Genetics and Molecular Biology, Volume: 31, Issue: 3, Published: 2008
  • Complex networks: the key to systems biology Review Article

    Costa, Luciano da F.; Rodrigues, Francisco A.; Cristino, Alexandre S.

    Abstract in English:

    Though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. Because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. The current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. The main concepts and models of complex networks are presented and illustrated in an accessible fashion. Three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks and metabolic networks. The key role of complex networks for systems biology is extensively illustrated by several of the papers reviewed.
  • Polymorphism of human haptoglobin and its clinical importance Review Article

    Wobeto, Vânia Peretti de Albuquerque; Zaccariotto, Tânia Regina; Sonati, Maria de Fátima

    Abstract in English:

    Haptoglobin (Hp) is a plasma glycoprotein, the main biological function of which is to bind free hemoglobin (Hb) and prevent the loss of iron and subsequent kidney damage following intravascular hemolysis. Haptoglobin is also a positive acute-phase protein with immunomodulatory properties. In humans, the HP locus is polymorphic, with two codominant alleles (HP1 and HP2) that yield three distinct genotypes/phenotypes (Hp1-1, Hp2-1 and Hp2-2). The corresponding proteins have structural and functional differences that may influence the susceptibility and/or outcome in several diseases. This article summarizes the available data on the structure and functions of Hp and the possible effects of Hp polymorphism in a number of important human disorders.
  • Clinical and molecular characteristics of sickle cell anemia in the northeast of Brazil Human and Medical Genetics

    Adorno, Elisângela Vitória; Zanette, Ângela; Lyra, Isa; Seixas, Magda Oliveira; Reis, Mitermayer Galvão; Gonçalves, Marilda Souza

    Abstract in English:

    Beta S-globin gene (βS-globin) haplotypes, markers for severe sickle cell anemia (SCA), and the alpha-thalassemia 2 gene 3.7 kb deletion (-α2(3.7 kb) thal) along with demographic and clinical data were investigated in SCA outpatients (n = 125, 63 female and 62 male) in the Brazilian state of Bahia, which has a high prevalence SCA. PCR-RFLP showed that the Central African Republic/Benin (CAR/BEN, 51.2%) haplotype was most frequent, followed by the Benin/Benin (Ben/Ben, 28.8%). At least one CAR haplotype was present in every outpatient with a history of cerebrovascular accident. The Cameroon (Cam), Senegal (Sen) and Arab-India haplotypes occurred in small numbers, as did atypical haplotypes. Fetal hemoglobin (HbF, %) was unevenly distributed. Compared to those > 18 y, those aged < 18 y had had fewer erythrocyte transfusions and high HbF levels (12.3% ± 7.01 to 7.9% ± 4.36) but a higher frequency of spleen sequestration and pneumonia. Compared with normal α - genes carriers values, the outpatients with -α2(3.7 kb) thal (determined by PCR analysis) had significantly higher mean hemoglobin concentration (Hb) (8.3 ± 1.34 g/dL, p = 0.018) and packed cell volume (PCV = 27.1% ± 4.26, p = 0.019) but low mean corpuscular volume (MCV = 86.1 fL = 10-15 L ± 9.56, p = 0.0004) and mean corpuscular hemoglobin (MCH = 26.6% ± 4.60, p = 0.039).
  • CYP21 gene mutations in Brazilian patients with 21-hydroxylase deficiency from the Amazon region Human and Medical Genetics

    Carvalho, Tarcísio André Amorim de; Souza, Izabel Cristina Neves de; Yoshioka, France Keiko Nascimento; Caldato, Milena Coelho Fernandes; Torres, Nilza Nei; Garcia, Lena Stilianidi; Guerreiro, João Farias

    Abstract in English:

    Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (P450c21, CYP21) accounts for about 95% of all CAH cases. The incidence of CYP21 gene mutations has been extensively studied in the last years, but in Brazil it has been investigated only in Southeast Brazilian patients. This study is the first report on the distribution of CYP21 mutations in patients from the Amazon region. Direct sequencing of the CYP21 gene identified at least one mutation in 96% of the studied chromosomes. The most common mutations found were IVS2-13A/C > G (36%), Q318X (12%), V281L (12%), 1760_1761insT (9%), Cluster E6 (7%), and P30L (7%). The worldwide most common mutations were identified among patients from the Amazon region at frequencies that may be expected for a population resulting from the admixture of Europeans (predominantly Portuguese), African Blacks and Amerindians, in proportions that differ from those estimated for South Brazilian populations. Interethnic mixture may explain the differences in the frequencies of some mutations between Brazilian patients from the Amazon and from the Southeast of the country. However, the differences found may also be due to variation in the number of patients with the different clinical forms of 21-hydroxylase deficiency in the studies carried out so far.
  • DNA methylation analysis of the tumor suppressor gene CDKN2B in Brazilian leukemia patients Human and Medical Genetics

