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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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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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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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Genomic DNA in Prokaryotes00:46

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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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Eukaryotic Compartmentalization01:37

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One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
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Eukaryotic Evolution01:24

Eukaryotic Evolution

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The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
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Related Experiment Video

Updated: May 9, 2025

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
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EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.

Guillaume Lentendu1, David Singer2, Sabine Agatha3

  • 1Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.

Molecular Ecology Resources
|April 30, 2025
PubMed
Summary
This summary is machine-generated.

A new database, EukFunc, offers a standardized way to functionally classify soil eukaryotes, including fungi, nematodes, and protists. This tool enhances ecological insights into soil biodiversity and ecosystem functions.

Keywords:
functional ecologyfungimicroeukaryotesmicroorganismsnematodesprotistssoil biodiversity

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Area of Science:

  • Soil ecology
  • Microbial ecology
  • Biodiversity research

Background:

  • Soil eukaryotes drive crucial ecosystem functions like carbon cycling and plant health.
  • Current methods lack a standardized, holistic approach for functional classification of soil eukaryotes.
  • Understanding soil eukaryome function is vital for soil system management.

Purpose of the Study:

  • To develop the first comprehensive functional reference database for soil eukaryotes.
  • To enable standardized functional classification of fungi, nematodes, and protists.
  • To facilitate deeper ecological insights into soil biodiversity and functions.

Main Methods:

  • Compiled EukFunc, a database of 14,060 soil eukaryotic species.
  • Classified species based on nutrient acquisition modes (e.g., symbiotroph, saprotroph, predator).
  • Integrated functional data into an R package for user-friendly analysis and metabarcoding annotation.

Main Results:

  • EukFunc categorizes species into functional classes: 40% symbiotrophs, 26% saprotrophs, 17% phototrophs, 16% predators.
  • The database includes detailed nutritional modes and interactions (prey/symbionts).
  • Analysis of alpine meadow soils demonstrated enhanced ecological understanding by integrating the entire soil eukaryome.

Conclusions:

  • EukFunc provides a standardized framework for functional annotation of soil eukaryotes.
  • The database streamlines analysis, improving efficiency and accuracy in ecological studies.
  • This resource is essential for advancing our understanding of soil ecosystem functions and services.