Mixture deconvolution remains one of the major challenges in the field of forensic science. Currently, genetic markers are used and studied in the field of forensic genetics, including short tandem repeat (STR), insertion/deletion polymorphism (InDel), single nucleotide polymorphism (SNP), InDel closely linked to STR (DIP-STR), SNP closely linked to STR (SNP-STR), InDel closely linked to SNP (DIP-SNP) and microhaplotype (MH), all of which have been studied for DNA mixture analysis and have their own advantages and disadvantages. Mini-haplotype (MiniHap), as a novel haplotype genetic marker, contains 5 or more SNPs. A previous study has substantiated its significant high polymorphic characteristics, and it is expected to have potential applications in individual identification, paternity testing, ancestry inference, and mixture deconvolution. In this study, we first screened 22 MiniHaps with high polymorphism potential and constructed a panel based on the QNome nanopore sequencing device. Subsequently, we tested 100 unrelated Chinese Han individuals to evaluate the sequencing performance, allele (haplotype) frequencies, effective number of alleles (Ae) and forensic parameters of the 22 MiniHaps markers included in this novel assay. Next, a series of mixture simulations (two- or three-person mixtures with mixing ratios of 1:1-1:99 or 1:1:1-1:8:1) based on three standard materials (9947 A, 9948 and 2800 M) were detected by this MiniHap panel to explore its potential for DNA mixture deconvolution. The average Ae value was 10.9574, and 52.38 % of MiniHap loci had Ae values greater than 12.0000. The mean values of genetic diversity (GD) and power of discrimination (PD) were 0.8717 and 0.9457, respectively. Notably, most MiniHaps (85.71 %) had PD values exceeding 0.9000. The combined match probability (CMP) and combined power of exclusion (CPE) of this MiniHap panel were 4.4505 × 10-31 and 0.999999999999999996653, respectively. Moreover, the results of mixture analysis demonstrated that this MiniHap panel allowed detecting the components of minor contributor (s) even in imbalanced mixture samples, with detection limits of 1:39 and 1:8:1 for two- and three-person mixtures, respectively. In summary, MiniHap markers have remarkable application potential in mixture deconvolution, and it is necessary to conduct in-depth research on MiniHap markers for mixture analysis in the future.

Methamphetamine (METH) is a highly addictive psychostimulant that causes physical and psychological damage and immune system disorder, especially in the liver which contains a significant number of immune cells. Dopamine, a key neurotransmitter in METH addiction and immune regulation, plays a crucial role in this process. Here, we developed a chronic METH administration model and conducted single-cell RNA sequencing (scRNA-seq) to investigate the effect of METH on liver immune cells and the involvement of dopamine receptor D1 (DRD1). Our findings reveal that chronic exposure to METH induces immune cell identity shifts from IFITM3+ macrophage (Mac) and CCL5+ Mac to CD14+ Mac, as well as from FYN+CD4+ T effector (Teff), CD8+ T, and natural killer T (NKT) to FOS+CD4+ T and RORα+ group 2 innate lymphoid cell (ILC2), along with the suppression of multiple functional immune pathways. DRD1 is implicated in regulating certain pathways and identity shifts among the hepatic immune cells. Our results provide valuable insights into the development of targeted therapies to mitigate METH-induced immune impairment.

Detecting dopamine (DA) in biological samples is vital to understand its crucial role in numerous physiological processes, such as motion, cognition, and reward stimulus. In this work, p-type graphene on sapphire, synthesized via chemical vapor deposition, serves as substrate for the preparation of p-type Cu2-xS films through solid-phase sulfurization. The optimized Cu2-xS/graphene heterostructure, prepared at 250 °C using a 15-nm copper film sulfurized for 2 h, exhibits superior electron transfer performance, ideal for electrochemical sensing. It is confirmed that the spontaneous charge transfer from graphene to Cu2-xS, higher Cu(II)/Cu(I) ratio ( 0.8), and the presence of well-defined nanocrystalline structures with an average size of 35 nm in Cu2-xS significantly contribute to the improved electron transfer of the heterostructure. The electrochemical sensor based on Cu2-xS/graphene heterostructure demonstrates remarkable sensitivity towards DA, with a detection limit as low as 100 fM and a dynamic range greater than 109 from 100 fM to 100 μM. Additionally, it exhibits excellent selectivity even in the presence of uric acid and ascorbic acid 100 times higher, alongside notable storage and measurement stability and repeatability. Impressively, the sensor also proves capable of detecting DA concentrations as low as 100 pM in rat serum, showcasing its potential for clinically relevant analytes and promising applications in sensitive, selective, reliable, and efficient point-of-care diagnostics.

