遗传 Pub Date : 2025-06-01 DOI: 10.16288/j.yczz.24-209

Yao Shen, Zhi-Yu Li, Feng-Cheng Miao, Ying-Ping Xiao, Hua Yang, Ya-Li Dang, Jian-Gang Ma

{"title":"Progresses on the prevalence and mechanism of vancomycin- resistant bacteria.","authors":"Yao Shen, Zhi-Yu Li, Feng-Cheng Miao, Ying-Ping Xiao, Hua Yang, Ya-Li Dang, Jian-Gang Ma","doi":"10.16288/j.yczz.24-209","DOIUrl":"https://doi.org/10.16288/j.yczz.24-209","url":null,"abstract":"Vancomycin, a glycopeptide antibiotic, serves as the last-resort treatment for infections caused by methicillin- resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE), and Clostridium difficile. However, the emergence of various vancomycin-resistant bacterial strains worldwide poses a significant challenge to clinical therapy. Adopting the \"One Health\" concept, we mainly present the prevalence of vancomycin-resistant bacteria over the past decade from 40 human, animal, environmental, and food sources across various regions, both domestically and internationally. The statistical results indicate that vancomycin-resistant bacteria are primarily concentrated in hospitals and their surrounding environments. The prevalence of resistant bacteria in hospital wastewater in South Africa reaches as high as 96.77%, followed by Pakistan and China's Taiwan region, where the resistance rates are 56.5% and 29.02%, respectively. The vancomycin average resistance rate in domestic human-source bacteria (1.41%) is overall higher than that in international human-source bacteria (0.47%). The prevalence of resistant bacteria in pediatric patients across various regions is relatively low (<1%). It is worth noting that although the use of vancomycin is prohibited in livestock farming, vancomycin- resistant bacteria can still be detected in livestock, related products and environment, posing a potential threat to human health. Based on the statistical analysis results, we summarize several common vancomycin resistance mechanisms and the transmission mechanisms, and clarify the differences in the prevalence of resistant bacteria across the \"human-animal-food-environment\" interface for further analyzing the distribution and transmission risks of vancomycin-resistant bacteria in different hosts worldwide. This review can also provide references for the prevention and control of antimicrobial resistance.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 6","pages":"650-659"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318181","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}

引用次数: 0

Study on population genomics of Bacillus anthracis based on multiple types of genetic variations. 基于多类型遗传变异的炭疽芽孢杆菌群体基因组学研究。

遗传 Pub Date : 2025-06-01 DOI: 10.16288/j.yczz.24-295

Zu-Ming Zhang, Hao Zhou, Xue-Zhi Huang, Duo-Yue Zhang, Jia-Yi Zhang, Yu Lin, Li-Wei Fang, Xiu-Chang Zhang, Yu-Jun Cui, Ya-Rong Wu, Yan-Jun Li

{"title":"Study on population genomics of Bacillus anthracis based on multiple types of genetic variations.","authors":"Zu-Ming Zhang, Hao Zhou, Xue-Zhi Huang, Duo-Yue Zhang, Jia-Yi Zhang, Yu Lin, Li-Wei Fang, Xiu-Chang Zhang, Yu-Jun Cui, Ya-Rong Wu, Yan-Jun Li","doi":"10.16288/j.yczz.24-295","DOIUrl":"https://doi.org/10.16288/j.yczz.24-295","url":null,"abstract":"Bacillus anthracis, the causative agent of the deadly infectious disease anthrax, is also a typical biological warfare agent. It primarily infects livestock such as cattle and sheep, as well as humans, causing significant economic losses to the livestock industry and posing a threat to human society. A more profound insight into the genetic diversity and evolutionary drivers of this species is essential for studying its virulence mechanisms and conducting anthrax surveillance and control. However, current research in this area is insufficient, particularly lacking population genomic studies based on multiple types of genetic variation. In this study, we collect and filter the genome sequences of 1,628 publicly available B. anthracis strains, and identify various types of variation in 1,347 high-quality sequences, including SNPs, indels, large fragment gains and losses, copy number variations (CNVs), and genome rearrangements. In total, we identify 26,635 SNPs, 9,997 indels, 21 large fragment gains and losses, 25 CNVs, and 5 inversions. Phylogenetic reconstruction reveals that this species can be divided into six major populations and 17 subgroups. By integrating population diversity and geographic distribution characteristics, we find that U.S. strains exhibit the highest genetic diversity, while African strains show significant geographic clustering. Additionally, through selection pressure analysis, we identify strong selection signals in four genes (rpoB, fusA, spo0F, GBAA_RS11385) related to drug resistance and sporulation. This study reconstructs the global population structure of B. anthracis and reveals key variations during the species' evolutionary process, providing targets for anthrax strain identification, tracing, and virulence mechanism research, as well as scientific support for the prevention and control of anthrax outbreaks.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 6","pages":"681-693"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318183","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}

