell line in vitro. Fluorescent microscopy of leukemic cells revealed Berberine nuclear localization. The results showed that Berberine inhibited leukemic cell growth in a time- and dose-dependent manner, that was associated with reactive oxygen species production intensification and caspase 3/7 activity increase with followed apoptosis induction. Berberine was used as a toxic and phototoxic agent for triple system synthesis along with DNA as a carrier and nanosilver as a plasmonic accelerator of Berberine electronic transitions and high energy emission absorbent centers. The proposed method allows to obtain the complex of DNA with Berberine molecules and silver nanoparticles. The optical properties of free components as well as their various combinations, including the final triple system DNA-Nanosilver-Berberine, were investigated. Obtained results support the possibility to use the triple system DNA-Nanosilver-Berberine as an alternative therapeutic agent for cancer treatment. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16105 SN - 2190-5517 VL - 9 SP - 945 EP - 956 PB - Springer ER - TY - JOUR A1 - Prylutska, Svitlana A1 - Grebinyk, Anna A1 - Ponomarenko, Stanislav A1 - Gövem, Defne A1 - Chumachenko, Vasyl A1 - Kutsevol, Nataliya A1 - Petrovsky, Mykola A1 - Ritter, Uwe A1 - Frohme, Marcus A1 - Piosik, Jacek A1 - Prylutskyy, Yuriy T1 - Toxicity of Water-Soluble D-g-PNIPAM Polymers in a Complex with Chemotherapy Drugs and Mechanism of Their Action In Vitro JF - International Journal of Molecular Sciences N2 - The application of a biocompatible polymer nanocarrier can provide target delivery to tumor tissues, improved pharmacokinetics, controlled drug release, etc. Therefore, the proposed strategy was to use the water-soluble star-like copolymers with a Dextran core and Poly(N-isopropylacrylamide) grafts (D-g-PNIPAM) for conjugation with the widely used chemotherapy drugs in oncology–Cisplatin (Cis-Pt) and Doxorubicin (Dox). The molecular characteristics of the copolymer were received using size-exclusion chromatography. The physicochemical characterization of the D-g-PNIPAM-Cis-Pt (or Dox) nanosystem was conducted using dynamic light scattering and FTIR spectroscopy. Using traditional biochemical methods, a comparative analysis of the enhancement of the cytotoxic effect of free Cis-Pt and Dox in combination with D-g-PNIPAM copolymers was performed in cancer cells of the Lewis lung carcinoma line, which are both sensitive and resistant to Dox; in addition, the mechanism of their action in vitro was evaluated. KW - star-like copolymer KW - drug KW - Lewis lung carcinoma KW - cytotoxicity Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18790 SN - 1422-0067 VL - 25 IS - 5 PB - MDPI 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 - 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 - 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. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-11415 SN - 1556-276X VL - 14 ER - TY - GEN A1 - Keil, Karolin A1 - Radke, Lars A1 - Tillich, Ulrich M. A1 - Frohme, Marcus T1 - Automatisierung des Bio-Plex Pro Analyseverfahrens T2 - Wissenschaftliche Beiträge 2015 N2 - Für den simultanen Nachweis mehrerer Analyten innerhalb einer Probe ist die Bead-basierte Multiplexanalytik ein häufig verwendetes Verfahren und wird beispielsweise zur Quantifizierung von Proteinen genutzt. Die aufwendige Durchführung der Assays soll durch Automatisierung einerseits dem Anwender abgenommen werden, während andererseits die Genauigkeit und Reproduzierbarkeit der Analyse gesteigert wird. Die Automatisierung des Bio-Plex Pro™ Assays ist mit dem Pipettierroboter Tecan Freedom EVO 200 umgesetzt worden. Es ist ein Skript mit der Software Freedom EVOware® entwickelt worden, welches die Probenvorbereitung des Assays vollständig übernimmt. Für einen Vergleich der manuellen und automatisierten Methode sind die humanen Zytokine IL-2, IL-4, IL-10, GM-CSF, IFN-γ und TNF-α in einer achtstufigen Standardverdünnungsreihe und in unterschiedlich konzentrierten Proben gemessen worden. Die Berechnung der Streuungen (Standardabweichung und Variationskoeffizient) der einzelnen Standardverdünnungsreihen sowie der Vergleich von gemessenen und erwarteten Konzentrationen der automatisierten und manuellen Methode zeigen, dass die Automatisierung neben der zeitlichen Optimierung auch die Genauigkeit und Reproduzierbarkeit der Analyse verbessert. N2 - Bead-based multpiplex analysis is frequently used for the simultaneous detection of multiple analytes within a sample. Such assays are commonly used to quantify proteins. The automation of the process relieves the user from the complex assay conductance and on the other hand increases the accuracy and reproducibility of the analysis. The automation of the Bio-Plex Pro™ assay has been successfully implemented with the pipetting-robot Tecan Freedom EVO 200. A script has been developed, using the Freedom EVOware® which has the ability to perform the complete assay procedure. For a comparison between manual and automated methods, the human cytokines IL-2, IL-4, IL-10, GM-CSF, IFN-γ and TNF-α were analysed by an eight-point standard dilution series and with samples of different concentrations. The calculation of the variances (standard deviation and coefficient of variation) of the single standard dilution series as well as the comparison of the observed and expected concentrations of the manual or automated method show the higher precision and reproducibility of the automated process in addition to its time-saving nature. