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1.  Assessment of genetic diversity in Brazilian barley using SSR markers 
Genetics and Molecular Biology  2016;39(1):86-96.
Abstract
Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.
doi:10.1590/1678-4685-GMB-2015-0148
PMCID: PMC4807376  PMID: 27007902
Domesticated barley; genetic diversity; Hordeum vulgare ssp. vulgare; Hordeum vulgare ssp. spontaneum; microsatellite markers
2.  Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers 
Genetics and Molecular Biology  2016;39(1):145-150.
Abstract
Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster and seven sequences ofD. simulans, both from South America, to check the number of repetitions of TPE, in order to clarify the evolutionary scenario of thehobo element in these populations. Our results showed a monomorphism in populations of both species in South America, with only three TPE repeats. Hence, we discuss and propose an evolutionary scenario of the invasion of the hobo element in populations of D. melanogaster and D. simulans.
doi:10.1590/1678-4685-GMB-2015-0049
PMCID: PMC4807377  PMID: 27007908
transposable elements; transposons; hAT; genomic evolution; molecular evolution
3.  The complex translocation (9;14;14) involving IGH and CEBPE genes suggests a new subgroup in B-lineage acute lymphoblastic leukemia 
Abstract
Many subtypes of acute lymphoblastic leukemia (ALL) are associated with specific chromosomal rearrangements. The complex translocation t(9;14;14), a variant of the translocation (14;14)(q11;q32), is a rare but recurrent chromosomal abnormality involving the immunoglobulin heavy-chain (IGH) and CCAAT enhancer-binding protein (CEBPE) genes in B-lineage ALL (B-ALL) and may represent a new B-ALL subgroup. We report here the case of a 5-year-old girl with B-ALL, positive for CD19, CD38 and HLA-DR. A direct technique and G-banding were used for chromosomal analysis and fluorescentin situ hybridization (FISH) with BAC probes was used to investigate a possible rearrangement of the IGH andCEBPE genes. The karyotype exhibit the chromosomal aberration 46,XX,del(9)(p21),t(14;14)(q11;q32). FISH with dual-color break-apartIGH-specific and CEPBE-specific bacterial artificial chromosome (BAC) probes showed a complex t(9;14;14) associated with a deletion of cyclin-dependent kinase inhibitor 2A (CDKN2A) and paired box gene 5 (PAX5) at 9p21-13 and duplication of the fusion gene IGH-CEBPE.
doi:10.1590/S1415-475738420140368
PMCID: PMC4807378  PMID: 27007892
acute lymphoblastic leukemia; CEBPE; FISH; IGH; translocation
4.  Human mesenchymal stem cells are resistant to cytotoxic and genotoxic effects of cisplatin in vitro  
Genetics and Molecular Biology  2016;39(1):129-134.
Abstract
Mesenchymal stem cells (MSCs) are known for their important properties involving multilineage differentiation potential., trophic factor secretion and localization along various organs and tissues. On the dark side, MSCs play a distinguished role in tumor microenvironments by differentiating into tumor-associated fibroblasts or supporting tumor growth via distinct mechanisms. Cisplatin (CIS) is a drug widely applied in the treatment of a large number of cancers and is known for its cytotoxic and genotoxic effects, both in vitro and in vivo. Here we assessed the effects of CIS on MSCs and the ovarian cancer cell line OVCAR-3, by MTT and comet assays. Our results demonstrated the resistance of MSCs to cell death and DNA damage induction by CIS, which was not observed when OVCAR-3 cells were exposed to this drug.
doi:10.1590/1678-4685-GMB-2015-0057
PMCID: PMC4807379  PMID: 27007906
Mesenchymal stem cells; Cisplatin; MTT; Comet assay; OVCAR-3 cells
5.  Functional abilities of cultivable plant growth promoting bacteria associated with wheat (Triticum aestivum L.) crops 
Genetics and Molecular Biology  2016;39(1):111-121.
Abstract
In the pursuit of sustainable agriculture, bioinoculants usage as providers of a crop's needs is a method to limit environmental damage. In this study, a collection of cultivable putative plant growth promoting (PGP) bacteria associated with wheat crops was obtained and this bacterial sample was characterized in relation to the functional diversity of certain PGP features. The isolates were obtained through classical cultivation methods, identified by partial 16S rRNA gene sequencing and characterized for PGP traits of interest. Functional diversity characterization was performed using Categorical Principal Component Analysis (CatPCA) and Multiple Correspondence Analysis (MCA). The most abundant genera found among the 346 isolates were Pseudomonas, Burkholderia, and Enterobacter. Occurrence of PGP traits was affected by genus, niche, and sampling site. A large number of genera grouped together with the ability to produce indolic compounds; phosphate solubilization and siderophores production formed a second group related to fewer genera, in which the genus Burkholderia has a great importance. The results obtained may help future studies aiming prospection of putative plant growth promoting bacteria regarding the desired organism and PGP trait.
doi:10.1590/1678-4685-GMB-2015-0140
PMCID: PMC4807380  PMID: 27007904
plant growth promoting bacteria; Categorical Principal Component Analysis; functional analysis; Burkholderia genus
6.  Lack of detection of human papillomavirus DNA in prostate carcinomas in patients from northeastern Brazil 
Genetics and Molecular Biology  2016;39(1):24-29.
Abstract
Prostate cancer is the second most common cancer among men in western populations, and despite its high mortality, its etiology remains unknown. Inflammatory processes are related to the etiology of various types of tumors, and prostate inflammation, in particular, has been associated with prostate cancer carcinogenesis and progression. Human papillomavirus (HPV) is associated with benign and malignant lesions in the anogenital tract of both females and males. The possible role of HPV in prostate carcinogenesis is a subject of great controversy. In this study, we aimed to examine the prevalence of HPV infections in prostate carcinomas of patients from northeastern Brazil. This study included 104 tissue samples from primary prostate carcinoma cases. HPV DNA was purified and then amplified using MY09/11 and GP5+/GP6+ degenerate primer sets that detect a wide range of HPV types, and with specific PCR primers sets for E6 and E7 HPV regions to detect HPV 16. None of the samples showed amplification products of HPV DNA for primer sets MY09/11 and GP5+/GP6+, or the specific primer set for the E6 and E7 HPV regions. HPV infection, thus, does not seem to be one of the causes of prostate cancer in the population studied.
doi:10.1590/1678-4685-GMB-2015-0122
PMCID: PMC4807381  PMID: 27007894
human papillomavirus; prostate cancer; prevalence; HPV PCR detection; molecular epidemiology
7.  Six1 induces protein synthesis signaling expression in duck myoblasts mainly via up-regulation of mTOR  
Genetics and Molecular Biology  2016;39(1):151-161.
Abstract
As a critical transcription factor, Six1 plays an important role in the regulation of myogenesis and muscle development. However, little is known about its regulatory mechanism associated with muscular protein synthesis. The objective of this study was to investigate the effects of overexpression ofSix1 on the expression of key protein metabolism-related genes in duck myoblasts. Through an experimental model where duck myoblasts were transfected with a pEGFP-duSix1 construct, we found that overexpression of duckSix1 could enhance cell proliferation activity and increase mRNA expression levels of key genes involved in the PI3K/Akt/mTOR signaling pathway, while the expression of FOXO1, MuRF1and MAFbx was not significantly altered, indicating thatSix1 could promote protein synthesis in myoblasts through up-regulating the expression of several related genes. Additionally, in duck myoblasts treated with LY294002 and rapamycin, the specific inhibitors ofPI3K and mTOR, respectively, the overexpression of Six1 could significantly ameliorate inhibitive effects of these inhibitors on protein synthesis. Especially, the mRNA expression levels of mTOR and S6K1 were observed to undergo a visible change, and a significant increase in protein expression of S6K1 was seen. These data suggested that Six1plays an important role in protein synthesis, which may be mainly due to activation of the mTOR signaling pathway.
doi:10.1590/1678-4685-GMB-2015-0075
PMCID: PMC4807382  PMID: 27007909
duck; Six1; protein metabolism signaling; mTOR; pEGFP-duSix1
8.  Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits 
Genetics and Molecular Biology  2016;39(1):97-110.
