Phylogenetic and size constrains on cranial ontogenetic allometry of spiny rats (Echimyidae, Rodentia).

Analysis of ontogenetic development is crucial for understanding the emergence of phenotypic discrepancies between animal taxa. The study of allometric trajectories within a phylogenetic context is a feasible approach to assess the morphological change across different evolutionary lineages. Here, we report the disparity of multivariate ontogenetic allometry in the Echimyidae, a taxonomically diverse rodent family, as well as the effects of size on the evolution of skull ontogeny. The ontogenetic trajectories of 15 echimyid operational taxonomic unities (12 genera plus one genus with three species) belonging to all subfamilies and major clades, when plotted in allometric space, revealed strong and significant phylogenetic signals. Allometric trajectories were found to be constrained by phylogenetic ancestry, with changes approximately adjusting to a Brownian motion model of evolution. Moreover, the occupation of allometric space by echimyid taxa was significantly correlated with adult size rather than with shape, suggesting that the variation in adult size might result in critically intrinsic and structural constraints on allometric coefficients. These findings disagreed with the hypothesis that allometric disparities might be mainly adaptive with undetectable phylogenetic signals.

Association of TP53 polymorphisms on the risk of Wilms tumor.

BACKGROUND: Molecular factors influencing Wilms tumor (WT) development remain largely unknown. TP53 mutations seem to be restricted to the anaplastic WT subtype. However, TP53 polymorphisms do not have a defined role in the disease. PROCEDURE: To assess the impact of TP53 mutations and polymorphisms (PIN2, PIN3, and PEX4) on risk of development, age at diagnosis, and survival in WT, we analyzed 46 blood DNA samples and 31 fresh tumor DNA samples from 52 patients with WT. Sequencing of TP53 exons 2-11 was performed. RESULTS: Tumor DNA analysis revealed TP53 pathogenic missense mutations (p.V197M, p.R213Q, p.R248W, and p.R337C) in four samples (12.9%). Blood DNA samples revealed a novel intronic mutation, IVS2 + 37C > T, in one patient (2.2%). Bilaterality was associated with a twofold decrease in survival (P = 0.00037). Diffuse anaplasia also presented a lower survival probability compared to patients with non-anaplastic tumors, or with focal anaplasia (P = 0.045). Patients with a TP53 somatic mutation showed survival probability of 37.5% versus 85.0% for patients with no somatic mutations, although the difference was not statistically significant (P = 0.0706). PIN3 duplicated allele was associated with a 20-month later mean age at diagnosis (P = 0.0084). TP53 PEX4 C allele showed an increased risk for WT development (P = 0.0379). No relationship was found between survival and gender, age at diagnosis, or the less frequent alleles of PIN2, PIN3, and PEX4. CONCLUSIONS: Our results demonstrate an association between PIN3 and age at diagnosis, as well as an association of PEX4 and risk of development of WT.

Prevalence of hepatitis C virus among users attending a voluntary testing centre in Rio Grande, southern Brazil: predictive factors and hepatitis C virus genotypes.

We estimated the prevalence of hepatitis C (HCV) infection and associated risk factors in 750 individuals attending the Voluntary Counseling and Testing Center of Rio Grande (VCT/RG), in Southern Brazil, and identified viral genotypes. Demographic data and risk factors for HCV transmission were also collected and analysed. Anti-HCV antibody-positive individuals were tested for HCV-RNA and genotyped by sequencing the 5' untranslated region of the viral genome. Prevalence estimates of anti-HCV and HCV-RNA were 6% and 5.5%, respectively. We identified genotypes 1 (67%), 2 (2%) and 3 (31%); the latter was more prevalent than in other regions of Brazil. Anti-HCV prevalence in VCT/RG users was similar to previous reports. Age, previous blood transfusion, sexual orientation and injecting drug use were independent predictors of HCV infection. The presence of multiple risk factors was also associated with a higher risk for HCV infection. HCV genotype was not associated with any variable analysed in this study.

Genetic diversity of neotropical primates: phylogeny, population genetics, and animal models for infectious diseases.

The classification of neotropical primates has been controversial, and different arrangements have been proposed based on disparate taxonomic criteria and on the traits selected for elucidating phylogenetic reconstructions, like morphologic characters, nuclear DNA and mitochondrial DNA. Population studies of some neotropical primates have been useful for assessing their extant genetic variability and for understanding their social structure and dynamics. Finally, neotropical primates have become valuable models for some human infectious deseases, especially for HIV studies related to viral resistance. In this review, we comment on these aspects that make neotropical primates a group of highly valuable species for basic and applied research.

