Low frequency of Y anomaly detected in Australian Brahman cow-herds

Indicine cattle have lower reproductive performance in comparison to taurine. A chromosomal anomaly characterized by the presence Y markers in females was reported and associated with infertility in cattle. The aim of this study was to investigate the occurrence of the anomaly in Brahman cows. Brahman cows (n = 929) were genotyped for a Y chromosome specific region using real time-PCR. Only six out of 929 cows had the anomaly (0.6%). The anomaly frequency was much lower in Brahman cows than in the crossbred population, in which it was first detected. It also seems that the anomaly doesn't affect pregnancy in the population. Due to the low frequency, association analyses couldn't be executed. Further, SNP signal of the pseudoautosomal boundary region of the Y chromosome was investigated using HD SNP chip. Pooled DNA of non-pregnant and pregnant cows were compared and no difference in SNP allele frequency was observed. Results suggest that the anomaly had a very low frequency in this Australian Brahman population and had no effect on reproduction. Further studies comparing pregnant cows and cows that failed to conceive should be executed after better assembly and annotation of the Y chromosome in cattle.

Efeito da utilização de diferentes critérios de controle de qualidade dos genótipos em estudos de associação e seleção genômica ampla

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Application of ionospheric corrections in the equatorial region for L1 GPS users

In the absence of the selective availability, which was turned off on May 1, 2000, the ionosphere can be the largest source of error in GPS positioning and navigation. Its effects on GPS observable cause a code delays and phase advances. The magnitude of this error is affected by the local time of the day, season, solar cycle, geographical location of the receiver and Earth's magnetic field. As it is well known, the ionosphere is the main drawback for high accuracy positioning, when using single frequency receivers, either for point positioning or relative positioning of medium and long baselines. The ionosphere effects were investigated in the determination of point positioning and relative positioning using single frequency data. A model represented by a Fourier series type was implemented and the parameters were estimated from data collected at the active stations of RBMC (Brazilian Network for Continuous Monitoring of GPS satellites). The data input were the pseudorange observables filtered by the carrier phase. Quality control was implemented in order to analyse the adjustment and to validate the significance of the estimated parameters. Experiments were carried out in the equatorial region, using data collected from dual frequency receivers. In order to validate the model, the estimated values were compared with ground truth. For point and relative positioning of baselines of approximately 100 km, the values of the discrepancies indicated an error reduction better than 80% and 50% respectively, compared to the processing without the ionospheric model. These results give an indication that more research has to be done in order to provide support to the L1 GPS users in the Equatorial region.

RINEX_HO: second- and third-order ionospheric corrections for RINEX observation files

When GNSS receivers capable of collecting dual-frequency data are available, it is possible to eliminate the first-order ionospheric effect in the data processing through the ionosphere-free linear combination. However, the second- and third-order ionospheric effects still remain. The first-, second- and third-order ionospheric effects are directly proportional to the total electron content (TEC), although the second- and third-order effects are influenced, respectively, by the geomagnetic field and the maximum electron density. In recent years, the international scientific community has given more attention to these kinds of effects and some works have shown that for high precision GNSS positioning these effects have to be taken into consideration. We present a software tool called RINEX_HO that was developed to correct GPS observables for second- and third-order ionosphere effects. RINEX_HO requires as input a RINEX observation file, then computes the second- and third-order ionospheric effects, and applies the corrections to the original GPS observables, creating a corrected RINEX file. The mathematical models implemented to compute these effects are presented, as well as the transformations involving the earth's magnetic field. The use of TEC from global ionospheric maps and TEC calculated from raw pseudorange measurements or pseudoranges smoothed by phase is also investigated.

Haptoglobin polymorphism correlated with coronary artery disease

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Allelic Frequencies of HPA-1 to 5 Human Platelet Antigens in Patients Infected With Hepatitis C Virus

Studies have suggested that hepatitis C virus (HCV) may infect not only hepatocytes but may also be carried by platelets. Platelets express more than 20 polymorphic antigenic determinants on their surface, which are called human platelet antigens (HPA), To determine the allele frequency of the HPA-1 to -5 in patients infected with HCV, blood samples were collected from 257 blood donors for the control group and from 191 patients infected with HCV. DNA was isolated and amplified for genes HPA-1 to -4 using PCR Sequence Specific Primers (PCR-SSP) and HPA-5 using PCR-Restriction Fragment Length Polymorphism (PCR-RFLP). The allelic and genotypic frequency of HPA-5a in patients infected with HCV was found to be significantly lower(P < 0.05) than in the controls, and HPA-5b from patients infected with HCV was significantly higher (P < 0.05) than in controls. The increase in HPA5b allelic frequency in HCV infection may indicate a possible association between HCV infection and HPAs. J. Med. Virol. 81:757-759, 2009. (C) 2009 Wiley-Liss, Inc.

