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DOE OSTI2022

Spectroscopy of Twisted Bilayer Graphene Correlated Insulators

Here we analytically compute the scanning tunneling microscopy (STM) signatures of integer-filled correlated ground states of the magic angle twisted bilayer graphene (TBG) narrow bands. After experimentally validating the strong-coupling approach at ± 4 electrons/moiré unit cell, we consider the spatial features of the STM signal for 14 different many-body correlated states and assess the possibility of Kekulé distortion (KD) emerging at the graphene lattice scale. Remarkably, we find that coupling the two opposite graphene valleys in the intervalley-coherent (IVC) TBG insulators does not always result in KD. As an example, we show that the Kramers IVC state and its nonchiral U(4) rotations do not exhibit any KD, while the time-reversal-symmetric IVC state does. Our results, obtained over a large range of energies and model parameters, show that the STM signal and Chern number of a state can be used to uniquely determine the nature of the TBG ground state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii ) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae . Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

Conversion↗

DOE OSTI2022

Status of the MicroBooNE Inclusive Single Photon Selection Using Wire-Cell Reconstruction

MicroBooNE is a Liquid Argon Time Project Chamber (LArTPC) detector whose primary design goal is to understand the “low-energy-excess” anomaly seen by MiniBooNE. MicroBooNE’s currently published results see no excess consistent with the MiniBooNE observation, therefore creating a need for searches in more channels. This note summarizes MicroBooNE’s inclusive single photon selection using Wire-Cell reconstruction and pattern recognition, which will be used to search for a low-energy-excess (LEE) anomaly in the inclusive single photon channel. The selection is similar to the Wire-Cell inclusive electron neutrino selection, but with a different signal definition and some modifications and additions to the pattern recognition tools. A selection with 15.2% efficiency and 18.5% purity is achieved for simulated Standard Model single photon events.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

An Update on MicroBooNE’s Inclusive Single Photon Low Energy Excess Search

The MicroBooNE detector is a Liquid Argon Time Project Chamber (LArTPC) detector whose primary design goal is to understand the "low-energy-excess" anomaly seen by MiniBooNE. MicroBooNE's currently published results see no excess consistent with the MiniBooNE observation, emphasizing a need for improved searches in more channels. This note summarizes MicroBooNE's inclusive single photon selection using Wire-Cell reconstruction and pattern recognition, which is used to search for a low-energy-excess (LEE) anomaly in the inclusive single photon channel. The selection is similar to the Wire-Cell inclusive electron neutrino selection, but with a different signal definition and some modifications and additions to the pattern recognition tools. A selection with 7.0% efficiency and 40.2% purity is achieved for our targeted single photon signal simulated events.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Status of the MicroBooNE inclusive single photon selection using Wire-Cell reconstruction

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa , a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme–substrate relationships. We focus on uridine diphosphate–glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa , presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1976

Polarization compensator for optical communications

An optical data communication system is provided whereby two orthogonal polarization states of a light beam carrier correspond to digital states. In such a system, automatic polarization compensation is provided by applying a dither modulating voltage to a cell exhibiting the electro-optic effect. The cell controls the relative phase of electric field components of an input light beam enabling the dither frequency component of the difference of the instantaneous powers in the two polarization states to be coherently detected. A signal derived from the coherent detection process is fed back to the cell via an integrator to form polarization bias compensating servo loop ot Type 1.

Fitzmaurice, M. W.↗

NASA NTRS1988

VLSI Architecture Of A Binary Up/Down Counter

Identical stages contain relatively-few logic gates. New algorithm simplifies design of binary up/down counter. Design suitable for very-large-scale integrated circuits. Contains simple "pipeline" array of identical cells. Programmable logic unit converts increment and decrement input signals to "U" and "D" signals required by algorithm of counter.

Hsu, In-Shek↗

NASA NTRS1993

Nearly steady flows in GONG prototype data

Doppler velocity images obtained with the GONG prototype instrument were analyzed to measure the nearly steady photospheric flows. The data consists of 88 images each of velocity, intensity, and modulation obtained at 20:00 UT on 88 days from July 1992 to February 1994. Each velocity image was temporally filtered to remove the p-mode oscillations, masked to exclude active regions, and then analyzed using spherical harmonics and orthogonal functions as described by Hathaway (1992). The spectral coefficients show very consistent results for the entire time interval with some evidence of year-to-year variations. The rotation profile agrees well with previous results and exhibits a north-south asymmetry that reverses sign during the 20 month interval. The residual rotation velocities exhibit structures with amplitudes of approximately 5 m/s that may be related to torsional oscillations. The meridional circulation is directed from the equator toward the poles with a peak velocity in the photosphere of approximately 50 m/s. The higher order components are very weak but indicate a divergent flow from the mid-latitudes (opposite that found for the June 1989 data). The convective limb shift is well fit by a 3rd order polynomial. The convection spectrum has a prominent peak at spherical harmonic degrees of l approximately 150 with very little signal in the low degree modes. Analysis of this signal shows that there is no evidence for giant cell convection at the level of approximately 10 m/s for all modes up to l = 32.

