Thomas J. Begley

Multi-dimensional DNA nanostructures isothermally assembled in hydrated ionic liquids

This paper demonstrates the isothermal assembly of DNA nanostructures and 3D crystals in hydrated ionic liquids, enhancing biostability and enabling cell internalization without thermal annealing.

Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis

This study examines how tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis across growth phases.

Oncogenes have the most distinct codon biases in the genome and codon signatures that oppose tumor suppressor genes

The paper compares codon usage bias between oncogenes and tumor suppressor genes in humans and mice, finding distinct patterns in humans and less distinct in mice.

The Wobble Uridine tRNA Writer MnmA Shapes Codon-Dependent Stress Response Systems

This study identifies MnmA as a key enzyme that regulates codon-dependent stress response systems in E. coli by affecting tRNA modifications and gene expression.

Lysosomal Profiling with LysoTracker for Quantitative Assessment of Cellular Senescence in Human Fibroblasts

This paper introduces a live-cell imaging protocol using LysoTracker Deep Red to quantify lysosomal remodeling as a marker of cellular senescence in human fibroblasts.

Synonymous codon usage defines functional gene families

The paper defines functional gene families in S. cerevisiae by analyzing codon usage patterns using a new statistical method called ASCS.

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa

The paper profiles tRNA modifications in Pseudomonas aeruginosa to uncover regulatory networks and validate gene annotations.

Loss of the s2U tRNA modification induces antibiotic tolerance and is linked to changes in ribosomal protein expression

The paper shows that loss of s2U tRNA modification in Yersinia pseudotuberculosis leads to antibiotic tolerance by reducing ribosomal protein translation.

Distinct age- and pathology-dependent epitranscriptome and translational dysfunction in a tauopathy mouse model

This study investigates age- and pathology-dependent changes in the epitranscriptome and translational dysfunction in a tauopathy mouse model, revealing significant alterations in tRNA biology and codon usage patterns.

Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate Protein Levels

The paper analyzes codon bias in human and mouse ORFeomes to identify species-specific pathways regulated by translation, showing that extreme codon bias affects protein levels in transcription factors.

Translational response to mitochondrial stresses is orchestrated by tRNA modifications.

The paper shows that tRNA modifications regulate the translational response to mitochondrial stress by altering codon decoding and pathway activity.

Angiogenin regulates mitochondrial stress and function via tRNA-derived fragments generation and impacting tRNA modifications.

This study shows that Angiogenin regulates mitochondrial stress and function by generating tRNA-derived fragments and altering tRNA modifications.

ROS-induced translational regulation--through spatiotemporal differences in codon recognition--is a key driver of brown adipogenesis

The paper shows that ROS-induced translational bias during brown adipogenesis supports mitochondrial biogenesis by preferentially translating G/C-ending codons through tRNA modification.

tRNA modifications inform tissue specific mRNA translation and codon optimization.

The paper shows that tRNA modifications influence tissue-specific mRNA translation and codon optimization by analyzing tRNA and mRNA data from seven mouse tissues.

Epitranscriptomic reprogramming is required to prevent stress and damage from acetaminophen

This study shows that acetaminophen induces epitranscriptomic reprogramming, and Alkbh8 is critical for regulating selenoprotein production and mitigating APAP toxicity.

Genome Profiling for Aflatoxin B1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B1-associated DNA Damage

The paper identifies 85 AFB1-resistant genes in yeast by screening a deletion library and finds that the CSM2/SHU complex is involved in error-free bypass of AFB1-induced DNA adducts.

Epitranscriptomic regulation of the response to the air pollutant naphthalene in mouse lungs: from the perspectives of specialized translation and tolerance linked to the writer ALKBH8

This study investigates the role of ALKBH8 in protecting mouse lungs from naphthalene toxicity, showing increased sensitivity in its deficiency and a protective effect on lung function.