Isolation and characterization of cDNA clones corresponding to two different human apoC-III alleles

We have recently reported that the human apolipoprotein A-I (apoA-I) and apolipoprotein C-III (apoC-III) genes are physically linked and that the presence of a DNA insertion in the apoA-I gene is correlated with apoA-I-apoC-III deficiency in patients with premature atherosclerosis. In addition, the presence of a polymorphic restriction endonuclease site (SacI) in the 3' noncoding region of apoC-III mRNA has been correlated with hypertriglyceridemia in humans. In this study, we report the isolation and characterization of cDNA clones containing the entire apoC-III mRNA coding sequence. The nucleotide-derived apoC-III amino acid sequence indicates that the apoC-III primary translational product contains a 20 amino acid N-terminal extension, which conforms with the general properties of known signal peptides, and is highly homologous to the recently reported rat apoC-III signal peptide. The DNA-derived apoC-III amino acid sequence differs from the previously reported apoC-III amino acid sequence at four amino acid residues. More specifically, at positions +32, +33, +37, +39, the DNA sequence predicts Glu, Ser, Gln, Ala, respectively, while the previously reported sequence specifies Ser, Gln, Ala, Gln, respectively. Finally, isolation and characterization of apoC-III cDNA clones, with or without the polymorphic SacI restriction site, indicated that the apoC-III nucleotide sequence corresponding to the Sac+ and Sac- clones differs at three nucleotide sites; however, the amino acid sequence specified by the Sac+ and Sac- alleles is identical.     

The effect of deleterious alleles on adaptation in asexual populations

We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.     

Genetic and dietary adaptation to malaria in human populations

Plasmodial invasion places a severe oxidant stress on parasitized erythrocytes which can result in red cell damage and removal within the reticuloendothelial system or lysis, thus interrupting the parasitic cycle. The basis of a number of genetic adaptations to malaria--including the hemoglobin variants, the thalassemias, and glucose-6-phosphate dehydrogenase deficiency--is an increased sensitivity of the variant erythrocytes to the oxidant stress of plasmodial parasitization. It is suggested that dietary adaptations of traditional cusines in human populations living in areas where malaria is endemic augment this oxidant stress. It appears that there are three components of this adaptive dietary pattern in most tropical populations: the consumption of 'oxidant fuels', moderate to high iron intake, and limitation of dietary antioxidant intake or storage. It is argued that this dietary pattern maximizes iron-mediated free radical production in parasitized erythrocytes and thus provides a form of diet-mediated antimalarial prophylaxis. African pastoral populations that are heavy consumers of milk appear to manifest a different adaptive pattern involving low intakes of para-aminobenzoic acid, vitamin E, and iron. Periodic food restriction may also contribute to this antimalarial effect.     

DNA diversity in modern East European human populations in view of demographic history and adaptation

The interaction of the human genome with the changing environment moulds the genetic structure of human populations. The variability of autosomal loci and the haplotype diversity was studied in geographically diverse populations from Russia and neighboring countries. Basic tendencies in variability were investigated concerning specific types of polymorphism. The results reveal marked differences between East European populations and those from the Asian part of Russia. The possible effects of climatic-geographic factors on the allele and haplotype frequencies have been studied for some loci. The existences of these correlations provide evidence of possible effect of both adaptation to natural environmental factors and large-scale population movements on the specificity and diversity of gene pool.     

Genetic and morphological similarity of two California gull populations with different life history traits

California Gulls nesting at Mono Lake (ML) have a modal clutch size of two eggs, while at Great Salt Lake (GSL) the mode is three. We used starch gel electrophoresis to determine whether the populations are genically different. Average individual heterozygosity at ML averages 2.67% and at GSL 2.95%, both slightly below the average for other birds. The average number of alleles per locus is 1.2 for both sites. Variation between sites is insignificant, with a genetic distance of 0.001 and an F_ST of 0.0044. Therefore, the clutch size differences are without genic correlates. In fact, at the loci studied, the two samples are indistinguishable from two random samples drawn from a panmictic unit. Five morphological characteristics also exhibited little between-site difference, in agreement with the electrophoretic analysis. A marked historical reduction (bottleneck) in the Mono Lake population seems not to have affected levels of genetic variation. We conclude that the clutch size differences are either recently evolved, and determined by loci not surveyed by us, or they are environmentally induced. At the population level, these gulls are similar to passerines in terms of heterozygosity and among population differentiation.     

