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S Easteal

Publications and source records attributed to S Easteal.

At least 19 recordsLinked to original sources
PubMed2001

The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution.

The complete sequence of the MC1R locus has been assembled, the coding region of the gene is intronless and placed within a 12 kb region flanked by the NULP1 and TUBB4 genes. The immediate promoter region has an E-box site with homology to the M-box consensus known to bind the microphthalmia transcription factor (MITF); however, promoter deletion analysis and transactivation studies have failed to show activation through this element by MITF. Polymorphism within the coding region, immediate 5' promoter region and a variable number tandem repeat (VNTR) minisatellite within the locus have been examined in a collection of Caucasian families and African individuals. Haplotype analysis shows linkage disequilibrium between the VNTR and MC1R coding region red hair variant alleles which can be used to estimate the age of these missense changes. Assuming a mean VNTR mutation rate of 1% and a star phylogeny, we estimate the Arg151Cys variant arose 7500 years before the present day, suggesting these variants may have arisen in the Caucasian population more recently than previously thought.

Amino Acid Sequence↗
PubMed2001

Differential expression of the actin-binding proteins, alpha-actinin-2 and -3, in different species: implications for the evolution of functional redundancy.

The alpha-actinins are a multigene family of four actin-binding proteins related to dystrophin. The two skeletal muscle isoforms of alpha-actinin (ACTN2 and ACTN3) are major structural components of the Z-line involved in anchoring the actin-containing thin filaments. In humans, ACTN2 is expressed in all muscle fibres, while ACTN3 expression is restricted to a subset of type 2 fibres. We have recently demonstrated that alpha-actinin-3 is absent in approximately 18% of individuals in a range of human populations, and that homozygosity for a premature stop codon (577X) accounts for most cases of true alpha-actinin-3 deficiency. Absence of alpha-actinin-3 is not associated with an obvious disease phenotype, raising the possibility that ACTN3 is functionally redundant in humans, and that alpha-actinin-2 is able to compensate for alpha-actinin-3 deficiency. We now present data concerning the expression of ACTN3 in other species. Genotyping of non-human primates indicates that the 577X null mutation has likely arisen in humans. The mouse genome contains four orthologues which all map to evolutionarily conserved syntenic regions for the four human genes. Murine Actn2 and Actn3 are differentially expressed, spatially and temporally, during embryonic development and, in contrast to humans, alpha-actinin-2 expression does not completely overlap alpha-actinin-3 in postnatal skeletal muscle, suggesting independent function. Furthermore, sequence comparison of human, mouse and chicken alpha-actinin genes demonstrates that ACTN3 has been conserved over a long period of evolutionary time, implying a constraint on evolutionary rate imposed by continued function of the gene. These observations provide a real framework in which to test theoretical models of genetic redundancy as they apply to human populations. In addition we highlight the need for caution in making conclusions about gene function from the phenotypic consequences of loss-of-function mutations in animal knockout models.

Actinin↗
PubMed2001

Association of a polymorphism of the dopamine transporter gene with externalizing behavior problems and associated temperament traits: a longitudinal study from infancy to the mid-teens.

There have been reports that a variable number of tandem repeats (VNTR) polymorphism situated in the 3' untranslated region of the dopamine transporter gene is associated with attention-deficit hyperactivity disorder. On the basis of these findings, we predicted an association of this polymorphism with hyperactivity, other externalizing behavior problems, and related temperament traits in a general population sample. The association was investigated using children participating in a longitudinal study of childhood temperament and development. DNA was taken from 660 children who had been assessed for temperament from 4-8 months to 15-16 years, and for behavior problems from 3-4 to 15-16 years. No significant associations were found at any age. There are a number of methodological differences from earlier studies that might explain the lack of associations with hyperactivity. It is also possible that the earlier findings are not replicable.

Adolescent↗
PubMed2001

Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins.

