Characteristic reaction paths of biochemical reaction systems with time scale separation

A technique has been developed for characterizing the in vivo behavior of key enzymes from intermediate measurements. The technique is based on the identification of characteristic reaction paths, and it depends on the time scale separation characteristics of the systems. It is shown that useful information can be obtained from the phase plots of properly selected intermediate pairs or combinations which typically show process insensitive algebraic relations approached on time scales short compared to those of most practical interest. These characteristic reaction paths provide useful global measures of enzyme activity. The mathematical basis of reaction path analysis is investigated using linear transformation techniques. General theorems are developed predicting the existence of characteristic reaction paths as asymptotic limits whenever there is effective time scale separation. These limits are reached when fast reactions are relaxed, and available evidence suggests that these conditions will occur for the majority of reaction networks.     

Lumping analysis of biochemical reaction systems with time scale separation

Due to the complexity of the systems, successful modelling of intracellular reaction networks must rely on lumping techniques which systematically reduce the number of variables and parameters. Fortunately, the time scale separation characteristics of biochemical systems provide opportunities for eliminating unnecessary details. Through the proper interpretation of eigenvalues and eigenvectors, this article presents a theoretical basis for systematic model reduction. Results are generalized as a semiheuristic basis for lumping systems without complete kinetic information. It is also illustrated that the simplified system can yield new insight which is otherwise unavailable.     

An anionic galactomannan polysaccharide gum from a newly-isolated lactose-utilizing bacterium. I. Strain description and gum characterization.

As part of an effort to obtain microorganisms able to produce polysaccharide gums from whey and whey permeate, soil samples from farm fields regularly treated with whey were screened for bacteria able to produce gums from lactose. The most promising organism isolated (ATCC 55046) is a facultative anaerobe, tentatively identified as a new Erwinia species on the basis of biochemical and morphological tests. The organism produces a polysaccharide gum from lactose and other sugars (herein named lactan gum) composed of mannose, galactose, and galacturonic acid with an approximate molar ratio of 5:3:2 and containing no organic acid modifying groups. The weight average molecular weight of the gum is approximately 7 x 10(6). Aqueous solutions of lactan gum exhibit shear-thinning and elastic flow behavior with an estimated power law model flow index of 0.26 at 1% (w/w) gum. The viscosity of aqueous 1% (w/w) lactan gum solutions is stable over a pH range of 2-11, being particularly stable in alkaline environments. Aqueous 1% (w/w) gum solutions at pH 5-11 show excellent thermostability, retaining at least 80% of the original viscosity after being heated to 121 degrees C for 15 min. These flow properties indicate potential industrial applications in food and nonfood products requiring a moderate degree of thickening, wet-end additives and coating agents for paper products, ceramics, detergents, and binders for building materials.     

Enemy at the Gates: Interaction-Specific Stomatal Responses to Pathogenic Challenge

Stomata regulate gas exchange and their closure in response to pathogens may, in some cases, contribute to resistance. However, in the cereal mildew and rust systems, stomatal closure follows establishment of compatible infections. In incompatible systems, expression of major (R) gene controlled hypersensitive responses (HR), causes drastic, permanent stomatal dysfunction: stomata become locked open following powdery mildew attack and locked shut following rust attack. Thus, stomatal locking can be a hitherto unsuspected negative consequence of R gene resistance that carries a physiological cost affecting plant performance.Key Words: stomata, rust, mildew, hypersensitive response, stomatal lock-up     

The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3

Background  

SH3 domains are small protein modules of 60–85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the α-spectrin SH3 domain (Spc-SH3).     

