Accurately Modulating Binuclear Metal Nodes of Metal-Organic Frameworks for Oxygen Evolution.

The accurate manipulation of the species and locations of catalytic centers is crucial for regulating the catalytic activity of catalysts, which is essential for their efficient design and development. Metal-organic frameworks (MOFs) with coordinated metal sites are ideal materials for investigating the origin of catalytic activity. In this study, we present a Ni2-MOF featuring novel Ni-based binuclear nodes with open metal sites (OMSs) and saturated metal sites (SMSs). The nickel was replaced by iron to obtain Ni1Fe1-MOF. In the electrocatalytic oxygen evolution reaction, Ni1Fe1-MOF exhibited an overpotential and Tafel slope of 370 mV@10 mA cm-2 and 87.06 mV dec-1, respectively, which were higher than those of Ni2-MOF (283 mV@10 mA cm-2 and 39.59 mV dec-1, respectively), demonstrating the superior performance of Ni1Fe1-MOF. Furthermore, theoretical calculations revealed that iron as an SMS may effectively regulate the electronic structure of the nickel catalytic center to reduce the free energy barrier ΔG*OH of the rate-determining step.

Compact highly sensitive Fabry-Perot temperature and gas pressure sensing probe fabricated by a femtosecond laser and PDMS.

A high sensitivity optical fiber temperature and gas pressure sensor with integrated micro-cavity is proposed. First, a single-mode optical fiber (SMF) is spliced with a section of capillary, and then the sensitive material polydimethylsiloxane (PDMS) is filled into the capillary to form a Fabry-Perot interferometer (FPI). Finally, a femtosecond laser is used to ablate the fiber core of the SMF to form the third reflecting surface, constituting two cascaded FPIs. When two FPIs have a similar free spectral range, a Vernier effect is produced. The temperature and gas pressure sensitivity of the sensor reached 14.41 nm/°C and 113.82 nm/MPa, respectively, after using the sensitive material and Vernier effect double sensitization technology. In addition, a fiber Bragg grating is cascaded with the sensor, which can realize the simultaneous measurement of temperature and gas pressure and eliminate cross-sensitivity.

Rapid detection of SARS-CoV-2 with CRISPR-Cas12a.

The recent outbreak of betacoronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is responsible for the Coronavirus Disease 2019 (COVID-19) global pandemic, has created great challenges in viral diagnosis. The existing methods for nucleic acid detection are of high sensitivity and specificity, but the need for complex sample manipulation and expensive machinery slow down the disease detection. Thus, there is an urgent demand to develop a rapid, inexpensive, and sensitive diagnostic test to aid point-of-care viral detection for disease monitoring. In this study, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated proteins (Cas) 12a-based diagnostic method that allows the results to be visualized by the naked eye. We also introduced a rapid sample processing method, and when combined with recombinase polymerase amplification (RPA), the sample to result can be achieved in 50 minutes with high sensitivity (1-10 copies per reaction). This accurate and portable detection method holds a great potential for COVID-19 control, especially in areas where specialized equipment is not available.

PcENO3 interacts with patchoulol synthase to positively affect the enzymatic activity and patchoulol biosynthesis in Pogostemon cablin.

Patchouli alcohol, a significant bioactive component of the herbal plant Pogostemon cablin, has considerable medicinal and commercial potential. Several genes and transcription factors involved in the biosynthesis pathway of patchouli alcohol have been identified. However, so far, regulatory factors directly interacting with patchouli synthase (PTS) have not been reported. This study was conducted to analyze the interaction between PcENO3 and PcPTS to explore the molecular regulation effect of PcENO3 on patchouli alcohol biosynthesis. PcENO3, a homologous protein of Arabidopsis ENO3 belonging to the enolase family, was identified and characterized. Subcellular localization experiments in Arabidopsis protoplast cells indicated that the PcENO3 protein was localized in both the cytoplasm and nucleus. The physical interaction between PcENO3 and PcPTS was confirmed through yeast two-hybrid (Y2H), GST pull-down, and bimolecular fluorescence complementation assays. Furthermore, the Y2H assay demonstrated that PcENO3 could also interact with JAZ proteins in the JA pathway. Enzymatic assays showed that the interaction with PcENO3 increased the catalytic activity of patchoulol synthase. Additionally, suppression of PcENO3 expression with VIGS (virus-induced gene silencing) decreased patchouli alcohol content compared to the control. These findings suggest that PcENO3 interacts with patchoulol synthase and modulates patchoulol biosynthesis by enhancing the enzymatic activity of PcPTS.