引用次数: 0

Onsite rapid detection method for genetically modified maize and soybean based on recombinase polymerase amplification. 基于重组酶聚合酶扩增的转基因玉米和大豆现场快速检测方法。

遗传 Pub Date : 2025-06-01 DOI: 10.16288/j.yczz.24-322

Jia-Tong Yan, Guan-Wei Chen, Qing-Mei Miao, Cheng Peng, Lei Yang, Xiao-Yun Chen, Xiao-Li Xu, Wei Wei, Jun-Feng Xu, Xiao-Fu Wang

{"title":"Onsite rapid detection method for genetically modified maize and soybean based on recombinase polymerase amplification.","authors":"Jia-Tong Yan, Guan-Wei Chen, Qing-Mei Miao, Cheng Peng, Lei Yang, Xiao-Yun Chen, Xiao-Li Xu, Wei Wei, Jun-Feng Xu, Xiao-Fu Wang","doi":"10.16288/j.yczz.24-322","DOIUrl":"https://doi.org/10.16288/j.yczz.24-322","url":null,"abstract":"With the commercial planting of transgenic maize and transgenic soybeans in China, in order to ensure the healthy development of China's biological breeding industry, it is urgent to develop on-site rapid detection techniques for transgenic maize and soybeans. In this study, a rapid detection method based on recombinase polymerase amplification (RPA) was proposed to overcome the shortcomings of on-site rapid detection of transgenic maize and soybean. Representative transgenic maize (Shuang Kang 12-5, DBN9936, MON810) and soybean (DBN9004, GTS40-3-2, SHZD32-1) were selected as test objects. According to their flanking sequence, specific primers and probes were designed and screened, and a RPA amplification system with high specificity and sensitivity of 20 copies for each transgenic event was established. In order to quickly obtain DNA, seed samples use nucleic acid release agents to obtain templates that can be used for RPA amplification. In order to eliminate the interference of chlorophyll in leaves on RPA fluorescence signal and quickly obtain DNA, leaf samples use the nucleic acid rapid integrated extraction device developed by our laboratory to quickly obtain DNA and eliminate the chlorophyll interference. Combined with a portable metal bath for initiating RPA amplification, a blue light gel cutter for visual detection, and a rapid on-site detection method for transgenic maize and soybean was constructed. The entire detection process required approximately 20 minutes, and the detection result was consistent with the result of conventional PCR. It is suitable for on-site rapid detection without large equipment, and has strong practicability and adaptability. The proposed approach provides technical support for on-site detection of transgenic crops and offers a reference for the application of other rapid nucleic acid detection technologies.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 6","pages":"694-707"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318179","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}

引用次数: 0

Analysis of regulatory mechanisms of enhancers in gastric cancer with double minute chromosomes based on bioinformatics. 基于生物信息学的双微小染色体胃癌增强子调控机制分析。

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-291

Meng-Ting An, Guan-Lin Guo, Jie Wu, Wen-Jing Sun, Xue-Yuan Jia

{"title":"Analysis of regulatory mechanisms of enhancers in gastric cancer with double minute chromosomes based on bioinformatics.","authors":"Meng-Ting An, Guan-Lin Guo, Jie Wu, Wen-Jing Sun, Xue-Yuan Jia","doi":"10.16288/j.yczz.24-291","DOIUrl":"https://doi.org/10.16288/j.yczz.24-291","url":null,"abstract":"Gastric cancer (GC) has a high incidence and mortality rate globally. Double minutes (DMs) are extrachromosomal circular chromosomes that carry amplified oncogenes or drug resistance genes, and they are closely associated with tumorigenesis and drug resistance. To investigate the role and regulatory mechanisms of double minutes in the malignant progression of gastric cancer, we utilize bioinformatics methods to analyze genomic copy number variation data from the CCLE cell line database and TCGA solid tumor database. We analyze and summarize the genomic features of tumor samples with double minutes. Based on these features, we classify gastric cancer samples. We use the FANTOM5 database, R package \"GenomicRanges\", Bedtools, and MEME SUITE to analyze the functions of the enhancers on double minutes and their regulated target genes in gastric cancer. Next, we apply the CIBERSORT package and the GDSC drug database to analyze immune cell infiltration and drug resistance in gastric cancer samples with and without double minutes from TCGA. The results show that the genome with a copy number greater than 10 and genomic fragments longer than 50 kb play a significant role. The regulatory role of double minutes enhancers affects drug resistance and tumor immunity, with disruptions in the enhancer-transcription factor-target gene regulatory loops also linked to tumor immunity. Furthermore, the target genes regulated by double minutes enhancers not only alter the expression of immune-related genes but also contribute to increased drug resistance to common chemotherapy agents in gastric cancer samples. High expression of drug resistance-related target genes in gastric cancer samples with double minutes is closely associated with poor prognosis. This study provides new insights for the treatment of gastric cancer patients with double minutes.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 5","pages":"558-572"},"PeriodicalIF":0.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013911","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}

