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S M Fullerton

Publications and source records attributed to S M Fullerton.

13 recordsLinked to original sources
PubMed2005

Population genetics of CAPN10 and GPR35: implications for the evolution of type 2 diabetes variants.

A positional cloning study of type 2 diabetes in Mexican Americans identified a region, termed "NIDDM1," on chromosome 2q37 with significant linkage evidence. Haplotype combinations at the calpain-10 gene (CAPN10) within this region were shown to increase diabetes risk in several populations. On the basis of the thrifty genotype hypothesis, variants that increase susceptibility to type 2 diabetes under modern lifestyle conditions provided a survival advantage in past environments by increasing the efficiency of energy use and storage. Here, our goal is to make inferences about the evolutionary forces shaping variation in genes in the NIDDM1 region and to investigate the population genetics models that may underlie the thrifty genotype hypothesis. To this end, we surveyed sequence variation in CAPN10 and in an adjacent gene, G-protein-coupled receptor 35 (GPR35), in four population samples from different ethnic groups. These data revealed two distinct deviations from the standard neutral model in CAPN10, whereas GPR35 variation was largely consistent with neutrality. CAPN10 showed a significant deficit of variation in the haplotype class defined by the derived allele at SNP44, a polymorphism that is significantly associated with diabetes in meta-analysis studies. This suggests that this haplotype class was quickly driven to high frequency by positive natural selection. Interestingly, the derived allele at SNP44 is protective against diabetes. CAPN10 also showed a local excess of polymorphism and linkage disequilibrium decay in intron 13. Simulations show that this pattern may be explained by long-standing balancing selection that maintains multiple selected alleles. Alternatively, it is possible that the local mutation and recombination rates changed since the divergence of human and chimpanzee; this scenario does not require the action of natural selection on intron 13 variation.

Calpain↗
PubMed2001

Impairment of the blood-nerve and blood-brain barriers in apolipoprotein e knockout mice.

Apolipoprotein E (apoE) is well characterized as a plasma lipoprotein involved in lipid and cholesterol metabolism. Recent studies implicating apoE in Alzheimer's disease and successful recovery from neurological injury have stimulated much interest in the functions of apoE within the brain. To explore the functions of apoE within the nervous system, we examined apoE knockout (KO) mice. Previously, we showed that apoE KO mice have a delayed response to noxious thermal stimuli associated with a loss and abnormal morphology of unmyelinated fibers in the sciatic nerve. From these data, we hypothesized that apoE KO mice could have an impaired blood-nerve barrier (BNB). In this report, we demonstrate functionally impaired blood-nerve and blood-brain barriers (BBB) in apoE KO mice using immunofluorescent detection of serum protein leakage into nervous tissue as a diagnostic for decreased BNB and BBB integrity. Extensive extravasation of serum immunoglobulin G (IgG) is detected in the sciatic nerve, spinal cord, and cerebellum of apoE KO but not WT mice. In a subpopulation of apoE KO mice, IgG also extravasates into discrete cortical and subcortical locations, including hippocampus. Loss of BBB integrity was additionally confirmed by the ability of exogenously supplied Evans blue dye to penetrate the BBB and to colocalize with IgG immunoreactivity in CNS tissue. These observations support a role for apoE in maintaining the integrity of the BNB/BBB and suggest a novel relationship between apoE and neural injury.

Animals↗
PubMed2000

Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism.

Three common protein isoforms of apolipoprotein E (apoE), encoded by the epsilon2, epsilon3, and epsilon4 alleles of the APOE gene, differ in their association with cardiovascular and Alzheimer's disease risk. To gain a better understanding of the genetic variation underlying this important polymorphism, we identified sequence haplotype variation in 5.5 kb of genomic DNA encompassing the whole of the APOE locus and adjoining flanking regions in 96 individuals from four populations: blacks from Jackson, MS (n=48 chromosomes), Mayans from Campeche, Mexico (n=48), Finns from North Karelia, Finland (n=48), and non-Hispanic whites from Rochester, MN (n=48). In the region sequenced, 23 sites varied (21 single nucleotide polymorphisms, or SNPs, 1 diallelic indel, and 1 multiallelic indel). The 22 diallelic sites defined 31 distinct haplotypes in the sample. The estimate of nucleotide diversity (site-specific heterozygosity) for the locus was 0.0005+/-0.0003. Sequence analysis of the chimpanzee APOE gene showed that it was most closely related to human epsilon4-type haplotypes, differing from the human consensus sequence at 67 synonymous (54 substitutions and 13 indels) and 9 nonsynonymous fixed positions. The evolutionary history of allelic divergence within humans was inferred from the pattern of haplotype relationships. This analysis suggests that haplotypes defining the epsilon3 and epsilon2 alleles are derived from the ancestral epsilon4s and that the epsilon3 group of haplotypes have increased in frequency, relative to epsilon4s, in the past 200,000 years. Substantial heterogeneity exists within all three classes of sequence haplotypes, and there are important interpopulation differences in the sequence variation underlying the protein isoforms that may be relevant to interpreting conflicting reports of phenotypic associations with variation in the common protein isoforms.

