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At least 163 records · Page 9

The case for relationship of the flavobacteria and their relatives to the green sulfur bacteria

Analysis of 16S rRNA sequences suggests, but does not convincingly demonstrate a specific relationship between the eubacterial phylum defined by the flavobacteria and their relatives and that defined by the green sulfur bacteria. Consequently, we have sequenced the 23S rRNA from several representatives of the former group and one of the latter in order to bring more data to bear upon this point. The 23S rRNA data alone strongly suggest a specific relationship between the two phyla, and, together with the 16S rRNA results, provides what we consider now to be a convincing case for this specific relationship.

NASA Discipline Number 52-30↗

High-performance liquid chromatography of oligoguanylates at high pH

Because of the stable self-structures formed by oligomers of guanosine, standard high-performance liquid chromatography techniques for oligonucleotide fractionation are not applicable. Previously, oligoguanylate separations have been carried out at pH 12 using RPC-5 as the packing material. While RPC-5 provides excellent separations, there are several limitations, including the lack of a commercially available source. This report describes a new anion-exchange high-performance liquid chromatography method using HEMA-IEC BIO Q, which successfully separates different forms of the guanosine monomer as well as longer oligoguanylates. The reproducibility and stability at high pH suggests a versatile role for this material.

Non-NASA Center↗

A kill curve for Phanerozoic marine species

A kill curve for Phanerozoic species is developed from an analysis of the stratigraphic ranges of 17,621 genera, as compiled by Sepkoski. The kill curve shows that a typical species' risk of extinction varies greatly, with most time intervals being characterized by very low risk. The mean extinction rate of 0.25/m.y. is thus a mixture of long periods of negligible extinction and occasional pulses of much higher rate. Because the kill curve is merely a description of the fossil record, it does not speak directly to the causes of extinction. The kill curve may be useful, however, to li inverted question markmit choices of extinction mechanisms.

NASA Discipline Number 52-40↗

Catalysis of hydrolysis and nucleophilic substitution at the P-N bond of phosphoimidazolide-activated nucleotides in phosphate buffers

Phosphoimidazolide-activated derivatives of guanosine and cytidine 5'-monophosphates, henceforth called ImpN's, exhibit enhanced rates of degradation in the presence of aqueous inorganic phosphate in the range 4.0 < or = pH < or = 8.6. This degradation is been attributed to (i) nucleophilic substitution of the imidazolide and (ii) catalysis of the P-N bond hydrolysis by phosphate. The first reaction results in the formation of nucleoside 5'-diphosphate and the second in nucleoside 5'-monophosphate. Analysis of the observed rates as well as the product ratios as a function of pH and phosphate concentration allow distinction between various mechanistic possibilities. The results show that both H2PO4- and HPO4(2-) participate in both hydrolysis and nucleophilic substitution. Statistically corrected biomolecular rate constants indicate that the dianion is 4 times more effective as a general base than the monoanion, and 8 times more effective as nucleophile. The low Bronsted value beta = 0.15 calculated for these phosphate species, presumed to act as general bases in facilitating water attack, is consistent with the fact that catalysis of the hydrolysis of the P-N bond in ImpN's has not been detected before. The beta nuc = 0.35 calculated for water, H2PO4-, HPO4(2-), and hydroxide acting as nucleophiles indicates a more associative transition state for nucleotidyl (O2POR- with R = nucleoside) transfers than that observed for phosphoryl (PO3(2-)) transfers (beta nuc = 0.25). With respect to the stability/reactivity of ImpN's under prebiotic conditions, our study shows that these materials would not suffer additional degradation due to inorganic phosphate, assuming the concentrations of phosphate, Pi, on prebiotic Earth were similar to those in the present oceans ([Pi] approximately 2.25 micromoles).

NASA Discipline Number 52-20↗

Continental-pelagic carbonate partitioning and the global carbonate-silicate cycle

A carbonate-silicate geochemical cycle model is developed and used to explore dynamic and climatic consequences of constraints on shallow-water carbonate burial and possible carbon loss to the mantle associated with sea-floor subduction. The model partitions carbonate deposition between shallow-water and deep-water environments and includes carbon fluxes between the mantle and lithosphere. When total lithospheric carbonate mass is constant, there are two stable steady states, one in which the carbonate burial flux is mostly continental and another in which it is mostly pelagic. The continental steady state is characterized by a low metamorphic CO2 flux to the atmosphere and predominantly shallow-water carbonate burial. The pelagic steady state is characterized by a high metamorphic CO2 flux and predominantly deep-water carbonate burial. For reasonable parameter values, when total lithospheric carbonate mass is allowed to vary, the model oscillates between predominantly continental and predominantly pelagic modes. Model results suggest that carbonate deposition patterns established during the Cenozoic may be pushing the Earth system from the continental to the pelagic mode on a time scale of 10(8) yr, with a possible consequent order-of-magnitude increase in the metamorphic CO2 flux to the atmosphere.

