实验基础

The isolation and subsequent characterization of microbial cells from within environmental samples is a difficult process. Flow cytometry and cell sorting, when combined with the application of fluorescent probes, have the capability for the detection and separation of diverse m ...

Microorganisms from extreme environments are often very difficult to cultivate, precluding detailed study by biochemical and physiological techniques. Recent advances in genomic sequencing and proteomic measurements of samples obtained from natural communities have a ...

Chemolithoautotrophic bacteria can be of industrial and environmental importance, but they present a challenge for systems biology studies, as their central metabolism deviates from that of model organisms and there is a much less extensive experimental basis for their gene annota ...

The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discov ...

The coordinated regulation of the expression of a group of genes by a specific transcription factor frequently lies at the heart of the ability of a bacterium to respond to an environmental signal, or to progress through a developmental program. Thus, in many situations, it is of interest to identify ...

Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subje ...

A rapid and inexpensive method to characterise chemical cell properties and identify the functional groups present in the cell wall is Fourier transform infrared spectroscopy (FTIR). Infrared spectroscopy is a well-established technique to identify functional groups in organ ...

Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring comple ...

C-isotope labeling is a commonly used technique for determining and quantifying pathways in microorganisms under various growth conditions. The experimental protocol consists of feeding the cell with a composition-defined substrate and measuring isotopic labeling patte ...

Through the characterization of metabolic pathways, metabolomics is able to illuminate the activities of a cell at the functional level. However, the metabolome, which is comprised of hundreds of chemically diverse metabolites, is rather difficult to monitor. Mass spectrometry (MS) ...

Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism’s physiological re ...

Recent advances in high-resolution imaging secondary ion mass spectrometry (SIMS) (J Biol 5: 20, 2006) have made isotopic tracing at the single-cell level a standard technique for microbial ecology and systems biology; elemental and metal cofactor analyses are also showing significa ...

A formalism for simulating coupled metabolic and electrophysiological processes is presented. The resulting chemical kinetic and electrophysiological equations are solved numerically to create a cell simulator. Metabolic features of this simulator were adapted from Kar ...

Annotation of prokaryotic sequences can be separated into structural and functional annotation. Structural annotation is dependent on algorithmic interrogation of experimental evidence to discover the physical characteristics of a gene. This is done in an effort to construct a ...

Most systems of interest in the natural and engineering sciences are multiscale in character. Typically available models are incomplete or uncertain. Thus, a probabilistic approach is required. We present a deductive multiscale approach to address such problems, focusing on virus a ...

The complexity of the metabolic networks in even the simplest organisms has raised new challenges in organizing metabolic information. To address this, specialized computer frameworks have been developed to capture, manage, and visualize metabolic knowledge. The leading datab ...

Genome-scale models of metabolism are valuable tools for using genomic information to predict microbial phenotypes. System-level mathematical models of metabolic networks have been developed for a number of microbes and have been used to gain new insights into the biochemical conv ...

One important aim of synthetic biology is to develop a self-replicating biological system capable of performing useful tasks. A mathematical model of a synthetic organism would greatly enhance its value by providing a platform in which proposed modifications to the system could be rapid ...

An essential idea in the area of Systems Biology is that a good understanding of interactions between components is crucial for developing deep knowledge of the functioning of the system as a whole. Network analysis is an approach uniquely suited to uncover patterns and organizing principl ...

Some aerobic photosynthetic bacteria produce a cocktail of carotenoids, some of them being of a high economic value. A good example is the photosynthetic Bradyrhizobium sp. strain ORS278, which synthesizes, in addition to the photosynthetic carotenoid spirilloxanthin, large amou ...