scholarly journals Admixture into and within sub-Saharan Africa

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
George BJ Busby ◽  
Gavin Band ◽  
Quang Si Le ◽  
Muminatou Jallow ◽  
Edith Bougama ◽  
...  
Keyword(s):  
Gene Flow ◽  
Geographic Region ◽  
Sub Saharan Africa ◽  
Genome Wide ◽  
A Genome ◽  
Depth Analysis ◽  
Shared Ancestry ◽  
Sub Saharan ◽  
Linguistic Groups ◽  
Insight Into

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

scholarly journals Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

2020 ◽  
Author(s):  
Catherine Stein ◽  
Penelope Bencheck ◽  
Jacquelaine Bartlett ◽  
Robert P Igo ◽  
Rafal S Sobota ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Sub Saharan Africa ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Chromosome 5 ◽  
Epigenetic Marks ◽  
Genome Wide ◽  
A Genome ◽  
Immunodeficiency Virus ◽  
Sub Saharan

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.

scholarly journals A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

2018 ◽  
Author(s):  
Veena Devi Ganeshan ◽  
Stephen O. Opiyo ◽  
Samuel K. Mutiga ◽  
Felix Rotich ◽  
David M. Thuranira ◽  
...  
Keyword(s):  
Association Study ◽  
Magnaporthe Oryzae ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Sub Saharan ◽  
Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

scholarly journals Inferring adaptive gene-flow in recent African history

2017 ◽  
Author(s):  
George Busby ◽  
Ryan Christ ◽  
Gavin Band ◽  
Ellen Leffler ◽  
Quang Si Le ◽  
...  
Keyword(s):  
Gene Flow ◽  
African Ancestry ◽  
The Gambia ◽  
Sub Saharan Africa ◽  
Histocompatibility Complex ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Multiple Regions ◽  
Novel Method ◽  
Sub Saharan

AbstractGene-flow from an ancestrally differentiated group has been shown to be a powerful source of selectively advantageous variants. To understand whether recent gene-flow may have contributed to adaptation among humans in sub-Saharan Africa, we applied a novel method to identify deviations in ancestry inferred from genome-wide data in 48 populations. Among the signals of ancestry deviation that we find in the Fula, an historically pastoralist ethnic group from the Gambia, are the region that encodes the lactose persistence phenotype, LCT/MCM6, which has the highest proportion of Eurasian ancestry in the genome. The region with the lowest proportion of non-African ancestry is across DARC, which encodes the Duffy null phenotype and is protective for Plasmodium vivax malaria. In the Jola from the Gambia and a Khoesan speaking group from Namibia we find multiple regions with inferred ancestry deviation including the Major Histocompatibility Complex. Our analysis shows the potential for adaptive gene-flow in recent human history.

scholarly journals Admixture into and within sub-Saharan Africa

2016 ◽  
Author(s):  
George Busby ◽  
Gavin Band ◽  
Quang Si Le ◽  
Muminatou Jallow ◽  
Edith Bougama ◽  
...  
Keyword(s):  
Large Scale ◽  
Haplotype Diversity ◽  
Geographic Region ◽  
Sub Saharan Africa ◽  
Agricultural Technologies ◽  
Population Movements ◽  
Crucial Component ◽  
Depth Analysis ◽  
Scale Population ◽  
Sub Saharan

Understanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa. We show that coastal African populations have experienced an influx of Eurasian haplotypes as a series of admixture events over the last 7,000 years, and that Niger-Congo speaking groups from East and Southern Africa share ancestry with Central West Africans as a result of recent population expansions associated with the adoption of new agricultural technologies. We demonstrate that most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of large-scale population movements over the last 4,000 years. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.

scholarly journals Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

2016 ◽  
Author(s):  
Bony De Kumar ◽  
Hugo J. Parker ◽  
Ariel Paulson ◽  
Mark E. Parrish ◽  
Irina Pushel ◽  
...  
Keyword(s):  
Es Cells ◽  
Hox Proteins ◽  
Binding Motifs ◽  
Functional Roles ◽  
Regulatory Interactions ◽  
Mouse Es Cells ◽  
Genome Wide ◽  
A Genome ◽  
Combinatorial Interactions ◽  
Insight Into

AbstractHoxa1 has diverse functional roles in differentiation and development. We have identified and characterized properties of regions bound by Hoxa1 on a genome-wide basis in differentiating mouse ES cells. Hoxa1 bound regions are enriched for clusters of consensus binding motifs for Hox, Pbx and Meis and many display co-occupancy of Pbx and Meis. Pbx and Meis are members of the TALE family and genome-wide analysis of multiple TALE members (Pbx, Meis, TGIF, Prep1 and Prep2) show that nearly all Hoxa1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins defines distinct classes of Hoxa1 targets and indicates a role as cofactors in modulating the specificity of Hox proteins. We also discovered extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes. This study provides new insight into a regulatory network involving combinatorial interactions between Hoxa1 and TALE proteins.

Professors without Borders: The Benefits of a Scholastic Mentoring Program

2018 ◽  
Author(s):  
Jennifer Maul
Keyword(s):  
Higher Education ◽  
Graduate Students ◽  
Sub Saharan Africa ◽  
Mentoring Program ◽  
Mentorship Program ◽  
Postgraduate Study ◽  
Industrialized Nations ◽  
Similar Program ◽  
Sub Saharan ◽  
Insight Into

Universities in sub-Saharan Africa currently struggle to maintain adequate faculty and resources to take on Ph.D. candidates. Expanding enrolment in recent decades has not been met with improvements in university facilities, and neglect from development agencies has made it difficult for the higher education sector to meet the demands of the knowledge economy. As a result African graduate students have few opportunities to pursue postgraduate study in the region and sub-Saharan Africa’s brain drain persists. In order to address the lack of opportunity for graduate study, the Professors without Borders program has been developed. Professors without Borders is a mentorship program, whereby graduate students in sub-Saharan Africa are partnered with professors and academics at universities in industrialized nations and the students are mentored during the course of their degree. The program aims to promote internationalization among universities as well as facilitate development. This report examines the motivation behind the program and its potential for success. The literature review on higher education in sub-Saharan African summarizes the problems facing the sector but indicates the potential for higher education to contribute to economic growth. In addition, the reception of the Professors without Borders idea among African universities indicates unanimously that such a mentorship program would be very much welcomed and beneficial to African Ph.D. students. The experience of a similar program known as BrainRetain by the Irish-Africa Partnership provides insight into the challenges and logistics of making such a mentorship program successful and sustainable.

scholarly journals The gut microbiome in konzo

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Matthew S. Bramble ◽  
Neerja Vashist ◽  
Arthur Ko ◽  
Sambhawa Priya ◽  
Céleste Musasa ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Bacterial Species ◽  
Sub Saharan Africa ◽  
Metagenomic Sequencing ◽  
Childbearing Age ◽  
Shotgun Metagenomic Sequencing ◽  
Republic Of The Congo ◽  
Study Population ◽  
Sub Saharan ◽  
Insight Into

AbstractKonzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.

scholarly journals Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

Science ◽  
2019 ◽  
Vol 365 (6448) ◽  
pp. eaaw6275 ◽  
Author(s):  
Mary E. Prendergast ◽  
Mark Lipson ◽  
Elizabeth A. Sawchuk ◽  
Iñigo Olalde ◽  
Christine A. Ogola ◽  
...  
Keyword(s):  
Iron Age ◽  
Food Production ◽  
Sub Saharan Africa ◽  
Eastern Africa ◽  
Multiphase Model ◽  
Later Stone Age ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Sub Saharan ◽  
Pastoral Neolithic

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African–related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African–related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

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