    Lima, Patrícia Santos Pereira; Molffeta, Greice Andreoti; Araujo, Amélia Góes de; Zago, Marco Antônio; Silva Jr., Wilson Araújo da

    Abstract in English:

    The aim of this work was to evaluate the methylation profile of the p15 (CDKN2B) gene in Brazilian patients with leukemia and to correlate the CDKN2B gene expression with the percentage of methylated CpG dinucleotides in its promoter region. Thirty-one samples from six patients with acute lymphocytic leukemia (ALL), four with chronic myeloid leukemia (CML), and 21 with acute myeloid leukemia (AML) were evaluated by MSP (Methylation-Specific PCR). The CDKN2B gene was found to be methylated in four (67%) of the six ALL samples and in 16 (76%) of the 21 AML samples, but in none of the four CML samples analyzed. We observed a correlation between the CDKN2B mRNA expression (RT-PCR) and the percentage of methylated CpG dinucleotides. Therefore, this study in Brazilian patients confirms that the CDKN2B gene is methylated in the majority of leukemia patients.
  • Assessment of the association between SMAD1 and HHIP gene variation and non-syndromic cleft-lip palate in Chilean case-parent trios Human and Medical Genetics

    Suazo, José; Santos, José Luis; Jara, Lilian; Blanco, Rafael

    Abstract in English:

    Nonsyndromic cleft lip/palate (NSCLP) is a congenital malformation with features of a complex genetic trait. Several studies have reported positive association and linkage between NSCLP and microsatellite markers in the 4q28-4q33 region particularly with the D4S192 (4q31) marker. We hypothesized that the candidate genes SMAD1 and HHIP (4q31) could be involved in the etiology of NSCLP based on previous positive linkage results and their important role in maxillofacial development. We evaluated the possible association between microsatellite markers located at less than 1 cM from these genes and NSCLP using a sample of 58 Chilean case-parent trios. Microsatellite markers were analyzed using the polymerase chain reaction (PCR) with fluorescent labeled primers. Electrophoresis of the PCR products was performed on a laser-fluorescent automatic DNA sequencer. The extended transmission disequilibrium test (ETDT) was used to analyze allelic transmissions from the parents to their affected progeny. No significant association due to linkage disequilibrium was detected between both markers and NSCLP.
  • Use of V H, D and J H immunoglobulin gene segments in Brazilian patients with chronic lymphocytic leukaemia (CLL) Human and Medical Genetics

    Pimentel, Beatriz Jatobá; Stefanoff, Cláudio Gustavo; Moreira, Aline Santos; Seuánez, Héctor N.; Zalcberg, Ilana Renault

    Abstract in English:

    Chronic lymphocytic leukaemia (CLL) is a haematological malignancy for which reliable prognostic markers are needed in view of its clinical heterogeneity. In approximately 50% of CLL patients, immunoglobulin (Ig) rearrangements are modified by somatic hypermutation (SHM), a process that represents a reliable prognostic indicator of favourable progression. In this study, we investigated SHM in 37 Brazilian CLL patients and identified the preferential involvement of specific immunoglobulin gene families and segments through PCR-amplified fragments or subcloned fragments. Forty-one rearrangements were observed and 37 of them were functional. A 98% homology cut-off with germinal sequences showed 18 patients (48.7%) with SHM. Unmutated cases showed a poorer clinical outcome. V H3 was the most frequent V H family, followed by V H4. The V H4-39 segment was the most frequently used, mainly in unmutated cases, while the V H3 family was predominant in mutated cases. The D3 and J H4/J H6 families were the most frequently observed.
  • Lack of mutations in the PVRL3 gene in North American caucasians with non-syndromic cleft lip/palate Human and Medical Genetics

    Sözen, Mehmet A.; Hecht, Jacqueline T.; Spritz, Richard A.

    Abstract in English:

    Cleft lip with or without cleft palate (CLP) is one of the most common birth defects. In about 70% of cases, CLP occurs as an isolated anomaly, denoted non-syndromic CLP (nsCLP). Genetic linkage and association studies have implicated many loci in susceptibility to nsCLP, including some members of the nectin gene family. We performed mutation screening of the PVRL3 gene that encodes nectin-3 in 73 unrelated Caucasian nsCLP patients and 105 unrelated controls from North America. We detected no sequence variants in the PVRL3 gene in either the nsCLP patients or the controls. These data suggest that PVRL3 is not an important susceptibility gene for nsCLP in the North American Caucasian population.
  • Population and mutation analysis of Y-STR loci in a sample from the city of São Paulo (Brazil) Human and Medical Genetics

    Soares-Vieira, José A.; Billerbeck, Ana E.C.; Iwamura, Edna S.M.; Mendonca, Berenice B.; Gusmão, Leonor; Otto, Paulo A.

