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{"title":"Progress on the quality control technology of next generation sequencing library.","authors":"Meng-Nan Cui, Yan Guo, Ya-Rong Wu, Guang-Qian Pei, Yu-Jun Cui","doi":"10.16288/j.yczz.23-262","DOIUrl":"10.16288/j.yczz.23-262","url":null,"abstract":"<p><p>As a key supporting technology in the fields of life sciences and medicine, high-throughput sequencing has developed rapidly and become increasingly mature. The workflow of this technology can be divided into nucleic acid extraction, library construction, sequencing, and data analysis. Among these, library construction is a pivotal step that bridges the previous and subsequent stages. The effectiveness of library construction is contingent on the quality of upstream samples and also impacts the data analysis following sequence data output. The selection and implementation of library construction quality control techniques are crucial for enhancing the reliability of results and reducing errors in sequencing data. This review provides an in-depth discussion of library construction quality control techniques, summarizing and evaluating their principles, advantages and disadvantages, and applicability. It also discusses the selection of relevant technologies in practical application scenarios. The aim is to offer theoretical foundations and references for researchers, disease prevention and control personnel, and others when choosing library quality control techniques, thereby promoting the quality and efficiency of high-throughput sequencing work.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"140-148"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Choroid plexus and its relations with age-related diseases.","authors":"Yun-Fei Yang, Yi-Dong Shen","doi":"10.16288/j.yczz.23-294","DOIUrl":"10.16288/j.yczz.23-294","url":null,"abstract":"<p><p>The choroid plexus is composed of epithelial cells situated on the basal layer. The tight junctions between adjacent choroid plexus epithelial cells establish the blood-cerebrospinal fluid barrier. This barrier, in conjunction with the blood-brain barrier, is crucial for the homeostasis of the brain microenvironment. The choroid plexus epithelium secretes cerebrospinal fluid, growth factors, neuropeptides, and lipids into the ventricles and also serves as a gateway for immune cells to enter the brain. The pathophysiology of aging and neurodegenerative diseases remains largely enigmatic, with an increasing body of research linking the choroid plexus to the etiology of these age-related disorders. In this review, we summarize the known relationship between the choroid plexus epithelium and age-related diseases, aiming to provide new therapeutic clues for these disorders.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"109-125"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of next-generation sequencing in the detection of low-abundance mutations.","authors":"Yang Luan, Xin-Yue You, Jin Yang","doi":"10.16288/j.yczz.23-309","DOIUrl":"10.16288/j.yczz.23-309","url":null,"abstract":"<p><p>Mutation accumulation in somatic cells contributes to cancer development, aging and many non-malignant diseases. The true mutation frequency in normal cells is extremely low, which presents a challenge in detecting these mutations at such low frequencies. The emergence of next-generation sequencing (NGS) technology enables direct detection of rare mutations across the entire genome of any species. This breakthrough overcomes numerous limitations of traditional mutation detection techniques that rely on specific detection models and sites. However, conventional NGS is limited in its application for detecting low-frequency mutations due to its high sequencing error rate. To address this challenge, high-accuracy NGS sequencing techniques based on molecular consensus sequencing strategies have been developed. These techniques have the ability to correct sequencing errors, resulting in error rates lower than 10^-7, are expected to serve as effective tools for low-frequency mutation detection. Error-corrected NGS (ecNGS) techniques hold great potential in various areas, including safety evaluation and research on environmental mutagens, risk assessment of cell and gene therapy drugs, population health risk monitoring, and fundamental research in life sciences. This review highlights a comprehensive review of the research progress in low-frequency mutation detection techniques based on NGS, and provides a glimpse into their potential applications. It also offers an outlook on the potential applications of these techniques, thereby providing valuable insights for further development, research, and application of this technology in relevant fields.