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W K Thomas

Publications and source records attributed to W K Thomas.

At least 19 recordsLinked to original sources
PubMed2004

Familial correlations, segregation analysis, and nongenetic correlates of soy isoflavone-metabolizing phenotypes.

Particular intestinal bacteria metabolize the soy isoflavone daidzein to equol and O-desmethylangolensin (O-DMA), metabolites that can be identified in urine. Individuals that harbor bacteria capable of producing equol or O-DMA are known as equol producers (approximately 30%-50% of the population) and O-DMA producers (approximately 80%-90% of the population), respectively. The equol-producer phenotype has been associated with sex hormone-related outcomes in several studies. However, the bacteria responsible for these phenotypes have not yet been identified and factors that influence the manifestation of these phenotypes are not well understood. To evaluate familial clustering of and nongenetic factors associated with these phenotypes, 410 individuals from 112 families participated in phenotyping (3-day soy challenge and Day 4 spot urine collection). In segregation analyses of the equol-producer phenotype, the Mendelian dominant model provided the most parsimonious fit to the data, suggesting that the pattern of inheritance of the equol-producer phenotype is consistent with an autosomal dominant trait. This phenotype was positively associated with education (p trend = 0.01), but not with sex, smoking, or several dietary factors. Results of the segregation analyses of the O-DMA-producer phenotype were inconclusive; no other models provided a more parsimonious fit to the data than the general model. This phenotype was inversely associated with age in a nonlinear model (p = 0.01), positively associated with age- and sex-adjusted height (odds ratio [OR] 10-cm increase = 0.38, 95% confidence interval [CI] = 0.15, 0.95) and body mass index (kg/m(2)) (OR = 0.91, 95% CI = 0.85, 0.96), but not with sex, education, smoking, or several dietary factors. These results suggest the equol-producer phenotype may be under some degree of genetic control and that there are likely other environmental factors not evaluated in the present analysis that contribute to both of these phenotypes. These results provide a foundation for further work to refine our understanding of heritable and environmental determinants of daidzein-metabolizing phenotypes.

Female↗
PubMed2000

High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.

Mutations in the mitochondrial genome have been implicated in numerous human genetic disorders and offer important data for phylogenetic, forensic, and population genetic studies. Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed a wide-scale screen for mutations in the mitochondrial genome that revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates, a highly biased mutational spectrum, multiple mutations affecting coding function, as well as mutational hotspots at homopolymeric nucleotide stretches.

Amino Acid Substitution↗
PubMed2000

Evolution of vulva development in the Cephalobina (Nematoda).

Ventral cord and vulva development are analyzed in a large sample of nematode species of the suborder Cephalobina. We find a specific range of evolutionary variations at distinct developmental steps. (1) Unlike Caenorhabditis elegans and relatives, the vulva is formed from the four precursor cells P(5-8).p or, exceptionally, from P(6, 7).p only. (2) The vulval competence group is restricted to these four cells or is larger. (3) The fates of more anterior and posterior Pn.p cells vary between closely related species (mostly cell death versus epidermal fate). (4) The mechanism of vulval cell fate patterning varies within a single genus, even between strains of the same species. (5) We describe the first example of a vulval cell lineage that is asymmetric between the anterior and the posterior sides of the vulva. For a selection of the investigated taxa, phylogenetic trees were constructed in order to map vulval characters and infer evolutionary polarities. We can conclude that in this group, death of the Pn.p cells probably constitutes a derived character state compared to a syncytial fate. Rhabditophanes sp. and Strongyloides ratti are placed as sister taxa, probably sharing an exclusive common ancestor in which the number of precursor cells forming the vulva was reduced from four to two.

Animals↗
PubMed1999

Morphological, molecular and biological characterization of Mehdinema alii (Nematoda: Diplogasterida) from the decorated cricket (Gryllodes sigillatus).

