Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module

Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.     

Solving the N-Queens problem with a binary Hopfield-type network

The application of a discrete Hopfield-type neural network to solving the NP-Hard optimization problem — the N-Queens Problem (NQP) — is presented. The applied network is binary, and at every moment each neuron potential is equal to either 0 or 1. The network can be implemented in the asynchronous mode as well as in the synchronous one with n parallel running processors. In both cases the convergence rate is up to 100%, and the experimental estimate of the average computational complexity is polynomial. Based on the computer simulation results and the theoretical analysis, the proper network parameters are established. The behaviour of the network is explained.     

Protein binding and stability of norepinephrine in human blood plasma. Involvement of prealbumin, alpha 1-acid glycoprotein and albumin

The binding of norepinephrine (NE) to plasma proteins of fresh human blood obtained from healthy volunteers was studied by ultrafiltration at different NE concentrations and incubation times at 37 degrees C. At 1.7 nM L-[3H]-NE binding was approximately 25%. The binding was rapid and was not influenced by the incubation time. [3H]-NE could be dissociated from its binding sites by acid precipitation and, after HPLC, showed to be unchanged NE. No difference in NE binding was found between plasma collected in EGTA-GSH or heparin solution. There was no degradation of NE when incubated in plasma at 37 degrees C for 10 h, even without the addition of antioxidants. Therefore, in the present study, binding represented interaction of unchanged NE with plasma proteins. The whole plasma binding was saturable over the range of 0.66 nM to 0.59 mM of NE. Scatchard plot of specific binding revealed high-affinity sites with a Kd of 5.4 nM and a Bmax of 3.9 fmoles.mg-1 protein, and low-affinity sites with a Kd of 2.7 microM and a Bmax of 3.3 pmoles.mg-1 protein. Electrophoretic characterization of NE-binding proteins showed that about 60% of bound NE was associated to albumin, and 20% to prealbumin. NE binding to pure human plasma proteins was also studied using ultrafiltration. Scatchard analyses revealed a single class of very high-affinity binding sites for prealbumin (Kd 4.9 nM), a single class of binding sites for alpha 1-acid glycoprotein (Kd 54 microM) and two classes of binding sites for albumin with high (Kd 1.7 microM) and low (Kd 0.8 mM) affinities respectively. The main results obtained in this study - a) reversibility of NE binding, b) stability of free and bound NE in plasma, c) involvement of the prealbumin as a specific binding protein - point out to a specific transport for NE in human blood plasma.     

Modeling the Role of Negative Cooperativity in Metabolic Regulation and Homeostasis

A significant proportion of enzymes display cooperativity in binding ligand molecules, and such effects have an important impact on metabolic regulation. This is easiest to understand in the case of positive cooperativity. Sharp responses to changes in metabolite concentrations can allow organisms to better respond to environmental changes and maintain metabolic homeostasis. However, despite the fact that negative cooperativity is almost as common as positive, it has been harder to imagine what advantages it provides. Here we use computational models to explore the utility of negative cooperativity in one particular context: that of an inhibitor binding to an enzyme. We identify several factors which may contribute, and show that acting together they can make negative cooperativity advantageous.     

Effect of mixing on biogas production during mesophilic anaerobic digestion of screened dairy manure in a pilot plant

The effect of mixing on biogas production of a 1.5‐m³ pilot continuous stirred tank reactor (CSTR) processing screened dairy manure was evaluated. Mixing was carried out by recirculation of reactor content with a mono pump. The experiment was conducted at a controlled temperature of 37±1°C and hydraulic retention times (HRTs) of 20 and 10 days. The effect of continuous and intermittent operation of the recirculation pump on biogas production was studied. At 10 days of HRT, the results showed a minimal influence of recirculation rate on biogas production and that continuous recirculation did not improve reactor performance. At 20 days of HRT, the recirculation rate did not affect reactor performance. Combination of low solid content in feed animal slurry and long HRTs results in minimal mixing requirements for anaerobic digestion.     

Advantages of Task-Specific Multi-Objective Optimisation in Evolutionary Robotics

The application of multi-objective optimisation to evolutionary robotics is receiving increasing attention. A survey of the literature reveals the different possibilities it offers to improve the automatic design of efficient and adaptive robotic systems, and points to the successful demonstrations available for both task-specific and task-agnostic approaches (i.e., with or without reference to the specific design problem to be tackled). However, the advantages of multi-objective approaches over single-objective ones have not been clearly spelled out and experimentally demonstrated. This paper fills this gap for task-specific approaches: starting from well-known results in multi-objective optimisation, we discuss how to tackle commonly recognised problems in evolutionary robotics. In particular, we show that multi-objective optimisation (i) allows evolving a more varied set of behaviours by exploring multiple trade-offs of the objectives to optimise, (ii) supports the evolution of the desired behaviour through the introduction of objectives as proxies, (iii) avoids the premature convergence to local optima possibly introduced by multi-component fitness functions, and (iv) solves the bootstrap problem exploiting ancillary objectives to guide evolution in the early phases. We present an experimental demonstration of these benefits in three different case studies: maze navigation in a single robot domain, flocking in a swarm robotics context, and a strictly collaborative task in collective robotics.     

Renal cortical intermediary metabolism in the recovery phase of postischemic acute renal failure in the dog.

Renal metabolism has been studied in eight dogs before and 48 hr after a 60-min period of renal ischemia induced by clamping the left renal artery with the simultaneous removal of the right kidney, and in 12 sham-operated animals. The study involved the measurement of renal uptake and production of lactate, glutamine, glutamate, alanine, ammonium, and oxygen, and the measurement of the tissue concentrations of ATP, glutamine, lactate, alpha-ketoglutarate, aspartate, and alanine in the renal cortex. Two days after a temporary renal ischemia, the remaining kidney showed a 22% decrease in glomerular filtration rate (GFR) and a 25% decrease in renal plasma flow. Fractional sodium and potassium excretions were similar to those of control dogs. Renal production or extraction of glutamine, glutamate, alanine, ammonium, and oxygen (all expressed by 100 ml of GFR) was not significantly different in basal conditions or 2 days after ischemia, but lactate extraction was reduced in postischemic kidneys (-101 +/- 29 vs -204 +/- 38 mumol/100 ml GFR in control dogs). The cortical concentrations of glutamine and glutamate were lower in postischemic than in control kidneys. No differences were found in cortical concentration of alpha-ketoglutarate, aspartate, lactate, pyruvate, or ATP, but total nucleotides and inorganic phosphate were decreased in postischemic kidneys. It is concluded that in the recovery phase of the ischemia, a decreased lactate uptake is the main metabolic change, and total ATP production is adapted to the decrease of GFR and sodium reabsorption.