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"126-139"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Progress on fluorescent RNA and fluorescent NA-based biosensing technology.","authors":"Fang-Ting Zuo, Ya-Qiang Zhang, Hui-Min Yang, Yi Yang, Xian-Jun Chen","doi":"10.16288/j.yczz.23-306","DOIUrl":"10.16288/j.yczz.23-306","url":null,"abstract":"<p><p>Fluorescent RNA is a kind of emerging RNA labeling technique that can be used for <i>in situ</i> labeling and imaging of RNA in live cells, which plays an important role in understanding the function and regulation mechanism of RNA. Biosensing technology based on fluorescent RNA can be applied in dynamic detection of small molecule metabolites and proteins in real time, offering valuable tools for basic life science research and biomedical sensing technology development. In this review, we introduce the development of genetically encoded fluorescent RNA, and the application of fluorescent RNA in RNA imaging and biosensing technology based on fluorescent RNA in biosensing in live cell. Meanwhile, we discuss the direction and challenge of future development of fluorescent RNA technology to provide valuable insights for further development and application of this technology in relevant fields.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"92-108"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and characterization analysis of the HDM gene family in melon (<i>Cucumis melo</i> L.).","authors":"Zhi Zhang, Jing Zhang, Jin Zhang, Agula Hasi, Jin-Feng Hao","doi":"10.16288/j.yczz.23-226","DOIUrl":"10.16288/j.yczz.23-226","url":null,"abstract":"<p><p>Histone demethylase (HDM) play crucial roles in regulating plant growth and environmental adaptation. In this study, the HDM gene family in melon was identified by bioinformatics methods and the expression patterns of the CmHDM family members in different melon tissues were analyzed using transcriptome data. The results showed that 20 <i>CmHDM</i> genes were identified in the melon genome, which were unevenly distributed across each chromosome. These members fall into two major categories: LSD1 and JmjC. The JmjC group could be further divided into five subgroups with different numbers. The results of collinearity analysis of intraspecific and interspecific relationships showed that there were only one pair of segmental duplication in melon <i>HDM</i> genes, and more collinearity in genetic relationship of <i>HDM</i> genes between melon and tomato. The numbers of conserved domains, exons and introns in each member vary and various <i>cis</i>-acting elements responding to hormones and environmental signals existed in the respective promoter regions. Expression analysis showed that the respective gene members were expressed at different levels in male flowers, female flowers, roots, stems, leaves, ovary, and mature fruits of melon. These results will contribute to the understanding on the potential functions of the <i>HDM</i> genes and their potential functions in regulating melon growth and environmental adaptation.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"168-180"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Paternal genetic structure analysis of the modern Han populations based on Y-SNP and Y-STR.","authors":"Xin Zhu, Xin Jin, Jun Liu, Lan Yang, Li-Xin Zou, Cai-Xia Li, Jiang Huang, Li Jiang","doi":"10.16288/j.yczz.23-260","DOIUrl":"10.16288/j.yczz.23-260","url":null,"abstract":"<p><p>The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. However, a comprehensive analysis of the global paternal genetic structure of Han populations is lacking. In this study, we performed Y-chromosome sequencing on 362 unrelated male samples from Chinese Han individuals collected from Qinghai, Sichuan and Liaoning provinces. We then integrated relevant data from reported studies. Our final dataset comprised 1830 samples from 16 Han populations across 15 provinces in China, encompassing information on 89 Y-SNPs and 16 Y-STRs. Statistical analyses were conducted to assess Y-STR haplotype diversity (HD) and Y-SNP haplogroup frequencies. Additionally, we employed principal component analysis (PCA), phylogenetic tree and haplotype network to explore genetic differentiation within Han populations and the genetic relationships between Han populations and ethnic minorities surrounding them. Our results demonstrated that the O-M175 haplogroup represents the predominant paternal lineage in Han