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Highlights: [•] HLFSS exhibited a richer aromatic profile compared with LSFSS. [•] GC-O analysis of two Chinese soy sauces pointed out 33–37 odourant areas. [•] The individual odourant affects the whole sensory attributes in real food matrix. [ABSTRACT FROM AUTHOR]

Hierarchical ZnO pine needles were successfully fabricated via a novel economical one-step self-assembly synthesis. The influences of the amount of metallic zinc powder added and reaction time on the size and morphology of the ZnO were studied in detail. The gas-sensing performance of the hierarchical ZnO pine needles was observed carefully, and it indicated that the sensor based on hierarchical ZnO pine needles showed a high selectivity, quick response and stability for a long time for ethanol gas. Furthermore, AC impedance spectroscopy of the sensor was also examined at different temperatures and in atmospheres of different gases to understand the gas-sensing mechanism, and the results indicate that the sensor has the lowest potential barrier height for the transition of space charges and the minimum resistance when it is exposed to ethanol gas at 400 °C. [ABSTRACT FROM AUTHOR]

Highlights: [•] Honeycomb Ag/ZnO heterostructures were prepared. [•] It shows rapid photocatalytic activity and excellent chemical stability. [•] BET surface area of the prepared Ag/ZnO heterostructures is 46.7m2/g. [•] The surface state was investigated by XPS. [•] Excellent photocatalytic activity depends on porous structure and heterostructures. [ABSTRACT FROM AUTHOR]

The Fe-doped ZnO with excellent porous features was successfully fabricated via a fast economical solution combustion synthesis. The morphology and the porous nature were characterized by SEM, TEM and BET – N2 adsorption–desorption analysis. The results of XRD Rietveld refinements and Raman spectra demonstrate that the dopant was successfully incorporated into the nanostructure ZnO lattice. The gas-sensing tests show that the sensors based on Zn0.97Fe0.03O have high sensitivity, quick response, excellent selectivity and long-time stability for detecting ethanol vapor. AC impedance spectroscopy and DC electrical conductivity measurements were used to investigate the gas-sensing mechanism, and the results demonstrate that the O− (300–400 °C) on the surface is the most reactive species with ethanol gas. [ABSTRACT FROM AUTHOR]

With the promotion of cold recycled mixture (CRM) in cold areas and the improvement of its application layer, the enhancement of the low-temperature performance of mixtures is particularly important. The applicability of the current low-temperature bending test method to CRM is controversial. Firstly, the low-temperature crack resistance of CRM with different gradations and emulsified asphalt contents was studied by the indirect tensile (IDT) test and the semi-circular bending (SCB) test. Thereafter, the low-temperature performance evaluation index suitable for CRM was put forward. Then, the low-temperature performance of CRM with different gradations, fiber types, and contents was evaluated by using the above low-temperature evaluation index. The results show that the low-temperature performance of CRM with different gradations and emulsified asphalt contents can be distinguished by fracture work (W) and fracture energy (Gf). Not only do the test results have little variability (about 12% and 15%, respectively), but also the correlation coefficient with the new asphalt film thickness is the highest (0.8595 and 0.8939, respectively). Compared with coarse gradation (AC-25) and fine gradation (AC-13), medium-gradation (AC-20) CRM has higher low-temperature performance, and polyester fiber can significantly improve the low-temperature performance of CRM. Compared with non-fiber, the W and Gf of CRM of polyester fiber (0.3% content) can be increased by at least 42% and 30%, respectively. [ABSTRACT FROM AUTHOR]

• A dolerite sill emplaced into the Guanmenshan Formation was dated at ca. 2060 Ma. • The lower part of Fanhe Group was deposited in the span of 2200–2060 Ma in the Rhyacian Period. • The lower part of Fanhe Group provides excellent stratigraphic records of the GOE and LJE in the NCC. The Great Oxidation Event (GOE) and Lomagundi-Jatuli Event (LJE) during Paleoprterozoic Era represent significant global environmental changes in Earth's history and their geological records have been identified from many ancient cratons. However, reliable records of GOE and LJE are rare in the North China Craton (NCC) due to high-grade metamorphism on Paleoproterozoic strata during Orosirian Period and poor age constraints. Weakly metamorphosed to unmetamorphosed Proterozoic strata termed as Fanhe Group of around 8 km thick are well preserved in Fanhe Basin in the Archean Longgang Block in northeastern NCC and the Guanmenshan Formation from the lower part of the Fanhe Group is characterized by positive δ 13C carb excursion of around +5‰. Since the Fanhe Group was usually considered as Meso-Neoproterozoic in ages, the reasons for positive δ 13C carb excursions in the lower Fanhe Group are unclear. Our new LA-(MC-)ICP-MS U-Pb dating on a dolerite sill intruding into the Guanmenshan Formation yields two upper intercept 207Pb/206Pb ages of 2065 ± 20 Ma (95% confidence, MSWD = 1.4, N = 26) and 2062 ± 22 Ma (95% confidence, MSWD = 1.05, N = 22), respectively. Combined with the weighted mean 207Pb/206Pb age of the youngest detrital zircon population of the Daposhan Formation (2199 ± 19 Ma, 95% confidence, N = 8, MSWD = 0.47) and their contact relations, the deposition ages of the Daposhan, Kangzhaungzi, Guanmenshan and Tongjiajie formations from the lower part of Fanhe Group were constrained to be Rhyacian Period from ca. 2200 Ma to ca. 2060 Ma, not Mesoproterozoic Era as previously regarded. These new age constraints provide solid evidence for the existence of weakly metamorphosed stratigraphic records of GOE and LJE in lower part of Fanhe Group in the NCC. Stratigraphic correlations with other ancient cratons show that the Guanmenshan Formation in Fanhe Basin in the northeastern NCC can be correlated with the Dashiling Formation of the Hutuo Group in the central NCC, the Lucknow Formation in West Australia, the Upper Pretoria Formation in South Africa, the Gordon Lake Formation in North America and the Tulomozero and Kuetsjärvi formations in Fennoscandia, and therefore the Fanhe Group provides excellent stratigraphic records to study GOE and LJE in the NCC. [ABSTRACT FROM AUTHOR]

Background: The cytological analysis of bronchoalveolar lavage fluid (BALF) plays an essential role in the differential diagnosis of respiratory diseases. In recent years, deep learning has demonstrated excellent performance in image processing and object recognition.Objectives: We aim to apply deep learning to the automated interpretation and analysis of BALF.Method: Visual images were acquired using an automated biological microscopy platform. We propose a three-step algorithm to automatically interpret BALF cytology based on a convolutional neural network (CNN). The clinical value was evaluated at the patient level.Results: Our model successfully detected most cells in BALF specimens and achieved a sensitivity, precision, and F1 score of over 0.9 for most cell types. In two tests in the clinical context, the algorithm outperformed experienced practitioners.Conclusion: The program can automatically provide the cytological background of BALF and augment clinical decision-making for clinicians. [ABSTRACT FROM AUTHOR]

