An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

BACKGROUND: Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data. RESULTS: In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG) as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML) schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here. CONCLUSION: The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at . Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data

XML schemas for common bioinformatic data types and their application in workflow systems

<p>Abstract</p> <p>Background</p> <p>Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.</p> <p>Results</p> <p>Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at <url>http://bioschemas.sourceforge.net</url>, the BioDOM library can be obtained at <url>http://biodom.sourceforge.net</url>.</p> <p>Conclusion</p> <p>The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.</p

XML-based approaches for the integration of heterogeneous bio-molecular data

Background: The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. Results: In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. Conclusion: XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources. </p

Combining protein structure prediction with experiments and functional information

Proteins are key players in all cells of living organisms. In particular, knowledge of the spatial protein structure may give fundamental insights into protein function and disease processes. For many years, the successful prediction of the structural and functional properties of proteins has been a major research field in bioinformatics. This field is also addressed in this work, which comprises an applied biomedical and a methodological part. Comprehensive application studies of bioinformatics approaches were performed, which primarily targeted autoinflammatory and neurodegenerative diseases. A variety of computational tools was used to analyze medically relevant proteins and to evaluate experimental data. Many bioinformatics methods were applied to predict the molecular structure and function of proteins. The results provided a rationale for the design, prioritization, and interpretation of experiments performed by cooperation partners. Some of the generated biological hypotheses were tested and confirmed by experiments. In addition, the application studies revealed limitations of current bioinformatics techniques, which led to suggestions for novel approaches. Three new computational methods were developed to support the prediction of the secondary and tertiary structure of proteins and the investigation of their interaction networks. First, consensus formation between three different methods for secondary structure prediction was shown to considerably improve the prediction quality and reliability. Second, in order to utilize experimental measurements in tertiary structure prediction, scoring functions were implemented that incorporate distance constraints into the alignment evaluation, thus increasing the fold recognition rate. Third, an automatic procedure for decomposing protein networks into interacting domains was designed to obtain a more detailed molecular view of protein-protein interactions, facilitating further functional and structural analyses.Proteinen kommt in allen Zellen lebender Organismen eine Schlüsselrolle zu. Insbesondere die Kenntnis der Raumstruktur von Proteinen kann fundamentale Einsichten in ihre Funktion und in Krankheitsprozesse liefern. Seit vielen Jahren ist die erfolgreiche Vorhersage struktureller und funktioneller Eigenschaften von Proteinen ein wichtiges Forschungsgebiet in der Bioinformatik. Dieses Gebiet ist auch Gegenstand der vorliegenden Arbeit, welche einen angewandten biomedizinischen und einen methodischen Teil umfasst. Es wurden umfangreiche Applikationsstudien von bioinformatischen Verfahren durchgeführt, die sich vornehmlich mit autoinflammatorischen und neurodegenerativen Erkrankungen befassten. Verschiedene Computerwerkzeuge wurden verwendet, um medizinisch relevante Proteine zu analysieren und experimentelle Daten auszuwerten. Es kamen viele Bioinformatikmethoden zur Anwendung, um die molekulare Struktur und Funktion von Proteinen vorherzusagen. Die Ergebnisse dienten als Grundlage für die Planung, Priorisierung und Interpretation von Experimenten, die von Kooperationspartnern durchgeführt wurden. Einige der generierten biologischen Hypothesen wurden durch Experimente überprüft und bestätigt. Zusätzlich deckten die Applikationsstudien Grenzen von Bioinformatikmethoden auf, was zu Vorschlägen für neuartige Verfahren führte. So wurden drei neue rechnerbasierte Methoden entwickelt, um die Vorhersage der Sekundär- und Tertiärstruktur von Proteinen sowie die Untersuchung ihrer Interaktionsnetzwerke zu unterstützen. Erstens wurde gezeigt, dass die Bildung eines Konsensus zwischen drei verschiedenen Methoden der Sekundärstrukturvorhersage die Vorhersagequalität und -verlässlichkeit erheblich verbessert. Zweitens wurden zur Nutzung experimenteller Messungen in der Tertiärstrukturvorhersage Bewertungsfunktionen implementiert, die Distanzbeschränkungen in die Alignmentevaluation einbinden, um die Faltungserkennungsrate zu erhöhen. Drittens wurde eine automatische Prozedur zur Dekomposition von Proteinnetzwerken in interagierende Domänen entworfen, um eine detailliertere molekulare Sicht von Interaktionen zwischen Proteinen zu erhalten. Hierdurch werden weitere Analysen zu Funktion und Struktur erleichtert

