Intra- and inter-tribal genetic variability in South American Indians

A review was made of all studies to date concerning the genetic polymorphisms of South American Indians. The observed inter-tribal variability was then compared with the intra-tribal variation encountered in seven Caingang and three Xavante Indian communities. The differing pattern of genetic variability observed within these two tribes was afterwards correlated with the information available about their breeding structure.     

MICA polymorphism in South American Indians

We have studied the MICA alleles of 196 unrelated subjects from three South American Indian tribes (Toba, Wichi and Terena). They are members of isolated tribes located in the Gran Chaco area in northeastern Argentina and in Mato Grosso do Sul in South Central Brazil. Of 55 previously known alleles, nine were observed in South American Indians, compared with 16 that were found in North American Caucasians, suggesting a more restricted allelic distribution of MICA in these tribes. In South American Indians, MICA*00201 was the most frequent allele, with a gene frequency of 33% in Toba, 47% in Wichi and 44% in Terena. MICA*00201, MICA*027 (external domain sequence like MICA*008/TM allele A5) and MICA*010 accounted for more than 90% of all the MICA genes in South American Indians. In North American Caucasians, MICA*00801 (*008/A5.1) accounted for 42% of the genes and was the most common allele. We observed a high degree of linkage disequilibrium between certain alleles of MICA and of HLA-B in the South American Indian populations. Phylogenetic trees constructed using gene frequencies of the transmembrane short tandem repeats in the populations reported here, and in other populations taken from published reports, suggest that South American Indians are more closely related to Asians than to Europeans.     

When growth models are not universal: evidence from marine invertebrates

The accumulation of body mass, as growth, is fundamental to all organisms. Being able to understand which model(s) best describe this growth trajectory, both empirically and ultimately mechanistically, is an important challenge. A variety of equations have been proposed to describe growth during ontogeny. Recently, the West Brown Enquist (WBE) equation, formulated as part of the metabolic theory of ecology, has been proposed as a universal model of growth. This equation has the advantage of having a biological basis, but its ability to describe invertebrate growth patterns has not been well tested against other, more simple models. In this study, we collected data for 58 species of marine invertebrate from 15 different taxa. The data were fitted to three growth models (power, exponential and WBE), and their abilities were examined using an information theoretic approach. Using Akaike information criteria, we found changes in mass through time to fit an exponential equation form best (in approx. 73% of cases). The WBE model predominantly overestimates body size in early ontogeny and underestimates it in later ontogeny; it was the best fit in approximately 14% of cases. The exponential model described growth well in nine taxa, whereas the WBE described growth well in one of the 15 taxa, the Amphipoda. Although the WBE has the advantage of being developed with an underlying proximate mechanism, it provides a poor fit to the majority of marine invertebrates examined here, including species with determinate and indeterminate growth types. In the original formulation of the WBE model, it was tested almost exclusively against vertebrates, to which it fitted well; the model does not however appear to be universal given its poor ability to describe growth in benthic or pelagic marine invertebrates.     

Esterase D in South American Indians.

Significant variation in the frequency of Esterase D isoenzymes was found in 1,070 individuals belonging to eight South American Indian tribes. The Es D1 allele shows frequencies varying from .36 to 1. A region of low prevalence of this allele seems to exist in northern Brazil, involving the Parakanan, Gorotire, and Krahó. The intratribal variation observed in eight Yanomama villages located in Brazil was not exceptional.     

N-glycans are not a universal signal for apical sorting of secretory proteins.

In MDCK cells, N-glycans have been shown to determine the sorting of secretory proteins and membrane proteins to the apical domain in the absence of a dominant basolateral targeting signal. We have examined the sorting of endogenous proteins in ECV304 cells in the presence and absence of tunicamycin, an inhibitor of N-linked glycosylation. A prominent apically secreted protein of 71 kDa was not N-glycosylated and continued to be secreted apically in the presence of tunicamycin. In contrast, other endogenous proteins that were N-glycosylated were secreted preferentially into the basolateral medium or without polarity. When rat growth hormone was expressed in MDCK and ECV304 cells, we observed 65 and 94% of the secretion to the basolateral medium, respectively. Introduction of a single N-glycan caused 83% of the growth hormone to be secreted at the apical surface in MDCK cells but had no significant effect on the polarity of secretion of growth hormone in ECV304 cells. These results indicate that not all cell lines recognise N-glycans as a signal for apical sorting and raises the possibility of using ECV304 cells as a model system for analysis of apical sorting molecules.     

