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At least 883 records · Page 49Linked to original sources
PubMed1971

Interconnected patterns of biogeography and evolution.

Analysis of the fauna of the carabid beetles of New Guinea reveals both a broad dispersal pattern and a local turnover pattern that together fit into a world-wide pattern of successive dispersals and replacements that run from large to small areas and from more to less favorable climates. This pattern coincides broadly with a world-wide pattern of species numbers. Evolution by group selection, proceeding most rapidly and effectively where species are most numerous, connects the patterns and can supply the force that gives direction to the dispersal pattern. Directional change at any level of complexity involves movement that results in the formation of diverse groups of units (which are themselves groups of smaller units) and differential survival. This process-generalized group selection-has been continuous from chemical evolution on the earth's surface, through the origin of life, and into successive interacting levels of organic evolution. A corollary is that evolution should make situations favorable to itself, by group selection, and has probably done so in (for example) tropical rain forest, where new information about group evolution may be sought.

Journal Article↗
PubMed1983

The primitive code and repeats of base oligomers as the primordial protein-encoding sequence.

Even if the prebiotic self-replication of nucleic acids and the subsequent emergence of primitive, enzyme-independent tRNAs are accepted as plausible, the origin of life by spontaneous generation still appears improbable. This is because the just-emerged primitive translational machinery had to cope with base sequences that were not preselected for their coding potentials. Particularly if the primitive mitochondria-like code with four chain-terminating base triplets preceded the universal code, the translation of long, randomly generated, base sequences at this critical stage would have merely resulted in the production of short oligopeptides instead of long polypeptide chains. We present the base sequence of a mouse transcript containing tetranucleotide repeats conserved during evolution. Even if translated in accordance with the primitive mitochondria-like code, this transcript in its three reading frames can yield 245-, 246-, and 251-residue-long tetrapeptidic periodical polypeptides that are already acquiring longer periodicities. We contend that the first set of base sequences translated at the beginning of life were such oligonucleotide repeats. By quickly acquiring longer periodicities, their products must have soon gained characteristic secondary structures--alpha-helical or beta-sheet or both.

Amino Acid Sequence↗
PubMed1991

Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics.

In contrast to the Darwinian theory of evolution by natural selection, the neutral theory emphasizes the great importance of random genetic drift (due to finite population size) and mutation pressure as the main causes of molecular evolution. In this paper, after a brief review of the neutral theory, recent data strongly supporting the neutral theory are presented. Also discussed are such topics as compensatory neutral evolution and an approach to a unified understanding of molecular and phenotypic evolution. It is concluded that random genetic drift acting on selectively neutral mutants must have played some very important role in organic evolution, including the origin of life and macroevolution.

Alleles↗
PubMed1993

Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane.

A 16-residue peptide [(Ala-Glu-Ala-Glu-Ala-Lys-Ala-Lys)2] has a characteristic beta-sheet circular dichroism spectrum in water. Upon the addition of salt, the peptide spontaneously assembles to form a macroscopic membrane. The membrane does not dissolve in heat or in acidic or alkaline solutions, nor does it dissolve upon addition of guanidine hydrochloride, SDS/urea, or a variety of proteolytic enzymes. Scanning EM reveals a network of interwoven filaments approximately 10-20 nm in diameter. An important component of the stability is probably due to formation of complementary ionic bonds between glutamic and lysine side chains. This phenomenon may be a model for studying the insoluble peptides found in certain neurological disorders. It may also have implications for biomaterials and origin-of-life research.

Amino Acid Sequence↗
PubMed1999

Carbonic anhydrase is an ancient enzyme widespread in prokaryotes.

Carbonic anhydrases catalyze the reversible hydration of CO(2) and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (gamma class) in a methanoarchaeon and our present finding that the beta class also extends into thermophilic species from the Archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. Here we show that carbonic anhydrase is widespread in the Archaea and Bacteria domains, and is an ancient enzyme. The occurrence in chemolithoautotrophic species occupying deep branches of the universal phylogenetic tree suggests a role for this enzyme in the proposed autotrophic origin of life. The presence of the beta and gamma classes in metabolically diverse species spanning the Archaea and Bacteria domains demonstrates that carbonic anhydrases have a far more extensive and fundamental role in prokaryotic biology than previously recognized.