The nematode Mehdinema alii was recovered from the decorated cricket Gryllodes sigillatus (Walker). Morphometric comparisons are presented from 3 populations. The nematode is characterized by dense arrays of spines on the cuticle of the anterior half of the body and a highly elongate, tubular stoma with a dorsal denticle in the glottoid region. Females have a protruding vulva. Young females are amphidelphic, but the anterior ovary disappears in older females bearing multiple developing juveniles. The male is monorchic with asymmetrically placed genital papillae, distally fused spicules, and a highly complex gubernaculum bearing 2 cuticularized thorns that protrude through a separate, postcloacal opening. Adult nematodes are located primarily in the hindgut, whereas juveniles or dauers occur mainly in the genital chamber of both male and female crickets. Male crickets are significantly more likely to be infected than females. This male-biased infection may be linked to the venereal transmission mechanism of the dauers. Although morphologically unusual in many respects, placement of M. alii in Diplogasterida is supported by both the morphology of the anterior digestive tract as well as analysis of its 18S rDNA sequence. These sequence data suggest that M. alii groups most closely with members of the Cylindrocorporidae.

Animals↗
PubMed1998

A molecular evolutionary framework for the phylum Nematoda.

Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.

Animals↗
PubMed1998

Embryonic axis specification in nematodes: evolution of the first step in development.

In 1828, von Baer proposed that the early stages of development must be the most conserved [1]. Others have since countered that the middle stages of development are the most conserved [2]. To address whether the earliest step in pattern formation can evolve, we have examined how asymmetry along the antero-posterior (AP) axis is generated in various nematode species. AP asymmetry is specified in Caenorhabditis elegans at fertilization by the sperm, which directs a cytoplasmic rearrangement that segregates critical factors such as the P granules to one side of the uncleaved embryo [3,4]. We found that AP asymmetry is generated differently in another nematode species: the sperm is not used to specify AP asymmetry, there are no signs of cytoplasmic movements, and P granules are segregated differently. Despite these differences, development from the two-cell stage is remarkably similar in the two species. We have reconstructed the evolutionary history of these mechanisms by analyzing the development of 30 nematode species and mapping the results onto a molecular phylogeny of the nematodes [5]. The results suggest that a new mechanism for axis specification evolved in an ancestor of some of the relatives of C. elegans. We conclude that this fundamental step in development can evolve without affecting other aspects of development.

Animals↗
PubMed1997

An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans.

Nematodes are known to be a useful system for studies of comparative development. Here we perform a molecular phylogenetic analysis to allow for the independent interpretation of the developmental and morphological changes observed among a selected set of nematode species. Our molecular phylogenetic analysis is based on coding regions of the genes for RNA polymerase II, the small subunit rRNA and an expansion segment of the large subunit rRNA. Sequences were compared from five species in the family (Rhabditidae) that includes the developmental model organism Caenorhabditis elegans and from an outgroup taxon Aduncospiculum halicti (Diplogasterina). The phylogenetic analysis does not support the monophyly of the subfamily Mesorhabditinae and identifies the unnamed strain PS1010 as a sister taxon of C. elegans despite its morphologically divergent buccal capsule. On the basis of the inferred framework, we can begin to interpret the evolution of vulval development and of morphological differences among these nematode species.

Animals↗
PubMed1994

A molecular evolutionary framework for eukaryotic model organisms.

BACKGROUND: Implicit in the characterization of a model organism is the hope that insights into its biology can be extended to other species. For this hope to be fulfilled, the phylogenetic position of the model organism within a larger evolutionary framework must be known. We focus here on major model organisms of developmental genetics and cell biology. We first consider the positions of the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster within a phylogeny of the major advanced metazoan groups. Then we consider the evolutionary relationships between fungi (represented by Saccharomyces cerevisiae and Schizosaccharomyces pombe), plants, and animals. RESULTS: We show, by a direct comparison with small subunit ribosomal RNA (18 S rRNA), that RNA polymerase II is an appropriate molecule for addressing the phylogenetic branchings in the early evolution of eukaryotes. The results from the analyses of newly determined and previously published sequences of the two largest subunits of RNA polymerase II suggest the following. Firstly, that plants and animals share a last common ancestor that excludes fungi, the lineage of which originated earlier. Secondly, that the lineage leading to the nematode Caenorhabditis elegans diverged earlier from the Metazoa than the lineages of arthropods, deuterostomes, annelids and molluscs. Finally, that deuterostomes arose from within protostomes. CONCLUSIONS: RNA polymerase II is well-suited for the elucidation of the evolutionary relationships among eukaryotes. We emphasize the implications of our results for other biological disciplines in addition to molecular evolution, as a phylogenetic framework allows predictions and inferences to be made about the existence of fundamental biological mechanisms elucidated in model organisms.

