Intestinal epithelial cells of Japanese flounder (Paralichthys olivaceus) as an in vitro model for studying intestine immune function based on transcriptome analysis.

Japanese flounder (Paralichthys olivaceus) is an economically crucial marine species, but diseases like hemorrhagic septicemia caused by Edwardsiella tarda have resulted in significant economic losses. E. tarda infects various hosts, and its pathogenicity in fish is not fully understood. Lipopolysaccharides (LPS) are components of the outer membrane of Gram-negative bacteria and are representative of typical PAMP molecules that cause activation of the immune system. The PoIEC cell line is a newly established intestinal epithelial cell line from P. olivaceus. In order to investigate whether it can be used as an in vitro model for studying the pathogenesis of E. tarda and LPS stimulation, we conducted RNA-seq experiments for the PoIECs model of E. tarda infection and LPS stimulation. In this study, transcriptome sequencing was carried out in the PoIEC cell line after treatment with LPS and E. tarda. A total of 62.52G of high-quality data from transcriptome sequencing results were obtained in nine libraries, of which an average of 87.96% data could be aligned to the P. olivaceus genome. Data analysis showed that 283 and 414 differentially expressed genes (DEGs) in the LPS versus Control (LPS-vs-Con) and E. tarda versus Control groups (Et-vs-Con), respectively, of which 60 DEGs were shared in two comparation groups. The GO terms were predominantly enriched in the extracellular space, inflammatory response, and cytokine activity in the LPS-vs-Con group, whereas GO terms were predominantly enriched in nucleus and positive regulation of transcription by RNA polymerase II in the Et-vs-Con group. KEGG analysis revealed that three immune-related pathways were co-enriched in both comparison groups, including the Toll-like receptor signaling pathway, C-type lectin receptor signaling pathway, and Cytokine-cytokine receptor interaction. Five genes were randomly screened to confirm the validity and accuracy of the transcriptome data. These results suggest that PoIEC cell line can be an ideal in vitro model for studies of marine fish gut immunity and pathogenesis of Edwardsiellosis.

Forensic characteristics and genetic structure of the Chinese Tibetan population revealed by 38 X-chromosomal InDel loci.

With the increasing importance of X-chromosome (Chr-X) genotyping in kinship identification, the exploitation of X chromosome genetic marker multiplex kits is increasing. The Human X-InDels amplification kit is a novel developed system which contained 38 X-chromosomal Insertion/deletion markers (X-InDels) and Amelogenin. Herein, we investigated the genetic diversity of the 38 X-InDels in the Tibetan ethnic minority (n = 792) from seven regions and evaluated the application potential of this novel panel. The rs16368 was the least variable locus, whereas the most polymorphic locus was the rs59605609 in Tibetan population. We confirmed three linkage groups with the haplotype diversities ranged from 0.5032 to 0.5976. The overall combined power of discrimination (PD) in males and females were 0.999999999582066 and 0.999999999999993, respectively. And the overall combined mean exclusion chance (MEC) values were not lower than 0.999125526990159. In addition, we explored the genetic relationships among the Tibetans in seven different regions via series of population comparison analyses, finding that the genetic relationship between the Ngari Tibetan and Chamdo Tibetan was the farthest, which was consistent with geographical distribution.

A highly sensitive fluorescence probe for on-site detection of nerve agent mimic diethylchlorophosphonate DCP.

Nerve agents are the most toxic chemical warfare agents that pose severe threat to human health and public security. In this work, we developed a novel fluorescent probe NZNN based on naphthylimide and o-phenylenediamine to detect nerve agent mimic diethylchlorophosphonate (DCP). DCP underwent a specific nucleophilic reaction with the o-phenylenediamine group of NZNN to produce a significant fluorescence turn-on response with high selectivity, exceptional linearity, bright fluorescence, rapid response (<6 s) and a low detection limit (30.1 nM). Furthermore, a portable sensing device was fabricated for real-time detection of DCP vapor with excellent performance. This portable and sensitive device is favorable for monitoring environmental pollution and defense against chemical warfare agents.

A practical chromogenic and fluorogenic dual-mode sensing platform for rapid quantification of sulfite in food.

