Analysis of DNA polymerase activity in vitro using non-radioactive primer extension assay in an automated DNA sequencer |
Genet. Mol. Res. 6 (2): 250-255 (2007)
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D.O. Lopes, C.G. Regis-da-Silva, A. Machado-Silva, A.M. Macedo, G.R. Franco, J.S. Hoffmann, C. Cazaux, S.D.J. Pena, S.M.R. Teixeira and C.R. Machado |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Although different DNA polymerases have distinct functions and substrate affinities, their general mechanism of action is similar. Thus, they can all be studied using the same technical principle, the primer extension assay employing radioactive tags. Even though fluorescence has been used routinely for many years for DNA sequencing, it has not been used in the in vitro primer extension assay. The use of fluorescence labels has obvious advantages over radioactivity, including safety, speed and ease of manipulation. In the present study, we demonstrated the potential of non-radioactive in vitro primer extension for DNA polymerase studies. By using an M13 tag in the substrate, we can use the same fluorescent M13 primer to study different substrate sequences. This technique allows quantification of the DNA polymerase activity of the Klenow fragment using different templates and under different conditions with similar sensitivity to the radioactive assay.
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Sex-biased gene flow in African Americans but not in American Caucasians |
Genet. Mol. Res. 6 (2): 256-261 (2007)
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Authors |
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V.F. Gonçalves, F. Prosdocimi, L.S. Santos, J.M. Ortega and S.D.J. Pena |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. We have previously shown evidence of strong sex-biased genetic blending in the founding and ongoing history of the Brazilian population, with the African and Amerindian contribution being highest from maternal lineages (as measured by mitochondrial DNA) and the European contribution foremost from paternal lineages (estimated from Y-chromosome haplogroups). The same phenomenon has been observed in several other Latin American countries, suggesting that it might constitute a universal characteristic of the Iberian colonization of the Americas. However, it has also recently been detected in the Black population of the United States. We thus wondered if the same could be observed in American Caucasians. To answer that question, we retrieved 1387 hypervariable I Caucasian mitochondrial DNA sequences from the FBI population database and established their haplogroups and continental geographical sources. In sharp contrast with the situation of the Caucasian population of Latin American countries, only 3.1% of the American Caucasian sequences had African and/or Amerindian origin. To explain this discrepancy we propose that the finding of elevated genomic contributions from European males and Amerindian or African females depends not only on the occurrence of directional mating, but also on the “racial” categorization of the children born from these relations. In this respect, social practices in Latin America and in the United States diverge considerably; in the former socially significant “races” are normally designated according to physical appearance, while in the latter descent appears to be the most important factor.
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Homology of polytene elements between Drosophila and Zaprionus determined by in situ hybridization in Zaprionus indianus |
Genet. Mol. Res. 6 (2): 262-276 (2007)
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S.R.C. Campos, T.T. Rieger and J.F. Santos |
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ABSTRACT. The drosophilid Zaprionus indianus due to its economical importance as an insect pest in Brazil deserves more investigation into its genetics. Its mitotic karyotype and a line-drawing map of its polytene chromosomes are already available. This paper presents a photomap of Z. indianus polytene chromosomes, which was used as the reference map for identification of sections marked by in situ hybridization with gene probes. Hybridization signals for Hsp70 and Hsr-w were detected, respectively, in sections 34B and 32C of chromosome V of Z. indianus, which indicates its homology to the chromosomal arm 3R of Drosophila melanogaster and, therefore, to Muller’s element E. The main signal for Hsp83 gene probe hybridization was in section 17C of Z. indianus chromosome III, suggesting its homology to arm 3L of D. melanogaster and to element D of Muller. The Ubi probe hybridized in sections 10C of chromosome II and 17A of chromosome III. Probably the 17A is the polyubiquitin locus, with homology to arm 3L of D. melanogaster and to the mullerian D element, as suggested also by Hsp83 gene location. The Br-C gene was mapped in section 1D, near the tip of the X chromosome, indicating its homology to the X chromosome of D. melanogaster and to mullerian element A. The Dpp gene probe hybridized mainly in the section 32A of chromosome V and, at lower frequencies to other sections, although no signal was observed as expected in the correspondent mullerian B element. This result led to the suggestion of a rearrangement including the Dpp locus in Z. indianus, the secondary signals possibly pointing to related genes of the TGF-b family. In conclusion, the results indicate that chromosomes X, III, V of Z. indianus are respectively correspondents to elements A, D, and E of Muller. At least chromosome V of Z. indianus seems to share synteny with the 3R arm of D. melanogaster, as indicated by the relative positions of Hsp70 and Hsr-w, although the Dpp gene indicates a disruption of synteny in its distal region.
