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Evolution. Darwin for all seasons.
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Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity.
Parmelioid lichens comprise about 1500 species and have a worldwide distribution. Numerous species are widely distributed and well known, including important bioindicators for atmospheric pollution. The phylogeny and classification of parmelioid lichens has been a matter of debate for several decades. Previous studies using molecular data have helped to establish hypotheses of the phylogeny of certain clades within this group. In this study, we infer the phylogeny of major clades of parmelioid lichens using DNA sequence data from two nuclear loci and one mitochondrial locus from 145 specimens (117 species) that represent the morphological and chemical diversity in these taxa. Parmelioid lichens are not monophyletic; however, a core group is strongly supported as monophyletic, excluding Arctoparmelia and Melanelia s. str., and including Parmeliopsis and Parmelaria. Within this group, seven well-supported clades are found, but the relationships among them remain unresolved. Stochastic mapping on a MC/MCMC tree sampling was employed to infer the evolution of two morphological and two chemical traits believed to be important for the evolutionary success of these lichens, and have also been used as major characters for classification. The results suggest that these characters have been gained and lost multiple times during the diversification of parmelioid lichens.
Role of minimization of chemical distances between amino acids in the evolution of the genetic code.
The allocation of codons in the genetic code makes possible a moderate minimization of the chemical distances between pairs of neighboring amino acids in the code. However, the code is neither a global nor a local optimum with respect to distance minimization. These findings do not support the physicochemical postulate that distance minimization was a major factor shaping the evolution of the genetic code. They agree with the coevolution theory, which proposes that genetic code evolution was predominantly determined by the concession of codons from precursor to product amino acids in an expansion of the code to accommodate new varieties of amino acids, with distance minimization playing a subsidiary role in deciding the choice of codons to be acquired by the product amino acids from the codon domains of the precursor amino acids.
The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome.
Metazoan genomes contain large numbers of genes that participate in responses to environmental stressors. We surveyed the sea urchin Strongylocentrotus purpuratus genome for homologs of gene families thought to protect against chemical stressors; these genes collectively comprise the 'chemical defensome.' Chemical defense genes include cytochromes P450 and other oxidases, various conjugating enzymes, ATP-dependent efflux transporters, oxidative detoxification proteins, and transcription factors that regulate these genes. Together such genes account for more than 400 genes in the sea urchin genome. The transcription factors include homologs of the aryl hydrocarbon receptor, hypoxia-inducible factor, nuclear factor erythroid-derived 2, heat shock factor, and nuclear hormone receptors, which regulate stress-response genes in vertebrates. Some defense gene families, including the ABCC, the UGT, and the CYP families, have undergone expansion in the urchin relative to other deuterostome genomes, whereas the stress sensor gene families do not show such expansion. More than half of the defense genes are expressed during embryonic or larval life stages, indicating their importance during development. This genome-wide survey of chemical defense genes in the sea urchin reveals evolutionary conservation of this network combined with lineage-specific diversification that together suggest the importance of these chemical stress sensing and response mechanisms in early deuterostomes. These results should facilitate future studies on the evolution of chemical defense gene networks and the role of these networks in protecting embryos from chemical stress during development.
Chemo-orientation using conspecific chemical cues in the stripe-necked terrapin (Mauremys leprosa).
Although chemical communication has been studied intensively in may reptilian species, little attention has been paid to the role that chemical signals play in aquatic reptiles, such as freshwater turtles. Here, I tested the hypothesis that the stripe-necked terrapin (Mauremys leprosa), an abundant freshwater turtle that inhabits the Iberian peninsula, is able to recognize chemical cues from conspecifics in the water and to modify its behavior in response to such cues. I compared the time spent by adult males and adult females in clean water to the time spent in water that presumably contained their own odor, odor from other males, and odor from other females, both during and outside the mating season. Results show that outside the mating season, both males and females avoid water that contains chemical cues from conspecifics of the opposite sex. During the mating season, male turtles clearly select water with chemical cues from females. Moreover, males prefer to occupy water from their home containers over clean water, and avoid water with chemical cues from other conspecific males. Conversely, during the mating season, females prefer to occupy water with chemical cues from other females, but do not select water from their home containers or water from males. The evolution of chemical communication in turtles, its relation to sexual selection processes, and the implications for turtle behavior are discussed.
[Chemical structure and photochemical activity of the abiogenic flavin substrate].
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Improved detection of long-range residual dipolar couplings in weakly aligned samples by Lee-Goldburg decoupling of homonuclear dipolar truncation.
Homonuclear (1)H residual dipolar couplings (RDCs) truncate the evolution of transverse (1)H magnetization of weakly aligned molecules in high-resolution NMR experiments. This leads to losses in sensitivity or resolution in experiments that require extended (1)H evolution times. Lee-Goldburg decoupling schemes have been shown to remove the effects of homonuclear dipolar couplings, while preserving chemical shift evolution in a number of solid-state NMR applications. Here, it is shown that the Lee-Goldburg sequence can be effectively incorporated into INEPT- or HMQC-type transfer schemes in liquid state weak alignment experiments in order to increase the efficiency of the magnetization transfer. The method is applied to the sensitive detection of (1)H(N)-(13)C long-range RDCs in a three-dimensional HCN experiment. As compared to a conventional HCN experiment, an average sensitivity increase by a factor of 2.4 is obtained for a sample of weakly aligned protein G. This makes it possible to detect 170 long-range (1)H(N)-(13)C RDCs for distances up to 4.9 angstroms.
