Genetic substructure analysis of three isolated populations in southwest China.

Southwest China is home to numerous ethnic minorities, as well as many geographically and genetically isolated groups. However, the genetic substructure of these ethnic groups, especially the paternal genetic structure between groups, has not been comprehensively analyzed. In this study, we used Y chromosome capture and Illumina sequencing technologies to investigate the paternal genetic structure of three isolated groups of male unrelated individuals, including Baima in Pingwu, Sichuan Province, Muya in Shimian, Sichuan Province, and Kongge in Jinghong, Yunnan Province. We calculated the frequencies of related haplogroups by the fixed-point compound amplification method and direct counting method, and used the Past3.0 software to perform principal component analysis to draw a population clustering tree. we observed that Kongge had 3 Y chromosome haplogroups, Baima had 4 Y chromosome haplogroups, and Muya had 5 Y chromosome haplogroups. The results showed that Kongge was most closely related to the Wa, and the Y chromosome types of the Baima and Muya were mainly concentrated in the D haplogroup and its lower reaches. It has the closest relationship with the Tibetans in Qamdo and Nyingchi. The study on the genetic structure of different ethnic groups has enriched the genetic relationship of isolated populations and provided a new perspective for understanding Chinese ethnic groups.

[A genetic sub-structure study of the Tibetan population in Southwest China].

Tibetan is a typical ethnic minority population in Southwest China, which can be divided into U-Tsang, Kham, Amdo, Jiarong and other sub-populations. However, the genetic structure of these sub-populations has not been comprehensively analyzed, especially from the perspective of paternal and maternal lineages. Based on genetic markers of autosomes, the Y chromosome and mitochondria, we studied four Tibetan populations (the U-Tsang population in Tibet Autonomous Region; the Kham population in Garze, Sichuan province; the Amdo population in Qinghai province and the Jiarong population in Aba, Sichuan province) to interpret their genetic structure. The mini-sequencing technology was used to detect the genotype of each maker. Meanwhile, the PowerPlex ?Y23 and DNA Typer TM Y26 kit were applied to genotype Y-STRs. Subsequently, the genetic structure was analyzed by heatmap and principal component analysis, ancestry component, haplogroup frequency, network map and multi-dimensional scaling analysis. The results showed that the four Tibetan populations could be divided into three sets based on the autosomal and Y-chromosomal genetic markers, in which set 1 was the U-Tsang population in the Tibetan Plateau, set 2 comprised of the Kham and Amdo populations in the surrounding areas of the plateau, and set 3 was the Jiarong population that resided in the Tibetan and Yi Corridor. No significant difference was observed in mitochondrial genetic markers among four Tibetan populations. In general, multi-category genetic information provides a new comprehensive insight into the Tibetan sub-population.

Sub-structure-based screening and molecular docking studies of potential enteroviruses inhibitors.

Rhinoviruses (RV), especially Human rhinovirus (HRVs) have been accepted as the most common cause for upper respiratory tract infections (URTIs). Pleconaril, a broad spectrum anti-rhinoviral compound, has been used as a drug of choice for URTIs for over a decade. Unfortunately, for various complications associated with this drug, it was rejected, and a replacement is highly desirable. In silico screening and prediction methods such as sub-structure search and molecular docking have been widely used to identify alternative compounds. In our study, we have utilised sub-structure search to narrow down our quest in finding relevant chemical compounds. Molecular docking studies were then used to study their binding interaction at the molecular level. Interestingly, we have identified 3 residues that is worth further investigation in upcoming molecular dynamics simulation systems of their contribution in stable interaction.

Population Genetic Analysis and Sub-Structuring of Theileria annulata in Sudan.

Theileria annulata, which causes tropical theileriosis, is a major impediment to improving cattle production in Sudan. Tropical theileriosis disease is prevalent in the north and central regions of Sudan. Outbreaks of the disease have been observed outside the known endemic areas, in east and west regions of the country, due to changes in tick vector distribution and animal movement. A live schizont attenuated vaccination based on tissue culture technology has been developed to control the disease. The parasite in the field as well as the vaccine strain need to be genotyped before the vaccinations are practiced, in order to be able to monitor any breakthrough or breakdown, if any, after the deployment of the vaccine in the field. Nine microsatellite markers were used to genotype 246 field samples positive for T. annulata DNA and the vaccine strain. North and central populations have a higher multiplicity of infection than east and west populations. The examination of principal components showed two sub-structures with a mix of all four populations in both clusters and the vaccine strain used being aligned with left-lower cluster. Only the north population was in linkage equilibrium, while the other populations were in linkage disequilibrium, and linkage equilibrium was found when all samples were regarded as single population. The genetic identity of the vaccine and field samples was 0.62 with the north population and 0.39 with west population. Overall, genetic investigations of four T. annulata populations in Sudan revealed substantial intermixing, with only two groups exhibiting regional origin independence. In the four geographically distant regions analyzed, there was a high level of genetic variation within each population. The findings show that the live schizont attenuated vaccine, Atbara strain may be acceptable for use in all Sudanese regions where tropical theileriosis occurs.