NASA Program Exobiology↗

Template-directed synthesis of oligonucleotides under eutectic conditions

One of the most important sets of model prebiotic experiments consists of reactions that synthesize complementary oligonucleotides from preformed templates under nonenzymatic conditions. Most of these experiments are conducted at 4 degrees C using 0.01-0.1 M concentrations of activated nucleotide monomer and template (monomer equivalent). In an attempt to extend the conditions under which this type of reaction can occur, we have concentrated the reactants by freezing at -18 degrees C, which is close to the NaCl-H2O eutectic at -21 degrees C. The results from this set of experiments suggest that successful syntheses can occur with poly(C) concentrations as low at 5 x 10(-4) M and 2MeImpG concentrations at 10(-3) M. It was also anticipated that this mechanism might allow the previously unsuccessful poly(A)-directed synthesis of oligo(U)s to occur. However, no template effect was seen with the poly(A) and ImpU system. The failure of these conditions to allow template-directed synthesis of oligo(U)s supports the previously proposed idea that pyrimidines may not have been part of the earliest genetic material. Because of the low concentrations of monomer and template that would be expected from prebiotic syntheses, this lower temperature could be considered a more plausible geologic setting for template-directed synthesis than the standard reaction conditions.

NASA Discipline Number 52-20↗

Attempted nonenzymatic template-directed oligomerizations on a polyadenylic acid template: implications for the nature of the first genetic material

Previous attempts to produce nonenzymatic template-directed oligomerizations of activated pyrimidines on polypurine templates have been unsuccessful. The only efficient reactions are those where the template is composed primarily of pyrimidines, especially cytosine. Because molecular evolution requires that a synthesized daughter polynucleotide be capable of acting as a template for the synthesis of the original polynucleotide, the one-way replication achieved thus far is inadequate to initiate an evolving system. Several uracil analogs were used in this investigation in order to search for possible replacements for uracil. The monomers used in this investigation were the imidazolides of UMP, xanthosine 5'-monophosphate, the bis-monophosphates of the acyclic nucleosides of uracil, and 2,4-quinazolinedione. The concentrations of various salts, buffers, pH, and temperature were among the different variables investigated in attempts to find conditions that would permit template-directed oligomerizations. Although the different monomers in this study demonstrated varying abilities to form very short oligomers, we were unable to detect any enhancement of this oligomerization that could be attributed to the poly(A) template. Although special conditions might be found that would allow purine-rich templates to work, these reactions cannot be considered robust. The results of our experiments suggest that pyrimidines were not part of the original replicating system on the primitive Earth. It has already been shown that ribose is an unlikely component of the first replicating systems, and we now suggest that phosphate was absent as well. This is due to the low solubility of phosphate in the present ocean (3 x 10(-6) M), as well as the difficulty of prebiotic activation of phosphates.

Non-NASA Center↗

Imaging Jupiter's aurorae from H3+ emissions in the 3-4 micrometers band

Since H3+ was first spectroscopically detected on Jupiter, there has been considerable interest in using this simple molecular ion to probe conditions existing in the planet's auroral regions. Here we present a series of images of Jupiter recorded at wavelengths sensitive to emission by H3+, which reveal the spatial distribution of excited H3+ molecular ions in the jovian ionosphere, as seen from Earth. We believe that they provide high-spatial-resolution images of polar aurorae on Jupiter. They suggest that the intensity of the auroral emission can vary on a timescale of an hour, a shorter period than had previously been noted. We also find that the spatial distribution of H3+ emissions correlates only partially with the loci of auroral activity inferred from ultraviolet and longer-wavelength infrared observations. The H3+ emission may therefore be controlled by auroral processes that are different from those responsible for the ultraviolet and infrared emissions.

Non-NASA Center↗

The timing of alkali metasomatism in paleosols

We have measured the concentrations of rubidium and strontium and 87Sr/86Sr values of whole-rock samples from three paleosols of different ages. The oldest of the three weathering horizons, the 2,760 Ma Mt. Roe #1 paleosol in the Fortescue Group of Western Australia, experienced addition of Rb, and probably Sr, at 2,168 +/- 10 Ma. The intermediate paleosol, developed on the Hekpoort Basalt in South Africa, is estimated to have formed at 2,200 Ma, and yields a Rb-Sr isochron age of 1,925 +/- 32 Ma. The youngest of the three paleosols, developed on the Ongeluk basalt in Griqualand West, South Africa ca. 1,900 Ma, yielded a Rb-Sr age of 1,257 +/- 11 Ma. The Rb-Sr systematics of all three paleosols were reset during post-weathering metasomatism related to local or regional thermal disturbances. The Rb-Sr systematics of the paleosols were not subsequently disturbed. The near-complete removal of the alkali and alkaline earth elements from these paleosols during weathering made them particularly susceptible to resetting of their Rb-Sr systematics. Paleosols of this type are therefore sensitive indicators of the timing of thermal disturbances.

NASA Discipline Number 52-20↗

Kingdoms in turmoil

How should the world's living organisms be classified? Into how many kingdoms should they be grouped? Scientists have been grappling with these questions since the time of Aristotle, drawing on a broad base of biological characteristics for clues. The fossil record, visible traits of living organisms and, more recently, results from cell biology have all shaped theories of biological classification. But last year a new and controversial concept emerged: a classification of life based solely on molecular traits. The focal point of the controversy is a tree of life, or "phylogeny", devised by Carl Woese of the University of Illinois, Otto Kandler of the University of Munich and Mark Wheelis of the University of California. The tree is unusual because, unlike all previous schemes, it is constructed solely from biochemical data such as DNA sequences rather than a range of different organism characteristics. But that is not all. The scheme also challenges the idea that life on Earth is best divided into five kingdoms, with the main split being between bacteria and all other organisms. Woese and his colleagues create three main groupings by dividing the bacteria in two and unifying all other organisms.

NASA Program Exobiology↗

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

NASA Program Exobiology↗

Laboratory studies of the newly discovered infrared band at 4705.2 cm-1 (2.1253 micrometers) in the spectrum of Io: the tentative identification of CO2

We discuss over 120 laboratory experiments pertaining to the identification of the new absorption band discovered by Trafton et al. (1991) at 4705.2 cm-1 (2.1253 micrometers) in the spectrum of Io. It is shown that this band is not due to overtones or combinations of the fundamental bands associated with the molecules (or their chemical complexes) already identified on Io, namely, SO2, H2S, and H2O. Thus, this band is due to a new, previously unidentified, component of Io. Experiments also demonstrate that the band is not due to molecular H2 frozen in SO2 frosts. Since the frequency of this band is very close to the first overtone of the nu 3 asymmetric stretching mode of CO2, we have investigated the spectral behavior of CO2 under a variety of conditions appropriate for Io. The profile of the Io band is not consistent with the rotational envelope expected for single, freely rotating, gaseous CO2 under Io-like conditions. It was found that pure, solid CO2 and CO2 intimately mixed in a matrix of solid SO2 and H2S produce bands with similar widths (5-10 cm-1), but that these bands consistently fall at frequencies about 10-20 cm-1 (approximately 0.007 micrometer) lower than the Io band. CO2 in SO2 : H2S ices also produces several additional bands that are not in the Io spectra. The spectral fit improves, however, as the CO2 concentration in SO2 increases, suggesting that CO2-CO2 interactions might be involved. A series of Ar : CO2 and Kr : CO2 matrix isolation experiments, as well as laboratory work done elsewhere, show that CO2 clustering shifts the band position to higher frequencies and provides a better fit to the Io band. Various laboratory experiments have shown that gaseous CO2 molecules have a propensity to cluster between 80 and 100 K, temperatures similar to those found on the colder regions of Io. We thus tentatively identify the newly discovered Io band at 4705.2 cm-1 (2.1253 micrometers) with CO2 multimers or "clusters" on Io. Whether these clusters are buried within an SO2 frost, reside on the surface, or are in a residual, steady-state "atmospheric aerosol" population over local coldtraps is not entirely clear, although we presently favor the latter possibility. The size of these clusters is not well defined, but evidence suggests groups of more than four molecules are required. The absorption strength of the 2 nu 3 CO2 cluster overtone determined in the laboratory, in conjunction with the observed strength of the Io band, suggests that the disk-integrated abundance of CO2 is less than 1% that of the SO2. Studies of the sublimation behavior of CO2 indicate that it probably resides predominantly in the cooler areas (< 100 K) of Io. The relative constancy of the Io feature over a variety of orbital phases suggests that the polar regions may contain much of the material. Some consequences of the physical properties of CO2 under conditions pertinent to Io are discussed. The presence of CO2 clusters on Io could be verified by the detection of any one of several other infrared bands associated with the CO2 molecule, of which the strongest are the nu 3 12CO2 asymmetric stretch fundamental near 2350 cm-1 (4.25 micrometers) and the nu 2 bending mode fundamental near 660 cm-1 (15.1 micrometers). Weaker bands that may also be detectable include the nu 3 13CO2 asymmetric stretch fundamental near 2280 cm-1 (4.39 micrometers), the 2 nu 2 + nu 3 combination/overtone band near 3600 cm-1 (2.78 micrometers), and the nu 1 + nu 3 combination band near 3705 cm-1 (2.70 micrometers).

NASA Center ARC↗

Microbial mats, stromatolites and the rise of oxygen in the Precambrian atmosphere

Microbial mats are stratified communities that develop within the environmental microgradients established at the interfaces of water and solid substrates (Cohen, 1989). Stromatolites, the lithified remains of layered accumulations of microbial mats, occur in rocks as old as 3.5 Ga (Lowe, 1980; Walter et al., 1980). These lithified microbial communities represent the most ancient, widespread ecosystems known, and it is useful to explore their role in the accumulation of free oxygen in the ancient atmosphere.

NASA Program Exobiology↗

PCR amplification of 16S rDNA from lyophilized cell cultures facilitates studies in molecular systematics

The sequence of the major portion of a Bacillus cycloheptanicus strain SCH(T) 16S rRNA gene is reported. This sequence suggests that B. cycloheptanicus is genetically quite distinct from traditional Bacillus strains (e.g., B. subtilis) and may be properly regarded as belonging to a different genus. The sequence was determined from DNA that was produced by direct amplification of ribosomal DNA from a lyophilized cell pellet with straightforward polymerase chain reaction (PCR) procedures. By obviating the need to revive cell cultures from the lyophile pellet, this approach facilitates rapid 16S rDNA sequencing and thereby advances studies in molecular systematics.

Non-NASA Center↗

Impacts and the origin of life

As living creatures, all of us have some interest in the question of how life originated. To some, the question is more religious than scientific; nonetheless, a small but dedicated group of scientists spend their careers trying to answer it from a rational standpoint. Logically, the question can be broken down into the three standard divisions of any mystery: When did life originate? Where did it originate? And how did it originate? Of these three sub-questions the last is by far the most difficult and I will make no attempt to address it here. I will however take a personal look at the two easier parts of the problem. In particular, I will outline my current view of the physical environment of the early Earth, and I will try to show how observations of other solar system bodies, especially our own Moon, provide clues as to when and where life could have originated.

Review↗

Vendian microfossils in metasedimentary cherts of the Scotia Group, Prins Karls Forland, Svalbard

Sedimentary rocks of the Scotia Group, Prins Karls Forland, Svalbard, have been metamorphosed to lower greenschist facies. Yet Scotia chert nodules contain abundant organic-walled microfossils belonging to at least seventeen taxa. Their black colour indicates that the fossils underwent substantial thermal alteration. However, it is suggested that preservation in a matrix of early diagenetic silica shielded them from the most destructive mechanical and chemical effects of metamorphism. Microbial mats and large acanthomorphic acritarchs suggest a coastal marine depositional environment; the acritarchs further indicate an early Vendian age for the sediments. The Scotia fossils bear a close resemblance to assemblages described from the Doushantuo Formation, China and elsewhere, demonstrating the broad geographical distribution of biostratigraphically important Vendian taxa. Briareus and Echinosphaeridium are described as new genera; Briareus borealis is described as a new species, while Echinosphaeridium maximum is proposed as a new combination.

Non-NASA Center↗

Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

NASA Discipline Number 52-20↗

Novel long-chain anteiso-alkanes and anteiso-alkanoic acids in Antarctic rocks colonized by living and fossil cryptoendolithic microorganisms

Saponified extracts of rock samples colonized by cryptoendolithic microbial communities from the McMurdo Dry Valleys of Southern Victoria Land, Antarctica, were separated into hydrocarbon and fatty acid fractions by silica gel column chromatography. Hydrocarbons and methyl esters of fatty acids were analyzed by capillary gas chromatography-mass spectrometry. Unusually, a suite of long-chain anteiso-alkanes (a-C20 to a-C30) and anteiso-alkanoic acids (a-C20 to a-C30) were detected in many samples, together with straight-chain, branched and/or cyclic and acyclic isoprenoid compounds. These novel compounds are probably derived from unidentified heterotrophic bacteria or symbiotic processes in a unique microbial community in the Antarctic cold desert and suggest the occurrence of a special biosynthetic pathway. Long-chain anteiso-alkanes are probably formed through microbial decarboxylation of corresponding anteiso-alkanoic acids. They may serve as new biomarkers in environmental and geochemical studies.

NASA Program Exobiology↗