Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses

Papillomaviruses are attractive models for studying the molecular evolution of DNA viruses because of the large number of isolates that exhibit genomic diversity and host species and tissue specificity. To examine their relationship, we selected two amino acid sequences, one of 52 residues within the early gene E1 and the other of 44 residues within the late gene L1, which allowed insertion- and deletion-free alignment of all accessible papillomavirus sequences. We constructed phylogenetic trees from the amino acid and corresponding nucleotide sequences from 28 published and 20 newly determined animal and human papillomavirus (HPV) genomic sequences by using distance matrix, maximum-likelihood, and parsimony methods. The trees agreed in all important topological aspects. One major branch with two clearly separated clusters contained 11 HPV types associated with epidermodysplasia verruciformis. A second major branch had all the papillomaviruses involved in genital neoplasia and, in distant relationship, the cutaneous papillomaviruses HPV type 2a (HPV-2a), HPV-3, and HPV-10 as well as the "butcher's" papillomavirus HPV-7 and two simian papillomaviruses. Four artiodactyl (even-toed hoofed mammal) papillomaviruses, the cottontail rabbit papillomavirus, and avian (chaffinch) papillomavirus type 1 formed a third major branch. Last, four papillomaviruses exhibited little affinity to any of these three branches; these were the cutaneous types HPV-1a, HPV-4, and HPV-41 and B-group bovine papillomavirus type 4. The phylogeny suggests that some branches of papillomavirus evolution are restricted to particular target tissues and that a general process of long-term papillomavirus-host coevolution has occurred. This latter hypothesis is still conjectural because of bias in the current data base for human types and the paucity of animal papillomavirus sequences. The comparison of evolutionary distances for the most closely related types with those of 28 subtypes and variants of HPV-2, HPV-5, HPV-6, HPV-16, and HPV-18 supports the type as a natural taxonomic unit, with subtypes and variants being expressions of minor intratype genomic diversity similar to that found in the natural populations of all biological species. An exception to this seems to be HPV-2c, which has an evolutionary distance from HPV-2a of the intertype magnitude and may eventually have to be regarded as a distinct type. We describe an experimental approach that estimates the taxonomic and phylogenetic positions of newly identified papillomaviruses without viral isolation and complete genomic sequencing.(ABSTRACT TRUNCATED AT 400 WORDS)

Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex?

Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which apparently indicates restricted recombination between alleles at different loci. The extent to which restricted recombination reflects limited migration between geographically isolated populations versus infrequent mixis of genotypes within populations is more difficult to determine. We examined the genetic structure of Rhizobium leguminosarum biovar phaseoli populations associated with wild and cultivated beans (Phaseolus spp.) over several spatial scales, ranging from individual host plants to throughout the Western Hemisphere. We observed significant linkage disequilibrium at scales at least as small as a cultivated plot. However, the amount of disequilibrium was much greater among isolates collected throughout the Western Hemisphere than among isolates from one area of Mexico, even when disequilibrium was quantified using an index that scales for allelic diversity. This finding suggests that limited migration between populations contributes substantially to linkage disequilibrium in Rhizobium. We also compared the genetic structure for R. leguminosarum bv. phaseoli taken from a cultivated plot with that for Escherichia coli obtained from one human host in an earlier study. Even at this fine scale, linkage disequilibrium in E. coli was very near the theoretical maximum level, whereas it was much less extreme in the local population of Rhizobium. Thus, the genetic structure for R. leguminosarum bv. phaseoli does not exclude the possibility of frequent mixis within local populations.

Does the VP1 gene of foot-and-mouth disease virus behave as a molecular clock?

We have carried out a phylogenetic study of the evolution of the VP1 gene sequence from different serological types and subtypes of foot-and-mouth disease virus (FMDV). The maximum-likelihood method developed by Hasegawa and co-workers (Hasegawa et al. 1985) for the estimation of evolutionary parameters and branching dates has been used to decide between alternative models of evolution: constant versus variable rates. The results obtained indicate that a constant rate model, i.e., a molecular clock, seems to be the most plausible one. However, additional information suggests the possibility that the appearance of serotype CS has been accompanied by an episode of rapid evolution (Villaverde et al. 1991). We discuss the possibility that this evolution of RNA viruses was due to episodic positive Darwinian selection, which would have helped the new variant to escape the immunogenic pressure from the hosts.

Primer design for specific diagnosis by PCR of highly variable RNA viruses: typing of foot-and-mouth disease virus

A PCR assay for the specific detection and identification of viral sequences that correlate with established serotypes of foot-and-mouth disease virus (FMDV) has been developed. A new analysis based on homology profiles among reported sequences was used for primer design. RNA replicase (3D) gene regions that showed high homology among FMDVs, and low homology to other picornaviruses, were used for PCR amplification. Specific and highly sensitive detection was achieved for RNA of FMDV types C, A, and O, either purified or extracted from vesicular fluids of infected animals, under reaction conditions permissive for the detection of variants present in the virus population. Similarly, serotype-specific primers were designed to amplify the carboxy-terminal end of VP1 gene of FMDV types either C, A, or O. The results of PCR amplification of 15 different FMDV RNAs using type-specific primers are in agreement with the serological typing of the corresponding viruses and show that the primer-selection procedure developed for FMDV constitutes a reliable method of viral diagnosis.

Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet

Muller's ratchet is an important concept in population genetics. It predicts that when mutation rates are high and a significant proportion of mutations are deleterious, a kind of irreversible ratchet mechanism will gradually decrease the mean fitness of small populations of asexual organisms. In contrast, sexual recombination may stop or reverse this mutational ratchet by recombinational repair of genetic damage. Experimental support for Muller's ratchet has previously been obtained in protozoa and in a tripartite RNA bacteriophage. We now show clear evidence that Muller's ratchet can operate on a nonsegmented nonrecombining pathogenic RNA virus of animals and humans. We did genetic bottleneck passages (plaque-to-plaque transfers) of vesicular somatitis virus (VSV) and then quantitated relative fitness of the bottleneck clones by allowing direct replication competition in mixed infections in cell culture. We document variable fitness drops (some severe) following only 20 plaque-to-plaque transfers of VSV. In some clones no fitness changes (or only insignificant changes) were observed. Surprisingly, the most regular and severe fitness losses occurred during virus passages on a new host cell type. These results again demonstrate the extreme genetic and biological variability of RNA virus populations. Muller's ratchet could have significant implications for variability of disease severity during virus outbreaks, since genetic bottlenecks must often occur during respiratory droplet transmissions and during spread of low-yield RNA viruses from one body site to another (as with human immunodeficiency virus). Likewise, the lower-probability generation of increased-fitness clones during repeated genetic bottleneck transfers of RNA viruses in nature might also affect disease pathogenesis in infected individuals and in host populations. Whenever genetic bottlenecks of RNA viruses occur, enhanced biological differences among viral subpopulations may result.

