Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server

N<inf>2</inf>O reduction during municipal wastewater treatment using a two-sludge SBR system acclimatized with propionate

A two-sludge denitrifying phosphorus removal process (A2N-SBR), acclimatized with propionate, was proposed as an efficient method for nitrous oxide (N2O) reduction during municipal wastewater treatment. Compared with the conventional nitrification-denitrification process (AO-SBR) operated in parallel, the A2N-SBR not only significantly improved total nitrogen and soluble phosphorus removal efficiencies by around 32.3% and 23.5%, respectively, but also greatly reduced N2O generation by around 31.5%. Moreover, like the anoxic stage of AO-SBR, nearly zero N2O (merely 0.054% of the removed nitrogen) was generated during the anoxic stage of A2N-SBR. The substantial N2O reduction achieved in the proposed A2N-SBR can be reasonably explained by: (i) the use of independent nitrification reactor resulting in higher activity of nitrifying bacteria and no occurrence of heterotrophic denitrification in aerobic stage, and (ii) the use of propionate as carbon source decreasing nitrite accumulation in anoxic stage. © 2013 Elsevier B.V

The treatability of trace organic pollutants in WWTP effluent and associated biotoxicity reduction by advanced treatment processes for effluent quality improvement

© 2019 Elsevier Ltd As increasing attention is paid to surface water protection, there has been demand for improvements of domestic wastewater treatment plant (WWTP) effluent. This has led to the application of many different advanced treatment processes (ATPs). In this study, the treatability of trace organic pollutants in secondary effluent (SE) and associated biotoxicity reduction by four types of ATPs, including coagulation, granular activated carbon (GAC) adsorption, ultraviolet (UV) photolysis and photocatalysis, and ozonation, were investigated at the bench-scale. The ATPs showed different removal capacity for the 48 chemicals, which were classified into seven categories. EDCs, herbicides, bactericides and pharmaceuticals were readily degraded, and insecticides, flame retardants, and UV filters were relatively resistant to removal. During these processes, the efficiency of the ATPs in reducing four biological effects were investigated. Of the four biological effects, the estrogenic activity from SE was not detected using the yeast estrogen screen. In contrast with genotoxicity and photosynthesis inhibition, bacterial cytotoxicity posed by SE was the most difficult biological effect to reduce with these ATPs. GAC adsorption and ozonation were the most robust treatment processes for reducing the three detected biotoxicities. UV photolysis and photocatalysis showed comparable efficiencies for the reduction of genotoxicity and photosynthesis inhibition. However, coagulation only performed well in genotoxicity reduction. The effect-based trigger values for the four bioassays, that were derived from the existing environmental quality standards and from HC5 (hazardous concentration for 5% of aquatic organisms), were all used to select and optimize these ATPs for ecological safety. Conducting ATPs in more appropriate ways could eliminate the negative effects of WWTP effluent on receiving water bodies

Enhanced nitrogen removal in constructed wetlands: Effects of dissolved oxygen and step-feeding

Four horizontal subsurface flow constructed wetlands (HSFCWs), named HSFCW1 (three-stage, without step-feeding), HSFCW2 (three-stage, with step-feeding), HSFCW3 (five-stage, without step-feeding) and HSFCW4 (five-stage, with step-feeding) were designed to investigate the effects of dissolved oxygen (DO) and step-feeding on nitrogen removal. High removal of 90.9% COD, 99.1% ammonium nitrogen and 88.1% total nitrogen (TN) were obtained simultaneously in HSFCW4 compared with HSFCW1-3. The excellent TN removal of HSFCW4 was due to artificial aeration provided sufficient DO for nitrification and the favorable anoxic environment created for denitrification. Step-feeding was a crucial factor because it provided sufficient carbon source (high COD: nitrate ratio of 14.3) for the denitrification process. Microbial activities and microbial abundance in HSFCW4 was found to be influenced by DO distribution and step-feeding, and thus improve TN removal. These results suggest that artificial aeration combined with step-feeding could achieve high nitrogen removal in HSFCWs. © 2014 Elsevier Ltd

Effects of interspecific competition on the growth of macrophytes and nutrient removal in constructed wetlands: A comparative assessment of free water surface and horizontal subsurface flow systems