    Abstract in English:

    The haplotypes of seven Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were determined in a sample of 634 healthy Brazilian males (190 adult individuals and 222 father-son pairs). The 412 adults were unrelated, and the 222 father-son pairs had their biological relationship confirmed using autosomal STRs (LR > 10,000). Among the 412 adults, a total of 264 different 7-loci haplotypes were identified, 210 of which were unique. The most frequent haplotype was detected in 31 instances, occurring with a frequency of 7.52%. The haplotype diversity index was calculated as 98.83%. Upon transmission of the 1,554 alleles, in 222 father-son pairs, six mutations were observed, with an average overall rate of 3.86 x 10-3 per locus. A haplotype with a duplicated DYS389I locus, and another with duplicated DYS389I, DYS389II, and DYS439 loci were detected in both fathers and their respective sons.
  • Leptin and hypothalamic gene expression in early- and late-maturing Bos indicus Nellore heifers Animal Genetics

    Vaiciunas, Aline; Coutinho, Luiz L.; Meirelles, Flávio V.; Pires, Alexandre V.; Silva, Luis Felipe P.

    Abstract in English:

    We investigated wether early-maturing or late-maturing Bos indicus Nellore heifers produced more leptin mRNA in adipose tissues and altered expression of hypothalamic genes related to leptin signaling. Six prepubertal and six pubertal heifers aged about 34 months and weighing 280 kg to 300 kg each were selected from a population of 100 Nellore heifers. Real-time PCR was used to quantify the expression of the leptin gene (LEP) in adipose tissues and the long isoform of the leptin receptor gene (Ob-Rb), the NK2 homeobox 1 hypothalamic marker gene NKX2-1, the suppressor of cytokine signaling 3 gene (SOCS-3), the neuropeptide Y genes (NPY) and the NPY G-protein coupled receptor genes NPY-Y1 and NPY-Y4 in the hypothalamus. Heifers attaining puberty earlier showed significantly greater LEP expression in adipose tissues (p < 0.05) and there was tissue interaction (p < 0.05). Hypothalamic expression of Ob-Rb, NKX2-1, NPY and SOCS-3 did not differ between groups, but in early-maturing heifers there was a tendency for lower expression of NPY-Y1 (8.3-fold less) and NPY-Y4 (14.3-fold less) compared to late-maturing heifers (p = 0.1). These results suggest that a combination of higher LEP expression, lower NPY-Y1 and NPY-Y4 expression could be a factor in regulating puberty in early-maturing B. indicus heifers.
  • Variance component estimates applying random regression models for test-day milk yield in Caracu heifers (Bos taurus Artiodactyla, Bovidae) Animal Genetics

    El Faro, Lenira; Cardoso, Vera Lucia; Albuquerque, Lucia Galvão de

    Abstract in English:

    Random regression models (RRM) were used to estimate covariance functions for 2,155 first-lactation milk yields of native Brazilian Caracu heifers. The models included contemporary group (defined as year-month of test and paddock) fixed effects, and quadratic effect of age of cow at calving. Genetic and permanent environmental effects were fitted by a random regression model and Legendre polynomials of days in milk (DIM). Schwarz's Bayesian information criteria (BIC) indicated that the best RRM assumed a six coefficient function for both random effects and a sixth order variance function for residual structure. Akaike's information criteria suggested a model with the same number of coefficients for both effects and a residual structure fitted by a step function with 15 variances. Phenotypic, additive genetic, permanent environmental and residual variances were higher at the beginning and declined during lactation. The RRM heritability estimates were 0.09 to 0.26 and generally higher at the beginning and end of lactation. Some unexpected negative genetic correlations emerged when higher order covariance functions were used. A model with four coefficients for additive genetic covariance function explains more parsimoniously the changes in genetic variation with DIM since the genetic parameter was more acceptable and BIC was close to that for a six coefficient covariance function.
  • Test-day milk yield as a selection criterion for dairy buffaloes (Bubalus bubalis Artiodactyla, Bovidae) Animal Genetics

    Tonhati, Humberto; Cerón-Muñoz, Mário Fernando; Oliveira, João Ademir de; El Faro, Lenira; Lima, André Luís Ferreira; Albuquerque, Lucia Galvão de