• The proposed strategy decouples protection and sampling configurations. • The proposed strategy leverages state estimation methods and relay deployments. • The proposed strategy makes full use of state features and relay features. Remedial countermeasures are introduced by communication-assisted protection (CAP) to cope with the impacts of insufficient sampling configurations on distribution network (DN) protection. To promote the flexibility of CAP applications and the robustness of CAP performance, a comprehensive feature recognition-based CAP (C-FRCAP) strategy retaining the advantages of the feature recognition method and the protective relay deployment in fault detection is proposed in this paper. State features are calculated from state estimation methods and adopted as complementary inputs in protective relays. In turn, relay features generated by the protective relays are employed in the process of feature recognition together with the calculated state features. Therefore, both the sampling resources and the protective relay resources are fully utilized. Different fault scenarios are screened to perform fault diagnosis and location. Cases of a general sampling configuration and cases with issues of lack and loss of samplings are investigated to demonstrate that the proposed strategy can flexibly adapt to different sampling conditions and make optimal decisions to mitigate the impacts of sampling issues. [ABSTRACT FROM AUTHOR]

Molasseswastewater contains largeamounts of glucose, and it can provide enough energy for microbial decomposition. The microbial fuel cell (MFC) in this study was demonstrated to be able to treat real wastewater with the benefit of harvesting electricity energy. Efficient operation of this MFC requires a molasses wastewater and preferably an inexpensive anode electrolyte. The results from a batch of experiments showed that molasses wastewater could not only serve as the electron acceptor in anode, but also generate electricity stably. A maximum voltage output of 514.5 mV and a maximum power density of 65.82 mW/m2 were recorded at external resistance of 1,000 Ω. The MFC not only effectively dealt with the molasseswastewater, the chemical oxygen demand removal rate is 81.22%, but also had a significant effect in the processing of analog silver wastewater. At the end of the experiment, after disassembling the device, silver precipitation was found stacked on the cathode carbon paper electrode, and some black sediment was found at the side of the proton membrane anode. [ABSTRACT FROM AUTHOR]

The presence of non-cutaneous vascular lesions in the syndrome of multiple enchondromas and subcutaneous hemangiomas, also named Maffucci syndrome, is exceedingly rare. Until now, non-cutaneous vascular lesions have been described in nine patients, while only three cases were present in the oral cavity; they were found in the tongue in two patients and in the lower lip in one patient. Herein, we report the second case of vascular lesions localized in the mucosa of lower lip in a patient with Maffucci syndrome. Histopathologic examination showed spindle cell hemangioma. [ABSTRACT FROM AUTHOR]

Expression Quantitative Trait Locus (eQTL) analysis is a powerful tool to study the biological mechanisms linking the genotype with gene expression. Such analyses can identify genomic locations where genotypic variants influence the expression of genes, both in close proximity to the variant (cis-eQTL), and on other chromosomes (trans-eQTL). Many traditional eQTL methods are based on a linear regression model. In this study, we propose a novel method by which to identify eQTL associations with information theory and machine learning approaches. Mutual Information (MI) is used to describe the association between genetic marker and gene expression. MI can detect both linear and non-linear associations. What’s more, it can capture the heterogeneity of the population. Advanced feature selection methods, Maximum Relevance Minimum Redundancy (mRMR) and Incremental Feature Selection (IFS), were applied to optimize the selection of the affected genes by the genetic marker. When we applied our method to a study of apoE-deficient mice, it was found that the cis-acting eQTLs are stronger than trans-acting eQTLs but there are more trans-acting eQTLs than cis-acting eQTLs. We compared our results (mRMR.eQTL) with R/qtl, and MatrixEQTL (modelLINEAR and modelANOVA). In female mice, 67.9% of mRMR.eQTL results can be confirmed by at least two other methods while only 14.4% of R/qtl result can be confirmed by at least two other methods. In male mice, 74.1% of mRMR.eQTL results can be confirmed by at least two other methods while only 18.2% of R/qtl result can be confirmed by at least two other methods. Our methods provide a new way to identify the association between genetic markers and gene expression. Our software is available from supporting information. [ABSTRACT FROM AUTHOR]

This article examines the impact of traditional Chinese culture on organ donation from the perspective of Confucianism, Buddhism, and Taoism. In each of these cultural systems, it appears that there are some particular sayings or remarks that are often taken in modern Chinese society to be contrary to organ donation, especially cadaveric organ donation. However, this article argues that the central concerns of Buddhism, Confucianism, and Taoism are “great love,” “ren,” and “dao,” which can be reasonably interpreted to support organ donation. The author understands that each cultural system, in order to play its cultural function, must have its central concerns as well as relevant ritual practices (li) that incarnate its religious and ethical commitments. That is, each plays a general cultural role, which influences organ donation in particular not merely through abstract or general ethical principles and teachings, but through a combination of ethical teachings and the forming of particular ritual practices. This article contends that the primary reason Chinese individuals fail to donate sufficient cadaveric organs for transplantation is not because particular remarks or sayings from each of these systems appear to conflict with donation. Neither is it that the central concerns of these systems cannot support cadaveric donation. Rather, it is that modern Chinese individuals have failed to develop and secure relevant ritual practices that support the central concerns of organ transplantation. The article concludes that in order to promote more donations, there is a need to form relevant ritual practices supporting organ donation in conformity with the central concerns of these cultural systems. [ABSTRACT FROM AUTHOR]

Background: Epithelial cells(EC)-derived interleukin-7 (IL-7) plays a crucial role in control of development and homeostasis of neighboring intraepithelial lymphocytes (IEL), and keratinocyte growth factor (KGF) exerts protective effects on intestinal epithelial cells and up-regulates EC-derived IL-7 expression through KGFR pathway. This study was to further investigate the molecular mechanism involved in the regulation of IL-7 expression by KGF in the intestine. Methods: Intestinal epithelial cells (LoVo cells) and adult C57BL/6J mice were treated with KGF. Epithelial cell proliferation was studied by flow cytometry for BrdU-incorporation and by immunohistochemistry for PCNA staining. Western blot was used to detect the changes of expression of P-Tyr-STAT1, STAT1, and IL-7 by inhibiting STAT1. Alterations of nuclear extracts and total proteins of IRF-1, IRF-2 and IL-7 following IRF-1 and IRF-2 RNA interference with KGF treatment were also measured with western blot. Moreover, IL-7 mRNA expressions were also detected by Real-time PCR and IL-7 protein level in culture supernatants was measured by enzyme linked immunosorbent assay(ELISA). Results: KGF administration significantly increased LoVo cell proliferation and also increased intestinal wet weight, villus height, crypt depth and crypt cell proliferation in mice. KGF treatment led to increased levels of P-Tyr-STAT1, RAPA and AG490 both blocked P-Tyr-STAT1 and IL-7 expression in LoVo cells. IRF-1 and IRF-2 expression in vivo and in vitro were also up-regulated by KGF, and IL-7 expression was decreased after IRF-1 and IRF-2 expression was silenced by interfering RNA, respectively. Conclusion: KGF could up-regulate IL-7 expression through the STAT1/IRF-1, IRF-2 signaling pathway, which is a new insight in potential effects of KGF on the intestinal mucosal immune system. [ABSTRACT FROM AUTHOR]

Abstract: Knowledge of phase equilibria of Fe–Ce–Bi is important for understanding respective effects of rare earth, low melting point elements, e.g. Bi, and the interaction between rare earth and low melting point elements in cast iron. By using a CALPHAD approach, the Ce–Bi binary system was assessed on the basis of reported thermodynamic and phase-equilibrium data and then extrapolated to Fe–Ce–Bi ternary system combined with the Fe–Ce and Fe–Bi binary systems assessed in literatures. Meanwhile, the interfacial reaction between Bi and Fe-45at%–Ce alloy at 773K was investigated to verify the reliability of thermodynamic calculations. It was clearly observed that a reaction layer containing CeBi2, Fe and liquid (Bi) exists in the couple, indicating the reaction path liquid (Bi)/CeBi2+Fe/Fe-45at%–Ce in this couple. The reaction path was further explained using a recently reported model by adopting the thermodynamics assessed herein. [Copyright &y& Elsevier]

