Contrasting patterns of nucleotide sequence variation at the glucose dehydrogenase (Gld) locus in different populations of Drosophila melanogaster

We have analyzed nucleotide sequence variation at the Glucose dehydrogenase (Gld) locus from four populations of Drosophila melanogaster from four continents. All four population samples show a significant reduction in silent variation compared to the neutral expectation. The levels of silent variation across all four populations are consistent with the predictions of the background selection model; however, Zimbabwe has a remarkably low level of variation. In the face of dramatically reduced silent polymorphism, an amino acid variant, leading to the common allozyme polymorphism at Gld, remains in low to intermediate frequency in all non-African samples. In the Chinese population sample, the ratio of replacement to silent variation is significantly elevated compared to the neutral expectation. The difference in patterns of variation across these population samples suggests that selection on Gld (or the Gld region) has been different in the Chinese population than in the other three.     

Simultaneous automated determination of glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase activities in whole blood

We have shown previously that the non-steroidal anti-inflammatory drug flufenamate (FFA) causes a maintained increase in [Ca2+]i and transient increases in a Ca(2+)-activated nonselective cation current (ICAN) and a Ca(2+)-activated slow, outward Cl- current (lo-slow) in molluscan neurons [Shaw T., Lee R.J., Partridge L.D. Action of diphenylamine carboxylate derivatives, a family of non-steroidal anti-inflammatory drugs, on [Ca2+]i and Ca(2+)-activated channels in neurons. Neurosci Lett 1995; 190:121-124]. Here we demonstrate that pretreatment of neurons with 10 microM thapsigargin eliminates the FFA-induced increase in [Ca2+]i and substantially reduces both ICAN and Io-slow supporting the hypothesis that the FFA-induced increase in [Ca2+]i results primarily from Ca2+ release from a thapsigargin-sensitive intracellular store. The [Ca2+]i response appears to be sustained, not by influx of extracellular Ca2+, but by inhibitory effects of FFA on Ca2+ removal from the cytosol. Inhibition of Ca2+ efflux may be an important component of the FFA-induced activation of both ICAN and Io-slow, as Ca2+ release by thapsigargin alone is not sufficient to activate either current. Our data also demonstrate that the effects of FFA on [Ca2+]i, ICAN and Io-slow are reversible and suggest that protein phosphorylation as well as an increase in [Ca2+]i are involved in the FFA-induced activation of Io-slow. Effects on neuronal Ca2+ handling as well as activation of ICAN or Io-slow may partially explain the analgesic effects of FFA.     

The gnd gene encoding a novel 6-phosphogluconate dehydrogenase and its adjacent region of Actinobacillus actinomycetemcomitans chromosomal DNA

Integrin alpha IIb beta 3 is necessary for platelet thrombus formation by virtue of its ability to bind fibrinogen and von Willebrand factor in a regulated fashion and to mediate platelet aggregation. Moreover, alpha IIb beta 3 transduces inward signals in response to ligand binding which promote cytoskeletal reorganization and other post-ligand binding events. Anchorage and signaling through alpha IIb beta 3 appear to be controlled by interactions of intracellular proteins with the cytoplasmic tails of alpha IIb and/or beta 3. The cytoplasmic tails and associated cytoskeletal components may function as a scaffold or nucleation site for the assembly of enzymes, substrates and adaptor molecules into a signaling complex. Identification of the components of this signaling complex and characterization of their dynamic interactions should lead to insights into the molecular basis of platelet activation defects and may provide a rationale for the development of new anti-thrombotic drugs.     

Multiple isotope effects as a probe of proton and hydride transfer in the 6-phosphogluconate dehydrogenase reaction

Primary solvent deuterium, primary substrate deuterium, multiple solvent deuterium/substrate deuterium, and multiple solvent deuterium/13C isotope effects on V/K6PG have been measured for the Candida utilis and sheep liver 6-phosphogluconate dehydrogenases (6PGDH). Proton inventory data suggest the presence of a significant medium effect in a step preceding hydride transfer and the presence of a kinetic solvent deuterium isotope effect on hydride transfer. Multiple isotope effect data confirm the presence of multiple solvent deuterium sensitive steps, likely including a conformational change preceding hydride transfer, hydride transfer, and decarboxylation.     