    Abstract in English:

    Due to the great demand for buffalo milk by-products the interest in technical-scientific information about this species is increasing. Our objective was to propose selection criteria for milk yield in buffaloes based on total milk yield, 305-day milk yield (M305), and test-day milk yield. A total of 3,888 lactations from 1,630 Murrah (Bubalus bubalis) cows recorded between 1987 and 2001, from 10 herds in the State of São Paulo, Brazil, were analyzed. Covariance components were obtained using the restricted maximum likelihood method applied to a bivariate animal model. Additive genetic and permanent environmental effects were considered as random, and contemporary group and lactation order as fixed effects. The heritability estimates were 0.22 for total milk yield and 0.19 for M305. For test-day yields, the heritability estimates ranged from 0.12 to 0.30, with the highest values being observed up to the third test month, followed by a decline until the end of lactation. The present results show that test-day milk yield, mainly during the first six months of lactation, could be adopted as a selection criterion to increase total milk yield.
  • Genetic polymorphisms at the leptin receptor gene in three beef cattle breeds Animal Genetics

    Almeida, Sabrina E.M.; Santos, Luciana B.S.; Passos, Daniel T.; Corbellini, Ângela O.; Lopes, Beatriz M.T.; Kirst, Cláudia; Terra, Gustavo; Neves, Jairo P.; Gonçalves, Paulo B.D.; Moraes, José C.F.; Weimer, Tania de Azevedo

    Abstract in English:

    The genetic diversity of a single nucleotide polymorphism (SNP) at the exon 20 (T945M) of the leptin receptor gene (LEPR) and of three short tandem repeats (STRs BM7225, BMS694, and BMS2145) linked to LEPR was investigated in three beef cattle herds (Brangus Ibagé, Charolais, and Aberdeen Angus). A cheap and effective new method to analyze the T945M polymorphism in cattle populations was developed and the possible role of these polymorphisms in reproduction and weight gain of postpartum cows was evaluated. High levels of genetic diversity were observed with the average heterozygosity of STRs ranging from 0.71 to 0.81. No significant association was detected between LEPR markers and reproductive parameters or daily weight gain. These negative results suggest that the LEPR gene polymorphisms, at least those herein described, do not influence postpartum cows production.
  • Morphological patterns of the heteropycnotic chromatin and nucleolar material in meiosis and spermiogenesis of some Pentatomidae (Heteroptera) Animal Genetics

    Souza, Hederson Vinicius de; Castanhole, Márcia Maria Urbanin; Bicudo, Hermione Elly Melara de Campos; Costa, Luiz Antônio Alves; Itoyama, Mary Massumi

    Abstract in English:

    Pentatomidae is a family of Heteroptera which includes several agriculture pests that have had different aspects of their meiosis and spermiogenesis analyzed. In the present study we analyzed the morphological patterns of the heteropycnotic chromatin and the nucleolar material of Mormidea v-luteum, Oebalus poecilus and Oebalus ypsilongriseus. The three species presented multilobate testes, with three lobes in M. v-luteum and four in the Oebalus species. A karyotype with 2n = 14 chromosomes (12A + XY) was observed in the three species. Several characteristics were common to the three species, such as the absence of a testicular harlequin lobe (a lobe which produces different types of spermatozoa, previously considered a general characteristic of this family), late migration of the sex chromosomes and semi-persistence of the nucleolus. The three species also shared some characteristics regarding the patterns of the heteropycnotic chromatin and nucleolar material, but differed in others mainly related to the location of the heteropycnotic chromatin in the spermatids and the morphology and distribution of the nucleolar material at zygotene. The differences were always between species from different genera, suggesting a relationship with their genetic divergence.
  • Cytogenetic analysis of three catfish species of the family Pseudopimelodidae (Teleostei, Siluriformes) Animal Genetics

    Martinez, Emanuel Ricardo Monteiro; Nirchio, Mauro; Granado, Angel; Foresti, Fausto; Oliveira, Claudio

    Abstract in English:

