Gene Reports最新文献_第7页

Association of the RNASE9 c.1+1G>A splice site variant with decreased sperm motility in Japanese men RNASE9 c.1+1G>A剪接位点变异与日本男性精子活力下降的关系

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-28 DOI: 10.1016/j.genrep.2025.102366

Shinichiro Saeki , Junko Otsuki , Noritoshi Enatsu , Xingqiang Wei , Naoto Mukaida , Ryota Okamoto , Saori Yoshimura , Keisuke Okada , Koji Chiba , Shoji Kokeguchi , Toshiroh Iwasaki , Yasuhiro Fujiwara , Mikiya Nakatsuka , Tetsuo Kunieda , Masahide Shiotani

This study aims to investigate the role of the RNASE9 gene mutation (c.1 + 1G > A) in male infertility, specifically focusing on its impact on sperm motility in patients with asthenozoospermia. Despite known genetic causes for azoospermia, the genetic basis of asthenozoospermia remains poorly understood. Given that RNASE9 is specifically expressed in the epididymis, where sperm maturation occurs, we hypothesized that mutations in RNASE9 might influence post-testicular sperm maturation. Whole-exome sequencing (WES) was performed on 20 Japanese patients with abnormal semen parameters to identify high-impact genetic variants. Variants were filtered based on allele frequencies in the 1000 Genomes Phase 3 East Asian (EAS) population and the Japanese 38KJPN database. RNASE9 was selected for further analysis, and the presence of the c.1 + 1G > A variant was confirmed in a cohort of 71 patients via Sanger sequencing. Sperm motility and other semen parameters were evaluated, and allele frequencies in asthenozoospermic, azoospermic, and normospermic groups were compared. The allele frequency of the RNASE9 (c.1 + 1G > A) variant was significantly higher in asthenozoospermic patients than in individuals with normal semen parameters (p = 0.022), while no significant difference was found in azoospermic patients. This suggests that the RNASE9 variant primarily affects sperm motility rather than sperm production. The RNASE9 (c.1 + 1G > A) mutation may contribute to reduced sperm motility in humans, likely impacting post-testicular sperm maturation. The findings provide new insights into the genetic factors affecting sperm motility, particularly in asthenozoospermia.

本研究旨在探讨RNASE9基因突变（c.1 + 1G >； A）在男性不育中的作用，特别关注其对弱精子症患者精子活力的影响。尽管已知无精子症的遗传原因，但对无精子症的遗传基础仍然知之甚少。鉴于RNASE9在精子成熟发生的附睾中特异性表达，我们假设RNASE9的突变可能影响睾丸后精子成熟。对20例精液参数异常的日本患者进行了全外显子组测序（WES），以确定高影响遗传变异。根据1000个基因组3期东亚（EAS）人群和日本38KJPN数据库的等位基因频率筛选变异。选择RNASE9进行进一步分析，通过Sanger测序在71例患者中证实存在c.1 + 1G >； A变体。评估精子活力和其他精液参数，并比较弱精子组、无精子组和正常精子组的等位基因频率。RNASE9 （c.1 + 1G >； A）变异的等位基因频率在无精子症患者中显著高于精液参数正常的个体（p = 0.022），而在无精子症患者中无显著差异。这表明RNASE9变异主要影响精子活力而不是精子产量。RNASE9 （c.1 + 1G >； A）突变可能导致人类精子活力降低，可能影响睾丸后精子成熟。这一发现为研究影响精子活力的遗传因素提供了新的见解，特别是在弱精子症中。

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引用次数: 0

Detection of Epstein-Barr virus coinfections based on LMP-1 gene diversity obtained by the high-throughput sequencing 基于高通量测序获得的LMP-1基因多样性检测Epstein-Barr病毒共感染

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-27 DOI: 10.1016/j.genrep.2025.102369

Marija Rozman , Ana Planinić , Kristian Bodulić , Dijana Škorić , Paola Gršković , Anita Stojanović Marković , Petra Korać , Snježana Židovec-Lepej

Background

Epstein-Barr virus (EBV) exhibits significant molecular diversity, commonly classified into distinct variants based on specific polymorphisms in the latent membrane protein-1 (LMP-1) gene. Traditional analyses have largely relied on Sanger sequencing, which may be limited in detecting mixed variant populations and recombination events.