引用次数: 0

Research advances in rice blast resistance genes. 水稻抗稻瘟病基因研究进展。

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-358

Zhan-Chun Wang, Gui-Tao Zhong, Bei-Bei Zhang, Yi-Lin Xie, Ding-Zhong Tang, Wei Wang

引用次数: 0

Screening and application of unstable genetically resistant strains in fission yeast. 裂变酵母不稳定遗传抗性菌株的筛选与应用。

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-266

Lu-Feng Dan, Yi-Wen Chu, Xin-Rong Wang, Xiang-Wei He

{"title":"Screening and application of unstable genetically resistant strains in fission yeast.","authors":"Lu-Feng Dan, Yi-Wen Chu, Xin-Rong Wang, Xiang-Wei He","doi":"10.16288/j.yczz.24-266","DOIUrl":"https://doi.org/10.16288/j.yczz.24-266","url":null,"abstract":"Reversible alterations at DNA sequence or epigenetic levels can result in phenotypes that are unstably inherited. The reversibility of these inheritable changes might be uniquely beneficial for adaption to possible fluctuations in environment. However, unstable changes are always ignored for the genetic instability in traditional studies, especially in the cause of drug resistance. In this study, we conduct a specific genetic screen in fission yeast using rapamycin (+caffeine) and obtain 173 resistant isolates. In contrast to the common strategy of isolating stable genetic mutants, we passage the cell culture with rapamycin resistance on drug free condition and test the resistance of offspring every five days, and obtain 14 strains that exhibit unstable resistance to rapamycin (the drug resistance is lost randomly among the cell progenies without drug selection pressure). Further studies show that the unstable genetic resistance of some strains is regulated by reversible DNA sequence alterationat the ssp1 gene locus. This study provides new insights and relevant scientific basis for the regulatory mechanism of unstable drug resistance in the process of rapamycin as a clinical anti-tumor drug, and a new possible target for solving the problem of drug resistance.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 5","pages":"589-599"},"PeriodicalIF":0.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044190","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}

引用次数: 0

The role and mechanism of UFMylation, a ubiquitin-like modification, in Mycobacterium tuberculosis infection immunity. 泛素样修饰ufmyation在结核分枝杆菌感染免疫中的作用及机制

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-259

Yi-Ran Liao, Qi-Ao Zhang, Pei-Bo Li, Jian-Ping Xie

引用次数: 0

Ancient genomes revealed the genetic history and interaction of prehistoric populations in the Ngari region of the western Tibetan Plateau. 古基因组揭示了青藏高原西部阿里地区史前种群的遗传历史和相互作用。

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-368

Fan Bai, Wei He, Yu Gao, Wan-Jing Ping, Qiao-Mei Fu

{"title":"Ancient genomes revealed the genetic history and interaction of prehistoric populations in the Ngari region of the western Tibetan Plateau.","authors":"Fan Bai, Wei He, Yu Gao, Wan-Jing Ping, Qiao-Mei Fu","doi":"10.16288/j.yczz.24-368","DOIUrl":"https://doi.org/10.16288/j.yczz.24-368","url":null,"abstract":"The Ngari Prefecture is located in the western part of the Tibetan Plateau. Despite its high altitude and harsh natural environment, it occupies a strategic position adjacent to northern Nepal, India, and Ladakh. As a crossroads connecting the Tibetan Plateau, Xinjiang Autonomous Region, Central Asia, and South Asia, it likely played an important role in early human migration. Archaeological studies in recent years have revealed that even before the establishment of the Tubo Dynasty in the seventh century, the Ngari region maintained extensive cultural connections with Kashmir, Nepal, Xinjiang, and other regions. Furthermore, its subsistence economy reflected strong interactions between Ngari and northern South Asia. Recent paleogenetic studies have demonstrated that the genetic components of the ancient population in the Ngari region originated from the southern part of the plateau, with multiple population expansions occurring from south to west. These studies have also confirmed that alongside cultural exchanges, the Ngari region began experiencing complex genetic interactions with ancient populations from neighboring Central and South Asia at least 2,300 years ago. In this review, we integrate findings from paleogenetics, archaeology, archaeobotany, and zooarchaeology in the Ngari region to systematically examine the genetic origins of the ancient western plateau population and analyze both intraregional cultural-genetic interactions within the Tibetan Plateau and those between Ngari populations and external groups. This synthesis provides important insights for understanding the complex relationships between ancient population movements and interactions in the western Tibetan Plateau, as well as the transformation patterns of regional archaeological cultures and subsistence economies.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 5","pages":"501-512"},"PeriodicalIF":0.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144048131","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}

