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At least 613 records · Page 34Linked to original sources
PubMed2002

Hypothetical clues suggesting that 'AU' and 'UA' were the first 'beginning' and 'end' codons: is their ancient polymerase extant present as a protein domain fossil in reverse transcriptase and telomerase?

Tryptophan and cysteine are excluded from the histones, except histone H3, presumably to decrease premature terminations, since the first two letters of their codons are the same as that of the termination codon UGA. Though tyrosine codon also begins with 'UG', any mutation in tyrosine codon causing premature termination is corrected more professionally by the suppressor tRNA system. Given this background, a hypothetical model for the first replication is proposed. The first termination codon is 'UA' and the first initiation codon is 'AU', in 'UAU' centred RNA rings, which are replicated both clockwise and counter-clockwise. Replication of these would result in the formation of palindromic strands, which may have led to the formation of palindromic sequences in the genome, such as those forming hairpin loops. Their polymerase may be extant in reverse transcriptase (RT), because of tendencies to 'turn the corner' and to form 'hairpin loops', when RT is used for DNA synthesis in vitro. The catalytic subunit of telomerase hTERT in close contact to its RNA template may be another site to find this ancient 'polymerase'.

Codon↗
PubMed1997

Sequence fossils, triplet expansion, and reconstruction of earliest codons.

mRNA sequences are known to carry a hidden periodical pattern (GCU)n, which may be considered a remnant of sequence organization of mRNA early in its evolution, dominated by codons for alanine and their point mutation derivatives. A similar pattern is characteristic of the master (consensus) tRNA sequence derived in 1981 by Eigen and Winkler-Oswatitsch. The master tRNA sequence is thought to represent one of the earliest mRNA. From analysis of literature and from our own calculations presented in this work, the (GCU)n pattern appears to be the most expandable in the norm and in disease. The speculation is put forward that (GCU)n and polyalanine have been key players at the beginning of the triplet code, and the first codons, apart from the GCU triplet, were point change derivatives of the generic triplet GCU, coding for amino acids present in the early prebiotic-biotic environment. The set of the earliest amino acids is derived on the basis of structural simplicity, presence in imitated prebiotic conditions and involvement with class II aminoacyl-tRNA synthetases. The set consists of six amino acids: Ala, Asp, Gly, Pro, Ser and Thr. All these amino acids are, indeed, encoded by the GCU triplet and its derivatives, as predicted. Thus, the pairs GCN (Ala), GAU (Asp), GGU (Gly), CCU (Pro), UCU (Ser) and ACU (Thr) can be viewed as an early triplet code.

Codon↗
PubMed2000

Fossil DNA.

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Animals↗
PubMed2000

EPR spectrum deconvolution and dose assessment of fossil tooth enamel using maximum likelihood common factor analysis.

In order to determine the components which give rise to the EPR spectrum around g = 2 we have applied Maximum Likelihood Common Factor Analysis (MLCFA) on the EPR spectra of enamel sample 1126 which has previously been analysed by continuous wave and pulsed EPR as well as EPR microscopy. MLCFA yielded agreeing results on three sets of X-band spectra and the following components were identified: an orthorhombic component attributed to CO2-, an axial component (CO3(3-)), as well as four isotropic components, three of which could be attributed to SO2-, a tumbling CO2- and a central line of a dimethyl radical. The X-band results were confirmed by analysis of Q-band spectra where three additional isotropic lines were found, however, these three components could not be attributed to known radicals. The orthorhombic component was used to establish dose response curves for the assessment of the past radiation dose, D(E). The results appear to be more reliable than those based on conventional peak-to-peak EPR intensity measurements or simple Gaussian deconvolution methods.

Animals↗
PubMed2002

Phylogeny, fossils, and model systems in the study of evolutionary developmental biology.

The emerging field of evolutionary developmental biology (evo-devo) continues to operate largely under a single paradigm. In this paradigm developmental regulatory genes and processes are compared among a collection of "model organisms" selected primarily on the basis of their historical utility in the study of development. This approach has proven to be extremely informative, revealing an unexpected deep evolutionary conservation among developmental genes and genetic systems. Despite its success, concern has been expressed regarding its limitations. We discuss the "model organism" paradigm in evo-devo research. Based on our interpretation of its limitations, we propose a separate but complementary approach that is centered on "model groups." These groups are selected on the basis of their taxonomic affinity and their relevance to questions of interest to evo-devo biologists. We further discuss the Tetraodontiformes (Teleostei, Pisces) as an example of a "model group" for the evo-devo study of vertebrate skeletal elements.

