Organic synthesis in experimental impact shocks.

Laboratory simulations of shocks created with a high-energy laser demonstrate that the efficacy of organic production depends on the molecular, not just the elemental composition of the shocked gas. In a methane-rich mixture that simulates a low-temperature equilibrium mixture of cometary material, hydrogen cyanide and acetylene were produced with yields of 5 x 10(17) molecules per joule. Repeated shocking of the methane-rich mixture produced amine groups, suggesting the possible synthesis of amino acids. No organic molecules were produced in a carbon dioxide-rich mixture, which is at odds with thermodynamic equilibrium approaches to shock chemistry and has implications for the modeling of shock-produced organic molecules on early Earth.

Continuous in vitro evolution of catalytic function.

A population of RNA molecules that catalyze the template-directed ligation of RNA substrates was made to evolve in a continuous manner in the test tube. A simple serial transfer procedure was used to achieve approximately 300 successive rounds of catalysis and selective amplification in 52 hours. During this time, the population size was maintained against an overall dilution of 3 x 10(298). Both the catalytic rate and amplification rate of the RNAs improved substantially as a consequence of mutations that accumulated during the evolution process. Continuous in vitro evolution makes it possible to maintain laboratory "cultures" of catalytic molecules that can be perpetuated indefinitely.

Low-temperature carbonate concretions in the Martian meteorite ALH84001: evidence from stable isotopes and mineralogy.

The martian meteorite ALH84001 contains small, disk-shaped concretions of carbonate with concentric chemical and mineralogical zonation. Oxygen isotope compositions of these concretions, measured by ion microprobe, range from delta18O = +9.5 to +20.5 per thousand. Most of the core of one concretion is homogeneous (16.7 +/- 1.2 per thousand) and over 5 per thousand higher in delta18O than a second concretion. Orthopyroxene that hosts the secondary carbonates is isotopically homogeneous (delta18O = 4.6 +/- 1.2 per thousand). Secondary SiO2 has delta18O = 20.4 per thousand. Carbon isotope ratios measured from the core of one concretion average delta13C = 46 +/- 8 per thousand, consistent with formation on Mars. The isotopic variations and mineral compositions offer no evidence for high temperature (>650 degrees C) carbonate precipitation and suggest non-equilibrium processes at low temperatures (< approximately 300 degrees C).

Enantiomeric excesses in meteoritic amino acids.

Gas chromatographic-mass spectral analyses of the four stereoisomers of 2-amino-2,3-dimethylpentanoic acid (dl-alpha-methylisoleucine and dl-alpha-methylalloisoleucine) obtained from the Murchison meteorite show that the L enantiomer occurs in excess (7.0 and 9.1%, respectively) in both of the enantiomeric pairs. Similar results were obtained for two other alpha-methyl amino acids, isovaline and alpha-methylnorvaline, although the alpha hydrogen analogs of these amino acids, alpha-amino-n-butyric acid and norvaline, were found to be racemates. With the exception of alpha-amino-n-butyric acid, these amino acids are either unknown or of limited occurrence in the biosphere. Because carbonaceous chondrites formed 4.5 billion years ago, the results are indicative of an asymmetric influence on organic chemical evolution before the origin of life.

Sequence, overproduction and purification of Vibrio proteolyticus ribosomal protein L18 for in vitro and in vivo studies.

A strategy suggested by comparative genomic studies was used to amplify the entire Vibrio proteolyticus (Vp) gene for ribosomal protein L18. Vp L18 and its flanking regions were sequenced and compared with the deduced amino acid (aa) sequences of other known L18 proteins. A 26-aa residue segment at the carboxy terminus contains many strongly conserved residues and may be critical for the L18 interaction with 5S rRNA. This approach should allow rapid characterization of L18 from large numbers of bacteria. Both Vp L18 and Escherichia coli (Ec) L18 were overproduced and purified using a T7 expression vector which fuses an N-terminal peptide segment (His-tag) containing 6 histidine residues to the recombinant protein. The purified fusion proteins, Vp His::L18 and Ec His::L18, were both found to bind to either the Vp 5S or Ec 5S rRNAs in vitro. Vp His::L18 protein was also shown to incorporate into Ec ribosomes in vivo. This His-tag strategy likely will have general applicability for the study of ribosomal proteins in vitro and in vivo.

Free-living spirochetes from Cape Cod microbial mats detected by electron microscopy.