The primates of the Neotropics: genomes and chromosomes.

The classification of neotropical primates has been controversial. Different arrangements have been proposed, depending on taxonomic criteria and on the traits selected for phylogenetic reconstructions. These include gross morphologic characters, karyotypic attributes and DNA sequence data of nuclear and mitochondrial genes and of repetitive genomic components. These approaches have substantially clarified the main intergeneric relationships although several intrageneric arrangements still remain to be elucidated. In this review, we compare karyologic and molecular data of this speciose group.

Cytochrome b polymorphisms and population structure of two species of Alouatta (Primates).

We carried out a phylogenetic and population study in Alouatta caraya and Alouatta belzebul based on cytochrome b DNA sequence data. Maximum Parsimony and Median-Joining analyses grouped A. caraya from different localities showing a population structure in accordance with geographic distribution. The relation between A. caraya haplotypes could be explained with respect to the species range in the Cerrado, one of the most ancient morphoclimatic domains of South America, and the Chaco. Conversely, A. belzebul from the Amazonas and Atlantic forests grouped in a paraphyletic arrangement without an evident geographic pattern. Recent geologic events resulting in the separation of A. belzebul might explain why these geographically distant groups shared similar haplotypes and why ancestral polymorphisms might have been maintained in this species. Time of divergence estimates indicated that the splitting of the Alouatta lineage leading to A. caraya occurred some 4.58 MYA while the lineage leading to A. belzebul emerged 4.14 MYA.

Multi-directional chromosome painting maps homologies between species belonging to three genera of New World monkeys and humans.

We mapped chromosomal homologies in two species of Chiropotes (Pitheciini, Saki Monkeys) and one species of Aotus (Aotinae, Owl Monkey) by multi-directional chromosome painting. Human chromosome probes were hybridized to Chiropotes utahicki, C. israelita and Aotus nancymae metaphases. Wooly Monkey chromosome paints were also hybridized to Owl Monkey metaphases. We established Owl Monkey chromosome paint probes by flow sorting and reciprocally hybridized them to human chromosomes. The karyotypes of the Bearded Saki Monkeys studied here are close to the hypothesized ancestral platyrrhine karytoype, while that of the Owl Monkey appears to be highly derived. The A. nancymae karyotype is highly shuffled and only three human syntenic groups were found conserved coexisting with 17 derived human homologous associations. A minimum of 14 fissions and 13 fusions would be required to derive the A. nancymae karyotype from that of the ancestral New World primate karyotype. An inversion between homologs to segments of human 10 and 16 suggests a link between Callicebus and Chiropotes, while the syntenic association of 10/11 found in Aotus and Callicebus suggests a link between these two genera. Future molecular cytogenetic work will be needed to determine whether these rearrangements represent synapomorphic chromosomal traits.

Identification of three novel RB1 mutations in Brazilian patients with retinoblastoma by "exon by exon" PCR mediated SSCP analysis.

AIMS: To carry out a retrospective study, screening for mutations of the entire coding region of RB1 and adjacent intronic regions in patients with retinoblastoma. METHODS: Mutation screening in DNA extracts of formalin fixed, paraffin wax embedded tissues of 28 patients using combined "exon by exon" polymerase chain reaction mediated single strand conformational polymorphism analysis, followed by DNA sequencing. RESULTS: Eleven mutations were found in 10 patients. Ten mutations consisted of single base substitutions; 10 were localised in exonic regions (eight nonsense, one missense, and one frameshift) and another one in the intron-exon splicing region. Three novel mutations were identified: a 2 bp insertion in exon 2 (g.5506-5507insAG, R73fsX77), a G to A transition affecting the last invariant nucleotide of intron 13 (g.76429G>A), and a T to C transition in exon 20 (g.156795T>C, L688P). In addition, eight C to T transitions, resulting in stop codons, were found in five different CGA codons (g.64348C>T, g.76430C>T, g.78238C>T, g.78250C>T, and g.150037C>T). Although specific mutation hotspots have not been identified in the literature, eight of the 11 mutations occurred in CGA codons and seven fell within the E1A binding domains (codons 393-572 and 646-772), whereas five were of both types-in CGA codons within E1A binding domains. CONCLUSIONS: CGA codons and E1A binding domains are apparently more frequent mutational targets and should be initially screened in patients with retinoblastoma. Paraffin wax embedded samples proved to be valuable sources of DNA for retrospective studies, providing useful information for genetic counselling.

Genetic differentiation in geographically close populations of the water rat Nectomys squamipes (Rodentia, Sigmodontinae) from the Brazilian Atlantic Forest

We examined the genetic structure and the effects of a bottleneck in populations of the water rat Nectomys squamipes, a primary host of Schistosoma mansoni. Eight microsatellite loci were studied in 7 populations from the Sumidouro region of the Brazilian state of Rio de Janeiro. Our data, covering a four-year period during which a bottleneck occurred, revealed substantial variation (6-31 alleles per locus) and high levels of both observed (0.718-0.789) and expected (0.748-0.832) heterozygosity. Most populations were in Hardy-Weinberg equilibrium without linkage disequilibrium between loci. Overall average genetic differentiation between populations (estimated with the F ST (theta) and R ST (rho) analogues was 0.037 for theta and 0.060 for rho. There was significant allelic and genotypic differentiation between populations, especially in pairwise comparisons that included the most geographically isolated population. Direct migration estimates showed a low rate of migration, indicating that infected N. squamipes populations had a limited ability to spread S. mansoni. When the pre- and post-bottleneck populations were compared there was no detectable reduction in heterozygosity or allele number, although a significant excess of heterozygosity was detected in the post-bottleneck population.

Morphologic, karyotypic, and molecular evidence of a new form of Chiropotes (primates, pitheciinae).

Morphologic, karyotypic, and molecular analyses were carried out in 25 specimens of a distinct morph of Chiropotes (henceforth termed Chiropotes sp.) obtained from a number of localities in the Brazilian Amazon. Pelage coloration clearly distinguishes the collected specimens and all other known species of this genus. A distinct karyotype was described for Chiropotes sp. It differs from C. satanas chiropotes by two pericentric inversions, and from C. satanas utahicki by three, which suggests that these taxa are reproductively isolated. Morphometric analyses did not show significant differentiation between these Chiropotes taxa. Molecular analyses confirmed the monophyly of the subfamily Pitheciinae and genera Chiropotes, Cacajao, and Pithecia (the latter appearing as the most basal lineage of the pithecine clade). The genetic distances between C. s. utahicki and Chiropotes sp. from Rio Negro were greater than those between three recognized species of Pithecia, but smaller than those between Cacajao calvus and Cacajao melanocephalus. The most appropriate name for Chiropotes sp. from Rio Negro is C. israelita. This species, C. s. chiropotes, and C. s. utahicki are allopatric. Pelage coloration, karyotype, and molecular analysis strongly indicate that C. chiropotes, C. utahicki, and Chiropotes israelita deserve species status.

Chromosome painting in Callicebus lugens, the species with the lowest diploid number (2n=16) known in primates.

Cytogenetic studies have shown that New World primates are karyologically diverse and highly derived. The genus Callicebus is the best example of this karyological diversity, with diploid numbers ranging from 2n=50 to 2n=16. We report on Callicebus lugens, which has the lowest diploid number (2n=16) yet found in the primate order and represents a striking example of extreme karyotypic shuffling. To better understand the genomic rearrangements that have resulted in this extremely low diploid number, we mapped chromosome homologies between C. lugens and humans by in situ hybridization. The total number of hybridization signals was 42, excluding the Y chromosome, with a total of 34 syntenic associations not found in humans. This species has one of the most derived karyotypes among the Platyrrhini. Fusion has been the predominant mode of karyological evolution, although fissions and inversions have also transformed the C. lugens karyotype. Remarkably in such a highly rearranged karyotype, the synteny of 11 human chromosomes (4, 5, 9, 12, 13, 14, 17, 18, 20, 21, and X) was maintained intact, even if most of these human-homologous gene clusters were translocated. Other human syntenies, such as homologues to human chromosomes 10 and 16, were highly fragmented. Comparisons of the C. lugens-human homology map with those of other New World primates have not yet helped establish a phylogenic arrangement between congeneric species or link Callicebus with any other genus.

Nectomys squamipes microsatellites and homologous loci in sigmodontine rodents.

Three monomorphic and four highly polymorphic microsatellites of Nectomys squamipes were isolated and characterised in a sample of 141 specimens from eight different Brazilian localities. These seven microsatellites and four others previously described in this species were tested in seven other nonfocus sigmodontine species. At least three loci were successfully amplified in every species, but none was amplified in all species. All sequenced products in nonfocus species showed (GT)(n) motifs as in N. squamipes. Several loci were amplified in Nectomys rattus and Oligoryzomys nigripes, while absence of PCR products was observed more frequently in Oxymycterus dasythricus and Akodon cursor. Two of three monomorphic loci in N. squamipes were polymorphic in other species.

Molecular analysis of HPRT1(+) somatic cell hybrids derived from a carrier of an HPRT1 mutation responsible for Lesch-Nyhan syndrome.