Efeitos da dieta deficiente ou suplementada com ácido fólico em ratas wistar durante a fase gestacional em parâmetros inflamatórios e neurotróficos nas mães e na prole adulta : risco para o desenvolvimento da esquizofrenia

Dissertação de mestrado apresentada ao Programa de Pós-Graduação em Ciências da Saúde da Universidade do Extremo Sul Catarinense - UNESC, para a obtenção do título de Mestre em Ciências da Saúde.A nutrição materna, em particular o aporte adequado de ácido fólico (AF), exerce um papel determinante para o desenvolvimento cerebral e pode influenciar na susceptibilidade a doenças na prole, inclusive a esquizofrenia. Com base nisso, o objetivo deste estudo foi investigar o efeito da dieta AIN 93, também conhecida como dieta controle, da dieta controle suplementada com AF em diferentes doses (5, 10 e 50 mg/kg) e da dieta deficiente em AF durante a gestação e lactação sobre os parâmetros inflamatórios em ratas Wistar mães, bem como avaliar o efeito das dietas maternas nestes marcadores inflamatórios e nos níveis cerebrais de neurotrofinas na prole adulta submetida ao modelo animal de esquizofrenia induzida por cetamina. Ratas Wistar foram divididas em 5 grupos conforme a dieta administrada: dieta controle; dieta controle suplementadas com AF nas doses de 5, 10 e 50 mg/kg e dieta deficiente em AF. Após o desmame, a prole foi submetida à sexagem e os filhotes machos foram agrupados conforme as dietas maternas para ser utilizados na idade adulta. As ratas mães foram decapitadas e o sangue coletado para análise dos níveis plasmáticos de interleucinas (IL): IL-4 e IL-6 e fator de necrose tumoral α (TNF-α). A prole adulta proveniente das ratas mães foi subdividida para a indução do modelo de esquizofrenia através da administração intraperitoneal (i.p) de cetamina (25 mg/kg) ou salina durante 7 dias. Após a última administração, os animais foram decapitados e as estruturas cerebrais, córtex frontal e hipocampo, dissecadas para análise dos níveis de citocinas (IL-4, IL-6 e TNF-α) e neurotrofinas: fator neurotrófico derivado do cérebro (BDNF) e fator de crescimento nervoso (NGF). Verificou-se um aumento da citocina anti-inflamatória (IL-4) e uma redução nos níveis plasmáticos de citocinas pró-inflamatórias (IL-6 e TNF-α) nas ratas mães que foram submetidas às dietas suplementadas com AF 5, 10 e 50 mg/kg, apontando um possível efeito anti-inflamatório do AF na fase gestacional. Na prole adulta submetida ao modelo animal de esquizofrenia, em geral, o AF demonstrou uma ação neuroprotetora nos níveis de IL-4, IL-6 e TNF-α, o que sugere um efeito persistente desta vitamina sobre a resposta inflamatória dos animais, confirmando ainda o efeito anti-inflamatório, conforme também observado nas ratas mães. A suplementação materna com AF demonstrou uma ação duradoura e neuroprotetora nos níveis de BDNF e NGF, em especial, no córtex frontal da prole adulta. Diante destes achados, deve-se mencionar a importância do AF durante a gestação e a lactação, não somente para a prole, mas para a saúde materna. Por fim, os resultados deste estudo contribuem para a compreensão da patogênese da esquizofrenia, além de reforçar o papel do AF materno como uma abordagem protetora para os transtornos neurodesenvolvimentais. Salienta-se, entretanto, a necessidade de mais estudos investigarem a ação da cetamina sobre parâmetros inflamatórios e nos fatores neurotróficos, bem como avaliarem os padrões de metilação do DNA, pois sabe-se que os mecanismos epigenéticos estão diretamente envolvidos em condições psiquiátricas, inclusive na esquizofrenia, enfatizando a continuidade desta pesquisa