© 2016 Elsevier Ltd. The outcome of competition between adjoining interspecific colonies of Phragmites and Typha in two large field pilot-scale free water surface (FWS) and subsurface flow (SSF) CWs is evaluated. According to findings, the effect of interspecific competition was notable for Phragmites australis, whereby it showed the highest growth performance in both FWS and SSF wetland. In a mixed-culture, P. australis demonstrates superiority in terms of competitive interactions for space between plants. Furthermore, the interspecific competition among planted species seemed to cause different ecological responses of plant species in the two CWs. For example, while relatively high density and shoot height determined the high aboveground dry weight of P. australis in the FWS wetland, this association was not evident in the SSF. Additionally, while plants nutrients uptake accounts for a higher proportion of the nitrogen removal in FWS, that in the SSF accounts for a higher proportion of the phosphorous removal

Regulation of G protein-coupled receptors by palmitoylation and cholesterol

Due to their membrane location, G protein-coupled receptors (GPCRs) are subject to regulation by soluble and integral membrane proteins as well as membrane components, including lipids and sterols. GPCRs also undergo a variety of post-translational modifications, including palmitoylation. A recent article by Zheng et al. in BMC Cell Biology demonstrates cooperative roles for receptor palmitoylation and cholesterol binding in GPCR dimerization and G protein coupling, underlining the complex regulation of these receptors

Laryngeal Reinnervation Using Ansa Cervicalis for Thyroid Surgery-Related Unilateral Vocal Fold Paralysis: A Long-Term Outcome Analysis of 237 Cases

To evaluate the long-term efficacy of delayed laryngeal reinnervation using the main branch of the ansa cervicalis in treatment of unilateral vocal fold paralysis (UVFP) caused by thyroid surgery.UVFP remains a serious complication of thyroid surgery. Up to now, a completely satisfactory surgical treatment of UVFP has been elusive.From Jan. 1996 to Jan. 2008, a total of 237 UVFP patients who underwent ansa cervicalis main branch-to-recurrent laryngeal nerve (RLN) anastomosis were enrolled as UVFP group; another 237 age- and gender-matched normal subjects served as control group. Videostroboscopy, vocal function assessment (acoustic analysis, perceptual evaluation and maximum phonation time), and electromyography were performed preoperatively and postoperatively. The mean follow-up period was 5.2±2.7 years, ranging from 2 to 12 years.>0.05, respectively). Postoperative laryngeal electromyography confirmed successful reinnervation of laryngeal muscle.Delayed laryngeal reinnervation with the main branch of ansa cervicalis is a feasible and effective approach for treatment of thyroid surgery-related UVFP; it can restore the physiological laryngeal phonatory function to the normal or a nearly normal voice quality

Design, synthesis of 4-hydroxyl-α-cyanocinnmaic acid derived compounds and their applications in chiral recognition of amino acids by mass spectrometry

2012-2013 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Effect of straw and polyacrylamide on the stability of land/water ecotone soil and the field implementation

© 2016 Elsevier B.V. Poor stability of land/water ecotone (L/WE) soil is a serious and increasing problem in the context of ecological restoration. Effective management by adding straw and polyacrylamide (PAM), i.e., SPAM, to soil may increase soil stability, including structure and fertility. Thus, it is important to explore the effects of SPAM on L/WE soil, as well as to determine the appropriate ratio of straw and PAM to achieve optimal increases. To investigate the soil properties and provide basis for ecological restoration, an indoor soil culture experiment, including nine straw and PAM combinations, was conducted. It was found that 3 g/kg straw with 1 g/kg PAM was optimal; thus, this scale was applied in engineering of Gonghu L/WE, which was turning Fishery to Lake. The survey explored changes in soil nutrients and structure, dry-sieved aggregate stability, and wet-sieved water aggregate stability under nine measures. Results indicated that the measurement of SPAM strongly affected soil properties, such as improvements in the fine sand and clay fraction, decreased coarse sand fraction and density, and enhanced content of the larger aggregates (>2 mm), organic matter (OM), availabl. e nitrogen (AN), available phosphorus (AP), and available potassium (AK). For soil nutrients, applying of Straw/PAM significantly improved the contents of OM/AN, respectively; showing an increasing trend with a dosage rate. Meanwhile, it was shown that SPAM was more effective than treating each individual component on AP and AK improvements. Regarding soil structure, application of PAM significantly increased contents of the dry-sieved aggregates and wet-sieved water-stable aggregates, especially aggregates >2 mm. Straw mulching only improved the content of dry-sieve medium size aggregates. However, when combining SPAM, the straw improved the medium particle size fraction, after which PAM converted a portion of the medium particles into >2.0 mm aggregates. Furthermore, the measure proved to be beneficial to land/water ecotone engineering