Linchuan Liao

Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele.

Tibetan is one of 56 ethnic groups in China, where a level of genetic sub-structure might be expected. Although a global analysis of Y-chromosomal haplotype diversity for 23 STR loci and Y-STR databases with PPY23 kit were created with collaborative effort, there was a lack of data for Tibetan population. In this study we evaluated 248 unrelated male individuals of Chinese Tibetan living in the Tibet Autonomous Region to explore the underlying genetic structure of Tibetan populations. These samples were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) by using PPY23 kit. A total of 224 different haplotypes were found. Haplotype diversity was 0.9990. Both Rst pairwise analyses and multidimensional scaling plot showed the genetic structure of Tibetan population was significantly different from some of Chinese ethnic groups and neighboring populations. There were few interesting null features at DYS448 observed by PPY23 that deserved some comment. It revealed that PPY23 marker set provided substantially stronger discriminatory power in Tibetan population.

A case study of SNPSTR efficiency in paternity testing with locus incompatibility

Instead of testing the additional STR loci, SNPSTR was included in the paternity testing for an alleged father-son duo case, with one inconsistency at the CSF1PO locus. We have chosen CSF1PO STR and five closely linked SNPs rs10077461, rs2569076, rs2228422, rs3733673 and rs3829987 to establish the SNPSTR and examined its potential use in paternity testing. A total of 152 haplotypes from 76 unrelated individuals were obtained by the nested-AS-PCR and 60 SNPSTR haplotypes were observed. The discrimination power of the SNPSTR haplotype was greater than either the STR or SNP haplotype alone. Its SNP part could be used to distinguish fathers from uncles. When SNPSTR was introduced into the calculation of parentage statistics, the paternity probability increased to 99.998%. Based on our findings, we concluded that SNPSTR could be considered a useful tool in forensic science.

An experimental study on investigating the postmortem interval in dichlorvos poisoned rats by GC/MS-based metabolomics

The estimation of the postmortem interval (PMI) is always a key issue in forensic science. Although many attempts based on metabolomics approaches have been proven to be feasible and accurate for PMI estimation, there have been no reports regarding the determination of the PMI in acute dichlorvos (DDVP) poisoning. In this study, all rats were killed by acute DDVP poisoning at a dose three fold the oral LD50 (240 mg/kg). Gas chromatography-mass spectrometry (GC/MS) was applied to investigate the metabolic profiling of blood samples at various times after death up to 72 h. A total of 39 metabolites were found to be associated with PMI, and the combinations of various numbers of metabolites were used to establish support vector regression (SVR) models to investigate the PMI. The SVR model constructed by 23 metabolites had a minimum mean squared error (MSE) of 5.49 h for the training set. Then, the SVR model was validated by prediction set with an MSE of 10.33 h, suggesting good predictive ability of the model for investigating the PMI. The findings demonstrated the great potential of GC/MS-based metabolomics combined with the SVR model in determining the PMI of DDVP poisoned rats and provided an experimental basis for the application of this approach in investigating the PMI of other toxicants.

Estimation of early postmortem interval in rats by GC–MS-based metabolomics

Accurately predicting the early postmortem interval (PMI) is of great significance in forensic practice. This study aimed to establish a novel method for estimating the early PMI by analyzing endogenous substances in the cardiac blood of male and female rats and compare different model for estimating early PMI using these data. Adult Sprague-Dawley (SD) rats (50% male) were sacrificed by suffocation. Then, cardiac blood was collected at various time intervals (0, 3, 6, 12, 24, 48, and 72 h) after death, and the collected samples were analyzed by gas chromatography-tandem mass spectrometry (GC-MS). The data were analyzed by multivariate statistical analysis. An orthogonal signal correction-partial least squares (OSC-PLS) regression model was constructed with whole endogenous metabolites to validate the PMI. The OSC-PLS regression model successfully predicted the PMI of the forecast set and no significant differences was observed between male and female rats. This is the first study to establish an OSC-PLS regression model for predicting PMI with the metabolome, which provides a new technical method and platform for estimating PMI through metabolomics.

Polymorphism study of nine SNPs associated with subjective response to alcohol in Chinese Han, Hui, Tibetan, Mongolian and Uygur populations

ABSTRACT Heavy alcohol drinking is a major public health problem, causing a large disease, social and economic burden in societies. Subjective response (SR) to alcohol is an intermediate characteristic of heavy drinking. A variety of candidate genes have been reported to be associated with SR to alcohol. In this study, we investigated nine single nucleotide polymorphisms (SNPs) related to SR to alcohol in healthy individuals from five Chinese ethnic groups, the Han, Hui, Tibetan, Mongolian and Uygur populations, and a total of 584 bloodstain samples were collected. The nine SNPs included four SNPs in alcohol-metabolizing genes (ADH1B, ADH1C, ALDH2 and CYP2E1*5B) and five SNPs in genes of neurobiological pathways (GABRA2, OPRM1, CHRNA3, HYKK and SLC6A4). A SNaPshot analysis method was developed to type these SNPs simultaneously, and all samples were typed successfully. Statistical analyses of the allele frequencies indicated that the frequencies of all SNPs, except for ADH1C, showed varying degrees of difference in the five studied ethnic groups. Tibetans showed the highest frequencies of risk alleles for heavy drinking at most loci. The genetic polymorphic differences found in this study revealed the variation in genetic susceptibility to heavy drinking in the studied populations.

A Preliminary Urinary Metabolomics Study of Sprague-Dawley Rats after Short-term Ketamine Administration by Proton Nuclear Magnetic Resonance Spectroscopy

Drug abuse has become a global problem. The mass spectrometry-based metabolic consequences of ketamine administration in anesthesia and therapy have been well studied, but to the best of our knowledge, metabolomic studies of ketamine abuse based on nuclear magnetic resonance (NMR) spectroscopy are still lacking. In this study, twenty Sprague–Dawley rats were randomly assigned into two groups: a control group (n = 10) and a ketamine group (n = 10). The animals in the ketamine group received intraperitoneal injections of ketamine twice daily at 12-h intervals at progressively increasing doses over a period of 9 days, while the control group received an equal volume of saline. The urine samples were collected for 24 h at days 0, 1, 3, 5, 7, and 9 for the metabolomics study. The metabolic changes in urine after short-term ketamine administration were analyzed by proton NMR coupled with multivariate statistical analysis. The results indicated that short-term ketamine exposure led to significant alterations of the metabolites in the urine of the rats. Specifically, 1,3,7-trimethyluric acid, 1,3-dimethyluric acid, acetoacetic acid, acetylglycine, creatine, sarcosine, dimethylglycine, glycine, and theobromine were significantly increased in the urine. Significant changes were also found in metabolites related to antioxidant and energy metabolism, including acetoacetic acid, succinate, 1,3,7-trimethyluric acid, 1,3-dimethyluric acid, creatine, and taurine. Our findings indicated that short-term ketamine administration leads to disorder of energy metabolism and oxidative stress. In addition, the modified metabolites identified could serve as the new biological markers and potential biological indices reflecting the underlying mechanism of ketamine abuse.