Objectives

This study aimed to evaluate whether high-throughput sequencing (HTS) using Oxford Nanopore Technology (ONT) provides a more comprehensive analysis of LMP-1 variants, particularly in samples previously identified as recombinants by Sanger sequencing.

Study design

Twenty-four peripheral blood samples from patients with EBV-associated infectious mononucleosis (IM), previously analysed by Sanger sequencing, were reevaluated using full-length LMP-1 sequencing via ONT.

Results

ONT sequencing enabled the reclassification of 11 samples initially identified as recombinants by Sanger sequencing as coinfections, based on the presence of dual polymorphisms at the same nucleotide positions. The remaining 12 samples showed concordant results with Sanger data, confirming their recombinant nature. Additionally, ONT identified an amino acid substitution at position 366 in 5/24 samples, leading to further reclassification of LMP-1 variants. In one case, ONT detected only a single LMP-1 variant (China1), contradicting earlier recombinant classification.

Conclusions

ONT-based HTS enables more detailed detection of LMP-1 recombinants and coinfections, offering a broader view of EBV molecular diversity compared to Sanger sequencing. This approach has potential implications for identifying high-risk EBV variants associated with malignancy and demonstrates feasibility for implementation in routine clinical virology. To our knowledge, this is the first study to apply ONT for comprehensive molecular analysis of EBV LMP-1 coinfections.

depstein - barr病毒（EBV）具有显著的分子多样性，通常根据潜伏膜蛋白-1 （LMP-1）基因的特定多态性分为不同的变体。传统的分析很大程度上依赖于桑格测序，这可能在检测混合变异群体和重组事件方面受到限制。本研究旨在评估使用牛津纳米孔技术（ONT）的高通量测序（HTS）是否能提供更全面的LMP-1变异分析，特别是在先前通过Sanger测序鉴定为重组的样品中。研究设计：先前通过Sanger测序分析的24例ebv相关传染性单核细胞增多症（IM）患者外周血样本，通过ONT使用全长LMP-1测序重新评估。结果基于在相同核苷酸位置存在双重多态性，ont测序使最初被Sanger测序鉴定为重组的11个样本重新分类为共感染。其余12个样品的结果与Sanger数据一致，证实了它们的重组性质。此外，ONT在5/24的样本中发现了366位的氨基酸替换，从而进一步对LMP-1变异进行了重新分类。在一个病例中，ONT仅检测到单个LMP-1变体（China1），这与早期的重组分类相矛盾。结论与Sanger测序相比，基于sont的HTS可以更详细地检测LMP-1重组和共感染，为EBV分子多样性提供了更广阔的视角。这种方法对识别与恶性肿瘤相关的高危EBV变异具有潜在的意义，并证明了在常规临床病毒学中实施的可行性。据我们所知，这是首次应用ONT对EBV LMP-1合并感染进行综合分子分析的研究。

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引用次数: 0

Genetic polymorphisms associated with Behçet's disease in Egypt, Tunisia, and Morocco: A systematic review 埃及、突尼斯和摩洛哥与behaperet病相关的遗传多态性：一项系统综述

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-27 DOI: 10.1016/j.genrep.2025.102368

Kahli Zineb , Ait Baha Atmane , Habbane Mouna , Hassani Idrissi Hind , El Bassyouni Najlâa , Moudatir Mina , Semlali Mohammed Youssef , Akhouayri Omar

This systematic review examines the genetic polymorphisms associated with Behcet disease in Africa, focusing on SNPs and HLA class I and II gene variants. A structured search was conducted in the PubMed, Scopus, Web of Science, and ScienceDirect databases, according to rigorous inclusion and exclusion criteria. The analysis shows that Egypt is the most active country in terms of publications, followed by Tunisia and Morocco. Certain genes were analyzed collectively in all three countries. The CTLA-4 + 49 A variant was more at risk in Tunisia (OR = 4.63) and Egypt (OR = 3.08), showing a high association with disease susceptibility. Other variants, such as VDR-ApaI-a (OR = 2.09 in Egypt) and VDR-FokI-F (OR = 1.89 in Tunisia), have moderate associations. Inflammation-related polymorphisms, as TNF-α 1031C (OR = 1.65 in Tunisia) and TNF-α 1211C (OR = 1.68 in Morocco), also presented significant associations, though less strong. These results demonstrate the existence of regional variations in genetic susceptibility to Behcet and the importance of population-specific studies. This is the first such review on the African continent and paves the way for further studies into the region's genetic determinants of the disease.

本系统综述研究了与非洲白塞病相关的遗传多态性，重点关注snp和HLA I类和II类基因变异。根据严格的纳入和排除标准，在PubMed、Scopus、Web of Science和ScienceDirect数据库中进行结构化搜索。分析显示，就出版物而言，埃及是最活跃的国家，其次是突尼斯和摩洛哥。对这三个国家的某些基因进行了集体分析。CTLA-4 + 49a变异在突尼斯（OR = 4.63）和埃及（OR = 3.08）的风险更高，显示与疾病易感性高度相关。其他变异，如VDR-ApaI-a（在埃及OR = 2.09）和VDR-FokI-F（在突尼斯OR = 1.89）具有中等相关性。炎症相关的多态性，如TNF-α 1031C（突尼斯的OR = 1.65）和TNF-α 1211C（摩洛哥的OR = 1.68）也表现出显著的相关性，尽管不那么强。这些结果表明白塞病的遗传易感性存在区域差异，以及进行人群特异性研究的重要性。这是在非洲大陆进行的首次此类审查，并为进一步研究该地区该病的遗传决定因素铺平了道路。

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引用次数: 0

Molecular and in silico analysis of pamidronate disodium interaction with type IV osteogenesis imperfecta caused by the ultra-rare COL1A1 Variant rs72656337 (c.3664G>T; p.Ala1222Ser) 帕米膦酸二钠与超罕见COL1A1变异rs72656337 （c.3664G>T; p.Ala1222Ser）所致IV型成骨不全相互作用的分子和计算机分析

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-27 DOI: 10.1016/j.genrep.2025.102367

Maryam Dhary Kamel

Type IV osteogenesis imperfecta (OI) is classically associated with heterozygous variants in COL1A1, the gene encoding the α1-chain of type I collagen. Here we explore whether an ultra-rare missense change located in the collagen C-terminal pro-peptide—rs72656337 (NM_000088.4:c.3664G > T; p.Ala1222Ser, equivalent to p.Ala26Ser within exon 48)—could influence the molecular interaction between collagen and pamidronate disodium, a nitrogen-containing bisphosphonate routinely administered to children with type IV OI. All COL1A1 coding single-nucleotide variants were mined from dbSNP-156, filtered for C-terminal location and rarity (allele frequency < 4 × 10⁻⁶ in gnomAD v4), yielding rs72656337 as the sole candidate for structural analysis. Using an in silico approach, examined the structural impact of the rs72656337 variant on the Collagen alpha-1(I) chain, focusing on how it affects protein conformation. Molecular docking in MOE placed pamidronate in a mixed acidic–basic pocket of the C-terminal region with a top docking score of −8.07 kcal mol⁻¹, forming hydrogen bonds to Asp59 (chain C) and Arg28 (chain B). Although direct collagen–pamidronate binding has not been demonstrated experimentally, our in-silico findings provide a testable framework for future biochemical assays and genotype-stratified studies in OI. As a hypothesis-generating study, our work motivates experimental validation (e.g., SPR/ITC with recombinant pro-peptides, hydroxyapatite-coated binding assays) and genotype-stratified clinical analyses to test whether C-terminal COL1A1 variants modify bisphosphonate efficacy in OI.