High sensitivity temperature sensor based on enhanced Vernier effect through two parallel Fabry-Perot cavities.

In this paper, an enhanced Vernier effect temperature sensor based on two parallel Fabry-Perot interferometers (FPIs) is proposed and demonstrated experimentally. Among them, F P I 1 is composed of a single-mode fiber (SMF), a quartz capillary, and AB glue filled in the capillary. F P I 2 is formed by filling a capillary with polyimide (PI) solution and inserting two-segment SMF from both sides of the capillary. Since AB glue and PI have good thermal sensitivity, F P I 1 and F P I 2 are highly sensitive to temperature. Due to their different structures, the temperature sensitivity of F P I 1 is negative, and that of F P I 2 is positive. When F P I 1 and F P I 2 with similar free spectral range are connected in parallel, they will act as reference cavities for each other, resulting in an enhanced Vernier effect, which enlarges the sensitivity of the sensor more. In the temperature range of 40°C-58°C, the temperature sensitivity of the sensor is as high as -13.09n m/∘ C, and the fitting coefficient is 0.9974. The experimental results show that in the enhanced Vernier effect sensor structure, only two FPIs with opposite temperature sensitivity are required, which does not increase the difficulty and cost of sensor manufacturing. In addition, the sensor has good stability and repeatability.

TMT-based proteomics analysis of the cerebral cortex of TauT knockout rats.

BACKGROUND: Taurine serves a variety of nutritional and physiological roles, and it is mostly transported in cells via taurine transporter (TauT). The effect of taurine transporter in cerebral cortex is still unknown. We employed TMT label-based proteomics to find differences in proteins in the cerebral cortex of TauT knockout rats in this investigation. The goal of this research was to see how TauT deletion affected protein alterations in brain tissue and to see if there was a new research area for TauT. METHODS: The cerebral cortex of TauT knockout rats and wild-type control rats were analyzed using TMT-based proteomics, and differentially expressed proteins were analyzed by bioinformatics analysis means such as GO and KEGG, the association between the proteins was found by PPI, and biologically significant and interesting proteins were selected for verification by WB and immunohistochemistry. RESULTS: There were total of 8275 proteins found, but only 35 differentially expressed proteins were identified (27 up-regulated and 8 down-regulated), and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the biological pathways and functional classification of the proteins. The results show that these differentially expressed proteins are mainly enriched in lysine degradation, cell cycle, chronic myeloid leukemia, and longevity regulating pathways-multiple species, renal cell carcinoma, pathways in cancer, etc. To verify the proteomic data, we analyzed the expression of Annexin6 and Pik3r2 by western blotting and immunofluorescence. The results are consistent with proteomics, which proves the reliability of our proteomics data. CONCLUSION: Through TMT-based proteomics, we have a comprehensive understanding of the effect of TauT knockout on the changes of other proteins in the cerebral cortex, providing new evidence for further understanding the function of TauT.

[Cloning of transcription factor PcFBA-1 in Pogostemon cabin and its interaction with FPPS promoter].