Analysis of genetic heterogeneity within the type strain of satellite tobacco mosaic virus reveals variants and a strong bias for G to A substitution mutations

Satellite tobacco mosaic virus (STMV) is a small plant virus that is dependent for its replication on the presence of a helper tobamovirus. RNase protection analysis of genomic RNA of the STMV type strain revealed that it was composed of two major genome types which differed at a single detectable site near nucleotide 753. Analyses of 42 full-length STMV clones for sequence heterogeneity resulted in the identification of 16 variants distinguishable by unique RNase protection assay patterns. Characterization of these variants confirmed the presence of a major heterogeneity site at nucleotide 751 and identified several sites of sequence microheterogeneity typical of an RNA quasispecies population. Mapping of the heterogeneity sites revealed an apparently random distribution along the length of the STMV genome, with no significant clustering or preference for noncoding regions. Infectivity experiments in tobacco showed that RNA transcripts of 13 of the 16 variant clones were infectious, indicating that most of the variants represent functional genomes coexisting in the type strain with the two major genome types. Sequence analyses revealed that most of the heterogeneity sites detected, including the major site of heterogeneity, were single base differences. Assessment of all the heterogeneity sites found in the total of 10,545 nt sequenced allowed us to estimate that the RNase protection assays detected approximately 50% of the differences present in the 16 clones studied. The nature of these differences was highly biased in that 18 of the 29 single base differences characterized (62%) were G to A substitutions.

Comparison of the sequence of the gene encoding African swine fever virus attachment protein p12 from field virus isolates and viruses passaged in tissue culture

Comparison of the amino acid sequence of the African swine fever virus attachment protein p12 from different field virus isolates, deduced from the nucleotide sequence of the gene, revealed a high degree of conservation. No mutations were found after adaptation to Vero cells, and a polypeptide with similar characteristics was present in an IBRS2-adapted virus. The sequence of the 5' flanking region was conserved among the isolates, whereas sequences downstream of the gene were highly variable in length and contained direct repeats in tandem that may account for the deletions found in different isolates. Protein p12 was synthesized in swine macrophages infected with all of the viruses tested.

Evolution of the capsid protein genes of foot-and-mouth disease virus: antigenic variation without accumulation of amino acid substitutions over six decades

The genetic diversification of foot-and-mouth disease virus (FMDV) of serotype C over a 6-decade period was studied by comparing nucleotide sequences of the capsid protein-coding regions of viruses isolated in Europe, South America, and The Philippines. Phylogenetic trees were derived for VP1 and P1 (VP1, VP2, VP3, and VP4) RNAs by using the least-squares method. Confidence intervals of the derived phylogeny (significance levels of nodes and standard deviations of branch lengths) were placed by application of the bootstrap resampling method. These procedures defined six highly significant major evolutionary lineages and a complex network of sublines for the isolates from South America. In contrast, European isolates are considerably more homogeneous, probably because of the vaccine origin of several of them. The phylogenetic analysis suggests that FMDV CGC Ger/26 (one of the earliest FMDV isolates available) belonged to an evolutionary line which is now apparently extinct. Attempts to date the origin (ancestor) of the FMDVs analyzed met with considerable uncertainty, mainly owing to the stasis noted in European viruses. Remarkably, the evolution of the capsid genes of FMDV was essentially associated with linear accumulation of silent mutations but continuous accumulation of amino acid substitutions was not observed. Thus, the antigenic variation attained by FMDV type C over 6 decades was due to fluctuations among limited combinations of amino acid residues without net accumulation of amino acid replacements over time.

Non-additive effects of multiple amino acid substitutions on antigen-antibody recognition

Synthetic peptides have been used to mimic the main antigenic site of foot-and-mouth disease virus (FMDV) of serotype C and of several variant isolates. This region includes multiple continuous B cell epitopes. The effect of single amino acid replacements, individually or in combination, on antigen specificity has been evaluated using monoclonal antibodies. Quantitative enzyme immunodot assays have shown that both additive and non-additive effects of multiple replacements occur in continuous B cell epitopes, with regard to antibody recognition. Antigenically critical single replacements may be compensated by other, non-critical replacements. Thus, the role of a single amino acid on antibody recognition depends on the sequence context in the antigenic domain. The non-additive effects of multiple replacements may modulate the extent of antigenic diversification of highly variable RNA viruses, and keep viruses confined within antigenic groups by precluding linear antigenic divergence.

Carbon catabolite repression can account for the temporal pattern of expression of a penicillin biosynthetic gene in Aspergillus nidulans

Aspergillus nidulans synthesizes penicillins as secondary metabolites when grown under certain culture conditions. Broths containing carbon (C) sources that give rise to carbon catabolite repression (CCR) support a much lower antibiotic yield than broths with non-repressing C sources. Steady-state levels of the isopenicillin N synthetase (IPNS) gene transcript are considerably reduced in mycelia grown with repressing C sources and are depressed in mycelia grown with sugars which do not cause CCR, indicating that penicillin biosynthesis is regulated by CCR through transcriptional control of structural genes. CCR is sufficient to explain the temporal window of expression of the IPNS gene during the growth cycle since (i) the transcript becomes derepressed as soon as the concentration of a repressing C source drops to non-repressing levels and (ii) derepressing C sources sustain derepressed IPNS transcription at all tested moments of the growth cycle. Several tested hypofunctional mutations in creA (the negatively acting regulatory gene which mediates CCR in A. nidulans) do not cause full derepression of IPNS transcript in the presence of a repressing C source. The slight degree of IPNS derepression caused by some creAd (derepressed) alleles parallels the strength of the mutation (as determined by the morphological effect they elicit).

Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures

Peach latent mosaic viroid (PLMVd), the causal agent of peach latent mosaic disease, has been sequenced and found to be a circular RNA molecule of 337 nucleotide residues, which adopts a branched conformation when it is folded in the model of lowest free energy. PLMVd exhibits limited homologies with other viroids and some satellite RNAs, but it does not have any of the central conserved sequences characteristic of the subgroups of typical viroids. However, a segment of approximately one-third of the PLMVd sequence has the elements required to form in the RNAs of both polarities the hammerhead structures proposed to act in the in vitro self-cleavage of avocado sunblotch viroid (ASBVd) and some satellite RNAs. Plus and minus partial- and full-length RNA transcripts of PLMVd containing the hammerhead structures displayed self-cleavage during transcription and after purification as predicted by these structures. These data are consistent with the high stability of the PLMVd hammerhead structures, more similar to the corresponding structures of some satellite RNAs than to those of ASBVd, and indicate that the self-cleavage reactions of PLMVd are most probably mediated by single hammerhead structures. Our results support the inclusion of PLMVd in a viroid subgroup represented by ASBVd, whose members are characterized by their ability to self-cleave in vitro, and probably in vivo, through hammerhead structures. A consensus phylogenetic tree has been obtained suggesting that PLMVd, together with ASBVd, may represent an evolutionary link between viroids and viroid-like satellite RNAs.

Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution

Sequencing of multiple recombinant clones generated from polymerase chain reaction-amplified products demonstrated that the degree of heterogeneity of two well-conserved regions of the hepatitis C virus (HCV) genome within individual plasma samples from a single patient was consistent with a quasispecies structure of HCV genomic RNA. About half of circulating RNA molecules were identical, while the remaining consisted of a spectrum of mutants differing from each other in one to four nucleotides. Mutant sequence diversity ranged from silent mutations to appearance of in-frame stop codons and included both conservative and nonconservative amino acid substitutions. From the relative proportion of essentially defective sequences, we estimated that most circulating particles should contain defective genomes. These observations might have important implications in the physiopathology of HCV infection and underline the need for a population-based approach when one is analyzing HCV genomes.

Identification and synthesis of a major conserved antigenic epitope of Trypanosoma cruzi

A gene sequence encoding an immunodominant protein with a repetitive epitope from the protozoan Trypanosoma cruzi, the causative agent of Chagas disease, was cloned and expressed. The identified 10-amino acid repeat is present within a high-molecular-weight trypomastigote antigen that appears specific to and conserved among T. cruzi isolates. More importantly, greater than 95% of T. cruzi infection sera, including both chronic and acute Chagas disease, contained elevated levels of antibody to a 15-amino acid synthetic peptide bearing the repetitive B-cell epitope. Considering the wide diversity of T. cruzi parasites, as well as the broad spectrum of clinical manifestations of Chagas disease, such a prevalent immune response among patients is significant and applicable to the control of Chagas disease through the diagnosis of T. cruzi infection.

Population structure and mitochondrial DNA gene flow in Old World populations of Drosophila subobscura

An extensive survey of mitochondrial DNA (mtDNA) restriction polymorphism in 156 isofemale lines from 29 different geographic populations of Drosophila subobscura distributed throughout the Old World was carried out. Ten restriction enzymes were used, five of which revealed restriction site polymorphism. Of the 31 restriction sites detected, 13 were found to be polymorphic. Comparisons with the mtDNA map of Drosophila yakuba indicate that the variable sites are mainly concentrated in protein genes, especially those corresponding to the NADH complex. A total of 13 different haplotypes were observed, two of which (haplotypes I and II) are quite frequent and widely distributed throughout the populations, whereas the other 11 with the exception of VIII, which deserves special attention, are each restricted to one population only and occur at low frequencies. The observed distribution of haplotypes, corroborated by a parsimonious unrooted tree, suggests an ancient origin of haplotypes I and II in the continent. In order to compare genetic structure according to mtDNA and allozymes, the 10 populations with higher population sizes were studied for 10 polymorphic allozymes also. One striking result is the high degree of population structure of the mtDNA when compared to that obtained for allozymes. If an island model is assumed, estimates of gene flow give values of 0.013 and 1.89 migrants per generation for mtDNA and allozymes, respectively. What is apparent from these estimates is that Drosophila subobscura populations are effectively subdivided for mtDNA genes at migration rates at which nuclear genes (allozymes) are almost panmictic.

Numerical taxonomy of Trypanozoon based on polymorphisms in a reduced range of enzymes

Numerical analyses of Trypanozoon taxonomy are presented, based on the isoenzyme data of Stevens et al. (1992). The previous study used a reduced range of enzymes compared with earlier work; the analyses indicate the value of this rationalized system. Both recently isolated trypanosome stocks and previously studied populations were included, allowing detailed comparison with earlier studies. Relationships between zymodemes were calculated with an improved similarity coefficient program, using Jaccard's coefficient (1908), and by Nei's method (1972). Dendrograms were constructed from the matrices produced with the group-average method. The groupings produced by both numerical methods were in close agreement, and the clusters of related principal zymodemes largely matched the species, subspecies and strain groups proposed by previous workers. Trypanozoon biochemical taxonomy is reviewed and the groupings reinforced by this study are: the mainly East African strain groups, busoga, zambezi, kakumbi, kiboko and sindo; T.b. gambiense and the bouaflé strain group from West Africa, and T. evansi; an intermediate bouaflé/busoga group was also recognized.

Genetic variation and quasi-species

During the past year the relative fitness, that is, overall replication ability, and the fitness gain of animal virus variants have been quantified, providing new insight into the dynamics for the generation of RNA virus quasi-species. Measurements of mutant frequencies and rates of genetic diversification have confirmed the extreme complexity of RNA virus and retrovirus populations.

