Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers

New antiretroviral drugs that offer large genetic barriers to resistance, such as the recently approved inhibitors of HIV-1 protease, tipranavir and darunavir, present promising weapons to avert the failure of current therapies for HIV infection. Optimal treatment strategies with the new drugs, however, are yet to be established. A key limitation is the poor understanding of the process by which HIV surmounts large genetic barriers to resistance. Extant models of HIV dynamics are predicated on the predominance of deterministic forces underlying the emergence of resistant genomes. In contrast, stochastic forces may dominate, especially when the genetic barrier is large, and delay the emergence of resistant genomes. We develop a mathematical model of HIV dynamics under the influence of an antiretroviral drug to predict the waiting time for the emergence of genomes that carry the requisite mutations to overcome the genetic barrier of the drug. We apply our model to describe the development of resistance to tipranavir in in vitro serial passage experiments. Model predictions of the times of emergence of different mutant genomes with increasing resistance to tipranavir are in quantitative agreement with experiments, indicating that our model captures the dynamics of the development of resistance to antiretroviral drugs accurately. Further, model predictions provide insights into the influence of underlying evolutionary processes such as recombination on the development of resistance, and suggest guidelines for drug design: drugs that offer large genetic barriers to resistance with resistance sites tightly localized on the viral genome and exhibiting positive epistatic interactions maximally inhibit the emergence of resistant genomes.

Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India

Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.

On states, on a lattice, with half-integral charge

In certain molecular models, and related one-dimensional field theories, localized objects appear with half-integral expectation values of charge. We consider whether these states are eigenstates of charge, with half-integral eigenvalue. We find that it is indeed so for a suitably diffuse definition of the charge operator in question. This diffuse charge operator has a spectrum which approaches a continuum. The analysis is made on a lattice, to avoid divergence ambiguities, and on a finite length, which is only subsequently made large. The half-integral charge phenomenon is not tied to solitons, but can also arise as an end effect.

Ultrasonic attenuation in strongly disordered electronic systems

The attenuation of long-wavelength phonons due to their interaction with electronic excitations in disordered systems is investigated here. Lattice strain couples to electronic stress, and thus ultrasonic attenuation measures electronic viscosity. The enhancement and critical divergence of electronic viscosity due to localization effects is calculated for the first time. Experimental consequences for the anomalous increase of ultrasonic attenuation in disordered metals close to the metal-insulator transition are discussed. In the localized regime, the appropriate model is one of electronic two-level systems (TLS’s) coupled to phonons. The TLS consists of a pair of states with one localized state occupied and the other unoccupied. The density of such low-excitation-energy TLS’s is nonzero due to long-range Coulomb interactions. The question of whether these could be significant low-energy excitations in glasses is touched upon.

Purification of a bacterial organophosphate-hydrolysing phosphatase by cibacron 3GA-Sepharose affinity chromatography

A phosphatase catalysing the hydrolysis of organophosphorus pesticides was purified to homogeneity using Cibacron 3GA-Sepharose CL 6B affinity chromatography. The enzyme which is localized in the periplasm of the bacterium Image NC5 was extracted by treating with 0.2M MgCl2, pH 8.4. The enzyme was adsorbed to the Cibacron-Sepharose at pH 7.0 and eluted with Tris-HCl buffer at pH 8.0, with 47 per cent recovery. The enzyme thus obtained was electrophoretically homogeneous. This simple affinity purification procedure enhances the potential for its use in large scale detoxification systems.

Studies on tryptophan residues of Abrus agglutinin Stopped-flow kinetics of modification and fluorescence-quenching studies

The presence of two essential tryptophan residues/molecule was implicated in the binding site of Abrus agglutinin [Patanjali, Swamy, Anantharam, Khan & Surolia (1984) Biochem. J. 217, 773-781]. A detailed study of the stopped-flow kinetics of the oxidation of tryptophan residues revealed three classes of tryptophan residues in the native protein. A discrete reorganization of tryptophan residues into two phases was observed upon ligand binding. The heterogeneity of tryptophan exposure was substantiated by quenching studies with acrylamide, succinimide and Cs+. Our study revealed the microenvironment of tryptophan residues to be hydrophobic, and also the presence of acidic amino acid residues in the vicinity of surface-localized tryptophan residues.

