Differences In Base Composition Research Articles

Metallurgical characterization of orthodontic brackets produced by Metal Injection Molding (MIM).

The aim of this study was to investigate the bonding base surface morphology, alloy type, microstructure, and hardness of four types of orthodontic brackets produced by Metal Injection Molding technology (Discovery, Extremo, Freedom, and Topic). The bonding base morphology of the brackets was evaluated by scanning electron microscopy (SEM). Brackets from each manufacturer were embedded in epoxy resin, and after metallographic grinding, polishing and coating were analyzed by x-ray energy-dispersive spectroscopic (EDS) microanalysis to assess their elemental composition. Then, the brackets were subjected to metallographic etching to reveal their metallurgical structure. The same specimen surfaces were repolished and used for Vickers microhardness measurements. The results were statistically analyzed with one-way analysis of variance and Student-Newman-Keuls multiple comparison test at the 0.05 level of significance. The findings of SEM observations showed a great variability in the base morphology design among the brackets tested. The x-ray EDS analysis demonstrated that each bracket was manufactured from different ferrous or Co-based alloys. Metallographic analysis showed the presence of a large grain size for the Discovery, Freedom, and Topic brackets and a much finer grain size for the Extremo bracket. Vickers hardness showed great variations among the brackets (Topic: 287 +/- 16, Freedom: 248 +/- 13, Discovery: 214 +/- 12, and Extremo: 154 +/- 9). The results of this study showed that there are significant differences in the base morphology, composition, microstructure, and microhardness among the brackets tested, which may anticipate significant clinical implications.

Stabilization against Hyperthermal Denaturation through Increased CG Content Can Explain the Discrepancy between Whole Genome and 16S rRNA Analyses

Based largely upon analysis of ribosomal RNA, a third domain of life, called archaea, had been proposed in addition to bacteria and eukaryotes. However, quantitative analysis of 73 whole genomes shows only a two-domain division of life: into eukaryotes and prokaryotes. Thousands of orthologous genes in archaea and bacteria show an essentially unimodal distribution of sequence identities. Thus, whole genome analyses indicate that archaea are a phylum of bacteria rather than a separate domain of life. In contrast, archaeal rRNA and that of hyperthermophilic bacteria differ from the rRNA of mesophilic bacteria. Thus, there is a bimodal distribution of rRNA sequence identities which differ by 12%. This discrepancy in rRNA and gene content based analyses of whole genomes is likely due to a 15% elevated C:G content of the rRNA of archaea and hyperthermophilic bacteria. The elevated C:G content is consistent with stabilization against thermal denaturation caused by additional hydrogen bonding (3 bonds) in C:G pairs compared to A:U pairs (2 bonds). Based upon this premise, there is no reliable way to correct rRNA for such differences in base composition and it is not possible to quantitatively compare hyperthermophiles with mesophiles by the rRNA method. Furthermore, quantitative study of whole genomes shows that the extent of change in both bacterial and archaeal genes, including rRNA, has reached a limit. Thus, direct sequence comparisons work with closely related genomes, but it is not possible to differentiate the most divergent prokaryotic species, which are currently designated as separate phyla. We believe that the differences in characteristics of archaeal species is based primarily upon selection of genes and pathways compatible with the extreme environmental lifestyle, i.e., hyperthermophily.

Discovering Rare Variants by Use of Melting Temperature Shifts Seen in Melting Curve Analysis

Two reports in this issue of Clinical Chemistry describe novel mutations in thrombophilia genes (1)(2). The authors of the reports describe variants detected by the identification of a melting temperature ( T m) different from the expected T m of the target mutation and from the T m of the wild-type sequence. The variants reported in this issue are A20218G in the prothrombin (factor II) gene and C1690T in the factor V gene. These cases add to the reported variants identified by fluorescent hybridization probes and melting analysis on the LightCycler. In addition to factor II and V variants, variants have been discovered similarly in genes coding for MTHFR and HFE (3)(4). Melting analyses, as performed on the LightCycler or similar instruments, can distinguish variants that lie within the region of the target probe. Differences in base composition, nucleotide position, and nearest-neighbor environments all affect T m. These differences are detected by monitoring fluorescence during an increase in temperature. Melting is visualized by a loss of fluorescence as the probes dissociate from the template. Differences in T m from the expected T m for wild-type and target mutations are indicative of a nontarget (a variant other than the mutation the assay was designed to detect) mutation or variant. In contrast, assays that use restriction enzymes, allele-specific amplification, or hybridization probes at a single detection temperature may not detect a variant or may show an indeterminate genotype (3)(4). With these 3 types of assays, when one allele carries the variant and the opposite allele is a wild type, the variant allele may be undetected, and the genotype would be reported as wild type. If the variant is in conjunction with a target mutation on the opposite allele, the genotype could be reported as a …

Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: A novel tool for the identification and differentiation of humans

In traditional approaches, mitochondrial DNA (mtDNA) variation is exploited for forensic identity testing by sequencing the two hypervariable regions of the human mtDNA control region. To reduce time and labor, single nucleotide polymorphism (SNP) assays are being sought to possibly replace sequencing. However, most SNP assays capture only a portion of the total variation within the desired regions, require a priori knowledge of the position of the SNP in the genome, and are generally not quantitative. Furthermore, with mtDNA, the clustering of SNPs complicates the design of SNP extension primers or hybridization probes. This article describes an automated electrospray ionization mass spectrometry method that can detect a number of clustered SNPs within an amplicon without a priori knowledge of specific SNP positions and can do so quantitatively. With this technique, the base composition of a PCR amplicon, less than 140 nucleotides in length, can be calculated. The difference in base composition between two samples indicates the presence of an SNP. Therefore, no post-PCR analytical construct needs to be developed to assess variation within a fragment. Of the 2754 different mtDNA sequences in the public forensic mtDNA database, nearly 90% could be resolved by the assay. The mass spectrometer is well suited to characterize and quantitate heteroplasmic samples or those containing mixtures. This makes possible the interpretation of mtDNA mixtures (as well as mixtures when assaying other SNPs). This assay can be expanded to assess genetic variation in the coding region of the mtDNA genome and can be automated to facilitate analysis of a large number of samples such as those encountered after a mass disaster.

Inhibition of DNA Polymerization and Antifungal Specificity of Furanocoumarins Present in Traditional Medicines¶

ABSTRACTAntifungal activity is positively correlated to furanocoumarin content in extracts of the traditional phytomedicine northern prickly ash (Zanthoxylum americanum Mill. [Rutaceae]). The specificity of these furanocoumarins in inhibiting replication of DNA was investigated with reference to significant base composition differences between fungal and mammalian mitochondrial DNA. We developed a polymerase chain reaction‐based assay to investigate whether (1) furanocoumarins inhibit DNA polymerization and (2) distinct furanocoumarins specifically inhibit DNA replication depending on base composition. Specific inhibition of DNA polymerization by 5‐methoxypsoralen and psoralen through high‐adenine and thymine (AT) (84.3%) and low‐AT (51.9%) DNA, respectively, suggests that furanocoumarins inhibit replicative functions of genomes or of regions within the genome that differ in base composition. Greater overall inhibition of DNA polymerization by Z. americanum husk extracts than with single or mixed furanocoumarins suggests that inhibitory compounds in addition to the major furanocoumarins are present in Z. americanum.

Inhibition of DNA polymerization and antifungal specificity of furanocoumarins present in traditional medicines.

Antifungal activity is positively correlated to furanocoumarin content in extracts of the traditional phytomedicine northern prickly ash (Zanthoxylum americanum Mill. [Rutaceae]). The specificity of these furanocoumarins in inhibiting replication of DNA was investigated with reference to significant base composition differences between fungal and mammalian mitochondrial DNA. We developed a polymerase chain reaction-based assay to investigate whether (1) furanocoumarins inhibit DNA polymerization and (2) distinct furanocoumarins specifically inhibit DNA replication depending on base composition. Specific inhibition of DNA polymerization by 5-methoxypsoralen and psoralen through high-adenine and thymine (AT) (84.3%) and low-AT (51.9%) DNA, respectively, suggests that furanocoumarins inhibit replicative functions of genomes or of regions within the genome that differ in base composition. Greater overall inhibition of DNA polymerization by Z. americanum husk extracts than with single or mixed furanocoumarins suggests that inhibitory compounds in addition to the major furanocoumarins are present in Z. americanum.

