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A challenging issue in designing computational methods for predicting the gene structure into exons and introns from a cluster of transcript (EST, mRNA) sequences, is guaranteeing both accuracy and efficiency in time and space, when large clusters of over than 20,000 ESTs and genes longer than 1Mb are processed. Traditionally, the problem has been faced by combining different tools, not specifically...
A rat model of ulcerative colitis (UC) was established using an immunological method involving local stimulation. After the UC rat model was established, HPM was administered to the UC rats (n = 8) for seven days. UC rats without HPM (n = 8) and normal rats (n = 8) were used as the controls. Hematoxylin and eosin staining was used to visualize the pathological changes in the rats' colonic mucosa....
Curcumin, the most active constituent of turmeric, is currently one of the major anticance new drugs and has been reported to enhance Heme Oxygenase-1(HO-1) in human brain when oxidative stress occur. Keeping the balance of HO-1 and HO-2 plays an important role in the brain. However, few researches study the effects of curcumin on the two isoenzymes of HO. Here we investigated the effects of curcumin...
This paper addresses robust stability of genetic regulatory networks (GRNs) with stochastic perturbation and discrete and distributed time-varying delays. Aside from discrete delays, there are few results about stability of GRNs with distributed delay. In this paper, noise perturbation and delays have been considered in both mRNA and protein dynamics. Based on Lyapunov functional approach and linear...
Gene regulatory networks are highly complex dynamical systems of biomolecular components - genes, mRNA, proteins. These components interact with each other and through those interactions determine gene expression levels, i.e., determine the rate of gene transcription to mRNA and, consequently, the rate of mRNA translation to proteins. In this paper, a particle filter with MCMC move step is employed...
Early patterning in the Drosophila melanogaster embryo occurs through a complicated network of interactions involving transcription factor proteins and the mRNA of their target genes. One such system is the pattern of hunchback mRNA and its regulation by Bicoid and Kru??ppel proteins. This system is well-studied, but there is disagreement amongst biologists on how exactly hunchback expression is regulated...
The possibilities of an in vitro translation system, based on cell components of the hyperthermophilic archaeon, Thermococcus kodakaraensis, to utilize at a lower temperature range were examined. Green fluorescence protein (GFP) was used as the reporter protein. Through optimization of several experimental conditions, the yield of active GFP production at 40??C increased 5-fold. The optimized system...
In this study, the effect of oleic oil on cytoactive, triglycerides (TG) accumulation, lipids drop and mRNA expression of peroxisome proliferator-activated receptor alpha (PPARalpha) and peroxisome proliferator-activated receptor gamma ( PPARgamma ) was measured in primary goose hepatocytes. Results were as follows: 1.5 mmol/L oleic oil had an inhibiting effect on the cell viability; oleic oil could...
In this paper we describe a new maximum likelihood approach to infer kinetic rate constants from time-course data and apply it to estimate the rate constants of the synthesis and degradation of the mRNA of Cdc20 protein, and the rate constant of the transcription of the cdc20 gene into Cdc20 protein. The Cdc20 protein plays a crucial role in eukaryotic cell cycle, as it codes for the cyclin antagonist...
The effects of three structurally related flavonols (kaempferol, quercetin, myricetin) on anti-proliferation and cell cycle arrest in human oesophageal adenocarcinoma OE33 cells were determined and compared by MTT assay and flow cytometry analysis. The results showed that three flavonols not only inhibited proliferation but also induced G2/M arrest in OE33 cells. Moreover, G2/M arrest-inducing activity...
The purpose of this experiment was to determine the effects of overfeeding on hepatic fat deposition at lipogenic genes expression. Overfeeding had effects on the body weight, liver weight, abdominal adipose weight and liver/body weight compared to control. In contrast, the dietary treatment had markedly difference in ALT, TG and H-cholesterol. In liver, the expression of aP2 mRNA was higher in geese...
Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics...
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by the degeneration of motor neurons. Although the cause of ALS is unknown, mutations in the gene that produces the SOD1 enzyme are associated with some cases of familial ALS. SOD1 is a powerful antioxidant that protects the body from damage caused by superoxide, a toxic free radical. It has been proposed that defects...
Transcribed exons in genes are joined together at donor and acceptor splice sites precisely and efficiently to generate mRNAs capable of being translated into proteins. The sequence variability in individual splice sites can be modeled using Shannon information theory. In the laboratory, the degree of individual splice site use is inferred from the structures of mRNAs and their relative abundance...
Codon usage bias is well established in different species from bacteria to mammals. A number of models have been proposed to show this bias as a balance between mutation and selection. Most of these models emphasize controlling the speed of protein translation from the mRNA and increasing the accuracy where this bias is dependent on the abundance and properties of the available tRNA. In this work,...
Hidden stop codons are nucleotide triples TAA, TAG, and TGA that appear in the second and third reading frames of a protein coding gene. Recent studies reported biological evidence suggesting that hidden stop codons are important in preventing misread of mRNA, which is often detrimental to the cell. We study the problem of designing protein-encoding genes with large number of hidden stop codons under...
In this paper we study the state estimation problem for a basic model of gene expression. The model describes the interaction between mRNA and protein(s) within the transcription- translation process. We first study some basic dynamic properties of the model, namely the existence of a unique equilibrium point, its stability and local observability. Then, we address the problem of estimating mRNA concentration...
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