Abstract: Background: IgY isolated from egg yolk has been widely used in immunodiagnostic tests, including tests to detect circulating antigen (soluble egg antigen or SEA) of Schistosoma japonicum. Results: A sandwich ELISA was established using a combination of anti-S. japonicum SEA-IgY polyclonal antibodies and IgM monoclonal antibodies. To explore sensitivity and specificity of the sandwich ELISA, serum samples from 43 patients infected with S. japonicum were tested. All acute cases and 91.3% of the chronic cases showed a positive reaction. Only 5% of the control sera from healthy persons gave a positive response. Cross-reactions with antibodies to nine other parasites were rare. Conclusion: The developed immunoassay is reasonably sensitive and specific. It could be used for field research and treatment efficacy assessments. [Copyright &y& Elsevier]

Protein-DNA interaction plays an important role in many biological processes. The classical methods and the novel technologies advanced have been developed for the interaction of protein-DNA. Recent developments of these methods and research achievements have been reviewed in this paper. [ABSTRACT FROM AUTHOR]

OBJECTIVE: To determine the function of Smad ubiquitin regulatory factor 2 (Smurf2) on the development of liver fibrosis and cirrhosis. METHODS: In vivo Smurf2 expression in fibrotic and cirrhotic rat and human liver tissues were measured using reverse transcription-polymerase chain reaction, Western blot (WB) and immunohistochemistry. In vitro Smurf2 levels were determined in LX-2 cell line with or without transforming growth factor (TGF)-β1 treatment; I, III, IV collagen and laminin levels were determined by ELISA. The recombinant plasmid pcDNA3.1-Smurf2 was transfected into LX-2 cells, and WB and ELISA were utilized to analyze the expression of TGF-β receptor type I (TβRI), Smad7, collagens and laminin with or without proteasome inhibitor MG-132. Coimmunoprecipitation was utilized to characterize the interactions among these factors and the ubiquitination levels. pcDNA3.1-Smad7 vector was transfected and subsequent examinations were conducted just as Smurf2. RESULTS: Smurf2 levels were elevated in the early period of fibrotic rat liver and TGF-β1-treated LX-2 cells but were reduced in the cirrhotic livers. Smurf2 overexpression in LX-2 cells reduced TβRI and Smad7 levels, which was accompanied by decreased collagen and laminin levels. Coimmunoprecipitation demonstrated that Smurf2 interacted with TβRI and Smad7, which increased TβRI and Smad7 ubiquitin levels. Smad7 overexpression reduced the TβRI level and was accompanied by decreased collagen and laminin levels. MG-132 could antagonize these effects. CONCLUSION: Smurf2 interacts with Smad7 to suppress TGF-β-mediated liver fibrosis through the ubiquitin-dependent degradation of TβRI during the early period of liver fibrosis. [ABSTRACT FROM AUTHOR]

Endothelial regeneration and dyslipidemia impair endothelium-dependent relaxation, while supplementation with fish oil (FO) prevents it. The genomic impact of different diets was compared in primary cultures derived from native and regenerated endothelial cells. Pigs were fed with high-cholesterol (CHL) or FO-rich diet. Partial in vivo removal of endothelium was performed to induce endothelial regeneration. Native and regenerated cells were harvested, cultured, and prepared for genomic (microarray experiments, real-time PCR) and proteomic (Western blotting) analysis. The analysis identified genomic changes induced by chronic CHL diet in native cultures resembling those induced by in vivo regeneration, as well as those that could be prevented by FO diet. At the protein level, the reduced and increased presences of endothelial nitric oxide synthase and F2, respectively, observed after regeneration combined with CHL diet were alleviated by FO. The comparison of the differential changes induced by regeneration in vivo in endothelial cells from both diet groups revealed a limited number of genes as the most likely contributors to reduction in endothelium-dependent relaxations in porcine coronary arteries lined with regenerated endothelium. [ABSTRACT FROM AUTHOR]

Abstract: Reconstruction of 3D curves from their stereo images is an important issue in computer vision. Based on deformation of the snake model and NURBS representation, we evolve the curve in the view of inverse optimization to finish reconstruction. This manner can reduce the need of matching multi-view space curve projections, meanwhile improve the reconstruction precision. Considering that the 2D data reconstruction exists error inevitably, based on two cameras, a discussion on its influence to stereo reconstruction is given next. Finally, the proposed approach is experimented with artificial and real data, and gains a satisfying reconstruction effect. [Copyright &y& Elsevier]

Cancer is the leading cause of death in the world. Development of minimally invasive biomarkers for early detection of cancer is urgently needed to reduce high morbidity and mortality associated with malignancy. MicroRNAs (miRNAs) are small regulatory RNAs that modulate the activity of specific mRNA targets and play important roles in a wide range of physiologic and pathologic processes. Recently, miRNAs were found to be dysregulated in a variety of diseases including cancer. Emerging evidence suggests that miRNAs are involved in tumor initiation and progression. Together, the different expression profiles of miRNAs in cancer, and the stability of circulating miRNAs, make them new potentially clinical biomarkers for cancer diagnosis, classification, therapeutic decisions, and prognosis. [ABSTRACT FROM AUTHOR]

In the past decade, a number of case–control studies have been carried out to investigate the relationship between the HHEX polymorphism and type 2 diabetes (T2D). However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the HHEX polymorphism and T2D. In total, 22 association studies on two HHEX polymorphisms (rs1111875 and rs7923837) and risk of T2D published before April 2010, including a total of 36 695 T2D cases and 51 800 controls were included. We also explored potential sources of heterogeneity. In a combined analysis, the summary per-allele odds ratio (OR) for T2D of the rs1111875 and rs7923837 polymorphism was 1.17 [95% confidence interval (CI): 1.13–1.21] and 1.23 (95% CI: 1.18–1.28), respectively. The haplotype analysis also showed significant association in the pooled international populations with an OR of 1.19 (95% CI: 1.15–1.22). In the subgroup analysis by ethnicity, significantly increased risks were found in Asians and Caucasians for these polymorphisms in almost all genetic models. Subgroup analysis also showed that ethnicity is the main source of heterogeneity between pooled studies. This meta-analysis demonstrated that the risk allele of HHEX polymorphisms (rs1111875 and rs7923837) is a risk factor for developing T2D. However, additional very large-scale studies are warranted to provide conclusive evidence on the effects of the HHEX gene on risk of T2D. [ABSTRACT FROM AUTHOR]

Abstract: We have fabricated carbon nanoscrolls (CNSs) from monolayer graphene and investigated temperature-dependent Raman scattering of CNSs. Firstly, monolayer graphene prefers to form stacked layers, rather than tubular-like structures. Secondly, Raman signals between CNSs and monolayer graphene are similar, except the ratios between G and 2D peaks’ intensities. Finally, the G and 2D band frequencies downshift with temperature increasing from 303K to 473K. The temperature coefficients for G and 2D bands are – (1.86±0.06)×10−2 cm−1/K and – (3.46±0.28)×10−2 cm−1/K, respectively, which are similar to those of monolayer graphene. Therefore, compared with monolayer graphene, CNSs show similar electronic band structure and different phonon dispersion. [ABSTRACT FROM AUTHOR]

