Asifullah Khan

Genetic History of Xinjiang’s Uyghurs Suggests Bronze Age Multiple-Way Contacts in Eurasia

The Uyghur people residing in Xinjiang, a territory located in the far west of China and crossed by the Silk Road, are a key ethnic group for understanding the history of human dispersion in Eurasia. Here we assessed the genetic structure and ancestry of 951 Xinjiangs Uyghurs (XJU) representing 14 geographical subpopulations. We observed a southwest and northeast differentiation within XJU, which was likely shaped jointly by the Tianshan Mountains, which traverses from east to west as a natural barrier, and gene flow from both east and west directions. In XJU, we identified four major ancestral components that were potentially derived from two earlier admixed groups: one from the West, harboring European (25-37%) and South Asian ancestries (12-20%), and the other from the East, with Siberian (15-17%) and East Asian (29-47%) ancestries. By using a newly developed method, MultiWaver, the complex admixture history of XJU was modeled as a two-wave admixture. An ancient wave was dated back to ∼3,750 years ago (ya), which is much earlier than that estimated by previous studies, but fits within the range of dating of mummies that exhibited European features that were discovered in the Tarim basin, which is situated in southern Xinjiang (4,000-2,000 ya); a more recent wave occurred around 750 ya, which is in agreement with the estimate from a recent study using other methods. We unveiled a more complex scenario of ancestral origins and admixture history in XJU than previously reported, which further suggests Bronze Age massive migrations in Eurasia and East-West contacts across the Silk Road.

The Microbial Pathology of Neu5Ac and Gal Epitopes

Glycans play a vital role in modulating many physiological and pathological phenomena of microbes and humans, such as bacterial adhesion, colonization, host-microbial interactions, cancer recognition, and blood group determination. The aim of the current review is to provide an account of the functions of N-acetyl sialic acid (Neu5Ac) and galactose (Gal) residues in microbial pathology. Specifically, an overview of the biosynthesis and metabolism of Neu5Ac and Gal residues in different bacterial species will provide a better understanding of microbial pathogenesis in the human body.

Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations.

The glycine amidinotransferase gene (GATM) plays a vital role in energy metabolism in muscle tissues and is associated with multiple clinically important phenotypes. However, the genetic diversity of the GATM gene remains poorly understood within and between human populations. Here we analyzed the 1,000 Genomes Project data through population genetics approaches and observed significant genetic diversity across the GATM gene among various continental human populations. We observed considerable variations in GATM allele frequencies and haplotype composition among different populations. Substantial genetic differences were observed between East Asian and European populations (FST = 0.56). In addition, the frequency of a distinct major GATM haplotype in these groups was congruent with population-wide diversity at this locus. Furthermore, we identified GATM as the top differentiated gene compared to the other statin drug response-associated genes. Composite multiple analyses identified signatures of positive selection at the GATM locus, which was estimated to have occurred around 850 generations ago in European populations. As GATM catalyzes the key step of creatine biosynthesis involved in energy metabolism, we speculate that the European prehistorical demographic transition from hunter-gatherer to farming cultures was the driving force of selection that fulfilled creatine-based metabolic requirement of the populations.

From Genes to Health – Challenges and Opportunities

In genome science, the advancement in high-throughput sequencing technologies and bioinformatics analysis is facilitating the better understanding of Mendelian and complex trait inheritance. Charting the genetic basis of complex diseases – including pediatric cancer, and interpreting huge amount of next-generation sequencing data are among the major technical challenges to be overcome in order to understand the molecular basis of various diseases and genetic disorders. In this review, we provide insights into some major challenges currently hindering a better understanding of Mendelian and complex trait inheritance, and thus impeding medical benefits to patients.