Amino Acid Sequence↗
PubMed1994

Phylogenetic analysis of the Coscoroba coscoroba using mitochondrial srRNA gene sequences.

In order to study the phylogenetic relationships among Coscoroba, goose, and swan lineages, sequences for the complete mitochondrial small ribosomal RNA (srRNA) gene were determined from five waterfowl species. Parsimony and distance analyses support the branching of Coscoroba prior to the divergence of geese and swans, and maximum likelihood analyses give almost equal support to that pattern and to the sister group relationship between Coscoroba and swans. The monophyly of the geese was confirmed at a statistically significant level. In sequence comparisons among waterfowl, transitions increase linearly with transversions, and so we conclude that the lack of complete resolution of Coscoroba's position is not due to sequence saturation alone, but also reflects relatively close branching times.

Animals↗
PubMed1994

The marsupial mitochondrial genome and the evolution of placental mammals.

The entire nucleotide sequence of the mitochondrial genome of the American opossum, Didelphis virginiana, was determined. Two major features distinguish this genome from those of other mammals. First, five tRNA genes around the origin of light strand replication are rearranged. Second, the anticodon of tRNA(Asp) is posttranscriptionally changed by an RNA editing process such that its coding capacity is altered. When the complete protein-coding region of the mitochondrial genome is used as an outgroup for placental mammals it can be shown that rodents represent an earlier branch among placental mammals than primates and artiodactyls and that artiodactyls share a common ancestor with carnivores. The overall rates of evolution of most of the mitochondrial genome of placentals are clock-like. Furthermore, the data indicate that the lineages leading to the mouse and rat may have diverged from each other as much as 35 million years ago.

Amino Acid Sequence↗
PubMed1994

Transgenic cattle resulting from biopsied embryos: expression of c-ski in a transgenic calf.

Producing transgenic cattle by microinjection of DNA into pronuclei has been inefficient and costly, in large part because of the cost of maintaining numerous nontransgenic pregnancies to term. We designed a system for early identification of transgenic embryos in which biopsies of embryos were assayed by polymerase chain reaction for presence of the transgene before embryo transfer. A total of 2555 embryos were microinjected with one of two DNA constructs. Of the 533 embryos biopsied, 112 were judged to be potentially transgenic and were transferred nonsurgically to recipients, resulting in production of 29 putative transgenic fetuses. One fetus and one calf (7% of offspring) were subsequently shown to be definitively transgenic. The calf was transgenic for a chicken c-ski cDNA, and several months after birth developed dramatic muscular hypertrophy followed by muscle degeneration. This phenotype was associated with expression of high levels of mRNA from the transgene.

Animals↗
PubMed1993

A recent origin of marmots.

The complete mitochondrial cytochrome b genes from four ground squirrels, a marmot, and a tree squirrel were sequenced and compared. A level of divergence three times lower than expected based on fossil evidence was found between the marmot and the ground squirrels. The observed divergence was similar to that found within the ground squirrels and is consistent with a recent divergence of marmots (Marmota) from true ground squirrels (Spermophilus).

Animals↗
PubMed1993

Method for producing transgenic bovine embryos from in vitro matured and fertilized oocytes.