William Bateson, Richard Goldschmidt, and Non-Genic Modes of Speciation

Sometimes a cross between two individuals that appear to belong to the same species produces a sterile offspring (i.e., their hybrid is sterile). Thus, the two individuals appear reproductively isolated from each other. If each could find a compatible mate, then new species might emerge. At issue is whether the form of hybrid sterility that precedes sympatric differentiation into species is, in the general case, of genic or non-genic origin. Several recent papers lend the authority of William Bateson to the genic hypothesis, referring to the "Bateson–Dobzhansky–Muller hypothesis". All these papers cite a 1996 paper that, in turn, cites a 1909 paper of Bateson. However, from 1902 until 1926 the latter espoused a non-genic hypothesis that today would be classified as "chromosomal". Analysis of Bateson's 1909 text reveals no recantation. Bateson's non-genic view was similar to that advanced by Richard Goldschmidt in the 1940s. However, Bateson proposed a contribution from parents of abstract factors that, together in their hybrids, complement to bring about a negative effect (hybrid sterility). In contrast, Goldschmidt proposed that normally parents contribute complementary factors making parental chromosomes compatible at meiosis in their hybrids, which hence are fertile (i.e., the parental factors work together to produce a positive effect). When the factors are not sufficiently complementary the parental chromosomes are incompatible in their hybrids, which hence are sterile. The non-genic Batesonian–Goldschmidtian abstractions are now being fleshed-out chemically in terms of DNA base-composition differences.

Teleost introns are characterized by a high A+T content

We previously observed that Antarctic fish genes contain intron sequences of high A+T content (60–70% average A+T) which are in stark contrast with adjacent protein coding-sequences. Here, we report that this disparity in intron/exon base composition is a common feature among teleosts. We analyzed 483 teleost genomic DNA sequences, containing 2583 introns, from 80 teleost genera that populate polar, temperate, or tropical habitats. Eighty-nine percent of teleost introns display an A+T content between 50–84% A+T with a mean of 60% A+T. In contrast, only 37% of teleost exons have an A+T content greater-than 50% with a mean of 48% A+T. A comparison to homologous mammalian genes showed a striking difference; in this case, introns and exons have similar base compositions, averaging 45–47% A+T. This indicates that most teleost genes exhibit a large difference in base composition between their introns and exons. There was no correlation of teleost intron A+T content to intron length or habitat temperature range. Thus, teleost intron sequences tend to show the common feature of being much higher in A+T content then neighboring exons.

The 5' leader of plant PgiC has an intron: the leader shows both the loss and maintenance of constraints compared with introns and exons in the coding region.

PgiC, a complex gene with 23 coding exons and 22 intervening introns, encodes the cytosolic isozyme of phosphoglucose isomerase (EC 5.3.1.9) in higher plants. Here, we report RNA ligase-mediated rapid amplification of cDNA ends experiments that showed that PgiC in Clarkia (Onagraceae) and Arabidopsis thaliana has an intron in the 5' leader. Comparison of the EMBL accessions of the cDNA and genomic sequences showed that this is also the case in rice (Oryza sativa), suggesting that a leader intron is generally present in higher plant PgiC. The intron is bounded by consensus 5'-GT and AG-3' splice sites but showed alternative splicing in Clarkia, resulting in mature transcripts that differ by 8-19 nt in length. The intron is located 18 or 10 nt upstream of the start codon in Clarkia, 2 nt upstream in Arabidopsis, and 9 nt in rice. PgiC in Clarkia was duplicated before the divergence of the extant species, many of which have two expressed genes PgiC1 and PgiC2. Full-length transcripts of both genes identified the transcription start and made it possible to identify the leader intron and leader exon (between the transcription start and leader intron) from previously obtained genomic sequences of both genes in other Clarkia species. These data permit the comparison of evolution in the leader exon and intron with the exons and introns of the coding region, a topic that has not been studied previously. Both the leader exon and the leader intron resemble introns of the coding region in base substitution rate and accumulation of gaps. But the leader intron splice junctions are not strictly conserved in position as are those of the coding region introns. Also, in base composition, the leader intron resembles the other introns, whereas the leader exon more nearly resembles the coding exons. A difference in base composition between coding exons and flanking introns is known to be important for the recognition of splice sites. Thus, the marked difference in base composition between the leader exon and leader intron is probably maintained by selection despite a high rate of sequence divergence.

Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-‘Synechococcus’ clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon The GenBank accession numbers for the ITS amplicon sequences reported in this paper are AF387607 (PCC 9511T), AF387610 (PCC 6307), AF387608 (PCC 7001) and AF387609 (PCC 7941).

PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of 'Synechococcus' (WH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 16S rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-'Synechococcus' strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted clade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems.

Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species.

