Proceedings of the National Academy of Sciences of the United States of America Channel

Dendrites of rod bipolar cells sprout in normal aging retina

Liets — Wed, 16 Jul 2008 11:57:16 -0700

The aging nervous system is known to manifest a variety of degenerative and regressive events. Here we report the unexpected growth of dendrites in the retinas of normal old mice. The dendrites of many rod bipolar cells in aging mice were observed to extend well beyond their normal strata within the outer plexiform layer to innervate the outer nuclear layer where they appeared to form contacts with the spherules of rod photoreceptors. Such dendritic sprouting increased with age and was evident at all retinal eccentricities.

Proceedings of the National Academy of Sciences of the United States of America Channel

Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry

cdupont — Thu, 20 Sep 2007 18:30:41 -0700

Because of the rise in atmospheric oxygen 2.3 billion years ago (Gya) and the subsequent changes in oceanic redox state over the last 2.3–1 Gya, trace metal bioavailability in marine environments has changed dramatically. Although theorized to have influenced the biological usage of metals leaving discernable genomic signals, a thorough and quantitative test of this hypothesis has been lacking. Using structural bioinformatics and whole-genome sequences, the Fe-, Zn-, Mn-, and Co-binding metallomes of 23 Archaea, 233 Bacteria, and 57 Eukarya were constructed.

Structural Bioinformatics

Phylogeny determined by protein domain content

Song — Thu, 19 Jul 2007 11:01:11 -0700

A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides the 174 taxa into Archaea, Bacteria, and Eukarya and satisfactorily sorts most of the major groups within these superkingdoms. The most challenging problem involved 119 Bacteria, many of which have reduced genomes. When a weighting factor was used that takes account of difference in genome size (number of considered folds), small-genome taxa were mostly grouped with their full-sized counterparts.

Structural Bioinformatics