bluuebunny/crossref_metadata_2025_split huggingface dataset:
Very low‐angle light scattering. A characterization method for high‐molecular‐weight DNA
Authors: Levine Harold I. , Fiel Robert J. , Billmeyer Fred W. 
Published: December 2004

AbstractA very low‐angle light‐scattering photometer is described with respect to optical features, scattering cell, correction factors, and absolute calibration in the angular range 2°–35°. An improved microfiltration apparatus was used to obtain essentially dust‐free aqueous solutions for very low‐angle light scattering. The instrument was calibrated with silicotungstic acid, an absolute molecular‐weight standard, and the calibration was confirmed with the use of several secondary standards.Very low‐angle light‐scattering measurements were made to determine the weight‐average molecular weight M̄r and z‐average radius of gyration Rg,z of a commerical preparation of calf‐thymus DNA. Microfiltration of the solutions allowed measurements down to 6°. The value M̄r = 20.0 × 106 obtained by extrapolating 6°–9° data to 0° is more than three times that from 30°–75° data (6.38 × 106) but ∼20% smaller than that from 10–35° data (23.7 × 106). The experimental errors in M̄r and Rg,z are estimated to be ±8% and ±14%, respectively. Combined 6°–75° data from two photometers fit well a theoretical scattering curve for a model wormlike coil of the same M̄r as the DNA sample.
Theoretical calculations of the helix–coil transition of DNA in the presence of large, cooperatively binding ligands
Authors: McGhee James D. 
Published: December 2004

AbstractTheoretical calculations are conducted on the helix–coil transition of DNA, in the presence of large, cooperatively binding ligands modeled after the DNA‐binding proteins of current biological interest. The ligands are allowed to bind both to helx and to coil, to cover up any number of bases or base pairs in the complex, and to interact cooperatively with their nearest neighbors. The DNA is treated in the infinite homogeneous Ising model approximation, and all calculations are done by Lifson's method of sequence‐generating functions. DNA melting curves are calculated by computer in order to expolore the effects on the transition of ligand size, binding constant, free activity, and ligand–ligand cooperativity. The calculations indicate that (1) at the same intrinsic free energy change per base pair of the complexes, small ligands, for purely entropic reasons, are more effective than are large ligands in shifting the DNA melting temperature; (2) the response of the DNA melting temperature to increased ligand binding constant K and/or free ligand activity L is adequately represented at high values of KL (but not at low KL) by a simple independent site model; (3) if curves are calculated with the total amount of added ligand remaining constant and the free ligand activity allowed to vary throughout the transition, biphasic melting curves can be obtained in the complete absence of ligand–ligand cooperativity. In an Appendix, the denaturation of poly[d(A‐T)] in the presence of the drug, netropsin, is used to verify some features of the theory and to illustrate how the theory can be used to obtain numerical estimates of the ligand binding parameters from the experimental melting curves.
Evidence for long‐range interactions in DNA. Analysis of melting curves of block polymers d(C15A15)·d(T15G15), d(C20A15)·d(T15G20), and d(C20A10)·d(T10G20)
Authors: Wartell Roger M. , Burd John F. 
Published: December 2004

AbstractThe influence of one DNA region on the stability of an adjoining region (telestability) was examined. Melting curves of three block DNA's, d(C15A15)·d(T15G15), d(C20A15)·d(T15G20), and d(C20A10)·d(T10G20) were analyzed in terms of the nearest neighbor Ising model. Comparisons of predicted and experimental curves were made in 0.01 M and 0.1 M sodium ion solutions. The nearest neighbor formalism was also employed to analyze block DNA transition in the presence of actinomycin, a G·C specific molecule. The results show that nearest neighbor base‐pair interaction cannot predict the melting curves of the block DNA's. Adjustments in theoretical parameters to account for phosphate repulsion assuming a B conformation throughout the DNA's do not alter this conclusion. Changes in the theoretical parameters, which provide good overall agreement, are consistent with a substantial stabilization of the A·T region nearest the G·C block. The melting temperature T A·T for the average A·T pari in d(C20A10)·d(T10G20), with 10 A·T pairs, appears to be 4°C greater than TA·T for d(C15A15)·d(T15G15) and d(C20A15)·d(T15G20), both with 15 A·T pairs. Actinomycin bound to the G·C end effectively stabilizes the A·T end by 9°C. These results indicate a long‐range contribution to the interactions governing DNA stability. A possible mechanism for these interactions will be discussed.
Reconstitution of collagen‐fold structure with stretching of gelatin film
Authors: Tanioka Akikiko , Miyasaka Keizo , Ishikawa Kinzo 
Published: December 2004

