Synthesis of compositionally unique DNA by terminal deoxynucleotidyl transferase

Studies on the composition and characterization of DNA product(s) synthesized by calf thymus terminal deoxynucleotidyl transferase were performed using homopolymeric single-stranded, calf thymus double-stranded, and native DNA resident in calf thymus chromatin preparations as priming DNA species. Synthesis was carried out using equimolar concentrations of all four deoxynucleoside triphosphates as substrates and Mg²⁺ or Mn²⁺ as an effective divalent cation. Irrespective of the nature of the priming DNA or the divalent cation, the DNA product contained 60–70% dGMP residues, 10–15% each of the two pyrimidine residues, and 5–10% dAMP residues. The product synthesized using chromatin DNA as initiator was predominantly single-stranded and its synthesis was resistant to actinomycin D. The predilection of terminal deoxynucleotidyl transfease to synthesize dGMP-rich products on natural or homopolymeric DNA primers suggests that such products may represent biologically important recognition signal sequences.     

The penetration of local anesthetics into the red blood cell membrane as studied by fluorescence quenching.

The local anesthetics procaine and tetracaine were found to quench the fluorescence of the probes N-octadecyl naphthyl-2-amine 6-sulfonic acid and 12-(9-anthroyl)stearic acid in the presence of erythrocyte membranes. This quenching was shown to be due to the aromatic amine of the procaine and tetracaine molecules. Lidocaine, an active anesthetic that does not contain an aromatic amine in the same position as does procaine and tetracaine did not quench either of the fluorophores. The preferential quenching of the fluorescent probes by procaine and tetracaine indicated a greater accessibility of tetracaine than of procaine to the hydrocarbon region of the membrane and a greater accessibility of procaine than of tetracaine at the membrane's surface. The addition of calcium was found to reverse the quenching of 12-(9-anthroyl)stearic acid by tetracaine in the presence of red cell membranes.     

Synthesis of four novel trisaccharides by induction of loose acceptor specificity in Gal beta 1----4 transferase (EC 2.4.1.22): Galp(beta 1----4)Glcp(X)Glc where X = beta 1----3: beta 1----4: beta 1----6: alpha 1----4.

Development of tandem mass spectral methods for direct linkage determination in oligosaccharides requires sets of trisaccharides differing only in one structural parameter. In this case, we chose the position of linkage to the reducing-end hexose. These sets of compounds would also be useful for the development of high-resolution separation techniques geared to resolve linkage types. Conventional organic synthesis of such a set could take as long as 2-5 months for each member of the set. Each trisaccharide would require 10-20 steps of synthesis. Instead, we utilized low pH to induce a loose acceptor specificity for bovine milk galactosyltransferase (lactose synthase: EC 2.4.1.22) and by this method, within 2 weeks, generated four novel oligosaccharides for NMR and mass spectral studies. The disaccharides cellobiose (beta 1----4), laminaribiose (beta 1----3), gentiobiose (beta 1----6) and maltose (alpha 1----4) acted as acceptors for EC 2.4.1.22 under these conditions. The beta 1----2-linked disaccharide, sophorose, was not commercially available and is not included in this study. The alpha-linked disaccharides were also examined, but except for the alpha 1----4 disaccharide maltose, were very poor acceptors under a variety of conditions. From these four acceptors, the following four novel trisaccharides were synthesized in micromole amounts, suitable for studies of linkage position using low-energy collision-induced-dissociation tandem mass spectrometry (FAB-MS-CID-MS), and for NMR: Galp(beta 1----4)Glcp(beta 1----3)-Glc, Galp(beta 1----4)Glcp(beta 1----4)Glc, Galp(beta 1----4)Glcp(beta 1----6)-Glc and Galp(beta 1----4)Glcp(alpha 1----4)Glc.     

Carbohydrate compositions of the rabbit plasminogen isozymes.