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A novel mutation in DAX1 gene causing different phenotypes in three siblings with adrenal hypoplasia congenita |
Genet. Mol. Res. 6 (2): 277-283 (2007)
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L.E.P. Calliari, C.A. Longui, M.N. Rocha, C.D.C. Faria, C. Kochi, M.R. Melo, M.B. Melo and O. Monte |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Adrenal hypoplasia congenita (AHC) is a rare disease that can be caused by many abnormalities, including an X-linked form. Mutations in the DAX1 gene have been assigned as the genetic cause of AHC. We describe here three siblings with AHC, clinically presented at different ages, two in the neonatal period and one oligosymptomatic during infancy. Molecular analysis was able to detect a novel mutation in exon 1 of the DAX1 gene, consisting of a transition of C to T at position 359, determining a stop codon at position 359 (Q359X). The mutated gene encodes a truncated protein missing a large portion of the ligand-binding domain (C-terminal domain). The recognition of the disease in the index case suggested the diagnosis in the other siblings. Interestingly, the same mutation is presented with different phenotypes, suggesting that first-degree family members of patients with DAX1 mutations should be carefully evaluated routinely.
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Preponderance of GC-rich sites in silver-stained nucleolus organizing regions of Rita rita (Hamilton) and Mystus gulio (Hamilton) (Bagridae, Pisces), as revealed by chromomycin A3-staining technique and scanning electron microscopic studies |
Genet. Mol. Res. 6 (2): 284-291 (2007)
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J.K. Das and A.R. Khuda-Bukhsh |
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ABSTRACT. The karyotypes of two species of catfish, Rita rita (Hamilton) (2n = 54; 14m + 34sm + 6st; NF = 102) and Mystus gulio (Hamilton) (2n = 58; 30m + 12sm + 2st + 14t, NF = 100) were studied through Giemsa-, silver- and chromomycin A3-staining techniques. The silver-stained karyotypes in both sexes of R. rita and M. gulio revealed that the nucleolus organizing regions were located terminally at the shorter arms (Tp) of one pair of submetacentric chromosomes, placed at positions Nos. 2 and 1, respectively, which was confirmed by scanning electron microscopy. Staining with a GC-specific fluorochrome, chromomycin A3, produced bright fluorescence in the Ag-positive nucleolus organizer regions, suggesting thereby that nucleolus organizing regions actually included GC-rich sites of active r-RNA genes in metaphase chromosomes of these two bagrids. Further such studies are needed due to the extreme paucity of data on fish.
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Amino acid profile in cassava and its interspecific hybrid |
Genet. Mol. Res. 6 (2): 292-297 (2007)
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Nagib M.A. Nassar and M.V. Sousa |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Cassava roots have a low-protein content (0.7-2%). Amino acids such as lysine and methionine are also low, and some research reports have indicated the absence of methionine. The amino acid profiles of a common cassava cultivar and an interspecific hybrid, namely ICB 300, were determined using the computerized amino acid analyzer Hitachi L-8500. The interspecific hybrid has 10 times more lysine and 3 times more methionine than the common cassava cultivar: lysine content was 0.010 g per 100 g in the common cassava cultivar while it reached 0.098 in the interspecific hybrid. Methionine in the common cassava cultivar was 0.014 g per 100 g whereas it reached 0.041 g per 100 g in the interspecific hybrid. Total amino acid content in the common cassava cultivar was 0.254 g per 100 g viz. a viz. 1.664 g per 100 g in the interspecific hybrid. The genetic variability of the profile and quantity of amino acids indicate the feasibility of selecting interspecific hybrids that are rich in both crude protein and amino acids. This is the first report of high true protein in cassava root.
