Research Progress on the Application of Human Oral Microbiome in Forensic Individual Identification.

The oral cavity is the second largest microbial bank in humans after the intestinal canal, colonizing a large number of microorganisms including viruses, bacteria, archaea, fungi and protozoa. The great number of microbial cells, good DNA stability, and individual has a unique microbial community, these characteristics make the human microbiome expected to become a new biomarker for forensic individual identification. This article describes the characteristics of human oral microorganisms and microbial molecular markers in detail, analyzes the potential application value of microorganisms in forensic individual identification, and reviews the research progress of human oral microorganisms in forensic individual identification.

Monitoring the Resistance of the Beet Armyworm (Lepidoptera: Noctuidae) to Four Insecticides in Southern China from 2014 to 2018.

The beet armyworm Spodoptera exigua (Hübner) is a serious polyphagous pest that infests vegetable crops worldwide and has rapidly developed resistance due to its long-term exposure to insecticides. The current resistance statuses to four insecticides exhibited by three field populations of beet armyworms collected in southern China from 2014 to 2018 were investigated. Monitoring data from five consecutive years demonstrated that all three tested S. exigua populations developed extremely high resistance to chlorantraniliprole in 2018 (220.58- to 2,597.39-fold). Two populations (Baiyun and Fengxian) developed low to moderate resistance to spinosad, whereas the Huangpi population remained susceptible (except in 2014, with RR of 6.11-fold). The RR of the Fengxian and Baiyun populations to indoxacarb steadily increased over the years, whereas that of the Huangpi population increased relatively slowly. The Baiyun and Fengxian populations developed moderate to high resistance to indoxacarb and methoxyfenozide, whereas the Huangpi population exhibited susceptibility to low resistance (1.06- to 6.45-fold) to indoxacarb and susceptibility to moderate resistance (1.53- to 14.22-fold) to methoxyfenozide. These results suggest that chlorantraniliprole should not be employed to control this pest in southern China. Reduced use of indoxacarb and methoxyfenozide or the use of alternating insecticides with low levels of resistance is recommended. Spinosad remains an effective insecticide for the management of S. exigua. To avoid the rapid development of insecticide resistance, rotations of insecticides with low levels of resistance and different modes of action based on the resistance patterns of S. exigua should be performed in southern China.

Bioconversion of steviol glycosides into steviol by Microbacterium barkeri.

The strain which degraded steviol glycosides to steviol (STE) was screened and isolated from soil samples. A phylogenetic tree was constructed and used to determine the taxonomic status of the strain. 16S rDNA sequence was ultimately used to identify the strain as Microbacterium barkeri XJ. The transformation product was detected and identified as STE by HPLC/LC-MS/IR analysis. The bioconversion rate of 1% (v/v) steviol glycosides (stevioside, rebaudioside A, rebaudioside C) into STE in basic medium were 100% within 24 h, 84 h and 144 h, respectively. The results indicated XJ was more effective than mixed flora in the bioconversion of steviol glycosides to STE.

Immunization with a peptide mimicking Lipoteichoic acid protects mice against Staphylococcus aureus infection.

Lipoteichoic acid (LTA), a major component of the cell wall of Staphylococcus aureus (S. aureus), is not generally considered as an ideal vaccine candidate since it is a thymus-independent antigen. In this study, we screened a 12-mer phage peptide library and identified a series of peptide sequences that can mimic the epitope of LTA. A tetra-branched multiple antigenic peptide, named MAP2-3, comprising one of the positive peptide sequences (GHKEDRQWCQHS), was synthesized. Immunization with MAP2-3 induced LTA-specific IgG antibodies, prolonged the survival time, and decreased the bacterial burden in organs of mice infected with S. aureus. Moreover, passive immunization with polyclonal anti-MAP2-3 sera reduced bacterial load in organs of mice with bacteremia, alleviated acute lung injury in mice with pneumonia, and decreased the size of lesions in mice with skin infection. The number of LTA-specific antibody-secreting cells in the spleen of MAP2-3 immunized mice were significantly higher than that in the control mice. In summary, as a surrogate of LTA, vaccination with MAP2-3 elicited humoral immune response and protected mice from S. aureus infection. This study provides a new option to design vaccines against S. aureus.

