A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli.

Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory events. Since the pioneering work of Covert and co-workers as well as Shlomi and co-workers it is debated, how regulation and metabolism synergistically characterize a coherent cellular state.

Variation of triacylglycerol profiles in unfermented and dried fermented cocoa beans of different origins.

Fermentation and drying are the two crucial processing steps required to produce cocoa beans with desired properties, especially taste and flavor. To understand their impact on the lipid profile of cocoa, the lipid composition of unfermented raw and fermented dried beans from six different origins was investigated using high-performance liquid chromatography-mass spectrometry methods. While the comparison of triacylglycerol profiles across the different origins showed only small variations in individual compound concentrations, the comparison along the fermentation status showed major differences regarding the occurrence of polar lipids.

Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans.

It is well known that the development of chocolate flavor is initiated during cocoa bean fermentation. Storage proteins undergo the most intensive breakdown yielding peptides and free amino acids, which both serve as flavor precursors. A comprehensive analysis of cocoa proteins and oligopeptides of non-fermented and fermented beans from various geographic origins allows the assessment of systematic differences with respect to their origin as well as fermentation status.

Degradation of cocoa proteins into oligopeptides during spontaneous fermentation of cocoa beans.

Degradation products of proteins produced during fermentation are believed to be the key precursors of a range of Maillard reactions that deliver the characteristic flavor and aroma of cocoa and chocolate. We have utilized UPLC-ESI-Q-q-TOF to identify and relatively quantify the largest collection of cocoa oligopeptides during a spontaneous fermentation time series using Ivory Coast cocoa beans. Peptides were identified, sequenced by tandem mass spectrometry and annotated based on their characteristic fragmentation pattern in the positive-ion mode.

Determination of hydroxycinnamic acids present in Rhododendron species.

Hydroxycinnamates including free hydroxycinnamic acids and their chlorogenic acid derivatives and glycosides have been profiled in leaf extracts of 98 Rhododendron species using LC-MS techniques. In total, 69 hydroxycinnamic acid derivatives were identified in the leaves of 98 Rhododendron species. Some derivatives serve as unique phytochemical marker for a single species, whereas other compounds are limited to certain subgenera.

The interdependent network of gene regulation and metabolism is robust where it needs to be.

Despite being highly interdependent, the major biochemical networks of the living cell-the networks of interacting genes and of metabolic reactions, respectively-have been approached mostly as separate systems so far. Recently, a framework for interdependent networks has emerged in the context of statistical physics. In a first quantitative application of this framework to systems biology, here we study the interdependent network of gene regulation and metabolism for the model organism Escherichia coli in terms of a biologically motivated percolation model.

Metabolome Comparison of Bioactive and Inactive Rhododendron Extracts and Identification of an Antibacterial Cannabinoid(s) from Rhododendron collettianum.

Introduction: The science of metabolomics offers the possibility to measure full secondary plant metabolomes with limited experimental effort to allow identification of metabolome differences using principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) of liquid chromatography mass spectrometry (LC-MS) data.

Objective: To demonstrate a bioinformatics driven hypothesis generator for identification of biologically active compounds in plant crude extracts, which is validated by activity guided fractionation.

Methodology: Crude extracts of Rhododendron leaves were tested for their antibacterial activity using agar diffusion and minimum inhibitory concentration assays.

Bioactivity in : A Systemic Analysis of Antimicrobial and Cytotoxic Activities and Their Phylogenetic and Phytochemical Origins.

The exceptional diversity of the genus has a strong potential for identification, characterization, and production of bioactive lead compounds for health purposes. A particularly relevant field of application is the search for new antibiotics. Here, we present a comparative analysis of nearly 90 species targeted toward the search for such candidate substances.