Evaluation of loci to predict ear morphology using two SNaPshot assays.

Human ear morphology prediction with SNP-based genotypes is growing in forensic DNA phenotyping and is scarcely explored in Pakistan as a part of EVCs (externally visible characteristics). The ear morphology prediction assays with 21 SNPs were assessed for their potential utility in forensic identification of population. The SNaPshot™ multiplex chemistries, capillary electrophoresis methods and GeneMapper™ software were used for obtaining genotypic data. A total of 33 ear phenotypes were categorized with digital photographs of 300 volunteers. SHEsis software was applied to make LD plot. Ordinal and multinomial logistic regression was implemented for association testing. Multinomial logistic regression was executed to construct the prediction model in 90% training and 10% testing subjects. Several influential SNPs for ear phenotypic variation were found in association testing. The model based on genetic markers predicted ear phenotypes with moderate to good predictive accuracies demonstrated with the area under curve (AUC), sensitivity and specificity of predicted phenotypes. As an additional EVC, the estimated ear phenotypic profiles have the possibility of determining the human ear morphology differences in unknown biological samples found in crimes that do not result in a criminal database hit. Furthermore, this can help in facial reconstruction and act as an investigational lead.

Evaluation of facial hair-associated SNPs: a pilot study on male Pakistani Punjabi population.

Variation in facial hair is one of the most conspicuous features of facial appearance, particularly in South Asia and Middle East countries. A genome-wide association study in Latin Americans has identified multiple genetic variants at distinct loci being associated with facial hair traits including eyebrow thickness, beard thickness, and monobrow. In this pilot study, we have evaluated 16 SNPs associated with facial hair traits in 58 male individuals from the Punjabi population of Pakistan. In our sample, rs365060 in EDAR and rs12597422 in FTO showed significant association with monobrow, rs6684877 in MACF1 showed significant association with eyebrow thickness, and two SNPs in LOC105379031 (rs9654415 and rs7702331) showed significant association with beard thickness. Our results also suggest that genetic association may vary between ethnic groups and geographic regions. Although more data are needed to validate our results, our findings are of value in forensic molecular photofitting research in Pakistan.

Genetic diversity and forensic application of Y-filer STRs in four major ethnic groups of Pakistan.

17 Y-chromosomal STRs which are part of the Yfiler Amplification Kit were investigated in 493 unrelated Pakistani individuals belonging to the Punjabi, Sindhi, Baloch, and Pathan ethnic groups. We have assessed the forensic parameters and population genetic structure for each group. Among the 493 unrelated individuals from four ethnic groups (128 Baloch, 122 Pathan, 108 Punjabi, and 135 Sindhi), 82 haplotypes were observed with haplotype diversity (HD) of 0.9906 in Baloch, 102 haplotypes with HD value of 0.9957 in Pathans, 80 haplotypes with HD value of 0.9924 in Punjabi, and 105 haplotypes with HD value of 0.9945 in the Sindhi population. The overall gene diversity for Baloch, Pathan, Punjabi, and Sindhi populations was 0.6367, 0.6479, 0.6657, and 0.6112, respectively. The results had shown us that Pakistani populations do not have a unique set of genes but share the genetic affinity with regional (Central Asia and Northern India) populations. The observed low gene diversity (heterozygosity) values may be because of endogamy trends and this observation is equally supported by the results of forensic parameters which are mostly static across 4 combinations (minimal STRs, extended 11 Y-STRs, Powerplex 12 Y System, and Yfiler 17 Y-STRs) of STRs in these four populations.

Tracing the Genetic Legacy of the Tibetan Empire in the Balti.

The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6-26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39-21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.

Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand line revealed by Y-chromosomal STRs.

