微生物学技术

Mycobacterium ulcerans is a slow-growing environmental bacterium that causes a severe skin disease known as Buruli ulcer. Rapid detection of M. ulcerans in clinical specimens is essential to ensure early diagnosis and prevention of disability. This chapter describes a real-time PCR m ...

Our aim was to develop and evaluate sensitive methods that would allow simultaneous direct identification of multiple potential pathogens in clinical specimens for diagnosis and epidemiological studies, using a multiplex PCR-based reverse line blot assay. We have previously de ...

Bartonella henselae is the causative agent of cat-scratch disease (CSD), usually presenting itself as a �self-limiting lymphadenopathy. In this chapter an internally controlled Taqman probe-based real-time PCR targeting the groEL gene of Bartonella spp. is described. This assay a ...

Mycoplasma pneumoniae is a significant cause of respiratory disease, accounting for approximately 20% of cases of community-acquired pneumonia. Although several diagnostic methods exist to detect M. pneumoniae in respiratory specimens, real-time PCR has emerged as a signific ...

Pneumocystis jirovecii is a common cause of life-threatening pneumonia among immunocompromised patients. Since P. jirovecii cannot be cultured, specific identification of it depends on examining respiratory specimens. In the last decade, PCR has been developed which allows the d ...

Recent advances in molecular biology and better understanding of the genetic basis of drug resistance have allowed rapid identification of mycobacteria and rapid detection of drug resistance of Mycobacterium tuberculosis present in cultured isolates or in respiratory specim ...

Systems biologists frequently seek to integrate complex data sets of diverse analytes into a comprehensive picture of an organism’s biological state under defined environmental conditions. Although one would prefer to collect these data from the same sample, technical limitati ...

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 ...