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PubMed2000

Health care savings from microbiological caries risk screening of toddlers: a cost estimation model.

OBJECTIVES: Modeling new biomedical technologies and determining their expected cost is necessary before initiating formal clinical trials. This paper estimates an economic model for the potential cost impact of microbiological screening of toddlers for caries risk compared to the traditional method of managing pediatric caries. METHODS: Potential cost savings were calculated based on screening test properties (sensitivity and specificity) derived from a population of 1,180 children aged 1 to 3 years with a caries prevalence of 15 percent. An algorithm was then developed to allocate prevalent and anticipate incident caries, treatment effectiveness assumptions, and existing regional treatment costs. RESULTS: The cost analysis model conservatively predicts savings of 7.3 percent from screening and early intervention. Cumulative dental treatment costs for a child at age 4 years are $367.90 if the child has been screened and $396.70 otherwise. The model further predicts that cost savings increase significantly as caries prevalence increases. CONCLUSIONS: Microbiologic risk assessment for pediatric caries may be an example of a preventive public health screening technique that results in both clinical benefits and cost savings. If the model is validated by randomized clinical trials, microbiologic screening could be used by pediatric primary care providers to identify toddlers who require early referral to dentists for further risk assessment and early caries management.

Algorithms↗
PubMed1999

CR6: A third member in the MyD118 and Gadd45 gene family which functions in negative growth control.

MyD118 and Gadd45 are two related genes which encode for proteins that play important roles in negative growth control, including both growth suppression and apoptosis. A strategy was employed to clone new members of the MyD118 and Gadd45 family of genes. Based on alignment of the deduced amino acid sequences, one cDNA clone was found to encode for the murine homologue of human CR6, originally cloned as an IL-2 immediate-early response gene. The murine and human CR6 proteins were observed to be 97% identical, indicating that CR6 is an evolutionarily conserved protein. Analysis of CR6 expression during hematopoietic cell development associated with growth arrest and apoptotic cell death, upon exposure of hematopoietic cells to a variety of growth arrest and apoptotic stimuli, and in a variety of murine tissues, has revealed that CR6 expression differs significantly from the expression of the related MyD118 and Gadd45 genes. Nevertheless, CR6, like MyD118 and Gadd45, suppressed colony formation of human lung carcinoma H1299 cells. These data suggest that CR6 plays similar, but not identical, roles to MyD118 and Gadd45 in negative control of cell growth.

Amino Acid Sequence↗
PubMed1991

[Results and analysis of poor results after conservative therapy of distal radius fracture].

The authors report on the results of a follow-up study of 120 conservatively treated distal radius fractures. Follow-up averaged 35 months (25 to 48 months). The quality of initial reduction has a crucial impact on the final outcome. 87 fractures showed nearly perfect anatomical reduction, of these, 48 resulted in excellent, 16 in good, 15 in satisfactory, and 8 in poor final anatomical outcomes. In comparison, in 33 fractures with unsuccessful initial reduction, only two cases gave excellent and 12 cases good results (42%); 11 fractures were considered satisfactory and 8 poor. The necessity of a second reduction was significantly lower in the first group of initially well-reduced fractures when compared to the second group: 8 (9.2%) to 14 (42.4%) respectively. Evaluation of the functional outcome according to the Sarmiento scheme showed a strong correlation between the AO fracture classification and the final outcome. In group A fractures, 78% gave excellent or good, 22% satisfactory or bad results. Type B fractures gave 82% excellent or good and 18% satisfactory or poor results. In group C, only 50% reached excellent or good results, the C 3 fractures having the worst prognosis, achieving excellent or good results in only 20% of the cases. Regression analysis demonstrated a significant correlation between anatomical and functional outcome.

Adult↗
PubMed2003

Long-term population isolation in the endangered tropical tree species Caesalpinia echinata Lam. revealed by chloroplast microsatellites.