Abstract: Neuropilin-2(Nrp2), which is a nontyrosine kinase transmembrane glycoprotein, can promote angiogenesis and is a poor prognostic factor in some human cancers. In the present study, to explore the expression and potential function of Nrp2 in salivary adenoid cystic carcinoma (SACC), immunohistochemistry was used to examine the Nrp2 expression in 50 SACCs and 20 normal salivary gland tissues nearby SACCs. The result showed that immunoreactivity for Nrp2 was detected in 47 of 50 SACCs, and its expression level had significant correlations with microvessel density, tumor size, TMN clinical stage, vascular invasion, and metastasis (P <0.05) of SACCs. In addition, inhibition of Nrp2 function by the receptor–ligand interaction-blocking antibody decreased cell migration, invasion, and angiogenic promotion without influences on the cell proliferation of Acc-3 cells. Taken together, the expression of Nrp2 protein is significantly correlated with tumor progression and angiogenesis in SACCs. These results suggest that Nrp2 may be a potential therapeutic target for SACCs. [ABSTRACT FROM AUTHOR]

Abstract: Jatropha curcas (Jatropha) is an oil-producing plant with multiple uses, especially the great potential of energy application. Germplasm collection and evaluation are essential for breeding new cultivars with high yield, good quality and wide adaptation. In the present study, we investigated genetic diversity of Chinese Jatropha germplasm by using ISSR markers. A set of 224 accessions including 219 from all the adaptation areas in China and five from Myanmar was adopted. Out of 100 UBC ISSR primers, 15 that had good reproducibility were selected to genotype the population. Among the 169 amplified bands, 127 (75.15%) were polymorphic which meant that Chinese Jatropha had high genetic diversity. Population genetics analysis showed that average Nei’s gene diversity (He) was 0.19, and average Shannon Information Index (I) was 0.292, indicating a relatively high genetic variation in the collections. The dendrogram based on Nei’s genetic distance showed that distinct genetic differentiation occurred in Chinese Jatropha, most of the mainland accessions were clustered into a sub-group (Ia), and accessions from Hainan Island and its neighboring Guangdong province were generally clustered into another sub-group (Ib). A core germplasm collection was established by SCR strategy. This core collection consisted of 46 accessions that accounted 20.54% of the initial collection, and maintained over 90% of observed alleles, polymorphic loci and polymorphism rate. Slight correlation of oil content variation and genetic diversity was observed. Tropical populations are the most important genetic resources and crosses between this tropics and the mainland are recommended for genetic improvement of Jatropha in China. [Copyright &y& Elsevier]

Abstract: The white-rot fungus Pycnoporus sp. SYBC-L1 produced large amount of laccase in submerged fermentation. Two laccase isozymes (LacI and LacII) were purified using (NH4)2SO4 fractionation, DEAE-cellulose and Sephadex G-100 column chromatography. The molecular masses of LacI and Lac II were 55.89 and 63.07kDa, respectively by SDS-PAGE. Both the laccases showed acidic pH optima and high catalytic activities at low temperature for oxidations of 2,6-dimethoxyphenol (DMP), 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonate acid) (ABTS), syringaldazine and guaiacol. LacI and LacII were not only with high cold adaptation, but also fairly stable at high temperature. The half-lives of LacI at 50, 60 and 70°C were 69.31, 2.58 and 0.13h, respectively, whereas LacII was more stable with half-lives of 256.72, 21.00 and 2.06h respectively. The best substrates for the enzymes were both found to be ABTS, in which the K m values of LacI and LacII were 0.0166 and 0.0435mM and the catalytic efficiencies were 19640.36 and 31172.64S−1 mM−1, respectively. EDTA and low concentration of Cu2+ and Mn2+ almost had non-inhibitions on their activities. LacII with syringaldehyde efficiently decolorized Remazol Brilliant Blue R. The high thermostabilities as well as cold adapted properties made Pycnoporus sp. SYBC-L1 laccases to be excellent candidates in harsh industry. [ABSTRACT FROM AUTHOR]

Lysophosphatidic acid (LPA), which is proposed to play an important role in normal physiological situations such as wound healing, vascular tone, vascular integrity and reproduction, may be involved in the etiology of some diseases such as atherosclerosis, cancer, obesity or myocardial infarction. Abnormal findings, including silent brain infarction (SBI), are frequently observed by magnetic resonance imaging (MRI) in patients with nonvalvular atrial fibrillation (NVAF). However, whether there is a relationship between LPA level and the prevalence of SBI has not been extensively studied. In the present study, the association between them was investigated. 235 patients with NVAF, 116 cases of SBI without NVAF and 120 cases of healthy volunteers (control group), who did not receive any antithrombotic therapy, were enrolled in this study. Plasma LPA levels in the NVAF with SBI group were significantly higher than that in the control group (p < 0.01), NVAF without SBI group (p < 0.01) and SBI without NVAF group (p < 0.01). The LPA levels are lower in the control group than in the NVAF without SBI and SBI without NVAF groups (p < 0.01), however, the latter two groups did not significantly differ from each other for LPA levels (p > 0.05) There were significant differences in the positive rate of platelet activation between each of the groups (p < 0.01). The positive rate of platelet activation was significantly higher in the NVAF with SBI group. We suggest that LPA might be a novel marker for estimation of the status of platelet activation and the risk factor for SBI onset in NVAF patients. We expected that plasma LPA levels could predict the occurrence of SBI in NVAF patients. [ABSTRACT FROM AUTHOR]

Ethnopharmacological relevance: Zhen-wu-tang (ZWT) is a blended traditional Chinese medicine specifically used for various kidney diseases. Aim of the study: The present study is to evaluate the effects of ZWT on diabetic nephropathy and investigate the potential anti-diabetic mechanisms. Materials and methods: Streptozotocin (STZ)-induced diabetic rats were orally administrated ZWT (80,320mg/kg b.w.) once a day, for a period of 12 weeks. Body weight, urinary volume, urine protein and blood biochemical parameters were measured every 3 weeks. At the end of the observation period, kidneys were isolated for histology, angiotensin II content determination, real time PCR and Western blot analyses. Results: ZWT (320mg/kg b.w.) prevented body weight loss, reduced polyurea, urinary protein excretion, serum creatinine and blood urea nitrogen, although it did not alter the hyperglycemia. It ameliorated glomerular hypertrophy and expansion of the mesangial area, swell and effacement of foot process. It also suppressed the increased expression of angiotensin II, nephrin and podocin. Conclusions: Data from this study suggest that ZWT possess a protective effect on renal damage of STZ-induced diabetic nephropathy in rats, by suppressing hyperactivity of renal renin–angiotensin system that turns in to modulate renal nephrin and podocin expressions, thereby protecting podocyte from injury. [Copyright &y& Elsevier]

