Dicty News
Electronic Edition
Volume 19, number 5
August 17, 2002

Please submit abstracts of your papers as soon as they have been
accepted for publication by sending them to dicty@northwestern.edu.

Back issues of Dicty-News, the Dicty Reference database and other useful
information is available at DictyBase--http://dictybase.org.


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  Abstracts
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Comparison of probe preparation methods for DNA microarrays


Patrick Farbrother, Silke Mller, Angelika A. Noegel and Ludwig Eichinger 


BioTechniques, accepted for publication, 08/05/2002.

The increasing amount of sequencing data provides the opportunity to 
produce DNA microarrays for a growing number of organisms. For spotted 
microarrays this demands a fast and cost-efficient method for the production 
of the thousands of DNA probes the microarrays consist of. Previous 
protocols state the need to highly amplify these probes and purify them by 
filtering methods. Here we compared three methods for probe amplification 
and purification. We found that signal intensities from probes amplified by 
single PCRs were either equal or only slightly lower than from probes with 
fivefold higher DNA concentrations. This is true over the full range of 
signal intensities, suggesting that the amount of a specific probe always 
exceeds the amount of the target being analyzed. For the purification of 
probes after amplification simple ethanol precipitation proved similar to 
a membrane binding method. Thus, rapid probe preparation for microarrays by 
single PCR amplification and ethanol precipitation is possible.

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Taxonomy, slime molds, and the questions we ask

Andrew R. Swanson*, Frederick W. Spiegel* and James C. Cavender**

*Department of Biological Sciences, University of Arkansas, Fayetteville, 
Arkansas 72701, **Department of Environmental and Plant Biology, Ohio 
University, Athens, Ohio 45701

Mycologia, in press

ABSTRACT

Taxonomic treatments often influence the way we both ask and attempt to answer 
certain biological questions.  The classical taxonomy of the dictyostelid 
cellular slime molds (Dictyosteliales) involves a convenient set of categories 
that were developed independent of phylogeny.  In order to test whether the 
characters supporting the classical taxonomy hold any phylogenetic signal, we 
subjected 19 described taxa belonging to two families (Acytosteliaceae and 
Dictyosteliaceae) and three genera (Acytostelium, Dictyostelium, and 
Polysphondylium) to rooted cladistic analyses using PAUP* v 4.0b4a.  Neither 
family nor any of the three genera were found to represent monophyletic 
groups.  These results confirm that the classical taxonomy used to delineate 
families and genera within these slime molds carries very little phylogenetic 
signal. Taxonomic character sets should be scrutinized phylogenetically in 
order to determine what information they provide about the relatedness of taxa 
within a group.  Because taxonomy often drives the nature of biological 
inquiry, caution should be exercised when drawing conclusions regarding the 
evolution of developmental systems in Dictyostelium.

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[End Dicty News, volume 19, number 5]