AbstractThe gelatin film is stretched more 100% over 75% relative humidity, while the dried gelatin extended only several percent. In this experiment the gelatin film was stretched in a solution of water and ethanol. The sample was extended to 650% of its initial length when ethanol/water was 1.5(w/w) at 30°C. The wide‐angle X‐ray diffraction photographs of drawn samples showed the three important layer lines with approximate spacing of 10 Å, 4 Å, and 3 Å, which verify the reconstitution of collagen triple helical structure. The sharp spots appeared near 10 Å on the equatirial axis, indicating the high orientation of peptide chains. These patterns become sharp and clear on increasing the extension ratio.The content of the triple helix was investigated by wide‐angle X‐ray diffraction and differential scanning calorimetry. The maximum renaturation percentage is 25% at the draw ratio of 7.5. Since the formation of a collagen triple helix requires three chains, in which each chain has only three repeatin amino acids, (Gly‐Pro‐X)n, and glycoprotein and other impurities interrupt helix formation, the more advanced renaturation will not be expected.
The optical birefringence of DNA solutions induced by oscillatory electric and hydrodynamic fields
Authors: Wilkinson Robert S. , Thurston George B. 
Published: December 2004

AbstractThe optical birefringence induced in DNA solutions by both oscillating hydrodynamic fields (flow birefringence) and oscillating electric fields (Kerr effect) is measured over a wide frequency range. The observed frequency response of the birefrigence is compared with theories for rigid ellipsoidal particles and for Gaussian chains. DNA at 6 × 105 molecular weight is found to exhibit rigid particle hydrodynamic behavior, while DNA at 5 × 106 molecular weight behaves like a flexible chain. Characterization of the hydrodynamic relaxation spectra for the DNA's by oscillatory flow birefringence allows precise comparison between theory and the experimental Kerr effect response. The dielectric model for DNA contains both permanent and dispersionless induced dipole moments. The dielectric behavior of DNA has the character of a permanent dipole but with anomalous low‐frequency dispersion in the Kerr effect. The existing theories do not adequately describe this dispersion. A fluctuation dipole mechanism with relaxation times comparable to those associated with the hydrodynamic motion could possibly demonstrate the observed polar behavior.
The effects of isolated N‐methylated residues on the conformational characteristics of polypeptides
Authors: Tonelli Alan E. 
Published: December 2004

AbstractConformational energies have been estimated for the tripeptide fragments L‐Ala‐N‐methyl‐L‐Ala‐L‐Ala, L‐Ala‐L‐Ala‐N‐methyl‐L‐Ala, L‐Ala‐Sar‐L‐Ala, and L‐Ala‐Gly‐N‐methyl‐L‐Ala. The peptide bonds connecting L‐Ala and Gly with N‐methyl‐L‐Ala and L‐Ala with Sar were permitted to adopt the planar cis as well as the usual trans conformation. Contour maps of the conformational energies of the central residue in these tripeptide fragments are presented and compared to the conformational energy maps previously calculated for unmethylated L‐Ala and Gly surrounded by residues which are also unmethylated. In generl it is observed that L‐Ala and Gly residues that are either N‐methylated in their conformational freedom relative to the same residues in an unmethylated polypeptide chain.
Switching of turn conformation in an aspartate anion peptide fragment by NH · · · O− hydrogen bonds
Authors: Onoda Akira , Yamamoto Hitoshi , Yamada Yusuke , Lee Keonil , Adachi Seiji , Okamura Taka‐aki , Yoshizawa‐Kumagaye Kumiko , Nakajima Kiichiro , Kawakami Toru , Aimoto Saburo , Ueyama Norikazu 
Published: January 2005

