Correction for non-uniform phosphate labeling of E. coli and phage RNAs synthesized in vivo

$\text{E. coli}$ cells grown to phosphate starvation incorporate ³²PO₄ unequally into the α position of the four ribonucleotide triphosphates during a short period of labeling. A method for determining the relative specific activities of nucleotides in RNA molecules synthesized under these conditions and correcting sequence data is described.     

Dansyl labeled proteins: Determination of extinction coefficient and number of bound residues with radioactive dansyl chloride

A method is described for preparing fluorescent conjugates of proteins labeled by reaction with methyl-C¹⁴-dansyl chloride and for determining their radioactivity by scintillation counting. The extinction coefficient of the bound dye varies in conjugates of different proteins and is considerably lower than the value generally employed to calculate degree of labeling. For assays of dansyl groups using absorption spectroscopy, a value of ? = 3.4 × 10³M^?1 cm^?1 will probably be approximately correct. However, the radioactive dye technique allows much more accurate determinations of degree of labeling, as well as of the extinction coefficient, which may be of interest in itself.     

Chemical modification of mitochondria. II. Effect of labeling on oxidative phosphorylation

The labeling of rat liver mitochondria (RLM) by the uncoupler 2,4-dinitro-5-(bromoacetoxyethoxy)phenol (DNBP) was studied and related to the effect of this molecule on oxidative phosphorylation. Alkylation of the cysteine residues was measured both with respect to incubation time of RLM with DNBP and with increasing DNBP concentration. At 3.3 × 10^?5m DNBP, the amount of S-carboxymethyl-cysteine formed was found to level off after about 3 min. The rate of ATP synthesis in RLM is reduced by increasing concentrations of DNBP and falls to zero, with either hydroxybutyrate or succinate as substrate, at 2 × 10^?4m DNBP. To characterize the effect of labeling on oxidative phosphorylation, the $\text{P}\text{O}$ ratio were measured after incubating RLM with DNBP for various times between 10 and 300 sec. The $\text{P}\text{O}$ ratio increases and tends to level off as the incubation time increases. No increase in $\text{P}\text{O}$ ratio was noted when RLM were similarly incubated with the nonlabeling uncoupler 2,4-dinitro-5-(acetoxyethoxy) phenol. Further, the effect of labeling on oxidative phosphorylation was determined with RLM which had been treated with DNBP and then washed free of the excess unreacted uncoupler. DNBP produces specific labeling in RLM which, when related to the effects of this uncoupler on oxidative phosphorylation, suggests that the labeled proteins may be involved in the primary energy transduction process.     

Analysis of mRNA 5'-terminal cap structures and internal N6-methyladenosine by reversed-phase high-performance liquid chromatography

A simple procedure for determining the complete methylation profile of an mRNA molecule in a single chromatographic separation is described. The mRNA is selectively hydrolyzed to its component nucleosides leaving its cap 0 (m⁷GpppN′) or cap 1 (m⁷GpppN′m) structure intact. The hydrolysis products, which can include cap 0, cap 1, 2′-O-methylnucleosides (N″m) of cap 2 (m⁷GpppN′mpN″m) and internal N⁶-methyladenosine, are separated on an octadecyl reverse-phase column using a mobile phase containing acetonitrile and ammonium formate, a weak ion-pairing reagent. methyl-³H-labeled poly(A)-containing mRNA is used to demonstrate the efficacy of the procedure.     

Photoaffinity labeling of benzodiazepine-receptors: Possible mechanism of reaction

Photoaffinity labeling of brain benzodiazepine-receptors with [³H]flunitrazepam ([³H]FNZ) results in the covalent linking of the ligand to [³H]FNZ-binding site. The major findings in benzodiazepine-receptor studies employing photoaffinity labeling are described; the covalent linking of [³H]FNZ is compared to its reversible binding; and a mechanism for the labeling reaction is postulated.     

Studies on characterization of the sodium-potassium transport adenosine-triphosphatase III: Synthesis of strophanthidin 3-[1-14C] bromoacetate for affinity labeling of the cardiotonic steroid site

The synthesis is described of strophanthidin 3-[1-¹⁴C]bromoacetate for affinity labeling of the cardiotonic steroid site of the (Na⁺ + K⁺)-activated adenosinetriphosphatase. The product is obtained radiopure and in reasonably good yield. Its specific activity is sufficiently high for affinity labeling of less than milligram quantities of current preparations of enzyme.     