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Analysis of blood processing conditions to obtain high-quality total RNA from human leukocyte concentrate |
Genet. Mol. Res. 6 (2): 298-307 (2007)
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I.A.G. Pérez, S.P. Santana, T.D. Argudin and D.O.P. Gardon |
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ABSTRACT. Blood samples are used as a biological source to discover biomarkers of hematological and non-hematological disorders. The present study shows the impact of different experimental conditions associated with cell lysis buffer, TRI-reagent protocol and blood cell storage buffer and their correlation with the quantity, quality and Adrenomedullin gene expression levels of total RNA when RT-PCR technique is used. A leukocyte cell bank protocol is also proposed for further mRNA expression analysis using RNAlater as storage buffer. There is evidence that total RNA isolated from leukocyte concentrate stored for 1 month at -70°C did not show significant differences concerning quality, purity and Adrenomedullin gene expression compared with the freshly processed leukocyte sample.
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Evidence of programmed cell death during microsporogenesis in an interspecific Brachiaria (Poaceae: Panicoideae: Paniceae) hybrid |
Genet. Mol. Res. 6 (2): 308-315 (2007)
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V.A. Fuzinatto, M.S. Pagliarini and C.B. Valle |
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ABSTRACT. Morphological changes have been investigated during plant programmed cell death (PCD) in the last few years due to the new interest in a possible apoptotic-like phenomenon existing in plants. Although PCD has been reported in several tissues and specialized cells in plants, there have been few reports of its occurrence during microsporogenesis. The present study reports a typical process of PCD during meiosis in an interspecific Brachiaria hybrid leading to male sterility. In this hybrid, some inflorescences initiated meiosis but it was arrested in zygotene/pachytene. From this stage, meiocytes underwent a severe alteration in shape showing substantial membrane blebbing; the cytoplasm became denser at the periphery; the cell nucleus entered a progressive stage of chromatin disintegration, and then the nucleolus disintegrated, and the cytoplasm condensed and shrunk. The oldest flowers of the raceme showed only the callose wall in the anthers showing obvious signs of complete sterility.
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A multiplex single-base extension protocol for genotyping Cdx2, FokI, BsmI, ApaI, and TaqI polymorphisms of the vitamin D receptor gene |
Genet. Mol. Res. 6 (2): 316-324 (2007)
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T.C.L. Lins, L.R. Nogueira, R.M. Lima, P. Gentil, R.J. Oliveira and R.W. Pereira |
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ABSTRACT. The well-described role of the vitamin D endocrine system in bone metabolism makes its receptor a widely investigated candidate gene in association studies looking for the genetic basis of complex bone-related phenotypes. Most association studies genotype five polymorphic sites along the gene using PCR-RFLP and allele-specific amplification methods, which may not be the better choice in large case/control or cross-sectional studies. In this case, genotyping SNPs in parallel and using automated allele-calling methods are important to decrease genotyping errors due to manual data handling and save sample in cases where the amount of DNA is limited. The aim of this study was to present a straightforward method based on multiplex PCR amplification followed by multiplex single-base extension as a simple way to genotype five vitamin D receptor gene polymorphisms in parallel, which may be implemented in medium- to large-scale case/control or cross-sectional studies. The results regarding method feasibility and optimization are presented by genotyping eight paternity trios and seven samples of Brazilian postmenopausal women who took part in an ongoing association study carried out by members of our group.
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Transferability of microsatellite loci from Cervidae species to the endangered Brazilian marsh deer, Blastocerus dichotomus |
Genet. Mol. Res. 6 (2): 325-330 (2007)
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K.C.E. Leite, R.G. Collevatti, T.R. Menegasso, W.M. Tomas and J.M.B. Duarte |
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ABSTRACT. Blastocerus dichotomus, the marsh deer, is the largest Brazilian Cervidae species. The species is endangered because of hunting and loss of its natural habitat, i.e., flood plain areas, because of hydroelectric power station construction and agricultural land expansion. In the present study, we tested 38 microsatellite loci from four Cervidae species: Odocoileus virginianus (7), Rangifer tarandus (17), Capreolus capreolus (7), and Mazama bororo (7). Eleven loci showed clear amplification, opening a new perspective for the generation of fundamental population genetic data for devising conservation strategies for B. dichotomus.
