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NASA NTRS1990

A new continuum model for suspensions of gyrotactic micro-organisms

A new continuum model is formulated for dilute suspensions of swimming micro-organisms with asymmetric mass distributions. Account is taken of randomness in a cell's swimming direction, p, by postulating that the probability density function for p satisfies a Fokker-Planck equation analogous to that obtained for colloid suspensions in the presence of rotational Brownian motion. The deterministic torques on a cell, viscous and gravitational, are balanced by diffusion, represented by an isotropic rotary diffusivity Dr, which is unknown a priori, but presumably reflects stochastic influences on the cell's internal workings. When the Fokker-Planck equation is solved, macroscopic quantities such as the average cell velocity Vc, the particle diffusivity tensor D and the effective stress tensor sigma can be computed; Vc and D are required in the cell conservation equation, and sigma in the momentum equation. The Fokker-Planck equation contains two dimensionless parameters, lambda and epsilon; lambda is the ratio of the rotary diffusion time Dr-1 to the torque relaxation time B (balancing gravitational and viscous torques), while epsilon is a scale for the local vorticity or strain rate made dimensionless with B. In this paper we solve the Fokker-Planck equation exactly for epsilon = 0 (lambda arbitrary) and also obtain the first-order solution for small epsilon. Using experimental data on Vc and D obtained with the swimming alga, Chlamydomonas nivalis, in the absence of bulk flow, the epsilon = 0 results can be used to estimate the value of lambda for that species (lambda approximately 2.2; Dr approximately 0.13 s-1). The continuum model for small epsilon is then used to reanalyse the instability of a uniform suspension, previously investigated by Pedley, Hill & Kessler (1988). The only qualitatively different result is that there no longer seem to be circumstances in which disturbances with a non-zero vertical wavenumber are more unstable than purely horizontal disturbances. On the way, it is demonstrated that the only significant contribution to sigma, other than the basic Newtonian stress, is that derived from the stresslets associated with the cells' intrinsic swimming motions.

NASA Discipline Number 28-20↗

NASA NTRS2001

Analysis of the myosins encoded in the recently completed Arabidopsis thaliana genome sequence

BACKGROUND: Three types of molecular motors play an important role in the organization, dynamics and transport processes associated with the cytoskeleton. The myosin family of molecular motors move cargo on actin filaments, whereas kinesin and dynein motors move cargo along microtubules. These motors have been highly characterized in non-plant systems and information is becoming available about plant motors. The actin cytoskeleton in plants has been shown to be involved in processes such as transportation, signaling, cell division, cytoplasmic streaming and morphogenesis. The role of myosin in these processes has been established in a few cases but many questions remain to be answered about the number, types and roles of myosins in plants. RESULTS: Using the motor domain of an Arabidopsis myosin we identified 17 myosin sequences in the Arabidopsis genome. Phylogenetic analysis of the Arabidopsis myosins with non-plant and plant myosins revealed that all the Arabidopsis myosins and other plant myosins fall into two groups - class VIII and class XI. These groups contain exclusively plant or algal myosins with no animal or fungal myosins. Exon/intron data suggest that the myosins are highly conserved and that some may be a result of gene duplication. CONCLUSIONS: Plant myosins are unlike myosins from any other organisms except algae. As a percentage of the total gene number, the number of myosins is small overall in Arabidopsis compared with the other sequenced eukaryotic genomes. There are, however, a large number of class XI myosins. The function of each myosin has yet to be determined.

NASA Discipline Plant Biology↗

NASA NTRS1998

Viruses in Antarctic lakes

Water samples collected from four perennially ice-covered Antarctic lakes during the austral summer of 1996-1997 contained high densities of extracellular viruses. Many of these viruses were found to be morphologically similar to double-stranded DNA viruses that are known to infect algae and protozoa. These constitute the first observations of viruses in perennially ice-covered polar lakes. The abundance of planktonic viruses and data suggesting substantial production potential (relative to bacteria] secondary and photosynthetic primary production) indicate that viral lysis may be a major factor in the regulation of microbial populations in these extreme environments. Furthermore, we suggest that Antarctic lakes may be a reservoir of previously undescribed viruses that possess novel biological and biochemical characteristics.