The nuclear large subunit (LSU) rRNA gene is a rich source of phylogenetic characters because of its large size, mosaic of slowly and rapidly evolving regions, and complex secondary structure variation. Nevertheless, many studies have indicated that inconsistency, bias, and gene-specific error (e.g., within-individual gene family variation, cryptic sequence simplicity, and sequence coevolution) can complicate animal phylogenies based on LSU rDNA sequences. However, most of these studies sampled small gene fragments from expansion segments--among animals only five nonchordate complete LSU sequences are published. In this study, we sequenced near-complete nuclear LSU genes from 11 representative daphniids (Crustacea). The daphniid expansion segment V6 was larger and showed more length variation (90-351 bp) than is found in all other reported LSU V6 sequences. Daphniid LSU (without the V6 region) phylogenies generally agreed with the existing phylogenies based on morphology and mtDNA sequences. Nevertheless, a major disagreement between the LSU and the expected trees involved a positively misleading association between the two taxa with the longest branches, Daphnia laevis and D. occidentalis. Both maximum parsimony (MP) and maximum likelihood (ML) optimality criteria recovered this association, but parametric simulations indicated that MP was markedly more sensitive to this bias than ML. Examination of data partitions indicated that the inconsistency was caused by increased nucleotide substitution rates in the branches leading to D. laevis and D. occidentalis rather than among-taxon differences in base composition or distribution of sites that are free to vary. These results suggest that lineage-specific rate acceleration can lead to long-branch attraction even in the conserved genes of animal species that are almost morphologically indistinguishable.

Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae.

Compositional changes are a major feature of genome evolution. Overlooking nucleotide composition differences among sequences can seriously mislead phylogenetic reconstructions. Large compositional variation exists among the members of the family Drosophilidae. Until now, however, base composition differences have been largely neglected in the formulations of the nucleotide substitution process used to reconstruct the phylogeny of this important group of species. The present study adopts a maximum-likelihood framework of phylogenetic inference in order to analyze five nuclear gene regions and shows that (1) the pattern of compositional variation in the Drosophilidae does not match the phylogeny of the species; (2) accounting for the heterogeneous GC content with Galtier and Gouy's nucleotide substitution model leads to a tree that differs in significant aspects from the tree inferred when the nucleotide composition differences are ignored, even though both phylogenetic hypotheses attain strong nodal support in the bootstrap analyses; and (3) the LogDet distance correction cannot completely overcome the distorting effects of the compositional variation that exists among the species of the Drosophilidae. Our analyses confidently place the Chymomyza genus as an outgroup closer than the genus Scaptodrosophila to the Drosophila genus and conclusively support the monophyly of the Sophophora subgenus.

The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?

Miyata et al. have suggested that the male-to-female mutation rate ratio (alpha) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of alpha. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of alpha are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of alpha, obtained using this method, need to be treated with caution.

Dynamic evolution of genomes and the concept of genome space.

A new era in the elucidation of genome evolution has been heralded with the availability of numerous genome sequences. With these data, it has been possible to study evolutionary processes at a greater level of detail in order to characterize features such as gene shuffling, genome rearrangements, base bias composition, and horizontal gene transfer. In this paper, we discuss the evolutionary implications of significant rearrangements within genomes as well as characteristic genomic regions that have been conserved across genomes. This is based on our analysis of orthologous and paralogous genes. We argue that genome plasticity has most likely contributed substantially to the dynamic evolution of genomes. We also describe the characteristic mosaic features of an archaea genome that is comprised of both bacterial and eukaryal elements. Here we investigate base compositional differences as well as the similarity of this species' genes to either bacteria or eukarya. We conclude that these features can be largely explained by the mechanism of horizontal gene transfer. Finally, we introduce the concept of genome space which is defined as the entire set of genomes of all living organisms. We explain its usefulness to describe as well as to gain deeper insight into the general features of the dynamic genomic evolutionary process.

Codon usage bias and base composition in MHC genes in humans and common chimpanzees.

Codon bias and base composition in major histocompatibility complex (MHC) sequences have been studied for both class I and II loci in Homo sapiens and Pan troglodytes. There is low to moderate codon bias for the MHC of humans and chimpanzees. In the class I loci, the same level of moderate codon bias is seen for HLA-B, HLA-C, Patr-A, Patr-B, and Patr-C, while at HLA-A the level of codon bias is lower. There is a correlation between codon usage bias and G+C content in the A and B loci in humans and chimps, but not at the C locus. To examine the effect of diversifying selection on codon bias, we subdivided class I alleles into antigen recognition site (ARS) and non-ARS codons. ARS codons had lower bias than non-ARS codons. This may indicate that the constraint of codon bias on nucleotide substitution may be selected against in ARS codons. At the class II loci, there are distinct differences between alpha and beta chain genes with respect to codon usage, with the beta chain genes being much more biased. Species-specific differences in base composition were seen in exon 2 at the DRB1 locus, with lower GC content in chimpanzees. Considering the complex evolutionary history of MHC genes, the study of codon usage patterns provides us with a better understanding of both the evolutionary history of these genes and the evolution of synonymous codon usage in genes under natural selection.

