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By sequencing the genomes of 34 mutation accumulation lines of a mismatch-repair defective strain of Escherichia coli that had undergone a total of 12,750 generations, we identified 1625 spontaneous base-pair substitutions spread across the E. coli genome. These mutations are not distributed at random but, instead, fall into a wave-like spatial pattern that(More)
We describe the Hox cluster in the radially symmetric sea urchin and compare our findings to what is known from clusters in bilaterally symmetric animals. Several Hox genes from the direct-developing sea urchin Heliocidaris erythrogramma are described. CHEF gel analysis shows that the Hox genes are clustered on a < or = 300 kilobase (kb) fragment of DNA,(More)
We have used Drosophila testis-specific beta2-tubulin to determine sequence requirements for different microtubules. The beta2-tubulin C-terminal tail has unique sperm-specific functions [Dev Biol 158:267-286 (2003)] and is also important for forming stable heterodimers with alpha-tubulin, a general function common to all microtubules [Mol Biol Cell(More)
Next-generation sequencing techniques are now commonly used to characterize structural variations (SVs) in population genomics and elucidate their associations with phenotypes. Many of the computational tools developed for detecting structural variations work by mapping paired-end reads to a reference genome and identifying the discordant read-pairs whose(More)
There is renewed interest in how the different body plans of extant phyla are related. This question has traditionally been addressed by comparisons between vertebrates and Drosophila. Fortunately, there is now increasing emphasis on animals representing other phyla. Pentamerally symmetric echinoderms are a bilaterian metazoan phylum whose members exhibit(More)
Axonemes of motile eukaryotic cilia and flagella have a conserved structure of nine doublet microtubules surrounding a central pair of microtubules. Outer and inner dynein arms on the doublets mediate axoneme motility [1]. Outer dynein arms (ODAs) attach to the doublets at specific interfaces [2-5]. However, the molecular contacts of ODA-associated proteins(More)
The relationship between the primary structure of the beta-tubulin C-terminal tail (CTT) and axoneme structure and function is explored using the spermatogenesis-specific beta2-tubulin of Drosophila. We previously showed that all beta-tubulins used for motile 9 + 2 axonemes contain a conserved sequence motif in the proximal part of the CTT, the beta-tubulin(More)
Background Discordant read pairs [1,2] – those deviating either from expected insert size range or correct relative orientation – have served as vital clues to identifying structural variants (SV) in genomes. Collecting discordant read pairs is the first step in SV detection and is often done by sequence alignment. When there are repetitive elements, such(More)
A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun(More)
Using Drosophila spermatogenesis as a model, we show that function of the beta-tubulin C-terminal tail (CTT) is not independent of the body of the molecule. For optimal microtubule function, the beta-tubulin CTT and body must match. beta2 is the only beta-tubulin used in meiosis and spermatid differentiation. beta1-tubulin is used in basal bodies, but beta1(More)
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