Stoichiometric network analysis

Stoichiometric network analysis is a systematic, general approach to the qualitative, nonlinear dynamics of chemical reaction mechanisms and other systems with stoichiometry. The advantage of a qualitative approach is that no rate constants are needed to determine qualitative features of the dynamics. If one is interested in stability, the approach yields inequalities among the steady-state concentrations and the rate of flow through sequences of important reactions. These parameters are often the ones most easily measured experimentally. By comparing such experiments with the inequalities derived from stoichiometric network analysis, one can often prove that certain mechanisms cannot account for oscillations or other types of observed dynamics. The approach covers far more than stability. The existence of steady states of zero concentration has an interesting mathematics and applies to chemical evolution. The folding of the manifold of steady states can be found by direct calculation and plays a role in switching enzymes on and off. The approach leads to theorems showing that some steady states are globally attracting or, possibly, that a region containing chaos or an oscillation is globally attracting. The subject of sensitivity analysis has been reformulated in this context. Algorithms that apply many of the theoretical results to chemical networks have been developed and combined into a computer program package.     

Lipopolysaccharide-induced NF-kappa B activation in mouse 70Z/3 pre-B lymphocytes is inhibited by mevinolin and 5''-methylthioadenosine: roles of protein isoprenylation and carboxyl methylation reactions.

We show that both the lipopolysaccharide (LPS)-induced activation of NF-kappa DNA binding and kappa gene expression are blocked by treating murine pre-B lymphocyte 70Z/3 cells with 5'-methylthioadenosine (MTA), an inhibitor of several S-adenosylmethionine-dependent methylation reactions. We further show that the LPS-induced incorporation of radioactivity from [methyl-3H]methionine into methyl ester-like linkages on a group of membrane polypeptides is also inhibited by MTA treatment, suggesting the involvement of protein methylation reactions in the LPS signal transduction pathway. We also find that NF-kappa B and kappa gene activation in LPS-treated 70Z/3 cells is blocked by mevinolin, an inhibitor that prevents protein isoprenylation. Interestingly, mevinolin-treated cells also exhibited a marked reduction in the methylation of membrane proteins. Neither MTA nor mevinolin significantly inhibited NF-kappa B activation by phorbol myristate acetate, suggesting that these agents act early in signal transduction. These results provide the first evidence that carboxyl methylated and/or isoprenylated proteins play an essential role in the LPS-signaling pathway.     

A comparison of strength and muscle endurance in strength-trained and untrained women

Muscular strength and fatigability of strength-trained (ST) and untrained (UT) women were compared during a 6-min bout of maximal rhythmic exercise involving the elbow flexor muscles given at a rate of 30 contractions.min-1. Fifteen ST and 15 UT subjects, aged 18-34 years and pair-matched for body size, were tested for differences in initial strength, final strength, absolute endurance, relative endurance, and rate of fatigue. Results revealed a significant difference in initial strength, final strength, and absolute endurance in favor of ST subjects. No significant difference was found for relative endurance, and rates of fatigue were similar for both groups. It is concluded that muscular strength and endurance are enhanced in women engaged in a training program designed primarily to increase muscular strength and hypertrophy, but fatigability is not affected.     

Targeting deletion (homoeologous chromosome pairing locus) or addition line single copy sequences from cereal genomes.

We describe here a protocol for obtaining clones containing sequences present in low copy-number from genomic DNA where moderately and highly repeated sequences predominate. Specific chromosomal regions can be targeted by using deletion or addition line material. We have used this protocol to identify a sequence which has been deleted in both the tetraploid and hexaploid wheat mutants for the homoeologous chromosome pairing locus.     

The 5S DNA units of bread wheat (Triticum aestivum)

A collection of 44 cloned 5S DNA units fromTriticum aestivum cv. Chinese Spring were grouped into 12 sequence-types based on sequence similarity and the respective consensus sequences were then produced. The relationship between these 12 consensus sequences (T. aestivum S 1-S 8 andT. aestivum L 1-L 4), together with two clones sequenced byGerlach andDyer, and the 5S DNA consensus sequences from diploidTriticum spp. were then determined by numerical methods. Both phenetic and cladistic analyses were carried out. The following wheat 5S DNA sequences were found to group with respective sequences from diploidTriticum spp.:T. aestivum S 4, S 6 withT. tauschii S;T. aestivum S 3 withT. monococcum S andT. monococcum S-Rus 7;T. aestivum L 1 andT. aestivum L-G&D withT. speltoides L;T. aestivum L 2, L 3 withT. tauschii L;T. aestivum L 4 withT. monococcum L andT. monococcum L-Rus 12. The analyses suggested that 5 out of the 65S Dna loci present in wheat were identified at the sequence level. The locus that could not be identified in this analysis was the5S Dna-B 1 locus. A group ofT. aestivum sequences (T. aestivum S 1, S 7, S 8, S-G&D) were found to be distinct from the other 5S DNA sequences in the data base. The existence of the distinct group of 5S DNA sequences suggests that there is a gap in our current understanding of wheat evolution with respect to the5S Dna loci.     

Effects of microhabitat and metabolic rate on food intake,growth and fecundity of two competing coral reef fishes

Spinyhead blennies (Acanthemblemaria spinosa) and roughhead blennies (A. aspera) are planktivorous hole-dwelling fishes that live in dead coral skeletons. Both species are known to choose shelters high above the reef surface (although spinyheads displace roughheads downwards). To test the hypothesis that this preference is due to greater plankton availability in higher locations, fish were placed on artificial habitats located 15 cm and 100 cm above the surface of a natural reef. Both species experienced higher feeding rates, growth rates, and fecundities in high locations, and spinyhead rates generally exceeded roughhead rates at a given height. Under laboratory conditions, oxygen consumption by spinyheads was 1.6 times greater than that of roughheads and this corresponds well with the 1.8 ratio of feeding rates under controlled aquarium conditions. This information provides a partial explanation for the observed microhabitat distribution and resulting coexistence of these competing species: it is hypothesized that spinyheads have an advantage in agonistic interactions because of their higher metabolic rates, thus excluding roughheads from high sites, but that roughheads can persist at low sites because their lower metabolic rates result in lower food demands. A model is presented that predicts varying occurrences and vertical distributions of these species in locations with different zooplankton densities.     

The L-isoaspartyl/D-aspartyl protein methyltransferase gene (PCMT1) maps to human chromosome 6q22.3-6q24 and the syntenic region of mouse chromosome 10.

We have mapped the genes for the human and mouse L-isoaspartyl/D-aspartyl protein carboxyl methyltransferase (EC 2.1.1.77) using cDNA probes. We determined that the human gene is present in chromosome 6 by Southern blot analysis of DNA from a panel of mouse-human somatic cell hybrids. In situ hybridization studies allowed us to confirm this identification and further localize the human gene (PCMT1) to the 6q22.3-6q24 region. By analyzing the presence of an EcoRI polymorphism in DNA from backcrosses of C57BL/6J and Mus spretus strains of mice, we localized the mouse gene (Pcmt-1) to chromosome 10, at a position 8.2 +/- 3.5 cM proximal to the Myb locus. This region of the mouse chromosome is homologous to the human 6q24 region.