Identify Golgi protein types with modified Mahalanobis discriminant algorithm and pseudo amino acid composition

The Golgi apparatus is an important eukaryotic organelle. Successful prediction of Golgi protein types can provide valuable information for elucidating protein functions involved in various biological processes. In this work, a method is proposed by combining a special mode of pseudo amino acid composition (increment of diversity) with the modified Mahalanobis discriminant for predicting Golgi protein types. The benchmark dataset used to train the predictor thus formed contains 95 Golgi proteins in which none of proteins included has ≥40% pairwise sequence identity to any other. The accuracy obtained by the jackknife test was 74.7%, with the ROC curve of 0.772 in identifying cis-Golgi proteins and trans-Golgi proteins. Subsequently, the method was extended to discriminate cis-Golgi network proteins from cis-Golgi network membrane proteins and trans-Golgi network proteins from trans-Golgi network membrane proteins, respectively. The accuracies thus obtained were 76.1% and 83.7%, respectively. These results indicate that our method may become a useful tool in the relevant areas. As a user-friendly web-server, the predictor is freely accessible at http://immunet.cn/SubGolgi/.     

Optimization of ultrasonic-stimulated solvent extraction of sinigrin from Indian mustard seed (Brassica Juncea L.) using response surface methodology

Introduction – Sinigrin, a major glucosinolate present in Indian mustard (Brassica juncea L.) seeds as the precursor of the anticancer compound allyl isothiocyanate, shows a wide range of biological activities. It's necessary to optimize the extraction methods and conditions, in order to improve the extraction productivity and save raw material. Objective – To systemically investigate and optimize the most important factors affected the productivity of sinigrin in the process of extraction using response surface methodology. Methodology – The ranges of three main factors including the ethanol concentration, extraction time and extraction temperature were selected by the one‐factor‐at‐a‐time method. The conditions of ultrasonic‐stimulated extraction of sinigrin from defatted Indian mustard seed powder were optimized by Box‐Behnken design to obtain the maximum productivity. Result – The predicted productivity (3.81%) was obtained using 57% ethanol concentration at 81°C for 60 min, with the coefficient of the model R² > 0.96 (n = 17). The actual productivity (3.84 ± 0.02%) of sinigrin under the optimized condition was increased by 70.67% compared with the result of conventional extraction. Meanwhile, HPLC, UV and IR were applied to examine if there is a difference between the ultrasonic‐stimulated solvent extraction and conventional extraction, and the improvement of productivity of sinigrin depended on the destruction of cell wall caused by the elimination of outer pectinous material was explained by SEM and composition content analysis. Conclusion – The ultrasonic‐stimulated solvent extraction was suggested to be a promising method to improve the productivity of sinigrin. And the results demonstrated that sinigrin productivity may be related to pectinous materials existed in the seeds. Copyright © 2010 John Wiley & Sons, Ltd.     

Removal of water-borne microorganisms in floating media filter-microfiltration system for water treatment

Floating plastic media pre-filter (PP) in combination with microfiltration membrane (MF) was applied to the removal of water-borne microorganism from surface water. The system was operated with and without coagulant addition. Jar-test results suggested that alum and polyaluminum chloride could effectively remove turbidity, fecal coliforms (FC) and algae at their optimum doses. Nevertheless, none of those coagulants could accomplish high coliphage (CP) removal. Microorganism removal in the system was increasing along with time in the PP unit operated at 5-m³/m²/h filtration rate but opposite trend was observed at higher filtration rates (10-15 m³/m²/h). Different coagulant types and filtration rates employed in the PP unit also affected microorganism removal in MF unit. The operation of PP unit at a filtration rate of 15 m³/m²/h and MF unit at a filtration rate of 0.6 m³/m²/d could achieve satisfactory turbidity and overall microorganism removal.     

Degradation of pentachlorophenol with the presence of fermentable and non-fermentable co-substrates in a microbial fuel cell

Pentachlorophenol (PCP) was more rapidly degraded in acetate and glucose-fed microbial fuel cells (MFCs) than in open circuit controls, with removal rates of 0.12 ± 0.01 mg/Lh (14.8 ± 1.0 mg/g-VSS-h) in acetate-fed, and 0.08 ± 0.01 mg/L h (6.9 ± 0.8 mg/g-VSS-h) in glucose-fed MFCs, at an initial PCP concentration of 15 mg/L. A PCP of 15 mg/L had no effect on power generation from acetate but power production was decreased with glucose. Coulombic balances indicate the predominant product was electricity (16.1 ± 0.3%) in PCP-acetate MFCs, and lactate (19.8 ± 3.3%) in PCP-glucose MFCs. Current generation accelerated the removal of PCP and co-substrates, as well as the degradation products in both PCP-acetate and PCP-glucose reactors. While 2,3,4,5-tetrachlorophenol was present in both reactors, tetrachlorohydroquinone was only found in PCP-acetate MFCs. These results demonstrate PCP degradation and power production were affected by current generation and the type of electron donor provided.     

Acid tolerance of an acid mine drainage bioremediation system based on biological sulfate reduction

The acid tolerance response of an AMD bioremediation system based on sulfate reduction was investigated. Efficient sulfate reduction was observed with a maximum sulfate reduction rate of 12.3±0.8 mg L(-1) d(-1) and easily available organic carbon was released during high acid treatment with an initial pH of 2.0. The rapid increase in sulfate reduction was observed when the extreme acid treatment with an initial pH of 1.0 was stopped. Column experiment on acid shock showed that efficient sulfate reduction was maintained while precipitation of Cu or Zn still occurred during extreme or high acid shock. More than 98% of Cu and 85% of Zn were removed in the high acid column experiment with influent pH of 2.0. The majority bacteria in the remediation system used for high acid drainage belonged to genera Clostridiaceae, Eubacterium, Pseudobutyrivibrio, and Clostridium. These findings showed high acid tolerance of the straw remediation system.     

