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Related Concept Videos

The Nucleolus02:55

The Nucleolus

The nucleolus is the most prominent substructure of the nucleus. When it was first discovered, it was considered to be an isolated organelle that forms fibrils and granules. In 1931, the relationship between the nucleolus and chromosomes was first described by Heitz. He observed that the appearance and size of nucleolus varies depending on the stage of the cell cycle. He also noticed constricted regions on different chromosomes clustered together at definite cell cycle stages. These regions,...
The Nucleolus02:55

The Nucleolus

The nucleolus is the most prominent substructure of the nucleus. When it was first discovered, it was considered to be an isolated organelle that forms fibrils and granules. In 1931, the relationship between the nucleolus and chromosomes was first described by Heitz. He observed that the appearance and size of nucleolus varies depending on the stage of the cell cycle. He also noticed constricted regions on different chromosomes clustered together at definite cell cycle stages. These regions,...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Nuclear Protein Sorting01:34

Nuclear Protein Sorting

Nuclear protein sorting is the selective trafficking of histones, polymerases, gene regulatory proteins into the nucleus and exporting RNAs and ribosomes to the cytosol. It is a tightly controlled process that regulates gene expression within a cell.
Proteins targeted to the nucleus carry nuclear localization signals or NLS recognized by import receptors in the cytosol. Similarly, proteins with nuclear export signals are recognized by export receptors. Import and export receptors are...
Nucleoid01:24

Nucleoid

The nucleoid represents a structurally and functionally distinct region within prokaryotic cells, where the cell's DNA and associated proteins are housed. Unlike eukaryotic cells, prokaryotes lack a membrane-bound nucleus, and the nucleoid facilitates the organization and accessibility of the genetic material within this constraint. The DNA in most bacteria and archaea exists as a single, circular, double-stranded molecule that is highly compacted through supercoiling and interactions with...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

NOPdb: Nucleolar Proteome Database--2008 update.

Yasmeen Ahmad1, François-Michel Boisvert, Peter Gregor

  • 1Wellcome Trust Centre for Gene Regulation & Expression and School of Computing, University of Dundee, Dundee DD1 5EH, UK.

Nucleic Acids Research
|November 6, 2008
PubMed
Summary
This summary is machine-generated.

A new system enhances the Nucleolar Proteome Database (NOPdb) to manage extensive mass spectrometry data. This update significantly expands the identified human nucleolar proteome, revealing over 4500 proteins.

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Area of Science:

  • Proteomics
  • Cell Biology
  • Bioinformatics

Background:

  • The Nucleolar Proteome Database (NOPdb) previously cataloged ~700 human proteins.
  • Managing large-scale proteomic datasets requires robust data handling systems.

Purpose of the Study:

  • To develop an updated experimental data handling system for the Nucleolar Proteome Database.
  • To analyze highly purified human nucleoli using mass spectrometry.
  • To expand the coverage of the human nucleolar proteome.

Main Methods:

  • Development of a dynamic relational database integrated with external web sources (IPI, Gene Ontology).
  • Utilized mass spectrometry to analyze purified human nucleoli from various cell lines.
  • Implemented an Application Programming Interface (API) for external data access.

Main Results:

  • Identified over 50,000 peptides from more than 4500 human proteins in purified nucleoli.
  • Achieved significantly enhanced coverage of the nucleolar proteome compared to NOPdb3.0.
  • Established a continuously updated, dynamic database accessible via an API.

Conclusions:

  • The enhanced NOPdb system successfully manages large proteomic datasets.
  • The study substantially increased the number of identified human nucleolar proteins.
  • The updated database provides a valuable, continuously improving resource for researchers.