Yanjun Ding

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.

A carbon dot-based hybrid fluorescent sensor for detecting free chlorine in water medium

A novel fluorescent sensor has been prepared for the quantitative detection of free chlorine in water medium. The sensor contains a fluorescent carbon dot (CD)–rhodamine B (RhB) nanohybrid, which exhibits their respective emission peaks at 445 and 580 nm under an excitation wavelength of 380 nm. The fluorescence of CDs could be quenched by free chlorine through the combination of chemical bonds and energy transfer while the peak of RhB almost remains constant, leading to color changes that can be recognized by the naked eye. The designed sensor could achieve the detection of free chlorine rapidly with a detection limit as low as 4 μM.

The complete mitochondria genome of Parasarcophaga albiceps (Diptera: Sarcophagidae).

Abstract Parasarcophaga albiceps is one of the forensically important fly species which belongs to the family Sarcophagidae. In this study, we report the complete mitochondrial genome of P. albiceps to provide a supplemental data for species identification. The 14 935 bp-long mitogenome is composed of 13 protein-encoding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding AT-rich region. The permutation of the genes is in conformity with that observed in the ancestral arthropod. The overall base compositions of A, G, C and T are 39.24%, 9.70%, 14.44%, and 36.62%, respectively. Phylogenetic analysis shows the composition of the P. albiceps mitochondrial genome, which is very similar to that of another eight species of Sarcophagidae. The monophyletic branches of the phylogenetic tree reveal that complete mitochondrial genome is suitable for discrimination between these species, providing high support for separation on congeneric species. Therefore, the molecular method applied to the sarcophagid species identification is feasible. The complete mitochondrial genome of P. albiceps is supposed to make contributions to enriching the dipteran mitochondrial genomes and provide a potential tool for species identification.

Overview of long non-coding RNA and mRNA expression in response to methamphetamine treatment in vitro

Long non-coding RNAs (lncRNAs) display multiple functions including regulation of neuronal injury. However, their impact in methamphetamine (METH)-induced neurotoxicity has rarely been reported. Here, using microarray analysis, we investigated the expression profiling of lncRNAs and mRNAs in primary cultured prefrontal cortical neurons after METH treatment. We observed a difference in lncRNA and mRNA expression between the experimental and sham control groups. Using bioinformatics, we analyzed the highest enriched gene ontology (GO) terms of biological process, cellular component, and molecular function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and pathway network analysis. Furthermore, an lncRNA-mRNA co-expression sub-network for aberrantly expressed terms revealed possible interactions of lncRNA NR_110713 and NR_027943 with their related genes. Afterwards, three lncRNAs (NR_110713, NR_027943, GAS5) and two mRNAs (Ddit3, Casp12) were targeted to validate the microarray data by qRT-PCR. This presented an overview of lncRNA and mRNA expression profiling and indicated that lncRNA might participate in METH-induced neuronal apoptosis by regulating the coding genes of neurons.

Estimation of postmortem interval by vitreous potassium evaluation with a novel fluorescence aptasensor

Estimation of postmortem interval (PMI) is a central role in medico-legal identification. Analysis of vitreous potassium ions (K+) concentration is frequently used by forensic workers to estimate PMI. This paper describes interdisciplinary research to introduce fluorescence sensing techniques into forensic medicine. On the basis of silver nanoclusters (AgNCs) probe stabilized by DNA, a simple and highly sensitive fluorescence aptasensor has been proposed to selectively detect K+ ions. The linear range for K+ ions was found to be 0.1 nM-1 mM, with limit of detection of 0.06 nM. Moreover, 63 vitreous humour cases within 36 h after death were further studied to verify the utility of K+ ions in estimating the PMI. By the fluorescence aptasensor method, a new formula was built to determine the postmortem interval based on K+ ions concentration: PMI(h) = −0.55 + 1.66 × CK+(r = 0.791). And the real significance of this research was demonstrated by additional 6 cases with known PMIs. In comparison with the conventional method, the presented aptasensor strategy is cost-effective and easy in measuring vitreous K+, which may be potentially a better way for estimation of PMI in medico-legal practice.

The complete mitochondria genome of Aldrichina grahami (Diptera: Calliphoridae)

Abstract Aldrichina grahami is a significant medical and forensic insect belonging to the family calliphoridae. In this study, we present the complete mitochondrial genome of A. grahami for the first time. The mitogenome was 14 903 bp in length, consisting of 22 transfer RNA genes, 2 ribosomal RNA genes and 13 protein-encoding genes. The overall base compositions of A, G, C and T were 39.14, 9.59, 13.65 and 37.62%, respectively. Phylogenetic analysis is conducted using 12 mitochondrial genomes from two families. The monophyletic branches of the phylogenetic tree reveal that the composition of the mitochondrial genome, particularly the gene lengths, is very similar to that of another Calliphoridae fly, C. vicina, but the interspecific variations between them was 5.4%, which could distinguish these two species explicitly. Phylogenetic analyses indicated that phylogenetic analysis of whole mt genome sequences resulted in much stronger support for the identification of A. grahami between other species. This article aimed to enrich the dipteran mitochondrial genomes and provides the complete mitochondrial genome and phylogenetic analyses of A. grahami for species identifications forensic purpose.

