相关实验视频

Updated: Jul 20, 2025

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

闪亮BioHEAT:一个交互闪亮的应用程序,以识别E.coli和B.subtilis中的表型驱动基因

Chen Wang¹, Harikumar Govindarajan¹, Panagiotis Katsonis¹

¹Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States.

Bioinformatics (Oxford, England)

|July 31, 2023

概括

鉴定驱动细菌如大肠杆菌和细菌细菌适应的基因至关重要. ShinyBioHEAT是一个新的网络工具,通过分析突变数据和蛋白质结构,简化了这一过程,即使对于没有计算专业知识的用户来说也是如此.

科学领域:

微生物学微生物学
计算生物学计算生物学
进化生物学进化生物学

背景情况:

在选择性压力下区分适应基因与中性突变是人口遗传学的关键挑战.
以前的方法将突变频率与功能影响分析结合起来,以确定大肠杆菌中的驱动基因.
这种方法成功地确定了在实验室进化和环境菌株中驱动适应的基因.

研究的目的:

开发一个用户友好的网络应用程序,用于识别模型细菌中的表型驱动基因.
为了使没有专业计算技能的研究人员能够进行进化分析.
促进识别适应性基因的方法的普遍采用.

主要方法:

开发ShinyBioHEAT,一个基于R Shiny的网络应用程序.
包括对两个模型细菌的分析:大肠杆菌 (E. coli) 和细菌细菌.
将突变频率数据与编码变异功能影响的进化分析进行整合.
对蛋白质结构的突变影响的动态可视化生成.

主要成果:

通过ShinyBioHEAT,可以对实验室进化数据进行透明和交互式分析.
该应用程序支持在大肠杆菌和B. subtilis.中识别表型驱动基因.
动态蛋白质结构可视化为预测的驱动基因提供直角验证.

结论:

在常见的细菌模型中,ShinyBioHEAT使适应基因的识别民主化.
该工具增强了对细菌适应负责的基因的发现.
它为研究细菌进化和适应的研究人员提供了宝贵的资源.

更多相关视频

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

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

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

Published on: December 7, 2021

相关概念视频

Chemotaxis in E. coli

Chemotaxis in E. coli

Chemotaxis in Escherichia coli is a sensory-driven motility mechanism that enables bacteria to navigate chemical gradients, moving toward beneficial environments while avoiding harmful conditions. This process relies on a signal transduction system integrating external chemical cues with flagellar motor control.Chemoreceptors and Signal DetectionE. coli detects chemical gradients through methyl-accepting chemotaxis proteins (MCPs), which are membrane-bound chemoreceptors that sense attractants...

Stringent Response in E. coli

Stringent Response in E. coli

Bacterial growth is closely tied to nutrient availability, with cells proliferating exponentially under favorable conditions and entering a stationary phase when resources become scarce. This transition is mediated by a regulatory mechanism known as the stringent response, which allows bacteria to adapt to nutrient deprivation by modulating gene expression and metabolic activity.During nutrient scarcity, intracellular amino acid levels decline. It results in the accumulation of uncharged tRNAs...