IV型成骨不全症（OI）通常与COL1A1的杂合变异有关，COL1A1是编码I型胶原α1链的基因。本研究探讨了位于胶原蛋白c端前肽rs72656337 （NM_000088.4:c）中的一种超罕见的错义变化。3664G >； T；p.a ala1222ser（相当于外显子48内的p.a ala26ser）可能影响胶原蛋白与帕米膦酸二钠（一种常规用于IV型OI患儿的含氮双膦酸盐）之间的分子相互作用。从dbSNP-156中挖掘所有COL1A1编码单核苷酸变异，对c端位置和稀有性进行筛选（gnomAD v4中等位基因频率<； 4 × 10−6），得到rs72656337作为结构分析的唯一候选。使用计算机方法，研究了rs72656337变异对胶原α -1(I)链的结构影响，重点研究了它如何影响蛋白质构象。在MOE中的分子对接将帕米膦酸盐置于C端酸碱混合口袋中，最高对接分数为−8.07 kcal mol−1，与Asp59（链C）和Arg28（链B）形成氢键。虽然胶原-帕米膦酸盐的直接结合尚未在实验中得到证实，但我们的计算机研究结果为未来的成骨不全症生化分析和基因型分层研究提供了可测试的框架。作为一项假设生成研究，我们的工作激发了实验验证（例如，重组前肽的SPR/ITC，羟基磷灰石包覆结合试验）和基因型分层临床分析，以测试c端COL1A1变异是否会改变双膦酸盐治疗成骨不全症的疗效。

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引用次数: 0

Mitochondrial genome sequencing and phylogenetic analysis of the freshwater snail Fukuia kurodai ooyagii (Pomatiopsidae) 淡水蜗牛kukuia kurodai ooyagii线粒体基因组测序及系统发育分析

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-21 DOI: 10.1016/j.genrep.2025.102365

Yuuki Ebata , Akira Ooyagi , Kazuo Umetsu , Takashi Kitano

Fukuia kurodai ooyagii is a freshwater snail endemic to the Shimokita Peninsula, Japan, yet little is known about its mitochondrial genome or phylogenetic position. To address this, we sequenced the mitochondrial genomes of five individuals. The genomes ranged from 16,145 to 16,169 bp and included all 37 typical animal mitochondrial genes. Gene arrangement and nucleotide composition were consistent with other Truncatelloidea species. The control region featured long inverted repeats and AT-repeat regions. Phylogenetic analysis placed F. kurodai ooyagii within the Pomatiopsidae family, with moderate support for a closer relationship to Tricula hortensis than to Oncomelania species. These results provide the first complete mitochondrial genome sequences for this species, confirming its evolutionary stability within Pomatiopsidae. However, due to the lack of mitochondrial data for other Fukuia and Blanfordia species, its precise taxonomic status remains uncertain. This study offers a foundation for future comparative analyses and highlights the need for broader taxon sampling and additional genomic data to resolve phylogenetic relationships within this group.

Fukuia kurodai ooyagii是日本下田半岛特有的淡水蜗牛，但对其线粒体基因组或系统发育位置知之甚少。为了解决这个问题，我们对五个人的线粒体基因组进行了测序。基因组范围为16,145 ~ 16,169 bp，包含了所有37个典型动物线粒体基因。基因排列和核苷酸组成与其他龙葵科物种一致。对照区具有较长的反向重复区和at重复区。系统发育分析表明，F. kurodai ooyagii属于Pomatiopsidae科，与hortensis的亲缘关系比与钉螺的亲缘关系更近。这些结果为该物种提供了第一个完整的线粒体基因组序列，证实了其在Pomatiopsidae中的进化稳定性。然而，由于缺乏其他Fukuia和Blanfordia物种的线粒体数据，其精确的分类地位仍然不确定。该研究为未来的比较分析提供了基础，并强调需要更广泛的分类群采样和额外的基因组数据来解决该群体内的系统发育关系。

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引用次数: 0

MeX_Docker: An integrated application for transposon identification and annotation based on the Docker platform MeX_Docker：基于Docker平台的转座子识别和标注集成应用

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-20 DOI: 10.1016/j.genrep.2025.102364

