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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 NTRS1992

Evolution of catalytic RNA in the laboratory

We are interested in the biochemistry of existing RNA enzymes and in the development of RNA enzymes with novel catalytic function. The focal point of our research program has been the design and operation of a laboratory system for the controlled evolution of catalytic RNA. This system serves as working model of RNA-based life and can be used to explore the catalytic potential of RNA. Evolution requires the integration of three chemical processes: amplification, mutation, and selection. Amplification results in additional copies of the genetic material. Mutation operates at the level of genotype to introduce variability, this variability in turn being expressed as a range of phenotypes. Selection operates at the level of phenotype to reduce variability by excluding those individuals that do not conform to the prevailing fitness criteria. These three processes must be linked so that only the selected individuals are amplified, subject to mutational error, to produce a progeny distribution of mutant individuals. We devised techniques for the amplification, mutation, and selection of catalytic RNA, all of which can be performed rapidly in vitro within a single reaction vessel. We integrated these techniques in such a way that they can be performed iteratively and routinely. This allowed us to conduct evolution experiments in response to artificially-imposed selection constraints. Our objective was to develop novel RNA enzymes by altering the selection constraints in a controlled manner. In this way we were able to expand the catalytic repertoire of RNA. Our long-range objective is to develop an RNA enzyme with RNA replicase activity. If such an enzyme had the ability to produce additional copies of itself, then RNA evolution would operate autonomously and the origin of life will have been realized in the laboratory.

Joyce, Gerald F.↗

NASA NTRS1994

Physiological and genetic characterization of plant growth and gravitropism in LED light sources

Among the many problems of growing plants in completely controlled environments, such as those anticipated for the space station and the CELSS program, is the need to provide light that is both adequate for photosynthesis and of proper quality for normal growth and development. NASA scientists and engineers have recently become interested in the possibility of utilizing densely packed, solid state, light emitting diodes (LED's) as a source for this light. Unlike more conventional incandescent or electrical discharge lamps, these sources are highly monochromatic and lack energy in spectral regions thought to be important for normal plant development. In addition, a recent observation by NASA scientist has suggested that infra-red LED's, that are routinely used as photographic safelights for plants grown in darkness, may interact with the ability of plants to detect gravity. In order to establish how plants respond to light from these LED light sources we carried out a series of experiments with known pigment mutants of the model mustard plant, Arabidopsis thaliana, growing in either a gravity field or on a clinostat to simulate a micro-gravity environment. Results indicate that only red light from the 665 nm LED's disrupts the ability of normal wildtype seedlings to detect a gravity stimulus. There was no consistent effect found for the far-red (735 nm) LED's or either of the infrared (880 nm or 935 nm) LED sources but both showed some effect in one or more of the genotypes tested. Of these five members of the phytochrome multigene family in Arabidopsis, only the phytochrome B pigment mutant (hy3) lacked the ability to detect gravity under all conditions. There was no effect of either micro-gravity (clinostat) or the infra-red LED's on the light induced inhibition of hypocotyl elongation. Measurements of the pigment phytochrome in oats also showed no photoconversion by 15 min irradiations with the infra-red LED's. We conclude that phytochrome B is required for the perception of gravity and that only red light is able to disrupt this perception. The infra-red LED's also do not appear to interact with gravity perception in Arabidopsis, but caution should be exercised if infra-red LED's are to be used as photographic safelights for these types of experiments.

