Biochemical network matching and composition

This paper looks at biochemical network matching and compositio

CHEMICAL AND PHYSICAL CHARACTERISTICS OF M. PSOAS MAIOR FROM ALENTEJANO PIGS AT A VARIOUS LIVE WEIGTHS

The present study was carried out to investigate the evolution of biochemical composition and physical traits of the chemical composition and physical characteristics of muscle Psoas major (PM adipose during growth of Alentejano pigs

Composition of Biochemical Networks using Domain Knowledge

Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain

Effect of plant-based feed ingredients on osmoregulation in the Atlantic salmon lens

Lenses of adult Atlantic salmon fed with a plant oil and plant protein-based diet (plant diet) were compared to lenses of fish fed a diet based on traditional marine ingredients (marine diet) with respect to biochemical composition and functionality ex vivo. After 12 months of feeding, plant diet-fed fish had smaller lenses with higher water contents and lower concentrations of histidine (His) and N-acetylhistidine (NAH) than fish fed with the marine diet. Cataract development in both dietary groups was minimal and no differences between the groups were observed. Lens fatty acid and lipid class composition differed minimally, although a significant increase in linoleic acid was observed. The lenses were examined for their ability to withstand osmotic disturbances ex vivo. Culture in hypoosmotic and hyperosmotic media led to increase and decrease of lens volume, respectively. Lenses from plant diet-fed fish were less resistant to swelling and shrinking, released less NAH into the culture medium, and accumulated His and NAH at higher rates than lenses from marine diet-fed fish. Culture in hypoosmotic medium resulted in higher cataract scores than in control and hyperosmotic medium. mRNA expression of selected genes, including glutathione peroxidase 4 and SPARC (secreted protein acidic and rich in cysteine), was affected by diet and osmotic treatment. It can be concluded that lenses of farmed Atlantic salmon are affected by the diet composition, both in biochemical composition and physiological functionality in relation to osmoregulation

Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs (Poster Presentation)

Copyright @ 2007 Gu et al; licensee BioMed Central LtdBiochemists often conduct experiments in-vivo in order to explore observable behaviours and understand the dynamics of many intercellular and intracellular processes. However an intuitive understanding of their dynamics is hard to obtain because most pathways of interest involve components connected via interlocking loops. Formal methods for modelling and analysis of biochemical pathways are therefore indispensable. To this end, ODEs (ordinary differential equations) have been widely adopted as a method to model biochemical pathways because they have an unambiguous mathematical format and are amenable to rigorous quantitative analysis. BioNessie http://www.bionessie.com webcite is a workbench for the composition, simulation and analysis of biochemical networks which is being developed in by the Systems Biology team at the Bioinformatics Research Centre as a part of a large DTI funded project 'BPS: A Software Tool for the Simulation and Analysis of Biochemical Networks' http://www.brc.dcs.gla.ac.uk/projects/dti_beacon webcite. BioNessie is written in Java using NetBeans Platform libraries that makes it platform independent. The software employs specialised differential equations solvers for stiff and non-stiff systems to produce model simulation traces. BioNessie provides a user-friendly interfact that comes up with an intuitive tree-based graphical layout, an edition function to SBML-compatible models and feature of data output

Evaluation of organic matter stability during the composting process of agroindustrial wastes.

Composting of wastes from citrus industrial processing (pastazzo and sludge) was studied in order to evaluate the evolution of organic matter during the process and to individuate chemical and/or biochemical techniques able to set the stability of the final product. Composts from two open-air piles of different composition were sampled every month during the whole period of composting (5 months) and the organic matter of each sample was characterised by chemical and biochemical techniques. Humification rate (HR%) and humification index (HI) were determined. Extracted organic matter of six samples collected for each compost was investigated by isoelectric-focusing technique (IEF). The biochemical analysis was based on the study of C-mineralisation after the addition of each collected sample to soil. Results obtained clearly demonstrated organic matter evolution during composting processes. Humification rates increased and humification indexes decreased over time, while extracted organic matter showed electrophoretic behaviour typical of stabilised organic compounds. Moreover, mineralisation patterns confirmed the increased level of organic matter stability during the composting process

Stable oxygen and carbon isotope compositional fields for skeletal and diagenetic components in New Zealand Cenozoic nontropical carbonate sediments and limestones: a synthesis and review

The stable oxygen isotope composition (d¹⁸O) of a precipitated carbonate depends mainly on the isotope composition, salinity, and temperature of the host fluid, whereas the stable carbon isotope composition (d¹³C) reflects the source of CO2 for precipitation, such as meteoric or sea water, shell dissolution, or various biochemical origins, including microbial oxidation of organic matter and methane. Despite the potentially complex array of controls, natural waters tend to show a characteristic range of isotope values which in turn are mimicked or tracked by the carbonate minerals precipitated from them. Consequently, plots of d¹⁸O versus d¹³C for carbonate materials can help identify their depositional and/or diagenetic environment(s)

Urban, Forest, and Agricultural AIS Data: Fine Spectral Structure

Spectra acquired by the Airborne Imaging Spectrometer (AIS) near Lafayette, IN, Ely, MN, and over the Stanford University campus, CA were analyzed for fine spectral structure using two techniques: the ratio of radiance of a ground target to the radiance of a standard and also the correlation coefficient of radiances at adjacent wavelengths. The results show ramp like features in the ratios. These features are due to the biochemical composition of the leaf and to the optical scattering properties of its cuticle. The size and shape of the ramps vary with ground cover

Changes of ultrasound characteristics of mango juice during fruit ripening

Attenuation and propagation velocity of ultrasound signals at 25 MHz were measured on clear mango juice samples using a pulse echo method. Ultrasound characteristics were determined with other physico-chemical characteristics on juice samples extracted from fruits undergoing ripening for three weeks at 23 °C and 80 % RH and periodically removed every two or three days. During fruit ripening, the changes of biochemical composition induced more effect on velocity than attenuation. Velocity were positively correlated to soluble solids content (R = 0.98), to sucrose content (R = 0.80) and negatively correlated to titratable acidity (R = -0.59) and fruit firmness (R = -0.76). A linear model based on soluble solids content and a PLS model based on all the physico-chemical characteristics were built to predict ultrasound velocity. Finally, the results obtained in this study showed that velocity is a relevant parameter linked to the major biochemical changes occurring during controlled fruit ripening. Due to high attenuation of ultrasound waves in mango peel and pulp tissues, confirmation of these results for whole fruit will be a challenge. (Résumé d'auteur

Biochemical characterisation during seed development of oil palm (Elaeis guineensis)

Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA