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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Generating Mixed Patterns of Residential Segregation: An Evolutionary Approach

The Schelling model of residential segregation has demonstrated that even the slightest preference for neighbors of the same race can be amplified into community-wide segregation. However, these models are unable to simulate mixed, coexisting patterns of segregation and integration, which have been seen to exist in cities. Using evolutionary model discovery we demonstrate how including social factors beyond racial bias when modeling relocation behavior enables the emergence of strongly mixed patterns. Our results indicate that the emergence of mixed patterns is better explained by multiple factors influencing the decision to relocate; the most important being the interaction of nonlinear, rapidly diminishing racial bias with a recent, historical tendency to move. Additionally, preference for less isolated neighborhoods or preference for neighborhoods with longer residing neighbors may produce weaker mixed patterns. Finally, this work highlights the importance of exploring the influence of multiple hypothesized factors of decision making, and their interactions, within agent rules, when studying emergent outcomes generated by agent-based models of complex social systems.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1999

Orthologs, paralogs and genome comparisons

During the past decade, ancient gene duplications were recognized as one of the main forces in the generation of diverse gene families and the creation of new functional capabilities. New tools developed to search data banks for homologous sequences, and an increased availability of reliable three-dimensional structural information led to the recognition that proteins with diverse functions can belong to the same superfamily. Analyses of the evolution of these superfamilies promises to provide insights into early evolution but are complicated by several important evolutionary processes. Horizontal transfer of genes can lead to a vertical spread of innovations among organisms, therefore finding a certain property in some descendants of an ancestor does not guarantee that it was present in that ancestor. Complete or partial gene conversion between duplicated genes can yield phylogenetic trees with several, apparently independent gene duplications, suggesting an often surprising parallelism in the evolution of independent lineages. Additionally, the breakup of domains within a protein and the fusion of domains into multifunctional proteins makes the delineation of superfamilies a task that remains difficult to automate.

Non-NASA Center↗
DOE OSTI2021

Deep representation learning improves prediction of LacI-mediated transcriptional repression

Significance The understanding of protein function increases with new experimental and evolutionary datasets. A major challenge is to apply machine learning to these datasets to capture essential features of protein function. Here, we analyze the experimentally determined repression function for tens of thousands of mutants of the LacI protein. This study provides a continuous, noncategorical repression value across a majority of all single mutations and for thousands of higher-order mutations. To develop a top-performing model for the prediction of repression by LacI, we compare several leading variant effect prediction algorithms. A deep representation learning paradigm, first trained across millions of proteins from all known protein families and then fine-tuned using LacI experimental data, offers the highest predictive performance of repression function.

42 ENGINEERING↗
NASA NTRS2003

Afferent innervation patterns of the saccule in pigeons

The innervation patterns of vestibular saccular afferents were quantitatively investigated in pigeons using biotinylated dextran amine as a neural tracer and three-dimensional computer reconstruction. Type I hair cells were found throughout a large portion of the macula, with the highest density observed in the striola. Type II hair cells were located throughout the macula, with the highest density in the extrastriola. Three classes of afferent innervation patterns were observed, including calyx, dimorph, and bouton units, with 137 afferents being anatomically reconstructed and used for quantitative comparisons. Calyx afferents were located primarily in the striola, innervated a number of type I hair cells, and had small innervation areas. Most calyx afferent terminal fields were oriented parallel to the anterior-posterior axis and the morphological polarization reversal line. Dimorph afferents were located throughout the macula, contained fewer type I hair cells in a calyceal terminal than calyx afferents and had medium sized innervation areas. Bouton afferents were restricted to the extrastriola, with multi-branching fibers and large innervation areas. Most of the dimorph and bouton afferents had innervation fields that were oriented dorso-ventrally but were parallel to the neighboring reversal line. The organizational morphology of the saccule was found to be distinctly different from that of the avian utricle or lagena otolith organs and appears to represent a receptor organ undergoing evolutionary adaptation toward sensing linear motion in terrestrial and aerial species.