Habitat fragmentation represents the single most serious threat to the survival of tropical ecosystems. In formulating strategies to counteract the detrimental effects of fragmentation, knowledge of the levels and patterns of genetic diversity within and between natural populations is vital to the establishment of any conservation programme. We utilized polymorphic chloroplast microsatellite markers to analyse genetic diversity in populations of the endangered tropical tree Caesalpinia echinata Lam. representing the entire extant range of the species. Levels of within-population diversity were low, with only two of seven populations studied displaying any variation. The vast majority of the genetic variation was partitioned between geographical regions (36%) and between populations within regions (55%). These levels of genetic structuring, coupled with a calculated pollen-to-seed flow ratio of approximately 6.7:1, suggest that there has been little gene flow between the three major geographical regions over an extended period. Thus, the current tripartite distribution of the species is more consistent with the existence of separate glacial refugia, rather than reflecting any anthropogenic effects.

Brazil↗
PubMed2004

Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen. nov., comb. nov., and description of the Bacteriovorax-Peredibacter clade as Bacteriovoracaceae fam. nov.

A phylogenetic analysis of Bdellovibrio-and-like organisms (BALOs) was performed. It was based on the characterization of 71 strains and on all consequent 16S rRNA gene sequences available in databases, including clones identified by data-mining, totalling 120 strains from very varied biotopes. Amplified rDNA restriction analysis (ARDRA) accurately reflected the diversity and phylogenetic affiliation of BALOs, thereby providing an efficient screening tool. Extensive phylogenetic analysis of the 16S rRNA gene sequences revealed great diversity within the Bdellovibrio (> 14 % divergence) and Bacteriovorax (> 16 %) clades, which comprised nine and eight clusters, respectively, exhibiting more than 3 % intra-cluster divergence. The clades diverged by more than 20 %. The analysis of conserved 16S rRNA secondary structures showed that Bdellovibrio contained motifs atypical of the delta-Proteobacteria, suggesting that it is ancestral to Bacteriovorax. While none of the Bdellovibrio strains were of marine origin, Bacteriovorax included separate soil/freshwater and marine-specific groups. On the basis of their extensive diversity and the large distance separating the groups, it is proposed that Bacteriovorax starrii be placed into a new genus, Peredibacter gen. nov., with Peredibacter starrii A3.12T (= ATCC 15145T = NCCB 72004T) as its type strain. Also proposed is a redefinition of the Bdellovibrio and the Bacteriovorax-Peredibacter lineages as two different families, i.e. 'Bdellovibrionaceae' and a new family, Bacteriovoracaceae. Also, a re-evaluation of oligonucleotides targeting BALOs is presented, and the implications of the large diversity of these organisms and of their distribution in very different environments are discussed.

Bdellovibrio↗
PubMed2005

Detection and differentiation of filarial parasites by universal primers and polymerase chain reaction-restriction fragment length polymorphism analysis.

Filarial nematode parasites are a serious cause of morbidity in humans and animals. Identification of filarial infection using traditional morphologic criteria can be difficult and lead to misdiagnosis. We report on a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based method to detect and differentiate a broad range of filarial species in a single PCR. The first internal transcribed spacer 1 (ITS1) along with the flanking 18S and 5.8S ribosomal DNA (rDNA) were isolated and cloned from Wuchereria bancrofti, Brugia malayi, and Brugia pahangi. Sequence analysis identified conserved sites in the 18S and 5.8S rDNA sequence that could be used as universal priming sites to generate ITS1-distinctive PCR products that were useful for distinguishing filariae at the genus level. The addition of a digestion of the ITS1 PCR product with the restriction endonuclease Ase I generated a fragment profile that allowed differentiation down to the species level for W. bancrofti, B. malayi, B. pahangi, Dirofilaria immitis, and D. repens. The PCR-RFLP of ITS1 rDNA will be useful in diagnosing and differentiating filarial parasites in human, animal reservoir hosts, and mosquito vectors in disease-endemic areas.

Animals↗
PubMed1998

Porcine CD5 gene and gene product identified on the basis of inter-species conserved cytoplasmic domain sequences.

Analysis of published CD5 amino acid sequences identified conserved sequences with potentially immunogenic epitopes. To obtain anti-porcine CD5, synthetic peptides representing conserved sequences identified in mouse, human, cattle and sheep CD5 cytoplasmic tail domains were linked to KLH and used to immunize rabbits. Anti-synthetic peptide serum reacted with an antigen extracted from porcine lymphocyte membrane which was consistent in size (67 kDa) with CD5. Murine monoclonal anti-porcine wCD5 (b53b7) and the anti-CD5 synthetic peptide serum react with the same ligand confirming that porcine wCD5 has conserved amino acid sequences similar to those of CD5 of several species. Analysis of porcine genome for CD5 gene sequences by PCR was conducted to verify the presence of CD5-like genes. Oligomeric primers were designed to identify CD5-like sequences by polymerase chain reaction in pigs and other species. Amplified DNA similar in size to that predicted for CD5 elements were amplified from a variety of animal genomes including that of pig. The porcine-derived fragment was cloned and shown to be 96% similar to mouse CD5. The use of published CD sequences for prediction of immunogenic peptides has provided a complimentary alternative to the more traditional approaches to production of CD-specific antibodies.

Amino Acid Sequence↗
PubMed2000

Multiple domains interacting with Gs in the porcine calcitonin receptor.

The molecular basis for Gs activation by the calcitonin (CT) receptor was investigated. Based upon the analysis of conserved regions in G protein-coupled receptors, two nonoverlapping regions in the heptahelical porcine CT receptor (CTR) were selected as candidate Gs-interacting domains: the third intracellular loop residues 327-344 (KLKESQEAESHMYLKAVR, P3 region) and the C-tail residues 404-418 (KRQWNQYQAQRWAGR, P4 region). To assess their Gs-interacting function, we expressed these sequences in hybrid insulin-like growth factor II receptors in which the receptor native Gi-interacting domain was converted to CTR sequences. In COS cells transfected with either P3- or P4-substituted hybrid receptor, membrane adenylyl cyclase activity significantly increased. The up-regulated activity of cAMP was confirmed by measuring the transcriptional activity of the cAMP response element in cells expressing either hybrid receptor. A mutant CTR lacking the P4 region maintained positive cAMP response but with an attenuated maximal capacity to produce cAMP. In contrast, we could not assess the function of the P3 region using a conventional deletion method, as CT bound poorly to cells transfected with either of the two P3-deficient CTRs (one lacking the P3 region and the other lacking P3 but having the P3 sequence in reverse orientation). These data suggest that the third intracellular loop and the C-tail in CTR have domain-specific roles in Gs activation and that the hybrid receptor approach used here, combined with a conventional mutagenesis approach, is useful for intact cell analysis and functional dissection of G protein-coupled receptors.

Adenylyl Cyclases↗
PubMed2003

NF-kappa B regulates BCL3 transcription in T lymphocytes through an intronic enhancer.

Exposure to soluble protein Ags in vivo leads to abortive proliferation of responding T cells. In the absence of a danger signal, artificially provided by adjuvants, most responding cells die, and the remainder typically become anergic. The adjuvant-derived signals provided to T cells are poorly understood, but recent work has identified BCL3 as the gene, of those tested, with the greatest differential transcriptional response to adjuvant administration in vivo. As an initial step in analyzing transcriptional responses of BCL3 in T cells, we have identified candidate regulatory regions within the locus through their evolutionary conservation and by analysis of DNase hypersensitivity. An evolutionarily conserved DNase hypersensitive site (HS3) within intron 2 was found to act as a transcriptional enhancer in response to stimuli that mimic TCR activation, namely, PHA and PMA. In luciferase reporter gene constructs transiently transfected into the Jurkat T cell line, the HS3 enhancer can cooperate not only with the BCL3 promoter, but also with an exogenous promoter from herpes simplex thymidine kinase. Deletional analysis revealed that a minimal sequence of approximately 81 bp is required for full enhancer activity. At the 5' end of this minimal sequence is a kappaB site, as confirmed by EMSAs. Mutation of this site in the context of the full-length HS3 abolished enhancer activity. Cotransfection with NF-kappaB p65 expression constructs dramatically increased luciferase activity, even without stimulation. Conversely, cotransfection with the NF-kappaB inhibitor IkappaBalpha reduced activation. Together, these results demonstrate a critical role for NF-kappaB in BCL3 transcriptional up-regulation by TCR-mimetic signals.

B-Cell Lymphoma 3 Protein↗
PubMed2005

Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design.

Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and isolated to some degree (e.g. sea loughs and offshore islands). While such features enable easier management, they may have important implications for the genetic structure of protected populations, the ability of populations to recover from local catastrophes and the potential for marine reserves to act as sources of propagules for surrounding areas. Here, we present a case study demonstrating genetic differentiation, isolation, inbreeding and reduced genetic diversity in populations of the dogwhelk Nucella lapillus in Lough Hyne Marine Nature Reserve (an isolated sea lough in southern Ireland), compared with populations on the local adjacent open coast and populations in England, Wales and France. Our study demonstrates that this sea lough is isolated from open coast populations, and highlights that there may be long-term genetic consequences of selecting reserves on the basis of isolation and ease of protection.

Analysis of Variance↗
PubMed2003

Identification and characterization of Fugu orthologues of mammalian interleukin-12 subunits.

We have isolated and characterized cDNAs and genes for pufferfish, Fugu rubripes, (Fugu) orthologues of mammalian interleukin (IL)-12 subunits (IL-12 p35 and IL-12 p40). The deduced amino acid sequences of the Fugu IL-12 subunits showed homology with mammalian IL-12 subunits (p35: 50.4-58.0% similarity; p40: 51.2-55.4% similarity). Phylogenetic analysis confirmed that Fugu IL-12 p35 and p40 genes cluster with their mammalian counterpart lineages. The genomic organization of each of the Fugu IL-12 subunit genes is similar to that of the corresponding mouse IL-12 subunit genes, although the Fugu genes are very compact due to small intron size. Comparative genomic analysis showed conserved syntenies within the IL-12 p35 and p40 regions between Fugu and human, indicating that the Fugu IL-12 p35 and p40 genes are orthologues for mammalian IL-12 p35 and p40 encoding genes, respectively. Expression of IL-12 p35 mRNA was observed in lymphoid tissues and several non-lymphoid tissues, while expression of IL-12 p40 mRNA was constitutive and nearly ubiquitous. In the spleen and head kidney, expression of IL-12 p35 was induced by polyriboinosinic polyribocytidylic acid [poly(I:C)] and not by lipopolysaccharide (LPS), while expression of IL-12 p40 was constitutive and unresponsive to both poly(I:C) and LPS. These results indicate that IL-12 levels are regulated by production of IL-12 p35 mRNA and suggest that IL-12 in fish may be involved in antiviral defense. This is the first report of the identification and characterization of IL-12 subunit cDNAs and genes in a non-mammalian vertebrate.

Amino Acid Sequence↗
PubMed2006

Structural assessment of single amino acid mutations: application to TP53 function.

Single amino acid substitution is the type of protein alteration most related to human diseases. Current studies seek primarily to distinguish neutral mutations from harmful ones. Very few methods offer an explanation of the final prediction result in terms of the probable structural or functional effect on the protein. In this study, we describe the use of three novel parameters to identify experimentally-verified critical residues of the TP53 protein (p53). The first two parameters make use of a surface clustering method to calculate the protein surface area of highly conserved regions or regions with high nonlocal atomic interaction energy (ANOLEA) score. These parameters help identify important functional regions on the surface of a protein. The last parameter involves the use of a new method for pseudobinding free-energy estimation to specifically probe the importance of residue side-chains to the stability of protein fold. A decision tree was designed to optimally combine these three parameters. The result was compared to the functional data stored in the International Agency for Research on Cancer (IARC) TP53 mutation database. The final prediction achieved a prediction accuracy of 70% and a Matthews correlation coefficient of 0.45. It also showed a high specificity of 91.8%. Mutations in the 85 correctly identified important residues represented 81.7% of the total mutations recorded in the database. In addition, the method was able to correctly assign a probable functional or structural role to the residues. Such information could be critical for the interpretation and prediction of the effect of missense mutations, as it not only provided the fundamental explanation of the observed effect, but also helped design the most appropriate laboratory experiment to verify the prediction results.

