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The ability to design and engineer organisms demands the ability to predict kinetic responses of novel regulatory networks built from well-characterized biological components. Surprisingly, few validated kinetic models of complex regulatory networks have been derived by combining models of the network components. A major bottleneck in producing such models is the difficulty of measuring in vivo rate constants for components of complex networks. We demonstrate that a simple, genetic approach to measuring rate constants in vivo produces an accurate kinetic model of the complex network that Saccharomyces cerevisiae employs to regulate the expression of genes encoding glucose transporters. The model predicts a transient pulse of transcription of HXT4 (but not HXT2 or HXT3) in response to addition of a small amount of glucose to cells, an outcome we observed experimentally. Our model also provides a mechanistic explanation for this result: HXT2-4 are governed by a type 2, incoherent feed forward regulatory loop involving the Rgt1 and Mig2 transcriptional repressors. The efficiency with which Rgt1 and Mig2 repress expression of each HXTgene determines which of them have a pulse of transcription in response to glucose. Finally, the model correctly predicts how lesions in the feed forward loop change the kinetics of induction of HXT4 expression. gene--regulatory networks | glucose transport | kinetic model | Saccharomyces cerevisiae | systems biology doi/ 10.1073/pnas.0912483107

A reliable model of glucose absorption after oral ingestion may facilitate simulation as well as pathophysiological studies. One of the difficulties for the development and quality assessment of such models has been the lack of gold standard data for their validation. Thus, while data on plasma concentrations of glucose are available, the rates of appearance in plasma of ingested glucose (Ra) were not available to develop such models. Here we utilize the recent availability of Ra data, estimated with a model-independent multiple tracer technique, to formulate a system model of intestinal glucose absorption. Two published and two new models are tested on this new data set. One of the two new models performed best: it is nonlinear, describes the Ra data well and its parameters are estimated with good precision. This model has important potential both in simulation contexts, e.g., it can be incorporated in whole-body models of the glucose regulatory system, as well as in physiological and clinical studies to quantitatively characterize possible impairment of glucose absorption in particular populations such as elderly and diabetic individuals. Index Terms--Gastric emptying, gastrointestinal system, meal, OGTT, parameter estimation, physiological model.

In humans, failure to express the fragile X mental retardation protein (FMRP) gives rise to fragile X syndrome, the most common form of inherited mental retardation. A fragile X knockout (fmr1 KO) mouse has been described that has some of the characteristics of patients with fragile X syndrome, including immature dendritic spines and subtle behavioral deficits. In our behavioral studies, fmr1 KO mice exhibited hyperactivity and a higher rate of entrance into the center of an open field compared with controls, suggesting decreased levels of anxiety. Our finding of impaired performance of fmr1 KO mice on a passive avoidance task is suggestive of a deficit in learning and memory. In an effort to understand what brain regions are involved in the behavioral abnormalities, we applied the [[sup.14]C]deoxyglucose method for the determination of cerebral metabolic rates for glucose (CM[R.sub.glc]). We measured CM[R.sub.glc] in 38 regions in adult male fmr1 KO and WT littermates. We found CM[R.sub.glc] was higher in all 38 regions in fmr1 KO mice, and in 26 of the regions, differences were statistically significant. Differences in CM[R.sub.glc] ranged from 12% to 46%, and the greatest differences occurred in regions of the limbic system and primary sensory and posterior parietal cortical areas. Regions most affected are consistent with behavioral deficiencies and regions in which FMRP expression is highest. Higher CM[R.sub.glc] in fragile X mice may be a function of abnormalities found in dendritic spines.