Sulfur dioxide (SO2) and its derivatives (HSO3- and SO32-) are widely used in food-processing. Whereas excessive consumption of sulfur dioxide and its derivatives (>0.70 mg·kg-1day-1) severely endangers human health. In this work, we rationally constructed a practical dual-mode probe (dicyanomethylene)-1-methyl-1,4-dihydroquinolin-2-yl)vinyl)-1-methylquinolinium (QMN), which underwent a specific 1, 4-Michael addition with sulfite to afford a noticeable color change from pale yellow to red along with a high-contrast fluorescence turn-on response at 598 nm. QMN has the advantages of rapid response, high signal-to-noise ratio, excellent selectivity, good water-solubility, large Stokes shift and low detection limit (LOD = 31.9 nM). QMN has been successfully used to on-site visually determine sulfite in a diversity of foods with satisfactory recoveries (91.33-111.33 %) and high accuracy (93.74-98.71 %). Furthermore, a portable smartphone-based fluorescence sensing platform was fabricated for on-site determination of sulfite in food with good performance.

A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing.

Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.

Oxidant-Free Electrochemical Direct Oxidative Benzyl Alcohols to Benzyl Aldehydes Using Three-Dimensional Printing PPAR Polyoxometalate.

The oxidation of benzyl alcohols is an important reaction in organic synthesis. Traditional methods for benzyl alcohol oxidation have not been widely utilized due to the use of significant amounts of precious metals and environmentally unfriendly reagents. In recent years, electrocatalytic oxidation has gained significant attention, particularly electrochemical anodic oxidation, which offers a sustainable alternative for oxidation without the need for external oxidants or reducing agents. Here, a copper monosubstituted phosphotungstate-based polyacrylate resins (Cu-LPOMs@PPAR) catalyst has been fabricated with immobilization and recyclability using 3D printing technology that can be successfully applied in the electrocatalytic oxidation of benzyl alcohol to benzaldehyde, achieving atom economy and reducing pollution. In this protocol, we obtain benzaldehyde in good yields with excellent functional group toleration under metal-free and oxidant-free conditions. This strategy could provide a new avenue for heterogeneous catalysts in application for enhancing the efficiency and selectivity of electrocatalytic oxidation processes.

CmVCall: An automated and adjustable nanopore analysis pipeline for heteroplasmy detection of the control region in human mitochondrial genome.

Genetic associations between human mitochondrial DNA (mtDNA) heteroplasmy and mitochondrial diseases, aging, and cancer have been elaborated, contributing a lot to the further understanding of mtDNA polymorphic spectrum in anthropology, population, and forensic genetics. In the past decade, heteroplasmy detection using Sanger sequencing and next generation sequencing (NGS) was hampered by the former's inefficiency and the latter's inherent bias due to amplification and mapping of short reads, respectively. Nanopore sequencing stands out for its ability to yield long contiguous segments of DNA, providing a new insight into heterogeneity authentication. In addition to MinION from Oxford Nanopore Technologies, an alternative nanopore sequencer QNome (Qitan Technology) has also been applied to various biological research and the forensic applicability of this platform has been proved recently. In this study, we evaluated the performance of four commonly used variant callers in the heterogeneity authentication of the control region of human mtDNA based on simulations of different ratios generated by mixing QNome nanopore sequencing reads of two synthetic sequences. Then, an open-source and python-based nanopore analytics pipeline, CmVCall was developed and incorporated multiple programs including reads filtering, removal of nuclear mitochondrial sequences (NUMTs), alignment, optional 'Correction' mode, and heterogeneity identification. CmVCall can achieve high precision, accuracy, and recall of 100%, 99.9%, and 92.3% with a 5% heteroplasmy level in 'Correction' mode. Moreover, blood, saliva, and hair shaft samples from monozygotic (MZ) twins were used for heterogeneity evaluation and comparison with the NGS data. Results of MZ twin samples showed that CmVCall could identify more point heteroplasmy sites, revealing significant levels of inter- and intra-individual mtDNA polymorphism. In conclusion, we believe that this analysis pipeline will lay a solid foundation for the development of a comprehensive nanopore analysis pipeline targeting the whole mitochondrial genome.

Ligand-protected metal nanoclusters as low-loss, highly polarized emitters for optical waveguides.

Photoluminescent molecules and nanomaterials have potential applications as active waveguides, but such a use has often been limited by high optical losses and complex fabrication processes. We explored ligand-protected metal nanoclusters (LPMNCs), which can have strong, stable, and tunable emission, as waveguides. Two alloy LPMNCs, Pt1Ag18 and AuxAg19-x (7 ≤ x ≤ 9), were synthesized and structurally determined. Crystals of both exhibited excellent optical waveguide performance, with optical loss coefficients of 5.26 × 10-3 and 7.77 × 10-3 decibels per micrometer, respectively, lower than those demonstrated by most inorganic, organic, and hybrid materials. The crystal packing and molecular orientation of the Pt1Ag18 compound led to an extremely high polarization ratio of 0.91. Aggregation enhanced the quantum yields of Pt1Ag18 and AuxAg19-x LPMNCs by 115- and 1.5-fold, respectively. This photonic cluster with low loss and high polarization provides a generalizable and versatile platform for active waveguides and polarizable materials.

