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Related Concept Videos

Conjugation01:19

Conjugation

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...
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Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains — Archaea and Bacteria. Bacteria include many common microorganisms, such as Salmonella and E. coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.
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iChip01:24

iChip

The cultivation of environmental microorganisms has long been hindered by the inability to replicate complex native conditions in vitro. The isolation chip (iChip) addresses this limitation by facilitating the growth of previously uncultivable microorganisms through in situ incubation. Designed for high-throughput microbial cultivation, the iChip comprises hundreds of microchambers, each capable of housing a single microbial cell. These microchambers are loaded with a mixture of molten agar and...
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Cell Inclusions01:27

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.

Dexi Bi1, Zhen Xu, Ewan M Harrison

  • 1State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China.

Nucleic Acids Research
|October 20, 2011
PubMed
Summary
This summary is machine-generated.

ICEberg is a new database for integrative and conjugative elements (ICEs) in bacteria. It provides comprehensive data and tools to study bacterial evolution, pathogenesis, and biotechnology.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Integrative and conjugative elements (ICEs) are mobile genetic elements crucial for bacterial evolution and adaptation.
  • ICEs possess modules for integration, excision, conjugation, and regulation, facilitating gene transfer and inheritance.
  • Many ICEs carry genes conferring traits like antibiotic resistance and virulence, impacting bacterial populations.

Purpose of the Study:

  • To introduce ICEberg, an integrated database for comprehensive information on bacterial ICEs.
  • To provide a centralized, explorable archive of predicted and experimentally supported ICE data.
  • To facilitate multi-disciplinary research on ICEs in prokaryotic evolution, pathogenesis, and biotechnology.

Main Methods:

  • Development of a curated database compiling information on ICEs from diverse bacterial species.
  • Inclusion of predicted and experimentally validated ICE data.
  • Integration of various bioinformatics tools for data analysis, including similarity search, sequence alignment, and genome context browsing.

Main Results:

  • ICEberg currently houses data on 428 ICEs from 124 bacterial species.
  • The database includes over 400 directly related references.
  • Accessible tools facilitate similarity searches, sequence alignments, genome context visualization, and phylogenetic analyses.

Conclusions:

  • ICEberg serves as a valuable resource for researchers studying bacterial ICEs.
  • The database promotes efficient and innovative exploration of ICEs and their roles.
  • Ongoing maintenance and updates will ensure ICEberg's continued utility for the scientific community.