P. Preeti , Mihir Nakul , Chhavi Dudeja , Abhishek Singh , Arushi Gupta , Yuktika Malhotra , Deepika Yadav , Kamal Rawal

Transposable elements (TEs) are mobile genetic elements that can disrupt genomic integrity, influencing gene regulation and contributing to various diseases, including cancer. The accurate identification and characterization of TEs in high-throughput sequencing data is essential for understanding their role in genomic instability and tumorigenesis. To streamline this process, we developed MeX_Docker, a pipeline that utilizes Docker containerization to overcome software dependency issues and ensure reproducibility across different computing environments. Docker provides a standardized, portable solution that allows researchers to deploy and run the pipeline seamlessly, eliminating common obstacles in bioinformatics workflows. MeX_Docker integrates widely-used tools such as FastQC, Fastp, SAMtools, TEfinder, and Ensembl Variant Effect Predictor (VEP) for efficient data preprocessing, alignment, TE calling, and annotation. The pipeline was applied to human paired end whole-genome sequencing cancer datasets (breast, lung, and colorectal cancers), successfully identifying reference and non-reference Alu and L1 elements. In a lung cancer sample, an in-frame insertion in the CATSPERD gene was detected, which was classified as benign polymorphism. These findings highlight the use of MeX_Docker as an efficient tool for studying the impact of transposable elements on genomic instability and their potential role in cancer biology.

转座因子（te）是一种可移动的遗传因子，可以破坏基因组完整性，影响基因调控并导致包括癌症在内的各种疾病。在高通量测序数据中准确识别和表征TEs对于了解它们在基因组不稳定性和肿瘤发生中的作用至关重要。为了简化这个过程，我们开发了MeX_Docker，这是一个利用Docker容器化来克服软件依赖问题并确保跨不同计算环境的可重复性的管道。Docker提供了一个标准化的、可移植的解决方案，允许研究人员无缝地部署和运行管道，消除了生物信息学工作流程中的常见障碍。MeX_Docker集成了广泛使用的工具，如FastQC， Fastp, SAMtools， TEfinder和Ensembl Variant Effect Predictor (VEP)，用于高效的数据预处理，对齐，TE调用和注释。该管道应用于人类配对末端全基因组测序癌症数据集（乳腺癌、肺癌和结直肠癌），成功鉴定了参考和非参考Alu和L1元件。在肺癌样本中，检测到CATSPERD基因框内插入，归类为良性多态性。这些发现突出了MeX_Docker作为研究转座因子对基因组不稳定性影响及其在癌症生物学中的潜在作用的有效工具的使用。

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引用次数: 0

Genome-wide identification, characterization, and expression analysis of the SKP1.1 family in Nicotiana benthamiana exposed to tailings dam wastewater 尾矿坝废水中本烟SKP1.1家族的全基因组鉴定、表征及表达分析

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-18 DOI: 10.1016/j.genrep.2025.102363

Junjie Wang , Xiaoqin Li , Xinghai Li , Yang Xu , Cuihua Xin , Jiangbo Guo

SKP1 (S-phase Kinase-associated Protein 1) functions as an adaptor protein connecting F-box proteins to Cullin1 in the SKP1-Cullin1-F-box (SCF) ubiquitin ligase complex, which performs essential functions in response to abiotic stresses. However, the specific roles of SKP1 in plant responses to tailings dam water stress remain unclear. This study identified 30 SKP1.1 family members in Nicotiana benthamiana through bioinformatics analysis. The expression patterns of NbSKP1.1 were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) when plants were subjected to tailings dam water stress. Results demonstrated that exposure to tailings dam water pollutants suppressed the expression of NbSKP1.1. Confocal imaging revealed that NbSKP1s (NbSKP1.1, NbSKP1.2, NbSKP1.3, and NbSKP1L1) exhibit dual localization in the nucleus and cytoplasm. This comprehensive analysis of the NbSKP1.1 family in plants establishes a foundation for future investigations into plant-environment interactions.