Deitzer, Gerald F.↗

NASA NTRS1995

Immune Alterations in Male and Female Mice after 2-Deoxy-D-Glucose Administration

Administration of 2-deoxy-D-glucose (2-DG), an analog of glucose which inhibits glycolysis by competitive antagonism for phosphohexose isomerase, results in acute periods of intracellular glucoprivation and hyperglycemia resulting in hyperphagia. In addition to these changes in the carbohydrate metabolism, injection of 2-DG results in alterations of both the endocrine and neurological systems as suggested by modifications in oxytocin and glucocorticoid levels and norepinephrine production. Moreover, alterations of the immune response, such as a decrease in the in vitro proliferation of splenocytes after mitogen-stimulation, were observed in mice injected with 2-DG. Sex, genotype and environment are among the factors that may modulate effects of catecholamines and hypothalamo-pituitary-adrenal axis on these immune changes. Sexual dimorphism in immune function resulting from the effects of sex hormones on immune effector cells has been shown in both animals and humans. These observations have important implications, especially with regard to higher incidence of many autoimmune diseases in females. Evidence exists that reproductive hormones influence the immune system and increase the risk of immunologically related disorders in both animals and humans. Indeed, immunological responses in stressful situations may also be confounded by fluctuations of sex hormones especially in females. Lymphocyte distribution, cytoldne production, and the ability of lymphocyte to proliferate in vitro were analyzed in male and female mice to determine if sex influenced 2-DG immunomodulation. In addition, the influence of hormones, especially sex hormones, on these changes were evaluated.

Dreau, Didier↗

NASA NTRS1997

Theories of Simplification and Scaling of Spatially Distributed Processes

The problem of scaling is at the heart of ecological theory, the essence of understanding and of the development of a predictive capability. The description of any system depends on the spatial, temporal, and organizational perspective chosen; hence it is essential to understand not only how patterns and dynamics vary with scale, but also how patterns at one scale are manifestations of processes operating at other scales. Evolution has shaped the characteristics of species in ways that result in scale displacement: Each species experiences the environment at its own unique set of spatial and temporal scales and interfaces the biota through unique assemblages of phenotypes. In this way, coexistence becomes possible, and biodiversity is enhanced. By averaging over space, time, and biological interactions, a genotype filters variation at fine scales and selects the arena in which it will face the vicissitudes of nature. Variation at finer scales is then noise, of minor importance to the survival and dynamics of the species, and consequently of minor importance in any attempt at description. In attempting to model ecological interactions in space, contributors throughout this book have struggled with a trade-off between simplification and "realistic" complexity and detail. Although the challenge of simplification is widely recognized in ecology, less appreciated is the intertwining of scaling questions and scaling laws with the process of simplification. In the context of this chapter simplification will in general mean the use of spatial or ensemble means and low-order moments to capture more detailed interactions by integrating over given areas. In this way, one can derive descriptions of the system at different spatial scales, which provides the essentials for the extraction of scaling laws by examination of how system properties vary with scale.

Levin, Simon A.↗

NASA NTRS2000

JavaGenes: Evolving Graphs with Crossover

Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

Globus, Al↗

NASA NTRS2004

Best of Breed

No team of engineers, no matter how much time they took or how many bottles of cabernet they consumed, would dream up an antenna that looked like a deer antler on steroids. Yet that's what a group at NASA Ames Research Center came up with-thanks to a little help from Darwin. NASA's Space Technology 5 nanosatellites, which are scheduled to start measuring Earth's magnetosphere in late 2004, requires an antenna that can receive a wide range of frequencies regardless of the spacecraft's orientation. Rather than leave such exacting requirements in the hands of a human, the engineers decided to breed a design using genetic algorithms and 32 Linux PCs. The computers generated small antenna-constructing programs (the genotypes) and executed them to produce designs (the phenotypes). Then the designs were evaluated using an antenna simulator. The team settled on the form pictured here. You won't find this kind of antenna in any textbook, design guide, or research paper. But its innovative structure meets a challenging set of specifications. If successfully deployed, it will be the first evolved antenna to make it out of the lab and the first piece of evolved hardware ever to fly in space.

Lohn, Jason↗

NASA NTRS2004

Shortcomings with Tree-Structured Edge Encodings for Neural Networks

In evolutionary algorithms a common method for encoding neural networks is to use a tree structured assembly procedure for constructing them. Since node operators have difficulties in specifying edge weights and these operators are execution-order dependent, an alternative is to use edge operators. Here we identify three problems with edge operators: in the initialization phase most randomly created genotypes produce an incorrect number of inputs and outputs; variation operators can easily change the number of input/output (I/O) units; and units have a connectivity bias based on their order of creation. Instead of creating I/O nodes as part of the construction process we propose using parameterized operators to connect to preexisting I/O units. Results from experiments show that these parameterized operators greatly improve the probability of creating and maintaining networks with the correct number of I/O units, remove the connectivity bias with I/O units and produce better controllers for a goal-scoring task.

Hornby, Gregory S.↗

NASA NTRS2004

Carnobacterium Pleistocaenium sp. nov.: A Novel Psychrotolerant, Facultative Anaerobe Isolated from Permafrost of the Fox Tunnel in Alaska

A novel, psychrotolerant, facultative anaerobe, strain FTRIT1(sup T), was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells with sizes 0.6-0.7 x 0.9-1.5 micrometers were observed. Growth occurred within the pH range 6.5-9.5 and optimum at pH 7.3-7.5. The temperature range of the new isolate was 0-28 C and optimum growth occurred at 24 C. The novel isolate requires NaCl (growth absent at 0 %) and growth was observed between 0 and 5% NaCl with optimum at 0.5% (w/v). The new isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were: acetate, ethanol and CO2. Strain FTRl was sensitive to ampicillin, tetracycline, chloramphenicol, rifampin, kanamycin, and gentamycin. The 16S rDNA sequence analysis showed 99.8% similarity of strain FTR1 with Carnobacterium alterfunditum, but the DNA-DNA hybridization between them demonstrated 39 plus or minus 5% homology. On the basis of genotypic and phenotypic characteristics, it is proposed that the strain FTR1(sup T) (= ATCC BAA-754(sup T) = JSM 12174(sup T) is assigned to the new species of the genus Carnobacterium with proposed name Carnobacterium pleistocaenium sp. nov.

Pikuta, Elena V.↗

NASA NTRS2003

The evolution of transcriptional regulation in eukaryotes

Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.

Review, Academic↗

NASA NTRS2003

Molecular and functional analyses of the contractile apparatus in lymphatic muscle

Lymphatics are necessary for the generation and regulation of lymph flow. Lymphatics use phasic contractions and extrinsic compressions to generate flow; tonic contractions alter resistance. Lymphatic muscle exhibits important differences from typical vascular smooth muscle. In this study, the thoracic duct exhibited significant functional differences from mesenteric lymphatics. To understand the molecular basis for these differences, we examined the profiles of contractile proteins and their messages in mesenteric lymphatics, thoracic duct, and arterioles. Results demonstrated that mesenteric lymphatics express only SMB smooth muscle myosin heavy chain (SM-MHC), whereas thoracic duct and arterioles expressed both SMA and SMB isoforms. Both SM1 and SM2 isoforms of SM-MHC were detected in arterioles and mesenteric and thoracic lymphatics. In addition, the fetal cardiac/skeletal slow-twitch muscle-specific beta-MHC message was detected only in mesenteric lymphatics. All four actin messages, cardiac alpha-actin, vascular alpha-actin, enteric gamma-actin, and skeletal alpha-actin, were present in both mesenteric lymphatics and arterioles. However, in thoracic duct, predominantly cardiac alpha-actin and vascular alpha-actin were found. Western blot and immunohistochemical analyses corroborated the mRNA studies. However, in arterioles only vascular alpha-actin protein was detected. These data indicate that lymphatics display genotypic and phenotypic characteristics of vascular, cardiac, and visceral myocytes, which are needed to fulfill the unique roles of the lymphatic system.

Non-NASA Center↗

NASA NTRS2003

Toll-like receptor 4-positive macrophages protect mice from Pasteurella pneumotropica-induced pneumonia

This study investigates Toll-like receptor 4 (TLR4)-positive macrophages in early recognition and clearance of pulmonary bacteria. TLR4 is a trans-membrane receptor that is the primary recognition molecule for lipopolysaccharide of gram-negative bacteria. The TLR4(Lps-del) mouse strains C57BL10/ScN (B10) and STOCK Abb(tm1) TLR4(Lps-del) Slc11a1(s)(B10 x C2D) are susceptible to pulmonary infections and develop pneumonia when naturally or experimentally infected by the opportunistic bacterium Pasteurella pneumotropica. Since these mice have the TLR4(Lps-del) genotype, we hypothesized that reconstitution of mice with TLR4-positive macrophages would provide resistance to this bacterium. A cultured macrophage cell line (C2D macrophages) and bone marrow cells from C2D mice were adoptively transferred to B10 and B10 x C2D mice by intraperitoneal injection. C2D macrophages increased B10 and B10 x C2D mouse resistance to P. pneumotropica. In C2D-recipient mice there was earlier transcription of tumor necrosis factor alpha and chemokines JE and macrophage inflammatory protein 2 (MIP-2) in the lungs of B10 and B10 x C2D mice, and there was earlier transcription of KC and MIP-1alpha in B10 x C2D mice. In addition, the course of inflammation following experimental Pasteurella challenge was altered in C2D recipients. C2D macrophages also protected B10 x C2D mice, which lack CD4(+) T cells. These data indicate that macrophages are critical for pulmonary immunity and can provide host resistance to P. pneumotropica. This study indicates that TLR4-positive macrophages are important for early recognition and clearance of pulmonary bacterial infections.

Non-NASA Center↗

NASA NTRS2002

Characteristics of genomic instability in clones of TK6 human lymphoblasts surviving exposure to 56Fe ions

Genomic instability in the human lymphoblast cell line TK6 was studied in clones surviving 36 generations after exposure to accelerated 56Fe ions. Clones were assayed for 20 characteristics, including chromosome aberrations, plating efficiency, apoptosis, cell cycle distribution, response to a second irradiation, and mutant frequency at two loci. The primary effect of the 56Fe-ion exposure on the surviving clones was a significant increase in the frequency of unstable chromosome aberrations compared to the very low spontaneous frequency, along with an increase in the phenotypic complexity of the unstable clones. The radiation-induced increase in the frequency of unstable chromosome aberrations was much greater than that observed previously in clones of the related cell line, WTK1, which in comparison to the TK6 cell line expresses an increased radiation resistance, a mutant TP53 protein, and an increased frequency of spontaneous unstable chromosome aberrations. The characteristics of the unstable clones of the two cell lines also differed. Most of the TK6 clones surviving exposure to 56Fe ions showed unstable cytogenetic abnormalities, while the phenotype of the WTK1 clones was more diverse. The results underscore the importance of genotype in the characteristics of instability after radiation exposure.

NASA Discipline Radiation Health↗

NASA NTRS2002

Do convergent developmental mechanisms underlie convergent phenotypes?

Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies convergence in anatomy. A switch in the ecology of sea urchins from feeding to nonfeeding larvae illustrates how convergence in development can be associated with convergence in anatomy. Comparisons to more distantly related taxa, however, suggest that this association may be limited to relatively close phylogenetic comparisons. Similarities in gene expression during development provide another window into the association between convergence in developmental processes and convergence in anatomy. Several well-studied transcription factors exhibit likely cases of convergent gene expression in distantly related animal phyla. Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons. Copyright 2002 S. Karger AG, Basel.

NASA Discipline Evolutionary Biology↗

NASA NTRS2002

Genetic predisposition to low bone mass is paralleled by an enhanced sensitivity to signals anabolic to the skeleton

The structure of the adult skeleton is determined, in large part, by its genome. Whether genetic variations may influence the effectiveness of interventions to combat skeletal diseases remains unknown. The differential response of trabecular bone to an anabolic (low-level mechanical vibration) and a catabolic (disuse) mechanical stimulus were evaluated in three strains of adult mice. In low bone-mineral-density C57BL/6J mice, the low-level mechanical signal caused significantly larger bone formation rates (BFR) in the proximal tibia, but the removal of functional weight bearing did not significantly alter BFR. In mid-density BALB/cByJ mice, mechanical stimulation also increased BFR, whereas disuse significantly decreased BFR. In contrast, neither anabolic nor catabolic mechanical signals influenced any index of bone formation in high-density C3H/HeJ mice. Together, data from this study indicate that the sensitivity of trabecular tissue to both anabolic and catabolic stimuli is influenced by the genome. Extrapolated to humans, these results may explain in part why prophylaxes for low bone mass are not universally effective, yet also indicate that there may be a genotypic indication of people who are at reduced risk of suffering from bone loss.

