Process Oriented Collaboration in Grid-Environments: A Case Study in the Construction Industry

This paper addresses the process-oriented collaboration based on a grid-based platform for the support of virtual organizations (VO), illustrated on the example of the construction industry. Distributed, organizational and IT-structures of teams involved in vintage complex projects cannot be managed with conventional methods in an appropriate manner. Both using a grid platform and grid-based services, in conjunction with semantic methods for consistency saving and goal-oriented process management can increase the efficiency of collaboration processes in large-scale projects. A hybrid grid- and web service-based architecture for the next generation of VO service and a gateway solution was developed integrating the process-oriented perspective and prototypically implemented. The problem, as well as the solution on the basis of the hybrid system architecture combing the benefits of the cutting-edge technologies, the methodical concept for modeling VO processes and their automated execution on a grid platform are discussed in detail

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16(INK4A) promoter in colon carcinoma cell lines

Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limited number of cytosines. Here, we present an oligonucleotide microarray that permits the parallel analysis of the methylation status of individual cytosines, thus combining high throughput and high resolution. The approach was used to study the CpG island in the promoter region of the tumour suppressor gene p16(INK4A). In total, 876 oligonucleotide probes of 21 nt in length were used to inspect the methylation status of 53 CpG dinucleotides, producing correct signals in colorectal cancer cell lines as well as control samples with a defined methylation status. The information was validated by established alternative methods. The overall methylation pattern was consistent for each cell line, while different between them. At the level of individual cytosines, however, significant variations between individual cells of the same type were found, but also consistencies across the panel of cancer cell lines were observed

Identification of single-point mutations in mycobacterial 16S rRNA sequences by confocal single-molecule fluorescence spectroscopy

We demonstrate the specific identification of single nucleotide polymorphism (SNP) responsible for rifampicin resistance of Mycobacterium tuberculosis applying fluorescently labeled DNA-hairpin structures (smart probes) in combination with single-molecule fluorescence spectroscopy. Smart probes are singly labeled hairpin-shaped oligonucleotides bearing a fluorescent dye at the 5′ end that is quenched by guanosine residues in the complementary stem. Upon hybridization to target sequences, a conformational change occurs, reflected in a strong increase in fluorescence intensity. An excess of unlabeled (‘cold’) oligonucleotides was used to prevent the formation of secondary structures in the target sequence and thus facilitates hybridization of smart probes. Applying standard ensemble fluorescence spectroscopy we demonstrate the identification of SNPs in PCR amplicons of mycobacterial rpoB gene fragments with a detection sensitivity of 10(−8) M. To increase the detection sensitivity, confocal fluorescence microscopy was used to observe fluorescence bursts of individual smart probes freely diffusing through the detection volume. By measuring burst size, burst duration and fluorescence lifetime for each fluorescence burst the discrimination accuracy between closed and open (hybridized) smart probes could be substantially increased. The developed technique enables the identification of SNPs in 10(−11) M solutions of PCR amplicons from M.tuberculosis in only 100 s

Genome-scale screen for DNA methylation-based detection markers for ovarian cancer.

The identification of sensitive biomarkers for the detection of ovarian cancer is of high clinical relevance for early detection and/or monitoring of disease recurrence. We developed a systematic multi-step biomarker discovery and verification strategy to identify candidate DNA methylation markers for the blood-based detection of ovarian cancer

M3 Project - Actor Based Simulation in VirtualWorlds

M3 Simulation is a simulation approach that actively involves real human actors in a virtual reality environment based on multidisciplinary simulation models. This actor based concept aims at integrated simulation of complex processes belonging to heterogeneous levels of reality, paying specific attention to real human behavior. The entities of the real system under consideration are represented in a consistent object-oriented way by agents simulated by environmental models. This distributed network-capable implementation of the M3 system combines environmental modeling with the intuitive graphic representation, complex communication and interaction structures of virtual worlds in order to support the process of investigation of complex real world systems

