A microcomputer program for analysis of nucleic acid hybridization data

The Aedes aegypti genome: complexity and organization

We describe the use of DNA reassociation kinetics to determine the total genome size and complexity together with the individual complexity and copy number of the single copy, middle repetitive and highly repeated DNA fractions of cell line and larval DNA from the mosquito, Aedes aegypti. The genome of Ae. aegypti is both large and complex, being one third the size of the human genome, and exhibits a short period interspersed repeat pattern. The implications of patterns of sequence arrangement and genome complexities for experiments aimed at isolating specific classes of DNA sequences, such as mobile genetic elements, are discussed.

Use of nonlinear regression to analyze enzyme kinetic data: application to situations of substrate contamination and background subtraction

In a recent publication, A. Lundin, P. Arner, and J. Hellmér [Anal. Biochem. 177, 125-131 (1989)] describe a method whereby kinetic substrate assays can be performed when the assay mixture includes a significant contaminating levels of substrate. Their method requires various rearrangements of the data, and involves three separate linear regression calculations. We show how the same data may be analyzed directly, and far more simply, by nonlinear regression. Unlike the linear regression method, nonlinear regression allows direct calculation of the actual values for Km, Vmax, and the concentration of contaminating substrate (as well as estimates of their standard errors); the former method gives only apparent values. The nonlinear regression technique is also statistically a more valid means of analysis, as the rearrangements required to give linearized equations will considerably distort the error distribution and render simple unweighted linear regression inappropriate. The ease of incorporating extra parameters into standard equations when nonlinear regression is used is further illustrated by fitting enzyme reaction data which describe a first-order process when a significant nonspecific background is present. For this equation no simple rearranged linear plot is possible, but nonlinear regression is easily applied to determine the kinetic parameters.

[3H]8-OH-DPAT labels the 5-hydroxytryptamine uptake recognition site and the 5-HT1A binding site in the rat striatum

The binding of [3H]8-hydroxy-2-(di-N-propylamino)-tetralin ([ 3H]8-OH-DPAT) to rat hippocampal and striatal membranes has been compared. In the hippocampus, low concentrations of [3H]8-OH-DPAT bound to a single, high affinity site which was sensitive to inhibition by spiperone, buspirone and ergotamine but not by mianserin, quipazine or (-)-propranolol. This is consistent with a selective labeling of the 5-HT1A receptor. In the striatum, [3H]8-OH-DPAT bound to two sites with high and low affinity (KD's 1.18 and 109 nM). The high affinity component was blocked by low concentrations of buspirone, spiperone and ergotamine. The low affinity component was blocked only by high concentrations of buspirone and spiperone, and was not displaced by ergotamine at concentrations up to 1 microM. The ergotamine-resistant component of striatal [3H]8-OH-DPAT binding was blocked by low concentrations of the 5-HT uptake inhibitors fluvoxamine and paroxetine, and by relatively low concentrations of 5-HT itself. Thus [3H]8-OH-DPAT labels the 5-HT transporter in the rat striatum. Unlike [3H]imipramine binding, the binding of [3H]8-OH-DPAT to the 5-HT transporter was independent of external sodium ions. It is therefore suggested that 8-OH-DPAT acts as substrate for the 5-HT transporter and labels the 5-HT recognition site of the transporter complex.

Heterogeneous 3H-rauwolscine binding sites in rat cortex: two alpha 2-adrenoceptor subtypes or an additional non-adrenergic interaction?