One-step, visual and sensitive detection of phorate in blood based on a DNA–AgNC aptasensor

The ingestion of organophosphate (Op) pesticides for attempting suicide has been a serious health issue recently. Phorate, a class of Op, has attracted attention in this regard and so the rapid diagnosis and detection of phorate is crucial for human health. In this study, a one-step and visual method for the rapid determination of phorate via an aptasensor based on DNA-templated silver nanoclusters (DNA–AgNCs) has been presented. The designed DNA–AgNC nanoprobe, containing a special structure with an intercalated aptamer, shows excellent stability. Introducing phorate to the system easily triggers the aggregation of DNA–AgNCs, producing a brown-to-colorless color change in the solution in only 6 minutes. Under the optimal conditions, the aptasensor can allow for the determination of phorate in the concentration range of 0–25 μg mL−1, using two linear equations: y = −2.308x + 0.996 (R2 = 0.977) for 0–0.125 μg mL−1 and y = −0.020x + 0.664 (R2 = 0.971) for 0.125–25 μg mL−1. The estimated detection limit of phorate was 0.012 ng mL−1. Moreover, the practicability of this proposed method was also validated by analyzing phorate-spiked human blood samples and the results were in agreement with those from gas chromatography/mass spectrometry (GC/MS) analysis. Therefore, this fabricated aptasensor is suitable for sensing phorate in complex biological samples, and shows high potential for clinical diagnosis or forensic toxicology analysis.

A rapid evaluation of acute hydrogen sulfide poisoning in blood based on DNA-Cu/Ag nanocluster fluorescence probe

Hydrogen sulfide (H2S) is a highly toxic gas as a cause of inhalational death. Accurate detection of H2S poisoning concentration is valuable and vital for forensic workers to estimate the cause of death. But so far, it is no uniform and reliable standard method to measure sulfide concentrations in H2S poisoning blood for forensic identification. This study introduces a fluorescence sensing technique into forensic research, in which a DNA-templated copper/silver nanocluster (DNA-Cu/AgNCs) fluorescence probe has been proposed to selective detection of S2−. Under an optimized condition, the proposed method can allow for determination of S2− in the concentration range of 10 pM to 1 mM with a linear equation: y = −0.432 lg[S2−] + 0.675 (R2 = 0.9844), with the limit of detection of 3.75 pM. Moreover, acute H2S poisoning mouse models were established by intraperitoneally injected different doses of Na2S, and the practical feasibility of the proposed fluorescence sensor has been demonstrated by 35 poisoning blood samples. This proposed method is proved to be quite simple and straightforward for the detection of H2S poisoning blood. Also it may provide a basis for sulfide metabolizing study in body, and it would be meaningful to further push forensic toxicology identification and clinical laboratory research.

The complete mitochondria genome of Calliphora vomitoria (Diptera: Calliphoridae)

Abstract Calliphora vomitoria is a significant insect which belongs to the Calliphoridae family. In this study, the mitochondrial genome of C. vomitoria was completely sequenced for species identification. The entire mitogenome was 16,134 bp in length, composing of 13 protein-encoding genes, 22 transfer RNA genes and two ribosomal RNA genes, and then the array of the genes was similar to the other insects have discovered. The overall base compositions of A, G, C and T were 39.40%, 9.37%, 13.08% and 37.13% respectively. What is more, phylogenetic analyses tree indicated that entire mitochondria genome sequences of C. vomitoria had high degree of identification among the species listed in. We hope that the results from the present study will provide useful dipteran mitochondrial genomes information for the further studies on genetic structure and phylogenetic analyses of C. vomitoria in the species identifications.

Trimethylamine in postmortem tissues as a predictor of postmortem interval estimation using the GC method

Trimethylamine (TMA), a simple amine in volatile compounds, indicating the spoilage degree of meat, related with the late postmortem interval (PMI) during the cadaver decomposition process. In this paper, a headspace gas chromatography (HS-GC) method has been successfully built to analyze the content of TMA in postmortem rat tissues (liver, myocardial and skeletal muscle tissues), which is used for PMI estimation with the wide range of PMI (0-720 h postmortem) at 16 °C ± 1 °C. Correspondingly, three equations about the relationship between the PMI and TMA content were established, in which they showed that the TMA content in all three tissues increased from the firstly detected time to 192 h and gradually decreased after 384 h. Furthermore, the TMA measurement in five human samples was carried out and the results (<35 h PMI) showed a good agreement about the change trend of TMA content between human and rat, which elucidated that this research might provide a new insight for the forensic scientist to band HS-GC technology together with TMA determination in the PMI estimation.