Substitution mutation induced migration anomaly of a D10S2325 allele on capillary electrophoresis.

Microvariants of short tandem repeat (STR) have been reported for different commercially available multiplex STR systems. Sequence length variations caused by variant mechanisms were the central cause of these abnormal phenomena. Here, we reported a novel electrophoretic mobility of the variant allele 13 of D10S2325 in the Investigator HDplex(TM) Kit, which was induced by a special sequence structure containing a poly-G tract (ttg ggg ggg) as a result of only one single base substitution in the flanking regions of the core repeat structure. This migration anomaly can pose a potential risk of wrong designation of some off-ladder alleles in STR loci. Furthermore, population genetic data of the Investigator HDplex(TM) Kit in the Chinese Han population are also reported.

Exploring of new Y-chromosome SNP loci using Pyrosequencing and the SNaPshot methods.

The single nucleotide polymorphisms on the Y chromosome (Y-SNP) have been considered to be important in forensic casework. However, Y-SNP loci were mostly population specific and lacked biallelic polymorphisms in the Asian population. In this study, we developed a strategy for seeking and genotyping new Y-SNP markers based on both Pyrosequencing and the SNaPshot methods. As results, 34 new biallelic markers were observed to be polymorphic in the Chinese Han population by estimation of allele frequencies of 103 candidate's Y-SNP loci in DNA pools using Pyrosequencing technology. Then, a multiplex system with 20 Y-SNP loci was genotyped using the SNaPshot™ multiplex kit. Twenty Y-SNP loci defined 56 different haplotypes, and the haplotype diversity was estimated to be 0.9539. Our result demonstrated that the strategy could be used as an efficient tool to search and genotype biallelic markers from a large amount of candidate loci. In addition, 20 Y-SNP loci constructed a multiplex system, which could provide supplementary information for forensic identification.

Photosynthetic responses to heat treatments at different temperatures and following recovery in grapevine (Vitis amurensis L.) leaves.

BACKGROUND: The electron transport chain, Rubisco and stomatal conductance are important in photosynthesis. Little is known about their combined responses to heat treatment at different temperatures and following recovery in grapevines (Vitis spp.) which are often grown in climates with high temperatures. METHODOLOGY/FINDINGS: The electron transport function of photosystem II, the activation state of Rubisco and the influence of stomatal behavior were investigated in grapevine leaves during heat treatments and following recovery. High temperature treatments included 35, 40 and 45°C, with 25°C as the control and recovery temperature. Heat treatment at 35°C did not significantly (P>0.05) inhibit net photosynthetic rate (P(n)). However, with treatments at 40 and 45°C, P(n) was decreased, accompanied by an increase in substomatal CO(2) concentration (C(i)), decreases in stomatal conductance (g(s)) and the activation state of Rubisco, and inhibition of the donor side and the reaction center of PSII. The acceptor side of PSII was inhibited at 45°C but not at 40°C. When grape leaves recovered following heat treatment, P(n), g(s) and the activation state of Rubisco also increased, and the donor side and the reaction center of PSII recovered. The increase in P(n) during the recovery period following the second 45°C stress was slower than that following the 40°C stress, and these increases corresponded to the donor side of PSII and the activation state of Rubisco. CONCLUSIONS: Heat treatment at 35°C did not significantly (P>0.05) influence photosynthesis. The decrease of P(n) in grape leaves exposed to more severe heat stress (40 or 45°C) was mainly attributed to three factors: the activation state of Rubisco, the donor side and the reaction center of PSII. However, the increase of P(n) in grape leaves following heat stress was also associated with a stomatal response. The acceptor side of PSII in grape leaves was responsive but less sensitive to heat stress.

Association between single-nucleotide polymorphisms in pre-miRNAs and the risk of asthma in a Chinese population.