引用次数: 0

Design and exploration of integrating bioinformatic analysis into comprehensive and exploratory epigenetic experiments. 设计和探索将生物信息学分析整合到综合性和探索性表观遗传学实验中。

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-217

Sai-Nan An, Huan-Chun Yang, Shan Jiang, Jing-Xuan Li, Gen-Fa Zhang

{"title":"Design and exploration of integrating bioinformatic analysis into comprehensive and exploratory epigenetic experiments.","authors":"Sai-Nan An, Huan-Chun Yang, Shan Jiang, Jing-Xuan Li, Gen-Fa Zhang","doi":"10.16288/j.yczz.24-217","DOIUrl":"https://doi.org/10.16288/j.yczz.24-217","url":null,"abstract":"As the most thoroughly studied epigenetic modification, DNA methylation-induced silencing of suppressor genes is closely related with the development of cancers. Bioinformatic analysis is an important research tool in the fields of life sciences, medicine, and so on. To introduce the application of bioinformatic analysis in cancer epigenetic research to students and to change the current situation that students usually passively perform experiments during the experimental teaching of genetics, we established a comprehensive and exploratory epigenetic experiment which was integrated with bioinformatic analysis. The implement of this experiment followed the principles of centering on students and cultivating scientific research capabilities. Students selected the genes that were potentially silenced by high DNA methylation in lung adenocarcinoma through bioinformatic analysis and literature review under the guidance of teachers and formulated experimental scheme by their own. They then conducted real-time PCR and methylation-specific PCR to explore whether DNA methylation caused the expression silencing of genes of interest and to identify the DNA methyltransferase responsible for the methylation of genes of interest. To comprehensively assess the capability of students, we designed diversified evaluation methods which intensify the assessment of experiment process. This experiment has the characteristics of interdisciplinarity, comprehensiveness, and inquiry, which can help to cultivate the scientific thinking and practical ability of students.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 5","pages":"600-608"},"PeriodicalIF":0.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053065","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}

引用次数: 0

Role of different Lyl1 transcripts in zebrafish primitive hematopoiesis. 不同Lyl1转录本在斑马鱼原始造血中的作用。

遗传 Pub Date : 2025-05-01 DOI: 10.16288/j.yczz.24-288

Jie-Hao Lin, Tong-Shu Yang, Wen-Qing Zhang, Wei Liu

{"title":"Role of different Lyl1 transcripts in zebrafish primitive hematopoiesis.","authors":"Jie-Hao Lin, Tong-Shu Yang, Wen-Qing Zhang, Wei Liu","doi":"10.16288/j.yczz.24-288","DOIUrl":"https://doi.org/10.16288/j.yczz.24-288","url":null,"abstract":"Primitive hematopoiesis is a crucial process in the organism, responsible for the transportation of oxygen and nutrients during early embryonic stages and laying the foundation for the immune system. During primitive hematopoiesis, hematopoietic-related transcription factors and their cofactors interact to form a complex regulatory network that controls the process of primitive hematopoiesis. Among the bHLH transcription factor family, SCL and LYL1 are key factors in embryonic hematopoiesis. SCL is responsible for initiating primitive hematopoiesis, while LYL1, a paralog of SCL, compensates for the hematopoietic impact of SCL deficiency in adulthood. However, the role of LYL1 in primitive hematopoiesis remains unclear. This study, through analysis of zebrafish blood cell scRNA-seq data, discovered high expression of CABZ01066694.1 in hematopoietic stem/progenitor cells. Sequence alignment revealed it as a short transcript of the lyl1 gene. Subsequently, using 5'RACE and sequencing, the study confirmed the existence of both long (lyl1f) and short (lyl1s) transcripts of lyl1 in zebrafish and humans, similar to mice. Further analysis of scRNA-seq and RNA-seq data from public databases showed that in zebrafish primitive hematopoietic cells, lyl1 primarily transcribes lyl1s. Finally, using Morpholino technology to knock down lyl1f and lyl1s separately, it was found that knocking down lyl1s hindered the production of primitive myeloid progenitors and primitive granulocytes, whereas knocking down lyl1f promoted the production of primitive macrophages. In conclusion, this study demonstrates the existence of long and short transcripts of lyl1 in zebrafish and humans, with distinct roles in regulating primitive myelopoiesis, providing new insights into the regulation of primitive hematopoiesis.","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 5","pages":"573-588"},"PeriodicalIF":0.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030771","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}

引用次数: 0

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