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Background: Pumpkin (Cucurbita moschata Duch.) productivity is severely hindered by powdery mildew worldwide. The causative agent of pumpkin PM is Podosphaera xanthii, a biotrophic fungus. To identify genes involved in the defense response to PM attack, we performed a transcriptomic analysis of a highly-resistant pumpkin genotype by RNA-sequencing. Pathogenesis-related protein 1 (PR1) is among the most abundantly produced proteins in plants responding to pathogen attacks. In this study, we identified and investigated the effects of CmPR1 gene from C. moschata for resistance to powdery mildew. Results: Subcellular localization assay in Arabidopsis protoplasts revealed that CmPR1 is a cytoplasmic protein in plants. The expression of CmPR1 gene was strongly induced by P. xanthii and exogenous ethylene, jasmonic acid and NaCl treatments, but repressed by hydrogen peroxide and salicylic acid treatments. Visual disease symptoms, histological observations of fungal growth and host cell death, and accumulation of H2O2 in transgenic tobacco plants indicated that CmPR1 overexpression significantly enhanced the resistance to Golovinomyces cichoracearum compared to wild type plants during powdery mildew pathogens infection, possibly due to inducing cell death and H2O2 accumulation near infected sites. The expression of PR1a was significantly induced in transgenic tobacco plants in response to G. cichoracearum, suggesting that CmPR1 overexpression positively modulates the resistance to powdery mildew via the SA signaling pathway. Conclusions: These findings indicate that CmPR1 is a defense response gene in C. moschata and and can be exploited to develop disease-resistant crop varieties.

Liver cancer is one of the deadliest cancers in the world. To find effective therapies for this cancer, it is indispensable to identify key genes, which may play critical roles in the incidence of the liver cancer. To identify key genes of the liver cancer with high accuracy, we integrated multiple microarray gene expression data sets to compute common differentially expressed genes, which will result more accurate than those from individual data set. To find the main functions or pathways that these genes are involved in, some enrichment analyses were performed including functional enrichment analysis, pathway enrichment analysis, and disease association study. Based on these genes, a protein-protein interaction network was constructed and analyzed to identify key genes of the liver cancer by combining the local and global influence of nodes in the network. The identified key genes, such as TOP2A, ESR1, and KMO, have been demonstrated to be key biomarkers of the liver cancer in many publications. All the results suggest that our method can effectively identify key genes of the liver cancer. Moreover, our method can be applied to other types of data sets to select key genes of other complex diseases.

MADS-box family transcription factors play essential roles in the growth and development of plants, and some MADS-box genes have also been found to participate in the stress-response. At present, little information regarding stress-related MADS-box genes is available in pepper. We isolated a MADS-box transcription factor gene from Capsicum annuum, which we named CaMADS. CaMADS expression is induced by low and high temperature, salt, and osmotic stress, and also by abscisic acid (ABA), salicylic acid (SA), methyl-jasmonic acid (MeJA), and CaCl2. To understand the function of CaMADS in the abiotic stress response, we generated pepper plants in which CaMADS expression was down-regulated using VIGS (Virus-induced Gene Silencing), and also transgenic Arabidopsis plants overexpressing CaMADS. We found that CaMADS-down-regulated seedlings were more seriously injured than WT after cold, NaCl, and mannitol treatment, and showed increased electrolyte leakage, malondialdehyde (MDA) levels, and lower chlorophyll content. CaMADS-overexpressing Arabidopsis plants were more tolerant to these stresses than WT, and showed significantly high survival rates and lower H2O2 and super oxide radical contents after cold treatment. CaMADS-overexpressing plants had higher germination rates and percentages of green cotyledons following NaCl and mannitol treatment. Root lengths and fresh weight in CaMADS-overexpressing plants were also significantly longer and higher, respectively, than in WT plants. Taken together, our results suggest that CaMADS functions as a positive stress-responsive transcription factor in the cold, salt, and osmotic stress signaling pathways.