Candidate SNPs for carcass and meat traits in Nelore animals and in their crosses with Bos taurus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hierarchical status and colour preference in Nile tilapia (Oreochromis niloticus)

We studied the colour preference of isolated Nile tilapia (Oreochromis niloticus) and whether previous residence or body size can affect environmental colour choice. In the first phase, a cylindrical tank was divided into five differently coloured compartments (yellow, blue, green, white and red), a single fish was introduced into the tank and the frequency at which this fish visited each compartment was recorded over a 2-day study period. An increasingly larger fish (approx +2 cm in length each time) was then added into the tank on each of days 3, 5 and 7 (=four fish in the tank by day 7), and the frequency at which each fish visited the different compartments of the tank was observed twice a day to obtain visit frequency data on the differently sized fishes. This experiment was replicated six times. In the first phase, the solitary fish established residence inside the yellow compartment on the first and second days. Following the introduction of a larger fish, the smaller fish was displaced from the occupied compartment. Nile tilapia possibly shows this preference for yellow as a function of its visual spectral sensitivity and/or the spectral characteristics of its natural environment. Moreover, body size is an important factor in determining hierarchical dominance and territorial defence, and dominant fish chose the preferred environmental colour compartment as their territory.

Population structure and stock assessment of Hoplias malabaricus (Characiformes: Erythrinidae) caught by artisanal fishermen in river-reservoir transition area in Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Association of matrix metalloproteinase-8 gene variation with breast cancer prognosis

Animal and cell studies indicate an inhibitory effect of matrix metalloproteinase-8 (MMP8) on tumorigenesis and metastasis. We investigated whether MMP8 gene variation was associated with breast cancer metastasis and prognosis in humans. We first studied nine tagging single nucleotide polymorphisms (SNP) in the MMP8 gene in 140 clinically and pathologically well-characterized breast cancer patients. Four of the SNPs were found to be associated with lymph node metastasis, the most pronounced being a promoter SNP (rs11225395) with its minor allele (T) associating with reduced susceptibility to lymph node metastasis (P = 0.02). This SNP was further evaluated for association with cancer relapse and survival among a cohort of similar to 1,100 breast cancer patients who had been followed for cancer recurrence and mortality for a median of 7.1 years. The T allele was associated with reduced cancer relapse and greater survival, particularly among patients with earlier stage cancer. Among patients of tumor-node-metastasis stage 0 to 11, the adjusted hazard ratio of disease-free survival was 0.7 [95% confidence interval (95% CI), 0.5-0.9] for patients carrying T allele compared with those homozygous for the C allele (P = 0.02). In vitro experiments showed that the T allele had higher promoter activity than the C allele in breast cancer cells. Electrophoretic mobility shift assays showed binding of nuclear proteins to the DNA sequence at the SNP site of the T allele but not that of the C allele. The data suggest that MMP8 gene variation may influence breast cancer prognosis and support the notion that MMP8 has an inhibitory effect on cancer metastasis.

Taxas de cruzamento em uma população natural de Cryptocarya Moschata Nees (Lauraceae)

O sistema de cruzamento da espécie arbórea de dossel da Mata Atlântica brasileira, Cryptocarya moschata, foi estudado a partir de material proveniente do Parque Estadual Carlos Botelho, São Miguel Arcanjo, São Paulo, Brasil. As taxas de cruzamento foram determinadas através de marcadores alozímicos obtidos de plântulas germinadas de coortes de sementes coletadas de 35 árvores. O valor médio da taxa de cruzamento de equilíbrio (estimador indireto) foi t^eq = 0.51. As estimativas das taxas de cruzamento uniloco e multilocos (estimadores diretos) foram t^s = 0.725± 0,041 e t^m = 0,884 ± 0,034, respectivamente, indicando um sistema de cruzamento predominantemente alogâmico. As taxas de cruzamento de árvores individuais variaram de 27 a 100 ( x¯ = 87,8) porcento, a partir de t^m calculado com as freqüências gênicas de pólen mantidas constantes ao nível populacional. A partir do modelo de par de irmãos (modelo de cruzamento correlacionado) de Ritland, a correlação entre duas progênies irmãs oriundas de autofecundação (r^s) e a correlação entre duas progênies irmãs oriundas de paternidade por exocruzamento (r^p) foram 35,7% e 99,0%, respectivamente. Esses resultados corroboram o fato de haver variação nas taxas de autocruzamento entre as diferentes árvores, podendo também indicar que quando há endogamia, a maior parte das sementes nas árvores são provavelmente irmãs-germanas.

