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Forensic Characterization, Genomic Variability and Ancestry Analysis of Six Populations from Odisha Using mtDNA SNPs and Autosomal STRs. 利用 mtDNA SNPs 和常染色体 STRs 对奥迪沙邦的六个人群进行法医特征描述、基因组变异性和祖先分析。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-07-22 DOI: 10.1007/s10528-024-10887-2
Jaison Jeevan Sequeira, Muktikanta Panda, Shivani Dixit, Ramkishan Kumawat, Mohammed S Mustak, Awdhesh Narayan Sharma, Gyaneshwer Chaubey, Pankaj Shrivastava
{"title":"Forensic Characterization, Genomic Variability and Ancestry Analysis of Six Populations from Odisha Using mtDNA SNPs and Autosomal STRs.","authors":"Jaison Jeevan Sequeira, Muktikanta Panda, Shivani Dixit, Ramkishan Kumawat, Mohammed S Mustak, Awdhesh Narayan Sharma, Gyaneshwer Chaubey, Pankaj Shrivastava","doi":"10.1007/s10528-024-10887-2","DOIUrl":"10.1007/s10528-024-10887-2","url":null,"abstract":"<p><p>Located on India's eastern coast, Odisha is known for its diverse tribes and castes. In the early days of genome sequencing technology, researchers primarily studied the Austroasiatic communities inhabiting this region to reconstruct the ancient origins and dispersal of this broad linguistic group. However, current research has shifted towards identifying population and individual-specific genome variation for forensic applications. This study aims to analyze the forensic efficiency and ancestry of six populations from Odisha. We assessed the SF mtDNA-SNP60™ PCR Amplification Kit by comparing it with PowerPlex® Fusion 6C System, a widely used autosomal STR (aSTR) kit, in an Indian cohort. Although the mtDNA SNP kit showed low discriminating power for individuals of a diverse population, it could identify deep lineage divergence. Also, we utilized mitochondrial and autosomal variation information to analyze the ancestry of six endogamous ethnic groups in Odisha. We observe two extremities-populations with higher West Asian affinity and those with East Asian affinity. This observation is in congruence with the existing information of their tribal and non-tribal affiliation. When compared with neighbouring populations from Central and Eastern India, multivariate analysis showed that the Brahmins clustered separately or with the Gopala, Kaibarta appeared as an intermediate, Pana and Kandha clustered with the Gonds, and Savara with the Munda tribes. Our findings indicate significant deep lineage stratification in the ethnic populations of Odisha and a gene flow from West and East Asia. The artefacts of unique deep lineage in such a diverse population will help in improving forensic identification. In addition, we conclude that the SF mtDNA-SNP60 PCR Amplification Kit may be used only as a supplementary tool for forensic analysis.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3497-3516"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Circ_0000758 Facilitates Bladder Cancer Cell Growth, Migration and Angiogenesis Via Severing as miR-1236-3p Sponge. Circ_0000758 作为 miR-1236-3p 海绵可促进膀胱癌细胞的生长、迁移和血管生成。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-06-13 DOI: 10.1007/s10528-024-10855-w
Qiang Chi, Zhiyong Wang, Hui Xu, Hongyang Li, Dianbin Song
{"title":"Circ_0000758 Facilitates Bladder Cancer Cell Growth, Migration and Angiogenesis Via Severing as miR-1236-3p Sponge.","authors":"Qiang Chi, Zhiyong Wang, Hui Xu, Hongyang Li, Dianbin Song","doi":"10.1007/s10528-024-10855-w","DOIUrl":"10.1007/s10528-024-10855-w","url":null,"abstract":"<p><p>Circular RNA (circRNA) has been reported to regulate the development of bladder cancer (BCa). However, the role of circ_0000758 in BCa progression is unknown. Circ_0000758 and miR-1236-3p expression, as well as ZEB2 mRNA expression were determined by qRT-PCR. BCa cell biological functions were determined by MTT assay, EdU assay, flow cytometry, wound healing assay and tube formation assay. Protein expression was detected by western blot analysis. RNA pull-down assay and dual-luciferase reporter assay were used to confirm RNA interaction. Xenograft mice models were constructed to assess the effect of circ_0000758 on BCa tumor growth. Circ_0000758 had increased expression in BCa tissues and cells. Circ_0000758 silencing could inhibit BCa cell growth, migration, angiogenesis in vitro, and tumor growth in vivo. Circ_0000758 served as a molecular sponge for miR-1236-3p, and miR-1236-3p inhibitor reversed circ_0000758 knockdown-mediated the inhibition effect on BCa cell progression. ZEB2 was targeted by miR-1236-3p, and its overexpression also revoked the suppressive effect of miR-1236-3p on BCa cell growth, migration, and angiogenesis. Besides, circ_0000758 knockdown also restrained BCa tumor growth. Circ_0000758 might promote BCa cell growth, migration, and angiogenesis by regulating the miR-1236-3p/ZEB2 axis.