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Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2023年第9期24卷 839-852页

作者： Yating FANG Man CHEN bofeng zhu Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification School of Forensic MedicineSouthern Medical UniversityGuangzhou510515China School of Basic Medical Sciences Anhui Medical UniversityHefei230031China Microbiome Medicine Center Department of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou510515China

The identification of tissue origin of body fluid can provide clues and evidence for criminal case *** establish an efficient method for identifying body fluid in forensic cases,eight novel body fluid-specific DNA methylation markers were selected in this study,and a multiplex single base extension reaction(SNaPshot)system for these markers was constructed for the identification of five common body fluids(venous blood,saliva,menstrual blood,vaginal fluid,and semen).The results indicated that the in-house system showed good species specificity,sensitivity,and ability to identify mixed biological *** the same time,an artificial body fluid prediction model and two machine learning prediction models based on the support vector machine(SVM)and random forest(RF)algorithms were constructed using previous research data,and these models were validated using the detection data obtained in this study(n=95).The accuracy of the prediction model based on experience was 95.79%;the prediction accuracy of the SVM prediction model was 100.00%for four kinds of body fluids except saliva(96.84%);and the prediction accuracy of the RF prediction model was 100.00%for all five kinds of body *** conclusion,the in-house SNaPshot system and RF prediction model could achieve accurate tissue origin identification of body fluids.

关键词： DNA methylation Body fluid Forensic identification Single base extension reaction(SNaPshot) Machine learning

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Angiogenesis in a 3D model containing adipose tissue stem cells and endothelial cells is mediated by canonical Wnt signaling

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Bone Research 2017年第4期5卷 330-342页

作者： Xiaoxiao Cai Jing Xie Yang Yao Xiangzhu Cun Shiyu Lin Taoran Tian bofeng zhu Yunfeng Lin State Key Laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengdu 610041China Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of StomatologyXi'an Jiaotong UniversityXi'an 710004China Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of StomatologyXi'an Jiaotong UniversityXi'an 710004China Department of Forensic Genetics School of Forensic MedicineSouthern Medical UniversityGuangzhou 510515China

Adipose-derived stromal cells （ASCs） have gained great attention in regenerative medicine. Progress in our understanding of adult neovascularization further suggests the potential of ASCs in promoting vascular regeneration, although the specific cues that stimulate their angiogenic behavior remain controversial In this study, we established a three-dimensional （3D） angiogenesis model by co-culturing ASCs and endothelial cells （ECs） in collagen gel and found that ASC-EC-instructed angiogenesis was regulated by the canonical Wnt pathway. Furthermore, the angiogenesis that occurred in implants collected after injections of our collagen gel- based 3D angiogenesis model into nude mice was confirmed to be functional and also regulated by the canonical Wnt pathway. Wnt regulation of angiogenesis involving changes in vessel length, vessel density, vessel sprout, and connection numbers occurred in our system. Wnt signaling was then shown to regulate ASC- mediated paracrine signaling during angiogenesis through the nuclear translocation of β-catenin after its cytoplasmic accumulation in both ASCs and ECs. This translocation enhanced the expression of nuclear cofactor Lef-1 and cyclin D1 and activated the angiogenic transcription of vascular endothelial growth factor A （VEGFA）, basic fibroblast growth factor （bFGF）, and insulin-like growth factor 1 （IGF-1）. The angiogenesis process in the 3D collagen model appeared to follow canonical Wnt signaling, and this model can help us understand the importance of the canonical Wnt pathway in the use of ASCs in vascular regeneration.

