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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994–2018) and four hyperendemic Lake Victoria fishing communities (2011–2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

Background The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use. Results We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes. Conclusions AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.

Allopolyploids↗
DOE OSTI2025

Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg

The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1977

Calculations of the effects of angular momentum on the early evolution of Jupiter

Early phases in the evolutionary development of a rotating cloud of gas and dust are investigated to determine whether physically reasonable initial conditions are likely to produce a planet-satellite system with the values of specific orbital angular momentum currently observed for Jupiter and its inner satellites. Spherically symmetric computations of Jupiter's evolutionary history are reviewed, and transport of angular momentum is considered along with evolutionary sequences of individual differentially rotating models with decreasing values of equatorial radius. The problem of accounting for the present specific orbital angular momenta of Jupiter and its regular satellites is examined qualitatively, and a range of possible angular-momentum distributions in an initially tidally unstable cloud is assessed. The results show that particular physically plausible angular-momentum distributions, which could either be established as initial conditions or be caused by angular-momentum transport, will lead to favorable situations for the formation of a central planet and a surrounding rotating cloud with specific angular momentum comparable to that of the regular satellites.

Bodenheimer, P.↗
NASA NTRS1980

Atmospheric lidar multi-user instrument system definition study

A spaceborne lidar system for atmospheric studies was defined. The primary input was the Science Objectives Experiment Description and Evolutionary Flow Document. The first task of the study was to perform an experiment evolutionary analysis of the SEED. The second task was the system definition effort of the instrument system. The third task was the generation of a program plan for the hardware phase. The fourth task was the supporting studies which included a Shuttle deficiency analysis, a preliminary safety hazard analysis, the identification of long lead items, and development studies required. As a result of the study an evolutionary Lidar Multi-User Instrument System (MUIS) was defined. The MUIS occupies a full Spacelab pallet and has a weight of 1300 kg. The Lidar MUIS laser provides a 2 joule frequency doubled Nd:YAG laser that can also pump a tuneable dye laser wide frequency range and bandwidth. The MUIS includes a 1.25 meter diameter aperture Cassegrain receiver, with a moveable secondary mirror to provide precise alignment with the laser. The receiver can transmit the return signal to three single and multiple photomultiple tube detectors by use of a rotating fold mirror. It is concluded that the Lidar MUIS proceed to program implementation.

Greco, R. V.↗
NASA NTRS1980

Cosmological considerations on the diffuse gamma-ray isotropic background

Bignami et al (1979) have recently studied the problem of the origin of the diffuse gamma-ray isotropic radiation. They have concluded that within standard cosmology with Lambda = 0 and p = 0, BL Lacertae objects and Seyfert galaxies can account for most of the diffuse radiation if they have not evolved in time. For QSOs, an evolutionary factor is allowed by the data. From the study of radio data, however, it is known that strong evolutionary effects are expected. The discrepancy cannot be explained by changing the geometry of the universe. Contrary to the case of standard cosmology, it is found that in order to fit the diffuse gamma-ray background, the evolutionary function required is almost identical to the one previously determined from the study of the log N-log S relation.

Canuto, V. M.↗
NASA NTRS1980

The effect of dense cores on the structure and evolution of Jupiter and Saturn

The evolutionary and static models of Jupiter and Saturn were calculated with homogeneous solar composition mantles and dense cores of material consisting of solar abundances of SiO2, MgO, Fe, and Ni. Evolutionary sequences for Jupiter were calculated with cores of mass ranging from 2 to 8% of the Jovian mass; the Saturn sequences ranged from cores of mass of 16 to 22% of total mass. Two envelope mixtures representative of the solar abundances were used: they contained mass fraction of 0.74 and 0.77 of hydrogen, respectively, and 0.24 and 0.21 mass fractions of helium. For Jupiter, the observations of the temperature at 1 bar pressure, of radius and of internal luminosity were best fit by evolutionary models with a core mass of about 6.5% and chemical composition of 0.77 mass fraction of hydrogen and 0.21 mass fraction of helium. The cooling time calculated for Saturn was 2.6 x 10 to the 9th yr, almost a factor of 2 less than the percentage of the solar system.