A method using 3-O-methyl-D-glucose and phloretin for the determination of intracellular water space of cells in monolayer culture.

A method is presented for determining the extent of methylation of tRNAs synthesized in mammalian and bacterial cell systems and is based upon determining the distribution of radioactivity associated with the guanine constituents of total cellular tRNA preparations previously labeled with [2-¹⁴C]guanosine and with [methyl]-³H or -¹⁴C]methionine. Whereas labeling with guanosine provides a means of assessing the extent of methylation of the [2-¹⁴C]guanine residues incorporated into tRNA, methionine labeling provides a measure of the percentage of [methyl-³H or -¹⁴C]methylated constituents that are methylated guanines. Analyses such as the above reveal that the tRNA of KB cells acquires approximately three times as many methyl groups as that of E. coli B tRNA. Coupled with the knowledge that both mammalian and bacterial tRNA preparations contain an average of 24 guanine residues per molecule, the above analyses further reveal that 7.2 and 2.4 methyl groups are incorporated into each tRNA molecule synthesized in exponentially growing KB- and E. coli B-cells, respectively. Additional information regarding the extent of formation of individual methylated constituents per tRNA molecule synthesized is presented.     

Systematic comparison of two novel,thiol-reactive prosthetic groups for <Superscript>18</Superscript>F labeling of peptides and proteins with the acylation agent succinimidyl-4-[<Superscript>18</Superscript>F]fluorobenzoate ([<Superscript>18</Superscript>F]SFB)

A systematic comparison of 4-[¹⁸F]fluorobenzaldehyde-O-(2-{2-[2-(pyrrol-2,5-dione-1-yl)ethoxy]-ethoxy}-ethyl)oxime ([¹⁸F]FBOM) and 4-[¹⁸F]fluorobenzaldehyde-O-[6-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-hexyl]oxime ([¹⁸F]FBAM) as prosthetic groups for the mild and efficient ¹⁸F labeling of cysteine-containing peptides and proteins with the amine-group reactive acylation agent, succinimidyl-4-[¹⁸F]fluorobenzoate ([¹⁸F]SFB), is described. All three prosthetic groups were prepared in a remotely controlled synthesis module. Synthesis of [¹⁸F]FBOM and [¹⁸F]FBAM was accomplished via oxime formation through reaction of appropriate aminooxy-functionalized labeling precursors with 4-[¹⁸F]fluorobenzaldehyde. The obtained radiochemical yields were 19% ([¹⁸F]FBOM) and 29% ([¹⁸F]FBAM), respectively. Radiolabeling involving [¹⁸F]FBAM and [¹⁸F]FBOM was exemplified by the reaction with cysteine-containing tripeptide glutathione (GSH), a cysteine-containing dimeric neurotensin derivative, and human native low-density lipoprotein (nLDL) as model compounds. Radiolabeling with the acylation agent [¹⁸F]SFB was carried out using a dimeric neurotensin derivative and nLDL. Both thiol-group reactive prosthetic groups show significantly better labeling efficiencies for the peptides in comparison with the acylation agent [¹⁸F]SFB. The obtained results demonstrate that [¹⁸F]FBOM is especially suited for the labeling of hydrophilic cysteine-containing peptides, whereas [¹⁸F]FBAM shows superior labeling performance for higher molecular weight compounds as exemplified for nLDL apolipoprotein constituents. However, the acylation agent [¹⁸F]SFB is the preferred prosthetic group for labeling nLDL under physiological conditions.     

The tritium labeling of small amounts of protein for analysis by electrophoresis on sodium dodecyl sulfate--polyacrylamide slab gels.

A simple and reproducible method for the tritium labeling of small amounts of proteins prior to analysis under denaturing conditions on polyacrylamide slab gels is described. The method involves the in vitro labeling of proteins by reductive methylation using formaldehyde and high specific activity [³H]potassium borohydride. Labeled proteins were detected by fluorography after fractionation on polyacrylamide slab gels in the presence of sodium dodecylsulfate. The overall procedure allows the analysis and molecular weight estimation of submicrogram quantities of protein.     