SKP1 （s期激酶相关蛋白1）在SKP1-Cullin1-F-box （SCF）泛素连接酶复合体中作为连接F-box蛋白和Cullin1的衔接蛋白，在应对非生物胁迫中发挥重要作用。然而，SKP1在植物对尾矿坝水分胁迫响应中的具体作用尚不清楚。本研究通过生物信息学分析，鉴定出30个本烟SKP1.1家族成员。采用实时荧光定量聚合酶链反应（qRT-PCR）技术评价了植物在尾矿坝水分胁迫下NbSKP1.1基因的表达谱。结果表明，暴露于尾矿坝水污染物可抑制NbSKP1.1的表达。共聚焦成像显示NbSKP1.1、NbSKP1.2、NbSKP1.3和NbSKP1L1在细胞核和细胞质中表现出双重定位。对植物中NbSKP1.1家族的全面分析为进一步研究植物与环境的相互作用奠定了基础。

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引用次数: 0

Detection of cas5 and virulence genes in Pseudomonas aeruginosa from cystic fibrosis, and burn wounds: Impact on biofilm and antibiotic resistance 囊性纤维化和烧伤创面铜绿假单胞菌cas5和毒力基因的检测：对生物膜和抗生素耐药性的影响

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-18 DOI: 10.1016/j.genrep.2025.102360

Yasir Adil Jabbar Alabdali

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and Cas (CRISPR associated proteins) are the acquired immune system in bacteria against foreign DNA pieces. Nevertheless, it is not known how prevalent cas5 (type I-C CRISPR-Cas) is and whether it has a clinical isolate phenotypic implication in Iraq. Pseudomonas aeruginosa is among the most harmful species of opportunistic pathogenic bacteria that lead to illness, particularly in patients with cystic fibrosis, burns, and wounds. Cas5 was found in 10 isolates (15.6 %) of P. aeruginosa in 64 clinical isolates of the bacteria, collected between January and April 2024 All of the total of ten cas5-positive isolates had the virulence genes plcH, plcN, lasB, toxA, exoS, and algD (100 %) present. Most notably, resistance to all the tested antibiotics was lower in cas5-positive isolates. These findings suggest the existence of the potential connection between cas5 carriage, antibiotic resistance and biofilm adherence.

Significance statement

The present study offers a clear understanding regarding the impact of the CRISPR-Cas5 system on the Pseudomonas aeruginosa resistance to antibiotics and presents new information that could be utilised to create an infection control strategy in patients with cystic fibrosis and burn injuries.

CRISPR （Clustered Regularly Interspaced Short Palindromic Repeats）和Cas （CRISPR相关蛋白）是细菌对抗外源DNA片段的获得性免疫系统。然而，目前尚不清楚cas5 （I-C型CRISPR-Cas）在伊拉克的流行程度，以及它是否具有临床分离表型意义。铜绿假单胞菌是导致疾病的最有害的机会致病菌之一，特别是在囊性纤维化、烧伤和伤口患者中。在2024年1 - 4月收集的64株铜绿假单胞菌临床分离株中，10株（15.6%）检出Cas5, 10株Cas5阳性分离株（100%）含有毒力基因plcH、plcN、lasB、toxA、exoS和algD。最值得注意的是，cas5阳性菌株对所有测试抗生素的耐药性较低。这些发现表明cas5携带、抗生素耐药性和生物膜粘附之间存在潜在的联系。本研究提供了关于CRISPR-Cas5系统对铜绿假单胞菌对抗生素耐药性影响的清晰认识，并提供了可用于创建囊性纤维化和烧伤患者感染控制策略的新信息。

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引用次数: 0

Evaluation of the antimicrobial activity of Arnebia euchroma extract and its influence on quorum sensing gene expression in Pseudomonas aeruginosa 紫草提取物抑菌活性评价及其对铜绿假单胞菌群体感应基因表达的影响

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-18 DOI: 10.1016/j.genrep.2025.102362

Leila Yadegari , Maryam Mohammadi-Sichani , Soodabeh Rostami

Background

Antibiotic resistance in Pseudomonas aeruginosa has become a significant public health concern, particularly in burn patients. This study aimed to evaluate the effect of Arnebia euchroma extract on the expression of the lasR and lasI genes, which are crucial for the pathogenicity of this bacterium.

