Der Umgang mit Wissen in F&E-Kooperationen am Beispiel des staatlichen Forschungsförderungsprogramms Kplus

Um Innovationen hervorzubringen, bedarf es Wissen. Unternehmen können dieses Wissen einerseits durch unternehmensinterne Forschung und Entwicklung generieren, andererseits von unternehmensexternen Quellen, wie beispielsweise durch F&E-Kooperationen erwerben. Wird aus gesamtwirtschaftlicher Sicht in bestimmten Fachgebieten zu wenig Forschung und Entwicklung betrieben, kann der Staat mittels Forschungsförderung lenkend eingreifen. In Österreich startete im Jahr 1998 das Kplus-Programm mit dem Ziel, den Wissenstransfer in Kooperationen zwischen Wissenschaft und Wirtschaft zu verstärken. Aus drei Ausschreibungsrunden gingen insgesamt 17 Kplus-Zentren hervor. Die vorliegende Arbeit legt den Schwerpunkt auf den Umgang mit Wissen in den einzelnen Kplus-Zentren in allen Phasen einer Kooperation. Hierfür fand im Zeitraum von Jänner 2009 bis Mai 2009 eine empirische Erhebung unter allen 17 Kplus-Zentren statt. Die Auswertung zeigt nicht nur wie von den Kooperationspartnern der Zugang zu bereits vorhandenem Wissen geregelt wurde, sondern auch die von den Partnern implementierten Maßnahmen zum Wissenstransfer während der siebenjährigen Kooperation. Abschließend wird die Frage beantwortet, ob von den wissenschaftlichen und wirtschaftlichen Partnern in den Kplus-Zentren Verwertungsrechte und Veröffentlichungen der neu gewonnenen Erkenntnisse angestrebt wurden.Innovation needs knowledge. Companies generate knowledge on the one hand, themselves in R&D, and on the other hand via external sources through research and development co-operations for example. If on a macroeconomic level there is too little research and development undertaken in certain scientific domains, the government encourages research via support programmes. In 1998 the Kplus-programme started in Austria with the aim to support cooperative research projects between science and industry. As a result of three calls for tender finally 17 Kplus competence centres started up. This diploma thesis describes the different forms of knowledge transfer in all phases of cooperation. For this purpose, a survey was done among all 17 Kplus competence centres from January to May 2009. Not only does the analysis point out how existing knowledge was regulated among the cooperation partners, but also details measures implemented to enable knowledge transfer throughout the seven year cooperation period. Finally, the question is answered, as to whether the scientific and economic partners in the Kplus centres have pursued exploitation rights and publications of new findings

A comparison between mobile and stationary gas chromatography–mass spectrometry devices for analysis of complex volatile profiles (advance online)

On-site analysis of volatile organic compounds (VOCs) with miniaturized gas chromatography–mass spectrometry (GC–MS)systems is a very rapidly developing field of application. While, on the one hand, major technological advances are improv-ing the availability of these systems on the market, on the other hand, systematic studies to assess the performance of suchinstruments are still lacking. To fill this gap, we compared three portable GC–MS devices to a state-of-the-art benchtop(stationary) system for analysis of a standard mixture of 18 VOCs. We systematically compared analytical parameters suchas the sensitivity and similarity of the signal response pattern and the quality of the obtained mass spectra. We found that theinvestigated mobile instruments (i) showed different response profiles with a generally lower number of identified analytes.Also, (ii) mass spectral reproducibility (% relative standard deviation (RSD) of the relative abundance of selective fragments)was generally worse in the mobile devices (mean RSD for all targeted fragments~9.7% vs. ~3.5% in the stationary system).Furthermore, mobile devices (iii) showed a poorer mass spectral similarity to commercial reference library spectra (>20%deviation of fragment ion relative intensity vs. ~10% in the stationary GC–MS), suggesting a less reliable identification ofanalytes by library search. Indeed, (iv) the performance was better with higher-mass and/or more abundant fragments, whichshould be considered to improve the results of library searches for substance identification. Finally, (v) the estimation ofthe signal-to-noise ratio (S/N) in mobile instruments as a measure of sensitivity revealed a significantly lower performancecompared to the benchtop lab equipment (with a ratio among medians of~8 times lower). Overall, our study reveals not only apoor signal-to-noise ratio and poor reproducibility of the data obtained from mobile instruments, but also unfavorable resultswith respect to a reliable identification of substances when they are applied for complex mixtures of volatiles

Evidence against GB virus C infection in dromedary camels

A recent publication described finding GB virus C (GBV-C) RNA in four of twenty two dromedary camel sera, and sequence analysis found that these viruses were phylogenetically clustered within human GBV-C isolates. Since all other GB viruses to date form monophyletic groups according to their host species, the close relationship between the sequences generated from camel sera and human GBV-C isolates seemed implausible, leading us to conduct an independent analysis of the sequences. Our investigation found three lines of evidence arguing against GBV-C infection in dromedary camels. First, strong evidence of artifactual sequence generation was identified for some of the sequences. Secondly, the sequence diversity within individual camel sera was ten- to one-hundred fifty two-fold greater than that described for GBV-C within a human host. Finally, GBV-C sequences generated from each camel shared near complete identity with human isolates previously described by the same laboratory. Taken together, these data strongly suggest laboratory contamination. We suggest that additional validation experiments are needed before it is possible to conclude that camels are permissive for GBV-C infection

