Analysis of Salivary Bacterial Community by Direct PCR and High Resolution Melting Curve and Its Forensic Applications.

OBJECTIVES: To develop a rapid test for salivary bacterial community based on direct PCR (dPCR) and high resolution melting (HRM) curve analysis, to evaluate its application value in forensic medicine. METHODS: The salivary bacteria were collected by centrifugation and then resuspended in Tris-EDTA (TE) buffer, and directly used as the template for amplification and HRM curve analysis (dPCR-HRM) of the 16S rDNA V4 region. The genotype confidence percentage (GCP) of the HRM profiles compared with the reference profile was calculated. The template DNA was extracted by traditional kit and then PCR-HRM (namely kPCR-HRM) was used as reference to validate the feasibility of dPCR-HRM. The gradient dilution templates, population samples and simulated salivary stains were analyzed by dPCR-HRM to evaluate its sensitivity, typing ability and adaptability. RESULTS: Using dPCR-HRM method, the HRM profiles of salivary bacterial community were obtained within 90 minutes. The GCP between dPCR-HRM and kPCR-HRM was greater than 95.85%. For general individuals, the HRM type of bacterial community could be determined with 0.29 nL saliva by dPCR-HRM. The 61 saliva samples could be divided into 10 types. The typing of salivary stains deposited within 8 h was the same as those of fresh saliva (GCP>90.83%). CONCLUSIONS: dPCR-HRM technology can be used for rapid typing of salivary bacterial community, and has the advantage of low cost and simple operation.

[One-step methylation variable position analysis technology in single-tube].

OBJECTIVE: To develop the single-tube one-step methylation variable position (MVP) analysis technology-single-tube post-digestion PCR-melting curve analysis (PDP-MCA). METHODS: Based on differentially methylated region (DMR) reported previously as the model, a set of primers with different melting temperatures of products in the two sides of MVP were designed. By using the FastDigest methylation-sensitive restriction enzyme (MSRE), DNA digestion, multiplex amplification, MCA detection and MCA profiles were performed in a single reaction tube. Same samples (peripheral venous blood, semen, and vaginal fluid, 5 samples each type) were tested by single-tube one step MVP and traditional MSRE-PCR MCA technology. To verify the feasibility of this method, the results were compared with that of the traditional technology. The MCA/HRM profiles of different samples were analyzed and compared. RESULTS: When the melting temperature of the fragments had a differential of 2 degrees C, the MCA melting peaks separated well, and MCA detection after multiplex amplification was successful. The single-tube PDP-MCA assay was developed, which integrated multiple reactions (digestion, amplification and detection) into one tube. By this method, the sample-specific profiles and data were analyzed in 2 h, which is similar to that of the traditional method. The rapid classifications of the samples were also realized. CONCLUSION: Multiplex MVPs can be analyzed in a single closed-tube. The single-tube PDP-MCA technology is a simple, fast, and automatable method. It can be used for detection of DNA methylation variations.

[Advances in the study of HIV-1 integrase inhibitors of alpha, gamma-diketo compounds].

HIV-1 integrase (IN) is an essential enzyme for retroviral replication. There is no analogue for this enzyme in human cells so that inhibition of IN will not bring strong effect on human body. Thus, HIV-1 IN has become a rational target for therapy of AIDS. This review provides a comprehensive report of alpha, gamma-diketo IN inhibitors discovered in recent years. Compilation of such data will prove to be beneficial in developing QSAR, pharmacophore hypothesis generation and validation, virtual screening and synthesis of compounds with higher activity.

[Advances in identification of semen stains].

Stain identification has long been a task in forensic biology. The identification of semen stain, one of the most common human stains, can provide crucial information for crime scene reconstruction and forensic investigation. Traditional detection of semen stain depends largely on the microscopic identification of spermatozoa, enzyme activity-based methods or antigen-antibody reactions. These morphological, proteinological and zymological approaches, however, are apparently inadequate in identifying tiny, admixed, degraded or contaminated samples. With the development of transcriptomics and epigenetics, many semen-specific mRNA markers, such as protamine-1 (PRM1) and -2 (PRM2), have been applied to semen and semen stain identification. Messenger RNA profiling shows great promise in identifying tissues as demonstrated by the recognition of specific markers. Further more, studies on tis-sue-specific differential DNA methylation will provide a scrumptious way of identifying difficult samples.