Non-NASA Center↗

NASA NTRS1995

Diverse Thermus species inhabit a single hot spring microbial mat

Through an effort to characterize aerobic chemoorganotrophic bacteria in the Octopus Spring cyano-bacterial mat community, we cultivated four Thermus isolates with unique 16S rRNA sequences. Isolates clustered within existing Thermus clades, including those containing Thermus ruber, Thermus aquaticus, and a subgroup closely related to T. aquaticus. One Octopus Spring isolate is nearly identical (99.9% similar) to isolates from Iceland, and two others are closely related to a T. ruber isolated from Russia. Octopus Spring isolates similar to T. aquaticus and T. ruber exhibited optimal growth rates at high (65-70 degrees C) and low (50 degrees C) temperatures, respectively, with the most abundant species best adapted to the temperature of the habitat (50-55 degrees C). Our results display a diversity of Thermus genotypes defined by 16S rRNA within one hot spring microbial community. We suggest that specialization to temperature and perhaps other local environmental features controls the abundance of Thermus populations.

Non-NASA Center↗

NASA NTRS1996

Gravitropism in roots of intermediate-starch mutants of Arabidopsis

Gravitropism was studied in roots of wild type (WT) Arabidopsis thaliana (L.) Heynh. (strain Wassilewskija) and three starch-deficient mutants that were generated by T-DNA insertional mutagenesis. One of these mutants was starchless while the other two were intermediate mutants, which had 51% and 60%, respectively, of the WT amount of starch as determined by light and electron microscopy. The four parameters used to assay gravitropism were: orientation during vertical growth, time course of curvature, induction, and intermittent stimulation experiments. WT roots were much more responsive to gravity than were roots of the starchless mutant, and the intermediate starch mutants exhibited an intermediate graviresponse. Our data suggest that lowered starch content in the mutants primarily affects gravitropism rather than differential growth because both phototropic curvature and growth rates were approximately equal among all four genotypes. Since responses of intermediate-starch mutants were closer to the WT response than to the starchless mutant, it appears that 51-60% of the WT level of starch is near the threshold amount needed for full gravitropic sensitivity. While other interpretations are possible, the data are consistent with the starch statolith hypothesis for gravity perception in that the degree of graviresponsiveness is proportional to the total mass of plastids per cell.

NASA Program Space Biology↗

NASA NTRS1990

Severely reduced gravitropism in dark-grown hypocotyls of a starch-deficient mutant of Nicotiana sylvestris

Gravitropism in dark-grown hypocotyls of the wild type was compared with a starch-deficient Nicotiana sylvestris mutant (NS 458) to test the effects of starch deficiency on gravity sensing. In a time course of curvature measured using infrared video, the response of the mutant was greatly reduced compared to the wild type; 72 hours after reorientation, curvature was about 10 degrees for NS 458 and about 70 degrees for wild type. In dishes maintained in a vertical orientation, wild-type hypocotyls were predominantly vertical, whereas NS 458 hypocotyls were severely disoriented with about 5 times more orientational variability than wild type. Since the growth rates were equal for both genotypes and phototropic curvature was only slightly inhibited in NS 458, the mutation probably affects gravity perception rather than differential growth. Our data suggest that starch deficiency reduces gravitropic sensitivity more in dark-grown hypocotyls than in dark- or light-grown roots in this mutant and support the hypothesis that amyloplasts function as statoliths in shoots as well as roots.

Non-NASA Center↗