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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
NASA NTRS1989

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

NASA Discipline Exobiology↗
NASA NTRS1988

Mychonastes desiccatus Brown sp. nova (Chlorococcales, Chlorophyta)--an intertidal alga forming achlorophyllous desiccation-resistant cysts

An intertidal Chlorella-like alga Mychonastes desiccatus Brown sp. nova, capable of forming achlorophyllous desiccation-resistant cysts, has been grown in unialgal culture. This small alga was first isolated from a dried sample of a well-studied microbial mat. The mat, located at North Pond, Laguna Figueroa, San Quintin, Baja California, Mexico, is a vertically-stratified microbial community which forms laminated sediments. Morphology, pigment composition and G+C content are within the range typical for the genus Chlorella s. 1. Unlike other chlorellae, however, upon desiccation M. desiccatus forms an achlorophyllous, lipid-filled cyst (thick-walled resting stage) in which no plastid is evident. Rewetting leads to chloroplast differentiation, excystment and recovery of the fully green alga. During desiccation, sporopollenin is deposited within a thickening cell wall. Encystment cannot be induced by growth in the dark. The formation of desiccation-induced cysts allows the alga to survive frequent and intermittent periods of dryness. These chlorellae tolerate wide ranges of acidity and temperature; they both grow and form cysts in media in which sodium ions are replaced with potassium. Although the cysts tolerate crystalline salts, the cell grow optimally in concentrations corresponding from three-quarters to full-strength seawater.

NASA Discipline Exobiology↗
NASA NTRS1988

Niebla ceruchis from Laguna Figueroa: dimorphic spore morphology and secondary compounds localized in pycnidia and apothecia

During and after the floods of 1979-80 Niebla ceruchis growing epiphytically on Lycium brevipes was one of the dominant aspects of the vegetation in the coastal dunal complex bordering the microbial mats at Laguna Figueroa, Baja California Norte, Mexico. The lichen on denuded branches of Lycium was far more extensively distributed than Lycium lacking lichen. Unusual traits of this Niebla ceruchis strain, namely localization of lichen compounds in the mycobiont reproductive structures (pycnidia and apothecia) and simultaneous presence of bilocular and quadrilocular ascospores, are reported. The abundance of this coastal lichen cover at the microbial mat site has persisted through April 1988.

NASA Discipline Exobiology↗
NASA NTRS1987

Adaptation, plant evolution, and the fossil record

The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases, environmental disruption appears to have been a major factor in shaping the fossil record. This does not mean that continuing adaptation was not important during this interval, but it may indicate that adaptive evolution was strongest in environments other than those best represented in the paleobotanical record.

NASA Discipline Exobiology↗
NASA NTRS1987

Paleobiology of distinctive benthic microfossils from the upper Proterozoic Limestone-Dolomite "Series," central East Greenland

Populations of Polybessurus bipartitus Fairchild ex Green et al., a large morphologically distinctive microfossil, occur in silicified carbonates of the Upper Proterozoic (700-800 Ma) Limestone-Dolomite "Series," central East Greenland. Large populations of well-preserved individuals permit reconstruction of P. bipartitus as a coccoidal unicell that "jetted" upward from the sediment by the highly unidirectional secretion of extracellular mucopolysaccharide envelopes. Reproduction by baeocyte formation is inferred on the basis of clustered envelope stalks produced by small cells. Sedimentological evidence indicates that P. bipartitus formed surficial crusts locally within a shallow peritidal carbonate platform. Among living microorganisms a close morphological, reproductive, and behavioral counterpart to Polybessurus is provided by populations of an as yet underscribed cyanobacterium found in coastal Bahamian environments similar to those in which the Proterozoic fossils occur. In general morphology and "jetting" behavior, this population resembles species of the genus Cyanostylon, Geitler (1925), but reproduces via baeocyte formation. Polybessurus is but one of the more than two dozen taxa in the richly fossiliferous biota of the Limestone-Dolomite "Series." This distinctive population, along with co-occurring filamentous cyanobacteria and other microfossils, contributes to an increasingly refined picture of ecological heterogeneity in late Proterozoic oceans.

