Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.4K
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.
20.4K
Protein Modifications in the RER01:26

Protein Modifications in the RER

6.7K
Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
6.7K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

4.9K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
4.9K
Ribosome Profiling02:24

Ribosome Profiling

4.0K
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...
4.0K
Gene Families01:57

Gene Families

9.7K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.7K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

14.5K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
14.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Local Anesthetic and Adjuvant Mixtures Show Unexpected pH-Dependent Crystallization Patterns in Human Cerebrospinal Fluid: A Semiquantitative In Vitro Trial.

Anesthesia and analgesia·2026
Same author

Comparison of local anaesthesia and regional anaesthesia (PSP/IPP) on QoR-15 in patients undergoing subpectoral implantation of cardiac implantable electronic devices (CIEDs)-a prospective, randomized, double-blinded, controlled pragmatic trial with two arms.

Trials·2025
Same author

Is It Time to Reassess Local Anesthetic and Adjuvant Mixtures? A Narrative Review of Practice, Evidence, and Risks.

Anesthesiology·2025
Same author

The PROSITE database for protein families, domains, and sites.

Nucleic acids research·2025
Same author

Safety and Stability of Additives and Medication Mixtures for the Anesthesiologist.

Advances in anesthesia·2025
Same author

Crystallization of local anesthetic and adjuvant mixtures: a chemical analysis of the crystal precipitate composition.

Regional anesthesia and pain medicine·2025

Related Experiment Video

Updated: Jan 4, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.1K

Enzyme annotation in UniProtKB using Rhea.

Anne Morgat1, Thierry Lombardot1, Elisabeth Coudert1

  • 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva 1211-4, Switzerland.

Bioinformatics (Oxford, England)
|November 6, 2019
PubMed
Summary

UniProtKB now uses Rhea for enzyme annotation, improving data quality and enabling advanced searches. This integration enhances biochemical reaction information accessibility and computational tractability.

More Related Videos

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

288
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K

Related Experiment Videos

Last Updated: Jan 4, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.1K
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

288
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • UniProtKB provides protein sequence and functional information.
  • Enzyme annotation in UniProtKB relied on textual descriptions of biochemical reactions.
  • There was a need for standardized, computationally tractable reaction data.

Purpose of the Study:

  • To enhance enzyme annotation quality in UniProtKB using the Rhea knowledgebase.
  • To integrate ChEBI ontology for standardized chemical entity representation.
  • To improve search and query functionalities for biochemical reactions.

Main Methods:

  • Replaced existing textual reaction descriptions in UniProtKB with Rhea equivalents.
  • Leveraged Rhea's expert-curated biochemical reactions and ChEBI ontology.
  • Developed enhanced search and query facilities for UniProt website, REST API, and SPARQL endpoint.

Main Results:

  • Rhea is now the standard for enzymatic reaction annotation in UniProtKB.
  • Improved search capabilities utilize chemical structure, nomenclature, and classification data.
  • Enhanced data accessibility and computational tractability for biochemical reactions.

Conclusions:

  • The integration of Rhea significantly improves UniProtKB's enzyme annotation.
  • Enhanced search and query tools facilitate deeper analysis of biochemical data.
  • This work establishes a new standard for representing enzymatic reactions in biological databases.