Catabolism of Tritiated Thymidine by Aquatic Microbial Communities and Incorporation of Tritium into RNA and Protein

The incorporation of tritiated thymidine by five microbial ecosystems and the distribution of tritium into DNA, RNA, and protein were determined. All microbial assemblages tested exhibited significant labeling of RNA and protein (i.e., nonspecific labeling), as determined by differential acid-base hydrolysis. Nonspecific labeling was greatest in sediment samples, for which ≥95% of the tritium was recovered with the RNA and protein fractions. The percentage of tritium recovered in the DNA fraction ranged from 15 to 38% of the total labeled macromolecules recovered. Nonspecific labeling was independent of both incubation time and thymidine concentration over very wide ranges. Four different RNA hydrolysis reagents (KOH, NaOH, piperidine, and enzymes) solubilized tritium from cold trichloroacetic acid precipitates. High-pressure liquid chromatography separation of piperidine hydrolysates followed by measurement of isolated monophosphates confirmed the labeling of RNA and indicated that tritium was recovered primarily in CMP and AMP residues. We also evaluated the specificity of [2-³H]adenine incorporation into adenylate residues in both RNA and DNA in parallel with the [³H]thymidine experiments and compared the degree of nonspecific labeling by [³H]adenine with that derived from [³H]thymidine. Rapid catabolism of tritiated thymidine was evaluated by determining the disappearance of tritiated thymidine from the incubation medium and the appearance of degradation products by high-pressure liquid chromatography separation of the cell-free medium. Degradation product formation, including that of both volatile and nonvolatile compounds, was much greater than the rate of incorporation of tritium into stable macromolecules. The standard degradation pathway for thymidine coupled with utilization of Krebs cycle intermediates for the biosynthesis of amino acids, purines, and pyrimidines readily accounts for the observed nonspecific labeling in environmental samples.     

Circulating T and B lymphocytes of the mouse. II. Lifespan

The average lifespan of circulating lymphocytes was investigated by determining the percentage of labeling of thoracic duct lymphocytes (TDL⁵) from mice injected with tritiated thymidine (³HT) for various periods. Percentage of labeling of TDL from normal CBA mice, which consist of approximately 85% T cells and 15% B cells, was found to be directly proportional to the time of ³HT administration. This technique thus failed to demonstrate the presence of more than one population of lymphocytes. Less than 50% of TDL were labeled after ³HT injection for 8 weeks.Percentage of labeling of TDL from nude mice (which consist solely of B cells) was likewise found to be directly proportional to the duration of ³HT injection but occurred at a rate three to four times faster than in non-T cell-depleted CBA mice. Further experiments, in which a marker for B cells was used, allowed the rate of ³HT labeling of B cells to be studied in normal CBA mice. These data corroborated the findings in nude mice and indicated that, with regard to lifespan, thoracic duct B cells consisted of a single population with an average lifespan of 5–7 weeks. Similarly it was calculated that the average lifespan of thoracic duct T cells was in the order of 4–6 months.Studies on the rate of formation of TDL during prolonged thoracic duct drainage of normal CBA mice indicated that the percentage of newly formed cells increased rapidly after 24-hr drainage. The total numbers of newly formed cells, however, were found to remain relatively constant throughout the period of drainage investigated (up to 9 days) except for a transient increase during the second and third day. Newly formed small lymphocytes were found to consist of approximately equal proportions of T cells, B cells, and other “mononuclear” cells which lacked surface markers for either T or B cells. The great majority of large lymphocytes, in contrast, were found to be neither T cells nor B cells and probably belonged to the plasma cell line. In nude mice, production of newly formed lymphocytes during prolonged thoracic duct drainage was found to be very low in comparison with normal CBA mice.     

Separation of cyclic 3',5'-AMP from ATP, ADP, and 5'-AMP by precipitation with inorganic compounds

The antibiotic anisomycin is a very useful tool in studying protein synthesis since it is a specific inhibitor of the peptidyl transferase centre of eukaryotic ribosomes (5–7). By tritium exchange labeling followed by chromatographic and electrophoretic purification, we have obtained [³H]anisomycin of specific activity 285 mCi/mmole, and the methodology followed is described in this paper. This method is useful in preparing tritium labeled antibiotics other than anisomycin provided that the nonradioactive compound has the following characteristics: (a) a chemical structure resistant to the method required for tritium labeling, (b) ionic groups, and (c) chromophore groups with absorption maxima in the uv or visible part of the spectrum. Since these circumstances concur frequently in a number of chemical structures, a method essentially similar to that described in this work might be widely used. The method was not applicable to amicetin, blasticidin S, and fusidic acid, as these antibiotics were broken down during the tritium labeling. However, gougerotin, a well known inhibitor of peptide bond formation by prokaryotic and eukaryotic ribosomes (2–7), has been tritiated and purified following a method very similar to that described in this contribution to [³H]gougerotin (110 mCi/mmole) (16).     