[Applications of Alu family in forensic DNA analysis].

Alu family is the primate specific short interspersed repetitive elements (SINEs). Its abundance and diversity distribution in genome, high methylation level and polymorphic for insertion make them ideally suitable as tools in forensic applications. The application of A4 lu sequence in forensic genomics, include DNA quantitation, race determination, species and gender identification, personal identification, paternity testing and whole-genome amplification. The principles and characteristics of these Alu-based techniques are also summarized. The prospect of Alu as forensic molecular marker is discussed as well.

[The application of PCR-SSCP in forensic mtDNA typing].

OBJECTIVE: To study the application of PCR-SSCP in forensic mtDNA typing. METHODS: Primers flanking the mtDNA HV-I and HV-II regions were designed. By PCR-SSCP techniques, 70 family trios and 140 unrelated Wuhan Han individuals were investigated and analyzed. RESULTS: In 70 family trios, the SSCP profiles in region HV-I and HV-II of children were not same to that of their fathers in 98.57% and 97.13% respectively but were identical with their mothers. In 140 unrelated Wuhan Han individuals, 21 haplotypes were found in HVI, GD = 0.9556; 16 haplotypes were found in HVII, GD = 0.9356. CONCLUSION: PCR-SSCP technique may be useful in forensic mtDNA typing, especially for screening the suspects.

[The multiplex analysis of epigenetic markers and genetic markers by post-digestion mutagenically separated PCR].

OBJECTIVE: To establish a novel method for the multiplex analysis of the methylation and single nucleotide polymorphism (SNP). METHODS: The imprinted SNP rs220028 was chosen as a model. Genomic DNA, after being digested with methylation sensitive restriction enzyme, were typed by mutagenically separated PCR (MS-PCR). The polymorphism of restriction site was excluded by PCR-RFLP. RESULTS: By post-digestion MS-PCR, the methylated allele was detected selectively, the maternal origin of which was confirmed by pedigree analysis; A=0.5085, G=0.4915,PIC=0.3749. CONCLUSION: The multiplex analysis of methylation markers and SNP can be achieved by post-digestion MS-PCR. The imprinted SNP locus rs220028 is a potentially useful marker in screening Prader-Willi/Angelman syndrome.

[Applications of DNA methylation markers in forensic medicine].

DNA methylation is a post-replication modification that is predominantly found in cytosines of the dinucleotide sequence CpG. Epigenetic information is stored in the distribution of the modified base 5-methylcytosine. DNA methylation profiles represent a more chemically and biologically stable source of molecular diagnostic information than RNA or most proteins. Recent advances attest to the great promise of DNA methylation markers as powerful future tools in the clinic. In the past decade, DNA methylation analysis has been revolutionized by two technological advances--bisulphite modification of DNA and methylation-specific polymerase chain reaction (MSP). The methylation pattern of human genome is space-time specific, sex-specific, parent-of-origin specific and disease specific, providing us an alternative way to solve forensic problems.

[A simple and rapid modified--new method for SNP typing by fragment length discrepant allele specific PCR].

