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相关概念视频

Horizontal Gene Transfer01:27

Horizontal Gene Transfer

1.3K
Horizontal gene transfer (HGT) is a process where genetic material moves between organisms within the same generation, unlike vertical gene transfer, which occurs from parent to offspring. HGT plays a crucial role in microbial evolution, adaptation, and survival, particularly in shared environments like the human gut.Mobile genetic elements such as plasmids, prophages, integrons, insertion sequences, and transposons facilitate this process. HGT occurs through three primary mechanisms:...
1.3K
Types of Genetic Transfer Between Organisms02:18

Types of Genetic Transfer Between Organisms

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Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and horizontal gene transfer. Vertical gene transfer occurs when genetic information is transferred from one generation to the next, which happens much more frequently than horizontal gene transfer. Both sexual and asexual reproduction are forms of vertical gene transfer, where one or more organisms pass some or all of their genome onto their progeny.
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Types of Genetic Transfer Between Organisms02:18

Types of Genetic Transfer Between Organisms

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Transduction01:16

Transduction

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Among the three main modes of HGT—transformation, conjugation, and transduction—transduction is unique in that it is mediated by bacteriophages, or bacterial viruses.Transduction occurs in two ways. Generalized transduction occurs during the lytic cycle of a bacteriophage infection. In this process, bacteriophages infect bacterial cells, replicate within them, and ultimately cause cell lysis, releasing newly assembled virions. Occasionally, random fragments of the bacterial genome...
1.1K
Conjugation01:19

Conjugation

1.8K
Conjugation is a form of horizontal gene transfer that primarily occurs in bacteria and some archaea, promoting genetic diversity and adaptation. Bacteria can acquire resistance genes through conjugative plasmids, allowing them to survive antibiotic treatments that would otherwise be lethal. This process involves direct contact between cells through specialized structures such as the sex pilus and is mediated by conjugative plasmids, including the F (fertility) factor.Conjugation requires...
1.8K
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

48.2K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
48.2K

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相关实验视频

Updated: Jan 8, 2026

Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
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Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli

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用于水平基因转移检测的基因组数据表示.

Andre Jatmiko Wijaya1,2, Aleksandar Anžel1, Hugues Richard2,3

  • 1Center for Artificial Intelligence in Public Health Research (ZKI-PH), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.

NAR genomics and bioinformatics
|December 12, 2025
PubMed
概括
此摘要是机器生成的。

机器学习模型可以更有效地检测抗微生物耐药性 (AMR) 基因的水平基因转移 (HGT). 最佳的基因组数据表示,如RCKmer,显著提高模型性能用于识别超级细菌.

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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相关实验视频

Last Updated: Jan 8, 2026

Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
06:56

Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 横向基因转移 (HGT) 通过移动遗传元素加速了抗菌素耐药性 (AMR) 的传播,推动了多抗药性病原体的进化.
  • 检测HGT的传统方法缺乏复杂转移事件的解决方案,阻碍了减轻AMR的努力.
  • 机器学习 (ML) 显示了改善HGT检测的希望,但其性能高度依赖于所选择的基因组数据表示.

研究的目的:

  • 评估不同基因组数据表示对ML模型HGT检测性能的影响.
  • 确定最佳的数据表示和ML模型组合,以准确检测HGT事件,特别是涉及AMR基因的事件.
  • 为基因监测和AMR基因转移的识别提供最先进的模型.

主要方法:

  • 使用五种不同的ML模型评估了44种不同的基因组数据表示.
  • 在四个不同的数据集中测试模型性能,以评估概括能力.
  • 使用F1分数和马修斯相关系数 (MCC) 等指标来量化性能.

主要成果:

  • 在HGT检测中ML模型的性能受到所使用的基因组数据表示的强烈影响.
  • 基于RCKmer的表示 (k=7) 与支持矢量机相结合,实现了最佳性能 (F1:0.959;MCC:0.908).
  • 在多个物种数据集上训练的模型表现出优异的概括性,突出了多样化的训练数据的好处.

结论:

  • 特定任务的基因组数据表示对于增强基于ML的基因组监测至关重要.
  • RCKmer表示为检测HGT事件提供了一种高度有效的方法,有助于识别AMR基因转移.
  • 这项研究提供了优化的模型,用于识别基因组岛屿,并了解物种之间的AMR基因流动.