NASA Discipline Exobiology↗
NASA NTRS1987

Comparison of automated pre-column and post-column analysis of amino acid oligomers

It has been shown that various amino acids will polymerize under plausible prebiotic conditions on mineral surfaces, such as clays and soluble salts, to form varying amounts of oligomers (n = 2-6). The investigations of these surface reactions required a quantitative method for the separation and detection of these amino acid oligomers at the picomole level in the presence of nanomole levels of the parent amino acid. In initial high-performance liquid chromatography (HPLC) studies using a classical postcolumn o-phthalaldehyde (OPA) derivatization ion-exchange HPLC procedure with fluorescence detection, problems encountered included lengthy analysis time, inadequate separation and large relative differences in sensitivity for the separated species, expressed as a variable fluorescent yield, which contributed to poor quantitation. We have compared a simple, automated, pre-column OPA derivatization and reversed-phase HPLC method with the classical post-column OPA derivatization and ion-exchange HPLC procedure. A comparison of UV and fluorescent detection of the amino acid oligomers is also presented. The conclusion reached is that the pre-column OPA derivatization, reversed-phase HPLC and UV detection produces enhanced separation, improved sensitivity and faster analysis than post-column OPA derivatization, ion-exchange HPLC and fluorescence detection.

NASA Discipline Exobiology↗
NASA NTRS1987

Atmospheric H2O2 measurement: comparison of cold trap method with impinger bubbling method

Collection of atmospheric H2O2 was performed by a cold trap method using dry ice-acetone as the refrigerant. The air was drawn by a pump into a glass gas trap immersed in the dry ice-acetone slush in a dewar flask at a flow rate of 2.5 l min-1 for approximately 2 h. Collection efficiency was > 99% and negligible interferences by O3, SO2 or organic matter with the collected H2O2 in the trap were observed. This method was compared with the air impinger bubbling method which has been previously described (Kok et al., 1978a, b, Envir. Sci. Technol. 12, 1072-1080). The measured total peroxide (H2O2 + organic peroxide) values in a series of aim samples collected by the impinger bubbling method (0.06-3.7 ppb) were always higher than those obtained by the cold trap method (0.02-1.2 ppb). Laboratory experiments suggest that the difference in values between the two methods probably results from the aqueous phase generation of H2O2 and organic peroxide in the impinger solution by a reaction of atmospheric O3 with olefinic and aromatic compounds. If these O3-organic compound reactions which occur in the impinger also occur in aqueous droplets in the atmosphere, the process could be very important for aqueous phase generation of H2O2 in clouds and rainwater.

NASA Discipline Exobiology↗
NASA NTRS1987

The evaporation path of seawater and the coprecipitation of Br- and K+ with halite

Brines and salt were sampled at the Morton Bahamas solar salt production facility on Great Inagua Island in the Bahamas. The brines were analyzed by ion chromatography to define more precisely than heretofore the evaporation path of seawater to the end of the halite facies. At Inagua, calcium carbonate begins to precipitate at a brine concentration factor of 1.8 times that of seawater. Gypsum begins to precipitate at a brine concentration of 3.8 times seawater, and halite at a concentration factor of 10.6. Three of the most concentrated brines from Inagua (40 times seawater) were evaporated further in the laboratory. Magnesium sulfate first precipitated at brine concentrations about 70 times those of seawater, and potassium-bearing phases began to precipitate for these brines at concentrations greater than 90 times those of seawater. The distribution of coefficients of Br- and K+ between brines and halite were determined by combining analytical data for the Inagua brines with measurements of the Br- and K+ content of halites from Inagua and of halite which had precipitated from Inagua brines during storage. The observed average value of DBr- is 0.032, in good agreement with some of the previous measurements. The measured values of DK+ are highly variable (0.001 to 0.021); DK+ for halite precipitated early in the halite facies is in the vicinity of 0.015.

NASA Discipline Exobiology↗
NASA NTRS1987

Antitropical distribution and evolution in the Indo-West Pacific Ocean

Antitropical distributions of continental shelf, Indo-West Pacific species are probably not due to transgression of the tropics during the glacial periods, isothermic submergence, island integration, rising Neogene temperatures, or the Mesozoic dispersal of fragments from a Pacific continental mass. Characteristics of common antitropical patterns, plus information from systematic works on a variety on a variety of animal and plant groups, indicate that the long discarded "relict theory" of Theel (1885) appears to best fit the evidence, for it provides a mechanism whereby antitropical distribution may be brought about. The relict theory is compatible with the concept that the East Indies part of the Indo-West Pacific has been functioning as a center of evolutionary origin. It suggests that antitropical and associated disjunct patterns are produced as an older species, that has spread out to occupy a broad range, loses ground and gradually becomes supplanted by a younger species that had subsequently evolved in the East Indies. As this process goes on, the older species becomes restricted to a few isolated localities on the fringe of its original range. These isolates are often found to the north and south of the equatorial region but may include relict populations at the western edge of the Indian Ocean.

