Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases

BACKGROUND:Protein kinases (PKs) have emerged as the largest family of signaling proteins in eukaryotic cells and are involved in every aspect of cellular regulation. Great progresses have been made in understanding the mechanisms of PKs phosphorylating their substrates, but the detailed mechanisms, by which PKs ensure their substrate specificity with their structurally conserved catalytic domains, still have not been adequately understood. Correlated mutation analysis based on large sets of diverse sequence data may provide new insights into this question. METHODOLOGY/PRINCIPAL FINDINGS:Statistical coupling, residue correlation and mutual information analyses along with clustering were applied to analyze the structure-based multiple sequence alignment of the catalytic domains of the Ser/Thr PK family. Two clusters of highly coupled sites were identified. Mapping these positions onto the 3D structure of PK catalytic domain showed that these two groups of positions form two physically close networks. We named these two networks as theta-shaped and gamma-shaped networks, respectively. CONCLUSIONS/SIGNIFICANCE:The theta-shaped network links the active site cleft and the substrate binding regions, and might participate in PKs recognizing and interacting with their substrates. The gamma-shaped network is mainly situated in one side of substrate binding regions, linking the activation loop and the substrate binding regions. It might play a role in supporting the activation loop and substrate binding regions before catalysis, and participate in product releasing after phosphoryl transfer. Our results exhibit significant correlations with experimental observations, and can be used as a guide to further experimental and theoretical studies on the mechanisms of PKs interacting with their substrates

Microwave ablation induces abscopal effect via enhanced systemic antitumor immunity in colorectal cancer

BackgroundThermal ablation is the primary procedure for the local treatment of lung metastases. It is known that radiotherapy and cryoablation can stimulate an abscopal effect, while the occurrence of abscopal effect induced by microwave ablation is less; the cellular and molecular mechanisms involved in the abscopal effect after microwave ablation should be further elucidated.MethodsCT26 tumor-bearing Balb/c mice were treated with microwave ablation with several combinations of ablation power and time duration. The growth of primary or abscopal tumors and the survival of mice were both monitored; moreover, immune profiles in abscopal tumors, spleens, and lymph nodes were examined by flow cytometry.ResultsMicrowave ablation suppressed tumor growth in both primary and abscopal tumors. Both local and systemic T-cell responses were induced by microwave ablation. Furthermore, the mice exhibiting significant abscopal effect after microwave ablation markedly elevated Th1 cell proportion both in the abscopal tumors and spleens.ConclusionsMicrowave ablation at 3 w–3 min not only suppressed tumor growth in the primary tumors but also stimulated an abscopal effect in the CT26-bearing mice via the improvement of systemic and intratumoral antitumor immunity

Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m6A) methylation is the most abundant type of post-transcriptional modification for mRNAs, but the pattern of inheritance from parents to hybrids and potential impact on heterosis are largely unknown. We constructed transcriptome-wide mRNA m6A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F1 hybrids. Generally, the transcriptome-wide pattern of m6A methylation tends to be conserved between accessions. Approximately 74% of m6A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m6A methylation is maintained after hybridization. We found a significant association between differential expression and differential m6A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m6A level between Col-0 and Ler is clearly different but tended to disappear at the allelic sites in the hybrids. Interestingly, many enriched biological functions of genes with differential m6A modification between parents and hybrids are also conserved, including many heterosis-related genes involved in biosynthetic processes of starch. Collectively, our study revealed the overall pattern of inheritance of mRNA m6A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation

Surface roughness detection of arteries via texture analysis of ultrasound images for early diagnosis of atherosclerosis

