DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines.

Accurate identification of protein-DNA binding sites is significant for both understanding protein function and drug design. Machine-learning-based methods have been extensively used for the prediction of protein-DNA binding sites. However, the data imbalance problem, in which the number of nonbinding residues (negative-class samples) is far larger than that of binding residues (positive-class samples), seriously restricts the performance improvements of machine-learning-based predictors. In this work, we designed a two-stage imbalanced learning algorithm, called ensembled hyperplane-distance-based support vector machines (E-HDSVM), to improve the prediction performance of protein-DNA binding sites. The first stage of E-HDSVM designs a new iterative sampling algorithm, called hyperplane-distance-based under-sampling (HD-US), to extract multiple subsets from the original imbalanced data set, each of which is used to train a support vector machine (SVM). Unlike traditional sampling algorithms, HD-US selects samples by calculating the distances between the samples and the separating hyperplane of the SVM. The second stage of E-HDSVM proposes an enhanced AdaBoost (EAdaBoost) algorithm to ensemble multiple trained SVMs. As an enhanced version of the original AdaBoost algorithm, EAdaBoost overcomes the overfitting problem. Stringent cross-validation and independent tests on benchmark data sets demonstrated the superiority of E-HDSVM over several popular imbalanced learning algorithms. Based on the proposed E-HDSVM algorithm, we further implemented a sequence-based protein-DNA binding site predictor, called DNAPred, which is freely available at http://csbio.njust.edu.cn/bioinf/dnapred/ for academic use. The computational experimental results showed that our predictor achieved an average overall accuracy of 91.7% and a Mathew's correlation coefficient of 0.395 on five benchmark data sets and outperformed several state-of-the-art sequence-based protein-DNA binding site predictors.

[The integrity study on PEG-PCL micelles transcellular transported across MDCK epithelial cell monolayer using FRET technology].

The integrity of poly(ethylene glycol)-co-poly(ε-caprolactone) (PEG-PCL) micelles transcellular transported across madin-darby canine kidney(MDCK) epithelial cells was investigated. Fluorescein isothiocyanate isomer I(FITC) was conjugated to PEG-PCL and the product PEG-PCL-FITC was identified by fluorescence spectra. Two micelles were prepared using the thin-film hydration method: 3,3'-dioctadecyloxacarbocyanine perchlorate (DiO) and 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) co-loaded PEG-PCL micelles (DiO-DiI-M), DiI loaded and PEG-PCL-FITC contained micelles(FITC-DiI-M). The size of the micelles was characterized by dynamic light scattering analysis using a Malvern Zetasizer Nano ZS and it turned out that the particle sizes of both micelles were about 30 nm with identical polydispersity index(PDI). The stability of the micelles in phosphate buffer saline(PBS) was monitored using fluorescence spectra and both micelles were stable within 4 h in PBS. The integrity of PEG-PCL micelles in the transcellular process across MDCK epithelial cell monolayer at 1 and 4 h was investigated using laser confocal scanning microscope and Förster resonance energy transfer(FRET) technology. The Person's coefficient and FRET efficiency of both Transwell layer and Receive layer were recorded. The results show that the FRET efficiency and Person's coefficient of the Receive layer was consistent with that of Transwell layer for both the micelles at 1 h, but decreased at 4 h and FITC-DiI-M decreased more significantly than Di O-DiI-M. The results indicated that the micelles could transport across the MDCK monolayer intactly at 1 h but some of them were disassembled during the 4 h transportation process.

[Distribution Prediction of Soil Heavy Metals Based on Remote Sensing Temporal-Spatial-Spectral Features and Random Forest Model].

Obtaining soil heavy metal content characteristics and spatial distribution is crucial for preventing soil pollution and formulating environmental protection policies. We collected 304 surface soil samples (0-20 cm) in the Changqing district. At the same time, the spectral, temporal, and spatial features of soil heavy metals were derived from multi-remote sensing data; the temporal-spatial-spectral features closely related to soil heavy metals were selected via correlation analysis and used as input independent variables. The measured soil arsenic (As) content was used as the dependent variable to establish a spatial prediction model based on the random forest (RF) algorithm. The results showed the following:the As content in the soils exceeded the background value by 43.17% but did not exceed the risk screening values and intervention values, indicating slight heavy metal pollution in the soil. The accuracy ranking of the spatial prediction models with one feature type from high to low was spatial features (ratio of performance to inter-quartile range (RPIQ)=3.87)>temporal features (RPIQ=2.57)>spectral features (RPIQ=2.50). The spatial features were the most informative for predicting soil heavy metals. The models using temporal-spatial, temporal-spectral, and spatial-spectral features were superior to those using only one feature type, and the RPIQ values were 4.81, 4.21, and 4.70, respectively. The RF model with temporal-spatial-spectral features achieved the highest spatial prediction accuracy (R2=0.90; root mean square error (RMSE)=0.77; RPIQ=5.68). The As content decreased from the northwest to the southeast due to Yellow River erosion and industrial activities. The spatial prediction of soil heavy metals incorporating remote sensing temporal-spatial-spectral features and the random forest model provides effective support for soil pollution prevention and environmental risk control.