Allelic diversity at the merozoite surface protein-1 (MSP-1) locus in natural Plasmodium falciparum populations: a brief overview

The merozoite surface protein-1 (MSP-1) locus of Plasmodium falciparum codes for a major asexual blood-stage antigen currently proposed as a major malaria vaccine candidate. The protein, however, shows extensive polymorphism, which may compromise its use in sub-unit vaccines. Here we compare the patterns of allelic diversity at the MSP-1 locus in wild isolates from three epidemiologically distinct malaria-endemic areas: the hypoendemic southwestern Brazilian Amazon (n = 54), the mesoendemic southern Vietnam (n = 238) and the holoendemic northern Tanzania (n = 79). Fragments of the variable blocks 2, 4a, 4b and 6 or 10 of this single-copy gene were amplified by the polymerase chain reaction, and 24 MSP-1 gene types were defined as unique combinations of allelic types in each variable block. Ten different MSP-1 types were identified in Brazil, 23 in Vietnam and 13 in Tanzania. The proportion of genetically mixed infections (isolates with parasites carrying more than one MSP-1 version) ranged from 39% in Brazil to 44% in Vietnam and 60% in Tanzania. The vast majority (90%) of the typed parasite populations from Brazil and Tanzania belonged to the same seven most frequent MSP-1 gene types. In contrast, these seven gene types corresponded to only 61% of the typed parasite populations from Vietnam. Non-random associations were found between allelic types in blocks 4a and 6 among Vietnamese isolates, the same pattern being observed in independent studies performed in 1994, 1995 and 1996. These results suggest that MSP-1 is under selective pressure in the local parasite population. Nevertheless, the finding that similar MSP-1 type frequencies were found in 1994 and 1996 argues against the prominence of short-term frequency-dependent immune selection of MSP-1 polymorphisms. Non-random associations between MSP-1 allelic types, however, were not detected among isolates from Brazil and Tanzania. A preliminary analysis of the distribution of MSP-1 gene types per host among isolates from Tanzania, but not among those from Brazil and Vietnam, shows significant deviation from that expected under the null hypothesis of independent distribution of parasites carrying different gene types in the human hosts. Some epidemiological consequences of these findings are discussed.     

Lipoprotein Lp(a): effects of allelic variation at the LPA locus

Concentrations of the lipoprotein Lp(a) vary widely in healthy individuals, but in many studies, high concentrations are strongly associated with cardiovascular disease. On the basis of lipid and protein composition, Lp(a) is a variant of the atherogenic low-density lipoprotein but differs in possessing the unique apolipoprotein(a) [apo(a)]. Lp(a) concentrations are controlled at the level of biosynthesis of the apo(a) protein, which is encoded by the LPA locus, and allelic differences at LPA are responsible for the bulk of variation in Lp(a) phenotype. In this article we describe several aspects of allelic variation at LPA reported in studies of human and baboons, including (1) polymorphisms for protein size, (2) families of alleles having distinct relationships between apo(a) size and Lp(a) concentration, (3) sequence polymorphisms, (4) a group of alleles whose protein products have a multibanded phenotype, and (5) allelic diversity of null phenotype alleles (whose protein products are not detected in the plasma). The data make clear that no single aspect of allelic variation at LPA is sufficient to fully explain the genetic control of Lp(a).     

Mitochondrial DNA haplotype frequencies in natural and experimental populations of Drosophila subobscura

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (>96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima's neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. Both populations were started with the two most frequent mitochondrial haplotypes, but at different initial frequencies. After 13 to 16 generations, haplotype II reached fixation in three cages and its frequency was 0.89 by generation 25 in the fourth cage. Random drift can be rejected as the force responsible for the observed changes in haplotype frequencies. There is not only statistical evidence of a linear trend favoring a mtDNA (haploid) fitness effect, but also of a significant nonlinear deviation that could be due to a nuclear component.     

Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis

The background selection hypothesis predicts a reduction in nucleotide site diversity and an excess of rare variants, owing to linkage associations with deleterious alleles. This effect is expected to be amplified in species that are predominantly self-fertilizing. To examine the predictions of the background selection hypothesis in self-fertilizing species, we sequenced 1,362 bp of adh1, a gene for alcohol dehydrogenase (Adh; alcohol:NAD+ oxidoreductase, EC 1.1.1.1), in a sample of 45 accessions of wild barley, Hordeum vulgare ssp. spontaneum, drawn from throughout the species range. The region sequenced included 786 bp of exon sequence (part of exon 4, all of exons 5-9, and part of exon 10) and 576 bp of intron sequence (all of introns 4-9). There were 19 sites polymorphic for nucleotide substitutions, 8 in introns, and 11 in exons. Of the 11 nucleotide substitutions in codons, 4 were synonymous and 7 were nonsynonymous, occurring uniquely in the sample. There was no evidence of recombination in the region studied, and the estimated effective population size (Ne) based on synonymous sites was approximately 1.8-4.2 x 10(5). Several tests reveal that the pattern of nonsynonymous substitutions departs significantly from neutral expectations. However, the data do not appear to be consistent with recovery from a population bottleneck, recent population expansion, selective sweep, or strong positive selection. Though several features of the data are consistent with background selection, the distributions of polymorphic synonymous and intron sites are not perturbed toward a significant excess of rare alleles as would be predicted by background selection.     