Alleles↗
PubMed2000

Polymorphism and divergence in the beta-globin replication origin initiation region.

DNA sequence polymorphism and divergence was examined in the vicinity of the human beta-globin gene cluster origin of replication initiation region (IR), a 1.3-kb genomic region located immediately 5' of the adult-expressed beta-globin gene. DNA sequence variation in the replication origin IR and 5 kb of flanking DNA was surveyed in samples drawn from two populations, one African (from the Gambia, West Africa) and the other European (from Oxford, England). In these samples, levels of nucleotide and length polymorphism in the IR were found to be more than two times as high as adjacent non-IR-associated regions (estimates of per-nucleotide heterozygosity were 0.30% and 0.12%, respectively). Most polymorphic positions identified in the origin IR fall within or just adjacent to a 52-bp alternating purine-pyrimidine ((RY)n) sequence repeat. Within- and between-populations divergence is highest in this portion of the IR, and interspecific divergence in the same region, determined by comparison with an orthologous sequence from the chimpanzee, is also pronounced. Higher levels of diversity in this subregion are not, however, primarily attributable to slippage-mediated repeat unit changes, as nucleotide substitution contributes disproportionately to allelic heterogeneity. An estimate of helical stability in the sequenced region suggests that the hypervariable (RY)n constitutes the major DNA unwinding element (DUE) of the replication origin IR, the location at which the DNA duplex first unwinds and new strand synthesis begins. These findings suggest that the beta-globin IR experiences a higher underlying rate of neutral mutation than do adjacent genomic regions and that enzyme fidelity associated with the initiation of DNA replication at this origin may be compromised. The significance of these findings for our understanding of eukaryotic replication origin biology is discussed.

Animals↗
PubMed2000

Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene.

A common strategy for genotyping large samples begins with the characterization of human single nucleotide polymorphisms (SNPs) by sequencing candidate regions in a small sample for SNP discovery. This is usually followed by typing in a large sample those sites observed to vary in a smaller sample. We present results from a systematic investigation of variation at the human apolipoprotein E locus (APOE), as well as the evaluation of the two-tiered sampling strategy based on these data. We sequenced 5.5 kb spanning the entire APOE genomic region in a core sample of 72 individuals, including 24 each of African-Americans from Jackson, Mississippi; European-Americans from Rochester, Minnesota; and Europeans from North Karelia, Finland. This sequence survey detected 21 SNPs and 1 multiallelic indel, 14 of which had not been previously reported. Alleles varied in relative frequency among the populations, and 10 sites were polymorphic in only a single population sample. Oligonucleotide ligation assays (OLA) were developed for 20 of these sites (omitting the indel and a closely-linked SNP). These were then scored in 2179 individuals sampled from the same three populations (n = 843, 884, and 452, respectively). Relative allele frequencies were generally consistent with estimates from the core sample, although variation was found in some populations in the larger sample at SNPs that were monomorphic in the corresponding smaller core sample. Site variation in the larger samples showed no systematic deviation from Hardy-Weinberg expectation. The large OLA sample clearly showed that variation in many, but not all, of OLA-typed SNPs is significantly correlated with the classical protein-coding variants, implying that there may be important substructure within the classical epsilon 2, epsilon 3, and epsilon 4 alleles. Comparison of the levels and patterns of polymorphism in the core samples with those estimated for the OLA-typed samples shows how nucleotide diversity is underestimated when only a subset of sites are typed and underscores the importance of adequate population sampling at the polymorphism discovery stage. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF261279.]

Alleles↗
PubMed1998

Peripheral sensory nerve defects in apolipoprotein E knockout mice.

Apolipoprotein E (apoE), a plasma lipoprotein involved in lipid metabolism, is also proposed to have important functions within the central and peripheral nervous systems. To investigate the function of apoE in the peripheral nervous system, we examined the structure of sciatic nerves in apoE-deficient (apoE KO) mice. In the normal peripheral nervous system, apoE is produced by nonmyelinating Schwann cells, suggesting a role for apoE in the support of unmyelinated thermal and nociceptive sensory afferents. Using electron microscopy, we have found that apoE KO mice have abnormal and reduced numbers of unmyelinated axons within the sciatic nerve. ApoE KO unmyelinated axons are irregularly shaped and separated by very little Schwann cell cytoplasm. ApoE KO myelinated fibers and myelin are ultrastructurally normal. Consistent with these morphological findings, apoE KO mice display reduced sensitivity to noxious thermal stimuli. These data provide in vivo support for the hypothesis that apoE promotes neuronal health and survival.