Microinjection and in vitro culture procedures were developed to produce transgenic bovine embryos after in vitro fertilization of in vitro matured oocytes. In Experiment I, zygotes were subjected to pronuclear microinjection of DNA 18 or 24 h following addition of spermatozoa to oocytes. Microinjections were performed in either Hepes-buffered TCM-199 or modified Dulbecco's phosphate-buffered saline without glucose. Viability of embryos was similar at both injection times and for both media, as determined by morphological evaluation after culturing embryos in vitro for 10 d. In Experiment II, microinjected embryos were cultured 1) in rabbit oviducts, 2) in vitro in a 5% CO(2) in air, or 3) in a 5% CO(2) / 5% O(2) / 90% N(2) incubator. There were no significant differences between the 2 in vitro culture environments. The in vitro culture systems supported development of embryos significantly better than the rabbit oviducts; 33% of cleaved ova developed to blastocysts in vitro vs 10% in vivo; 98% of transferred ova were recovered from the rabbit oviducts. From both experiments, 6 of 92 blastocysts were positive for the microinjected DNA as determined by a polymerase chain reaction followed by gel electrophoresis.

Journal Article↗
PubMed1993

Effects of cumulus cells on culture of bovine embryos derived from oocytes matured and fertilized in vitro.

Bovine zygotes derived from oocytes matured and fertilized in vitro were cultured in vitro. In Exp. 1, zygotes were vortexed to remove cumulus cells and then cultured in oviduct epithelial cell-conditioned TCM-199 medium with or without added cumulus cells. Embryos cultured without cumulus cells developed to blastocysts significantly less often than those cultured with added cumulus cells, 3 vs 38% of cleaved ova (P < .05). Co-culture of embryos with cumulus cells during the first 48 h only, or for the duration of the culture period, resulted in development rates similar to those of controls that were not vortexed. In Exp. 2, denuded zygotes were centrifuged (15,850 x g, 3 min) at room temperature to facilitate visualization of pronuclei. Centrifuged zygotes were either placed directly into conditioned medium for culture (with or without added cumulus cells) or DNA was first microinjected into their cytoplasm or a pronucleus. All microinjected embryos were co-cultured with added cumulus cells. Centrifugation and microinjection did not reduce viability significantly when embryos were co-cultured with cumulus cells. Development was reduced significantly when embryos were cultured without cumulus cells. Thus, when oviduct epithelial cell-conditioned medium was used, cumulus cell co-culture was beneficial during the early cleavage stages of in vitro-derived zygotes, including those that received DNA microinjection.

Animals↗
PubMed1992

Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent.

Initial amplification and sequencing of a 366-bp fragment of the cytochrome b gene by a conserved primer pair (MVZ 03 and MVZ 04) revealed a nonfunctional copy of the gene with two deletions (one of which is 17 bp in length and the other of which is 3 bp in length) in Chroeomys jelskii, a South American akodontine rodent. By means of an alternative primer to MVZ 03--namely, MVZ 05--from the region of the tRNA for glutamic acid, a functional copy of cytochrome b was subsequently amplified. Both primer pairs amplify functional sequence when applied to purified mitochondrial DNA (mtDNA). Restriction-endonuclease digestion of purified mtDNA from C. jelskii did not reveal any additional sets of bands that would suggest heteroplasmy in the mitochondrial genome. When probed with both functional and nonfunctional gene fragments, MboI restriction digests revealed the same pattern, providing further evidence that the nonfunctional copy must be located in the nucleus. Observed differences in the mitochondrial and nuclear sequences from two populations are consistent with a faster rate of change in mtDNA than in nuclear DNA.

Animals↗
PubMed1991

Rearrangements of mitochondrial transfer RNA genes in marsupials.

The nucleotide sequences of the mitochondrial origin of light-strand replication and the five tRNA genes surrounding it were determined for three marsupials. The region was found to be rearranged, leaving only the tRNA(Tyr) gene at the same position as in placental mammals and Xenopus. Distribution of the same rearranged genotype among two marsupial families indicates that the events causing the rearrangements took place in an early marsupial ancestor. The putative mitochondrial light-strand origin of replication in marsupials contains a hairpin structure similar to other vertebrate origins and; in addition, extensive flanking sequences that are not found in other vertebrates. Sequence comparisons among the marsupials as well as placentals indicate that the tRNA(Tyr) gene has been evolving under more constraints than the other tRNA genes.

Animals↗