MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study

Background  

The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quantify the importance of multi-SNP interactions, few of them could handle the genome wide data due to the combinatorial explosive search space and the difficulty to statistically evaluate the high-order interactions given limited samples.     

Social Networks Shape the Transmission Dynamics of Hepatitis C Virus

Hepatitis C virus (HCV) infects 170 million people worldwide, and is a major public health problem in Brazil, where over 1% of the population may be infected and where multiple viral genotypes co-circulate. Chronically infected individuals are both the source of transmission to others and are at risk for HCV-related diseases, such as liver cancer and cirrhosis. Before the adoption of anti-HCV control measures in blood banks, this virus was mainly transmitted via blood transfusion. Today, needle sharing among injecting drug users is the most common form of HCV transmission. Of particular importance is that HCV prevalence is growing in non-risk groups. Since there is no vaccine against HCV, it is important to determine the factors that control viral transmission in order to develop more efficient control measures. However, despite the health costs associated with HCV, the factors that determine the spread of virus at the epidemiological scale are often poorly understood. Here, we sequenced partial NS5b gene sequences sampled from blood samples collected from 591 patients in São Paulo state, Brazil. We show that different viral genotypes entered São Paulo at different times, grew at different rates, and are associated with different age groups and risk behaviors. In particular, subtype 1b is older and grew more slowly than subtypes 1a and 3a, and is associated with multiple age classes. In contrast, subtypes 1a and 3b are associated with younger people infected more recently, possibly with higher rates of sexual transmission. The transmission dynamics of HCV in São Paulo therefore vary by subtype and are determined by a combination of age, risk exposure and underlying social network. We conclude that social factors may play a key role in determining the rate and pattern of HCV spread, and should influence future intervention policies.     

Maintenance of pluripotency in mouse embryonic stem cells cultivated in stirred microcarrier cultures

The development of efficient and reproducible culture systems for embryonic stem (ES) cells is an essential pre‐requisite for regenerative medicine. Culture scale‐up ensuring maintenance of cell pluripotency is a central issue, because large amounts of pluripotent cells must be generated to warrant that differentiated cells deriving thereof are transplanted in great amounts and survive the procedure. This study aimed to develop a robust scalable cell expansion system, using a murine embryonic stem cell line that is feeder‐dependent and adapted to serum‐free medium, thus representing a more realistic model for human ES cells. We showed that high concentrations of murine ES cells can be obtained in stirred microcarrier‐based spinner cultures, with a 10‐fold concentration of cells per volume of medium and a 5‐fold greater cell concentration per surface area, as compared to static cultures. No differences in terms of pluripotency and differentiation capability were observed between cells grown in traditional static systems and cells that were replated onto the traditional system after being expanded on microcarriers in the stirred system. This was verified by morphological analyses, quantification of cells expressing important pluripotency markers (Oct‐4, SSEA‐1, and SOX2), karyotype profile, and the ability to form embryoid bodies with similar sizes, and maintaining their intrinsic ability to differentiate into all three germ layers. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Mucopolysaccharidosis I, II, and VI: Brief review and guidelines for treatment

Mucopolysaccharidoses (MPS) are rare genetic diseases caused by the deficiency of one of the lysosomal enzymes involved in the glycosaminoglycan (GAG) breakdown pathway. This metabolic block leads to the accumulation of GAG in various organs and tissues of the affected patients, resulting in a multisystemic clinical picture, sometimes including cognitive impairment. Until the beginning of the XXI century, treatment was mainly supportive. Bone marrow transplantation improved the natural course of the disease in some types of MPS, but the morbidity and mortality restricted its use to selected cases. The identification of the genes involved, the new molecular biology tools and the availability of animal models made it possible to develop specific enzyme replacement therapies (ERT) for these diseases. At present, a great number of Brazilian medical centers from all regions of the country have experience with ERT for MPS I, II, and VI, acquired not only through patient treatment but also in clinical trials. Taking the three types of MPS together, over 200 patients have been treated with ERT in our country. This document summarizes the experience of the professionals involved, along with the data available in the international literature, bringing together and harmonizing the information available on the management of these severe and progressive diseases, thus disclosing new prospects for Brazilian patients affected by these conditions.     