A method for selection of mutations at the tdk locus in Escherichia coli

Mutants of Escherichia coli which are resistant to 5-fluorodeoxyuridine all have mutations which map at a single locus at 27.5 min on the genetic map of E. coli. Extracts prepared from each mutant were deficient in thymidine kinase activity measured in vitro. Simple selective conditions which allowed detection of one mutant in the presence of 10(7) wild-type bacteria were found. These results show that loss of thymidine kinase activity is the usual mechanism for 5-fluorodeoxyuridine resistance and that all such mutations occur at the locus previously designated tdk.     

A 2.8 A resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with coenzyme and substrate analogues

The three-dimensional structure of 6-phosphogluconate dehydrogenase (6PGDH) from the parasitic protozoan Trypanosoma brucei has been solved at 2.8 A resolution. This pentose phosphate pathway enzyme is NADP-dependent; NADPH generated in the reaction protects against oxidative stress. The enzyme crystallises in the space-group P3121 with a dimer in the asymmetric unit and cell dimensions a=b=135.13 A, c=116.74 A, alpha=beta=90 degrees, gamma=120 degrees. The structure has refined to R=18.6% (Rfree=27.3%) with good geometry. The amino acid sequence of T. brucei 6PGDH is only 35% identical to that of the sheep liver enzyme and significant activity differences have been observed. The active dimer assembles with the C-terminal tail of one subunit threaded through the other, forming part of the substrate binding site. The tail of T. brucei 6PGDH is shorter than that of the sheep enzyme and its terminal residues associate tightly with the second monomer. The three-dimensional structure shows this generates additional interactions between the subunits close to the active site; the coenzyme binding domain is thereby associated more tightly with the helical domain. Three residues, conserved in all other known sequences, are important in creating a salt bridge between monomers close to the substrate binding site. The differences could explain the 200-fold enhanced affinity observed for the substrate analogue 6-phospho-2-deoxy-D-gluconate and suggest targets for anti-parasite drug design. The coenzyme binding domain of 6PGDH has a beta-alpha-beta fold; while in most species the "fingerprint" sequence is GxAxxG, in the T. brucei enzyme it is GxGxxG. Additional interactions between the enzyme and the coenzyme bis-phosphate are likely in the parasite 6PGDH, accounting for greater inhibition (40-fold) of 2'5'-ADP. While the core of the T. brucei dimer was restrained during refinement, several conformational differences have been found between the monomers; those at the coenzyme binding site suggest the molecule could be asymmetric during the enzyme reaction.     

Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum

Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal group that inhabits cold and temperate terrestrial and marine environments. To date these organisms have resisted isolation in pure culture, and so their phenotypic and genotypic characteristics remain largely unknown. To characterize these archaea, and to extend methodological approaches for characterizing uncultivated microorganisms, we initiated genomic analyses of the nonthermophilic crenarchaeote Cenarchaeum symbiosum found living in association with a marine sponge, Axinella mexicana. Complex DNA libraries derived from the host-symbiont population yielded several large clones containing the ribosomal operon from C. symbiosum. Unexpectedly, cloning and sequence analysis revealed the presence of two closely related variants that were consistently found in the majority of host individuals analyzed. Homologous regions from the two variants were sequenced and compared in detail. The variants exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping region. Our study not only indicates the potential for characterizing uncultivated prokaryotes by genome sequencing but also identifies the primary complication inherent in the approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic populations.     

On the locus of visual selection: Evidence from focused attention tasks.

