We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910 individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing regions of the African pan-genome missing from the reference genome. Our analysis revealed 296,485,284 bp in 125,715 distinct contigs present in the African-descended populations, demonstrating that the African pan-genome contains ~10% more DNA than the current human reference genome. Although the functional significance of nearly all of this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes while the rest appear to be intergenic.

After vaccination with tetanus toxoid (TT), TT-specific immune responses in humans infected with Schistosoma mansoni were assessed. Peripheral blood mononuclear cells (PBMC) from vaccinated infected subjects and vaccinated uninfected controls were evaluated for their ability to produce cytokines characteristic of Th1 or Th2 cells (interferon [IFN]-gamma or interleukin [IL]-4, respectively) after in vitro restimulation with TT. TT-specific IFN-gamma production by PBMC from infected subjects was inversely related to infection intensity and was significantly lower than TT-specific IFN-gamma production by control PBMC. PBMC from all of the infected subjects and 3 of the 5 controls analyzed by reverse transcriptase-polymerase chain reaction transcribed the IL-4 gene in response to TT restimulation. Together, these results suggest that S. mansoni-infected persons mount a Th2-like response to the bystander antigen TT, while uninfected persons mount a Th1- or Th0-like response.

Background: Helminthic infections and allergic disease are highly prevalent in many areas of the world. It is known that IgE antibodies are involved in the pathogenesis of both helminthiasis and atopy. However, the consequences of the presence of helminthic infections in atopic patients are still not completely understood. Methods: Subjects infected by Schistosoma mansoni with more than 200 eggs/g of feces (n = 42) and uninfected subjects (n = 133) were selected from an endemic area of schistosomiasis. The history of allergy and results of the immediate hypersensitivity prick tests with inhalant allergen extracts were registered. Total IgE and IgE specific to S. mansoni and aeroallergens were measured in serum by ELISA. Results: The proportion of individuals with a positive skin test to allergens was higher in the uninfected group (24.3%) than in the group with more than 200 eggs/g of feces (4.8%). The odds of atopy (defined as a positive test for at least one of the antigens) were 5 times higher (odds ratio = 7.0; 95% confidence interval = 1.6–31.1%; p = 0.01) in the uninfected group, after taking into account the potential influence of gender and age. While there was a tendency for higher total and S. mansoni-specific IgE levels in infected patients, an opposite trend, that is higher aeroallergen-specific IgE, was observed in uninfected subjects. Conclusions: There was a strong and statistically significant inverse association between the immediate skin test response to common aeroallergens and infection by S. mansoni. The results indicate that immediate hypersensitivity reactions may be suppressed in S. mansoni-infected individuals.

The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.

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Helminthic infections have been shown to inhibit allergy skin-prick tests and to modify the course of asthma. We evaluated Dermatophagoides pteronyssinus-specific immune responses in patients with asthma by measuring levels of T helper 2 (Th2) cytokines in peripheral blood mononuclear cell (PBMC) cultures. PBMCs from Schistosoma mansoni-infected patients with asthma living in an area of polyhelminthic endemicity produced lower levels of interleukin (IL)-5 and IL-4 in response to D. pteronyssinus antigen (Ag) 1 than did PBMCs from helminth-free patients with asthma. In contrast, D. pteronyssinus Ag 1-specific production of IL-10 was higher in helminth-infected patients than in helminth-free patients. The addition of recombinant human IL-10 to D. pteronyssinus Ag 1-stimulated cultures of PBMCs from helminth-free patients led to down-modulation of production of IL-5. After helminth-infected patients with asthma received antihelminthic treatment, there was down-modulation of D. pteronyssinus Ag 1-specific production of IL-10 in vitro. S. mansoni-infected patients with asthma produce lower levels of Th2 cytokines than do helminth-free patients with asthma, and this modulation is likely done by IL-10.

In areas where schistosomiasis is endemic, a negative correlation is observed between atopy and helminth infection, associated with a low prevalence of asthma. We investigated whether Schistosoma mansoni infection or injection of parasite eggs can modulate airway allergic inflammation in mice, examining the mechanisms of such regulation. We infected BALB/c mice with 30 S. mansoni cercariae or intraperitoneally injected 2,500 schistosome eggs, and experimental asthma was induced by ovalbumin (OVA). The number of eosinophils in bronchoalveolar lavage fluid was higher in the asthmatic group than in asthmatic mice infected with S. mansoni or treated with parasite eggs. Reduced Th2 cytokine production, characterized by lower levels of interleukin-4 (IL-4), IL-5, and immunoglobulin E, was observed in both S. mansoni-treated groups compared to the asthmatic group. There was a reduction in the number of inflammatory cells in lungs of S. mansoni-infected and egg-treated mice, demonstrating that both S. mansoni infection and the egg treatment modulated the lung inflammatory response to OVA. Only allergic animals that were treated with parasite eggs had increased numbers of CD4 ؉ CD25 ؉ Foxp3 ؉ T cells and increased levels of IL-10 and decreased production of CCL2, CCL3, and CCL5 in the lungs compared to the asthmatic group. Neutralization of IL-10 receptor or depletion of CD25 ؉ T cells in vivo confirmed the critical role of CD4 ؉ CD25 ؉ Foxp3 ؉ regulatory T cells in experimental asthma modulation independent of IL-10.The prevalence of allergic diseases such as asthma has increased markedly over the past few decades (5). The immune response to allergens is characterized by eosinophilic inflammation of the airways, airway hyperreactivity, and immunoglobulin E (IgE) production by B cells (39). The immune etiology of asthma is complex. Genetic and immunological analyses of atopic individuals have revealed that Th2 cytokines are usually associated with allergies (23, 25). Furthermore, Th2 cells which produce interleukin-4 (IL-4), IL-5, and IL-13 mediate the inflammatory reaction in the lung. Production of IL-5 increases differentiation, recruitment, and survival of eosinophils and therefore plays an important role in the development of pulmonary eosinophilia during allergic disorders (26). Moreover, IL-13 is important for IgE production, mucus hyperplasia, and eosinophilia (34). The levels of these cytokines are higher in allergic patients and play a direct role in the inflammatory response.It has been suggested that people in developing countries suffer less from allergic disease than those who live in industrialized countries because the former are frequently exposed to bacteria and helminth infections associated with poverty and lack of basic sanitary conditions (21). Both helminth infections and allergic diseases are associated with Th2 cytokines and high levels of IgE and eosinophilia. Though they appear to have similar immune responses, a negative correlation between helminth infection and allergic disease has been obse...