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DNA sequencing of a pathogenicity-related plasmid of an avian septicemic Escherichia coli strain |
Genet. Mol. Res. 6 (2): 331-337 (2007)
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E.G. Stehling, T.A. Campos, V. Azevedo, M. Brocchi and W.D. Silveira |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. A 43-MDa conjugative plasmid isolated from an avian septicemic Escherichia coli (APEC) strain possessing genes related to the adhesion and invasion capacities of in vitro-cultured cells was sequenced. The results demonstrated that the 43-MDa plasmid harbors bacterial pathogenicity-related sequences which probably allow the wild-type pathogenic strain to adhere to and invade tissues and to cause septicemia in poultry. The existence of homology sequences to sequences belonging to other human pathogenic Enterobacteriaceae like Escherichia coli O157:H7, Shigella and Salmonella was also observed. The presence of these sequences in this plasmid could indicate that there is horizontal genetic transfer between bacterial strains isolated from different host species. In conclusion, the present study suggests that APEC strains harbor high-molecular weight plasmids that present pathogenicity-related sequences and that these are probably responsible for the pathogenicity exhibited by these strains. The presence of human pathogenicity-associated sequences in APEC conjugative plasmids suggests that these strains could represent a zoonotic risk.
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Genetic structure in Brazilian breeding colonies of the Roseate Spoonbill (Platalea ajaja, Aves: Threskiornithidae) |
Genet. Mol. Res. 6 (2): 338-347 (2007)
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Authors |
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C.I. Miño and S.N. Del Lama |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Roseate Spoonbills (Platalea ajaja, Linnaeus) are wading birds present in two of the most important Brazilian wetlands: the Pantanal wetlands and Rio Grande do Sul marshes. Natural populations of these species have not been previously studied with variable nuclear molecular markers. In order to support decision making regarding the management and conservation of these populations, we estimated and characterized the distribution of genetic variability among five Brazilian breeding colonies. The average observed heterozygosity in Brazilian Roseate Spoonbill populations (Ho = 0.575) did not differ significantly from the value determined in a U.S. wild-caught sample of 15 individuals, using data generated by the same set of microsatellite loci. Considering that the U.S. population underwent a recent reduction in size, we discuss this result supposing that the U.S. population was not genetically affected or that both populations had suffered a bottleneck. Global FST indicated the lack of genetic differentiation among colonies, indicating the occurrence of past and/or present gene flow among them. Analysis of molecular variance revealed that most of the genetic variation is distributed within the colonies. Results are explained by a recent origin of colonies or by high levels of gene flow. Management decisions should take into consideration the fact that, even in the presence of high genetic exchange, ecological adaptations to different environments are important for species survival.
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Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog |
Genet. Mol. Res. 6 (2): 348-357 (2007)
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D.C. Salim, A.A. Akimoto, C.B. Carvalho, S.F. Oliveira, C.K. Grisolia, J.R. Moreira and M.N. Klautau-Guimarães |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.