Archaea↗
PubMed2007

Protein architecture chronology deduced from structures of amino acid synthases.

Inferring the protein architecture chronology is one of central topics in origin of life study and has been given much attention. Based on an amino acid evolutionary model that late amino acids were bio-synthesized prior to early counterparts, we addressed the issue by examining the structures of amino acid synthases. Despite the limited structural information on amino acid synthases, our deduction revealed that alpha/beta was the oldest protein class, which is in good agreement with the prior fold-usage-based conclusion.

Amino Acid Sequence↗
PubMed2002

From stem cells to tissue-specific differentiation.

Stem cells have been isolated from embryonic, foetal and adult sources. Embryonic stem cells, derived from the pre-implantation embryo, can be expanded indefinitely in vitro. When reintroduced into the blastocyst they contribute to all lineages in vivo. In vitro, differentiated derivatives of embryonic stem cells are obtained by manipulating culture conditions. Embryonic germ cells, derived from the primordial germ cells, display the same degree of pluripotential differentiation. Adult stem cells that repopulate the tissue of origin throughout life possess the ability to differentiate into phenotypes not restricted to the tissue and, in some cases, to the germ layer from which they derive. Although the pluripotential differentiation capability of these stem-cell populations is supported by an increasing amount of evidence, a better understanding of the mechanisms that control differentiation is required for their exploitation in the treatment of human diseases.

Journal Article↗
PubMed1984

Photochemistry of the atmosphere of Titan: comparison between model and observations.

The photochemistry of simple molecules containing carbon, hydrogen, nitrogen, and oxygen atoms in the atmosphere of Titan has been investigated using updated chemical schemes and our own estimates of a number of key rate coefficients. Proper exospheric boundary conditions, vertical transport, and condensation processes at the tropopause have been incorporated into the model. It is argued that he composition, climatology, and evolution of Titan's atmosphere are controlled by five major processes: (a) photolysis and photosensitized dissociation of CH4; (b) conversion of H to H2 and escape of hydrogen; (c) synthesis of higher hydrocarbons; (d) coupling between nitrogen and hydrocarbons; (e) coupling between oxygen and hydrocarbons. Starting with N2, CH4, and H2O, and invoking interactions with ultraviolet sunlight, energetic electrons, and cosmic rays, the model satisfactorily accounts for the concentrations of minor species observed by the Voyager IRIS and UVS instruments. Photochemistry is responsible for converting the simpler atmospheric species into more complex organic compounds, which are subsequently condensed at the tropopause and deposited on the surface. Titan might have lost 5.6 x 10(4), 1.8 x 10(3), and 4.0 g cm-2, or the equivalent of 8, 0.25, and 5 x 10(-4) bars of CH4, N2, and CO, respectively, over geologic time. Implications of abiotic organic synthesis on Titan for the origin of life on Earth are briefly discussed.

Atmosphere↗
PubMed2001

Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis.

Polymeric compounds similar to oligonucleotides are relevant to the origin of life and particularly to the concept of an RNA world. Although short oligomers of RNA can be synthesized nonenzymatically under laboratory conditions by second-order reactions in concentrated solutions, there is no consensus on how these polymers could have been synthesized de novo on the early Earth from dilute solutions of monomers. To address this question in the context of an RNA world, we have explored ice eutectic phases as a reaction medium. When an aqueous solution freezes, the solutes become concentrated in the spaces between the ice crystals. The increased concentration offsets the effect of the lower temperature and accelerates the reaction. Here we show that in the presence of metal ions in dilute solutions, frozen samples of phosphoimidazolide-activated uridine react within days at -18 degrees C to form oligouridylates up to 11 bases long. Product yields typically exceed 90%, and approximately 30% of the oligomers include one or more 3'-5' linkages. These conditions facilitate not only the notoriously difficult oligouridylate synthesis, but also the oligomerization of activated cytidylate, adenylate, and guanylate. To our knowledge, this represents the first report to indicate that ice matrices on the early Earth may have accelerated certain prebiotic polymerization reactions.