关键词： Angiogenesis in a 3D model containing adipose tissue stem cells and endothelial cells is mediated by canonical Wnt signaling Wnt

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Genetic polymorphisms of 44 Y chromosomal genetic markers in the Inner Mongolia Han population and its genetic relationship analysis with other reference populations

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Forensic Sciences Research 2022年第3期7卷 510-517页

作者： Xiaoye Jin Guohui Xing Chunhua Yang Xingru Zhang Wei Cui Chong Chen bofeng zhu Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of StomatologyXi’an Jiaotong UniversityXi’anChina College of Forensic Science Xi’an Jiaotong University Health Science CenterXi’anChina Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of StomatologyXi’an Jiaotong UniversityXi’anChina People’s Hospital of Arong Banner Hulun Buir CityChina Multi-Omics Innovative Research Center of Forensic Identification Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina

Y chromosomal genetic markers in the non-recombining region are commonly used for human evolution research,familial searching,and forensic male differentiation since they strictly follow paternal inheritance.Y chromosomal short tandem repeats(Y-STRs)possess extraordinarily advantages in forensic applications because of their high polymorphisms and special genetic ***,we assessed the genetic diversities of 41 Y-STRs and three Y chromosomal insertion/deletion(Y-InDels)loci in the Chinese Inner Mongolia Han population;besides,genetic differentiation analyses among the studied Han population and other previously reported populations were conducted based on 27 same ***,425 alleles were observed in 324 Inner Mongolia Han individuals for these *** diversities of these Y-markers distributed from 0.0306 to *** haplotype diversity and discriminatory capacity of these Y-markers in the Inner Mongolia Han population were 0.9999 and 0.98457,*** resolution comparisons of different Y-marker groups in the studied Han population revealed that higher haplotype resolution could be achieved for these 44 *** genetic analyses of the Inner Mongolia Han population and other reference populations demonstrated that the studied Han population had relatively closer genetic affinities with Northern Han Chinese populations than Southern Han and other minority *** sum up,these 44 Y-markers can be utilized as a valuable tool for male differentiation in the Inner Mongolia Han population.

关键词： Forensic sciences forensic genetics Y chromosomal STR InDel Inner Mongolia Han male differentiation

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Genetic and structural characterization of 20 autosomal short tandem repeats in the Chinese Qinghai Han population and its genetic relationships and interpopulation differentiations with other reference populations

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Forensic Sciences Research 2018年第2期3卷 145-152页

作者： Zhanhai Wang Bin Lu Xiaoye Jin Jiangwei Yan Haotian Meng bofeng zhu The Public Security Bureau of Qinghai Province XiningChina Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of StomatologyXi'an Jiaotong UniversityXi'anChina Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of StomatologyXi'an Jiaotong UniversityXi'anChina Research Center of Stomatology Stomatological HospitalXi'an Jiaotong UniversityXi'anChina Beijing Institute of Genomics Chinese Academy of SciencesBeijingChina

China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%.Qinghai Province is located in the northeastern part of the Qinghai-Tibet Plateau,has an area of 72.12 km2,and is the fourth largest province in *** the present study,we investigated the genetic polymorphisms of 20 short tandem repeat (STR) loci in a Qinghai Han population,as well as its genetic relationships with other populations.A total of 273 alleles were identified in 2 000 individuals at 20 loci,and the allelic frequency ranged from 0.0002 to *** 20 STR loci showed a relatively high polymorphic rate in the studied *** and expected heterozygosities ranged 0.613 0-0.907 5 and 0.614 8-0.920 0,*** combined power of discrimination,and the probability of exclusion in duo and trio cases were 0.999 999 999 999 999 999 999 999 34,0.9999960 and 0.9999999965,*** of interpopulation differentiation revealed that the most significant differences were found between the Qinghai Han and Malaysian,while no significant differences were found between the Qinghai Han and Han people from Shaanxi and *** results of principal component analysis,multidimensional scaling analysis and phylogenetic reconstructions also suggested the close relationships between the Qinghai Han and other two Han *** present results,therefore,indicated that these 20 STR loci could be used for paternity testing and individual identification in forensic applications,and may also provide information for the studies of genetic relationships between Qinghai Han and other groups.