Comparison of capsid protein VP1 of the viruses used for the production and challenge of foot-and-mouth disease vaccines in Spain

A significant frequency of amino acid substitutions, that affect important antigenic sites on capsid protein VP1, has been found among viral preparations used for the production and for challenge, in protection assays, of foot-and-mouth disease (FMD) vaccines. The amino acid substitutions present in one of the viruses studied abolished its reactivity with two neutralizing monoclonal antibodies that recognized different epitopes on VP1. Thus, the results obtained illustrate the high potential for antigenic variation introduced by the multiple cycles of growth usually undergone by the strains used for the production and challenge of FMD vaccines.

RNA virus populations as quasispecies

RNA virus mutation frequencies generally approach maximum tolerable levels, and create complex indeterminate quasispecies populations in infected hosts. This usually favors extreme rates of evolution, although periods of relative stasis or equilibrium, punctuated by rapid change may also occur (as for other life forms). Because complex quasispecies populations of RNA viruses arise probabilistically and differentially in every host, their compositions and exact roles in disease pathogenesis are indeterminate and their directions of evolution, and the nature and timing of "new" virus outbreaks are unpredictable.

Studies on antigenic variability of C strains of foot-and-mouth disease virus by means of synthetic peptides and monoclonal antibodies

Peptides representing the sequence of the immunodominant loop of foot-and-mouth disease virus strain C-S8 (YTASARGDLAHLTTTHARHLP, residues 136-156 of VP1) and of several variant viruses have been prepared by solid phase methods. In addition, five peptides with single-residue replacements at Leu147 (Ile, Nle, Val, Ala, Gly) have been synthesized. Tosyl and dinitrophenyl protections for histidine have been compared, the latter being found to give better synthetic products. The peptides have been tested in an immunodot assay against a panel of monoclonal antibodies directed towards the VP1 loop. Immunochemical results are discussed on the basis of the mobility of the region reproduced by the peptides and the nature of the side chain of residue 147.

Molecular cloning and expression of the VP1 gene of foot-and-mouth disease virus C1 in E. coli: effect on bacterial cell viability

The VP1 gene of foot-and-mouth disease virus (serotype C1) has been cloned in Escherichia coli Clts cells, under the control of the bacteriophage lambda pL promoter. The expressed VP1 protein was complete and non-fused, and its molecular weight was indistinguishable from that of the VP1 obtained from virions. Cells harbouring the recombinant vectors exhibited symptoms of plasmid instability and toxicity and died in a few weeks even when never exposed to inducing conditions. A new plasmid clone in which a segment of the VP1 gene was fused with contiguous genes of the viral genome was very stable. The expressed partial VP1 protein contains the two major immunogenic domains of the virion. This system can be used as a tool to design an immunogenic VP1, and to explore possible synthetic vaccines against foot-and-mouth disease.

Null mutants of Saccharomyces cerevisiae Cu,Zn superoxide dismutase: characterization and spontaneous mutation rates

Deletion-replacement mutations of the Saccharomyces cerevisiae Cu,Zn superoxide dismutase gene were constructed. They were exquisitely sensitive to redox cycling drugs and showed slight sensitivity to other agents. The aerobic spontaneous mutation rate was three- to fourfold higher in sod1 delta 1 mutants, while the anaerobic rate was similar to that of the wild type.

Evolution of the G and P genes of human respiratory syncytial virus (subgroup A) studied by the RNase A mismatch cleavage method

The G and P genes of human respiratory syncytial viruses (subgroup A), isolated between 1961 and 1989, were analyzed by RNase A one-dimensional fingerprinting, using the Long strain as the reference. Total RNA extracted from cells infected with the different isolates was hybridized to radiolabeled antisense G or P RNA probes of the Long virus. The RNA:RNA heteroduplexes were digested with RNase A and the resistant products analyzed by gel electrophoresis. Comparative analysis of the cleavage patterns revealed extensive genetic heterogeneity in both genes among viruses isolated in different epidemics. In contrast, 13 viruses isolated in Montevideo during a 3-month period showed much more restricted heterogeneity; thus, 11 viruses represented the predominant type of this outbreak and only 2 other viruses generated different RNA cleavage patterns distantly related to the major type. Statistical analysis of the results obtained indicated progressive accumulation of genetic changes with time along cocirculating evolutionary lineages within the same antigenic subgroup of RS virus. The results are discussed in terms of a model for RS virus evolution.

Fixation of mutations at the VP1 gene of foot-and-mouth disease virus. Can quasispecies define a transient molecular clock?

The number of nucleotide (nt) substitutions found in the VP1 gene (encoding viral capsid protein) between any two of 16 closely related isolates of foot-and-mouth disease virus (FMDV) has been quantified as a function of the time interval between isolations [Villaverde et al., J. Mol. Biol. 204 (1988) 771-776]. One of them (isolate C-S12) includes some replacements found in isolates that preceded it and other replacements found in later isolates. The study has revealed alternating periods of rapid evolution and of relative genetic stability of VP1. During a defined period of acute disease, the rate of fixation of replacements at the VP1 coding segment was 6 x 10(-3) substitutions per nt per year. Only small differences in the rate of evolution were observed between subsegments within the VP1 gene. The observation of a relatively constant rate of evolution during a disease episode was unexpected. We propose that such constancy may be a consequence of random sampling of mutants from the FMDV quasispecies, followed by their amplification in susceptible hosts (to generate a new quasispecies). Successive sampling and amplification events may result in a steady accumulation of mutations.

Two modes of balancing selection in Drosophila melanogaster: overcompensation and overdominance

Overdominance is often invoked to account for the extensive polymorphisms found in natural populations of organisms; overcompensation, however, may be equally or more important. Overcompensation occurs when limiting resources are better exploited by a genetically mixed than by a uniform population, and is often causally related to frequency-dependent selection. We have designed experiments to test whether overcompensation occurs in Drosophila melanogaster, using the Sod locus as a marker. Tests are made at each of two densities and two temperatures for cultures with desired genetic compositions. Both temperature and density have statistically significant effects on the per-female productivity of the cultures. More important, there are strong effects due to overcompensation. Cultures that are more polymorphic are also more productive than less polymorphic ones even when the level of individual heterozygosity is the same in all. There is also overdominance for the Sod locus: the heterozygotes are more productive than either homozygote at every temperature and density, and the differences are statistically significant in several cases. These results corroborate previous studies showing that overdominance may contribute to the maintenance of the Sod polymorphisms. Moreover, our results indicate that the significance of overcompensation as a mechanism to account for polymorphism in natural populations deserves further investigation.