NASA Discipline Neuroscience↗
DOE OSTI2022

The influence of Hickson-like compact group environment on galaxy luminosities

Compact groups of galaxies are devised as extreme environments where interactions may drive galaxy evolution. In this work, we analysed whether the luminosities of galaxies inhabiting compact groups differ from those of galaxies in loose galaxy groups. We computed the luminosity functions of galaxy populations inhabiting a new sample of 1412 Hickson-like compact groups of galaxies identified in the Sloan Digital Sky Survey Data Release 16. We observed a characteristic absolute magnitude for galaxies in compact groups brighter than that observed in the field or loose galaxy systems. We also observed a deficiency of faint galaxies in compact groups in comparison with loose systems. Our analysis showed that the brightening is mainly due to galaxies inhabiting the more massive compact groups. In contrast to what is observed in loose systems, where only the luminosities of Red (and Early) galaxies show a dependency with group mass, luminosities of Red and Blue (also Early and Late) galaxies in compact groups are affected similarly as a function of group virial mass. When using Hubble types, we observed that elliptical galaxies in compact groups are the brightest galaxy population, and groups dominated by an elliptical galaxy also display the brightest luminosities in comparison with those dominated by spiral galaxies. Moreover, we show that the general luminosity trends can be reproduced using a mock catalogue obtained from a semi-analytical model of galaxy formation. These results suggest that the inner extreme environment in compact groups prompts a different evolutionary history for their galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2014

Towards Co-evolution of Membrane Transport and Metabolism

Protocellular boundaries were inextricably connected to the metabolism they encapsulated: to be inheritable, early metabolism must have led to an increased rate of growth and division of vesicles and, similarly, transport through vesicle boundaries must have supported the evolution of metabolism. Even though explaining how this coupling emerged and evolved in the absence of the complex machinery of modern cells is one of the key issues in studies on the origin of life, little is known about the biochemical and biophysical processes that might have been involved. This gap in our knowledge is a major impediment in efforts to construct scenarios for the origin of life and laboratory models of protocells. A combination of experimental and computational studies carried out by us and our collaborators is aimed at helping to close this gap. Properties of membranes might have contributed to the selection of RNA as an early biopolymer. A kinetic mechanism was proposed (Sacerdote & Szostak, 2005) in which ribose was supplied more quickly than other aldopentoses to primordial cells for preferential incorporation of ribonucleotides into nucleic acids. This proposal is based on a finding that ribose permeates membranes an order of magnitude faster than its diastereomers, arabinose and xylose. Our computer simulations, which yield permeation rates in excellent agreement with experiment, and kinetic modeling explain this phenomenon in terms of inter- and intramolecular interactions involving exocyclic hydroxyl groups attached to carbon atoms of the pyranose ring (Wei and Pohorille, 2009). They also constrain scenarios for the formation of the earliest nucleic acids (Wei and Pohorille, 2013). In one scenario, sugars permeate protocellular walls and subsequently are used to synthesize nucleic acids inside protocells. As long as this process proceeds at the rate faster than 6x10(exp -3)/s, ribose derivatives will be available for synthesis easier than their diastereomers. If nucleosides or their activated derivatives are synthesized outside protocells and subsequently transported across protocellular membranes the kinetic mechanism does not apply because all diastereomers, which have their sugars in the furanose rather than pyranose form, permeate the membrane at approximately the same rate. Properties of membranes might have been also coupled to metabolism involving peptides. Recently, Adamala and Szostak (2013) have shown that a dipeptide inside fatty-acid vesicles catalyzes the formation of another dipeptide that binds to vesicle walls and, by doing so, promotes their growth at the expense of other vesicles. This coupling of metabolism, permeability of vesicles and their growth is the first demonstration of evolutionary advantage imparted by small, membrane-bound peptides. Building on this work we have calculated the rate at which different blocked amino acids are delivered to a protocell for synthesis of dipeptides. We have further shown that the dipeptides are located at the water-membrane interface rather than in the center of the bilayer. On these basis it is anticipated that other dipeptides containing aromatic, but not necessarily hydrophobic amino acids (e.g. tyrosine) could have the same catalytic effects. Insight from these studies allows for estimating the rate of vesicle growth and the rates of dipeptide synthesis required to keep the system in balance. These results, in combination with our earlier studies, lead to a general scenario for evolution from membrane-bound dipeptides to ion channels in the origin of life.