Rwanda is known as the heart of Africa, reflecting the history of the world. Colonization and genocide have led to Rwanda's existing genetic structure. Herein, we used massively parallel sequencing to analyze 296 loci in 185 Rwandans and constructed a database for Rwandan forensic data for the first time. We found the following results: First, forensic parameters demonstrated that all loci were highly informative and could be used for forensic identification and paternity tests in Rwandans. Second, we found that the differences in genetic background between Rwandans and other African populations were similar but slight, as indicated by the massively parallel sequencing panel. Rwandans belonged to the African population and were inseparable from populations from neighboring countries. Also, Rwandans were closer to the European and American populations because of colonization, war, and other reasons. There was no scientific basis for racial classification established by colonization. Further research still needs to be carried out on more loci and larger Rwandan samples.

The Tibetan-Yi Corridor (TYC) region between Tibet and the rest of east Asia has served as a crossroads for human migrations for thousands of years. The lack of whole-genome sequencing data specific to the TYC populations has hindered the understanding of the fundamental patterns of migration and divergence between humans in east Asia and southeast Asia. Here, we provide 248 individual whole genomes from the 16 TYC and 3 outgroup populations to elucidate historical relationships. We find that the Tibetan plateau forms an important barrier to gene flow, with a more Tibetan-like ancestry in northern populations and a southern east Asian-related ancestry in south populations. An isolated population, Achang, shows a prolonged isolation and genetic drift compared to other TYC populations. We also note that previous claims regarding the history and structure of TYC populations inferred by linguistics are incompatible with the genetic evidence.

Many villages in the Tibetan-Yi Corridor were isolated and inaccessible by car. Credit: Shengbin Li

Insertion/deletion (InDel) polymorphisms, as ideal forensic markers, show useful characteristics of both SNPs and STRs, such as low mutation rate, short amplicon size and general applicability of genotyping platform, and have been used in human identification, population genetics and biogeographic research in recent years. X-chromosome genetic markers are significant in population genetic studies and indispensable complements in some complex forensic cases. However, the population genetic studies of X-chromosome InDel polymorphisms (X-InDels) still need to be explored. In this study, the forensic utility of a novel panel including 38 X-InDel markers was evaluated in a sample of Han population from Henan province in China. It is observed that the heterozygosities ranged from 0.0054 to 0.6133, and the combined discrimination power was 1–9.18 × 10−17 for males and 1–7.22 × 10−12 for females respectively. The mean exclusion chance in trios and duos were 0.999999319 and 0.999802969 respectively. Multiple biostatistics methods, such as principal component analysis, genetic distances analysis, phylogenetic reconstruction, and structure analysis was used to reveal the genetic relationships among the studied Henan Han group and other 26 reference groups from 1,000 Genomes Project. As expected, the Henan Han population was clustered with East Asian populations, and the most intimate genetic relationships existed in three Han Chinese populations from Henan, Beijing and South China, and showed significant differences compared with other continental groups. These results confirmed the suitability of the 38 X-InDel markers both in individual identification and parentage testing in Han Chinese population, and simultaneously showed the potential application in population genetics.

