Africans Research Articles

Population genetic variation of SLC6A4 gene, associated with neurophysiological development

The serotonin transporter 5-HTT is encoded by a single gene SLC6A4. Polymorphisms in SLC6A4 has been associated with a wide variety of neurological and psychiatric disorders including increased risk of posttraumatic stress disorder, higher likelihood for depression, obsessive-compulsive disorder (OCD), increased hostility and criminal behaviour. Genes associated with complex diseases often exhibit strong signatures of purifying selection compared to others. Further, discernible population specific variation in the signature of natural selection have been observed for several complex disease-related genes. In this project we aimed to investigate the population genetic variation of the serotonin transporter gene (SLC6A4), focussing on the single nucleotide polymorphisms (SNPs). To this end, we employed 2504 individuals around the globe available in 1000 Genome project Phase III data and classified them into five ethnic groups: Americans (AMR), Europeans (EUR), Africans (AFR), East Asians (EAS) and South Asians (SAS). Principal component analysis (PCA) performed on all annotated SNPs of SLC6A4 depicted clear clustering between Africans and the rest of the world along PC1, and East Asians and other non-African populations along PC2. Further, these SNPs were found to be under strong selection pressure especially among East Asian populations with significantly high positive cross-population extended haplotype homozygosity scores compared to Africans, indicating that SLC6A4 has likely undergone a strong selective sweep among the East Asians in the recent past. Our study can potentially explain the association between polymorphisms in SLC6A4, and major depression and suicidal tendencies among people of East Asian ancestry and the absence of such associations among people of European ancestry.

Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform.

Genetic polymorphisms of enzymes and transporters associated with the absorption, distribution, metabolism, and elimination (ADME) of drugs are one of the major factors that contribute to interindividual variations in drug response. In the present study, we aimed to elucidate the pharmacogenetic profiles of the Korean population using the Affymetrix Drug Metabolizing Enzyme and Transporters (DMET™) platform. A total of 1,012 whole blood samples collected from Korean subjects were genotyped using the DMET™ plus microarray. In total, 1,785 single nucleotide polymorphism (SNP) markers for 231 ADME genes were identified. The genotype and phenotype of 13 clinically important ADME genes implemented in the Clinical Pharmacogenetics Implementation Consortium guidelines were compared among different ethnic groups. Overall, the genotype frequencies of the Korean population were similar to those of the East Asian population. Several genes, notably CYP2C19 and VKORC1, showed marked differences in Koreans compared to Europeans (EURs) or Africans (AFRs). The percentage of CYP2C19 poor metabolizers was 15% in Koreans and less than 3% in EURs or AFRs. The frequencies of causative SNPs of the VKORC1 gene for the low warfarin dose phenotype were 90%, 60%, and 10% in Koreans, EURs and AFRs, respectively. Our findings can be utilized for optimal pharmacotherapy in Korean patients.

Racial Differences Effects on Oral Health and Periodontal Diseases Extent, Staging and Grading among the Multi-Ethnic Expatriates in Aseer Region, Saudi Arabia

Background: Given the increase in the numbers of expatriates in Saudi Arabia and the shortage of information about expatriates’ oral health and periodontal disease severity and progression. Objectives: This study aimed to evaluate the effects of the racial differences on oral health and periodontal disease extent, staging, and grading among the multi-ethnic expatriates in the Aseer region, Saudi Arabia. Materials and Methods: This cross-sectional study was carried out on 300 expatriates in Aseer region, Saudi Arabia. They were divided into three equal racial different groups (n = 100), Arabs (AR), Asians (AS), and Africans (AF). The interviews of all participants were completed then the clinical examinations of periodontal diseases extent, staging, and grading parameters were performed. Statistical analysis was done by ANOVA test, Tukey’s test, and Chi-square test. The statistical significance level was determined at p < 0.05. Results: There were statistically significant differences in the comparison between the three ethnic/racial groups in clinical parameters except in GBI, PCR, FI, TFO, and BC, where there were no statistically significant differences in the comparison between the three ethnic/racial groups. There were differences associated with age, gender, smoking, and diabetes, without statistically significant differences among the three racial groups. Conclusion: We concluded that most participants in this study had a generalized severe grade 4 plaque-induced gingivitis and localized periodontitis stage III grade B.

Genetics of Circulating Resistin Level, a Biomarker for Cardiovascular Diseases, Is Informed by Mendelian Randomization and the Unique Characteristics of African Genomes.

