Using a systems-based approach to overcome reductionist strategies in the development of diagnostics

Systems biology is a recent addition to the necessary but insufficient reductionist approach used in biological research. Systems biology is focused on understanding living things as a function of their various interactions at multiple levels: not simply as a sum of all their individual parts at any one level. This integrative approach yields predictive models of the normal state, the disease state and therapeutic actions. Although molecular biology has collected an enormous amount of information, including the sequencing of the entire human genome in the year 2000, few real-world applications have resulted from this molecular approach. The pharmaceutical industry's R&D expenditure has increased substantially since 2000, but the number of approved therapeutics has dropped simultaneously, due in part to over-reliance on reductionist genomic, and not systems, approaches. Instead of using reductionist genomics approaches alone, genomics should be incorporated into a multi-level systems biology approach to develop diagnostics and therapeutics.

The Systems Biology of Stem Cell Released Molecules—Based Therapeutics

Most therapeutics are based on the traditional method of reductionism where a clinically defined condition is broken down into a defined biochemical pathway underlying the condition, then a target in the pathway is identified, followed by developing a drug to interact with the target, modifying the target such that the disease is ameliorated. Biology acts as a system, therefore reductionist approaches to developing therapeutics are limited in therapeutic value because disease or traumatized tissue involves multiple underlying pathways, only a part of the pathways underlying the disease is manipulated by the traditional therapeutic. Much data regarding stem cells shows that their beneficial effects are not restricted to their ability to differentiate, but is more likely due in large part to their ability to release a multitude of molecules. Stem cells release potent combinations of factors that modulate the composition of the cellular milieu to evoke a multitude of responses from neighboring cells. Therefore, stem cells represent a natural systems-based biological factory for the production and release of a multitude of molecules that interact with the system of biomolecular circuits underlying an indication. Current research includes efforts to define, stimulate, enhance, and harness stem cell released molecules (SRM) to develop systems-therapeutics.

Tracer-based metabolomics: concepts and practices

Tracer-based metabolomics is a systems biology tool that combines advances in tracer methodology for physiological studies, high throughput "-omics" technologies and constraint based modeling of metabolic networks. It is different from the commonly known metabolomics or metabonomics in that it is a targeted approach based on a metabolic network model in cells. Because of its complexity, it is the least understood among the various "-omics." In this review, the development of concepts and practices of tracer-based metabolomics is traced from the early application of radioactive isotopes in metabolic studies to the recent application of stable isotopes and isotopomer analysis using mass spectrometry; and from the modeling of biochemical reactions using flux analysis to the recent theoretical formulation of the constraint based modeling. How these newer experimental methods and concepts of constraint-based modeling approaches can be applied to metabolic studies is illustrated by examples of studies in determining metabolic responses of cells to pharmacological agents and nutrient environment changes.

Ethanol diversely alters palmitate, stearate, and oleate metabolism in the liver and pancreas of rats using the deuterium oxide single tracer

OBJECTIVE

To determine tissue-specific effects of alcohol on fatty acid synthesis and distribution as related to functional changes in triglyceride transport and membrane formation.

METHODS

Tissue fatty acid profile and de novo lipogenesis were determined in adult male Wistar rats after 5 weeks of ethanol feeding using deuterated water and gas chromatography/mass spectrometry. Liver and pancreas fatty acid profiles and new synthesis fractions were compared with those from control rats on an isocaloric diet.

RESULTS

Fatty acid ratios in the liver indicated that there was a more than 2-fold accumulation of stearate to that of palmitate, with an apparent decrease in oleate content. On the other hand, in the pancreas, there was a 17% decrease in the stearate-to-palmitate ratio, whereas the oleate-to-palmitate ratio was increased by 30%. The fractions of deuterium-labeled palmitate and stearate were substantially reduced in the liver and pancreas of the alcohol-treated animals. Deuterium labeling of oleate was reduced in the liver but not in the pancreas, consistent with the oleate/stearate ratios in these tissues.

CONCLUSIONS

Long-term alcohol exposure results in opposite effects on the desaturase activity in the liver and pancreas, limiting fatty acid transport in the liver but promoting the exocrine function of the pancreas.