The Hazara population across Durand line has experienced extensive interaction with Central Asian and East Asian populations. Hazara individuals have typical Mongolian facial appearances and they called themselves descendants of Genghis Khan's army. The people who speak the Balochi language are called Baloch. Previously, a worldwide analysis of Y-chromosomal haplotype diversity for rapidly mutating (RM) Y-STRs and with PowerPlex Y23 System (Promega Corporation Madison, USA) kit was created with collaborative efforts, but Baloch and Hazara population from Pakistan and Hazara population from Afghanistan were missing. In the current study, Yfiler Plus PCR Amplification Kit loci were examined in 260 unrelated Hazara individuals from Afghanistan, 153 Hazara individuals, and 111 Balochi individuals from Baluchistan Pakistan. For the Hazara population from Afghanistan and Pakistan overall, 380 different haplotypes were observed on these 27 Y-STR loci, gene diversities ranged from 0.51288 (DYS389I) to 0.9257 (DYF387S1), and haplotype diversity was 0.9992. For the Baloch population, every individual was unique at 27 Y-STR loci; gene diversity ranged from 0.5718 (DYS460) to 0.9371(DYF387S1). Twelve haplotypes were shared between 178 individuals, while only two haplotypes among these twelve were shared between 87 individuals in Hazara populations. Rst and Fst pairwise genetic distance analyses, multidimensional scaling plot, neighbor-joining tree, linear discriminatory analysis, and median-joining network were performed, which shed light on the history of Hazara and Baloch populations. The results of our study showed that the Yfiler Plus PCR Amplification Kit marker set provided substantially stronger discriminatory power in the Baloch population of Pakistan and the Hazara population across the Durand line.

Phylogenetic relationship and genetic history of Central Asian Kazakhs inferred from Y-chromosome and autosomal variations.

The Xinjiang Uyghur Autonomous Region of China (XUARC) with 47 ethnic groups is a very colorful ethnic region of China, harboring abundant genetic and cultural diversity. The Kazakhs are the third largest ethnic group (7.02%) after Uyghur (46.42%) and Han (38.99%) in Xinjiang, but their genetic diversity and forensic characterization are poorly understood. In the current study, we genotyped 15 autosomal short tandem repeat (STR) loci and ten Y-STRs in 889 individuals (659 male and 230 female) collected from Kazak population of the Ili Kazak Autonomous Prefecture using AGCU Expressmarker 16 and 10Y-STR Kit (EX16 + 10Y). For autosomal STRs, we observed a total of 174 different alleles ranging from 6 to 34.2 repeat units and FGA showed the greatest power of discrimination (20 alleles) in Ili Kazakh population. We have not observed departures from Hardy-Weinberg equilibrium (HWE) after sequential Bonferroni correction and only found a minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The combined power of exclusion (CPE) was 0.99999998395 and combined power of discrimination (CPD) was 99.999999999999999798%. For Y-STRs, we observed a total of 496 different haplotypes in these ten Y-STR loci. The gene diversities ranged from 0.5023 (DYS391) to 0.8357 (DYS385a/b). The overall haplotype diversity (GD) was 0.9985 with random matching probability (RMP) of 0.0015. The results of population genetic analysis based on both autosomal and Y-chromosome STRs demonstrated that the genetic affinity among populations is generally consistent with ethnic, linguistic, and continental geographical classifications.

Genetic structure and forensic characteristics of Saraiki population from Southern Punjab, Pakistan, revealed by 20 Y-chromosomal STRs.

Pakistan harbors more than 18 major ethnic groups which speak 60 different languages. People speaking Saraiki languages are known as Saraiki or Multani. They are mainly residents of Southern Punjab including Multan, Dear Ghazi Khan, Rajanpur, and Rahim Yar khan. Here, we reported the data of 20 Y-chromosomal short tandem repeats (Y-STRs) genotyped with the Goldeneye® 20Y kit in 154 unrelated Saraiki individuals. We observed 141 different haplotypes on 20 Y-STR loci and the gene diversity (GD) ranged from 0.6566 (DYS448) to 0.9538 (DYS385a, b). The overall haplotype diversity was 0.9989 at 20 Y-STRs loci. Furthermore, we performed population genetic analyses by including data from 26 other South Asian populations. The presented haplotype data was recently included in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

Genetic characterization of 15 autosomal STRs in the interior Sindhi population of Pakistan and their phylogenetic relationship with other populations.

