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PubMed2004

The TNA-family of nucleic acid systems: properties and prospects.

This report summarizes the content of the author's lecture given at the 9th ISSOL Conference on the 'Origin of Life' in Oaxaca on 2 July 2002*. The report consists of introductory remarks followed by a reproduction of the authentic sequence of slides shown during the lecture. Each slide figure is accompanied with a short commentary on the figure's content. The lecture dealt with the structure and the properties of TNA (alpha-threofuranosyl nucleic acid) and included results of some more recent chemical investigations that had been inspired by the simplicity of TNA's molecular architecture.

Base Pairing↗
PubMed2003

Organic-inorganic interactions in petroleum-producing sedimentary basins.

Petroleum deposits form as a consequence of the increased temperatures that accompany progressive burial of organic matter deep within sedimentary basins. Recent advances in petroleum geochemistry suggest that inorganic sedimentary components participate in organic transformations associated with this process. Water is particularly important because it facilitates reaction mechanisms not available in dry environments, and may contribute hydrogen and oxygen for the formation of hydrocarbons and oxygenated alteration products. These findings suggest that petroleum generation and stability is influenced by subsurface chemical environments, and is a simple function of time, temperature and the composition of sedimentary organic matter.

Evolution, Chemical↗
PubMed2005

Geometry of multiple-spin systems as reflected in 13C-{1H} dipolar spectra measured at Lee-Goldburg cross-polarization.

Theoretical calculation and analysis of (13)C-{(1)H} dipolar spectra of small-size spin clusters is presented. Dipolar spectra simulated using the time-independent average Hamiltonian are compared with the dipolar profiles obtained by 2D and 3D (1)H-(13)C correlation experiments employing Lee-Goldburg off-resonance cross-polarization (LG-CP). It is demonstrated that the structural parameters such as interatomic distances as well as mutual orientation of internuclear vectors can be derived from the dipolar profiles of simple spin clusters. Simplified analysis of the dipolar spectra based on isolated-like spin-pair approach can be used only if interacting spin cluster is reduced to the three-spin system in which the angle between both internuclear vectors ranges from 45 degrees to 135 degrees . For other local arrangements of spin systems the produced dipolar spectra must be analyzed with high caution. Contributions of all interacting spins to dipolar evolution of (13)C magnetization are mutually mixed and cannot be easily separated. However, simplification of the dipolar spectra is achieved by selective excitation. Enhanced selectivity of LG-CP transfer due to the initial (1)H chemical-shift-evolution period makes it possible to construct the dipolar spectra from (1)H-(13)C cross-peak intensities for every detected (1)H-(13)C spin-pair. Consequently, isolated-like spin pair evolution of the detected (1)H-(13)C coherence dominates to the resulting dipolar profile, while the influence of other interacting spins is suppressed. However, this suppression is not quite complete and analysis of the selective dipolar spectra based on isolated-like spin-pair approach cannot be used generally. Especially evolution of long-range (1)H-(13)C coherence is still significantly affected by spin states of other coupled hydrogen atoms.

Algorithms↗
PubMed1976

Ia antigens: isolation, chemical modification and structural characterization.

The results described above, with respect to the similarity of basic structural features of Ia and H-2 antigens (see Table V), led to the evolutionary concept presented in Figure 10 according to which these antigens are the products of tandem-duplicated genes. The evolution of MHC-gene products is reflected by the basic structure of these molecules. This structure is compatible with basic repetitive units of molecular weight 12,000 as suggested by the selective cleavage of the intact protein by, for example, papain.

Animals↗
PubMedDate not supplied

[Interneuronal synapses with electrical and chemical mechanisms of transmission and the evolution of the central nervous system].

It becomes increasingly evident that not only chemical but also electrotonic synapses are characteristic feature of the vertebrate brain. Experiments carried out on the isolated perfused central nervous system of lampreys and frogs have shown that in cyclostomes spinal motoneurons receive at least 4 different electrotonic inputs: from giant reticulospinal axons, from smaller descending fibers intrinsic to the cord, from primary afferents and ventral roots. In amphibian motoneurons it is possible to identify 3 electrotonically mediated monosynaptic actions: from primary afferents, recurrent, and reticulospinal. The exact mode of transmission of monosynaptic excitation 1a and supraspinal actions in mammals remains to be elucidated. The trends of evolutionary development of synaptic transmissional processes and synaptic organization in vertebrate nervous system are discussed.