Cholesterol-Esterifying Enzymes in Developing Rat Brain

A cholesterol-esterifying enzyme which incorporates exogenous fatty acids into cholesterol esters in the presence of ATP and coenzyme A was demonstrated in 15-day-old rat brain. This enzyme was maximally active at pH 7.4 and distinct from the cholesterol-esterifying enzyme reported earlier (Eto and Suzuki, 1971), which has a pH optimum at 5.2 and does not require cofactors. Properties of the two enzymes have been compared. Both the enzymes showed negligible esterification with acetate and were maximally active with oleic acid. The pH 5.2 enzyme esterified desmosterol, lanosterol and cholesterol at about the same rate, while the pH 7.4 enzyme was only 50% as active ith lanosterol as it was with cholesterol and desmosterol. Phosphatidyl serine stimulated the pH 5.2 enzyme but not the pH 7.4 enzyme. Phosphatidyl choline and sodium taurocholate showed no effect on either of the enzymes. Both the enzymes were associated with particulate fractions, but the pH 7.4 enzyme was localized more in the microsomes. Purified myelin showed 2.6-fold and 1.5-fold higher specific activities of pH 5.2 and 7.4 enzymes respectively, when compared with homogenate. About 7-10% of total activity of both the enzymes was associated with purified myelin. Brain stem and spinal cord showed higher specific activity of pH 5.2 enzyme than cerebral cortex and cerebellum, while pH 7.4 enzyme specific activity was higher in cerebellum and brain stem than in cerebral cortex and spinal cord. Microsomal pH 7.4 activity showed progressive increase prior to the active period of myelination, reaching a maximum on the 15th day after birth and declined to 20% of the peak activity by 30 days. In contrast, pH 5.2 enzyme reached maximum activity about the 6th day after birth and remained at this level well into adulthood. In 15-day-old rat brain, pH 7.4 enzyme had five to six times higher specific activity than pH 5.2 enzyme, while in adults the activities were equal. The pH 7.4 enzyme showed a threefold higher specific activity than pH 5.2 enzyme in myelin from 15-day-old rats, but in adults the reverse was true. Key Words: Cholesterol esterifying enzymes-Developing rat brain-Myelination. Jagannatha H. M. and Sastry P. S. Cholesterol-esterifying enzymes in developing rat brain. J. Neurochem. 36, 1352- 1360 (1981).

Highly Enhanced Thermopower in Two-Dimensional Electron Systems at Millikelvin Temperatures

We report experimental observation of an unexpectedly large thermopower in mesoscopic two-dimensional (2D) electron systems in GaAs/AlGaA heterostructures at sub-Kelvin temperatures and zero magnetic field. Unlike conventional nonmagnetic high-mobility 2D systems, the thermopower in our devices increases with decreasing temperature below 0.3 K, reaching values in excess of 100 mu V/K, thus exceeding the free electron estimate by more than 2 orders of magnitude. With support from a parallel study of the local density of states, we suggest such a phenomenon to be linked to intrinsic localized states and many-body spin correlations in the system.

ESR and optical studies of Mo5+ and W5+ ions in phosphomolybdate and phosphotungstate glasses

ESR and optical studies of phosphomolybdate and phosphotungstate glasses are discussed. Both the ESR and optical results indicate that molybdenum or tungsten ions are present in distorted octahedral environments in these glasses. In addition, ESR spectra of Mo5+ and W5+ ions show that the d electrons are localized on molybdenum and tungsten sites respectively. The variation of gperpendicular and gshort parallel values has been examined using appropriate structural models of these glasses.

Valence bond analysis of the Kondo chain Hamiltonian

Accurate extrapolations for the ground state energy per site of the one - dimensional Kondo chain system is obtained from exact finite system calculations carried out employing a valence bond scheme. An analysis of the ground state wave function indicates that the localized spin is quenched for all nonzero values of the Kondo exchange constant in one dimension.

Mordenite-incorporated PVA-PSSA membranes as electrolytes for DMFCs

Composite membranes with mordenite (MOR) incorporated in poly vinyl alcohol (PVA)–polystyrene sulfonic acid (PSSA) blend tailored with varying degree of sulfonation are reported. Such a membrane comprises a dispersed phase of mordenite and a continuous phase of the polymer that help tuning the flow of methanol and water across it. The membranes on prolonged testing in a direct methanol fuel cell (DMFC) exhibit mitigated methanol cross-over from anode to the cathode. The membranes have been tested for their sorption behaviour, ion-exchange capacity, electrochemical selectivity and mechanical strength as also characterized by Fourier transform infrared spectroscopy and thermogravimetric analysis. Water release kinetics has been measured by magnetic resonance imaging (NMR imaging) and is found to be in agreement with the sorption data. Similarly, methanol release kinetics studied by volume-localized NMR spectroscopy (point resolved spectroscopy, PRESS) clearly demonstrates that the dispersion of mordenite in PVA–PSSA retards the methanol release kinetics considerably. A peak power-density of 74 mW/cm2 is achieved for the DMFC using a PVA–PSSA membrane electrolyte with 50% degree of sulfonation and 10 wt.% dispersed mordenite phase. A methanol cross-over current as low as 7.5 mA/cm2 with 2 M methanol feed at the DMFC anode is observed while using the optimized composite membrane as electrolyte in the DMFC, which is about 60% and 46% lower than Nafion-117 and PVA–PSSA membranes, respectively, when tested under identical conditions.