Animals↗
PubMed1997

A gene tree for beta-globin sequences from Melanesia.

We have analyzed allelic sequence variation in sixty-one 3-kb beta-globin sequences from the Melanesian population of Vanuatu to demonstrate the value of (1) turning to the autosomal nuclear genome for studies on the evolution of modern humans and (2) using new analytical methods based on a coalescent model. After excluding recombination events, beta-globin sequence variants were connected in a unique gene tree. A gene tree provides more information for inferences on the population genealogy than simple summary statistics such as the average pairwise sequence difference. Estimates of the time to the most recent common ancestor (MRCA) and of the ages of each mutation, conditional on the gene tree, were made using new maximum likelihood methods assuming a coalescent model. We found that allelic beta-globin variation coalesces to a single shared ancestral haplotype over a time scale of approximately 900,000 years. Three major haplotypes (A1, B1, C3) that are older than 200,000 years identify ancestral diversity contemporaneous with the single MRCA for mitochondrial variation.

Animals↗
PubMed1997

Archaic African and Asian lineages in the genetic ancestry of modern humans.

A 3-kb region encompassing the beta-globin gene has been analyzed for allelic sequence polymorphism in nine populations from Africa, Asia, and Europe. A unique gene tree was constructed from 326 sequences of 349 in the total sample. New maximum-likelihood methods for analyzing gene trees on the basis of coalescence theory have been used. The most recent common ancestor of the beta-globin gene tree is a sequence found only in Africa and estimated to have arisen approximately 800,000 years ago. There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained. Modest differences in levels of beta-globin diversity between Africa and Asia are better explained by greater African effective population size than by greater time depth. There may have been a reduction of Asian effective population size in recent evolutionary history. Characteristically Asian ancestry is estimated to be older than 200,000 years, suggesting that the ancestral hominid population at this time was widely dispersed across Africa and Asia. Patterns of beta-globin diversity suggest extensive worldwide late Pleistocene gene flow and are not easily reconciled with a unidirectional migration out of Africa 100,000 years ago and total replacement of archaic populations in Asia.

Africa↗
PubMed1996

Camstatins are peptide antagonists of calmodulin based upon a conserved structural motif in PEP-19, neurogranin, and neuromodulin.

Unbridled increases in intracellular ionized calcium can result in neuronal damage and death. Since many of the deleterious effects of calcium are mediated by calmodulin, we have sought to identify neuronal proteins that inhibit activation of this ubiquitous protein. PEP-19 is a 7.6-kDa neuron-specific protein, which contains a motif similar to the calmodulin binding domains of neuromodulin (GAP-43) and neurogranin (RC3). Here we show that PEP-19 binds calmodulin in an analogous calcium-independent manner with an apparent Kd near 1.2 microM. Furthermore, using the calmodulin-dependent enzyme neuronal nitric oxide synthase, we demonstrate that native PEP-19 is also an antagonist of enzyme activity. Based on the PEP-19 sequence, a series of peptide calmodulin antagonists termed camstatins were synthesized. These analogs define the minimally active domain of PEP-19 and provide a structure/activity relationship for calmodulin antagonism. There was a positive correlation between the binding affinities of the camstatins for calmodulin and their potencies as neuronal nitric oxide synthase inhibitors. Despite the similar IQ motif in PEP-19 and neuromodulin or neurogranin, PEP-19 was not a substrate for protein kinase C. The properties of PEP-19 suggest that it could fulfill a role in neuroprotection.

Amino Acid Sequence↗
PubMed1994

Molecular and population genetic analysis of allelic sequence diversity at the human beta-globin locus.

Allelic sequence polymorphism at the beta-globin locus was investigated in a group of 36 Melanesians. A 3-kilobase fragment containing the gene and its flanking regions was sequenced in 60 normal (beta A) and 12 thalassemic (intron 1, position 5, G-->C) chromosomes. Haplotype relationships between linked polymorphisms were derived by allele-specific PCR amplification and sequencing. Seventeen nucleotide polymorphisms and 2 length variants were identified, and these sites segregated as 17 sequence haplotypes in the normal chromosomes. This haplotype diversity is higher than that expected on the basis of the nucleotide polymorphism observed and is probably due to recombination and gene conversion. Nucleotide diversity at synonymous sites in the sample is 0.14%, suggesting an average age of sequence divergence of approximately 450,000 years, consistent with that expected for a neutrally evolving human nuclear locus.

Alleles↗