Using complex web-based software called Ingenuity Pathway Analysis?®, the researchers were able to systematically map out pathways, or chains of genes, and subpathways that contribute to various aspects of inflammation.

We basically organized the inflammation-associated genes in a systematic way, said Matthew Loza, Ph.D., of the Center for Human Genomics at Wake Forest University School of Medicine, and lead author of the study. Before, a random list of genes involved in inflammation was all you had. We started with that same list, but then built these networks to bring all these different genes together.

The study, which was recently published by the Public Library of Science in its online journal PLoS One, has also led to the development of two customized panels for analyzing genetic variations in the inflammation pathways -- one for European and one for African descent populations. In a laboratory, these panels are analyzed using special laboratory equipment and computer systems. Researchers can obtain the custom inflammation panel through Affymetrix Corporation.

This is so significant because inflammation is a very hot topic, and many research groups want to study it, said Bao-Li Chang, Ph.D., assistant professor of pediatrics at Wake Forest and senior author for the study. We have provided researchers with the tool to effectively and efficiently accomplish their goals.

wfubmc/

The second featured protocol is from Dr. Rusty Lansford's lab at Caltech (quad.bicltech/~fraserlab/people/lansford/). It describes how to insert a DNA vector into very young bird (quail and chicken) embryos using a method called electroporation. The DNA vector contains a gene of interest attached to a fluorescent marker, which allows the researchers to track the fluorescently labeled cells using imaging techniques. Lansford's group uses this method to investigate mechanisms of brain and heart development in birds.

In Lansford's protocol, the DNA is electroporated into shell-less bird eggs. There are several advantages to using shell-less eggs: each embryo can be more accurately positioned during electroporation, and the researchers can ensure that all embryos used in the experiment are at the same stage in development. The protocol is freely available here: www.cshprotocols/cgi/content/full/2007/24/pdb.prot4894.

cshl/