DNA from ancient human remains provides perspectives on the origin of our species and the relationship between molecular and morphological variation. We report analysis of mtDNA from the remains of 10 ancient Australians. These include the morphologically gracile Lake Mungo 3 [ approximately 60 thousand years (ka) before present] and three other gracile individuals from Holocene deposits at Willandra Lakes (<10 ka), all within the skeletal range of living Australians, and six Pleistocene/early Holocene individuals (15 to <8 ka) from Kow Swamp with robust morphologies outside the skeletal range of contemporary indigenous Australians. Lake Mungo 3 is the oldest (Pleistocene) "anatomically modern" human from whom DNA has been recovered. His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations. This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. The other ancient Australian individuals we examined have mtDNA sequences descended from the most recent common ancestor of living humans. Our results indicate that anatomically modern humans were present in Australia before the complete fixation of the mtDNA lineage now found in all living people. Sequences from additional ancient humans may further challenge current concepts of modern human origins.

Africa, Eastern↗
PubMed2000

Identification, characterization, and crystal structure of the Omega class glutathione transferases.

A new class of glutathione transferases has been discovered by analysis of the expressed sequence tag data base and sequence alignment. Glutathione S-transferases (GSTs) of the new class, named Omega, exist in several mammalian species and Caenorhabditis elegans. In humans, GSTO 1-1 is expressed in most tissues and exhibits glutathione-dependent thiol transferase and dehydroascorbate reductase activities characteristic of the glutaredoxins. The structure of GSTO 1-1 has been determined at 2.0-A resolution and has a characteristic GST fold (Protein Data Bank entry code ). The Omega class GSTs exhibit an unusual N-terminal extension that abuts the C terminus to form a novel structural unit. Unlike other mammalian GSTs, GSTO 1-1 appears to have an active site cysteine that can form a disulfide bond with glutathione.

Amino Acid Sequence↗
PubMed2000

Association of smoking and personality with a polymorphism of the dopamine transporter gene: results from a community survey.

In studies that used mixed volunteer samples, Lerman et al. [1999: Health Psychol 18:14-20] and Sabol et al. [1999: Health Psychol 18:7-13] reported on an association of smoking with a polymorphism of the dopamine transporter gene. We attempted to replicate this association in a nonvolunteer community sample of 861 Caucasians. No associations were found with either smoking initiation or smoking cessation. Sabol et al. [1999] also reported on an association of the dopamine transporter polymorphism with the personality trait of novelty seeking. However, we failed to find any associations with a range of personality traits, including a scale of fun seeking that correlates with novelty seeking. These negative findings suggest that either the original associations are not replicable or that any association is very small.

Adult↗
PubMed2000

COMT and DRD3 polymorphisms, environmental exposures, and personality traits related to common mental disorders.

In a community sample of 2,327 Caucasians, we tested the hypotheses that polymorphisms in the COMT and DRD3 genes are associated with personality traits conferring vulnerability to anxiety, depression, or alcohol misuse, or with current symptoms of these; and that the association is stronger in persons who also have been exposed to stressor experiences. To conserve resources and to allow replication, the genetic analysis was undertaken in two stages. For the COMT polymorphism, no statistically significant associations were found in the first sample of 862 persons. The remainder of the sample was therefore not analysed for that gene. For the DRD3 polymorphism, those in the first sample with at least one of the Ser(9) alleles had significantly higher scores in neuroticism (p=0.006) and behavioral inhibition (p=0.003). There was a trend, failing to meet the 1% significance criterion, for those with this genotype also to have higher depression and anxiety. The groups did not differ in alcohol use. In persons with the Ser(9) allele who were also exposed to stressors, there was a higher level of depression at the 5% level; and the depression level was higher in homozygotes. But when the remainder of the sample (1,465) was analysed, none of the associations reached statistical significance. We conclude that neither the COMT nor DRD3 polymorphisms are associated with anxiety, depression, or alcohol abuse. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:102-107, 2000

Catechol O-Methyltransferase↗
PubMed2000

Assessing candidate genes as risk factors for mental disorders: the value of population-based epidemiological studies.

