SERVIÇOS E PRODUTOS DO SIBi/USP: descrição dos processos essenciais, gerenciais e de apoio

O Modelo de Gestão do Sistema Integrado de Bibliote cas da Universidade de São Paulo (SIBi/USP) incorpora conceitos e ferramentas de ger enciamento que permeiam as organizações modernas para garantir melhores índice s de desempenho sistêmico e prestar serviços com qualidade e eficiência aos usuários. C omo parte do Modelo está a identificação e a descrição detalhada dos processos de trabalho do Sistema, assim como o estabelecimento de alguns indicadores de desempenho . A partir do trabalho inicial, foi elaborado um levantamento complementar para identif icação dos processos que abrangessem o conjunto do Sistema de forma ampla. O s dados foram dispostos em planilhas para melhor visualização, especialmente q uanto aos macro processos, processos, sub processos e atividades. Os processos foram sepa rados em essenciais, gerenciais e de apoio, além de elencadas as atividades pertinentes a cada um deles, bem como as instruções técnicas e fluxos de trabalho. Foram est abelecidos alguns indicadores, tendo por referência os da IFLA já estudados por outro Grupo de Trabalho. Daquele estudo quatro indicadores foram testados e validados pelo SIBi/US P por meio de aplicação piloto em algumas das Bibliotecas do Sistema e outros foram d efinidos no estudo atual. Com isso foi possível mapear os processos e as atividades desenv olvidas pelo conjunto de Bibliotecas sendo que cada Biblioteca, em função de sua especia lidade e especificidade pode adequar o seu mapeamento. A definição de um núcleo básico d e indicadores objetiva viabilizar a concretização da missão e dos objetivos em consonân cia com a política do SIBI/USP

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.

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.

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.

Petrogenesis of syntectonic granites emplaced at the transition from thrusting to transcurrent tectonics in post-collisional setting: Whole-rock and Sr-Nd-Pb isotope geochemistry in the Neoproterozoic Quatro Ilhas and Mariscal Granites, Southern Brazil

The Neoproterozoic post-collisional period in southern Brazil (650-580 Ma) is characterized by substantial volumes of magma emplaced along the active shear zones that compose the Southern Brazilian Shear Belt. The early-phase syntectonic magmatism (630-610 Ma) is represented by the porphyritic, high-K, metaluminous to peraluminous Quatro Ilhas Granitoids and the younger heterogranular, slightly peraluminous Mariscal Granite. Quatro II has Granitoids include three main petrographic varieties (muscovite-biotite granodiorite mbg; biotite monzogranite - bmz: and leucogranite - lcg) that, although sharing some significant geochemical characteristics, are not strictly comagmatic, as shown by chemical and Sr-Nd-Pb isotope data. The most primitive muscovite-biotite granodiorite was produced by contamination of more mafic melts (possibly with some mantle component) with peraluminous crustal melts; the biotite monzogranite, although more felsic, has higher Ca, MgO,TiO2 and Ba, and lower K2O, FeOt, Sr and Rb contents, possibly reflecting some mixing with coeval mafic magmas of tholeiitic affinity; the leucogranite may be derived from pure crustal melts. The Mariscal Granite is formed by two main granite types which occur intimately associated in the same pluton, one with higher K (5-6.5 wt.% K2O) high Rb and lower CaO, Na2O, Ba and Zr as compared to the other (3-5 wt.% of K2O). The two Mariscal Granite varieties have compositional correspondence with fine-grained granites (fgg) that occur as tabular bodies which intruded the Quatro Ilhas Granoitoids before they were fully crystallized, and are inferred to correspond to the Mariscal Granite feeders, an interpretation that is reinforced by similar U-Pb zircon crystallization ages. The initial evolution of the post-collisional magmatism, marked by the emplacement of the Quatro Ilhas Granitoids varieties, activated sources that produced mantle and crustal magmas whose emplacement was controlled both by flat-lying and transcurrent structures. The transition from thrust to transcurrent-related tectonics coincides with the increase in the proportion of crustal-derived melts. The transcurrent tectonics seems to have played an essential role in the generation of mantle-derived magmas and may have facilitated their interaction with crustal melts which seem to be to a large extent the products of reworking of orthogneiss protoliths. (C) 2012 Elsevier B.V. All rights reserved.

