Multifunctional polycondensation distributions: A kinetic approach to mixed monomer systems

The size distributions of a number of multifunctional polycondensations which contained mixtures of monomers of different functionalities were derived from kinetic reaction schemes. The distributions obtained were in agreement with those derived by other authors on similar systems. The distribution functions differed, however, from those obtained by a kinetic method by using mean functionalities of the monomer mixtures; the reasons for the differences were explored. Size distribution parameters also obtained were used to consider the differences between actually observed gel points and gel points calculated for multifunctional polycondensing systems.     

Distributions in nonself-condensing polycondensations: A kinetic approach

The size distributions of a number of different polycondensations with nonself-condensing monomers were calculated by a kinetic method. The results of linear polycondensations with and without reversibility or stoichiometry and of multifunctional polycondensations are exactly the same as those obtained by Flory with probability methods and do not differ, when comparable, from the size distributions produced by the polycondensation of self-condensing monomers. Size distributions were also obtained for reactions in which the order of reaction changes with conditions or during reaction. These results clearly show that a Flory distribution is obtained as long as the principle of equal reactivity applies at any given instant, although this reactivity may vary in the course of the reaction.     

Thymine-dimer and action-spectrum evidence for indirect photoreactivation in Escherichia coli

Abstract— Cells of Escherichia coli B and B phr- were labeled with tritiated thymidine, exposed to inactivating ultraviolet radiation at 254 nm, given photoreactivation (PR) treatment immediately thereafter, and then immediately hydrolyzed and assayed for thymine-containing dimers. It was found that (1) PR treatment of strain B phr- does not split thymine dimers and (2) the amount of splitting of thymine dimers in strain B at 334 nm is only 45 per cent of the amount of splitting observed at 405 nm for the same amount of biological PR. These findings show that all of the PR in E. coli B phr-, and part of the PR at 334 nm in E. coli B, is indirect (does not use PR enzyme) and is not due to thymine-dimer splitting. Action spectra for PR in Escherichia' coli strains B_s-1 and B/r were obtained. At wavelengths below 366 nm (the indirect PR region), PR is relatively much more efficient in strain B/r in logarithmic phase than in strain B/r in stationary phase or in strain B_s-l. This is consistent with the expectation that indirect PR would not be exhibited by strains, such as B_s-1 that lack dark-repair ability, or by certain strains in the stationary phase, such as B/r, which, upon plating, have a ‘built-in’ growth delay that can permit optimal dark repair, but indirect PR would be exhibited by intermediate cases, such as in strain B (which is less resistant to u.v. than strain B/r) or in strain B/r in logarithmic phase. These findings support the hypothesis that indirect PR results from enhancement of dark repair.     

Fractionation and characterization of phenolic resins by high-performance liquid chromatography and gel-permeation chromatography combined with ultraviolet, refractive index, mass spectrometry and light-scattering detection

HPLC and gel permeation chromatographic (GPC) characterization of complex phenol-formaldehyde resins is described. Reversed-phase HPLC fingerprints the phenolic monomers, dimers and some oligomers. The molecular masses of these phenolic compounds were determined using an ion trap mass spectrometer. GPC analyzes tetrahydrofuran-soluble phenolic polymers beyond HPLC capability. The molecular mass distribution and structural information of the phenolics was determined by both conventional and laser light-scattering calibration methods. GPC with both UV and refractive index detection provides weight concentration of phenolic resin and the molar concentration of the phenol unit in the oligomers or polymers.     

EF-Tu binding peptides identified,dissected, and affinity optimized by phage display

The highly abundant GTP binding protein elongation factor Tu (EF-Tu) fulfills multiple roles in bacterial protein biosynthesis. Phage-displayed peptides with high affinity for EF-Tu were selected from a library of approximately 4.7 x 10(11) different peptides. The lack of sequence homology among the identified EF-Tu ligands demonstrates promiscuous peptide binding by EF-Tu. Homolog shotgun scanning of an EF-Tu ligand was used to dissect peptide molecular recognition by EF-Tu. All homolog shotgun scanning selectants bound to EF-Tu with higher affinity than the starting ligand. Thus, homolog shotgun scanning can simultaneously optimize binding affinity and rapidly provide detailed structure activity relationships for multiple side chains of a polypeptide ligand. The reported peptide ligands do not compete for binding to EF-Tu with various antibiotic EF-Tu inhibitors, and could identify an EF-Tu peptide binding site distinct from the antibiotic inhibitory sites.     