Metabolism↗
DOE OSTI2025

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

The Nature and Evolutionary History of GRO J1744-28

GRO J1744-28 is the first known X-ray source to display bursts, periodic pulsations, and quasi-periodic oscillations. This source may thus provide crucial clues that will lead to an understanding of the differences in the nature of the X-ray variability from various accreting neutron stars. The orbital period is 11.8 days, and the measured mass function of 1.31 x 10(exp -4) solar mass is one of the smallest among all known binaries. If we assume that the donor star is a low-mass giant transferring matter through the inner Lagrange point, then we can show that its mass is lower than approximately 0.7 solar mass and probably closer to 0.25 solar mass. Higher mass, but unevolved, donor stars are shown to be implausible. We also demonstrate that the current He core mass of the donor star lies in the range of 0.20-0.25 solar mass. Thus, this system is most likely in the final stages of losing its hydrogen-rich envelope, with only a small amount of mass remaining in the envelope. If this picture is correct, then GRO J1744-28 may well represent the closest observational link that we have between the low-mass X-ray binaries and recycled binary pulsars in wide orbits. We have carried out a series of binary evolution calculations and explored, both systematically and via a novel Monte Carlo approach, the range of initial system parameters and input physics that can lead to the binary parameters of the present-day GRO J1744-28 system. The input parameters include both the initial total mass and the core mass of the donor star, the neutron-star mass, the strength of the magnetic braking, the mass-capture fraction, and the specifics of the core mass/radius relation for giants. Through these evolution calculations, we compute probability distributions for the current binary system parameters (i.e., the total mass, core mass, radius, luminosity, and K-band magnitude of the donor star, the neutron star mass, the orbital inclination angle, and the semimajor axis of the binary). Our calculations yield the following values for the GRO J1744-28 system parameters (with 95% confidence limits in parentheses): donor star mass: 0.24 solar mass (0.2-0.7 solar mass); He core mass of the donor star: 0.22 solar mass (0.20-0.25 solar mass); neutron-star mass: 1.7 solar mass (1.39-1.96 solar mass); orbital inclination angle: 18deg (7deg-22deg); semi- major axis: 64 lt-s (60-67 lt-s); radius of the donor star: 6.2 solar radius(6-9 solar radius); luminosity of donor star: 23 solar luminosity (15-49 solar luminosity), and long-term mass transfer rate at the current epoch: 5 x 10(exp -10)solar mass/yr (2 x 10(exp -10) to 5 x 10(exp -9)solar mass/yr). We deduce that the magnetic field of the underlying neutron star lies in the range of approximately 1.8 x 10(exp 11)G to approximately 7 x 10(exp 11)G, with a most probable value of 2.7 x 10(exp 11)G. This is evidently sufficiently strong to funnel the accretion flow onto the magnetic polar caps and suppress the thermonuclear flashes that would otherwise give rise to the type 1 X-ray bursts observed in most X-ray bursters. We present a simple paradigm for magnetic accreting neutron stars where X-ray pulsars, GRO J1744-28, the Rapid Burster, and the type 1 X-ray bursters may form a continuum of possible behaviors among accreting neutron stars, with the strength of the neutron-star magnetic field serving as a crucial parameter that determines the mode of X-ray variability from a given object.

Rappaport, S.↗
NASA NTRS2008

Distributed Aviation Concepts and Technologies

Aviation has experienced one hundred years of evolution, resulting in the current air transportation system dominated by commercial airliners in a hub and spoke infrastructure. While the first fifty years involved disruptive technologies that required frequent vehicle adaptation, the second fifty years produced a stable evolutionary optimization of decreasing costs with increasing safety. This optimization has resulted in traits favoring a centralized service model with high vehicle productivity and cost efficiency. However, it may also have resulted in a system that is not sufficiently robust to withstand significant system disturbances. Aviation is currently facing rapid change from issues such as environmental damage, terrorism threat, congestion and capacity limitations, and cost of energy. Currently, these issues are leading to a loss of service for weaker spoke markets. These catalysts and a lack of robustness could result in a loss of service for much larger portions of the aviation market. The impact of other competing transportation services may be equally important as casual factors of change. Highway system forecasts indicate a dramatic slow down as congestion reaches a point of non-linearly increasing delay. In the next twenty-five years, there is the potential for aviation to transform itself into a more robust, scalable, adaptive, secure, safe, affordable, convenient, efficient and environmentally friendly system. To achieve these characteristics, the new system will likely be based on a distributed model that enables more direct services. Short range travel is already demonstrating itself to be inefficient with a centralized model, providing opportunities for emergent distributed services through air-taxi models. Technologies from the on-demand revolution in computers and communications are now available as major drivers for aviation on-demand adaptation. Other technologies such as electric propulsion are currently transforming the automobile industry, and will also significantly alter the functionality of future distributed aviation concepts. Many hurdles exist, including technology, regulation, and perception. Aviation has an inherent governmental role not present in other recent on-demand transformations, which may pose a risk of curtailing aviation democratization .

