Studies of transcription regulation are often focused on binding of transcription factors (TFs) to a small number of promoters of interest. It is often assumed that TFs are in great excess to their binding sites (TFBSs) and competition for TFs between DNA sites is seldom considered. With increasing evidence that TFBSs are exceedingly abundant for many TFs and significant variations in TF and TFBS numbers occur during growth, the interplay between a TF and all TFBSs should not be ignored. Here, we use additional decoy DNA sites to quantitatively analyze how the relative abundance of a TF to its TFBSs impacts the steady-state level and onset time of gene expression for the auto-activated Escherichia coli PhoB response regulator. We show that increasing numbers of decoy sites progressively delayed transcription activation and lowered promoter activities. Perturbation of transcription regulation by additional TFBSs did not require extreme numbers of decoys, suggesting that PhoB is approximately at capacity for its DNA sites. Addition of decoys also converted a graded response to a bi-modal response. We developed a binding competition model that captures the major features of experimental observations, providing a quantitative framework to assess how variations in TFs and TFBSs influence transcriptional responses.

Binding of transcription factor (TF) proteins to regulatory DNA sites is key to accurate control of gene expression in response to environmental stimuli. Theoretical modeling of transcription regulation is often focused on a limited set of genes of interest, while binding of the TF to other genomic sites is seldom considered. The total number of TF binding sites (TFBSs) affects the availability of TF protein molecules and sequestration of a TF by TFBSs can promote bistability. For many signaling systems where a graded response is desirable for continuous control over the input range, biochemical parameters of the regulatory proteins need be tuned to avoid bistability. Here we analyze the mono-/bistable parameter range for positively autoregulated two-component systems (TCSs) in the presence of different numbers of competing TFBSs. TCS signaling, one of the major bacterial signaling strategies, couples signal perception with output responses via protein phosphorylation. For bistability, competition for TF proteins by TFBSs lowers the requirement for high fold change of the autoregulated transcription but demands high phosphorylation activities of TCS proteins. We show that bistability can be avoided with a low phosphorylation capacity of TCSs, a high TF affinity for the autoregulated promoter or a low fold change in signaling protein levels upon induction. These may represent general design rules for TCSs to ensure uniform graded responses. Examining the mono-/bistability parameter range allows qualitative prediction of steady-state responses, which are experimentally validated in the E. coli CusRS system.

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The present study aimed to develop and evaluate a nutritional and nursing risk assessment method for diabetic inpatients to improve healthcare and risk management. Diabetic inpatients diagnosed according to the World Health Organization guidelines, together with their nursing staff, were divided into two groups for nutritional and nursing risk assessment. Data from one group were used to establish the assessment method, and data from the other group were used to evaluate the reliability and effectiveness of the method. To establish the method, various risk variables in the nutritional and nursing processes were evaluated by logistic regression analysis; the score and probability of the risk variables were determined based on odds ratios. The overall nutritional and nursing risk for individual inpatients was then judged by the accumulated scores. The analysis showed that there were a number of risk factors, including age and body mass index. The risk was shown to increase with increasing score for the inpatients, and the χ2 test (P<0.01) was used to indicate a significant association. When the score was 50, the sensitivity and specificity of the method used to detect the nutritional and nursing risk were 88.3 and 66.5%, respectively, with predictive positive and negative rates of 12.83 and 98.53%, respectively. Therefore, the method is simple, cost-effective and fast; it can be used to screen a large number of patients by nursing staff and can also be used by patients themselves. Overall, the method is an effective and practicable nutritional and nursing risk assessment and educational tool.