Heterozygous carriers of HPRT1 mutations responsible for Lesch-Nyhan syndrome can be detected by analysis of somatic cell hybrids derived from peripheral blood lymphocytes and Hprt1-negative cells of rodent origin followed by selection in culture medium containing hypoxanthine, aminopterine, and thymidine (HAT). The parental origin of the X chromosome containing the normal HPRT1 allele in HPRT1(+) hybrid cell lines can be determined by molecular haplotyping attributable to highly polymorphic X-linked markers. We used this procedure to study a presumed carrier whose paternal active X chromosome always segregated in the cell hybrids derived from her. Conversely, her maternal X chromosome was systematically absent in most cell hybrids, or when present, it was inactive and coexisted with an active, paternal X chromosome. These results clearly demonstrated that the proband was a heterozygous carrier of a mutation responsible for HPRT1 deficiency.

Molecular phylogenetics of howler monkeys (Alouatta, Platyrrhini). A comparison with karyotypic data.

Molecular phylogenetic analyses of seven Brazilian Alouatta species, based on cytochrome b DNA sequence data were carried out. Parsimony and neighbor joining topologies grouped Alouatta belzebul and A. fusca as sister groups in one clade while another, well-supported clade contained A. seniculus as the most basal offshoot, followed by A. nigerrima as a sister lineage of A. macconnelli/A. stramineus. Estimates of inter-specific sequence divergence were generally low, and estimates of the time of divergence indicated that the main Alouatta lineages emerged during a short evolutionary interval. A comparison with karyotypic data confirmed the molecular topology showing a closer relationship between A. macconnelli and A. stramineus in respect to A. nigerrima. It also showed that the XX/XY sex chromosome system was maintained in several lineages while the X1X2Y/X1X1X2X2 system appeared independently at least three times during the radiation of howler monkeys. Moreover, the X1X2Y1Y2/X1X1X2X2 system might have appeared once or, alternatively, twice and independently.

Induction and characterization of hypoxanthine-phosphoribosyltransferase (Hprt-) deficient cell lines of Akodon cursor (Rodentia, Sigmodontinae).

Hypoxanthine-phosphoribosyltransferase negative (Hprt-) cell lines derived from an Akodon cursor liposarcoma were obtained by induced mutagenesis. All but one Hprt- cell line lacked Hprt mRNA transcripts while one (AKO 3) coded for a truncated protein. Cell fusion and karyotypic analyses showed that one cell line (AKO 1-15) could be successfully used for constructing hybrid panels and allow for a clear identification of human chromosomes in hybrid cells.

Can molecular data place each neotropical monkey in its own branch?

Four different DNA datasets, representative of all extant neotropical primate genera, were tandemly aligned, comprising some 6,763 base pairs (bp) with 2,086 variable characters and 674 informative sites. Maximum Parsimony, Maximum Likelihood and Neighbor-Joining analyses suggested three monophyletic families (Atelidae, Pitheciidae and Cebidae) that emerged almost at the same time during primate radiation. Combined molecular data showed congruent branching inside the atelid clade, placing Alouatta as the most basal lineage followed by Ateles and a more derived branch including Brachyteles and Lagothrix as sister groups. In the Pitheciidae, Callicebus was the most basal lineage with respect to Pithecia and to the more derived sister groups (Cacajao and Chiropotes). Conjoint analysis strongly supported the monophyly of the Cebidae, grouping Aotus, Cebus and Saimiri with the small callitrichines. Within callitrichines, Cebuella merged with Callithrix, Callimico appeared as a sister group of Callithrix/Cebuella, Leontopitecus as a sister group of the previous clade, and Saguinus was the earliest callitrichine offshoot. Two major points remained to be clarified in platyrrhine phylogeny: (i) the exact branching pattern of Aotus, Cebus, Saimiri and the callitrichines, and (ii), which two of these three families (Atelidae, Pitheciidae and Cebidae) are more closely related to one another.

Gene assignment in Ateles paniscus chamek (Platyrrhini, Primates). Allocation of 18 markers of human syntenic groups 1, 2, 7, 14, 15, 17 and 22.

Eighteen markers allocated to human syntenic groups 1, 2, 7, 14, 15, 17 and 22 were assigned to the chromosome complement of the neotropical primate Ateles paniscus chamek. These new allocations and existing gene charts in this species were compared with chromosome painting patterns produced by human chromosome probes in the congeneric species A teles geoffroyi and with available data on the human genome and gene mapping. These comparisons showed congruent findings in Ateles and provided good evidence of how several human syntenic groups were evolutionarily rearranged.