Animals↗
PubMed2002

Fossil fuel and wood combustion as recorded by carbon particles in Lake Erie sediments 1850-1998.

Carbon particle analysis was performed on a dated sediment core from Lake Erie in order to explore the inputs of pollution from incomplete combustion of coal, oil, and wood. Carbon particles were isolated from the sediment by chemical digestion, and elemental carbon content was determined by CHN analysis. The type of carbon particle (from burning coal, oil, and wood) and particle size and relative abundance were determined using scanning electron microscopy on 100 particles from each core section. The elemental carbon content in the Lake Erie core ranges from 2.5 to 7.4 mg of carbon/g of sediment (1850-1998), and the maximum carbon content in the sediment occurs in the late 1960s to early 1970s. It is shown that particle mass is a better predictor than particle number of historical energy consumption records. This is especially clear for wood where variable particle volumes play a significant role in determining the record of elemental carbon mass from wood burning. Lake Erie core's content of total carbon and carbon particle type is in agreement with U.S. energy consumption records, except that a wood maximum occurs during 1905-1917, about 36 yr after the U.S. consumption maximum from 1870 to 1880.

Air Pollutants↗
PubMed2006

Dispersion modeling of polycyclic aromatic hydrocarbons from combustion of biomass and fossil fuels and production of coke in Tianjin, China.

A USEPA, procedure, ISCLT3 (Industrial Source Complex Long-Term), was applied to model the spatial distribution of polycyclic aromatic hydrocarbons (PAHs) emitted from various sources including coal, petroleum, natural gas, and biomass into the atmosphere of Tianjin, China. Benzo[a]pyrene equivalent concentrations (BaPeq) were calculated for risk assessment. Model results were provisionally validated for concentrations and profiles based on the observed data at two monitoring stations. The dominant emission sources in the area were domestic coal combustion, coke production, and biomass burning. Mainly because of the difference in the emission heights, the contributions of various sources to the average concentrations at receptors differ from proportions emitted. The shares of domestic coal increased from approximately 43% at the sources to 56% at the receptors, while the contributions of coking industry decreased from approximately 23% at the sources to 7% at the receptors. The spatial distributions of gaseous and particulate PAHs were similar, with higher concentrations occurring within urban districts because of domestic coal combustion. With relatively smaller contributions, the other minor sources had limited influences on the overall spatial distribution. The calculated average BaPeq value in air was 2.54 +/- 2.87 ng/m3 on an annual basis. Although only 2.3% of the area in Tianjin exceeded the national standard of 10 ng/m3, 41% of the entire population lives within this area.

Air Movements↗
PubMed2004

Natural aromatic steroids as potential molecular fossils from the fruiting bodies of the ascomycete Daldinia concentrica.

The identification of aromatic steroid hydrocarbons bearing a methyl group at positions 1, 2, 3, 4, or 6 in sediments and petroleum has been puzzling since possible steroidal precursors have not yet been reported in living organisms. Two new aromatic steroids, (17beta,20R,22E,24R)-19-norergosta-1,3,5,7,9,14,22-heptaene (1) and (17beta,20R,22E,24R)-1-methyl-19-norergosta-1,3,5,7,9,14,22-heptaene (2), were isolated from the ascomycete Daldinia concentrica, of which compound 2 bears an unusual methyl group at position 1. We propose that the origin of these compounds is derived from the transformation undergone by their precursor due to microbial action. Compounds 1 and 2 could be the long-sought, biological precursor steroids for organic matter in Earth's subsurface.

Ascomycota↗
PubMed2004

Earth's oldest (approximately 3.5 Ga) fossils and the 'Early Eden hypothesis': questioning the evidence.

We question the biogenicity of putative bacterial and cyanobacterial 'microfossils' from 3465 Ma Apex cherts of the Warrawoona Group in Western Australia. They are challenged on the basis of integrated multidisciplinary evidence obtained from field and fabric mapping plus new high-resolution research into their context, sedimentology, filament morphology, 'septation' and arrangement. They cannot be distinguished from (and are reinterpreted as) secondary artefacts of amorphous carbon that formed during devitrification of successive generations of carbonaceous hydrothermal dyke vein quartz. Similar structures occur within associated carbonaceous volcanic glass. The null hypothesis of an abiotic or prebiotic origin for such ancient carbonaceous matter is sustained until mutually supporting contextural, morphological and geochemical evidence for a bacterial rather than abiotic origin is forthcoming.

Earth, Planet↗