Search NASA⌕ Search

SEARCH · Search NASA

Results for “Genotype”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

Evolutionary Biology↗
DOE OSTI2025

Genome assembly UWOPS 85-398.1-1

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.

Sampaio, Jose P. [UCIBIO, Departamento de Ciências↗
DOE OSTI2025

Genome assembly UFMG-CM Y6992

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.

Sampaio, Jose P. [UCIBIO, Departamento de Ciências↗
NASA NTRS1980

Effect of graded physical load on the state of the liver from morphometric data and biochemical blood indices of rats against a background of hypokinesia

Tests were conducted on 100 sexually immature inbred August and Wistar male rats in order to determine the effects hypokinesia, physical load and phenamine on the liver. Weight and linear dimension fell in hypokinesia; total serum protein lowered and aldolase and cholesterol and beta-lipoprotein levels rose. Blood sugar content rose and liver glycogen fell. Interlinear differences of these indices are found. Rehabilitated physical loading against hypokinesia background diminished and at times completely prevented its negative effect. Extent of correction depended on animal species. Evidence of genotypical conditionality of organism adaptation to physical load in hypokinesia was found.

Nikityuk, B. A.↗
NASA NTRS1981

Development of guayule (Parthenium argentatum) research in cell culture

Utilizing the lateral buds of known high rubber producing plants as explants in culture medium specifically designed to engender shoot development and to prevent callus formation, unlimited numbers of replicate plants can be produced. Each has the same genotype as the parent. This procedure has long been used to rid plants of virus, the latter generally does not occur in the embryonic tissues of the bud; it also, by virtue of its axenic nature, eliminates all microorganisms characteristic of the parent plant. Auxins were found essential to callus formation, but since the latter is known to bring about chromosomal aberrations, it was avoided. The cytokinin benzylaminopurine strongly stimulated shoot growth, and the number of regenerated buds on the inoculum was proportional to its concentration. These buds produced shoots several centimeters in length which were caused to root on medium containing indolebutyric acid. Transferred to the septic condition of soil, the plantlets were gradually brought into full sunlight where they showed a brief vegetative growth with production of mature leaves, and flowered.

Ball, E. A.↗
NASA NTRS1982

Energy metabolism and lifespan

An experiment to determine how the longevity of individual animals and genotypes within species depended on body weight and metabolic rate is described.

Sacher, G.↗
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↗