Biological Evolution↗
PubMed2004

Meteors do not break exogenous organic molecules into high yields of diatomics.

Meteoroids that dominate the Earth's extraterrestrial mass influx (50-300 microm size range) may have contributed a unique blend of exogenous organic molecules at the time of the origin of life. Such meteoroids are so large that most of their mass is ablated in the Earth's atmosphere. In the process, organic molecules are decomposed and chemically altered to molecules differently from those delivered to the Earth's surface by smaller (<50 microm) micrometeorites and larger (>10 cm) meteorites. The question addressed here is whether the organic matter in these meteoroids is fully decomposed into atoms or diatomic compounds during ablation. If not, then the ablation products made available for prebiotic organic chemistry, and perhaps early biology, might have retained some memory of their astrophysical nature. To test this hypothesis we searched for CN emission in meteor spectra in an airborne experiment during the 2001 Leonid meteor storm. We found that the meteor's light-emitting air plasma, which included products of meteor ablation, contained less than 1 CN molecule for every 30 meteoric iron atoms. This contrasts sharply with the nitrogen/iron ratio of 1:1.2 in the solid matter of comet 1P/Halley. Unless the nitrogen content or the abundance of complex organic matter in the Leonid parent body, comet 55P/Tempel-Tuttle, differs from that in comet 1P/Halley, it appears that very little of that organic nitrogen decomposes into CN molecules during meteor ablation in the rarefied flow conditions that characterize the atmospheric entry of meteoroids approximately 50 microm-10 cm in size. We propose that the organics of such meteoroids survive instead as larger compounds.

Meteoroids↗
PubMed2005

Quality classification of tandem mass spectrometry data.

UNLABELLED: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICAT and Mascot, which can relate experimental spectra to the theoretical ones derived from protein databases, thus removing much of the manual input needed in the identification process. However, the time-consuming validation of the peptide identifications is still the bottleneck of many proteomic studies. One way to further streamline this process is to remove those spectra that are unlikely to provide a confident or valid peptide identification, and in this way to reduce the labour from the validation phase. RESULTS: We propose a prefiltering scheme for evaluating the quality of spectra before the database search. The spectra are classified into two classes: spectra which contain valuable information for peptide identification and spectra that are not derived from peptides or contain insufficient information for interpretation. The different spectral features developed for the classification are tested on a real-life material originating from human lymphoblast samples and on a standard mixture of 9 proteins, both labelled with the ICAT-reagent. The results show that the prefiltering scheme efficiently separates the two spectra classes.

Algorithms↗
PubMed2005

Development of the mammalian female reproductive tract.

The female reproductive tract (FRT), which includes the oviduct, uterus, cervix and vagina, is critical for mammalian reproduction. Recent research using knockout mice has contributed substantially to our understanding of the molecular mechanisms governing FRT development. Aside from satisfying our curiosities about the origin of life, these studies have provided us with a better understanding of FRT disorders and ways to improve female fertility. Here we review genes that are involved in various stages of sexual duct formation and development in mammals. In addition, the effect of exogenous estrogen such as DES on FRT development is also discussed.

Animals↗
PubMed1998

Template-directed photoligation of oligodeoxyribonucleotides via 4-thiothymidine.