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3031-3046"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141309367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India. 首次揭示印度不同农业气候条件下山羊感染 Bovicola caprae 的系统发育多样性。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-07-13 DOI: 10.1007/s10528-024-10886-3
Aman D Moudgil, Anil K Nehra, Ankur Sharma, Santosh Patel, Sukhdeep Vohra
{"title":"First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India.","authors":"Aman D Moudgil, Anil K Nehra, Ankur Sharma, Santosh Patel, Sukhdeep Vohra","doi":"10.1007/s10528-024-10886-3","DOIUrl":"10.1007/s10528-024-10886-3","url":null,"abstract":"<p><p>Bovicola caprae is an important obligate ectoparasite of goats worldwide including India. The present study aimed at the molecular confirmation, phylogenetics and population structure analyses of B. caprae infesting goats of three different agro-climatic locations in India, by targeting the mitochondrial cytochrome C oxidase subunit 1 (cox1) genetic marker. The phylogenetic tree exhibited the presence of two different lineages of B. caprae. The sequences generated herein clustered in lineage 2 along with the GenBank™ archived sequences from China and Iran. The sequences generated herein also showed the circulation of sub-lineages of B. caprae in India based on the analysis of pairwise genetic distances between sequences and median-joining haplotype network. The population structure analyses revealed low nucleotide (0.00353 ± 0.00291 and 0.02694 ± 0.00363) and high haplotype (0.667 ± 0.314 and 0.618 ± 0.104) diversities for the present study isolates as well as for the complete dataset, respectively, which evinced a recent demographic expansion. High genetic differentiation (F<sub>ST</sub> value = 0.97826) and low gene flow (N<sub>m</sub> = 0.00556) were also recorded in the different lineages/populations. In conclusion, the present study addressed the research gap and provided the first insight into the phylogenetics of the goat louse B. caprae and highlighted the circulation of sub-lineages of the ectoparasite in India.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3465-3478"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bioinformatic Analysis Reveals the Association of Human N-Terminal Acetyltransferase Complexes with Distinct Transcriptional and Post-Transcriptional Processes. 生物信息学分析揭示了人类 N 端乙酰转移酶复合物与不同转录过程和转录后过程的关联。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-06-12 DOI: 10.1007/s10528-024-10860-z
C Koufaris, C Demetriadou, V Nicolaidou, A Kirmizis
{"title":"Bioinformatic Analysis Reveals the Association of Human N-Terminal Acetyltransferase Complexes with Distinct Transcriptional and Post-Transcriptional Processes.","authors":"C Koufaris, C Demetriadou, V Nicolaidou, A Kirmizis","doi":"10.1007/s10528-024-10860-z","DOIUrl":"10.1007/s10528-024-10860-z","url":null,"abstract":"<p><p>N-terminal acetyltransferases (NAT) are the protein complexes that deposit the abundant N-terminal acetylation (Nt-Ac) on eukaryotic proteins, with seven human complexes currently identified. Despite the increasing recognition of their biological and clinical importance, NAT regulation remains elusive. In this study, we performed a bioinformatic investigation to identify transcriptional and post-transcriptional processes that could be involved in the regulation of human NAT complexes. First, co-expression analysis of independent transcriptomic datasets revealed divergent pathway associations for human NAT, which are potentially connected to their distinct cellular functions. One interesting connection uncovered was the coordinated regulation of the NatA and proteasomal genes in cancer and immune cells, confirmed by analysis of multiple datasets and in isolated primary T cells. Another distinctive association was of NAA40 (NatD) with DNA replication, in cancer and non-cancer settings. The link between NAA40 transcription and DNA replication is potentially mediated through E2F1, which we have experimentally shown to bind the promoter of this NAT. Second, the coupled examination of transcriptomic and proteomic datasets revealed a much greater intra-complex concordance of NAT subunits at the protein compared to the transcript level, indicating the predominance of post-transcriptional processes for achieving their coordination. In agreement with this concept, we also found that the effects of somatic copy number alterations affecting NAT genes are attenuated post-transcriptionally. In conclusion, this study provides novel insights into the regulation of human NAT complexes.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"2987-3008"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Small but Mighty: Genetic Diversity of the Thai Ridgeback Dog Population. 小而强大:泰国脊背犬种群的遗传多样性。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-06-12 DOI: 10.1007/s10528-024-10858-7
Chadaphon Thatukan, Chananya Patta, Worapong Singchat, Wattanawan Jaito, Nichakorn Kumnan, Piangjai Chalermwong, Thitipong Panthum, Wongsathit Wongloet, Pish Wattanadilokchatkun, Thanyapat Thong, Syed Farhan Ahmad, Narongrit Muangmai, Kyudong Han, Akihiko Koga, Prateep Duengkae, Ratthanin Patcharakulvorawat, Kornsorn Srikulnath
{"title":"Small but Mighty: Genetic Diversity of the Thai Ridgeback Dog Population.","authors":"Chadaphon Thatukan, Chananya Patta, Worapong Singchat, Wattanawan Jaito, Nichakorn Kumnan, Piangjai Chalermwong, Thitipong Panthum, Wongsathit Wongloet, Pish Wattanadilokchatkun, Thanyapat Thong, Syed Farhan Ahmad, Narongrit Muangmai, Kyudong Han, Akihiko Koga, Prateep Duengkae, Ratthanin Patcharakulvorawat, Kornsorn Srikulnath","doi":"10.1007/s10528-024-10858-7","DOIUrl":"10.1007/s10528-024-10858-7","url":null,"abstract":"<p><p>Originating in Thailand, the Thai Ridgeback dog is known for its unique fur ridge that grows in the opposite direction along its back. Selective breeding and a limited populations in Thailand have led to significant close inbreeding among related individuals. The current Thai Ridgeback population is assumed to have experienced a loss of genetic diversity and bottleneck events. Furthermore, studies on the genetic diversity and structure of Thai Ridgeback dogs are limited. Therefore, the aim of this study was to assess the genetic diversity in Thai Ridgeback dogs. Microsatellite genotyping and mitochondrial DNA D-loop sequences were used to assess genetic diversity in 105 Thai Ridgeback dogs from various farms throughout Thailand. Significant genetic diversity and minimal inbreeding were observed in the current Thai Ridgeback population. Signs of bottlenecks were not observed because the exchange of genetic material among Thai Ridgeback owners effectively preserved the genetic diversity. Moreover, the genetic parameters in this study supported owner-to-owner exchanges animals for mating programs. To sustain the genetic diversity of Thai Ridgeback dogs, the use of genetic parameters to manage genetic closeness while preserving breed characteristics is essential. These data are crucial for ensuring demographic stability, which is pivotal for long-term conservation and effective population management.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"2967-2986"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and Characterization of LBD Gene Family in Pseudoroegneria libanotica Reveals Functions of PseLBD1 and PseLBD12 in Response to Abiotic Stress. Pseudoroegneria libanotica LBD 基因家族的鉴定和特征描述揭示了 PseLBD1 和 PseLBD12 在应对非生物胁迫时的功能。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-06-08 DOI: 10.1007/s10528-024-10859-6
Xunzhe Yang, Xiang Li, Xia Wang, Chen Chen, Dandan Wu, Yiran Cheng, Yi Wang, Lina Sha, Houyang Kang, Songqing Liu, Xing Fan, Yinglong Chen, Yonghong Zhou, Haiqin Zhang
