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1.  Monitoring of adenovirus serotypes in environmental samples by combined PCR and melting point analyses 
Virology Journal  2013;10:190.
Human adenoviruses are promising candidates for addressing health risks associated with enteric viruses in environmental waters. Relatively harmless but common, these DNA viruses persist within the population and are generally considered extremely stable, remaining infectious in water for long periods of time. Group-specific or single species detection of human adenoviruses in environmental samples is usually based on polymerase chain reaction assays. Simultaneous identification of specific species or serotypes needs additional processing. Here we present a simple molecular approach for the monitoring of serotypic diversity in the human adenovirus populations in contaminated water sites.
Diversity patterns of human adenoviruses in environmental samples, collected in an outdoor artificial stream and pond simulation system, were analyzed using a closed tube polymerase chain reaction method with subsequent melting point analysis.
Human adenovirus serotype 41 was the most prominent adenovirus serotype detected in environmental water samples, but melting point analyses indicated the presence of additional adenovirus serotypes.
Based on investigations with spiked and environmental samples, a combination of qPCR and melting point analysis was shown to identify adenovirus serotypes in sewage contaminated water.
PMCID: PMC3706342  PMID: 23758742
Adenovirus; Environment; Melting point analysis; qPCR; Sewage; Viral indicator; Virus stability
2.  The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels 
BMC Genomics  2013;14:185.
The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.
To build the N. furzeri transcript catalogue, thirteen cDNA libraries were sequenced using Sanger, 454/Roche and Solexa/Illumina technologies yielding about 39 Gb. In total, 19,875 protein-coding genes were identified and annotated. Of these, 71% are represented by at least one transcript contig with a complete coding sequence. Further, transcript levels of young and old fish of the strains GRZ and MZM-0403, which differ in lifespan by twofold, were studied by RNA-seq. In skin and brain, 85 differentially expressed genes were detected; these have a role in cell cycle control and proliferation, inflammation and tissue maintenance. An RNA-seq experiment for zebrafish skin confirmed the ageing-related relevance of the findings in N. furzeri. Notably, analyses of transcript levels between zebrafish and N. furzeri but also between N. furzeri strains differed largely, suggesting that ageing is accelerated in the short-lived N. furzeri strain GRZ compared to the longer-lived strain MZM-0403.
We provide a comprehensive, annotated N. furzeri transcript catalogue and a first transcriptome-wide insight into N. furzeri ageing. This data will serve as a basis for future functional studies of ageing-related genes.
PMCID: PMC3605293  PMID: 23496936
Nothobranchius furzeri; Model fish species; Ageing; Transcriptome assembly; Transcript catalogue; Gene expression; RNA-seq
3.  Substrate-mediated effects in photothermal patterning of alkanethiol self-assembled monolayers with microfocused continuous-wave lasers 
In recent years, self-assembled monolayers (SAMs) have been demonstrated to provide promising new approaches to nonlinear laser processing. Most notably, because of their ultrathin nature, indirect excitation mechanisms can be exploited in order to fabricate subwavelength structures. In photothermal processing, for example, microfocused lasers are used to locally heat the substrate surface and initiate desorption or decomposition of the coating. Because of the strongly temperature-dependent desorption kinetics, the overall process is highly nonlinear in the applied laser power. For this reason, subwavelength patterning is feasible employing ordinary continuous-wave lasers. The lateral resolution, generally, depends on both the type of the organic monolayer and the nature of the substrate. In previous studies we reported on photothermal patterning of distinct types of SAMs on Si supports. In this contribution, a systematic study on the impact of the substrate is presented. Alkanethiol SAMs on Au-coated glass and silicon substrates were patterned by using a microfocused laser beam at a wavelength of 532 nm. Temperature calculations and thermokinetic simulations were carried out in order to clarify the processes that determine the performance of the patterning technique. Because of the strongly temperature-dependent thermal conductivity of Si, surface-temperature profiles on Au/Si substrates are very narrow ensuring a particularly high lateral resolution. At a 1/e spot diameter of 2 µm, fabrication of subwavelength structures with diameters of 300–400 nm is feasible. Rapid heat dissipation, though, requires high laser powers. In contrast, patterning of SAMs on Au/glass substrates is strongly affected by the largely distinct heat conduction within the Au film and in the glass support. This results in broad surface temperature profiles. Hence, minimum structure sizes are larger when compared with respective values on Au/Si substrates. The required laser powers, though, are more than one order of magnitude lower. Also, the laser power needed for patterning decreases with decreasing Au layer thickness. These results demonstrate the impact of the substrate on the overall patterning process and provide new perspectives in photothermal laser patterning of ultrathin organic coatings.
PMCID: PMC3304314  PMID: 22428098
femtosecond lasers; nonlinear laser processing; self-assembled monolayers; subwavelength patterning; ultrathin resists
4.  High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research 
Genome Biology  2009;10(2):R16.
A genomic analysis of the annual fish Nothobranchius furzeri, a vertebrate with the shortest known life span in captivity and which may provide a new model organism for aging research.
The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research.
To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred.
Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.
PMCID: PMC2688266  PMID: 19210790
5.  Mapping of quantitative trait loci controlling lifespan in the short-lived fish Nothobranchius furzeri – a new vertebrate model for age research 
Aging Cell  2012;11(2):252-261.
The African annual fish Nothobranchius furzeri emerged as a new model for age research over recent years. Nothobranchius furzeri show an exceptionally short lifespan, age-dependent cognitive/behavioral decline, expression of age-related biomarkers, and susceptibility to lifespan manipulation. In addition, laboratory strains differ largely in lifespan. Here, we set out to study the genetics of lifespan determination. We crossed a short- to a long-lived strain, recorded lifespan, and established polymorphic markers. On the basis of genotypes of 411 marker loci in 404 F2 progeny, we built a genetic map comprising 355 markers at an average spacing of 5.5 cM, 22 linkage groups (LGs) and 1965 cM. By combining marker data with lifespan values, we identified one genome-wide highly significant quantitative trait locus (QTL) on LG 9 (P < 0.01), which explained 11.3% of the F2 lifespan variance, and three suggestive QTLs on LG 11, 14, and 17. We characterized the highly significant QTL by synteny analysis, because a genome sequence of N. furzeri was not available. We located the syntenic region on medaka chromosome 5, identified candidate genes, and performed fine mapping, resulting in a c. 40% reduction of the initial 95% confidence interval. We show both that lifespan determination in N. furzeri is polygenic, and that candidate gene detection is easily feasible by cross-species analysis. Our work provides first results on the way to identify loci controlling lifespan in N. furzeri and illustrates the potential of this vertebrate species as a genetic model for age research.
PMCID: PMC3437503  PMID: 22221414
lifespan; Nothobranchius furzeri; genetic linkage map; QTL mapping; synteny

Results 1-5 (5)