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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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The Eukaryotic Promoter Region02:40

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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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Eukaryotic RNA Polymerases00:58

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.

Susanne Warrenfeltz1, Evelina Y Basenko2, Kathryn Crouch3

  • 1Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA. swfeltz@uga.edu.

Methods in Molecular Biology (Clifton, N.J.)
|May 16, 2018
PubMed
Summary
This summary is machine-generated.

The Eukaryotic Pathogen Database Resources (EuPathDB) provide integrated data and tools for studying pathogen biology. This resource supports researchers in discovering biological relationships and advancing drug and vaccine development.

Keywords:
BioinformaticsFungiGenomicsOrthologyParasitePathogenProteomicsSequence analysisTranscriptomics

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Understanding pathogen biology is crucial for developing new drugs and vaccines.
  • Accessible genomic and functional data accelerates biological and translational discovery.
  • The Eukaryotic Pathogen Database Resources (EuPathDB) offer integrated data mining capabilities.

Purpose of the Study:

  • To describe the guiding concepts and data mining capabilities of EuPathDB.
  • To facilitate hypothesis-driven research in eukaryotic pathogen biology.
  • To support the discovery of biological relationships from large datasets.

Main Methods:

  • EuPathDB integrates pre-analyzed genomic, functional genomic, and population data for over 170 species.
  • The resource provides advanced search, data visualization, and analysis tools.
  • A user-friendly graphical interface requires no prior computational expertise.

Main Results:

  • EuPathDB encompasses 13 sites supporting diverse eukaryotic pathogens and related species.
  • The platform facilitates the discovery of meaningful biological relationships.
  • It empowers researchers without computational backgrounds to mine complex biological data.

Conclusions:

  • EuPathDB is a valuable resource for advancing research on eukaryotic pathogens.
  • Its integrated data and user-friendly tools accelerate biological discovery and translational research.
  • The platform supports the development of novel drugs and vaccines by enhancing pathogen biology knowledge.