[Estimation of vegetation canopy water content using Hyperion hyperspectral data].

Vegetation canopy water content (VCWC) has widespread utility in agriculture, ecology and hydrology. Based on the PROSAIL model, a novel model for quantitative inversion of vegetation canopy water content using Hyperion hyperspectral data was explored. Firstly, characteristics of vegetation canopy reflection were investigated with the PROSAIL radiative transfer model, and it was showed that the first derivative at the right slope (980 - 1 070 nm) of the 970 nm water absorption feature (D98-1 070) was closely related to VCWC, and determination coefficient reached to 0.96. Then, bands 983, 993, 1 003, 1 013, 1 023, 1 033, 1 043, 1 053 and 1 063 nm of Hyperion data were selected to calculate D980-1 070, and VCWC was estimated using the proposed method. Finally, the retrieval result was verified using field measured data in Yingke oasis of the Heihe basin. It indicated that the mean relative error was 12.5%, RMSE was within 0.1 kg x m(-2) and the proposed model was practical and reliable. This study provides a more efficient way for obtaining VCWC of large area.

Oxidative damage to RNA and expression patterns of MTH1 in the hippocampi of senescence-accelerated SAMP8 mice and Alzheimer's disease patients.

Mammalian MTH1 protein, a MutT-related protein, catalyzes the hydrolysis of 8-oxo-7,8-dihydroguanosine triphosphate (8-oxoGTP) to monophosphate, thereby preventing incorporation of 8-oxo-7,8-dihydroguanine (8-oxoguanine) into RNA. In this study, we applied immunohistochemistry to follow the expression of MTH1 and the amount of 8-oxoguanine in RNA during aging. There were increased amounts of 8-oxoguanine in RNA in the CAl and CA3 subregions of hippocampi of 8- and 12-month-old SAMP8 mice, which exhibited early aging syndromes and declining learning and memory abilities compared to those of age-matched control SAMR1 mice. The expression levels of MTH1 in the hippocampi of 8- and 12-month-old SAMP8 mice were significantly lower than those of control mice. Therefore, in this mouse model, age-related accumulation of 8-oxoguanine in RNA is correlated with decreased expression of MTH1. Increased amounts of 8-oxoguanine in the RNA, and decreased expression of MTH1 were also observed in the hippocampi of patients suffering from Alzheimer's disease. These results suggest that MTH1 deficiency might be a causative factor for aging and age-related disorders.

Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites.

AIM AND OBJECTIVE: The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding sites. Nevertheless, the severe class imbalance phenomenon, where the number of nonbinding (majority) residues is far greater than that of binding (minority) residues, has a negative impact on the performance of such machine-learning-based predictors. MATERIALS AND METHODS: In this study, we aim to relieve the negative impact of class imbalance by Boosting Multiple Granular Support Vector Machines (BGSVM). In BGSVM, each base SVM is trained on a granular training subset consisting of all minority samples and some reasonably selected majority samples. The efficacy of BGSVM for dealing with class imbalance was validated by benchmarking it with several typical imbalance learning algorithms. We further implemented a protein-nucleotide binding site predictor, called BGSVM-NUC, with the BGSVM algorithm. RESULTS: Rigorous cross-validation and independent validation tests for five types of proteinnucleotide interactions demonstrated that the proposed BGSVM-NUC achieves promising prediction performance and outperforms several popular sequence-based protein-nucleotide binding site predictors. The BGSVM-NUC web server is freely available at http://csbio.njust.edu.cn/bioinf/BGSVM-NUC/ for academic use.

Anti-ulcer and anti-Helicobacter pylori potentials of the ethyl acetate fraction of Physalis alkekengi L. var. franchetii (Solanaceae) in rodent.

