Nick Davis
Massachusetts Institute of Technology
8 Papers
8 Citations
Nick Davis is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Transfer RNA & Protein aggregation. The author has an hindex of 5, co-authored 7 publications.
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Papers
Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.
Jennifer Hu,Jennifer Hu,Daniel Yim,Daniel Yim,Duanduan Ma,Sabrina M. Huber,Sabrina M. Huber,Nick Davis,Jo Marie Bacusmo,Sidney Vermeulen,Jieliang Zhou,Thomas J. Begley,Michael S. DeMott,Stuart S. Levine,Valérie de Crécy-Lagard,Peter C. Dedon,Peter C. Dedon,Bo Cao,Bo Cao,Bo Cao +19 more
TL;DR: The absolute quantification RNA-sequencing (AQRNA-seq) method presented in this article minimizes biases and provides a direct linear correlation between sequencing read count and copy number for all small RNAs in a sample.
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Helicobacter pylori Eradication in Patients with Immune Thrombocytopenic Purpura: A Review and the Role of Biogeography
Paul L. Beck,Galit H. Frydman,Nick Davis,James G. Fox +3 more
- 01 Mar 2015
TL;DR: In this article, the authors proposed a pathophysiological link between ITP and chronic Helicobacter pylori infection, which is typically a diagnosis of exclusion, assigned by clinicians after ruling out other identifiable etiologies.
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tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast.
Joana F Tavares,Nick Davis,Ana Poim,Andreia Reis,Stefanie Kellner,Inês Sousa,Ana R. Soares,Gabriela Moura,Peter C. Dedon,Manuel A. S. Santos +9 more
TL;DR: It is shown that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, and that stress response proteins whose genes are enriched in codons decoded by tRNAs are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains.
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Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast
Leticia Pollo-Oliveira,Roland Klassen,Nick Davis,Akif Ciftci,Jo Marie Bacusmo,Maria Martinelli,Michael S. DeMott,Thomas J. Begley,Peter C. Dedon,Raffael Schaffrath,Valérie de Crécy-Lagard +10 more
- 18 Feb 2020
TL;DR: Proteomic analysis of the t6A-deficient strain (sua5 mutant) revealed a global mistranslation leading to protein aggregation without regard to physicochemical properties or t 6A-dependent or biased codon usage in parent genes, but loss of sua5 led to increased expression of soluble proteins for mitochondrial function, protein quality processing/trafficking, oxidative stress response, and energy homeostasis.
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The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12
Leticia Pollo-Oliveira,Nick Davis,Intekhab Hossain,Peiying Ho,Yifeng Yuan,Pedro Salguero García,Cécile Pereira,Shane Byrne,Jiapeng Leng,Melody Sze,Crysten E. Blaby-Haas,Agnieszka Sekowska,A. Barba Montoya,Thomas J. Begley,Antoine Danchin,Daniel P. Aalberts,Alexander Angerhofer,John Hunt,Ana Conesa,Peter C. Dedon,Valérie de Crécy-Lagard +20 more
TL;DR: Downstream analysis of the transcriptomic data suggested that the absence of Q triggers an atypical oxidative stress response, confirmed by the detection of slightly elevated reactive oxygen species (ROS) levels in the mutant, increased sensitivity to hydrogen peroxide and paraquat, and a subtle growth phenotype in a strain prone to accumulation of ROS.
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