Ternary vanadium sulfides

Ternary vanadium sulfides, MxVS2 (M = Fe, Co, Ni), with Image , were prepared and studied. The Image and Image series are isostructural with V5S8 and V3S4, respectively, while compounds with Image appear to have the hexagonal Cr2S3 structure. Structures of NiV2S4 and NiV4S8 were refined from powder X-ray diffraction intensities. Magnetic and electrical properties reveal that M ions in these sulfides exist in the divalent state having localized moments, while the vanadium 3 d electrons are itinerant.

Enzymatic acylation of 1-alkyl-, 1-alkenyl-and 1-acyl glycero-3-phosphorylethanolamine in developing rat brain

Rat brain particulate fractions were shown to acylate [32P]1-alkyl-sn-glycero-3-phosphorylethanolamine (GPE). While the main product is 1-alkyl-2-acyl GPE, about 12 per cent of the radioactivity was also found in 1-alkenyl-2-acyl GPE. The acyl transferase activity was completely dependent on added ATP and CoA and it was localized mainly in the microsomal fraction. A comparative study of acyl transferase activities to 1-alkyl-, 1-alkenyl-, and 1-acyl GPE by crude mitochondrial fraction and microsomes of 10, 16 and 22-day-old rat brains showed a progressive increase in activity with development. In the 22-day-old rat brain the order of activity towards the three substrates is as follows: 1-acyl GPE ± 1-alkenyl GPE ± 1-alkyl GPE with a crude mitochondrial fraction and 1-acyl GPE ± 1-alkyl GPE ± 1-alkenyl GPE with microsomes.

Study of linear and nonlinear optical properties of dendrimers using density matrix renormalization group method

We have used the density matrix renormalization group (DMRG) method to study the linear and nonlinear optical responses of first generation nitrogen based dendrimers with donor acceptor groups. We have employed Pariser–Parr–Pople Hamiltonian to model the interacting pi electrons in these systems. Within the DMRG method we have used an innovative scheme to target excited states with large transition dipole to the ground state. This method reproduces exact optical gaps and polarization in systems where exact diagonalization of the Hamiltonian is possible. We have used a correction vector method which tacitly takes into account the contribution of all excited states, to obtain the ground state polarizibility, first hyperpolarizibility, and two photon absorption cross sections. We find that the lowest optical excitations as well as the lowest excited triplet states are localized. It is interesting to note that the first hyperpolarizibility saturates more rapidly with system size compared to linear polarizibility unlike that of linear polyenes.

Unusual effects of anisotropic bonding in Cu(II) and Ni(II) oxides with K2NiF4 structure

Geometric constraints present in A2BO4 compounds with the tetragonal-T structure of K2NiF4 impose a strong pressure on the B---OII---B bonds and a stretching of the A---OI---A bonds in the basal planes if the tolerance factor is t congruent with RAO/√2 RBO < 1, where RAO and RBO are the sums of the A---O and B---O ionic radii. The tetragonal-T phase of La2NiO4 becomes monoclinic for Pr2NiO4, orthorhombic for La2CuO4, and tetragonal-T′ for Pr2CuO4. The atomic displacements in these distorted phases are discussed and rationalized in terms of the chemistry of the various compounds. The strong pressure on the B---OII---B bonds produces itinerant σ*x2−y2 bands and a relative stabilization of localized dz2 orbitals. Magnetic susceptibility and transport data reveal an intersection of the Fermi energy with the d2z2 levels for half the copper ions in La2CuO4; this intersection is responsible for an intrinsic localized moment associated with a configuration fluctuation; below 200 K the localized moment smoothly vanishes with decreasing temperature as the d2z2 level becomes filled. In La2NiO4, the localized moments for half-filled dz2 orbitals induce strong correlations among the σ*x2−y2 electrons above Td reverse similar, equals 200 K; at lower temperatures the σ*x2−y2 electrons appear to contribute nothing to the magnetic susceptibility, which obeys a Curie-Weiss law giving a μeff corresponding to S = 1/2, but shows no magnetic order to lowest temperatures. These surprising results are verified by comparison with the mixed systems La2Ni1−xCuxO4 and La2−2xSr2xNi1−xTixO4. The onset of a charge-density wave below 200 K is proposed for both La2CuO4 and La2NiO4, but the atomic displacements would be short-range cooperative in mixed systems. The semiconductor-metallic transitions observed in several systems are found in many cases to obey the relation Ea reverse similar, equals kTmin, where varrho = varrho0exp(−Ea/kT) and Tmin is the temperature of minimum resistivity varrho. This relation is interpreted in terms of a diffusive charge-carrier mobility with Ea reverse similar, equals ΔHm reverse similar, equals kT at T = Tmin.