Grossman, A. S.↗
NASA NTRS1985

What are mycoplasmas - The relationship of tempo and mode in bacterial evolution

In phenotype the mycoplasmas are very different from ordinary bacteria. However, genotypically (i.e., phylogenetically) they are not. On the basis of ribosomal RNA homologies the mycoplasmas belong with the clostridia, and indeed have specific clostridial relatives. Mycoplasmas are, however, unlike almost all other bacteria in the evolutionary characteristics of their ribosomal RNAs. These RNAs contain relatively few of the highly conserved oligonucleotide sequences characteristic of normal eubacterial ribosomal RNAs. This is interpreted to be a reflection of an elevated mutation rate in mycoplasma lines of descent. A general consequence of this would be that the variation associated with a mycoplasma population is augmented both in number and kind, which in turn would lead to an unusual evolutionary course, one unique in all respects. Mycoplasmas, then, are actually tachytelic bacteria. The unusual evolutionary characteristics of their ribosomal RNAs are the imprints of their rapid evolution.

Woese, C. R.↗
NASA NTRS1991

Thioredoxin and evolution

Comparisons of primary structure have revealed significant homology between the m type thioredoxins of chloroplasts and the thioredoxins from a variety of bacteria. Chloroplast thioredoxin f, by comparison, remains an enigma: certain residues are invariant with those of the other thioredoxins, but a phylogenetic relationship to bacterial or m thioredoxins seems distant. Knowledge of the evolutionary history of thioredoxin f is, nevertheless, of interest because of its role in photosynthesis. Therefore, we have attempted to gain information on the evolutionary history of chloroplast thioredoxin f, as well as m. Our goal was first to establish the utility of thioredoxin as a phylogenetic marker, and, if found suitable, to deduce the evolutionary histories of the chloroplast thioredoxins. To this end, we have constructed phylogenetic (minimal replacement) trees using computer analysis. The results show that the thioredoxins of bacteria and animals fall into distinct phylogenetic groups - the bacterial group resembling that derived from earlier 16s RNA analysis and the animal group showing a cluster consistent with known relationships. The chloroplast thioredoxins show a novel type of phylogenetic arrangement: one m type aligns with its counterpart of eukaryotic algae, cyanobacteria and other bacteria, whereas the second type (f type) tracks with animal thioredoxin. The results give new insight into the evolution of photosynthesis.

Buchanan, B. B.↗
NASA NTRS1992

Ultraviolet studies of Cepheids

We discuss whether with new evolutionary tracks we still have a problem fitting the Cepheids and their evolved companions on the appropriate evolutionary tracks. We find that with the Bertelli et al. tracks with convective overshoot by one pressure scale height the problem is essentially removed, though somewhat more mixing would give a better fit. By using the results of recent nonlinear hydrodynamic calculations, we find that we also have no problem matching the observed pulsation periods of the Cepheids with those expected from their new evolutionary masses, provided that Cepheids with periods less than 9 days are overtone pulsators. We investigate possible mass loss of Cepheids from UV studies of the companion spectrum of S Mus and from the ultraviolet spectra of the long period Cepheid l Carinae. For S Mus with a period of 9.6 days we derive an upper limit for the mass loss of M less than 10(exp -9) solar mass, if a standard velocity law is assumed for the wind. For l Carinae with a period of 35.5 days we find a probable mass loss of M is approximately 10(exp -5+/-2) solar mass.

Boehm-Vitense, Erika↗
NASA NTRS1993

Trace of planetary nebula evolution by distance-independent parameters

Using existing infrared and radio data on a sample of 432 planetary nebulae, we derived a number of distance-independent parameters for comparison with evolutionary models of planetary nebulae. We find that many of the observed properties of planetary nebulae can be explained by current central star evolutionary models, even if the time scales are subject to significant change by a factor of up to an order of magnitude. Specifically, we find that the evolutionary tracks are well separated in the radio surface brightness-central star temperature plane, therefore allowing us to determine the core mass of individual planetary nebulae. We also obtain the luminosity and gravity of the central stars of individual nebulae, from their temperature and core mass, without relying on the distance assumptions. We find that our results of the core mass are in good agreement with those of Mendez et al. (1992) and Tylenda et al. (1991). A systematic, large discrepancy is found between the luminosity found in this work and that found by Gathier and Pottasch (1986).