Interaction of group I cations with iota,kappa and lambda carrageenans studied by multinuclear n.m.r.

Results are reported for ²³Na, ³⁹K, ⁸⁷Rb and ¹³³Cs n.m.r. on kappa and iota carrageenans over a range of temperatures. Results for ²³Na and ³⁹K n.m.r. for lambda carrageenan are also given over the same range of temperatures. A variety of behaviour is observed which, in general, does not correlate with the rheological behaviour in these systems. It is concluded that non-specific ion interactions are of importance in determining rheological behaviour.     

Alterations of fatty acyl turnover in macrophage glycerolipids induced by stimulation. Evidence for enhanced recycling of arachidonic acid

Glycerophospholipid biosynthesis by the de novo pathway was assessed in mouse peritoneal macrophages by pulse-labeling with [U-¹⁴C]glycerol. Phosphatidylcholine (PC), which amounts to about 35% of total cellular phospholipids, exhibited the highest rate of glycerol uptake, followed by phosphatidylinositol (PI) and phosphatidylethanolamine (PE). Remodeling of PC molecular species by deacylation/reacylation was established by determining the redistribution of glycerol label over 2 h after a 1 h pulse of [U-¹⁴C]glycerol and by determining incorporation of ¹⁸O from H₂ ¹⁸O-containing media. These data suggest that stearic and arachidonic acid enter PC primarily by the remodeling pathway but that small amounts of highly unsaturated molecular species, including 1,2-diarachidonoyl PC, are rapidly synthesized de novo, and subsequently remodeled or degraded. Treatment of the cells with the ionophore A23187 resulted in the selective enhancement of arachidonate turnover in PC, PI and neutral lipid, as well as enhanced de novo PI synthesis. [U-¹⁴C]Glycerol labeling experiments suggest that arachidonic acid liberated by Ca²⁺-dependent phospholipase A₂ activity is also reacylated in part through de novo glycerolipid biosynthesis, leading to the formation and remodeling of 1,2-diarachidonoyl PC and other highly polyunsaturated molecular species.     

A radiometric method for developing the alkaline sucrose gradient sedimentation patterns of DNA from nondividing cells.

A radiometric method for developing the alkaline sucrose gradient sedimentation patterns of DNA from nonlabeled cells is described. The principle of the method is the labeling of the DNA contained in the gradient fractions by means of the binding of a labeled amino acid to DNA in the presence of formaldehyde. The procedure involves incubation of the fractions with the labeling reagent, filtration of the incubation mixtures through nitrocellulose filters, and radiometry of the filters. The relationship between the radioactivity on the filters and the DNA concentration in the sample is linear; the DNA detection sensitivity is sufficient to escape overloading of the gradients. It was shown that the nonlabeled mammalian cell DNA sedimentation patterns developed by the method described and those of DNA from the same cells labeled with [³H]thymidine in vivo are identical.     

PIGMENT TURNOVER IN THE MARINE DIATOM THALASSIOSIRA WEISSFLOGII. II. THE 14CO2-LABELING KINETICS OF CAROTENOIDS1

The biosynthesis and turnover of the pigments fucoxanthin, diadinoxanthin (DD), and diatoxanthin (DT) were studied in exponentially growing cultures of the diatom Thalassiosira weissflogii (Grunow) Fryxell and Hasle to investigate the dependence of pigment turnover on algal growth rates and light intensity. ¹⁴C-bicarbonate was used as a tracer. The labeling kinetics of fucoxanthin and DT were described satisfactorily by a simple precursor-pigment model with two free parameters, the precursor and pigment turnover rate. At growth irradiances < 200 μE · m^?2· s^?1, labeling kinetics of DD indicated the presence of two kinetically distinct DD pools and at least one precursor pool. The average growth rate-normalized pigment turnover rate of fucoxanthin was 0. The growth rate-normalized turnover rate of DT, determined only at high light irradiances (> 200 μE·m^?2·s^?1), was 1.3. At high light irradiances, the growth rate-normalized turnover rate of DD was 1.8. At low light irradiances, the turnover rates of the two DD pools were 3.7 and 0, respectively. The corresponding pigment turnover times were on the order of days to weeks, depending on the growth rate of the cultures. A comparison of pigment pool sizes, pigment turnover rates, and precursor turnover rates suggests that fucoxanthin is synthesized from a pool of DD and that DD and DT are synthesized from a common precursor, possibly β-carotene. No evidence was seen for dynamic xanthophyll cycling. This suggests that the commonly known “xanthophyll cycle” is the simple unidirectional conversion of DD into DT, or of DT into DD, in response to rapid irradiance changes.     

