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PubMed1988

Analysis of lipophilic pigments from a phototrophic microbial mat community by high performance liquid chromatography.

As assay for lipophilic pigments in phototrophic microbial mat communities using reverse phase-high performance liquid chromatography was developed which allows the separation of 15 carotenoids and chloropigments in a single 30 min program. Lipophilic pigments in a laminated mat from a commercial salina near Laguna Guerrero Negro, Baja California Sur, Mexico reflected their source organisms. Myxoxanthophyll, echinenone, canthaxanthin, and zeaxanthin were derived from cyanobacteria; chlorophyll c, and fucoxanthin from diatoms; chlorophyll a from cyanobacteria and diatoms; bacteriochlorophylls a and c, bacteriophaeophytin a, and gamma-carotene from Chloroflexus spp.; and beta-carotene from a variety of phototrophs. Sensitivity of detection was 0.6-6.1 ng for carotenoids and 1.7-12 ng for most chloropigments. This assay represents a significant improvement over previous analyses of lipophilic pigments in microbial mats and promises to have a wider application to other types of phototrophic communities.

Bacteria↗
PubMed1997

An analysis of the metabolic theory of the origin of the genetic code.

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature.

Amino Acids↗
PubMed1999

CRITICA: coding region identification tool invoking comparative analysis.

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

Algorithms↗
PubMed1999

Exploring for a record of ancient Martian life.

The immediate task facing exopaleontology is to define a strategy to explore Mars for a fossil record during the decade-long exploration program that lies ahead. Consideration of the quality of paleontological information preserved under different geological conditions is important if we are to develop a strategy with broad applicability. The preservation of microbial fossils is strongly influenced by the physical, chemical, and biological factors of the environment which, acting together, determine the types of information that will be captured and retained in the rock record. In detrital sedimentary systems, preservation is favored by rapid burial in fine-grained, clay-rich sediments. In chemical sedimentary systems, preservation is enhanced by rapid entombment in fine-grained chemical precipitates. For long-term preservation, host rocks must be composed of stable minerals that are resistant to chemical weathering and that form an impermeable matrix and closed chemical system to protect biosignatures from alteration during subsequent diagenesis or metamorphism. In this context, host rocks composed of highly ordered, chemically stable mineral phases, like silica (e.g., cherts) or phosphate (e.g., phosphorites), are especially favored. Such lithologies tend to have very long crustal residence times and, along with carbonates and shales, are the most common host rocks for the Precambrian microfossil record on Earth. Although we make the defensible assumption that Mars was more like the Earth early in its history, clearly, the geological and historical differences between the two planets are many. Such differences must be carefully considered when adapting an Earth-based strategy to Mars.

Carbonates↗
PubMed1994

The collision of Jupiter and Comet Shoemaker-Levy 9.

A simple description of the disruption and deceleration of 100-m- to 5-km-diameter comets striking Jupiter is combined with numerical simulations of the subsequent explosions to predict the fate of Comet Shoemaker-Levy 9. Kilometer-size objects of density 1 g/cm3 explode at about the 10-bar level; a fragment of the same diameter but of density 0.3 g/cm3 explodes at about the 2-bar level. Detailed numerical simulations of the first 3 min of the explosion were performed using the astrophysical hydrodynamics program ZEUS-3D. Our numerical simulations begin either with hot cylinders with dimensions suggested by the disruption and deceleration model or with an initial wake constructed from a moving line charge. In all cases, extensive plumes of hot gas are expelled from the atmosphere. The models with wakes evolve about twice as fast as the initially confined models. Models of both types generate similar pressure waves into the planet. Temperatures and negative hydrogen ion opacities were computed by solving a battery of Saha equations. For atmospheric entry, light curves were computed assuming thermal radiation by clean jovian air with a surface area consistent with the (changing) cross-sectional area of the impactor. On entry the largest bolides could be very bright, possibly as bright as Jupiter for observers placed to see them, although for kilometer-size impactors the luminosity peak is obscured by clouds. The timescale is about 10 sec. For the fireball, light curves were computed from the numerical simulations assuming a grey atmosphere. Metals from the vaporized comet provide electrons that dramatically increase the opacity of Jovian air at low temperature; the resulting effective radiating temperature of the fireball is of order 3000 K. The fireball rises through and above the atmosphere, brightening at first as its surface area increases, but later fading to invisibility as its temperature drops and its opacity plummets. The timescale is about 100 sec.

Astronomy↗