Engineering topics
Liu, Kevin
Publications and source records attributed to Liu, Kevin.
Novel small molecule FGF 23 inhibitors increase serum phosphate and improve skeletal abnormalities in Hyp mice
We report that excess fibroblast growth factor 23 (FGF23) causes hereditary hypophosphatemic rickets, such as X-linked hypophosphatemia (XLH) and tumor induced osteomalacia (TIO). A small molecule that specifically binds to FGF23 to prevent activation of the FGFR/a-Klotho complex has potential advantages over the currently approved systemically administered FGF23 blocking antibody. Using structure-based drug design we previously identified ZINC13407541 (N-[[2-(2-phenylethenyl)cyclopenten-1-yl]methylidene]hydroxylamine) as a small molecule antagonist for FGF23. Additional structure-activity studies developed a series of ZINC13407541 analogues with enhanced drug-like properties. In this study, we tested in a pre-clinical Hyp mouse homologue of XLH a direct connect analogue (8n) [(E)-2-(4-(tert-butyl)phenyl)cyclopent-1-ene-1-carbaldehyde oxime] that exhibited the greatest stability in microsomal assays, and 13a [(E)-2-((E)-4-methylstyryl)benzaldehyde oxime] that exhibited increased in vitro potency. Using cryo-electron microscopy (Cryo-EM) structure and computational docking, we identified a key binding residue (Q156) of the FGF23 antagonists, ZINC13407541 and its analogues (8n and 13a) in the N-terminal domain of FGF23 protein. Site-directed mutagenesis and bimolecular fluorescence complementation (BiFC)-fluorescence resonance energy transfer (FRET) assay confirmed the binding site of these three antagonists. We found that pharmacological inhibition of FGF23 with either of these compounds blocked FGF23 signaling and increased serum phosphate and 1,25(OH)2D concentrations in Hyp mice. Long-term parenteral treatment with 8n or 13a also enhanced linear bone growth, increased mineralization of bone, and narrowed the growth plate in Hyp mice. The more potent 13a compound had greater therapeutic effects in Hyp mice. Further optimization of these FGF23 inhibitors may lead to versatile drugs to treat excess FGF23-mediated disorders.
Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs
RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.
Crowd-Sourced Data and Analysis Tools for Advancing the Chemical Vapor Deposition of Graphene: Implications for Manufacturing
Industrial production of graphene by chemical vapor deposition (CVD) requires more than the ability to synthesize large domain, high-quality graphene in a lab reactor. The integration of graphene in the fabrication process of electronic devices requires the cost-effective and environmentally friendly production of graphene on dielectric substrates, but current approaches can only produce graphene on metal catalysts. Sustainable manufacturing of graphene should also conserve the catalyst and reaction gases, but today the metal catalysts are typically dissolved after synthesis. Progress toward these objectives is hindered by the hundreds of coupled synthesis parameters that can strongly affect CVD of low-dimensional materials and poor communication in the published literature of the rich experimental data that exists in individual laboratories. We report here on a platform, "graphene recipes for synthesis of high quality material" (Gr-ResQ: pronounced graphene rescue), which includes powerful new tools for data-driven graphene synthesis. At the core of Gr-ResQ is a crowd-sourced database of CVD synthesis recipes and associated experimental results. The database captures similar to 300 parameters ranging from synthesis conditions such as a catalyst material and preparation steps, to ambient lab temperature and reactor details, as well as resulting Raman spectra and microscopy images. These parameters are carefully selected to unlock the potential of machine-learning models to advance synthesis. A suite of associated tools enable fast, automated, and standardized processing of Raman spectra and scanning electron microscopy images. To facilitate community-based efforts, Gr-ResQ provides tools for cyber-physical collaborations among research groups, allowing experiments to be designed, executed, and analyzed by different teams. Gr-ResQ also allows publication and discovery of recipes via the Materials Data Facility, which assigns each recipe a unique identifier when published and collects parameters in a search index. We envision that this holistic approach to data-driven synthesis can accelerate CVD recipe discovery and production control and open opportunities for advancing not only graphene but also many other 1D and 2D materials.
Mars 2020 Center Differential Pivot Restraint: Flexurized Spring System Providing Compliance for Rover Mobility Deployment Prior to Landing
The Center Differential Pivot Restraint (CDPR) for the Mars 2020 mission is designed to constrain motion of the rover differential and to dampen out the load response of during rover’s mobility deployment event in Entry, Descent, and Landing (EDL) phase of the mission. For Mars 2020, it was required to redesign the mechanism to save minimum 33% of the mass from the previous Mars Science Laboratory (MSL) design. The new mechanism architecture used a monolithic spring-like flexure to act as the system compliance, resulting in 50% mass savings from the MSL design. Along the design and prototype testing process, several mechanism design principles were re-affirmed as well as lessons learned about potential race conditions.
VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage
Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutralizing and non-broadly neutralizing branches of an antibody-developmental tree. Because sequences of antibodies isolated from the fusion peptide (FP)-targeting VRC34-antibody lineage suggested it might be suitable for such rare mutation analysis, we carried out next-generation sequencing (NGS) on B cell transcripts from donor N123, the source of the VRC34 lineage, and functionally and structurally characterized inferred intermediates along broadly neutralizing and poorly neutralizing developmental branches. The broadly neutralizing VRC34.01 branch required the rare heavy-chain mutation Y33P to bind FP, whereas the early bifurcated VRC34.05 branch did not require this rare mutation and evolved less breadth. Our results demonstrate how a required rare mutation can restrict development and shape the maturation of a broad HIV-1-neutralizing antibody lineage.