Absence of AKT1 Mutations in Glioblastoma

Background: Oncogenic activation of the PI3K signalling pathway plays a pivotal role in the development of glioblastoma multiforme (GBM). A central node in PI3K downstream signalling is controlled by the serine-threonine kinase AKT1. A somatic mutation affecting residue E17 of the AKT1 gene has recently been identified in breast and colon cancer. The E17K change results in constitutive AKT1 activation, induces leukaemia in mice, and accordingly, may be therapeutically exploited to target the PI3K pathway. Assessing whether AKT1 is activated by somatic mutations in GBM is relevant to establish its role in this aggressive disease. Methodology/Principal Findings: We performed a systematic mutational analysis of the complete coding sequence of the AKT1 gene in a panel of 109 tumor GBM samples and nine high grade astrocytoma cell lines. However, no somatic mutations were detected in the coding region of AKT1. Conclusions/Significance: Our data indicate that in GBM oncogenic deregulation of the PI3K pathway does not involve somatic mutations in the coding region of AKT1

From digital archive to digital edition

Contemporary techniques allow us to handle some 100.000 pages of digitized manuscripts. If it is possible to bring collections of this size at low costs to the desktop of the researcher, the environment of historical research will change fundamentally. To explore these possibilities the Duderstadt Municipal Archive (Stadtarchiv Duderstadt, Germany) and the Max-Planck-Institut für Geschichte in Göttingen started a project in 1996. This project aims at developing a computerised version of the files of an entire archive. The older records of the archive are completely digitized and then put at the user's disposal together with registers. The aim is to create a research System which offers not only access to the sources in a way which preserves the originals, but also many facilities for the researcher that go beyond the ordinary work with originals. The second part of this paper goes to the opposite extreme. The possibility of integrating information into a database system opens completely new approaches to the source that can go far beyond a single text. Apart from visualizing information that Gould never he represented in a printed edition, the dynamic digital edition gives access to the various readings of a manuscript and thus deals with the aspects of the source's tradition. A software tool has been developed which supports the creation of digital editions to be build upon digitized collections, such as the one we present here. This project would not exist without the generous sponsoring of the Volkswagen-Stiftung

Sdhd and Sdhd/H19 Knockout Mice Do Not Develop Paraganglioma or Pheochromocytoma

BACKGROUND: Mitochondrial succinate dehydrogenase (SDH) is a component of both the tricarboxylic acid cycle and the electron transport chain. Mutations of SDHD, the first protein of intermediary metabolism shown to be involved in tumorigenesis, lead to the human tumors paraganglioma (PGL) and pheochromocytoma (PC). SDHD is remarkable in showing an 'imprinted' tumor suppressor phenotype. Mutations of SDHD show a very high penetrance in man and we postulated that knockout of Sdhd would lead to the development of PGL/PC, probably in aged mice. METHODOLOGY/PRINCIPAL FINDINGS: We generated a conventional knockout of Sdhd in the mouse, removing the entire third exon. We also crossed this mouse with a knockout of H19, a postulated imprinted modifier gene of Sdhd tumorigenesis, to evaluate if loss of these genes together would lead to the initiation or enhancement of tumor development. Homozygous knockout of Sdhd results in embryonic lethality. No paraganglioma or other tumor development was seen in Sdhd KO mice followed for their entire lifespan, in sharp contrast to the highly penetrant phenotype in humans. Heterozygous Sdhd KO mice did not show hyperplasia of paraganglioma-related tissues such as the carotid body or of the adrenal medulla, or any genotype-related pathology, with similar body and organ weights to wildtype mice. A cohort of Sdhd/H19 KO mice developed several cases of profound cardiac hypertrophy, but showed no evidence of PGL/PC. CONCLUSIONS: Knockout of Sdhd in the mouse does not result in a disease phenotype. H19 may not be an initiator of PGL/PC tumorigenesis

Probing the SELEX Process with Next-Generation Sequencing

Background SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. Methodology We have performed a semi-automated SELEX procedure on the model target streptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. Conclusions High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts