The photochemistry of the paleoatmosphere

Targeting nitric oxide as a key modulator of sepsis, arthritis and pain

Nitric oxide (NO) is produced by enzymatic activity of neuronal (nNOS), endothelial (eNOS), and inducible nitric oxide synthase (iNOS) and modulates a broad spectrum of physiological and pathophysiological conditions. The iNOS isoform is positively regulated at transcriptional level and produces high levels of NO in response to inflammatory mediators and/or to pattern recognition receptor signaling, such as Toll-like receptors. In this review, we compiled the main contributions of our group for understanding of the role of NO in sepsis and arthritis outcome and the peripheral contributions of NO to inflammatory pain development. Although neutrophil iNOS-derived NO is necessary for bacterial killing, systemic production of high levels of NO impairs neutrophil migration to infections through inhibiting neutrophil adhesion on microcirculation and their locomotion. Moreover, neutrophil-derived NO contributes to multiple organ dysfunction in sepsis. In arthritis, NO is chief for bacterial clearance in staphylococcal-induced arthritis; however, it contributes to articular damage and bone mass degradation. NO produced in inflammatory sites also downmodulates pain. The mechanism involved in analgesic effect and inhibition of neutrophil migration is dependent on the activation of the classical sGC/cGMP/PKG pathway. Despite the increasing number of studies performed after the identification of NO as an endothelium-derived relaxing factor, the underlying mechanisms of NO in inflammatory diseases remain unclear.

Evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky

Life originated in anoxia, but many organisms came to depend upon oxygen for survival, independently evolving diverse respiratory systems for acquiring oxygen from the environment. Ambient oxygen tension (PO2) fluctuated through the ages in correlation with biodiversity and body size, enabling organisms to migrate from water to land and air and sometimes in the opposite direction. Habitat expansion compels the use of different gas exchangers, for example, skin, gills, tracheae, lungs, and their intermediate stages, that may coexist within the same species; coexistence may be temporally disjunct (e.g., larval gills vs. adult lungs) or simultaneous (e.g., skin, gills, and lungs in some salamanders). Disparate systems exhibit similar directions of adaptation: toward larger diffusion interfaces, thinner barriers, finer dynamic regulation, and reduced cost of breathing. Efficient respiratory gas exchange, coupled to downstream convective and diffusive resistances, comprise the "oxygen cascade"-step-down of PO2 that balances supply against toxicity. Here, we review the origin of oxygen homeostasis, a primal selection factor for all respiratory systems, which in turn function as gatekeepers of the cascade. Within an organism's lifespan, the respiratory apparatus adapts in various ways to upregulate oxygen uptake in hypoxia and restrict uptake in hyperoxia. In an evolutionary context, certain species also become adapted to environmental conditions or habitual organismic demands. We, therefore, survey the comparative anatomy and physiology of respiratory systems from invertebrates to vertebrates, water to air breathers, and terrestrial to aerial inhabitants. Through the evolutionary directions and variety of gas exchangers, their shared features and individual compromises may be appreciated.

The early role of nitric oxide in evolution

Nitric oxide (NO), which today serves many different purposes in regulating complex cellular functions, must have played a crucial role in the early stages of the evolution of life. The formation of NO may have been a critical defence mechanism for primitive microorganisms at a time when life faced the problem of rising atmospheric levels of ozone (03) formed upon photolysis of oxygen (Oz), which occurred shortly after the development of respiration in cyanobacteria. The production of NO by organisms would have allowed neutralization of toxic 03 by chemical reaction outside the cell, thus acting as a protective mechanism against oxidative destruction, allowing evolutionary advantage. Later, NO production might have allowed the control of reactive OZ species within cells before the development of specific electron-accepting enzymes. The pathway of NO formation was then consequently developed further to serve other useful functions. Although mammalian cells produce NO from L-arginine, the origin of this ability might have arisen from the essential process of either nitrification or denitrification in prokaryotic cells.

The catalytic potential of cosmic dust: implications for prebiotic chemistry in the solar nebula and other protoplanetary systems

The synthesis of important prebiotic molecules is fundamentally reliant on basic starting ingredients: water, organic species [e.g., methane (CH(4))], and reduced nitrogen compounds [e.g., ammonia (NH(3)), methyl cyanide (CH(3)CN) etc.]. However, modern studies conclude that the primordial Earth's atmosphere was too rich in CO, CO(2), and water to permit efficient synthesis of such reduced molecules as envisioned by the classic Miller-Urey experiment. Other proposed sources of terrestrial nitrogen reduction, like those within submarine vent systems, also seem to be inadequate sources of chemically reduced C-H-O-N compounds. Here, we demonstrate that nebular dust analogs have impressive catalytic properties for synthesizing prebiotic molecules. Using a catalyst analogous to nebular iron silicate condensate, at temperatures ranging from 500K to 900K, we catalyzed both the Fischer-Tropsch conversion of CO and H(2) to methane and water, and the corresponding Haber-Bosch synthesis of ammonia from N(2) and H(2). Remarkably, when CO, N(2), and H(2) were allowed to react simultaneously, these syntheses also yielded nitrogen-containing organics such as methyl amine (CH(3)NH(2)), acetonitrile (CH(3)CN), and N-methyl methylene imine (H(3)CNCH(2)). A fundamental consequence of this work for astrobiology is the potential for a natural chemical pathway to produce complex chemical building blocks of life throughout our own Solar System and beyond.

Bolide impacts and the oxidation state of carbon in the Earth's early atmosphere

A one-dimensional photochemical model was used to examine the effect of bolide impacts on the oxidation state of Earth's primitive atmosphere. The impact rate should have been high prior to 3.8 Ga before present, based on evidence derived from the Moon. Impacts of comets or carbonaceous asteroids should have enhanced the atmospheric CO/CO2 ratio by bringing in CO ice and/or organic carbon that can be oxidized to CO in the impact plume. Ordinary chondritic impactors would contain elemental iron that could have reacted with ambient CO2 to give CO. Nitric oxide (NO) should also have been produced by reaction between ambient CO2 and N2 in the hot impact plumes. High NO concentrations increase the atmospheric CO/CO2 ratio by increasing the rainout rate of oxidized gases. According to the model, atmospheric CO/CO2 ratios of unity or greater are possible during the first several hundred million years of Earth's history, provided that dissolved CO was not rapidly oxidized to bicarbonate in the ocean. Specifically, high atmospheric CO/CO2 ratios are possible if either: (1) the climate was cool (like today's climate), so that hydration of dissolved CO to formate was slow, or (2) the formate formed from CO was efficiently converted into volatile, reduced carbon compounds, such as methane. A high atmospheric CO/CO2 ratio may have helped to facilitate prebiotic synthesis by enhancing the production rates of hydrogen cyanide and formaldehyde. Formaldehyde may have been produced even more efficiently by photochemical reduction of bicarbonate and formate in Fe(++)-rich surface waters.

Constraints on nebular dynamics and chemistry based on observations of annealed magnesium silicate grains in comets and in disks surrounding Herbig Ae/Be stars

Understanding dynamic conditions in the Solar Nebula is the key to prediction of the material to be found in comets. We suggest that a dynamic, large-scale circulation pattern brings processed dust and gas from the inner nebula back out into the region of cometesimal formation-extending possibly hundreds of astronomical units (AU) from the sun-and that the composition of comets is determined by a chemical reaction network closely coupled to the dynamic transport of dust and gas in the system. This scenario is supported by laboratory studies of Mg silicates and the astronomical data for comets and for protoplanetary disks associated with young stars, which demonstrate that annealing of nebular silicates must occur in conjunction with a large-scale circulation. Mass recycling of dust should have a significant effect on the chemical kinetics of the outer nebula by introducing reduced, gas-phase species produced in the higher temperature and pressure environment of the inner nebula, along with freshly processed grains with "clean" catalytic surfaces to the region of cometesimal formation. Because comets probably form throughout the lifetime of the Solar Nebula and processed (crystalline) grains are not immediately available for incorporation into the first generation of comets, an increasing fraction of dust incorporated into a growing comet should be crystalline olivine and this fraction can serve as a crude chronometer of the relative ages of comets. The formation and evolution of key organic and biogenic molecules in comets are potentially of great consequence to astrobiology.

Oceanic protection of prebiotic organic compounds from UV radiation

It is frequently stated that UV light would cause massive destruction of prebiotic organic compounds because of the absence of an ozone layer. The elevated UV flux of the early sun compounds this problem. This applies to organic compounds of both terrestrial and extraterrestrial origin. Attempts to deal with this problem generally involve atmospheric absorbers. We show here that prebiotic organic polymers as well as several inorganic compounds are sufficient to protect oceanic organic molecules from UV degradation. This aqueous protection is in addition to any atmospheric UV absorbers and should be a ubiquitous planetary phenomenon serving to increase the size of planetary habitable zones.