A batch procedure for the assay of cyclic nucleotide phosphodiesterase.

A procedure for the assay of cyclic nucleotide phosphodiesterase is described in which labeled cyclic nucleotide is separated from labeled nucleoside by the batchwise addition of ethanolic slurries of Dowex 2 fluoride. Under the conditions described there is no detectable adsorption of nucleoside by the anion exchanger, which removes more than 95% of the tritium in boiled samples of [8-³H]cAMP or [8-³H]cGMP. Linear time courses and enzyme vs activity relationships are described for 10^?3 and 10^?7m cAMP and 10^?4m cGMP. The method is limited by interference by neutral salts and by the enzymatic conversion of adenosine into inosine.     

Kinetics of C-14 Translocation in Soybean: II. Kinetics in the Leaf

The kinetics of ¹⁴C-assimilates in the soybean leaf were studied in pulse labeling and steady state labeling experiments. ¹⁴C-Sucrose apparently served as the ultimate source, at least, of translocated ¹⁴C-sucrose. However, since the specific activity of leaf sucrose reached a maximum within 5 minutes after pulse labeling, whereas that of exported sucrose did not reach a maximum until at least 20 minutes, it appeared that there were two sucrose compartments in the leaf. A possible physical basis for the two compartments may be the mesophyll (a photosynthetic compartment) and a specialized “paraveinal mesophyll” (a nonphotosynthetic compartment), through which photosynthate must pass on its way to the veins.     

CHROMOSOMAL BASIS OF DOSAGE COMPENSATION IN DROSOPHILA : III. Early Completion of Replication by the Polytene X-Chromosome in Male: Further Evidence and Its Implications

Thymidine-³H labeling patterns on the X (section 1 A to 12 E of Bridges' map) and 2 R (section 56 F to 60 F of Bridges' map) segments in the salivary gland chromosomes of Drosophila melanogaster have been analyzed in male and female separately. The observed patterns fit, with a few exceptions, in a continuous to discontinuous labeling sequence. In nuclei with similar labeling patterns on the 2R segment in both sexes, the number of labeled sites on the X in male is always less than in female X's. The labeling frequency of the different sites on the male X is considerably lower than those on the female X's, while the sites on the 2R segment have very similar frequency in the two sexes. The rate of thymidine-³H incorporation (as judged by visual grain counting) is relatively higher in male X than in female X's. It is concluded that the model sequence of replication in polytene chromosomes follows a continuous to discontinuous labeling sequence, and that the single X in male completes its replication earlier than either the autosomes in male or the X's in female. This asynchronous and faster rate of replication by the polytene X-chromosome in male substantiates the hypothesis of hyperactivity of the single X in male as the chromosomal basis of dosage compensation in Drosophila.     

Antigen-specific helper activity in serum of mice primed with sheep red cells. I. Definition of the test system and comparison with other systems

An adoptive transfer system is described to measure serum helper activity in the primary antibody response to sheep red blood cells (SRBC). Mice injected with a high dose of cyclophosphamide and reconstituted with rabbit anti-thymocyte serum-treated spleen cells were used as recipients. Serum obtained 9 hr after ip injection of normal mice with 2 × 10⁸ SRBC (S(SRBC)) injected i.v. in the recipients caused a significant enhancement of the antibody response to 2 × 10⁷ SRBC. The serum helper activity was not generated in thymectomized animals and could be absorbed from S(SRBC) by normal and formalinized SRBC. The SRBC-specific serum helper activity (SSHA) is heat labile (30 min 56 °C) and shows allogeneic restriction. Another test system described in literature for measuring T-cell help in vivo was less suited to measure SSHA in the response to 2 × 10⁷ SRBC. A system using normal mice injected with 10⁵ SRBC for determining specific immune response-enhancing factor (SIREF), demonstrated SIREF activity in S(SRBC). It did, however, not measure SSHA, as absorption of S(SRBC) with formalinized SRBC did not abolish the activity in that system.