Poly (A)(+) Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines

We report the first quantitative and qualitative analysis of the poly (A)(+) transcriptome of two human mammary cell lines, differentially expressing (human epidermal growth factor receptor) an oncogene over-expressed in approximately 25% of human breast tumors. Full-length cDNA populations from the two cell lines were digested enzymatically, individually tagged according to a customized method for library construction, and simultaneously sequenced by the use of the Titanium 454-Roche-platform. Comprehensive bioinformatics analysis followed by experimental validation confirmed novel genes, splicing variants, single nucleotide polymorphisms, and gene fusions indicated by RNA-seq data from both samples. Moreover, comparative analysis showed enrichment in alternative events, especially in the exon usage category, in ERBB2 over-expressing cells, data indicating regulation of alternative splicing mediated by the oncogene. Alterations in expression levels of genes, such as LOX, ATP5L, GALNT3, and MME revealed by large-scale sequencing were confirmed between cell lines as well as in tumor specimens with different ERBB2 backgrounds. This approach was shown to be suitable for structural, quantitative, and qualitative assessment of complex transcriptomes and revealed new events mediated by ERBB2 overexpression, in addition to potential molecular targets for breast cancer that are driven by this oncogene.

Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation

Background: Schizophrenia is likely to be a consequence of DNA alterations that, together with environmental factors, will lead to protein expression differences and the ultimate establishment of the illness. The superior temporal gyrus is implicated in schizophrenia and executes functions such as the processing of speech, language skills and sound processing. Methods: We performed an individual comparative proteome analysis using two-dimensional gel electrophoresis of 9 schizophrenia and 6 healthy control patients' left posterior superior temporal gyrus (Wernicke's area - BA22p) identifying by mass spectrometry several protein expression alterations that could be related to the disease. Results: Our analysis revealed 11 downregulated and 14 upregulated proteins, most of them related to energy metabolism. Whereas many of the identified proteins have been previously implicated in schizophrenia, such as fructose-bisphosphate aldolase C, creatine kinase and neuron-specific enolase, new putative disease markers were also identified such as dihydrolipoyl dehydrogenase, tropomyosin 3, breast cancer metastasis-suppressor 1, heterogeneous nuclear ribonucleoproteins C1/C2 and phosphate carrier protein, mitochondrial precursor. Besides, the differential expression of peroxiredoxin 6 (PRDX6) and glial fibrillary acidic protein (GFAP) were confirmed by western blot in schizophrenia prefrontal cortex. Conclusion: Our data supports a dysregulation of energy metabolism in schizophrenia as well as suggests new markers that may contribute to a better understanding of this complex disease.

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Background: Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus. Results: Two thousand six hundred and forty one single nucleotide polymorphisms ( SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. Conclusion: The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.

Renal hypothermia: Experience in pigs and clinical trial

Purpose: This study was designed to compare the effectiveness of two methods of inducing renal hypothermia through laparoscopy in pigs and humans. Materials and Methods: Twelve pigs were divided into four groups of three animals each. Both kidneys of the animals in Groups A, B, and C were submitted to pelvic irrigation with cold saline (4 degrees C) for 20 minutes, with flow rates of 5 mL/min, 10 mL/min, and 15 mL/min, respectively. In Group D renal hypothermia was induced by intracorporeal ice slush applied to the surface for 20 minutes. All maneuvers were performed laparoscopically and renal cortex temperature was measured by a thermocouple needle. Five human patients also underwent laparoscopic partial nephrectomy due to renal cell carcinoma. In one case renoprotection was induced by retrograde endoscopic cold saline perfusion at a flow rate of 10 mL/min. In the remaining four patients we induced renal hypothermia via laparoscopic application of ice slush. The renal temperature of the human patients was also monitored using a thermocouple needle. Results: In the pigs, at 20 minutes of renal pelvis perfusion the mean renal temperature, the temperature drop, and saline flow per gram of kidney were: Group A, -29.5 degrees C +/- 1.1 (-6.3 degrees C; 0.10 mL); Group B, -22.8 degrees C +/- 1.1 (-13.1 degrees C; 0.22 mL); and Group C, -21.1 degrees C +/- 0.9 (-14.9 degrees C; 0.31 mL). In Group D the mean renal cortex temperature at 20 minutes was 13.6 degrees C +/- 1.2, a drop of -22.5 degrees C. There were striking differences among the groups (P < 0.0001). The laparoscopic partial nephrectomy was uneventful in all five human patients. The lowest renal cortex temperature was 32.5 degrees C, seen in the patient who submitted to pelvic irrigation with cold saline, and the mean temperature drop was 19.1 degrees C +/- 2.5 degrees C in the patients who submitted to ice slush-induced renal hypothermia. Conclusions: Induction of renal hypothermia using intracorporeal ice slush confers lower kidney temperatures than endoscopically-induced cold saline perfusion.

