Modeling technique for optimal recovery of immiscible light hydrocarbons as free product from contaminated aquifer

Contamination sites associated with light non-aqueous phase liquids {LNAPL) are numerous and represent difficult cleanup problems. Remediation methods for cleanup of LNAPL fluids in subsurface systems are continuously evolving with the development of various technologies for pump.-and~treat, soil venting, and in-situ bioremediation. Evaluating the effectiveness of remediation techniques as well as attempting to improve their efficiency has been a focus of many researchers, These efforts have included the development of computer simulation models to predict and analyze the fluid movement, entrapment, and mobilization of three~phase systems in porous media. The capability of computer models that not only simulate but optimize remediation processes are in great need. Simulation/optimization (S/0) models allow engineers to optimize processes and to make cost-effective design and management decisions when evaluating remediation strategies. An innovative approach is presented to optimize pumping to immobilize and recover the free product of a floating contaminant consisting of LNAPL\u27s. This determines the best pumping strategy to capture and remove the free oil product not left behind as residual oil. The approach combines detailed simulation, statistical analysis, and operations research optimization. This modeling technique derives regression equations describing system response to unit pumping stimuli. The statistical approach develops regression equations that represent free oil area within the system versus pumping. These equations are derived for multiple time steps and used in the S/0 model to determine the optimized pumping rates required to minimize free oil area and entrapped oil while maximizing free oil recovery and immobilizing the plume via a pump and oil recovery system. When compared with standard simulation techniques, this approach can save substantial computational time and improve remediation strategy design. Utilized is a modified version of US/REMAX, a linear or nonlinear simulation/optimization (S/0) model. US/REMAX can be used to analyze and optimize a variety of groundwater management problems. The modified version incorporates system responses generated externally using ARMOS plus regression analysis. ARMOS is a Z~D areal multiphase flow model. It has the capability of simulating spill, leakage, redistribution, or recovery of LNAPL materials. Application to a representative field problem illustrates the S/O model utility for problem analysis and remediation design. Potential applications of such an S/0 model are numerous providing optimized strategies for recovery of LNAPL spills

X-ray Structures of the Signal Recognition Particle Receptor Reveal Targeting Cycle Intermediates

The signal recognition particle (SRP) and its conjugate receptor (SR) mediate cotranslational targeting of a subclass of proteins destined for secretion to the endoplasmic reticulum membrane in eukaryotes or to the plasma membrane in prokaryotes. Conserved active site residues in the GTPase domains of both SRP and SR mediate discrete conformational changes during formation and dissociation of the SRP·SR complex. Here, we describe structures of the prokaryotic SR, FtsY, as an apo protein and in two different complexes with a non-hydrolysable GTP analog (GMPPNP). These structures reveal intermediate conformations of FtsY containing GMPPNP and explain how the conserved active site residues position the nucleotide into a non-catalytic conformation. The basis for the lower specificity of binding of nucleotide in FtsY prior to heterodimerization with the SRP conjugate Ffh is also shown. We propose that these structural changes represent discrete conformational states assumed by FtsY during targeting complex formation and dissociation

S/O Modeling Technique for Optimal Containment of Light Hydrocarbons in Contaminated Unconfined Aquifers

An innovative approach is presented to minimize pumping for immobilizing a floating plume of a light non-aqueous phase liquid (LNAPL). The best pumping strategy is determined to contain the free oil product and provide for gradient control of the water table. This approach combined detailed simulation, statistical analysis, and optimization. This modeling technique uses regression equations that describe system response to variable pumping stimuli. The regression equations were developed from analysis of systematically performed simulations of multiphase flow in an areal region of an unconfined aquifer. Simulations were performed using ARMOS, a finite element model. ARMOS can be used simulate a spill, leakage from subsurface storage facilities and recovery of hydrocarbons from trenches or pumping wells to design remediation schemes. Two gradient control points were located inside the area of the symmetric floating plume. Air-oil interface drawdowns with respect to water pumping rates were taken from ARMOS simulations at the two locations. These drawdowns were used to calculate elevation changes in air-oil table elevations (Zao) between the control points. These elevation changes of Zao between Points #1 and #2 versus pumping were plotted and fitted by statistical regression analysis for a pumping range of 150m3/day to 240m3/day. The resulting regression equation was used to represent system response to pumping in the simulation/optimization (S/0) model called Utah State Model for Optimizing Management of Stream/ Aquifer Systems Using the Response Matrix Method (US!REMAX). The containment problem was then optimized by US/REMAX to determine the minimum pumping rate required to reverse the water table gradient and immobilize the floating plume. Once regression equations are developed the optimal pumping state for alternative containment goals and scenarios can be quickly determined. A range of gradient control values can be easily evaluated to determine minimized pumping rates. Then, their impacts can be compared between alternatives for minimum pumping versus time to containment, residual or trapped oil volumes, and free oil area at containment time