Genetic structure of a population can be influenced by evolutionary processes and cultural histories which can alter the frequencies of different variants at particular genetic markers. These characteristics make DNA evidence suitable for forensic applications. Little relevant data are available from the interior Sindhi population; thus, in the current study, we have investigated 15 autosomal STRs in 181 unrelated individuals belonging to the interior parts of Sindh Pakistan, to establish its lineage and parameters of forensic interest. These STRs revealed a high power of discrimination (CPD), power of exclusion (CPE) and matching probability (CMP) are 0.9999999999999999968997, 0.99998612 and 3.1003 × 10-18 respectively. The genetic distances, neighbour-joining (NJ) tree, interactivity test and principal component analysis (PCA) based on 15 autosomal STR loci showed that the interior Sindhi population had a closer genetic relationship with Pakistani populations and distant relationships with regional (India and Afghanistan) populations. The present findings exhibited that STRs included in AmpFLSTR Identifiler kit (Applied Biosystems) are genetically polymorphic in the interior Sindhi population of Pakistan. This study provides valuable population genetic data for the genetic information study, forensic human individual identification and paternity testing.

Population data of 23 Y STRs from Manchu population of Liaoning Province, Northeast China.

Mongol-like-horsemen-turned-merchants from Manchuria are known as Manchus, originally their homeland was centered around what is nowadays the city of Shenyang in Northeast China. Previously, worldwide analysis of Y-chromosomal haplotype diversity for 23 STR loci and Y-STR databases with PowerPlex® Y23 System (Promega Corporation Madison, USA) kit were created with collaborative efforts, but Manchu population data was missing. In current study, PowerPlex® Y23 System loci were examined in 328 unrelated Manchu male individuals from Xiuyan and Huanren Manchu autonomous counties in Liaoning province, to calculate the forensic parameters of the 23 STR loci. A total of 323 different haplotypes were observed on these 23 Y-STR loci. The gene diversities ranged from 0.3820 (DYS391) to 0.9696 (DYS385a, b). The overall haplotype diversity was 0.9999 ± 0.0002 at PowerPlex® Y23 System. Rst pairwise analyses, multidimensional scaling plot, and linear discriminatory analysis showed the genetic structure of Manchu population was significantly different from some of Chinese populations like Tibetan and Uyghur. Results of our study showed that PowerPlex® Y23 System marker set provided substantially stronger discriminatory power in Manchu population of China.

Genetic characterization of Y-chromosomal STRs in Hazara ethnic group of Pakistan and confirmation of DYS448 null allele.

Pakistan harbors 18 major ethnic groups and Hazara is one of the distinct but smaller groups comprising 0.090% of the total population. Hazara individuals have typical Mongolian facial features and they claim to be descendants of Genghis Khan's army in the first quarter of the thirteenth century AD. In this study, we genotyped 153 unrelated males living in Quetta, Baluchistan, Pakistan, for a total of 26 (n = 153) to 30 (n = 47) Y-chromosomal STR loci. One hundred forty unique haplotypes were developed for Hazara population using the PowerPlex Y23 loci. The Y-STR locus showed a genetic diversity ranging from 0.2384 to 0.7918, and an overall discrimination capacity (DC) of 91.5%. The Hazara population samples were profiled for three additional Y-STRs (DYS388, DYS449 and DYS460), which increased the number of unique haplotypes to 144 while the DC increased to 94.11% in Hazara Population of Pakistan. Interestingly, null alleles were observed at DYS448 in 25 individuals of Hazara population. The Hazaras showed significant differences from other local populations of Pakistan as well as neighboring populations, but had considerable genetic affinities to Kazakhs and Mongols.

Evaluation of 13 rapidly mutating Y-STRs in endogamous Punjabi and Sindhi ethnic groups from Pakistan.

Y-chromosomal short tandem repeats (Y-STRs) are commonly used to study population histories, discover ancestral relationships, and identify males for criminal justice purposes. Y-STRs being largely in forensic use have low haplotype diversity in some populations and cannot discriminate between paternal male relatives. Rapidly mutating Y-STRs (RM Y-STRs) were breakthrough and have been paid much attention. A set of 13 rapidly mutating (RM) Y-STRs (DYF387S1, DYF399S1, DYF403S1a/b1/b2, DYF404S1, DYS449, DYS518, DYS526I/II, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) typically reveals higher haplotype diversities than the commercially available Y-STR sets and allows differentiating male relatives for which commercial Y-STR sets are usually not informative. Here, we amplified the 13 RM Y-STRs in 168 (37 Sindhi and 131 Punjabi) individuals from Pakistani population, which is characterized by high rates of endogamy. The haplotype diversity and discrimination capacity were 1. Allelic frequencies ranged from 0.0060 to 0.5060, while gene diversity ranged from 0.6759 (DYS526a) to 0.9937 (DYF399S1). A total 319 different alleles were observed. Results of our study showed that RM Y-STRs provided substantially stronger discriminatory power in Pakistani populations.

Population background exploration and genetic distribution analysis of Pakistan Hazara via 23 autosomal STRs.

Background: Short tandem repeats (STRs) have gained considerable attention in family search (Y-chromosomal STRs), complex paternity identification (X-chromosomal STRs), routine forensic personal identification (autosomal STRs) and population genetics.Aim: To explore the forensic characteristics of 23 autosomal STRs included in the Huaxia Platinum system in the South Pakistan Hazara population and investigate the genetic similarities and differences between Hazara and 54 worldwide reference populations.Subjects and methods: Variation of the 23 autosomal STRs included in the Huaxia Platinum system was first investigated and reported in a sample of 261 Quetta Hazara in Balochistan Province, Southwest Pakistan.Results: The combined power of discrimination is 0.999999999999999999999999999 and combined power of exclusion is 0.99999999989596 in Quetta Hazara. Comprehensive population comparisons between Hazara and another 13 Eurasian populations based on genotype data, as well as between Hazara and 54 worldwide populations based on the allele frequency distribution, were conducted. Multidimensional scaling plots, principal component analysis, and neighbour-joining phylogenetic trees consistently demonstrated that Pakistan Hazara harbours close affinities with neighbouring Turkic-speaking populations. Model-based genetic structure analysis further suggests that Quetta Hazara derives about half its ancestry directly from the East Asians.Conclusion: Twenty-five forensic-related markers included in the Huaxia Platinum system can be used for forensic practice in the Central Asia Hazara population. Quetta Hazara has a close genetic relationship with the Turkic-speaking populations of Uyghur and Kazakh. Further whole-genome sequencing of Hazara needs to be conducted to validate the observed genetic structure and reconstruct the fine-scale population history of Hazara.

Total polyphenol quantitation using integrated NIR and MIR spectroscopy: A case study of Chinese dates (Ziziphus jujuba).

INTRODUCTION: Polyphenols are the foremost measure of phytochemicals in Chinese dates due to their many potential health benefits such as averting cancers, reducing the risk of coronary artery disease, diuretic activity, myocardial stimulant, coronary dilator and muscle relaxant. OBJECTIVE: To quantitate the polyphenols in Chinese dates using a data fusion approach with near-infrared (NIR) and mid-infrared (MIR) spectroscopy. MATERIAL AND METHODS: A total of 80 Chinese dates samples were used for data acquisition from both NIR and MIR spectroscopy. The efficient spectral intervals were extracted by the synergy interval partial least square (Si-PLS) algorithm as input variables for NIR-MIR fusion model. A genetic algorithm (GA) was used to construct the model based on NIR-MIR fusion. The performance of the developed models was evaluated using correlation coefficients of calibration (R2 ) and prediction (r2 ), root mean square error of prediction (RMSEP), bias and residual prediction deviation (RPD). RESULTS: The data fusion model based on the GA was superior compared to NIR and MIR build model. The optimal GA-fusion model yielded R2  = 0.9621, r2  = 0.9451, RPD = 2.44, calibration set bias = 0.004 and prediction set bias = 0.061, computing only 15 variables. CONCLUSION: These findings reveal that integration of NIR and MIR is possible for the prediction of total polyphenol content in Chinese dates.

Population data and phylogenetic structure of Han population from Jiangsu province of China on GlobalFiler STR loci.

Forensic statistical parameters based on allelic frequencies of commonly used short tandem repeats were estimated for the Han population of Jiangsu province from P.R. China. The 6-dye GlobalFiler™ PCR amplification kit incorporates 21 autosomal STRs, providing reliable DNA typing results with enhanced the power of discrimination. Here, we analyzed the GlobalFiler™ STR loci in 516 unrelated individuals from Jiangsu Han population. A total of 256 alleles were observed ranging between 5 and 35.2 repeat units, and SE33 showed the greatest power of discrimination (34 alleles) in Jiangsu Han population. Most of the loci were found to be in the Hardy-Weinberg equilibrium after the Bonferroni correction with the exception of D3S1358. The combined power of exclusion (CPE) was 0.999999996353609, and the combined match probability (CMP) was 3.64 × 10-25. Phylogenetic parameters including pairwise genetic distances showed that Han population living in Jiangsu had closest genetic relationship with other East Asian populations. The present study provides precise reference database for forensic applications and population genetic studies.

Population data of 17 Y-STRs (Yfiler) from Punjabis and Kashmiris of Pakistan.

Pakistan harbors 16 major ethnic groups including Punjabis (56% of total population) and Kashmiri (6% of total population). Here, we report data of 17 Y-chromosomal short tandem repeats (Y-STRs) genotyped with the AmpFlSTR Y-filer™ PCR Amplification kit in 94 Punjabis and 101 Kashmiris. The estimated haplotype diversity was higher in Punjabis (0.996) than that in Kashmiris (0.983). Furthermore, we performed population genetic analyses by including data from six other Pakistani groups. The presented haplotype data were recently included in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

Rice bran nutraceutics: A comprehensive review.

Agro-industry yields ample quantity of several byproducts with considerable importance. These byproducts are mostly under-utilized, often used as animal feed or rejected as waste; hence their true potential is not harnessed. The use of such superfluous resources is of not only economic significance but also a form of commercial recycling. Rice bran is an important byproduct of rice milling industry with a global potential of 29.3 million tons annually. It is gaining great attention of the researchers due to its nutrient-rich composition, easy availability, low cost, high antioxidant potential, and promising effects against several metabolic ailments. Bioactive components of rice bran, mainly γ-oryzanol, have been reported to possess antioxidant, anti-inflammatory, hypocholesterolemic, anti-diabetic, and anti-cancer activities. Rice bran oil contains appreciable quantities of bioactive components and has attained the status of "Heart oil" due to its cardiac-friendly chemical profile. Nutraceutics have successfully been extracted from rice bran using several extraction techniques such as solvent extraction, supercritical fluid extraction, microwave-, and ultrasonic-assisted extraction. Current paper is an attempt to highlight bioactive moieties of rice bran along with their extraction technologies and health benefits.

Combating Mineral Malnutrition through Iron and Zinc Biofortification of Cereals.

 Iron and zinc are 2 important nutrients in the human diet. Their deficiencies in humans lead to a variety of health-related problems. Iron and zinc biofortification of cereals is considered a cost-effective solution to overcome the malnutrition of these minerals. Biofortification aims at either increasing accumulation of these minerals in edible parts, endosperm, or to increase their bioavailability. Iron and zinc fertilization management positively influence their accumulation in cereal grains. Regarding genetic strategies, quantitative genetic studies show the existence of ample variation for iron and zinc accumulation as well as inhibitors or promoters of their bioavailability in cereal grains. However, the genes underlying this variation have rarely been identified and never used in breeding programs. Genetically modified cereals developed by modulation of genes involved in iron and zinc homeostasis, or genes influencing bioavailability, have shown promising results. However, iron and zinc concentration were quantified in the whole grains during most of the studies, whereas a significant proportion of them is lost during milling. This makes it difficult to realistically assess the effectiveness of the different strategies. Moreover, modifications in the accumulation of toxic elements, like cadmium and arsenic, that are of concern for food safety are rarely determined. Trials in living organisms with iron- and zinc-biofortified cereals also remain to be undertaken. This review focuses on the common challenges and their possible solutions related to agronomic as well as genetic iron and zinc biofortification of cereals.