Non-NASA Center↗

NASA NTRS1984

Prochloron--a status report

Prochloron is a genus of prokaryotic algae with photosynthetic pigments like those of chlorophytes. Prochlorophytes are almost invariably found associated as symbionts with marine protochordates (didemnid ascidians), and so far none has been successfully grown in sustained culture away from in host. Based on materials collected from nature, information of various sorts (biochemical, physiological, cytological and fine-structural) has been obtained, indicating many resemblances (and probably close phylogenetic affinities) between prochlorophytes and cyanophytes. Nevertheless they are distinguished by certain unique combinations of characters. Some of the data support the symbiogenesis theory for the origin of green-plant chloroplasts. Other possibilities are briefly discussed.

Review, Tutorial↗

NASA NTRS2000

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

Review, Tutorial↗

NASA NTRS1999

Iron isotope biosignatures

The (56)Fe/(54)Fe of Fe-bearing phases precipitated in sedimentary environments varies by 2.5 per mil (delta(56)Fe values of +0.9 to -1. 6 per mil). In contrast, the (56)Fe/(54)Fe of Fe-bearing phases in igneous rocks from Earth and the moon does not vary measurably (delta(56)Fe = 0.0 +/- 0.3 per mil). Experiments with dissimilatory Fe-reducing bacteria of the genus Shewanella algae grown on a ferrihydrite substrate indicate that the delta(56)Fe of ferrous Fe in solution is isotopically lighter than the ferrihydrite substrate by 1.3 per mil. Therefore, the range in delta(56)Fe values of sedimentary rocks may reflect biogenic fractionation, and the isotopic composition of Fe may be used to trace the distribution of microorganisms in modern and ancient Earth.

NASA Center JPL↗

NASA NTRS1998

Nonphotic entrainment of the human circadian pacemaker

In organisms as diverse as single-celled algae and humans, light is the primary stimulus mediating entrainment of the circadian biological clock. Reports that some totally blind individuals appear entrained to the 24-h day have suggested that nonphotic stimuli may also be effective circadian synchronizers in humans, although the nonphotic stimuli are probably comparatively weak synchronizers, because the circadian rhythms of many totally blind individuals "free run" even when they maintain a 24-h activity-rest schedule. To investigate entrainment by nonphotic synchronizers, we studied the endogenous circadian melatonin and core body temperature rhythms of 15 totally blind subjects who lacked conscious light perception and exhibited no suppression of plasma melatonin in response to ocular bright-light exposure. Nine of these fifteen blind individuals were able to maintain synchronization to the 24-h day, albeit often at an atypical phase angle of entrainment. Nonphotic stimuli also synchronized the endogenous circadian rhythms of a totally blind individual to a non-24-h schedule while living in constant near darkness. We conclude that nonphotic stimuli can entrain the human circadian pacemaker in some individuals lacking ocular circadian photoreception.

NASA Discipline Regulatory Physiology↗

NASA NTRS1996

Diversity of eukaryotic microorganisms: computer-based resources, "The Handbook of Protoctista" and its "Glossary"

The kingdom Protoctista comprises some 30 phyla, including the eukaryotic anaerobes that permanently lack mitochondria, the Phylum Archaeprotista, with its three classes: (i) Archamoebae, e.g., Pelomyxa, Mastigina, (ii) Metamonada, e.g., Giardia, Pyrsonympha, and (iii) Parabasalia, e.g., Trichomonas, Calonympha, and the Phylum Microspora (Microsporidia), e.g., Vairimorpha. These and all algae, protozoa, labyrinthulids, "water molds" (oomycota, plasmodiophorans, hyphochytrids, chytrids, etc.) and other eukaryotes excluded from plants, animals and fungi are detailed in the Handbook of Protoctista. The Illustrated Glossary of Protoctista contains descriptions of the morphology and taxonomy of these microorganisms, including the many equivalent and homologous structures with different names. The Glossary has also been made into a Macintosh-compatible CD-ROM disk.

NASA Discipline Number 52-30↗

NASA NTRS1996

Characterization of Anopheles darlingi (Diptera: Culicidae) larval habitats in Belize, Central America

Surveys for larvae of Anopheles darlingi Root were conducted in April, May, and August 1994 in riverine habitats of central Belize (Cayo and Belize districts). An. darlingi was present during both the dry and wet seasons. Larvae were encountered most frequently in patches of floating debris along river margins. The floating mats were often formed by bamboo hanging over the banks and dense submersed bamboo roots. Larvae were found less frequently in lake margins, small lagoons, and ground pools with submersed roots and patches of floating leaves or vegetation. In addition to their association with floating debris, larvae of An. darlingi were associated positively with shade and submersed plants in riverine environments. Samples from river habitats showed the larvae of Anopheles albimanus Wiedemann to be strongly associated with sun-exposed sites containing green or blue-green algae. Unlike An. darlingi, An. albimanus was an ubiquitous mosquito, the immatures of which occurred in a wide variety of riverine and nonriverine aquatic habitats. Based on published reports and our experience, the association of An. darlingi with river systems was verified, and its distribution in Central America and Mexico was mapped.

NASA Discipline General Space Life Sciences↗

NASA NTRS1994

Bioregenerative life-support systems

Long-duration future habitation of space involving great distances from Earth and/or large crew sizes (eg, lunar outpost, Mars base) will require a controlled ecological life-support system (CELSS) to simultaneously revitalize atmosphere (liberate oxygen and fix carbon dioxide), purify water (via transpiration), and generate human food (for a vegetarian diet). Photosynthetic higher plants and algae will provide the essential functions of biomass productivity in a CELSS, and a combination of physicochemical and bioregenerative processes will be used to regenerate renewable resources from waste materials. Crop selection criteria for a CELSS include nutritional use characteristics as well as horticultural characteristics. Cereals, legumes, and oilseed crops are used to provide the major macronutrients for the CELSS diet. A National Aeronautics and Space Administration (NASA) Specialized Center of Research and Training (NSCORT) was established at Purdue University to establish proof of the concept of the sustainability of a CELSS. The Biosphere 2 project in Arizona is providing a model for predicted and unpredicted situations that arise as a result of closure in a complex natural ecosystem.

NASA Discipline Life Support Systems↗

NASA NTRS1994

Proterozoic and early Cambrian protists: evidence for accelerating evolutionary tempo

In rocks of late Paleoproterozoic and Mesoproterozoic age (ca. 1700-1000 million years ago), probable eukaryotic microfossils are widespread and well preserved, but assemblage and global diversities are low and turnover is slow. Near the Mesoproterozoic-Neoproterozoic boundary (1000 million years ago), red, green, and chromophytic algae diversified; molecular phylogenies suggest that this was part of a broader radiation of "higher" eukaryotic phyla. Observed diversity levels for protistan microfossils increased significantly at this time, as did turnover rates. Coincident with the Cambrian radiation of marine invertebrates, protistan microfossils again doubled in diversity and rates of turnover increased by an order of magnitude. Evidently, the Cambrian diversification of animals strongly influenced evolutionary rates, within clades already present in marine communities, implying an important role for ecology in fueling a Cambrian explosion that extends across kingdoms.

Non-NASA Center↗

NASA NTRS1992

Recent evidence for evolution of the genetic code

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

Review↗

NASA NTRS1992

Biodiversity: molecular biological domains, symbiosis and kingdom origins

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still behave as if there were only two important kingdoms (plants and animals).