The carbohydrate compositions of the two affinity-chromatography-resolved isozymes of rabbit plasminogen and plasmin as well as the isoelectric-focusing-resolved subforms of each plasminogen isozyme have been investigated in detail. The first plasminogen isozyme as well as its subforms all possess four to five residues of N-acetylglucosamine, two residues of N-acetylgalactosamine, three residues of mannose and five residues of galactose per molecule of protein. Additionally, we previously reported three residues of sialic acid present on this protein molecule. The corresponding plasmin heavy chain for this isozyme contains essentially all of the carbohydrate, and the plasmin light chain appears devoid of carbohydrate. On the other hand, the second plasminogen isozyme as well as its subforms all possess only trace amounts of N-acetylglucosamine, two residues of N-acetylgalactosamine, less than one residue of mannose and three residues of galactose per molecule of protein. In addition, we have previously reported two residues of sialic acid for this molecule. Here, also, all carbohydrate appears on the heavy chain of the plasmin, which is prepared by activation of this particular plasminogen. Thus, the carbohydrate differences which we reported earlier in rabbit plasminogen isozymes are confirmed and extended.     

Localization of the ATP binding site on alpha-tubulin

The binding site for ATP to tubulin was established by use of the photoaffinity label [gamma-32P]N3ATP. Photolysis of the analog in the presence of tubulin resulted in covalent modification of the protein as revealed by autoradiography of electropherograms. Scanning the autoradiograms showed that the ATP analog was bound mainly to the alpha subunit of the tubulin dimer; the alpha subunit was two to three times more radioactive than was the beta subunit. The location of a particular site on the alpha subunit was further defined by peptide maps. The alpha and beta subunits from affinity-labeled tubulin were separated and digested with Staphylococcus protease. Radioactivity was found predominantly in one peptide band from the alpha subunit. The location of the [gamma-32P]N3ATP binding site on the alpha subunit distinguishes it from the previously known exchangeable GTP binding site which is on the beta subunit. Moreover, excess GTP did not compete with [gamma-32P]N3ATP binding. The ATP binding site is distinct from the nonexchangeable GTP binding site. The GTP content of tubulin was the same after dialysis in 0.5 mM ATP as it was following dialysis against ATP-free buffer. Proof that the binding site for [gamma-32P]N3ATP is the same as that for ATP was obtained by competition experiments. In the presence of ATP, photolysis of the affinity analog did not label the alpha subunit preferentially.     

The enthalpy of oxidation of flavin mononucleotide

The oxidation enthalpy of reduced flavin mononucleotide at pH 7.0 in 0.2 m phosphate buffer has been studied by determining the heat associated with the reaction: FMNH₂ + 2 Fe(CN)^?3₆ ? FMN + 2 Fe(CN)^?4₆ + 2 H⁺. (a) (The quinone, semiquinone, and hydroquinone forms of FMN are represented as FMN, FMNH, and FMNH₂, respectively.) Calorimetric experiments were performed in a flow microcalorimeter which was modified to prevent sample contamination by oxygen. The enthalpy observed for reaction (a), after correction for dilution and buffer effects, was ?39.2 ± 0.4 kcal (mole FMNH₂)^?1 at 25 °C. The potential difference, ΔE′, developed by reaction (a) was determined potentiometrically and corresponded to a free energy change, ΔG′, of ?30.3 kcal (mole FMNH₂)^?1. The resulting entropy change, ΔS′, was thus calculated to be ?29.8 e.u. Reaction (a) was also studied at temperatures of 7 °C and 35.5 °C. ΔC_p′ for the reaction was calculated as ?155 ± 18 cal deg^?1 (mole FMNH₂)^?1 at 20 °C. ΔH′ for the reaction (b), FMNH₂ ? FMN + H₂, (b) was calculated as +14.2 ± 0.7 kcal mole^?1 at 25 °C, relative to the enthalpy of the hydrogen electrode being identically equal to zero at all values of pH and temperature. The free energy at pH 7.0 for reaction (b), calculated from the potential was found to be ?9.7 kcal mole^?1, which resulted in an entropy for reaction (b) of 80.2 e.u. A thermal titration of reaction (a) was used to calculate the thermodynamic parameters for the formation of semiquinone dimer according to the reaction FMNH₂ + FMN ? (·FMNH)₂. (c) The free energy, enthalpy, and entropy changes for reaction (c) were estimated to be ?6.1 kcal mole^?1, ?7 kcal mole^?1, and ?3 e.u., respectively.     