Novel Quantitative Real-Time LCR for the Sensitive Detection of SNP Frequencies in Pooled DNA: Method Development, Evaluation and Application

BACKGROUND: Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. METHODS: The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. CONCLUSIONS: The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. SIGNIFICANCE: The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food

The replication of plastid minicircles involves rolling circle intermediates

Plastid genomes of peridinin-containing dinoflagellates are unique in that its genes are found on multiple circular DNA molecules known as ‘minicircles’ of ∼2–3 kb in size, carrying from one to three genes. The non-coding regions (NCRs) of these minicircles share a conserved core region (250–500 bp) that are AT-rich and have several inverted or direct repeats. Southern blot analysis using an NCR probe, after resolving a dinoflagellate whole DNA extract in pulsed-field gel electrophoresis (PFGE), revealed additional positive bands (APBs) of 6–8 kb in size. APBs preferentially diminished from cells treated with the DNA-replication inhibitor aphidicolin, when compared with 2–3 kb minicircles, implicating they are not large minicircles. The APBs are also exonuclease III-sensitive, implicating the presence of linear DNA. These properties and the migration pattern of the APBs in a 2D-gel electrophoresis were in agreement with a rolling circle type of replication, rather than the bubble-forming type. Atomic force microscopy of 6–8 kb DNA separated by PFGE revealed DNA intermediates with rolling circle shapes. Accumulating data thus supports the involvement of rolling circle intermediates in the replication of the minicircles

The replication of plastid minicircles involves rolling circle intermediates

Plastid genomes of peridinin-containing dinoflagellates are unique in that its genes are found on multiple circular DNA molecules known as ‘minicircles’ of ∼2–3 kb in size, carrying from one to three genes. The non-coding regions (NCRs) of these minicircles share a conserved core region (250–500 bp) that are AT-rich and have several inverted or direct repeats. Southern blot analysis using an NCR probe, after resolving a dinoflagellate whole DNA extract in pulsed-field gel electrophoresis (PFGE), revealed additional positive bands (APBs) of 6–8 kb in size. APBs preferentially diminished from cells treated with the DNA-replication inhibitor aphidicolin, when compared with 2–3 kb minicircles, implicating they are not large minicircles. The APBs are also exonuclease III-sensitive, implicating the presence of linear DNA. These properties and the migration pattern of the APBs in a 2D-gel electrophoresis were in agreement with a rolling circle type of replication, rather than the bubble-forming type. Atomic force microscopy of 6–8 kb DNA separated by PFGE revealed DNA intermediates with rolling circle shapes. Accumulating data thus supports the involvement of rolling circle intermediates in the replication of the minicircles

TbPIF5 Is a Trypanosoma brucei Mitochondrial DNA Helicase Involved in Processing of Minicircle Okazaki Fragments

Trypanosoma brucei's mitochondrial genome, kinetoplast DNA (kDNA), is a giant network of catenated DNA rings. The network consists of a few thousand 1 kb minicircles and several dozen 23 kb maxicircles. Here we report that TbPIF5, one of T. brucei's six mitochondrial proteins related to Saccharomyces cerevisiae mitochondrial DNA helicase ScPIF1, is involved in minicircle lagging strand synthesis. Like its yeast homolog, TbPIF5 is a 5′ to 3′ DNA helicase. Together with other enzymes thought to be involved in Okazaki fragment processing, TbPIF5 localizes in vivo to the antipodal sites flanking the kDNA. Minicircles in wild type cells replicate unidirectionally as theta-structures and are unusual in that Okazaki fragments are not joined until after the progeny minicircles have segregated. We now report that overexpression of TbPIF5 causes premature removal of RNA primers and joining of Okazaki fragments on theta structures. Further elongation of the lagging strand is blocked, but the leading strand is completed and the minicircle progeny, one with a truncated H strand (ranging from 0.1 to 1 kb), are segregated. The minicircles with a truncated H strand electrophorese on an agarose gel as a smear. This replication defect is associated with kinetoplast shrinkage and eventual slowing of cell growth. We propose that TbPIF5 unwinds RNA primers after lagging strand synthesis, thus facilitating processing of Okazaki fragments

Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi

Abstract Kinetoplastid flagellates are known for several unusual features, one of which is their complex mitochondrial genome, known as kinetoplast (k) DNA, composed of mutually catenated maxi- and minicircles. Trypanosoma lewisi is a member of the Stercorarian group of trypanosomes which is, based on human infections and experimental data, now considered a zoonotic pathogen. By assembling a total of 58 minicircle classes, which fall into two distinct categories, we describe a novel type of kDNA organization in T. lewisi. RNA-seq approaches allowed us to map the details of uridine insertion and deletion editing events upon the kDNA transcriptome. Moreover, sequencing of small RNA molecules enabled the identification of 169 unique guide (g) RNA genes, with two differently organized minicircle categories both encoding essential gRNAs. The unprecedented organization of minicircles and gRNAs in T. lewisi broadens our knowledge of the structure and expression of the mitochondrial genomes of these human and animal pathogens. Finally, a scenario describing the evolution of minicircles is presented