AbstractAspartic acid protease model peptides Z–Phe–Asp(COOH)–Thr–Gly–Ser–Ala–NHCy (1) and AdCO–Asp(COOH)–Val–Gly–NHBzl (3), and their aspartate anions (NEt4)[Z–Phe–Asp(COO−)–Thr–Gly–Ser–Ala–NHCy] (2) and (NEt4)[AdCO–Asp(COO−)–Val–Gly–NHBzl] (4), having an invariant primary sequence of the Asp–X(Thr,Ser)—Gly fragment, were synthesized and characterized by 1H‐NMR, CD, and infrared (IR) spectroscopies. NMR structure analyses indicate that the Asp Oδ atoms of the aspartate peptide 2 are intramolecularly hydrogen‐bonded with Gly, Ser, Ala NH, and Ser OH, supporting the rigid β‐turn‐like conformation in acetonitrile solution. The tripeptide in the aspartic acid 3 forms an inverse γ‐turn structure, which is converted to a β‐turn‐like conformation because of the formation of the intramolecular NH · · · O− hydrogen bonds with the Asp Oδ in 4. Such a conformational change is not detected between dipeptides AdCO–Asp(COOH)–Va–NHAd (5) and (NEt4)[AdCO–Asp(COO−)–Val–NHAd] (6). The pKa value of side‐chain carboxylic acid (5.0) for 3 exhibits a lower shift (0.3 unit) from that of 5 in aqueous polyethyleneglycol lauryl ether micellar solution. NMR structure analyses for 3 in an aqueous micellar solution indicate that the preorganized turn structure, which readily forms the NH · · · O− hydrogen bonds, lowers the pKa value and that resulting hydrogen bonds stabilize the rigid conformation in the aspartate anion state. We found that the formation of the NH · · · O− hydrogen bonds involved in the hairpin turn is correlated with the protonation and deprotonation state of the Asp side chain in the conserved amino acid fragments. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Conformational aspects of polypeptide structure XIV. Synthesis of L‐glutamate oligomers via active ester and azide coupling reactions
Authors: Goodman Murray , Rosen Ira G. , Safdy Max 
Published: December 2004

AbstractIn this paper we have once again shown the general utility of the modified active ester synthesis using a dipeptide active ester. We have also demonstrated that the acyl azide coupling method using the modifications of Rudinger and Honzl, and Schwyzer make a good general method for the synthesis of complex oligopeptides. This method employs reactions known to give products of high optical purity in reasonable yields. The use of the t‐butyloxycarbonyl hydrazyl (CBH) blocking group provides a good route to hydrazides of esters of glutamic acid. The classical route to prepare hydrazides involves the displacement of an ester with hydrazine. Such a pathway is clearly impossible because of the γ‐esters. Finally we demonstrated that trifluoroethanol is an excellent solvent for catalytic hydrogenation reactions.
Conformational aspects of polypeptide structure XV. Synthesis of co‐oligomeric peptides of glutamic‐aspartic acids and glutamic acid‐glycine
Authors: Goodman Murray , Rosen Ira G. 
Published: December 2004

AbstractWe have synthesized three series of co‐oligomers of the following type:
magnified image
where Z represents the carbobenzoxy blocking group and the subscripts can assume various small integral values.The first series includes the dimer (a = 1, b = 0), trimer (a = 1, b = 1) and pentamers (a = 2, b = 1) and was prepared using the p‐nitrophenyl ester technique. The second series is made up of dimer (n = 1, m = 0), trimer (n = 1, m = 1), pentamer (n = 2, m = 1), heptamer (n = 3, m = 1) and undecamer (n = 5, m = 1) and was prepared using mixed anhydrides and modified azide reactions. Lastly, the third series is composed of an octamer (w = 0, x = 3, y = 2) a decamer (w = 0, x = 3, y = 4) and an undecamer (w = 2, x = 3, y = 2). This group of compounds was synthesized by using p‐nitrophenyl ester and modified azide reactions.
Three‐component theory for the approach to sedimentation equilibrium in a density gradient
Authors: Hearst John E. 
Published: December 2004

AbstractA three‐component theory for the approach to sedimentation equilibrium in a density gradient is developed starting from the ‐phenomenological equations of irreversible thermodynamics. It is concluded that in the limit of infinitely dilute macromolecule, the properties of the solvated molecule are being measured as might be expected.
Crosslinked synthetic polypeptides. I. Preparation and characterization of crosslinked poly Glu51‐Lys33Tyr16 and of poly Glu52Lys33Tyr15 no. 3
Authors: Marfey Peter S. , Gill Thomas J. , Kunz Heinz W. 
Published: December 2004

