Comprehensive genome methylation and whole genome expression analysis in penile carcinoma: Uncovering new molecular markers

Background: Penile carcinoma (PeCa) is frequently associated with high morbidity rates. Unlikely of the vast majority of tumors, there is no molecular markers described that are able to assist in diagnosis and prognosis or with potential to be therapeutic targets in PeCa. Patients and methods: DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies) and large-scale expression analysis (4x44K Whole Human Genome Microarray, Agilent Technologies) were performed in 35 and 37 PeCa, respectively. Quantitative bisulfite pyrosequencing (qBP) and RT-qPCR were used to validate the findings in 93 samples. HPV status was assessed using the Linear Array HPV Genotyping kit (Roche Molecular Diagnostics, CA, USA). Results: Methylome analysis revealed 171 hypermethylated and 449 hypomethylated CpGs sites and the transcriptome profiling showed 2986 down- and 2817 over-expressed genes. HPV positivity was found in 32.7% of the cases, mainly the HPV16. The integrative analysis in 32 PeCa revealed a panel of 96 genes with inverse correlation between methylation and gene expression levels. The CpG hypermetlylation and gene downexpression, was confirmed for TWIST1, RSOP2, SOX3, SOX17, CD133, OTX2, HOXA3 and MEIS. In addition, BIRC5, DNMT1 and DNMT3B presented low levels of methylation and overexpression. The comparison of the results with clinical findings revealed that LIN28A, NKX2.2, NKX2.3, LHX5, BDNF, FOXA1 and CDX2 were associated with poor prognosis features. Conclusion: Putative prognostic markers were detected revealing that DNA methylation modulates the expression of several genes in PeCa. These data may prove instrumental for biomarker discovery in clinics and molecular epidemiology of PeCa.

Isotope analysis (δ 13c) of pulpy whole apple juice

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

Análise do consumo de extato hidrossolúvel de soja na qualidade do tecido ósseo de ratos jovens adultos

Pós-graduação em Ciência Animal - FMVA

Qualidade dos processos mecanizados de semeadura e colheita na cultura da soja

Pós-graduação em Agronomia (Produção Vegetal) - FCAV

Confidence in Communication: Can My Whole Class Achieve This?

In this action research study of my classroom of Algebra 2 students, I investigated the confidence levels and communication skills of these students. I discovered that students who have higher confidence levels are comfortable in their classroom situations. The students with increased levels of confidence also have more open communication with those they respect. As a result of this research, I plan to continue with the implementation of communication skills. I will also look to next school year as a place to start executing a plan to be more available and involved in the active learning process of my students.

G93-1167 Spider Mite Management in Corn and Soybeans

This NebGuide describes the two common spider mites found in Nebraska corn and soybeans, their natural enemies and management. Two species of spider mites, the Banks grass mite and twospotted spider mite, commonly feed on Nebraska corn. Banks grass mites (BGM) feed almost exclusively on grasses, including corn and sorghum. Twospotted spider mites (TSM) not only feed on many species of grasses, but also on soybeans, fruit trees and a variety of vegetables and ornamental plants. Although these two species are somewhat similar in appearance, they differ in several biological characteristics and in their susceptibility to pesticides. Banks grass mites usually appear earlier in the season, feed mostly on the lower leaves of the corn plant, and in Nebraska are moderately susceptible to many of the commonly used miticides. On the other hand, TSM tend to appear in mid to late season, increase rapidly, feed over the entire plant, and often are not consistently controlled by available pesticides.

Whole genome sequencing analysis of Plasmodium vivax using whole genome capture

Background: Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important human pathogen. Whole genome analysis methods on patient-derived material are thus likely to have a substantial impact on our understanding of P. vivax pathogenesis and epidemiology. For example, it will allow study of the evolution and population biology of the parasite, allow parasite transmission patterns to be characterized, and may facilitate the identification of new drug resistance genes. Because parasitemias are typically low and the parasite cannot be readily cultured, on-site leukocyte depletion of blood samples is typically needed to remove human DNA that may be 1000X more abundant than parasite DNA. These features have precluded the analysis of archived blood samples and require the presence of laboratories in close proximity to the collection of field samples for optimal pre-cryopreservation sample preparation. Results: Here we show that in-solution hybridization capture can be used to extract P. vivax DNA from human contaminating DNA in the laboratory without the need for on-site leukocyte filtration. Using a whole genome capture method, we were able to enrich P. vivax DNA from bulk genomic DNA from less than 0.5% to a median of 55% (range 20%-80%). This level of enrichment allows for efficient analysis of the samples by whole genome sequencing and does not introduce any gross biases into the data. With this method, we obtained greater than 5X coverage across 93% of the P. vivax genome for four P. vivax strains from Iquitos, Peru, which is similar to our results using leukocyte filtration (greater than 5X coverage across 96% of the genome). Conclusion: The whole genome capture technique will enable more efficient whole genome analysis of P. vivax from a larger geographic region and from valuable archived sample collections.

