PubMed Health⌕ Search

Biomedical subjects

G J Olsen

Publications and source records attributed to G J Olsen.

At least 19 recordsLinked to original sources
PubMed1992

Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods.

The evolutionary relationships of the onychophorans (velvet worms) and the monophyly of the arthropods have generated considerable debate. Cladistic analyses of 12S ribosomal RNA sequences indicate that arthropods are monophyletic and include the onychophorans. Maximum parsimony analyses and monophyly testing within arthropods indicate that myriapods (millipedes and centipedes) form a sister group to all other assemblages, whereas crustaceans (shrimps and lobsters) plus hexapods (insects and allied groups) form a well-supported monophyletic group. Parsimony analysis further suggests that onychophorans form a sister group to chelicerates (spiders and scorpions) and crustaceans plus hexapods, but this relationship is not well supported by monophyly testing. These relationships conflict with current hypotheses of evolutionary pathways within arthropods.

Animals↗
PubMed1992

The Ribosomal Database Project.

The Ribosomal Database Project (RDP) complies ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various software packages for handling, analyzing and displaying sequences. In addition, the RDP offers (or will offer) certain analytic services. At present the project is in an intermediate stage of development.

Base Sequence↗
PubMed1992

Evolutionary relationships among sulfur- and iron-oxidizing eubacteria.

Some 37 reverse transcriptase, partial 16S rRNA sequences from sulfur- and/or iron-oxidizing eubacteria, including sequences from species of the genera Thiobacillus, Thiothrix, Thiomicrospira, Acidophilium, "Leptospirillum," Thiovulum, and Chlorobium, have been determined. In addition, 16S sequences from a number of unnamed sulfur- and/or iron-oxidizing bacteria from hydrothermal vent sites, from invertebrate-bacterial endosymbioses, and from various mineral recovery operations also have been determined. The majority of sequences place their bacterial donors in one or another of the subdivisions of the Proteobacteria. However, three unnamed facultatively thermophilic iron-oxidizing isolates, Alv, BC, and TH3, are affiliated with the gram-positive division. One H2S-oxidizer, from the genus Thiovulum, is affiliated with Campylobacter, Wolinella, and other genera in what appears to be a new subdivision of the Proteobacteria. Three "Leptospirillum"-helical vibrioid isolates, BU-1, LfLa, and Z-2, exhibit no clear phylum level affiliation at all, other than their strong relationship to each other. A picture is emerging of an evolutionary widespread capacity for sulfur and/or iron oxidation among the eubacteria.

Bacteria↗
PubMed1990

Structure detection through automated covariance search.

This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential secondary and tertiary structural interactions, but also provides the covariation evidence that supports the proposed bondings, and any counterevidence that can be detected in the known sequences. A small number of previously unknown higher-order structural features have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. We are systematically studying mitochondrial rRNA, seeking tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. To test hypotheses suggested by an examination of our program's output, our colleagues in biology are sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosomal structure.

Algorithms↗
PubMed1989

Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review.

The most incisive a priori approach to inferring the higher order structure of large RNAs has proven to be the use of phylogenetic comparisons. This article provides guidelines to the method, using as an illustration the elucidation of the secondary structure of the catalytic RNA subunit of ribonuclease P (RNase P). The resultant structure is compared to the possibilities that are predicted thermodynamically for the RNase P RNA sequences of nine eubacteria.

Bacillus subtilis↗
PubMed1989

A brief note concerning archaebacterial phylogeny.

Critical analysis of the recently proposed alternative to the normal archaebacterial tree, the new eocyte tree, shows that the latter's central topology, in which the eubacteria branch from an entirely different section of the unrooted archaebacterial tree than the eukaryotes, is consistent with an artifact. The effects of the alignment used and the particular composition of the sequence quartets analyzed to infer this tree are discussed in detail.

Archaea↗
PubMed1988

Molecular phylogeny of the animal kingdom.

A rapid sequencing method for ribosomal RNA was applied to the resolution of evolutionary relationships among Metazoa. Representatives of 22 classes in 10 animal phyla were used to infer phylogenetic relationships, based on evolutionary distances determined from pairwise comparisons of the 18S ribosomal RNA sequences. The classical Eumetazoa are divided into two groups. Cnidarians arose from a protist ancestry different from the second group, the Bilateria. Within the Bilateria, an early split gave rise to Platyhelminthes (flatworms) and the coelomate lineage. Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.

Animals↗
PubMed1988

The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme.