Lesions of the frontal bone in American Indians

Over 1,400 adult skulls from archeological sites along the Atlantic Seaboard, in the Midwest and in the Southwest were examined for frontal lesions. A late prehistoric site in Delaware yielded the highest frequency. Next was a late prehistoric site in Illinois, but here the high frequency may reflect in part the collector's special interest in bone pathology. By contrast, the historic and early prehistoric sites yielded the lowest frequencies. Like Hooton and Snow, the only previous American investigators who have recorded frontal lesions in detail, the present authors agree that most of the occurrences in skulls from Archaic and early Pueblo sites are due to trauma. However, in the other groups studied most of the lesions appear to be inflammatory and to have a rather constant location on the frontal. Some are accompanied by lesions on the parietals and on certain long bones. After healing bone remodelling gradually eliminates much of the original disfigurement. Examples of lesions in different stages are illustrated. The appearance of some of the inflammatory lesions suggests syphilis, but satisfactory proof of this is not yet forthcoming. Hopefully, these findings will rekindle interest in the problem and stimulate further efforts to reach correct diagnoses.     

Assessing Accuracy of Genotype Imputation in American Indians

Background

Genotype imputation is commonly used in genetic association studies to test untyped variants using information on linkage disequilibrium (LD) with typed markers. Imputing genotypes requires a suitable reference population in which the LD pattern is known, most often one selected from HapMap. However, some populations, such as American Indians, are not represented in HapMap. In the present study, we assessed accuracy of imputation using HapMap reference populations in a genome-wide association study in Pima Indians.

Results

Data from six randomly selected chromosomes were used. Genotypes in the study population were masked (either 1% or 20% of SNPs available for a given chromosome). The masked genotypes were then imputed using the software Markov Chain Haplotyping Algorithm. Using four HapMap reference populations, average genotype error rates ranged from 7.86% for Mexican Americans to 22.30% for Yoruba. In contrast, use of the original Pima Indian data as a reference resulted in an average error rate of 1.73%.

Conclusions

Our results suggest that the use of HapMap reference populations results in substantial inaccuracy in the imputation of genotypes in American Indians. A possible solution would be to densely genotype or sequence a reference American Indian population.     

Serum clusterin levels are not increased in presymptomatic Alzheimer's disease

Increased plasma levels of clusterin have recently been found to be associated with severity and progression in Alzheimer's disease (AD). We have investigated clusterin levels in serum of elderly people with presymptomatic AD from a population-based prospective cohort study. During 10 years follow-up, 43 participants were diagnosed with AD after on average 4.2 years (±2.6 years SD) after the initial blood sampling. At the time of blood sampling, these participants showed normal cognitive function. For each presymptomatic AD case, a control was matched on gender and age. Furthermore, the selected controls had to remain dementia-free and still be alive at the end of follow-up. Quantitative serum clusterin levels were measured with a newly developed multiple reaction monitoring (MRM) assay. Results of the assay showed no significant difference in clusterin levels between presymptomatic AD and controls (p-value 0.54). In conclusion, serum clusterin is not an early, presymptomatic biomarker for AD.     

Twelve Thousand Years: American Indians in Maine

Twelve Thousand Years: American Indians in Maine. Bruce J. Bourque. with Steven L. Cox and Ruth H. Whitehead. Lincoln: University of Nebraska Press, 2001.368 pp.     

American Indians without tribes in the twenty-first century

Among American Indians and Alaska Natives, most aspects of ethnicity are tightly associated with the person's tribal origins. Language, history, foods, land and traditions differ among the hundreds of tribes indigenous to the USA. With this in mind, we ask why almost one million American Indians failed to respond to the tribal affiliation part of the Census 2000 race question. We investigate four hypotheses about why one-third of multiracial American Indians and one-sixth of single-race American Indians did not write any response to the tribal affiliation question: (1) survey item non-response that undermines all fill-in-the-blank questions; (2) a non-salient tribal identity; (3) a genealogy-based affiliation; and (4) a mestizo identity, which does not require a tribe. We use multivariate logistic regression models and high-density restricted-use Census 2000 data. We find support for the first two hypotheses and note that predictors differ substantially for single-race versus multiple-race American Indians.     

A genome-wide association study of BMI in American Indians

Numerous studies have been done to understand genetic contributors to BMI, but only a limited number of studies have been done in nonwhite groups such as American Indians. A genome-wide association study (GWAS) for BMI was therefore performed in Pima Indians. BMI measurements from a longitudinal study of 1,120 Pima Indians and 454,194 single-nucleotide polymorphisms (SNPs) from the 1 million Affymetrix SNP panel were used (35% of SNPs were excluded due to minor allele frequency <0.05). Data included BMI measured at multiple examinations collected from 1965 to 2004, as well as the maximum BMI at one of these visits. General and within-family tests were performed using a maximum-likelihood based mixed model procedure. No SNP reached a genome-wide significance level (estimated at P < 4.94 × 10(-7)). For repeated measures analyses, the strongest associations for general and within-family tests mapped to two different regions on chromosome 6 (rs9342220 (P = 1.39 × 10(-6)) and rs7758764 (P = 2.51 × 10(-6)), respectively). For maximum BMI, the strongest association for the general tests mapped to chromosome 4 (rs17612333; P = 1.98 × 10(-6)) and to chromosome 3 (rs11127958; P = 1.53 × 10(-6)) for the within-family tests. Further analysis is important because only a few of these regions have been previously implicated in a GWAS and genetic susceptibility may differ by ethnicity.