populations, with frequencies ranging from 60.53% (Qinghai Han) to 92.7% (Guangdong Han). Moreover, the subclades downstream of O-M175 showed distinct regional variations in their distribution patterns. The O2-M122 haplogroup was prevalent in all Han populations and demonstrated a gradual decline in frequency from north to south. Conversely, the distribution frequency of the O1b-M268 haplogroup decreased from south to north, particularly showed significant presence among Han populations in the Lingnan region. Haplogroup O1a-M119 distributed more frequently in the central Han populations. Our findings revealed that Chinese Han populations can be categorized into three subgroups: northern, central, and southern. Notably, there were significant differences among Han in Qinghai and other regions. Regarding the genetic relationships between Han populations and surrounding ethnic minorities, we observed a closer genetic affinity between different Han populations, but northern Han demonstrated a stronger relationship with the Hui ethnic group, while southern Han exhibited a closer connection with the Gelao and Li ethnic groups. In summary, this study presented a systematic analysis of haplogroup distribution, genetic substructure of Han populations and genetic relationships between Han populations and surrounding ethnic minorities based on 89 Y-SNPs and 16 Y-STRs systematically. Our research supplemented valuable insights into population genetics and forensic genetics, and provided data support for the forensic application of Y chromosome. The integration of Y-SNP haplogroups with Y-STR haplotypes offers enhanced understanding of the genetic substructure within Han populations, which holds significance for both population genetics research and forensic science applicati","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"149-167"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of chromosomal genetic characteristics and identification of structural variation in the offspring of hexaploid triticale×hexaploid wheat.","authors":"Man-Yu Yang, Fang-Jie Yao, Zu-Jun Yang, En-Nian Yang","doi":"10.16288/j.yczz.23-212","DOIUrl":"10.16288/j.yczz.23-212","url":null,"abstract":"<p><p>Hexaploid triticale is an important genetic resource for genetic improvement of common wheat, which can broaden the genetic basis of wheat. In order to lay a foundation for the subsequent research and utilization of triticale germplasm materials, the chromosomal genetic characteristics of cross and backcross offspring of hexaploid triticale×hexaploid wheat were investigated in the process of transferring rye chromatin from hexaploid triticale to hexaploid wheat. Hybrid and backcross combinations were prepared with hexaploid triticale 16yin171 as the maternal parent and hexaploid wheat Chuanmai62 as the paternal parent. The chromosomes in root tip cells of F₁, BC₁F₁ and BC₁F₂ plants were traced and identified non-denaturing florescence in situ hybridization (ND-FISH). The results indicated that the backcross setting rate of hybrid F₁ was 2.61%. The transmission frequency of 2R chromosome was the highest in BC₁F₁ plants while the transmissibility of rye chromosome in BC₁F₂ plant was 6R>4R>2R, and the 5B-7B wheat translocation in BC₁F₂ plants showed severe segregation. A total of 24 structural variant chromosomes were observed both in BC₁F₁ and BC₁F₂ plants, including chromosome fragments, isochromosomes, translocations, and dicentric chromosomes. In addition, the seed length and 1000-grain weight of some BC₁F₂ plants were better than that of the hexaploid wheat parent Chuanmai 62. Therefore, multiple backcrosses should be adopted as far as possible to make the rapid recovery of group D chromosomes, ensuring the recovery of fertility in offspring, when hexaploid tritriale is used as a bridge to introduce rye genetic material into common wheat. At the same time, the potential application value of chromosomal structural variation materials should be also concerned.