Bright near-infrared circularly polarized electrochemiluminescence from Au9Ag4 nanoclusters.

Metal nanoclusters are excellent electrochemiluminescent luminophores owing to their rich electrochemical and optical properties. However, the optical activity of their electrochemiluminescence (ECL) is unknown. Herein, we achieved, for the first time, the integration of optical activity and ECL, i.e., circularly polarized electrochemiluminescence (CPECL), in a pair of chiral Au9Ag4 metal nanocluster enantiomers. Chiral ligand induction and alloying were employed to endow the racemic nanoclusters with chirality and photoelectrochemical reactivity. S-Au9Ag4 and R-Au9Ag4 exhibited chirality and bright-red emission (quantum yield = 4.2%) in the ground and excited states. The enantiomers showed mirror-imaged CPECL signals at 805 nm owing to their highly intense and stable ECL emission in the presence of tripropylamine as a co-reactant. The ECL dissymmetry factor of the enantiomers at 805 nm was calculated to be ±3 × 10-3, which is comparable with that obtained from their photoluminescence. The obtained nanocluster CPECL platform shows the discrimination of chiral 2-chloropropionic acid. The integration of optical activity and ECL in metal nanoclusters provides the opportunity to achieve enantiomer discrimination and local chirality detection with high sensitivity and contrast.

Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations.

Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (Ae), informativeness (In), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The Ae values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had Ae values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean In value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.

Impact of the metal core on the electrochemiluminescence of a pair of atomically precise Au20 nanocluster isomers.

Although the electrochemiluminescence (ECL) of metal nanoclusters has been reported, revealing the correlation between structure and ECL at an atomic level is highly challenging. Here, we reported the impact of the metal core of Au20(SAdm)12(CHT)4 (Au20-AC for short; SAdm = 1-adamantanethiolate; CHT= cyclohexanethiol) and its isomer Au20(TBBT)16 (TBBT = 4-tert-butylthiophenol) on their solution-state and solid-state electrochemiluminescence. In self-annihilation ECL experiments, Au20-AC showed a strong cathodic ECL but a weak anodic ECL, while the ECL signal of Au20(TBBT)16 was weak and barely detectable. Density functional theory (DFT) calculations showed that the Au7 kernel of [Au20-AC]- is metastable, weakening its anodic ECL. Au20-AC in solution-state displayed an intense co-reactant ECL in the near-infrared region, which is 7 times higher than that of standard Ru(bpy)32+. The strongest solid-state ECL emissions of Au20-AC and Au20(TBBT)16 were at 860 and 770 nm, respectively - 15 nm red-shifted for Au20-AC and 20 nm blue-shifted for Au20(TBBT)16, compared to their corresponding solid-state photoluminescence (PL) emissions. This work shows that ECL is significantly affected by the subtle differences of the metal core, and offers a potential basis for sensing and immunoassay platforms based on atomically precise emissive metal nanoclusters.

Molecular engineering of fluorescence probe for real-time non-destructive visual screening of meat freshness.

Spoiled meat poses a great challenge to food security and human health, which should be addressed by the early monitoring and warning of the meat freshness. We herein exploited a molecular engineering strategy to construct a set of fluorescence probes (PTPY, PTAC, and PTCN) with phenothiazine as fluorophore and cyanovinyl as recognition site for the facile and efficient monitoring of meat freshness. These probes produce an obvious fluorescence color transition from dark red to bright cyan in response to cadaverine (Cad) through the nucleophilic addition/elimination reaction. The sensing performances were elaborately improved to achieve quick response (16 s), low detection limit (LOD = 3.9 nM), and high contrast fluorescence color change by enhancing the electron-withdrawing strength of cyanovinyl moiety. Furthermore, PTCN test strips were fabricated for portable and naked-eye detection of Cad vapor with fluorescence color change from crimson to cyan, and accurate determination of Cad vapor level with RGB color (red, green, blue) mode analysis. The test strips were employed to detect the freshness of real beef samples, and demonstrated a good capability of non-destructive, non-contact and visual screening meat freshness on site.

Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing.

Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.

Design and fabrication of a differential-pressure optical fiber grating sensor for monitoring the flow rate of fluid.