Spirochetes from microbial mats and anaerobic mud samples collected in salt marshes were studied by light microscopy, whole mount and thin section transmission electron microscopy. Enriched in cellobiose-rifampin medium, selective for Spirochaeta bajacaliforniensis, seven distinguishable spirochete morphotypes were observed. Their diameters ranged from 0.17 micron to > 0.45 micron. Six of these morphotypes came from southwest Cape Cod, Massachusetts: five from Microcoleus-dominated mat samples collected at Sippewissett salt marsh and one from anoxic mud collected at School Street salt marsh (on the east side of Eel Pond). The seventh morphotype was enriched from anoxic mud sampled from the north central Cape Cod, at the Sandy Neck salt marsh. Five of these morphotypes are similar or identical to previously described spirochetes (Leptospira, Spirochaeta halophila, Spirochaeta bajacaliforniensis, Spirosymplokos deltaeiberi and Treponema), whereas the other two have unique features that suggest they have not been previously described. One of the morphotypes resembles Spirosymplokos deltaeiberi (the largest free-living spirochete described), in its large variable diameter (0.4-3.0 microns), cytoplasmic granules, and spherical (round) bodies with composite structure. This resemblance permits its tentative identification as a Sippewissett strain of Spirosymplokos deltaeiberi. Microbial mats samples collected in sterile Petri dishes and stored dry for more than four years yielded many organisms upon rewetting, including small unidentified spirochetes in at least 4 out of 100 enrichments.

Search for past life on Mars: possible relic biogenic activity in martian meteorite ALH84001.

Fresh fracture surfaces of the martian meteorite ALH84001 contain abundant polycyclic aromatic hydrocarbons (PAHs). These fresh fracture surfaces also display carbonate globules. Contamination studies suggest that the PAHs are indigenous to the meteorite. High-resolution scanning and transmission electron microscopy study of surface textures and internal structures of selected carbonate globules show that the globules contain fine-grained, secondary phases of single-domain magnetite and Fe-sulfides. The carbonate globules are similar in texture and size to some terrestrial bacterially induced carbonate precipitates. Although inorganic formation is possible, formation of the globules by biogenic processes could explain many of the observed features, including the PAHs. The PAHs, the carbonate globules, and their associated secondary mineral phases and textures could thus be fossil remains of a past martian biota.

Sequence of the bchG gene from Chloroflexus aurantiacus: relationship between chlorophyll synthase and other polyprenyltransferases.

The sequence of the Chloroflexus aurantiacus open reading frame thought to be the C. aurantiacus homolog of the Rhodobacter capsulatus bchG gene is reported. The BchG gene product catalyzes esterification of bacteriochlorophyllide a by geranylgeraniol-PPi during bacteriochlorophyll a biosynthesis. Homologs from Arabidopsis thaliana, Synechocystis sp. strain PCC6803, and C. aurantiacus were identified in database searches. Profile analysis identified three related polyprenyltransferase enzymes which attach an aliphatic alcohol PPi to an aromatic substrate. This suggests a broader relationship between chlorophyll synthases and other polyprenyltransferases.

Ground-based detectability of terrestrial and Jovian extrasolar planets: observations of CM Draconis at Lick Observatory.

The detection of terrestrial-sized extrasolar planets from the ground has been thought to be virtually impossible due to atmospheric scintillation limits. However, we show that this is not the case especially selected (but nevertheless main sequence) stars, namely small eclipsing binaries. For the smallest of these systems, CM Draconis, several months to a few years of photometric observations with 1-m-class telescopes will be sufficient to detect the transits of any short-period planets of sizes > or = 1.5 Earth radii (RE), using cross-correlation analysis with moderately good photometry. Somewhat larger telescopes will be needed to extend this detectability to terrestrial planets in larger eclipsing binary systems. (We arbitrarily define "terrestrial planets" herein as those whose disc areas are closer to that of Earth's than Neptune's i.e., less than about 2.78 RE.) As a "spin-off" of such observations, we will also be able to detect the presence of Jovian-mass planets without transits using the timing of the eclipse minima. Eclipse minima will drift in time as the binary system is offset by a sufficiently massive planet (i.e., one Jupiter mass) about the binary/giant-planet barycenter, causing a periodic variation in the light travel time to the observer. We present here an outline of present observations taking place at the University of California Lick Observatory using the Crossley 0.9-m telescope in collaboration with other observatories (in South Korea, Crete, France, Canary Islands, and New York) to detect or constrain the existence of terrestrial planets around main sequence eclipsing binary star systems, starting with CM Draconis. We demonstrate the applicability of photometric data to the general detection of gas giant planets via eclipse minima timings in many other small-mass eclipsing binary systems as well.