Squamosa promoter binding protein (SBP)-box genes are plant-specific transcription factors involved in plant growth and development, morphogenesis and biotic and abiotic stress responses. However, these genes have been understudied in pepper, especially with respect to defense responses to Phytophthora capsici infection. CaSBP11 is a SBP-box family gene in pepper that was identified in our previous research. Silencing CaSBP11 enhanced the defense response of pepper plants to Phytophthora capsici. Without treatment, the expression of defense-related genes (CaBPR1,CaPO1,CaSAR8.2 and CaDEF1) increased in CaSBP11-silenced plants. However, the expression levels of these genes were inhibited under transient CaSBP11 expression. CaSBP11 overexpression in transgenic Nicotiana benthamiana decreased defense responses, while in Arabidopsis, it induced or inhibited the expression of genes in the salicylic acid and jasmonic acid signaling pathways. CaSBP11 overexpression in sid2-2 mutants induced AtNPR1, AtNPR3, AtNPR4, AtPAD4, AtEDS1, AtEDS5, AtMPK4 and AtNDR1 expression, while AtSARD1 and AtTGA6 expression was inhibited. CaSBP11 overexpression in coi1-21 and coi1-22 mutants, respectively, inhibited AtPDF1.2 expression and induced AtPR1 expression. These results indicate CaSBP11 has a negative regulatory effect on defense responses to Phytophthora capsici. Moreover, it may participate in the defense response of pepper to Phytophthora capsici by regulating defense-related genes and the salicylic and jasmonic acid-mediated disease resistance signaling pathways.

Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation. To address this problem, we propose a novel computational approach, TFBSImpute, for predicting additional TF binding profiles by leveraging information from available ChIP-seq TF binding data. TFBSImpute fuses the dataset to a 3-mode tensor and imputes missing TF binding signals via simultaneous completion of multiple TF binding matrices with positional consistency. We show that signals predicted by our method achieve overall similarity with experimental data and that TFBSImpute significantly outperforms baseline approaches, by assessing the performance of imputation methods against observed ChIP-seq TF binding profiles. Besides, motif analysis shows that TFBSImpute preforms better in capturing binding motifs enriched in observed data compared with baselines, indicating that the higher performance of TFBSImpute is not simply due to averaging related samples. We anticipate that our approach will constitute a useful complement to experimental mapping of TF binding, which is beneficial for further study of regulation mechanisms and disease.

The Nystrom-Clenshaw-Curtis (NCC) quadrature, which was proposed in [S. Y. Kang, I. Koltracht, and G. Rawitscher, Math. Comp. 72, 729–756 (2003)], is a highly accurate numerical method for solving integral equations with semi-smooth kernel. In this paper, we introduce the basic idea of the NCC quadrature and derive an NCC quadrature for Volterra integral equations with proportional delays. Numerical results are presented to illustrated the high accuracy of the method.

Ubiquitous cell membrane proteins called aquaporins are members of major intrinsic proteins (MIPs), which control the specific transport of water molecules across cell membranes. A pepper aquaporin gene (CaAQP), which exhibits the structural features of tonoplast intrinsic proteins of the MIP subfamily, was isolated from the leaves of chilling-treated seedlings of pepper (Capsicum annuum L.) cv. P70. Assays indicated high levels of expression in young seeds, green fruits and flower buds and low levels of expression in the stems, leaves and roots of pepper. The expression patterns were strongly and rapidly induced by HgCl2, low temperature, abscisic acid, fluridone and osmotic stresses. The responsiveness of pepper seedlings pretreated with abscisic acid at low temperatures demonstrated up-regulation of CaAQP by chilling, which is potentially involved in ABA signalling. Our results indicated that overexpression of CaAQP decreased chilling stress in transgenic plants, likely by increasing the stomatal aperture under stress, increasing the rate of membrane damage during the recovery stage, thereby affecting the intercellular CO2 concentration with lower stomatal conductance and transpiration rates. VIGS of CaAQP in pepper plants caused significant growth retardation. These results suggested that CaAQP played a crucial role in the plant response to abiotic stresses.