Abstract
The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.
doi:10.1590/1678-4685-GMB-2015-0126
PMCID: PMC4807383  PMID: 27007903
gametic phase disequilibrium; GWAS; candidate gene
9.  Identification and characterization of MAGO and Y14 genes in Hevea brasiliensis  
Genetics and Molecular Biology  2016;39(1):73-85.
Abstract
Mago nashi (MAGO) and Y14 proteins are highly conserved among eukaryotes. In this study, we identified two MAGO (designated as HbMAGO1 andHbMAGO2) and two Y14 (designated as HbY14aand HbY14b) genes in the rubber tree (Hevea brasiliensis) genome annotation. Multiple amino acid sequence alignments predicted that HbMAGO and HbY14 proteins are structurally similar to homologous proteins from other species. Tissue-specific expression profiles showed that HbMAGO and HbY14 genes were expressed in at least one of the tissues (bark, flower, latex, leaf and root) examined. HbMAGOs and HbY14s were predominately located in the nucleus and were found to interact in yeast two-hybrid analysis (YTH) and bimolecular fluorescence complementation (BiFC) assays. HbMAGOs and HbY14s showed the highest transcription in latex and were regulated by ethylene and jasmonate. Interaction between HbMAGO2 and gp91phox (a large subunit of nicotinamide adenine dinucleotide phosphate) was identified using YTH and BiFC assays. These findings suggested that HbMAGO may be involved in the aggregation of rubber particles in H. brasiliensis.
doi:10.1590/1678-4685-GMB-2014-0387
PMCID: PMC4807384  PMID: 27007901
interaction; Hevea brasiliensis; Mago nashi; Y14 proteins
10.  Genetic analysis of reciprocal differences in the inheritance of in vitro characters in pearl millet 
Genetics and Molecular Biology  2016;39(1):54-61.
Abstract
Reciprocal differences persist in nature because of the unequal contribution of cytoplasmic determinants from male and female gametes to the zygote. The inheritance of genetic differences is an important factor that influences various traits, including somatic embryogenesis and regeneration in vitro. In this report, we estimate the cytoplasmic and maternal effects in pearl millet and their adequacy in describing the observed reciprocal differences based on an in depth study of the parents, F2s and reciprocal backcross progenies needed for fitting genetical models. Our study revealed that of the two characters examined, embryogenic callus quantity and regeneration frequency, the former showed a greater proportion of cytoplasmic nuclear interaction whereas the latter showed a greater role of nuclear factors. Additive-maternal effects influenced total callus quantity and dominance-maternal effects influenced total callus quantity, embryogenic callus quantity and regeneration frequency. Dwarfing was associated with the production of large quantities of embryogenic callus that had visually recognizable characteristics. The phenotypic nature of dwarf parents (green dwarf with long narrow leaves) with a genetic basis for a given character controlled by nuclear and cytoplasmic determinants can be exploited for other breeding programs.
doi:10.1590/1678-4685-GMB-2014-0380
PMCID: PMC4807385  PMID: 27007899
cytoplasmic inheritance; d2 dwarf; in vitro regeneration; pearl millet; reciprocal differences
11.  Cytogenetic variation of repetitive DNA elements in Hoplias malabaricus (Characiformes - Erythrinidae) from white, black and clear water rivers of the Amazon basin 
Genetics and Molecular Biology  2016;39(1):40-48.
Abstract
Hoplias malabaricus is a common fish species occurring in white, black and clear water rivers of the Amazon basin. Its large distribution across distinct aquatic environments can pose stressful conditions for dispersal and creates possibilities for the emergence of local adaptive profiles. We investigated the chromosomal localization of repetitive DNA markers (constitutive heterochromatin, rDNA and the transposable element REX-3) in populations from the Amazonas river (white water), the Negro river (black water) and the Tapajós river (clear water), in order to address the variation/association of cytogenomic features and environmental conditions. We found a conserved karyotypic macrostructure with a diploid number of 40 chromosomes (20 metacentrics + 20 submetacentrics) in all the samples. Heteromorphism in pair 14 was detected as evidence for the initial differentiation of an XX/XY system. Minor differences detected in the amount of repetitive DNA markers are interpreted as possible signatures of local adaptations to distinct aquatic environments.
doi:10.1590/1678-4685-GMB-2015-0099
PMCID: PMC4807386  PMID: 27007897
cytogenomics; FISH; rDNA; REX 3; Tapajós river
12.  Genotypic diversity of the Killer Cell Immunoglobulin-like Receptors (KIR) and their HLA class I Ligands in a Saudi population 
Genetics and Molecular Biology  2016;39(1):14-23.
Abstract
Killer Cell Immunoglobulin-like Receptors (KIR) have been used as good markers for the study of genetic predisposition in many diseases and in human genetic population dynamics. In this context, we have investigated the genetic diversity of KIR genes and their main HLA class I ligands in Saudi population and compared the data with other studies of neighboring populations. One hundred and fourteen randomly selected healthy Saudi subjects were genotyped for the presence or absence of 16 KIR genes and their HLA-C1, -C2, -Bw4Thr80 and Bw4Ile80 groups, using a PCR-SSP technique. The results show the occurrence of the framework genes (3DL2, 3DL3 and 2DL4) and the pseudogenes (2DP1 and 3DP1) at highest frequencies. All inhibitory KIR (iKIR) genes appeared at higher frequencies than activating genes (aKIR), except for 2DS4 with a frequency of 90.35%. A total of 55 different genotypes were observed appearing at different frequencies, where 12 are considered novel. Two haplotypes were characterized, AA and Bx (BB and AB), which were observed in 24.5% and 75.5% respectively of the studied group. The frequencies of iKIR + HLA associations were found to be much higher than aKIR + HLA. KIR genes frequencies in the Saudi population are comparable with other Middle Eastern and North African populations.
doi:10.1590/1678-4685-GMB-2015-0055
PMCID: PMC4807387  PMID: 27007893
KIR diversity; gene polymorphism; molecular evolution; PCR SSP; population viability analysis
13.  Protective effects of acerola juice on genotoxicity induced by iron in vivo  
Genetics and Molecular Biology  2016;39(1):122-128.
Abstract
Metal ions such as iron can induce DNA damage by inducing reactive oxygen species (ROS) and oxidative stress. Vitamin C is one of the most widely consumed antioxidants worldwide, present in many fruits and vegetables, especially inMalpighia glabra L., popularly known as acerola, native to Brazil. Acerola is considered a functional fruit due to its high antioxidant properties and phenolic contents, and therefore is consumed to prevent diseases or as adjuvant in treatment strategies. Here, the influence of ripe and unripe acerola juices on iron genotoxicity was analyzed in vivo using the comet assay and micronucleus test. The comet assay results showed that acerola juice exerted no genotoxic or antigenotoxic activity. Neither ripe nor unripe acerola juices were mutagenic to animals treated with juices, in micronucleus test. However, when compared to iron group, the pre-treatment with acerola juices exerted antimutagenic activity, decreasing significantly micronucleus mean values in bone marrow. Stage of ripeness did not influence the interaction of acerola compounds with DNA, and both ripe and unripe acerola juices exerted protective effect over DNA damage generated by iron.
doi:10.1590/1678-4685-GMB-2015-0157
PMCID: PMC4807388  PMID: 27007905
genotoxicity; comet assay; micronucleus; acerola juice; iron
14.  The prognostic value of the serum ferritin in a southern Brazilian cohort of patients with Gaucher disease 
Genetics and Molecular Biology  2016;39(1):30-34.
