Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA.

We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present.

An ancient RNase H1 splice junction mutant preserved in a 19-million-year-old genetic fossil in ape genomes.

A retroprocessed pseudogene (retropseudogene) descended from the gene encoding ribonuclease (RNase) H1 has been found in ape genomes that preserves a splice junction mutation event that altered the carboxyl-terminal end of the enzyme. The GT --> GC transition mutant at the 5' splice junction of RNase H1 exon 7/intron 7 led to the absence of exon 8 and more than 1 kb of intron 7 sequence being substituted. Comparison of source gene and pseudogene sequences indicates that the retrotranscription event occurred 19 million years ago. Present in these sequences is an in-frame stop and several available polyadenylation signals, suggesting that the mutant allele could have been translated. At the present time, the genetic fossil is the only evidence that the mutation ever occurred, and thus represents an archival marker of an ancient genetic event in primate evolution.

Molecular archeology of an SP100 splice variant revisited: dating the retrotranscription and Alu insertion events.

BACKGROUND: SP100 is a nuclear protein that displays a number of alternative splice variants. In Old World monkeys, apes and humans one of these variants is extended by a retroprocessed pseudogene, HMG1L3, whose antecedent gene is a member of the family of high-mobility-group proteins, HMG1. This is one of only a few documented cases of a retropseudogene being incorporated into another gene as a functional exon. In addition to the HMG1L3 insertion, Old World monkey genomes also contain an Alu sequence within the last SP100-HMG intron. PCR amplification of the 3' end of the SP100 gene using genomic DNAs from human and New World and Old World monkey species, followed by direct sequencing of the amplicons has made dating the HMG1L3 and Alu insertion events possible. RESULTS: PCR amplifications confirm that the HMG1L3 retrotransposition into the SP100 locus occurred after divergence of New World and Old World monkey lineages, some 35-40 million years ago. PCR amplification also shows that an upstream Alu sequence was inserted in the last SP100-HMG intron after divergence of the Old World monkey and ape lineages. Direct sequencing of the Alu in five Old World monkey species places the latter event at around 19 million years ago. Finally, ten single base mutations and one deletion in the Alu differentiate African from Asian Old World monkey species. CONCLUSIONS: PCR and DNA sequence analysis of 'genetic fossils' such as retropseudogenes and Alu elements in primates give details as to the timing of such events and can reveal sequence features useful for other molecular phylogenetic applications.

Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates.

BACKGROUND: The serine hydroxymethyltransferase processed pseudogene SHMT-ps1 has been suggested to be unique to the order Primates because of the failure to amplify this sequence by PCR from genomic DNAs of any non-primate mammal species. Here, 'molecular beacon' probes specific to SHMT-ps1 were used in an attempt to verify this suggestion. RESULTS: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates. The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians. CONCLUSIONS: These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

Use of high specific activity StarFire oligonucleotide probes to visualize low-abundance pre-mRNA splicing intermediates in S. pombe.

An oligonucleotide labeling system was developed that can produce radiolabeled hybridization probes with tenfold or more higher specific activity than is obtained by traditional 5'-end-labeling with polynucleotide kinase. Yet the system is as rapid and simple as kinase labeling. The reaction uses the Klenow fragment of E. coli DNA polymerase to add alpha-32P-dA residues to the 3'-end of an oligonucleotide in a primer-extension reaction. Unlike other methods of radioactive tailing (e.g., terminal transferase), a single species is produced of both known length and known specific activity. The reaction is efficient, and over 90% of probe molecules are routinely labeled. Using this method of labeling, an oligonucleotide was shown to be tenfold more sensitive in detecting target DNA sequences in a dot blot hybridization assay, compared to the same oligonucleotide labeled using polynucleotide kinase. Northern blots of Schizosaccharomyces pombe RNA were probed with an oligonucleotide specific for intron 1 of the tf2d gene, a TATA-box binding transcription factor. Kinase-labeled tf2d probe detected only unspliced RNA, while the same oligonucleotide labeled using the new method detected both unspliced tf2d RNA and rare pre-mRNA splicing intermediates.

Serotonin transporter gene (5-HTT) polymorphisms and compulsive buying.

We examined a panel of 21 patients diagnosed with compulsive buying for two DNA sequence polymorphisms found in the gene that encodes the serotonin transport (5-HTT). One polymorphism, found in the promoter region of the 5-HTT gene, involves a 44-base pair (bp) deletion, and the other, found in the second intron, is due to variable numbers of a repeat sequence. We also typed a panel of 38 psychiatrically normal controls for both 5-HH markers. When compared to this control panel, no significant differences were seen for either 5-HTT marker among the compulsive buyers.

Serine hydroxymethyltransferase pseudogene, SHMT-ps1: a unique genetic marker of the order primates.

The serine hydroxymethyltransferase (SHMT) gene family is composed of three distinct loci. The cytosolic (cSHMT) and mitochondrial (mSHMT) genes constitute the functional members of the gene family, while the third member, SHMT-ps1, is a processed pseudogene descended from cSHMT. PCR analysis of 38 primate and nonprimate mammal species indicates that the reverse transcription event that gave rise to SHMT-ps1 might have occurred after the divergence of the primates from the rest of the mammals. In addition, direct sequencing of primate PCR products has revealed several features--including two deletions, an insertion, and two single base mutations--that are unique to specific phylogenetic branches of the order Primates. These unique features make the SHMT-ps1 locus a useful marker in molecular studies of the primates.

The Bal I and Msp I polymorphisms in the dopamine D3 receptor gene display, linkage disequilibrium with each other but no association with Tourette syndrome.

The D3-dopamine receptor gene, DRD3, has been considered as a candidate gene in several disorders in which the dopaminergic system has been implicated including Tourette syndrome and schizophrenia. The DRD3 studies to date have all used as the gene marker a Bal I polymerase chain reaction restriction fragment length polymorphism (PCR RFLP). There have been recent reports on a second marker, an Msp I PCR RFLP, that lies 40 kb downstream. We have typed a sample of 16 Tourette syndrome families with both markers and observed significant linkage disequilibrium between the two markers but no apparent association of either marker with Tourette syndrome.

Nucleotide sequence, chromosome localization, and evolutionary conservation of a serine hydroxymethyltransferase-processed pseudogene.

The nucleotide sequence and chromosomal localization of a human pseudogene is reported. Sequence data suggest that this pseudogene was derived via reverse transcription from the gene encoding the cytosolic isoform of the enzyme serine hydroxymethyltransferase. In addition, a heteroduplex analysis of this pseudogene among several species of nonhuman primate indicates a relatively high degree of sequence conservation.

A developmental-genetic model of alcoholism: implications for genetic research.

The research for biological-genetic markers of alcoholism is discussed in the context of a multifactorial, heterogeneous, developmental model of the disease. It is suggested that the strategies used in both linkage and association studies require modification to accommodate this more complex model. It is also suggested that several extant associations of genetic markers with alcoholism represent true secondary interactive phenomena that alter the outcome of primary alcoholism genotypes at the phenotype level.

Platelet MAO activity in type I and type II alcoholism.

Lowered activity of the enzyme MAOB in the platelets and other tissues of alcoholics than of nonalcoholics is the most replicated biological finding in genetic research in alcoholism. Data presented here and elsewhere also indicate that the relationship between MAOB activity and alcoholism extends to the clinical subtypes referred to as Type I and Type II alcoholism. A detailed examination of the relationship between in vitro platelet MAOB activity levels, alcoholic subtype, and general mental health status among the relatives of the probands suggests that low MAOB activity is a marker of increased risk overall and that the families of Type II alcoholics have a higher genetic risk loading than do the families of Type I alcoholics. This increased genetic loading is probably due to the classification of Type II alcoholics on the basis of features related to severity of illness and additional psychiatric features such as personality disorders. Although the families of alcoholics tend to have higher levels of psychiatric illness compared to the general population, the overall risk is compounded in the families of Type II alcoholics, and these differences in underlying risk are reflected in the observed differences in MAOB activities. Thus, MAOB is not a biological/genetic marker of alcoholism sensu stricto but is rather a biological/genetic marker of an underlying pathophysiologic process leading to alcoholism and other psychiatric illness. The task now before us is to understand this process and how the activity of MAOB is involved.

Association of monoamine oxidase (MAO) activity with alcoholism and alcoholic subtypes.

A familial/genetic study of platelet monoamine oxidase (MAO) activity in alcoholics was carried out. MAO activities were determined using phenylethylamine (PEA) as substrate at Km concentration (1.2 microM) and at saturating concentration (12.0 microM). Complex segregation analysis of familial data indicated a single major gene mode of transmission of activity at both substrate concentrations. In addition, the present sample size (13 families, 108 members) proved sufficient to allow correlation analysis of enzyme activity with affection status and clinical subtypes of affecteds. MAO activity was significantly correlated with alcoholism at both Km and saturating substrate concentrations and a significant correlation between low MAO activity and Cloninger Type II alcoholism was seen at Km substrate concentration. These results confirm a hierarchical cosegregation of platelet MAO activity and alcoholism suggesting that MAO activity warrants continued status as a marker in alcoholism.

A familial/genetic study of plasma serine and glycine concentrations.

Plasma serine and glycine concentrations were assayed in a sample of 28 nuclear families (n = 108). Complex segregation analysis of these familial data reveals significant genetic control of concentrations via a single major gene locus. The serine and glycine metabolizing enzyme serine hydroxymethyltransferase (SHMT) is suggested as the most likely candidate for this single major gene locus.

A genetic familial study of monoamine oxidase B activity and concentration in alcoholics.

Platelet monoamine oxidase B (MAO B) activity and concentration were studied in a small sample of alcoholic families (n = 8) and in 20 unrelated, nonalcoholic controls. Complex segregation analyses of familial data indicated that both activity and concentration are controlled by a single major gene locus with a multifactorial background effect accounting for 0-50% of the variance. When the alcoholic family members (n = 24) were compared with the controls, all determinations of activity display significant differences, whereas MAO B concentration levels showed no difference. These results indicated that the lowered MAO B activities frequently reported among alcoholics do not reflect a change in the number of MAO B macromolecules expressed in platelets, but could be caused by the presence of an inhibitor or by a polymorphic or variant form of the enzyme.

Why there is no gene for alcoholism.

The search for and recognition of biological and genetic markers of alcoholism are discussed in the context of a heuristic model of human alcoholism as a complex, multilocus, heterogeneous disorder. Implications of this model for the interpretation of results from both linkage and association studies are presented.