Nanoscale Molecular Characterization of Hair Cuticle Cells Using Integrated Atomic Force Microscopy-Infrared Laser Spectroscopy.

The hair cuticle provides significant protection from external sources, as well as giving rise to many of its bulk properties, e.g., friction, shine, etc. that are important in many industries. In this work, atomic force microscopy-infrared spectroscopy (AFM-IR) has been used to investigate the nanometer-scale topography and chemical structure of human hair cuticles in two spectral regions. AFM-IR combines atomic force microscopy with a tunable infrared laser and circumvents the diffraction limit that has impaired traditional infrared spectroscopy, facilitating surface-selective spectroscopy at ultra-spatial resolution. This high resolution was exploited to probe the protein secondary structures and lipid content, as well as specific amino acid residues, e.g., cystine, within individual cuticle cells. Characterization across the top of individual cells showed large inhomogeneity in protein and lipid contributions that suggested significant changes to physical properties on approaching the hair edge. Additionally, the exposed layered sub-structure of individual cuticle cells allowed their chemical compositions to be assessed. The variation of protein, lipid, and cystine composition in the observed layers, as well as the measured dimensions of each, correspond closely to that of the epicuticle, A-layer, exocuticle, and endocuticle layers of the cuticle cell sub-structure, confirming previous findings, and demonstrate the potential of AFM-IR for nanoscale chemical characterization within biological substrates.

Engineering of layered, lipid-encapsulated drug nanoparticles through spray-drying.

Drug-containing nanoparticles have been synthesized through the spray-drying of submicron droplet aerosols by using matrix materials such as lipids and biopolymers. Understanding layer formation in composite nanoparticles is essential for the appropriate engineering of particle substructures. The present study developed a droplet-shrinkage model for predicting the solid-phase formation of two non-volatile solutes-stearic acid lipid and a set of drugs, by considering molecular volume and solubility. Nanoparticle formation was simulated to define the parameter space of material properties and process conditions for the formation of a layered structure with the preferential accumulation of the lipid in the outer layer. Moreover, lipid-drug demarcation diagrams representing a set of critical values of ratios of solute properties at which the two solutes precipitate simultaneously were developed. The model was validated through the preparation of stearic acid-isoniazid nanoparticles under controlled processing conditions. The developed model can guide the selection of solvents, lipids, and processing conditions such that drug loading and lipid encapsulation in composite nanoparticles are optimized.

A multiple-dimension liquid chromatography coupled with mass spectrometry data strategy for the rapid discovery and identification of unknown compounds from a Chinese herbal formula (Er-xian decoction).

It is very important to rapidly discover and identify the multiple components of traditional Chinese medicine (TCM) formula. High performance liquid chromatography with high resolution tandem mass spectrometry (HPLC-HRMS/MS) has been widely used to analyze TCM formula and contains multiple-dimension data including retention time (RT), high resolution mass (HRMS), multiple-stage mass spectrometric (MSn), and isotope intensity distribution (IID) data. So it is very necessary to exploit a useful strategy to utilize multiple-dimension data to rapidly probe structural information and identify chemical compounds. In this study, a new strategy to initiatively use the multiple-dimension LC-MS data has been developed to discover and identify unknown compounds of TCM in many styles. The strategy guarantees the fast discovery of candidate structural information and provides efficient structure clues for identification. The strategy contains four steps in sequence: (1) to discover potential compounds and obtain sub-structure information by the mass spectral tree similarity filter (MTSF) technique, based on HRMS and MSn data; (2) to classify potential compounds into known chemical classes by discriminant analysis (DA) on the basis of RT and HRMS data; (3) to hit the candidate structural information of compounds by intersection sub-structure between MTSF and DA (M,D-INSS); (4) to annotate and confirm candidate structures by IID data. This strategy allowed for the high exclusion efficiency (greater than 41%) of irrelevant ions in er-xian decoction (EXD) while providing accurate structural information of 553 potential compounds and identifying 66 candidates, therefore accelerating and simplifying the discovery and identification of unknown compounds in TCM formula.

Revealing latitudinal patterns of mitochondrial DNA diversity in Chileans.