    Cytogenetic analyses performed in Cephalosilurus apurensis, Microglanis aff. cottoides and Pseudopimelodus bufonius revealed that the three species have 2n = 54 chromosomes: C. apurensis presented six metacentric (M), 28 submetacentric (SM), 14 subtelolocentric (ST), and six acrocentric (A) chromosomes, while M. aff. cottoides showed 10M, 32SM, 10ST and 2A, and P. bufonius had 12M, 30SM and 12ST. The nucleolus organizer regions (NORs) were present on the short arm of a middle-sized ST pair, identified as pair 19, in C. apurensis NORs were found on the short arm of a middle-sized ST (pair 23) and on the long arm of a middle-sized ST (pair 22) in M. aff. cotttoides and on the short arm of three middle-sized ST pairs, identified as pairs 9, 10 and 11, in P. bufonius. C-banding revealed a very small amount of constitutive heterochromatin in the chromosomes of all species, including the NORs. The occurrence of 2n = 54 in all species of the family Pseudopimelodidae and its absence among species of the closely related Pimelodidae and Heptapteridae may be important in identifying Pseudopimelodidae species.
  • Karyotypic analyses and morphological comments on the endemic and endangered Brazilian painted tree rat Callistomys pictus (Rodentia, Echimyidae) Animal Genetics

    Ventura, Karen; Ximenes, Gilson Evaristo Iack; Pardini, Renata; Sousa, Marcos A. Nóbrega de; Yonenaga-Yassuda, Yatiyo; Silva, Maria José de J.

    Abstract in English:

    The genus Callistomys belongs to the rodent family Echimyidae, subfamily Echimyinae, and its only living representative is Callistomys pictus, a rare and vulnerable endemic species of the state of Bahia, Brazil. Callistomys has been previously classified as Nelomys, Loncheres, Isothrix and Echimys. In this paper we present the karyotype of Callistomys pictus, including CBG and GTG-banding patterns and silver staining of the nucleolus organizer regions (Ag-NORs). Comments on Callistomys pictus morphological traits and a compilation of Echimyinae chromosomal data are also included. Our analyses revealed that Callistomys can be recognized both by its distintinctive morphology and by its karyotype.
  • Developmental genetic analysis of fruit shape traits under different environmental conditions in sponge gourd (Luffa cylindrical (L) Roem. Violales, Cucurbitaceae) Plant Genetics

    Zhang, Sheng; Hu, Jin; Xu, Shengchun

    Abstract in English:

    Analysis of genetic main effects and genotype × environment (GE) interaction effects for the fruit shape traits fruit length and fruit circumference in the sponge gourd (Luffa cylindrical (L) Roem. Violales, Cucurbitaceae) was conducted for diallel cross data from two planting seasons. A genetic model including fruit direct effects and maternal effects and unconditional and conditional variances analysis was used to evaluate the development of the fruit at four maturation stages. The variance analysis results indicated that fruit length and circumference were simultaneously affected by fruit direct genetic effects and maternal effects as well as GE interaction effects. Fruit direct genetic effects were relatively more important for both fruit shape traits during the whole developmental period. Gene activation was mostly due to additive effects at the first maturation stage and dominance effects were mainly active during the other three stages. The fruit shape trait correlation coefficients due to different genetic effects and the phenotypic correlation coefficients varied significantly for the various maturation stages. The results indicate that it is relatively easy to improve the two fruit shape traits for market purposes by carefully selecting the parents at the first maturation stage 3 days after flowering instead of at fruit economic maturation.
  • Analysis of the genetic relationships from different genetic systems between the amylose content and the appearance quality of indica rice across environments Plant Genetics

    Ge, Guo-Ke; Shi, Chun-Hai; Wu, Jian-Guo; Ye, Zi-Hong

    Abstract in English:

    The genetic relationships between amylose content (AC) and appearance quality traits of indica rice (Oryza sativa L.) were investigated using conditional analysis and unconditional analysis in present experiment. The results from the unconditional analysis indicated that AC of rice positively correlated with brown rice (BR, i.e., dehulled but unmilled rice) length (BRL), width (BRW) and thickness (BRT), but was negatively correlated with the ratio of length to width (RLW). The conditional analysis showed that weight of brown rice (WBR) negatively affected the genetic relationships between AC and the appearance quality traits of rice except between AC and BRW, while the genetic relationships between AC and most appearance quality traits were negatively affected by protein content (PC). However, these influences were not apparent due to the impact of WBR or PC on the most covariance components of the different genetic systems between AC and the appearance quality traits. The conditional analysis showed that it was possible to improve AC while significantly reduce BRL and BRT under maintaining WBR. Furthermore, AC could be improved when BRL was reduced under maintaining PC, but BRW and BRT could be significantly increased.
  • Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization Plant Genetics

    Robledo, Germán; Seijo, Guillermo

    Abstract in English:

    Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH) of the 5S and 45S rRNA genes and heterochromatic 4'-6-diamidino-2-phenylindole (DAPI) positive bands. We used chromosome landmarks identified by these markers to construct the first Arachis species ideogram in which all the homologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome constitution (D genome) of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes.
  • Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers Plant Genetics

