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Biomedical subjects

D B Goldstein

Publications and source records attributed to D B Goldstein.

At least 55 records · Page 3Linked to original sources

Microsatellite variation in North American populations of Drosophila melanogaster.

Computer database searching for microsatellites can be particularly effective for organisms like Drosophila melanogaster for which there are extensive sequence data. Here we demonstrate that 17 out of 18 such microsatellites are also highly polymorphic in natural populations of Drosophila, and that this variation is easily scorable with PCR followed by electrophoresis on high-resolution agarose. This form of variation is likely to be of great value in studies of the genomic distribution of polymorphism, population structure, the relation between intraspecific polymorphism and interspecific divergence and the mutation rate and pattern of mutations of microsatellites. In this preliminary survey of 15 lines, we find that the variance in repeat count is most strongly correlated with the maximum count, that perfect repeats are significantly more variable than imperfect repeats and that repeats which are split by an imperfection have unexpectedly low variance given the size of the perfectly repeated portion.

Alleles↗

Genetic absolute dating based on microsatellites and the origin of modern humans.

We introduce a new genetic distance for microsatellite loci, incorporating features of the stepwise mutation model, and test its performance on microsatellite polymorphisms in humans, chimpanzees, and gorillas. We find that it performs well in determining the relations among the primates, but less well than other distance measures (not based on the stepwise mutation model) in determining the relations among closely related human populations. However, the deepest split in the human phylogeny seems to be accurately reconstructed by the new distance and separates African and non-African populations. The new distance is independent of population size and therefore allows direct estimation of divergence times if the mutation rate is known. Based on 30 microsatellite polymorphisms and a recently reported average mutation rate of 5.6 x 10(-4) at 15 dinucleotide microsatellites, we estimate that the deepest split in the human phylogeny occurred about 156,000 years ago. Unlike most previous estimates, ours requires no external calibration of the rate of molecular evolution. We can use such calibrations, however, to test our estimate.

Animals↗

Population structure, fitness surfaces, and linkage in the shifting balance process.

Wright first introduced the idea that random genetic drift and classical mass-action selection might combine in such a way as to allow populations to find the highest peak in complicated adaptive surfaces. His theory assumes large but structured populations, in which mating is spatially local. If gene flow is sufficiently low, and the subpopulations (demes) are small enough, they will be subject to genetic drift. Distant demes drift independently, allowing many independent searches of the adaptive surface to take place. A deme that has shifted to a higher peak can, by emigration, cause the rest of the demes to shift to the higher peak. The probability of this shift depends on the migration rate. Previous studies have concluded that very little migration is necessary to effect the shift in adaptive peaks that characterizes the last phase of Wright's Shifting Balance Process (SBP). Here we present the results of a computer study that investigates the roles of dispersal distance, the degree of epistasis in the fitness surface, and recombination on the shifting balance process. In particular, we measure their effect on the population's mean fitness. We show that over a range of dispersal distances the advantage of the SBP is a monotonically increasing function of the amount of epistasis. Our results show that the extent of dispersal that results in the greatest effect of the SBP in increasing mean fitness depends on the extent of epistasis. Finally, for low levels of epistasis, higher recombination performs better, while for intermediate levels, lower recombination results in a greater advantage of the SBP.

Adaptation, Biological↗

An evaluation of genetic distances for use with microsatellite loci.

Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

Computer Simulation↗

A comparison of two methods for constructing evolutionary distances from a weighted contribution of transition and transversion differences.

Since the initial work of Jukes and Cantor (1969), a number of procedures have been developed to estimate the expected number of nucleotide substitutions corresponding to a given observed level of nucleotide differentiation assuming particular evolutionary models. Unlike the proportion of different sites, the expected number of substitutions that would have occurred grows linearly with time and therefore has had great appeal as an evolutionary distance. Recently, however, a number of authors have tried to develop improved statistical approaches for generating and evaluating evolutionary distances (Schöniger and von Haeseler 1993; Goldstein and Polock 1994; Tajima and Takezaki 1994). These studies clearly show that the estimated number of nucleotide substitutions is generally not the best estimator for use in reconstruction of phylogenetic relationships. The reason for this is that there is often a large error associated with the estimation of this number. Therefore, even though its expectation is correct (i.e., on average the expected number of substitutions is proportional to time--but see Tajima 1993), it is not expected to be as useful as estimators designed to have a lower variance.

Algorithms↗

Least squares estimation of molecular distance--noise abatement in phylogenetic reconstruction.