Non-enzymatic, template-directed ligation of oligonucleotides in aqueous solution has been of great interest because of its potential synthetic and biomedical utility and implications for the origin of life. Though there are many methods for template-directed chemical ligation of oligonucleotides, there are only three reported photochemical methods. In the first report, template-directed photoligation was effected by cyclobutane dimer formation between the 5'- and 3'-terminal thymidines of two oligonucleotides with >290 nm light, which also damages DNA itself. To make the photochemistry of native DNA more selective, we have replaced the thymidine at the 5'-end of one oligonucleotide with 4-thiothymidine (s4T) and show that it photoreacts at 366 nm with a T at the 3'-endof another oligonucleotide in the presence of a complementary template. When a single mismatch is introduced opposite either the s4T or its adjoining T, the ligation efficiency drops by a factor of five or more. We also show that by linking the two ends of the oligonucleotides together, photoligation can be used to form circular DNA molecules and to 'photopadlock' circular DNA templates. Thus, s4T-mediated photo-ligation may have applications to phototriggered antisense-based or antigene-based genetic tools, diagnostic agents and drugs, especially for those situations in which chemical or enzyme-mediated ligation isundesirable or impossible, for example inside a cell.

Base Sequence↗
PubMed2001

Aminoacyl-tRNA synthetases database.

Aminoacyl-tRNA synthetases (AARSs) are at the center of the question of the origin of life. They constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. AARSs arose early in evolution and are believed to be a group of ancient proteins. They are responsible for attaching amino acid residues to their cognate tRNA molecules, which is the first step in the protein synthesis. The role they play in a living cell is essential for the precise deciphering of the genetic code. The analysis of AARSs evolutionary history was not possible for a long time due to a lack of a sufficiently large number of their amino acid sequences. The emerging picture of synthetases' evolution is a result of recent achievements in genomics [Woese,C., Olsen,G.J., Ibba,M. and Söll,D. (2000) Microbiol. Mol. Biol. Rev., 64, 202-236]. In this paper we present a short introduction to the AARSs database. The updated database contains 1047 AARS primary structures from archaebacteria, eubacteria, mitochondria, chloroplasts and eukaryotic cells. It is the compilation of amino acid sequences of all AARSs known to date, which are available as separate entries via the WWW at http://biobases.ibch.poznan.pl/aars/.

Amino Acid Sequence↗
PubMed2001

Comparison of the rates of prebiotic formation and hydrolysis of RNA under hydrothermal environments and its implications on the chemical evolution of RNA.

In order to evaluate the possibility of the RNA world hypothesis from the viewpoint of hydrothermal origin of life, parallel investigations on the formation and decomposition of RNA are indispensable under hydrothermal conditions. In this report, comparison of the rates of the template-directed formation and hydrolytic decomposition of RNA in aqueous solution at elevated to high temperatures was carried out. Furthermore, it was elucidated that these prebiotic reactions are relatively so slow compared with modern enzymatic reactions. Based on the considerations, it is predicted that RNA world would be possible at high temperatures.

Environment↗
PubMed1993

tRNA-rRNA interactions and peptidyl transferase.

The extent to which ribosomal RNA is directly involved in the function of ribosomes has important implications for both the mechanism of translation and the molecular origins of life. Detailed evidence has accumulated that places the anticodon and acceptor ends of tRNA in close proximity to conserved features of rRNA in the ribosome. Recent studies are providing evidence that these features are important for ribosomal function.

Base Sequence↗
PubMed2005

Modelling biological complexity: a physical scientist's perspective.

We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter. The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.

Animals↗
PubMed1987

Complexes of DNA hairpins and a single-stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage.

The emergence of a simple translation device consisting of an assembler strand (primordial mRNA) and RNA hairpins (primordial tRNA) is presumed to be an important step leading to the origin of life. The assumption of a non-enzymatic interaction of primordial tRNA and mRNA is experimentally approached. DNA hairpins containing five or more adenosine residues in the loop are able to bind to complementary oligonucleotides covalently bound to cellulose. The exact number of base pairs formed between the hairpins and the assembler strand is determined by two methods applied to DNA hairpin/assembler complexes. The melting temperature of a complex is measured and the cleavage pattern by nuclease from mung bean is determined. The loop of the smallest hairpin able to bind consists of five adenosine residues and only three base pairs are formed. This supports the idea of a primordial recognition similar to the contemporary codon-anticodon interaction.

Biological Evolution↗