关键词： Genetic polymorphisms forensic genetics phylogenetic reconstruction short tandem repeat

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Gingipain from Porphyromonas gingivalis causes insulin resistance by degrading insulin receptors through direct proteolytic effects

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International Journal of Oral Science 2024年第3期16卷 539-552页

作者： Fen Liu bofeng zhu Ying An Zhifei Zhou Peiying Xiong Xuan Li Yang Mi Tongqiang He Faming Chen Buling Wu Shenzhen Stomatology Hospital(Pingshan) Southern Medical UniversityShenzhenChina Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research Laboratory Center of StomatologyDepartment of Paediatric DentistryCollege of StomatologyXi’an Jiaotong UniversityXi’anChina State Key Laboratory of Oral&Maxillofacial Reconstruction and Regeneration National Clinical Research Center for Oral DiseasesShaanxi International Joint Research Center for Oral DiseasesDepartment of PeriodontologySchool of StomatologyThe Fourth Military Medical UniversityXi’anChina Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification School of Forensic MedicineSouthern Medical UniversityGuangzhouChina Microbiome Medicine Center Department of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhouChina Department of Stomatology General Hospital of Tibetan Military CommandLhasaChina Department of Stomatology Center Shenzhen HospitalSouthern Medical UniversityShenzhenChina Department of Obstetrics Northwest Women’s and Children’s HospitalXi’anChina

Periodontitis is a critical risk factor for the occurrence and development of *** gingivalis may participate in insulin resistance(IR)caused by periodontal inflammation,but the functional role and specific mechanisms of *** in IR remain *** the present study,clinical samples were analysed to determine the statistical correlation between *** and IR *** culturing of hepatocytes,myocytes,and adipocytes,and feeding mice *** orally,the functional correlation between *** and IR occurrence was further studied both in vitro and in *** data suggested that the amount of *** isolated was correlated with the Homeostatic Model Assessment for IR *** vitro studies suggested that coculture with *** decreased glucose uptake and insulin receptor(INSR)protein expression in hepatocytes,myocytes,and *** fed *** tended to undergo *** was detectable in the liver,skeletal muscle,and adipose tissue of experimental *** distribution sites of gingipain coincided with the downregulation of *** proteolysed the functional insulin-binding region of *** with *** significantly decreased the INSR–insulin binding *** out gingipain from *** alleviated the negative effects of *** on IR in *** together,these findings indicate that distantly migrated *** may directly proteolytically degrade INSR through gingipain,thereby leading to *** results provide a new strategy for preventing diabetes by targeting periodontal pathogens and provide new ideas for exploring novel mechanisms by which periodontal inflammation affects the systemic metabolic state.

关键词： gingivalis inflammation resistance

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Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci

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Forensic Sciences Research 2022年第2期7卷 181-188页

作者： Jiuyang Ding Haoliang Fan Yongsong Zhou zhuo Wang Xiao Wang Xuheng Song bofeng zhu Pingming Qiu Shanghai Key Laboratory of Forensic Medicine Shanghai Forensic Service PlatformAcademy of Forensic ScienceShanghaiChina School of Forensic Medicine Southern Medical UniversityGuangzhouChina School of Basic Medicine and Life Science Hainan Medical UniversityHaikouChina Multi-Omics Innovative Research Center of Forensic Identification Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina Department of Psychiatry The First Clinical Medical CollegeShanxi Medical UniversityTaiyuanChina Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of StomatologyXi’an Jiaotong UniversityXi’anChina Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of StomatologyXi’an Jiaotong UniversityXi’anChina

As a result of the expansion of old Tibet on the Qinghai-Tibet Plateau,Tibetans diverged into three main branches,Ü-Tsang,Amdo,and Kham Tibetan.Ü-Tsang Tibetans are geographically distributed across the wide central and western portions of the Qinghai-Tibet Plateau while Lhasa is the central gathering place for Tibetan *** AGCU Y30,a 6-dye fluorescence kit including 30 slowly and moderately mutated Y-STR loci,has been validated for its stability and sensitivity in different biomaterials and diverse Chinese populations(Han and other minorities),and widely used in the practical work of forensic ***,the 30 Y-STR profiling of Tibetan,especially forÜ-Tsang Tibetan,were *** utilized the AGCU Y30 to genotype 577Ü-Tsang Tibetan unrelated males from Lhasa in the Tibet Autonomous Region of China to fill up the full and accurate Y-STR profiles.A total of 552 haplotypes were observed,536(97.10%)of which were *** hundred and ninety-four alleles were observed at 26 single copy loci and the allelic frequencies ranged from 0.0017 to *** the two multi-copy loci DYS385a/b and DYS527a/b,64 and 36 allelic combinations were observed,*** gene diversity(GD)values ranged from 0.3079 at DYS391 to 0.9142 at DYS385a/b and the overall haplotype diversity(HD)was 0.9998,and its discrimination capacity(DC)was *** population genetic analyses demonstrated that LhasaÜ-Tsang Tibetan had close relationships with other Tibetan populations from Tibet and Qinghai,especially withÜ-Tsang *** the perspective of Y haplogroups,the admixture of the southward Qiang people with dominant haplogroup O-M122 and the northward migrations of the initial settlers of East Asia with haplogroup D-M175 hinted the Sino-Tibetan homologous,thus,we could not ignore the gene flows with other Sino-Tibetan populations,especially for Han Chinese,to characterize the forensic genetic landscape of Tibetan.