A fiber Bragg grating (FBG) flow sensor is designed and fabricated, in which two FBGs are fixed on the front and other side of the metal diaphragm, and differential pressure is used to monitor the flow rate of fluid. The temperature sensitivity of these two FBGs is 0.030 and 0.029 nm/°C, which is almost the same, suggesting that the influence of temperature on the flow measurement can be effectively eliminated. The static pressure sensitivity of these two FBGs can be up to 86.7 nm/MPa and 68.6 nm/MPa, respectively; accordingly, the static pressure sensitivity of the sensor overall is 155.3 nm/MPa. Furthermore, the flow rate sensitivity is 0.00029 L/s. This FBG flow sensor exhibits high sensitivity, high accuracy, and a low start-up flow rate. Furthermore, the cross effect between the temperature and strain on the sensing sensitivity is eliminated, which makes this FBG flow sensor suitable for real-time monitoring of the trace flow rate in oil and gas wells.

Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection.

Y-chromosomal haplogroups determined by Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal biogeographic ancestry inference, which has attracted a lot of interest in the forensic community. Recently, a comprehensive Y-SNP tool with dominant markers targeting haplogroups in R, E and I branches has been reported, which allows the inference of 640 Y haplogroups. It had a very good performance and could provide a high level of Y haplogroup resolution in most populations. However, the predominant haplogroups in the Chinese populations are O, C and N, suggesting that more Y-SNPs under these clades are needed to achieve the population-specific high resolution. Herein, aiming at the Chinese population, we presented a largely improved custom Y-SNP MPS panel that contains 256 carefully ascertained Y-SNPs based on our previous studies, and evaluated this panel via a series of tests, including the tests for concordance, repeatability, sensitivity, specificity, and stability, as well as the mixture, degraded and case-type sample analysis. The preliminary developmental validation demonstrated that this panel was highly reliable, sensitive, specific, and robust. In the sensitivity test, even when the DNA input was reduced to as low as 0.5 ng, the sample could still be assigned to the correct Y haplogroup. For mixture analysis, even the 1:99 (Male: Female) mixtures had no effects on the assignation of the Y haplogroup of the male contributor. In summary, this assay has provided a high-resolution Y-chromosomal haplogrouping workflow to determine a male's paternal lineage and/or paternal biogeographic ancestry and could be widely used for Chinese Y-chromosomal haplogroups dissection.

Applying resonance Rayleigh scattering and spectrofluorimetric techniques for the selective determination of neomycin sulfate using Congo red as a probe: Applications for wastewater analysis.

Two simple, sensitive, and low-cost fluorescence spectroscopy methods for neomycin (NEO) detection were developed. Both methods were based on the interaction between NEO and Congo red (CR) in acidic buffer medium to form an ion-association complex. The quenching effect of the formed ion-association complex on the fluorescence of CR at 421 nm is a basic principle of fluorescence analysis, whilst the resonance Rayleigh scattering (RRS) method was used to enhance the resonance Rayleigh scattering spectrum at 384 nm by adding NEO. Experimental conditions such as pH, temperature, reaction time, CR concentration, and the ionic strength of the two methods were investigated and optimized. In addition, the effect of common coexisting substances on the method was tested and the results showed good selectivity. The composition of ion-association complexes, the reaction mechanism, and reasons for the enhanced intensity of RRS are discussed. Under optimum conditions, the responses of the fluorescence spectrophotometry and RRS methods showed good linearity with NEO concentrations in the range 0.2-3.0 µg ml-1 and 0.1-3.0 µg ml-1 , respectively. The detection limits of fluorescence spectrophotometry and RRS spectroscopy techniques were 0.02 µg ml-1 and 0.01 µg ml-1 , respectively. Finally, the two methods were applied to the analysis of wastewater and the results were satisfactory.

Enhancement of Congo Red-Neomycin Resonance Rayleigh Scattering by Dodecyl Trimethyl Ammonium Bromide and its Application.

A simple, rapid, and convenient method for the determination of neomycin based on the ion association method was proposed. In Britton-Robinson buffer solution, neomycin could react with Congo red to form an ionic association, which in turn reacted with dodecyl trimethyl ammonium bromide to form a ternary ionic association. The three were combined in a 1 : 1 : 1 ratio, which significantly enhanced the resonant Rayleigh scattering intensity at 468 nm. The obtained resonant Rayleigh scattering sensor showed a linear relationship with neomycin in the range of 0.07∼1 µg·mL-1. The limit of detection was 0.02 µg·mL-1, and the limit of quantification was 0.037 µg·mL-1. The experimental conditions were optimized. The method was verified based on the ICH rule. The established method could be applied to the analysis of the acceptable recovery rate of neomycin in powdered veterinary drugs.

Versatile Superatom Complex Nanocluster for the Construction of Framework Materials.