The Effects of Radiation and Emitted Light Transport on the Positional Response of 11 cm × 42.5 cm × 5.5 cm NaI(Tl) Detectors
Experiments were performed with 30 11 cm x 42.5 x cm 5.5 cm NaI(Tl) detectors to better understand their positional response. Spectra were collected using 0.02 to 0.15 MBq point sources of 241 Am, 137 Cs, 60 Co, and 133 Ba positioned on lines parallel and perpendicular to the long axis of the crystal along both the narrow and wide detector faces as well as at different distances from them. A greater density of positions was sampled at the ends of the detector, and repeated measurements were made to examine potential gain drifts during the experiment. Spectroscopic peak counts, spectroscopic pulse heights, and net counts were analyzed. Empirical equations were fit to the aforementioned data for each specific source energy as a function of source position. In addition, a Monte Carlo radiation transport code was used to simulate the expected positionally variable response based solely upon radiation absorption. The simulated radiation transport efficiency functions were compared to the experimental data. The effects of the geometric radiation efficiency, the attenuation and scattering of emitted light within the scintillation crystal, and combined effects such as non-uniformity of the photomultiplier tube photocathode response and crystal irregularities were then distinguished. Functions describing each effect were derived. The results suggest potential new corrections to data obtained with large scintillation detectors as well as a novel approach to partial positional gamma-ray detection with minimal collimation, given that the energy resolution is within reason for particular photopeaks.
Calibration and Statistical Performance of Al2O3: C Optically Stimulated Luminescent Dosimeters With and Without Annealing Using a 137Cs Source
A series of experiments were conducted using commercially available Al 2 O 3 :C optically stimulated luminescent dosimeters to provide a technical basis for their precise calibration and statistical performance at irradiated air kerma doses between 0.02 mGy and 5 mGy using 137 Cs. This study examines the dose response linearity, studies the background signal for annealed dosimeters, and compares the statistical performance of dosimeters that were annealed and not annealed prior to their irradiation and readout. The average and standard deviation for the response of groups of dosimeters annealed and nonannealed prior to their irradiation were determined at each delivered dose. The batch of dosimeters that were annealed prior to their irradiation exhibited a coefficient of variation in its mean dose response below 10% when using three or more irradiation trials at each delivered air kerma dose between 0.02 mGy and 5m Gy. The reader calibration factor was calculated using the response of the annealed batch of dosimeters and was determined to be 756 ± 7 photomultiplier tube counts perm Gy. Best estimates of the individual sensitivity factors were determined to be between 0.79 and 1.12 for the annealed batch of dosimeters. The minimum number of irradiations required to accurately determine the sensitivity factor of each individual dosimeter is reported with the recommended reader and dosimeter calibration procedures.
Modular Active Self-Assembling Space Telescope Swarms
The Phase I study included a detailed exploration of a specific mission concept based on this architecture - a 31-meter diameter version of the LUVOIR (Large Ultraviolet Optical Infrared Surveyor) mission concept with the same wavelength coverage and wave-front quality requirements. The study focused on establishing the feasibility of the proposed concept with respect to what were identified as the most challenging aspects of the mission: the ability to find orbital solutions using solar sail propulsion for both the initial transfers and subsequent rendezvous trajectories; and the ability to generate the required final primary mirror surface out of uniformly polished individual module mirrors using deformation via mechanical degrees of freedom. As a result of the Phase I work it was shown that both orbital and optical solutions are feasible, but will require technology advancement in multiple key areas. In particular, improvements to solar sail areal densities and loading factors will allow us to more easily find fully general solutions for the transfer trajectories, while lower mass, ultra-precise cryogenic linear actuators will likely be needed to form the final mirror shape. However, it was found that current state of the art in solar sails was sufficient for rendezvous trajectories once on-orbit, that the requisite wave-front quality could be achieved with actuation requirements not more stringent than those being carried by LUVOIR, and that there exists a well-defined design space in which the module spacecraft designs can be optimized. The technology development required to progress this work overlaps significantly with numerous NASA technology roadmaps, as well as the Exoplanet Exploration Program's technologies gap list, meaning that continued development of this concept would directly benefit a variety of NASA programs, as well as enabling the completely unique capabilities provided by a 31-meter optical space telescope...Our architecture requires only a single module type allowing us to directly leverage the cost and efficiency benefits of true mass production, in direct contrast to previously explored self-assembling swarm concepts, which typically include multiple module types.
Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1
A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. In conclusion, the N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.
Setup and Characterization of a 137 CS Dosimetry Calibration Source in a Space-constrained Environment
Proper characterization of 137 Cs sources used for dosimeter calibration and performance testing is crucial for accurate and precise knowledge of air kerma rate and delivered dose. A 269 GBq 137 Cs source was relocated to a new facility, which had a footprint of approximately 2.8 m × 3.6 m and a 3.4 m high ceiling. A small room size, such as in the new facility, may significantly increase backscatter from the walls or room return. Due to the limited source strength, a relatively close irradiation position of 1.00 m from the source was selected to decrease required exposure times. Proximity to the small but cylindrical source has the potential to alter the 1/r 2 relationship (inverse square law) of air kerma rate with distance associated with point sources. Practical tutorials concerning dosimetry irradiation facilities are largely absent from the archival literature. For those reasons, standard characterization experiments were repeated multiple times, great care was taken with positioning, several experiments were added to the standard ones, an ion chamber and dosimeters were used rather than film for greater accuracy and precision, and practical details of the process were recorded. The impacts of room size and finite source dimensions were quantified and mitigated by the efforts reported here. Finally, recommendations for simple but thorough facility characterization, beam calibration, and quality control resulted.
Design of Interrogation Protocols for Radiation Dose Measurements Using Optically-Stimulated Luminescent Dosimeters
Not provided.
Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody
The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. In this paper, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. Finally, these results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.