Diversity of lactic acid bacteria of the bioethanol process

Background  

Bacteria may compete with yeast for nutrients during bioethanol production process, potentially causing economic losses. This is the first study aiming at the quantification and identification of Lactic Acid Bacteria (LAB) present in the bioethanol industrial processes in different distilleries of Brazil.     

DNA sequencing of 13 cytokine gene fragments of Aotus infulatus and Saimiri sciureus, two non-human primate models for malaria

Aotus and Saimiri are non-human primate models recommended by the World Health Organization for experimental studies in malaria, especially for vaccine pre-clinical trials. However, research using these primates is hindered by the lack of specific reagents to evaluate immune responses to infection or vaccination. As a step toward developing molecular tools for cytokine expression studies in these species, primer pairs for 18 cytokine gene fragments were designed based on human DNA sequences and used to amplify the corresponding genes in Aotus infulatus and Saimiri sciureus genomic DNA samples. IFNγ, TNFα, LTA, IL2, IL3, IL4, IL5, IL6, IL10, IL12, IL13, CSF2 and TGFβ2 gene fragments were amplified and sequenced. Primer pairs for IL8, IL17, IL18, IL27 and MIF failed to generate amplification products. When compared to the available corresponding human and non-human primate sequences, most--except IL3 and IL4--showed identity degrees above 90%. Small variations in sequence can help to explain the failure to amplify certain genes or the amplification only at lower annealing temperatures as compared to human DNA samples for several primer pairs. The sequences made available provide the basis for designing molecular tools such as primers for real time PCR specific for A. infulatus and/or S. sciureus. The nucleotide sequences reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned accession numbers DQ985386 to DQ985389, DQ989356 to DQ989369, FJ89020 to FJ89024, and FJ89029.     

Paleogenetic and taphonomic analysis of human bones from Moa, Beirada, and Zé Espinho Sambaquis, Rio de Janeiro, Brazil

The present paper discusses mtDNA and taphonomy of human remains from Moa, Beirada, and Zé Espinho sambaquis of Saquarema, state of Rio de Janeiro, Brazil. New human bone dating by 14C-AMS for Moa archeological site (3810+50 BP - GX-31826-AMS) is included. Preservation of microscopic lamellae and DNA is not related to the macroscopic integrity of the bones. Results here suggest that the preservation of amplifiable DNA fragments may have relation to the preservation of the lamellar arrangement as indicated by optical microscopic examination (polarized light). In 13 human bone fragments from Moa, Beirada, and Zé Espinho it was possible to sequence mtDNA from the 3 individuals of Moa, and from 1 of 4 individuals of Beirada, whose bones also show extensive areas with preserved lamellar structures. The 6 human bone fragments of Zé Espinho and 3 of the 4 fragments of Beirada showed extensive destruction of cortical microstructure represented by cavities, intrusive minerals, and agglomerated microscopic bodies of fungi and bacteria; it was not possible to extract mtDNA from these samples. The results support the hypothesis that the preservation of the microscopic osteon organization is a good predictor for DNA preservation. It was also confirmed the C haplogroup antiquity in Brazil.     

Antitumor Activity of the Essential Oil from the Leaves of Croton regelianus and Its Component Ascaridole

Croton regelianus Muell. Arg. , popularly known as ‘velame‐de‐cheiro’, is a native plant from the Northeast of Brazil used in folk medicine to treat diseases of different kinds, including malignant tumors. In this study, the in vitro and in vivo antitumor effects of the essential oil from the leaves of C. regelianus and ascaridole, one of the main constituents, were investigated. In vitro, the essential oil and ascaridole displayed cytotoxicity, showing IC₅₀ values in the range of 22.2 to 48.0 μg/ml in HL‐60 and SF‐295 cell lines for the essential oil, and 6.3 to 18.4 μg/ml in HL‐60 and HCT‐8 cells lines for ascaridole, respectively. The in vivo study, using sarcoma 180 as a tumor model, demonstrated inhibition rates of 28.1 and 31.8% for essential oil, at the 50 and 100 mg/kg, while ascaridole inhibition rates were 33.9% at 10 mg/kg and 33.3% at 20‐mg/kg doses. Histopathological examination showed that the organs were only weakly affected by the treatment. In conclusion, ascaridole has an interesting antitumor activity in sarcoma 180 murine model, probably related to the described cytotoxic activity, and, moreover, its presence in the essential oil from the leaves of C. regelianus could explain, at least in part, the ethnopharmacological use of this plant in the treatment of cancer.     