Use of Nepeta clarkei extracts for controlling honey bee pathogenic bacteria and mosquito larvae

ABSTRACT Honeybee (Apis mellifera) population is going down across the globe due to honeybee pathogens. This greatly influences the bee-associated commercial food products production. Likewise, mosquitoes are prominent vector responsible for spreading life-threatening human diseases, including malaria and dengue. The plant-based insecticides are a better substitute to the recent control practices of honeybee pathogenic bacteria and mosquito. Here, we performed in vitro screening of Nepeta clarkei Hook. f. (Labiatae) aqueous extracts against three honey bee gut bacterial isolates including Paenibacillus larvae an infamous honeybee bacterial pathogen. The inhibitory zone was produced in the range of 6–14 mm diameters against three honey bee bacterial isolates. Likewise, fourth instars larvae of Culex (Diptera/Culicidae) were also subjected to check the possible larvicidal efficacy of N. clarkei. A normal media supplemented with N. clarkei in different concentrations (0.025% 0.05%, 0.1%, 0.15%, and 0.2%) affected the growth of larvae significantly. The lethal concentration at which 50% of larvae failed to become pupate was found to be 0.1% after 24 h of exposure. Considerable reductions in larval growth and pupal development of mosquito suggested that this plant should be utilized in mosquito control programmes.

Population genetic structure of domain I of apical membrane antigen-1 in Plasmodium falciparum isolates from Hazara division of Pakistan

BackgroundThe Plasmodium falciparum apical membrane antigen-1 (PfAMA1) is considered as an ideal vaccine candidate for malaria control due to its high level of immunogenicity and essential role in parasite survival. Among the three domains of PfAMA1 protein, hyper-variable region (HVR) of domain I is the most immunogenic. The present study was conducted to evaluate the extent of genetic diversity across HVR domain I of the pfama1 gene in P. falciparum isolates from Hazara division of Pakistan.MethodsThe HVR domain I of the pfama1 was amplified and sequenced from 20 P. falciparum positive cases from Hazara division of Pakistan. The sequences were analysed in context of global population data of P. falciparum from nine malaria endemic countries. The DNA sequence reads quality assessment, reads assembling, sequences alignment/phylogenetic and population genetic analyses were performed using Staden, Lasergene v. 7.1, MEGA7 and DnaSP v.5 software packages respectively.ResultsTotal 14 mutations were found in Pakistani isolates with 12 parsimony informative sites. During comparison with global isolates, a novel non-synonymous mutation (Y240F) was found specifically in a single Pakistani sample with 5% frequency. The less number of mutations, haplotypes, recombination and low pairwise nucleotide differences revealed tightly linked uniform genetic structure with low genetic diversity at HVR domain I of pfama1 among P. falciparum isolates from Hazara region of Pakistan. This uniform genetic structure may be shaped across Pakistani P. falciparum isolates by bottleneck or natural selection events.ConclusionThe Pakistani P. falciparum isolates were found to maintain a distinct genetic pattern at HVR pfama1 with some extent of genetic relationship with geographically close Myanmar and Indian samples. However, the exact pattern of gene flow and demographic events may infer from whole genome sequence data with large sample size of P. falciparum collected from broad area of Pakistan.

Genome-wide comparison of allele-specific gene expression between African and European populations

Transcriptomic diversity across human populations reflects differential regulatory mechanisms. Allelic-imbalanced gene expression is a genetic regulatory mechanism that contributes to human phenotypic variation. To systematically investigate genome-wide allele-specific expression (ASE), we analyzed RNA-Seq data from European and African populations provided by the Geuvadis project. We identified 11 sites in 8 genes showing ASE in both Europeans and Africans, and 9 sites in 9 genes showing population-specific ASE, including both novel and known ASE signals. Notably, the top signal of differentiated ASE between inter-continental populations was observed in DNAJC15, of which the derived allele of rs12015, a single nucleotide polymorphism (SNP), showed significantly higher expression than did the ancestral allele specifically in European individuals. We identified a unique haplotype of DNAJC15, where a few SNPs highly differentiated between European and African populations were strongly linked to sites with high ASE. Among these, SNP rs17553284 affected the binding of several transcription factors as well as the genotype-dependent expression of DNAJC15. Therefore, we speculated that rs17553284 could be a regulatory causal variant that mediates the ASE of rs12015. We found several variations in ASE between intercontinental populations. The highly differentiated ASE genes identified here may implicate in the phenotypic variations among populations that are both evolutionarily and medically important.