Amino Acid Sequence↗
PubMed2003

A protein kinase from Colletotrichum trifolii is induced by plant cutin and is required for appressorium formation.

When certain phytopathogenic fungi contact plant surfaces, specialized infection structures (appressoria) are produced that facilitate penetration of the plant external barrier; the cuticle. Recognition of this hydrophobic host surface must be sensed by the fungus, initiating the appropriate signaling pathway or pathways for pathogenic development. Using polymerase chain reaction and primers designed from mammalian protein kinase C sequences (PKC), we have isolated, cloned, and characterized a protein kinase from Colletotrichum trifolii, causal agent of alfalfa anthracnose. Though sequence analysis indicated conserved sequences in mammalian PKC genes, we were unable to induce activity of the fungal protein using known activators of PKC. Instead, we show that the C. trifolii gene, designated LIPK (lipid-induced protein kinase) is induced specifically by purified plant cutin or long-chain fatty acids which are monomeric constituents of cutin. PKC inhibitors prevented appressorium formation and, to a lesser extent, spore germination. Overexpression of LIPK resulted in multiple, abnormally shaped appressoria. Gene replacement of lipk yielded strains which were unable to develop appressoria and were unable to infect intact host plant tissue. However, these mutants were able to colonize host tissue following artificial wounding, resulting in typical anthracnose lesions. Taken together, these data indicate a central role in triggering infection structure formation for this protein kinase, which is induced specifically by components of the plant cuticle. Thus, the fungus is able to sense and use host surface chemistry to induce a protein kinase-mediated pathway that is required for pathogenic development.

Amino Acid Sequence↗
PubMed2004

SP-transcription factors are involved in basal MVP promoter activity and its stimulation by HDAC inhibitors.

The major vault protein (MVP) has been implicated in multidrug resistance, cellular transport, and malignant transformation. In this study we aimed to identify crucial MVP promoter elements that regulate MVP expression. By mutation as well as deletion analysis a conserved proximal GC-box element was demonstrated to be essential for basal human MVP promoter transactivation. Binding of Sp-family transcription factors but not AP2 to this element in vitro and in vivo was shown by EMSA and ChIP assays, respectively. Inhibition of GC-box binding by a dominant-negative Sp1-variant and by mithramycin A distinctly attenuated MVP promoter activity. In Sp-null Drosophila cells, the silent human MVP promoter was transactivated by several human Sp-family members. In human cells the MVP promoter was potently stimulated by the histone deacetylase (HDAC) inhibitors butyrate (NaB) and trichostatin A (TSA), resulting in enhanced MVP expression. This stimulation was substantially decreased by mutation of the single GC-box and by application of mithramycin A. Treatment with HDAC inhibitors led to a distinct decrease of Sp1 but increase of Sp3 binding in vivo to the respective promoter sequence as demonstrated by ChIP assays. Summarising, this study identifies variations in Sp-transcription factor binding to a single proximal GC-box element as critical for basal MVP promoter activation and its stimulation by HDAC inhibitors.

Animals↗
PubMed2006

Differences in the umbrella effects of African amphibians and mammals based on two estimators of the area of occupancy.

Conservation organizations are collecting large-scale data regarding distribution and threats to vertebrate taxa. These data sets will enable planners to systematically identify large-scale conservation priorities; however, they will cover only a tiny proportion of living organisms. Therefore, it is essential to investigate to what extent the areas selected for conservation actions can provide protection for other species. We analyzed the umbrella effect between amphibians and mammals across mainland Africa. We built habitat suitability models within the geographic ranges of 1654 species, based on data collected in the framework of the World Conservation Union (IUCN) Global Amphibian Assessment and IUCN Global Mammal Assessment. We applied systematic reserve selection algorithms to two sets of estimators of the area of occupancy of amphibians and mammals (geographic ranges and estimated suitable areas) and thus selected four reserve systems. We then quantified the protection that each of the four systems provided for amphibians and mammals. Reserves selected for amphibians and mammals were comparable in area, with the former concentrated in the Afrotropical region and the latter more evenly dispersed. Mammal reserves left fewer gaps in species coverage among amphibians than the reverse, but amphibian reserves included a larger proportion of each mammal's area of occupancy than the reverse. For both taxa, setting reserves to include estimated suitable areas instead of ranges resulted in the clustering of reserves in the tropics. Furthermore, it efficiently protected hidden gaps (species with unsuitable portions of their range inside protected areas) in the other taxon and included a higher proportion of the area of occupancy of the other taxon. Overall, amphibians and mammals in Africa acted as an umbrella for a high proportion of species in the other taxon. Focusing on estimated suitable areas instead of ranges improved the umbrella effect of both taxa.