Farnesyl diphosphate synthase(FPPS) is a key enzyme at the branch point of the sesquiterpene biosynthetic pathway, but there are no reports on the transcriptional regulation of FPPS promoter in Pogostemon cabin. In the early stage of this study, we obtained the binding protein PcFBA-1 of FPPS gene promoter in P. cabin. In order to explore the possible mechanism of PcFBA-1 involved in the regulation of patchouli alcohol biosynthesis, this study performed PCR-based cloning and sequencing analysis of PcFBA-1, analyzed the expression patterns of PcFBA-1 in different tissues by fluorescence quantitative PCR and its subcellular localization using the protoplast transformation system, detected the binding of PcFBA-1 protein to the FPPS promoter in vitro with the yeast one-hybrid system, and verified its transcriptional regulatory function by dual-luciferase reporter gene assay. The findings demonstrated that the cloned PcFBA-1 had an open reading frame(ORF) of 1 131 bp, encoding a protein of 376 amino acids, containing two conserved domains named F-box-like superfamily and FBA-1 superfamily, and belonging to the F-box family. Moreover, neither signal peptide nor transmembrane domain was contained, implying that it was an unstable hydrophilic protein. In addition, as revealed by fluorescence quantitative PCR results, PcFBA-1 had the highest expression in leaves, and there was no significant difference in expression in roots or stems. PcFBA-1 protein was proved mainly located in the cytoplasm. Furthermore, yeast one-hybrid screening and dual-luciferase reporter gene assay showed that PcFBA-1 was able to bind to FPPS promoter both in vitro and in vivo to enhance the activity of FPPS promoter. In summary, this study identifies a new transcription factor PcFBA-1 in P. cabin, which directly binds to the FPPS gene promoter to enhance the promoter activity. This had laid a foundation for the biosynthesis of patchouli alcohol and other active ingre-dients and provided a basis for metabolic engineering and genetic improvement of P. cabin.

An electrographic AV optimization for the maximum integrative atrioventricular and ventricular resynchronization in CRT.

BACKGROUND: Atrioventricular (AV) delay could affect AV and ventricular synchrony in cardiac resynchronization therapy (CRT). Strategies to optimize AV delay according to optimal AV synchrony (AVopt-AV) or ventricular synchrony (AVopt-V) would potentially be discordant. This study aimed to explore a new AV delay optimization algorithm guided by electrograms to obtain the maximum integrative effects of AV and ventricular resynchronization (opt-AV). METHODS: Forty-nine patients with CRT were enrolled. AVopt-AV was measured through the Ritter method. AVopt-V was obtained by yielding the narrowest QRS. The opt-AV was considered to be AVopt-AV or AVopt-V when their difference was < 20 ms, and to be the AV delay with the maximal aortic velocity-time integral between AVopt-AV and AVopt-V when their difference was > 20 ms. RESULTS: The results showed that sensing/pacing AVopt-AV (SAVopt-AV/PAVopt-AV) were correlated with atrial activation time (Pend-As/Pend-Ap) (P < 0.05). Sensing/pacing AVopt-V (SAVopt-V/PAVopt-V) was correlated with the intrinsic AV conduction time (As-Vs/Ap-Vs) (P < 0.01). The percentages of patients with more than 20 ms differences between SAVopt-AV/PAVopt-AV and SAVopt-V/PAVopt-V were 62.9% and 57.1%, respectively. Among them, opt-AV was linearly correlated with SAVopt-AV/PAVopt-AV and SAVopt-V/PAVopt-V. The sensing opt-AV (opt-SAV) = 0.1 × SAVopt-AV + 0.4 × SAVopt-V + 70 ms (R2 = 0.665, P < 0.01) and the pacing opt-AV (opt-PAV) = 0.25 × PAVopt-AV + 0.5 × PAVopt-V + 30 ms (R2 = 0.560, P < 0.01). CONCLUSION: The SAVopt-AV/PAVopt-AV and SAVopt-V/PAVopt-V were correlated with the atrial activation time and the intrinsic AV conduction interval respectively. Almost half of the patients had a > 20 ms difference between SAVopt-AV/PAVopt-AV and SAVopt-V/PAVopt-V. The opt-AV could be estimated based on electrogram parameters.

Serum Prealbumin and Echocardiography Parameters Predict Mortality in Peritoneal Dialysis Patients.

AIM: Protein-energy malnutrition and cardiovascular (CV) disease predisposes patients with end-stage renal disease (ESRD) on dialysis to a high risk of early death, but the prognostic value of prealbumin (PAB) and echocardiographic indices in ESRD patients treated with maintenance peritoneal dialysis (PD) remains unclear. METHODS: A total of 211 PD patients (mean age 49.2 ± 15.4 years, 51.7% male) were prospectively studied. PAB and echocardiography parameters were recorded at baseline. Follow-up (mean ± SD: 33.7 ± 17.3 months) was conducted based on hospital records, clinic visits, and telephone reviews, to record death events and their causes. RESULTS: In the Cox proportional hazards model, PAB and the echocardiographic parameters listed below were found to be optimal predictors of all-cause mortality: PAB (p = 0.003), aortic root diameter (ARD) (p = 0.004), interventricular septum end-diastolic thickness (IVSd) (p = 0.046), and left ventricular end-diastolic diameter index (LVEDDI) (p = 0.029). Of the above-mentioned factors, PAB (p = 0.018), ARD (p = 0.031), and IVSd (p = 0.037) were independent predictors of CV mortality in PD patients. Of note, malnutrition, degradation of the aorta, and myocardial hypertrophy are also known death risk factors in the general population. The all-cause mortality and CV death rate significantly increased as the number of risk factors increased, reaching values as high as 40 and 22% in patients who had all of the risk factors, i.e., abnormal PAB, ARD, and IVSd (p < 0.001 and p = 0.011). CONCLUSION: In PD patients, low serum PAB and abnormal echocardiographic parameters together were significantly associated with all-cause mortality and CV death, independently of other risk factors. These risk factors for death in PD are similar to those in the general population. Noticeably, the combination of echocardiographic parameters and PAB could provide additional predictive value for mortality in PD patients. In light of these findings, more studies in an optimal model containing PAB and echocardiographic parameters for the prediction of outcomes in ESRD are required.

Two novel genetic variants in the STK38L and RAB27A genes are associated with glioma susceptibility.

Glioma is the most common malignant primary brain tumors with poor prognosis. Genome wide association studies (GWAS) of glioma in populations with Western European ancestry were completed in the US and UK. However, our previous results strongly suggest the genetic heterogeneity could be important in glioma risk. To systematically investigate glioma risk-associated variants in Chinese population, we performed a multistage GWAS of glioma in the Han Chinese population, with a total of 3,097 glioma cases and 4,362 controls. In addition to confirming two associations reported in other ancestry groups, this study identified one new risk-associated locus for glioma on chromosome 12p11.23 (rs10842893, pmeta = 2.33x10-12, STK38L) as well as a promising association at 15q15-21.1 (rs4774756, pmeta = 6.12x10-8, RAB27A) in 3,097 glioma cases and 4,362 controls. Our findings demonstrate two novel association between the glioma risk region marked by variant rs10842893 and rs4774756) and glioma risk. These findings may advance the understanding of genetic susceptibility to glioma.

Cadmium induces ovarian granulosa cell damage by activating PERK-eIF2α-ATF4 through endoplasmic reticulum stress.

This study aimed to investigate whether cadmium induces ovarian granulosa cell damage by activating protein kinase R-like endoplasmic reticulum kinase (PERK)-eIF2α-ATF4 through endoplasmic reticulum (ER) stress and to elucidate the underlying regulation mechanism. Two models of cadmium exposure were established. In one model, ovarian granulosa cells isolated from 21-day-old female Sprague Dawley rats were cultured in vitro for 36 h and exposed to CdCl2 (0, 5, 10, and 20 µM), and in another model, a human ovarian granulosa tumor cell line (COV434) was used to construct the binding immunoglobulin protein (BIP)-knockdown cell line sh-BIP and exposed to 0 and 20 µM CdCl2. After exposure to cadmium for 12 h, the expression mRNA and protein levels of BIP, p-PERK, and p-eIF2α were determined in the two models. miRNAs related to BIP were also detected in granulosa cells after cadmium exposure. We found that mRNA and protein levels of all factors were upregulated in each cadmium-dose group, except for BIP mRNA expression in the 5 µM Cd group. The BIP gene was knocked down in COV434 cells before exposure to cadmium. All factors were upregulated in COV434 cells exposed to Cd, and the expression of the p-eIF2α protein was downregulated in sh-BIP cells exposed to Cd. In addition, no differences in BIP-related miRNAs were detected in cadmium-exposed rat ovarian granulosa cells versus the control group. Cadmium induces ovarian granulosa cell damage by inducing ER stress.

Prognostic Significance of Serum Cysteine-Rich Protein 61 in Patients with Acute Heart Failure.