Diurnal variations in learning performance in chickens

Diurnal variations in the learning performance of young chicks were investigated using a visual discrimination task which requires birds to discrminate grains from a background of pebbles. Chicks accustomed to receiving fresh food daily in the morning were found to learn well during the day, in that they pecked almost exclusively at grains; but during the night they pecked indiscriminately at grains and pebbles. This occurred even though food was available ad libitum. Chicks accustomed to receiving fresh food daily in the evening learnt the task during the day, and also late at night. Thus the shape of the performance cycle depends in part on environmental factors. Other factors, such as activity, which may contribute to, or co-vary with, this variation in learning performance were investigated.     

Biosynthesis of the beta and beta' subunits of RNA polymerase in Escherichia coli

The amounts of the β and β′ subunits of the DNA-dependent RNA polymerase relative to the amount of total protein synthesized have been determined under a number of growth conditions in two strains of Escherichia coli. The results of these measurements have been expressed as the relative rate of synthesis of core RNA polymerase, α_p, assuming the four constituent subunits (2α, 1β and 1β′) to be synthesized in equivalent amounts.This quantity, α_p, was found not to vary greatly with the growth rate μ. For glucose-grown cells of E. coli B/r (μ = 1.5 doublings/h) α_p = 1.4%, corresponding to about 7000 molecules of core RNA polymerase per cell. For slowgrowing cells the value obtained for α_p is lower and for fast-growing cells somewhat 3 higher. The comparison of these values with the number of RNA polymerase molecules estimated to be actively engaged in RNA synthesis indicates that both slow- and fast-growing cells contain a surplus of RNA polymerase, if the catalytic unit is assumed to be the monomer of core RNA polymerase.In addition to the measurements of cells during balanced growth at various rates, α_p has been determined during the transition from one growth rate to another and during synchronous growth. During a shift-up the rate of synthesis of polymerase follows closely the rate of total protein synthesis, α_p being nearly constant for a period of twenty minutes after the shift. In a synchronously dividing culture of E. coli B/r, α_p was seen to be fairly constant during two cycles of synchronous division. It appears that α_p is rather insensitive to the effect of gene doubling during the cell cycle.     

The effects of heparin on endogenous DNA polymerase activity of rat liver nuclei and chromatin fractions

1. 1. Heparin activates endogenous DNA polymerase activity in isolated rat hepatic nuclei to a synthesis rate two to three times the control values, when added in amounts as small as 10% of total nuclear DNA.

2. 2. Cations such as polylysine, polyornithine and unfractionated histones form insoluble complexes with heparin and reverse its effect in either order of addition.

3. 3. Autoradiography demonstrates many apparent new sites of DNA synthesis in heparin-treated nuclei, both in previously inactive and in previously active nuclei.

4. 4. Electron microscopy shows a dramatic change in the chromatin pattern upon treatment with heparin; fiber diameters are significantly decreased, probably indicating loss of supercoiling.

5. 5. The response to heparin of the endogenous polymerase activity in three chromatin fractions is examined. Two of the three fractions show patterns similar to whole nuclei; the third, a high specific activity fraction, has a distinctively different pattern of response to heparin.

6. 6. The kinetic data combined with the behavior of the high specific activity chromatin fraction indicate that the heparin effect on endogenous DNA synthesis may have more than one component.