Identification of novel nuclear protein interactions with the N-terminal part of filamin A

Since certain missense mutations in the N-terminal part of filamin A (FLNA) cause inherited skeletal malformation, we screened for proteins that bind to this part of FLNA. We identified two nuclear proteins that are specifically associated with the N-terminal region of FLNA. This suggests more extensive nuclear function of filamin than expected.     

Biodiesel production from rubber seed oil using poly (sodium acrylate) supporting NaOH as a water-resistant catalyst

Poly (sodium acrylate) supporting NaOH (NaOH/NaPAA) was prepared by in situ polymerization of aqueous solution of acrylic acid with an over-neutralization by adding excess of NaOH. NaOH/NaPAA presented a promising selectivity for water absorbency and good water retention with negligible swelling capacity in the organic solvents of methanol, glycerol, rubber seed oil methyl esters, and rubber seed oil. NaOH/NaPAA catalysts showed a basic strength of 15.0 < H_ < 18.4 and their basicity increased with the increase of the NaOH loading amount. NaOH/NaPAA catalysts exhibited almost the same catalytic activity in the transesterification of rubber seed oil with methanol under the optimized reaction conditions compared to conventional homogeneous NaOH catalyst. Furthermore, the functional absorbent/catalyst system presented a good water resistance in the transesterification which retained high catalytic activity when a water concentration in the reaction system was less than 2 wt.%.     

A cell permeable peptide analog as a potential-specific PET imaging probe for prostate cancer detection

Non-invasive detection of prostate cancer or metastases still remains a challenge in the field of molecular imaging. In our recent work of screening arginine- or lysine-rich peptides for intracellular delivery of a therapeutic agent into prostate cancer cells, an arginine-rich cell permeable peptide (NH₂GR₁₁) was found with an unexpectedly preferential uptake in prostate cancer cell lines. The goal of this work was to develop this peptide as a positron emission tomography (PET) imaging probe for specific detection of distant prostate cancer metastases. The optimal length of arginine-rich peptides was evaluated by the cell uptake efficiency of three fluorescein isothiocyanate (FITC)-tagged oligoarginines (NHGR₉, NHGR₁₁, and NHGR₁₃) in four human prostate cell lines (LNCaP, PZ-HPV-7, DU145, and PC3). Of the three oligoarginines, NH₂GR₁₁ showed the highest cell uptake and internalization efficiency with its subcellular localization in cytosol. The biodistribution of FITC-NHGR₉, FITC-NHGR₁₁, and FITC-NHGR₁₃ performed in control nude mice displayed the unique preferential accumulation of FITC-NHGR₁₁ in the prostate tissue. Further in vivo evaluation of FITC-NHGR₁₁ in PC3 tumor-bearing nude mice revealed elevated uptake of this peptide in tumors as compared to other organs. In vivo pharmacokinetics evaluated with ⁶⁴Cu-labeled NH₂GR₁₁ showed that the peptide was rapidly cleared from the blood (t _1/2 = 10.7 min) and its elimination half-life was 17.2 h. The PET imaging specificity of ⁶⁴Cu-labled NH₂GR₁₁ was demonstrated for the detection of prostate cancer in a comparative imaging experiment using two different human cancer xenograft models.     

Effect of using suboptimal alignments in template-based protein structure prediction

Computational protein structure prediction remains a challenging task in protein bioinformatics. In the recent years, the importance of template-based structure prediction is increasing because of the growing number of protein structures solved by the structural genomics projects. To capitalize the significant efforts and investments paid on the structural genomics projects, it is urgent to establish effective ways to use the solved structures as templates by developing methods for exploiting remotely related proteins that cannot be simply identified by homology. In this work, we examine the effect of using suboptimal alignments in template-based protein structure prediction. We showed that suboptimal alignments are often more accurate than the optimal one, and such accurate suboptimal alignments can occur even at a very low rank of the alignment score. Suboptimal alignments contain a significant number of correct amino acid residue contacts. Moreover, suboptimal alignments can improve template-based models when used as input to Modeller. Finally, we use suboptimal alignments for handling a contact potential in a probabilistic way in a threading program, SUPRB. The probabilistic contacts strategy outperforms the partly thawed approach, which only uses the optimal alignment in defining residue contacts, and also the re-ranking strategy, which uses the contact potential in re-ranking alignments. The comparison with existing methods in the template-recognition test shows that SUPRB is very competitive and outperforms existing methods.     

Synthesis and docking study of 2-phenylaminopyrimidine Abl tyrosine kinase inhibitors

Six analogs of imatinib, an Abl kinase inhibitor clinically used as a first-line therapeutic agent for chronic myeloid leukaemia (CML), have been synthesized and characterized. And their potency as Abl kinase inhibitors have been screened by a robust virtual screening method developed based on the crystal structure (PDB code 2hyy) of Abl-imatinib complex using Surflex-Docking. The docking results are consistent with the inhibitory potency of the compounds characterized by MS method. And the H-bonds between imatinib analogs and Thr315 and Met318 residues in Abl kinase are shown to be crucial for achieving accurate poses and high binding affinities for the ATP-competitive kinase inhibitors.