Tokyo Institute of Technology · Biochemistry, Genetics and Molecular Biology
Professor Timothy J. Stasevich's research lab specializes in developing and applying advanced imaging and biophysical techniques to study dynamic cellular processes at the single-molecule level. Key research directions include live-cell imaging of protein synthesis using nascent chain tracking, quantitative analysis of chromatin dynamics through endogenous labeling of histone modifications and RNA polymerase II phosphorylation, and the development of novel probes for genomic locus visualization. The lab also investigates the fundamental physics of surface diffusion and step dynamics in epitaxial systems, particularly on copper and silver surfaces, using lattice-gas models and statistical mechanics. These interdisciplinary efforts bridge molecular biology, biophysics, and materials science to uncover mechanisms of gene regulation and surface phenomena at the nanoscale.
Figures are computed from collected data and may differ slightly.
Although messenger RNA (mRNA) translation is a fundamental biological process, it has never been imaged in real time in vivo with single-molecule precision. To achieve this, we developed nascent chain tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify protein synthesis dynamics at the single-mRNA level. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 seconds. Polysomes contain
Histone acetylation and RNA polymerase II phosphorylation are associated with transcriptionally active chromatin, but their spatiotemporal relationship in live cells remains poorly understood. To address this problem, we combine Fab-based labeling of endogenous protein modifications with single-molecule tracking to quantify the dynamics of chromatin enriched with histone H3 lysine-27 acetylation (H3K27ac) and RNA polymerase II serine-5 phosphorylation (RNAP2-Ser5ph). Our analysis reveals that ch
We present ab initio calculations of a variety of different lattice-gas interaction energies between Cu adatoms on Cu(001) and Cu(111). We find the next-nearest-neighbor (NNN) interactions to be negligible on Cu(111), explaining the success of the nearest-neighbor (NN) Ising model when describing the Cu(111) step stiffness. On Cu(001), however, we find that NNN interactions are roughly $(1∕7)$ the attractive NN interaction strength. On both surfaces, we find longer-range pair interactions to be
For hexagonal nets, descriptive of {111} fcc surfaces, we derive from combinatoric arguments a simple, low-temperature formula for the orientation dependence of the surface step line tension and stiffness, as well as the leading correction, based on the Ising model with nearest-neighbor (NN) interactions. Our formula agrees well with experimental data for both Ag and Cu{111} surfaces, indicating that NN interactions alone can account for the data in these cases (in contrast to results for Cu{001
Abstract In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here, we demonstrate a new method to see endogenous genomic loci using synthetic zinc‐finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag‐specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps: First, we develop an anti‐FLAG frankenbody that c
Within the solid-on-solid (SOS) approximation, we carry out a calculation of the orientational dependence of the step stiffness on a square lattice with nearest- and next-nearest-neighbor interactions. At low temperature our result reduces to a simple, transparent expression. The effect of the strongest trio (three-site, nonpairwise) interaction can easily be incorporated by modifying the interpretation of the two pairwise energies. The work is motivated by a calculation based on nearest neighbo
The decoration of hexagonal Ag/Ag(111) monolayer islands by chains of C60, observed via STM at 300 K, dramatically changes the nanocrystalline shape and fluctuations of the islands. We tune coverage so that a single chain of C60 fully decorates each Ag island boundary, forming a closed circular "necklace." We model the C60-induced rounding in terms of competing energetic and entropic effects. We thereby characterize the decorated-step fluctuations and estimate the C60-Ag and C60-C60 attractions
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