     

Proton-nuclear magnetic resonance study of peracetylated derivatives of ten oligosaccharides isolated from human milk

Proton-nuclear magnetic resonance (NMR) spectra of peracetylated derivatives of ten structurally related oligosaccharides isolated from human milk were measured for solutions in CDCl3 at 360 MHz. The following oligosaccharides were investigated: Gal beta 1 leads to 4Glc-ol (1), GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc-ol (2), Gal beta 1 leads to 4GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc-ol (3), Gal beta 1 leads to 3GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc-ol (4), Gal beta 1 leads to 3GlcNAc(4 comes from 1Fuc alpha) beta 1 leads to 3Gal beta 1 leads to 4Glc-ol (5), Fuc alpha 1 leads to 2Gal beta 1 leads to 3GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc-ol (6), Fuc alpha 1 leads to 2Gal beta 1 leads to 3GlcNAc(4 comes from 1Fuc alpha)beta 1 leads to 3Gal beta 1 leads to 4Glc-ol (7), Fuc alpha 1 leads to 2Gal beta 1 leads to 4Glc-ol(3 comes from 1Fuc alpha) (8), and a 1:3 mixture of Fuc alpha 1 leads to 2Gal beta 1 leads to 4Glc-ol (9) and Gal beta 1 leads to 4Glc-ol(3 comes from 1Fuc alpha) (10). Owing to the strong downfield shifts of the resonances of protons linked to acetoxylated carbons, the problems of signal overlap are less severe and the spin systems of all constituent sugar residues can be assigned fully. The sites of glycosidic linkage can be recognized by the high-field position of the signals of protons linked to those sites; for example, type 1 (Gal beta 1 leads to 3GlcNAc) and type 2(Gal beta 1 leads to 4GlcNAc) saccharide chains can be distinguished. The sequence can be established by observing a nuclear Overhauser effect involving the anomomeric and the aglyconic proton.     

Specificity reversal in phospholipase A2 hydrolysis of lipid mixtures

The activity and specificity of phospholipase A₂ from cobra venom ($\text{Naja naja naja}$) toward binary mixtures of phosphatidylcholine and phosphatidylethanolamine in mixed micelles with the nonionic surfactant Triton X-100 were examined. In mixtures containing 5–50 mol % phosphatidylcholine, the rate for phosphatidylethanolamine hydrolysis was enhanced greatly over that for phosphatidylcholine. This is in marked contrast to previous studies with individual phospholipid species in mixed micelles where phosphatidylcholine was found to be the preferred substrate and phosphatidylethanolamine was found to be a very poor substrate. Possible explanations for this specificity reversal are considered.     

Relationships among adult females in captive vervet monkeys: Testing a model of rank-related attractiveness

Data from three captive groups of vervet monkeys (Cercopithecus aethiops sabaeus) were used to test predictions from Seyfarth's (1977) model of rank-related attractiveness. Grooming patterns among adult females were consistent with the model's predictions. There was also evidence that females compete for access to the alpha female, as would be predicted by the model. This study failed to provide evidence for reciprocal support in agonistic encounters based on proximity relationships, independent of kinship.     

Molecular organization in bacterial cell membranes: IV. Isolation by preparative electrophoresis in sodium dodecylsulphate and properties of the two major polypeptide groups of a “soluble” fraction from Streptomyces albus membranes