Early and late selection models of attention disagree about whether visual objects are identified before or after selection, with recent evidence of interference from to-be-ignored stimuli favoring late selection over early selection accounts. However, these tests may not have permitted optimal attentional focusing. In 4 experiments subjects identified an attentionally cued target letter embedded among distractors. Only minimal effects of information appearing in to-be-ignored locations were observed. This striking efficiency of selection provides support for early selection theories and calls into question some late selection theories holding that stimuli throughout the display are immediately and fully identified prior to attentional selection. In order to explain the larger pattern of results across a variety of focused- and divided-attention paradigms, a hybrid model is advanced with a flexible locus for visual selection. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Variation in the sequence of a mitochondrial NADH dehydrogenase I gene fragment among six natural populations of Schistosoma japonicum from China

The present study investigated the level of genetic variation among Schistosoma japonicum populations of different geographical origins from mainland China. Polymerase chain reaction-based methods were employed to determine the sequence for a subunit of the mitochondrial NADH dehydrogenase I gene for populations from Zhejiang, Anhui, Jiangxi, Hunan, Hubei and Sichuan. No variation was detectable in the NADH dehydrogenase I sequence within populations from Zhejiang and Hubei, whereas sequence variation of 0.2% was detected within populations from Anhui, Jiangxi, Hunan and Sichuan. Pairwise comparison of the sequences representing the six different populations revealed genetic differences ranging from 0 to 0.6%.     

Genetic variation at the apoA-IV gene locus and response to diet in familial hypercholesterolemia

Plasma lipid response to dietary fat and cholesterol is, in part, genetically controlled. The apolipoprotein A-IV (apoA-IV protein; APOA4, gene) has been shown to influence the response to dietary changes in normolipidemic individuals. The response to diet in subjects with familial hypercholesterolemia (FH) is also variable, and no studies are available on the influence of APOA4 mutations on dietary response in these subjects. We studied the effect of 2 common apoA-IV genetic variants (Gln360-->His and Thr347-->Ser) on the lipid response to the National Cholesterol Education Program type I (NCEP-I) diet in 67 FH heterozygotes (43 women and 24 men). Subjects were studied at baseline (after consuming for 1 month a diet with 35% fat [10% saturated] and 300 mg/d cholesterol) and after 3 months of consuming a low-fat diet. No sex-related differences were found, and results were combined for men and women. The APOA4-360 mutation was assessed in 67 subjects, 51 with genotype 1/1 and 16 with genotype 1/2. The APOA4-2 allele was associated with marginally significantly lower (P=0.049) low density lipoprotein (LDL) cholesterol levels and significantly lower (P=0.027) apoB levels independent of diet effects. After consuming an NCEP-I diet, carriers of the APOA4-2 allele showed a significantly lower reduction in apoB concentration (6.2%) than 1/1 subjects (14.1%; P=0.036); however, no significant differences in response were noted for LDL cholesterol. The APOA4-347 mutation was assessed in 63 individuals, 44 with the A/A allele and 19 with the A/T and T/T alleles. No significant differences were observed in baseline or post-NCEP-I diet values for these 2 groups in total, LDL, and high density lipoprotein cholesterol and plasma apoB levels. After dietary intervention, A/A individuals showed significant reductions in plasma triglyceride and very low density lipoprotein cholesterol levels; no changes were found in carriers of the T allele. Haplotype analysis suggested that in these FH subjects, the APOA4-360-2 allele was associated with lower plasma lipid levels during the NCEP-I diet period, whereas no significant effects were observed for the APOA4-347-T allele.     

Genetic diversity at a single locus under viability selection and facultative apomixis: equilibrium structure and deviations from Hardy-Weinberg frequencies

We extensively analyze the maintenance of genetic variation and deviations from Hardy-Weinberg frequencies at a diallelic locus under mixed mating with apomixis and constant viability selection. Analytical proofs show that: (1) at most one polymorphic equilibrium exists, (2) polymorphism requires overdominant or underdominant selection, and (3) a simple, modified overdominance condition is sufficient to maintain genetic variation. In numerical analyses, only overdominant polymorphic equilibria are stable, and these are stable whenever they exist, which happens for approximately 78% of random fitness and mating parameters. The potential for maintaining both alleles increases with increasing apomixis or outcrossing and decreasing selfing. Simulations also indicate that equilibrium levels of heterozygosity will often be statistically indistinguishable from Hardy-Weinberg frequencies and that adults, not seeds, should usually be censused to maximize detecting deviations. Furthermore, although both censuses more often have an excess rather than a deficit of heterozygotes, analytical sign analyses of the fixation indices prove that, overall, adults are more likely to have an excess and seeds a deficit at equilibrium.     