    Veasey, Elizabeth Ann; Borges, Aline; Rosa, Mariana Silva; Queiroz-Silva, Jurema R.; Bressan, Eduardo de Andrade; Peroni, Nivaldo

    Abstract in English:

    We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6% (w/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering the presence or absence of bands. The results were subjected to analysis of molecular variance (AMOVA), and cluster and principal coordinate analyses. Spatial structure was assessed using Mantel's test to compare genetic and geographic distances. Each primer pair generated between three and ten clearly scorable polymorphic fragments. Cluster analyses showed a Jaccard's index from 0.3 to 1.0, indicating high genetic and intravarietal diversity. Accessions from all 19 communities were not spatially structured (r = 0.15, p < 0.054), with AMOVA indicating that most of the variability (58.2%) was distributed within households and only 18.1% of the variability was distributed between households within communities. The outcrossing mating system of sweet potato, and anthropic factors such as selection of different varieties and their maintenance within household small plots and home gardens, as well as an extensive exchange system between agriculturists, may all be contributing to these results.
  • Inheritance and identification of molecular markers associated with spot blotch (Cochliobolus sativus L.) resistance through microsatellites analysis in barley Plant Genetics

    Kuldeep, Tyagi; Nandan, Rajiv; Kumar, Uttam; Prasad, Lal Chand; Chand, Ramesh; Joshi, Arun Kumar

    Abstract in English:

    Spot blotch resistant (IBON 18) and susceptible (RD 2508) lines were crossed to investigate inheritance of resistance and to identify simple sequence repeats (SSRs) associated with resistance. F1 resistance was intermediate and suggested additive nature of inheritance. Three additive genes was noted in the distribution of F3, F4 and F5 generations. In F6 and F6-7, the quantitative and qualitative approaches also suggested the control of three resistance genes. The parents and the RILs (F6/F6-7) were grown in four environments and spot blotch severity recorded. Forty five SSR primers, specific for chromosomes 1 (7H) and 5 (1H), were applied. Of these, 12 were polymorphic between the parents, and between the resistant and susceptible bulks. Three markers BMS 32, BMS 90 and HVCMA showed association with resistance, which was further confirmed through selective genotyping. The co-segregation data on the molecular markers (BMS 32, BMS 90 and HVCMA) and spot blotch severity on 173 RILs was analyzed by single marker linear regression approach. Significant regression suggested linkage among BMS 32, BMS 90 and HVCMA and the three resistant genes (designated as Rcs-qtl-5H-1, Rcs-qtl-5H-2 and Rcs-qtl-1H-1.) respectively. These markers explained 28%, 19% and 12% of variation respectively, for spot blotch resistance among the RILs.
  • Expression, purification and DNA-binding activities of two putative ModE proteins of Herbaspirillum seropedicae (Burkholderiales, Oxalobacteraceae) Genetics of Microorganisms

    Souza, André L.F.; Chubatsu, Leda S.; Souza, Emanuel M.; Pedrosa, Fábio O.; Monteiro, Rose A.; Rego, Fabiane G.M.; Rigo, Liu U.

    Abstract in English:

    In prokaryotes molybdenum is taken up by a high-affinity ABC-type transporter system encoded by the modABC genes. The endophyte β-Proteobacterium Herbaspirillum seropedicae has two modABC gene clusters and two genes encoding putative Mo-dependent regulator proteins (ModE1 and ModE2). Analysis of the amino acid sequence of the ModE1 protein of H. seropedicae revealed the presence of an N-terminal domain containing a DNA-binding helix-turn-helix motif (HTH) and a C-terminal domain with a molybdate-binding motif. The second putative regulator protein, ModE2, contains only the helix-turn-helix motif, similar to that observed in some sequenced genomes. We cloned the modE1 (810 bp) and modE2 (372 bp) genes and expressed them in Escherichia coli as His-tagged fusion proteins, which we subsequently purified. The over-expressed recombinant His-ModE1 was insoluble and was purified after solubilization with urea and then on-column refolded during affinity chromatography. The His-ModE2 was expressed as a soluble protein and purified by affinity chromatography. These purified proteins were analyzed by DNA band-shift assays using the modA2 promoter region as probe. Our results indicate that His-ModE1 and His-ModE2 are able to bind to the modA2 promoter region, suggesting that both proteins may play a role in the regulation of molybdenum uptake and metabolism in H. seropedicae.
  • Antigenotoxic effects of Mandevilla velutina (Gentianales, Apocynaceae) crude extract on cyclophosphamide-induced micronuclei in Swiss mice and urethane-induced somatic mutation and recombination in Drosophila melanogaster Mutagenesis

