Molecular preservation.

The differing patterns of molecular abundances in organisms are fundamental to the understanding of the biomolecular palaeontological record. All organisms contain DNA, RNA, protein, polysaccharides and lipid components, together with glycolipids, lipopolysaccharides and other complex molecules. Certain biopolymers, however, are restricted in their distributions; for example, lignin, cutin and sporopollenin are found only in terrestrial plants. The detailed chemical structures, namely the bond types present and their precise intramolecular environments, determine resistance to degradation. Observations of biomolecular preservation are compared with predictions based on chemical structure and on conditions encountered during decay.     

Fluorescence correlation spectroscopy. II. An experimental realization

This paper describes the first experimental application of fluorescence correlation spectroscopy, a new method for determining chemical kinetic constants and diffusion coefficients. These quantities are measured by observing the time behaviour of the tiny concentration fluctuations which occur spontaneously in the reaction system even when it is in equilibrium. The equilibrium of the system is not disturbed during the experiment. The diffusion coefficients and chemical rate constants which determine the average time behaviour of these spontaneous fluctuations are the same as those sought by more conventional methods including temperature-jump or other perturbation techniques. The experiment consists essentially in measuring the variation with time of the number of molecules of specified reactants in a defined open volume of solution. The concentration of a reactant is measured by its fluorescence; the sample volume is defined by a focused laser beam which excites the fluorescence. The fluorescent emission fluctuates in proportion with the changes in the number of fluorescent molecules as they diffuse into and out of the sample volume and as they are created or eliminated by the chemical reactions. The number of these reactant molecules must be small to permit detection of the concentration fluctuations. Hence the sample volume is small (10^?8 ml) and the concentration of the solutes is low (～ 10^?9 M). We have applied this technique to the study of two prototype systems: the simple example of pure diffusion of a single fluorescent species, rhodamine 6G, and the more interesting but more challenging example of the reaction of macromolecular DNA with the drug ethidium bromide to form a fluorescent complex. The increase of the fluorescence of the ethidium bromide upon formation of the complex permits the observation of the decay of concentration fluctuations via the chemical reaction and consequently the determination of chemical rate constants.     

Carbon-13 NMR in conformational analysis of nucleic acid fragments. Heteronuclear chemical shift correlation spectroscopy of RNA constituents.

The assignment of the non-quaternary 13C resonances by means of two-dimensional heteronuclear chemical shift correlation spectroscopy is presented for several oligoribonucleotides: The dimers m6(2)AU, m6(2)Am6(2)A and mpUm6(2)A and the trimers m6(2)AUm6(2)A and m4(2)Cm4(2)Cm6(2)A. The temperature and concentration dependency of the 13C chemical shifts are studied with emphasis on the behaviour of the dimer m6(2)AU. The present study shows that in the 5-50 mM range the concentration-dependent chemical shift changes of the ribose carbons are negligible compared to chemical shift changes due to intramolecular events. All compounds studied show a surprising correlation between the chemical shifts of the carbon atoms of the ribose ring and the sugar conformational equilibrium as expressed by the percentage N or S conformer. Thus the chemical shift data can be used to obtain the thermodynamical parameters of the two-state N/S equilibrium. Parameters deduced for m6(2)AU are Tm = 306 K and delta S = -25 cal mol-1 K-1, which values are in satisfactory agreement with results obtained earlier from 1H NMR and from Circular Dichroism.     

Correlations between chromosome segments and fitness in Drosophila melanogaster III. Differential genetic responses to zinc sulfate and selenocystine.

Genetic X environmental interactions are examined at an intrachromosomal level in Drosophila melanogaster. With respect to two fitness components, egg production and egg-to-adult viability, evidence is provided that different segments of the X chromosome are affected differently by each of the chemical substances, zinc sulfate and selenocystine. The extent of a segment's effect on a trait is not always parallelled by the extent of its association with that trait's sensitivity to chemical treatment. Both attributes are functions of the genetical background. The degree of dominance of each segment is not always greater in the chemical environments, a finding inconsistent with Parson's concept of "extreme-environment heterosis".     

Molecular effects of nitrosamine toxicity.

Nitrosamines are toxic chemical compounds found low in quantity, but widespread in the environment. This work investigated the kinetics of chemical reaction of activated nitrosamines with various organic substrates. The mechanism by which nitrosamines react demonstrates possible pathways in which the toxicity is expressed. Once activated nitrosamines are very reactive. Chemical compounds which can act as nucleophilic substrates may be alkylated by the activated nitrosamines. A broad category of chemical compounds are shown to be suitable substrates for nitrosamine induced alkylation. This large category of substrates suggests a substantial potential for toxic activity in vivo. By investigating the reaction kinetics of activated nitrosamines a greater understanding of their toxic effects may be possible.     

