Taxonomic classification of metagenomic sequences

Gerlach W. Taxonomic classification of metagenomic sequences. Bielefeld: Universität; 2012.Bacteria, archaea and microeukaryotes can be found in almost every habitat present in nature, in particular in soil, sediments and sea water. They typically live in complex communities with different kinds of symbiotic associations which include relationships with larger organisms like animals or plants. Examples are microbial communities in the gut or on the skin of animals and humans, or bacteria that live in symbiosis with plants. The vast majority of such microbes are unculturable and thus cannot be sequenced by means of traditional methods. The recently upcoming discipline of metagenomics provides various in vivo- and in silico-tools to overcome this limitation. In particular, high-throughput sequencing techniques like 454 or Solexa-Illumina make it possible to explore those microbes by studying whole natural microbial communities and analysing their biological diversity as well as the underlying metabolic pathways. A current limitation of theses technologies is that they can sequence only DNA fragments of a limited length. With this limitation it is usually not possible to recover complete microbial genomes. In addition, the DNA fragments are drawn randomly from the microbial communities and the exact species of origin is unknown. Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences. However, the taxonomic classification of metagenomic sequences from novel species without close homologues in the biological sequence databases poses a challenge due to the high number of wrong taxonomic predictions on lower taxonomic ranks. In this thesis we present CARMA3, a novel method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches. CARMA3 accepts protein-encoding DNA sequences, protein sequences, and 16S-rDNA sequences as input. In addition, we present WebCARMA, a web application for the analysis of protein-encoding DNA sequences with CARMA3 without the need for a local installation. We evaluate our novel method in different experiments using simulated and real shotgun metagenomes and show that CARMA3 makes fewer wrong taxonomic predictions (at the same sensitivity) than other BLAST-based methods. In the last experiment we show that also very short reads can, in principle, be used to describe the taxonomic content of a metagenome

Spatial localization of knowledge-transfer channels and face-to-face contacts: A survey of the Jena university-industry linkages

In this paper we examine the knowledge-Transfer Channels of the universities and public research institutes in Jena. The empirical study is based on a survey of 297 personal interviews with researchers of both types of organisations. Our study focuses on three questions: (a) The importance and multitude of existing transfer channels, (b) their geographic distribution and (c) the importance of face-to-face contacts. With regard to the first question the analysis reveals some shortcomings of the usual channels considered in many empirical studies. Above all, informal transfer channels play an important role and in addition the multitude of transfer channels at hand turns out to be large. These outcomes suggest a very cautious interpretation of the claimed influences of transfer mechanisms like patents, joint publications and so on. As to the regional distribution of the linkages our results confirm the relevance of geographical proximity. A substantial part of the relevant transfer co-operations concentrate on the city and region. Finally, we examine the idea that 'distance matters' is due to the necessity of face-to-face contacts. By means of asking the researchers directly we found the puzzling result, that knowledge-transfer rests significantly upon personal contacts, but that this does not imply a bias towards geographical proximity. --

Forms and regional distribution of knowledge transfer by German universities

For the first time the transfer activities of two different German university types - the Friedrich Schiller University (FSU) and the University of Applied Sciences Jena (FH Jena) - were documented in parallel over all departments and channels of technology transfers with regard to their regional significance. Five groups of transfer activities are distinguished in the study: (1) those oriented on human capital, (2) those oriented on classic research and development, (3) those oriented on enterprises, (4) those oriented on direct transfers and (5) informal knowledge transfer channels. The results show that the traditional R&D-activities of the universities for the region are embedded into important supplemental transfer channels. In addition the radii of the external relations of the two universities are complementary: FH Jena has a stronger regional bearing, while FSU is more strongly active supra-regionally and internationally. It is possible that stronger support of the university faculty's activities establishing knowledge transfer could increase the regional economic impact of such activity. --innovation systems,technology transfer,regional development,Universities,know-how-transfer

Zusammenlegung von Arbeitslosen- und Sozialhilfe: Wirkungen auf Löhne, Beschäftigung und gewerkschaftliche Tarifpolitik

In the context of the so-called Hartz reforms, the previous unemployment assistance and the social assistance for individuals who are in need but capable of work were combined into a uniform basic benefit for those seeking employment. After a brief description of the problems associated with the old institutions, the regulations of the new unemployment benefit II are outlined. Then the effects of the reform are analysed. As the new system was introduced only recently, it is not yet possible to examine the actual effects empirically. The impact analysis can only be geared towards the theoretically expected effects. For this a partial analytical labour market model is used. It is shown that the incentives for suppliers of labour have been increased only slightly and that a conversion of the increase in supply into additional employment is uncertain. Positive employment effects are expected in the medium term if wage disparity is increased at the lower end of the range and complementary ways of promoting employment are used

Taxonomic classification of metagenomic shotgun sequences with CARMA3

The vast majority of microbes are unculturable and thus cannot be sequenced by means of traditional methods. High-throughput sequencing techniques like 454 or Solexa-Illumina make it possible to explore those microbes by studying whole natural microbial communities and analysing their biological diversity as well as the underlying metabolic pathways. Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences. However, the taxonomic classification of metagenomic sequences from novel species without close homologue in the biological sequence databases poses a challenge due to the high number of wrong taxonomic predictions on lower taxonomic ranks. Here we present CARMA3, a new method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches. We show that our method makes fewer wrong taxonomic predictions (at the same sensitivity) than other BLAST-based methods. CARMA3 is freely accessible via the web application WebCARMA from http://webcarma.cebitec.uni-bielefeld.de

Spatial localization of knowledge-transfer channels and face-to-face contacts: A survey of the Jena university-industry linkages

In this paper we examine the knowledge-Transfer Channels of the universities and public research institutes in Jena. The empirical study is based on a survey of 297 personal interviews with researchers of both types of organisations. Our study focuses on three questions: (a) The importance and multitude of existing transfer channels, (b) their geographic distribution and (c) the importance of face-to-face contacts. With regard to the first question the analysis reveals some shortcomings of the usual channels considered in many empirical studies. Above all, informal transfer channels play an important role and in addition the multitude of transfer channels at hand turns out to be large. These outcomes suggest a very cautious interpretation of the claimed influences of transfer mechanisms like patents, joint publications and so on. As to the regional distribution of the linkages our results confirm the relevance of geographical proximity. A substantial part of the relevant transfer co-operations concentrate on the city and region. Finally, we examine the idea that 'distance matters' is due to the necessity of face-to-face contacts. By means of asking the researchers directly we found the puzzling result, that knowledge-transfer rests significantly upon personal contacts, but that this does not imply a bias towards geographical proximity

Formen und regionale Verteilung des Wissenstransfers von Hochschulen: Eine repräsentative Fallstudie für Jena

Neu an dieser Studie ist, dass zum ersten Mal umfassend die Transferaktivitäten von zwei unterschiedlichen Hochschultypen - in diesem Fall der Friedrich Schiller Universität (FSU) und der Fachhochschule Jena (FH Jena) - parallel und über alle Fächer hinweg hinsichtlich ihrer regionalen Bedeutung erfasst wurden. Unterschieden werden fünf Gruppen von Transferaktivitäten: (1) humankapitalorientierte, (2) auf die klassische Forschung und Entwicklung orientierte, (3) unternehmensorientierte, (4) direkt transferorientierte und (5) informelle Kanäle des Wissenstransfers. Es ergibt sich das Bild, dass die traditionellen FuE - Aktivitäten der Hochschulen für die Region eingebettet sind in wichtige ergänzende Transferkanäle. Komplementär sind außerdem die Radien in den Außenbeziehungen der beiden Hochschulen: die FH Jena hat den einen stärkeren regionalen Bezug, während die FSU stärker überregional und international aktiv ist. Möglicherweise könnte eine stärkere Unterstützung von Gründungsaktivitäten der Hochschullehrer die regionale wirtschaftliche Bedeutung ihres Wissenstransfers weiter erhöhen

Forms and regional distribution of knowledge transfer by German universities

For the first time the transfer activities of two different German university types - the Friedrich Schiller University (FSU) and the University of Applied Sciences Jena (FH Jena) - were documented in parallel over all departments and channels of technology transfers with regard to their regional significance. Five groups of transfer activities are distinguished in the study: (1) those oriented on human capital, (2) those oriented on classic research and development, (3) those oriented on enterprises, (4) those oriented on direct transfers and (5) informal knowledge transfer channels. The results show that the traditional R&D-activities of the universities for the region are embedded into important supplemental transfer channels. In addition the radii of the external relations of the two universities are complementary: FH Jena has a stronger regional bearing, while FSU is more strongly active supra-regionally and internationally. It is possible that stronger support of the university faculty's activities establishing knowledge transfer could increase the regional economic impact of such activity

Löhne und Beschäftigung: Was wissen wir mehr als vor 25 Jahren? (Wages and employment * what more do we know than 25 years ago?)

"This article, which serves as the introduction to the special issue focusing on 'wages and employment', deals with the key developments of the past 25 years in this area of research. First, the latest insights and findings of macro- and microeconomic theory as well as of empirical knowledge on the explanation and quantification of the relationship between wage level, wage structure and employment as well as of employment structure are the centre of attention, with the relevant progress in econometry also being acknowledged. Then, the importance of wage rigidities is dealt with, which are significant both from a macro- and a microeconomic point of view, and which have been at the centre of scientific and economic-policy discussions particularly in recent years. Finally, wage-policy conclusions are examined briefly. What becomes obvious is that a negative relationship between wages and employment can be detected far more clearly nowadays than a quarter of a century ago. This is equally true on the basis of theoretical and empirical analysis with a micro- and macroeconomic background, even if, when based on disequilibrium models, for the latter no positive employment effects due to reductions in real wages can be expected in times of recession." (Author's abstract, IAB-Doku) ((en))Lohntheorie, Beschäftigung, Lohnstarrheit

Investitionen, Weiterbildung und betriebliche Reorganisation (Investments, further training and company reorganization)

"The correlations between investments, reorganization and further training existing at company level are examined in this paper. A production theory approach in conjunction with an optimisation calculation of the companies shows that the variables focused on here are mutually dependent on one another. If the model analysis is expanded by a few plausibility considerations on possible company developments, the initially simple and clearly manageable structure becomes more complex and counter-effects can occur. This is why it is not possible to formulate any clear hypotheses on the interdependency effects of the variables of investments, reorganization and further training as a point of departure for an empirical analysis. The empirical study is based on the data of the IAB establishment panel of the years 1997-2000. The focus of research is a simultaneous triangular equation model with further training, reorganization and investments as the variables to be studied. The key results are: there is a mutually interdependent relationship between reorganization measures and investments. Although further training is encouraged by real capital investments, the reverse correlation cannot be found. Clear relationships between further training and reorganization measures only exist if individual measures are analysed. All in all, simultaneous relationships between investments, reorganization measures and further training schemes can be empirically proven. Delayed adjustment processes partly interfere with them." (Author's abstract, IAB-Doku) ((en))organisatorischer Wandel, IAB-Betriebspanel, Unternehmensorganisation, Arbeitsorganisation, Investitionen, betriebliche Weiterbildung, Produktinnovation, Westdeutschland, Ostdeutschland, Bundesrepublik Deutschland