Moore, Mark D.↗
DOE OSTI2025

Naturally ornate RNA-only complexes revealed by cryo-EM

The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, each empty except for a disordered loop. Extensive intramolecular and intermolecular A-minor interactions, kissing loops, an unusual A–A helix and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Toward Consistent High-Fidelity Quantum Learning on Unstable Devices via Efficient In-Situ Calibration

In the near-term noisy intermediate-scale quantum (NISQ) era, high noise will significantly reduce the fidelity of quantum computing. What's worse, recent works reveal that the noise on quantum devices is not stable, that is, the noise is dynamically changing over time. This leads to an imminent challenging problem: At run-time, is there a way to efficiently achieve a consistent high-fidelity quantum system on unstable devices? To study this problem, we take quantum learning (a.k.a., variational quantum algorithm) as a vehicle, which has a wide range of applications, such as combinatorial optimization and machine learning. A straightforward approach is to optimize a variational quantum circuit (VQC) with a parameter-shift approach on the target quantum device before using it; however, the optimization has an extremely high time cost, which is not practical at run-time. To address the pressing issue, in this paper, we proposed a novel quantum pulse-based noise adaptation framework, namely QuPAD. In the proposed framework, first, we identify that the CNOT gate is the fidelity bottleneck of the conventional VQC, and we employ a more robust parameterized multi-qubit gate (i.e., Rzx gate) to replace CNOT gate. Second, by benchmarking Rzx gate with different parameters, we build a fitting function for each coupling qubit pair, such that the deviation between the theoretic output of Rzx gate and its on-device output under a given pulse amplitude and duration can be efficiently predicted. On top of this, an evolutionary algorithm is devised to identify the pulse amplitude and duration of each Rzx gate (i.e., calibration) and find the quantum circuits with high fidelity. Experiments show that the runtime on quantum devices of QuPAD with 8–10 qubits is less than 15 minutes, which is up to 270 x faster than the parameter-shift approach. In addition, compared to the vanilla VQC as a baseline, QuPAD can achieve 59.33% accuracy gain on a classification task, and average 66.34% closer to ground state energy for molecular simulation.

Hu, Zhirui↗
DOE OSTI2021

The Swan: Data-driven Inference of Stellar Surface Gravities for Cool Stars from Photometric Light Curves

Stellar light curves are well known to encode physical stellar properties. Precise, automated, and computationally inexpensive methods to derive physical parameters from light curves are needed to cope with the large influx of these data from space-based missions such as Kepler and TESS. Here we present a new methodology that we call “The Swan,” a fast, generalizable, and effective approach for deriving stellar surface gravity (logg) for main-sequence, subgiant, and red giant stars from Kepler light curves using local linear regression on the full frequency content of Kepler long-cadence power spectra. With this inexpensive data-driven approach, we recover logg to a precision of ~0.02 dex for 13,822 stars with seismic logg values between 0.2 and 4.4 dex and ~0.11 dex for 4646 stars with Gaia-derived logg values between 2.3 and 4.6 dex. We further develop a signal-to-noise metric and find that granulation is difficult to detect in many cool main-sequence stars (T {sub eff} ≲ 5500 K), in particular K dwarfs. By combining our logg measurements with Gaia radii, we derive empirical masses for 4646 subgiant and main-sequence stars with a median precision of ~7%. Finally, we demonstrate that our method can be used to recover logg to a similar mean absolute deviation precision for a TESS baseline of 27 days. Our methodology can be readily applied to photometric time series observations to infer stellar surface gravities to high precision across evolutionary states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Stellar migration and chemical enrichment in the milky way disc: a hybrid model

ABSTRACT We develop a hybrid model of galactic chemical evolution that combines a multiring computation of chemical enrichment with a prescription for stellar migration and the vertical distribution of stellar populations informed by a cosmological hydrodynamic disc galaxy simulation. Our fiducial model adopts empirically motivated forms of the star formation law and star formation history, with a gradient in outflow mass loading tuned to reproduce the observed metallicity gradient. With this approach, the model reproduces many of the striking qualitative features of the Milky Way disc’s abundance structure: (i) the dependence of the [O/Fe]–[Fe/H] distribution on radius Rgal and mid-plane distance |z|; (ii) the changing shapes of the [O/H] and [Fe/H] distributions with Rgal and |z|; (iii) a broad distribution of [O/Fe] at sub-solar metallicity and changes in the [O/Fe] distribution with Rgal, |z|, and [Fe/H]; (iv) a tight correlation between [O/Fe] and stellar age for [O/Fe] > 0.1; (v) a population of young and intermediate-age α-enhanced stars caused by migration-induced variability in the Type Ia supernova rate; (vi) non-monotonic age–[O/H] and age–[Fe/H] relations, with large scatter and a median age of ∼4 Gyr near solar metallicity. Observationally motivated models with an enhanced star formation rate ∼2 Gyr ago improve agreement with the observed age–[Fe/H] and age–[O/H] relations, but worsen agreement with the observed age–[O/Fe] relation. None of our models predict an [O/Fe] distribution with the distinct bimodality seen in the observations, suggesting that more dramatic evolutionary pathways are required. All code and tables used for our models are publicly available through the Versatile Integrator for Chemical Evolution (VICE; https://pypi.org/project/vice).

