Ribosome biogenesis and function in development and disease

C Ni, M Buszczak - Development, 2023 - journals.biologists.com
Although differential transcription drives the development of multicellular organisms, the
ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation …

A synthetic biology approach for vaccine candidate design against delta strain of SARS-CoV-2 revealed disruption of favored codon pair as a better strategy over …

P Gurjar, N Karuvantevida, IV Rzhepakovsky, AA Khan… - Vaccines, 2023 - mdpi.com
The SARS-CoV-2 delta variant (B. 1.617. 2) appeared for the first time in December 2020
and later spread worldwide. Currently available vaccines are not so efficacious in curbing …

Using protein-per-mRNA differences among human tissues in codon optimization

X Hernandez-Alias, H Benisty, LG Radusky, L Serrano… - Genome Biology, 2023 - Springer
Background Codon usage and nucleotide composition of coding sequences have profound
effects on protein expression. However, while it is recognized that different tissues have …

Human tissues exhibit diverse composition of translation machinery

AS Anisimova, NM Kolyupanova, NE Makarova… - International Journal of …, 2023 - mdpi.com
While protein synthesis is vital for the majority of cell types of the human body, diversely
differentiated cells require specific translation regulation. This suggests the specialization of …

Dicodon-based measures for modeling gene expression

AM Alonso, L Diambra - Bioinformatics, 2023 - academic.oup.com
Motivation Codon usage preference patterns have been associated with modulation of
translation efficiency, protein folding, and mRNA decay. However, new studies support that …

Cellular energy regulates mRNA degradation in a codon-specific manner

P Tomaz da Silva, Y Zhang, E Theodorakis… - Molecular Systems …, 2024 - embopress.org
Codon optimality is a major determinant of mRNA translation and degradation rates.
However, whether and through which mechanisms its effects are regulated remains poorly …

An insight into codon pattern analysis of autophagy genes associated with virus infection

S Singhal, U Kumar, T Alqahtani… - Current …, 2023 - ingentaconnect.com
Introduction: Apoptosis and autophagy are the two fundamental processes involved in
maintaining homeostasis, and a common stimulus may initiate the processes. Autophagy …

Synonymous codon variant analysis for autophagic genes dysregulated in neurodegeneration

R Khandia, MK Pandey, IV Rzhepakovsky… - Molecular …, 2023 - Springer
Neurodegenerative disorders are often a culmination of the accumulation of abnormally
folded proteins and defective organelles. Autophagy is a process of removing these …

[PDF][PDF] Synonymous codon usage regulates translation initiation

CL Barrington, G Galindo, AL Koch, ER Horton… - Cell reports, 2023 - cell.com
Nonoptimal synonymous codons repress gene expression, but the underlying mechanisms
are poorly understood. We and others have previously shown that nonoptimal codons slow …

[HTML][HTML] Monitoring integrated stress response in live Drosophila

PV Lidsky, J Yuan, KA Lashkevich, SE Dmitriev… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Cells exhibit stress responses to various environmental changes. Among these responses,
the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling …