A novel point mutation in a class IV glucose-6-phosphate dehydrogenase variant (G6PD São Paulo) and polymorphic G6PD variants in São Paulo State, Brazil

In this study, we used red cell glucose-6-phosphate dehydrogenase (G6PD) activity to screen for G6PD-deficient individuals in 373 unrelated asymptomatic adult men who were working with insecticides (organophosphorus and carbamate) in dengue prevention programs in 27 cities in São Paulo State, Brazil. Twenty-one unrelated male children suspected of having erythroenzymopathy who were attended at hospitals in São Paulo city were also studied. Fifteen of the 373 adults and 12 of the 21 children were G6PD deficient. G6PD gene mutations were investigated in these G6PD-deficient individuals by using PCR-RFLP, PCR-SSCP analysis and DNA sequencing. Twelve G6PD A-202A/376G and two G6PD Seattle844C, as well as a new variant identified as G6PD São Paulo, were detected among adults, and 11 G6PD A-202A/376G and one G6PD Seattle844C were found among children. The novel mutation c.660C > G caused the replacement of isoleucine by methionine (I220M) in a region near the dimer interface of the molecule. The conservative nature of this mutation (substitution of a nonpolar aliphatic amino acid for another one) could explain why there was no corresponding change in the loss of G6PD activity (64.5% of normal activity in both cases).     

Genetic characterization of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats

Based on nine microsatellite loci, the aim of this study was to appraise the genetic diversity of 42 cassava (Manihot esculenta) landraces from selected regions in Brazil, and examine how this variety is distributed according to origin in several municipalities in the states of Minas Gerais, São Paulo, Mato Grosso do Sul, Amazonas and Mato Grosso. High diversity values were found among the five above-mentioned regions, with 3.3 alleles per locus on an average, a high percentage of polymorphic loci varying from 88.8% to 100%, an average of 0.265 for observed heterozygosity and 0.570 for gene diversity. Most genetic diversity was concentrated within the regions themselves (H_S = 0.52). Cluster analysis and principal component based scatter plotting showed greater similarity among landraces from São Paulo, Mato Grosso do Sul and Amazonas, whereas those from Minas Gerais were clustered into a sub-group within this group. The plants from Mato Grosso, mostly collected in the municipality of General Carneiro, provided the highest differentiation. The migration of human populations is one among the possible reasons for this closer resemblance or greater disparity among plants from the various regions.     

Diversity of somatic coliphages in coastal regions with different levels of anthropogenic activity in São Paulo State, Brazil

Bacteriophages are the most abundant and genetically diverse viruses on Earth, with complex ecology in both quantitative and qualitative terms. Somatic coliphages (SC) have been reported to be good indicators of fecal pollution in seawater. This study focused on determining the concentration of SC and their diversity by electron microscopy of seawater, plankton, and bivalve samples collected at three coastal regions in São Paulo, Brazil. The SC counts varied from <1 to 3.4 × 10³ PFU/100 ml in seawater (73 samples tested), from <1 to 4.7 × 10² PFU/g in plankton (46 samples tested), and from <1 to 2.2 × 10¹ PFU/g in bivalves (11 samples tested). In seawater samples, a relationship between the thermotolerant coliforms and Escherichia coli and SC was observed at the three regions (P = 0.0001) according to the anthropogenic activities present at each region. However, SC were found in plankton samples from three regions: Baixada Santista (17/20), Canal de São Sebastião (6/14), and Ubatuba (3/12). In seawater samples collected from Baixada Santista, four morphotypes were observed: A1 (4.5%), B1 (50%), C1 (36.4%), and D1 (9.1%). One coliphage, Siphoviridae type T1, had the longest tail: between 939 and 995 nm. In plankton samples, Siphoviridae (65.8%), Podoviridae (15.8%), Microviridae (15.8%), and Myoviridae (2.6%) were found. In bivalves, only the morphotype B1 was observed. These SC were associated with enteric hosts: enterobacteria, E. coli, Proteus, Salmonella, and Yersinia. Baixada Santista is an area containing a high level of fecal pollution compared to those in the Canal de São Sebastião and Ubatuba. This is the first report of coliphage diversity in seawater, plankton, and bivalve samples collected from São Paulo coastal regions. A better characterization of SC diversity in coastal environments will help with the management and evaluation of the microbiological risks for recreation, seafood cultivation, and consumption.     

Genotype by environment interaction in Nelore cattle from five Brazilian states

Records from 75,941 Nelore cattle were used to determine the importance of genotype by environment interaction (GEI) in five Brazilian states. (Co)variance components were estimated by single-trait analysis (with yearling weight, W450, considered to be the same trait in all states) and multiple-trait analysis (with the record from each state considered to be a different trait). The direct heritability estimates for yearling weight were 0.51, 0.39, 0.44, 0.37 and 0.41 in the states of Goiás, Mato Grosso, São Paulo, Mato Grosso do Sul and Minas Gerais, respectively. The across-state genetic correlation estimates between Goiás and Mato Grosso, Goiás and Minas Gerais, São Paulo and Minas Gerais, and Mato Grosso do Sul and Minas Gerais ranged from 0.67 to 0.75. These estimates indicate that GEIs are biologically important. No interactions were observed between Goiás and São Paulo, Goiás and Mato Grosso do Sul, Mato Grosso and São Paulo, Mato Grosso and Mato Grosso do Sul, Mato Grosso and Minas Gerais, or São Paulo and Mato Grosso do Sul (0.82 to 0.97). Comparison of single and multiple-trait analyses showed that selection based on the former was less efficient in the presence of GEI, with substantial losses (up to 10%) during selection.     

Allozyme differentiation of two populations of the genus Neoplecostomus Eigenmann & Eigenmann, 1888 (Teleostei, Loricariidae) from the upper Paraná River basin, Brazil

Allozyme electrophoresis was used to examine 12 enzymatic systems in two populations of the genus Neoplecostomus from the Paraná River basin. Samples of Neoplecostomus sp. 1 were collected in Paraitinguinha stream of the Tietê River basin, in the municipality of Salesópolis, São Paulo State, and those of Neoplecostomus sp. 2 from São Domingos stream of the Rio Grande River basin, in the municipality of Muzambinho, Minas Gerais State. The genetic variability of the two populations was estimated by Nei’s expected heterozygosity and was considered lower than average for populations of freshwater fish. The proportion of polymorphic loci was low (only 5.26% for the locus Idh). The low frequency of heterozygosity for both populations revealed a high fixation of alleles for each locus. Homozygote excess was observed in both populations. The values of Nei’s genetic identity and the presence of loci with different allele frequencies in both populations may imply that the two populations belong to different species. The genetic variability between populations was compared to other data for loricariids.     

Allozyme comparison of two populations of Rineloricaria (Siluriformes, Loricariidae) from the Ivaí River, upper Paraná River basin, Brazil

Two allopatric morphotypes of the genus Rinelocaria were compared through the allozyme electrophoresis technique: one morphotype, R. pentamaculata, from the Keller River in the middle stretch of the Ivaí River basin and the other, R. aff. pentamaculata, from the São João River in the upper portion of the Ivaí River basin. The morphotype from the São João River was collected upstream from the São João waterfall, which is about 80 m deep. Twelve enzymatic systems (AAT, ADH, EST, GCDH, G3PDH, GPI, IDH, LDH, MDH, ME, PGM and SOD) were analyzed, which allowed to score 22 loci. Only lociAat-2, Est-3 and Mdh-C showed polymorphism. The two samples differed in allele frequencies at the three polymorphic loci. The average expected heterozygosity for all loci was 0.0806 ± 0.0447 in the Keller River sample. For the São João River morphotype, this value was 0.0489 ± 0.0350. Nei'' s genetic identity and distance between the two populations were respectively 0.9789 and 0.0213. Wright''s F_IS , F_IT and F_ST over all loci were estimated as 0.3121, 0.4021 and 0.1309, respectively. We consider that the two morphotypes represent species in statunascendi.     

Genetic characterization of 12 heterologous microsatellite markers for the giant tropical tree Cariniana legalis (Lecythidaceae)

Twelve microsatellite loci previously developed in the tropical tree Cariniana estrellensis were genetically characterized in Cariniana legalis. Polymorphisms were assessed in 28 C. legalis individuals found between the Pardo and Mogi-Guaçu River basins in the state of São Paulo, Brazil. Of the 12 loci, 10 were polymorphic and exhibited Mendelian inheritance. The allelic richness at each locus ranged from 2-11, with an average of 7 alleles per locus, and the expected heterozygosity ranged from 0.07-0.88. These loci showed a high probability of paternity exclusion. The characteristics of these heterologous microsatellite markers indicate that they are suitable tools for investigating questions concerning population genetics in C. legalis.     

Molecular epidemiology of Neisseria meningitidis serogroup B in Brazil

Background

Neisseria meningitidis serogroup B has been predominant in Brazil, but no broadly effective vaccine is available to prevent endemic meningococcal disease. To understand genetic diversity among serogroup B strains in Brazil, we selected a nationally representative sample of clinical disease isolates from 2004, and a temporally representative sample for the state of São Paulo (1988–2006) for study (n = 372).

Methods

We performed multi-locus sequence typing (MLST) and sequence analysis of five outer membrane protein (OMP) genes, including novel vaccine targets fHbp and nadA.

Results

In 2004, strain B:4:P1.15,19 clonal complex ST-32/ET-5 (cc32) predominated throughout Brazil; regional variation in MLST sequence type (ST), fetA, and porB was significant but diversity was limited for nadA and fHbp. Between 1988 and 1996, the São Paulo isolates shifted from clonal complex ST-41/44/Lineage 3 (cc41/44) to cc32. OMP variation was associated with but not predicted by cc or ST. Overall, fHbp variant 1/subfamily B was present in 80% of isolates and showed little diversity. The majority of nadA were similar to reference allele 1.

Conclusions

A predominant serogroup B lineage has circulated in Brazil for over a decade with significant regional and temporal diversity in ST, fetA, and porB, but not in nadA and fHbp.     

Scenario of the spread of the invasive species Zaprionus indianus Gupta, 1970 (Diptera, Drosophilidae) in Brazil

Zaprionus indianus was first recorded in Brazil in 1999 and rapidly spread throughout the country. We have obtained data on esterase loci polymorphisms (Est2 and Est3), and analyzed them, using Landscape Shape Interpolation and the Monmonier Maximum Difference Algorithm to discover how regional invasion occurred. Hence, it was apparent that Z. indianus, after first arriving in São Paulo state, spread throughout the country, probably together with the transportation of commercial fruits by way of the two main Brazilian freeways, BR 153, to the south and the surrounding countryside, and the BR 116 along the coast and throughout the north-east.     

Elmidae (Coleoptera, Byrrhoidea) larvae in the state of São Paulo, Brazil: Identification key, new records and distribution

The family Elmidae Curtis, 1830 has cosmopolitan distribution and most species inhabit riffles on streams and rivers, hence the name “riffle beetle”. In recent years, this family has been featured in papers addressing the assessment and environmental monitoring of water quality. In Brazil, studies on the family remain scarce and the present investigation is a pioneering study in the state of São Paulo. This study aims to propose a taxonomic key for the identification of larvae of Elmidae genera known to occur in the State, as well as to report new records and the distribution of these genera. The material analyzed was collected from various locations in each of 15 drainage basins from 2005 to 2010. The identification key includes 12 genera (Austrolimnius Carter & Zeck, 1929, Heterelmis Sharp, 1882, Hexacylloepus Hinton, 1940, Hexanchorus Sharp, 1882, Huleechius Brown, 1981, Macrelmis Motschulsky, 1859, Microcylloepus Hinton, 1935, Neoelmis Musgrave, 1935, Phanocerus Sharp, 1882, Potamophilops Grouvelle, 1896, Stegoelmis Hinton, 1939 and Xenelmis Hinton, 1936) known in Brazil as well as three morphotypes designated herein as Genus A, Genus M and Genus X. The genus Hexanchorus is recorded for the first time in the state of São Paulo.     

Relatedness,parentage, and philopatry within a Natterer’s bat (<Emphasis Type="Italic">Myotis nattereri</Emphasis>) maternity colony

Given their cryptic behaviour, it is often difficult to establish kinship within microchiropteran maternity colonies. This limits understanding of group formation within this highly social group. Following a concerted effort to comprehensively sample a Natterer’s bat (Myotis nattereri) maternity colony over two consecutive summers, we employed microsatellite DNA profiling to examine genetic relatedness among individuals. Resulting data were used to ascertain female kinship, parentage, mating strategies, and philopatry. Overall, despite evidence of female philopatry, relatedness was low both for adult females and juveniles of both sexes. The majority of individuals within the colony were found to be unrelated or distantly related. However, parentage analysis indicates the existence of a number of maternal lineages (e.g., grandmother, mother, or daughter). There was no evidence suggesting that males born within the colony are mating with females of the same colony. Thus, in this species, males appear to be the dispersive sex. In the Natterer’s bat, colony formation is likely to be based on the benefits of group living, rather than kin selection.     

Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea)

Oysters (Ostreidae) manifest a high degree of phenotypic plasticity, whereby morphology is of limited value for species identification and taxonomy. By using molecular data, the aim was to genetically characterize the species of Crassostrea occurring along the Brazilian coast, and phylogenetically relate these to other Crassostrea from different parts of the world. Sequencing of the partial cytochrome oxidase c subunit I gene (COI), revealed a total of three species of Crassostrea at 16 locations along the Brazilian coast. C. gasar was found from Curuçá (Pará state) to Santos (São Paulo state), and C. rhizophorae from Fortim (Ceará state) to Florianópolis (Santa Catarina state), although small individuals of the latter species were also found at Ajuruteua beach (municipality of Bragança, Pará state). An unidentified Crassostrea species was found only on Canela Island, Bragança. Crassostrea gasar and C. rhizophorae grouped with C. virginica, thereby forming a monophyletic Atlantic group, whereas Crassostrea sp. from Canela Island was shown to be more similar to Indo-Pacific oysters, and either arrived in the Atlantic Ocean before the convergence of the Isthmus of Panama or was accidentally brought to Brazil by ship.     

Reproductive sharing in relation to group and colony-level attributes in a cooperative breeding fish

The degree to which group members share reproduction is dictated by both within-group (e.g. group size and composition) and between-group (e.g. density and position of neighbours) characteristics. While many studies have investigated reproductive patterns within social groups, few have simultaneously explored how within-group and between-group social structure influence these patterns. Here, we investigated how group size and composition, along with territory density and location within the colony, influenced parentage in 36 wild groups of a colonial, cooperatively breeding fish Neolamprologus pulcher. Dominant males sired 76% of offspring in their group, whereas dominant females mothered 82% of offspring in their group. Subordinate reproduction was frequent, occurring in 47% of sampled groups. Subordinate males gained more paternity in groups located in high-density areas and in groups with many subordinate males. Dominant males and females in large groups and in groups with many reproductively mature subordinates had higher rates of parentage loss, but only at the colony edge. Our study provides, to our knowledge, the first comprehensive quantification of reproductive sharing among groups of wild N. pulcher, a model species for the study of cooperation and social behaviour. Further, we demonstrate that the frequency of extra-pair parentage differs across small social and spatial scales.     

Cytogenotoxicity biomarkers in fat snook Centropomus parallelus from Cananéia and São Vicente estuaries, SP, Brazil

The aquatic environment receives many contaminants that can induce damages at the molecular, biochemical, cellular and physiological levels. Centropomus parallelus, an important food resource for local populations, is a predator fish that feeds on small fishes and benthic invertebrates, thus being vulnerable to the bioconcentration and biomagnification processes. This study aimed to evaluate cytogenotoxic responses in erythrocytes from C. parallelus juveniles collected in the Cananéia and São Vicente estuaries, both in winter and in summer. After anesthesia, blood samples were collected by caudal puncture. Blood smears were prepared on glass slides and stained with May-Grünwald-Giemsa dye. Two thousand cells were analyzed per slide (1000x), and nuclear abnormalities (NA) and micronuclei (MN) were scored. The São Vicente sample showed MN and NA frequencies (%/1000 cells) of 0.325 and 3.575, in winter, and of 0.125 and 2.935 in summer respectively; the Cananéia sample showed frequencies of 0.0325 and 0.03, in winter, and of 0.065 and 0.355 in summer, respectively. The rates found in São Vicente were significantly higher than those found in Cananéia, evidencing that the levels of pollution in that estuary were high enough to induce genetic damages.     

Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese

Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D'') extent in three genomic regions: Xq13.3, NRY and HLA. In addition, we examine the distribution of DXS1225-DXS8082 haplotype diversity in Azoreans and mainland Portuguese. Allele distribution has demonstrated that the São Miguel population is genetically very diverse; haplotype analysis revealed 100% discriminatory power for X- and Y-markers and 94.3% for HLA markers. Standardized multiallelic D'' in these three genomic regions shows values lower than 0.33, thereby suggesting there is no extensive LD in the São Miguel population. Data regarding the distribution of DXS1225-DXS8082 haplotypes indicate that there are no significant differences among all the populations studied, (Azorean geographical groups, the Azores archipelago and mainland Portugal). Moreover, in these as well as in other European populations, the most frequent DXS1225-DXS8082 haplotype is 210-219. Even though São Miguel islanders and Azoreans do not constitute isolated populations and show LD for only very short physical distances, certain characteristics, such as the absence of genetic structure, the same environment and the possibility of constructing extensive pedigrees through church and civil records, offer an opportunity for dissecting the genetic background of complex diseases in these populations.     

Food habits of the Broad‐snouted Caiman (Caiman latirostris: Crocodylia,Alligatoridae) in northwestern Uruguay

The food habits of the Broad‐snouted Caiman (Caiman latirostris) were studied in northwestern Uruguay. The most common prey were insects, the shrimp Pseudopalaemon bouvieri, the snail Pomacea canaliculata, fish and birds. Spiders, crabs, amphibians, snakes, turtles and mammals were consumed less frequently. Arthropods were the most frequent prey for juvenile caiman. Fish and snails were consumed by all size classes. The proportion of stomach contents with invertebrates decreased with increasing caiman size, and that with vertebrates was greater in the diet of larger caiman. Diet composition and ontogenetic shift are similar to that of other crocodilians considered as opportunistic generalist predators.

Se estudiaron los hábitos alimenticios del Yacaré (Caiman latirostris) en el noroeste de Uruguay. Las presas más comunes fueron insectos, el camarón Pseudopalaemon bouvieri, el caracol Pomacea canaliculata, peces y aves. Arañas, cangrejos, anfibios, serpientes, tortugas y mamíferos fueron consumidos menos frecuentemente. Los artrópodos fueron las presas más frecuentes de juveniles. Peces y aves fueron consumidos por todos los tamaños. La proporción de contenidos estomacales con invertebrados disminuyó al aumentar el tamaño de los caimanes, y la de vertebrados fue mayor en los individuos de mayor tamaño. La composición y cambio ontogenético en la dieta resultan similares a los de crocodilianos considerados predadores generalistas oportunistas.     

Three new species of Atopsyche Banks (Trichoptera, Hydrobiosidae) from Brazil

Three new species of Atopsyche Banks (Hydrobiosidae) from Brazil are described and illustrated: Atopscyhe (Atopsaura) blahniki sp. n., Atopsyche (Atopsyche) parauna sp. n., and Atopsyche (Atopsaura) galharada sp. n. Additional illustrations of the male genitalia of Atopsyche urumarca Schmid are provided, including its populational variation. Also, we provide new state records for 2 species: Atopsyche (Atopsyche) urumarca from São Paulo, and Atopsyche (Atopsaura) plancki Marlier from Santa Catarina.     