Zuckerkandl and Pauling (1962, "Horizons in Biochemistry," pp. 189-225, Academic Press, New York) first noticed that the degree of sequence similarity between the proteins of different species could be used to estimate their phylogenetic relationship. Since then models have been developed to improve the accuracy of phylogenetic inferences based on amino acid or DNA sequences. Most of these models were designed to yield distance measures that are linear with time, on average. The reliability of phylogenetic reconstruction, however, depends on the variance of the distance measure in addition to its expectation. In this paper we show how the method of generalized least squares can be used to combine data types, each most informative at different points in time, into a single distance measure. This measure reconstructs phylogenies more accurately than existing non-likelihood distance measures. We illustrate the approach for a two-rate mutation model and demonstrate that its application provides more accurate phylogenetic reconstruction than do currently available analytical distance measures.

Amino Acid Sequence↗

The evolution of interference: reduction of recombination among three loci.

Crossover events along chromosomes do not occur independently, but influence the probability of other nearby events. The most common interaction between nearby crossover events is inhibitory: a crossover event tends to reduce the probability of other such events nearby, and this is called positive interference. A crossover event may increase the probability of events nearby, and this rare phenomenon is called negative interference. In this paper, we use numerical methods to investigate how interference among three loci would evolve if it were under the genetic control of a fourth, selectively neutral locus. We first discuss the effect of interference on the overall rate of recombination among the three loci, and then show that, under a variety of conditions, interference evolves in the same way as would be predicted based upon its effect on the overall rate of recombination. That is, the overall rate evolves in the same direction as would the rate at a locus that controls recombination between two loci directly. We then check for the existence of viability-analogous Hardy-Weinberg equilibria in the four-locus model of interference modification.

Crossing Over, Genetic↗

Recombination and the evolution of diploidy.

With two copies of every gene, a diploid organism is able to mask recessive deleterious mutations. In this paper we present the analysis of a two-locus model designed to determine when the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases ("alternation of generations"). It is hypothesized that diploidy will be favored whenever masking occurs ("the masking hypothesis"). Using analytical methods, we confirm that this masking hypothesis is essentially correct under free recombination: as long as the heterozygous expression of deleterious alleles is sufficiently masked by the wild-type allele, diploidy is favored over haploidy. When the rate of recombination is lower, however, diploidy is much less likely to be favored over haploidy. In fact, according to our model, the evolution of diploidy is impossible without significant levels of recombination even when masking is fairly strong.

Biological Evolution↗

Heterozygote advantage and the evolution of a dominant diploid phase.

The life cycle of eukaryotic, sexual species is divided into haploid and diploid phases. In multicellular animals and seed plants, the diploid phase is dominant, and the haploid phase is reduced to one, or a very few cells, which are dependent on the diploid form. In other eukaryotic species, however, the haploid phase may dominate or the phases may be equally developed. Even though an alternation between haploid and diploid forms is fundamental to sexual reproduction in eukaryotes, relatively little is known about the evolutionary forces that influence the dominance of haploidy or diploidy. An obvious genetic factor that might result in selection for a dominant diploid phase is heterozygote advantage, since only the diploid phase can be heterozygous. In this paper, I analyze a model designed to determine whether heterozygote advantage could lead to the evolution of a dominant diploid phase. The main result is that heterozygote advantage can lead to an increase in the dominance of the diploid phase, but only if the diploid phase is already sufficiently dominant. Because the diploid phase is unlikely to be increased in organisms that are primarily haploid, I conclude that heterozygote advantage is not a sufficient explanation of the dominance of the diploid phase in higher plants and animals.

Alleles↗

Formation of fatty acid ethyl esters during chronic ethanol treatment in mice.

Ethyl esters of long-chain fatty acids are formed in the liver and brain of mice after 1-6 days of ethanol intoxication. This observation extends the reports of Lange and co-workers who detected these compounds as unusual metabolites of ethanol in human tissues [E. A. Laposata and L. G. Lange, Science 231, 497 (1986)]. Ethyl esters of oleic and linoleic acids, and, in smaller amounts, ethyl esters of palmitic and stearic acids were found in the livers of mice that had been treated with ethanol by inhalation. In the brain, only the esters of unsaturated fatty acids were found, in lower amounts than in liver. All the fatty acid ethyl esters seemed to have reached steady-state levels in the tissues after 3 or 4 days of alcohol treatment. When incorporated into synaptosomal plasma membranes in vitro, in intramembrane concentrations estimated to resemble those observed in the mice, these esters reduced the fluorescence anisotropy, i.e. they disordered the membranes.