BACKGROUND: It is now possible to routinely collect DNA for the investigation of genetic risk factors in psychiatric epidemiology. However, concerns have been raised about the investigation of genetic risk factors in population surveys and in case-control studies with population controls, because of spurious associations arising through population stratification. To overcome this problem, some geneticists advocate the use of family controls and studies on isolated populations. However, such approaches may not be the best for psychiatric epidemiology. METHOD: A critical analysis is made of arguments against the investigation of genetic risk factors in studies with population controls. RESULTS: It is argued that concerns about population stratification have been overblown. It is simply a form of confounding and can occur in studies of environmental as well as genetic risk factors. Epidemiologists have traditionally dealt with this and other types of confounding by matching on potential confounders in the design of the study, or stratification by confounders in the analysis. Family controls overcome population stratification, but not other forms of confounding. They are a good choice when the sole interest is genetic risk factors, but psychiatric epidemiologists are typically interested in both genetic and environmental factors. Family controls are poor for examining environmental risk factors because they can give rise to over-matching. Isolated populations may produce genetic associations that do not generalize to other populations, and they may have a restricted range of environments. CONCLUSION: We conclude that population surveys and case-control studies using population controls are suitable for the investigation of both genetic and environmental risk factors and have greater public health relevance than alternative designs.

Epidemiologic Studies↗
PubMed2000

Evolutionary rate acceleration of cytochrome c oxidase subunit I in simian primates.

We present an analysis of the evolutionary rates of the cytochrome c oxidase subunit I genes of primates and other mammals. Five primate genes were sequenced, and this information was combined with published data from other species. The sequences from simian primates show approximately twofold increases in their nonsynonymous substitution rate compared to those from other primates and other mammals. The species range and the overall magnitude of this rate increase are similar to those previously identified for the cytochrome c oxidase subunit II and cytochrome b genes.

Animals↗
PubMed2000

Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study.

Mutations in BRCA1 (ref. 1) confer an increased risk of female breast cancer. In a genome-wide scan of linkage disequilibrium (LD), a high level of LD was detected among microsatellite markers flanking BRCA1 (ref. 3), raising the prospect that positive natural selection may have acted on this gene. We have used the predictions of evolutionary genetic theory to investigate this further. Using phylogeny-based maximum likelihood analysis of the BRCA1 sequences from primates and other mammals, we found that the ratios of replacement to silent nucleotide substitutions on the human and chimpanzee lineages were not different from one another (P=0.8), were different from those of other primate lineages (P=0.004) and were greater than 1 (P=0.04). This is consistent with the historic occurrence of positive darwinian selection pressure on the BRCA1 protein in the human and chimpanzee lineages. Analysis of genetic variation in a sample of female Australians of Northern European origin showed evidence for Hardy-Weinberg (HW) disequilibrium at polymorphic sites in BRCA1, consistent with the possibility that natural selection is affecting genotype frequencies in modern Europeans. The clustering of between-species variation in the region of the gene encoding the RAD51-interaction domain of BRCA1 suggests the maintenance of genomic integrity as a possible target of selection.

Adaptation, Biological↗
PubMed2000

Association of a functional polymorphism of the serotonin transporter gene with anxiety-related temperament and behavior problems in children: a longitudinal study from infancy to the mid-teens.

A polymorphism in the promoter region of the serotonin transporter gene (5-HTTLPR) has been associated with anxiety-related personality traits in adults. Initial studies showed that the short allele was associated with higher neuroticism, anxiety and harm avoidance. However, most attempts to replicate these findings have been negative. Because the association of candidate polymorphisms with behavioral traits may vary with stage of development, we investigated the association using participants in a longitudinal study of childhood temperament. DNA was available for 660 children who had been assessed for temperament from 4-8 months to 15-16 years, and for behaviour problems from 3-4 years to 15-16 years. No significant associations were found at most ages. However, at ages 13-14 years and 15-16 years, the long/long genotype was associated with higher anxiety. These findings do not support an association of the short allele with anxiety-related traits in early life.

