ABSTRACT It remains debatable how many genes and how various the mechanisms are behind human adaptation to extreme environments, such as high altitudes. Despite extensive studies on Tibetans, Andeans and Ethiopians, new insights are expected to be provided with careful analysis of underrepresented highlanders living in a different geographical region, such as the Tajiks, who reside on the Pamir Plateau at an average altitude exceeding 4000 meters. Moreover, genetic admixture, as we observed in the current whole-genome deep-sequencing study of Xinjiang Tajiks (XJT), offers a unique opportunity to explore how admixture may facilitate adaptation to high-altitude environments. Compared with other extensively studied highlanders, XJT showed pronounced admixture patterns: most of their ancestry are derived from West Eurasians (34.5%–48.3%) and South Asians (21.4%–40.0%), and some minor ancestry from East Asians and Siberians (3.62%–17.5%). The greater genetic diversity in XJT than in their ancestral source populations provides a genetic basis for their adaptation to high-altitude environments. The admixture gain of functional adaptive components from ancestral populations could facilitate adaptation to high-altitude environments. Specifically, admixture-facilitated adaptation was strongly associated with skin-related candidate genes that respond to UV radiation (e.g. HERC2 and BNC2) and cardiovascular-system-related genes (e.g. MPI and BEST1). Notably, no adaptive variants of genes showing outstanding natural selection signatures in the Tibetan or Andean highlanders were identified in XJT, including EPAS1 and EGLN1, indicating that a different set of genes contributed to XJT's survival on the Pamir Plateau, although some genes underlying natural selection in XJT have been previously reported in other highlanders. Our results highlight the unique genetic adaptations in XJT and propose that admixture may play a vital role in facilitating high-altitude adaptation. By introducing and elevating diversity, admixture likely induces novel genetic factors that contribute to the survival of populations in extreme environments like the highlands.
Abstract The objective of this work was to propose a hybrid model to predict the concentration of PM2.5 in three cities of China. PM2.5 is one of the most important pollution worldwide, therefore effective prevention and control are beneficial to human’s production and life. A hybrid model, CEEMD-MFO-SVR-GRA-BPNN, was proposed to predict the concentration of PM2.5. The proposed model is the combination of (1) complementary ensemble empirical mode decomposition (CEEMD) to decompose the original PM2.5 concentration data; (2) support vector regression (SVR) to give a regressed prediction model in which parameters was optimized via moth-flame optimization algorithm (MFO); (3) grey relational analysis (GRA) to select atmospheric factors with distinguished effect on PM2.5; and (4) back propagation neural network (BPNN) to reduce the forecasting residual. The hybrid model was evaluated in three cities, Guiyang, Lijiang and Guangzhou of China, in which the environments and geographical locations are different. The implementation of the proposed model and well-known CEEMD-MFO-SVR, CEEMD- WOA-SVR, EEMD-MFO-SVR, EMD-MFO-SVR and MFO-SVR, BPNN-meteorology models, were compared. The results show that the prediction of the proposed hybrid model is more accurate than the compared models.
Abstract Background Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. Results We analyzed the whole-genome deep sequencing data (~30×) of five native trios from Malaysia, and discovered approximately 6.9 million single nucleotide variants (SNVs), 1.2 million small insertions and deletions (indels), and 9,000 copy number variants (CNVs) in the 15 samples. We found 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify autosomal de novo variants and estimated the mutation rates to be 0.81×10-8–1.33×10-8 , 1.0×10-9–2.9×10-9 , and ~0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for accurate haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example was a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. Conclusion Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.
Additional file 2: Table S4. Functional enrichment of genes underlying the mutation hotspots, loss-of-function variants, de novo variants, copy number variants and novel insertions.
The Ras superfamily of small guanosine triphosphatases (GTPases) are a large group of small GTP-binding proteins, which play crucial roles in basic cellular processes in all eukaryotes. In this study, by analyzing the gene structure, temporal and spatial expression patterns, a total of 108 Ras superfamily genes were identified in the genome of the Pacific white shrimp Litopenaeus vannamei . We found these genes included not only the classical Ras GTPase superfamily members, but also some unconventional and novel Ras GTPase proteins, which have unknown functions and unique expression patterns. All Ras superfamily genes of L. vannamei were highly conserved within the core G domain and closely related in phylogeny, but they might have two different evolutionary origins. In addition, different Ras GTPase genes exhibited distinct expression patterns in different tissues, development/molting stages and WSSV infection samples of L. vannamei , suggesting that they may have a high functional specialization, and play important roles in regulating the biological processes of cell differentiation, growth and development, immune response, etc. This study provides important clues for the structure, classification, evolution and function of Ras superfamily in shrimp.
Background Man who has sex with man (MSM) is one of the high risk groups for spreading HIV/AIDS. It was reported that the most prevalent human immunodeficiency virus type 1 (HIV-1) strain among MSM is subtype B; however, T cell immunity remains unknown across the HIV-1 B genome in this population. Methods Using Elispot assay with synthetic peptides spanning the sequence of HIV-1 consensus B, HIV-1-specific cytotoxic T-cell lymphocyte responses were quantified among 3 treated and 19 untreated HIV-1 infected MSM from Beijing, China. Cross-sectional association between viral loads and cellular immune responses were analyzed. Results Peptide pools corresponding to each HIV-1 protein were used for Env, Gag, Pol, Nef, Tat/Rev, Vpr/Vpu and Vif. The results showed that the magnitude of T cell responses in the 3 treated HIV+ MSM group [median, 770 spot forming cells (SFCs) per 106 peripheral blood mononuclear cells (PBMCs)] might be significantly lower than that in the 19 untreated HIV+ MSM group (median, 6175 SFCs per 106 PBMCs). Nef, Gag and Pol are the most frequently targeted HIV-1 antigens; and 16 subjects (73%) were identified with vigorous T cell immunity against each of these three proteins. The overall magnitude of T cell immunity closely related to its breadth (r=0.72, P<0.05) and was inversely but weakly associated with viral loads (r=-0.15). Further analysis showed that both Gag (r=-0.24) and Pol specific T cells (r=-0.12) contributed to this inverse association whereas Nef specific T cells showed no association with viral loads. Conclusions The magnitude of HIV-1 specific T cells is inversely but weakly associated with viral loads among MSM; HIV-specific T cell responses against conservative sequences (Gag and Pol) are the main contributors to this association among Chinese HIV+ MSM. These findings have important implications for vaccine design. Chin Med J2006;119(23):1958–1965
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