A5033713990- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- Fungal Infections and Studies
- Bacteriophages and microbial interactions
- Robotics and Sensor-Based Localization
- Antifungal resistance and susceptibility
- Zebrafish Biomedical Research Applications
- Advanced Vision and Imaging
- Interactive and Immersive Displays
- Genomics and Phylogenetic Studies
- Adipose Tissue and Metabolism
- Autism Spectrum Disorder Research
- Machine Learning in Bioinformatics
- Congenital heart defects research
- Genetics and Neurodevelopmental Disorders
- Carbohydrate Chemistry and Synthesis
- Neural dynamics and brain function
- Fungal and yeast genetics research
- Neuroscience and Neuropharmacology Research
- Tuberculosis Research and Epidemiology
- Phytoplasmas and Hemiptera pathogens
- Viral Infections and Immunology Research
- Mycobacterium research and diagnosis
- RNA Research and Splicing
Jackson Laboratory
2018-2024
Stony Brook University
2014-2023
Most amino acids can be encoded by several synonymous codons, which are used at unequal frequencies. The significance of codon usage remains unclear. One hypothesis is that frequent codons translated relatively rapidly. However, there little direct, in vivo, evidence regarding codon-specific translation rates. In this study, we generate high-coverage data using ribosome profiling yeast, analyze a novel algorithm, and deduce events the A- P-sites ribosome. Different decoded different rates...
Gait and posture are often perturbed in many neurological, neuromuscular, neuropsychiatric conditions. Rodents provide a tractable model for elucidating disease mechanisms interventions. Here, we develop neural-network-based assay that adopts the commonly used open field apparatus mouse gait analysis. We quantitate both with high precision across 62 strains of mice. characterize four mutants known deficits demonstrate multiple autism spectrum disorder (ASD) models show deficits, implying...
The amino sugar N-acetylglucosamine (GlcNAc) is increasingly recognized as an important signaling molecule in addition to its well-known structural roles at the cell surface. In human fungal pathogen Candida albicans, GlcNAc stimulates several responses including induction of genes needed for catabolism and a switch from budding filamentous hyphal growth. We identified two growth on (RON1 NGS1) found that mutants lacking these fail induce catabolism. NGS1 was also other sugars, such maltose,...
The fungal pathogen Candida albicans can transition from budding to hyphal growth, which promotes biofilm formation and invasive growth into tissues. Stimulation of adenylyl cyclase form cAMP induces morphogenesis. failure cells lacking (cyr1Δ) hyphae has suggested that signaling is essential for growth. However, cyr1Δ mutants also grow slowly have defects in morphogenesis, making it unclear whether inducers must stimulate cAMP, or if normal basal levels are required maintain cellular health...
Drugs of abuse induce neuroadaptations, including synaptic plasticity, that are critical for transition to addiction, and genes pathways regulate these neuroadaptations potential therapeutic targets.
The RNA exosome is a conserved complex for degradation with two ribonucleolytic subunits, Dis3 and Rrp6. Rrp6 3′–5′ exonuclease, but it also has structural role in helping target RNAs to the activity. relative importance of exonuclease activity targeting probably differs between different substrates, this poorly understood. To understand contributions activities individual substrates Schizosaccharomyces pombe , we compared levels an rrp6 null mutant those point specifically defective A wide...
ABSTRACT During protein synthesis, the ribosome shifts along messenger RNA (mRNA) by exactly three nucleotides for each amino acid added to being translated. However, in special cases, sequence of mRNA somehow induces shift forward either two or four nucleotides. This “reading frame” which is translated, and gives rise an otherwise unexpected protein. Such “programmed frameshifts” are well-known viruses, including coronavirus, a few cases programmed frameshifting also known cellular genes....
The Shine-Dalgarno motif occurs in front of prokaryotic start codons, and is complementary to the 3' end 16S ribosomal RNA. Hybridization between sequence anti-Shine-Dalgarno region the16S rRNA (CCUCCU) directs ribosome AUG mRNA for translation. Shine-Dalgarno-like motifs (AGGAGG E. coli) are depleted from open reading frames most prokaryotes. This may be because hybridization at Shine-Dalgarnos inside genes would slow translation or induce internal initiation. However, we analyzed 128...
1 Abstract Gait and whole body posture are sensitive measures of the proper functioning numerous neural circuits, often perturbed in many neurological, neuromuscular, neuropsychiatric illnesses. Rodents provide a tractable model for elucidating disease mechanisms interventions, however, studying gait rodent models requires specialized methods remains challenging. Here, we develop simple assay that allows adoption commonly used open field apparatus analysis. We leverage modern networks to...
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Codon pair bias is the species-specific phenomenon that pairs of adjacent codons appear in genomes with frequencies different than would be predicted under an independence assumption, and thus indicative evolutionary selection. The synthetic attenuated virus engineering (SAVE) paradigm to design vaccines creates weak viruses by designing coding sequences favor underrepresented codon pairs. Designing genes which achieve absolute minimum arbitrary distribution computationally difficult. In...
Abstract Drugs of abuse induce neuroadaptations, including synaptic plasticity, that are critical for transition to addiction, and genes pathways regulate these neuroadaptations potential therapeutic targets. Tropomodulin 2 ( Tmod2 ) is an actin-regulating gene plays important role in synapse maturation dendritic arborization has been implicated substance-abuse intellectual disability humans. Here we mine the KOMP2 data find Tmod knockout mice show emotionality phenotypes predictive...
Each genome encodes some codons more frequently than their synonyms (codon usage bias), but are also arranged into specific pairs pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular proper juxtaposition. We therefore hypothesized that pairing could likewise attenuate Mtb genes. explored role bias recoding ( rpoB, mmpL3, ndh ) assessing...
During normal protein synthesis, the ribosome shifts along messenger RNA (mRNA) by exactly three nucleotides for each amino acid added to being translated. However, in special cases, sequence of mRNA somehow induces slip, which "reading frame" is translated, and gives rise an otherwise unexpected protein. Such "programmed frameshifts" are well-known viruses, including coronavirus, a few cases programmed frameshifting also known cellular genes. there no good way, either experimental or...