Two polypeptide fractions have been purified from a “soluble” fraction of n-butanol-extracted Streptomyces albus membranes by preparative electrophoresis in sodium dodecylsulphate. They accounted for approx. 80% of the protein of the fraction (i.e. 20% of the total membrane protein). The ultraviolet spectrum of Group 1 (relative mobility 1.0) revealed the presence of nucleotide material, while that of Group 3 (relative mobility 0.65±0.05) showed the presence of a possibly aggregated protein-like material. About 100 and 30% of the protein contents (Lowry method) of Groups 3 and 1, respectively, were recovered as amino acid residues. These results confirm the protein nature of both fractions and suggest an overestimation of the protein value in Group 1. Both polypeptide groups can be classified as “extrinsic” membrane proteins on the basis of their similar amino acid composition (Vanderkooi, G. and Capaldi, R. A. (1972) Ann. N.Y. Acad. Sci. 195, 135–138). Three N-terminal amino acids were found in each fraction: one common (alanine), methionine, leucine or isoleucine (Group 3) and glutamic acid, lysine (Group 1). The sedimentation coefficients calculated were 2.46 S for Group 3 and 1.54 S for Group 1. Analysis of the isolated groups by gel electrophoresis under non-dissociating conditions or with Triton X-100, gave aggregate-like patterns.Sodium dodecylsulphate electrophoresis revealed an anomalous staining behaviour of Group 3 depending upon the dissociating conditions. The whole “soluble” fraction bound 0.40 mg dodecylsulphate /mg protein (0.55 mg detergent/mg protein corrected for overestimation). After dialysis, the fraction retained 10% of the bound dodecylsulphate. Circular dichroism of the isolated groups after exhaustive dialysis showed similar spectra, although of lower dichroism, to those obtained by other authors on soluble enzymes treated with sodium dodecylsulphate. Strong acid conditions were required to change the CD spectra of the polypeptides.     

Bile acids LIII: Application of reverse-phase high-pressure liquid chromatography to the analysis of conjugated bile acids in bile samples

The common conjugated bile acids of deproteinated bile from the human or the rat can be separated by high-pressure liquid chromatography and quantitated within 30 min with a 4-mm × 30-cm “fatty-acid analysis” column (Waters Associates) in 2-propanol/8.8 mm potassium phosphate buffer (pH 2.5) 160:340, coupled to a uv flow detector set at 193-nm wavelength. Detection limits were at least 0.1 nmol for the tauro-conjugates and 0.2 nmol for the glyco-derivatives.     

Reduction and subsequent oxidation of a cytochrome b of human neutrophils after stimulation with phorbol myristate acetate.

The level of nerve growth factor-like immunoreactivity in the lower limb muscles, the site where the dystrophic mice are effected, of both normal and dystrophic mice was studied by solid-phase radioimmunoassay. Nerve growth factor-like immunoreactivity levels of the homozygous dystrophic mice were about two times lower than those of the heterozygous dystrophic mice at 10–11 weeks and 7–8 weeks of age. The levels in 4–5 week old homozygous mice were too low for detection and remarkable differences between the homozygous and the heterozygous mice were observed at this age. These differences in the level of nerve growth factor-like immunoreactivity suggest that the factor may have some relation to the disease.     

Analysis of polypeptide molecular weights by electrophoresis in urea

Ten proteins of differing disulfide contents and isoionic points were subjected to disc gel electrophoresis in the presence of 8 urea-0.9 acetic acid to evaluate the use of this technique in determining polypeptide molecular weights. Comparison of the electrophoretic mobilities before and after reduction of the proteins' disulfide bonds demonstrated that only after all disulfide bonds were broken, could their molecular weights be estimated with any degree of accuracy. The expression of the electrophoretic mobilities as a function of the proteins' effective hydrodynamic sizes, thereby taking into account the extent of constraint by disulfide bonds, allowed a comparison of disulfide cross-linked and linear forms of the protein polypeptides. The extent to which intrinsic charge affects a protein's electrophoretic mobility was estimated by comparing alpha-lactalbumin and lysozyme, two proteins of identical size but vastly different isoionic points. They exhibited a 20% difference in mobilities. An apparent slow reduction of disulfide bonds was observed to occur when proteins were exposed to reducing agent at low pH in 8 urea.     

The mechanism of cobalamin binding to hog intrinsic factor

Chicken brain Arylsulfatase A (E.C.3.1.6.1) was immobilized by interaction with Concanavalin A. The immobilized enzyme retained its catalytic activity and this enzyme can be reused without appreciable loss of activity. The storage stability of bound and soluble enzymes was comparable and binding of enzyme to Concanavalin A increases its thermal stability. Kinetic studies indicated that bound enzyme shows similar anomalous kinetics as that of free enzyme but slight change was observed in relation to pH optima, Km value and activation energy.     