{"title":"Identification and Characterization of LBD Gene Family in Pseudoroegneria libanotica Reveals Functions of PseLBD1 and PseLBD12 in Response to Abiotic Stress.","authors":"Xunzhe Yang, Xiang Li, Xia Wang, Chen Chen, Dandan Wu, Yiran Cheng, Yi Wang, Lina Sha, Houyang Kang, Songqing Liu, Xing Fan, Yinglong Chen, Yonghong Zhou, Haiqin Zhang","doi":"10.1007/s10528-024-10859-6","DOIUrl":"10.1007/s10528-024-10859-6","url":null,"abstract":"<p><p>The lateral organ boundaries domain (LBD) plays a vital role as a transcriptional coactivator within plants, serving as an indispensable function in growth, development, and stress response. In a previous study, we found that the LBD genes of Pseudoroegneria libanotica (a maternal donor for three-quarter of perennial Triticeae species with good stress resistance, holds great significance in exploring its response mechanisms to abiotic stress for the Triticeae tribe) might be involved in responding to drought stress. Therefore, we further identified the LBD gene family in this study. A total of 29 PseLBDs were identified. Among them, 24 were categorized into subclass I, while 5 fell into subclass II. The identification of cis-acting elements reveals the extensive involvement of PseLBDs in various biological processes in P. libanotica. Collinearity analysis indicates that 86% of PseLBDs were single-copy genes and have undergone a single whole-genome duplication event. Transcriptomic differential expression analysis of PseLBDs under drought stress reveals that the most likely candidates for responding to abiotic stress were PseLBD1 and PseLBD12. They have been demonstrated to respond to drought, salt, heavy metal, and heat stress in yeast. Furthermore, it is plausible that functional divergence might have occurred among their orthologous genes in wheat. This study not only establishes a foundation for a deeper understanding of the biological roles of PseLBDs in P. libanotica but also unveils novel potential genes for enhancing the genetic background of crops within Triticeae crops, such as wheat.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"2857-2878"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolome and Genome Analysis of a Novel Endophytic Fungus Aureobasidium pullulans KB3: Discovery of Polyketones and Polyketone Biosynthesis Pathway. 新型内生真菌 Aureobasidium pullulans KB3 的代谢组和基因组分析:发现多酮和多酮生物合成途径。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-06-15 DOI: 10.1007/s10528-024-10866-7
Shuai Wang, Jia-Nuo He, Ying-Jie Wang, Wen-Ya Zhao, Qing-Xia Yang, Ya-Na Wang, Yang Zhang, Li-Ping Zhang, Hong-Wei Liu
{"title":"Metabolome and Genome Analysis of a Novel Endophytic Fungus Aureobasidium pullulans KB3: Discovery of Polyketones and Polyketone Biosynthesis Pathway.","authors":"Shuai Wang, Jia-Nuo He, Ying-Jie Wang, Wen-Ya Zhao, Qing-Xia Yang, Ya-Na Wang, Yang Zhang, Li-Ping Zhang, Hong-Wei Liu","doi":"10.1007/s10528-024-10866-7","DOIUrl":"10.1007/s10528-024-10866-7","url":null,"abstract":"<p><p>Endophytic fungi associated with plants may contain undiscovered bioactive compounds. Under standard laboratory conditions, most undiscovered compounds are inactive, whereas their production could be stimulated under different cultivation conditions. In this study, six endophytic fungi were isolated from the bark of Koelreuteria paniculata in Quancheng Park, Jinan City, Shandong Province, one of which was identified as a new subspecies of Aureobasidium pullulans, named A. pullulans KB3. Additionally, metabolomic tools were used to screen suitable media for A. pullulans KB3 fermentation, and the results showed that peptone dextrose medium (PDM) was more beneficial to culture A. pullulans KB3 for isolation of novel compounds. Sphaerolone, a polyketone compound, was initially isolated from A. pullulans KB3 via scaled up fermentation utilizing PDM. Additionally, the whole-genome DNA of A. pullulans KB3 was sequenced to facilitate compound isolation and identify the biosynthesis gene clusters (BGCs). This study reports the multi-omics (metabolome and genome) analysis of A. pullulans KB3, laying the foundation for discovering novel compounds of silent BGCs and identifying their biosynthesis pathway.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3047-3064"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141320375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MicroRNA-204-5p Attenuates Oxidative Stress, Apoptosis and Inflammation by Targeting TXNIP in Diabetic Cataract. MicroRNA-204-5p通过靶向TXNIP减轻糖尿病性白内障患者的氧化应激、细胞凋亡和炎症反应
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-06-19 DOI: 10.1007/s10528-024-10863-w
Xiang Cao, Zhixin Jiang, Xiaofei Bu, Qingyu Li, Ye Tian, Zijiao Xu, Boyang Zhang, Xiaoyong Yuan
