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At least 703 records · Page 39Linked to original sources
PubMed1996

Molecular mechanisms of biocatalytic desulfurization of fossil fuels.

The development of biocatalytic desulfurization of petroleum fractions may allow its use in place of conventional hydrodesulfurization (HDS). Dibenzothiophene (DBT) is representative of a broad range of sulfur heterocycles found in petroleum that are recalcitrant to desulfurization via HDS. Rhodococcus sp. strain IGTS8 has the ability to convert DBT to 2-hydroxybiphenyl (HBP) with the release of inorganic sulfur. The conversion of DBT to HBP is catalyzed by a multienzyme pathway consisting of two monooxygenases and a desulfinase. The final reaction catalyzed by the desulfinase appears to be the rate limiting step in the pathway. Each of the enzymes has been purified to homogeneity and their kinetic and physical properties studied. Neither monooxygenase has a tightly bound cofactor and each requires an NADH-FMN oxidoreductase for activity. An NADH-FMN oxidoreductase has been purified from Rhodococcus and is a protein of approximately 25,000 molecular weight with no apparent sequence homology to any other protein in the databases. We describe a unique sulfur acquisition system that Rhodococcus uses to obtain sulfur from very stable heterocyclic molecules.

Biodegradation, Environmental↗
PubMed1998

A technique for establishing the identity of 'isolated' fossil hominin limb bones.

Associated skeletons, which are specimens preserving more than one body part from the same individual, are especially important for taxonomic and functional analyses. This study concentrates on the subset of associated skeletons which preserve the reciprocal surfaces of a joint. It uses laser scanning to explore whether the shapes of the reciprocal surfaces of a joint of an individual are significantly more congruent than the surfaces of randomly-matched pairings taken from the same species. Laser scanning was used to capture the distal articular surface of the left tibia of OH35 and the trochlear articular surface of the talus of OH8, both from Bed I, Olduvai Gorge, Tanzania. The degree of congruency between those articular surfaces was tested against the congruency of the talocrural joint of AL 288-1 (Australopithecus afarensis), and the congruency of both associated and randomly-matched talocrural joints of modern humans, chimpanzees and gorillas. The results suggest that OH35 and OH8 do not come from the same individual and may not come from the same species. Although this analysis leaves open the taxonomic affinity of OH35, it demonstrates the potential of laser scanning for capturing 3D data in palaeoanthropology. It also demonstrates the potential for using the relative congruency of reciprocal joint surfaces as a test of the likelihood that isolated limb bones are components of a single individual.

Animals↗
PubMed2000

The study of morphological variation in the hominid fossil record: biology, landmarks and geometry.

This review considers some recent advances in shape analysis based on landmark data, and focuses on the application of these methods to the study of skeletal evolution in primates. These advances have provoked some controversy. The major aims of this review are to put these debates in context and to provide an overview for the nonmathematician. The purpose of morphometric studies is considered, together with issues relating to the nature, significance and identification of landmarks before turning to a review of available technologies for the analysis of morphological variation. These are considered in terms of underlying models and assumptions in order to clarify when each is appropriate. To illustrate the application of these methods, 3 example studies are presented. The first examines differences amongst ancient and modern adult human crania using 2-dimensional data. The second illustrates the extension of these methods into 3 dimensions in a study of facial growth in monkeys. The third presents an application to the analysis of the form of the hominoid talus. The review ends with an account of available software resources for shape analysis.

Adult↗
PubMedDate not supplied

Determining the role that ecological and developmental constraints play in controlling disparity: examples from the crinoid and blastozoan fossil record.

It is widely believed that morphological constraints are responsible for the observed pattern of decreasing major morphological innovation in both the Metazoa and Metaphytes over geological time. This is readily seen as the decreasing trend of origination of higher taxa: phyla, classes, and orders. Currently, there are two competing evolutionary hypotheses that have been proposed to explain this phenomenon: (1) the empty ecospace hypothesis and (2) the developmental constraint hypothesis. To distinguish between hypotheses 1 and 2, the change of morphological innovation before and after several mass extinction events was measured in the Crinoidea and Blastozoa. Mass extinction intervals provided a means in which to remove ecospace limiting constraints and allow the developmental constraint hypothesis to be thoroughly tested. Within the Crinoidea, disparity was measured before and after three mass extinctions. Within the Blastozoa, disparity was measured before and after two mass extinctions. For each taxon, three suites of characters were analyzed: ecological, nonecological, or "developmental" and a combination of the two previous suites plus 50 additional characters. Four different measures of disparity were used to analyze each character suite. In the majority of the cases investigated, disparity rebounds to comparable levels or in some cases higher levels in both the Crinoidea and Blastozoa. The results indicate that developmental constraints are not responsible for the decrease in disparity throughout the geologic range of the taxa. The more likely scenario is that increasingly structured ecological guilds have made it much more difficult to allow large increases in disparity.

Animals↗
PubMedDate not supplied

Fins to limbs: what the fossils say.

A broad phylogenetic review of fins, limbs, and girdles throughout the stem and base of the crown group is needed to get a comprehensive idea of transformations unique to the assembly of the tetrapod limb ground plan. In the lower part of the tetrapod stem, character state changes at the pectoral level dominate; comparable pelvic level data are limited. In more crownward taxa, pelvic level changes dominate and repeatedly precede similar changes at pectoral level. Concerted change at both levels appears to be the exception rather than the rule. These patterns of change are explored by using afternative treatments of data in phylogenetic analyses. Results highlight a large data gap in the stem group preceding the first appearance of limbs with digits. It is also noted that the record of morphological diversity among stem tetrapods is somewhat worse than that of basal crown group tetrapods. The pre-limbed evolution of stem tetrapod paired fins is marked by a gradual reduction in axial segment numbers (mesomeres); pectoral fins of the sister group to limbed tetrapods include only three. This reduction in segment number is accompanied by increased regional specialization, and these changes are discussed with reference to the phylogenetic distribution of characteristics of the stylopod, zeugopod, and autopod.