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From geochemistry and biochemistry to prebiotic evolution … we necessarily enter into Gánti’s fluid automata |
Genet. Mol. Res. 6 (2): 358-373 (2007)
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H.F. Hoenigsberg |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. The present study is just an overview of the opening of the geochemical stage for the appearance of life. But that opening would not have been sufficient for the intellectual discovery of the origin of life! The excellent works and many commendable efforts that advance this explanation have not shown the fundamental elements that participate in the theoretical frame of biological evolution. The latter imply the existence of evolutionary transitions and the production of new levels of organization. In this brief analysis we do not intend to introduce the audience to the philosophy of biology. But we do expect to provide a modest overview, in which the geochemical chemolithoautotrophic opening of the stage should be seen, at most, as the initial metabolism that enabled organic compounds to follow the road where a chemical fluid machinery was thus able to undertake the more “sublime” course of organic biological evolution. We think that Tibor Gánti’s chemoton is the most significant contribution to theoretical biology, and the only course now available to comprehend the unit of evolution problem without the structuralist and functionalist conflict prevalent in theoretical biology. In our opinion Gánti’s chemoton theory travels to the “locus” where evolutionary theory dares to extend itself to entities at many levels of structural organization, beyond the gene or the group above. Therefore, in this and subsequent papers on the prebiotic conditions for the eventual appearance of the genetic code, we explore the formation and the presence of metal sulfide minerals, from the assembly of metal sulfide clusters through the precipitation of nanocrystals and the further reactions resulting in bulk metal sulfide phases. We endeavor to characterize pristine reactions and the modern surfaces, utilizing traditional surface science techniques and computational methods. Moreover, mechanistic details of the overall oxidation of metal sulfide minerals are set forth. We hope that this paper will lead our audience to accept that in a chemically oscillating system the chemoton is a model fluid state automaton capable of growth and self-reproduction. This is not simply a matter of transmitting a pattern, as in inorganic crystals; such self-reproduction must be more complex than crystal growth. Indeed that is what Gánti’s theoretical and abstract model offers to us all: we finally have a philosophy of evolutionary units in theoretical biology.
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Selection and estimation of the heritability of sunflower (Helianthus annuus) pollen collection behavior in Apis mellifera colonies |
Genet. Mol. Res. 6 (2): 374-381 (2007)
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M. Basualdo, E.M. Rodríguez, E. Bedascarrasbure and D. De Jong |
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ABSTRACT. We selected honey bee colonies (Apis mellifera L.) with a high tendency to collect sunflower pollen and estimated the heritability of this trait. The percentage of sunflower pollen collected by 74 colonies was evaluated. Five colonies that collected the highest percentages of sunflower pollen were selected. Nineteen colonies headed by daughters of these selected queens were evaluated for this characteristic in comparison with 20 control (unselected) colonies. The variation for the proportion of sunflower pollen was greater among colonies of the control group than among these selected daughter colonies. The estimated heritability was 0.26 ± 0.23, demonstrating that selection to increase sunflower pollen collection is feasible. Such selected colonies could be used to improve sunflower pollination in commercial fields.
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Genetic diversity of microsatellite loci in Leopardus pardalis, Leopardus wiedii and Leopardus tigrinus |
Genet. Mol. Res. 6 (2): 382-389 (2007)
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A.B. Grisolia, V.R. Moreno, F. Campagnari, M.P. Milazzotto, J.F. Garcia, C.H. Adania and E.B. Souza |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. The microsatellite loci FCA045, FCA077, FCA008, and FCA096 are highly variable molecular markers which were used to determine the genetic diversity in 148 captive Leopardus sp. The PCR-amplified products of microsatellite loci were characterized in ABI Prism 310 Genetic Analyzer. Allele numbers, heterozygosity, polymorphism information content, exclusive allele number, and shared alleles were calculated. Sixty-five alleles were found and their sizes ranged from 116 to 216 bp in four microsatellite loci. The heterozygosity ranged from 0.36 to 0.81 in Leopardus pardalis, 0.57 to 0.67 in L. tigrinus and 0.80 to 0.92 in L. wiedii. The polymorphism information content was from 0.80 to 0.88 in L. pardalis, 0.76 to 0.88 in L. tigrinus and 0.77 to 0.90 in L. wiedii. The margay (L. wiedii) showed the highest index of polymorphism among the three species in this study. These results imply that microsatellite DNA markers can help in the study of the genetic diversity of Leopardus specimens.