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-3524 SN - 0949-8214 VL - 19 SP - 15 EP - 19 ER - TY - JOUR A1 - Gossing, Wilhelm A1 - Frohme, Marcus A1 - Radke, Lars T1 - Biomarkers for Liquid Biopsies of Pituitary Neuroendocrine Tumors JF - Biomedicines N2 - Pituitary neuroendocrine tumors (PitNET) do not only belong to the most common intracranial neoplasms but seem to be generally more common than has been thought. Minimally invasive liquid biopsies have the potential to improve their early screening efficiency as well as monitor prognosis by facilitating the diagnostic procedures. This review aims to assess the potential of using liquid biopsies of different kinds of biomarker species that have only been obtained from solid pituitary tissues so far. Numerous molecules have been associated with the development of a PitNET, suggesting that it often develops from the cumulative effects of many smaller genetic or epigenetic changes. These minor changes eventually pile up to switch critical molecules into tumor-promoting states, which may be the key regulatory nodes representing the most potent marker substances for a diagnostic test. Drugs targeting these nodes may be superior for the therapeutic outcome and therefore the identification of such pituitary-specific cellular key nodes will help to accelerate their application in medicine. The ongoing genetic degeneration in pituitary adenomas suggests that repeated tumor profiling via liquid biopsies will be necessary for personalized and effective treatment solutions. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13307 SN - 2227-9059 VL - 8 IS - 6 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 - Kuhls, Katrin A1 - Moskalenko, Olga A1 - Sukiasyan, Anna A1 - Manukyan, Dezdemonia A1 - Melik-Andreasyan, Gayane A1 - Atshemyan, Liana A1 - Apresyan, Hripsime A1 - Strelkova, Margarita V. A1 - Jaeschke, Anja A1 - Wieland, Ralf A1 - Frohme, Marcus A1 - Cortes, Sofia A1 - Keshishyan, Ara T1 - Microsatellite based molecular epidemiology of Leishmania infantum from re-emerging foci of visceral leishmaniasis in Armenia and pilot risk assessment by ecological niche modeling JF - PLoS Neglected Tropical Diseases N2 - Leishmaniasis is a vector-borne disease caused by protozoan parasites of the genus Leishmania. In Armenia visceral leishmaniasis (VL) is re-emerging since 1999 after a long break of 30 years, with 167 cases recorded until 2019. Molecular diagnosis of VL was implemented only in 2016, and the causative agent was identified as L. infantum. In the present study we expanded the investigation of the causative agent to a characterization at strain level and the identification of its phylogenetic position among the L. infantum genotypes circulating worldwide. This is the first study addressing genetic diversity and population structure of L. infantum in Armenia and in Transcaucasia. Armenia is an extremely interesting region due to its bio-geographic specificities e.g. the high number of different climates in this small mountainous country and the observed high diversity of sand fly species, part of which occurring in very high altitudes. Ecological niche modeling based on registered VL cases and sand fly vectors collected in active VL foci revealed that the risk of further spread of VL is very high due to climate change. Studies of this region should be expanded to enable targeted control measures. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14004 SN - 1935-2735 VL - 15 IS - 4 SP - e0009288 PB - Public Library of Science (PLoS) ER - TY - JOUR A1 - Kagel, Heike A1 - Frohme, Marcus A1 - Glökler, Jörn T1 - Photoacids in biochemical applications JF - Journal of Cellular Biotechnology N2 - BACKGROUND: After excitation with light photoacids can change the pH in a solution by release of a proton. They have been used mostly for excited state proton transfer studies. In this review the general functionality and mechanisms and the subdivision of photoacids is explained. STATE OF THE ART: Different uses of photoacids are described, covering a wide range of various biochemical topics, focusing on biochemical applications. Examples for the introduced subdivisions are covered. CONCLUSIONS AND OUTLOOK: The areas in which photoacids can be employed are diverse. Photoacids have a promising future in biotechnology and biochemistry and should be considered for upcoming applications, especially in non-invasive control of biochemical reactions. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16123 SN - 2352-3697 VL - 4 IS - 1-2 SP - 23 EP - 30 PB - IOS Press ER - TY - GEN A1 - Michel, Stephanie A1 - Jork, Nadine A1 - Rockmann, Christian A1 - Grohme, Markus A1 - Franke, Philipp A1 - Menzel, Detlef A1 - Frohme, Marcus T1 - Charakterisierung des mikrobiellen Symbioms von Blutegeln T2 - Wissenschaftliche Beiträge 2013 N2 - Die medizinischen Blutegel, Hirudo medicinalis und Hirudo verbana, werden wegen ihrer kurativen Wirkung in der Humanmedizin angewandt. Während des Blutsaugens injizieren sie über ihren Speichel eine Vielzahl bioaktiver, derzeit noch unbekannter Moleküle. Eine vollständige Aufklärung aller Inhaltsstoffe mit Wirkmechanismen ist für die Entwicklung von neuen Pharmaka von großem Interesse. Vor diesem Hintergrund wurden verschiedene Organe beider Arten auf ihre Besiedlung durch symbiontische Bakterien untersucht. Dazu wurden die Bakterien zunächst unter geeigneten Bedingungen kultiviert und mittels biochemischer Methoden charakterisiert. Die Identifizierung der Symbionten erfolgte durch Polymerasekettenreaktion (PCR) und Sequenzierung der 16S rDNA. Die biochemischen Tests ergaben, dass die kultivierbaren Bakterien Amylase positiv, Gram negativ und Ornithin Decarboxylase negativ sind. Mit Hilfe von datenbankgestützten Analysen der 16S rDNA-Sequenzen konnte Aeromonas veronii biovar sobria nachgewiesen werden. Hochdurchsatzsequenzierungen der gesamtgenomischen DNA des Bakteriums aus H. medicinalis zeigten deutliche Abweichungen zum Referenzgenom von Aeromonas veronii B565. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-3084 SN - 0949-8214 VL - 17 SP - 8 EP - 12 ER - TY - GEN A1 - Sinning, Denise A1 - Köhler, Kernt A1 - Litzke, Lutz-Ferdinand A1 - Schönian, Gabriele A1 - Frohme, Marcus A1 - Kuhls, Katrin T1 - Leishmania siamensis als Erreger von autochthoner kutaner Leishmaniose bei Pferden in Deutschland - eine neue Infektionskrankheit in Mitteleuropa? T2 - Wissenschaftliche Beiträge 2014 N2 - Aus mitteleuropäischer Sicht ist die durch Parasiten verursachte und von Sandmücken übertragene Leishmaniose eine in Ländern tropischer und subtropischer Regionen auftretende Infektionskrankheit. In zunehmendem Maße werden jedoch autochthone Fälle in Mitteleuropa, insbesondere in Süddeutschland, verzeichnet. Dies ist vermutlich auf die globale Erwärmung und die Ausdehnung des Verbreitungsgebietes der Sandmücken nach Norden zurückzuführen. Die vorliegende Arbeit befasst sich mit der Identifizierung und phylogenetischen Charakterisierung der Erreger dieser Fälle. Dazu wurden verschiedene Marker im Leishmaniengenom sequenziert und mit bekannten Arten verglichen. Die untersuchte DNA stammte von autochthonen kutanen Leishmaniosen bei Pferden und einem Rind, die in den letzten zehn Jahren in Deutschland und der Schweiz auftraten. Aufgrund identischer Sequenzen konnten die Parasiten als L. siamensis identifiziert bzw. verifiziert werden, eine erst im Jahr 2008 neu beschriebene Art, die in Thailand humane viszerale Leishmaniose verursacht. Die phylogenetischen Analysen zeigten die Ähnlichkeit von L. siamensis mit weiteren bisher nicht identifizierten Stämmen aus Martinique und Ghana, die kutane Leishmaniose bei Menschen verursachen. Um die Frage zu beantworten, ob sich die Leishmaniose zu einer in Mitteleuropa endemischen zoonotischen Krankheit entwickeln könnte, müssen weitere Studien über kompatible Vektoren, mögliche Reservoire und zur Virulenz durchgeführt werden. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-3295 SN - 0949-8214 VL - 18 SP - 17 EP - 25 ER - TY - GEN A1 - Lange, Janine A1 - Messaoudi, Hamza A1 - Das, Susanta Kumar A1 - Grunwald, Rüdiger A1 - Schrader, Sigurd A1 - Frohme, Marcus A1 - Heinrich, Friedhelm T1 - Analyse komplexer biologischer Proben mittels oberflächenverstärkter Ramanspektroskopie (SERS) T2 - Wissenschaftliche Beiträge 2014 N2 - Diese Studie beschäftigt sich mit dem Nachweis biologischer Proben mit Hilfe der Raman-Mikroskopie. Um ausreichende Signalintensitäten auch bei niedrigen Konzentrationen zu erhalten, wurde insbesondere der Effekt der oberflächenverstärkten Raman-Streuung (SERS) näher untersucht. Als Proben dienten DNA aus Hering-Sperma und das Protein Albumin. Zur Verstärkung des Raman-Spektrums wurden zwei unterschiedliche Methoden verwendet. Zum Einen wurden in einem chemischen Reduktionsprozess Nanosilberpartikel hergestellt und den biologischen Proben zugemischt. Zum Anderen wurden mit Hilfe laserangeregter periodischer Oberflächenstrukturierung (LIPSS) erzeugte nanostrukturierte Silberoberflächen als Substrate für die Proben verwendet. Diese Methode wurde bislang nicht für die SERS-Analyse biologischer Proben eingesetzt. Erste hier präsentierte Messungen zeigen, dass beide Verfahren signifikante SERS-Verstärkungen liefern und potentiell leistungsstarke Methoden für die zerstörungsfreie Analyse biologischer Proben darstellen. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-3300 SN - 0949-8214 VL - 18 SP - 27 EP - 32 ER - TY - CHAP A1 - Chumachenko, Dmytro A1 - Nechyporenko, Alina A1 - Frohme, Marcus ED - Shakhovska, Natalia ED - Chrétien, Stéphane ED - Izonin, Ivan ED - Campos, Jaime T1 - Impact of Russian War on COVID-19 Dynamics in Germany: the Simulation Study by Statistical Machine Learning T2 - Proceedings of the 5th International Conference on Informatics & Data-Driven Medicine, Lyon, France, November 18 - 20, 2022 N2 - The new coronavirus COVID-19 has been spreading worldwide for almost three years. The global community has developed effective measures to contain and control the pandemic. However, new factors are emerging that are driving the dynamics of COVID-19. One of these factors was the escalation of Russia's war in Ukraine. This study aims to test the hypothesis of the influence of migration flows caused by the Russian war in Ukraine on the dynamics of the epidemic process in Germany. For this, a model of the COVID-19 epidemic process was built based on the polynomial regression method. The model's adequacy was tested 30 days before the start of the escalation of the Russian war in Ukraine. To assess the impact of the war on the dynamics of COVID-19, the model was used to calculate the forecast of cumulative new and fatal cases of COVID-19 in Germany in the first 30 days after the start of the escalation of the Russian war in Ukraine. Modeling showed that migration flows from Ukraine are not a critical factor in the growth of the dynamics of the incidence of COVID-19 in Germany, but they influenced the number of cases. The next stage of the study is the development of more complex models for a detailed analysis of population dynamics, identifying factors influencing the epidemic process in the context of the Russian war in Ukraine, and assessing their information content. KW - epidemic model KW - machine learning KW - polynomial regression KW - war KW - COVID-19 KW - infectious disease simulation Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19074 UR - https://ceur-ws.org/Vol-3302/short4.pdf VL - 3302 SP - 78 EP - 85 PB - RWTH Aachen 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 - Alekseeva, Victoriia A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Gargin, Vitaliy A1 - Meniailov, Ievgen A1 - Chumachenko, Dmytro T1 - Intelligent Decision Support System for Differential Diagnosis of Chronic Odontogenic Rhinosinusitis Based on U-Net Segmentation JF - Electronics N2 - The share of chronic odontogenic rhinosinusitis is 40% among all chronic rhinosinusitis. Using automated information systems for differential diagnosis will improve the efficiency of decision-making by doctors in diagnosing chronic odontogenic rhinosinusitis. Therefore, this study aimed to develop an intelligent decision support system for the differential diagnosis of chronic odontogenic rhinosinusitis based on computer vision methods. A dataset was collected and processed, including 162 MSCT images. A deep learning model for image segmentation was developed. A 23 convolutional layer U-Net network architecture has been used for the segmentation of multi-spiral computed tomography (MSCT) data with odontogenic maxillary sinusitis. The proposed model is implemented in such a way that each pair of repeated 3 × 3 convolutions layers is followed by an Exponential Linear Unit instead of a Rectified Linear Unit as an activation function. The model showed an accuracy of 90.09%. To develop a decision support system, an intelligent chatbot allows the user to conduct an automated patient survey and collect patient examination data from several doctors of various profiles. The intelligent information system proposed in this study made it possible to combine an image processing model with a patient interview and examination data, improving physician decision-making efficiency in the differential diagnosis of Chronic