Staining Plant Cells with Silver. III. The Mechanism

Silver does not stain all cytological structures with the same intensity. The chemical basis for differential silver staining is unclear, but differences in protein side groups available to react with silver are likely involved. These include amine, carboxyl, phosphate, sulfhydryl and hydroxyl moieties. Here we report an investigation of the chemical groups that could be involved in salt-nylon silver staining of onion root tip squashes. Based on the results, we conclude that SN silver staining primarily depends on the presence of tyrosine hydroxyl groups, and we propose a mechanism for staining.     

Chemical composition distribution of bacterial copolyesters.

Poly(3-hydroxybutyrate) [P(3HB)] and its copolymers with hydroxyalkanoates are naturally occurring thermoplastic materials produced by bacteria. There are many potential uses for these copolyesters owing to their biodegradability and biocompatibility. The physical properties of the copolyesters vary depending on the chemical structure as well as the composition of the comonomers. Usually, we expect, copolymers to have a narrow chemical composition distribution (CCD). Several reports, however, have pointed out that some bacterial copolyesters have broad and/or multimodal CCD. Fractionation based on the chemical composition has also been reported for several bacterial copolyester samples. In this review, the literature concerning CCD and fractionation based on chemical composition is summarized. The width of CCD is approximated based on the data of diad sequence distribution. Generality of the complex CCD in bacterial copolyesters is also discussed.     

CELL PENETRATION BY ACIDS : VI. THE CHLOROACETIC ACIDS.

Measurements of the penetration of tissue from Chromodoris zebra are believed to show that a determining factor in penetration involves the establishment of a critical pH (near 3.5) in relation to superficial cell proteins. The rapidity with which this state is produced depends upon acid strength, and upon some property of the acid influencing the speed of absorption; hence it is necessary to compare acids within groups of chemical relationship. The actual speed of penetration observed with any acid is dependent upon two influences: preliminary chemical combination with the outer protoplasm, followed by diffusion. The variation of the temperature coefficient of penetration velocity with the concentration of acid, and the effect of size (age) of individual providing the tissue sample agree in demonstrating the significant part played by diffusion. In comparing different acids, however, their mode of chemical union with the protoplasm determines the general order of penetrating ability.     

Fluorescence correlation spectroscopy. I. Conceptual basis and theory

We describe a method for determining chemical kinetic constants and diffusion coefficients by measuring the rates of decay of spontaneous concentration fluctuations. The equilibrium of the system is not disturbed during the measurement. We measure the number of molecules of a specified type in a defined open volume as a function of time and compute the time course of the deviations from the thermodynamic mean concentration. The method is based on the principle that the rates of decay of spontaneous microscopic fluctuations are determined by the same phenomenological rate coefficients as those of macroscopic departures from equilibrium which result from external perturbations. Hence, an analysis of fluctuations yields the same chemical rate constants and diffusion coefficients as are measured by conventional procedures. In practice the number of the specified molecules is measured by a property such as absorbance or fluorescence which is specific and sensitive to chemical change. The sample volume is defined by a light beam which traverses the cell. As the molecules appear in or disappear from the light beam, either due to diffusion or chemical reaction, their concentration fluctuations give rise to corresponding fluctuations of the intensity of absorbed or emitted light. This paper presents the theory needed to derive chemical rate constants and diffusion coefficients from these fluctuations in light intensity. The theory is applied to three examples of general interest: pure diffusion in the absence of chemical reaction; the binding of a small rapidly diffusing ligand to a larger slowly diffusing macromolecule; and a unimolecular isomerization. The method should be especially useful in studying highly cooperative systems, relatively noncooperative systems with intermediate states closely spaced in free energy, small systems, and systems not readily subject to perturbations of state.     

Design and analysis of experiments on mutagenicity. II. Assays involving microorganisms.

The design and statistical analysis of mutagenicity experiments involving microorganisms and a single dose of mutagen are discussed. Test statistics are derived for use in determining the mutagenicity of a chemical when survival data are available and also when such data are not available. One's likelihood (power) of correctly concluding a chemical is mutagenic is examined, and minimum total sample sizes required for 95% power are presented. It is found that one generally has greater power when survival data are available. Required precision is estimating survival is discussed in reference to type-1 and type-2 errors. The proper use of the formulae and figures presented is illustrated by examples.     

Phosphorus-31 Fourier transform nuclear magnetic resonance study of mononucleotides and dinucleotides. 1. Chemical shifts.