Fertility and viability at the Sod locus in Drosophila melanogaster: non-additive and asymmetric selection

Experiments were designed to test in Drosophila melanogaster the effect of mating type at the Sod locus on fertility and viability. The experiments show that fertility is neither additive (or multiplicative) nor symmetric, i.e. that the fertility of a mating type cannot be predicted from the average fertility of the two genotypes involved in the mating. There is no significant male x female interaction with respect or progeny viability; but the interaction is significant for productivity, i.e. when fertility and viability are jointly taken into account. There is overdominance with respect to female fertility, but not with respect to male fertility or to viability. There also is alloprocoptic selection with respect to fertility and with respect to productivity, i.e. mating between like homozygotes are less fertile and productive than matings between dissimilar homozygotes. Selection at the Sod locus yields stable polymorphic equilibria, with the frequency of the F allele predicted at P = 0.641 or 0.695, respectively for low and high larval density.

Identification of neutralizing antigenic sites on VP1 and VP2 of type A5 foot-and-mouth disease virus, defined by neutralization-resistant variants

Five neutralizing monoclonal antibodies (nMAbs) obtained against type A5 Spain-86 foot-and-mouth disease virus were used to generate a series of neutralization-resistant variants. In vitro and in vivo assays showed that the variants were fully refractory to neutralization by the selecting nMAb. On the basis of cross-neutralization and binding assays, two neutralizing antigenic sites have been located on the virus surface; one, located near the C-terminus of VP1, displayed a linear epitope, and the second, located on VP2, displayed two conformational epitopes. Nucleotide sequencing of RNA of the parental and variant capsid protein-coding region P1 has placed the amino acid changes at position 198 of VP1 for the first site and at positions 72 and 79 of VP2 for the related epitopes in the second site. The relative importance of these two sites in the biological properties of foot-and-mouth disease virus is discussed.

Trypanosoma cruzi: flow cytometric analysis of developmental stage differences in DNA

Flow cytometry and DNA binding-specific fluorescent reagents were used to compare the total DNA, G-C, and A-T content of the epimastigote and trypomastigote stages of Trypanosoma cruzi stocks. Significant total DNA differences of 2-12% between epimastigotes and trypomastigotes were found in three of six stocks studied. The epimastigote G-C content of five of six stocks was 4-8% higher than trypomastigotes, whereas the trypomastigote A-T content was 2.5-13% higher than the epimastigote A-T content. Although no obvious developmental stage association between total DNA and base composition was found, intrastage associations do exist. These observations were unaffected by nucleoprotein extraction implying that the observed differences between trypomastigotes and epimastigotes are not a consequence of nucleoprotein interference with DNA-binding fluorochromes. The nuclei and kinetoplasts of four T. cruzi stocks were isolated and analyzed. Developmental stage differences in nuclear and kinetoplast DNA are stock-dependent and base composition-dependent; both organelles contribute to the observed differences in DNA of intact cells. We found a nearly linear association between the percentage of total kinetoplast DNA, G-C, and A-T content. During metacyclogenesis, the G-C content decreases by approximately 7% as epimastigotes transform into metacyclic trypomastigotes. The decrease in G-C content precedes changes in morphology or in complement resistance. If the DNA changes are causally connected to developmental stage transformations in T. cruzi remains to be determined. However, our results could facilitate studies of the molecular genetic processes the parasite uses to successfully complete various phases of its life cycle and, consequently, the disease process it evokes.

Ecological determinants of life-history evolution

Density-dependent natural selection has been studied, empirically with laboratory populations of Drosophila melanogaster. Populations kept at very high and low population density have become differentiated with respect to important fitness-related traits. There is now some understanding of the behavioural and physiological basis of these differences. These studies have identified larval competitive ability and efficiency of food utilization as traits that are negatively correlated with respect to effects on fitness. Theory that illuminates and motivates additional research with this experimental system has been lacking. Current research has focused on models that incorporate many details of Drosophila ecology in laboratory environments.

Expression of bovine superoxide dismutase in Drosophila melanogaster augments resistance of oxidative stress

Superoxide dismutases (SOD) play a major role in the intracellular defense against oxygen radical damage to aerobic cells. In eucaryotes, the cytoplasmic form of the enzyme is a 32-kDa dimer containing two copper and two zinc atoms (CuZn SOD) that catalyzes the dismutation of the superoxide anion (O2-) to H2O2 and O2. Superoxide-mediated damage has been implicated in a number of biological processes, including aging and cancer; however, it is not certain whether endogenously elevated levels of SOD will reduce the pathological events resulting from such damage. To understand the in vivo relationship between an efficient dismutation of O2- and oxidative injury to biological structures, we generated transgenic strains of Drosophila melanogaster overproducing CuZn SOD. This was achieved by microinjecting Drosophila embryos with P-elements containing bovine CuZn SOD cDNA under the control of the Drosophila actin 5c gene promoter. Adult flies of the resulting transformed lines which expressed both mammalian and Drosophila CuZn SOD were then used as a novel model for evaluating the role of oxygen radicals in aging. Our data show that expression of enzymatically active bovine SOD in Drosophila flies confers resistance to paraquat, an O2(-)-generating compound. This is consistent with data on adult mortality, because there was a slight but significant increase in the mean lifespan of several of the transgenic lines. The highest level of expression of the active enzyme in adults was 1.60 times the normal value. Higher levels may have led to the formation of toxic levels of H2O2 during development, since flies that died during the process of eclosion showed an unusual accumulation of lipofuscin (age pigment) in some of their cells. In conclusion, our data show that free-radical detoxification has a minor by positive effect on mean longevity for several strains.