Odontogenic Rhinosinusitis. The proposed solution is the first comprehensive solution in this area. KW - CT data KW - deep learning KW - image segmentation KW - U-Net KW - decision support system KW - chronic odontogenic rhinosinusitis KW - machine learning KW - artificial intelligence Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17088 SN - 2079-9292 VL - 12 IS - 5 PB - MDPI ER - TY - CHAP A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Omelchenko, Vladyslav A1 - Alekseeva, Victoriia A1 - Lupyr, Andrii A1 - Gargin, Vitaliy ED - Shakhovska, Natalia ED - Kovác, Michal ED - Izonin, Ivan ED - Chrétien, Stéphane T1 - Identification of Personality Based on the Sphenoid Sinus Structure Using Machine Learning T2 - Proceedings of the 6th International Conference on Informatics & Data-Driven Medicine, Bratislava, Slovakia, November 17-19, 2023 N2 - The aim of our study is to develop a new, simple, and effective method for identification of personality based on the characteristics of the sphenoid sinus structure, using machine learning for subsequent implementation into routine medical practice in Ukraine. The study involved 200 multislice computed tomography (MSCT) scans of individuals of various genders and ages. During the study, we obtained results with an accuracy exceeding 70%. KW - identification of personality KW - multislice computed tomography KW - deep learning Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-3609-1 UR - https://ceur-ws.org/Vol-3609/short2.pdf VL - 3609 SP - 167 EP - 173 PB - CEUR-WS.org 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 - 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 - tardigrade 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 - Grebinyk, Anna A1 - Yashchuk, Valeriy A1 - Bashmakova, Nataliya A1 - Gryn, Dmytro A1 - Hagemann, Tobias A1 - Naumenko, Antonina A1 - Kutsevol, Nataliya A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - A New Triple System DNA-Nanosilver-Berberine for Cancer Therapy JF - Applied Nanoscience N2 - The isoquinoline quaternary alkaloid Berberine possesses a variety of pharmacological properties that suggests its promising application for an anticancer delivery system design utilizing its ability to intercalate DNA.In the current work we have investigated the effects of Berberine on the human T-cell leukemia cell line in vitro.Fluorescent microscopy of leukemic cells revealed Berberine nuclear localization. The results showed that Berberine inhibited leukemic cell growth in a time-and dose-dependent manner, that was associated with reactive oxygen species production intensification and caspase 3/7 activity increase with followed apoptosis induction.Berberine was used as a toxic and phototoxic agent for triple system synthesis along with DNA as a carrier and nanosilver as a plasmonic accelerator of Berberine electronic transitions and high energy emission absorbent centers.The proposed method allows to obtain the complex of DNA with Berberine molecules and silver nanopoarticles. The optical properties of free components as well as their various combinations, including the final triple system DNA-Nanosilver-Berberine, were investigated. Obtained results support the possibility to use the triple system DNA-Nanosilver-Berberine as an alternative therapeutic agent for cancer treatment. KW - berberine KW - apoptosis KW - nanosilver KW - DNA delivery system Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10628 SN - 2190-5517 ER - TY - GEN A1 - Gossing, Wilhelm A1 - Radke, Lars A1 - Frohme, Marcus A1 - Biering, Henrik T1 - ECS-Komplex – ein neuer Biomarker bei Wachstumshormonstörungen? T2 - Wissenschaftliche Beiträge 2016 N2 - Störungen im Metabolismus des Wachstumshormons können sich als Wachstumshormonmangel oder -überschuss (Akromegalie) äußern. In beiden Fällen handelt es sich um seltene Krankheiten, die aufwendig behandelt werden müssen, da jeder Patient anders auf seine jeweilige Medikation anspricht. Zur Bestimmung des individuellen Ansprechverhaltens auf die medikamentöse Behandlung wird Insulin-like Growth Factor 1 verwendet, das jedoch als unzuverlässig für die Therapiekontrolle gilt. Um die Diagnostik und Therapie von Wachstumshormonstörungen zu verbessern, wurde in dieser Pilotstudie der Nutzen des neuen potenziellen Biomarkers Elongin B/C-Cullin5-Socs-box Komplex (ECS-Komplex) überprüft. Die fünf Proteine des Komplexes üben zusammen einen negativen Feedback-Mechanismus auf den Wachstumshormonrezeptor aus und regulieren ihn in Abhängigkeit vom Wachstumshormonspiegel im Blut. Für diese Pilotstudie wurden vier Patienten mit Wachstumshormondefizienz und 15 Patienten mit Akromegalie rekrutiert. Die Messung von Unterschieden in der Expression der Gene auf RNA-Ebene in Blutproben der Patienten erlaubt erste Aussagen über deren Eignung als therapeutische Marker für diese Krankheiten. N2 - Growth hormone (GH) dysfunctions can occur as a GH-deficiency (GHD) or an overproduction of GH, leading to acromegaly. Both are rare diseases, which have to be treated for many years before the correct individual dosage is found and a mitigation of symptoms can be achieved. Current medical therapy is determined by the levels of the insulin-like growth factor-1, which is considered to be an unreliable theranostic tool. In order to improve the diagnosis and therapy of patients with GH-dysfunctions, we investigated the benefits of the novel potential biomarker Elongin B/C-Cullin5-Socs-box complex (ECS-complex). Together, these proteins regulate the growth hormone receptor levels according to the blood GH concentration through a negative feedback loop. For this study, we were able to recruit four patients with a GHD and 15 patients with acromegaly. The detected differential expression of the ECS-complex in patients with growth hormone dysfunctions allows for first conclusions about the potential of those proteins as predictive biomarker molecules for individualized therapies. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5308 SN - 0949-8214 VL - 20 SP - 23 EP - 29 ER - TY - JOUR A1 - Kober, Liane A1 - Meyer-Alert, Henriette A1 - Grienitz, Desirée A1 - Hollert, Henner A1 - Frohme, Marcus T1 - Intact cell mass spectrometry as a rapid and specific tool for the differentiation of toxic effects in cell-based ecotoxicological test systems JF - Analytical and Bioanalytical Chemistry N2 - In the last few decades, MALDI-TOF MS has become a useful technique not only in proteomics, but also as a fast and specific tool for whole cell analysis through intact cell mass spectrometry (IC-MS). The present study evaluated IC-MS as a novel tool for the detection of distinct patterns that can be observed after exposure to a certain toxin or concentration by utilizing the eukaryotic fish cell line RTL-W1. Two different viability assays were performed to define the range for IC-MS investigations, each of which employing copper sulfate, acridine, and β-naphthoflavone (BNF) as model compounds for several classes of environmental toxins. The IC-MS of RTL-W1 cells revealed not only specific spectral patterns for the various toxins, but also that the concentration used had an effect on RTL-W1 profiles. After the exposure with copper sulfate and acridine, the spectra of RTL-W1 showed a significant increase of certain peaks in the higher mass range (m/z >7000), which is probably attributed to the apoptosis of RTL-W1. On the contrary, exposure to BNF showed a distinct change of ion abundances only in the lower mass range (m/z <7000). Furthermore, a set of mass peaks could be identified as a specific biomarker for a single toxin treatment, so IC-MS demonstrates a new method for the distinction of toxic effects in fish cells. Due to fast sample preparation and high throughput, IC-MS offers great potential for ecotoxicological studies to investigate cellular effects of different substances and complex environmental samples. KW - RTL-W1 KW - intact cell mass spectrometry KW - MALDI KW - acridine KW - β-Naphthoflavone KW - copper sulfate Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5900 SN - 1618-2650 VL - 407 IS - 25 SP - 7721 EP - 7731 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 - 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 - 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 - http://iiste.org/Journals/index.php/FSQM/article/view/39645 SN - 2225-0557 VL - 69 SP - 44 EP - 52 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 - 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 - 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 - Pfeil, Juliane A1 - Siptroth, Julienne A1 - Pospisil, Heike A1 - Frohme, Marcus A1 - Hufert, Frank T. A1 - Moskalenko, Olga A1 - Yateem, Murad A1 - Nechyporenko, Alina T1 - Classification of Microbiome Data from Type 2 Diabetes Mellitus Individuals with Deep Learning Image Recognition JF - Big Data and Cognitive Computing N2 - Microbiomic analysis of human gut samples is a beneficial tool to examine the general well-being and various health conditions. The balance of the intestinal flora is important to prevent chronic gut infections and adiposity, as well as pathological alterations connected to various diseases. The evaluation of microbiome data based on next-generation sequencing (NGS) is complex and their interpretation is often challenging and can be ambiguous. Therefore, we developed an innovative approach for the examination and classification of microbiomic data into healthy and diseased by visualizing the data as a radial heatmap in order to apply deep learning (DL) image classification. The differentiation between 674 healthy and 272 type 2 diabetes mellitus (T2D) samples was chosen as a proof of concept. The residual network with 50 layers (ResNet-50) image classification model was trained and optimized, providing discrimination with 96% accuracy. Samples from healthy persons were detected with a specificity of 97% and those from T2D individuals with a sensitivity of 92%. Image classification using DL of NGS microbiome data enables precise discrimination between healthy and diabetic individuals. In the future, this tool could enable classification of different diseases and imbalances of the gut microbiome and their causative genera. KW - human intestinal microbiome KW - next-generation sequencing KW - type 2 diabetes KW - deep learning KW - image classification Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17184 SN - 2504-2289 VL - 7 IS - 1 PB - MDPI 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 - 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 - Sukiasyan, Anna A1 - Keshishyan, Ara A1 - Manukyan, Dezdemonia A1 - Melik-Andreasyan, Gayane A1 - Atshemyan, Liana A1 - Apresyan, Hripsime A1 - Strelkova, Margarita V. A1 - Frohme, Marcus A1 - Cortes, Sofia A1 - Kuhls, Katrin T1 - Re-Emerging Foci of Visceral Leishmaniasis in Armenia – First Molecular Diagnosis of Clinical Samples JF - Parasitology N2 - Visceral leishmaniasis (VL) was firstly reported in Armenia in 1913. Following a considerable increase of the number of cases until the mid 1950s, the diseases disappeared after 1969 and re-emerged in 1999. Scientific literature about VL in Armenia is available only in Russian or Armenian. This paper presents a historical overview about leishmaniasis in Armenia based on this literature as well as an epidemiological update since the re-emergence of the disease. In 1999- 2016, 116 indigenous VL cases were recorded mainly in children in 8 of the 11 districts, however VL is underreported because of lack of trained medical personal and diagnostic facilities. The aim of this work was to apply for the first time molecular diagnosis of VL in Armenia. Out of 25 VL suspected patients, 22 were positive by microscopy and PCR. Genotyping using ITS1-PCR-RFLP and sequencing identified the causative agent of VL in Armenia as Leishmania infantum. The present work is an important step towards the inclusion of molecular techniques in the current diagnosis of VL in Armenia and the establishment of local molecular diagnostic facilities. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12018 SN - 1469-8161 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 - GEN A1 - Gering, Vanessa A1 - Kober, Liane A1 - Brödel, Oliver A1 - Koskei, Richard A1 - Mugendi, Beatrice A1 - Frohme, Marcus T1 - LC-MS/MS als Methode zur Detektion und Quantifizierung der Inhaltsstoffe in Kaffee T2 - Wissenschaftliche Beiträge 2017 N2 - Kaffee ist das wohl populärste Heißgetränk weltweit. Zwei botanische Arten sind für den Weltmarkt von Bedeutung und unterscheiden sich bezüglich ihres Anbaugebietes und der Inhaltsstoffe. Kaffee enthält über 850 bisher identifizierte Aromastoffe, welche den Geschmack bilden. Außerdem haben die Prozessierung der geernteten Kirsche bis zur Bohne, das Röstprofil und das Aufbrühen einen großen Einfluss darauf. In dieser Arbeit wurde die Auswirkung der Prozessierungsmethode auf ausgewählte Inhaltsstoffe mit Hilfe der Flüsssig-Chromatographie-Tandem-Massenspektroskopie (LC-MS/MS) untersucht. Dafür wurden drei Prozessierungsmethoden, die unterschiedlich viel Wasser für das Ablösen des Fruchtfleisches von den Kaffeekirschen benötigen, und zwei Kultursorten miteinander verglichen. Die Ergebnisse zeigten einen geringfügig höheren Gehalt der zwei wichtigsten Inhaltsstoffe Koffein und Chlorogensäure in den Bohnen, bei deren Prozessierung im Eco-Pulper-Verfahren weniger Wasser eingesetzt wurde. Bis auf einen verringerten Gehalt an Saccharose wurde für weitere wichtige Inhaltsstoffe (Acrylamid, Niacin, Zitronensäure und Vanillin) kein signifikanter Unterschied bei höherem Wassereinsatz gefunden. Insofern man die untersuchten Inhaltsstoffe als Qualitätsmarker betrachtet, ist im Vergleich zu den anderen Prozessierungsmethoden das Eco-Pulper-Verfahren die beste Wahl, insbesondere da es als wassersparende Methode einen entscheidenden Beitrag zur Nachhaltigkeit des Kaffeeanbaus leistet. N2 - Coffee is the most popular soft drink in the world. Two botanical species of coffee are important for the world market and differ not only in their area of cultivation but also their components. Coffee contains more than 850 aromatic compounds which constitute its taste and flavour. Also, the method selected for the processing from the harvested cherry to the bean, the roasting profile, and the method of brewing are relevant. In this work, liquid chromatography tandem-mass-spectroscopy (LC-MS/MS) is used to investigate how the processing method influences selected aromatic compounds. Thus, three different processing methods differing in the amount of water needed for separating the coffee beans from the cherries, and two cultivars were compared. The results showed slightly higher concentrations of the caffeine and chlorogenic acid components in coffee processed with less water (the eco-pulper method). Apart from a reduced sucrose concentration, we found no significant difference in other important compounds (acrylamide, niacin, citric acid and vanillin) when plenty of water was used. Taking the investigated compounds as quality markers, the eco-pulper method is the best choice among the processing methods, especially since it conserves water, which could therefore significantly contribute to a sustainable cultivation of coffee. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9362 SN - 0949-8214 VL - 21 SP - 7 EP - 12 ER - TY - GEN A1 - Kober, Liane A1 - Hanschke, Christian A1 - Macholz, Rainer A1 - Frohme, Marcus T1 - Die einfache Extraktion und Quantifizierung von sprengstofftypischen Verbindungen in Bodenproben über LC-MS/MS T2 - Wissenschaftliche Beiträge 2018 N2 - Die Kontamination von Flächen mit Rüstungsaltlasten durch sprengstofftypische Verbindungen (STV) wie 2,4,6-Trinitrotoluol (TNT) ist nach wie vor ein großes Risiko für Gesundheit und Umwelt. Die Hochdruckflüssigchromatographie (HPLC) ist in Kombination mit der Tandem-Massenspektrometrie (MS/MS) ein besonders sensitives und exaktes Verfahren zur Konzentrationsbestimmung derartiger Umweltkontaminanten. Jedoch benötigen die derzeit eingesetzten Methoden zur Extraktion und Quantifizierung viel Zeit und Bodenmaterial. Wir haben daher eine 20-minütige LC-MS/MS-Methode entwickelt, die in einer Probe simultan acht STV qualitativ und quantitativ nachweisen kann. Im Vergleich zur EPA-Referenzmethode konnte bei der Extraktion die eingesetzte Bodenmenge von 10 g auf 2 g reduziert und die Extraktionsdauer von 18 h auf 30 min verkürzt werden. Die abschließende Validierung zeigte eine gute Reproduzierbarkeit und mit etablierten Protokollen vergleichbare Detektions- (LOD) und Quantifizierungslimits (LOQ), so dass die optimierten Methoden für eine schnelle und zuverlässige Analyse von Realproben eingesetzt werden konnten. N2 - Soil contamination on former military sites with explosives-related compounds (STV) such as 2,4,6-trinitrotoluene (TNT) is still a major health and environmental threat. High pressure liquid chromatography (HPLC) combined with tandem mass spectrometry (MS/MS) is a very sensitive and precise method to detect such environmental contaminants. However, currently used extraction and quantification methods often need a long time and a high sample amount. Thus, we developed an LC-MS/MS method that detects and quantifies eight explosives simultaneously in only 20 min. Compared to the EPA reference method, the amount of soil was reduced from 10 g to 2 g and the extraction time shortened from 18 h to 30 min. The validation revealed a good reproducibility of the fast analysis process. Limits of detection (LOD) and quantification (LOQ) were comparable to established protocols. Hence, the optimized methods were used for a fast and reliable quantification of STV in soil samples of a former military site. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10219 SN - 0949-8214 VL - 22 SP - 7 EP - 16 ER - TY - JOUR A1 - Sandig, Grit A1 - von Horsten, Hans Henning A1 - Radke, Lars A1 - Blanchard, Véronique A1 - Frohme, Marcus A1 - Giese, Christoph A1 - Sandig, Volker A1 - Hinderlich, Stephan T1 - Engineering of CHO Cells for the Production of Recombinant Glycoprotein Vaccines with Xylosylated N-glycans JF - Bioengineering N2 - Xylose is a general component of O-glycans in mammals. Core-xylosylation of N-glycans is only found in plants and helminth. Consequently, xylosylated N-glycans cause immunological response in humans. We have used the F-protein of the human respiratory syncytial virus (RSV), one of the main causes of respiratory tract infection in infants and elderly, as a model protein for vaccination. The RSV-F protein was expressed in CHO-DG44 cells, which were further modified by co-expression of β1,2-xylosyltransferase from Nicotiana tabacum. Xylosylation of RSV-F N-glycans was shown by monosaccharide analysis and MALDI-TOF mass spectrometry. In immunogenic studies with a human artificial lymph node