BACKGROUND/AIMS: Cyr61-cysteine-rich protein 61 (CCN1/CYR61) is a multifunctional matricellular protein involved in the regulation of fibrogenesis. Animal experiments have demonstrated that CCN1 can inhibit cardiac fibrosis in cardiac hypertrophy. However, no study has been conducted to assess the relation between serum CCN1 and prognosis of acute heart failure (AHF). METHODS: We measured the serum CCN1 levels of 183 patients with AHF, and the patients were followed up for 6 months. The associations between CCN1 levels and some clinical covariates, especially left ventricular ejection fraction (LVEF), estimated glomerular filtration rate (eGFR), atrial fibrillation and age, were estimated. The AHF patients were followed up for 6 months. The endpoint was all-cause mortality. Kaplan-Meier curve analysis and multivariable Cox proportional hazards analysis were employed to evaluate the prognostic ability of CCN1. We used calibration, discrimination and reclassification to assess the mortality risk prediction of adding CCN1. RESULTS: Serum CCN1 concentrations in AHF patients were significantly increased compared with those in individuals without AHF (237 pg/ml vs. 124.8 pg/ml, p< 0.001). CCN1 level was associated with the level of NT-proBNP (r=0.349, p< 0.001) and was not affected by LVEF, eGFR, age or atrial fibrillation in AHF patients. Importantly, Kaplan-Meier curve analysis illustrated that the AHF patients with serum CCN1 level > 260 pg/ ml had a lower survival rate (p< 0.001). Multivariate Cox hazard analysis suggests that CCN1 functions as an independent predictor of mortality for AHF patients (LgCCN1, hazard ratio 5.825, 95% confidence interval: 1.828-18.566, p=0.003). In addition, the inclusion of CCN1 in the model with NT-proBNP significantly improved the C-statistic for predicting death (0.758, p< 0.001). The integrated discrimination index was 0.019 (p< 0.001), and the net reclassification index increased significantly after addition of CCN1 (23.9%, p=0.0179). CONCLUSIONS: CCN1 is strongly predictive of 6-month mortality in patients with AHF, suggesting serum CCN1 as a promising candidate prognostic biomarker for AHF patients.

ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives.

Motivation: Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. Existing prediction methods use randomly selected non-validated sites as non-ubiquitination sites to train ubiquitination site prediction models. Results: We propose an evolutionary screening algorithm (ESA) to select effective negatives among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. The ESA selects non-validated sites least likely to be ubiquitination sites as training negatives. Moreover, the ESA and ESA-UbiSite use a set of well-selected physicochemical properties together with a support vector machine for accurate prediction. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy and a Matthews's correlation coefficient of 0.48, better than existing prediction methods. The ESA increased ESA-UbiSite's test accuracy from 0.75 to 0.92 and can improve other post-translational modification site prediction methods. Availability and Implementation: An ESA-UbiSite-based web server has been established at http://iclab.life.nctu.edu.tw/iclab_webtools/ESAUbiSite/ . Contact: syho@mail.nctu.edu.tw. Supplementary information: Supplementary data are available at Bioinformatics online.

Taurine Promotes the Cartilaginous Differentiation of Human Umbilical Cord-Derived Mesenchymal Stem Cells in Vitro.

Taurine has been reported to influence osteogenic differentiation, but the role of taurine on cartilaginous differentiation using human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) remains unclear. In this study, we investigated the effect of taurine (0, 1, 5 and 10 mM) on the proliferation and chondrogenesis of hUC-MSCs by analyzing cell proliferation, accumulation of glycosaminoglycans and expression of cartilage specific mRNA. The results show though taurine did not affected the proliferation of hUC-MSCs, 5 mM of taurine is sufficient to enhanced the accumulation of glycosaminoglycans and up-regulate cartilage specific mRNA expression, namely collagen type II, aggrecan and SOX9. Taurine also inhibits chondrocyte dedifferentiation by reducing expression of collagen type I mRNA. Taken together, our study reveals that taurine promotes and maintains the chondrogenesis of hUC-MSCs.

Inhibition of LDHA Deliver Potential Anticancer Performance in Renal Cell Carcinoma.