Computational fluid dynamics were used to study the three-dimensional unsteady flows in a closed pipeline system with a screw-type centrifugal pump during rapid starting period. The unsteady Reynold time-averaged Navier-Stokes equations, RNG have been used to solve the unsteady, incompressible, viscous turbulent effects. The sliding mesh technique is proposed to resolve the transient flows caused by the started impeller. Combined with the characteristics of the motor, the screw-type centrifugal pump was started by two different way of linear and exponential acceleration. The automatic update of the rotational speed variation of field around the impeller was realized by FLUENT UDF. The transient variation of the pressure at the pump inlet and outlet, the global performance characteristics and the transient flow evolutions were obtained under different start-up modes. The results show that the rapid starting period presents obvious transient effect; the transient head, power curves changing with time reveal the transient attachment head and additional power part. Compared with the linear mode, the transient flow, shaft power, efficiency tend to a steady state value within a relatively short period in setting start time and maintain a quasi-periodic fluctuations.

There is still no animal model available that can mimic all the cognitive, behavioral, biochemical, and histopathological abnormalities observed in patients with Alzheimer's disease (AD). We undertook to consider the interaction between genetic factors, including amyloid precursor protein (APP) and presenilin-1 (PS1), and environmental factors, such as Aluminum (Al) in determining susceptibility outcomes when studying the pathogenesis of AD. In this article, we provide an AD model in APP/PS1 transgenic mice triggered by Al. The animal model was established via intracerebral ventricular microinjection of aluminum chloride once a day for 5 days in APP/PS1 transgenic mice. Twenty wild type (WT) mice and 20 APP/PS1 transgenic (TG) mice were separately divided into 2 groups (control and Al group), and a stainless steel injector with stopper was used for microinjection into the left-lateral cerebral ventricle of each mouse. The Morris water maze task was used to evaluate behavioral function of learning and memory ability on the 20th day after the last injection. This AD model's brain was analyzed by: (1) amyloid β immunohistochemical staining; (2) Tunnel staining; (3) apoptotic rates; (4) caspase-3 gene expression. Here, decrease of cognitive ability and neural cells loss were shown in APP/PS1 transgenic mice exposed to Al, which were more extensive than those in APP/PS1 TG alone and WT mice exposed to Al alone. These findings indicate that there is a close relationship between over-expression of APP and PS1 genes and Al overload. It is also suggested that APP/PS1 TG mice exposed to Al have potential value for improving AD models.

Antibody phage display is a powerful biomolecular selection technology now routinely used for refining antibody diversity towards analytes of both therapeutic and diagnostic interest. Post selection, automated robotic systems can be utilised to pick, express and analyse large numbers of putative analyte-specific clones allowing the parallel screening of thousands of antibodies in less time. Most screening techniques involve a spatial addressing process whereby the selected antibodies are extracted from the cells and analysed to verify specificity. Using a simple 'on-plate' growth and screening approach, we show that antibody-expressing clones can be simultaneously cultured and analysed rapidly in antigen-coated ELISA plate wells yielding high binding signals and saving valuable selection time, while also eliminating the necessity for antibody extraction. The utilisation of the 'on-plate' technique for the screening of Fab and scFv antibodies, and a comparative analysis with commonly used antibody extraction processes, are described.

In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Although several recent studies have demonstrated that a wealth of insights can be gained by integrative analysis of these data, owing to cost, time or sample material availability, it is not always possible for researchers to obtain binding profiles for every proteins in every sample of interest, which considerably limits the power of integrative studies. In this paper, we propose a novel method called Low Rank Convex Co-Embedding (LRCCE) for imputing new ChIP-seq datasets. In LRCCE, a diverse collection of available ChIP-seq data are fused together by mapping proteins, samples, and genomic positions simultaneously into the Euclidean space, thereby making their underling associations directly evaluable using simple calculations. In contrast with previous approaches which mainly use of the local correlations between available datasets, LRCCE can better estimate the overall data structure by formulating the representation learning of all involved entities as a single unified optimization problem. Experimental evaluations on the ENCODE data illustrate the usefulness of the proposed model.

We cloned a dehydrins gene CaDHN1 from pepper and the expression of CaDHN1 was markedly upregulated by cold, salt, osmotic stresses and salicylic acid (SA) treatment. Dehydrins (DHNs) are a subfamily of group 2 late embryogenesis-abundant (LEA) proteins that are thought to play an important role in enhancing abiotic stress tolerance in plants. In this study, a DHN EST (Expressed Sequence Tag) was obtained from 6 to 8 true leaves seedlings of pepper cv P70 (Capsicum annuum L.) by our laboratory. However, the DHN gene in pepper was not well characterized. According to this EST sequence, we isolated a DHN gene, designated as CaDHN1, and investigated the response and expression of this gene under various stresses. Our results indicated that CaDHN1 has the DHN-specific and conserved K- and S- domain and encodes 219 amino acids. Phylogenetic analysis showed that CaDHN1 belonged to the SKn subgroup. Tissue expression profile analysis revealed that CaDH N1 was expressed predominantly in fruits and flowers. The expression of CaDHN1 was markedly upregulated in response to cold, salt, osmotic stresses and salicylic acid (SA) treatment, but no significant change by abscisic acid (ABA) and heavy metals treatment. Loss of function of CaDHN1 using the virus-induced gene silencing (VIGS) technique led to decreased tolerance to cold-, salt- and osmotic-induced stresses. Overall, these results suggest that CaDHN1 plays an important role in regulating the abiotic stress resistance in pepper plants.

The F-box protein family is characterized by an F-box motif that has been shown to play an important role in regulating various developmental processes and stress responses. In this study, a novel F-box-containing gene was isolated from leaves of pepper cultivar P70 (Capsicum annuum L.) and designated CaF-box. The full-length cDNA is 2088 bp and contains an open reading frame of 1914 bp encoding a putative polypeptide of 638 amino acids with a mass of 67.8 kDa. CaF-box was expressed predominantly in stems and seeds, and the transcript was markedly upregulated in response to cold stress, abscisic acid (ABA) and salicylic acid (SA) treatment, and downregulated under osmotic and heavy metal stress. CaF-box expression was dramatically affected by salt stress, and was rapidly increased for the first hour, then sharply decreased thereafter. In order to further assess the role of CaF-box in the defense response to abiotic stress, a loss-of-function experiment in pepper plants was performed using a virus-induced gene silencing (VIGS) technique. Measurement of thiobarbituric acid reactive substances (TBARS) and electrolyte leakage revealed stronger lipid peroxidation and cell death in the CaF-box-silenced plants than in control plants, suggesting CaF-box plays an important role in regulating the defense response to abiotic stress resistance in pepper plants.

In the present paper, silver colloid films prepared by self-assembly method were used as surface-enhanced Raman scattering (SERS) active substrates to achieve trace detection of antibiotics in water. Silver colloids were prepared using the microwave heating method, and silver colloids films were prepared with self-assembly method. The enhancement of sliver colloid films to antibiotics was analysed by changing the pH value of silver colloid and times of films. Significant effects of pH value on silver colloid films were observed. And the silver colloid films with five times, prepared by silver colloids with pH 4 had the best enhancement factor. They were used as SERS active substrates to detect three antibiotics (chloramphenicol, ciprofloxacin, enrofloxacin). The experimental limits of detection were 120, 15, 120 nmol x L(-1), respectively. These results show that such substrate has a very high sensitivity and application value, and might be able to be used for trace detection of antibiotics in aquiculture.

