Cooperative adaptive responses in gene regulatory networks with many degrees of freedom.

Cells generally adapt to environmental changes by first exhibiting an immediate response and then gradually returning to their original state to achieve homeostasis. Although simple network motifs consisting of a few genes have been shown to exhibit such adaptive dynamics, they do not reflect the complexity of real cells, where the expression of a large number of genes activates or represses other genes, permitting adaptive behaviors. Here, we investigated the responses of gene regulatory networks containing many genes that have undergone numerical evolution to achieve high fitness due to the adaptive response of only a single target gene; this single target gene responds to changes in external inputs and later returns to basal levels. Despite setting a single target, most genes showed adaptive responses after evolution. Such adaptive dynamics were not due to common motifs within a few genes; even without such motifs, almost all genes showed adaptation, albeit sometimes partial adaptation, in the sense that expression levels did not always return to original levels. The genes split into two groups: genes in the first group exhibited an initial increase in expression and then returned to basal levels, while genes in the second group exhibited the opposite changes in expression. From this model, genes in the first group received positive input from other genes within the first group, but negative input from genes in the second group, and vice versa. Thus, the adaptation dynamics of genes from both groups were consolidated. This cooperative adaptive behavior was commonly observed if the number of genes involved was larger than the order of ten. These results have implications in the collective responses of gene expression networks in microarray measurements of yeast Saccharomyces cerevisiae and the significance to the biological homeostasis of systems with many components.

Circuit architecture explains functional similarity of bacterial heat shock responses.

Heat shock response is a stress response to temperature changes and a consecutive increase in amounts of unfolded proteins. To restore homeostasis, cells upregulate chaperones facilitating protein folding by means of transcription factors (TFs). We here investigate two heat shock systems: one characteristic to gram negative bacteria, mediated by transcriptional activator σ(32) in E. coli, and another characteristic to gram positive bacteria, mediated by transcriptional repressor HrcA in L. lactis. We construct simple mathematical models of the two systems focusing on the negative feedbacks, where free chaperones suppress σ(32) activation in the former, while they activate HrcA repression in the latter. We demonstrate that both systems, in spite of the difference at the TF regulation level, are capable of showing very similar heat shock dynamics. We find that differences in regulation impose distinct constraints on chaperone-TF binding affinities: the binding constant of free σ(32) to chaperone DnaK, known to be in 100 nM range, set the lower limit of amount of free chaperone that the system can sense the change at the heat shock, while the binding affinity of HrcA to chaperone GroE set the upper limit and have to be rather large extending into the micromolar range.

Weber's law for biological responses in autocatalytic networks of chemical reactions.

Biological responses often obey Weber's law, according to which the magnitude of the response depends only on the fold change in the external input. In this study, we demonstrate that a system involving a simple autocatalytic reaction shows such a response when a chemical is slowly synthesized by the reaction from a faster influx process. We also show that an autocatalytic reaction process occurring in series or in parallel can obey Weber's law with an oscillatory adaptive response. Considering the simplicity and ubiquity of the autocatalytic process, our proposed mechanism is thought to be commonly observed in biological reactions.

Cytokeratin 8/18 as a new marker of mouse liver preneoplastic lesions.

To search for a reliable biomarker of preneoplastic lesions arising early in mouse hepatocarcinogenesis the proteomes of microdissected basophilic foci, hepatocellular adenomas (HCAs), carcinomas (HCCs) and normal-appearing liver of B6C3F1 mice initiated with diethylnitrosamine (DEN) were analysed on anionic (Q10) surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) ProteinChip arrays. Significant overexpression of cytokeratin 8 (CK8; m/z 54, 565), cytokeratin 18 (CK18; m/z 47,538) proteins was found in basophilic foci as well as in HCAs and HCCs. Furthermore, immunohistochemistry demonstrated profound overexpression of CK8 and CK18 proteins (CK8/18) in all basophilic foci, mixed cell type foci, HCAs and HCCs in B6C3F1 and C57BL/6J mice initiated with DEN. A strong correlation between CK8/18-positive foci development and multiplicity of liver tumors in B6C3F1 and C57Bl/6J mice was further observed. Moreover, formation of CK8 and CK18 complexes due to CK8 phosphorylation at Ser73 and Ser431 was found to be strongly associated with neoplastic transformation of mice liver basophilic foci. Elevation of CK8/18 was strongly correlated with induction of cell proliferation in basophilic foci and tumors. In conclusion, our data imply that CK8/18 is a novel reliable marker of preneoplastic lesions arising during mouse hepatocarcinogenesis which might be used for prediction of tumor development and evaluation of environmental agents as well as drugs and food additives using mouse liver tests.