Our previous investigations showed that mobilized endothelial progenitor cells (EPCs) are enriched in non-tumor tissues (NT) surrounding hepatocellular carcinoma (HCC), compared to in tumor tissues (TT). This particular recruitment of EPCs is worth investigating further. The mobilization, recruitment, homing, and incorporation of EPCs into tumors require the participation of multiple factors, including angiogenic factors, adherent molecules, endothelial cells, hypoxic environment, etc. Therefore, we hypothesized that NT might be a hypoxic and highly angiogenic area, into which many more EPCs are recruited and homed. In the last three years, we evaluated the hypoxic condition, angiogenic factors and angiogenic index using frozen tissues or tissue microarrays from 105 patients who had undergone hepatectomy for HCC, and here we review our results and the studies of others. All results showed the expression of Hypoxia-inducible factor-1α was higher in NT than in TT. The expression of VEGFA, bFGF, TGF-β, MCP-1, MMP-9, TIMP-2, and endostatin in NT was significantly higher than in normal liver and TT. Meanwhile, the expression of CD105-the surface marker of activated endothelial cells-was also higher in NT than in TT at the protein and mRNA levels. These investigations showed that NT is a hypoxic and highly angiogenic area, which may be the 'niche' of EPCs. The particular background in HCC may be related to liver cirrhosis. Therefore, non-tumor tissues surrounding HCC may be the 'niche' of endothelial progenitor cells. [ABSTRACT FROM AUTHOR]

A set of simple TLC and HPLC-PDA-MS methods were developed for detection of counterfeit herbal dietary supplements by the qualitative and quantitative analysis of eight phosphodiesterase type 5 inhibitors (PDE5-Is), sildenafil, hongdenafil, homosildenafil, hydroxyhomosildenafil, vardenafil, pseudovardenafil, tadalafil, and aminotadalafil. The analytical approach is simple for rapid screening with TLC and reliable with HPLC-PDA-MS. Good linearity (r2 > 0.999 over the concentration range of 8.1 to 211.2 μg/ml), sensitivity (limits of quantification 0.04-0.09 μg/ml), accuracy (97.03-101.25%), and precision (RSD (%) < 1.32%) were achieved for all analytes. The methods were applied for detection of 36 commercial herbal dietary supplements suspected containing PDE5-Is. In addition, the characteristic MS fragmentations of three main typical structures, sildenafil, vardenafil, and tadalafil, were discussed and summarized, which are very helpful in rapid screening identification and determination of suspected chemicals not claimed in herbal products. Results have demonstrated that established TLC and HPLC-PDA-MS methods are good confirmation and quantification test schemes for the eight target compounds. [ABSTRACT FROM AUTHOR]

Several publications have showed that the number of metastatic lymph node (LN) should be taken into consideration in nodal category of esophageal cancer, but seldom considered extent of involved regional LNs. The aim of this study is to evaluate the significance of the extent of regional LN metastasis on survival in patients with esophageal cancer. A total of 245 thoracic esophageal cancer patients underwent transthoracic esophagectomy with standard lymphadenectomy between January 2000 and December 2006 were included in the study. Data including demographic factors, pathologic findings, LN parameters and survival outcomes were collected. The survival experience was depicted using Kaplan-Meier method. A multivariate Cox proportional hazard model was used to screen the significant prognostic factors. The univariate analysis to further explore the significant prognostic factor was done by log-rank test. After a median follow-up of 53.2 months, the 5-year survival rate was 46.3% for the entire cohort. Cox model regression indicated that the LN status and perigastric nodal status, aside from residual tumor status, histological tumor type and depth of invasion, were the independent prognostic factors. Patients without LN metastasis had better 5-year survival than those with positive nodes (64.2% vs. 18.9%, X2= 35.875, P < 0.001). However, For those patients with nodal involvement, there was no difference in 5-year survival between patients with involved nodes <3 and ≥3 (27.8% vs. 0%, X2= 0.925, P= 0.336). When considering the location of LN metastasis, patients could be further stratified according to whether the perigastric nodes were involved or not (37.5% vs. 10.0%, X2= 4.295, P= 0.038). In conclusion, involved LN number had no prognostic implication in nodal involved patients based on our data. Whereas, perigastric nodal involvement should be used to refine the N category (N0, no nodal metastasis, N1, non-perigastric node metastasis, N2, perigastric node metastasis) for the future esophageal cancer staging criteria. [ABSTRACT FROM AUTHOR]

Background: We investigated the distribution and clinical significance of mobilized endothelial progenitor cells (EPCs) in hepatocellular carcinoma (HCC). We found that many more EPCs were recruited to nonmalignant liver tissue (especially into adjacent non-tumor tissues (AT)) than to tumor vessels. These results suggest that the mechanism underlying the recruitment of EPCs into microvessels in AT merits further investigation Methods: Angiogenic factors were detected in three tissue microarrays comprising normal liver, paired tumor tissue (TT) and AT from 105 patients (who had undergone hepatectomy for HCC) using immunohistochemistry. Also, the number of EPCs (positive for Sca-1, Flk-1 and c-Kit) in the blood and liver of cirrhotic mice were determined by flow cytometry and immunohistochemistry. The distribution of these labeled EPCs in tumor and non-tumor tissues was then studied. Results: The results from the tissue microarrays showed that the expression levels of VEGF-A, bFGF, TGF-β, MCP-1, TSP-1, MMP-9, TIMP-2, and endostatin were significantly higher in AT than in either normal liver or TT (p < 0.05), but no significant difference was found in the expression levels of COX-2 and NOS-2 between AT and TT. The expression of VEGF-A, bFGF, TGF-β, MCP-1, TSP-1, MMP-9, TIMP-2, endostatin, COX-2, and NOS-2 in normal liver tissue was weaker than that in AT or TT. In cirrhotic mice, the number of circulating endothelial progenitor cells gradually increased, before decreasing again. In this mouse model, increased numbers of EPCs were recruited and homed specifically to the cirrhotic liver. Conclusions: Both liver cirrhosis and HCC led to increased expression of pro-angiogenic factors, which resulted in the recruitment of EPCs into AT. Also, EPCs were mobilized, recruited and homed to cirrhotic liver. The unique pathology of HCC coupled with liver cirrhosis may, therefore, be associated with the distribution and function of EPCs. [ABSTRACT FROM AUTHOR]

Abstract: Epithelioid vascular proliferations comprise a wide morphologic spectrum, ranging from reactive hyperplasia via benign tumor to malignant conditions. Epithelioid angiomatous nodule (EAN) is a recently recognized benign vascular proliferation with distinct clinical and pathological features. We review the literature and present six additional EANs in the head and neck examined by immunohistochemistry. This series comprised an equal number of males (n=3) and females (n=3) aged 13–45 years (mean 25.8 years). The sites of origin included the tongue (n=2), skin of the lip (n=2), periorbital and temporal skin (n=1), and nose (n=1). A painless solitary nodule (n=4) was the most common presentation. The lesions were distributed in the epidermis and subcutis, with a characteristic unilobular solid proliferation of polygonal epithelioid endothelial cells with intracytoplasmic primitive lumina. The distinction of EAN from other lesions of the heterogeneous group with epithelioid vascular proliferation can usually be made on the basis of the clinical and morphological features. This series indicates that the distribution of EAN in the head and neck region is not uncommon, which is in contrast to what was initially thought. EAN may be a variant of epithelioid hemangioma. [Copyright &y& Elsevier]

