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Related Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Translation01:31

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life
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...
Post-translational Translocation of Proteins to the RER01:27

Post-translational Translocation of Proteins to the RER

A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...

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Related Experiment Video

Updated: Jul 2, 2026

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

Leveraging semantic knowledge in IRB databases to improve translation science.

John F Hurdle1, Jeffery Botkin, Thomas C Rindflesch

  • 1National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.

AMIA ... Annual Symposium Proceedings. AMIA Symposium
|August 13, 2008
PubMed
Summary

Research administrative databases (RADs), like those from Institutional Review Boards (IRBs), are valuable, mine-able data sources. Existing semantic extraction tools show promise for analyzing this data, with potential for improvement.

Related Experiment Videos

Last Updated: Jul 2, 2026

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

Area of Science:

  • Informatics
  • Health Informatics
  • Data Science

Background:

  • Research administrative databases (RADs) are underutilized data sources.
  • Institutional Review Board (IRB) databases manage significant research information.
  • Informaticists have overlooked the potential of RADs for data mining.

Purpose of the Study:

  • To assess the mine-ability of RADs using existing text-mining tools.
  • To evaluate the performance of the SemRep semantic knowledge extraction system on IRB data.
  • To demonstrate the feasibility of extracting structured information from IRB abstracts.

Main Methods:

  • Extracted 1,876 titles and abstracts from an IRB database.
  • Formatted extracted data into a pseudo-MEDLINE format.
  • Processed the formatted data using the SemRep semantic knowledge extraction system.

Main Results:

  • SemRep demonstrated comparable performance on IRB abstracts versus MEDLINE citations.
  • After excluding non-healthcare studies, SemRep extracted an average of 7.3 semantic relations per IRB abstract.
  • Extraction precision for IRB abstracts was 70%, compared to 78% for MEDLINE citations.

Conclusions:

  • RADs, exemplified by IRB data, are mine-able with current informatics tools.
  • Existing semantic extraction tools can successfully process RAD data.
  • Tuning extraction tools for RAD structures is expected to enhance performance.