Methods

Five P. aeruginosa strains were isolated from burn wounds, identified with selective media and differential tests. The methanolic extract of A. euchroma was prepared by maceration and tested for antimicrobial activity. Antibiotic susceptibility was assessed using the disc diffusion method. The presence of lasI and lasR genes in clinical strains was confirmed by PCR, and their expression levels were quantified by Real-Time PCR. Active compounds in the extract were identified using gas chromatography–mass spectrometry.

Results

The A. euchroma root extract exhibited significant antibacterial effects, forming clear inhibition zones on agar plates. Its minimum inhibitory concentration ranged from 62.5 to 250 μg/mL, while the minimum bactericidal concentration was between 125 and 250 μg/mL. All tested P. aeruginosa isolates were positive for the lasI and lasR genes, with gene expression significantly reduced in the presence of the extract. The extract inhibited over 75 % of lasI and lasR expression, comparable to tobramycin. Diacetone alcohol, alpha-terpinenyl acetate, and xanthosine were identified as the most abundant compounds in the root.

Conclusion

The findings suggest that A. euchroma extract has potential as an antimicrobial and quorum sensing inhibitor. However, further studies with larger strain collections and in vivo validation are needed to confirm its therapeutic relevance.

铜绿假单胞菌的抗生素耐药性已成为一个重要的公共卫生问题，特别是在烧伤患者中。本研究旨在评价紫草提取物对该细菌致病性关键基因lasR和lasI表达的影响。方法从烧伤创面分离5株铜绿假单胞菌，采用选择性培养基和鉴别试验进行鉴定。采用浸渍法制备了赤藓醇提物，并进行了抑菌活性试验。采用椎间盘扩散法评估抗生素敏感性。通过PCR证实临床菌株中存在lasI和lasR基因，Real-Time PCR检测其表达量。采用气相色谱-质谱联用技术对提取物中的活性成分进行鉴定。结果真彩根提取物具有明显的抑菌作用，在琼脂平板上形成明显的抑菌带。其最低抑菌浓度为62.5 ~ 250 μg/mL，最低杀菌浓度为125 ~ 250 μg/mL。所有测试的铜绿假单胞菌分离株lasI和lasR基因均呈阳性，在提取物存在下基因表达显著降低。该提取物抑制了超过75%的lasI和lasR表达，与妥布霉素相当。二丙酮醇、-萜烯乙酸酯和黄嘌呤是根中含量最多的化合物。结论赤原草提取物具有抗菌和群体感应抑制剂的作用。然而，进一步的研究需要更大的菌株收集和体内验证来证实其治疗相关性。

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引用次数: 0

A study of the cutting-edge general-purpose compressors’ performance on the normalized genome sequence 基于归一化基因组序列的前沿通用压缩器性能研究

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports

Pub Date : 2025-10-17 DOI: 10.1016/j.genrep.2025.102358

Subhankar Roy , Arnab Charit , Mriganka Patra , Ananya Sadhukhan , Diya Chakraborty , Partha Ghosh , Kingshuk Chatterjee , Anirban Mukhopadhyay

Advanced general-purpose compressors like gzip and zstd have difficulties when compressing genome sequences. The lack of sequence-specific traits and limited-scale features leads to inferior performance. However, molecular sequence databases have preferred these compressors for years. To get around these limitations, this article proposes a compressor called NGC (Normalized Genome Compressor) to make general-purpose compressors work better to compress genome sequences. NGC is a reference-free compression tool consisting of two phases. Initially, it takes the primary domain of the genome, i.e., A, C, G, and T, and then proceeds with normalization. In the subsequent phase, based on user specifications, it utilizes one of the eight general-purpose compressors, including 7-zip, paq8px, bsc, gzip, zstd, bzip2, zpaq, or cmix. We compare the standard version (S) of each compressor, known as the S-compressor, the sequence normalized file (nf), and the S-compressor applied to the nf format, referred to as the proposed compressor (P-compressor). Subsequently, we evaluate the performance of NGC in two genome datasets, including seventeen and eleven primary genome sequences, respectively. The result is the weighted average compression ratio (WACR) for the initial dataset of 4.13 for P-gzip vs. 3.63 for S-gzip and 4.8 for P-zstd vs. 4.3 for S-zstd. P-gzip is