ETHNOPHARMACOLOGICAL RELEVANCE: Physalis alkekengi L. var. franchetii (Solanaceae) has been widely used in Chinese folk medicine due to its wide distribution throughout the country, for the treatment of a wide range of diseases including heat and cold, sore throat, fever, fungal infection, inflammation, toothache, rheumatism, burn, analgesic, ulcer and urinary diseases. However, the effect of P. alkekengi var. franchetii on ulcer and Helicobacter pylori infection has not been reported to date. AIM OF THE STUDY: This study was designed to investigate the anti-inflammatory, anti-ulcer, anti-Helicobacter pylori and analgesic properties of ethyl acetate fraction of the crude aqueous methanolic extract from the aerial parts of the plant P. alkekengi L. var. franchetii in rodents. MATERIALS AND METHODS: Acute toxicity of the crude extract of P. alkekengi L. var. franchetii (PAF) was evaluated in rats. The petroleum ether fraction (PEF), butanol fraction (BF), ethyl acetate fraction (EAF) and aqueous fraction (AF) of crude aqueous methanolic extract from PAF were screened for anti-inflammatory and anti-ulcer potential at doses of 100, 250 and 500mg/kg (p.o.), using carrageenin-induced hind paw edema and ethanol-induced gastric lesions test in rats. In vitro anti-Helicobacter pylori activity of EAF was assayed subsequently. In addition, three doses of EAF were evaluated for analgesic activity using hot plate and writhing tests, respectively. Finally, we performed a phytochemical analysis of EAF. RESULTS: Four fractions of crude extract from PAF significantly reduced the paw volume in carrageenin-induced hind paw edema model at different doses (100, 250 and 500mg/kg, p.o.). The fraction EAF at a dose of 500mg/kg exhibited the highest (75.92%) (0.150 ± 0.045***, ***p < 0.001) anti-inflammatory potential, which is similar to indomethacin (***P < 0.001)（0.120 ± 0.014***, 80.74% inhibition of inflammation） at 5mg/kg. Pretreatment with EAF (500mg/kg, p.o.) significantly reduced the intensity of gastric mucosal damage and showed higher gastroprotective activity (90.6%) when compared to the standard drug famotidine (84.6%). In addition, EAF fraction also showed a moderate (P < 0.05) anti-Helicobacter pylori activity with a minimal inhibition concentration (MIC) of 500µg/ml. Furthermore, pain sensation was effectively inhibited at 500mg/kg, p.o. of EAF as manifested by an increase (p < 0.001) of latency time in hot plate from 30 to 90min and a decrease (p < 0.001) in count of writhing induced by acetic acid. By HPLC, we determined some steroid, terpenoid and flavonoids (four compounds): kaempferol, quercetin, Blumenol A and physalindicanols A, which were isolated from the ethyl acetate fraction and identified using 1H NMR and 13C NMR spectra analysis. CONCLUSION: This study demonstrated the anti-inflammatory, anti-ulcer, anti-Helicobacter pylori and analgesic properties of EAF of the crude extract from PAF thus justifying its traditional usage.

Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation.

Soil microorganisms play a crucial role in cycling soil nutrients and providing organic nutrients for plant growth and development. Fertilisation balances soil fertility and quality, and affects soil microbial communities. Fertilisation is a frontier subject in agricultural and environmental sciences. Here we showed that the application of high-carbon basal fertiliser treatment could improve the tobacco yield and quality when compared to chemical fertiliser, high-carbon basal fertiliser and mixed high-carbon chemical fertiliser. The potential reason is that different fertiliser treatments influence soil fertility, such as nitrogen, phosphorus, and other contents, besides soil organic matter. Further experiments revealed that populations of bacteria, fungi and actinomycetes fluctuated during tobacco development under different fertilisation treatments. Then we performed high-throughput sequencing of the 16S rRNA gene, and the results showed that the fertilisation treatments had significant effects on the microbial community, particularly within the finer taxonomic divisions or non-dominant taxa. Moreover, proteobacteria and fungal genera had significantly different relative abundances during tobacco growth under various tobacco developmental stages and fertilisation treatments. These results indicated that mixed high-carbon chemical fertiliser could improve soil fertility by influencing the soil microorganism, and that the fertilisation treatments impacted on the structure and composition of the microbial community, and especially the diversity of non-dominant taxa. However, more studies are needed to confirm their reliability.

Norcantharidin enhances bortezomib-antimyeloma activity in multiple myeloma cells in vitro and in nude mouse xenografts.

Norcantharidin (NCTD), the demethylated analog of the Chinese medicine cantharidin, exhibits anti-myeloma activity by inactivating nuclear factor-κB (NF-κB), which is implicated in multiple myeloma (MM) cell survival and resistance to bortezomib (BTZ). We investigated whether NCTD could potentiate the anti-tumor activity of BTZ in MM. NCTD inhibited the proliferation of MM cells and potentiated the anti-myeloma effects of BTZ by down-regulating IKKα and p-IκBα, which induced the accumulation of IκBα and inhibited the constitutive activation of NF-κB. This effect was correlated with the suppression of NF-κB-regulated gene products. Furthermore, a chemotherapy-potentiating effect of NCTD on BTZ was also observed in vivo. Our study demonstrated that NCTD and BTZ exhibit significant therapeutic effects on MM through the NF-κB signal pathway in vitro and in vivo. Future studies will investigate the combined effects of NCTD and BTZ in patients with MM.