A phosphorus-31 nuclear magnetic resonance (NMR) study of adenine, uracil, and thymine mononucleotides, their cyclic analogues, and the corresponding dinucleotides is reported. From the pH dependence of phosphate chemical shifts, pKa values of 6.25-6.30 are found for all 5'-mononucleotides secondary phosphate ionization, independently from the nature of the base and the presence of a hydroxyl group at the 2' position. Conversely, substitution of a hydrogen atom for a 2'-OH lowers the pKa of 3'-monoribonucleotides from 6.25 down to 5.71-5.85. This indication of a strong influence of the 2'-hydroxyl group on the 3'-phosphate is confirmed by the existence of a 0.4 to 0.5 ppm downfield shift induced by the 2'-OH on the phosphate resonance of 3'-monoribonucleotides, and 3',5'-cyclic nucleotides and dinucleotides with respect to the deoxyribosyl analogues. Phosphate chemical shifts and titration curves are affected by the ionization and the type of the base. Typically, deviations from the theoretical Henderson-Hasselbalch plots are observed upon base titration. In addition, purine displays a more deshielding influence than pyrimidine on the phosphate groups of most of the mononucleotides (0.10 to 0.25 ppm downfield shift) with a reverse situation for dinucleotides. These effects together with the importance of stereochemical arrangement (furanose ring pucker, furanose-phosphate backbone conformation, O-P-O bond angle) on the phosphate chemical shifts are discussed.     

Conformation of the eosinophil chemotactic tetrapeptides and analogues in dimethyl sulfoxide. 1H n.m.r. studies

Proton nuclear magnetic resonance parameters are reported for DMSO-d6 solutions of the eosinophil chemotactic tetrapeptides, Val1-Gly2-Ser3-Glu4 and Ala1-Gly2-Ser3-Glu4, as well as three analogues of the Val1 tetrapeptide, D-Val1, Ala2 and Ala3. The synthesis of Val-(S)-[alpha-2 H1] Gly-Ala-Glu, in which the glycine has been stereospecifically deuterated in the H alpha 3 position, has allowed the assignment of the 1H resonances belonging to individual H alpha 2 and H alpha 3 glycine methylene protons. Simulation of the glycine ABX spin system yields two vicinal coupling constants which are consistent with a highly preferred conformation about the glycine HN-C alpha bond. The chemical shifts, coupling constants, temperature coefficients of amide proton chemical shifts and calculated side chain rotamer populations are reported for all peptides. The coupling constant analysis and temperature coefficients of amide proton chemical shifts together suggest that a type I beta-turn conformation is preferred by the Ala3 analogue. The 1H n.m.r. parameters of the other peptides suggest that these can also adopt a beta-turn conformation in DMSO. There are, however, considerable differences in the extent of conformational averaging undergone by the various peptides.     

The application of 1H NMR chemical shift calculations to diastereotopic groups in proteins.

We have calculated chemical shifts for a range of diastereotopic protons in proteins (i.e. methylene protons, and the methyl groups of valine and leucine residues), using a recently optimised method for chemical shift calculation. The calculations are based on crystal structure coordinates, and have been compared with experimental stereospecific assignments. The results indicate that chemical shifts can be used to suggest stereospecific assignments with about 80% probability of being correct, in cases where both the experimental and the calculated chemical shift differences between a pair of diastereotopic protons are greater than 0.3 ppm. Inaccurate calculations are shown to be caused in most cases by differences between crystal and solution structures. Furthermore, chemical shift calculations based on NMR structures are shown to be capable of acting as a further constraint on structure, by limiting the range of side-chain conformations adopted in structures calculated from NMR data.     

Chemical images: technical approaches and issues.

Chemical mapping techniques using Raman microscopy are introduced, and using an example of a pharmaceutical tablet, the practical aspects of data collection and processing to produce a chemical image of the sample are detailed. Issues related to data processing, instrument standards, chemical image reportable errors, and the interpretation of chemical images are presented to encourage debate, develop solutions, and promote use in other challenging scientific applications. applications.     

The preferred conformations of protected homodito homoheptamethionine peptides. A1 H n.m.r. study in deuterochloroform medium

Detailed analyses of the conformations of the homo-oligopeptide series, Boc-(L-Met)n-OME n = 2--7, in deuterochloroform have been carried out with proton n.m.r. and IR spectroscopy. Well-resolved high field n.m.r. spectra with assignments for the NH and alpha-CH resonances of these homo-methionine peptides are presented. Extensive n.m.r. concentration-dependent chemical shift studies are combined with IR results to delineate the involvement of the various methionine NH protons in intra- and/or intermolecular hydrogen bonding. N.m.r. chemical shift dependencies with temperature and solvent, DMSO-d6, are used to explore the strength of the hydrogen bonds for the various oligopeptides. At low concentrations, where peptide aggregation is absent, the dipeptide is found to be disordered. The tetra- to heptapeptides possess intramolecular hydrogen bonded seven-membered rings at internal residues. The number of internal rings and the oligopeptide self-association increase with increasing peptide chainlength. At intermediate concentrations associations of peptide molecules with folded structures occur with initial association at the C-terminal region. At high concentrations, "in-register" associated extended beta structures are formed.     