Contrasted crustal sources as defined by whole-rock and Sr-Nd-Pb isotope geochemistry of neoproterozoic early post-collisional granitic magmatism within the Southern Brazilian Shear Belt, Camboriu, Brazil

The early phase of post-collisional granitic magmatism in the Camboriu region, south Brazil, is represented by the porphyritic biotite +/- hornblende Rio Pequeno Granite (RPG; 630-620 Ma) and the younger (similar to 610 Ma), equigranular, biotite +/- muscovite Serra dos Macacos Granite (SMG). The two granite types share some geochemical characteristics, but the more felsic SMG constitutes a distinctive group not related to RPG by simple fractionation processes, as indicated by its lower FeOt, TiO2, K2O/Na2O and higher Zr Al2O3, Na2O, Ba and Sr when compared to RPG of similar SiO2 range. Sr-Nd-Pb isotopes require different sources. The SMG derives from old crustal sources, possibly related to the Paleoproterozoic protoliths of the Camboriu Complex, as indicated by strongly negative epsilon Nd-t (-23 to -24) and unradiogenic Pb (e.g., Pb-206/Pb-204 = 16.0-16.3; Pb-207/Pb-204 = 15.3-15.4) and confirmed by previous LA-MC-ICPMS data showing dominant zircon inheritance of Archean to Paleoproterozoic age. In contrast, the RPG shows less negative epsilon Nd-t (-12 to -15) and a distinctive zircon inheritance pattern with no traces of post-1.6 Ga sources. This is indicative of younger sources whose significance in the regional context is still unclear; some contribution of mantle-derived magmas is indicated by coeval mafic dykes and may account for some of the geochemical and isotopic characteristics of the least differentiated varieties of the RPG. The transcurrent tectonics seems to have played an essential role in the generation of mantle-derived magmas despite their emplacement within a low-strain zone. It may have facilitated their interaction with crustal melts which seem to be to a large extent the products of reworking of Paleoproterozoic orthogneisses from the Camboriu Complex. (C) 2012 Elsevier Ltd. All rights reserved.

Vasovagal reactions in whole blood donors at three REDS-II blood centers in Brazil

BACKGROUND: In Brazil little is known about adverse reactions during donation and the donor characteristics that may be associated with such events. Donors are offered snacks and fluids before donating and are required to consume a light meal after donation. For these reasons the frequency of reactions may be different than those observed in other countries. STUDY DESIGN AND METHODS: A cross-sectional study was conducted of eligible whole blood donors at three large blood centers located in Brazil between July 2007 and December 2009. Vasovagal reactions (VVRs) along with donor demographic and biometric data were collected. Reactions were defined as any presyncopal or syncopal event during the donation process. Multivariable logistic regression was performed to identify predictors of VVRs. RESULTS: Of 724,861 donor presentations, 16,129 (2.2%) VVRs were recorded. Rates varied substantially between the three centers: 53, 290, and 381 per 10,000 donations in Recife, Sao Paulo, and Belo Horizonte, respectively. Although the reaction rates varied, the donor characteristics associated with VVRs were similar (younger age [18-29 years], replacement donors, first-time donors, low estimated blood volume [EBV]). In multivariable analysis controlling for differences between the donor populations in each city younger age, first-time donor status, and lower EBV were the factors most associated with reactions. CONCLUSION: Factors associated with VVRs in other locations are also evident in Brazil. The difference in VVR rates between the three centers might be due to different procedures for identifying and reporting the reactions. Potential interventions to reduce the risk of reactions in Brazil should be considered.

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the similar to 12-Mb genome of CAT-1, when compared with the reference S228c genome, contains similar to 36,000 homozygous and similar to 30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.

Whole-rock geochemistry and Sr-Nd isotopic composition of the pre-rift sequence of the Camamu Basin, northeastern Brazil

Whole-rock geochemistry, combined with Sr-Nd isotopic composition of pelitic sedimentary rocks, have been considered to be useful parameters to estimate not only their provenance but also to make inferences about their depositional environment as well as the weathering processes they have been through. The basal sedimentary units of the basins of the northeastern Brazilian continental margin, particularly those of the pre-rift sequence, have been subject of interest of studies based on chemical and isotopic data, since they lack fossil content to establish their age and, therefore, stratigraphic correlations are difficult. The major and trace element contents as well as Sr-Nd isotopic compositions of whole-rock shale samples from five outcrops attributed to the pre-rift supersequence of the Camamu Basin were analyzed with the purpose of characterizing and obtaining further information that would allow a better correlation between the sites studied. The geochemical data suggest that the rocks exposed in the studied outcrops are part of the same sedimentary unit and that they might be correlated to the Capianga Member of the Alianca Formation of the Reconcavo Basin, exposed to the north of the Camamu Basin. The chemical index of alteration (CIA) suggests conditions associated with a humid tropical/subtropical climate at the time of deposition. Nd isotopic compositions indicate provenance from the Paleoproterozoic rocks of the Sao Francisco craton. The results presented here, therefore, show that the combined use of chemical and isotopic analyses may be of great interest to characterize and correlate lithologically homogeneous clastic sedimentary sequences. (C) 2012 Elsevier Ltd. All rights reserved.

