Difference Analysis Based on 16S rRNA Sequencing of Different Soil Bacterial Communities

Abstract

Objective To study the structure and differences of bacterial communities in different soils, and to explore the effectiveness of 16S rRNA sequencing in identification of different soil. Methods Soil samples from 7 places in Shanghai were collected, then bacterial genomic DNA were extracted from them. The fragments of hypervariable region from 16S rRNA sequences were sequenced with high-throughput sequencing techniques. The results were quantified or visualized with bioinformatics software. The differences in diversity and abundance among the three kinds of bacterial communities in soil samples from grassland, forests and beaches were compared and analyzed. Results The statistical differences that existed among the alpha diversity indexes of bacterial communities in soil samples of grassland, forests and beaches had statistical significance. The relative abundance and diversity of bacterial communities in these three kinds of soil were significantly different. Grassland soil had higher Acidobacteria abundance, forest soil had higher Proteobacteria abundance, beach soil had higher Actinobacteria abundance. However, the differences in soil bacterial communities in artificial grasslands, natural grasslands and industrial district grasslands did not have statistical significance. Conclusion 16S rRNA sequencing can effectively distinguish different soils. This method may be able to provide clues for first crime scene inference in criminal cases.

Progress in the 16S rRNA Gene Sequencing in Forensic Science

Forensic microorganism is one of the hotspots of forensic science research. Due to its conservatism and specificity, the 16S rRNA gene is found to be an ideal marker for forensic identification. With the rapid development of high throughput sequencing technology, the research on microorganisms has been gradually applied to many fields such as environment and health care. In the field of forensic science, the results of forensic microbiology research, represented by 16S rRNA gene sequencing, are also gradually applied to forensic practice, such as biological samples identification, individual identification, postmortem interval estimation, and regional inference, which not only provide clues for the investigation of cases but also complement and assist traditional methods. This paper describes the research methods and related sequencing technologies of 16S rRNA gene sequencing, summarizes its research progress, and discusses the application value and potential of 16S rRNA in forensic science.

[Establishment of DNA Genetic Marker Identification System for Plant Evidence]

OBJECTIVES

To establish a species identification system based on DNA genetic markers for plant evidence.

METHODS

Two hundred common plants in Shanghai were collected and identified by morphological characteristics. The primers of gene segments rbcL, matK, and ITS were designed and amplified. The PCR amplicon was detected by agarose gel electrophoresis. After the sequencing, the universality and the identification capacity of the three markers were evaluated.

RESULTS

The success rate of amplification was in order of rbcL （99.5%） > matK （92.5%） > ITS （86.0%）. The identification capacity of the combination of rbcL and matK was better than that of rbcL or matK, by which most plant species could be identified to the genus or higher. ITS was not suitable to be a unique marker because of its unstable result, but it still could be a powerful supplement. The identification capacity of the combination of rbcL, matK and ITS was higher than that of rbcL and matK, by which most plant species could be identified to the genus or lower.

CONCLUSIONS

The identification system with the combination of rbcL, matK and ITS as markers has excellent universality for plant evidence, which can distinguish most plant species to the genus or lower.

[Efficiency Analysis of EX16+10Y Kit on Detection of the Uygur Population in Xinjiang Province]

OBJECTIVES

To analyse the efficiency of EX16+10Y kit on the forensic detection of the Uygur in Xinjiang province.

METHODS

The blood samples were extracted from 4 620 male individuals of Uygur in Xinjiang province, and amplified by EX16+10Y kit. The typing of amplification products was performed by 3130xl genetic analyzer.

RESULTS

The genotyping graphs of 15 autosomal STR loci and 10 Y-chromosomal STR loci from 4 620 male individuals of Uygur in Xinjiang province were acquired completely. The genotype distribution of 15 autosomal STR loci was consistent with Hardy-Weinberg equilibrium. The heterozygosity, polymorphism information content and discrimination power of STR loci were 0.637-0.838, 0.580-0.860 and 0.811-0.978, respectively. There were 766 haplotypes in 10 Y -chromosomal STR loci.

CONCLUSIONS

The test results of EX16+10Y kit is accurate and trustworthy, which can simultaneously be used for the individual identification and the screening of paternal pedigree in practical work.

[Analysis of related factors of recurrent otitis media with effusion in children]

Objective:To investigate the influencing factors of recurrent episodes of otitis media with effusion in children.Method:A retrospective summary of the clinical data of 210 cases of children with otitis media with effusion, 75 cases of recurrence after treatment, 135 cases were recovered, the recurrence of the related factors and after symptomatic treatment effect is analyzed.Result:Logistic regression analysis results found that adenoid hypertrophy (Ⅲ°, Ⅳ°), tonsil hypertrophy (Ⅳ°) and sinusitis (including choanal polyp), a positive allergens, upper respiratory tract infection, the stomach esophagus regurgitation, cleft palate, younger age has significant effect on recurrence of otitis media with effusion, have significant difference (P< 0.05). And the influence of duration, gender, passive smoking history and previous medical history of otitis media with effusion has no obvious statistical significance (P> 0.05). Through the comparison among different age groups, adenoidectomy Ⅲ °, Ⅳ ° hypertrophy tract infections in > 3-6 years old group has significant effect (P< 0.05), recurrent respiratory tract infections in less than 3 years old group and the group of children aged > 3-6 years OME recurrence has significant effect (P< 0.05). By tympanocentesis or tympanostomy tube insertion and according to different conditions to take symptomatic treatment, 75 cases (123 ears) were cured 96 ears (78.05%), 19 ears were improved (15.45%), the total effective rate was 93.50%, ineffective in 8 ears (6.50%).Conclusion:Adenoid hypertrophy (Ⅲ°, Ⅳ°), tonsil hypertrophy (Ⅳ°), sinusitis, nasal polyps, allergic diseases and upper respiratory tract infection gastroesophageal reflux, cleft palate and younger age may be adverse factors related to recurrent otitis media with effusion in children, the clinical doctors should pay attention to these symptoms, according to different causes, adopt individualized treatment plan, make children get the best treatment as soon as possible.

The influence of emission control on particle number size distribution and new particle formation during China's V-Day parade in 2015

Temporary strict emission control strategies were conducted to ensure good air quality for China's V-Day parade (August 20-September 3, 2015) in Beijing and nearby cities. The influence of the emission control on particle number size distribution (PNSD) was evaluated based on the long-term measurements of PNSD at a rural site (Shangdianzi) located northeast of Beijing. This study also presented the comparison results of PNSD during the parade in 2015 and the Olympics in 2008 (August 8-23), as well as the same period without strict emission control in 2010-2013 (August 20-September 3). Compared with the same period in 2010-2013 and 2008 Olympics, the accumulation mode particle number concentration showed a significant reduction in 2015, and the PM₁ mass concentration decreased by approximately 60-90%. The alleviation of the PM₁ was also associated with the weather conditions. The back trajectories analysis results showed that the southerly air mass passing through the polluted areas accounted for 14% of the total back trajectories in 2015, which contributed to approximately 60% in the other years. During the control period in 2015, there were six new particle formation (NPF) events observed, with a higher frequency, but a lower formation rate and growth rate than the same period in 2010-2013. The comparison of the condensation sink (CS), sulfuric acid, solar radiation and relative humidity among the different years indicated that at Shangdianzi station, the first factor in determining the NPF occurrence was the CS, and the second factor could be the concentration level of precursor vapors participating in the NPF event (e.g., sulfuric acid).

[Research Progress on Gene Alterations of Amelogenin Locus in Gender Identification]

There are two kinds of amelogenin gene mutation, including mutation in primer-binding region of amelogenin gene and micro deletion of Y chromosome encompassing amelogenin gene, and the latter is more common. The mechanisms of mutation in primer-binding region of amelogenin gene is nucleotide point mutation and the mechanism of micro deletion of Y chromosome encompassing amelogenin gene maybe non-allelic homologous recombination or non-homologous end-joining. Among the population worldwide, there is a notably higher frequency of amelogenin gene mutations in Indian population, Sri Lanka population and Nepalese population which reside within the Indian subcontinent. Though amelogenin gene mutations have little impact on fertility and phenotype, they might cause incorrect result in gender identification. Using composite-amplification kit which including autosomal STR locus, amelogenin gene locus and multiple Y-STR locus, could avoid wrong gender identification caused by amelogenin gene mutation.

[Identification of Vaginal Fluid Using Microbial Signatures]

OBJECTIVES

To investigate the specific microbial signatures in vaginal fluid.

METHODS

Vaginal fluid （16 samples）, saliva （16 samples）, feces （16 samples）, semen （8 samples）, peripheral blood （8 samples）, urine （5 samples）, and nasal secretion （4 samples） were collected respectively. The 16S rRNA genes of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae were amplified. PCR production was detected via a 3130xl Genetic Analyzer.

RESULTS

The detected number of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae were 15, 5, 8, 14, and 3 in all vaginal fluid samples, respectively. Lactobacillus crispatus and Lactobacillus jensenii existed specifically in vaginal fluid.

CONCLUSIONS

There is a potential application value to detect Lactobacillus crispatus and Lactobacillus jensenii for the identification of vaginal fluid.

Source Identification of Human Biological Materials and Its Prospect in Forensic Science

Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction.

The HumD21S11 system of short tandem repeat DNA polymorphisms in Japanese and Chinese

HumD21S11 is a short tandem repeat DNA polymorphic system with a complex basic structure of (TCTA)4-6 (TCTG)5-6 (TCTA)3 TA (TCTA)3 TCA (TCTA)2 TCCA TA (TCTA)n. Using the allelic ladder prepared by us, the distribution of alleles among Japanese and Chinese was investigated, and four new alleles 28.2, 34, 35.2, and 36.2, were discovered. DNA sequencing was performed on the newly found alleles as well as on family samples and led to the discovery of different gene structures within alleles 28 and 32. Forensic materials, including hairs and seminal stains, were tested in parallel with blood samples from the same individual and were successfully typed for D21S11.

Complete culture medium is better than low folate medium for detecting increased chromosome aberrations in smokers in 48-h lymphocyte cultures

We compared chromosome breakage in parallel, 48-h lymphocyte cultures established from smokers and nonsmokers using minimal essential medium (MEM) and MEM without folate (MEM-FA). There was a statistically significant, higher frequency of aberrations for smokers than for nonsmokers in cells cultured in MEM, but not in those cultured in MEM-FA. Thus, these data support the recommendation of the World Health Organization (1985) that population monitoring studies for exposure assessment should not use a low folate medium.