Hathaway, David H.↗

NASA NTRS1999

Instrumentation and Methods to Measure Dynamic Forces During Exercise Using the Horizontal Exercise Machine

It is hypothesized that bone loss experienced by astronauts in zero gravity conditions may be curtailed by appropriate exercise. According to Wolf's law, bone regenerates when muscles produce stresses by pulling on the bone during daily activity and/or exercise on Earth. To use this theory to prevent or decrease bone loss, one needs to quantify musculoskeletal loads and relate them to bone density changes. In the context of the space program, it is desirable to determine musculoskeletal loads during exercise so that one may make similar measurements on Earth and in space. In this manner, load measurements on Earth may be used as reference to generate similar loads during exercise in space. A research project to investigate the effects of high-resistive exercise to decrease bone density loss underzero-gravity conditions is being carried out in Life Sciences Research Laboratories at NASA JSC. The project consists of a bed-rest study whereby subjects remain in horizontal position for seventeen weeks. During the study, a subset of those subjects executes a regime of resistive exercises in the horizontal exercise machine (HEM). The HEM was designed so that subjects remain horizontal while exercising to minimize gravity loading even during exercise. Bone density of each subject is measured throughout the duration of their participation. The objective of the study is to determine if the resistive exercises are effective in diminishing or eliminating bone loss. My participation in this project relates to instrumentation, measurement, and processing of signals from displacement sensors (optical encoders) and load-cells. Measurement of displacements will be used to determine the motion of the body during exercise, and load measurements will be used (along with displacement data) to determine forces and torques exerted on each section of the body during exercise. Further, I have assisted in specifying new sensors to be added to the HEM and to a new prototype resistive exercise machine called the Interim Resistive Exercise Device (IRED). New load cells and encoders should be mounted in these devices to obtain more complete kineto-dynamic information. This report includes a description of the instrumentation that was built to perform measurements in the HEM and the IRED, along with the software that was developed to collect the measurements. It also includes examples of measurements taken in the HEM. Finally, a plan is laid out that describes how these measurements may be used to determine forces exerted by muscles for each exercise.

Figueroa, Fernando↗

NASA NTRS1997

Peptide Folding and Translocation Across the Water-Membrane Interface

The ability of small peptides to organize at aqueous interfaces was examined by performing a series of large-scale, molecular dynamics computer simulations of several peptides composed of two amino acids, nonpolar leucine (L) and polar glutamine (Q). The peptides differed in size and sequence of the amino acids. Studies on dipeptides LL, LQ, QL and QQ were extended to two heptamers, LQQLLQL and LQLQLQL, designed to maximize interfacial stability of an alpha-helix and a beta-strand, respectively, by exposing polar side chains to water and nonpolar side chains to a nonpolar phase. Finally, a transition of an undecamer, composed entirely of leucine residues, from a disordered structure in water to an alpha-helix in a nonpolar phase representing the interior of the membrane was investigated. Complete folding of a peptide in solution was accomplished for the first time in computer simulations. The simulations revealed several basic principles governing the sequence-dependent organization of peptides at interfaces. Short peptides tend to accumulate at interfaces and acquire ordered structures, providing that they have a proper sequence of polar and nonpolar amino acids. The dominant factor determining the interfacial structure of peptides is the hydrophobic effect, which is manifested at aqueous interfaces as a tendency for polar and nonpolar groups of the solute to segregate into the aqueous and nonpolar phases, respectively. If peptides consist of nonpolar residue's only, they become inserted into the nonpolar phase. As demonstrated by the example of the leucine undecamer, such peptides fold into an alpha-helix as they partition into the nonpolar medium. The folding proceeds through an intermediate, called 3-10-helix, which remains in equilibrium with the alpha-helix. Once in the nonpolar environment, the peptides can readily change their orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with changing external conditions may have provided a simple mechanism of transmitting signals from the environment to the interior of a cell.