Lipid and selenium sources on fatty acid composition of intramuscular fat and muscle selenium concentration of Nellore steers

The objective of this study was to evaluate the effect of lipid and selenium sources in diets for finishing Nellore steers on the fatty acid composition and selenium concentration of the longissimus muscle. Fifty Nellore steers (body weight = 458 +/- 39 kg) were assigned to one of six dietary treatments: 1) diet containing sunflower seed and inorganic selenium; 2) sunflower seed and organic selenium; 3) whole cottonseed and inorganic selenium; 4) whole cottonseed and organic selenium; 5) soybeans and inorganic selenium; and 6) soybeans and organic selenium. Diets were formulated with the same amount of nitrogen and calories and supplied once daily to steers in collective pens, with three animals per pen, for 120 d. At the end of the trial, steers were slaughtered and samples of the longissimus muscle were collected for fatty acid and selenium analysis. Effect of selenium sources was detected for selenium concentration in the longissimus muscle. Organic selenium had higher concentrations in the meat compared with inorganic selenium. The total saturated, monounsaturated and polyunsaturated fatty acids did not differ between the sources of lipids and selenium. For selenium sources, no differences were observed between the concentrations of polyunsaturated fat. Also, no differences in C18:2 cis-9 trans-11 concentrations were noted; however, steers fed sunflower seed presented greater proportions of this fatty acid in the meat. The results indicated that the use of sunflower seed, cottonseed or soybeans and organic or inorganic selenium in feedlot diets to Nellore cattle does not alter the great part of the fatty acid profile of the longissimus muscle. However, the inclusion of sunflower seed in the diet increases the meat CLA cis-9, trans-11, which is desirable and beneficial for the health of consumers.

Screening, immobilization and utilization of whole cell biocatalysts to mediate the ethanolysis of babassu oil

The screening. biomass growth of lipase-producing fungus isolated from different sources and available at URM (University Recife Mycologia). as well as, the immobilization and utilization of the whole cells for the transesterification of babassu oil were investigated. Rhizopus oryzae (URM 3231, 4692), Mucor circinelloides (URM 4140, 4182) and Penicillium citrinum URM 4216 were considered to be good intracellular lipase producers whereas those from Mucor hiemalis URM 4144 and Mucor piriformis URM 4145 were weaker. Fungi biomass containing high lipase activities was immobilized on different biomass support particles (BSPs) and with the exception of Penicillium citrinum URM 4216 all the other fungi strains exhibited high lipase activity (20-50 Ug(-1)) when immobilized in situ using polyurethane foam particles. Transesterification activities of the immobilized whole cells were evaluated in the ethanolysis reaction with babassu oil and the highest performance was attained by M. circinelloides URM 4182 giving 83.22 +/- 3.68% ester yield in less than 96 h reaction. The biocatalyst operational stability was also assessed and an inactivation profile was found to follow the Arrhenius model, revealing values of 26 days and 2.6 x 10(-2)day(-1), for half-life and a deactivation coefficient, respectively. The purified product (biodiesel) exhibited viscosity (6.63 cSt) close to the value to attend specifications by the ASTM 06751 to be used as biofuel. Results are favorable compared with data already reported in the literature and demonstrated that M. circinelloides URM 4182 whole cells is a cheaper biocatalyst that can be used in the biodiesel synthesis. (C) 2012 Elsevier B.V. All rights reserved.

Whole blood genome-wide gene expression profile in males after prolonged wakefulness and sleep recovery

Pellegrino R, Sunaga DY, Guindalini C, Martins RC, Mazzotti DR, Wei Z, Daye ZJ, Andersen ML, Tufik S. Whole blood genome-wide gene expression profile in males after prolonged wakefulness and sleep recovery. Physiol Genomics 44: 1003-1012, 2012. First published September 4, 2012; doi: 10.1152/physiolgenomics.00058.2012.-Although the specific functions of sleep have not been completely elucidated, the literature has suggested that sleep is essential for proper homeostasis. Sleep loss is associated with changes in behavioral, neurochemical, cellular, and metabolic function as well as impaired immune response. Using high-resolution microarrays we evaluated the gene expression profiles of healthy male volunteers who underwent 60 h of prolonged wakefulness (PW) followed by 12 h of sleep recovery (SR). Peripheral whole blood was collected at 8 am in the morning before the initiation of PW (Baseline), after the second night of PW, and one night after SR. We identified over 500 genes that were differentially expressed. Notably, these genes were related to DNA damage and repair and stress response, as well as diverse immune system responses, such as natural killer pathways including killer cell lectin-like receptors family, as well as granzymes and T-cell receptors, which play important roles in host defense. These results support the idea that sleep loss can lead to alterations in molecular processes that result in perturbation of cellular immunity, induction of inflammatory responses, and homeostatic imbalance. Moreover, expression of multiple genes was downregulated following PW and upregulated after SR compared with PW, suggesting an attempt of the body to re-establish internal homeostasis. In silico validation of alterations in the expression of CETN3, DNAJC, and CEACAM genes confirmed previous findings related to the molecular effects of sleep deprivation. Thus, the present findings confirm that the effects of sleep loss are not restricted to the brain and can occur intensely in peripheral tissues.