    Silva, Regildo Márcio Gonçalves da; Sousa, Neila Coelho de; Graf, Ulrich; Spanó, Mário Antônio

    Abstract in English:

    A Mandevilla velutina crude extract was investigated using the mouse micronucleus test (MNT) and the Drosophila melanogaster somatic mutation and recombination test (SMART) using standard (ST) and high bioactivation (HB) crosses. The MNT used 10 mg, 20 mg or 40 mg per 100 g of body weight (bw) of extract with and without 0.2 mg per 100 g bw peritoneal cyclophosphamide. There was no genotoxicity in the negative control or extract only groups and, compared to the cyclophosphamide control, there was a significant reduction in micronucleated polychromatic erythrocytes in all the groups given extract plus cyclophosphamide. For SMART larvae were fed 5 or 10 mg mL-1 of extract for seven days with and without 0.89 mg mL-1 of urethane given on day seven. The ST and HB flies showed no significant differences in spots between the negative control and the extract only groups. The number of urethane-induced spots was reduced by the highest concentration of extract for the ST flies and by both concentrations of extract for the HB flies. The results suggest that M. velutina extract is not genotoxic but is antigenotoxic.
  • Antimutagenic activity of cashew apple (Anacardium occidentale Sapindales, Anacardiaceae) fresh juice and processed juice (cajuína) against methyl methanesulfonate, 4-nitroquinoline N-oxide and benzo[a]pyrene Mutagenesis

    Melo-Cavalcante, Ana Amelia; Picada, Jaqueline N.; Rubensam, Gabriel; Henriques, João A.P.

    Abstract in English:

    Cashew apple juice (CAJ), produced from the native Brazilian cashew tree (Anacardium occidentale), and has been reported to have antibacterial, antifungal, antitumor, antioxidant and antimutagenic properties. Both the fresh unprocessed juice and the processed juice (cajuína in Portuguese) has been shown to consist of a complex mixture containing high concentrations of anacardic and ascorbic acids plus several carotenoids, phenolic compounds and metals. We assessed both types of juice for their antimutagenic properties against the direct mutagens methyl methanesulfonate (MMS) and 4-nitroquinoline-N-oxide (4-NQO) and the indirect mutagen benzo[a]pyrene (BaP) using pre-treatment, co-treatment and post-treatment assays with Salmonella typhimurium strains TA100, TA102, and TA97a. In pre-treatment experiments with strains TA100 and TA102 the fresh juice showed high antimutagenic activity against MMS but, conversely, co-treatment with both juices enhanced MMS mutagenicity and there was an indication of toxicity in the post-treatment regime. In pre-, co-, and post-treatments with TA97a as test strain, antimutagenic effects were also observed against 4-NQO and BaP. These results suggest that both fresh and processed CAJ can protect the cells against mutagenesis induced by direct and indirect mutagens.
  • Allozyme variation among three populations of the armored catfish Hypostomus regani (Ihering, 1905) (Siluriformes, Loricariidae) from the Paraná and Paraguay river basins, Brazil Evolutionary Genetics

    Zawadzki, Cláudio H.; Renesto, Erasmo; Peres, Maria Dolores; Paiva, Suzana

    Abstract in English:

    Three Brazilian populations of the armored catfish Hypostomus regani (Ihering, 1905) were sampled, one from the Corumbá Reservoir in Goiás state, another from the Itaipu Reservoir in Paraná state and a third from the Manso Reservoir in Mato Grosso state. Allozyme electrophoresis was used to establish the genetic structure of the species, with the analysis of liver, heart and muscles tissues allowing the scoring of 25 loci from 14 enzymatic systems. Although no diagnostic loci were found, some exclusive rare alleles were recorded for the three populations. The genetically most similar populations were those from Corumbá and Itaipu, and the most distant were the populations from Manso and Corumbá. The allozyme data showed three structured populations belonging to the same species H. regani (F ST = 0.173).
  • A biogeographical population genetics perspective of the colonization of cats in Latin America and temporal genetic changes in Brazilian cat populations Evolutionary Genetics

    Ruiz-García, Manuel; Alvarez, Diana

    Abstract in English:

    We used nine morphological genes to analyze cat populations from Mexico, the Dominican Republic, the Colombian, Brazilian and Peruvian Amazon, Bolivia and Brazil. Most populations were in Hardy-Weinberg equilibrium at the O locus. The highest allele frequencies so far detected at world level for alleles I (inhibitor) and L (long hair) were found at La Paz (Bolivia). The analyses revealed at least five cat gene pools in Latin America: These findings suggest that the current genetic distribution of cats in Latin America correlates with the colonization of the Americas during the XIV to XVIII centuries. Additionally, the cat populations of São Paulo, Rio de Janeiro and Manaus were sampled, to compare their 1996-2003 genetic profiles with those obtained in 1983. Generally, these genetic profiles seem temporally stable, which is important for comparing cat populations sampled in different years and decades.
  • Complete sequence and organization of the mitochondrial genome of Cyclemys atripons (Testudines, Geoemydidae) Evolutionary Genetics