Non-NASA Center↗

NASA NTRS2004

Earth's Early Biosphere and the Biogeochemical Carbon Cycle

Our biosphere has altered the global environment principally by influencing the chemistry of those elements most important for life, e g., C, N, S, O, P and transition metals (e.g., Fe and Mn). The coupling of oxygenic photosynthesis with the burial in sediments of photosynthetic organic matter, and with the escape of H2 to space, has increased the state of oxidation of the Oceans and atmosphere. It has also created highly reduced conditions within sedimentary rocks that have also extensively affected the geochemistry of several elements. The decline of volcanism during Earth's history reduced the flow of reduced chemical species that reacted with photosynthetically produced O2. The long-term net accumulation of photosynthetic O2 via biogeochemical processes has profoundly influenced our atmosphere and biosphere, as evidenced by the O2 levels required for algae, multicellular life and certain modem aerobic bacteria to exist. When our biosphere developed photosynthesis, it tapped into an energy resource that was much larger than the energy available from oxidation-reduction reactions associated with weathering and hydrothermal activity. Today, hydrothermal sources deliver globally (0.13-1.1)x10(exp l2) mol yr(sup -1) of reduced S, Fe(2+), Mn(2+), H2 and CH4; this is estimated to sustain at most about (0.2-2)xl0(exp 12)mol C yr(sup -1) of organic carbon production by chemautotrophic microorganisms. In contrast, global photosynthetic productivity is estimated to be 9000x10(exp 12) mol C yr(sup -1). Thus, even though global thermal fluxes were greater in the distant geologic past than today, the onset of oxygenic photosynthesis probably increased global organic productivity by some two or more orders of magnitude. This enormous productivity materialized principally because oxygenic photosynthesizers unleashed a virtually unlimited supply of reduced H that forever freed life from its sole dependence upon abiotic sources of reducing power such as hydrothermal emanations and weathering. Communities sustained by oxygenic photosynthesis apparently thrived wherever supplies of sunlight, moisture and nutrients were sufficient. Prior to the development of oxygenic photosynthesis, the net global effect of the ancient global biosphere was to facilitate chemical equilibrium between reduced species from thermal activity and weathering and more oxidized constituents in the surface environment. But even this ancient biosphere might have been globally pervasive. The global geothermal heat flow was substantially higher during Earth's first billion years, and thus reduced chemical species might have persisted in sunlit aquatic environments. Perhaps the substantial decline in thermal activity between 4000 and 3000 Ma created a driver for oxygenic photosynthesis to develop.

DesMarais, David↗

NASA NTRS2005

Path Planning Algorithms for the Adaptive Sensor Fleet

The Adaptive Sensor Fleet (ASF) is a general purpose fleet management and planning system being developed by NASA in coordination with NOAA. The current mission of ASF is to provide the capability for autonomous cooperative survey and sampling of dynamic oceanographic phenomena such as current systems and algae blooms. Each ASF vessel is a software model that represents a real world platform that carries a variety of sensors. The OASIS platform will provide the first physical vessel, outfitted with the systems and payloads necessary to execute the oceanographic observations described in this paper. The ASF architecture is being designed for extensibility to accommodate heterogenous fleet elements, and is not limited to using the OASIS platform to acquire data. This paper describes the path planning algorithms developed for the acquisition phase of a typical ASF task. Given a polygonal target region to be surveyed, the region is subdivided according to the number of vessels in the fleet. The subdivision algorithm seeks a solution in which all subregions have equal area and minimum mean radius. Once the subregions are defined, a dynamic programming method is used to find a minimum-time path for each vessel from its initial position to its assigned region. This path plan includes the effects of water currents as well as avoidance of known obstacles. A fleet-level planning algorithm then shuffles the individual vessel assignments to find the overall solution which puts all vessels in their assigned regions in the minimum time. This shuffle algorithm may be described as a process of elimination on the sorted list of permutations of a cost matrix. All these path planning algorithms are facilitated by discretizing the region of interest onto a hexagonal tiling.

Stoneking, Eric↗

NASA NTRS2005

Overview of Biomineralization and Nanobacteria

Biomineralization is a frequently used term in nanotechnology, astrobiology, geology, and medicine. In the process of biomineralization, a living organism provides a chemical environment that controls the nucleation and growth of unique mineral phases. Often these materials exhibit hierarchical structural order, leading to superior physical properties, not found either in their inorganic counterparts or in synthetic materials. Biomineralization is widespread in the biosphere and hundreds of different minerals are produced or assisted by a variety of organisms from bacteria to humans. Teeth, bones, kidney stones, and skeletons of algae, mussels, and magnetotactic bacteria are all examples of biomineralization. We do not fully understand the control mechanism of biomineralization either in primitive or in developed organisms. The presence of organic molecules, among other characteristics, can influence the coherence length for X-ray scattering in biogenic crystals. Control over biomineral properties can be accomplished at a myriad of levels, including the regulation of particle size, shape, crystal orientation, polymorphic structure, defect texture, and particle assembly. In the latter case, cellular processes enable control in both the spatial and temporal domain in such a way that hierarchical composite structures can be built which increase the toughness and durability of the material, which is invaluable for load-bearing materials such as bones, teeth, mollusk shells, etc. Durability of biominerals produces remarkably preserved bacterial and cyanobacterial microfossils from billions of years-old samples. The differentiation between microfossils and nonbiogenic artifacts has been a lively discussion subject in astrobiology especially in the last decade. Clearly, more detailed information on the mechanism of biomineralization, and the effect of organic matter on crystal formation/fossilization would help focus such discussions.