Objective: The objective was to investigate the clinical and radiological characteristics of central giant cell granulomas (CGCGs) of the jaws.Methods: A retrospective analysis of a 20-year database was performed regarding both clinical and radiological features of 22 patients affected with CGCGs of the jaws.Results: Fourteen women and 8 men were included with the age range of 7-81 years (mean 31.7 years). Among the 22 lesions, 16 were located in the mandible and 6 in the maxilla. Painless swelling was the most common clinical feature in 18 of all cases. Limited mouth opening was noted in 2 patients where the lesions involved the condyle. Radiographically, 13 lesions were homogeneously osteolytic and 9 lesions were trabeculated. Fifteen lesions were unilocular and 14 lesions presented with well-defined but not sclerotic margins. CT images in 5 patients clearly showed the trabeculation within the lesions. The follow-up ranged from 1.5 to 11 years with a mean period of 5 years. Three out of 9 aggressive and 1 out of 13 nonaggressive lesions developed recurrence.Conclusions: Diagnosis of CGCGs of the jaws depends on both correct interpretation of clinical, radiographic and pathological data. Differentiation between aggressive and nonaggressive CGCGs should be considered to improve individual treatment planning. [ABSTRACT FROM AUTHOR]

A new natural coumarin, angepubebisin (1), and a new furan, angepubefurin (2), together with the five known compounds, umbelliferone, angelol B (3), ulopterol (4), peucedanol (5), and scopoletin, were isolated from the roots of Angelica pubescens Maxim. f. biserrata Shan et Yuan. The structures of angepubebisin (1) and known compounds were determined by spectroscopic methods, including IR, UV, EI-MS, HR-FTICR-MS, 1D-, and 2D-NMR spectral analyses, and angepubefurin (2) was determined by HR-FTICR-MS and X-ray diffraction analyses. [ABSTRACT FROM AUTHOR]

Abstract: A proliferation-inducing ligand (APRIL) is a novel member of the tumor necrosis factor (TNF) family, which is involved in immune regulation. In this study, the cDNA of dog APRIL (dAPRIL) was amplified from dog spleen by RT-PCR. The open reading frame (ORF) of dAPRIL encodes a protein of 250-amino acid, containing a predicted transmembrane domain and a putative furin protease cleavage site like other mammalian APRILs. The amino acid identities between biologically soluble dAPRIL and its pig, human, rabbit and mouse counterparts are 91%, 86%, 88% and 86%, respectively, dramatically higher than most other known cytokines. The result of real-time PCR revealed that dAPRIL is expressed in various tissues and is elevated in thymus and spleen. Recombinant soluble dAPRIL (dsAPRIL) fused with NusA.tag was efficiently produced in Origami B (DE3) pLysS expression host strain. In vitro, purified dsAPRIL was able to co-stimulate the proliferation of dog splenic B cells in response to anti-IgM. These findings indicate that dAPRIL plays an important role in survival/proliferation of dog B cells and provide the basis for investigation on the roles of APRIL in this important domestic species. [Copyright &y& Elsevier]

Summary: A new hypocrellin A-producing strain, Shiraia sp. SUPER-H168, was isolated from tissues of bamboo, Brachystachyum densiflorum. The morphology of this strain was characterized with a light microscope and a scanning electronic microscope. The mycelia, conidia, pycnidia of fungus were observed. Small pycnidia (10–20μm in length) full of small conidia appeared on the mycelia, which were first reported in this study. The 18S rDNA region of this strain was amplified and sequenced. Then a neighbor-joining tree of 18S rDNA was constructed. According to the result of analysis, the strain SUPER-H168 was proved to belong to the genus Shiraia. Hypocrellin A was produced by solid-state fermentation, extracted by acetone, isolated by preparative RP-HPLC, and identified by RP-HPLC, ESI-MS and ultraviolet–visible absorbing scanning with diode array detection. The HA production could reach 2.02mg/g dry solid substrate. [Copyright &y& Elsevier]

ZnO nanoflowers (NFs) and silver-decorated ZnO (Ag@ZnO) NFs arrays were prepared by two/three-step progress of magnetron sputtering, hydrothermal and magnetron sputtering method, respectively. The effect of silver nanoparticles (NPs) on the visible emission performance of ZnO arrays was described. The results show that the ultraviolet emission (UVE) peak of ZnO NFs array is concentrated at 380 nm red-shifted to longer wavelength after being decorated with Ag NPs in the diameter of 18–50 nm. It is very interesting that the intensity of the visible emission (VE) is enhanced by the VE ratio of 1.43 for the Ag@ZnO NFs arrays of 0.03 mol/L. However, for the Ag@ZnO NFs arrays of 0.015 mol/L, the UVE peak blue shift from 387 nm to 384 nm, indicating a slight decrease in emission intensity due to the decorating Ag NPs of 10–20 nm. The enhancement of VE is considered as the synergistic effect of competition between the increase of exciton concentration and the enhancement of Ag NPs local field. The Z-scan measurement of the opening was performed at 800 nm, revealing the contribution of metal NPs. Ag@ZnO NFs arrays with remarkable nonlinear optical properties are a potential nanomaterial for the development of multifunctional optoelectronic devices. • The Ag@ZnO NFs arrays were designed by two-step HT-MS categories. • The influence of the morphology of Ag NPs and ZnO on PL characteristics has been studied. • The contribution of Ag NPs to the ultrafast NA of the Ag@ZnO NFs was discussed. [ABSTRACT FROM AUTHOR]

Estuarine sediments are crucial repositories and incubators of molybdenum (Mo) during its transport from rivers to the ocean. Here, Mo mobility and related processes in estuarine sediments were explored using high-resolution dialysis (HR-Peeper) and diffusive gradients in thin films (DGT) techniques. Better correlations were observed between dissolved Mn and Mo than between dissolved Fe and Mo, implying that Mn geochemistry plays a key role in dissolved Mo mobility via molybdate adsorption onto abundant Mn oxides and its substantial release upon intense Mn reduction. As a result, oxic intertidal sediments functioned as Mo sinks, and anoxic subtidal sediments functioned as Mo sources. The opposite vertical distributions between DGT-Labile S and DGT-Labile Mo indicated that the availability of labile Mo can be blocked by aqueous sulfide. However, the corresponding high concentrations of DGT-Labile S and dissolved Mo at subtidal sites demonstrated that the abundant dissolved Mo remobilized via Mn reduction was not effectively solidified by sulfide. Simulation with the DIFS model further verified that redox conditions and induced physicochemical processes are crucial factors controlling Mo mobility, with relatively low dissolved Mo concentrations but an adequate and steady resupply capacity of the bioavailable molybdate in intertidal sediments. [Display omitted] • High-resolution distributions of mobile Mo in estuarine sediments are determined. • Geochemistry of Mn dominates dissolved Mo mobility, while S controls DGT-Labile Mo. • Inter- and subtidal sediments are dissolved Mo sinks and sources, respectively. • Intertidal sediments provide a steady resupply capacity of labile Mo in sediments. [ABSTRACT FROM AUTHOR]

Abstract: Glutathione (GSH), as the major small-molecule antioxidant in cells, has been implicated in the regulation of cell proliferation and apoptosis. Salvicine (SAL), a novel diterpenoid quinone compound, exhibits potent antitumor activities both in vitro and in vivo by poisoning topoisomerase II (Topo II) and has entered Phase II clinical trials for cancer therapy. Herein, we provide further evidence that SAL-induced DNA double-strand breaks (DSBs) and apoptosis by GSH depletion drives H2O2 generation and Topo II inhibition. Our data reveal that treatment with SAL results in a pronounced increase in intracellular H2O2 and is accompanied by the occurrence of DNA DSBs and apoptosis in epithelial HeLa cells. Furthermore, SAL was also noted to trigger a dramatic depletion of intracellular GSH via its direct reaction with GSH. Importantly, the introduction of GSH and overexpression of catalase antagonized SAL-mediated DNA DSBs and apoptosis, and the GSH synthesis inhibitor dl-buthionine-[S,R]-sulfoximine reduced SAL-mediated H2O2 generation, indicating that SAL-mediated H2O2 generation is derived from intracellular GSH depletion. Notably, SAL-mediated Topo II inhibition was also concentration-dependently reversed by GSH. Furthermore, we found that Topo II-defective HL-60/MX2 cells were almost completely resistant to SAL-induced DNA DSBs, suggesting that, in addition to its direct inhibitory effect on Topo II, SAL-mediated H2O2 generation may also trigger DNA DSBs via poisoning of Topo II. All these findings together suggest that GSH-depletion-driven H2O2 generation and Topo II inhibition are both critical for SAL-induced DNA DSBs and apoptosis. [Copyright &y& Elsevier]

Point-of-care testing (POCT) demands for rapidly obtaining test results by means of portable analytical instruments and auxiliary reagents at the sampling site. It's important for tumor marker to be recognized and detected in early clinical diagnosis. Many studies focused on producing small portable devices that would allow fast, accurate, and on-site detection. This study aimed to report a magnetic quantitative lateral flow immunoassay (LFIA) system based on poly (acrylic acid) (PAA)-modified gold magnetic nanoparticles (PGMNs) for detecting prostate-specific antigen (PSA) qualitatively and quantitatively. The result was easily achievable with a portable magnetic reader within 15 min. Under optimal conditions, as low as 0.17 ng/mL PSA could be detected. The method was validated using a well-established Solin electrochemiluminescence immunoassay and showed high consistency in detecting 84 serum samples (R 2 = 0.98). The quantitative LFIA based on PGMNs established in this study was proven to be rapid, accurate, sensitive, and inexpensive. As a POCT, it can be potentially developed for the quantitative diagnosis of other disease-related protein biomarkers. [Display omitted] • The detection of Prostate-specific antigen (PSA) can be completed within 15 min. • As low as 0.17 ng/mL PSA could be detected with high accuracy and specificity. • This detection system can be extended for any desired protein markers. [ABSTRACT FROM AUTHOR]

Abstract: Methionine aminopeptidase and N-terminal acetyltransferase are two enzymes that contribute most to the N-terminal acetylation, which has long been recognized as a frequent and important kind of co-translational modifications [R.A. Bradshaw, W.W. Brickey, K.W. Walker, N-terminal processing: the methionine aminopeptidase and N alpha-acetyl transferase families, Trends Biochem. Sci. 23 (1998) 263–267]. The combined action of these two enzymes leads to two types of N-terminal acetylated proteins that are with/without the initiator methionine after the N-terminal acetylation. To accurately predict these two types of N-terminal acetylation, a new method based on feature selection has been developed. 1047 N-terminal acetylated and non-acetylated decapeptides retrieved from Swiss-Prot database (http://cn.expasy.org) are encoded into feature vectors by amino acid properties collected in Amino Acid Index database (http://www.genome.jp/aaindex). The Maximum Relevance Minimum Redundancy method (mRMR) combining with Incremental Feature Selection (IFS) and Feature Forward Selection (FFS) is then applied to extract informative features. Nearest Neighbor Algorithm (NNA) is used to build prediction models. Tested by Jackknife Cross-Validation, the correct rate of predictors reach 91.34% and 75.49% for each type, which are both better than that of 84.41% and 62.99% acquired by using motif methods [S. Huang, R.C. Elliott, P.S. Liu, R.K. Koduri, J.L. Weickmann, J.H. Lee, L.C. Blair, P. Ghosh-Dastidar, R.A. Bradshaw, K.M. Bryan, et al., Specificity of cotranslational amino-terminal processing of proteins in yeast, Biochemistry 26 (1987) 8242–8246; R. Yamada, R.A. Bradshaw, Rat liver polysome N alpha-acetyltransferase: substrate specificity, Biochemistry 30 (1991) 1017–1021]. Furthermore, the analysis of the informative features indicates that at least six downstream residues might have effect on the rules that guide the N-terminal acetylation, besides the penultimate residue. The software is available upon request. [Copyright &y& Elsevier]

Abstract: Terpenoids serve as both constitutive and inducible defense chemicals in many plant species, and volatile terpenes participate in plant a indirect defense by attracting natural enemies of the herbivores. The rice (Oryza sativa L.) genome contains about 50 genes encoding putative terpene synthases (TPSs). Here we report that two of the rice sesquiterpene synthase genes, OsTPS3 and OsTPS13, encode (E)-β-caryophyllene synthase and (E,E)-farnesol synthase, respectively. In vitro, the recombinant protein of OsTPS3 catalyzed formation of (E)-β-caryophyllene and several other sesquiterpenes, including β-elemene and α-humulene, all being components of inducible volatiles of rice plants. The transcript levels of OsTPS3 exhibit a circadian rhythm of fluctuation, and its expression was also greatly induced by methyl jasmonate (MeJA). In addition, expression of OsTPS3 in transgenic plants of Arabidopsis thaliana resulted in emitting high quantities of OsTPS3 products. We also overexpressed OsTPS3 in rice plants which then produced more (E)-β-caryophyllene after MeJA treatment. Finally, we found that the MeJA-treated transgenic rice plants attracted more parasitoid wasps of Anagrus nilaparvatae than the wild-type. These results demonstrate that OsTPS3, an enzyme catalyzing the formation of volatile sesquiterpenes, plays a role in indirect defense of rice plants. [Copyright &y& Elsevier]

Abstract: Transcription factor binds to sequence specific sites in regulatory region to control nearby gene’s expression. It is termed as the major regulator of transcription. However, identifying DNA binding preference of transcription factors systematically is still a challenge. By using the nearest neighbor algorithm, a novel computational approach was developed to predict transcription factor DNA binding preference based on the gene ontology [M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, G. Sherlock, Gene Ontology: tool for the unification of biology, Nat. Genet. 25 (2000) 25–29.] and 0/1 encoding system of nucleotide. The overall success rate of Jackknife cross-validation test for our predictor reaches 76.6%, which indicates the DNA binding preference is closely correlated with its biological functions and computational method developed in this contribution could be a powerful tool to investigate transcription factor DNA binding preference, especially for those novel transcription factors with little prior knowledge on its DNA binding preference. [Copyright &y& Elsevier]

Abstract: The tetrapeptide Bz-Arg-Gly-Asp-Ser-NH2 (Bz-RGDS-NH2) was successfully synthesized by a combination of chemical and enzymatic methods in this study. Firstly, the precursor tripeptide Gly-Asp-Ser-NH2 (GDS-NH2) was synthesized by a novel chemical method in four steps including chloroacetylation of l-aspartic acid, synthesis of chloroacetyl l-aspartic acid anhydride, the synthesis of ClCH2COAsp-SerOMe and ammonolysis of ClCH2COAsp-SerOMe. Secondly, lipase (PPL) was used to catalyze the formation of Bz-RGDS-NH2 in aqueous water-miscible organic cosolvent systems using Bz-Arg-OEt as the acyl donor and GDS-NH2 as the nucleophile. The optimum conditions were Bz-Arg-OEt 50mM; GDS-NH2 400mM; 10°C, 0.1M phosphate buffer, pH 7.5; 60% DMF or 58% DMSO, PPL: 10mgml−1 with the maximum yields of the tetrapeptide of 73.6% for DMF and 70.4% for DMSO, respectively. The secondary hydrolysis of the tetrapeptide product did not take place due to the absence of amidase activity of lipase. [Copyright &y& Elsevier]