The territory of Chile is particularly long and narrow, which combined with its mountainous terrain, makes it a unique scenario for human genetic studies. We obtained 995 control region mitochondrial DNA (mtDNA) sequences from Chileans representing populations living at different latitudes of the country from the North to the southernmost region. The majority of the mtDNA profiles are of Native American origin (∼88%). The remaining haplotypes are mostly of recent European origin (∼11%), and only a minor proportion is of recent African ancestry (∼1%). While these proportions are relatively uniform across the country, more structured patterns of diversity emerge when examining the variation from a phylogeographic perspective. For instance, haplogroup A2 reaches ∼9% in the North, and its frequency decreases gradually to ∼1% in the southernmost populations, while the frequency of haplogroup D (sub-haplogroups D1 and D4) follows the opposite pattern: 36% in the southernmost region, gradually decreasing to 21% in the North. Furthermore, there are remarkable signatures of founder effects in specific sub-clades of Native American (e.g. haplogroups D1j and D4p) and European (e.g. haplogroups T2b3 and K1a4a1a+195) ancestry. We conclude that the magnitude of the latitudinal differences observed in the patterns of mtDNA variation might be relevant in forensic casework.

Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations.

Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics.

The multiethnic ancestry of Bolivians as revealed by the analysis of Y-chromosome markers.

We have analyzed the specific male genetic component of 226 Bolivians recruited in five different regions ("departments"), La Paz, Cochabamba, Pando, Beni, and Santa Cruz. To evaluate the effect of geography on the distribution of genetic variability, the samples were also grouped into three main eco-geographical regions, namely, Andean, Sub-Andean, and Llanos. All the individuals were genotyped for 17 Y-STR and 32 Y-SNP markers. The average Y-chromosome Native American component in Bolivians is 28%, and it is mainly represented by haplogroup Q1a3a, while the average Y-chromosome European ancestry is 65%, and it is mainly represented by haplogroup R1b1-P25. The data indicate that there exists significant population sub-division in the country in terms of continental ancestry. Thus, the partition of ancestries in Llanos, Sub-Andean, and Andean regions is as follows (respectively): (i) Native American ancestry: 47%, 7%, and 19%, (ii) European ancestry: 46%, 86%, and 75%, and (iii) African ancestry: 7%, 7%, and 6%. The population sub-structure in the country is also well mirrored when inferred from an AMOVA analysis, indicating that among-population variance in the country reaches 9.74-11.15%. This suggests the convenience of using regional datasets for forensic applications in Bolivia, instead of using a global and single country database. By comparing the Y-chromosome patterns with those previously reported on the same individuals on autosomal SNPs and mitochondrial DNA (mtDNA), it becomes clear that Bolivians show a strong gender-bias.

SNP variation with latitude: Analysis of the SNPforID 52-plex markers in north, mid-region and south Chilean populations.

Chile is a disproportionately long and narrow country defined by the southern Andes and Pacific coastline where a level of genetic sub-structure resulting from distances of several thousand kilometers might be expected across the most distantly separated regions. Although STR databases created for the Chilean Legal Medical Service indicate an absence of sub-structure, such a characteristic requires further exploration when introducing additional forensic markers. Notably, Single Nucleotide Polymorphisms (SNPs) have a much lower mutation rate than STRs and can show more stable distributions of genetic variation if population movement is restricted. In this study we evaluated 451 Chilean urban samples from the North, North-Central, Central, South-Central and South regions of Chile for the 52 SNPs of the SNPforID forensic identification panel to explore the underlying genetic structure of Chilean populations. Results reveal similar genetic distances between groups suggesting a single SNP database for the whole of Chile is appropriate. To further understand the genetic composition of Chilean populations that comprise the bulk of individuals with both European and Native American ancestries, ancestral membership proportions were evaluated and pairwise comparisons to other American populations were made.

The utility of mitochondrial and y chromosome phylogenetic data to improve correction for population stratification.

Genome-wide association (GWA) studies have become a standard approach for discovering and validating genomic polymorphisms putatively associated with phenotypes of interest. Accounting for population structure in GWA studies is critical to attain unbiased parameter measurements and control Type I error. One common approach to accounting for population structure is to include several principal components derived from the entire autosomal dataset, which reflects population structure signal. However, knowing which components to include is subjective and generally not conclusive. We examined how phylogenetic signal from mitochondrial DNA (mtDNA) and chromosome Y (chr:Y) markers is concordant with principal component data based on autosomal markers to determine whether mtDNA and chr:Y phylogenetic data can help guide principal component selection. Using HAPMAP and other original data from individuals of multiple ancestries, we examined the relationships of mtDNA and chr:Y phylogenetic signal with the autosomal PCA using best subset logistic regression. We show that while the two approaches agree at times, this is independent of the component order and not completely represented in the Eigen values. Additionally, we use simulations to demonstrate that our approach leads to a slightly reduced Type I error rate compared to the standard approach. This approach provides preliminary evidence to support the theoretical concept that mtDNA and chr:Y data can be informative in locating the PCs that are most associated with evolutionary history of populations that are being studied, although the utility of such information will depend on the specific situation.