A5060545658- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- DNA and Nucleic Acid Chemistry
- Bacteriophages and microbial interactions
- Immune Cell Function and Interaction
- Biotin and Related Studies
- Genomics and Chromatin Dynamics
- CAR-T cell therapy research
- Force Microscopy Techniques and Applications
- Astrophysics and Star Formation Studies
- Astro and Planetary Science
- Advanced biosensing and bioanalysis techniques
- Orbital Angular Momentum in Optics
- Analytical chemistry methods development
- Cancer-related molecular mechanisms research
- Metamaterials and Metasurfaces Applications
- Microfluidic and Capillary Electrophoresis Applications
- Analytical Chemistry and Chromatography
- interferon and immune responses
- T-cell and B-cell Immunology
- SARS-CoV-2 and COVID-19 Research
- Mitochondrial Function and Pathology
- Microfluidic and Bio-sensing Technologies
Baylor College of Medicine
2024
Dynamic Imaging (United Kingdom)
2021
Stanford University
2011-2020
Dynamic Systems (United States)
2019
Center for Astrophysics Harvard & Smithsonian
2008
Amherst College
2006-2008
Harvard University Press
2007
SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell's machinery. Subcellular localization of its viral could, thus, play important roles in replication antiviral immune response. We perform computational modeling subcellular residency across eight neighborhoods. compare hundreds genomes with human transcriptome other coronaviruses. predict genome sgRNAs to be enriched toward mitochondrial matrix nucleolus, that 5′ 3′ untranslated regions contain strongest, most...
Rho termination factor is an essential hexameric helicase responsible for terminating 20–50% of all mRNA synthesis in Escherichia coli. We used single-molecule force spectroscopy to investigate Rho–RNA binding interactions at the utilization site λtR1 terminator. Our results are consistent with complexes adopting two states: one that binds 57 ± 2 nt RNA across six primary sites, and another 85 sites plus a single secondary situated center hexamer. The data serve establish translocates 5′ →...
Bacterial RNases catalyze the turnover of RNA and are essential for gene expression quality surveillance transcripts. In Escherichia coli, exoribonucleases RNase R polynucleotide phosphorylase (PNPase) play critical roles in degrading RNA. Here, we developed an optical-trapping assay to monitor translocation individual enzymes along RNA-based substrates. Single-molecule records motion reveal be highly processive: one molecule can unwind over 500 bp a structured substrate. However, enzyme...
Subcellular localization is essential to RNA biogenesis, processing, and function across the gene expression life cycle. However, specific nucleotide sequence motifs that direct are incompletely understood. Fortunately, new sequencing technologies have provided transcriptome-wide atlases of localization, creating an opportunity leverage computational modeling. Here we present RNA-GPS, a machine learning model uses nucleotide-level features predict eight different subcellular locations—the...
SUMMARY We introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced nanometer-resolution map of human transcriptome, revealing extensive and exquisite patterns localization diverse classes transcript isoforms. uncover radial organization nuclear which is gated at inner surface pore cytoplasmic export processed transcripts. identify two pathways messenger mitochondria, each associated with...
The spectral energy distributions (SEDs), spanning the mid-infrared to millimeter wavelengths, of a sample 13 high-mass protostellar objects (HMPOs) were studied using large archive 2-D axisymmetric radiative transfer models.Measurements from Spitzer GLIMPSE and MIPSGAL surveys MSX survey used in addition our own at submillimeter wavelengths construct SEDs, which then fit models.These models assumed that stars all masses form via accretion allowed us make estimates for masses, luminosities...
Critical contacts made between the RNA polymerase (RNAP) holoenzyme and promoter DNA modulate not only strength of binding, but also frequency timing escape during transcription. Here, we describe a single-molecule optical-trapping assay to study transcription initiation in real time, use it map formed σ70 RNAP from E. coli T7A1 promoter, as well observe remodeling those transition elongation phase. The strong binding identified certain well-known regions, such -35 -10 elements, do...
In an optically active liquid the diffraction angle depends on circular polarization state of incident light beam. We report observation differential in isotropic chiral medium, and we demonstrate that double is alternate means to determine handedness (enantiomeric excess) a solution.
Furqan M. Fazal1 and Howard Y. Chang1,2 1Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA 2Howard Hughes Medical Institute, University School of Medicine, Correspondence: howchang{at}stanford.edu
Abstract We introduce APEX‑seq, a method for RNA sequencing based on direct proximity labeling of using the peroxidase enzyme APEX2. APEX‑seq in nine distinct subcellular locales produced nanometer-resolution spatial map human transcriptome as resource, revealing extensive and exquisite patterns localization diverse classes transcript isoforms. should be widely applicable to many systems, enabling comprehensive investigations transcriptome.
RNA structure is intimately connected to each step of gene expression. Recent advances have enabled transcriptome-wide maps secondary structure, termed structuromes. However, previous whole-cell analyses lacked the resolution unravel dynamic regulation across subcellular states. Here we reveal structuromes in three compartments — chromatin, nucleoplasm and cytoplasm. The cytotopic substantially expand structural information, enable detailed investigation central role linking transcription,...
Invariant natural killer T (iNKT) cells can potently inhibit graft-versus-host-disease (GVHD) in animal models through the production of Interleukin-4. Once considered a homogeneous population, it is now well established that murine iNKT differentiate during thymic development into three distinct sublineages, distinguished based on expression transcription factors and effector molecules: Th1-like (iNKT1) cells, Th2-like (iNKT2) Th17-like (iNKT17) cells. In this study, we investigated immune...