Africa↗
PubMed2004

Divergence of conserved non-coding sequences: rate estimates and relative rate tests.

In many eukaryotic genomes only a small fraction of the DNA codes for proteins, but the non-protein coding DNA harbors important genetic elements directing the development and the physiology of the organisms, like promoters, enhancers, insulators, and micro-RNA genes. The molecular evolution of these genetic elements is difficult to study because their functional significance is hard to deduce from sequence information alone. Here we propose an approach to the study of the rate of evolution of functional non-coding sequences at a macro-evolutionary scale. We identify functionally important non-coding sequences as Conserved Non-Coding Nucleotide (CNCN) sequences from the comparison of two outgroup species. The CNCN sequences so identified are then compared to their homologous sequences in a pair of ingroup species, and we monitor the degree of modification these sequences suffered in the two ingroup lineages. We propose a method to test for rate differences in the modification of CNCN sequences among the two ingroup lineages, as well as a method to estimate their rate of modification. We apply this method to the full sequences of the HoxA clusters from six gnathostome species: a shark, Heterodontus francisci; a basal ray finned fish, Polypterus senegalus; the amphibian, Xenopus tropicalis; as well as three mammalian species, human, rat and mouse. The results show that the evolutionary rate of CNCN sequences is not distinguishable among the three mammalian lineages, while the Xenopus lineage has a significantly increased rate of evolution. Furthermore the estimates of the rate parameters suggest that in the stem lineage of mammals the rate of CNCN sequence evolution was more than twice the rate observed within the placental amniotes clade, suggesting a high rate of evolution of cis-regulatory elements during the origin of amniotes and mammals. We conclude that the proposed methods can be used for testing hypotheses about the rate and pattern of evolution of putative cis-regulatory elements.

Animals↗
PubMed2004

Contributions of Portuguese cattle breeds to genetic diversity using marker-estimated kinships.

The quantitative assessment of genetic diversity within and between populations is important for decision-making in genetic conservation plans. In our study, we applied the livestock core set method to define the contribution of 15 cattle breeds, 11 of which are Portuguese indigenous cattle breeds, to genetic diversity. In livestock core set theory genetic diversity is defined as the maximum genetic variance that can be obtained in a random-mating population that is bred from the populations present in that core set. Two methods to estimate marker-estimated kinships to obtain the contributions to the core set were used in this study: the weighted log-linear model (WLM) and the weighted log-linear mixed model (WLMM). The breeds that contributed most to diversity in the core set were Holstein-Friesian followed by the Portuguese Mertolenga and Cachena for both WLM and WLMM methods. The ranking of relative contributions of cattle breeds was maintained when we considered only the Portuguese cattle breeds. Furthermore, we were able to identify the marginal contributions and respective losses of diversity for each of the 11 Portuguese cattle breeds when we considered a subset of populations that are not threatened of being lost (the Safe set composed of the four exotic breeds present in this study). When WLM was used losses in genetic diversity ranged from 2.68 to 0.65% while the loss in founder genome equivalents ranged from 37.37 to 8.43% for Mertolenga and Brava de Lide breeds respectively. When WLMM was used losses in genetic diversity and founder genome equivalents were less extreme than for the WLM method, ranging from 1.27 to 0.69 and 26.8 to 12.99 respectively.

Animals↗
PubMed1994

The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis.

The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.

Animals↗