Modified-live infectious bovine rhinotracheitis virus vaccine expressing monomer and dimer forms of foot-and-mouth disease capsid protein epitopes on surface of hybrid virus particles

Modified-live, attenuated infectious bovine rhinotracheitis (IBR) hybrid virus vaccines have been constructed by inserting in the major IBRV glycoprotein gIII gene chemically synthesized deoxyribonucleotide sequences encoding the bovine growth hormone signal sequence and monomeric or dimeric forms of the foot and mouth disease virus (FMDV) VP 1 epitope sequences. The foreign DNA sequences were inserted at the N-terminal end of the IBRV gIII coding sequence and were driven by the IBRV gIII promoter. The sequences encoding the first 38 and the first 21 amino acids of the IBRV gIII were deleted from the hybrid viruses containing inserts of the monomeric and dimeric FMDV epitope sequences, respectively, to avoid redundant signal sequences. Plaque immunoassay experiments with guinea pig and bovine anti-FMDV peptide antisera, and with anti-IBRV gIII monoclonal antibodies demonstrated that IBRV-FMDV fusion proteins were expressed in virus-infected MDBK cells. Immunoelectron microscopy analyses demonstrated that the IBRV-FMDV fusion proteins were expressed as repeated structures on the surface of virus particles. Experiments showed that the recombinant IBRV-FMDV viruses protected cattle from IBRV (Cooper) challenge and induced anti-FMDV peptide antibodies, thereby demonstrating that the FMDV epitopes were expressed in vivo.

Expression of bovine superoxide dismutase in Drosophila melanogaster augments resistance of oxidative stress

Superoxide dismutases (SOD) play a major role in the intracellular defense against oxygen radical damage to aerobic cells. In eucaryotes, the cytoplasmic form of the enzyme is a 32-kDa dimer containing two copper and two zinc atoms (CuZn SOD) that catalyzes the dismutation of the superoxide anion (O2-) to H2O2 and O2. Superoxide-mediated damage has been implicated in a number of biological processes, including aging and cancer; however, it is not certain whether endogenously elevated levels of SOD will reduce the pathological events resulting from such damage. To understand the in vivo relationship between an efficient dismutation of O2- and oxidative injury to biological structures, we generated transgenic strains of Drosophila melanogaster overproducing CuZn SOD. This was achieved by microinjecting Drosophila embryos with P-elements containing bovine CuZn SOD cDNA under the control of the Drosophila actin 5c gene promoter. Adult flies of the resulting transformed lines which expressed both mammalian and Drosophila CuZn SOD were then used as a novel model for evaluating the role of oxygen radicals in aging. Our data show that expression of enzymatically active bovine SOD in Drosophila flies confers resistance to paraquat, an O2(-)-generating compound. This is consistent with data on adult mortality, because there was a slight but significant increase in the mean lifespan of several of the transgenic lines. The highest level of expression of the active enzyme in adults was 1.60 times the normal value. Higher levels may have led to the formation of toxic levels of H2O2 during development, since flies that died during the process of eclosion showed an unusual accumulation of lipofuscin (age pigment) in some of their cells. In conclusion, our data show that free-radical detoxification has a minor by positive effect on mean longevity for several strains.

Relationships among the positive strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases

The sequences of 50 RNA-dependent RNA polymerases (RDRPs) from 43 positive strand and 7 double strand RNA (dsRNA) viruses have been compared. The alignment permitted calculation of distances among the 50 viruses and a resultant dendrogram based on every amino acid, rather than just those amino acids in the conserved motifs. Remarkably, a large subgroup of these viruses, including vertebrate, plant, and insect viruses, forms a single cluster whose only common characteristic is exploitation of insect hosts or vectors. This similarity may be due to molecular constraints associated with a present and/or past ability to infect insects and/or to common descent from insect viruses. If common descent is important, as it appears to be, all the positive strand RNA viruses of eucaryotes except for the picornaviruses may have evolved from an ancestral dsRNA virus. Viral RDRPs appear to be inherited as modules rather than as portions of single RNA segments, implying that RNA recombination has played an important role in their dissemination.

Elevated paraquat resistance can be used as a bioassay for longevity in a genetically based long-lived strain of Drosophila

A long-lived (L) strain of Drosophila melanogaster, derived from a normal-lived (R) strain by artificial selection, has a significantly different adult longevity. Previous work has shown that 1) the two strains age in the same manner, 2) the major genes responsible for much of the L strain's extended longevity are located on the 3rd chromosome, and 3) the extended longevity phenotype is significantly modulated by the larval environment. In this report, we investigate the resistance of the L and R strains to the lethal effects of dietary paraquat. We show that, within the limitations of our described chromosomal and environmental manipulations, the extended longevity phenotype always accompanies the phenotype of elevated paraquat resistance. In addition, reversed selection applied to the L strain results in the simultaneous decrease of both life span and paraquat resistance. Thus, the presence or absence of the latter phenotype may be used as a bioassay for the presence or absence of the extended longevity phenotype, without any necessary implication of causality. Use of this bioassay should greatly speed up the genetic analysis of this system by allowing us to identify long-lived animals at a young age. Finally, we show that the age-related loss of elevated paraquat resistance in both strains precedes all the other age-related functional decrements which we have previously noted in this system.

Genomic variation of Trypanosoma cruzi: involvement of multicopy genes

By using improved pulsed field gel conditions, the karyotypes of several strains of the protozoan parasite Trypanosoma cruzi were analyzed and compared with those of Leishmania major and two other members of the genus Trypanosoma. There was no difference in chromosome migration patterns between different life cycle stages of the T. cruzi strains analyzed. However, the sizes and numbers of chromosomal bands varied considerably among T. cruzi strains. This karyotype variation among T. cruzi strains was analyzed further at the chromosomal level by using multicopy genes as probes in Southern hybridizations. The chromosomal location of the genes encoding alpha- and beta-tubulin, ubiquitin, rRNA, spliced leader RNA, and an 85-kilodalton protein remained stable during developmental conversion of the parasite. The sizes and numbers of chromosomes containing these sequences varied among the different strains analyzed, implying multiple rearrangements of these genes during evolution of the parasites. During continuous in vitro cultivation of T. cruzi Y, the chromosomal location of the spliced leader gene shifted spontaneously. The spliced leader gene encodes a 35-nucleotide RNA that is spliced in trans from a 105-nucleotide donor RNA onto all mRNAs in T. cruzi. The spliced leader sequences changed in their physical location in both the cloned and uncloned Y strains. Associated with the complex changes was an increase in the infectivity of the rearranged variant for tissue culture cells. Our results indicate that the spliced leader gene clusters in T. cruzi undergo high-frequency genomic rearrangements.

On the analysis of viability data: an example with Drosophila

Larval competition experiments involving two wild type and eight mutant strains of Drosophila melanogaster have been carried out following the substitution procedure proposed by Mather and Caligari (1981). Our main goal has been to compare the competitive abilities of two phenotypically indistinguishable strains (wild and Oregon-R) by means of their responses with eight different mutants. Prior to the analyses of viability data, we have studied the normalizing effect of several transformations in order to determine which was best suited for the analyses. The differences found among the five transformations tested and the untransformed data were not very great. The folded power transformation (Mosteller and Tukey, 1977) was finally chosen. No constant pattern in the responses of the two wild type strains to the mutant competitors was detected. This leads us to conclude that the nature of the competition between the two wild type strains cannot be predicted from a knowledge of their competition with other strains.

The major 85-kD surface antigen of the mammalian form of Trypanosoma cruzi is encoded by a large heterogeneous family of simultaneously expressed genes

Trypanosoma cruzi is an obligate intracellular protozoan parasite. The parasite mammalian stage surface antigens exhibit extensive antigenic diversity. We have characterized a family of T. cruzi genes that code for a polymorphic set of 85-kD surface antigens, the SA85-1 antigens. The family contains greater than 100 genes and pseudogenes, of which a minimum of nine are transcribed. The gene family is expressed in the mammalian stage only. A subset of the gene family is present in two telomere-linked copies in the genome. Telomere linkage of other expressed SA85-1 genes has not been demonstrated. We have shown that at least three members of the SA85-1 gene family encode antigens at the surface of the mammalian stage of the parasite. Interestingly, these three antigens are expressed on all the trypanosomes examined. This suggests that T. cruzi simultaneously expresses a large repertoire of similar, but diverse antigens at its surface. Thus, T. cruzi exhibits extensive antigenic diversity in a system unique from that of African trypanosomes, perhaps reflecting its intracellular niche.

Mitochondrial DNA evolution in experimental populations of Drosophila subobscura

When two mitochondrial DNA (mtDNA) haplotypes of Drosophila subobscura compete in experimental populations with discrete generations, one or the other approaches fixation, depending on the nuclear background with which they are associated. The approach to fixation, however, is strongly dependent on the effective number of females in the population, Nf. Whether or not the ultimate fate of a given mtDNA haplotype is determined by random genetic drift depends on Nf as well as on the relative fitnesses. Our experimental results show that the mtDNA polymorphisms observed in natural populations are affected by interactions among nuclear polymorphisms, random genetic drift, and direct selection on the mtDNA haplotypes.

Genetic exchange and evolutionary relationships in protozoan and helminth parasites

The study of genetic exchange systems and the use of genetic analysis has been relatively limited in parasites leading to considerable gaps in our basic knowledge. This lack of knowledge makes it difficult to draw firm conclusions as to how these systems evolved. An additional problem is also raised by the difficulties in defining evolutionary distances particularly with the unicellular protozoa, using classical ultrastructural and cytological criteria. While these difficulties have by no means been overcome, the use of rapid sequencing techniques applied to the ribosomal genes has allowed measurement of evolutionary distances, and considerable advances in our understanding of the genetic exchange systems in a few parasitic protozoa have recently been made. The conclusions from these recent sets of analyses are reviewed and then examined together in order to discuss the evolution of genetic exchange systems in parasitic protozoa. The evolutionary distances defined by ribosome sequence analysis show that parasites are an extremely divergent group, with distances which, in some cases, are orders of magnitude greater than the distances between mammals and fish; furthermore these studies suggest that the parasitic protozoa or their free-living ancestors are extremely ancient. These findings support the view that parasitism has occurred independently many times and that the parasitic life-style has been adopted by evolutionarily distinct groups. The recent observation of a non-obligatory genetic system in the diploid but evolutionary ancient kinetoplastid Trypanosoma brucei suggests that diploidy and meiosis are extremely old. The observation, in parasitic protozoa and helminths, that selfing or non-obligatory mating is a common feature suggests that these processes may be strategies to overcome the cost of meiosis. In this context, the question of what selective forces maintain genetic exchange is discussed.

The biometrical genetics of competitive parameters in Drosophila melanogaster

Despite the importance of competition as an evolutionary determinant in natural populations there have been few studies of the genetical control of competitive ability. Here, we report the results of a biometrical analysis of four continuously varying traits which, between them, describe the competitive interactions in mixed cultures of Drosophila melanogaster. The analysis involved the parental, F1, F2 and backcross generations (including all reciprocals) derived from crosses between two highly inbred lines isolated from the Texas population of D. melanogaster. The competitive performance of each genotype in monoculture and in duoculture with a phenotypically distinct tester were assessed using a yield-density regression analysis. Appropriate genetic models were fitted using a variance weighted least squares procedure and the resulting genetic components of the generation means used to define the genetical architecture of competition. Of the four competitive parameters investigated here the e-value, which describes the competitive performance of the indicator genotype at a fixed reference density, was found to be determined by simple additive genetic effects with no evidence of significant dominance. Conversely, competitive performance in monoculture (intra-genotypic competition) did display a significant net dominance component and the observed values in the F1 and parental generations indicated some degree of heterosis. Of the two competitive parameters determining performance in duoculture (inter-genotypic sensitivity and inter-genotypic pressure) the former was found to have a complex genetic determination involving not only additive and dominance components of the progeny's own genotype but also dominance components of the F1 maternal genotypes. There were also additive-dominance and dominance-dominance non-allelic interactions. Heterosis was evident, determined both by the progeny's own genotype and by one of the F1 maternal genotypes.(ABSTRACT TRUNCATED AT 250 WORDS)

A clonal theory of parasitic protozoa: the population structures of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas, and Trypanosoma and their medical and taxonomical consequences

We propose a general theory of clonal reproduction for parasitic protozoa, which has important medical and biological consequences. Many parasitic protozoa have been assumed to reproduce sexually, because of diploidy and occasional sexuality in the laboratory. However, a population genetic analysis of extensive data on biochemical polymorphisms indicates that the two fundamental consequences of sexual reproduction (i.e., segregation and recombination) are apparently rare or absent in natural populations of the parasitic protozoa. Moreover, the clones recorded appear to be stable over large geographical areas and long periods of time. A clonal population structure demands that the medical attributes of clones be separately characterized; ubiquitous clones call for priority characterization. Uniparental reproduction renders unsatisfactory Linnean taxonomy; this needs to be supplemented by the "natural clone" as an additional taxonomic unit, which is best defined by means of genetic markers.