Genetic adaptation in emergence time ofClunio populations to different tidal conditions

Summary 1. The emergence times of intertidalClunio-species (Diptera, Chironomidae) are correlated with special tidal conditions in such a way that the immediately following reproduction of the short-lived imagos can take place on the exposed habitat.2. If the habitat of aClunio-species is situated in the middle tidal region and exposed twice a day by the tidal cycle (T = 12.4 h), a tidal rhythm of emergence with an average period of 12.4 hours may result (example:Clunio takahashii).3. If the habitat is located in the lower tidal zone, exposed only at about the time of the spring tides, a semilunar rhythm of emergence is expected (examples:Clunio marinus andClunio mediterraneus). These semilunar rhythms are correlated with certain conditions of low tide which occur at the coastal locations every 15 days at about the same time of day. The semilunar rhythm is therefore exactly characterized by two dates: the lunar emergence time (a few successive days around full and new moon) and the diurnal emergence time.4. According to experimental investigations on the control of the emergence rhythm, the midges are able to determine both dates in advance.5. Coastal populations differ in their lunar and diurnal emergence times. These differences correspond to the time of low tide which exists at each location during the emergence days of the semilunar rhythm.6. Crossbreeding between stocks of different populations showed that the differences in diurnal emergence time are gene-controlled.

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Genetische Adaptation der Schlüpfzeiten vonClunio-Populationen an verschiedene Gezeitenbedingungen

Kurzfassung Die Schlüpfzeiten der in der Gezeitenzone lebendenClunio-Arten (Diptera, Chironomidae) sind mit bestimmten Wasserstandsbedingungen synchronisiert, und zwar derart, daß die unmittelbar anschließende Fortpflanzung der kurzlebigen Imagines auf dem trockengefallenen Habitat stattfinden kann. Wenn das Habitat einerClunio-Art in der mittleren Gezeitenzone liegt und parallel zu dem halbtägigen Gezeitenzyklus (T = 12,4 h) zweimal täglich auftaucht, dann kann sich eine 12,4stündige Schlüpfperiodik einstellen (Beispiel:Clunio takahashii). Wenn das Habitat in der unteren Gezeitenzone liegt und nur um die Zeit der Springtiden auftaucht, dann ist eine 15tägige (semilunare) Schlüpfperiodik zu erwarten (Beispiele:Clunio marinus undC. mediterraneus). Diese 15tägige Schlüpfperiodik ist synchronisiert mit bestimmten Niedrigwasserbedingungen, die an einem Küstenort alle 15 Tage jeweils um die gleiche Tageszeit auftreten. Sie wird daher durch zwei Daten eindeutig gekennzeichnet: (1) die lunaren Schlüpftage (wenige aufeinanderfolgende Tage um Voll- und Neumond) und (2) die tägliche Schlüpfzeit. Wie experimentelle Untersuchungen über die Steuerung der Schlüpfperiodik zeigten, können die Tiere beide Daten richtig vorausbestimmen. Die einzelnen Küstenpopulationen unterscheiden sich allerdings in Anpassung an die örtlichen Gezeiten- und Standortbedingungen recht auffällig in ihren lunaren und täglichen Schlüpfzeiten. Kreuzungsversuche zwischen Laboratoriumsstämmen verschiedener Populationen belegen, daß die Unterschiede in der täglichen Schlüpfzeit genkontrolliert sind.