Behavior of endo-xylanases on wheat milling products in relation with variable solid loading conditions.

To investigate the incubation conditions encountered by enzymes in cereal-based product transformation processes, this study aims to provide comprehensive information on the effect of low (18 %) to high (72 %) solid loading on the behavior of bacterial and fungal xylanases towards wheat grain fractions, i.e. white flour, ground whole grain and bran. Both enzymes are effective from 30 % water content. A water content of 50 % appears as the threshold for optimal arabinoxylan solubilisation. The specificity of enzymes was influenced by low hydration conditions, particularly in wheat bran, which contains arabinoxylan with diverse structures. Especially the bacterial xylanase became more tolerant to arabinose substitution as the water content decreased. Time Domain-NMR measurements revealed four water mobility domains in all the fractions. The water populations corresponding to 7.5 nm to 15 nm pores were found to be the most restrictive for enzyme activity. These results define the water content limits for the optimal xylanase action in cereal products.

Preliminary study on mitochondrial DNA analysis from different sports items.

Criminals often attempt to conceal blood-stained weapons used in violent crimes, making forensic evidence crucial in solving cases. This study explores the recovery and extraction of trace DNA from sports equipment, including cricket bats, table tennis racquets, and hockey sticks, which are frequently implicated in such incidents. Our research evaluates various double swab collection methods for retrieving trace DNA from these sports items, emphasizing those associated with blunt force trauma. We also compare presumptive and confirmatory tests to establish a direct correlation. This research consistently demonstrated robust DNA recovery, surpassing a 50 % threshold across all tests. Specifically, DNA recovery from buried samples reached an impressive 87 %, while washed samples still yielded a substantial 80 % efficiency. We conducted a comparative analysis between presumptive and confirmatory testing methods, establishing a direct correlation between the two. Variability in DNA recovery efficiency was observed and attributed to factors like the type of surface the items contacted, and ambient humidity levels. In addition to presenting robust DNA recovery rates, statistical analyses were employed to compare methods, establishing correlations and highlighting the influence of environmental factors on DNA recovery efficiency. These findings have significant implications for forensic investigations involving silent weapons crafted from sports equipment, emphasizing the need for standardized protocols and consideration of environmental factors in DNA analysis.

Simultaneous quantitation of free fatty acid in rice by synergetic data fusion of colorimetric sensor arrays, NIR, and MIR spectroscopy.

This study evaluated the feasibility of colorimetric sensor array (CSA), near-infrared (NIR) and mid-infrared (MIR) spectroscopy for quantitation of free fatty acids in rice using data fusion. Purposely, different data sets of low-level (CSA-NIRLL, CSA-MIRLL, and NIR-MIRLL) and mid-level (CSA-NIRML, CSA-MIRML, and NIR-MIRML) fusion were adopted to enhance the statistical parameters. The model performance was evaluated using coefficient of determination for prediction, (R2p), root mean square error of prediction (RMSEP) and residual predictive deviation (RPD). Synergetic low-level and mid-level fusion model yielded 0.7707 ≤ R2p ≤ 0.8275, 14.4 ≤ RMSEP ≤ 16.3 and 2.19 ≤ RPD ≤ 2.48; and 0.7788 ≤ R2p ≤ 0.8571, 12.4 ≤ RMSEP ≤ 16.8 and 2.12 ≤ RPD ≤ 2.88, respectively. The CSA-NIRML model delivered an optimal performance for prediction of free fatty acid. The integration of CSA, NIR and MIR was feasible and could improve the prediction accuracy of free fatty acids in rice.