SABIO-RK: Curated Kinetic Data of Biochemical Reactions

SABIO-RK ("http://sabio.villa-bosch.de/SABIORK/":http://sabio.villa-bosch.de/SABIORK/) is a curated, web-accessible database for modellers and wet-lab scientists to get comprehensive information about biochemical reactions and their kinetic properties. It integrates data from different origin in order to facilitate the access to reaction kinetics data and corresponding information. Since most of the kinetic data is exclusively found in the literature SABIO-RK offers data manually extracted from the literature and related information obtained from other publicly available biological databases. For instance, the kinetic data are related to reactions, organisms, tissues and cellular locations. The type of the kinetic mechanism and corresponding rate equations are presented together with their parameters and experimental conditions. Additionally, SABIO-RK also includes data about the detailed mechanism for some of the reactions based on literature information. This not only includes the graphical representation of the mechanism but also the single reaction steps with their corresponding kinetic data.

The data in SABIO-RK are extracted manually from literature and the selection of articles is not restricted to any biological source (e.g. organisms or organism classifications). All the data are curated and annotated by biological experts using a web-based input interface. To support the curation process and data integration we have implemented different constraints in the input interface and offer several controlled vocabularies as lists of values, as well as additional semi-automatic consistency checks to avoid errors and inconsistencies in the database. Controlled vocabularies and annotations to external resources and ontologies were used to identify and relate the data to their biological context. All these efforts to unify and integrate the data augment the content and the semantics of the SABIO-RK database entries to enable a comprehensive understanding and comparison of the data for the user.

SABIO-RK can be accessed via a web-based user interface or via web-services. The user interface allows the definition of complex queries by specifying reactions and reaction participants, kinetic parameters, environmental conditions or literature sources. Links to other databases based on the annotations of the
data enable the user to gather further information for example for compounds, reactions or proteins. Selected data about reactions and their kinetics, together with their annotations, can be exported in SBML (Systems Biology Mark-up Language), a widely used standard exchange format in systems biology

Classification of Chemical Compounds to Support Complex Queries in a Pathway Database

Data quality in biological databases has become a topic of great discussion. To provide high quality data and to deal with the vast amount of biochemical data, annotators and curators need to be supported by software that carries out part of their work in an (semi-) automatic manner. The detection of errors and inconsistencies is a part that requires the knowledge of domain experts, thus in most cases it is done manually, making it very expensive and time-consuming. This paper presents two tools to partially support the curation of data on biochemical pathways. The tool enables the automatic classification of chemical compounds based on their respective SMILES strings. Such classification allows the querying and visualization of biochemical reactions at different levels of abstraction, according to the level of detail at which the reaction participants are described. Chemical compounds can be classified in a flexible manner based on different criteria. The support of the process of data curation is provided by facilitating the detection of compounds that are identified as different but that are actually the same. This is also used to identify similar reactions and, in turn, pathways

The PinK Study - Methodology of the Baseline Survey of a Prospective Cohort Study of Couples Undergoing Fertility Treatment

Der Methodenbericht beschreibt die Basiserhebung der PinK-Studie "Paare in Kinderwunschbehandlung". Ziel der Studie ist ein besseres Verständnis der Situation von Paaren mit unerfülltem Kinderwunsch und umfassende Erkenntnisse über die Wege in die Kinderwunschbehandlung. Der Ansatz der Studie ist interdisziplinär. Sie ist als prospektive Kohortenstudie in einem klinischen Umfeld angelegt. Zielgruppe der Studie sind Paare mit unerfülltem Kinderwunsch, die zwischen Juli 2012 und Mai 2013 ein Kinderwunschzentrum in Rheinland-Pfalz oder in der hessischen Landeshauptstadt aufgesucht haben. Als Erhebungsinstrument kamen schriftliche Fragebögen zum Einsatz, die den Patienten durch das Personal der Kinderwunschzentren übergeben wurden. Der finale Datensatz enthält alle bis Ende Juli 2013 zurückgesendete Fragebögen. Es haben 323 Frauen und 242 Männer an der Befragung teilgenommen, darunter 234 Paare, für die vollständige Informationen zu beiden Partnern vorliegen. Der Datensatz ermöglicht damit neben Geschlechtervergleichen auch Paaranalysen. Die Gesamtrücklaufquote liegt bei 31% mit teilweise erheblichen Unterschieden zwischen den Kliniken - mögliche Ursachen und Folgen werden diskutiert. Die Studienpopulation wird hinsichtlich zentraler soziodemografischer Merkmale beschrieben.This paper describes the realization of the baseline survey of the study ‘PinK- Paare in Kinderwunschbehandlung’ (couples undergoing fertility treatment). The study aims at a broader and better understanding of the situation of couples with an unfulfilled desire to have a child and of pathways leading couples to the fertility clinic. The approach of the study is interdisciplinary. It is designed as a prospective cohort study in a clinical setting. The study population consists of couples with an unfulfilled desire to have a child who presented themselves in a fertility clinic in the German state of Rhineland-Palatinate (RP) or in the capital city of the state of Hesse between July 2012 and May 2013. Self-administered questionnaires were used to gather information from patients at fertility clinics. These were handed out to the patients by the staff at the fertility clinics. Questionnaires returned by the end of July 2013 were included in the data set. The final sample consists of 323 female and 242 male respondents. In 234 couples, both partners participated. The overall response rate is 31%, with considerable variation across the clinics - reasons for and consequences of this are discussed. The final sample is described in terms of the distribution of core socio-demographic variables