Background: Haplotype provides significant insights into understanding genomes at both individual and population levels. However, research on many non-model organisms is still based on independent genetic variations due to the lack of haplotype.Results: We conducted haplotype assembling for Equus asinu, a non-model organism that plays a vital role in human civilization. We described the hybrid single individual assembled haplotype of the Dezhou donkey based on the high-depth sequencing data from single-molecule real-time sequencing (×30), Illumina short-read sequencing (×211), and high-throughput chromosome conformation capture (×56). We assembled a near-complete haplotype for the high-depth sequenced Dezhou donkey individual and a phased cohort for the resequencing data of the donkey population.Conclusion: Here, we described the complete chromosome-scale haplotype of the Dezhou donkey with more than a 99.7% phase rate. We further phased a cohort of 156 donkeys to form a donkey haplotype dataset with more than 39 million genetic variations.

SCOPE:Hepatic steatosis and insulin resistance (IR) are risk factors for many metabolic syndromes such as NAFLD and T2DM. ApoA4 improves glucose hemostasis by increasing glucose-stimulated insulin secretion and glucose uptake via PI3K-Akt activation in adipocytes. However, whether ApoA4 has an effect on hepatic steatosis or IR remains unclear.METHODS AND RESULTS:ApoA4-knockout (KO) aggravates diet-induced obesity, hepatic steatosis, and IR in mice promoted by increased hepatic lipogenesis gene expression based on RNA-seq data. Conversely, liver-specific overexpression of ApoA4 via AAV-ApoA4 transduction reverses the effect in ApoA4-KO mice, accompanied by suppressed hepatic lipogenesis, increased lipolysis, and fatty acid oxidation. Short-term treatment with recombinant ApoA4 protein improves glucose clearance and liver insulin sensitivity, and reduces hepatic lipogenesis gene expression in the absence of insulin. Moreover, in primary hepatocytes and a hepatic cell line, ApoA4 improves hepatic glucose uptake via IRS-PI3K-Akt signaling and decreases fat deposition and hepatic lipogenesis gene expression by inhibiting SREBF1 activity.CONCLUSION:ApoA4 restricts hepatic steatosis by inhibiting SREBF1-mediated lipogenesis and improves insulin sensitivity and glucose uptake via IRS-PI3K-Akt signaling in the liver. These findings indicate that ApoA4 may serve as a therapeutic target for obesity-associated NAFLD.

The liver immune microenvironment is a key element in the development of hepatic inflammation in NAFLD. ApoA4 deficiency increases the hepatic lipid burden, insulin resistance, and metabolic inflammation. However, the effect of ApoA4 on liver immune cells and the precise immune cell subsets that exacerbate fatty liver remain elusive. The aim of this study was to profile the hepatic immune cells affected by ApoA4 in NAFL. We performed scRNA-seq on liver immune cells from WT and ApoA4-deficient mice administered a high-fat diet. Immunostaining and qRT–PCR analysis were used to validate the results of scRNA-seq. We identified 10 discrete immune cell populations comprising macrophages, DCs, granulocytes, B, T and NK&NKT cells and characterized their subsets, gene expression profiles, and functional modules. ApoA4 deficiency led to significant increases in the abundance of specific subsets, including inflammatory macrophages (2-Mφ-Cxcl9 and 4-Mφ-Cxcl2) and activated granulocytes (0-Gran-Wfdc17). Moreover, ApoA4 deficiency resulted in higher Lgals3, Ctss, Fcgr2b, Spp1, Cxcl2, and Elane levels and lower Nr4a1 levels in hepatic immune cells. These genes were consistent with human NAFLD-associated marker genes linked to disease severity. The expression of NE and IL-1β in granulocytes and macrophages as key ApoA4 targets were validate in the presence or absence of ApoA4 by immunostaining. The scRNA-seq data analyses revealed reprogramming of liver immune cells resulted from ApoA4 deficiency. We uncovered that the emergence of ApoA4-associated immune subsets (namely Cxcl9+ macrophage, Cxcl2+ macrophage and Wfdc17+ granulocyte), pathways, and NAFLD-related marker genes may promote the development of NAFL. These findings may provide novel therapeutic targets for NAFL and the foundations for further studying the effects of ApoA4 on immune cells in various diseases.