关键词： Forensic sciences forensic genetics Y-STR Ü-Tsang Tibetan phylogenetic analysis AGCU Y30 O-M122

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An interpretation of the genetic polymorphism and population genetic background of Ankang Han population via a novel InDel panel

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Forensic Sciences Research 2022年第4期7卷 694-701页

作者： Wei Cui Xiaoye Jin Yating Fang Qiong Lan Jiangwei Lan Man Chen Shuyan Mei Tong Xie bofeng zhu Multi-Omics Innovative Research Center of Forensic Identification Department of Forensic Genetics School of Forensic MedicineSouthern Medical UniversityGuangzhouChina Department of Forensic Medicine Guizhou Medical UniversityGuiyangChina Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina

In this research,genotyping data of 43 InDel loci in 311 Han individuals in Ankang City,Shaanxi Province,China were detected using a self-developed five-dye multiplex amplification *** allelic frequencies and forensic parameters of all InDel loci were *** combined power of discrimination and probability of exclusion values were 0.99999999999999999882739 and 0.999887424,respectively,which demonstrated that this 43-InDel panel was powerful for individual identifications in Ankang Han ***,genetic distances,pairwise F_(ST)values,principal component analyses,phylogenetic trees and STRUCTURE analyses were performed to investigate the genetic affinities between Ankang Han and reference *** genetic investigations indicated that Ankang Han population had a close genetic relationship with Southern Han population compared with other reference groups.

关键词： Forensic sciences forensic genetics forensic parameter InDel Population genetics Ankang Han population

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Forensic Validation Studies of a Novel 35-InDel Multiplex Polymerase Chain Reaction System

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Journal of Forensic Science and Medicine 2023年第4期9卷 303-308,I0004-I0011页

作者： Tong Xie Hui Xu Congying Zhao Yating Fang Yongsong Zhou Qiong Lan Chunmei Shen bofeng zhu Department of Laboratory Medicine Guangzhou Key Laboratory of Forensic Multi-Omics for Precision IdentificationSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina Department of Laboratory Medicine Nanfang HospitalSouthern Medical UniversityGuangzhouChina Department of Laboratory Medicine Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anShaanxiChina

Background:A difficulty associated with forensic applications is the detection of degraded biological *** to the large amplicon sizes of short tandem repeat alleles,valid genotyping results cannot be obtained from degraded biological ***,insertion/deletion(InDel)polymorphisms have been used in forensic applications for their widespread distributions in the human genome,short amplicon sizes,and low mutation ***:Human identification InDel panels have mostly been designed for European ***,our laboratory independently developed a multiplex polymerase chain reaction(PCR)system with 35 polymorphic InDel loci to be used for human identification in *** validation studies were conducted on this novel 35-InDel multiplex PCR ***:The 35 InDel loci were screened in the database,and then used with the traditional PCR amplification and capillary electrophoresis platform combined with five-color fluorescence parallel detection *** studies were performed on this novel panel,including accuracy,repeatability and reproducibility,species specificity,sensitivity,stability,forensic case sample detection,and mixture *** addition,forensic efficiency assessments were conducted in populations from different ***:The data of validated studies indicated that the novel 35-InDel panel was accurate,stable,and efficient for forensic *** human identification,the cumulative power of discrimination values for the these 35 InDel loci in East Asian,South Asian,European,American,and African populations were 0.999999999999995,0.999999999999995,0.999999999999971,0.9999999999999960,and 0.999999999998166,***:In this study,a set of 35 InDel loci were conducted in a multiplex amplification system for human identification of degraded DNA sample,and this new assay was efficient and *** present results suggested that the 35-InDel panel was a reliable tool for foren