Secondary structure models for the ribonuclease (RNAase) P RNAs of Bacillus subtilis and E. coli were derived by a phylogenetic comparative analysis of published sequences as well as four novel ones. The RNAase P RNA genes from Bacillus megaterium, Bacillus brevis, Bacillus stearothermophilus, and Pseudomonas fluorescens were cloned, sequenced, and compared with the other available sequences. Regions of pairing were identified by the occurrence of homologous complementary sequences that vary among the compared molecules. A common core of primary and secondary structure can be identified in all these RNAase P RNAs. The previously noted striking differences between the Bacillus and the enteric RNAase P RNAs arise not only from point mutations, but from the addition or deletion of structural domains. The primary and secondary structural features that are common to all of the RNAase P RNAs are likely to be the elements involved in the binding and cleavage of tRNA precursors, and in the interaction with the RNAase P protein.

Bacillus↗
PubMed1988

Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme.

The Bacillus subtilis ribonuclease P consists of a protein and an RNA. At high ionic strength the reaction is protein-independent; the RNA alone is capable of cleaving precursor transfer RNA, but the turnover is slow. Kinetic analyses show that high salt concentrations facilitate substrate binding in the absence of the protein, probably by decreasing the repulsion between the polyanionic enzyme and substrate RNAs, and also slow product release and enzyme turnover. It is proposed that the ribonuclease P protein, which is small and basic, provides a local pool of counter-ions that facilitates substrate binding without interfering with rapid product release.

Bacillus subtilis↗
PubMed1988

Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells.

Examination of collections of 16S rRNA sequences revealed sequence domains that were unique to (and invariant within) the three primary lines of cellular descent: the archaebacteria, the eubacteria, and the eucaryotes. Oligodeoxynucleotides complementary to these conserved sequence domains were synthesized and used as hybridization probes. Each of the radiolabeled probes specifically hybridized to nylon membrane-bound 16S rRNA from the targeted kingdom. A probe complementary to a universally conserved sequence in 16S rRNAs was used as a positive control, while its complement provided a negative control for nonspecific binding. The abilities of the probes to bind specifically to whole, fixed cells representing a broad array of phylogenetic diversity were tested in whole-cell dot blot assays. Again, all of the probes specifically bound the targeted groups. By microautoradiography, the method was extended to permit phylogenetic identification of single cells microscopically.

Animals↗
PubMed1988

Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences.

The 16S rRNAs from the bacterial endosymbionts of six marine invertebrates from diverse environments were isolated and partially sequenced. These symbionts included the trophosome symbiont of Riftia pachyptila, the gill symbionts of Calyptogena magnifica and Bathymodiolus thermophilus (from deep-sea hydrothermal vents), and the gill symbionts of Lucinoma annulata, Lucinoma aequizonata, and Codakia orbicularis (from relatively shallow coastal environments). Only one type of bacterial 16S rRNA was detected in each symbiosis. Using nucleotide sequence comparisons, we showed that each of the bacterial symbionts is distinct from the others and that all fall within a limited domain of the gamma subdivision of the purple bacteria (one of the major eubacterial divisions previously defined by 16S rRNA analysis [C. R. Woese, Microbiol. Rev. 51: 221-271, 1987]). Two host specimens were analyzed in five of the symbioses; in each case, identical bacterial rRNA sequences were obtained from conspecific host specimens. These data indicate that the symbioses examined are species specific and that the symbiont species are unique to and invariant within their respective host species.

Animals↗
PubMed1988

Evolutionary relationships among cyanobacteria and green chloroplasts.

The 16S rRNAs from 29 cyanobacteria and the cyanelle of the phytoflagellate Cyanophora paradoxa were partially sequenced by a dideoxynucleotide-terminated, primer extension method. A least-squares distance matrix analysis was used to infer phylogenetic trees that include green chloroplasts (those of euglenoids, green algae, and higher plants). The results indicate that many diverse forms of cyanobacteria diverged within a short span of evolutionary distance. Evolutionary depth within the surveyed cyanobacteria is substantially less than that separating the major eubacterial taxa, as though cyanobacterial diversification occurred significantly after the appearance of the major eubacterial groups. Three of the five taxonomic sections defined by Rippka et al. (R. Rippka, J. Deruelles, J. B. Waterbury, M. Herdman, and R. Y. Stanier, J. Gen. Microbiol. 111:1-61, 1979) (sections II [pleurocapsalean], IV [heterocystous, filamentous, nonbranching], and V [heterocystous, filamentous, branching]) are phylogenetically coherent. However, the other two sections (I [unicellular] and III [nonheterocystous, filamentous]) are intermixed and hence are not natural groupings. Our results not only support the conclusion of previous workers that the cyanobacteria and green chloroplasts form a coherent phylogenetic group but also suggest that the chloroplast lineage, which includes the cyanelle of C. paradoxa, is not just a sister group to the free-living forms but rather is contained within the cyanobacterial radiation.

Base Sequence↗