Alcoholism↗

Plasticizers as contaminants in commercial ethanol.

A batch of 95% ethanol caused unusually strong disordering of biomembranes, which could be detected either by fluorescence anisotropy in synaptosomal membranes or by electron paramagnetic resonance spectroscopy in erythrocyte membranes. The contaminated batches of ethanol were visibly fluorescent when evaporated on filter paper. The adulterants were separated by capillary gas chromatography and the ubiquitous pollutant dioctylphthalate was identified by its low resolution electron impact mass spectrum. The remaining peaks, which were not recognized by any of the available mass spectral libraries, were identified by high resolution electron impact and chemical ionization mass spectrometry and low resolution tandem mass spectrometry using fast atom bombardment ionization; they were triethylene glycol esters and aryl phosphates. All the contaminants are industrial plasticizers. Distillation resulted in loss of the strong disordering properties of the alcohol.

Animals↗

The alcohol withdrawal syndrome. A view from the laboratory.

Animal models of the alcohol-dependent state, now readily available in many species, show that a withdrawal reaction can be produced whenever intoxication has been continuously maintained, even for short periods of time. The development of the tolerant/dependent state resembles a physiological adaptation in two ways: (1) the animal is no longer much affected by the drug, and (2) withdrawal reveals a condition of CNS hyperexcitability that is the opposite of the primary drug effect. This adaptation is believed to arise in response to ethanol's disordering effect in cell membranes (increased membrane fluidity). Spectrometric techniques such as electron spin resonance and fluorescence polarization reveal that cell membranes of ethanol-withdrawn animals are often abnormally rigid and resistant to ethanol-induced disorder, and it is thought that these changes may correspond to physical dependence and tolerance, respectively. Alterations in the chemical composition of the membranes can often (but not always) explain the abnormal physical properties. The relation between membrane order and ethanol-induced behavioral states is not known in detail, but these observations form a basis for a rational picture of the biochemical changes responsible for the withdrawal syndrome.

Alcoholism↗

Effect of alcohol on cellular membranes.

Ethanol disrupts the physical structure of cell membranes. The most fluid membranes, including those that are low in cholesterol, are the most easily disordered by ethanol. Although the membrane-disordering effect is small, there is pharmacological, temporal, and genetic evidence that it is important. Animals that are resistant to ethanol intoxication because of their genetic background or because of previous exposure to ethanol are found to have brain membranes that are not easily disordered in vitro. An exception is the increased behavioral sensitivity in aging animals, which is not matched by changes in their membranes. When animals are treated chronically with ethanol, their membranes become stiffer, a response that can be regarded as adaptive. Ethanol may favor the uptake of cholesterol or saturated fatty acids into membranes, thus reducing its own effect.

Aging↗

Cholesterol blocks the disordering effects of ethanol in biomembranes.

To assess the relation between the physical order of a membrane and its sensitivity to ethanol, we enriched biomembranes with cholesterol, both in vivo and in vitro. Japanese quail of the SEA line (selectively bred for susceptibility to experimental atherosclerosis) were treated for 9 to 16 weeks with a diet that contained 2% cholesterol. This regimen increased the cholesterol content of serum and erythrocytes. The cholesterol content of brain synaptosomal plasma membranes (SPM) was unaffected by the high cholesterol diet. In other experiments, isolated mouse synaptosomal plasma membranes were incubated with cholesterol/phospholipid (C/P) vesicles; different amounts of cholesterol were transferred according to the sterol content of the donor vesicles. Membrane order was determined in both types of membranes by a sensitive electron paramagnetic resonance (EPR) technique. The order parameter with 5- and 12-doxylstearic acid increased along with the cholesterol content. As expected, ethanol disordered membranes (decreased the order parameter) in a concentration-related manner. The slope of the concentration response curve was less steep in high cholesterol than low cholesterol membranes, indicating that cholesterol enrichment partially blocks the membrane action of ethanol in both types of membranes.

Animals↗

The effects of drugs on membrane fluidity.