Resistin, a protein linked with inflammation and cardiometabolic diseases, is one of few proteins for which genome-wide association studies consistently report variants within and near the coding gene (RETN). Here, we took advantage of the reduced linkage disequilibrium in African populations to infer genetic causality for circulating resistin levels by performing genome-wide association studies, whole-exome analysis, fine mapping, Mendelian randomization, and transcriptomic data analyses. Genome-wide association studies and fine-mapping analyses for resistin were performed in 5621 African-ancestry individuals, including 3754 continental Africans and 1867 African Americans. Causal variants identified were subsequently used as an instrumental variable in Mendelian randomization analyses for homeostatic modeling-derived insulin resistance index, body mass index, and type 2 diabetes. The lead variant (rs3219175, in the promoter region of RETN) for the single locus detected was the same for continental Africans (P=5.0×10-111) and for African Americans (9.5×10-38), respectively explaining 12.1% and 8.5% of variance in circulating resistin. Fine-mapping analyses and functional annotation revealed this variant as likely causal affecting circulating resistin levels as a cis-eQTL increasing RETN expression. Additional variants regulating resistin levels were upstream of RETN with genes PCP2, STXBP2, and XAB2 showing the strongest association using integrative analysis of genome-wide association studies with transcriptomic data. Mendelian randomization analyses did not provide evidence for resistin increasing insulin resistance, body mass index, or type 2 diabetes risk in African-ancestry populations. Taking advantage of the fine-mapping resolution power of African genomes, we identified a single variant (rs3219175) as the likely causal variant responsible for most of the variability in circulating resistin levels. In contrast to findings in some other ancestry populations, we showed that resistin does not seem to increase insulin resistance and related cardiometabolic traits in African-ancestry populations.

Type 1 diabetes loci display a variety of native American and African ancestries in diseased individuals from Northwest Colombia.

BACKGROUNDType 1 diabetes (T1D) is a complex disease with a higher incidence in Europeans than other populations. The Colombians Living in Medellin (CLM) is admixed with ancestry contributions from Europeans, Native Americans (NAT) and Africans (AFR).AIMOur aim was to analyze the genetic admixture component at candidate T1D loci in Colombian individuals with the disease.METHODSSeventy-four ancestry informative markers (AIMs), which tagged 41 T1D candidate loci/genes, were tested by studying a cohort of 200 Northwest Colombia diseased individuals. T1D status was classified by testing for glutamic acid decarboxylase (GAD-65 kDa) and protein tyrosine-like antigen-2 auto-antibodies in serum samples. Candidate loci/genes included HLA, INS, PTPN22, CTLA4, IL2RA, SUMO4, CLEC16A, IFIH1, EFR3B, IL7R, NRP1 and RNASEH1, amongst others. The 1,000 genome database was used to analyze data from 94 individuals corresponding to the reference CLM. As the data did not comply with a normal distribution, medians were compared between groups using the Mann-Whitney U-test.RESULTSBoth T1D patients and individuals from CLM displayed mainly European ancestry (61.58 vs 62.06) followed by Native American (27.34 vs 27.46) and to a lesser extent the AFR ancestry (10.28 vs 10.65) components. However, compared to CLM, ancestry of T1D patients displayed a decrease of NAT ancestry at gene EFR3B (24.30 vs 37.10) and an increase at genes IFIH1 (32.07 vs 14.99) and IL7R (52.18 vs 39.18). Also, for gene NRP1 (36.67 vs 0.003), we observed a non-AFR contribution (attributed to NAT). Autoimmune patients (positive for any of two auto-antibodies) displayed lower NAT ancestry than idiopathic patients at the MHC region (20.36 vs 31.88). Also, late onset patients presented with greater AFR ancestry than early onset patients at gene IL7R (19.96 vs 6.17). An association analysis showed that, even after adjusting for admixture, an association exists for at least seven such AIMs, with the strongest findings on chromosomes 5 and 10 (gene IL7R, P = 5.56 × 10-6 and gene NRP1, P = 8.70 × 10-19, respectively).CONCLUSIONAlthough Colombian T1D patients have globally presented with higher European admixture, specific T1D loci have displayed varying levels of Native American and AFR ancestries in diseased individuals.

Biobibliografía de los jesuitas de la estancia de Alta Gracia (Córdoba-Argentina).