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Colony membership is reflected by variations in cuticular hydrocarbon profile in a Neotropical paper wasp, Polistes satan (Hymenoptera, Vespidae) |
Genet. Mol. Res. 6 (2): 390-396 (2007)
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I.C. Tannure-Nascimento, F.S. Nascimento, I.C. Turatti, N.P. Lopes, J.R. Trigo and R. Zucchi |
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ABSTRACT. Nestmate recognition is one the most important features in social insect colonies. Although epicuticular lipids or cuticular hydrocarbons have both structural and defensive functions in insects, they also seem to be involved in several aspects of communication in wasps, bees and ants. We analyzed and described for the first time the cuticular hydrocarbons of a Neotropical paper wasp, Polistes satan, and found that variation in hydrocarbon profile was sufficiently strong to discriminate individuals according to their colony membership. Therefore, it seems that small differences in the proportion of these compounds can be detected and used as a chemical-based cue by nestmates to detect invaders and avoid usurpation.
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Minimization of transcriptional temporal noise and scale invariance in the yeast genome |
Genet. Mol. Res. 6 (2): 397-414 (2007)
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R.C. Ferreira, F. Bosco, P.B. Paiva and M.R.S. Briones |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. The analysis of transcriptional temporal noise could be an interesting means to study gene expression dynamics and stochasticity in eukaryotes. To study the statistical distributions of temporal noise in the eukaryotic model system Saccharomyces cerevisiae, we analyzed microarray data corresponding to one cell cycle for 6200 genes. We found that the temporal noise follows a lognormal distribution with scale invariance at the genome, chromosomal and sub-chromosomal levels. Correlation of temporal noise with the codon adaptation index suggests that at least 70% of all protein-coding genes are a noise minimization core of the genome. Accordingly, a mathematical model of individual gene expression dynamics was proposed, using an operator theoretical approach, which reveals strict conditions for noise variability and a possible global noise minimization/optimization strategy at the genome level. Our model and data show that minimal noise does not correspond to genes obeying a strictly deterministic dynamics. The natural strategy of minimization consists in equating the mean of the absolute value of the relative variation of the expression level (a) with noise (h). We hypothesize that the temporal noise pattern is an emergent property of the genome and shows how the dynamics of gene expression could be related to chromosomal organization.
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Technical Note Description of electrophoretic and chromatographic hemoglobin profile of Rhinoclemmys punctularia |
Genet. Mol. Res. 6 (2): 415-421 (2007)
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C.R. Bonini-Domingos, M.B. Silva, R.M. Romero, P.J.A. Zamaro, L.S. Ondei, C.E.S. Zago, S.B. Moreira and C.G. Salgado |
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ABSTRACT. Studies of the hemoglobin pattern in Brazilian reptiles are important for determining ecological and phylogenetic relationships, but they are scarce. Peripheral blood samples were obtained from 7 males and 18 females of Rhinoclemmys punctularia. The hematological profile was based on the total hemoglobin and hematocrit values. The hemoglobin profile was obtained using electrophoretic procedures at different pH, isoelectric focusing, globin chain electrophoresis, and HPLC. The hematocrit (31 ± 2%) and total hemoglobin (7.5 ± 0.2 g/dL) values did not indicate gender variations. Alkaline pH electrophoresis of the total blood samples treated with 1% saponin demonstrated the presence of four well-defined hemoglobin fractions, one major component (fraction I), showing cathodic migration and three others faster than fraction I with anodic migration. When the samples were precipitated with chloroform, only two hemoglobin fractions were observed, similar to fractions I and III from the first procedure. Isoelectric focusing and HPLC showed the same pattern. With acid and neutral pH electrophoresis, two fractions with anodic migration were observed. The globin chain identification at alkaline pH showed two fractions, but four fractions were observed at acidic pH, suggesting that different polypeptide chains are involved in the hemoglobin molecule. The chromatographic separation of the total blood sample demonstrated that the major fraction comprised 81.9% and the minor 18.1%. The results obtained demonstrated a similarity between these hemoglobin components and those of some Chelidae reported in the literature for both land and aquatic animals, reflecting the adaptation to environmental conditions.
