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相关概念视频

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Light Acquisition02:16

Light Acquisition

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In order to produce glucose, plants need to capture sufficient light energy. Many modern plants have evolved leaves specialized for light acquisition. Leaves can be only millimeters in width or tens of meters wide, depending on the environment. Due to competition for sunlight, evolution has driven the evolution of increasingly larger leaves and taller plants, to avoid shading by their neighbors with contaminant elaboration of root architecture and mechanisms to transport water and nutrients.
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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
503
Reporter Genes02:11

Reporter Genes

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Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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相关实验视频

Updated: Jan 8, 2026

Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects
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Published on: March 16, 2010

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通过使用可解释的深度学习,研究多种番茄品种中的cis调节元素和基因表达.

Xiang Ji1, Cong Wang1, He Zhang1

  • 1Qingdao Agricultural University, Qingdao, 266109, China.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
|December 22, 2025
PubMed
概括

我们开发了一个可解释的深度学习模型,L-CRE,以了解cis调节元件 (CREs) 如何控制番茄的基因表达. 该模型准确地预测了基因表达,并确定了关键的调节区域,包括转录因子结合部位.

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Co-localization of Cell Lineage Markers and the Tomato Signal
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Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease
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Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

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相关实验视频

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Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects
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Co-localization of Cell Lineage Markers and the Tomato Signal
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Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease
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科学领域:

  • 基因组学就是基因组学.
  • 计算生物学 计算生物学
  • 植物科学 植物科学

背景情况:

  • 基因表达是由 cis 调节元件 (CREs) 调节的,但它们的精确影响是复杂的.
  • 了解非编码的调节元素对于破译基因表达模式至关重要.

研究的目的:

  • 开发一种可解释的深度学习模型 (L-CRE) 以基于CREs预测基因表达水平.
  • 确定影响番茄基因表达的关键基因组区域和调控机制.

主要方法:

  • 改进了现有的模型,并开发了L-CRE深度学习框架.
  • 分析了四种番茄品种的基因侧边区域.
  • 进行解释性分析,以评估基因组区域对预测的贡献.

主要成果:

  • 对于高和低基因表达水平,L-CRE实现了86.9%的峰值预测准确度.
  • 确定了关键的基因组区域,显著影响基因表达预测.
  • 发现这些区域往往含有转录因子结合位.
  • 通过实验数据验证识别的监管要素.

结论:

  • L-CRE模型提供了一种可靠的方法来预测基因表达和理解调节机制.
  • 确定了关键的基因组区域和转录因子结合部位,为番茄基因调节提供了洞察力.
  • 这项研究推进了功能基因组学,并为作物遗传改进提供了工具.