NASA Discipline Exobiology↗
NASA NTRS1987

Control of matric water potential by temperature differential

A method for controlling relative humidity based on temperature differentials, rather than on salt solutions, is described. This method has the following advantages: (1) it does not exhibit the anomalous CO2 solution effects that we have found to occur with salt solutions; (2) humidity is continuously adjustable without sample removal; (3) circulation of the atmosphere results in short equilibration times.

NASA Discipline Exobiology↗
NASA NTRS1987

Pharmacological activities in thermal proteins: relationships in molecular evolution

The model of protobiological events that has been presented in these pages has increasing relevance to pharmacological research. The thermal proteins that function as key substances in the proteinoid theory have recently been found to prolong the survival of rat forebrain neurons in culture and to stimulate the growth of neurites. A search for such activity in thermal proteins added to cultures of modern neurons was suggested by the fact that some of the microspheres assembled from proteinoids rich in hydrophobic amino acids themselves generate fibrous outgrowths.

NASA Discipline Exobiology↗
NASA NTRS1987

Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

NASA Discipline Exobiology↗
NASA NTRS1987

Symbiont acquisition as neoseme: origin of species and higher taxa

We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

NASA Discipline Exobiology↗
NASA NTRS1987

Racemization and the origin of optically active organic compounds in living organisms

The organic compounds synthesized in prebiotic experiments are racemic mixtures. A number of proposals have been offered to explain how asymmetric organic compounds formed on the Earth before life arose, with the influence of chiral weak nuclear interactions being the most frequent proposal. This and other proposed asymmetric syntheses give only sight enantiomeric excess and any slight excess will be degraded by racemization. This applies particularly to amino acids where half-lives of 10(5)-10(6) years are to be expected at temperatures characteristic of the Earth's surface. Since the generation of chiral molecules could not have been a significant process under geological conditions, the origins of this asymmetry must have occurred at the time of the origin of life or shortly thereafter. It is possible that the compounds in the first living organisms were prochiral rather than chiral; this is unlikely for amino acids, but it is possible for the monomers of RNA-like molecules.

NASA Discipline Exobiology↗
NASA NTRS1987

Phylogenetic diversity and position of the genus Campylobacter

RNA sequence analysis has been used to examine the phylogenetic position and structure of the genus Campylobacter. A complete 5S rRNA sequence was determined for two strains of Campylobacter jejuni and extensive partial sequences of the 16S rRNA were obtained for several strains of C. jejuni and Wolinella succinogenes. In addition limited partial sequence data were obtained from the 16S rRNAs of isolates of C. coli, C. laridis, C. fetus, C. fecalis, and C. pyloridis. It was found that W. succinogenes is specifically related to, but not included, in the genus Campylobacter as presently constituted. Within the genus significant diversity was noted. C. jejuni, C. coli and C. laridis are very closely related but the other species are distinctly different from one another. C. pyloridis is without question the most divergent of the Campylobacter isolates examined here and is sufficiently distinct to warrant inclusion in a separate genus. In terms of overall position in bacterial phylogeny, the Campylobacter/Wolinella cluster represents a deep branching most probably located within an expanded version of the Division containing the purple photosynthetic bacteria and their relatives. The Campylobacter/Wolinella cluster is not specifically includable in either the alpha, beta or gamma subdivisions of the purple bacteria.

NASA Discipline Exobiology↗
NASA NTRS1987

Phosphorus in foraminiferal sediments from North Atlantic Ridge cores and in pure limestones

Samples of foraminiferal ooze from two North Atlantic cores were cleaned and progressively dissolved. Most of the P, Fe, and Mn was released during the first of two reductive cleaning steps. Most of the remainder of these elements and most of the Ca were released during the final acid dissolution step. The P in these samples is present largely in Fe- and Mn-rich coatings, not as a constituent of the foraminiferal shells themselves. Our results are consistent with those of earlier studies. The concentration of P in carbonate oozes in which it is clearly associated with coatings is similar to that of modern calcareous sediments in general, and with that of reasonably pure limestones of all ages. Phosphorus is apparently associated with (Fe, Mn)-oxide coatings in many carbonate sediments. The rate of removal of P from the oceans as a constituent of such sediments depends on the rate of formation of (Fe, Mn) coatings, not on the rate of incorporation of P into calcium carbonate.

NASA Discipline Exobiology↗