Zhang, C. Y.↗
NASA NTRS1994

Counts of galaxies in a merger model

A model for the photometric evolution of galaxies has been developed and has been applied to the problem of galaxy counts. The integrated colors of galaxies are calculated using the most recently computed evolutionary tracks from Maeder and collaborators complemented with evolutionary tracks derived by other authors. The asymptotic giant branch lifetime is left as a free parameter. A series of cosmological models using different values of the cosmological constant, lambda(sub 0), and the density parameter, omega(sub 0), have been computed. The universality hypothesis of the luminosity function of galaxies has been abandoned. The influence of galaxy merging on the counts has been considered in a simple manner by assuming that the number of strongly interacting galaxies in a comoving volume increases with redshift as a power law given by (1 + z)(exp 3.8). Taking a Schechter parametrization for the luminosity function of the different types of galaxies, we are able to reproduce the observations reasonably well. We have also considered models with a Gaussian distribution for the luminosity function of the brighter galaxies that provide a poorer fit to the observations. It is shown that galaxy count data are not yet able to make unambiguous cosmological statements since evolutionary assumptions are critical. In particular, an omega(sub 0) = 1, lambda(sub 0) = 0 cosmology is shown to be consistent with the data.

Colin, P.↗
NASA NTRS1994

Nonaxisymmetric evolution in protostellar disks

We present a two-dimensional, multigridded hydrodynamical simulation of the collapse of an axisymmetric, rotating, 1 solar mass protostellar cloud, which forms a resolved, hydrotastic disk. The code includes the effects of physical viscosity, radiative transfer and radiative acceleration but not magnetic fields. We examine how the disk is affected by the inclusion of turbulent viscosity by comparing a viscous simulation with an inviscid model evolved from the same initial conditions, and we derive a disk evolutionary timescale on the order of 300,000 years if alpha = 0.01. Effects arising from non-axisymmetric gravitational instabilities in the protostellar disk are followed with a three-dimensional SPH code, starting from the two-dimensional structure. We find that the disk is prone to a series of spiral instabilities with primary azimulthal mode number m = 1 and m = 2. The torques induced by these nonaxisymmetric structures elicit material transport of angular momentum and mass through the disk, readjusting the surface density profile toward more stable configurations. We present a series of analyses which characterize both the development and the likely source of the instabilities. We speculate that an evolving disk which maintains a minimum Toomre Q-value approximately 1.4 will have a total evolutionary span of several times 10(exp 5) years, comparable to, but somewhat shorter than the evolutionary timescale resulting from viscous turbulence alone. We compare the evolution resulting from nonaxisymmetric instabilities with solutions of a one-dimensional viscous diffusion equation applied to the initial surface density and temperature profile. We find that an effective alpha-value of 0.03 is a good fit to the results of the simulation. However, the effective alpha will depend on the minimum Q in the disk at the time the instability is activated. We argue that the major fraction of the transport characterized by the value of alpha is due to the action of gravitational torques, and does not arise from inherent viscosity within the smoothed particle hydrodynamics method.

Laughlin, Gregory↗
NASA NTRS1994

Rapidly rotating polytropes in general relativity

We construct an extensive set of equilibrium sequences of rotating polytropes in general relativity. We determine a number of important physical parameters of such stars, including maximum mass and maximum spin rate. The stability of the configurations against quasi-radial perturbations is diagnosed. Two classes of evolutionary sequences of fixed rest mass and entropy are explored: normal sequences which behave very much like Newtonian evolutionary sequences, and supramassive sequences which exist solely because of relativistic effects. Dissipation leading to loss of angular momentum causes a star to evolve in a quasi-stationary fashion along an evolutionary sequence. Supramassive sequences evolve towards eventual catastrophic collapse to a black hole. Prior to collapse, the star must spin up as it loses angular momentum, an effect which may provide an observational precursor to gravitational collapse to a black hole.

Cook, Gregory B.↗
NASA NTRS1994

GHRS Spectroscopy of individual stars in R136a

The installation of the Corrective Optics Space Telescope Axial Replacement (COSTAR) Instrument on the Hubble Space Telescope (HST) makes it possible to observe stars in very crowded regions with high spatial and spectral purity. To demonstrate this capability, we have used the Goddard High Resolution Spectrograph (GHRS) to obtain spectra of two stars in the dense center of the 30 Doradus ionizing cluster: R136a5, and its nearest neighbor, R136a2, only 0.17 sec away. R136a5 is shown to ben an O3f/WN star, while R136a2 is a WN4-w star. From both Wide Field/Planetary Camera (WFPC) photometry and GHRS, spectroscopy we estimate the following properties of R136a5: T(sub eff) = 42,500 K, R = 16.4 solar radius, L(sub bol) = 8 x 10(exp 5) solar luminosity, and M approx. equals 50 solar mass -- all indicating that, despite its spectral type, R136a5, as indicated by the strength of He II lambda 1640 emission. The observed mass-loss rate, dot-M = 1.8 x 10(exp -5) solar mass/yr, is an order of magnitude higher than is assumed by current stellar evolutionary models. We argue that this high rate of mass loss will alter drastically the evolutionary path of R136a5. If so, evolutionary models for massive stars require substantial revision.

Heap, Sara R.↗
NASA NTRS1995

Tests of two convection theories for red giant and red supergiant envelopes

Two theories of stellar envelope convection are considered here in the context of red giants and red supergiants of intermediate to high mass: Boehm-Vitense's standard mixing-length theory (MLT) and Canuto & Mazzitelli's new theory incorporating the full spectrum of turbulence (FST). Both theories assume incompressible convection. Two formulations of the convective mixing length are also evaluated: l proportional to the local pressure scale height (H(sub P)) and l proportional to the distance from the upper boundary of the convection zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red phase of core helium burning. Since the theoretically predicted effective temperatures for cool stars are known to be sensitive to the assigned value of the mixing length, this quantity has been individually calibrated for each evolutionary sequence. The calibration is done in a composite Hertzsprung-Russell diagram for the red giant and red supergiant members of well-observed Galactic open clusters. The MLT model requires the constant of proportionality for the convective mixing length to vary by a small but statistically significant amount with stellar mass, whereas the FST model succeeds in all cases with the mixing lenghth simply set equal to z. The structure of the deep stellar interior, however, remains very nearly unaffected by the choices of convection theory and mixing lenghth. Inside the convective envelope itself, a density inversion always occurs, but is somewhat smaller for the convectively more efficient MLT model. On physical grounds the FST model is preferable, and seems to alleviate the problem of finding the proper mixing length.

Stothers, Richard B.↗
NASA NTRS1997

Improving Search Properties in Genetic Programming

With the advancing computer processing capabilities, practical computer applications are mostly limited by the amount of human programming required to accomplish a specific task. This necessary human participation creates many problems, such as dramatically increased cost. To alleviate the problem, computers must become more autonomous. In other words, computers must be capable to program/reprogram themselves to adapt to changing environments/tasks/demands/domains. Evolutionary computation offers potential means, but it must be advanced beyond its current practical limitations. Evolutionary algorithms model nature. They maintain a population of structures representing potential solutions to the problem at hand. These structures undergo a simulated evolution by means of mutation, crossover, and a Darwinian selective pressure. Genetic programming (GP) is the most promising example of an evolutionary algorithm. In GP, the structures that evolve are trees, which is a dramatic departure from previously used representations such as strings in genetic algorithms. The space of potential trees is defined by means of their elements: functions, which label internal nodes, and terminals, which label leaves. By attaching semantic interpretation to those elements, trees can be interpreted as computer programs (given an interpreter), evolved architectures, etc. JSC has begun exploring GP as a potential tool for its long-term project on evolving dextrous robotic capabilities. Last year we identified representation redundancies as the primary source of inefficiency in GP. Subsequently, we proposed a method to use problem constraints to reduce those redundancies, effectively reducing GP complexity. This method was implemented afterwards at the University of Missouri. This summer, we have evaluated the payoff from using problem constraints to reduce search complexity on two classes of problems: learning boolean functions and solving the forward kinematics problem. We have also developed and implemented methods to use additional problem heuristics to fine-tune the searchable space, and to use typing information to further reduce the search space. Additional improvements have been proposed, but they are yet to be explored and implemented.

Janikow, Cezary Z.↗
NASA NTRS1998

Toward Evolvable Hardware Chips: Experiments with a Programmable Transistor Array

Evolvable Hardware is reconfigurable hardware that self-configures under the control of an evolutionary algorithm. We search for a hardware configuration can be performed using software models or, faster and more accurate, directly in reconfigurable hardware. Several experiments have demonstrated the possibility to automatically synthesize both digital and analog circuits. The paper introduces an approach to automated synthesis of CMOS circuits, based on evolution on a Programmable Transistor Array (PTA). The approach is illustrated with a software experiment showing evolutionary synthesis of a circuit with a desired DC characteristic. A hardware implementation of a test PTA chip is then described, and the same evolutionary experiment is performed on the chip demonstrating circuit synthesis/self-configuration directly in hardware.

Stoica, Adrian↗