Engineering topics

Hung, Li-Wei

Publications and source records attributed to Hung, Li-Wei.

10 records

DOE OSTI2023

Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism

BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae, where both are symmetric trimers composed of three “binding”-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera

In vitro display technologies based on phage and yeast have a successful history of selecting single-chain variable fragment (scFv) antibodies against various targets. However, single-chain antibodies are often unstable and poorly expressed in Escherichia coli. Here, we explore the feasibility of converting scFv antibodies to an intrinsically fluorescent format by inserting the monomeric, stable fluorescent protein named thermal green, between the light- and heavy-chain variable regions. Our results show that the scTGP format maintains the affinity and specificity of the antibodies, improves expression levels, allows one-step fluorescent assay for detection of binding and is a suitable reagent for epitope binning. We also report the crystal structure of an scTGP construct that recognizes phosphorylated tyrosine on FcεR1 receptor of the allergy pathway.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Debris Disk Results from the Gemini Planet Imager Exoplanet Survey's Polarimetric Imaging Campaign

We report the results of a ∼4 yr direct imaging survey of 104 stars to resolve and characterize circumstellar debris disks in scattered light as part of the Gemini Planet Imager (GPI) Exoplanet Survey. We targeted nearby (≲150 pc), young (≲500 Myr) stars with high infrared (IR) excesses (L {sub IR}/L {sub ⋆} > 10{sup −5}), including 38 with previously resolved disks. Observations were made using the GPI high-contrast integral field spectrograph in H-band (1.6 μm) coronagraphic polarimetry mode to measure both polarized and total intensities. We resolved 26 debris disks and 3 protoplanetary/transitional disks. Seven debris disks were resolved in scattered light for the first time, including newly presented HD 117214 and HD 156623, and we quantified basic morphologies of five of them using radiative transfer models. All of our detected debris disks except HD 156623 have dust-poor inner holes, and their scattered-light radii are generally larger than corresponding radii measured from resolved thermal emission and those inferred from spectral energy distributions. To assess sensitivity, we report contrasts and consider causes of nondetections. Detections were strongly correlated with high IR excess and high inclination, although polarimetry outperformed total intensity angular differential imaging for detecting low-inclination disks (≲70°). Based on postsurvey statistics, we improved upon our presurvey target prioritization metric predicting polarimetric disk detectability. We also examined scattered-light disks in the contexts of gas, far-IR, and millimeter detections. Comparing H-band and ALMA fluxes for two disks revealed tentative evidence for differing grain properties. Finally, we found no preference for debris disks to be detected in scattered light if wide-separation substellar companions were present.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Revised astrometric calibration of the Gemini Planet Imager

We present a revision to the astrometric calibration of the Gemini Planet Imager (GPI), an instrument designed to achieve the high contrast at small angular separations necessary to image substellar and planetary-mass companions around nearby, young stars. We identified several issues with the GPI data reduction pipeline (DRP) that significantly affected the determination of the angle of north in reduced GPI images. As well as introducing a small error in position angle measurements for targets observed at small zenith distances, this error led to a significant error in the previous astrometric calibration that has affected all subsequent astrometric measurements. We present a detailed description of these issues and how they were corrected. We reduced GPI observations of calibration binaries taken periodically since the instrument was commissioned in 2014 using an updated version of the DRP. These measurements were compared to observations obtained with the NIRC2 instrument on Keck II, an instrument with an excellent astrometric calibration, allowing us to derive an updated plate scale and north offset angle for GPI. This revised astrometric calibration should be used to calibrate all measurements obtained with GPI for the purposes of precision astrometry.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

The Gemini Planet Imager Exoplanet Survey: Dynamical Mass of the Exoplanet β Pictoris b from Combined Direct Imaging and Astrometry

Herein, we present new observations of the planet β Pictoris b from 2018 with the Gemini Planet Imager (GPI), the first GPI observations following conjunction. Based on these new measurements, we perform a joint orbit fit to the available relative astrometry from ground-based imaging, the Hipparcos Intermediate Astrometric Data (IAD), and the Gaia DR2 position, and demonstrate how to incorporate the IAD into direct imaging orbit fits. We find a mass consistent with predictions of hot-start evolutionary models and previous works following similar methods, though with larger uncertainties: $12.8^{+5.3}_{–3.2} M_{Jup}$. Our eccentricity determination of ${0.12}_{-0.03}^{+0.04}$ disfavors circular orbits. We consider orbit fits to several different imaging data sets, and find generally similar posteriors on the mass for each combination of imaging data. Our analysis underscores the importance of performing joint fits to the absolute and relative astrometry simultaneously, given the strong covariance between orbital elements. Time of conjunction is well-constrained within 2.8 days of 2017 September 13, with the star behind the planet's Hill sphere between 2017 April 11 and 2018 February 16 (±18 days). Following the recent radial velocity detection of a second planet in the system, β Pic c, we perform additional two-planet fits combining relative astrometry, absolute astrometry, and stellar radial velocities. These joint fits find a significantly smaller mass (8.0 ± 2.6 M Jup) for the imaged planet β Pic b, in a somewhat more circular orbit. We expect future ground-based observations to further constrain the visual orbit and mass of the planet in advance of the release of Gaia DR4.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

MAD using INRAD and Radiography [Slides]

We have previously evaluated Intrinsic Radiation Detection Algorithms from vendors for the Department of Homeland Security. These algorithms have limited spectra capability due to both the relatively low spectral content of the signal due to the use of PVT in the Radiation Portal detectors as well as relatively simple algorithms which are based on energy windowing and other simple algorithms to perform classification of Special Nuclear Material. Current detection algorithms are suceptible to nuissance alarms due to Naturally Occuring Radiation (NORM) and variations in background suppression. In this work, we propose to fuse the intrinsic radiation and radiographic data in conjunction with well-established machine learning algorithms to developed enhanced Threat Object detection capability.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

NASA NTRS2018

GPI Spectra of HR8799 C, D, and E in H-K Bands with KLIP Forward Modeling

We demonstrate KLIP forward modeling spectral extraction on Gemini Planet Imager coronagraphic data of HR8799, using PyKLIP. We report new and re-reduced spectrophotometry of HR8799 c, d, and e from H-K bands. We discuss a strategy for choosing optimal KLIP PSF subtraction parameters by injecting fake sources and recovering them over a range of parameters. The K1/K2 spectra for planets c and d are similar to previously published results from the same dataset. We also present a K band spectrum of HR8799e for the first time and show that our H-band spectra agree well with previously published spectra from the VLT/SPHERE instrument. We compare planets c, d, and e with M, L, and T-type field objects. All objects are consistent with low gravity mid-to-late L dwarfs, however, a lack of standard spectra for low gravity late L-type objects lead to poor fit for gravity. We place our results in context of atmospheric models presented in previous publications and discuss differences in the spectra of the three planets.

planets and satellites: gaseous planets { stars: i↗