DNA polymorphisms as tools for spinal cord injury research

Study Design: Data mining of single nucleotide polymorphisms (SNPs) in gene pathways related to spinal cord injury (SCI). Objectives: To identify gene polymorphisms putatively implicated with neuronal damage evolution pathways, potentially useful to SCI study. Setting: Departments of Psychiatry and Orthopedics, Faculdade de Medicina, Universidade de Sao Paulo, Brazil. Methods: Genes involved with processes related to SCI, such as apoptosis, inflammatory response, axonogenesis, peripheral nervous system development and axon ensheathment, were determined by evaluating the `Biological Process` annotation of Gene Ontology (GO). Each gene of these pathways was mapped using MapViewer, and gene coordinates were used to identify their polymorphisms in the SNP database. As a proof of concept, the frequency of subset of SNPs, located in four genes (ALOX12, APOE, BDNF and NINJ1) was evaluated in the DNA of a group of 28 SCI patients and 38 individuals with no SC lesions. Results: We could identify a total of 95 276 SNPs in a set of 588 genes associated with the selected GO terms, including 3912 nucleotide alterations located in coding regions of genes. The five non-synonymous SNPs genotyped in our small group of patients, showed a significant frequency, reinforcing their potential use for the investigation of SCI evolution. Conclusion: Despite the importance of SNPs in many aspects of gene expression and protein activity, these gene alterations have not been explored in SCI research. Here we describe a set of potentially useful SNPs, some of which could underlie the genetic mechanisms involved in the post trauma spinal cord damage.

Thermochronology of central Ribeira Fold Belt, SE Brazil: Petrological and geochronological evidence for long-term high temperature maintenance during Western Gondwana amalgamation

The studied sector of the central Ribeira Fold Belt (SE Brazil) comprises metatexites, diatexites, charnockites and blastomylonites. This study integrates petrological and thermochronological data in order to constrain the thermotectonic and geodynamic evolution of this Neoproterozoic-Ordovician mobile belt during Western Gondwana amalgamation. New data indicate that after an earlier collision stage at similar to 610 Ma (zircon, U-Pb age), peak metamorphism and lower crust partial melting, coeval with the main regional high grade D(1) thrust deformation, occurred at 572-562 Ma (zircon, U-Pb ages). The overall average cooling rate was low (<5 degrees C/Ma) from 750 to 250 degrees C (at similar to 455 Ma; biotite-WR Rb-Sr age), but disparate cooling paths indicate differential uplift between distinct lithotypes: (a) metatexites and blastomylonites show a overall stable 3-5 degrees C/Ma cooling rate; (b) charnockites and associated rocks remained at T>650 degrees C during sub-horizontal D(2) shearing until similar to 510-470 Ma (garnet-WR Sm-Nd ages) (1-2 degrees C/Ma), being then rapidly exhumed/cooled (8-30 degrees C/Ma) during post-orogenic D(3) deformation with late granite emplacement at similar to 490 Ma (zircon, U-Pb age). Cooling rates based on garnet-biotite Fe-Mg diffusion are broadly consistent with the geochronological cooling rates: (a) metatexites were cooled faster at high temperatures (6 degrees C/Ma) and slowly at low temperatures (0.1 degrees C/Ma), decreasing cooling rates with time; (b) charnockites show low cooling rates (2 degrees C/Ma) near metamorphic peak conditions and high cooling rates (120 degrees C/Ma) at lower temperatures, increasing cooling rates during retrogression. The charnockite thermal evolution and the extensive production of granitoid melts in the area imply that high geothermal gradients were sustained fora long period of time (50-90 Ma). This thermal anomaly most likely reflects upwelling of asthenospheric mantle and magma underplating coupled with long-term generation of high HPE (heat producing elements) granitoids. These factors must have sustained elevated crustal geotherms for similar to 100 Ma, promoting widespread charnockite generation at middle to lower crustal levels. (C) 2010 Elsevier B.V. All rights reserved.