    Zhang, Li; Nie, Liu-wang; Zhang, Ying; Rui, Jin-long; Zhang, Yan-yun

    Abstract in English:

    The Black Bridged Leaf Turtle, Cyclemys atripons (Testudines; Cryptodira; Geoemydidae), is a poorly known species within the genus Cyclemys. We determined the complete nucleotide sequence of the Cyclemys atripons mitochondrial genome (mtDNA) and found it to be 16,500 base pairs (bp) in length, with the genome organization, gene order and base composition being identical to that of the typical vertebrate. However, unlike for most turtle mtDNA so far reported, an extra base was not found in the NADH3 gene. The C. atripons control region of mtDNA was 981 bp long. Comparisons with three other geoemydids showed that the C. atripons control region contained a highly variable region at the 3' end composed of AT enriched tandem repeats containing a fifteen-unit 5'-A (AT)3-3' variable number of tandem repeats (VNTRs).
  • RAPD fingerprinting of the ornamental fish Badis badis (Hamilton 1822) and Dario dario (Kullander and Britz 2002) (Perciformes, Badidae) from West Bengal, India Evolutionary Genetics

    Brahmane, Manoj P.; Mitra, Krishna; Mishra, Sudhanshu S.

    Abstract in English:

    We used random amplification of polymorphic DNA (RAPD) to generate species-specific diagnostic fragment patterns for the molecular identification of the ornamental aquarium fish species Badis badis and Dario dario. Seven arbitrary oligodecamer primers produced a total of 116 bands of which 98.23% were polymorphic. The size of the amplified products was in the range 340 bp to 2170 bp. Intraspecies genetic similarity was 0.879 ± 0.023 for B. badis and 0.840 ± 0.014 for D. dario while interspecies genetic similarity was 0.602 ± 0.017, with cluster analysis displaying separate taxonomic and evolutionary status for these fish. The results show that RAPD was useful for the molecular identification of aquarium fish species, with morphological traits also being important.
  • Novel 12S mtDNA findings in sloths (Pilosa, Folivora) and anteaters (Pilosa, Vermilingua) suggest a true case of long branch attraction Evolutionary Genetics

    Barros, Maria Claudene; Sampaio, Iracilda; Schneider, Horacio

    Abstract in English:

    We sequenced 12S RNA mtDNA for the majority of the extant species of sloths and anteaters and compared our results with previous data obtained by our group using 16S RNA mtDNA in the same specimens and to GenBank sequences of the extinct giant sloth Mylodon. Our results suggest that pigmy-anteaters may be a case of the long-branch attraction phenomenon and also show the large genetic difference between the Amazonian and Atlantic forest three-toed sloths, contrasting with the small differences observed between the two non-Atlantic forest forms of sloths. These results have important implications for the taxonomy of sloths and anteaters and strongly suggest the placement of pigmy anteaters in their own family (Cyclopidae) and raising the taxonomic status of Bradypus torquatus to a genus.
  • Extinction of mammalian populations in conservation units of the Brazilian Cerrado by inbreeding depression in stochastic environments Evolutionary Genetics

    Silva, Marcel Müller Fernandes Pereira da; Diniz-Filho, José Alexandre Felizola

    Abstract in English:

    Despite methodological and theoretical advances in conservation genetics, data on genetic variation on broad regional spatial scales are still scarce, leading conservation planners to use general heuristic or simulation models for an integrated analysis of genetic, demographic and landscape parameters. Here, we extended previous results by evaluating spatial patterns of extinction by inbreeding depression under stochastic variation of environments for mammalian populations in 31 conservation units of the Brazilian Cerrado. We observed a large spatial variation of times to extinction, for different conservation units and body-size classes of species. For small-bodied species (500 g), the population times to extinction in the conservation units were usually longer than 200 years, whereas for medium-bodied (5 kg) and large-bodied (50 kg) species this time was considerably shorter, and only a few units would maintain viable populations for more than 100 years. These figures are consistent with the current status of mammalian conservation in Brazil, and hopefully the simulated scenarios can be integrated to patterns of human occupation and habitat loss in the biome, in order to furnish overall guidelines for biodiversity conservation.
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