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Microbial analysis, micropatterning methods featured in Cold Spring Harbor Protocols

Posted on: Wednesday, 1 July 2009, 16:13 CDT

Microbial populations have traditionally been studied in carefully controlled, laboratory-grown cultures. New metagenomic approaches are being developed to study these organisms in environmental or medical samples. The July issue of Cold Spring Harbor Protocols (www.cshprotocols.org/TOCs/toc7_09.dtl) presents a method developed by Holger Daims from the University of Vienna (http://www.microbial-ecology.net/daims.asp) for quantifying populations of microorganisms in a variety of naturally occurring conditions such as plankton samples or biofilms. "Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples" combines fluorescent in situ hybridization using rRNA-targeted probes with digital image analysis . The results show an organism's "biovolume fraction" in a given sample; this indicates the share of biochemical reaction space occupied by the quantified population and can be more relevant ecologically than absolute cell numbers. The article is freely available on the website for Cold Spring Harbor Protocols (http://cshprotocols.cshlp.org/cgi/content/full/2009/7/pdb.prot5253).

Micropatterning methods are rapidly becoming standard approaches for investigating cellular behaviors such as growth and migration. "Adhesive Micropatterns for Cells: A Microcontact Printing Protocol" from Matthieu Piel and colleagues at the Institut Curie (http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_gb/id_equipe/329.htm) offers a simple, fast, and efficient method for generating micropatterns for cellular studies. Employing an elastomeric stamp to print proteins on the substrate of choice, this technique does not require much of the expensive equipment and technical expertise needed for most micropatterning methods, making it easier to implement in biology laboratories. The authors have provided a movie that illustrates the technique step-by-step as part of the protocol. The article is freely accessible on the website for Cold Spring Harbor Protocols (http://cshprotocols.cshlp.org/cgi/content/full/2009/7/pdb.prot5255).


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