Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data

BACKGROUND: Technological improvements have shifted the focus from data generation to data analysis. The availability of large amounts of data from transcriptomics, protemics and metabolomics experiments raise new questions concerning suitable integrative analysis methods. We compare three integrative analysis techniques (co-inertia analysis, generalized singular value decomposition and integrative biclustering) by applying them to gene and protein abundance data from the six life cycle stages of Plasmodium falciparum. Co-inertia analysis is an analysis method used to visualize and explore gene and protein data. The generalized singular value decomposition has shown its potential in the analysis of two transcriptome data sets. Integrative Biclustering applies biclustering to gene and protein data. RESULTS: Using CIA, we visualize the six life cycle stages of Plasmodium falciparum, as well as GO terms in a 2D plane and interpret the spatial configuration. With GSVD, we decompose the transcriptomic and proteomic data sets into matrices with biologically meaningful interpretations and explore the processes captured by the data sets. IBC identifies groups of genes, proteins, GO Terms and life cycle stages of Plasmodium falciparum. We show method-specific results as well as a network view of the life cycle stages based on the results common to all three methods. Additionally, by combining the results of the three methods, we create a three-fold validated network of life cycle stage specific GO terms: Sporozoites are associated with transcription and transport; merozoites with entry into host cell as well as biosynthetic and metabolic processes; rings with oxidation-reduction processes; trophozoites with glycolysis and energy production; schizonts with antigenic variation and immune response; gametocyctes with DNA packaging and mitochondrial transport. Furthermore, the network connectivity underlines the separation of the intraerythrocytic cycle from the gametocyte and sporozoite stages. CONCLUSION: Using integrative analysis techniques, we can integrate knowledge from different levels and obtain a wider view of the system under study. The overlap between method-specific and common results is considerable, even if the basic mathematical assumptions are very different. The three-fold validated network of life cycle stage characteristics of Plasmodium falciparum could identify a large amount of the known associations from literature in only one study

Forschung am Rande des paläographischen Zweifels: Die EDV-basierte Erfassung individueller Schriftzüge im Projekt DAmalS

Das Pilotprojekt DAmalS (Datenbank zur Authentifizierung mittelalterlicher Schreiberhände) hat es sich zum Ziel gesetzt, neue Kriterien zur Unterscheidung von Schreiberhänden in mittelalterlichen deutschsprachigen Handschriften aufzustellen und zuverlässigere Methoden und Werkzeuge für diese Aufgabe zu entwickeln. DAmalS beruht auf den drei Säulen einer elementgetreuen Basistransliteration in XML, computerbasierten graphetischen Analysen und einem neuartigen Verfahren der bildorientierten Mustererkennung. Diese Säulen sind in eine Datenbankstruktur integriert, welche sowohl die Archivierung als auch die technisch hochkomplexe Verarbeitung der Bildund Textdokumente leistet. Auf diese Weise bietet DAmalS eine Art Brille, durch die paläographische ExpertInnen bei ihrer Schriftbegutachtung unterstützt werden. In einer weiteren Ausbaustufe soll das Projekt DAmalS in ein neues Projekt namens MOSES (Musterorientiertes System zur Erfassung von Schriftindividualität) eingebettet werden, welches sich auf neuzeitliche und aktuelle handgeschriebene Materialien ausdehnen lässt, um dann z. B. auch für forensische Zwecke hilfreich zu sein

Peroxidase gene discovery from the horseradish transcriptome

BACKGROUND: Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. RESULTS: In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. CONCLUSIONS: This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes

Long-term results of a nationwide general ultrasound screening system for developmental disorders of the hip: the Austrian hip screening program

Background The Financial Standard Accounting Board (FASB) is concerned the deterioration of utility of the financial information. For this reason, FASB opened a process of consultations and deliberations with object of including it in its calendar: it was obvious the importance of the investments on innovation, but the generally accepted accounting principles in USA (US GAAP) didn’t allow their recognition like asset. So, our question is, with independence of accounting treatment for R&D, do the investors consider them important? Aims This paper aims to examine the value-relevance of R&D expenditures, using a regression model based on the Ohlson equity-valuation framework. We contribute evidence about the direction that the international standards should follow. Instrument and Sample The instrument consists in different specifications of a valuation model, in other words, of Ohlson Model (1995). The sample is composed by U.S listed firms automotive over a 10-year period (1995-2004). Results and Conclusions Our findings show the association between current and the lagged R&D expenditure and stock price is negative and significant. These findings indicate that the investors consider that current R&D is an expense and is not an asset.Antecedentes El Financial Accounting Standard Board preocupado ante el deterioro de la utilidad de la información financiera, abrió un proceso de consultas y deliberaciones con objeto de incluir esta preocupación en su agenda: quedaba patente la importancia de las inversiones conductoras de la innovación, pero los principios de contabilidad generalmente aceptados en el ámbito estadounidense (conocidos por las siglas US GAAP) no permitían su reconocimiento como activos. La cuestión que nos planteamos es: ¿Con independencia del tratamiento contable asignado a las partidas de I+D, los inversores las consideran relevantes? Objetivo En el presente trabajo de investigación trataremos de contrastar la relevancia del valor de los gastos de I+D corriente y con retardo de un ejercicio económico. Metodología y muestra Usando como función base el modelo de Ohlson (1995), introducimos variantes del mismo y con ellas, fijamos nuestro objetivo en la modelización del precio de cotización. La muestra está formada por empresas que cotizan en Estados Unidos y que pertenecen al sector del automóvil. El horizonte temporal analizado comprende 10 años. Resultado y conclusiones Nuestros resultados muestran que los inversores consideran que los gastos de I+D corriente y los del ejercicio anterior no aportan valor añadido a las compañías, es decir, que los valoran como cualquier otro gasto del ejercicio y que, por tanto, no son relevantes para estimar el valor de mercado de las compañías que forman nuestra muestra

FascinatE newsletter 1

This FascinatE newsletter explains how gesture recognition will be used in the FascinatE system, how our first test shoot went at a Premier League football match, and explains about up and coming events