7 results on '"Niekamp, Hauke"'
Search Results
2. Intracellular accumulation of subviral HBsAg particles and diminished Nrf2 activation in HBV genotype G expressing cells lead to an increased ROI level
- Author
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Peiffer, Kai-Henrik, Akhras, Sami, Himmelsbach, Kiyoshi, Hassemer, Matthias, Finkernagel, Malin, Carra, Gert, Nuebling, Michael, Chudy, Michael, Niekamp, Hauke, Glebe, Dieter, Sarrazin, Christoph, Zeuzem, Stefan, and Hildt, Eberhard
- Published
- 2015
- Full Text
- View/download PDF
3. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples
- Author
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Arulandhu, Alfred J., primary, Staats, Martijn, additional, Hagelaar, Rico, additional, Voorhuijzen, Marleen M., additional, Prins, Theo W., additional, Scholtens, Ingrid, additional, Costessi, Adalberto, additional, Duijsings, Danny, additional, Rechenmann, François, additional, Gaspar, Frédéric B., additional, Barreto Crespo, Maria Teresa, additional, Holst-Jensen, Arne, additional, Birck, Matthew, additional, Burns, Malcolm, additional, Haynes, Edward, additional, Hochegger, Rupert, additional, Klingl, Alexander, additional, Lundberg, Lisa, additional, Natale, Chiara, additional, Niekamp, Hauke, additional, Perri, Elena, additional, Barbante, Alessandra, additional, Rosec, Jean-Philippe, additional, Seyfarth, Ralf, additional, Sovová, Tereza, additional, Van Moorleghem, Christoff, additional, van Ruth, Saskia, additional, Peelen, Tamara, additional, and Kok, Esther, additional
- Published
- 2017
- Full Text
- View/download PDF
4. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples
- Author
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Arulandhu, Alfred J., Staats, Martijn, Hagelaar, Rico, Voorhuijzen, Marleen M., Prins, Theo W., Scholtens, Ingrid, Costessi, Adalberto, Duijsings, Danny, Rechenmann, François, Gaspar, Frédéric B., Barreto Crespo, Maria Teresa, Holst-Jensen, Arne, Birck, Matthew, Burns, Malcolm, Haynes, Edward, Hochegger, Rupert, Klingl, Alexander, Lundberg, Lisa, Natale, Chiara, Niekamp, Hauke, Perri, Elena, Barbante, Alessandra, Rosec, Jean Philippe, Seyfarth, Ralf, Sovova, Tereza, Van Moorleghem, Christoff, van Ruth, Saskia, Peelen, Tamara, Kok, Esther, Arulandhu, Alfred J., Staats, Martijn, Hagelaar, Rico, Voorhuijzen, Marleen M., Prins, Theo W., Scholtens, Ingrid, Costessi, Adalberto, Duijsings, Danny, Rechenmann, François, Gaspar, Frédéric B., Barreto Crespo, Maria Teresa, Holst-Jensen, Arne, Birck, Matthew, Burns, Malcolm, Haynes, Edward, Hochegger, Rupert, Klingl, Alexander, Lundberg, Lisa, Natale, Chiara, Niekamp, Hauke, Perri, Elena, Barbante, Alessandra, Rosec, Jean Philippe, Seyfarth, Ralf, Sovova, Tereza, Van Moorleghem, Christoff, van Ruth, Saskia, Peelen, Tamara, and Kok, Esther
- Abstract
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
- Published
- 2017
5. Charakterisierung der phänotypischen Resistenz von Hepatitis-B-Virus Mutanten gegenüber antiviralen Nukleosid- und Nukleotidanaloga
- Author
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Niekamp, Hauke and Justus Liebig University Giessen
- Subjects
resistance ,ddc:500 ,overlength constructs ,Resistenz ,Primerdomäne ,HBV ,Überlängenkonstrukte ,primer domain ,Tenofovir - Abstract
Zurzeit sind etwa 240 Mio. Menschen auf der Welt chronisch mit dem Hepatitis-B-Virus (HBV) infiziert. Im Gegensatz zu einer akuten Infektion sollte die chronische Hepatitis B therapiert werden, um das Risiko von oft fatalen Folgeerkrankungen zu minimieren. Die Therapie mit Interferon alpha ist nur bei einem Teil der Patienten erfolgreich. Daher bleibt vielen Patienten nur eine Therapie mit Inhibitoren der viralen Reversen Transkriptase. Diese muss jedoch meist lebenslang erfolgen, da die ungewöhnlich hohe Variabilität dieses DNA-Virus eine Resistenzbildung begünstigt. Deshalb ist eine optimale und individualisierte Therapie von großer Bedeutung. Mithilfe genotypischer Analysen der HBV-Genome können bereits bekannte virale Resistenzmutationen identifiziert und so die antivirale Behandlung angepasst werden. Aber nur mit einer phänotypischen Charakterisierung können neue, bislang unbekannte HBV-Varianten eindeutig identifiziert und mit einer Resistenz verknüpft werden.Der bereits in der Arbeitsgruppe von PD Dr. D. Glebe am Institut für Medizinische Virologie der Universität Gießen etablierte phänotypische Assay zur viralen Resistenzbestimmung des HBV wurde weiter optimiert, um auch für HBV-Mutanten mit sehr geringer Replikation noch verlässlichere und genauere Resistenzdaten ermitteln zu können. Die Verlässlichkeit des verwendeten Assays konnte in einer Ringstudie mit einer ebenfalls am Projekt beteiligten Arbeitsgruppe bestätigt werden.Außerdem wurde eine neue Methode für den Replikationsnachweis von 1.5-fachen Überlängenkonstrukten entwickelt. Zumindest HBV-Isolate mit einer ausreichend starken Replikation können daher jetzt