     

Repeatability of adaptation in experimental populations of different sizes

The degree to which evolutionary trajectories and outcomes are repeatable across independent populations depends on the relative contribution of selection, chance and history. Population size has been shown theoretically and empirically to affect the amount of variation that arises among independent populations adapting to the same environment. Here, we measure the contribution of selection, chance and history in different-sized experimental populations of the unicellular alga Chlamydomonas reinhardtii adapting to a high salt environment to determine which component of evolution is affected by population size. We find that adaptation to salt is repeatable at the fitness level in medium (N_e = 5 × 10⁴) and large (N_e = 4 × 10⁵) populations because of the large contribution of selection. Adaptation is not repeatable in small (N_e = 5 × 10³) populations because of large constraints from history. The threshold between stochastic and deterministic evolution in this case is therefore between effective population sizes of 10³ and 10⁴. Our results indicate that diversity across populations is more likely to be maintained if they are small. Experimental outcomes in large populations are likely to be robust and can inform our predictions about outcomes in similar situations.     

Efficient introduction of cloned mutant alleles into the Escherichia coli chromosome.

An efficient method for moving mutations in cloned Escherichia coli DNA from plasmid vectors to the bacterial chromosome was developed. Cells carrying plasmids that had been mutated by the insertion of a resistance gene were infected with lambda phage containing homologous cloned DNA, and resulting lysates were used for transduction. Chromosomal transductants (recombinants) were distinguished from plasmid transductants by their ampicillin-sensitive phenotype, or plasmid transductants were avoided by using a recBC sbcB E. coli strain as recipient. Chromosomal transductants were usually haploid when obtained in a nonlysogen because of selection against the lambda vector and partially diploid when obtained in a lysogen. Pure stocks of phage that carry the resistance marker and transduce it at high frequency were obtained from transductant bacteria. The lambda-based method for moving mutant alleles into the bacterial chromosome described here should be useful for diverse analyses of gene function and genome structure.     

Donor age reflects the replicative lifespan of human fibroblasts in culture

Human fibroblasts, which have a finite lifespan in cultures, have been widely used as a model system for cellular aging, and frequently used as one model of human aging. But whether cellular aging contributes to organismal aging has been controversial. To reinvestigate this question, we cultured human fibroblasts from the skin of one individual volunteer collected at different ages. Over a period of 27 years (donor age 36 years to 62 years), we obtained skin cells four times at appropriate intervals, and established eight fibroblast lines. These human fibroblasts have presented evidence for a correlation between donor age and proliferative lifespan in vitro . This result parallels the fact that telomeric DNA size cultured fibroblasts decrease with the increase in donor age. These cell lines had a normal diploid human chromosome constitution and will be useful in studies of human biology including aging.     

Vocal frequency change reflects different responses to anthropogenic noise in two suboscine tyrant flycatchers

Anthropogenic noise is prevalent across the globe and can exclude birds from otherwise suitable habitat and negatively influence fitness; however, the mechanisms responsible for species' responses to noise are not always clear. One effect of noise is a reduction in effective acoustic communication through acoustic masking, yet some urban songbirds may compensate for masking by noise through altering their songs. Whether this vocal flexibility accounts for species persistence in noisy areas is unknown. Here, we investigated the influence of noise on habitat use and vocal frequency in two suboscine flycatchers using a natural experiment that isolated effects of noise from confounding stimuli common to urban habitats. With increased noise exposure, grey flycatcher (Empidonax wrightii) occupancy declined, but vocal frequency did not change. By contrast, ash-throated flycatcher (Myiarchus cinerascens) occupancy was uninfluenced by noise, but individuals in areas with greater noise amplitudes vocalized at a higher frequency, although the increase (≈200 kHz) may only marginally improve communication and may represent a secondary effect from increased vocal amplitude. Even so, the different flycatcher behavioural responses suggest that signal change may help some species persist in noisy areas and prompt important questions regarding which species will cope with an increasingly noisy world.     