Animals↗
PubMed1995

Specific effect of magnesium ion on 2',3'-cyclic AMP synthesis from adenosine and trimeta phosphate in aqueous solution.

Phosphorylation of adenosine by trimetaphosphate was investigated using various catalysts in aqueous solution under mild conditions at pH approximately 7.0 and at 41 degrees C. The product was primarily 2',3'-cyclic AMP together with smaller amounts of ATP. Magnesium ion was found to have a remarkable catalytic effect of approximately one hundred times greater than the other chemicals tested. The mechanism for the specific effect of magnesium ion is discussed.

Adenosine↗
PubMed1995

Plasma processing of interstellar PAHs into solar system kerogen.

Processes resulting in the formation of hydrocarbons of carbonaceous chondrites and the identity of the interstellar molecular precursors involved are an objective of investigations into the origin of the solar system and perhaps even life on earth. We have combined the resources and experience of an astronomer and physicists doing laboratory simulations with those of a chemical expert in the analysis of meteoritic hydrocarbons, in a project that investigated the conversion of polycyclic aromatic hydrocarbons (PAHs) formed in stellar atmospheres into alkanes found in meteorites. Plasma hydrogenation has been found in the University of Alabama at Birmingham Astrophysics Laboratory to produce from the precursor PAH naphthalene, a new material having an IR absorption spectrum (Lee, W. and Wdowiak, T.J., Astrophys. J. 417, L49-L51, 1993) remarkably similar to that obtained at Arizona State University of the benzene-methanol extract of the Murchison meteorite (Cronin, J.R. and Pizzarello, S., Geochim. Cosmochim. Acta 54, 2859-2868, 1990). There are astrophysical and meteoritic arguments for PAH species from extra-solar sources being incorporated into the solar nebula, where plasma hydrogenation is highly plausible. Conversion of PAHs into alkanes could also have occurred in the interstellar medium. The synthesis of laboratory analogs of meteoritic hydrocarbons through plasma hydrogenation of PAH species is underway, as is chemical analysis of those analogs. The objective is to clarify this heretofore uninvestigated process and to understand its role during the origin of the solar system as a mechanism of production of hydrocarbon species now found in meteorites. Results have been obtained in the form of time-of-flight spectroscopy and chemical analysis of the lab analog prepared from naphthalene.

Alkanes↗
PubMed1983

Biological diversity, chemical mechanisms, and the evolutionary origins of bioluminescent systems.

A diversity of organisms are endowed with the ability to emit light, and to display and control it in a variety of ways. Most of the luciferins (substrates) of the various phylogenetically distant systems fall into unrelated chemical classes, and, based on still limited data, the luciferases (enzymes) and reaction mechanisms are distinctly different. Based on its diversity and phylogenetic distribution, it is estimated that bioluminescence may have arisen independently as many as 30 times in the course of evolution. However, there are several examples of cross-phyletic similarities among the substrates; some of these may be accounted for nutritionally, but in other cases they may have evolved independently.

Animals↗
PubMed2003

[Synthesis and biological activity of pseudonucleotides based on the evolution hypothesis of the glycocomponent of nucleic acid].

Joyce et al. proposed the hypothesis that the sugar moiety of nucleic acid evolved from some achiral, stable and acyclic sugar into the ribose or the deoxyribose. According to their hypothesis, we designed and synthesized new pseudonucleotides having pentaerythritol moiety as a sugar moiety of nucleic acid and estimated their biological activities. Although all chemicals were not toxic to Lepidium sativum, Rhodotolula rubra and Cercospora kikuchi in the eucaryotes, three compounds having adenine, benzimidazole or 6-chloropurine residue as the base component of nucleotide exhibited the growth inhibiting activity to a prokaryote Spirulina platensis at 100 ppm. In the plaque formation test with Vero cells, a chemical with 6-chloropurine moiety inhibited 65.7% of plaque formation by Herpes simplex virus(HSV-1) at 500 ppm. Three chemicals with 6-chloropurine, 2-mercaptomethylbenzimidazole or guanine as the nucleic base moiety inhibited 62.3, 63.1 and 52.5% of plaque formation by Parainfluenza virus(PIFV) at 500 ppm, respectively. The prepared chemicals exhibited no effect on the Vero cells at the same concentration.

