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dictyNews Volume 19 Number 05
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]