Determination of Opiates in Whole Blood and Vitreous Humor: A Study of the Matrix Effect and an Experimental Design to Optimize Conditions for the Enzymatic Hydrolysis of Glucuronides

Faculty of Medicine University of Sao Paulo

Stereoselective Bioreduction of 1-(4-Methoxyphenyl)ethanone by Whole Cells of Marine-Derived Fungi

Nine strains of marine-derived fungi (Aspergillus sydowii Ce15, A. sydowii Ce19, Aspergillus sclerotiorum CBMAI 849, Bionectria sp. Ce5, Beauveria felina CBMAI 738, Cladosporium cladosporioides CBMAI 857, Mucor racemosus CBMAI 847, Penicillium citrinum CBMAI 1186, and Penicillium miczynskii Gc5) were screened, catalyzing the asymmetric bioreduction of 1-(4-methoxyphenyl) ethanone 1 to its corresponding 1-(4-methoxyphenyl) ethanol 2. A. sydowii Ce15 and Bionectria sp. Ce5 produced the enantiopure (R)-alcohol 2 (>99% ee) in accordance with the anti-Prelog rule and, the fungi B. felina CBMAI 738 (>99% ee) and P. citrinum CBMAI 1186 (69% ee) in accordance with the Prelog rule. Stereoselective bioreduction by whole cells of marine-derived fungi described by us is important for the production of new reductases from marine-derived fungi.

Whole-body computerized tomography and concomitant spine and head injuries A study of 355 cases

The authors present a prospective study on the coexistence of spinal injury (SI) and severe traumatic brain injury (TBI) in patients who were involved in traffic accidents and arrived at the Emergency Department of Hospital das Clinicas of the University of Sao Paulo between September 1, 2003 and December 31, 2009. A whole-body computed tomography was the diagnostic method employed in all cases. Both lesions were observed simultaneously in 69 cases (19.4%), predominantly in males (57 individuals, 82.6%). Cranial injuries included epidural hematoma, acute subdural hematoma, brain contusion, ventricular hemorrhage and traumatic subarachnoid hemorrhage. The transverse processes were the most fragile portion of the vertebrae and were more susceptible to fractures. The seventh cervical vertebra was the most commonly affected segment, with 24 cases (34.78%). The distribution of fractures was similar among the other cervical vertebrae, the first four thoracic vertebrae and the lumbar spine. Neurological deficit secondary to SI was detected in eight individuals (11.59%) and two individuals (2.89%) died. Traumatic subarachnoid hemorrhage was the most common intracranial finding (82.6%). Spinal surgery was necessary in 24 patients (34.78%) and brain surgery in 18 (26%). Four patients (5.79%) underwent cranial and spinal surgeries. The authors conclude that it is necessary a judicious assessment of the entire spine of individuals who presented in coma after suffering a brain injury associated to multisystemic trauma and whole-body CT scan may play a major role in this scenario.

Cholesterol-lowering effect of whole lupin (Lupinus albus) seed and its protein isolate

This study describes the hypocholesterolaemic effect of whole lupin and its protein in hamsters. The diets were: casein (control group HC), lupin protein isolate (group HPI) and whole lupin seed (group HWS). Diets from HPI and HWS promoted a significant reduction of total cholesterol and non-HDL cholesterol in the hamsters' plasma as compared with HC. The true digestibility of HPI and HC groups were similar and differed significantly from the HWS one, which in turn showed a significant difference in total sterol excretion as compared to the former groups. Histological analysis of the liver revealed that animals fed on HPI and HWS diets presented a low level of steatosis (level 1) as compared to the ones fed on HC diet (level 4). Our findings demonstrate that protein isolate from Lupinus albus from Brazil has a metabolic effect on endogenous cholesterol metabolism and a protector effect on development of hepatic steatosis. (C) 2011 Elsevier Ltd. All rights reserved.

Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes

Background: Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlotterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome. Results: We reanalyzed the dataset published by Metta and Schlotterer and found several issues that led us to a different conclusion. In particular, Metta and Schlotterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schltterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlotterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes. Conclusions: The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors' view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.

Hollow-fiber liquid-phase microextraction and gas chromatography-mass spectrometry of barbiturates in whole blood samples

Here, we present a method for measuring barbiturates (butalbital, secobarbital, pentobarbital, and phenobarbital) in whole blood samples. To accomplish these measurements, analytes were extracted by means of hollow-fiber liquid-phase microextraction in the three-phase mode. Hollow-fiber pores were filled with decanol, and a solution of sodium hydroxide (pH 13) was introduced into the lumen of the fiber (acceptor phase). The fiber was submersed in the acidified blood sample, and the system was subjected to an ultrasonic bath. After a 5 min extraction, the acceptor phase was withdrawn from the fiber and dried under a nitrogen stream. The residue was reconstituted with ethyl acetate and trimethylanilinium hydroxide. An aliquot of 1.0 mu L of this solution was injected into the gas chromatograph/mass spectrometer, with the derivatization reaction occurring in the hot injector port (flash methylation). The method proved to be simple and rapid, and only a small amount of organic solvent (decanol) was needed for extraction. The detection limit was 0.5 mu g/mL for all the analyzed barbiturates. The calibration curves were linear over the specified range (1.0 to 10.0 mu g/mL). This method was successfully applied to postmortem samples (heart blood and femoral blood) collected from three deceased persons previously exposed to barbiturates.

Vitrification of primordial germ cells using whole embryos for gene-banking in loach, Misgurnus anguillicaudatus

In gene-banking, primordial germ cells (PGCs), which are embryonic precursor cells of germ cells, are useful for cryopreservation because PGCs have a potential to differentiate into both eggs and sperm via germ-line chimera. Here, we have established vitrification methods for PGCs cryopreservation using 12- to 17-somite stage embryos in loach, Misgurnus anguillicaudatus, which were dechorionated, removed their yolk and injected with green fluorescent protein (GFP) -nos1 3'UTR mRNA to visualize their PGCs. In order to optimize cryopreservation medium for vitrification, the toxicity of cryoprotectants was analyzed. Different concentrations (2, 3, 4, 5 m) of dimethyl sulfoxide (DMSO), methanol (MeOH), ethylene glycol (EG) and propylene glycol (PG) as cryoprotectants were tested. Then, 5 m DMSO showed significantly-high toxicity. Based on this information, combinations called DMP (2 m (14.2% [v/v]) DMSO, 2 m (8.1% [v/v]) MeOH and 2 m (14.4% [v/v]) PG), DP (2 m (14.2% [v/v]) DMSO and 4 m (28.7% [v/v]) PG) and DE (2.1 m (15% [v/v]) DMSO and 2.7 m (15% [v/v]) EG) were evaluated for their toxicities and efficacy of PGCs cryopreservation using two types of equilibration step: direct immersion of cryopreservation media (one-step) and serial exposure to half and full concentration of cryopreservation media (two-step). Viable PGCs were obtained from post-thaw embryos which were cryopreserved by DP and DE with both 1- and 2-step equilibrations. Despite DP showing the highest toxicity, it gave the highest survival rate of embryonic cells after cryopreservation. When PGCs recovered from vitrified embryos were transplanted into host embryos at the blastula stage, the transplanted PGCs were able to migrate to a host genital ridge similarly as endogenous PGCs. It suggests that our methods could be useful to create a germ-line chimera for the production of gametes from PGCs of cryopreserved embryos.