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Recognition of α-helix transmembrane domains with an amphipathy scale generated by molecular dynamics using only the primary sequence of proteins
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Genet. Mol. Res. 6 (2): 422-433 (2007)
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F.M. Mazzé, C.A. Fuzo, P. Ciancaglini and L. Degrève |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane segments, by examining a large sample of membrane proteins with α-helix segments. The candidates were selected based on an amphipathy coefficient value range and the minimum number of residues in a segment. We compared our results with the transmembrane segments previously identified in the PDB_TM database by the TMDET algorithm. We expected that the hydrophobic segments would be identified using only the primary structures of the proteins and the amphipathy scale. However, some of these hydrophobic segments may pertain to hydrophobic pockets not included in transmembrane regions. We found that our amphipathy scale could identify α-helix transmembrane regions with a probability of success of 76% when all segments were included and 90% when all membrane proteins were included.
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Estimates of genetic parameters for Holstein cows for test-day yield traits with a random regression cubic spline model |
Genet. Mol. Res. 6 (2): 434-444 (2007)
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B.J. DeGroot, J.F. Keown, L.D. Van Vleck and S.D. Kachman |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Genetic parameters were estimated with restricted maximum likelihood for individual test-day milk, fat, and protein yields and somatic cell scores with a random regression cubic spline model. Test-day records of Holstein cows that calved from 1994 through early 1999 were obtained from Dairy Records Management Systems in Raleigh, North Carolina, for the analysis. Estimates of heritability for individual test-days and estimates of genetic and phenotypic correlations between test-days were obtained from estimates of variances and covariances from the cubic spline analysis. Estimates were calculated of genetic parameters for the averages of the test days within each of the ten 30-day test intervals. The model included herd test-day, age at first calving, and bovine somatropin treatment as fixed factors. Cubic splines were fitted for the overall lactation curve and for random additive genetic and permanent environmental effects, with five predetermined knots or four intervals between days 0, 50, 135, 220, and 305. Estimates of heritability for lactation one ranged from 0.10 to 0.15, 0.06 to 0.10, 0.09 to 0.15, and 0.02 to 0.06 for test-day one to test-day 10 for milk, fat, and protein yields and somatic cell scores, respectively. Estimates of heritability were greater in lactations two and three. Estimates of heritability increased over the course of the lactation. Estimates of genetic and phenotypic correlations were smaller for test-days further apart.
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Gene flow from transgenic to nontransgenic soybean plants in the Cerrado region of Brazil |
Genet. Mol. Res. 6 (2): 445-452 (2007)
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S. Abud, P.I.M. de Souza, G.R. Vianna, E. Leonardecz, C.T. Moreira, F.G. Faleiro, J.N. Júnior, P.M.F.O. Monteiro, E.L. Rech and F.J.L. Aragão |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Evaluation of transgenic crops under field conditions is a fundamental step for the production of genetically engineered varieties. In order to determine if there is pollen dispersal from transgenic to nontransgenic soybean plants, a field release experiment was conducted in the Cerrado region of Brazil. Nontransgenic plants were cultivated in plots surrounding Roundup Ready transgenic plants carrying the cp4 epsps gene, which confers herbicide tolerance against glyphosate herbicide, and pollen dispersal was evaluated by checking for the dominant gene. The percentage of cross-pollination was calculated as a fraction of herbicide-tolerant and -nontolerant plants. The greatest amount of transgenic pollen dispersion was observed in the first row, located at one meter from the central (transgenic) plot, with a 0.52% average frequency. The frequency of pollen dispersion decreased to 0.12% in row 2, reaching 0% when the plants were up to 10 m distance from the central plot. Under these conditions pollen flow was higher for a short distance. This fact suggests that the management necessary to avoid cross-pollination from transgenic to nontransgenic plants in the seed production fields should be similar to the procedures currently utilized to produce commercial seeds.