Origin of biochemical organization

The problems of the origin of life and biochemical evolution are analyzed in the context of the biochemical organization concept proposed earlier by the authors. The traditional view according to which the evolution of biological systems occurred from lower levels to systems of higher levels is criticized. It is suggested that the formation of the cell and biological systems of lower levels (subcellular structures, supramolecular structures, biomacromolecules) occurred in a coordinated manner. The liposome and inorganic hypotheses of the origin of life are discussed. Regosome model based on ideas of Nussinov and Mekler which combines advantages of the liposome and inorganic hypotheses has been adopted and modernized. It is suggested that the initial metabolism of protocells based itself on C2-C3-compounds. Autodevelopment of catalytic systems of protocells is discussed.

Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems

Thermodynamic calculations provide the means to quantify the chemical disequilibrium inherent in the mixing of reduced hydrothermal fluids with seawater. The chemical energy available for metabolic processes in these environments can be evaluated by taking into account the pressure and temperature dependence of the apparent standard Gibbs free energies of reactions in the S-H2-H2O system together with geochemical constraints on pH, activities of aqueous sulfur species and fugacities of H2 and/or O2. Using present-day mixing of hydrothermal fluids and seawater as a starting point, it is shown that each mole of H2S entering seawater from hydrothermal fluids represents about 200,000 calories of chemical energy for metabolic systems able to catalyze H2S oxidation. Extrapolating to the early Earth, which was likely to have had an atmosphere more reduced than at present, shows that this chemical energy may have been a factor of two or so less. Nevertheless, mixing of hydrothermal fluids with seawater would have been an abundant source of chemical energy, and an inevitable consequence of the presence of an ocean on an initially hot Earth. The amount of energy available was more than enough for organic synthesis from CO2 or CO, and/or polymer formation, indicating that the vicinity of hydrothermal systems at the sea floor was an ideal location for the emergence of the first chemolithoautotrophic metabolic systems.

Earth's early atmosphere

Ideas about atmospheric composition and climate on the early Earth have evolved considerably over the last 30 years, but many uncertainties still remain. It is generally agreed that the atmosphere contained little or no free oxygen initially and that oxygen concentrations increased markedly near 2.0 billion years ago, but the precise timing of and reasons for its rise remain unexplained. Likewise, it is usually conceded that the atmospheric greenhouse effect must have been higher in the past to offset reduced solar luminosity, but the levels of atmospheric carbon dioxide and other greenhouse gases required remain speculative. A better understanding of past atmospheric evolution is important to understanding the evolution of life and to predicting whether Earth-like planets might exist elsewhere in the galaxy.

Photochemistry of CO and H2O: analysis of laboratory experiments and applications to the prebiotic Earth's atmosphere

The role photochemical reactions in the early Earth's atmosphere played in the prebiotic synthesis of simple organic molecules was examined. We have extended an earlier calculation of formaldehyde production rates to more reduced carbon species, such as methanol, methane, and acetaldehyde. We have simulated the experimental results of Bar-Nun and Chang (1983) as an acid in the construction of our photochemical scheme and as a way of validating our model. Our results indicate that some fraction of CO2 and H2 present in the primitive atmosphere could have been converted to simple organic molecules. The exact amount is dependent on the partial pressure of CO2 and H2 in the atmosphere and on what assumptions are made concerning the shape of the absorption spectra of CO2 and H2O. In particular, the results are most sensitive to the presence or absence of absorption at wavelengths longward of 2000 angstroms. We also find that small quantities of CH4 could have been present in the prebiotic Earth's atmosphere as the result of the photoreduction of CO.

Prebiotic ribose synthesis: a critical analysis

The discovery of catalytic ability in RNA has given fresh impetus to speculations that RNA played a critical role in the origin of life. This question must rest on the plausibility of prebiotic oligonucleotide synthesis, rather than on the properties of the final product. Many claims have been published to support the idea that the components of RNA were readily available on the prebiotic earth. In this article, the literature cited in support of the prebiotic availability of one subunit, D-ribose, is reviewed to determine whether it justifies the claim. Polymerization of formaldehyde (the formose reaction) has been the single reaction cited for prebiotic ribose synthesis. It has been conducted with different catalysts: numerous basic substances, neutral clays and heat, and various types of radiation. Ribose has been identified (yields are uncertain, but unlikely to be greater than 1%) in reactions run with concentrated (0.15 M or greater) formaldehyde. It has been claimed in reactions run at lower concentration, but characterization has been inadequate, and experimental details have not been provided. The complex sugar mixture produced in the formose reaction is rapidly destroyed under the reaction conditions. Nitrogenous substances (needed for prebiotic base synthesis) would interfere with the formose reaction by reacting with formaldehyde, the intermediates, and sugar products in undesirable ways. The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.