Ciftcioglu, N.↗

NASA NTRS2005

Morphology and Elemental Composition of Recent and Fossil Cyanobacteria

Cyanobacteria (cyanophyta, cyanoprokaryota, and blue-green algae) are an ancient, diverse and abundant group of photosynthetic oxygenic microorganisms. Together with other bacteria and archaea, the cyanobacteria have been the dominant life forms on Earth for over 3.5 billion years. Cyanobacteria occur in some of our planets most extreme environments - hot springs and geysers, hypersaline and alkaline lakes, hot and cold deserts, and the polar ice caps. They occur in a wide variety of morphologies. Unlike archaea and other bacteria, which are typically classified in pure culture by their physiological, biochemical and phylogenetic properties, the cyanobacteria have historically been classified based upon their size and morphological characteristics. These include the presence or absence of heterocysts, sheath, uniseriate or multiseriate trichomes, true or false branching, arrangement of thylakoids, reproduction by akinetes, binary fission, hormogonia, fragmentation, presence/absence of motility etc. Their antiquity, distribution, structural and chemical differentiation, diversity, morphological complexity and large size compared to most other bacteria, makes the cyanobacteria ideal candidates for morphological biomarkers in returned Astromaterials. We have obtained optical (nomarski and phase contrast)/fluorescent (blue and green excitation) microscopy images using an Olympus BX60 compound microscope and Field Emission Scanning Electron Microscopy images and EDAX elemental compositions of living and fossil cyanobacteria. The S-4000 Hitachi Field Emission Scanning Electron Microscope (FESEM) has been used to investigate microfossils in freshly fractured interior surfaces of terrestrial rocks and the cells, hormogonia, sheaths and trichomes of recent filamentous cyanobacteria. We present Fluorescent and FESEM Secondary and Backscattered Electron images and associated EDAX elemental analyses of recent and fossil cyanobacteria, concentrating on representatives of the genera Calothnx, Leptolyngbya, Lyngbya, Planktolyngbya and Oscillatoria.

SaintAmand, Ann↗

NASA NTRS2007

Considerations on Terrestrial Iron Depositing Analogs to Earliest Mars

Iron oxide and hydroxide minerals, including hematite, can mineralize and preservemicrofossils and physical biomarkers (Allen at al., 2004). Preserved remnants of phototrophic microorganisms are recognized as biosignatures of past life on Earth (Schopf, 2006). To date, two types of surface iron depositing environments have been studied as analogs to possible habitable environments on earliest Mars: the highly acidified Rio Tinto River (Iberian Belt, Spain) [Gomez Ortis et al., 2007], and the nearneutral iron depositing Chocolate Pots Hot Spring (Yellowstone National Park, US) [Parenteau at al., 2005]. While phototrophs in the Rio Tinto are only represented by eukaryotic algae (Amaral Zettler et all., 2002), Chocolate Pots is mainly populated with cyanobacteria (Pierson et all., 2000; Brown et all., 2007). Which of these environments is the closer analog to a potentially habitable early Mars? Paleobiological data, combined with recent "tree of life" interpretations, suggest that phototrophic eukaryotes evolved not earlier than 2.5 - 2.8 b.y. after Earth s accretion (4.6 b.y.), while cyanobacteria and /or their iron-tolerant predecessors evolved between 1 - 1.5 b.y. after accretion (Brown et al., 2007). Lindsay and Brasier (2002) postulated that microbial life on Mars surface could have lasted no more than 1-1.5 b.y. after Mars accretion (also 4.6 b.y.). Recent multispectral mapping of Mars suggests that near-neutral wet environments prevailed at approximately this time (Bibring, et al., 2006). Thus, near-neutral iron depositing hot springs such as Chocolate Pots Hot Spring seem to be the more likely habitable analogs for earliest Mars.

Brown, Igor I.↗