Animals↗
PubMed2005

Degradation of wine distillery wastewaters by the combination of aerobic biological treatment with chemical oxidation by Fenton's reagent.

The degradation of wine distillery wastewaters by aerobic biological treatment has been investigated in a batch reactor. The evolution of the chemical oxygen demand, biomass and total contents of polyphenolic and aromatic compounds was followed through each experiment. According to the Contois model, a kinetic expression for the substrate utilization rate is derived, and its biokinetic constant is evaluated. The final effluents of the aerobic biological experiments were oxidized by Fenton's reagent. The evolution of chemical oxygen demand, hydrogen peroxide concentration and total contents of polyphenolic and aromatic compounds was followed through each experiment. A kinetic model to interpret the experimental data is proposed. The kinetic rate constant of the global reaction is determined.

Bacteria, Aerobic↗
PubMed1995

Organic analysis of hydrogen cyanide polymers: prebiotic and extraterrestrial chemistry.

Hydrogen cyanide polymerizes readily to a black solid from which a yellow-brown powder can be extracted by water and further hydrolyzed to alpha-amino acids. These macromolecules could be major components of the dark matter observed on many bodies in the outer solar system, including comets and asteroids. Primitive Earth might therefore have been covered with HCN polymers through bolide bombardment or be terrestrial synthesis. Several instrumental methods were used for the separation and identification of these intriguing polymeric materials, including photoacoustic Fourier transform infrared spectroscopy, supercritical fluid extraction chromatography and pyrolysis mass spectrometry. Our integrated analytical approach revealed fragmentation patterns and chemical functionalities consistent with the presence of polymeric peptide precursors both in HCN polymers and in the Murchison meteorite.

Astronomy↗
PubMed2001

Design of graph-based evolutionary algorithms: a case study for chemical process networks.

This paper describes the adaptation of evolutionary algorithms (EAs) to the structural optimization of chemical engineering plants, using rigorous process simulation combined with realistic costing procedures to calculate target function values. To represent chemical engineering plants, a network representation with typed vertices and variable structure will be introduced. For this representation, we introduce a technique on how to create problem specific search operators and apply them in stochastic optimization procedures. The applicability of the approach is demonstrated by a reference example. The design of the algorithms will be oriented at the systematic framework of metric-based evolutionary algorithms (MBEAs). MBEAs are a special class of evolutionary algorithms, fulfilling certain guidelines for the design of search operators, whose benefits have been proven in theory and practice. MBEAs rely upon a suitable definition of a metric on the search space. The definition of a metric for the graph representation will be one of the main issues discussed in this paper. Although this article deals with the problem domain of chemical plant optimization, the algorithmic design can be easily transferred to similar network optimization problems. A useful distance measure for variable dimensionality search spaces is suggested.

Algorithms↗
PubMed1975

Energetics of abiogenic chemical systems.

After recalling the energy consumption necessary to produce the main categories of biochemicals from the equilibrium state of an hydrogenated atmosphere, the primary processes by which energy can be absorbed in a mixture of methane and ammonia in the presence of aqueous solutions are defined. From the very first excitations, unsaturated products are formed. In fact, this formation of atmospheric precursors is the primordial state of a photochemically induced redox dismutation. The evolution of solutions obtained from the dissolution of these atmospheric precursors in aqueous media is described from experimental data and analysed on energetic grounds. The relaxation of energy accumulated in such solutions involves non enzymic archetypes of the main categories of metabolic processes; in particular some unsaturated atmospheric precursors must be looked upon as primordial representatives of biochemical dehydrating agents. Absorption of light energy in the solutions obtained from the evolution of precursors happens near the visible range and should govern their further evolution. In fact, biochemicals which were previously detected as products of model experiments are not present in these solutions. They were probably obtained during analytical procedures from products of the evolution of atmospheric precursors which are unstable against decreases of pH. Cyclic autocatalytic effects must be involved in the further evolution of the models of the first aqueous solutions. Their possible role in the appearance of optical dissymmetry is emphasized on theoretical grounds.