auch unter der vollständigen Kontrolle ihres natürlichen Promotors phänotypisch charakterisiert werden.Im Rahmen eines vom BMBF-geförderten Projekts zur Molekularen Diagnostik (HOPE-Projekt) wurden in dieser Arbeit 26 HBV-Isolate aus chronisch infizierten Patienten auf ihre Resistenz gegen die vier bedeutendsten antiviralen Medikamente (Lamivudin, Adefovir, Entecavir und Tenofovir) getestet. Ein Großteil der Ergebnisse bestätigte die bisherigen Erkenntnisse über die Resistenzentwicklung. Einige Phänotypen konnten jedoch anhand der bekannten Resistenzmutationen nicht erklärt werden. So wurde eine Kreuzresistenz auf Grundlage der Lamivudin-Resistenzmutationen rtM204I/V gegen Adefovir und Tenofovir detektiert, die außerhalb des HOPE-Projekts bisher nicht beschrieben wurde. Außerdem wurde ein vermindertes Ansprechen auf hohe Entecavirkonzentrationen im phänotypischen Assay festgestellt.Die außergewöhnlich hohe Adefovir- und Tenofovirresistenz des bereits zuvor charakterisierten multiresistenten Isolats FvB 150 1 war allein mit den bekannten Mutationen rtA181T und rtN236T nicht zu erklären. Es konnte gezeigt werden, dass neben diesen beiden Mutationen der Austausch T76S in der Primerdomäne für die hohen Resistenzen verantwortlich ist. Damit wurde erstmals ein Aminosäureaustausch außerhalb der Reversen Transkriptase der HBV-Polymerase als Resistenzmutation identifiziert.Unabhängig davon wurden weitere virale Varianten getestet, die in einer kürzlich publizierten Studie beschrieben wurden. Sie wurden gehäuft in Patienten, die während der Therapie einen virologischen Durchbruch der HBV-Infektion erlitten hatten, gefunden und standen daher im Verdacht einen Einfluss auf die Resistenzentwicklung zu haben. Die ermittelten phänotypischen Daten zeigten jedoch, dass es sich bei den Austauschen rtS78T, rtL229F/V und rtM309K wahrscheinlich nicht um Resistenzmutationen handelte., Currently, about 240 million people in the world are chronically infected with the hepatitis B virus. An acute infection does not require a specific therapy, whereas the chronic Hepatitis B has to be treated to minimize the risk of a secondary disease like cirrhosis of the liver and hepatocellular carcinoma. The therapy with interferon alpha is by far not in all cases successful. Therefore, for many patients remain only an inevitable life-long treatment with reverse transcriptase inhibitors. In addition, the high variability of the virus favors the development of resistance. Hence an optimal adapted therapy is very important. Genotypic analyzes can only identify already known resistance mutations. But the clear link of a new mutation to resistance is only possible with the results of a phenotypic characterizationThe already in the group of PD Dr. D. Glebe at the Institute of Medical Virology of the University of Giessen established phenotypic assay for resistance testing was further optimized in order to obtain more reliable and accurate resistance data even with HBV-mutants with very low viral replication. The reliability of the assay was confirmed in a collaborative study with a working group, which is also involved in the project.In addition, a new PCR-based method for the quantification of the viral replication of 1.5-fold HBV over length constructs was developed. With this qPCR at least HBV isolates with a sufficiently strong replication can be characterized under the full control of its natural promoter to analyze its effect of the replication strength.In the context of the BMBF-funded HOPE-project 26 isolates from chronic infected patients were tested for their resistance to the four major antiviral drugs (lamivudine, adefovir, entecavir and tenofovir). The majority of the results confirmed the previous findings on the development of resistance. However, some phenotypes could not be explained based on the known resistance mutations. Thus, cross-resistance was detected on the basis of lamivudine resistance mutations rtM204I/V to adefovir and tenofovir and the phenotypic data showed a reduced response on high entecavir concentrations, which both have not been described outside the HOPE-project before.The extremely high adefovir and tenofovir resistance of the previously characterized multidrug-resistant isolate FvB 150-1 could not be explained solely by the known mutations rtA181T and rtN236T. It could be shown that in addition the substitution T76S located in the priming domain is responsible for this high resistance. The mutation T76S is the first known resistance mutation of HBV, which is located outside of the reverse transcriptase.Regardless of the HOPE-project the influence of some substitutions were tested, which were described in a recently published study. The mutations were found more often in patient with virological breakthrough than in untreated patients. However, the determined phenotypic data showed that the exchanges rtS78T, rtL229F/V and rtM309K probably not acted as resistance mutations.