关键词： 35-InDel panel human identification insertion/deletion polymorphism validation study

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Comprehensive analyses for genetic diversities of 19 autosomal STRs in Chinese Kazak group and its phylogenetic relationships with other continental populations

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Forensic Sciences Research 2022年第2期7卷 163-171页

作者： Yijie Wang Xiaoye Jin Wenqing Zhang Wei Cui Tingting Kong Chong Chen Yuxin Guo Haotian Meng bofeng zhu Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of StomatologyXi’an Jiaotong UniversityXi’anChina Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of StomatologyXi’an Jiaotong UniversityXi’anChina College of Forensic Medicine Xi’an Jiaotong University Health Science CenterXi’anChina

Short tandem repeats(STRs)play an essential role in forensic genetics due to their high degree of polymorphisms,wide distributions and easy detection *** this study,allelic frequencies and forensic statistical parameters of the 19 autosomal STR loci in a Kazak ethnic group were calculated,and its genetic relationships with reference populations were assessed in order to understand population structure better and enrich population genetic data for forensic practice in Chinese Kazak ethnic *** were 226 identified alleles with the corresponding allelic frequencies ranging from 0.0008 to 0.5295 in the 628 unrelated healthy Kazak individuals in Xinjiang Uygur Autonomous *** autosomal STRs were conformed to the Hardy-Weinberg equilibrium after Bonferroni’s *** cumulative power of discrimination and the combined probability of exclusion of all the 19 autosomal STRs were 0.999999999999999999999997162 and 0.999999994484,***,the DA distances and Fixation index values of pairwise populations,principal component analysis,multidimensional scaling analysis,phylogenetic tree analysis and structure analysis were conducted to probe the genetic relationships between the Kazak group and other reference *** population genetic results showed that these 19 autosomal STR loci were characterised by high genetic diversities in the Kazak ***,the studied Kazak group had close genetic relationships with the Uyghur group and the Uzbek *** present results may facilitate understanding the genetic background of the Chinese Xinjiang Kazak group.

关键词： Forensic sciences forensic genetics Kazak ethnic group autosomal STRs population genetics interpopulation differentiation phylogenetic reconstruction

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Diversity distributions of killer cell immunoglobulin-like receptor genes and their ligands in the kazak ethnic minority

Diversity distributions of killer cell immunoglobulin-like r...

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第十二次全国医学遗传学学术会议

作者： Wang Hongdan Liao Shixiu zhu bofeng Medical Genetic Institute of Henan Province People's Hospital of Henan Province School of Medicine Xi'an Jiaotong University

Purpose To explore 17 killer cell immunoglobulin-like receptors(KIRs) gene and their ligands(human leukocyte antigen HLA-A and -B) polymorphisms in the Kazak individuals. Methods:17 killer cell immunoglobulin-like receptors(KIR) genes and KIR ligands(human leukocyte antigen HLA-A and -B) were detected by using a polymerase chain reaction-sequence-specific primer(PCR-SSP).Methods Neighbor-joining phylogenetic tree between the studing population and its neighboring ethnic groups was constructed using the observed carrier frequencies of 13 KIR loci by SPSS *** In the 110 unrelated healthy Kazak individuals living in Xinjiang Uygur Autonomous Region of China,we found the observed carrier frequencies of the 13 KIR genes ranged from 0.16 to 0.96;KIR2DL4,3DL2,3DL3 and 3DP1 were found to be present in every *** a total of 48 different KIR gene profiles were also *** the present study findings reveal the high polymorphism of KIRs in the Kazak population,demonstrate the KIR/HLA association in the study population,and enrich the KIR and HLA gene *** obtained KIR data will further the understanding of genetic relationships among populations in different geographic areas,and assist in answering questions regarding KIR/HLA relationships.

关键词： KIR PCR-SSP kazak ethnic minority

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