A5002558752- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Fuel Cells and Related Materials
- RNA Research and Splicing
- Light effects on plants
- Microbial Metabolic Engineering and Bioproduction
- Fungal and yeast genetics research
- Algal biology and biofuel production
- Mitochondrial Function and Pathology
- Photoreceptor and optogenetics research
- Circadian rhythm and melatonin
- Legume Nitrogen Fixing Symbiosis
- Photosynthetic Processes and Mechanisms
- Marine and coastal ecosystems
- Genetic and Environmental Crop Studies
- Cancer-related gene regulation
- Forensic and Genetic Research
- Marine and coastal plant biology
- Synthesis and biological activity
- Computational Drug Discovery Methods
- Plant Genetic and Mutation Studies
- Cancer-related molecular mechanisms research
- HVDC Systems and Fault Protection
- Antioxidant Activity and Oxidative Stress
- Spaceflight effects on biology
University of Michigan
2018-2024
Koç University
2015-2019
Post-transcriptional modifications to messenger RNAs (mRNAs) have the potential alter biological function of this important class biomolecules. The study mRNA is a rapidly emerging field, and full complement chemical in mRNAs not yet established. We sought identify quantify present yeast using an ultra-high performance liquid chromatography tandem mass spectrometry method detect 40 nucleoside variations parallel. observe six modified nucleosides with high confidence highly purified samples...
While the centrality of posttranscriptional modifications to RNA biology has long been acknowledged, function vast majority modified sites remains be discovered. Illustrative this, there is not yet a discrete biological role assigned for one most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m
Significance Pseudouridine is among the most-abundant RNA modifications. We present a framework for conceptualizing how eukaryotic pseudouridine synthases select their substrates. This work reveals structure of yeast synthase 7 (Pus7) and presents cell-based biochemical investigations enzyme binding activity. demonstrate that Pus7 interacts promiscuously with RNAs containing UG U AR sequences. Our observations raise question why these enzymes only modify <5% sequences in transcriptome,...
Abstract Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to generation reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise response mechanism non-phototrophic yet be elucidated. In this study, we investigated effect BL Vibrio cholerae by using genetics transcriptome profiling. Genome-wide analysis revealed transcription 6.3% V. genes were regulated BL. We further...
Light is crucial for many biological activities of most organisms, including vision, resetting circadian rhythm, photosynthesis, and DNA repair. The cryptochrome/photolyase family (CPF) represents an ancient group UV-A/blue light sensitive proteins that perform different functions such as repair, photoreception, transcriptional regulation. CPF widely distributed throughout all marine prokaryotes. bacterium Vibrio cholerae was previously shown to have a CPD photolyase repairs UV-induced...
Virtual screening of chemical libraries following experimental assays drug candidates is a common procedure in structure-based discovery. However, virtual with millions compounds requires lot time for computing and data analysis. A priori classification the as low- high-binding free energy sets decreases number experiments. This also reduces required computational resources. Data analysis demanding since compound can be described by more than one thousand attributes that make any very...
Ribosome speed is dictated by multiple factors including substrate availability, cellular conditions, and product (peptide) formation. Translation slows during the synthesis of cationic peptide sequences, potentially influencing expression thousands proteins. Available evidence suggests that ionic interactions between positively charged nascent peptides negatively ribosome exit tunnel impede translation. However, this hypothesis was difficult to test directly because inability decouple...
ABSTRACT While the centrality of post-transcriptional modifications to RNA biology has long been acknowledged, function vast majority modified sites remains be discovered. Illustrative this, there is not yet a discrete biological role assigned for one most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m 5 U54). Here, we uncover contributions m U54 both tRNA maturation and protein synthesis. Our mass spectrometry analyses demonstrate that cells lacking enzyme...
Damage to the mitochondrial genome (mtDNA) can lead diseases for which there are no clearly effective treatments. Since function and biogenesis controlled by nutrient environment of cell, it is possible that perturbation conserved, nutrient-sensing pathways may successfully treat disease. We found restricting glucose or otherwise reducing activity protein kinase A (PKA) pathway improved proliferation Saccharomyces cerevisiae cells lacking mtDNA transcriptional response loss reduced in with...
ABSTRACT Post-transcriptional nucleoside modifications have long been recognized as key modulators of non-coding RNA structure and function. There is an emerging appreciation that the chemical modification protein-coding messenger RNAs (mRNAs) also plays critical roles in cell. Although there are over 100 known found biology only a handful identified mRNAs. We sought to identify quantify present mRNAs yeast cells using high throughput ultra-high performance liquid chromatography-tandem mass...
Abstract Damage to the mitochondrial genome (mtDNA) can lead diseases for which there are no clearly effective treatments. Since function and biogenesis controlled by nutrient environment of cell, it is possible that perturbation conserved, nutrient-sensing pathways may successfully treat disease. We found restricting glucose or otherwise reducing activity protein kinase A (PKA) pathway improved proliferation Saccharomyces cerevisiae cells lacking mtDNA transcriptional response loss reduced...