Single-nucleotide polymorphisms (SNPs) in pre-miRNAs may alter microRNA (miRNA) expression levels or processing and contribute to susceptibility to a wide range of diseases. We investigated the correlation between four SNPs (rs11614913, rs3746444, rs2910164, and rs229283) in pre-miRNAs and the risk of asthma in 220 asthma patients and 540 controls using polymerase chain reaction-restriction fragment length polymorphism methodology and DNA-sequencing. There were significant differences in the genotype and allelic distribution of rs2910164G/C and rs2292832C/T polymorphisms among cases and controls. The CC genotype and C allele of rs2910164G/C were significantly associated with a decreased risk of asthma (CC vs. GG, odds ratio [OR] = 0.51, 95% confidence interval [CI]: 0.31-0.82; C vs. G, OR = 0.74, 95% CI: 0.59-0.93). Similarly, the TT genotype and T allele of rs2292832C/T were significantly associated with a decreased risk of asthma (TT vs. CC, OR = 0.56, 95% CI: 0.33-0.95; T vs. C, OR = 0.71, 95% CI: 0.53-0.95). However, no significant association between the other two polymorphisms (i.e., rs11614913C/T and rs3746444C/T) and the risk of asthma was observed. Our data indicate that rs2910164G/C and rs2292832C/T may play a role in the development of asthma.

Potent anti-tumor effect generated by a novel human papillomavirus (HPV) antagonist peptide reactivating the pRb/E2F pathway.

Human papillomavirus type 16 (HPV16) E7 is a viral oncoprotein believed to play a major role in cervical cancer. In this study, an antagonist peptide against HPV16E7 protein was first identified from screening the c7c phage display peptide library. The binding specificity and affinity of the selected peptide to HPV16E7 were tested by competitive enzyme-linked immunosorbent assay (ELISA). The antagonist peptide showed obvious anti-tumor efficacy both in cell lines and animal tumor models. Significant cell proliferation inhibition with high specificity was noted when HPV16-positive cells were treated with the peptide. This anti-tumor efficacy was resulted from overriding the activities of HPV16E7 and reactivating the pRb/E2F pathway, as shown by a series of experiments. Flow cytometry analysis revealed that the selected peptide induced G1 arrest in a dose-dependent manner. Competitive ELISA, pull down, and Co-IP experiments indicated that the selected peptide disrupted the interaction between HPV16E7 and pRb proteins both in vitro and in vivo. Luciferase reporter assay verified that transcription activities of E2F were suppressed by the peptide through restoration of pRb. RT-PCR and Western blot revealed that it reduced cyclins A, D1, and E1 expression, and led to HPV16E7 protein degradation, but pRb protein stabilization. The current study suggests that this specific peptide may serve as a potential therapeutic agent for HPV16-positive cervical cancer.

Characteristics of eight X-STR loci for forensic purposes in the Chinese population.

X-chromosomal short tandem repeats (ChrX STRs) loci are used for forensic practice in recent years. Considering the unique heredity characteristics of ChrX, recombination and linkage disequilibrium (LD) among ChrX STR loci vary between male and female and different populations as well. However, there is a lack of data for analysis of recombination and linkage disequilibrium on ChrX STR loci in the Chinese population. In this work, a total of 303 unrelated individuals (203 males and 100 females) in the Chinese Han population were analyzed with Mentype Argus X-8 PCR amplification kit (DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101, and DXS10134-DXS7423). The recombination and linkage disequilibrium of the eight ChrX STR loci were investigated with HapMap LD plots and software ARLEQUIN 3.1. Allele frequencies of the eight loci and further population forensic genetic parameters were obtained. Our results revealed hotspots for recombination, and there was no obvious evidence for LD among the eight loci in the Chinese population. Our work implied that single locus frequencies rather than haplotype frequencies should be applied for forensic practice in the Chinese population.

Association of tumor necrosis factor gene polymorphisms with susceptibility to dilated cardiomyopathy in a Han Chinese population.

Tumor necrosis factor (TNF) is an immunomodulatory cytokine that plays an important role in many inflammatory and autoimmune diseases. We investigated the correlation between single-nucleotide polymorphisms of the TNF gene [i.e., TNF-α (308), TNF-α (857), TNF-α (863), TNF-α (1031), and TNF-ß (+252)] and dilated cardiomyopathy (DCM). A total of 110 DCM patients and 110 control subjects were genotyped using polymerase chain reaction-restriction fragment length polymorphism and DNA-sequencing assay. GA=AA genotypes of TNF-α (308) were significantly associated with increased risk of DCM compared with GG genotype (odds ratio[OR]=1.92; 95% confidence intervals [CI], 1.05-3.52). Similarly, GA=AA of TNF-ß (+252) was significantly associated with increased risk of DCM compared with GG genotype (OR=1.97; 95% CI, 1.14-3.38). Additionally, A allele of TNF-α (-308) and TNF-ß (+252) was associated with a 1.76-fold increased risk of DCM compared with G allele (OR=1.76; 95% CI, 1.05-2.95 and OR=1.79; 95% CI, 1.22-2.63, respectively). However,no association between DCM and TNF-α (857), TNF-α (1031), and TNF-α (863) was observed. TNF gene polymorphisms may be associated with risk of DCM.