Molecular polymorphism of O alleles in five populations of different ethnic origins

Sequences of exons 6 and 7 of the O allele of the ABO gene were studied in 317 individuals of the O phenotype from five different ethnic groups (Basques, Berbers, Akans from the Ivory Coast, and Amerindians: Cayapas from Ecuador and Aymaras from Bolivia). Twenty-one O alleles were characterized, among which 9 differed from all O alleles reported to date. The nine alleles differed from either the O01 allele (four out of nine) or O02 allele (five out of nine) by one to three point mutations. The number of different O alleles in population samples varied greatly: the highest number (13) was observed in Akans, and the lowest (5) in Amerindians. Some rare alleles previously reported by others at low frequencies were found with high frequencies in the Akans. The results also revealed a decreasing frequency of Ov7 alleles from south to north (Akans, Berbers, Basques). Berbers and Basques share two rare alleles, Ov6 and O03, which were not encountered in the other populations studied here.     

Postglacial colonization history reflects in the genetic structure of natural populations of Festuca rubra in Europe

We conducted a large‐scale population genetic survey of genetic diversity of the host grass Festuca rubra s.l., which fitness can be highly dependent on its symbiotic fungus Epichloë festucae, to evaluate genetic variation and population structure across the European range. The 27 studied populations have previously been found to differ in frequencies of occurrence of the symbiotic fungus E. festucae and ploidy levels. As predicted, we found decreased genetic diversity in previously glaciated areas in comparison with nonglaciated regions and discovered three major maternal genetic groups: southern, northeastern, and northwestern Europe. Interestingly, host populations from Greenland were genetically similar to those from the Faroe Islands and Iceland, suggesting gene flow also between those areas. The level of variation among populations within regions is evidently highly dependent on the postglacial colonization history, in particular on the number of independent long‐distance seed colonization events. Yet, also anthropogenic effects may have affected the population structure in F. rubra. We did not observe higher fungal infection rates in grass populations with lower levels of genetic variability. In fact, the fungal infection rates of E. festucae in relation to genetic variability of the host populations varied widely among geographical areas, which indicate differences in population histories due to colonization events and possible costs of systemic fungi in harsh environmental conditions. We found that the plants of different ploidy levels are genetically closely related within geographic areas indicating independent formation of polyploids in different maternal lineages.     

Characterization of human glucocerebrosidase from different mutant alleles.

Human cDNA was mutagenized to duplicate six naturally occurring mutations in the gene for glucocere-brosidase. The mutant genes were expressed in NIH 3T3 cells. The abnormal human enzymes were purified by immunoaffinity chromatography and characterized. The Asn370----Ser mutant protein differed from normal enzyme in its inhibition by both conduritol B epoxide and glucosphingosine demonstrating that the 370 mutant enzyme has an abnormal catalytic site. In addition, the 370 mutant enzyme is less activated by saposin C, but more stimulated by phosphatidylserine than the wild type enzyme. The Arg463----Cys mutant protein was normal with respect to conduritol B epoxide and glucosphingosine inhibition, but was less activated by both saposin C and phosphatidylserine. The Arg120----Gln mutant protein was catalytically inactive. The Leu444----Pro, the pseudopattern, and the Pro415----Arg mutants appear to have reduced amounts of enzyme protein in cells. The studies demonstrated that mutations in the gene for glucocerebrosidase have different effects on the catalytic activity and stability of the enzyme.     