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HPLC determination of hemoglobins to establish reference values with the aid of statistics and informatics |
Genet. Mol. Res. 6 (2): 453-460 (2007)
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L.S. Ondei, P.J.A. Zamaro, P.H. Mangonaro, C.R. Valêncio and C.R. Bonini-Domingos |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. The purpose of the present study was to establish reference values for hemoglobins (Hb) using HPLC, in samples containing normal Hb (AA), sickle cell trait without alpha-thalassemia (AS), sickle cell trait with alpha-thalassemia (ASH), sickle cell anemia (SS), and Hb SC disease (SC). The blood samples were analyzed by electrophoresis, HPLC and molecular procedures. The Hb A2 mean was 4.30 ± 0.44% in AS, 4.18 ± 0.42% in ASH, 3.90 ± 1.14% in SS, and 4.39 ± 0.35% in SC. They were similar, but above the normal range. Between the AS and ASH groups, only the amount of Hb S was higher in the AS group. The Hb S mean in the AS group was 38.54 ± 3.01% and in the ASH it was 36.54 ± 3.76%. In the qualitative analysis, using FastMap, distinct groups were seen: AA and SS located at opposite extremes, AS and ASH with overlapping values and intermediate distribution, SC between heterozygotes and the SS group. Hb S was confirmed by allele-specific polymerase chain reaction. The Hb values established will be available for use as a reference for the Brazilian population, drawing attention to the increased levels of Hb A2, which should be considered with caution to prevent incorrect diagnoses.
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Y chromosome microdeletions in Brazilian fertility clinic patients |
Genet. Mol. Res. 6 (2): 461-469 (2007)
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J.T. Arruda, B.M. Bordin, P.R. Santos, W.E.J.C. Mesquita, R.C.P.C. Silva, M.C.S. Maia, M.S. Approbato, R.S. Florêncio, W.N. Amaral, M.A. Rocha Filho and K.K.V.O. Moura |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Microdeletions in Yq are associated with defects in spermatogenesis, while those in the AZF region are considered critical for germ cell development. We examined microdeletions in the Y chromosomes of patients attended at the Laboratory of Human Reproduction of the Clinical Hospital of the Federal University of Goiás as part of a screening of patients who plan to undergo assisted reproduction. Analysis was made of the AZF region of the Y chromosome in men who had altered spermograms to detect possible microdeletions in Yq. Twenty-three patients with azoospermia and 40 with severe oligozoospermia were analyzed by PCR for the detection of six sequence-tagged sites: sY84 and sY86 for AZFa, sY127 and sY134 for AZFb, and sY254 and sY255 for AZFc. Microdeletions were detected in 28 patients, including 10 azoospermics and 18 severe oligozoospermics. The patients with azoospermia had 43.4% of their microdeletions in the AZFa region, 8.6% in the AZFb region and 17.4% in the AZFc region. In the severe oligozoospermics, 40% were in the AZFa region, 5% in the AZFb region and 5% in the AZFc region. We conclude that microdeletions can be the cause of idiopathic male infertility, supporting conclusions from previous studies.
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First-trimester prenatal diagnosis of pyruvate kinase deficiency in an Indian family with the pyruvate kinase-Amish mutation |
Genet. Mol. Res. 6 (2): 470-475 (2007)
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P.S. Kedar, S. Nampoothiri, S. Sreedhar, K. Ghosh, K. Shimizu, H. Kanno and R.B. Colah |
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Abstract | Abstract HTML | Full Text HTML | Full Text PDF |
ABSTRACT. Pyruvate kinase (PK) deficiency is a rare red cell glycolytic enzymopathy. The purpose of the present investigation was to offer prenatal diagnosis for PK deficiency to a couple who had a previous child with severe enzyme deficiency and congenital non-spherocytic hemolytic anemia. PK deficiency was identified in the family by assaying the enzyme activity in red cells. Chorionic villus sampling was performed in an 11-week gestation and the mutation was located in exon 10 of the PKLR gene characterized by polymerase chain reaction and using restriction endonuclease digestion with the MspI enzyme, which was confirmed by DNA sequencing on the ABI 310 DNA sequencer. Both the parents were heterozygous for the 1436G→A [479 Arg→His] mutation in exon 10 and the proband was homozygous for this mutation. The fetus was also heterozygous for this mutation and the pregnancy was continued. Prenatal diagnosis allowed the parents with a severely affected child with PK deficiency to have the reproductive choice of having the fetus tested in a subsequent pregnancy.
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