Heroin addiction is a chronic and complex brain disease. Nicotinic acetylcholine receptors (nAChRs) have been shown as major control points in many of the neurological and physiological disorders involved in heroin addiction. In the present study, thirty-three SNPs across nine nAChR genes were selected and probed for their associations with heroin addiction phenotypes in 801 unrelated northwestern Chinese Han patients. We found that rs2565055 in CHRNA2 gene was associated with daily dose of methadone treatment, and rs2672215, rs2672216 and rs2741865 in CHRNA10 gene were associated with the duration of the transition from first use to dependence (DTFUD). Cox multivariable regression analysis revealed that rs3743075, rs6495309 in CHRNA3, rs2304297 in CHRNA6, and rs1948 in CHRNB4 were associated with sexual desire in patients with heroin addiction. These findings were further supported by the identification of a haplotype block spanning CHRNA5, CHRNA3, and CHRNB4 that is correlated with changes in sexual desire after long-term heroin use. Our findings highlight associations between polymorphisms in nAChRs genes and the phenotypes of heroin addiction in the Chinese Han population. We suggest several nAChRs subunits as potential novel targets for the treatment of heroin addiction.

Abstract Background Previous cytogenetic studies show that the karyotypes of species in Ciconiiformes vary considerably, from 2n = 52 to 78. Their karyotypes include different numbers of small to minute bi-armed chromosomes that have evolved probably by fusions of two ancestral microchromosomes, besides macrochromosomes and dot-like microchromosomes. However, it is impossible to define the inter-species homologies of such small-sized bi-armed chromosomes based on chromosome morphology and banding characteristics. Although painting probes from the chicken (Gallus gallus, GGA) chromosomes 1–9 and Z have been widely used to investigate avian chromosome homologies, GGA microchromosome probes are rarely used in these studies because most GGA microchromosome probes generated by flow sorting often contain multiple GGA microchromosomes. In contrast, the stone curlew (Burhinus oedicnemus, BOE, Charadriiformes) has an atypical low diploid chromosome number (42) karyotype and only 4 pairs of dot-like microchromosomes; a set of chromosome-specific painting probes that cover all BOE chromosomes has been generated. To get a genome-wide view of evolutionary chromosomal rearrangements in different lineages of Ciconiiformes, we used BOE painting probes instead of GGA painting probes to analyze the karyotypes of three ciconiiform species belonging to two different families: the eastern grey heron (Ardea cinerea, ACI, 2n = 64, Ardeidae), the little egret (Egretta garzetta, EGA, 2n = 64, Ardeidae) and the crested ibis (Nipponia nippon, NNI, 2n = 68, Threskiornithidae). Results BOE painting probes display the same hybridization pattern on chromosomes of ACI and EGA, while a different hybridization pattern is observed on chromosomes of NNI. BOE autosome probes detected 21 conserved homologous segments and 5 fusions on the sixteen pairs of recognizable chromosomes of ACI and EGA, while 16 conserved homologous segments and 4 fusions were found on the twelve pairs of recognizable chromosomes of NNI. Only a portion of smaller bi-armed chromosomes in the karyotypes of the ciconiiform species could have evolved from fusions of ancestral microchromosomes. In particular BOE 5, which is the result of a fusion between two segments homologous to GGA 7 and 8 respectively, was retained also as either a single chromosome in ACI (ACI 5) and EGA (EGA 5) or had fused with a part of the BOE 10 equivalent in NNI (NNI 5). Conclusion Our painting results indicate that different chromosome rearrangements occur in different ciconiiform lineages. Some of the small-sized bi-armed chromosomes in ACI, EGA and NNI are derived from the fusions of two microchromosomes, indicating that microchromosome fusions play an important role in ciconiiform chromosome evolution. The fusion segment homologous to GGA 7 and 8 is a potential cytogenetic signature that unites Ardeidae and Threskiornithidae.