Abstract
The clinical utility of serum ferritin as a biomarker of disease severity and prognosis in Gaucher disease (GD) is still debated. Here, we aimed to evaluate ferritin and its relation to clinicolaboratory parameters of GD patients seen at the Reference Center for Gaucher Disease of Rio Grande do Sul, Brazil, so as to gather evidence on the utility of ferritin as a biomarker of this condition. A retrospective chart review was performed collecting pre-and posttreatment data from GD patients. Eighteen patients with ferritin levels available before and after treatment were included in the study. Nine of these participants were males, and seventeen had type I GD. All patients were given either enzyme replacement (n = 16) or substrate reduction therapy (n = 2), and ferritin was found to decrease from 756 [318-1441] ng/mL at baseline to 521 [227-626] ng/mL (p=0.025) after 28.8 month soft treatment. Serum ferritin levels did not correlate with measures of disease severity, but showed an association with age at onset of treatment (ρ= 0.880; n = 18; p < 0.001). In conclusion, although serum ferritin did not correlate with disease severity, after a median 28.8 months of treatment, clinical outcomes had clearly improved, and ferritin levels had decreased.
doi:10.1590/1678-4685-GMB-2015-0125
PMCID: PMC4807389  PMID: 27007895
ferritin; biomarkers; Gaucher disease; iron metabolism
15.  Antioxidant responses of wheat plants under stress 
Abstract
Currently, food security depends on the increased production of cereals such as wheat (Triticum aestivum L.), which is an important source of calories and protein for humans. However, cells of the crop have suffered from the accumulation of reactive oxygen species (ROS), which can cause severe oxidative damage to the plants, due to environmental stresses. ROS are toxic molecules found in various subcellular compartments. The equilibrium between the production and detoxification of ROS is sustained by enzymatic and nonenzymatic antioxidants. In the present review, we offer a brief summary of antioxidant defense and hydrogen peroxide (H2O2) signaling in wheat plants. Wheat plants increase antioxidant defense mechanisms under abiotic stresses, such as drought, cold, heat, salinity and UV-B radiation, to alleviate oxidative damage. Moreover, H2O2 signaling is an important factor contributing to stress tolerance in cereals.
doi:10.1590/1678-4685-GMB-2015-0109
PMCID: PMC4807390  PMID: 27007891
abiotic stress; antioxidant enzymes; hydrogen peroxide signaling; wheat; Triticum aestivum
16.  Multiple introductions and gene flow in subtropical South American populations of the fireweed, Senecio madagascariensis(Asteraceae) 
Genetics and Molecular Biology  2016;39(1):135-144.
Abstract
Non-indigenous plants exhibit different attributes that make them aggressive competitors with indigenous plants and serious threats to biodiversity.Senecio madagascariensis (fireweed, Asteraceae), a native from southern Africa, is a strong competitor in agricultural activities and has toxic alkaloids that may result in high cattle mortality. In Brazil, this weed was collected for the first time in 1995 and has since spread quickly throughout the Pampas region. To better understand the invasion of the fireweed in South America, we used a genetic characterization with internal transcribed spacer (ITS) and microsatellite markers. Based on the ITS data, the southern Brazil populations of S. madagascariensis shared genetic homology with samples taken from the Hawaiian Islands and South Africa. Microsatellite analysis showed the genetic diversity split in two clusters, perhaps intimating the independent introduction of each species into South America. Although fireweed was introduced recently in southern Brazil, the considerable levels of genetic diversity, gene flow, and inbreeding may indicate success in the species establishment in this environment.
doi:10.1590/1678-4685-GMB-2015-0167
PMCID: PMC4807391  PMID: 27007907
Microsatellites; ITS; Pampas; weed; spread
17.  Tetrasomy 3q26.32-q29 due to a supernumerary marker chromosome in a child with pigmentary mosaicism of Ito 
Genetics and Molecular Biology  2016;39(1):35-39.
Abstract
Pigmentary mosaicism of Ito (PMI) is a skin abnormality often characterized by hypopigmentation of skin, following, in most cases, the Blaschko lines, usually associated with extracutaneous abnormalities, especially abnormalities of the central nervous system (CNS). It is suggested that this pattern arises from the presence and migration of two cell lineages in the ectoderm layer during the embryonic period and embryonic cell migration, with different gene expression profiles associated with pigmentation. Several types of chromosomal aberrations, with or without mosaicism, have been associated with this disorder. This study comprised clinical description and cytogenetic analysis of a child with PMI. The G-banded karyotype analysis revealed a supernumerary marker chromosome in 76% of the analyzed metaphases from peripheral blood lymphocytes. Array genomic hybridization analysis showed a copy number gain between 3q26.32-3q29, of approximately 20.5 Mb. Karyotype was defined as 47,XX,+mar[38]/46,XX[12].arr 3q26.32-3q29(177,682,859- 198,043,720)x4 dn. Genes mapped in the overlapping region among this patient and three other cases described prior to this study were listed and their possible involvement on PMI pathogenesis is discussed.