Anesthetics almost always disorder or "fluidize" membranes, i.e. the drugs increase the mobility of spin labels and reduce order parameters. This effect is universal at high concentrations above the clinical range, but in some kinds of membranes low concentrations of drugs have an ordering effect. Drugs that carry charges, including many local anesthetics, often stiffen membranes, as do long-chain alcohols or fatty acids that mimic natural membrane components. The potencies of short-chain alcohols correlate well with lipid solubility, but a cutoff is reached at 10-12 carbons, where pharmacological actions become weak or absent despite a progressive increase in lipid solubility. The cutoff is partly explained by the ordering action of the long chains and partly by the difficulty of administering such water-insoluble drugs in vivo. The idea of membrane disorder does not exclude some specificity. Closely related drugs may have different molecular shapes and may be capable of forming hydrogen bonds with different orientations, affecting their ability to make membrane more fluid. Perhaps for this reason, there is a remarkable stereospecificity in the disordering effect of anesthetic steroids, chloralose, and long-chain alkenols. Some specificity is mediated by different membrane environments. The drug action may actually reverse from order to disorder on addition of cholesterol, but in other experimental systems cholesterol blocks a disordering effect, and we cannot yet explain the action of drugs in different biomembranes. Further, drugs may have differential solubilities in membranes of different composition. This cannot always be predicted from octanol:water partition coefficients because branched molecules are differentially excluded from structured bilayers. Charged drugs react quite differently with charged and neutral phospholipids and may have differential actions on the two sides of the bilayer because of the asymmetry of the phospholipid distribution. The deeper reaches of the membrane seem particularly sensitive to disordering, even by drugs that presumably reside near the surface. Thus, proteins whose midregions are sensitive to disordering may be especially disrupted by drugs. This is a new field of pharmacology, currently applied only to a small group of drugs. But an understanding of the physiocochemical actions of drugs in hydrophobic regions of cells will clearly be needed for full understanding of membrane-bound drug receptors, enzymes, and transport systems. This is just a beginning.

Alcohols↗

Genetic influences on the central nervous system depressant and membrane-disordering actions of ethanol and sodium valproate.

The effects of the two central nervous system (CNS) depressant drugs ethanol and sodium valproate were compared using two pairs of mouse lines that had been selected from a heterogeneous stock for differential sensitivity to ethanol. The LS/SS lines differ in sensitivity to ethanol-induced sedation, and the WSP/WSR lines differ in the severity of their withdrawal convulsions after chronic ethanol treatment. We used these lines to test the hypothesis that ethanol and valproate act by the same mechanism. CNS depressant action was assessed by determining the brain drug concentration at which the mice lost their ability to balance on a stationary wooden dowel. LS mice were about twice as sensitive as SS mice to valproate-induced ataxia, in agreement with their reported relative sensitivity to ethanol. The WSR and WSP mice did not differ significantly in sensitivity to ethanol or valproate in this test. The intrinsic order and sensitivity to disordering of synaptosomal plasma membranes prepared from the four lines were measured using fluorescence polarization with the probe 1,6-diphenyl-1,3,5-hexatriene and EPR spectroscopy with 5-doxylstearic acid. No differences in the intrinsic membrane order of the four lines were detected with either technique. The sensitivities of the membranes from the four lines to ethanol- or valproate-induced disordering were not significantly different when measured by fluorescence polarization, but EPR spectroscopy revealed line differences in disordering sensitivity that correlated with the relative sensitivity of the four lines to the CNS depressant action of these drugs. These studies show that genetic factors modulate sensitivity to ethanol and valproate in a similar manner both in vivo and in vitro, suggesting that these drugs act by the same membrane-disordering mechanism.

Animals↗

Membrane-disordering potency and anticonvulsant action of valproic acid and other short-chain fatty acids.

The cell membrane-disordering potencies of sodium valproate, the sodium salts of other short-chain fatty acids, and ethanol were compared using fluorescence polarization with the probe 1,6-diphenyl-1,3,5-hexatriene. Valproate was about 7 times more potent in fluidizing synaptosomal plasma membranes than ethanol, a prototypic disordering agent. The disordering potency of the straight-chain fatty acids pentanoate through octanoate increased by a factor of 2.2 with each additional methylene group. The sedative potencies of the drugs were assessed by determining the brain concentration at which Swiss Webster mice lost the ability to balance on a stationary wooden dowel. Relative anticonvulsant potency was measured by determining the ED50 for protection against pentylenetetrazol-induced seizures and then determining the brain levels of drug that were actually achieved at the time of seizure protection. The ability of the fatty acids and ethanol to disorder membranes in vitro correlated closely with their ability to cause sedation and protect mice against pentylenetetrazol-induced seizures. These data suggest that valproic acid might exert some of its effects by disordering brain cell membranes--the proposed mechanism of action of ethanol and the general anesthetics.

Animals↗