司法鉴定质量事关司法鉴定的公信力和诉讼质量,不断提高司法鉴定质量是所有司法鉴定行业从业人员必须重视和不断完善的重要工作.本文分析了目前社会司法鉴定机构中普遍存在的质量问题,从政策法规、机构内部管理、标准建设三方面内容探讨如何进一步提高司法鉴定质量和公信力.

Rwanda is one of the smallest countries of Africa, where forensic genetic studies are rarely being conducted and very few DNA databases have been developed. Short tandem repeats (STRs) polymorphisms were investigated in 505 unrelated Rwandese by using the HUMDNA TYPING (Yanhuang) Kit. The following STRs were targeted: D3S1358, D13S317, D7S820, D16S539, SE33, D10S1248, D5S818, D21S11, TPOX, D1S1656, D6S1043, D19S433, D22S1045, D8S1179, Penta E, D2S441, D12S391, D2S1338, vWA, Penta D, TH01, D18S51, CSF1PO and FGA. The purpose of this study was to elucidate the genetic diversity and explore the potential of applying these 24 STR in 505 Rwandan population in forensics. A total of 360 alleles, with corresponding allele frequencies in the range from 0.001 to 0.442, were found in the Rwandan population. SE33 presented the highest polymorphism (PIC=0.921) among these 24 loci, whereas D13S317 presented the lowest one (PIC=0.671). No deviation from the Hardy-Weinberg equilibrium was observed for any of the 24 loci. The forensic parameters, including the combined power of discrimination (PD and the combined exclusion power, have demonstrated that this panel of 24 STRs is highly informative and useful for forensic applications such as individuals' identification and paternity tests. Additionally, the genetic distances between Rwanda population and other 24 published populations were calculated based on 8 overlapping loci with the polygenetic tree revealing significant clusters in the populations associated with their geographic locations and their historical relationship.

Substance addiction is a chronic and complicated disease involving genetic and environmental factors. Coregulated by the above factors, perturbations of the gut microbiome have been shown to have an essential role in the development of many neuropsychiatric disorders, including addiction. However, shifts in the gut microbiome during different stages of morphine addiction remain uncharacterized. In the present study, we harvested fecal samples from mice at the acquisition (both the control and morphine groups), extinction and reinstatement stages of morphine-induced conditioned place preference (CPP). Gut microbiome profiles were detected with 16S ribosomal RNA gene sequencing. We observed an increase in community richness following morphine conditioning, and it decreased after 4 weeks of abstinence. The abundance of Verrucomicrobia increased and Bacteroides decreased at the acquisition of morphine-induced CPP, while a recovery trend was found at the extinction stage. Several discriminative genera were identified for the characterization of different stages of morphine CPP. Functional analysis of taxa with differential abundance between CPP stages was mainly enriched in the pathways of amino acid metabolism. Taken together, our findings will extend the association between dysbiosis of the gut microbiome and the opioid-induced rewarding or reinforcing behaviors.

Parentage testing is routinely performed by genotyping short tandem repeat (STR) through capillary electrophoresis in the present. However, ambiguous or even misjudged paternity based on STRs happens from time to time in cases where only one putative parent is available. We analyzed STR data of 7,818,969 unrelated pairs and 75 close-relative pairs and found that although the probability of a random false match between non-relatives was 4.22 × 10–6, the incidence of false or ambiguous paternity results between children and first-degree relatives of their true parent was as high as 18.67%. These results highlight the risk of false inclusion of a relative or even non-relatives in parentage testing with STRs. We then validated all ambiguous STR results by targeted sequencing with a custom panel containing 4,830 individual identification single nucleotide polymorphisms (IISNP), found that the ratio of mismatch loci to total SNPs was 1.78–6.95% in close relatives compared with 10.93–13.49% in unrelated pairs. Last, we reported three real cases with undetermined paternity by STRs and rectified them by dissecting with our IISNP panel. These results suggested that high-density IISNP panel can be used to identify and rectify misjudged cases effectively.