Nitrated fibrinogen is a biomarker of oxidative stress in venous thromboembolism

The pathogenesis of venous thromboembolism (VTE) is linked to inflammation and oxidant production, although specific markers for these pathways with pathological relevance to VTE have not been explored. The coagulant protein fibrinogen is posttranslationally modified by nitric oxide-derived oxidants to nitrated fibrinogen in both acute and chronic inflammatory states. Therefore, nitrated fibrinogen may serve as a marker of inflammation and oxidative stress in VTE. To test this hypothesis we enrolled subjects (n=251) presenting with suspected VTE at the University of Pennsylvania Hospital emergency department, 50 (19.9%) of whom were positive by imaging or 90-day follow-up. Mean nitrated fibrinogen was elevated in VTE-positive (62.7 nM, 95% CI 56.6-68.8) compared to VTE-negative patients (54.2 nM, 95% CI 51.4-57.1; P<0.01). Patients in the highest quartile of nitrated fibrinogen had an increased risk of VTE compared with patients in the lowest quartile (OR 3.30; 95% CI 1.25-8.68; P<0.05). This risk persisted after univariate adjustment for age, active cancer, and recent surgery, but not after multivariate adjustment. Mean fibrinogen levels measured either by the Clauss assay or by ELISA were not different between VTE-negative and VTE-positive patients. These data indicate that nitrated fibrinogen is an oxidative risk marker in VTE, providing a novel mechanistic link between oxidant production, inflammation, and VTE.     

Subcellular localization of tyrosine-nitrated proteins is dictated by reactive oxygen species generating enzymes and by proximity to nitric oxide synthase

Using high-resolution immuno-electron microscopy the steady-state subcellular distribution of tyrosine-nitrated proteins in different cells and tissues was evaluated. In quiescent eosinophils and neutrophils in the bone marrow intracellular nitrated proteins were mainly restricted to the peroxidase-containing secretory granules. The inducible nitric oxide synthase (iNOS) was expressed in the same granules. Proteins nitrated on tyrosine residues were also abundant in the cytosol of circulating erythrocytes. In the vasculature, nitrated proteins were mainly located in mitochondria and endoplasmic reticulum of the endothelial cells, fibroblasts, and smooth muscle cells. Endogenous nitrated proteins were also found in chondrocytes in cartilage, where it was typically associated with the cytoplasmic interface of the endoplasmic reticulum membrane. Nitrated proteins were also prominent in the peroxisomes of liver hepatocytes and of secretory cells in the lacrimal gland. Challenge of mouse dendritic cells with lipopolysaccharide induced iNOS protein expression in cytosol and peroxisomes and was associated with an increased 3-nitrotyrosine formation in cytosol, mitochondria, and peroxisomes. These data indicate that nitric oxide-dependent protein tyrosine nitration is a physiologically relevant process localized within specific subcellular compartments in close proximity to iNOS and to enzymes capable of peroxidative chemistry and reactive oxygen species production.     

Birth weight,sex and childhood cancer: A report from the United Kingdom Childhood Cancer Study

Birth weight has been linked to the risk of developing childhood cancer, in particular childhood leukaemia. However, despite many childhood cancers having a male predominance and boys generally weighing more than girls at birth few studies have reported sex-specific associations. The relationship between birth weight and childhood cancer risk was examined using information from a national case-control study. Children (0–14 years) newly diagnosed with cancer in GB were ascertained between 1991 and 1996 (n = 3651) and for comparison, controls matched on sex, month and year of birth were identified from primary care population registers (n = 6337). Birth weights were obtained from the Office of National Statistics for all targeted subjects born in England and Wales. Overall, cases were, on average, 30 g heavier at birth than controls (p = 0.003) with differences seen by cancer type; those diagnosed with hepatic tumours weighing around 500 g less than controls at birth (p < 0.0001) and those with leukaemia being, on average, 50 g heavier than those without (p = 0.001). An interaction between birth weight and sex was found for acute leukaemia (χ² = 11.2, p = 0.04) and when data were stratified by sex, an association between high birth weight and risk of ALL was seen with girls (>4000 g, OR 1.86, 95% CI 1.38–2.50, χ² for trend 20.2, p < 0.0001). Our results support the hypothesis that birth weight is an important determinant for childhood cancer. In addition, the data are consistent with the notion that childhood leukaemia has a prenatal origin.