model, the engineered RSV-F protein revealed improved vaccination efficacy. KW - CHO KW - glycoengineering KW - respiratory syncytial virus KW - vaccine KW - xylose Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9620 SN - 2306-5354 VL - 4 IS - 2 ER - TY - JOUR A1 - Gossing, Wilhelm A1 - Radke, Lars A1 - Biering, Henrik A1 - Diederich, Sven A1 - Mai, Knut A1 - Frohme, Marcus T1 - The ElonginB/C-Cullin5-SOCS-Box-Complex Is a Potential Biomarker for Growth Hormone Disorders JF - Biomedicines N2 - Insulin-like growth factor 1 (IGF-1) is the standard biochemical marker for the diagnosis and treatment control of acromegaly and growth hormone deficiency (GHD). However, its limitations necessitate the screening for new specific and sensitive biomarkers. The elonginB/C-cullin5-SOCS-box-complex (ECS-complex) (an intracellular five-protein complex) is stimulated by circulating growth hormone (GH) and regulates GH receptor levels through a negative feedback loop. It mediates the cells’ sensitivity for GH and therefore, represents a potent new biomarker for those diseases. In this study, individual ECS-complex proteins were measured in whole blood samples of patients with acromegaly (n = 32) or GHD (n = 12) via ELISA and compared to controls. Hierarchical clustering of the results revealed that by combining the three ECS-complex proteins suppressor of cytokine signaling 2 (SOCS2), cullin-5 and ring-box protein 2 (Rbx-2), 93% of patient samples could be separated from controls, despite many patients having a normal IGF-1 or not receiving medical treatment. SOCS2 showed the best individual diagnostic performance with an overall accuracy of 0.93, while the combination of the three proteins correctly identified all patients and controls. This resulted in perfect sensitivity and specificity for all patient groups, which demonstrates potential benefits of the ECS-complex proteins as clinical biomarkers for the diagnostics of GH-related diseases and substantiates their important role in GH metabolism. KW - acromegaly KW - growth hormone deficiency KW - biomarker KW - SOCS2 KW - liquid biopsy KW - pituitary Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13802 SN - 2227-9059 VL - 9 IS - 2 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 - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grynyuk, I. A1 - Kolp, Benjamin A1 - Hurmach, V. A1 - Sliva, T. A1 - Amirkhanov, V. 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 - Prylutska, Svitlana A1 - Grynyuk, I. A1 - Grebinyk, Anna A1 - Hurmach, V. A1 - Shatrava, Iu. A1 - Sliva, T. A1 - Amirkhanov, V. 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 - CHAP A1 - Messaoudi, Hamza A1 - Das, Susanta Kumar A1 - Lange, Janine A1 - Heinrich, Friedhelm A1 - Schrader, Sigurd A1 - Frohme, Marcus A1 - Grunwald, Rüdiger T1 - Femtosecond laser induced nanostructuring for surface enhanced Raman spectroscopy N2 - The formation of periodical nanostructures with femtosecond laser pulses was used to create highly efficient substrates for surface-enhanced Raman spectroscopy (SERS). We report about the structuring of silver and copper substrates and their application to the SERS of DNA (herring sperm) and protein molecules (egg albumen). The maximum enhancement factors were found on Ag substrates processed with the second harmonic generation (SHG) of a 1-kHz Ti:sapphire laser and structure periods near the SHG wavelength. In the case of copper, however, the highest enhancement was obtained with long-period ripples induced with at fundamental wavelength. This is explained by an additional significant influence of nanoparticles on the surface. Nanostructured areas in the range of 1.25 mm2 were obtained in 10 s. The surfaces were characterized by scanning electron microscopy, Fast Fourier Transform and Raman spectroscopy. Moreover, the role of the chemical modification of the metal structures is addressed. Thin oxide layers resulting from working in atmosphere which improve the biocompatibility were indicated by vibration spectra. It is expected that the detailed study of the mechanisms of laser-induced nanostructure formation will stimulate further applications of functionalized surfaces like photocatalysis, selective chemistry and nano-biology. KW - laser-induced periodic surface structure KW - surface enhanced Raman spectroscopy KW - SERS KW - metal nanostructure KW - bio-molecule KW - DNA KW - femtosecond laser KW - ultrashort pulse Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15252 SP - 61 EP - 68 PB - Society of Photo-Optical Instrumentation Engineers (SPIE) 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 - Fischbach, Jens A1 - Loh, Qiuting A1 - Bier, Frank Fabian A1 - Lim, Theam Soon A1 - Frohme, Marcus A1 - Glökler, Jörn T1 - Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method JF - Scientific Reports N2 - We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate. KW - biochemical assay KW - fluorescent dye KW - screening Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9248 SN - 2045-2322 VL - 7 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 - 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 - 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 - CHAP A1 - Alekseeva, Victoriia A1 - Reshetnik, Viktor A1 - Frohme, Marcus A1 - Kachailo, Irina A1 - Murizyna, Irina A1 - Nechyporenko, Alina ED - Chumachenko, Dmytro ED - Kaur, Jasleen ED - Yakovlev, Sergiy ED - Morita, Plinio P. T1 - Investigation of the Impact of Insulin Resistance on the Bone Density of the Upper Wall of the Maxillary Sinus T2 - Proceedings of the 3rd International Workshop of IT-professionals on Artificial Intelligence, ProfIT AI 2023, Waterloo, Canada, November 20-22, 2023 N2 - The aim of our study was to investigate the impact of insulin resistance on the bone density of the upper wall of the maxillary sinus. Materials and Methods: The study included 100 female participants aged 18 to 44 years, divided into two groups. The first group consisted of individuals with insulin resistance, while the control group comprised individuals without signs of insulin resistance. In each group, we conducted an investigation of the radiological density of the upper wall of the maxillary sinus using uncertainty calculations. Results of the study suggest a potential influence of insulin resistance on the density of bone tissue around the nasal sinuses, specifically the upper wall of the maxillary sinus in our case. This parameter was found to be minimal in the group of individuals with insulin resistance. It is particularly noteworthy that both minimum and maximum bone density decreased in this group. Conclusions. The research focused on how insulin resistance affects the density of the upper wall of the maxillary sinus. By employing uncertainty calculations, the study revealed that insulin resistance is associated with a decrease in the minimum density of the upper wall of the maxillary sinus. This tendency may act as a catalyst for the emergence of significant inflammatory alterations in the nasal sinuses, serving as a foundation for the initiation of complications. KW - bone density KW - multispiral computer tomography KW - uncertainty KW - paranasal sinus KW - resistance to insulin Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-3641-3 UR - https://ceur-ws.org/Vol-3641/short1.pdf VL - 3641 SP - 216 EP - 223 PB - CEUR-WS.org ER - TY - JOUR A1 - Herkenhoff, Marcos Edgar A1 - Bovolenta, Luiz A. A1 - Brödel, Oliver A1 - dos Santos, Lucilene D. 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 - Radke, Lars A1 - Sandig, Grit A1 - Lubitz, Annika A1 - Schließer, Ulrike A1 - von Horsten, Hans Henning A1 - Blanchard, Véronique A1 - Keil, Karolin A1 - Sandig, Volker A1 - Giese, Christoph A1 - Hummel, Michael A1 - Hinderlich, Stephan A1 - Frohme, Marcus T1 - In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor JF - Bioengineering N2 - Subunit vaccines often require adjuvants to elicit sustained immune activity. Here, a method is described to evaluate the efficacy of single vaccine candidates in the preclinical stage based on cytokine and gene expression analysis. As a model, the recombinant human respiratory syncytial virus (RSV) fusion protein (RSV-F) was produced in CHO cells. For comparison, wild-type and glycoengineered, afucosylated RSV-F were established. Both glycoprotein vaccines were tested in a commercial Human Artificial Lymph Node in vitro model (HuALN®). The analysis of six key cytokines in cell culture supernatants showed well-balanced immune responses for the afucosylated RSV-F, while immune response of wild-type RSV-F was more Th1 accentuated. In particular, stronger and specific secretion of interleukin-4 after each round of re-stimulation underlined higher potency and efficacy of the afucosylated vaccine candidate. Comprehensive gene expression analysis by nCounter gene expression assay confirmed the stronger onset of the immunologic reaction in stimulation experiments with the afucosylated vaccine in comparison to wild-type RSV-F and particularly revealed prominent activation of Th17 related genes, innate immunity, and comprehensive activation of humoral immunity. We, therefore, show that our method is suited to distinguish the potency of two vaccine candidates with minor structural differences. KW - glycoengineering KW - fucosylation KW - RSV KW - F-protein KW - NanoString Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9831 SN - 2306-5354 VL - 4 IS - 3 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 - INPR A1 - Hollmann, Susanne A1 - Kremer, Andreas A1 - Baebler, Špela A1 - Trefois, Christophe A1 - Gruden, Kristina A1 - Rudnicki, Witold R. A1 - Tong, Weida A1 - Gruca, Aleksandra A1 - Bongcam-Rudloff, Erik A1 - Evelo, Chris T. A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Šafránek, David A1 - Regierer, Babette A1 - D'Elia, Domenica T1 - The need for standardisation in life science research - an approach to excellence and trust. [version 1; peer review: 3 approved] T2 - F1000Research N2 - Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation. KW - Open Data KW - Open Access KW - Open Science KW - FAIR Principles KW - standardisation KW - education KW - quality management Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13891 SN - 2046-1402 VL - 9 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 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Buchelnikov, Anatoliy A1 - Tverdokhleb, Nina A1 - Grebinyk, Sergii A1 - Evstigneev, Maxim A1 - Matyshevska, Olga A1 - Cherepanov, Vsevolod A1 - Prylutskyy, Yuriy A1 - Yashchuk, Valeriy A1 - Naumovets, Anton A1 - Ritter, Uwe A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - C60 Fullerene as an Effective Nanoplatform of Alkaloid Berberine Delivery into Leukemic Cells JF - Pharmaceutics N2 - A herbal alkaloid Berberine (Ber), used for centuries in Ayurvedic, Chinese, Middle-Eastern, and native American folk medicines, is nowadays proved to function as a safe anticancer agent. Yet, its poor water solubility, stability, and bioavailability hinder clinical application. In this study, we have explored a nanosized carbon nanoparticle—C60 fullerene (C60)—for optimized Ber delivery into leukemic cells. Water dispersions of noncovalent C60-Ber nanocomplexes in the 1:2, 1:1, and 2:1 molar ratios were prepared. UV–Vis spectroscopy, dynamic light scattering (DLS), and atomic force microscopy (AFM) evidenced a complexation of the Ber cation with the negatively charged C60 molecule. The computer simulation showed that π-stacking dominates in Ber and C60 binding in an aqueous solution. Complexation with C60 was found to promote Ber intracellular uptake. By increasing C60 concentration, the C60-Ber nanocomplexes exhibited higher antiproliferative potential towards CCRF-CEM cells, in accordance with the following order: free Ber < 1:2 < 1:1 < 2:1 (the most toxic). The activation of caspase 3/7 and accumulation in the sub-G1 phase of CCRF-CEM cells treated with C60-Ber nanocomplexes evidenced apoptosis induction. Thus, this study indicates that the fast and easy noncovalent complexation of alkaloid Ber with C60 improved its in vitro efficiency against cancer cells. KW - C60 fullerene KW - berberine KW - noncovalent nanocomplex KW - UV–Vis KW - DLS and AFM measurements KW - drug release KW - leukemic cell KW - uptake KW - cytotoxicity KW - apoptosis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12932 SN - 1999-4923 VL - 11 IS - 11 PB - MDPI ER - 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 - 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 VL - 14 ER -