Cytokeratin 8/18 overexpression and complex formation as an indicator of GST-P positive foci transformation into hepatocellular carcinomas.

Screening of the proteome of microdissected glutathione S-transferase placental form (GST-P) positive foci and normal-appearing liver on anionic (Q10), and cationic (CM10) surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) ProteinChip arrays demonstrated significant overexpression of cytokeratin 8 (CK8; m/z 54,020), cytokeratin 18 (CK18; m/z 47,760), microsomal cytochrome 5A (m/z 15,224) and histone type 2 H2aa3 (m/z 15,964) in the livers of rats initiated with diethylnitrosamine (DEN) followed by 10 weeks on phenobarbital (PB) at a dose of 500 ppm. Furthermore, formation of CK8 and CK18 complexes due to CK8 phosphorylation at Ser73 and Ser431 was found to be strongly associated with promotion of hepatocarcinogenesis by PB and the development of hepatocellular carcinomas. The data were confirmed by immunohistochemistry and real-time Q-PCR and profound overexpression of CK8 and CK18 (CK8/18) proteins and mRNAs were detected in several large size GST-P positive foci and liver tumors. A strong correlation between CK8/18 positive foci development and multiplicity of hepatocellular carcinomas was further observed. Moreover, elevation of CK8/18 was strongly associated with induction of cell proliferation in GST-P positive foci and tumors. In conclusion, our data imply that CK8/18 overexpression, those two cytokeratins complex formation associated with histone type 2 H2aa3 up-regulation and intermediate filament reorganization may drive neoplastic transformation of GST-P positive foci during rat hepatocarcinogenesis leading to the formation of hepatocellular carcinomas.

Enhancement of preneoplastic lesion yield by Chios Mastic Gum in a rat liver medium-term carcinogenesis bioassay.

The mastic (Pistacia lentiscus var. chia) tree is native throughout the Mediterranean region and has long proved a source of food additives and medical treatments. To investigate the modifying effects of Chios Mastic Gum on rat liver carcinogenesis, 6-week-old male F344 rats were subjected to the established rat liver medium-term carcinogenesis bioassay (Ito-test). At the commencement, rats (groups 1-4) were intraperitoneally injected with 200 mg/kg body weight of diethylnitrosamine (DEN). After two weeks, mastic was added to CRF (Charles River Formula)-1 powdered basal diet at doses of 0, 0.01, 0.1 and 1% in groups 1-4, respectively. At week 3, all rats were underwent two-thirds partial hepatectomy. The experiment was terminated at week 8. As results show, liver weights were significantly increased in a mastic dose-dependent manner among groups 1-4. The numbers (/cm(2)) and the areas (mm(2)/cm(2)) of glutathione S-transferase placental form (GST-P)-positive cell foci (>or=0.2 mm in diameter) were significantly increased in the DEN-1% group compared to the DEN-alone group, along with the average areas per foci and larger-sized foci (>or=0.4 mm). 5-Bromo-2'-deoxyuridine (BrdU)+GST-P double-immunohistochemistry showed the highest BrdU-labeling indices within GST-P foci in the DEN-1% group. 8-hydroxydeoxyguanosine (8-OHdG) levels in liver DNA did not vary, while real-time quantitative polymerase chain reaction (PCR) analysis of livers revealed many up- or down-regulated genes in the DEN-1% group. In conclusion, this is the first report to display a promotion potential of Chios Mastic Gum on the formation of preneoplastic lesions in the established rat liver medium-term carcinogenesis bioassay.

