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Related Concept Videos

DNA Bacteriophages01:26

DNA Bacteriophages

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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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Lytic Cycle of Bacteriophages01:30

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Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
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Viral Replication: Lytic Cycle01:20

Viral Replication: Lytic Cycle

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Bacteriophages, or phages, are viruses that specifically infect bacteria. Among them, T-even bacteriophages, such as T4, exhibit a well-characterized lytic replication cycle in Escherichia coli (E. coli). This process ensures the rapid proliferation of the virus while ultimately leading to the destruction of the bacterial host.Attachment and DNA InjectionThe infection process begins with the recognition and binding of the T4 phage to the E. coli cell surface. Tail fibers of the phage...
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Lysogenic Cycle of Bacteriophages00:43

Lysogenic Cycle of Bacteriophages

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In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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What are Viruses?00:50

What are Viruses?

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Overview
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Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System
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Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System

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Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes.

Daniel A Russell1

  • 1Department of Biological Sciences, University of Pittsburgh, 344 Crawford Hall, 4249 Fifth Ave, Pittsburgh, PA, 15260, USA. dar78@pitt.edu.

Methods in Molecular Biology (Clifton, N.J.)
|November 15, 2017
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) provides affordable access to genomic data. Our workflow refines NGS for high-quality bacteriophage genome completion, ensuring accurate downstream analysis.

Keywords:
454AceUtilConsedCoverageDNA sequencingGalaxyGenome terminiIlluminaIon TorrentLibrary preparationNewblerPAUSEPhagesDBSanger

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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Area of Science:

  • Genomics
  • Microbiology
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) technologies have democratized genomic data generation.
  • Current NGS platforms and software are optimized for large genomes and metagenomic samples, not individual bacteriophages.
  • Bacteriophage genomes, primarily coding regions, demand high-quality sequence data to avoid errors in annotation and analysis.

Purpose of the Study:

  • To present a specialized workflow for sequencing, assembling, and finishing bacteriophage genomes using NGS.
  • To establish a high standard for phage genome completion, crucial for reliable annotation and analysis.
  • To adapt NGS methodologies for the unique challenges of single bacteriophage genome sequencing.

Main Methods:

  • Utilized Illumina, Ion Torrent, and 454 sequencing platforms.
  • Developed a specific workflow tailored for bacteriophage genome sequencing and assembly.
  • Incorporated significant human oversight and expertise throughout the process.

Main Results:

  • Achieved high-standard complete genome sequences for bacteriophages.
  • Demonstrated the effectiveness of the specialized workflow across multiple NGS platforms.
  • Highlighted the necessity of meticulous quality control for phage genome projects.

Conclusions:

  • A tailored workflow is essential for high-quality bacteriophage genome completion using NGS.
  • Human expertise remains critical in achieving high standards despite advancements in sequencing and assembly algorithms.
  • This approach ensures the integrity of phage genomic data for subsequent research.