Population dynamics of mitochondria II. Turnover and ageing of rat liver mitochondria

Membrane-bound multi-protein complexes in mitochondria are provisionally classified into four categories based on possible mechanism of their assembly and degradation. These mechanisms may be investigated by the use of pulse-labeled radioactive markers which are not re-utilizable. Age dependent assembly is defined as that mechanism by which one or more of the pulse-labeled subunits are assembled into a complex, only while this complex is assembled. If the labeled sub-units can be taken up by the complex randomly during its life-span, then the mechanism is called age-independent assembly. Age-dependent degradation was defined as that mechanism by which the labeled subunits are decomposed, only when the complex is being degraded as an entity. If the labeled subunits are decomposed randomly, the mechanism is called age-independent degradation. Four categories are made by combining each of the assembly and degradation mechanisms. A differential equation was obtained to describe the fate of labeled sub-units that follow the age-dependent assembly and age-dependent degradation. Also derived was an equation for the age-independent assembly and age-dependent degradation. The other two categories which involve the age-independent degradation after age-dependent or age-independent assembly are described by single exponential kinetics. Practical application of the equations is illustrated with the use of experimental data on mitochondrial turnover found in the literature which suggests that the pulse-labeled proteins in rat liver mitochondria may follow the age-dependent assembly and degradation. The present attempts to introduce the concept of ageing into multi-protein complexes in mitochondria are the extensions of the steady state theory of mutation by Eyring & Stover (1970).     

The effect of beta-adrenergic blockade on leg blood flow with repeated maximal contractions of the triceps surae muscle group in man

The effect of beta-adrenergic blockade on torque output and leg blood flow was examined in seven healthy young men during repeated maximal isometric voluntary contractions of the triceps surae muscle group. Exercise was performed in either a bent- or straight-leg position during each of four drug treatments: placebo, propranolol, metoprolol, oxprenolol. Contractions were sustained for 5 s with 5 s relaxation for a total of 10 min followed by a 10-min recovery. Leg blood flow was measured during the 5 s relaxation separating contractions using strain gauge plethysmography. Torque output decreased during the 10-min contractions with no differences between the four drug treatments. Leg blood flow was lower with beta-blockade during the initial stages of exercise and recovery in the bent-leg position but no differences were observed after 3 min exercise or recovery. Leg blood flow in the straight-leg position was not different between any of the four drug treatments, but it was significantly less than in bent-leg exercise. The lower blood flows during the initial stages of exercise in the beta-blocked conditions probably reflect a slowing of the central cardiovascular response because of beta 1-receptor blockade of the heart rather than on the beta 2-receptors effects on peripheral vascular resistance. It is concluded that local vasodilator substances released from the working muscle may play a more important role than beta 2-receptor stimulation of smooth muscle in skeletal muscle resistance vessels in regulating local muscle blood flow during maximal exercise of the triceps surae muscle group.     

Neuroendocrine control of moulting cycle in mealworms: Histology and autoradiography of cephalic components

Fluctuations in the activities of the cephalic neuroendocrine system of larval mealworms (Tenebrio molitor) have been investigated by autoradiographic and histological techniques. Shortly after ecdysis, the proteinaceous granules in the cytoplasm of the ‘A’ type medial neurosecretory cells of the brain undergo a marked increase in numbers per cell and in chromophilia; both numbers and stain density reach a maximum about two-thirds of the way through interval between ecdyses and then both decline precipitously. The cyclic histological changes are nicely correlated with overall patterns of protein synthesis, as demonstrated by incorporation of ³H-amino acids into the medial cells. Paradoxically no cyclicity was observed downstream: no fluctuations in numbers or chromophilia of stainable inclusions were detected in the axons of the medial neurosecretory cells, in the corresponding efferent nerves to the corpora cardiaca, or within the cardiaca themselves. Mechanisms are proposed to account for this apparent paradox, and the patterns of protein synthesis within the ‘A’ type medial neurosecretory cells are correlated with previously determined fluctuations in moulting hormone activity.