Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle

BACKGROUND: A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a living cell can coordinate the activities of many genes and carry out complex functions. Therefore, identifying TRMs is helpful for understanding gene regulation. RESULTS: Integrating gene expression and ChIP-chip data, we develop a method, called MOdule Finding Algorithm (MOFA), for reconstructing TRMs of the yeast cell cycle. MOFA identified 87 TRMs, which together contain 336 distinct genes regulated by 40 TFs. Using various kinds of data, we validated the biological relevance of the identified TRMs. Our analysis shows that different combinations of a fairly small number of TFs are responsible for regulating a large number of genes involved in different cell cycle phases and that there may exist crosstalk between the cell cycle and other cellular processes. MOFA is capable of finding many novel TF-target gene relationships and can determine whether a TF is an activator or/and a repressor. Finally, MOFA refines some clusters proposed by previous studies and provides a better understanding of how the complex expression program of the cell cycle is regulated. CONCLUSION: MOFA was developed to reconstruct TRMs of the yeast cell cycle. Many of these TRMs are in agreement with previous studies. Further, MOFA inferred many interesting modules and novel TF combinations. We believe that computational analysis of multiple types of data will be a powerful approach to studying complex biological systems when more and more genomic resources such as genome-wide protein activity data and protein-protein interaction data become available

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data

Abstract Background ChIP-chip data, which indicate binding of transcription factors (TFs) to DNA regions in vivo, are widely used to reconstruct transcriptional regulatory networks. However, the binding of a TF to a gene does not necessarily imply regulation. Thus, it is important to develop methods to identify regulatory targets of TFs from ChIP-chip data. Results We developed a method, called Temporal Relationship Identification Algorithm (TRIA), which uses gene expression data to identify a TF's regulatory targets among its binding targets inferred from ChIP-chip data. We applied TRIA to yeast cell cycle microarray data and identified many plausible regulatory targets of cell cycle TFs. We validated our predictions by checking the enrichments for functional annotation and known cell cycle genes. Moreover, we showed that TRIA performs better than two published methods (MA-Network and MFA). It is known that co-regulated genes may not be co-expressed. TRIA has the ability to identify subsets of highly co-expressed genes among the regulatory targets of a TF. Different functional roles are found for different subsets, indicating the diverse functions a TF could have. Finally, for a control, we showed that TRIA also performs well for cell-cycle irrelevant TFs. Conclusion Finding the regulatory targets of TFs is important for understanding how cells change their transcription program to adapt to environmental stimuli. Our algorithm TRIA is helpful for achieving this purpose.</p

On the Adaptive Design Rules of Biochemical Networks in Evolution

Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive) to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process

Warm-Mix Asphalt Study: Test Track Construction and FirstLevel Analysis of Phase 3b HVS and Laboratory Testing (Rubberized Asphalt, Mix Design #2)

This is one of two reports describing the third phase of a warm-mix asphalt study that compares the performance of two rubberized asphalt control mixes with that of seven mixes produced with warm-mix technologies. The control mixes were produced and compacted at conventional hot-mix asphalt temperatures (&gt;300 F [150°C]), while the warm-mixes were produced and compacted at temperatures between 36°F (20°C) and 60°F (35°C) lower than the controls. The mixes, test track, Heavy Vehicle Simulator (HVS) and laboratory testing are discussed. Key findings from the study include: Adequate compaction can be achieved on rubberized warm-mixes at lower temperatures. Optimal compaction temperatures will differ. Equal and potentially better rutting performance can be achieved provided that standard specified limits for hot-mix asphalt are met. Test results indicate that use of the warm-mix technologies did not significantly influence performance when compared to control specimens. However, the mixes produced with chemical surfactant technologies did appear to be influenced in part by the lower mix production and construction temperatures, which would have resulted in less oxidation of the binder and consequent lower stiffness of the mix. Rutting performance, fatigue performance and moisture sensitivity did not appear to be affected. The warm-mixes produced using water-foaming technologies appeared to have lower moisture resistance compared to the other warm-mixes. Smoke and odors are significantly reduced on warm-mixes compared to hot-mixes, while workability is considerably better on warm-mixes compared to hot-mixes. The HVS and laboratory testing completed in this phase have provided no results to suggest that warm-mix technologies should not be used in rubberized asphalt in California

Onion-induced anaphylactic shock rapidly evolving to allergic right ventricular myocardial infarction and subsequent cardiogenic shock

AbstractThe type II variant of Kounis syndrome is defined as a rare allergic myocardial angina or infarction event in patients with preexisting quiescent coronary artery disease. Various causative factors have been implicated in the etiology of Kounis syndrome. However, reports highlighting the importance of recognizing a decreased preload caused by allergic right ventricular (RV) myocardial infarction and subsequent cardiogenic shock from ongoing anaphylactic shock are rare. Here we report the case of a 54-year-old male who initially presented with anaphylactic shock after ingesting onions. His condition silently progressed to RV infarction and cardiogenic shock within 2 hours of symptom onset. Under such instances, it is crucial to promptly identify RV infarction and cardiogenic shock by repeatedly performing electrocardiography at frequent intervals

An Adaptive Gaze Tracking System in the Diverse Environment

oai:ojs.ijiis.org:article/124For understanding the learning effect, the gaze tracking is a more objective method to collect the data on eye movement and used to analyze the learning behaviors. In order to provide an analysis tool to apply in diverse environments, an adaptive gaze tracking system is proposed in this paper. This system can offer helpful suggestions for educators when improving the instruction. Additionally, the experimental results show that the estimation of gaze points was successful even when the distance and head rotation alter

Attenuated Cardiac Mitochondrial-Dependent Apoptotic Effects by Li-Fu Formula in Hamsters Fed with a Hypercholesterol Diet

Apoptosis involves in the pathogenesis of various cardiac abnormalities. This study intends to evaluate the effects of Li-Fu formula on cardiac apoptosis induced by hyper-cholesterol diet. Twenty-four male Golden Syrian hamsters were randomly divided into Control, Cholesterol and Li-Fu formula groups. Histopathological analysis, western blotting and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assays were performed to measure the effects of Li-Fu formula on left ventricle. Significantly reduced TUNEL-positive cells and mitochondria- dependent apoptosis were observed in the left ventricle of hamsters from Li-Fu formula group compared to the Cholesterol group. Additionally, induced cardiac insulin like growth factor I receptor (IGFIR)-dependent survival pathway was detected in the Li-Fu formula group compared to the Cholesterol group. Besides, minor fibrosis, increased collagen deposition, and myofibril disarray was detected in the Cholesterol group, whereas the reductions of collagen deposition and myofibril disarray were observed in the Li-Fu formula group. This study demonstrated that Li-Fu formula not only reduced the mitochondria-dependent apoptosis and fibrosis, but also enhanced the IGF-I survival pathway in the left ventricle from high cholesterol-fed hamsters. We suggest the protective effects of Li-Fu formula on cardiac apoptosis and therapeutic potentials against cardiovascular disease