Xiaoliang Fu

Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing

Decomposition is a complex process involving the interaction of both biotic and abiotic factors. Microbes play a critical role in the process of carrion decomposition. In this study, we analysed bacterial communities from live rats and rat remains decomposed under natural conditions, or excluding sarcosaphagous insect interference, in China using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 1,394,842 high-quality sequences and 1,938 singleton operational taxonomic units were obtained. Bacterial communities showed notable variation in relative abundance and became more similar to each other across body sites during the decomposition process. As decomposition progressed, Proteobacteria (mostly Gammaproteobacteria) became the predominant phylum in both the buccal cavity and rectum, while Firmicutes and Bacteroidetes in the mouth and rectum, respectively, gradually decreased. In particular, the arrival and oviposition of sarcosaphagous insects had no obvious influence on bacterial taxa composition, but accelerated the loss of biomass. In contrast to the rectum, the microbial community structure in the buccal cavity of live rats differed considerably from that of rats immediately after death. Although this research indicates that bacterial communities can be used as a “microbial clock” for the estimation of post-mortem interval, further work is required to better understand this concept.

Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group

Abstract Population genetic data of 21 autosomal short tandem repeats (STRs) were obtained in a sample of 106 unrelated healthy individuals of Bai ethnic minority born in the Dali Bai Autonomous Prefecture in Yunnan Province. We observed 138 alleles with corresponding allelic frequencies ranging from 0.005 to 0.575. The genotypic frequency distributions at those STR loci were consistent with Hardy–Weinberg equilibrium (Bonferronis correction was used for Hardy–Weinberg equilibrium tests). The combined probability of exclusion, power of discrimination, probability of matching value for all 21 STR loci were 0.9999975729, 0.999999999999999999872 and 1.28×10 −19 , respectively. The population data in this study showed significant differences from the previously published population data of Tibetan and Salar groups in some loci.

Genetic polymorphism of 29 STR loci in the Hunan Han population from China

Genotype frequencies at each locus, power of discrimination (PD), power of exclusion (PE), probability of matching (PM), polymorphism information content (PIC), observed heterozygosity (Ho) and Hardy– Weinberg equilibrium (HWE) were evaluated with modified PowerStat (version 1.2) program [5]. Linkage disequilibrium (LD) analysis was performed using Genepop version 4.2 software package (http://genepop. curtin.edu.au). The allele frequency distributions among groups were compared using Arlequin version 3.5 software package [6]. Pairwise genetic distance among populations was calculated according to Nei’s formula by using Phylogeny Inference Package (Phylip) version 3.69 [7]. A Neighbour-Joining (NJ) phylogenetic tree was constructed and viewed with TreeView softwar [8]. The current study was approved by the Third Xiangya Hospital of Central South University (approval code: 2016-S041). The allele frequencies and population genetics parameters of the 29 STR loci are summarized in Table S1. We detected 403 alleles across the 29 STR loci, with the largest number of 50 variants at the SE33 locus and the least number of 6 alleles at the TPOX locus. Genotyping results should be combined with the standard DNA allelic ladder to avoid genotyping errors because of the complex internal sequence structure of the SE33 locus [9]. The P-value for Hardy–Weinberg testing did not significantly deviate from HWE after Bonferroni correction (P = 0.05/29 = 0.0017), only D21S2055 (P = 0.0002) and D7S1517 (P = 0.0012) had minor departures from HWE because of errors in random sampling. Among the 29 STR loci, the SE33 locus was the most informative marker, with a PD value of 0.9930 and a PIC value of 0.9500, whereas the TPOX locus presented the lowest forensic efficiency, with a PD value of 0.7590 and a PIC value of 0.5200. The Ho ranged from 0.5930 (TPOX) to 0.9240 (Penta E). The combined PM and combined PE for the 29 STR loci were 1.34 £ 10¡36 and 0.999 999 999 998, respectively. Pairwise LD tests demonstrated that only 18 pairs (Table S2) of the loci remained in LD for 406 pairwise

Developing a new nonbinary SNP fluorescent multiplex detection system for forensic application in China

Nonbinary single‐nucleotide polymorphisms (SNPs) are potential forensic genetic markers because their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In this study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent‐labeled SNaPshot multiplex SNP typing method. The allele frequencies and genetic parameters of these 20 nonbinary SNPs were determined among 314 unrelated individuals from Han populations from China. The total power of discrimination was 0.9999999999994, and the cumulative probability of exclusion was 0.9986. Moreover, the result of the combination of this 20 nonbinary SNP assay with the 20 nonbinary SNP assay we previously developed demonstrated that the cumulative probability of exclusion of the 40 nonbinary SNPs was 0.999991 and that no significant linkage disequilibrium was observed in all 40 nonbinary SNPs. Thus, we concluded that this new system consisting of new 20 nonbinary SNPs could provide highly informative polymorphic data which would be further used in forensic application and would serve as a potentially valuable supplement to forensic DNA analysis.