doi:10.1590/1678-4685-GMB-2015-0033
PMCID: PMC4807392  PMID: 27007896
Pigmentary mosaicism of Ito; tetrasomy; supernumerary marker chromosome; array genomic hybridization
18.  The PIN1 family gene PvPIN1 is involved in auxin-dependent root emergence and tillering in switchgrass 
Genetics and Molecular Biology  2016;39(1):62-72.
Abstract
Switchgrass (Panicum virgatum L.; family Poaceae) is a warm-season C4 perennial grass. Tillering plays an important role in determining the morphology of aboveground parts and the final biomass yield of switchgrass. Auxin distribution in plants can affect a variety of important growth and developmental processes, including the regulation of shoot and root branching, plant resistance and biological yield. Auxin transport and gradients in plants are mediated by influx and efflux carriers. PvPIN1, a switchgrass PIN1-like gene that is involved in regulating polar transport, is a putative auxin efflux carrier. Neighbor-joining analysis using sequences deposited in NCBI databases showed that the PvPIN1gene belongs to the PIN1 family and is evolutionarily closer to the Oryza sativa japonica group. Tiller emergence and development was significantly promoted in plants subjected toPvPIN1 RNA interference (RNAi), which yielded a phenotype similar to that of wild-type plants treated with the auxin transport inhibitor TIBA (2,3,5-triiodobenzoic acid). A transgenic approach that inducedPvPIN1 gene overexpression or suppression altered tiller number and the shoot/root ratio. These data suggest that PvPIN1plays an important role in auxin-dependent adventitious root emergence and tillering.
doi:10.1590/1678-4685-GMB-2014-0300
PMCID: PMC4807393  PMID: 27007900
Auxin transporter; PvPIN1 gene; TIBA treatment; tillering; switchgrass
19.  Genetic analysis reveals candidate species in the Scinax catharinae clade (Amphibia: Anura) from Central Brazil 
Genetics and Molecular Biology  2016;39(1):49-53.
Abstract
Scinax (Anura: Hylidae) is a species-rich genus of amphibians (113 spp.), divided into five species groups by morphological features. Cladistic analyses however revealed only two monophyletic clades in these groups: Scinax catharinae and Scinax ruber. Most species from the S. catharinae clade are found in Atlantic rainforest, except for Scinax canastrensis,S. centralis, S. luizotavioi, S. machadoi,S. pombali and S. skaios. In the present work, specimens of Scinax collected in Chapada dos Guimarães, central Brazil, were morphologically compatible with species from theS. catharinae group. On the other hand, genetic analysis based on mitochondrial (16S and 12S) and nuclear (rhodopsin) sequences revealed a nucleotide divergence of 6 to 20% between Scinax sp. and other congeners from the Brazilian savannah (Cerrado). Accordingly, Bayesian inference placed Scinax sp. in the S. catharinae clade with high support values. Hence, these findings strongly indicate the presence of a new species in the S. catharinae clade from the southwestern portion of the Brazilian savannah. To be properly validated as a novel species, detailed comparative morphological and bioacustic studies with other taxa from Brazil such asS. canastrensis, S. centralis, S. luizotavioi, S. machadoi, S. pombali and S. skaios are required.
doi:10.1590/1678-4685-GMB-2015-0037
PMCID: PMC4807394  PMID: 27007898
Amphibians; DNA barcode; Cerrado; rDNA
20.  Comparative study of curcumin and curcumin formulated in a solid dispersion: Evaluation of their antigenotoxic effects 
Genetics and Molecular Biology  2015;38(4):490-498.