The genetic structure and mating system of Acrocomia aculeata (Arecaceae)

Acrocomia aculeata is a perennial, fruit-producing palm tree, native to tropical forests. Its fruits have spurred interest because of their significant potential for use in the cosmetic industry and as feedstock for biofuel. In the present study, the genetic structure and mating system in Acrocomia aculeata were analyzed, using eight nuclear micro-satellite loci and samples from São Paulo and Minas Gerais states, Brazil. By means of Bayesian analysis, these populations were clustered into two or three groups. A high multilocus outcrossing rate suggests that outcrosses were predominant, although a certain degree of biparental inbreeding also occurred. Thus, although monoecious and self-compatible, there is every indication that A. aculeata bears a mixed reproductive system, with a predominance of outcrossing. Given the genetic structure revealed hereby, future conservation strategies and germplasm collecting should be focussed on sampling and preserving individuals from different clusters.     

BF Integrase Genes of HIV-1 Circulating in S?o Paulo,Brazil, with a Recurrent Recombination Region

Although some studies have shown diversity in HIV integrase (IN) genes, none has focused particularly on the gene evolving in epidemics in the context of recombination. The IN gene in 157 HIV-1 integrase inhibitor-naïve patients from the São Paulo State, Brazil, were sequenced tallying 128 of subtype B (23 of which were found in non-B genomes), 17 of subtype F (8 of which were found in recombinant genomes), 11 integrases were BF recombinants, and 1 from subtype C. Crucially, we found that 4 BF recombinant viruses shared a recurrent recombination breakpoint region between positions 4900 and 4924 (relative to the HXB2) that includes 2 gRNA loops, where the RT may stutter. Since these recombinants had independent phylogenetic origin, we argue that these results suggest a possible recombination hotspot not observed so far in BF CRF in particular, or in any other HIV-1 CRF in general. Additionally, 40% of the drug-naïve and 45% of the drug-treated patients had at least 1 raltegravir (RAL) or elvitegravir (EVG) resistance-associated amino acid change, but no major resistance mutations were found, in line with other studies. Importantly, V151I was the most common minor resistance mutation among B, F, and BF IN genes. Most codon sites of the IN genes had higher rates of synonymous substitutions (dS) indicative of a strong negative selection. Nevertheless, several codon sites mainly in the subtype B were found under positive selection. Consequently, we observed a higher genetic diversity in the B portions of the mosaics, possibly due to the more recent introduction of subtype F on top of an ongoing subtype B epidemics and a fast spread of subtype F alleles among the B population.     

The karyotype of three Brazilian Terrarana frogs (Amphibia, Anura) with evidence of a new Barycholos species

A recent substantial rearrangement of the 882 described eleutherodactyline frog species has considerably improved the understanding of their systematics. Nevertheless, many taxonomic aspects of the South American eleutherodactyline species remain unknown and require further investigation using morphological, cytogenetic and molecular approaches. In this work, the karyotypes of the Brazilian species Ischnocnema juipoca (Atibaia and Campos do Jordão, SP), Barycholos cf. ternetzi (Uberlândia, MG, and Porto Nacional, TO), and Pristimantis crepitans (Chapada dos Guimarães and São Vicente, MT) were analyzed using Giemsa staining, Ag-NOR labeling, and C-banding techniques. All individuals had a diploid number of 22 chromosomes, but the Fundamental Numbers were different among species. The herein described low chromosome number of Pristimantis crepitans is unique within this genus, suggesting that cytogenetically this species is not closely related either to its congeneric species or to Ischnocnema. In addition, karyotype differences, mainly in the NOR position, clearly distinguished the two Barycholos populations, besides indicating the existence of a so far undescribed species in this genus. A taxonomic review could clarify the systematic position of P. crepitans and verify the hypothetic new Barycholos species.