\sim

91.101 times and P-zstd is

\sim

22.734 times faster than the S-compressor. The outcomes for the remaining six compressors are likewise beneficial. The findings indicate that the use of a general-purpose compressor in the nf significantly enhances the results.

高级通用压缩器（如gzip和zstd）在压缩基因组序列时存在困难。缺乏序列特异性特征和有限规模特征导致性能较差。然而，分子序列数据库多年来一直倾向于使用这些压缩器。为了克服这些限制，本文提出了一种称为NGC（归一化基因组压缩器）的压缩器，以使通用压缩器更好地压缩基因组序列。NGC是一个无参考的压缩工具，由两个阶段组成。最初，它取基因组的主要域，即A、C、G和T，然后进行归一化。在后续阶段，根据用户规范，它使用8个通用压缩器之一，包括7-zip、paq8px、bsc、gzip、zstd、bzip2、zpaq或cmix。我们比较了每个压缩器的标准版本(S)，称为S压缩器，序列规范化文件（nf），以及应用于nf格式的S压缩器，称为建议压缩器（p压缩器）。随后，我们在两个基因组数据集（分别包括17个和11个初级基因组序列）中评估了NGC的性能。结果是初始数据集的加权平均压缩比（WACR）， P-gzip为4.13，S-gzip为3.63，P-zstd为4.8，S-zstd为4.3。P-gzip和P-zstd分别比S-compressor快~ 91.101倍和22.734倍。其余6台压缩机的结果同样是有益的。研究结果表明，在nf中使用通用压缩器可显著提高结果。

{"title":"A study of the cutting-edge general-purpose compressors’ performance on the normalized genome sequence","authors":"Subhankar Roy , Arnab Charit , Mriganka Patra , Ananya Sadhukhan , Diya Chakraborty , Partha Ghosh , Kingshuk Chatterjee , Anirban Mukhopadhyay","doi":"10.1016/j.genrep.2025.102358","DOIUrl":"10.1016/j.genrep.2025.102358","url":null,"abstract":"<div><div>Advanced general-purpose compressors like gzip and zstd have difficulties when compressing genome sequences. The lack of sequence-specific traits and limited-scale features leads to inferior performance. However, molecular sequence databases have preferred these compressors for years. To get around these limitations, this article proposes a compressor called NGC (<u>N</u>ormalized <u>G</u>enome <u>C</u>ompressor) to make general-purpose compressors work better to compress genome sequences. NGC is a reference-free compression tool consisting of two phases. Initially, it takes the primary domain of the genome, i.e., A, C, G, and T, and then proceeds with normalization. In the subsequent phase, based on user specifications, it utilizes one of the eight general-purpose compressors, including 7-zip, paq8px, bsc, gzip, zstd, bzip2, zpaq, or cmix. We compare the standard version (S) of each compressor, known as the S-compressor, the sequence normalized file (nf), and the S-compressor applied to the nf format, referred to as the proposed compressor (P-compressor). Subsequently, we evaluate the performance of NGC in two genome datasets, including seventeen and eleven primary genome sequences, respectively. The result is the weighted average compression ratio (WACR) for the initial dataset of 4.13 for P-gzip vs. 3.63 for S-gzip and 4.8 for P-zstd vs. 4.3 for S-zstd. P-gzip is <span><math><mo>∼</mo></math></span>91.101 times and P-zstd is <span><math><mo>∼</mo></math></span>22.734 times faster than the S-compressor. The outcomes for the remaining six compressors are likewise beneficial. The findings indicate that the use of a general-purpose compressor in the nf significantly enhances the results.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102358"},"PeriodicalIF":0.9,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358388","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}

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