Structure and genetic relationships between Brazilian naturalized and exotic purebred goat domestic goat (Capra hircus) breeds based on microsatellites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Locus no cromossomo 19 influencia positivamente o número de oócitos recuperados em ciclos estimulados

Objective: To evaluate if identified loci associated with normal age of menopause variation and early menopause can account for the poor response to controlled ovarian stimulation. Methods: A total of 71 patients, with age ≤ 35 years old, undergoing intracytoplasmic sperm injection were tested for three of the four newly identified genetic variants associated with normal variation in menopausal age and early menopause. Patients were divided into two groups: poor responder group (PR group, n=21) and normoresponder group (NR group, n=50). The influence of risk allele frequency on the response to controlled ovarian stimulation (COS) was evaluated. Logistic regression models were used. Results: There was no significant difference in the incidence of the genetic variants between NR and PR group. The risk allele for chromosome 19 variant (rs4806660) demonstrated a protective effect. The presence of a risk allele, either in homozygosis or in heterozygosis, was associated with an increased response to COS, resulting in an elevated number of follicles (Coef: 2.54, P= 0.041) and retrieved oocytes (Coef: 1.41, P= 0.041). Conclusions: Genetic variants rs244715, rs9379896 and rs4806660 are not risk factors for poor ovarian response. Instead, rs4806660 is associated with higher number of follicles and retrieved oocytes. It could be hypothesized that rs4806660 is associated with an increased response to gonadotrophin stimulus. © Todos os direitos reservados a SBRA - Sociedade Brasileira de Reprodução Assistida.

European Ancestry Predominates in Neuromyelitis Optica and Multiple Sclerosis Patients from Brazil

Background: Neuromyelitis optica (NMO) is considered relatively more common in non-Whites, whereas multiple sclerosis (MS) presents a high prevalence rate, particularly in Whites from Western countries populations. However, no study has used ancestry informative markers (AIMs) to estimate the genetic ancestry contribution to NMO patients. Methods: Twelve AIMs were selected based on the large allele frequency differences among European, African, and Amerindian populations, in order to investigate the genetic contribution of each ancestral group in 236 patients with MS and NMO, diagnosed using the McDonald and Wingerchuck criteria, respectively. All 128 MS patients were recruited at the Faculty of Medicine of Ribeirão Preto (MS-RP), Southeastern Brazil, as well as 108 healthy bone marrow donors considered as healthy controls. A total of 108 NMO patients were recruited from five Neurology centers from different Brazilian regions, including Ribeirão Preto (NMO-RP). Principal Findings: European ancestry contribution was higher in MS-RP than in NMO-RP (78.5% vs. 68.7%) patients. In contrast, African ancestry estimates were higher in NMO-RP than in MS-RP (20.5% vs. 12.5%) patients. Moreover, principal component analyses showed that groups of NMO patients from different Brazilian regions were clustered close to the European ancestral population. Conclusions: Our findings demonstrate that European genetic contribution predominates in NMO and MS patients from Brazil. © 2013 Brum et al.

Isolation and characterization of SNPs within HSC70 gene in the freshwater prawn Macrobrachium amazonicum

We report the discovery of 13 synonymous single nucleotide polymorphisms (SNPs) within a fragment of HSC70 gene in Macrobrachium amazonicum. Polymorphisms were assessed using the reference sequence of the HSC70 gene in Macrobrachium rosenbergii to the primers design. The minor allele frequency ranged from 0.011 to 0.213. None of the SNPs deviated significantly from Hardy-Weinberg equilibrium. These SNPs will be useful to access the genetic variation of populations and to the study of their relations with characteristics of interest for aquaculture. Both cases, favoring the conservation of the natural stocks of Amazon river prawn. © 2013 Springer Science+Business Media Dordrecht.