ABSTRACT
BACKGROUND: Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in combination with stable isotope labeling experiments. However, before the mass spectrometric data can be used it has to be corrected for biases caused by naturally occurring stable isotopes, by the analytical technique(s) employed, or by the biological sample itself. Finally the MS data and the labeling information it contains have to be assembled into a data format usable by flux analysis software (of which several dedicated packages exist). Currently the processing of mass spectrometric data is time-consuming and error-prone requiring peak by peak cut-and-paste analysis and manual curation. In order to facilitate high-throughput metabolic flux analysis, the automation of multiple steps in the analytical workflow is necessary. RESULTS: Here we describe iMS2Flux, software developed to automate, standardize and connect the data flow between mass spectrometric measurements and flux analysis programs. This tool streamlines the transfer of data from extraction via correction tools to ¹³C-Flux software by processing MS data from stable isotope labeling experiments. It allows the correction of large and heterogeneous MS datasets for the presence of naturally occurring stable isotopes, initial biomass and several mass spectrometry effects. Before and after data correction, several checks can be performed to ensure accurate data. The corrected data may be returned in a variety of formats including those used by metabolic flux analysis software such as 13CFLUX, OpenFLUX and 13CFLUX2. CONCLUSION: iMS2Flux is a versatile, easy to use tool for the automated processing of mass spectrometric data containing isotope labeling information. It represents the core framework for a standardized workflow and data processing. Due to its flexibility it facilitates the inclusion of different experimental datasets and thus can contribute to the expansion of flux analysis applications.
Subject(s)
Isotope Labeling/statistics & numerical data , Mass Spectrometry/statistics & numerical data , Metabolic Networks and Pathways , Software , Systems Biology/methodsABSTRACT
Research on plant metabolism is currently experiencing the common use of various omics methods creating valuable information on the concentrations of the cell's constituents. However, little is known about in vivo reaction rates, which can be determined by Metabolic Flux Analysis (MFA), a combination of isotope labeling experiments and computer modeling of the metabolic network. Large-scale applications of this method so far have been hampered by tedious procedures of tissue culture, analytics, modeling and simulation. By streamlining the workflow of MFA, the throughput of the method could be significantly increased. We propose strategies for these improvements on various sub-steps which will move flux analysis to the medium-throughput range and closer to established methods such as metabolite profiling. Furthermore, this may enable novel applications of MFA, for example screening plant populations for traits related to the flux phenotype.
Subject(s)
Carbon Isotopes/metabolism , Metabolic Networks and Pathways , Metabolomics/methods , Plants/metabolism , Algorithms , Computer Simulation , High-Throughput Screening Assays , Magnetic Resonance Spectroscopy , Mass Spectrometry , Phenotype , Tissue Culture TechniquesABSTRACT
A micro earthquake survey in 1990 provided high resolution digital recordings of 313 local events. An array of 58 portable seismological stations was deployed for 89 days covering an area of about 26000km2 in northeastern Venezuela including the El Pilar fault zone and the broad plate boundary between Caribbean and South American tectonic plates. Each recording instrument was equipped with a 3-component short period geophone and provided a direct and analogue recording of three seismic channels and a time-code on audio cassettes at three gain levels with a total dynamic range over 90 dB. The inversion employed 1382 P- and 780 S- arrival times with timing errors less than 0.1s. Although for the S-onsets only phases on the horizontal components were considered, the obtained results did not fit in with the well constrained P-velocity. The results presented in cross-sections reveal features like thrust faults with imbricate structure dipping to the north along the El Pilar fault zone. Basal decollements and deepseated thrusting could be the explanations for back thrust, ratated or tilted faults.(AU)
Subject(s)
Earthquakes , Monitoring Stations , Research , Venezuela , TomographyABSTRACT
Se presenta el análisis de amenaza sísmica de Venezuela en términos de aceleración maxima esperada con probabilidad de excedencia de 19
para 50 y 100 años de vida útil de las instalaciones. El resultado de este análisis tiene como objetivo desarrollar un nuevo mapa de zonificación sísmica con fines de ingeniería para Venezuela y sustituir el vigente de la norma COVENIN 1756-82 (AU)