Mass-independent isotopic compositions in terrestrial and extraterrestrial solids and their applications.
In 1983, Thiemens and Heidenreich reported the first chemically produced mass-independent isotope effect. This work has been shown to have a wide range of applications, including atmospheric chemistry, solar system evolution, and chemical physics. This work has recently been reviewed (Weston, R. E. Chem. Rev. 1999, 99, 2115-2136; Thiemens, M. H. Science 1999, 283, 341-345). In this Account, observations of mass-independent isotopic compositions in terrestrial and Martian solids are reviewed. A wide range of applications, including formation and transport of aerosols in the present atmosphere, chemistry of ancient atmospheres and oceans, history and coupling of the atmosphere-surface in the Antarctic dry valleys, origin and evolution of oxygen in the Earth's earliest environment, and the chemistry of the atmosphere and surface of Mars, are discussed.
Chemical etiology of nucleic acid structure.
Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.
Novel RNA catalysts for the Michael reaction.
BACKGROUND: In vitro selected ribozymes with nucleotide synthase, peptide and carbon-carbon bond forming activity provide insight into possible scenarios on how chemical transformations may have been catalyzed before protein enzymes had evolved. Metabolic pathways based on ribozymes may have existed at an early stage of evolution. RESULTS: We have isolated a novel ribozyme that mediates Michael-adduct formation at a Michael-acceptor substrate, similar to the rate-limiting step of the mechanistic sequence of thymidylate synthase. The kinetic characterization of this catalyst revealed a rate enhancement by a factor of approximately 10(5). The ribozyme shows substrate specificity and can act as an intermolecular catalyst which transfers the Michael-donor substrate onto an external 20-mer RNA oligonucleotide containing the Michael-acceptor system. CONCLUSION: The ribozyme described here is the first example of a catalytic RNA with Michael-adduct forming activity which represents a key mechanistic step in metabolic pathways and other biochemical reactions. Therefore, previously unforeseen RNA-evolution pathways can be considered, for example the formation of dTMP from dUMP. The substrate specificity of this ribozyme may also render it useful in organic syntheses.
Graded Autocatalysis Replication Domain (GARD): kinetic analysis of self-replication in mutually catalytic sets.
A Graded Autocatalysis Replication Domain (GARD) model is proposed, which provides a rigorous kinetic analysis of simple chemical sets that manifest mutual catalysis. It is shown that catalytic closure can sustain self replication up to a critical dilution rate, lambda c, related to the graded extent of mutual catalysis. We explore the behavior of vesicles containing GARD species whose mutual catalysis is governed by a previously published statistical distribution. In the population thus generated, some GARD vesicles display a significantly higher replication efficiency than most others. GARD thus represents a simple model for primordial chemical selection of mutually catalytic sets.
STUDIES OF A MAMMALIAN ENZYME SYSTEM FOR PRODUCING EVOLUTIONARY EVIDENCE ON MAN.
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Chemistry between the stars.
Life--as we know it--is a chemical process, based on water and carbon compounds. Complex organic molecules are made primarily from the biogenic elements--carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur--that formed deep within massive ancient stars. How did these elements travel from their stellar birthplaces across time and space to make up the life-form that is reading these words? In this article, we'll take a look at the chemical processes that set the stage for the origin of life.
Composite pulsed field gradients with refocused chemical shifts and short recovery time.
An improved self-compensating pulsed field gradient (PFG) technique that combines antiphase gradient pairs with broadband frequency-modulated 180 degrees pulses is proposed. The antiphase gradient pairs lead to superb system recovery. In addition, evolution under chemical shift and heteronuclear J coupling are refocused during the PFG, making it appear effectively instantaneous. This new approach makes it possible to obtain high-resolution phase-sensitive 2D spectra for the PFG version of many experiments such as COSY, DQF-COSY, and HSQC without adding extra compensating delays or pulses. While reasonable suppression of unwanted magnetization is achieved, this method also gives satisfactory retention of desired signals. As a bonus, the field-frequency lock is not perturbed during the experiments.
Carbonaceous components in the comet Halley dust.
Cometary grains containing large amounts of carbon and/or organic matter (CHON) were discovered by in situ measurements of comet Halley dust composition during VEGA and GIOTTO flyby missions. In this paper, we report the classification of these cometary grains by means of cluster analysis, discuss the resulting compositional groups, and compare them with substances observed or hypothesized in meteorites, interplanetary dust particles, and the interstellar medium. Grains dominated by carbon and/or organic matter (CHON grains) represent approximately 22% of the total population of measured cometary dust particles. They usually contain a minor abundance of rock-forming elements as well. Grains having organic material are relatively more abundant in the vicinity of the nucleus than in the outer regions of the coma, which suggests decomposition of the organics in the coma environment. The majority of comet Halley organic particles are multicomponent mixtures of carbon phases and organic compounds. Possibly, the cometary CHON grains may be related to kerogen material of an interstellar origin in carbonaceous meteorites. Pure carbon grains, hydrocarbons and polymers of cyanopolyynes, and multi-carbon monoxides are present in cometary dust as compositionally simple and distinctive components among a variety of others. There is no clear evidence of significant presence of pure formaldehyde or HCN polymers in Halley dust particles. The diversity of types of cometary organic compounds is consistent with the interstellar dust model of comets and probably reflects differences in composition of precursor dust. Preservation of this heterogeneity among submicron particles suggests the gentle formation of cometary nucleus by aggregation of interstellar dust in the protosolar nebula without complete mixing or chemical homogenization at the submicron level.