Adolescent↗
PubMed2000

TrExML: a maximum-likelihood approach for extensive tree-space exploration.

MOTIVATION: Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified. RESULTS: This paper presents the Advanced Stepwise Addition Algorithm for exploring tree-space and two algorithms for generating all binary trees on a set of sequences. The Advanced Stepwise Addition Algorithm has been implemented in TrExML, a phylogenetic program for maximum-likelihood analysis of nucleotide sequences. TrExML is shown to be more effective at finding near optimal trees than a similar program, fastDNAml, implying that TrExML offers a better approach to account for phylogenetic uncertainty than has previously been possible. A program, TreeGen, is also described; it generates binary trees on a set of sequences allowing for extensive exploration of tree-space using other programs. AVAILABILITY: TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html.

Algorithms↗
PubMed2000

How important is DNA replication for mutagenesis?

Rates of mutation and substitution in mammals are generally greater in the germ lines of males. This is usually explained as resulting from the larger number of germ cell divisions during spermatogenesis compared with oogenesis, with the assumption made that mutations occur primarily during DNA replication. However, the rate of cell division is not the only difference between male and female germ lines, and mechanisms are known that can give rise to mutations independently of DNA replication. We investigate the possibility that there are other causes of male-biased mutation. First, we show that patterns of variation at approximately 5,200 short tandem repeat (STR) loci indicate a higher mutation rate in males. We estimate a ratio of male-to-female mutation rates of approximately 1.9. This is significantly greater than 1 and supports a greater rate of mutation in males, affecting the evolution of these loci. Second, we show that there are chromosome-specific patterns of nucleotide and dinucleotide composition in mammals that have been shaped by mutation at CpG dinucleotides. Comparable patterns occur in birds. In mammals, male germ lines are more methylated than female germ lines, and these patterns indicate that differential methylation has played a role in male-biased vertebrate evolution. However, estimates of male mutation bias obtained from both classes of mutation are substantially lower than estimates of cell division bias from anatomical data. This discrepancy, along with published data indicating slipped-strand mispairing arising at STR loci in nonreplicating DNA, suggests that a substantial percentage of mutation may occur in nonreplicating DNA.

Animals↗
PubMed2000

Association of a functional polymorphism of the monoamine oxidase A gene promoter with personality and psychiatric symptoms.

A functional polymorphism in the promoter of the monoamine oxidase gene has recently been described by Sabol et al. This polymorphism is a strong candidate for associations with personality traits and psychiatric symptoms. We report relevant data from a general population sample of 850 Caucasian Australians. We found no associations with anxiety and depression symptoms, with personality traits that predispose to anxiety (neuroticism, behavioral inhibition, negative affect) or to a personality trait related to antisocial behavior (psychoticism).

Adult↗
PubMed1999

Molecular evidence for the early divergence of placental mammals.

Paleontological and molecular data suggest quite different patterns for the early evolution of placental mammals. Paleontological evidence indicates a radiation, with most of the extant orders diverging at approximately the same time, close to the Cretaceous-Tertiary boundary, 65 Myr ago. Molecular evidence suggests a branching pattern of evolution that started much earlier. Resolving this discrepancy requires a consideration of the assumptions that underlie both approaches. It is argued here that the pattern indicated by the molecular approach is the most likely to be correct. If it is correct then either: 1) A diversity of placental mammals remains to be sampled from the Cretaceous, or 2) The placental orders diverged phylogenetically long before they diversified morphologically, implying a decoupling of the evolutionary processes associated with speciation and adaptation. The adaptive diversification of placental mammals may have required the demise of the dinosaurs at the end of the Cretaceous, but it occurred in lineages that had a long prior history of independent existence. 1999.

Animals↗
PubMed1999

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