Salicylic acid alleviates decreases in photosynthesis under heat stress and accelerates recovery in grapevine leaves.

BACKGROUND: Although the effect of salicylic acid (SA) on photosynthesis of plants including grapevines has been investigated, very little is yet known about the effects of SA on carbon assimilation and several components of PSII electron transport (donor side, reaction center and acceptor side). In this study, the impact of SA pretreatment on photosynthesis was evaluated in the leaves of young grapevines before heat stress (25 degrees C), during heat stress (43 degrees C for 5 h), and through the following recovery period (25 degrees C). Photosynthetic measures included gas exchange parameters, PSII electron transport, energy dissipation, and Rubisco activation state. The levels of heat shock proteins (HSPs) in the chloroplast were also investigated. RESULTS: SA did not significantly (P < 0.05) influence the net photosynthesis rate (Pn) of leaves before heat stress. But, SA did alleviate declines in Pn and Rubisco activation state, and did not alter negative changes in PSII parameters (donor side, acceptor side and reaction center QA) under heat stress. Following heat treatment, the recovery of Pn in SA-treated leaves was accelerated compared with the control (H2O-treated) leaves, and, donor and acceptor parameters of PSII in SA-treated leaves recovered to normal levels more rapidly than in the controls. Rubisco, however, was not significantly (P < 0.05) influenced by SA. Before heat stress, SA did not affect level of HSP 21, but the HSP21 immune signal increased in both SA-treated and control leaves during heat stress. During the recovery period, HSP21 levels remained high through the end of the experiment in the SA-treated leaves, but decreased in controls. CONCLUSION: SA pretreatment alleviated the heat stress induced decrease in Pn mainly through maintaining higher Rubisco activation state, and it accelerated the recovery of Pn mainly through effects on PSII function. These effects of SA may be related in part to enhanced levels of HSP21.

[Analysis and application of haplotype in forensic medicine].

Haplotype is a lineable combination of alleles at multiple loci that are transmitted together on chromosome or mitochondrion. In October 2002, the international HapMap project started and aimed at mapping the haplotype blocks of human being and discovering the Tag SNPs by determining the DNA sequence variation patterns, variation frequency and their relationship. This review summarizes the formation and distribution of the haplotype and the current three haplotype-analysis methods including the methodology of experiment, the deduction from pedigrees and the statistic method. When an allele linkage disequilibrium occurs, the genetic probability would be evaluated by haplotype. The importance of haplotype has been recognized and its application has been gradually increased in forensic sciences. The current focus on haplotype study in forensic science involves Chromosome Y, Mitochondrial DNA and Chromosome X, which are useful supplements of genetic marks.

CYP1A1 and CYP1B1 genetic polymorphisms and uterine leiomyoma risk in Chinese women.

PURPOSE: The aim of the study was to evaluate the association of CYP1A1 and CYP1B1 polymorphisms with uterine leiomyoma in Chinese women. METHODS: We investigated 100 women with clinically diagnosed uterine leiomyoma and 110 healthy normal subjects from Chinese women. The genetic distribution of two CYP1A1 polymorphisms at MspI, Ile462Val and four CYP1B1 polymorphisms at Arg48Gly, Ala119Ser, Leu432Val, Asp449Asp were analyzed by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing method. RESULTS: All the SNPs showed polymorphisms in Chinese women. The genotype A/G and the allele G on Ile462Val was significantly different between uterine leiomyoma patients and controls (P < 0.05). CONCLUSION: These results suggest that the genotype of CYP1A1 Ile462Val was associated with the increased risk of uterine leiomyomas in Chinese women.

[Multiple amplification of 16S rRNA gene and Cytb gene in mitochondrial DNA for species identification].