The cell kinetics of the adaptation of the human esophagus to organ culture

Summary The adaptation of normal human esophageal explants to organ culture for the first 33 d of in vitro growth was evaluated using histomorphology and [³H]TdR autoradiography combined with mitotic blockade. On the 3rd d in culture, extensive desquamation of superficial cells reduced the epithelium to about four cell layers. Thereafter, the epithelium remained atrophic, with a relative increase in basal and suprabasal cells. The percentage of cells synthesizing DNA was greatest from Day 4 through 8, just after desquamation, and reached a maximum on Day 4 (24 h [³H]TdR labeling index of 62%). The labeling index (LI) fluctuated, thereafter, but remained high (26% on Day 33). During the last 6 h of each [³H]TdR labeling interval, mitosis was blocked by colcemid. The 6 h mitotic rate (MR) was a reasonably constant fraction of the LI (maximum at 4 d: MR=1.44%), but was much lower than predicted by [³H]TdR labeling indicating the loss of large numbers of cells after DNA synthesis but before or during mitosis. Unlabeled mitotic figures appeared between Days 1 to 3 and 6 to 33, suggesting that the epithelium initially contained a considerable population of cells arrested or delayed in G₂ and continued to generate cells that remained in premitosis longer than 24 h. These results indicate that the atrophy observed in vitro is characterized by a relative increase in the basal and suprabasal cell category, a high replication rate, initial recruitment of cells arrested in premitosis, and rapid cell turnover with significant loss of cells at the premitotic or mitotic step, or both. Thus it seems that human esophageal epithelium grown in organ culture is a satisfactory substrate for experimentation (for example, in vitro carcinogenesis) that requires cell replication. However, there are major differences between the kinetics of esophageal epithelium in vivo and in vitro. Supported in part by Contract NOI-CP-75909 and NOI-CP-25604-59 from the National Cancer Institute, Bethesda, MD.     

Genetic differentiation in life history between Daphnia galeata populations: an adaptation to local predation regimes?

Species of the water flea Daphnia exhibit constitutive as wellas phenotypically inducible anti-predator defence strategies,involving life history, morphological and behavioural traits.We explored the hypothesis of genetic differentiation in anti-predatordefence strategies using Daphnia clones originating from twodifferent water bodies: Tjeukemeer (the Netherlands) and FishPond (Belgium). Both water bodies are inhabited by zooplanktivorousfish. In contrast to Tjeukemeer, Fish Pond is also inhabitedby larvae of the phantom midge Chaoborus. The life history responsesof the two sets of clones to kairomones from fish (Perca), tokairomones from Chaoborus, and to a mixture of both were compared.Clones from Tjeukemeer and Fish Pond showed strong responsesto the presence of fish kairomone, with reductions in adultand neonate body length, in age at first reproduction and inthe total number of neonates produced during the first threeadult instars. Responses to Chaoborus kairomone were much lesspronounced, although there was a tendency towards an increasein the number of neonates in the first brood. Significant inter-populationgenetic differences were found for all the investigated traits.However, there was no indication for genetic adaptation of theFish Pond clones to negative size-selective predation by Chaoborus.Compared to Tjeukemeer clones, Fish Pond clones had a lowersize at first reproduction, produced smaller neonates and produceda higher number of neonates in their first brood. This suggestsadaptation to positive rather than to negative size selectivepredation. Genetic differences between populations were observedmainly for constitutive life history traits, rather than forphenotypic shifts in response to the presence of predator kairomones.     

Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC(2)F(3)-derived lines developed using "Elgin" as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC(3)F(3)-derived lines developed with "Williams 82" as the recurrent parent and PI 90566-1 as the donor parent (W population). The two populations were evaluated with 1,536 SNP markers and during 2?years for seed yield and other agronomic traits. Genotypic and phenotypic data were analyzed using the programs MapQTL and QTLNetwork to identify major QTL and epistatic QTL. In the E population, two yield QTL were identified by both MapQTL and QTLNetwork, and the PI 436684 alleles were associated with yield increases. In the W population, a QTL allele from PI 90566-1 accounted for 30?% of the yield variation; however, the PI region was also associated with later maturity and shorter plant height. No epistasis for seed yield was identified in either population. No yield QTL was previously reported at the regions where these QTL map indicating that exotic germplasm can be a source of new alleles that can improve soybean yield.