Low temperature is one of the major factors limiting pepper (Capsicum annuum L.) production during winter and early spring in non-tropical regions. Application of exogenous abscisic acid (ABA) effectively alleviates the symptoms of chilling injury, such as wilting and formation of necrotic lesions on pepper leaves; however, the underlying molecular mechanism is not understood. The aim of this study was to identify genes that are differentially up- or downregulated in ABA-pretreated hot pepper seedlings incubated at 6°C for 48 h, using a suppression subtractive hybridization (SSH) method. A total of 235 high-quality ESTs were isolated, clustered and assembled into a collection of 73 unigenes including 18 contigs and 55 singletons. A total of 37 unigenes (50.68%) showed similarities to genes with known functions in the non-redundant database; the other 36 unigenes (49.32%) showed low similarities or unknown functions. Gene ontology analysis revealed that the 37 unigenes could be classified into nine functional categories. The expression profiles of 18 selected genes were analyzed using quantitative RT-PCR; the expression levels of 10 of these genes were at least two-fold higher in the ABA-pretreated seedlings under chilling stress than water-pretreated (control) plants under chilling stress. In contrast, the other eight genes were downregulated in ABA-pretreated seedlings under chilling stress, with expression levels that were one-third or less of the levels observed in control seedlings under chilling stress. These results suggest that ABA can positively and negatively regulate genes in pepper plants under chilling stress.

To study the effect of necrostatin (Nec-1) on apoptosis induced by aluminum (Al), and approach the mechanism.Neural cell death model was made by 4 mmol/L Al treated neuroblastoma cells (SH-SY5Y). Cell viabilities were detected at different concentrations of Al and/or Nec-1. Hoechst 33342/PI double staining was used to observe apoptosis and (or) necrosis that were quantified by flow cytometry using Annexin V/PI double staining. Apoptotic pathway was tested by activities of Caspase-3, Caspase-8 and Caspase-9. In addition, the expression of NF-kappa B and Cyt-c was measured by immunocytochemistry.Cell viabilities were significantly decreased with the increasing concentrations of Al (P0.05), which could be significantly upregulated by 60 micromol/L Nec-1 (P0.05) and were correlated with the concentrations of Nec-1 (P0.05, P0.01). Apoptosis and necrosis were observed under fluorescent microscope and quantified by flow cytometry, which suggested an increasing trend of apoptotic and necrotic rates (P0.05, P0.01). Whereas, Nec-1 could not only decrease the necrotic rate but also apoptotic rate as well (P0.05, P0.01). Data of Nec-1 on caspases activities showed that Nec-1 could not affect Caspase-9 activity (P0.05) and Cty-c protein expression as well (P0.05). However, Nec-1 could reduce Caspase-8 activity significantly (P0.05, P0.01) and increase NF-kappa B protein expression (P0.05, P0.01) and finally decrease Caspase-3 activity (P0.05).Nec-1 could reduce cell apoptosis induced by Al, through Caspase-8 pathway, and up-regulate the expression of NF-kappa B protein.

Nanocrystalline powders of Cu-Zn alloy in size ranging from 10 to 140 nm was prepared from α-Cu-Zn alloy wire containing 39.8 at.% Zn by an electrical explosion method. The particles are identified from x-ray diffraction as a mixture of the α, β, γ, and e phases of Cu-Zn alloy. Most of the particles are hexagonal in shape, with only a small part being spherical and cubic. The composition of Zn in the explosion products varied from 6.9 to 45.2 at.% in different particles as determined by energy dispersive x-ray spectrometer. A possible mechanism for the formation of the alloy nanocrystalline powders is proposed, in which a redistribution process occurred caused by strong collision and diffusion between the two kinds of atoms during the powder formation.

To study the effects of benzo[a]pyrene (B[a]P) on capability of learning and memory and the content of amino acid neurotransmitters in hippocampus of rats.Thirty-two healthy, male SD rats were randomly divided into 4 groups according to their weights after intubated into ventricles: the solvent control group, 2.5, 5.0 and 10.0 mmol/L groups. 10 microl of B[a]P olive oil solutions, of different concentrations 2.5, 5.0 and 10.0 mmol/L, were injected into rats' lateral ventricles, respectively. Rats in the solvent control group were injected into the same volume of olive oil as that in B[a]P group. Rats' capability of learning and memory was tested by Morris water maze. The content of amino acid neurotransmitters in rats' hippocampus were determined by high performance liquid chromatogram with a fluorescence detector.Compared with the controls, the performances of learning and memory of rats decreased significantly in B[a]P treated groups (P0.01). Levels of glutamate (Glu) were lower significantly in treated groups than that in controls (P0.01). No significant differences were found in contents of aspartic acid (Asp), glycine (Gly) and aminobutyric acid (GABA) among the four groups.B[a]P can damage rats' spatial learning and memory, and which could be related to decreased contents of excitatory amino acids in hippocampus.