Abstract: The tetrapeptide Bz–Arg–Gly–Asp–Ser–NH2 (Bz–RGDS–NH2) as a precursor of cellular adhesion motif of RGDS was synthesized by a combination of chemical and enzymatic methods in this study for the first time. First of all, the precursor tripeptide Gly–Asp–Ser–NH2 (GDS–NH2) was synthesized by a novel chemical method in four steps including chloroacetylation of l-aspartic acid, synthesis of chloroacetyl l-aspartic acid anhydride, synthesis of ClCH2COAsp–SerOMe and ammonolysis of ClCH2COAsp–SerOMe. Secondly, trypsin-catalyzed synthesis of Bz–RGDS–NH2 using Bz–Arg–OEt (Bz–R–OEt) as the acyl donor and GDS–NH2 as the nucleophile under kinetic control in low-water organic media was carried out. The reaction conditions optimized are pH 8.0, 30°C, 14h, in ethanol/Tris–HCl buffer system (97:3, v/v). The yield of Bz–RGDS–NH2 is 68.3±1.74% for pre-treated trypsin prepared by dissolving trypsin powder in 0.1M Tris–HCl buffer (pH 8.0) and lyophilizing for 24h in a freeze-drier with −55°C, 4×10−4–1×10−2 mbar. Compared to trypsin powder, pre-treated trypsin (pH memory) displays higher catalytic activity and stability in low-water organic media, the yield at pH 8.0 increased by 7%. The secondary hydrolysis of the tetrapeptide product did not take place in this low-water organic medium. [Copyright &y& Elsevier]

Abstract: To understand the transcriptional regulatory mechanism, it is indispensable to identify transcription factors (TF) from the whole genome and to classify transcription factors into different classes. New computational approaches have been developed to identify TFs/non-TFs, and furthermore to classify TFs into four different classes, based on the protein functional domain composition [K.C. Chou, Y.D. Cai, Using functional domain composition and support vector machines for prediction of protein subcellular location, J. Biol. Chem. 277 (2002) 45765–45769]. We trained and tested our method on a non-redundancy dataset consisting of 74 transcription factors collected from TRANSFAC v7.0 [V. Matys, O.V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, N. Voss, P. Stegmaier, B. Lewicki-Potapov, H. Saxel, A.E. Kel, E. Wingender, TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes, Nucleic Acids Res. 34 (2006) D108–D110] and 1558 non-transcription factors from UniProtKB/Swiss-Prot Release 49.3 of 21-Mar-2006. The overall success rates of jackknife cross-validation tests reached 98.4% for TF/non-TF identification and 97.2% for classifications of TF classes: basic domains, zinc-coordinating DNA-binding domains, helix-turn-helix, and β-scaffold factors. [Copyright &y& Elsevier]

Abstract: A method of modified integrated pulsed amperometric detection with multicycle step waveform (Multi-IPAD) following high-performance liquid chromatography (HPLC) was applied for the determination of tetracyclines (TCs) including dimethyltetracycline (DMTC), oxytetracycline (OTC) and tetracycline (TC). The key advantages of the Multi-IPAD are the abilities to enhance sensitivity and reproducibility and the ability to keep working electrode clean through the use of a high-frequent waveform alteration in integration step and the use of a cleaning potential, which is quite different from conventional three-step potential waveform. The analyses were carried out using the mobile phase of acetonitrile–water mixture solution (10:90, v/v) containing 1% perchloric acid on a C18 column at a flow rate of 0.21mL/min. The IPAD waveform parameters were optimized to maximize the signal-to-noise ratio (S/N) and successfully applied for the sensitive detection of TCs. The detection limits (S/N=3, 20μL injected) were 0.07mg/L for DMTC, 0.08mg/L for OTC and 0.05mg/L for TC. The peak height relative standard deviations (RSDs) of every compound for replicate injection (n =15) determined were below 4.6%. [Copyright &y& Elsevier]

Abstract: Given the sequence of a protein, how can we predict whether it is a membrane protein or non-membrane protein? If it is, what membrane protein type it belongs to? Since these questions are closely relevant to the function of an uncharacterized protein, their importance is self-evident. Particularly, with the explosion of protein sequences entering into databanks and the relatively much slower progress in using biochemical experiments to determine their functions, it is highly desired to develop an automated method that can be used to give a fast answers to these questions. By hybridizing the functional domain (FunD) and pseudo-amino acid composition (PseAA), a new strategy called FunD–PseAA predictor was introduced. To test the power of the predictor, a highly non-homologous data set was constructed where none of proteins has ⩾25% sequence identity to any other. The overall success rates obtained with the FunD–PseAA predictor on such a data set by the jackknife cross-validation test was 85% for the case in identifying membrane protein and non-membrane protein, and 91% in identifying the membrane protein type among the following 5 categories: (1) type-1 membrane protein, (2) type-2 membrane protein, (3) multipass transmembrane protein, (4) lipid chain-anchored membrane protein, and (5) GPI-anchored membrane protein. These rates are much higher than those obtained by the other methods on the same stringent data set, indicating that the FunD–PseAA predictor may become a useful high throughput tool in bioinformatics and proteomics. [Copyright &y& Elsevier]

Abstract: Regulating most physiological processes by controlling the activation, synthesis, and turnover of proteins, proteases play pivotal regulatory roles in conception, birth, digestion, growth, maturation, ageing, and death of all organisms. Different types of proteases have different functions and biological processes. Therefore, it is important for both basic research and drug discovery to consider the following two problems. (1) Given the sequence of a protein, can we identify whether it is a protease or non-protease? (2) If it is, what protease type does it belong to? Although the two problems can be solved by various experimental means, it is both time-consuming and costly to do so. The avalanche of protein sequences generated in the post-genetic era has challenged us to develop an automated method for making a fast and reliable identification. By hybridizing the functional domain composition and pseudo-amino acid composition, we have introduced a new method called “FunD-PseAA predictor” that is operated in a hybridization space. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has ⩾25% sequence identity to any other. The overall success rate thus obtained by the jackknife cross-validation test in identifying protease and non-protease was 92.95%, and that in identifying the protease type was 94.75% among the following six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Demonstration was also made on an independent dataset, and the corresponding overall success rates were 98.36% and 97.11%, respectively, suggesting the FunD-PseAA predictor is very powerful and may become a useful tool in bioinformatics and proteomics. [Copyright &y& Elsevier]

Abstract: Prediction of protein classification is an important topic in molecular biology. This is because it is able to not only provide useful information from the viewpoint of structure itself, but also greatly stimulate the characterization of many other features of proteins that may be closely correlated with their biological functions. In this paper, the LogitBoost, one of the boosting algorithms developed recently, is introduced for predicting protein structural classes. It performs classification using a regression scheme as the base learner, which can handle multi-class problems and is particularly superior in coping with noisy data. It was demonstrated that the LogitBoost outperformed the support vector machines in predicting the structural classes for a given dataset, indicating that the new classifier is very promising. It is anticipated that the power in predicting protein structural classes as well as many other bio-macromolecular attributes will be further strengthened if the LogitBoost and some other existing algorithms can be effectively complemented with each other. [Copyright &y& Elsevier]