The PinK Study - Methodology of the Follow-up Survey of a Cohort Study of Couples Undergoing Fertility Treatment

The paper describes the follow-up survey of the PinK study 'Paare in Kinderwunschbehandlung' (couples undergoing fertility treatment). This interdisciplinary study aims at a broader and better understanding of the situation of couples with an unfulfilled desire to have a child. The focus in the follow-up survey is on the situation of the couples one year after their first visit to a fertility clinic in Rhineland-Palatinate or in the capital of Hesse, Wiesbaden. Approximately one year after the baseline survey, self-administered questionnaires were sent to respondents who had signed a written agreement to remain in the study. The field period lasted from June 2013 to August 2014. The final sample consists of 140 women and 93 men. In 89 couples both partners participated. The longitudinal data set includes 224 respondents. The share of baseline survey participants who also participated in the follow-up is 39.6 %. This report describes the study design and materials for the follow-up as well as the sample and analyses the selectivity of dropouts from the baseline sample

Dual PI3K/mTOR inhibitor NVP-BEZ235 enhances radiosensitivity of head and neck squamous cell carcinoma (HNSCC) cell lines due to suppressed Double-Strand Break (DSB) repair by non-homologous end joining

The PI3K/Akt/mTOR pathway is frequently altered in human papillomavirus (HPV)-positive and negative squamous cell carcinoma of the head and neck (HNSCC) and overstimulation is associated with poor prognosis. PI3K drives Akt activation and constitutive signaling acts pro-proliferative, supports cell survival, DNA repair, and contributes to radioresistance. Since the small molecule NVP-BEZ235 (BEZ235) is a potent dual inhibitor of this pathway, we were interested whether BEZ235 could be an efficient radiosensitizer. The 50 nM BEZ235 was found to abrogate endogenous and irradiation-induced phosphorylation of Akt (Ser473). The anti-proliferative capacity of the drug resulted in an increase in G1-phase cells. Repair of radiation-induced DNA double-strand breaks (DSBs) was strongly suppressed. Reduction in DSB repair was only apparent in G1- but not in G2-phase cells, suggesting that BEZ235 primarily affects non-homologous end joining. This finding was confirmed using a DSB repair reporter gene assay and could be attributed to an impaired phosphorylation of DNA-PKcs (S2056). Cellular radiosensitivity increased strongly after BEZ235 addition in all HNSCC cell lines used, especially when irradiated in the G0 or G1 phase. Our data indicate that targeting the PI3K/Akt/mTOR pathway by BEZ235 with concurrent radiotherapy may be considered an effective strategy for the treatment of HNSCC, regardless of the HPV and Akt status

EnzymeML : a data exchange format for biocatalysis and enzymology

EnzymeML is an XML‐based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modeling tools, and databases. EnzymeML supports the scientific community by introducing a standardized data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An application programming interface in Python supports the integration of software tools for data acquisition, data analysis, and publication. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modeling using the modeling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO‐RK.Deutsche ForschungsgemeinschaftBiotechnology and Biological Sciences Research CouncilGerman Federal Ministry of Education and ResearchUniversity of LiverpoolKlaus Tschira FoundationProjekt DEA

Mitochondrial DNA copy number and function decrease with age in the short-lived fish Nothobranchius furzeri. Aging Cell

Summary Among vertebrates that can be kept in captivity, the annual fish Nothobranchius furzeri possesses the shortest known lifespan. It also shows typical signs of aging and is therefore an ideal model to assess the role of different physiological and environmental parameters on aging and lifespan determination. Here, we used Nothobranchius furzeri to study whether aging is associated with mitochondrial DNA (mtDNA) alterations and changes in mitochondrial function. We sequenced the complete mitochondrial genome of N. furzeri and found an extended control region. Large-scale mtDNA deletions have been frequently described to accumulate in other organisms with age, but there was no evidence for the presence of detectable age-related mtDNA deletions in N. furzeri. However, mtDNA copy number significantly decreased with age in skeletal muscle, brain, liver, skin and dorsal fin. Consistent with this finding, expression of Pgc-1a that encodes a transcriptional coactivator of mitochondrial biogenesis and expression of Tfam and mtSsbp both encoding mtDNA binding factors was downregulated with age. The investigation of possible changes in mitochondrial function revealed that the content of respiratory chain complexes III and IV was reduced in skeletal muscle with age. In addition, ADP-stimulated and succinate-dependent respiration was decreased in mitochondria of old fish. These findings suggest that despite the short lifespan, aging in N. furzeri is associated with a decline in mtDNA copy number, the downregulation of mtDNA-associated genes and an impairment of mitochondrial function