Animals↗
PubMed2004

A new phlebotomine fossil species Trichopygomyia killickorum sp. n. (Diptera: Psychodidae) found in the Dominican Republic amber.

A description is given of male sandfly found in a piece of amber from Dominican Republic that dates from the Miocene period (20-15 m.y.a). It is assigned to the genus Trichopygomyia Barreto. The position of the spines on the style and the shape of the dorsal lobes of the paramere separate this fly from other species of the genus: it is here named Trichopygomyia killickorum sp. n.

Amber↗
PubMed2005

Reconstructing early sponge relationships by using the Burgess Shale fossil Eiffelia globosa, Walcott.

The relationships of the sponge classes are controversial, particularly between the calcareous and siliceous sponges. Specimens of the putative calcarean Eiffelia globosa Walcott from the Burgess Shale show the presence of diagnostic hexactinellid spicules integrated into the skeletal mesh. The arrangement of these spicules in Eiffelia is shown to be precisely equivalent to that of early protospongioid hexactinellids, and sponge growth occurred through an identical pattern to produce identical skeletal body morphology. The difference in spicule composition of the classes is interpreted through the observation of taphonomic features of Eiffelia that suggest the presence of at least two mineralogically distinct layers within the spicules. These results support molecular analyses that identify the calcarean-silicisponge transition as the earliest major sponge branch and suggest that the heteractinids were paraphyletic with respect to the Hexactinellida.

Animals↗
PubMed2006

Genomic fossils as a snapshot of the human transcriptome.

Processed pseudogenes (PPGs) are cDNA sequences that were generated through reverse transcription of mature, spliced mRNAs and have subsequently been reinserted at a new genomic location. These cDNA sequences are usually no longer transcribed and are considered "dead on arrival." Here we show that PPGs can be used to generate a map of the transcriptome. By analyzing thousands of human PPGs, we were able to discover hundreds of transcript variants so far unidentified. An experimental verification of a subset of these variants by RT-PCR indicates that most of them are still active in the human transcriptome. Furthermore, we demonstrate that PPGs can enable the identification of ancient splice variants that were expressed ancestrally but are now extinct. Our results show that the genome itself carries a "virtual cDNA library" that can readily be used to analyze both present and ancestral transcripts. Our approach can be applied to sequenced metazoan genomes to computationally annotate splicing variation even when expressed sequences are unavailable.

Alternative Splicing↗
PubMed1990

The earliest fossil evidence for sexual dimorphism in primates.

Recently obtained material of the early Eocene primate Notharctus venticolus, including two partial skulls from a single stratigraphic horizon, provides the geologically earliest evidence of sexual dimorphism in canine size and shape in primates and the only unequivocal evidence for such dimorphism in strepsirhines. By analogy with living platyrrhines, these data suggest that Notharctus venticolus may have lived in polygynous social groups characterized by a relatively high level of intermale competition for mates and other limited resources. The anatomy of the upper incisors and related evidence imply that Notharctus is not as closely related to extant lemuriform primates as has been recently proposed. The early Eocene evidence for canine sexual dimorphism reported here, and its occurrence in a nonanthropoid, indicates that in the order Primates such a condition is either primitive or evolved independently more than once.

Animals↗
PubMed1991

Laventiana annectens, new genus and species: fossil evidence for the origins of callitrichine New World monkeys.

A previously unidentified middle Miocene primate from the La Venta deposits of Colombia is intermediate between squirrel monkeys (Saimiri) and callitrichines (marmosets and tamarins) in the morphology of the lower molars, mandible, and talus. Laventiana annectens is closely related to Saimiri and to Cebus (capuchin monkeys) yet resembles the probable callitrichine morphotype, demonstrating that archaic relatives of a Saimiri-like stock were suitable structural ancestors for the enigmatic callitrichines. Laventiana is also more primitive than Saimiri (= Neosaimiri) fieldsi from the same fauna, further increasing the likelihood that the latter is a lineal ancestor of modern squirrel monkeys.

Animals↗
PubMed1994

Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation.

We propose a phylogeny for the evolution of tRNA that is based on the ubiquity and conservation of tRNA-like structures in the replication of contemporary genomes. This phylogeny is unique in suggesting that the function of tRNA in replication dates back to the very beginnings of life on earth, before the advent of templated protein synthesis. The origin we propose for tRNA has distinct implications for the order in which other components of the modern translational apparatus evolved. We further suggest that the "top half" of modern tRNA-a coaxial stack of the acceptor stem on the T psi C arm--is the ancient structural and functional domain and that the "bottom half" of tRNA--a coaxial stack of the dihydrouracil arm on the anticodon arm--arose later to provide additional specificity.

Animals↗
PubMed1999

Diversity of Holocene life forms in fossil glacier ice.

Studies of biotic remains of polar ice caps have been limited to morphological identification of plant pollen and spores. By using sensitive molecular techniques, we now demonstrate a much greater range of detectable organisms; from 2000- and 4000-year-old ice-core samples, we obtained and characterized 120 clones that represent at least 57 distinct taxa and reveal a diversity of fungi, plants, algae, and protists. The organisms derive from distant sources as well as from the local arctic environment. Our results suggest that additional taxa may soon be readily identified, providing a plank for future studies of deep ice cores and yielding valuable information about ancient communities and their change over time.

Base Sequence↗