AbstractCrosslinked synthetic polypeptides of poly Glu51Lys33Tyr16 (mol. wt. 31,000) and of poly Glu52Lys33Tyr15 (No. 3) (mol. wt. 52,000) containing from one to six crosslinks per molecule have been prepared by use of FFDNB, WRK and ICD reagents.The monomeric fractions of these derivatives were isolated by Sephadex G‐100 chromatography. The number of crosslinks per molecule of DNPene derivatives was determined by total hydrolysis of the derivatives, isolation of O, N∈‐DNPene‐Tyr‐Lys bridges by paper chromatography and then spectrophotometric quantitation. The number of the amide‐type crosslinks in Am derivatives was established by their deamination followed by total hydrolysis and quantitation of the remaining lysine residues. Crosslinked derivatives appear to have a more compact structure, as judged by their behavior on the Sephadex columns and by their intrinsic viscosities. They were further characterized in regard to their amino acid composition, average number of the crosslinks per molecule, nitrogen content, solubility, root‐mean‐square end‐to‐end distance, and their spectral properties. Their properties recommend them as useful models for the study of the tertiary structure of proteins in solution.
Statistical mechanics of noncovalent bonds in polyamino acids. II. Combinatorial formulation for short chains, including hydrophobic bonding in random coil
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractA combinatorial formulation of the partition function is developed for short polypeptide chains, where summations can be evaluated. From the complete combinatorial expression it is possible to assess the validity of any approximations which are made in evaluating the partition function. It is shown that it is an excellent approximation to consider the hydrogen‐bonded portion of a short (20 residues) chain as consisting of a single helical sequence of any size, with all sizes of helical sequences being about equally probable at the transition temperature. Another approximation, involving a linear dependence of the energy and entropy on the number of hydrogen bonds, helps to clarify the nature of the intermediate states in the denaturation process. Expressions are developed which incorporate the effect of hydrophobic bonds on the stability of the α‐helix, and the binding of water to the random coil. It is concluded that hydrophobic bonds in helical sequences can greatly stabilize the helix, but that similar bonds in the random coil can largely offset this stabilization.
Statistical mechanics of noncovalent bonds in polyamino acids. III. Interhelical hydrophobic bonds in short chains
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractA partition function is derived for a simple model of interacting helices in a short (20 residues) chain of poly‐L‐alanine. It is found that interhelical hydrophobic bonds effect a marked stabilization of helical forms, and give rise to a sharp transition of the type found in many proteins.
Statistical mechanics of noncovalent bonds in polyamino acids. IV. Matrix treatment of hydrophobic bonds in the random coil and of the helix–coil transition for chains of arbitrary length
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractThe Lifson‐Roig matrix theory of the helix–coil transition in polyglycine is extended to situations where side‐chain interactions (hydrophobic bonds) are present both in the helix and in the random coil, as discussed for short chains in paper II of this series. It is shown that the conditional probabilities of occurrence of any number and size of hydrophobic pockets in the random coil can be adequately described by a 2 × 2 matrix. This is combined with the Lifson‐Roig 3 × 3 matrix to produce a 4 × 4 matrix which represents all possible combinations of any amount and size sequence of α‐helix with random coil containing all possible types of hydrophobic pockets in molecules of any given chain length.
A practical method for partial purification of the organism of psittacosis grown in chicken embryo yolk sac
Authors: Shirey William N. , Dorsey Warren G. , Patrick William C. 
Published: December 2004

AbstractA procedure described for the partial purification of suspensions of the organisms of psittacosis utilizes tryptic digestion, calcium chloridedextran sulfate precipitation, and centrifugation through a sucrose barrier. More than 40% of the organisms in the original suspension are recovered in 80% of the original volume, with approximately 95% of the lipids and 85% of the proteins removed. This method is suggested as a preliminary purification procedure in laboratories desiring relatively large amounts of purified agent for studies on metabolism, physical properties, or antigenicity of the organism. Significant aspects of the investigations leading to the selection of the procedures are included.
Mass transfer and mixing rates in fermentation vessels
Authors: Blakebrough N. , Sambamurthy K. 
Published: December 2004

AbstractThe effects on mass‐transfer and overall mixing rates of varying impeller geometry and operating speed have been studied for flat‐bladed turbines in laboratory fermentors, in aerated aqueous solutions, and in unaerated and aerated suspensions (1.6% w/v) of paper pulp. In the absence of suspended solid, oxygen absorption rates could be correlated directly with power input. In the pulp suspension, oxygen absorption at a given power input was influenced by impeller geometry and operating speed. The data for the three‐phase system can be correlated by a dimensionless equation relating oxygen‐transfer rates and mixing times to the geometrical and operating parameters of the impellers.
Power requirement in non‐newtonian fermentation broth
Authors: Taguchi Hisaharu , Miyamoto Saburo 
Published: December 2004