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 1","pages":"63-77"},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of Mycobacterium biofilm development and novel measures against antibiotics resistance.","authors":"Abulimiti Abudukadier, Qi-Ao Zhang, Pei-Bo Li, Jian-Ping Xie","doi":"10.16288/j.yczz.23-205","DOIUrl":"10.16288/j.yczz.23-205","url":null,"abstract":"<p><p>Currently, there are over 170 recognized species of Mycobacterium, the only genus in the family Mycobacteriaceae. Organisms belonging to this genus are quite diverse with respect to their ability to cause disease in humans. The Mycobacterium genus includes human pathogens (Mycobacterium tuberculosis complex and Mycobacterium leprae) and environmental microorganisms known as non-tuberculosis mycobacteria (NTM). A common pathogenic factor of Mycobacterium is the formation of biofilms. Bacterial biofilms are usually defined as bacterial communities attached to the surface, and are also considered as shared spaces of encapsulated microbial cells, including various extracellular polymeric substrates (EPS), such as polysaccharides, proteins, amyloid proteins, lipids, and extracellular DNA (EDNA), as well as membrane vesicles and humic like microorganisms derived refractory substances. The assembly and dynamics of the matrix are mainly coordinated by second messengers, signaling molecules, or small RNAs. Fully deciphering how bacteria provide structure for the matrix, thereby promoting extracellular reactions and benefiting from them, remains a challenge for future biofilm research. This review introduces a five step development model for biofilms and a new model for biofilm formation, analyses the pathogenicity of biofilms, their interactions with bacteriophages and host immune cells, and the key genes and regulatory networks of mycobacterial biofilms, as well as mycobacterial biofilms and drug resistance, in order to provide a basis for clinical treatment of diseases caused by biofilms.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 1","pages":"34-45"},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular and evolutionary mechanisms of self-incompatibility in angiosperms.","authors":"Hong Zhao, Yong-Biao Xue","doi":"10.16288/j.yczz.23-300","DOIUrl":"10.16288/j.yczz.23-300","url":null,"abstract":"<p><p>As an intraspecific outcrossing mechanism, self-incompatibility (SI) widely adopted by hermaphroditic plants is usually controlled by a polymorphic multi-allelic S locus. Typically, six molecular types of SI have been found, including type-I controlled by the pistil S S-RNase and pollen S SLFs commonly spread in Plantaginaceae, Solanaceae, Rosaceae and Rutaceae, type-II by SRK and SCR in Brassicaceae, type-III by PrsS and PrpS in Papaveraceae, type-IV by CYP-GLO2-KFB-CCM-PUM in Primulaceae, type-V by TsSPH1-TsYUC6-TsBAHD in Turneraceae and type-VI by HPS10-S and DUF247I-S in Poaceae, with type-I characterized as a non-self recognition system but types-II, -III and -VI self ones. Furthermore, remarkable progresses have been made in their origin and evolutionary mechanisms recently. Among them, type-I SI possessed a single origin in the most recent common ancestor of eudicots and types II-V dynamically evolved following its losses, while type-VI SI exclusively existed in monocot Poaceae may be regained after the loss of the ancient type-I. Here, we mainly review the molecular and evolutionary mechanisms of angiosperm SI systems, thus providing a helpful reference for their theoretical research and breeding application.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 1","pages":"3-17"},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genes that escape from X-chromosome inactivation and sexual dimorphism of systemic lupus erythematosus.","authors":"Qian Ma, Shao-Lan Zhou, Jie Dang, Zheng-Hao Huo, Zhan-Bing Ma","doi":"10.16288/j.yczz.23-214","DOIUrl":"10.16288/j.yczz.23-214","url":null,"abstract":"<p><p>X chromosome inactivation can balance the effects of the two X chromosomes in females, and emerging evidence indicates that numerous genes on the inactivated X chromosome have the potential to evade inactivation. The mechanisms of escape include modification of DNA, RNA, histone, epitope, and various regulatory proteins, as well as the spatial structure of chromatin. The study of X chromosome inactivation escape has paved the way for investigating sex dimorphism in human diseases, particularly autoimmune diseases. It has been demonstrated that the presence of TLR7, CD40L, IRAK-1, CXCR3, and CXorf21 significantly contributes to the prevalence of SLE (systemic lupus erythematosus) in females. This article mainly reviews the molecular mechanisms underlying these genes that escape from X-chromosome inactivation and sexual dimorphism of systemic lupus erythematosus. Therefore, elucidating the molecular mechanisms underlying sexual dimorphism in SLE is not only crucial for diagnosing and treating the disease, but also holds theoretical significance in comprehensively understanding the development and regulatory mechanisms of the human immune system.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 1","pages":"18-33"},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}