Abstract
Curcumin (CMN) is the principal active component derived from the rhizome of Curcuma longa (Curcuma longa L.). It is a liposoluble polyphenolic compound that possesses great therapeutic potential. Its clinical application is, however, limited by the low concentrations detected following oral administration. One key strategy for improving the solubility and bioavailability of poorly water-soluble drugs is solid dispersion, though it is not known whether this technique might influence the pharmacological effects of CMN. Thus, in this study, we aimed to evaluate the antioxidant and antigenotoxic effects of CMN formulated in a solid dispersion (CMN SD) compared to unmodified CMN delivered to Wistar rats. Cisplatin (cDDP) was used as the damage-inducing agent in these evaluations. The comet assay results showed that CMN SD was not able to reduce the formation of cDDP-DNA crosslinks, but it decreased the formation of micronuclei induced by cDDP and attenuated cDDP-induced oxidative stress. Furthermore, at a dose of 50 mg/kg b.w. both CMN SD and unmodified CMN increased the expression of Tp53 mRNA. Our results showed that CMN SD did not alter the antigenotoxic effects observed for unmodified CMN and showed effects similar to those of unmodified CMN for all of the parameters evaluated. In conclusion, CMN SD maintained the protective effects of unmodified CMN with the advantage of being chemically water soluble, with maximization of absorption in the gastrointestinal tract. Thus, the optimization of the physical and chemical properties of CMN SD may increase the potential for the therapeutic use of curcumin.
doi:10.1590/S1415-475738420150046
PMCID: PMC4763312  PMID: 26537603
Curcuma longa; antigenotoxicity; micronucleus test; DNA damage; comet assay
21.  Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine 
Genetics and Molecular Biology  2015;38(4):484-489.
Abstract
The core microbiota of a neutral mine drainage and the surrounding high heavy metal content soil at a Brazilian copper mine were characterized by 16S rDNA pyrosequencing. The core microbiota of the drainage was dominated by the generalist genus Meiothermus. The soil samples contained a more heterogeneous bacterial community, with the presence of both generalist and specialist bacteria. Both environments supported mainly heterotrophic bacteria, including organisms resistant to heavy metals, although many of the bacterial groups identified remain poorly characterized. The results contribute to the understanding of bacterial communities in soils impacted by neutral mine drainage, for which information is scarce, and demonstrate that heavy metals can play an important role in shaping the microbial communities in mine environments.
doi:10.1590/S1415-475738420150025
PMCID: PMC4763313  PMID: 26537607
mine drainage; soil; 16S rDNA pyrosequencing; core microbiota; generalist and specialist OTUs
22.  DNA damage in the kidney tissue cells of the fish Rhamdia quelen after trophic contamination with aluminum sulfate 
Genetics and Molecular Biology  2015;38(4):499-506.
Abstract
Even though aluminum is the third most common element present in the earth's crust, information regarding its toxicity remains scarce. It is known that in certain cases, aluminum is neurotoxic, but its effect in other tissues is unknown. The aim of this work was to analyze the genotoxic potential of aluminum sulfate in kidney tissue of the fish Rhamdia quelen after trophic contamination for 60 days. Sixty four fish were subdivided into the following groups: negative control, 5 mg, 50 mg and 500 mg of aluminum sulfate per kg of fish. Samples of the posterior kidney were taken and prepared to obtain mitotic metaphase, as well as the comet assay. The three types of chromosomal abnormalities (CA) found were categorized as chromatid breaks, decondensation of telomeric region, and early separation of sister chromatids. The tests for CA showed that the 5 mg/kg and 50 mg/kg doses of aluminum sulfate had genotoxic potential. Under these treatments, early separation of the sister chromatids was observed more frequently and decondensation of the telomeric region tended to increase in frequency. We suggest that structural changes in the proteins involved in DNA compaction may have led to the decondensation of the telomeric region, making the DNA susceptible to breaks. Moreover, early separation of the sister chromatids may have occurred due to changes in the mobility of chromosomes or proteins that keep the sister chromatids together. The comet assay confirmed the genotoxicity of aluminum sulfate in the kidney tissue of Rhamdia quelen at the three doses of exposure.
doi:10.1590/S1415-475738420140327
PMCID: PMC4763314  PMID: 26692157
fish; metal contamination; chromosomal abnormalities; comet assay
23.  NCAPG is differentially expressed during longissimus muscle development and is associated with growth traits in Chinese Qinchuan beef cattle 
Genetics and Molecular Biology  2015;38(4):450-456.