AbstractPower requirements in the agitation of non‐Newtonian fermentation broths with and without aeration were measured by a strain gage‐type dynamometer. Broth from the production of gluc‐amylase by Endomyces species and carboxymethyl cellulose solutions were used as non‐Newtonian fluids. In gas–liquid agitation systems, the correlation between Pg and P02 ND3/Q0.56 observed by Michel and Miller was found to be applicable to non‐Newtonian fluids in laminar and transition regions. This was particularly true for fluids with apparent viscosities larger than 300 cp. The impeller diameter and impeller blade width had considerable effects on power consumption in a nongassed system. It was suggested, therefore, that Pg/P0 should be correlated by a dimensionless term involving some impeller‐size factors.
Dissolved oxygen measurements in pilot‐ and production‐scale novobiocin fermentations
Authors: Steel R. , Maxon W. D. 
Published: December 2004

AbstractDissolved oxygen measurements were made in pilot (20 and 250 l.) and production scale (15,000 l.) novobiocin fermentations. Bulk mixing was found to be incomplete in pilot tanks with turbine impellers of D/T = 0.40 (where D is impeller diameter, and T is tank diameter) but appeared homogeneous with impellers of D/T = 0.69. In the former case, the respiration rate was presumably limited by insufficient oxygen supply in areas of poor bulk mixing, whereas, in the latter case, the major resistance was between the bulk of the liquid and the cell (intraclump resistance). Higher agitator speeds decreased the gas–liquid resistance proportionally more than they reduced the liquid‐cell resistance. In production fermentors, dissolved oxygen measurements indicated that bulk mixing was complete with each of the three impeller sizes tested (D/T = 0.28, 0.33, and 0.43), but that the respiration rate was again limited, mainly by a resistance between the bulk of the liquid and the cell.
Mass culture of red halophilic bacteria
Authors: Kushner D. J. 
Published: December 2004

AbstractExtremely halophilic bacteria, which are able to grow in, and require, saturated or near‐saturated salt solutions are both of historical interest and of practical importance as food spoilage organisms. In addition, because of the environment in which they live, their membranes, enzymes, and ribosomes have unusual or unique properties that make them especially worthy of physiological study. A simple method for growing large quantities of extreme halophiles is described, and various growth media, both complex and synthetic are discussed.
Propagation of Bacillus popilliae in laboratory fermentors
Authors: Sharpe E. S. 
Published: December 2004

AbstractThe insect pathogen Bacillus popilliae Dutky causes a fatal milky disease of Japanese beetle larvae. Spores of the bacterium offer a biological means of controlling this insect. While satisfactory sporulation in vitro has not yet been accomplished, conditions have been developed for the proliferation of vegetative cells in shaken flasks and aerated fermentors. Vegetative cultures are maintained by frequent transfer or by lyophilization. Media based on yeast extract are used routinely, but corn steep liquor and casein hydrolyzates afford comparable yields of 5 × 108 cells/ml. in 16–24 hr. Nutritional requirements have been established for growth in a synthetic medium. Oxygen availability affects the pathway of carbohydrate catabolism and is necessary for optimal growth. In rapidly growing cultures, a short period of maximum viability is characteristically followed by rapid death of the cells. When inoculum size and transfer time are suitably manipulated, viable cell yields reach 1–2 × 109/ml. Alternative methods of propagation, including the addition of particulate carbon, and procedures designed either to neutralize acids or to remove metabolic products by dialysis, do not markedly enhance the yield of cells per volume of medium, although viability may be prolonged.
Effect of manganese and other heavy metals on submerged citric acid fermentation of molasses
Authors: Clark D. S. , Ito K. , Horitsu H. 
Published: December 2004

AbstractThe addition of as little as 2 ppb of manganese to ferrocyanide‐treated beet molasses during citric acid fermentation by Aspergillus niger NRC A‐1‐233 caused a 10% reduction in acid yield and undesirable change in the morphology of the organism from the normal pelletlike form to the filamentous from. Still smaller additions (0.4‐2ppb) caused undesirable pellet clumping, while greater additions (2‐100 ppb) gave further decreases in yield. The yield obtained at 100 ppb was less than 25% of that obtained at 1 ppb or less. None of the other metals tested (Al3+, Ca2+, Co2+, Cu2+, Fe2+, Mg2+, Ni2+, Zn2+) visibly changed pellet morphology, and only Al3+, Fe2+, and Zn2+ at relatively higher concentrations (5–25ppm) reduced acid yield. The adverse effect of manganese on growth and acid production was not affected by addition of the other metals.