Conditions for self-consistent aggregation by chemotactic particles.

We have numerically studied chemotactic aggregation of microorganisms by introducing a model consisting of elements with intracellular dynamics, random walks with a state-dependent turnover rate, and secretion of attractant. Three phases with and without aggregation, as well as partial aggregation, were obtained as to the diffusion and degradation rates of the attractant, and conditions for cellular aggregation were analyzed. The size of aggregated clusters was shown to be independent of cell density, as is consistent with experiment.

Relationship between regulatory pattern of gene expression level and gene function.

Regulation of gene expression levels is essential for all living systems and transcription factors (TFs) are the main regulators of gene expression through their ability to repress or induce transcription. A balance between synthesis and degradation rates controls gene expression levels. To determine which rate is dominant, we analyzed the correlation between expression levels of a TF and its regulated gene based on a mathematical model. We selected about 280,000 expression patterns of 355 TFs and 647 regulated genes using DNA microarray data from the Gene Expression Omnibus (GEO) data repository. Based on our model, correlation between the expressions of TF-regulated gene pairs corresponds to tuning of the synthesis rate, whereas no correlation indicates excessive synthesis and requires tuning of the degradation rate. The gene expression relationships between TF-regulated gene pairs were classified into four types that correspond to different gene regulatory mechanisms. It was surprising that fewer than 20% of these genes were governed by the familiar regulatory mechanism, i.e., through the synthesis rate. Moreover, we performed pathway analysis and found that each classification type corresponded to distinct gene functions: cellular regulation pathways were dominant in the type with synthesis rate regulation and terms associated with diseases such as cancer, Parkinson's disease, and Alzheimer's disease were dominant in the type with degradation rate regulation. Interestingly, these diseases are caused by the accumulation of proteins. These results indicated that gene expression is regulated structurally, not arbitrarily, according to the gene function. This funding is indicative of a systematic control of transcription processes at the whole-cell level.

Condition for intracellular adaptive dynamics for chemotaxis.

Chemotaxis is ubiquitously performed by bacteria. They sense and move toward a region with a higher concentration of an attractive chemical by changing the rate of tumbling for random walk. We numerically studied several models with internal adaptive dynamics to examine the validity of the condition for chemotaxis proposed by Oosawa and Nakaoka [J. Theor. Biol. 66, 747 (1977)], which states that the time scale of tumbling frequency must be smaller than that of adaptation and greater than that of sensing. Suitable renormalization of the time scales showed that the condition holds for a variety of environments and for both short- and long-term behavior.

Dynamics of coupled adaptive elements: bursting and intermittent oscillations generated by frustration in networks.

Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of two variables that show such adaptation dynamics, we studied a coupled dynamical system containing such elements to examine the diverse dynamics in the system and classified the behaviors on the basis of the network structure that determined the interaction among elements. For a system with two elements, two types of behaviors, perfect adaptation and simple oscillation, were observed. For a system with three elements, in addition to these two types of dynamics, rapid-burst-type oscillation and a slow cycle were discovered; depending on the initial conditions, these two types of dynamics coexisted. These behaviors are a result of the characteristic dynamics of each element, i.e., fast response and slow adaptation processes. The behaviors depend on the network structure (in specific, a combination of positive or negative feedback among elements). Cooperativity among elements due to a positive feedback loop leads to simple oscillation, whereas frustration involving alternating positive and negative interactions among elements leads to the coexistence of rapid bursting oscillation and a slow cycle. These behaviors are classified on the basis of the frustration indices defined by the network structure. The period of the slow cycle is much longer than the original adaptation time scale, while the burst-type oscillation is a continued response that does not involve any adaptation. We briefly discuss the universal applicability of our results to a network of a larger number of elements and their possible relevance to biological systems.