PURPOSE: Lactate dehydrogenase A (LDHA), which functions as a crucial enzyme in transforming from pyruvate into lactate, has been reported to be overexpressed in various advanced cancer and its silencing has turned out to be tumor suppressive. Previous studies have showed that the expression of LDHA was higher in renal cell carcinoma (RCC) than that in corresponding normal renal tissue. However, the function of LDHA in RCC, and its possible mechanism in tumor progression, has not been investigated. METHODS: MTT and cell cycle assay were performed to explore the growth of the renal cells. Transwell assay for the migration and invasion and tube formation were conducted to detect the metastatic properties of the renal cancer. RESULTS: Here, we show that siRNA-mediated knockdown of LDHA inhibits cell proliferation by decreasing cell cycle and promoting apoptosis in renal cancer cell lines. Mechanistically, LDHA siRNA treatment altered the expression of cell cycle- and apoptosis-related proteins, including p21, cyclin D1, Bcl-2 and Bax. In addition, LDHA siRNA treatment leads to markedly diminished migratory and invasive ability by reducing the expression of matrix metalloproteinase (MMP)-2 and MMP-9. CONCLUSIONS: These findings are consistent with the view that LDHA, as an oncogene, might be a potential therapeutic target in RCC.

[Effects of aqueous extracts of gecko on stemness of hepatocellular carcinoma].

To explore the effects and mechanism of aqueous extracts of gecko on cancer stem cells properties of hepatocellular carcinoma. In vitro, MTT assay was used to detect the cells growth in Huh7 and Hep3B. Spheroid-forming assay and flow cytometry were performed to observe the the stemness of Huh7 and Hep3B cells. The protein expressions of ß-catenin, CD44, c-Myc, CCND1, Sox2, Oct4, Nanog and ABCG2 were detected by Western blot. Interacting proteins were detected by co-immunoprecipitation; and a subcutaneous xenograft model was used to detect the stemness of hepatoma carcinoma cells. The results indicated that aqueous extracts of gecko induced cell growth inhibition in a dose- and time-dependent manner, with the IC50 of (0.750±0.112) g•mL⁻¹ for Huh7 and (0.454±0.039) g•mL⁻¹ for Hep3B, respectively. The number and size of tumor spheres formed by hepatoma carcinoma cells were decreased after treatment by aqueous extracts of gecko(P<0.05); the proportions of cells staining with putative markers for cancer stem cells, such as CD133 and CD44, were decreased(P<0.05). After treatment with aqueous extracts of gecko, the expression levels of ß-catenin, CD44, c-Myc, CCND1, Sox2, Oct4, Nanog and ABCG2 were decreased. Co-immunoprecipitation results showed that the aqueous extracts of gecko could inhibit the interaction between LRP6 and Frizzled6, indicating that the aqueous extracts of gecko could inhibit the proliferation of hepatoma cells, the formation of tumor spheres and the proportion of tumor stem cells, and inhibit the Wnt signaling pathway by targeting LRP6 to prevent the formation of LRP6 and Frizzled6 complexes.

A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area.

BACKGROUND: Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein structures, in this study, our aim was to design predictors for estimating relative solvent accessibility (RSA) of amino acid residues to discover protein folding characteristics from sequences. METHODS: The proposed 20 real-value RSA predictors were designed on the basis of the support vector regression method with a set of informative physicochemical properties (PCPs) obtained by means of an optimal feature selection algorithm. Then, molecular dynamics simulations were performed for validating the knowledge discovered by analysis of the selected PCPs. RESULTS: The RSA predictors had the mean absolute error of 14.11% and a correlation coefficient of 0.69, better than the existing predictors. The hydrophilic-residue predictors preferred PCPs of buried amino acid residues to PCPs of exposed ones as prediction features. A hydrophobic spine composed of exposed hydrophobic residues of an α-helix was discovered by analyzing the PCPs of RSA predictors corresponding to hydrophobic residues. For example, the results of a molecular dynamics simulation of wild-type sequences and their mutants showed that proteins 1MOF and 2WRP_H16I (Protein Data Bank IDs), which have a perfectly hydrophobic spine, have more stable structures than 1MOF_I54D and 2WRP do (which do not have a perfectly hydrophobic spine). CONCLUSIONS: We identified informative PCPs to design high-performance RSA predictors and to analyze these PCPs for identification of novel protein folding characteristics. A hydrophobic spine in a protein can help to stabilize exposed α-helices.

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides.