- Published
- 2013
- Full Text
- View/download PDF
6. Entecavir allows an unexpectedly high residual replication of HBV mutants resistant to lamivudine
- Author
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Geipel, Andreas, Seiz, Pia L., Niekamp, Hauke, Neumann-Fraune, Maria, Zhang, Ke, Kaiser, Rolf, Protzer, Ulrike, Gerlich, Wolfram H., Glebe, Dieter, Geipel, Andreas, Seiz, Pia L., Niekamp, Hauke, Neumann-Fraune, Maria, Zhang, Ke, Kaiser, Rolf, Protzer, Ulrike, Gerlich, Wolfram H., and Glebe, Dieter
- Abstract
Background: Entecavir is an efficient inhibitor of HBV reverse transcriptase (RT) and widely used for therapy of chronic hepatitis B. Entecavir treatment of HBV patients with lamivudine-resistant viral strains, however, often fails, but the mechanism of cross-resistance development is not fully understood. Methods: Using non-linear regression models, dose-response curves of cloned HBV strains from patients pre-treated with RT inhibitors were established in human hepatoma cell lines after transfection with HBV genomes containing HBV polymerase genes from patient isolates. 50% and 90% inhibitory concentrations (IC50 and IC90) and corresponding antiviral resistance factors (RF50 and RF90) were calculated. Results: The entecavir dose-response curve of lamivudine-resistant HBV RT mutants rtM204 for the replication of HBV decreased less than expected with increasing drug dose. Remarkably, due to the flat dose-response curves, RF90 values against entecavir of samples with rtM204 substitutions were up to 30x higher than their RF50 values. Conclusions: The unexpectedly high IC90 indicates a strong residual replication capacity of lamivudine-resistant HBV rtM204 variants under entecavir therapy, although IC50 values are initially within the therapeutic range of entecavir. This characteristic favours rapid selection of additional mutants with overt resistance against entecavir. Thus, the current phenotypic resistance assays should include determination of IC90.
- Published
- 2015
7. Entecavir allows an unexpectedly high residual replication of HBV mutants resistant to lamivudine.
- Author
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Geipel A, Seiz PL, Niekamp H, Neumann-Fraune M, Zhang K, Kaiser R, Protzer U, Gerlich WH, and Glebe D
- Subjects
- Antiviral Agents therapeutic use, Cell Line, Tumor, Cells, Cultured, DNA, Viral, Guanine pharmacology, Guanine therapeutic use, Hepatitis B drug therapy, Humans, Inhibitory Concentration 50, Lamivudine pharmacology, Lamivudine therapeutic use, Microbial Sensitivity Tests, Antiviral Agents pharmacology, Drug Resistance, Viral, Guanine analogs & derivatives, Hepatitis B virology, Hepatitis B virus drug effects, Hepatitis B virus genetics, Mutation, Virus Replication drug effects
- Abstract
Background: Entecavir is an efficient inhibitor of HBV reverse transcriptase (RT) and widely used for therapy of chronic hepatitis B. Entecavir treatment of HBV patients with lamivudine-resistant viral strains, however, often fails, but the mechanism of cross-resistance development is not fully understood., Methods: Using non-linear regression models, dose-response curves of cloned HBV strains from patients pre-treated with RT inhibitors were established in human hepatoma cell lines after transfection with HBV genomes containing HBV polymerase genes from patient isolates. 50% and 90% inhibitory concentrations (IC50 and IC90) and corresponding antiviral resistance factors (RF50 and RF90) were calculated., Results: The entecavir dose-response curve of lamivudine-resistant HBV RT mutants rtM204 for the replication of HBV decreased less than expected with increasing drug dose. Remarkably, due to the flat dose-response curves, RF90 values against entecavir of samples with rtM204 substitutions were up to 30× higher than their RF50 values., Conclusions: The unexpectedly high IC90 indicates a strong residual replication capacity of lamivudine-resistant HBV rtM204 variants under entecavir therapy, although IC50 values are initially within the therapeutic range of entecavir. This characteristic favours rapid selection of additional mutants with overt resistance against entecavir. Thus, the current phenotypic resistance assays should include determination of IC90.
- Published
- 2015
- Full Text
- View/download PDF
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