Expression levels of IL-27 and IL-17 in multiple myeloma patients: a higher ratio of IL-27:IL-17 in bone marrow was associated with a superior progression-free survival.

The goal of the study was to investigate the levels of interleukin-27 (IL-27) and IL-17 in bone marrow (BM) and peripheral blood (PB) of multiple myeloma (MM). The levels of IL-27 and IL-17 were determined in MM patients and controls using ELISA. The results showed a decreased IL-27 and elevated IL-17 level in MM patients and a negative association of IL-27 with IL-17. The ratio of IL-27:IL-17 in BM of newly diagnosed MM was significantly decreased and correlated with the progression of disease. Multivariate analysis showed that a higher ratio of IL-27:IL-17 in BM was associated with a superior progression-free survival (HR=0.160; 95% CI: 0.058-0.443; p<0.001). Our results suggest that there might be a possible competitive role of IL-27 and IL-17 in MM.

[Norcantharidin potentialize the chemosensitivity of adriamycin through the NF-κB/IκBα signaling pathway].

OBJECTIVE: To explore the synergetic effect of norcantharidin (NCTD) and adriamycin (ADR) on the proliferation and apoptosis of multiple myeloma (MM) cells. METHODS: Human MM cell line U266 cells were treated with NCTD alone (10 µmol/L) or in combination with ADR (0.25 µmol/L). MTT and Annexin V/PI staining were used to determine cell viability and apoptosis. The protein expression of nuclear factor-κB P65 (NF-κB P65), phosphorylated NF-κB p65 (p-NF-κB p65), NF-κB P65 inhibitor IκBα, phosphorylated IκBα (p-IκBα), survivin, Bcl-2 and Bax were determined by Western blot. Immunohistochemistry was used to determine the expression of vascular endothelial growth factor (VEGF). RESULTS: (1) NCTD potentiated the cytotoxicity and pro-apoptotic effects induced by ADR. The combination of NCTD and ADR had synergistic anti-proliferation effect. (2) Combination of ADR and NCTD downregulated the expression of nuclear NF-κB P65 and cytoplasm p-IκBα induced by ADR. The expression of nuclear NF-κB P65 and cytoplasm p-IκBα decreased from 2.08 ± 0.29 and 0.39 ± 0.07 to 0.48 ± 0.08 and 0.02 ± 0.01 respectively, while the expression of the cytoplasm NF-κB P65 and IκBα were unchanged in the ADR alone group and the combined group. (3) The expression of survivin and bcl-2 decreased from 0.31 ± 0.05 and 0.23 ± 0.05 to 0.03 ± 0.02 and 0.05 ± 0.02, while the expression of Bax increased from 0.46 ± 0.06 to 0.62 ± 0.08 respectively in ADR alone group and combined group. (4) The positive rate of VEGF in ADR group and combination group were (44.6 ± 4.4)% and (27.0 ± 2.1)% respectively, indicating that NCTD could potentiate the inhibition effect on VEGF induced by ADR. CONCLUSIONS: The results suggest that NCTD can potentialize the chemosensitivity of multiple myeloma cells to ADR through regulating NF-κB/IκBα signaling pathway and NF-κB-regulated gene products including survivin, Bcl-2, Bax and VEGF.

Age-related alterations in the expression of MTH2 in the hippocampus of the SAMP8 mouse with learning and memory deterioration.

MutT-related proteins degrade 8-oxo-7,8-dihydrodeoxyguanosine triphosphate (8-oxo-dGTP), a mutagenic substrate for DNA synthesis in the nucleotide pool, thereby preventing DNA replication errors. MTH2 (Mut T homolog 2), which belongs to this family of proteins, possesses 8-oxo-7,8-dihydro-2'-deoxyguanosine triphosphatase (8-oxo-dGTPase) activity and appears to function in the protection of the genetic material from the untoward effects of endogenous oxygen radicals. To examine the roles of MTH2 in the aging process, we used the senescence-accelerated prone mouse 8 (SAMP8), which exhibits early aging syndromes and declining abilities of learning and memory. Immunohistochemical and western blot analysis revealed that the level of MTH2 protein in the hippocampus of the SAMP8 mouse progressively decreases beginning from four months after birth, whereas no such change was observed in the control senescence-accelerated resistant mouse 1 (SAMR1). Under these conditions, 8-oxoguanine accumulates in the nuclear DNA in the CA1 and CA3 subregions of the hippocampus of SAMP8 in an age-dependent manner. In SAMR1 mice, accumulation of 8-oxoguanine in the DNA was not observed. These results suggest that the MTH2 deficiency might be one of the causative factors for accelerated aging.