Metamorphic P-T evolution of granulites in the central Ribeira Fold Belt, SE Brazil

Pseudosections, geothermobarometric estimates and careful petrographic observations of gneissic migmatites and granulites from Neoproterozoic central Ribeira Fold Belt (SE Brazil) were performed in order to quantify the metamorphic P-T conditions during prograde and retrograde evolution of the Brasiliano Orogeny. Results establish a prograde metamorphic trajectory from amphibolite facies conditions to metamorphic peak (T = 850 +/- 50 A degrees C; P = 8 +/- 1 kbar) that promoted widespread dehydrationmelting of 30 to 40% of the gneisses and high-grade granitization. After the metamorphic peak, migmatites evolved with cooling and decompression to T a parts per thousand 500 A degrees C and P a parts per thousand 5 kbar coupled with aH2O increase, replacing the high-grade paragenesis plagioclase-quartz-K-feldspar-garnet by quartz-biotite-sillimanite-(muscovite). Cordierite absence, microtextural observations and P-T results constrain the migmatite metamorphic evolution in the pseudosections as a clockwise P-T path with retrograde cooling and decompression. High-temperature conditions further dehydrated the lower crust with biotite and amphibole-dehydration melting and granulite formation coupled with 10% melt generation. Granulites can thus be envisaged as middle to lower crust dehydrated restites. Granulites were slowly (nearly isobarically) cooled, followed by late exhumation/retrograde rapid decompression and cooling, reflecting a two step P-T path. This retrograde evolution, coupled with water influx, chemically reequilibrated the rocks from granulite to amphibolite/greenschist facies, promoting the replacement of the plagioclase-quartz-garnet-hypersthene peak assemblage by quartz-biotite- K-feldspar symplectites.

P-T-Fluid evolution and graphite deposition during retrograde metamorphism in Ribeira Fold Belt, SE Brazil: Oxygen fugacity, fluid inclusions and C-O-H isotopic evidence

Combined fluid inclusion (FI) microthermometry, Raman spectroscopy, X-ray diffraction, C-O-H isotopes and oxygen fugacities of granulites from central Ribeira Fold Belt, SE Brazil, provided the following results: i) Magnetite-Hematite fO(2) estimates range from 10(-11.5) bar (QFM + 1) to 10(-18.3) bar (QFM - 1) for the temperature range of 896 degrees C-656 degrees C, implying fO(2) decrease from metamorphic peak temperatures to retrograde conditions; ii) 5 main types of fluid inclusions were observed: a) CO(2) and CO(2)-N(2) (0-11 mol%) high to medium density (1.01-0.59 g/cm(3)) FI; b) CO(2) and CO(2)-N(2) (0-36 mol%) low density (0.19-0.29 g/cm(3)) FI; c) CO(2) (94-95 mol%)-N(2) (3 mol%)-CH(4) (2-3 mol%)-H(2)O (water phi(v) (25 degrees C) = 0.1) FI; d) low-salinity H(2)O-CO(2) FI; and e) late low-salinity H(2)O FI; iii) Raman analyses evidence two graphite types in khondalites: an early highly ordered graphite (T similar to 450 degrees C) overgrown by a disordered kind (T similar to 330 degrees C); iv) delta(18)O quartz results of 10.3-10.7 parts per thousand, imply high-temperature CO(2) delta(18)O values of 14.4-14.8 parts per thousand, suggesting the involvement of a metamorphic fluid, whereas lower temperature biotite delta(18)O and delta D results of 7.5-8.5 parts per thousand and -54 to -67 parts per thousand respectively imply H(2)O delta(18)O values of 10-11 parts per thousand and delta D(H2O) of -23 to -36 parts per thousand suggesting delta(18)O depletion and increasing fluid/rock ratio from metamorphic peak to retrograde conditions. Isotopic results are compatible with low-temperature H(2)O influx and fO(2) decrease that promoted graphite deposition in retrograde granulites, simultaneous with low density CO(2), CO(2)-N(2) and CO(2)-N(2)-CH(4)-H(2)O fluid inclusions at T = 450-330 degrees C. Graphite delta(13)C results of -10.9 to -11.4 parts per thousand imply CO(2) delta(13)C values of -0.8 to -1.3 parts per thousand suggesting decarbonation of Cambrian marine carbonates with small admixture of lighter biogenic or mantle derived fluids. Based on these results, it is suggested that metamorphic fluids from the central segment of Ribeira Fold Belt evolved to CO(2)-N(2) fluids during granulitic metamorphism at high fO(2), followed by rapid pressure drop at T similar to 400-450 degrees C during late exhumation that caused fO(2) reduction induced by temperature decrease and water influx, turning carbonic fluids into CO(2)-H(2)O (depleting biotite delta(18)O and delta D values), and progressively into H(2)O. When fO(2) decreased substantially by mixture of carbonic and aqueous fluids, graphite deposited forming khondalites. (C) 2010 Elsevier Ltd. All rights reserved.

