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Analysis of Microbes, Immune Response Featured in Cold Spring Harbor Protocols

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Metagenomics, the study of DNA isolated from samples of naturally occurring microbial populations, is rapidly growing. Improvements to cloning and sequencing techniques are allowing researchers to study microorganisms in environmental samples, and new knowledge of species interactions and community dynamics is emerging. The identification of microorganisms in these samples is of vital importance to interpreting the results of such studies.

In the January issue of Cold Spring Harbor Protocols, Annelie Wendeberg of the Helmholtz Centre for Environmental Research presents a protocol for "Fluorescence In Situ Hybridization for the Identification of Environmental Microbes."

The methods described allow the phylogenetic identification of microorganisms in environmental samples by means of fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes followed by signal amplification with catalyzed reporter deposition (CARD). As one of January's featured articles, it is freely available on the journal's website.

The enzyme-linked immunospot (ELISPOT) assay is considered by many to be the gold standard for monitoring cellular immune responses. The method is sensitive, quantitative and amenable to high-throughput screening. Until recently, the ELISPOT assay has been limited to the characterization of only one effector molecule.

Since the maintenance of both IFN-g and IL-2 by pathogen-specific T cells has been linked to a more favorable clinical outcome in human immunodeficiency virus (HIV) and Leishmania infections, an ELISPOT assay able to characterize both of these effector molecules would be helpful for monitoring immune responses to certain infectious agents.