Accurately controlling the assembly of nanometer-sized building blocks presents an important but significant challenge for the construction of functional framework materials, which requires the development of highly stable versatile nanosized assembly modules with multiple coordination sites. In this study, [Ag23(SAdm)12]3+ (Ag23, in which SAdm = 1-adamantanethiol, i.e., C10H15S), a chiral superatom complex nanocluster, was synthesized and assembled into various topologies. We constructed two kinds of framework materials, i.e., superatom complex inorganic framework (SCIF) and superatom complex organic framework (SCOF) materials, including [Ag23(SAdm)12](SbF6)2X (Ag23-1; X = Cl-/SbF6-, a SCIF), [Ag23(SAdm)12](SbF6)3 (Ag23-2, a SCIF), [Ag23(SAdm)12](SbF6)3(bpy)3 (Ag23-bpy, a SCOF, in which bpy = 4,4'-bipyridine, i.e., C10H8N2), and [Ag23(SAdm)12](SbF6)3(dpbz)3 (Ag23-dpbz, a SCOF, in which dpbz = 1,4-bis(4-pyridyl)benzene, i.e., C16H12N2), owing to strong interactions between the versatile Ag23 and the inorganic and organic linkers. Ag23-1, Ag23-2, and Ag23-bpy exhibit two superstructures with interpenetrating frameworks and adamantane-like, hexagonal, and cubic topologies, while Ag23-dpbz displays three superstructures with interpenetrating frameworks and cubic topologies. Ag23-dpbz exhibits the largest specific surface area as well as the strongest photoluminescence and electrochemiluminescence signals owing to its dense network arrangement. This work contributes to the construction of nanocluster-based framework materials and helps to elucidate the effect of the assembly mode on the material properties and functionalities.

Epigenome-wide screening of CpG markers to develop a multiplex methylation SNaPshot assay for age prediction.

Age prediction can provide important information about the contributors of biological evidence left at crime scenes. DNA methylation has been regarded as the most promising age-predictive biomarker. Measuring themethylation level at the genome-wide scaleis an important step to screen specific markers for forensic age prediction. In present study, we screened out five age-related CpG sites from the public EPIC BeadChip data and evaluated them in a training set (115 blood) by multiplex methylation SNaPshot assay. Through full subset regression, the five markers were narrowed down to three, namely cg10501210 (C1orf132), cg16867657 (ELOVL2), and cg13108341 (DNAH9), of which the last one was a newly discovered age-related CpG site. An age prediction model was built based on these three markers, explaining 86.8% of the variation of age with a mean absolute deviation (MAD) of 4.038 years. Then, the multiplex methylation SNaPshot assay was adjusted according to the age prediction model. Considering that bloodstains are one of the most common biological samples in practical cases, three validation sets composed of 30 blood, 30 fresh bloodstains and 30 aged bloodstains were used for evaluation of the age prediction model. The MAD of each set was estimated as 4.734, 4.490, and 5.431 years, respectively, suggesting that our age prediction model was applicable for age prediction for blood and bloodstains in Chinese Han population of 11-71 age. In general, this study describes a workflow of screening CpG markers from public chip data and presents a 3-CpG markers model for forensic age prediction.

Development and validation of a forensic multiplex InDel assay: The AGCU InDel 60 kit.

Marker sets based on insertion/deletion polymorphisms (InDels) combine the characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms and have served as effective complementary or stand-alone systems for human identification in forensics. We developed a novel multiplex amplification detection system, designated the AGCU InDel 60 kit, containing 57 autosomal InDels, 2 Y-chromosomal InDels, and the amelogenin locus and validated the kit in a series of studies, which included tests of the PCR conditions; tests for sensitivity, species specificity, reproducibility, stability, and mock case samples; degradation studies; and a population study. The results indicated that the AGCU InDel 60 kit was accurate, specific, reproducible, stable, and robust. Complete DNA profiles were obtained even with 125 pg of human DNA. In tests of artificially degraded samples, we found that the number of alleles detected by the validated kit was considerably greater than that detected by the STR-based AGCU 21+1 kit, even as the degree of degradation increased. Additionally, 564 unrelated individuals from three Han groups were investigated using this novel system, and the values of combined power of discrimination and combined power of exclusion were not less than 1-4.9026 × 10-24 and 1-3.1123 × 10-5 , respectively. Thus, the results indicated that the novel kit was more powerful than the previous version of the InDel kit (the AGCU InDel 50 kit). Our results suggest that the AGCU InDel 60 kit can serve as an efficient tool for human forensics and a supplementary kit for population genetics research.