Distinct Merkel Cell Polyomavirus Molecular Features in Tumour and Non Tumour Specimens from Patients with Merkel Cell Carcinoma

Merkel Cell Polyomavirus (MCPyV) is associated with Merkel Cell carcinoma (MCC), a rare, aggressive skin cancer with neuroendocrine features. The causal role of MCPyV is highly suggested by monoclonal integration of its genome and expression of the viral large T (LT) antigen in MCC cells. We investigated and characterized MCPyV molecular features in MCC, respiratory, urine and blood samples from 33 patients by quantitative PCR, sequencing and detection of integrated viral DNA. We examined associations between either MCPyV viral load in primary MCC or MCPyV DNAemia and survival. Results were interpreted with respect to the viral molecular signature in each compartment. Patients with MCC containing more than 1 viral genome copy per cell had a longer period in complete remission than patients with less than 1 copy per cell (34 vs 10 months, P = 0.037). Peripheral blood mononuclear cells (PBMC) contained MCPyV more frequently in patients sampled with disease than in patients in complete remission (60% vs 11%, P = 0.00083). Moreover, the detection of MCPyV in at least one PBMC sample during follow-up was associated with a shorter overall survival (P = 0.003). Sequencing of viral DNA from MCC and non MCC samples characterized common single nucleotide polymorphisms defining 8 patient specific strains. However, specific molecular signatures truncating MCPyV LT were observed in 8/12 MCC cases but not in respiratory and urinary samples from 15 patients. New integration sites were identified in 4 MCC cases. Finally, mutated-integrated forms of MCPyV were detected in PBMC of two patients with disseminated MCC disease, indicating circulation of metastatic cells. We conclude that MCPyV molecular features in primary MCC tumour and PBMC may help to predict the course of the disease.     

Distribution and population structure of four Central Amazonian high-várzea timber species

Amazonian white-water (várzea) floodplains harbor many commercially important timber species which in Brazil are harvested following regulations of the Federal Environmental Agency (IBAMA). Although it is well-known that tree physiology, growth, and species distribution of Amazonian floodplain trees is linked to the heights and durations of the periodical inundations, information about timber stocks and population dynamics is lacking for most tree species. We investigated timber stocks and the population structure of four intensely logged tree species in a western Brazilian várzea forest on an area totaling 7.5 ha. Spatial distribution was investigated in all trees as a function of inundation height and duration and the distance to the river channel, and additionally for saplings (trees <10 cm diameter at breast height––DBH) as a function of the relative photosynthetically active radiation (rPAR). The diameter-class distribution in Hura crepitans and Ocotea cymbarum indicated that populations are subject to density variations that possibly are traced to small-scale flood variability. In all species, saplings concentrated at higher topographic elevations than the mature tree populations, which suggest that the physical ‘escape’ from a flooded environment is an important acclimation to flooding. While Ocotea cymbarum and Guarea guidonia were high-density wood species characterized by random dispersion and a pronounced shade-tolerance, Hura crepitans and Sterculia apetala presented lower wood density, aggregated dispersion, and were more light-demanding. All species presented exploitable stems according to the current harvest regulations, with elevated abundances in comparison to other Amazonian forest types. However, stem densities are below the harvest rates indicating that the harvest regulations are not sustainable. We recommend that the forest management in várzea forests should include specific establishment rates of timber species in dependence of the peculiar site conditions to achieve sustainability.