BACKGROUND: Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular processes, are characterized as a separate class of enzymes and share no structural similarity with their eukaryotic counterparts. However, in silico methods for predicting BY-kinases have not been developed yet. Since these enzymes are involved in key regulatory processes, and are promising targets for anti-bacterial drug design, it is desirable to develop a simple and easily interpretable predictor to gain new insights into bacterial tyrosine phosphorylation. This study proposes a novel SCMBYK method for predicting and characterizing BY-kinases. RESULTS: A dataset consisting of 797 BY-kinases and 783 non-BY-kinases was established to design the SCMBYK predictor, which achieved training and test accuracies of 97.55 and 96.73%, respectively. Furthermore, the leave-one-phylum-out method was used to predict specific bacterial phyla hosts of target sequences, gaining 97.39% average test accuracy. After analyzing SCMBYK-derived propensity scores, four characteristics of BY-kinases were determined: 1) BY-kinases tend to be composed of α-helices; 2) the amino-acid content of extracellular regions of BY-kinases is expected to be dominated by residues such as Val, Ile, Phe and Tyr; 3) BY-kinases structurally resemble nuclear proteins; 4) different domains play different roles in triggering BY-kinase activity. CONCLUSIONS: The SCMBYK predictor is an effective method for identification of possible BY-kinases. Furthermore, it can be used as a part of a novel drug repurposing method, which recognizes putative BY-kinases and matches them to approved drugs. Among other results, our analysis revealed that azathioprine could suppress the virulence of M. tuberculosis, and thus be considered as a potential antibiotic for tuberculosis treatment.

Estimating survival time of patients with glioblastoma multiforme and characterization of the identified microRNA signatures.

BACKGROUND: Though glioblastoma multiforme (GBM) is the most frequently occurring brain malignancy in adults, clinical treatment still faces challenges due to poor prognoses and tumor relapses. Recently, microRNAs (miRNAs) have been extensively used with the aim of developing accurate molecular therapies, because of their emerging role in the regulation of cancer-related genes. This work aims to identify the miRNA signatures related to survival of GBM patients for developing molecular therapies. RESULTS: This work proposes a support vector regression (SVR)-based estimator, called SVR-GBM, to estimate the survival time in patients with GBM using their miRNA expression profiles. SVR-GBM identified 24 out of 470 miRNAs that were significantly associated with survival of GBM patients. SVR-GBM had a mean absolute error of 0.63 years and a correlation coefficient of 0.76 between the real and predicted survival time. The 10 top-ranked miRNAs according to prediction contribution are as follows: hsa-miR-222, hsa-miR-345, hsa-miR-587, hsa-miR-526a, hsa-miR-335, hsa-miR-122, hsa-miR-24, hsa-miR-433, hsa-miR-574 and hsa-miR-320. Biological analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on the identified miRNAs revealed their influence in GBM cancer. CONCLUSION: The proposed SVR-GBM using an optimal feature selection algorithm and an optimized SVR to identify the 24 miRNA signatures associated with survival of GBM patients. These miRNA signatures are helpful to uncover the individual role of miRNAs in GBM prognosis and develop miRNA-based therapies.

AVE 0991 attenuates cardiac hypertrophy through reducing oxidative stress.

AVE 0991, the nonpeptide angiotensin-(1-7) (Ang-(1-7)) analog, is recognized as having beneficial cardiovascular effects. However, the mechanisms have not been fully elucidated. This study was designed to investigate the effects of AVE 0991 on cardiac hypertrophy and the mechanisms involved. Mice were underwent aortic banding to induce cardiac hypertrophy followed by the administration of AVE 0991 (20 mg kg·day (-1)) for 4 weeks. It was shown that AVE 0991 reduced left ventricular hypertrophy and improved heart function, characterized by decreases in left ventricular weight and left ventricular end-diastolic diameter, and increases in ejection fraction. Moreover, AVE 0991 significantly down-regulated mean myocyte diameter and attenuate the gene expression of the hypertrophic markers. Furthermore, AVE 0991 inhibited the expression of NOX 2 and NOX 4, meaning that AVE 0991 reduced oxidative stress of cardiac hypertrophy mice. Our data showed that AVE 0991 treatment could attenuate cardiac hypertrophy and improve heart function, which may be due to reduce oxidative stress.