OBJECTIVE: To establish a fluorescent multiple amplification system of 16S rRNA and Cytb genes located in mitochondrial DNA for species identification. METHODS: A pair of primers of 16S rRNA gene and Cytb gene of the mitochondrial DNA was designed with the software Primer 5.0 to construct a multiple amplification system. The amplified products from human and five species of animals, including cattle, pig, dog, chicken and grass carp were analyzed by 310 Genetic Analyzer. RESULTS: The amplified products of these samples showed two peaks. The common one was 358bp and the specific one different in unique species was between 231bp and 256bp. CONCLUSION: The multiplex amplification system can exactly distinguish the species of human from five common animals.

[Computer-aided molecular modeling and activity estimation for ligand screening with specific phage clone as the target].

OBJECTIVE: To investigate the interaction between tumor necrosis factor alpha (TNF alpha) mimotopes and TNF alpha-binding peptides screened from random phage display peptide library with TNF alpha mimotopes displayed on phage clone as the target, the computational docking program AutoDock (with confirmation calculations using Discover) was used to predict and analyze the binding modes of LLT-18 (TNF alpha binding peptide, sequence EHMALTYPFRPP) with TNF alpha, after which LCS-7 (TNF alpha mimic phage clone, displayed positive sequence c-RRPAQSG-c) was docked to LLT-18 manually. The binding between LLT-18 and TNF alpha or LCS-7 was stabilized predominantly through electrostatic interaction and H-bond formation. The Arg residues in TNF alpha or LCS-7 were important for their interaction with LLT-18. For LLT-18, the key amino acid residues were Glu1, His2, Met3 and Tyr7. These results suggest the feasibility of screening ligand to single epitope with specific phage clone as the target, and of predicting the interaction between small peptides by computer-aided molecular modeling.

[A study of paternity testing with considering mutation].

OBJECTIVE: To formulate recommendations in the evaluation of results of genetic analyses in paternity testing under considering mutations. METHODS: A total of 15 short tandem repeat(STR) loci were employed for this study, which were included CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, PentaD and PentaE. Both 100 cases of true trio and 100 cases of false trio were investigated. RESULTS: The numbers of mismatch alleles in different STR loci were observed in 100 cases of false trio. The different distributions of paternity index were obtained, including the changes of paternity index in each case of true trio under simulated mutations. CONCLUSION: In order to avoid the effect of mutations, the exclusion of paternity was never considered on the basis of a single locus. The threshold values of the combined probability of exclusion and the paternity index were important for both exclusion and inclusion of paternity. The scientific evidence for paternity testing can be obtained when both the combined probability of exclusion and the paternity index meet the threshold values. However, when either the combined probability of exclusion or the paternity index can not meet the threshold values, more genetic markers should be added.

[Polymorphism of five short tandem repeat systems in Chinese Han population in Chengdu].

OBJECTIVE: To obtain population genetic data of loci D11S4951, D11S4957, GATA193H05, D2S2951, and D6S2421 in Han population in Chengdu area and to validate the value of their forensic application. METHODS: Blood samples were collected in EDTA tubes from unrelated individuals. DNAs were extracted with Chelex-100 and were analyzed by PCR and horizontal PAGE followed by silver staining. RESULTS: Alleles 7, 10, 8, 6 and 8 were found in 5 STR loci, respectively. No deviations from Hardy-Weinberg balance were observed. The heterozygosities observed were 0.743, 0.772, 0.833, 0.650 and 0.800, respectively. The chances of exclusion were 0.497, 0.549, 0.662, 0.356 and 0.599, and the discrimination powers were 0.863, 0.912, 0.947, 0.829 and 0.931. CONCLUSION: All of the five loci studied may be useful markers for individual identification and paternity testing.

[Inhibition of IFN-gamma receptor signaling by hepatitis C virus non-structural protein NS4B].

The function of NS4B is incompletely understood. The aim of the study is to understand the influence of NS4B on anti-viral response. After cell line stably expressing NS4B established, the influence of IFN-alpha of different concentration on VSV was studied using plaque assay; cell expression profiling caused by NS4B was studied using DNA microarray, and the IFNGR1 fluorescence intensity was analyzed. Our data showed that HCV-NS4B could suppress immuno-associated gene expression, in particular, IFN-gamma receptor signal transduction-related genes. Taken together, NS4B could play some roles in HCV resistance to IFN therapy.