La contribución apunta a identificar y valorar las casi desconocidas figuras que a lo largo de 124 años formaron y desarrollaron la estancia jesuítica de Alta Gracia. Hoy transformada en una importante ciudad de la provincia de Córdoba, que conservó la antigua iglesia y edificio que los albergó. Aquí se mencionan las biografías de cada uno de los jesuitas que hemos podido localizar y que administraron o murieron en la estancia bajo distintas circunstancias. Igualmente constituyen solo una parte de la po-blación estable que comenzó a surgir en 1643, con una amplia mayoría de africanos y afroamericanos esclavizados.

Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes Project data set.

To assess the statistical significance of associations between variants and traits, genome-wide association studies (GWAS) should employ an appropriate threshold that accounts for the massive burden of multiple testing in the study. Although most studies in the current literature commonly set a genome-wide significance threshold at the level of P=5.0 × 10−8, the adequacy of this value for respective populations has not been fully investigated. To empirically estimate thresholds for different ancestral populations, we conducted GWAS simulations using the 1000 Genomes Phase 3 data set for Africans (AFR), Europeans (EUR), Admixed Americans (AMR), East Asians (EAS) and South Asians (SAS). The estimated empirical genome-wide significance thresholds were Psig=3.24 × 10−8 (AFR), 9.26 × 10−8 (EUR), 1.83 × 10−7 (AMR), 1.61 × 10−7 (EAS) and 9.46 × 10−8 (SAS). We additionally conducted trans-ethnic meta-analyses across all populations (ALL) and all populations except for AFR (ΔAFR), which yielded Psig=3.25 × 10−8 (ALL) and 4.20 × 10−8 (ΔAFR). Our results indicate that the current threshold (P=5.0 × 10−8) is overly stringent for all ancestral populations except for Africans; however, we should employ a more stringent threshold when conducting a meta-analysis, regardless of the presence of African samples.

Differential Natural Selection of Human Zinc Transporter Genes between African and Non-African Populations.

Zinc transporters play important roles in all eukaryotes by maintaining the rational zinc concentration in cells. However, the diversity of zinc transporter genes (ZTGs) remains poorly studied. Here, we investigated the genetic diversity of 24 human ZTGs based on the 1000 Genomes data. Some ZTGs show small population differences, such as SLC30A6 with a weighted-average FST (WA-FST = 0.015), while other ZTGs exhibit considerably large population differences, such as SLC30A9 (WA-FST = 0.284). Overall, ZTGs harbor many more highly population-differentiated variants compared with random genes. Intriguingly, we found that SLC30A9 was underlying natural selection in both East Asians (EAS) and Africans (AFR) but in different directions. Notably, a non-synonymous variant (rs1047626) in SLC30A9 is almost fixed with 96.4% A in EAS and 92% G in AFR, respectively. Consequently, there are two different functional haplotypes exhibiting dominant abundance in AFR and EAS, respectively. Furthermore, a strong correlation was observed between the haplotype frequencies of SLC30A9 and distributions of zinc contents in soils or crops. We speculate that the genetic differentiation of ZTGs could directly contribute to population heterogeneity in zinc transporting capabilities and local adaptations of human populations in regard to the local zinc state or diets, which have both evolutionary and medical implications.

Population-specific differences in gene conversion patterns between human SUZ12 and SUZ12P are indicative of the dynamic nature of interparalog gene conversion

Nonallelic homologous gene conversion (NAHGC) resulting from interparalog recombination without crossover represents an important influence on the evolution of duplicated sequences in the human genome. In 17q11.2, different paralogous sequences mediate large NF1 deletions by nonallelic homologous recombination with crossover (NAHR). Among these paralogs are SUZ12 and its pseudogene SUZ12P which harbour the breakpoints of type-2 (1.2-Mb) NF1 deletions. Such deletions are caused predominantly by mitotic NAHR since somatic mosaicism with normal cells is evident in most patients. Investigating whether SUZ12 and SUZ12P have also been involved in NAHGC, we observed gene conversion tracts between these paralogs in both Africans (AFR) and Europeans (EUR). Since germline type-2 NF1 deletions resulting from meiotic NAHR are very rare, the vast majority of the gene conversion tracts in SUZ12 and SUZ12P are likely to have resulted from mitotic recombination during premeiotic cell divisions of germ cells. A higher number of gene conversion tracts were noted within SUZ12 and SUZ12P in AFR as compared to EUR. Further, the distinctive signature of NAHGC (a high number of SNPs per paralog and a high number of shared SNPs between paralogs), a characteristic of many actively recombining paralogs, was observed in both SUZ12 and SUZ12P but only in AFR and not in EUR. A novel polymorphic 2.3-kb deletion in SUZ12P was identified which exhibited a high allele frequency in EUR. We postulate that this interparalog structural difference, together with low allelic recombination rates, could have caused a reduction in NAHGC between SUZ12 and SUZ12P during human evolution.

&lt;em&gt;A Matter of “Knowledge in the Blood”? Unperforming Racial and Ethnic Prejudice in Tertiary Educational Spaces in South Africa&lt;/em&gt;

Although the relatively new state of South Africa has been dubbed the rainbow nation by its iconic first president, Nelson Mandela, the much- anticipated shift from apartheid segregation to an inclusive constitutional democracy has been plagued by racial and ethnic prejudice, intermittent civil protests and violent crime. The shift in po liti cal power has not been accompanied by concomitant transformation towards a truly nonracial democratic state. Jansen (2011) singles out the institutional racism that has continued to corrode the social fabric of South Africa in schools, colleges, and universities. He further asserts that in order to deal with such prejudice, direct confrontation does not work, nor does the performance of truth and reconciliation narratives. This article argues that tackling racial and ethnic conflicts requires an understanding of what constitutes knowledge in the blood. The received knowledge embedded in people's minds and hearts through intergenera- tional transmission tends to trigger nostalgic memories that have hindered young South Af ri cans from moving towards a truly

Diaspora Sounds from Caribbean Central America

Bearing a proud, militant history of resistance to slavery, the Garinagu1 comprise a unique African-Amerindian maroo people dating to the early seventeenth century, when indigenous Carib and Arawak-speaking peoples of the eastern Caribbean took in Afri cans escaped from bondage. In their native St. Vincent, the Garinagu (or Black Caribs, as they were known during the colonial era) resisted French and English forces who sought to take control of the island's cultivable lands.

Slavery in the Lower South

If you ask Americans about the origins of slavery in this country, most would doubtlessly tell you that it all began at \h_^z:a^m the his tory of Africans in colonial North America is not synonymous with slavery. In the Lower South, indigenous sla very predated the arrival of Africans; in deed, some of the first Africans to reach the shores of what would later become the United States were free. Moreover, both free and enslaved Africans arrived more than a century before 1619. A free African named Juan Garrido accompa nied Juan Ponce de Leon when he claimed La Florida for Spain in 1513. Africans, free and slave, were also present in all of the major Spanish expeditions through the Lower South. Wherever these Afri cans traveled, they encountered Native Americans held in slavery. During the early years of Spanish settlement, most slaves were not Africans. At first, Spain's Queen Isabella forbade the enslave *?t ' ... ;^**.:>..-..... -:'i*J

The Seeds of Change

Little could Christopher Columbus realize upon reaching America's shores in 1492 that he was about to set in motion processes of encounter and ex that would dramatically alter life in both the New and Old Worlds. Indeed, who could have foretold that, as a conse quence of the tiny flotilla's voyage, Afri cans would one day become the dominant ethnic group in the Caribbean, that New World foods such as potatoes and corn would become major crops in Asia, or that tomatoes would transform cuisine in Europe? Nonetheless, Columbus began a process of that even tually altered the world's flora and fauna, reordered the ethnic compo sition of entire countries, and changed the diet and health of peoples every where. This fascinating story is the subject of Seeds of Change, the quincentenary exhibition of the Na tional Museum of Natural History at the Smithsonian Institution. Sched uled to open in Washington 12 Octo ber 1991 (and to travel broadly thereaf ter), the exhibition will demonstrate that the New World underwent rapid and pro found transformations because of certain seeds of change that the Europeans introduced, sometimes deliberately, some times accidentally. Columbus and those who followed

The archaeology of racism and ethnicity on southern plantations

Ethnic studies have recently received great em phasis in American historical archaeology. Three groups have commonly been studied: blacks or Af rican Americans, Hispanics, and Overseas Chinese (Staski n.d.). Each of these groups is seen as hav ing an emic identity within the historic period be ing studied, an identity which is connected to the identity held by members of the present groups that descend from these historical ancestors (Staski n.d.). Indeed, a major reason why these three groups are studied is the desire of these present groups to understand their ancestors. Due to prob lems with biased or incomplete written records (Deetz 1977:7-8), archaeology is embraced as a method of inquiry, of building a bridge of under standing between these present groups and their forebears. Such studies assume a continuity between the historical ethnic groups and their present descen dants, so that, for instance, in the case of African Americans, a certain category or definition of eth nicity will be common between an 18th-century slave and a modern black person. To date, archae ology has attempted to describe this connection, first, by establishing the presence and vitality of past ethnic groups from the archaeological record?for example, Ferguson's identification of Colono ceramics as the products of black crafts women (Ferguson 1980) and not of Native Amer icans, as had been thought previously (Noel Hume 1962a)?and second, by studying the "normative lives" of members of past groups. In the second instance, a narrative of everyday life is devised from which historical, social, or personal infer ences can be drawn by the group's modern stu dents. Neither of these approaches is, in any way, wrong or misdirected. The social purpose they serve, especially in revealing the proud history of groups who have been unjustly discredited in the past or present, is vitally important. In this pur pose, archaeology may serve well in creating a bond between present members of ethnic groups and their honored heritage as a way of fostering a strong, positive ethnic identity. Still, however, in simple procedural or technical terms, some prob lems may be encountered in fulfilling these most necessary functions. One problem is that any study which proceeds simply on the basis of identifying ethnic markers, but stops at this basic level, will likely prove too simplistic to be of much value. Colono ceramics again provide an example. Recent research (Fer guson n.d.) reveals that these ceramics are not sim ply the product of enslaved African Americans, but rather of Creole cultures created as adaptive responses to complex interactions between Afri cans, Native Americans, and Europeans, interac tions which, furthermore, varied by the different geographical and cultural arenas in which they took place. Using Colono ceramics as a simple ethnic marker which equates with African Ameri cans is an inaccurate oversimplification. A more serious problem concerns the uncritical acceptance of a simple equation between past and present ethnic groups. A Gambian Muslim, kid napped in Africa in the late 18th century, for ex ample, is certainly the ancestor of a modern black family (Haley 1976). Important questions remain, however, such as: Was his experience, as an Af rican, a Gambian, a Muslim, or as a slave in America, similar at all to the experience of a mod ern black American? Was this historical figure's own identity that of a black, an African, a Gam bian, or a Muslim, a combination of these, or all of them in some succession? Certain broad similari ties between this ancestor and his descendants may occur. The most unfortunate, perhaps, is the fact that each has experienced or will experience forms of oppression that are based in their ethnicity. Can these experiences be equated, and will each there fore have a similar ethnic identity? Archaeologists often assume that these questions have been an

The Madness of Africa(ns): Or, Anthropology's Reason

The Madness of Africa(ns): Or, Anthropology's Reason

Democracy on Trial in Africa

Africans visualize Western democracy as being "on trial" with respect to its ability to extirpate racism in southern Africa and in the United States, its willingness to al low Africans freely to determine their own social and economic goals and means for attaining them, and its capacity for mak ing adequate technical and financial assistance available in com petition with the Communist countries. The West feels that African states are in danger of sacrificing liberty to the pursuit of equality and that the burden of proof is on them to demon strate that the one-party states now prevalent can be "demo cratic," that civil liberties will be restored where they have been abridged in the case of emergencies, and that "African socialism" will not slide over into doctrinaire communism. Af ricans are sometimes accused of "abandoning" democratic pre cepts and practices bequeathed to them under colonialism. No colonial power ever tried to govern democratically. The new nations are involved in "experiments in democracy" for the first time. Some of their special problems may demand special political measures. It is probable that, as literacy levels rise and political conditions become more stable and if, and when, sustained self-generating economic growth takes place, some of the democratic values never known to the Afri can masses as well as some of those known to leaders but sacri ficed to achieve national unity and rapid modernization will emerge.

The Party System and Democracy in Africa

ANY people believe there is some special connection be tween the democratic form of government and the party system, so that one cannot exist without the other. This belief is strengthened by the fact that the freedom to form as many parties as people want is seen to be incompatible with a to talitarian r?gime. An ideal Communist government is run by a single party composed of the working class; a Fascist government is similarly run by one party in the interests of the capitalist class. This type of thinking is based on a misconception of the true nature of democracy. It confuses cause and effect. There were parties before the advent of democracy. The first political parties in Britain, for example, are believed to have come into being in the reign of Charles II. This was long before the Reform Act of 1832, which was the bare beginning of change in the direction of democracy. At present there are political parties in countries which do not even admit the correctness of the thinking behind democracy. Has not the U.N.'s 17-nation committee on colonialism ruled that there is no self-government? let alone full democracy?in South ern Rhodesia because of the denial of equal voting rights to Afri cans? And yet Southern Rhodesia has political parties which fight and win elections and form governments. South Africa also has parties which have been governing the country for over 50 years against the will of the majority of the people. No one can suggest South Africa enjoys anything like democracy. The same conclusion is reached if we look at the circumstances M