Ligand binding and isolated tissue data have provided evidence for the existence of two, tissue-specific, alpha 2-adrenoceptor subtypes in various rodent and non-rodent species. Thus it has been proposed that the complex binding of alpha 2-antagonists to rat cortical membranes is due to the presence of both subtypes in this tissue. We have previously shown that the alpha 2-antagonist 3H-rauwolscine binds to two sites on rat cortical membranes: a high affinity component characterised pharmacologically as an alpha 2-binding site, and a low affinity, spiperone-sensitive, serotonergic-like component. By the use of computerised non-linear curve-fitting, and the inclusion of (in the incubation buffer of displacement experiments) a concentration of spiperone previously shown to selectively occlude the low affinity component of the 3H-rauwolscine saturation isotherm, we have determined the rank order of affinity at each of the two sites. Whereas the rank order of affinity at the high affinity site retains the pharmacological profile of a single, monophasic alpha 2-binding site, that at the low affinity component is markedly different and is similar to that at the putative 5HT1A subtype. These data, together with the additional, functional serotonergic interactions of rauwolscine and yohimbine, indicate that there is no evidence to support the existence of heterogeneous alpha 2-binding sites, as measured by 3H-rauwolscine binding, on rat cortical membranes. Furthermore, we present evidence that the specific, low affinity serotonergic interaction of 3H-rauwolscine could be avoided by a more judicial estimation of specific binding.

Stereoselective blockade of central [3H]5-hydroxytryptamine binding to multiple sites (5-HT1A, 5-HT1B and 5-HT1C) by mianserin and propranolol

The interaction of the enantiomers of mianserin and propranolol with the binding of [3H]5-hydroxytryptamine ([3H]5-HT) to the 5-HT1A, 5-HT1B and 5-HT1C sites, and with the binding of [3H]ketanserin to the 5-HT2 site, has been evaluated in rat brain membranes. A stereoselective interaction at the 5-HT1A, 5-HT1B and 5-HT1C sites was demonstrated for both compounds, with (+)-mianserin being a more potent displacer than (-)-mianserin and (-)-propranolol being more potent than (+)-propranolol. Only mianserin interacted in a stereoselective manner with the 5-HT2 site, (+)-mianserin being the more potent isomer. The stereoselective association of mianserin and propranolol with the 5-HT1A, 5-HT1B and 5-HT1C sites may prove useful in the characterization of these sites.

Kinetic analysis of the triggered exocytosis/endocytosis secretory cycle in cultured bovine adrenal medullary cells

Cultured bovine adrenal medullary cells are an excellent preparation for quantitative analysis of the secretory exocytosis/endocytosis cycle. In this paper we examine the kinetics of endocytosis after stimulation of secretion. Membrane retrieval was monitored by uptake of the fluid phase marker horseradish peroxidase. Horseradish peroxidase was found to be suitable because it can be washed off completely, assayed quantitatively, and its uptake increases linearly with concentration. If this marker is present during stimulation, the rate of uptake is initially slower than catecholamine secretion but faster at a later time, suggesting that the formation of endocytotic vesicles follows exocytosis. To monitor the time-dependent concentration of secretory vesicle-plasma membrane fusion product (omega-profiles), secretion was halted at various time intervals after stimulation and the excess membrane allowed to transform into endocytotic vesicles in the presence of horseradish peroxidase. By adding horseradish peroxidase at various times after inhibition of secretion, the time course of membrane retrieval could be measured directly. All our results are consistent with a two-step kinetic model in which exocytosis and membrane retrieval are consecutive events. The estimated volumes of the compartments involved are roughly equal. The rate of endocytosis is strongly temperature-dependent but unaffected by extracellular calcium in the range of 10(-8)-2.5 X 10(-3) M, suggesting that calcium is not required at the site of endocytotic membrane fusion. Membrane retrieval is also unaffected by Lanthanum (1 mM) but is slowed by hypertonic media.

Estimation of gene expression in heterocysts of Anabaena variabilis by using DNA-RNA hybridization

In the filamentous cyanobacterium Anabaena variabilis, specialized cells called heterocysts occur in a regular pattern along the filament and are the sites of nitrogen fixation. We used two different types of DNA-excess RNA hybridization techniques to estimate the number of genes expressed in recently differentiated, mature heterocysts. In the first, RNA and DNA were incubated in a phosphate buffer at 60 degrees C, and the hybrids were separated from the unhybridized material by hydroxylapatite chromatography. In the second, the nucleic acids were incubated at 50 degrees C in a buffer containing 50% formamide, and the fraction of DNA in duplexes was assayed by S1 nuclease digestion. Both techniques revealed that approximately 65% of the A. variabilis genome was expressed in vegetative cells and 45% of the genome was expressed in heterocysts. Two experiments were conducted to estimate the number of heterocyst-specific mRNA transcripts. In one, hybridization of heterocyst RNA to a null DNA probe (DNA not transcribed in vegetative cells) revealed that heterocyst-specific transcripts were encoded by 25% of the DNA sense strand, representing approximately 1,000 genes (assuming each to be 1,500 nucleotides in length). The second approach, in which total cell DNA was hybridized to a mixture of heterocyst and vegetative cell RNA, indicated that 14.7% of the DNA sense strand, or about 600 genes, was transcribed exclusively in the heterocyst. The remaining 900 to 1,300 transcripts present in the heterocyst appeared to be constitutively produced in both vegetative cells and heterocysts. The heterocyst-specific transcripts were present in abundant copies in the cell, while transcripts that occurred in both cell types were present at much lower frequency.

Identification of multiple binding sites for [3H]5-hydroxytryptamine in the rat CNS

Recent studies indicate that there may be multiple subtypes of [3H]5-hydroxytryptamine ([3H]5-HT) binding sites. Mianserin and spiperone inhibited the specific binding of [3H]5-HT (2-3 nM) to rat brain cortical membranes with shallow displacement curves. The displacement data for spiperone were best described by the presence of three independent binding sites, for which spiperone had high, medium, and low affinities. The displacement data for mianserin were best fitted by two independent, high- and low-affinity sites. The inclusion of mianserin (250 nM) to inhibit [3H]5-HT binding to the mianserin-sensitive site selectively blocked one of the sites discriminated by spiperone. These results suggest the presence of three binding sites for [3H]5-HT, one blocked by low concentrations of spiperone (5-HT1A), one blocked by low concentrations of mianserin (5-HT1C), and one blocked only by high concentrations of both mianserin and spiperone (5-HT1B). Regional differences in the relative densities of the three sites were observed. The hippocampus was rich in 5-HT1A sites, whereas the striatum contained mainly 5-HT1B and 5-HT1C sites. Selective degeneration of 5-HT-containing nerve terminals induced by the neurotoxin 5,7-dihydroxytryptamine increased binding to all three sites in the cerebral cortex. Binding of [3H]5-HT to the three sites was differentially modulated by CaCl2 and guanylimidodiphosphate. The present data suggest the presence of three independent 5-HT1 binding sites having different affinities for mianserin and spiperone and having different regional distributions.

Human oestrogen receptor cDNA: sequence, expression and homology to v-erb-A

We have cloned and sequenced the complete complementary DNA of the oestrogen receptor (ER) present in the breast cancer cell line MCF-7. The expression of the ER cDNA in HeLa cells produces a protein that has the same relative molecular mass and binds oestradiol with the same affinity as the MCF-7 ER. There is extensive homology between the ER and the erb-A protein of the oncogenic avian erythroblastosis virus.

The effect of synthetic analogues of chymostatin upon protein degradation in isolated skeletal muscle

A series of peptides based on the structure of the proteinase inhibitor chymostatin were tested for their toxicity and ability to suppress protein degradation in the isolated mouse diaphragm. The inhibitory activities of the analogues were very similar, in marked contrast to their disparate abilities as inhibitors of chymotrypsin. Toxicity was determined by measurement of the rates of protein synthesis and of leakage of lactate dehydrogenase into the incubation medium. No significant toxicity was measurable at concentrations of inhibitor that were effective at suppressing proteolysis. The structural features of the chymostatin molecule may be less than optimal for suppression of proteolysis in muscle.