Although the newly available ChIP-seq data provides immense opportunities for comparative study of regulatory activities across different biological conditions, due to cost, time or sample material availability, it is not always possible for researchers to obtain binding profiles for every protein in every sample of interest, which considerably limits the power of integrative studies. Recently, by leveraging related information from measured data, Ernst et al. proposed ChromImpute for predicting additional ChIP-seq and other types of datasets, it is demonstrated that the imputed signal tracks accurately approximate the experimentally measured signals, and thereby could potentially enhance the power of integrative analysis. Despite the success of ChromImpute, in this paper, we reexamine its learning process, and show that its performance may degrade substantially and sometimes may even fail to output a prediction when the available data is scarce. This limitation could hurt its applicability to important predictive tasks, such as the imputation of TF binding data. To alleviate this problem, we propose a novel method called Local Sensitive Unified Embedding (LSUE) for imputing new ChIP-seq datasets. In LSUE, the ChIP-seq data compendium are fused together by mapping proteins, samples, and genomic positions simultaneously into the Euclidean space, thereby making their underling associations directly evaluable using simple calculations. In contrast to ChromImpute which mainly makes use of the local correlations between available datasets, LSUE can better estimate the overall data structure by formulating the representation learning of all involved entities as a single unified optimization problem. Meanwhile, a novel form of local sensitive low rank regularization is also proposed to further improve the performance of LSUE. Experimental evaluations on the ENCODE TF ChIP-seq data illustrate the performance of the proposed model. The code of LSUE is available at https://github.com/ekffar/LSUE .

To investigate the relationship between the genotypes of hepatitis B virus and the clinical and liver pathological features of patients with chronic hepatitis in the Zhoushan Islands.One hundred eighty HBV DNA positive chronic hepatitis patients with HBV markers were enrolled in this study. They were at least second generation Zhoushan Island residents. One hundred forty-seven of them were males and 33 were females with an average age of 39.0+/-11.3. Among the 180 patients, 17 had ASC, 57 had mild CHB, 48 moderate CHB, 9 severe CHB, 6 SHB, 39 LC, and 4 had HCC. The genotypes of their serum HBV were detected by using PCR integrated with Tagman MGB probe technology, and their serum HBV markers, HBV DNA and liver functions were also examined. Out of 180 patients, 129 accepted a liver biopsy. A pathological evaluation was then performed.HBVs of genotype C, 135 cases (75.0%), of B, 40 cases (22.2%), and of B+C, 5 cases (2.8%) were found among these 180 patients. No genotype A or D HBV were found. The proportions of genotype C virus were 7/17, 86/114, 34/39, 6/6 in ASC, CHB, LC and SHB patients. In the hepatocellular carcinoma patients, there were 2 each of genotype B and C. Among the 99 patients with genotype C HBV, 84 cases (84.8%) showed moderate and severe inflammation histologically in their livers and among the 30 patients with B, 7 cases (23.3%) showed moderate to severe inflammation in their livers (z = 6.47, P less than 0.01). The proportion of genotype C HBV was significantly different from that of genotype B HBV in those that showed moderate and severe (S3-4) liver fibrosis. In patients infected with genotype C HBV who had moderate and severe liver pathological changes, their clinical manifestations reflected better the histological alterations of their livers.Genotypes C, B and B+C HBV were found in CHB patients in the Zhoushan Islands of China, and type C was the predominant one. The liver pathological damage level of genotype C HBV infected patients is more serious than that of genotype B.