Analysis of competitive interactions in triocultures of Drosophila melanogaster

Competitive interactions in complex mixtures of genotypes have rarely been studied despite their obvious importance in both natural and commercial populations. Here, we describe a procedure for the analysis of competition in tripartite mixtures of Drosophila melanogaster genotypes. We have utilised a substitution design coupled with a yield-density regression analysis which describes intra- and inter-genotypic competitive effects in terms of simple linear parameters. The experimental design allows any of the competitors to be considered as the primary or indicator genotype and also incorporates variation in the relative proportions of the two associate competitors. The regression parameters are used to derive estimates of the competitive pressure exerted by each associate on the indicator genotype and also the response or sensitivity of the indicator to the competitive pressure which it faces in mixed culture. The results indicate that the joint pressure exerted by the paired associate genotypes in trioculture is equal to the sum of the individual pressures of those associates. This additive relationship holds for a variety of indicator genotypes isolated from the Texas population and appears to be a general property of Drosophila competition. We identified one indicator genotype which consistently departed from this relationship although additivity of joint pressures could be restored in combination with particular associate genotypes. The possible role of larval interference in the determination of these interactions is discussed.

Regeneration of a functional RNA virus genome by recombination between deletion mutants and requirement for cowpea chlorotic mottle virus 3a and coat genes for systemic infection

RNAs 1 and 2 of the tripartite cowpea chlorotic mottle virus (CCMV) genome are sufficient for RNA replication in protoplasts, whereas systemic infection of cowpea plants additionally requires RNA3, which encodes the 3a noncapsid protein and coat protein. By using biologically active CCMV cDNA clones, we find that deletions in either RNA3 gene block systemic infection. Thus, though some plant RNA viruses are able to spread systemically without encapsidation, both the coat and 3a genes are required for systemic infection of cowpeas by CCMV. When plants were coinoculated with CCMV RNAs 1 and 2 and both the 3a and coat deletion mutants of RNA3, 30-60% rapidly developed systemic infection. Progeny RNA recovered from systemically infected leaves in such infections contained neither of the starting deletion mutants but rather a single full-length RNA3 component with both genes intact. Nucleotide substitutions introduced into the coat protein deletion mutant as an artificial marker were recovered in the full-length progeny RNA, confirming its recombinant nature. Intermolecular RNA recombination in planta can, therefore, rescue a complete infectious genome from coinoculated mutants independently disabled for systemic spread. These results have implications for the repair of defective genomes produced by frequent natural replication errors, the possible emergence of newly adapted RNA viruses upon coinfection of new hosts, and further studies of RNA virus recombination.

Further studies on substrates inducing metacyclogenesis in Trypanosoma cruzi

Epimastigotes of Trypanosoma cruzi, Peru strain, incubated in Contreras' artificial triatomine urine transformed into metacyclic trypomastigotes when 10 mM L-glutamine, L-asparagine or D-fructose was added to the medium. Metacyclogenesis with these substrates was comparable to the percent metacyclic morphotype formation induced by L-proline and significantly greater than that stimulated by 10 mM D-glucose. Sodium acetate (10 mM) increased transformation induced by L-proline, and L-hydroxyproline (10 mM) increased transformation induced by D-fructose. Phosphoenolpyruvate (10 mM) inhibited L-proline-induced metacyclic trypomastigote stage formation. Three antimetabolites, azetidine 2-carboxylate (5 mM), malonic acid (1 mM), and desthiobiotin (5 mM), completely inhibited D-fructose-induced but not L-proline-induced transformation. The Costa Rica, Y, and CL strains of T. cruzi showed different patterns of percent metacyclogenesis with substrates that induce transformation in the Peru strain.

Characterization and grouping of Trypanosoma cruzi stocks by DNA base-specific fluorochromes and discriminant analysis

Fluorochromes with G-C and A-T specificity were used for a single-cell DNA analysis of the blood-stream forms of 14 Trypanosoma cruzi stocks in a cytofluorometric assay. The kinetoplast contained 22.3%-37.9% of the total DNA G-C base content and 42.7%-63.5% of the total DNA A-T base content. In spite of these differences, the mean base A-T/G-C ratio of the total DNA was 1.11 and was nearly constant in all stocks. The G-C base ratio of kinetoplast/nucleus resulted in a grouping corresponding with the peanut agglutinin (PNA)- and wheat germ agglutinin (WGA)-type characteristics of the T. cruzi stocks. The discriminant analysis revealed relationships, in that each stock contained some trypanosomes with DNA fluorescence characteristics of common to at least one other stock. After chromomycin A3 staining, the mean hit rates for the classification into group 1 PNA and the WGA group were 99% and 96%, respectively, and the respective rates obtained after DAPI application were 84% and 94%.

Larval competition in Drosophila melanogaster: effects on development time

The effects on development time of larval competition that is interrupted at different times are analyzed in an experiment with constant larval density and varying proportions of two competing strains. Interruption of competition is carried out by means of the overfeeding technique, which allows for the study of individuals that, after several days under competition stress, either complete their development in crowded conditions or migrate to a vial with fresh food where the rest of their development takes place. Results of mean development time and within-vial variance of development time show that individuals under strong competition stress can arrest their development retaining the capability to resume it, once they are exposed to fresh food. The effects of competition are observed sooner on development time than on viabilities, which is in agreement with Ohba's observations (Biol. J. Okayama Univ. 7:87-125, 1961), but the observed effects are not always coincident for both fitness components.