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  1. Abstract

    Transcription factors (TF) require access to target sites within nucleosomes to initiate transcription. The target site position within the nucleosome significantly influences TF occupancy, but how is not quantitatively understood. Using ensemble and single-molecule fluorescence measurements, we investigated the targeting and occupancy of the transcription factor, Gal4, at different positions within the nucleosome. We observe a dramatic decrease in TF occupancy to sites extending past 30 base pairs (bp) into the nucleosome which cannot be explained by changes in the TF dissociation rate or binding site orientation. Instead, the nucleosome unwrapping free energy landscape is the primary determinant of Gal4 occupancy by reducing the Gal4 binding rate. The unwrapping free energy landscape defines two distinct regions of accessibility and kinetics with a boundary at 30 bp into the nucleosome where the inner region is over 100-fold less accessible. The Gal4 binding rate in the inner region no longer depends on its concentration because it is limited by the nucleosome unwrapping rate, while the frequency of nucleosome rewrapping decreases because Gal4 exchanges multiple times before the nucleosome rewraps. Our findings highlight the importance of the nucleosome unwrapping free energy landscape on TF occupancy and dynamics that ultimately influences transcription initiation.

  2. Free, publicly-accessible full text available August 1, 2023
  3. Abstract

    Imaging through diffusers presents a challenging problem with various digital image reconstruction solutions demonstrated to date using computers. Here, we present a computer-free, all-optical image reconstruction method to see through random diffusers at the speed of light. Using deep learning, a set of transmissive diffractive surfaces are trained to all-optically reconstruct images of arbitrary objects that are completely covered by unknown, random phase diffusers. After the training stage, which is a one-time effort, the resulting diffractive surfaces are fabricated and form a passive optical network that is physically positioned between the unknown object and the image plane to all-optically reconstruct the object pattern through an unknown, new phase diffuser. We experimentally demonstrated this concept using coherent THz illumination and all-optically reconstructed objects distorted by unknown, random diffusers, never used during training. Unlike digital methods, all-optical diffractive reconstructions do not require power except for the illumination light. This diffractive solution to see through diffusers can be extended to other wavelengths, and might fuel various applications in biomedical imaging, astronomy, atmospheric sciences, oceanography, security, robotics, autonomous vehicles, among many others.

  4. Quaternary ammonium compounds (QAC, e.g., cetyltrimethylammonium bromide, (CTAB)) are widely used as surfactants and disinfectants. QAC already are commonly found in wastewaters, and their concentration could increase, since QAC are recommended to inactivate the SARS-CoV-2 (COVID-19) virus. Exposure of bacteria to QAC can lead to proliferation of antibiotic resistance genes (ARG). In particular, O2-based membrane biofilm reactors (O2-MBfRs) achieved excellent CTAB biodegradation, but ARG increased in their biofilms. Here, we applied meta-transcriptomic analyses to assess the impacts of CTAB exposure and operating conditions on microbial community's composition and ARG expression in the O2-MBfRs. Two opportunistic pathogens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia, dominated the microbial communities and were associated with the presence of ARG. Operating conditions that imposed stress on the biofilms, i.e., limited supplies of O2 and nitrogen or a high loading of CTAB, led to large increases in ARG expression, particularly for genes conferring antibiotic-target protection. Important within the efflux pumps was the Resistance-Nodulation-Division (RND) family, which may have been active in exporting CTAB from cells. Oxidative stress appeared to be the key factor that triggered ARG proliferation by selecting intrinsically resistant species and accentuating the expression of ARG. Our findings suggest that means to mitigate the spread ofmore »ARG, such as shown here in a O2-based membrane biofilm reactor, need to consider the impacts of stressors, including QAC exposure and stressful operating conditions.« less
  5. Redox-switchable polymerization has drawn increasing attention, in particular for the ring-opening polymerization (ROP) of biomass-derived monomers. However, an understanding of how the switch determines the observed changes is still limited. In this study, DFT calculations were employed to understand the redox-switchable ROP mechanism of ε-caprolactone catalyzed by group 4 metal complexes bearing [OSSO]-type ferrocene ligands. Our results suggest that two oxidized forms show higher reactivity because of the higher Lewis acidity of their catalytic metal centers in comparison with that of the corresponding reduced states. In one case, however, a lower activity of the oxidized species was observed that is likely due to the increased stability of the substrate-catalyst intermediate leading to a high activation barrier. In addition, other analogous metal complexes were computationally modelled by changing the metal center or modifying the ancillary ligand with different bridging-heteroatoms, and the results provide useful information on the development of new redox-switchable polymerization catalysts.