OBJECTIVE: To establish a new method for single nucleotide polymorphism (SNP) typing based on allele specific PCR: fragment length discrepant allele specific PCR (FLDAS-PCR), and study the influence on specific extension by introducing a mismatch at the third or fourth 3'-terminal base of allele specific primers. METHODS: For SNP loci rs759117 and rs760887, two allele specific forward primers, with different length and a mismatch introduced at the third or fourth 3'-terminal base, and a public reverse primer were designed for SNP typing. The genotyping of SNP was determined by the two allele specific fragments different in size after polyacrylamide gel and silver staining. RESULTS: The different homozygote genotypes comprised a single band with different size respectively, and the heterozygote genotypes comprised two bands. Typing results were completely consistent with those by direct sequencing. Non-specific primer extension was decreased remarkably after introducing a mismatch at the third or fourth 3'-terminal base of allele specific primers, and the stringency of PCR reaction was cut down. CONCLUSION: FLDAS-PCR is a simple, rapid and efficient new method for SNP typing. During FLDAS-PCR, specific primers with a mismatch at the third or fourth 3'-terminal base have more power to identify two alleles.

6r, a novel oxadiazole analogue of ethacrynic acid, exhibits antitumor activity both in vitro and in vivo by induction of cell apoptosis and S-phase arrest.

This study investigated the in vitro and in vivo antitumor effects of 5-[2,3-Dichloro-4-(2-methylene-1-oxobutyl) phenoxymethyl]-3-methyl-1,2,4- oxadiazole (6r), a novel ethacrynic acid (EA) derivative. The in vitro effect of 6r on cell proliferation of human colon, leukemia, prostate, lung, breast, ovarian and cervical tumor cell lines was assessed using MTT assay and the in vivo effect was determined with an SW620 xenografts nude mice model. The effect of 6r on expressions of GST P1-1 and apoptosis-related proteins were measured by western blotting and the effect on cell apoptosis was analysed by Hoechst 33258 nuclear staining as well as by cell surface staining of annexin V/propidium iodide. The effect on cell cycle was assessed by flow cytometry. Results showed that 6r inhibit proliferation of a range of human cancer cells in vitro and growth of SW620 tumor xenografts in vivo. The anti-proliferative effect of 6r is associated with cell apoptosis as a result of increased ratio of cellular Bax/bcl-2 expression and subsequent cytochrome-c and caspase-3 activation. Unlike EA, 6r did not show any influence on cellular GST P1-1 expression and its anti-proliferative action was associated with cell cycle arrest in G1/S-phase. In conclusion, 6r has the potential to be developed as a chemotherapeutic agent by induction of cell apoptosis but not regulating GST P1-1.

XRCC1 codon 280 and ERCC2 codon 751 polymorphisms and risk of esophageal squamous cell carcinoma in a Chinese population.

Numerous candidate genes have been proposed as susceptibility factors for the development of esophageal squamous cell carcinoma (ESCC). XRCC1 (X-ray cross-complementing group 1) codon 280 and ERCC2 (excision repair cross complementing group 2) codon 751 polymorphisms were studied in ESCC in a Chinese population. The aim of this study is to investigate the potential association between single-nucleotide polymorphisms (SNP) of XRCC1 codon 280 His and ERCC2 codon 751 Gln polymorphisms and ESCC. Peripheral blood samples of 200 cases and 200 age-and-gender matching controls were collected from a Chinese population and the two polymorphisms were studied by means of polymerase chain reaction (PCR) restriction fragment length polymorphism techniques. Our results showed that XRCC1 codon 280 His allele had no significant difference between ESCC patients and normal controls (P > 0.05), while ERCC2 codon 751Gln allele was associated with a borderline decrease of ESCC (odds ratio [OR] = 0.628, 95% confidence interval [CI]: 0.400-0.986).

Caffeoyl naphthalenesulfonamide derivatives as HIV integrase inhibitors.

HIV-1 integrase (IN) is an essential enzyme for retroviral replication and a rational target for the design of anti-AIDS drugs. In the present study, we have designed, synthesized and tested a series of caffeoyl naphthalenesulfonamide derivatives as HIV integrase inhibitors. Among these compounds, we found that HIV integrase inhibitory activities of compounds III-3 and III-4 were more potent than L-chicoric acid (IC(50)=11.8 microg/mL) and others were comparable to L-chicoric acid. Furthermore, the structure-activity relationships of these compounds were studied. The information gathered from this paper will be useful in the development and design of HIV-1 integrase inhibitors in the future.