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly, excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.

Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster.

Both natural selection and mutational biases contribute to variation in codon usage bias within Drosophila species. This study addresses the cause of codon bias differences between the sibling species, Drosophila melanogaster and D. simulans. Under a model of mutation-selection-drift, variation in mutational processes between species predicts greater base composition differences in neutrally evolving regions than in highly biased genes. Variation in selection intensity, however, predicts larger base composition differences in highly biased loci. Greater differences in the G+C content of 34 coding regions than 46 intron sequences between D. melanogaster and D. simulans suggest that D. melanogaster has undergone a reduction in selection intensity for codon bias. Computer simulations suggest at least a fivefold reduction in Nes at silent sites in this lineage. Other classes of molecular change show lineage effects between these species. Rates of amino acid substitution are higher in the D. melanogaster lineage than in D. simulans in 14 genes for which outgroup sequences are available. Surprisingly, protein sizes are larger in D. melanogaster than in D. simulans in the 34 genes compared between the two species. A substantial fraction of silent, replacement, and insertion/deletion mutations in coding regions may be weakly selected in Drosophila.

Selection of hammerhead ribozymes for optimum cleavage of interleukin 6 mRNA

Four GUC triplets in the coding region of the MRNA of interleukin 6 (IL-6) were examined for their suitabilty to serve as a target for hammerhead ribozome-mediated cleavage. This selection procedure was performed with the intention to downregulate IL-6 production as a potential treatment of those diseases in which IL-6 overexpression is involved. Hammerhead ribozymes and their respective short synthetic substrates (19-mers) were synthesized for these four GUC triplets. Notwithstanding the identical catalytic core sequences, the difference in base composition of the helices involved in substrate binding caused substantial variation in cleavage activity. The cleavage reactions on the 1035 nucleotide IL-6 mRNA transcript revealed that two ribozymes were able to cleave this substrate, showing a decrease in catalytic efficiency to 1/30 and 1/300 of the short substrate. This study indicates that the GUC triplet located at nucleotide 510 of the mRNA of IL-6 is the best site for hammerhead ribozyme-mediated cleavage. We suggest that in future targeting of chemically modified hammerhead ribosomes for cleavage of IL-6 RNA should be directed at this location.

Rapid genomic evolution of a non-virulent Coxsackievirus B3 in selenium-deficient mice results in selection of identical virulent isolates

Previous work from our laboratory demonstrated that selenium deficiency in the mouse allows a normally benign (amyocarditic) cloned and sequenced Coxackievirus to cause significant heart damage. Furthermore, Coxsackievirus recovered from the hearts of selenium-deficient mice inoculated into selenium-adequate mice still induced significant heart damage, suggesting that the amyocarditic Coxsackievirus had mutated to a virulent phenotype. Here we report that sequence analysis revealed six nucleotide changes between the virulent virus recovered from the selenium-deficient host and the avirulent input virus. These nucleotide changes are consistent with known differences in base composition between virulent and avirulent strains of Coxsackievirus. To the best of our knowledge, this is the first report of a specific nutritional deficiency driving changes in a viral genome, permitting an avirulent virus to acquire virulence due to genetic mutation.

Insulin-like Growth Factor II Intron Sequences Support the Hominoid Rate-Slowdown Hypothesis

Nucleotide sequences were obtained from the approximately 1.7 kb intron 7 of the insulin-like growth factor II gene in human and representatives of both Old World and New World monkeys and analyzed with additional published noncoding regions (both introns and flanking regions) that differ substantially in base composition (GC content). Relative rate tests, utilized to examine differential rates of molecular evolution between humans and Old World monkeys, support the hypothesis that the rate of nucleotide substitution is slower in humans than in Old World monkeys. Comparisons of approximately 4,300 nucleotide positions revealed a significantly higher evolutionary rate in the Old World monkey lineage than in the human lineage for both intron sequences and flanking regions. The data indicate that the molecular clock hypothesis is not applicable to the human and Old World monkey lineages and that the hominoid rate slowdown is a general phenomenon - it is not unique to a particular gene region and is not influenced by regional differences in base composition.