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2001

MHD Energy Bypass Scramjet Engine

Revolutionary rather than evolutionary changes in propulsion systems are most likely to decrease cost of space transportation and to provide a global range capability. Hypersonic air-breathing propulsion is a revolutionary propulsion system. The performance of scramjet engines can be improved by the AJAX energy management concept. A magneto-hydro-dynamics (MHD) generator controls the flow and extracts flow energy in the engine inlet and a MHD accelerator downstream of the combustor accelerates the nozzle flow. A progress report toward developing the MHD technology is presented herein. Recent theoretical efforts are reviewed and ongoing experimental efforts are discussed. The latter efforts also include an ongoing collaboration between NASA, the US Air Force Research Laboratory, US industry, and Russian scientific organizations. Two of the critical technologies, the ionization of the air and the MHD accelerator, are briefly discussed. Examples of limiting the combustor entrance Mach number to a low supersonic value with a MHD energy bypass scheme are presented, demonstrating an improvement in scramjet performance. The results for a simplified design of an aerospace plane show that the specific impulse of the MHD-bypass system is better than the non-MHD system and typical rocket over a narrow region of flight speeds and design parameters. Equilibrium ionization and non-equilibrium ionization are discussed. The thermodynamic condition of air at the entrance of the engine inlet determines the method of ionization. The required external power for non-equilibrium ionization is computed. There have been many experiments in which electrical power generation has successfully been achieved by magneto-hydrodynamic (MHD) means. However, relatively few experiments have been made to date for the reverse case of achieving gas acceleration by the MHD means. An experiment in a shock tunnel is described in which MHD acceleration is investigated experimentally. MHD has several potential aerospace applications. The first is to improve the performance of hypersonic air-breathing engines for space launch and cruise vehicles. The second is to improve the performance of a high enthalpy wind tunnel. The third is to control a hypersonic vehicle. With such applications in mind, theoretical and experiments are being conducted at the NASA Ames Research Center to develop the MHD technology.

Mehta, Unmeel B.↗
DOE OSTI2020

Geometry-Driven Detection, Tracking and Visual Analysis of Viscous and Gravitational Fingers

Viscous and gravitational flow instabilities cause a displacement front to break up into finger-like fluids. The detection and evolutionary analysis of these fingering instabilities are critical in multiple scientific disciplines such as fluid mechanics and hydrogeology. However, previous detection methods of the viscous and gravitational fingers are based on density thresholding, which provides limited geometric information of the fingers. The geometric structures of fingers and their evolution are important yet little studied in the literature. In this work, we explore the geometric detection and evolution of the fingers in detail to elucidate the dynamics of the instability. Additionally, we propose a ridge voxel detection method to guide the extraction of finger cores from three-dimensional (3D) scalar fields. After skeletonizing finger cores into skeletons, we design a spanning tree based approach to capture how fingers branch spatially from the finger skeletons. Finally, we devise a novel geometric-glyph augmented tracking graph to study how the fingers and their branches grow, merge, and split over time. Feedback from earth scientists demonstrates the usefulness of our approach to performing spatio-temporal geometric analyses of fingers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Origin and evolution of HIV-1 subtype A6

Background: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. Methods: For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. Results: Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. Conclusion: The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Early prediction of antigenic transitions for influenza A/H3N2

Influenza A/H3N2 is a rapidly evolving virus which experiences major antigenic transitions every two to eight years. Anticipating the timing and outcome of transitions is critical to developing effective seasonal influenza vaccines. Using a published phylodynamic model of influenza transmission, we identified indicators of future evolutionary success for an emerging antigenic cluster and quantified fundamental trade-offs in our ability to make such predictions. The eventual fate of a new cluster depends on its initial epidemiological growth rate––which is a function of mutational load and population susceptibility to the cluster––along with the variance in growth rate across co-circulating viruses. Logistic regression can predict whether a cluster at 5% relative frequency will eventually succeed with ~80% sensitivity, providing up to eight months advance warning. As a cluster expands, the predictions improve while the lead-time for vaccine development and other interventions decreases. However, attempts to make comparable predictions from 12 years of empirical influenza surveillance data, which are far sparser and more coarse-grained, achieve only 56% sensitivity. By expanding influenza surveillance to obtain more granular estimates of the frequencies of and population-wide susceptibility to emerging viruses, we can better anticipate major antigenic transitions. This provides added incentives for accelerating the vaccine production cycle to reduce the lead time required for strain selection.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/~mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages. (c) 2002 Elsevier Science (USA).

Non-NASA Center↗