Pohorille, Andrew↗

NASA NTRS2002

Hemichordates and the Origin of Chordates

At the start of the period of the NASA grant three years ago, we had no information on the organization and development of the body axis of the hemichordate, Saccoglossus kowalevskii. Now we have substantial findings about the anteroposterior axis and dorsoventral axis, and based on this information, we have new insights about the origin of chordates from ancestral deuterostomes. We found ways to obtain and preserve large numbers of embryos and hatched juveniles. We can now collect about 40,000 embryos in the month of September, the time of S. kowalevskii spawning at Woods Hole. Excellent cDNA libraries were prepared from three developmental stages. From these libraries, we directly isolated about 30 gene ortholog sequences by screening and pcr techniques, all of these sequences of interest in the inquiry about the animal's organization and development. We also performed a mid-sized EST project (60,000 randomly picked clones, many of these arrayed). About half of these have been analyzed so far by blastx and are suitable for direct use of clones. We have obtained about 50 interesting sequences from this set. The rest still await analysis. Thus, at this time we have isolated orthologs of 80 genes that are known to be expressed in chordates in conserved domains and known to have interesting roles in chordate organization and development. The orthology of the S. kowalevskii sequences has been verified by neighbor joining and parsimony methods, with bootstrap estimates of validity. The S. kowalevskii sequences cluster with other deuterostome sequences, namely, other hemichordates, echinoderms, ascidians, amphioxus, or vertebrates, depending on what sequences are available in the database for comparison. We have used these sequences to do high quality in situ hybridization on S. kowalevskii embryos, and the results can be divided into three sections-those concerning the anteroposterior axis of S. kowalevskii in comparison to the same axis of chordates, those concerning the dorsoventral axis of S. kowalevskii in comparison to the same axis of chordates, and those concerning the signals and transcription factors found in the endoderm, of S. kowalevskii compared to the signals and transcription factors in the endo-mesodermal cells of Spemann's organizer of chordates.

Gerhart, John↗

NASA NTRS1997

Development of the Lidar Atmospheric Sensing Experiment (LASE): An Advanced Airborne DIAL Instrument

The Lidar Atmospheric Sensing Experiment (LASE) Instrument is the first fully-engineered, autonomous Differential Absorption Lidar (DIAL) System for the measurement of water vapor in the troposphere (aerosol and cloud measurements are included). LASE uses a double-pulsed Ti:Sapphire laser for the transmitter with a 30 ns pulse length and 150 mJ/pulse. The laser beam is "seeded" to operate on a selected water vapor absorption line in the 815-nm region using a laser diode and an onboard absorption reference cell. A 40 cm diameter telescope collects the backscattered signals and directs them onto two detectors. LASE collects DIAL data at 5 Hz while onboard a NASA/Ames ER-2 aircraft flying at altitudes from 16-21 km. LASE was designed to operate autonomously within the environment and physical constraints of the ER-2 aircraft and to make water vapor profile measurements across the troposphere to better than 10% accuracy. LASE has flown 19 times during the development of the instrument and the validation of the science data. This paper describes the design, operation, and reliability of the LASE Instrument.

Moore, Alvah S., Jr.↗

NASA NTRS2017

Effects of Ionizing Radiation on Murine Gene Expression in Skin and Bone

Long duration spaceflight causes a negative calcium balance and reduces bone density in astronauts. The potential for exposure to space radiation to contribute to lasting decrements in bone mass is not yet understood. Sustained changes to bone mass have a relatively long latency for development, however skin is a radiation sensitive organ and changes in skin gene expression may serve as an early radiation biomarker of exposures and may correlate with adverse effects on skeletal tissue. Previous studies have shown that FGF18 gene expression levels of hair follicles collected from astronauts on the ISS rose over time. In the hair follicle, FGF18 signaling mediates radioresistance in the telogen by arresting the cell cycle, and FGF18 has the potential to function as a radioprotector. In bone, FGF18 appears to regulate cell proliferation and differentiation positively during osteogenesis and negatively during chondrogenesis. Cellular defense responses to radiation are shared by a variety of organs, hence in this study, we examined whether radiation induced gene expression changes in skin may be predictive of the responses of skeletal tissue to radiation exposure. We have examined oxidative stress and growth arrest pathways in mouse skin and long bones by measuring gene expression levels via quantitative polymerase chain reaction (qPCR) after exposure to total body irradiation (TBI). To investigate the effects of irradiation on gene expression, we used skin and femora (cortical shaft) from the following treatment groups: control (normally loaded, sham-irradiated), and TBI (0.5 Gy Fe-56 600 MeV/n and 0.5 Gy H-1 150 MeV/n). Animals were euthanized one and 11 days post-IR. Statistical analysis was performed via a Student's ttest. In skin samples one day after IR, skin expression of FGF18 was significantly greater (3.8X) than sham-irradiated controls (3.8X), but did not differ 11 days post TBI. Expression levels of other radiation related genes (Nfe2l2, Trp53, Cdkn1a, FoxO3, Gadd45g, SOD1), was not different due to TBI at either time point. In bone (femora) TBI significantly increased (3.8X) expression of the pro-bone resorption cytokine, MCP-1, one day after TBI. FGF18 expression in skin and MCP- 1 expression in bone were found to be positively correlated (P less than 0.002, r=0.8779). Further, microcomputed tomography analysis of tibae from these animals showed reduced fractional cancellous bone volume (-21.7%) at 11 days post exposure. These results suggest that early radiation induced changes in FGF18 gene expression in skin may have value for predicting subsequent loss of cancellous bone mass.