Abstract
Based on RNA-seq analysis, we recently found that the bovine NCAPG (non-SMC condensin I complex, subunit G) gene is differentially expressed during development of the longissimus muscle. In the present study, we validated this result and, using quantitative real-time PCR analysis, identified two adjacent genes, LCORL and DCAF16, that are more abundant in fetal muscle tissue; further analysis of tissue-specific expression patterns indicated high abundance of NCAPG in muscle. Since no polymorphisms were detected in a previous study of Qinchuan cattle, we extended our investigation to examine the occurrence of single-nucleotide polymorphisms (SNPs) in the NCAPG gene. Three SNPs, i.e., one located in the intron region (g47747: T > G), a synonymous mutation (g52535: A > G) and a missense mutation (g53208: T > G) that leads to a change in the amino acid of interest (pIle442Met), were detected in a population of Qinchuan beef cattle (n = 300). Association analysis showed that these SNPs were significantly associated with the growth traits of Qinchuan beef cattle. Our results indicate that the bovine NCAPG gene may be involved in the development of the longissimus muscle. These polymorphisms in the NCAPG gene may be useful for marker-assisted selection of optimal body size in Qinchuan beef cattle.
doi:10.1590/S1415-475738420140287
PMCID: PMC4763315  PMID: 26692155
association analysis; growth traits; longissimus muscle; NCAPG expression; single nucleotide polymorphism
24.  Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale 
Genetics and Molecular Biology  2015;38(4):513-518.
Abstract
Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalis musimon, were used as probes for hybridization on genomic DNA and on metaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 are sequences respectively belonging to the 1.715 and 1.714 DNA satellite I families. Southern blots and fluorescence in situ hybridization experiments showed completely coherent results: the Bovini probe Bt1 hybridized only to members of the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1 hybridized only to members of the Caprini tribe and not to members of Bovini. Hybridization signals were detected in the heterochromatic regions of every acrocentric autosome, except for two pairs of autosomes from Capra hircus that did not show hybridization to probe Om1. No signal was detected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1 showed almost 100% homology with a bacterial sequence reported in Helicobacter pylori.
doi:10.1590/S1415-475738420150094
PMCID: PMC4763316  PMID: 26692159
Bovidae; satellite DNA; fluorescence in situ hybridization; pericentromeric region
25.  Genetic variation for growth and selection in adult plants of Eucalyptus badjensis  
Genetics and Molecular Biology  2015;38(4):457-464.
Abstract
The aim of this study was to evaluate Eucalyptus badjensis concerning the genetic variation for growth traits and the potential of the species in supporting a breeding programme. The field trial was a provenance/progeny test established in Campina da Alegria, Santa Catarina, Brazil (latitude 26°52′05.1″ S, longitude 51°48′47.5″ W, altitude 1,015 m) in a soil classified as Latossolic Alumino-Ferric Brown Nitosol. The experiment comprised 60 open-pollinated progenies from the provenances Glenbog and Badja State Forest, New South Wales, Australia. Ten replicates and plots with six plants in row were used. At the age of 17 years, 279 trees were assessed for diameter of the bole at breast height (DBH), total tree height (H) and volume of wood with bark (Vol). After submitting the data to statistical genetic analysis, the overall means for DBH, H and Vol were 45.17 cm, 33.30 m and 2.84 m3, and the estimates of additive coefficient of variation [CV^a(%)] were 12.59%, 5.91% and 26.51%, respectively. Heritability coefficients of additive effects (h^a2) were also estimated and the following values were found: 0.443, 0.312 and 0.358. Thirty-nine trees from 25 different progenies were selected. The expected means of the provenances after improvement were 50.02 cm, 34.35 m and 3.47 m3 for DBH, H and Vol, respectively.
doi:10.1590/S1415-475738420150041
PMCID: PMC4763317  PMID: 26692156
eucalypt; progeny test; genetic parameters; breeding; genetic gain

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