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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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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.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Updated: May 21, 2025

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
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Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

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Information storage across a microbial community using universal RNA barcoding.

Prashant B Kalvapalle1,2,3, August Staubus2,4, Matthew J Dysart1,2,3

  • 1Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA.

Nature Biotechnology
|March 19, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed a novel RNA barcoding method to track gene transfer in wastewater microbiomes. This technique reveals the broad host range of plasmid conjugation, advancing microbiome engineering and environmental studies.

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Genetics

Background:

  • Traditional gene transfer studies in microbial communities face sensitivity limitations.
  • Monitoring mobile DNA host range is crucial for understanding microbial ecology.
  • Existing methods like reporter genes and metagenomics have drawbacks in complex environments.

Purpose of the Study:

  • To develop a sensitive method for recording gene transfer events in a wastewater microbiome.
  • To identify the host range of plasmid conjugation using a novel barcoding approach.
  • To enable microbiome engineering and study environmental influences on gene transfer.

Main Methods:

  • Utilized a synthetic catalytic RNA (ribozyme) to barcode a conserved ribosomal RNA (rRNA) segment.
  • Employed amplicon sequencing to detect both native and modified rRNA.
  • Used plasmids with different origins of replication (pBBR1, ColE1) for multiplexed barcoding.

Main Results:

  • Identified microbial community members from 20 taxonomic orders participating in plasmid conjugation with an Escherichia coli donor.
  • Observed variations in the 16S rRNA barcode signal across different amplicon sequence variants.
  • Demonstrated differences in host range based on the plasmid's origin of replication.

Conclusions:

  • The developed RNA-addressable modification method provides a sensitive tool for studying gene transfer without relying on translation.
  • This technique enhances our understanding of microbial community interactions and gene mobility.
  • The method has potential applications in microbiome engineering and investigating environmental factors affecting gene transfer and cellular uptake.