space radiation↗

DOE OSTI2025

An Arbitrary Time Interval Generator Base on Vernier Clocks with 0.67 ps Adjustable Steps Implemented in FPGA

In TDC testing and timing system implementations, it is often necessary to generate signal pulses with finely adjustable time intervals. In delay cell–based schemes, the adjustment resolution is constrained by the propagation delay of the cells—typically 15–20 ps per step—and is sensitive to temperature and supply voltage variations. This document presents a fully digital approach that uses two vernier clocks, generated by two stages of cascaded phase-locked loops (PLLs) with a slight frequency difference, to achieve adjustable timing intervals through accumulated phase differences. The scheme was validated on two families of low-cost FPGA devices, achieving adjustable step sizes of 0.67 ps and 0.97 ps.

Wu, Jin-yuan [Fermilab] (ORCID:0000000344329521)↗

DOE OSTI2021

TRIM27-mediated ubiquitination of PPARγ promotes glutamate-induced cell apoptosis and inflammation

Neurotoxicity induced by glutamate (Glu) is often used to study the signaling mechanism of neurological disorders. The identification of specific genetic factors that cause Glu-induced neurotoxicity provides evidence for the common pathways of neuronal apoptosis and inflammation. TRIM27 has been found to induce apoptosis and inflammation. Nevertheless, there is little evidence that TRIM27 is associated with Glu-induced neurotoxicity. We found that TRIM27 expression was increased in epilepsy patients and in HT22 cells following Glu treatment. Glu-mediated cell apoptosis, decreased PPARγ expression, and increased levels of cleaved Caspase-3 and IL-1β expression in HT22 cells were significantly inhibited by TRIM27 knockdown. TRIM27 overexpression significantly induced cell apoptosis and expression of cleaved Caspase-3 and IL-1β, but inhibited PPARγ expression in HT22 cells, which were reversed by ROZ, suggesting the involvement of PPARγ in TRIM27-mediated cell apoptosis and inflammation in HT22 cells. Mechanically, TRIM27 ubiquitinates and degrades PPARγ, following induces cleaved Caspase-3 and IL-1β expression. Clinically, increased expression of TRIM27 in epilepsy patients was associated with decreased PPARγ expression. Taken together, our study suggests that TRIM27-mediated ubiquitination of PPARγ promotes Glu-induced HT22 cell apoptosis and IL-1β release.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1997

Intracellular pH changes in human aortic smooth muscle cells in response to fluid shear stress

The smooth muscle cell (SMC) layers of human arteries may be exposed to blood flow after endothelium denudation, for example, following balloon angioplasty treatment. These SMCs are also constantly subjected to pressure driven transmural fluid flow. Flow-induced shear stress can alter SMC growth and metabolism. Signal transduction mechanisms involved in these flow effects on SMCs are still poorly understood. In this work, the hypothesis that shear stress alters the intracellular pH (pHi) of SMC is examined. When exposed to venous and arterial levels of shear stress, human aortic smooth muscle cells (hASMC) undergo alkalinization. The alkalinization plateau persisted even after 20 min of cell exposure to flow. Addition of amiloride (10 micromoles) or its 5-(N-ethyl-N-isopropyl) analog (EIPA, 10 micromoles), both Na+/H+ exchanger inhibitors, attenuated intracellular alkalinization, suggesting the involvement of the Na+/H+ exchanger in this response. The same concentrations of these inhibitors did not show an effect on pHi of hASMCs in static culture. 4-Acetamido-4'-isothio-cyanatostilbene-2,2'-disulfonic acid (SITS, 1 mM), a Cl-/HCO3- exchange inhibitor, affected the pHi of hASMCs both in static and flow conditions. Our results suggest that flow may perturb the Na+/H+ exchanger leading to an alkalinization of hASMCs, a different response from the flow-induced acidification seen with endothelial cells at the same levels of shear stress. Understanding the flow-induced signal transduction pathways in the vascular cells is of great importance in the tissue engineering of vascular grafts. In the case of SMCs, the involvement of pHi changes in nitric oxide production and proliferation regulation highlights further the significance of such studies.

NASA Discipline Cell Biology↗