The Galileo probe mass spectrometer: composition of Jupiter's atmosphere.

The composition of the jovian atmosphere from 0.5 to 21 bars along the descent trajectory was determined by a quadrupole mass spectrometer on the Galileo probe. The mixing ratio of He (helium) to H2 (hydrogen), 0.156, is close to the solar ratio. The abundances of methane, water, argon, neon, and hydrogen sulfide were measured; krypton and xenon were detected. As measured in the jovian atmosphere, the amount of carbon is 2.9 times the solar abundance relative to H2, the amount of sulfur is greater than the solar abundance, and the amount of oxygen is much less than the solar abundance. The neon abundance compared with that of hydrogen is about an order of magnitude less than the solar abundance. Isotopic ratios of carbon and the noble gases are consistent with solar values. The measured ratio of deuterium to hydrogen (D/H) of (5 +/- 2) x 10(-5) indicates that this ratio is greater in solar-system hydrogen than in local interstellar hydrogen, and the 3He/4He ratio of (1.1 +/- 0.2) x 10(-4) provides a new value for protosolar (solar nebula) helium isotopes. Together, the D/H and 3He/4He ratios are consistent with conversion in the sun of protosolar deuterium to present-day 3He.

Synthesis of long prebiotic oligomers on mineral surfaces.

Most theories of the origin of biological organization assume that polymers with lengths in the range of 30-60 monomers are needed to make a genetic system viable. But it has not proved possible to synthesize plausibly prebiotic polymers this long by condensation in aqueous solution, because hydrolysis competes with polymerization. The potential of mineral surfaces to facilitate prebiotic polymerization was pointed out long ago. Here we describe a system that models prebiotic polymerization by the oligomerization of activated monomers--both nucleotides and amino acids. We find that whereas the reactions in solution produce only short oligomers (the longest typically being a 10-mer), the presence of mineral surfaces (montmorillonite for nucleotides, illite and hydroxylapatite for amino acids) induces the formation of oligomers up to 55 monomers long. These are formed by successive 'feedings' with the monomers; polymerization takes place on the mineral surfaces in a manner akin to solid-phase synthesis of biopolymers.

The infrared spectrum of the Galactic center and the composition of interstellar dust.

We have obtained 5-8 micrometers spectra of the Galactic center from the Kuiper Airborne Observatory at resolving powers of approximately 50, approximately 150, and approximately 300. These spectra show absorption features at 5.5, 5.8, 6.1, and 6.8 micrometers. Together with previously observed features in the 3 micrometers region, these features are compared with laboratory spectra of candidate materials. The 3.0 and 6.1 micrometers features are due to the OH stretching and bending variations of H2O and are well fitted by water of hydration in silicates (e.g., talc). The 3.0 micrometer band is equally well fitted by ice mixtures containing 30% H2O, but such mixtures do not provide a good fit to the observed 6.1 micrometer band. The 3.4 and 6.8 micrometers features are identified with the CH stretching and deformation modes in CH2 and CH3 groups in saturated aliphatic hydrocarbons. The 6.1 micrometer band shows a short wavelength shoulder centered on 5.8 micrometer, attributed to carbonyl (C double bond O) groups in this interstellar hydrocarbon dust component. Finally, the narrow 5.5 micrometer feature is also attributed to carbonyl groups, but in the form of metal carbonyls [e.g., Fe(CO)4]. We have derived column densities and abundances along the line of sight toward the Galactic center for the various identified dust components. This analysis shows that hydrocarbon grains contain only 0.08 of the elemental abundance of C and contribute only a relatively minor fraction (0.1) of the total dust volume. Most of the interstellar dust volume is made up of silicates (approximately 0.6). Small graphite grains, responsible for the 2200 angstroms bump, account for 0.07 of the total dust volume. The remaining one-quarter of the interstellar dust volume consists of a material(s) without strong IR absorption features. Likely candidates include large graphite grains, diamonds, or amorphous carbon grains, which all have weak or no IR active modes. Finally, various models for the origin of the hydrocarbon dust component of the interstellar dust are discussed. All of them face some problems in explaining the observations, in particular, the absence of the spectroscopic signature of hydrocrbon grains in sources associated with molecular clouds.

Feedback shift register sequences versus uniformly distributed random sequences for correlation chromatography.

Two alternative input sequences are commonly employed in correlation chromatography (CC). They are sequences derived according to the algorithm of the feedback shift register (i.e., pseudo random binary sequences (PRBS)) and sequences derived by using the uniform random binary sequences (URBS). These two sequences are compared. By applying the "cleaning" data processing technique to the correlograms that result from these sequences, we show that when the PRBS is used the S/N of the correlogram is much higher than the one resulting from using URBS.