研究赣南地区汉族人群29个Y-STR基因座的遗传多态性以及与国内多个民族群体的遗传关系,探讨其在群体遗传学和法医学中的实际应用价值.采用DNATyperTM Y29试剂盒对1532例赣南地区健康男性无关个体进行Y-STR基因座扩增,3730型遗传分析仪进行毛细管电泳检测,运用GeneMapper IDX1.4软件对数据结果进行Y-STR分型,计算29个Y-STR基因座的等位基因频率及单倍型频率等遗传学参数.应用Mega-X软件对选取的群体构建进化树,用YHRD在线工具软件的分子方差分析(AMOVA),计算群体间遗传距离,同时构建多维尺度图(MDS).经分析,29个Y-STR基因座在赣南汉族人群中的基因多样性(GD)值范围为0.3815～0.8766,除了DYS508、DYS437、DYS391和DYS438基因座外,其余25个基因座GD值均高于0.5,且单倍型多样性为0.999924,表明29个Y-STR基因座在赣南汉族人群中有较高的遗传多态性.与其他地区汉族人群比较,赣南汉族与福建汉族遗传距离最近(遗传距离Rst值是0.0002),与黑龙江汉族遗传距离最远(Rst值是0.0249);与其他地区少数民族人群比较,赣南汉族与云南白族遗传距离最近(Rst值是0.0059),与甘孜藏族遗传距离最远(Rst值是0.4689).研究表明,这29个Y-STR基因座在赣南汉族人群中具有较好的遗传多态性分布,能够满足家系排查及法医学检案的要求,所得的数据可为该地区的群体遗传学和法医学研究与应用提供基础数据支持.

This article explores the role of ApoA4 in a CCl4-induced chronic liver injury (CLI) mouse model. C57BL/6J mice (WT) and ApoA4 knock-out (KO) mice were divided into CCl4 CLI (WT-CCl4 and KO-CCl4) and olive oil solvent control groups (WT-Veh and KO-Veh). Some of the KO-CCl4 mice were additionally treated with recombinant mouse ApoA4 and primary mouse T lymphocyte injections. After 6 weeks, histological analyses, biochemical and superoxide dismutase (SOD) and malondialdehyde (MDA) assays, flow cytometry of immune cells and qRT-PCR analyses were performed. KO mice after treatment with CCl4 showed reduced hepatic SOD and enhanced serum MDA activities leading to worsening liver injury and fibrosis compared with WT-CCl4, accompanied by enhanced hepatic alpha smooth muscle actin (α-SMA), tissue inhibitor of metalloproteinases-1 (TIMP-1) and collagen type I alpha 1 chain (COL1A1) transcriptions, elevated macrophage M1 levels, enhanced tumor necrosis factor-alpha (TNF-α), Interleukin 6 (IL-6) and C-C Motif Chemokine Ligand 5 (CCL5), but reduced Interleukin 10 (IL-10), monocyte chemotactic protein 1 (MCP-1), C-C Motif Chemokine Receptor 2 (CCR2), C-X3-C Motif Chemokine Receptor 1 (CX3CR1) and C-X-C Motif Chemokine Ligand 9 (CXCL9) transcription, as well as reduced CD3+, CD4+ and CD8+ T cell percentages in hepatic tissue, blood cells and spleen. In addition, CD11b+CD115+, CD11b+/Ly6Chigh, CD11b+/LyC6- and CD11b+/Ly6Cint cells were enhanced, which partly reversed by ApoA4 protein and T cell injections. In conclusion, we propose that ApoA4 might be involved in liver protection via inhibiting fibrotic mediators and inflammatory cytokines, suppression of pro-inflammatory hepatic M1 cell invasion and regulation of CD8+ T and CD4+ T lymphocytes.

寒辞去冬雪,暖带入春风.2020 年已经向我们走来.在这辞旧迎新之际,我们谨代表《西安交通大学学报 ( 医学版 )》编委会及编辑部同仁向多年来一直关心、支持本刊发展的编委、作者、读者、审稿人及各届朋友致以新春的问候,祝福大家在新的一年里,身体健康,事业顺遂.