{"title":"MicroRNA-204-5p Attenuates Oxidative Stress, Apoptosis and Inflammation by Targeting TXNIP in Diabetic Cataract.","authors":"Xiang Cao, Zhixin Jiang, Xiaofei Bu, Qingyu Li, Ye Tian, Zijiao Xu, Boyang Zhang, Xiaoyong Yuan","doi":"10.1007/s10528-024-10863-w","DOIUrl":"10.1007/s10528-024-10863-w","url":null,"abstract":"<p><p>Diabetic cataract (DC) is a major cause of blindness in diabetic patients and it is characterized by early onset and rapid progression. MiR-204-5p was previously identified as one of the top five down-regulated miRNAs in human DC lens tissues. We aimed to determine the expression of miR-204-5p in human lens epithelial cells (HLECs) and explore its effects and mechanisms in regulating the progression of DC. The expression of miR-204-5p in the anterior capsules of DC patients and HLECs was examined by RT-qPCR. Bioinformatics tools were then used to identify the potential target of miR-204-5p. The relationship between miR-204-5p and the target gene was confirmed through a dual luciferase reporter assay. Additionally, the regulatory mechanism of oxidative stress, apoptosis, and inflammation in DC was investigated by overexpressing miR-204-5p using miR-204-5p agomir. The expression of miR-204-5p was downregulated in the anterior capsules of DC patients and HLECs. Overexpression of miR-204-5p reduced ROS levels, pro-apoptosis genes (Bid, Bax, caspase-3), and IL-1β production in HG-treated HLECs. TXNIP was the direct target of miR-204-5p by dual luciferase reporter assay. Therefore, this study demonstrated that miR-204-5p effectively reduced oxidative damage, apoptosis, and inflammation in HLECs under HG conditions by targeting TXNIP. Targeting miR-204-5p could be a promising therapeutic strategy for the potential treatment of DC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3139-3156"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides. 球茎纤毛虫质体的重复序列、密码子使用偏差和系统发育分析
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-07-02 DOI: 10.1007/s10528-024-10874-7
Yangying Gan, Jingyao Ping, Xiaojing Liu, Caixia Peng
{"title":"Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides.","authors":"Yangying Gan, Jingyao Ping, Xiaojing Liu, Caixia Peng","doi":"10.1007/s10528-024-10874-7","DOIUrl":"10.1007/s10528-024-10874-7","url":null,"abstract":"<p><p>Annonaceae is the largest family in Magnoliales, exhibiting the greatest diversity among and within genera. In this study, we conducted an analysis of repetitive sequences and codon usage bias in the previously acquired plastome of Miliusa glochidioides. Using a concatenated dataset of shared genes, we constructed the phylogenetic relationships among 27 Annonaceae species. The results showed that the size of the plastomes in the Annonaceae ranged from 159 to 202 kb, with the size of the inverted repeat region ranging from 40 to 65 kb. Within the plastome of M. glochidioides, we identified 42 SSRs, 36 tandem repeats, and 9 dispersed repeats. These SSRs consist of three nucleotide types and eight motif types, with a preference for A/T bases, primarily located in the large single-copy regions and intergenic spacers. Tandem and dispersed repeat sequences were predominantly detected in the IR region. Through codon usage bias analysis, we identified 30 high-frequency codons and 11 optimal codons. The plastome of M. glochidioides demonstrated relatively weak codon usage bias, favoring codons with A/T endings, primarily influenced by natural selection. Phylogenetic analysis revealed that all four subfamilies formed monophyletic groups, with Cananga odorata (Ambavioideae) and Anaxagorea javanica (Anaxagoreoideae) successively nested outside Annonoideae + Malmeoideae. These findings improve our understanding of the plastome of M. glochidioides and provide additional insights for studying plastome evolution in Annonaceae.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3329-3346"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exosomal miR-17-92 Cluster from BMSCs Alleviates Apoptosis and Inflammation in Spinal Cord Injury. 来自 BMSCs 的外泌体 miR-17-92 簇可缓解脊髓损伤中的细胞凋亡和炎症。
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-08-01 Epub Date: 2024-07-03 DOI: 10.1007/s10528-024-10876-5
Wei Wang, Fei Yao, Haiyuan Xing, Fan Yang, Li Yan
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