Graph-theoretic methods for the analysis of chemical and biochemical networks. I. Multistability and oscillations in ordinary differential equation models

A chemical mechanism is a model of a chemical reaction network consisting of a set of elementary reactions that express how molecules react with each other. In classical mass-action kinetics, a mechanism implies a set of ordinary differential equations (ODEs) which govern the time evolution of the concentrations. In this article, ODE models of chemical kinetics that have the potential for multiple positive equilibria or oscillations are studied. We begin by considering some methods of stability analysis based on the digraph of the Jacobian matrix. We then prove two theorems originally given by A. N. Ivanova which correlate the bifurcation structure of a mass-action model to the properties of a bipartite graph with nodes representing chemical species and reactions. We provide several examples of the application of these theorems.     

Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP.

An analysis is presented in which are evaluated correlations among chemical structure, mutagenicity to Salmonella, and carcinogenicity to rats and mice among 301 chemicals tested by the U.S. NTP. Overall, there was a high correlation between structural alerts to DNA reactivity and mutagenicity, but the correlation of either property with carcinogenicity was low. If rodent carcinogenicity is regarded as a singular property of chemicals, then neither structural alerts nor mutagenicity to Salmonella are effective in its prediction. Given this, the database was fragmented and new correlations sought between the derived sub-groups. First, the 301 chemicals were segregated into six broad chemical groupings. Second, the rodent cancer data were partially segregated by target tissue. Using the previously assigned structural alerts to DNA reactivity (electrophilicity), the chemicals were split into 154 alerting chemicals and 147 non-alerting chemicals. The alerting chemicals were split into three chemical groups; aromatic amino/nitro-types, alkylating agents and miscellaneous structurally-alerting groups. The non-alerting chemicals were subjectively split into three broad categories; non-alerting, non-alerting containing a non-reactive halogen group, and non-alerting chemical with minor concerns about a possible structural alert. The tumor data for all 301 chemicals are re-presented according to these six chemical groupings. The most significant findings to emerge from comparisons among these six groups of chemicals were as follows: (a) Most of the rodent carcinogens, including most of the 2-species and/or multiple site carcinogens, were among the structurally alerting chemicals. (b) Most of the structurally alerting chemicals were mutagenic; 84% of the carcinogens and 66% of the non-carcinogens. 100% of the 33 aromatic amino/nitro-type 2-species carcinogens were mutagenic. Thus, for structurally alerting chemicals, the Salmonella assay showed high sensitivity and low specificity (0.84 and 0.33, respectively). (c) Among the 147 non-alerting chemicals less than 5% were mutagenic, whether they were carcinogens or non-carcinogens (sensitivity 0.04).     

Chemical dependency in women. Meeting the challenges of accurate diagnosis and effective treatment.

Women dependent on alcohol or prescribed or nonprescribed psychoactive drugs present special diagnostic challenges to physicians. Chemical dependency likewise has adverse effects on women who are nonusers through the disease of co-dependency. The natural history of chemical dependency in women includes sex-specific differences in presenting signs and symptoms. Collateral medical history may come from a variety of community sources. Diagnoses may also use sex-specific criteria, with simultaneous diagnoses of chemical dependency and co-dependency considered.     

Olfaction and the common chemical sense: some psychophysical contrasts.

Three experiments explored the olfactory and the common chemical attributes of sensations produced by various concentrations of n-butyl alcohol. These two attributes combine in an almost-linear fashion to produce the overall perceived intensity of the stimulus. Common chemical intensity makes only a small contribution to overall magnitude at low concentrations, but its proportional contribution increases with concentration. In like manner, speed of response (i.e., reciprocal of reaction time) to the common chemical attribute increases more rapidly than that to odor. Nevertheless, odor always makes its appearance sooner than the common chemical attribute, even when the two attributes are matched in perceived magnitude. Repeated inhalations cause odor intensity to decrease slightly but cause common chemical intensity to increase dramatically. The results obtained from the normal subjects studied here agree with those obtained from subjects with unilateral destruction of the trigeminal nerve.     

Neurokinin A and B.

The chemical features, pharmacological and biochemical characteristics of novel mammalian tachykinin peptides, neurokinin A and neurokinin B are described and are compared with those of substance P, a representative of tachykinin family.