Zhilong Li

An investigation of a set of DIP-STR markers to detect unbalanced DNA mixtures among the southwest Chinese Han population

The resolution of DNA mixtures is still a difficult problem that is worthy of further study. A common method applied for analysing mixtures is the use of autosomal STR markers as well as related calculation software based on genotypes; however, these markers have a limitation in detecting minor DNA in unbalanced mixtures if major DNA constitutes over 95% of the stain. Novel biomarkers, such as Y-STR, DIP-STR and SNP-STR, have been shown to perform well in distinguishing DNA donors in this type of mixture. DIP-STR can successfully target minor DNA in 1000-fold background DNA using two separate allele-specific primers. However, whether this method can successfully detect minor DNA primarily depends on the distribution of the DIPs in a population. Until now, only Swiss population data have been reported; therefore in this study, we selected 10 DIP-STR markers that performed well in the Swiss population and investigated whether these markers were also useful among the southwest Chinese Han population. The allele frequencies were estimated based on 152 samples, and six of the ten DIP-STR makers had a relatively high probability of informative markers (I value), which indicated their potential usefulness in the southwest Chinese Han population. A comparative study of DIP-STR markers and autosomal STR markers demonstrated that DIP-STR markers detected minor DNA at a ratio of 1:1000, while autosomal STR markers often failed to genotype minor DNA because of strong background noises caused by large amount of major DNA. However, the discrimination power was not high enough using these six DIPs alone. Therefore, we suggest that development of a panel with more loci is imperative and that a panel combined with DIP-STR and SNP-STR markers may be a possible way to achieve better discrimination power.

Circular RNA expression profile in mouse cortex after traumatic brain injury

Traumatic brain injury (TBI) causes high rates of worldwide death and morbidity because of the complex secondary injury cascade. Circular ribonucleic acid (RNA) (circRNA), a type of RNA that forms a covalently closed continuous loop, may be involved in the regulation of secondary injury because it is expressed widely in the brain and contributes to a large class of post-transcriptional regulators. Deep RNA sequencing (RNA-seq) and bioinformatic analysis were performed to investigate the expression profile and function of circRNAs in the mouse cortex after controlled cortical impact (CCI). A total of 19,794 circRNAs were identified, and 1315 were annotated in circBase. There were 191 filtered differentially expressed circRNAs (98 for up-regulated and 93 for down-regulated). The gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that inflammation, cell death, and repair of damage were the main biological processes and molecular mechanisms related to altered circRNAs. The pathway-circRNA interaction network revealed three core circRNAs and five corepathways related to TBI. The circRNA-messenger RNA (mRNA) interaction network and competitive endogenous RNA (ceRNA) analysis suggested potential microRNA (miRNA) sponges and target mRNAs. In addition to five optimal circRNA-miRNA-mRNA pairs were analyzed, circRNA_16895-miRNA myosin-10 (Myo 10) was predicted to regulate fragment crystallizable gamma receptors (FcγR)-mediated phagocytosis pathway. Four circRNAs were selected for quantitative real-time polymerase chain reaction analysis to validate the sequencing data. Our results provide promising functions of circRNAs aberrantly expressed in TBI to explore molecular mechanisms and potential therapeutic targets for its therapy.

Rapidly mutating Y-STRs study in Chinese Yi population

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic analysis and population genetics. With low to moderate mutation rates, conventional Y-STR panels, including commercially available Y-STR kits, enable the identification of male pedigrees but typically fail to differentiate related male individuals. The introduction of rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) with higher mutation rates (μ > 10−2) has been demonstrated to increase the discrimination capacity of unrelated men and the differentiation rate of related men compared with standard Y-STRs. To date, several studies have been performed worldwide. Here, 260 father–son pairs from Chinese Yi population were investigated, and 18.8% of them were differentiated with the 13 RM Y-STR markers, which was close to the theoretical estimate of 19.5% based on the mutation rates of these markers. Among the 57 mutations observed, repeat gains were more common than repeat losses (1.48:1), and one-step mutations were more common than two-step mutations (27.5:1). Locus-specific mutation rates ranged from < 3.85 × 10−3 (95% CI 0.00–1.41 × 10−2) to 3.85 × 10−2 (95% CI 1.86 × 10−2–6.96 × 10−2), with an average mutation rate of 1.46 × 10−2 (95% CI 1.11 × 10−2–1.89 × 10−2). Furthermore, we combined the father–son pair data from the present study with the data from the previous studies, generating an overall mutation rate of 1.70 × 10−2. The high differentiation rate obtained in the present study indicates the suitability of RM Y-STRs to distinguish paternal lineages in Chinese Yi population.

Semen-specific miRNAs: Suitable for the distinction of infertile semen in the body fluid identification?

Non-protein coding RNA, miRNAs (microRNAs), are a class of promising molecular biomarkers for forensic body fluid identification (BFI) as their small size and tissue-specific expression manners. A number of studies have shown that semen can be distinguished from forensic-related body fluids (such as menstrual blood, venous blood, vaginal fluid, saliva, etc.) using semen-specific miRNAs through microassay screening and RT-qRCR. Infertility is becoming a global health problem, affecting 10%-15% of couples worldwide, and half of the cases are the result of male factors (Lian et al., 2009 [1]). Forensic researchers have to consider the impact of semen infertility on semen identification with a high incidence of infertility. In the present study, normal semen (NS) and four other types of infertile semen samples, including asthenospermia (AS), oligospermia (OS), azoospermia (AZ), oligospermia and asthenospermia (OSAS) semen, were collected. The expression levels of a set of semen-specific miRNA markers (miR-10a, miR-10b, miR-135a, miR-135b, miR-888 and miR-891a) were evaluated using a real-time quantitative PCR technique with a specific fluorescence-labelled TaqMan probe. The results showed the significantly high expression of these miRNAs in normal semen, and the molecules have semen specificity. Nevertheless, a distinct down-regulation in the expression of infertile samples compared with normal semen samples was observed. Moreover, differences in the results of selected optimal biomarkers between the discriminant function and two-dimensional scatter plots were also detected. The goal of the present study was to identify a small set of semen-specific miRNAs that efficiently and accurately distinguish semen (fertile and infertile) from other forensic-related body fluids. The results of the present study suggest that attention should be paid to infertile semen samples when using miRNAs to identify semen samples, for which would have a far-reaching impact on forensic identification.