There is a strong research interest in identifying the surface roughness of the carotid arterial inner wall via texture analysis for early diagnosis of atherosclerosis. The purpose of this study is to assess the efficacy of texture analysis methods for identifying arterial roughness in the early stage of atherosclerosis. Ultrasound images of common carotid arteries of 15 normal mice fed a normal diet and 28 apoE−/− mice fed a high-fat diet were recorded by a high-frequency ultrasound system (Vevo 2100, frequency: 40 MHz). Six different texture feature sets were extracted based on the following methods: first-order statistics, fractal dimension texture analysis, spatial gray level dependence matrix, gray level difference statistics, the neighborhood gray tone difference matrix, and the statistical feature matrix. Statistical analysis indicates that 11 of 19 texture features can be used to distinguish between normal and abnormal groups (p<0.05). When the 11 optimal features were used as inputs to a support vector machine classifier, we achieved over 89% accuracy, 87% sensitivity and 93% specificity. The accuracy, sensitivity and specificity for the k-nearest neighbor classifier were 73%, 75% and 70%, respectively. The results show that it is feasible to identify arterial surface roughness based on texture features extracted from ultrasound images of the carotid arterial wall. This method is shown to be useful for early detection and diagnosis of atherosclerosis.Lili Niu, Ming Qian, Wei Yang, Long Meng, Yang Xiao, Kelvin K. L. Wong, Derek Abbott, Xin Liu, Hairong Zhen

Milk enhances intestinal absorption of green tea catechins in in vitro digestion/Caco-2 cells model

The effect of milk on the absorption of polyphenols is still controversial so far. In order to determine the impact of milk addition on green tea catechins bioaccessibility and intestinal absorption an in vitro digestion/Caco-2 cell model was applied. Green tea extract (GTE) was solubilized in distilled water at 23 °C and 100 °C, combined with skimmed milk (GTE + 10% milk and GTE + 25% milk) and subjected to simulated gastric and intestinal digestion, followed by transepithelial absorption in Caco-2 cells monolayers. In the mixture with milk, gallated catechins: ECG and EGCG showed binding to milk proteins while EC and EGC seemed to have weaker affinity. Catechins were stable during gastric incubation and very sensitive to intestinal digestion. Bioaccessibility of green tea catechins brewed at 100 °C was higher than brewed at 23 °C. Catechins from digested GTE with 10% and 25% milk exhibited enhanced intestinal permeability in Caco-2 model in comparison to non-digested GTE and digested GTE without milk. Apparent permeability coefficients (Papp) of EGCG and ECG in digested GTE with 25% milk were significantly higher compared to those in GTE with 10% milk, and amounted to 2.41 × 10− 6 cm/s and 1.39 × 10− 6 cm/s. The recoveries of all catechins in GTE with milk in Caco-2 cells after 2 h incubation were significantly higher than that without milk. To summarize, these data suggest that milk addition may increase catechin bioavailability by enhancing their transepithelial absorption and uptake from green tea extract

Transition Metal Catalyzed Direct Amination of the Cage B(4)–H Bond in <i>o</i>‑Carboranes: Synthesis of Tertiary, Secondary, and Primary <i>o</i>‑Carboranyl Amines

Transition metal catalyzed regioselective amination of the cage B(4)–H bond in <i>o</i>-carboranes has been achieved for the first time using <i>O</i>-benzoyl hydroxylamines or organic azides as the amination reagents, leading to the preparation of a series of tertiary and secondary carboranyl amines. Both amination reactions proceeded under mild conditions without the addition of any external oxidants. Hydrogenolysis of the resultant product 4-N­(CH₂Ph)₂-<i>o</i>-carborane afforded the primary carboranyl amine, 4-amino-<i>o</i>-carborane, in quantitative yield

Transition Metal Catalyzed Direct Amination of the Cage B(4)–H Bond in <i>o</i>‑Carboranes: Synthesis of Tertiary, Secondary, and Primary <i>o</i>‑Carboranyl Amines

Transition metal catalyzed regioselective amination of the cage B(4)–H bond in <i>o</i>-carboranes has been achieved for the first time using <i>O</i>-benzoyl hydroxylamines or organic azides as the amination reagents, leading to the preparation of a series of tertiary and secondary carboranyl amines. Both amination reactions proceeded under mild conditions without the addition of any external oxidants. Hydrogenolysis of the resultant product 4-N­(CH₂Ph)₂-<i>o</i>-carborane afforded the primary carboranyl amine, 4-amino-<i>o</i>-carborane, in quantitative yield

Modeling of User Perceived Webserver Availability

We propose to use Markov regenerative process (MRGP) models to study the availability of Internet-based services perceived by a Web user, which capture the interactions between the service facility and the user. The necessity of the sophisticated MRGP modeling is evidenced by the comparisons with the corresponding continuous time Markov chain (CTMC) models, which show that the popular convenient CTMC models tend to overestimate user-perceived service unavailabilities by 26% to 125%. We stud