Entorhinal cortex grid cells can map to hippocampal place cells by competitive learning

'Grid cells' in the dorsocaudal medial entorhinal cortex (dMEC) are activated when a rat is located at any of the vertices of a grid of equilateral triangles covering the environment. dMEC grid cells have different frequencies and phase offsets. However, cells in the dentate gyrus (DG) and hippocampal area CA3 of the rodent typically display place fields, where individual cells are active over only a single portion of the space. In a model of the hippocampus, we have shown that the connectivity from the entorhinal cortex to the dentate granule cells could allow the dentate granule cells to operate as a competitive network to recode their inputs to produce sparse orthogonal representations, and this includes spatial pattern separation. In this paper we show that the same computational hypothesis can account for the mapping of EC grid cells to dentate place cells. We show that the learning in the competitive network is an important part of the way in which the mapping can be achieved. We further show that incorporation of a short term memory trace into the associative learning can help to produce the relatively broad place fields found in the hippocampus.     

Genetic Parallel Programming: design and implementation

This paper presents a novel Genetic Parallel Programming (GPP) paradigm for evolving parallel programs running on a Multi-Arithmetic-Logic-Unit (Multi-ALU) Processor (MAP). The MAP is a Multiple Instruction-streams, Multiple Data-streams (MIMD), general-purpose register machine that can be implemented on modern Very Large-Scale Integrated Circuits (VLSIs) in order to evaluate genetic programs at high speed. For human programmers, writing parallel programs is more difficult than writing sequential programs. However, experimental results show that GPP evolves parallel programs with less computational effort than that of their sequential counterparts. It creates a new approach to evolving a feasible problem solution in parallel program form and then serializes it into a sequential program if required. The effectiveness and efficiency of GPP are investigated using a suite of 14 well-studied benchmark problems. Experimental results show that GPP speeds up evolution substantially.     

Predicting proteinase specificities from free energy calculations

The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96).     

Efficient biodegradation of naphthalene by a newly characterized indigenous Achromobacter sp. FBHYA2 isolated from Tehran Oil Refinery Complex

A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30 °C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals (aliphatic and aromatic hydrocarbons) was also investigated. No biosurfactant was detected during bacterial growth on any aliphatic/aromatic hydrocarbons. The results of hydrophobicity measurements showed no significant difference between naphthalene- and LB-grown cells. The capability of the strain FBHYA2 to degrade naphthalene completely and rapidly without the need to secrete biosurfactant may make it an ideal candidate to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sites.     

Optimization of the removal of phenol by soybean seed coats using response surface methodology

Peroxidase from soybean seed coats catalyzes the oxidation and polymerization of aromatic compounds in the presence of H(2)O(2). The present study investigated the optimization of the phenol removal from wastewaters by direct using of soybean seed coats that can be extended to large scale, as a cost-effective option in comparison to pure enzyme. A central composite design was used to evaluate the effect of the following factors on the phenol removal: H(2)O(2) concentration (1-40 mmol/L), polyethylene glycol (PEG) concentration (0-1 g/L) and the amount of soybean seed coats (10-60 g/L). The results showed that PEG concentration had no significant effect on phenol conversion. Additionally, by increasing the amount of soybean seed coats, the extent of phenol conversion was increased and a higher concentration of H(2)O(2) was required to reach the maximum phenol conversion. Under optimum conditions for 1 mmol/L initial phenol, 50 g/L soybean seed coats, 14 mmol/L H(2)O(2) and 0.8 g/L PEG, the phenol conversion after 30 min was 78%. After 2 h, the catalyzed process was capable of achieving 90-92% removal of the total phenol from synthetic wastewater. A cubic model was also developed that was verified by predicting some independent experimental results.     

Treatment performance of a constructed wetland during storm and non-storm events in Korea

The efficiency of a free water surface flow constructed wetland (CW) in treating agricultural discharges from stream was investigated during storm and non-storm events between April and December, 2009. Physico-chemical and water quality constituents were monitored at five sampling locations along the flow path of the CW. The greatest reduction in pollutant concentration was observed after passing the sedimentation zone at approximately 4% fractional distance from the inflow. The inflow hydraulic loading, flow rates and pollutant concentrations were significantly higher and variable during storm events than non-storm (baseflow) condition (p <0.001) that resulted to an increase in the average pollutant removal efficiencies by 10 to 35%. The highest removal percentages were attained for phosphate (51 ± 22%), ammonium (44 ± 21%) and phosphorus (38 ± 19%) while nitrate was least effectively retained by the system with only 25 ± 17% removal during non-storm events. The efficiency of the system was most favorable when the temperature was above 15 °C (i.e., almost year-round except the winter months) and during storm events. Overall, the outflow water quality was better than the inflow water quality signifying the potential of the constructed wetland as a treatment system and capability of improving the stream water quality.     

Comparison between a moving bed bioreactor and a fixed bed bioreactor for biological phosphate removal and denitrification

Moving bed bioreactors (MBBR) and fixed bed bioreactors (FBBR) were compared for biological phosphorus removal and denitrification. The sorption denitrification P-elimination (S-DN-P) process was selected for this study. Results indicated that all nutrients were removed by the FBBR process compared with the MBBR process: 19.8% (total COD), 35.5% (filtered COD), 27.6% (BOD(5)), 62.2% (acetate), 78.5% (PO(4)-P), and 54.2% (NO(3)-N) in MBBR; 49.7% (total COD), 54.0% (filtered COD), 63.2% (BOD(5)), 99.6% (acetate), 98.6% (PO(4)-P), and 75.9% (NO(3)-N) in FBBR. The phosphate uptake and NO(3)-N decomposition in the FBBR process during the denitrification phase were much higher than for the MBBR process despite being of shorter duration. Results obtained from this study are helpful in elucidating the practical implications of using MBBR and FBBR for the removal of bio-P and denitrification from wastewater.