Seasonal variability and detection range modeling of baleen whale calls in the Gulf of Alaska, 1999-2002

Five species of large whales, including the blue (Balaenoptera musculus), fin (B. physalus), sei (B. borealis), humpback (Megaptera novaeangliae), and North Pacific right (Eubalaena japonica), were the target of commercial harvests in the Gulf of Alaska (GoA) during the 19th through mid-20th Centuries. Since this time, there have been a few summer time visual surveys for these species, but no overview of year-round use of these waters by endangered whales primarily because standard visual survey data are difficult and costly. From October 1999-May 2002, moored hydrophones were deployed in six locations in the GoA to record whale calls. Reception of calls from fin, humpback, and blue whales and an unknown source, called Watkins' whale, showed seasonal and geographic variation. Calls were detected more often during the winter than during the summer, suggesting that animals inhabit the GoA year-round. To estimate the distance at which species-diagnostic calls could be heard, parabolic equation propagation loss models for frequencies characteristic of each of each call type were run. Maximum detection ranges in the subarctic North Pacific ranged from 45 to 250 km among three species (fin, humpback, blue), although modeled detection ranges varied greatly with input parameters and choice of ambient noise level.     

Stochastic pairwise alignments and scoring methods for comparative protein structure modeling

Despite recent advances in fold recognition algorithms that identify template structures with distant homology to the target sequence, the quality of the target-template alignment can be a major problem for distantly related proteins in comparative modeling. Here we report for the first time on the use of ensembles of pairwise alignments obtained by stochastic backtracking as a means to improve three-dimensional comparative protein models. In every one of the 35 cases, the ensemble produced by the program probA resulted in alignments that were closer to the structural alignment than those obtained from the optimal alignment. In addition, we examined the lowest energy structure among these ensembles from four different structural assessment methods and compared these with the optimal and structural alignment model. The structural assessment methods consisted of the DFIRE, DOPE, and ProsaII statistical potential energies and the potential energy from the CHARMM protein force field coupled to a Generalized Born implicit solvent model. The results demonstrate that the generation of alignment ensembles through stochastic backtracking using probA combined with one of the statistical potentials for assessing three-dimensional structures can be used to improve comparative models.     

Quantum chemical study of the mechanism of action of vitamin K carboxylase (VKC). IV. Intermediates and transition states

We studied proposed steps for the enzymatic formation of gamma-carboxyglutamic acid by density functional theory (DFT) quantum chemistry. Our results for one potentially feasible mechanism show that a vitamin K alkoxide intermediate can abstract a proton from glutamic acid at the gamma-carbon to form a carbanion and vitamin K epoxide. The hydrated carbanion can then react with CO2 to form gamma-carboxyglutamic acid. Computations at the B3LYP/6-311G** level were used to determine the intermediates and transition states for the overall process. The activation free energy for the gas-phase path is 22 kcal/mol, with the rate-limiting step for the reaction being the attack of the carbanion on CO2. Additional solvation studies, however, indicate that the formation of the carbanion step can be competitive with the CO2 attack step in high-dielectric systems. We relate these computations to the entire vitamin K cycle in the blood coagulation cascade, which is essential for viability of vertebrates.     

Interaction of radiatively cooled plasma jets with neutral gases for laboratory astrophysics studies

A supersonic (Mach～2–3), radiatively cooled plasma jet is produced by the ablation of aluminium plasma from a radial foil, a disc subjected to a ～1.4 MA, 250 ns current from the MAGPIE pulsed-power generator. The ablated plasma converges on axis, producing a steady and collimated jet with axial velocities reaching ～100 km/s. The study of jet-ambient interactions is achieved by introducing a neutral gas above the foil using a fast valve with a supersonic gas nozzle. The system has flexibility to study different interaction geometries in order to vary critical dimensionless parameters for astrophysical studies. In particular the effects of radiative cooling on the working surface of the jet are strongly affected by varying the gas composition. Experimental results are compared to numerical simulations using the 3-D MHD code GORGON.