The role of lysine-256 in the structure and function of sheep liver recombinant serine hydroxymethyltransferase

The active site lysine residue, K256, involved in Schiffs base linkage with pyridoxal-5'-phosphate (PEP) in sheep liver recombinant serine hydroxymethyltransferase (rSHMT) was changed to glutamine or arginine by site-directed mutagenesis. The purified K256Q and K256R SHMTs had less than 0.1% of catalytic activity with serine and H(4)folate as substrates compared to rSHMT. The mutant enzymes also failed to exhibit the characteristic visible absorbance spectrum (lambda(max) 425 nm) and did not produce the quinonoid intermediate (lambda(max) 495 nm) upon the addition of glycine and H(4)folate. The mutant enzymes were unable to catalyze aldol cleavage of beta-phenylserine and transamination of D-alanine. These results suggested that the mutation of the lysine had resulted in the inability of the enzyme to bind to the cofactor. Therefore, the K256Q SHMT was isolated as a dimer and the K256R SHMT as a mixture of dimers and tetramers which were converted to dimers slowly. On the other hand, rSHMT was stable as a tetramer for several months, further confirming the role of PLP in maintenance of oligomeric structure. The mutant enzymes also failed to exhibit the increased thermal stability upon the addition of serine, normally observed with rSHMT. The enhanced thermal stability has been attributed to a change in conformation of the enzyme from open to closed form leading to reaction specificity. The mutant enzymes were unable to undergo this conformational change probably because of the absence of bound cofactor

Assembly of physalis mottle virus capsid protein in Escherichia coli and the role of amino and carboxy termini in the formation of the icosahedral particles

The coat protein gene of physalis mottle tymovirus (PhMV) was over expressed in Escherichia coli using pET-3d vector. The recombinant protein was found to self assemble into capsids in vivo. The purified recombinant capsids had an apparent s value of 56.5 S and a diameter of 29(±2) nm. In order to establish the role of amino and carboxy-terminal regions in capsid assembly, two amino-terminal deletions clones lacking the first 11 and 26 amino acid residues and two carboxy-terminal deletions lacking the last five and ten amino acid residues were constructed and overexpressed. The proteins lacking N-terminal 11 (PhCPN1) and 26 (PhCPN2) amino acid residues self assembled into T = 3 capsids in vivo, as evident from electron microscopy, ultracentrifugation and agarose gel electrophoresis. The recombinant, PhCPN1 and PhCPN2 capsids were as stable as the empty capsids formed in vivo and encapsidated a small amount of mRNA. The monoclonal antibody PA3B2, which recognizes the epitope within region 22 to 36, failed to react with PhCPN2 capsids while it recognized the recombinant and PhCPN1 capsids. Disassembly of the capsids upon treatment with urea showed that PhCPN2 capsids were most stable. These results demonstrate that the N-terminal 26 amino acid residues are not essential for T = 3 capsid assembly in PhMV. In contrast, both the proteins lacking the C-terminal five and ten amino acid residues were present only in the insoluble fraction and could not assemble into capsids, suggesting that these residues are crucial for folding and assembly of the particles

Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase

The Sec6/8 complex, also known as the exocyst complex, is an octameric protein complex that has been implicated in tethering of secretory vesicles to specific regions on the plasma membrane. Two subunits of the Sec6/8 complex, Exo84 and Sec5, have recently been shown to be effector targets for active Ral GTPases. However, the mechanism by which Ral proteins regulate the Sec6/8 activities remains unclear. Here, we present the crystal structure of the Ral-binding domain of Exo84 in complex with active RalA. The structure reveals that the Exo84 Ral-binding domain adopts a pleckstrin homology domain fold, and that RalA interacts with Exo84 via an extended interface that includes both switch regions. Key residues of Exo84 and RalA were found that determine the specificity of the complex interactions; these interactions were confirmed by mutagenesis binding studies. Structural and biochemical data show that Exo84 and Sec5 competitively bind to active RalA. Taken together, these results further strengthen the proposed role of RalA-regulated assembly of the Sec6/8 complex