Distribution of ABCB1 polymorphisms among Brazilians: impact of population admixture

Introduction: Interethnic admixture is a source of cryptic population structure that may lead to spurious genotype-phenotype associations in pharmacogenomic studies. We studied the impact of population stratification on the distribution of ABCB1 polymorphisms (1236C > T, 2677G > T/A and 3435C > T) among Brazilians, a highly admixed population with Amerindian, European and African ancestral roots. Methods: Individual DNA from 320 healthy adults was genotyped with a panel of ancestry informative markers, and the proportions of African component of ancestry (ACA) were estimated. ABCB1 genotypes were determined by the single base extension/termination method. We describe the association between ABCB1 polymorphisms and ACA by fitting a linear proportional odds logistic regression model to the data. Results: The distribution of the ABCB1 2677G > T/A and 3435C > T, but not the 1236C > T, SNPs displayed a significant trend for decreasing frequency of the T alleles and TT genotypes from White to Intermediate to Black individuals. The same trend was observed in the frequency of the T/nonG/T haplotype at the 1236, 2677 and 3435 loci. When the population sample was proportioned in quartiles, according to the individual ACA estimates, the frequency of the T allele and TT genotype at each locus declined progressively from the lowest (< 0.25 ACA) to the highest (> 0.75 ACA) quartile. Linear proportional odds logistic regression analysis confirmed that the odds of having the T allele at each locus decreases in a continuous manner with the increase of the ACA, throughout the ACA range (0.13-0.94) observed in the overall population sample. A significant association was also detected between the individual ACA estimates and the presence of the T/nonG/T haplotype in the overall population. Conclusion: Self-identification according to the racial/color categories proposed by the Brazilian Census is insufficient to properly control for population stratification in pharmacogenomic studies of ABCB1.

Expression Profile of Rat Hippocampal Neurons Treated with the Neuroprotective Compound 2,4-Dinitrophenol: Up-Regulation of cAMP Signaling Genes

2,4-Dinitrophenol (DNP) is classically known as a mitochondrial uncoupler and, at high concentrations, is toxic to a variety of cells. However, it has recently been shown that, at subtoxic concentrations, DNP protects neurons against a variety of insults and promotes neuronal differentiation and neuritogenesis. The molecular and cellular mechanisms underlying the beneficial neuroactive properties of DNP are still largely unknown. We have now used DNA microarray analysis to investigate changes in gene expression in rat hippocampal neurons in culture treated with low micromolar concentrations of DNP. Under conditions that did not affect neuronal viability, high-energy phosphate levels or mitochondrial oxygen consumption, DNP induced up-regulation of 275 genes and down-regulation of 231 genes. Significantly, several up-regulated genes were linked to intracellular cAMP signaling, known to be involved in neurite outgrowth, synaptic plasticity, and neuronal survival. Differential expression of specific genes was validated by quantitative RT-PCR using independent samples. Results shed light on molecular mechanisms underlying neuroprotection by DNP and point to possible targets for development of novel therapeutics for neurodegenerative disorders.

Transcriptome analysis of Taenia solium cysticerci using Open Reading Frame ESTs (ORESTES)

Background: Human infection by the pork tapeworm Taenia solium affects more than 50 million people worldwide, particularly in underdeveloped and developing countries. Cysticercosis which arises from larval encystation can be life threatening and difficult to treat. Here, we investigate for the first time the transcriptome of the clinically relevant cysticerci larval form. Results: Using Expressed Sequence Tags (ESTs) produced by the ORESTES method, a total of 1,520 high quality ESTs were generated from 20 ORESTES cDNA mini-libraries and its analysis revealed fragments of genes with promising applications including 51 ESTs matching antigens previously described in other species, as well as 113 sequences representing proteins with potential extracellular localization, with obvious applications for immune-diagnosis or vaccine development. Conclusion: The set of sequences described here will contribute to deciphering the expression profile of this important parasite and will be informative for the genome assembly and annotation, as well as for studies of intra- and inter-specific sequence variability. Genes of interest for developing new diagnostic and therapeutic tools are described and discussed.