Amino Acids↗
PubMed2004

GFT NMR experiments for polypeptide backbone and 13Cbeta chemical shift assignment.

(4,3)D, (5,3)D and (5,2)D GFT triple resonance NMR experiments are presented for polypeptide backbone and (13)C(beta) resonance assignment of (15)N/(13)C labeled proteins. The joint sampling of m = 2, 3 or 4 indirect chemical shift evolution periods of 4D and 5D NMR experiments yields the measurement of 2(m) - 1 linear combinations of shifts. To obtain sequential assignments, these are matched in corresponding experiments delineating either intra or interresidue correlations. Hence, an increased set of matches is registered when compared to conventional approaches, and the 4D or 5D information allows one to efficiently break chemical shift degeneracy. Moreover, comparison of single-quantum chemical shifts obtained after a least squares fit using either the intra or the interresidue data demonstrates that GFT NMR warrants highly accurate shift measurements. The new features of GFT NMR based resonance assignment strategies promise to be of particular value for establishing automated protocols.

Carbon Isotopes↗
PubMed2006

Drug evolution concept in drug design: 2. Chimera method.

The drug evolution method represents a novel approach towards efficient rational drug design by implementing the drug evolution concept to the creation and development of general chemical libraries with the purpose of allowing the identification of drug candidates with improved odds and lesser costs than the traditional drug design strategies. As another example of successful translation of the biological evolution into chemical evolution, the chimera method comprises the grafting of selected building blocks, identified through a basic search within a drug library, onto the same substitution sites on a rationally chosen scaffold. The method allows the creation of a library containing both drugs and prospective drug candidates without any priorly required knowledge on the pursued disease or molecular target. Two libraries having scaffolds derived from para-aminobenzoic acid and salicylic acid have exemplified the application of the chimera method. The validation of the method has been achieved through the high number of recognized drugs within the library, which exhibit in the same time a wide variety of therapeutic activities and interact with a broad spectrum of molecular targets. The drug-enriched chimera libraries are expected to provide a highly efficient access to novel drug candidates whose unspecified therapeutic effects should be further revealed through high-throughput screening.

4-Aminobenzoic Acid↗
PubMed1980

The living state and cancer.

Most inanimate systems are build of closed-shell molecules in which electrons lack excitability and mobility. These electrons can be rendered reactive and mobile by taking out some of them, desaturating the system electronically. Single electrons can be taken out of molecules by transfer to an external acceptor, creating two radicals that form a biradical having no net charge. The living state is such an electronically desaturated state. The universal electron acceptor of the biosphere is oxygen. Before light and O2 appeared, a weak electron acceptor could occur through linkage of two C=O groups to glyoxal and addition of a methyl group. The resulting methylglyoxal, being a weak acceptor, could lead to only a low degree of desaturation and thus to formation of only the simple life forms extant during this dark and anaerobic period--the alpha period. During the subsequent aerobic beta period, more highly differentiated life forms could develop because of occurrence of O2, a strong electron acceptor leading to a greater degree of desaturation. When dividing, however, beta-type cells return partially to the proliferative alpha state. The process of electron (charge) transfer, described here in two models, depends on the dielectric constant of the medium and the relative concentration of SH and methylglyoxal. Structure-building proteins that perform the main biological functions carry with them this chemical mechanism of their desaturation. Central to the mechanism is the NH2 of lysine that attaches a methylglyoxal. Through folding of the side chain, the CO groups of resulting Schiff bases can come in touch with the NH's of the peptide chain and accept electrons from it, desaturating it. Ascorbic acid is the catalyst of this charge transfer, which brings protein into the living state. Purified protein is inanimate matter. Manganese and oxygen form part of the chemical mechanism of desaturation, and the charge transfer reactions studied were found to be autocatalytic. It follows from the above observations that a cancer cell is a cell trapped in the alpha state.

Aldehydes↗