Fossil preservation and the stratigraphic ranges of taxa.

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation.

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.

Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3'-5' phosphodiester bonds.

We have found that nonenzymatic, template-directed ligation reactions of oligoribonucleotides display high selectivity for the formation of 3'-5' rather than 2'-5' phosphodiester bonds. Formation of the 3'-5'-linked product is favored regardless of the metal ion catalyst or the leaving group, and for several different ligation junction sequences. The degree of selectivity depends on the leaving group: the ratio of 3'-5'- to 2'-5'-linked products was 10-15:1 when the 5'-phosphate was activated as the imidazolide, and 60-80:1 when the 5'-phosphate was activated by the formation of a 5'-triphosphate. Comparison of oligonucleotide ligation reactions with previously characterized single nucleotide primer extension reactions suggests that the strong preference for 3'-5'-linkages in oligonucleotide ligation is primarily due to occurence of ligation within the context of an extended Watston-Crick duplex. The ability of RNA to correctly self-assemble by template-directed ligation is an intrinsic consequence of its chemical structure and need not be imposed by an external catalyst (i.e., an enzyme polymerase); RNA therefore provides a reasonable structural basis for a self-replicating system in a prebiological world.

Extraterrestrial helium trapped in fullerenes in the Sudbury impact structure.

Fullerenes (C60 and C70) in the Sudbury impact structure contain trapped helium with a 3He/4He ratio of 5.5 x 10(-4) to 5.9 x 10(-4). The 3He/4He ratio exceeds the accepted solar wind value by 20 to 30 percent and is higher by an order of magnitude than the maximum reported mantle value. Terrestrial nuclear reactions or cosmic-ray bombardment are not sufficient to generate such a high ratio. The 3He/4He ratios in the Sudbury fullerenes are similar to those found in meteorites and in some interplanetary dust particles. The implication is that the helium within the C60 molecules at Sudbury is of extraterrestrial origin.

Infrared emission spectra of candidate interstellar aromatic molecules.

Interstellar dust is responsible, through surface reactions, for the creation of molecular hydrogen, the main component of the interstellar clouds in which new stars form. Intermediate between small, gas-phase molecules and dust are the polycyclic aromatic hydrocarbons (PAHs). Such molecules could account for 2-30% of the carbon in the Galaxy, and may provide nucleation sites for the formation of carbonaceous dust. Although PAHs have been proposed as the sources of the unidentified infrared emission bands that are observed in the spectra of a variety of interstellar sources, the emission characteristics of such molecules are still poorly understood. Here we report laboratory emission spectra of several representative PAHs, obtained in conditions approximating those of the interstellar medium, and measured over the entire spectral region spanned by the unidentified infrared bands. We find that neutral PAHs of small and moderate size can at best make only a minor contribution to these emission bands. Cations of these molecules, as well as much larger PAHs and their cations, remain viable candidates for the sources of these bands.

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.

Reflectance spectroscopy and geochemical analyses of Lake Hoare sediments, Antarctica: implications for remote sensing of the Earth and Mars.

Visible to infrared reflectance spectroscopic analyses (0.3-25 micromoles) have been performed on sediments from the Dry Valleys region of Antarctica. Sample characterization for these sediments includes extensive geochemical analyses and X-ray diffraction (XRD). The reflectance spectra and XRD indicate major amounts of quartz, feldspar, and pyroxene in these samples and lesser amounts of carbonate, mica, chlorite, amphibole, illite, smectite, and organic matter. Calcite is the primary form of carbonate present in these Lake Hoare sediments based on the elemental abundances and spectroscopic features. The particle size distribution of the major and secondary components influences their detection in mixtures and this sensitivity to particle size is manifested differently in the "volume scattering" and "surface scattering" infrared regions. The Christiansen feature lies between these two spectral regimes and is influenced by the spectral properties of both regions. For these mixtures the Christiansen feature was found to be dependent on physical parameters, such as particle size and sample texture, as well as the mineralogy. Semiquantitative spectroscopic detection of calcite and organic material has been tested in these quartz- and feldspar-rich sediments. The relative spectral band depths due to organics and calcite correlate in general with the wt% C from organic matter and carbonate. The amounts of organic matter and carbonate present correlate with high Br and U abundances and high Ca and Sr abundances, respectively. Variation in the elemental abundances was overall minimal, which is consistent with a common sedimentary origin for the forty-two samples studied here from Lake Hoare.