Proteomic analysis of dorsolateral prefrontal cortex indicates the involvement of cytoskeleton, oligodendrocyte, energy metabolism and new potential markers in schizophrenia

Schizophrenia is likely to be a consequence of serial alterations in a number of genes that, together with environmental factors, will lead to the establishment of the illness. The dorsolateral prefrontal cortex (Brodmann`s Area 46) is implicated in schizophrenia and executes high functions such as working memory, differentiation of conflicting thoughts, determination of right and wrong concepts, correct social behavior and personality expression. We performed a comparative proteome analysis using two-dimensional gel electrophoresis of pools from 9 schizophrenia and 7 healthy control patients` dorsolateral prefrontal cortex aiming to identify, by mass spectrometry, alterations in protein expression that could be related to the disease. In schizophrenia-derived samples, our analysis revealed 10 downregulated and 14 upregulated proteins. These included alterations previously implicated in schizophrenia, such as oligodendrocyte-related proteins (myelin basic protein and transferrin), as well as malate dehydrogenase, aconitase, ATP synthase subunits and cytoskeleton-related proteins. Also, six new putative disease markers were identified, including energy metabolism, cytoskeleton and cell signaling proteins. Our data not only reinforces the involvement of proteins previously implicated in schizophrenia, but also suggests new markers, providing further information to foster the comprehension of this important disease. (C) 2008 Elsevier Ltd. All rights reserved.

Lithium reduces Gsk3b mRNA levels: implications for Alzheimer Disease

There is evidence of increased systemic expression of active GSK3B in Alzheimer`s disease patients, which apparently is associated with the formation of senile plaques and neurofibrillary tangles. Due to its central role in the pathogenesis of AD, GSK3B is currently a promising target of the pharmaceutical industry. Whilst trials with specific GSK inhibitors in AD are under way, major attention has been focused on the neuroprotective effects of lithium. Whereas the direct and indirect inhibitory effects of lithium over GSK3 activity have been documented by several groups, its effects over Gsk3 transcription have not yet been addressed. We used quantitative PCR to evaluate the transcriptional regulation of Gsk3a and Gsk3b in lithium-treated primary cultures of rat cortical and hippocampal neurons. We found a significant and dose-dependent reduction in the expression of Gsk3b, which was specific to hippocampal cells. This same effect was further confirmed in vivo by measuring Gsk3 expression in different brain regions and in peripheral leukocytes of adult rats treated with lithium. Our studies show that LiCl can modulate Gsk3b transcription in vitro and in vivo. This observation suggest new regulatory effects of lithium over Gsk3b, contributing to the better understanding of its mechanisms of action, offering a new and complementary explanation for Gsk3b modulation and reinforcing its potential for the inhibition of key pathological pathways in Alzheimer`s disease.

Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: Preliminary evidence

An abnormality in neurodevelopment is one of the most robust etiologic hypotheses in schizophrenia (SZ). There is also strong evidence that genetic factors may influence abnormal neurodevelopment in the disease. The present study evaluated in SZ patients, whose brain structural data had been obtained with magnetic resonance imaging (MRI), the possible association between structural brain measures, and 32 DNA polymorphisms,located in 30 genes related to neurogenesis and brain development. DNA was extracted from peripheral blood cells of 25 patients with schizophrenia, genotyping was performed using diverse procedures, and putative associations were evaluated by standard statistical methods (using the software Statistical Package for Social Sciences - SPSS) with a modified Bonferroni adjustment. For reelin (RELN), a protease that guides neurons in the developing brain and underlies neurotransmission and synaptic plasticity in adults, an association was found for a non-synonymous polymorphism (Va1997Leu) with left and right ventricular enlargement. A putative association was also found between protocadherin 12 (PCDH12), a cell adhesion molecule involved in axonal guidance and synaptic specificity, and cortical folding (asymmetry coefficient of gyrification index). Although our results are preliminary, due to the small number of individuals analyzed, such an approach could reveal new candidate genes implicated in anomalous neurodevelopment in schizophrenia. (c) 2007 Elsevier Ireland Ltd. All rights reserved.

Pharmacogenetics of Warfarin: Development of a Dosing Algorithm for Brazilian Patients

A dosing algorithm including genetic (VKORC1 and CYP2C9 genotypes) and nongenetic factors (age, weight, therapeutic indication, and cotreatment with amiodarone or simvastatin) explained 51% of the variance in stable weekly warfarin doses in 390 patients attending an anticoagulant clinic in a Brazilian public hospital. The VKORC1 3673G>A genotype was the most important predictor of warfarin dose, with a partial R(2) value of 23.9%. Replacing the VKORC1 3673G>A genotype with VKORC1 diplotype did not increase the algorithm`s predictive power. We suggest that three other single-nucleotide polymorphisms (SNPs) (5808T>G, 6853G>C, and 9041G>A) that are in strong linkage disequilibrium (LD) with 3673G>A would be equally good predictors of the warfarin dose requirement. The algorithm`s predictive power was similar across the self-identified ""race/color"" subsets. ""Race/color"" was not associated with stable warfarin dose in the multiple regression model, although the required warfarin dose was significantly lower (P = 0.006) in white (29 +/- 13 mg/week, n = 196) than in black patients (35 +/- 15 mg/week, n = 76).