Enzyme variation at the aspartate aminotransferase locus in members of the Anopheles gambiae complex (Diptera: Culicidae)

The enzyme aspartate aminotransferase (AAT) currently is used to identify Anopheles quadriannulatus Theobald, the animal-biting, nonmalaria vector species of the Anopheles gambiae complex. Samples of An. quadriannulatus from South Africa and An. gambiae Giles s.str. from the island of Grand Comoros and the People's Republic of Congo have shown variation in electromorph frequencies that indicate that AAT has five alleles. The three slowest alleles are found in An. quadriannulatus and the three fastest in An. gambiae, An. arabiensis Patton and An. merus D?nitz. One of these is common to both An. quadriannulatus and An. gambiae. This overlap indicates a potential misidentification of 0.3% of unknown females with a further 2.1% being unidentifiable. However, all of the specimens in the overlap area were classified correctly using octanol dehydrogenase (ODH). Variation at the ODH locus in An. quadriannulatus is recorded for the first time, with four of 157 specimens being heterozygous for the fast allele. The probability of both AAT and ODH giving an incorrect or indecisive identification is 0.0005. The slowest AAT alleles were present in samples from a single locality, indicating the lack of gene flow between subpopulations of An. quadriannulatus in close geographic proximity in the Shingwedzi area, South Africa. A modified method for multiple gel casting is given.     

Dynamic balance of segregation distortion and selection maintains normal allele sizes at the myotonic dystrophy locus

Myotonic dystrophy (DM), an autosomal dominant neurological disorder, is caused by CTG-repeat expansions at the DMPK locus, with affected individuals having > or = 50 repeats of this trinucleotide. Reduced reproductive fitness of affected individuals and decreased viability of congenital DM have been noted. Expanded CTG-repeat alleles are highly unstable, predominantly yielding even higher repeat sizes. Preferential transmission of longer alleles from heterozygous mothers within the normal size range of alleles also is observed. In view of these observations, it is worth examining how DM has been maintained in human populations for hundreds of generations. We present an analysis of the dynamic properties of a model of joint effects of segregation distortion and selection (intensity of which increases with allele sizes of an individual's genotype). Our mathematical formulation and numerical analyses demonstrate that a weak segregation distortion during female meiosis, together with selection of comparable intensity (within the normal allele size range), can maintain an equilibrium distribution of allele frequencies. Genetic drift, acting in conjunction with the occasional contraction of alleles by mutation, can contribute to the balance of segregation distortion and mutation, in the sense that even weaker selection can explain the observed allele frequencies. The model is applied to CTG-repeat size distributions at the DMPK locus, observed in normal individuals from world populations.     

Enzymatic variability in natural populations of Aedes aegypti (Diptera:Culicidae) from Brazil

Yellowfever mosquitoes, Aedes aegypti (L), were collected from 3 towns located within 70 km of each other in the State of Sao Paulo to evaluate the protein variability of natural populations. Electrophoretic analysis permitted the identification of 6 loci responsible for the production of leucine aminopeptidase, 3 for esterases and malic enzyme, 2 for malate dehydrogenase, isocitrate dehydrogenase and alpha-glycerophosphate dehydrogenase, and 1 for phosphoglucomutase. For the 3 populations, the range for alleles per locus (1.63-2.03), the proportion of polymorphic loci (37.5-50.0%), and the expected mean heterozygosity (0.48-0.53) were greater than reported for other populations of A. aegypti. Although the 3 populations were similar genetically, the 1.8% differentiation was significant.     

Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in a group of filamentous fungi

In filamentous fungi, het loci (for heterokaryon incompatibility) are believed to regulate self/nonself-recognition during vegetative growth. As filamentous fungi grow, hyphal fusion occurs within an individual colony to form a network. Hyphal fusion can occur also between different individuals to form a heterokaryon, in which genetically distinct nuclei occupy a common cytoplasm. However, heterokaryotic cells are viable only if the individuals involved have identical alleles at all het loci. One het locus, het-c, has been characterized at the molecular level in Neurospora crassa and encodes a glycine-rich protein. In an effort to understand the role of this locus in filamentous fungi, we chose to study its evolution by analyzing het-c sequence variability in species within Neurospora and related genera. We determined that the het-c locus was polymorphic in a field population of N. crassa with close to equal frequency of each of the three allelic types. Different species and even genera within the Sordariaceae shared het-c polymorphisms, indicating that these polymorphisms originated in an ancestral species. Finally, an analysis of the het-c specificity region shows a high occurrence of nonsynonymous substitution. The persistence of allelic lineages, the nearly equal allelic distribution within populations, and the high frequency of nonsynonymous substitutions in the het-c specificity region suggest that balancing selection has operated to maintain allelic diversity at het-c. Het-c shares this particular evolutionary characteristic of departing from neutrality with other self/nonself-recognition systems such as major histocompatibility complex loci in mammals and the S (self-incompatibility) locus in angiosperms.