Showing papers by "Sao Paulo State University published in 2009"

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Stability Predicts Genetic Diversity in the Brazilian Atlantic Forest Hotspot

Abstract: Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.

Lanthanide-Containing Light-Emitting Organic-Inorganic Hybrids: A Bet on the Future

Abstract: Interest in lanthanide-containing organic-inorganic hybrids has grown considerably during the last decade, with the concomitant fabrication of materials with tunable attributes offering modulated properties. The potential of these materials relies on exploiting the synergy between the intrinsic characteristics of sol-gel derived hosts (highly controlled purity, versatile shaping and patterning, excellent optical quality, easy control of the refractive index, photosensitivity, encapsulation of large amounts of isolated emitting centers protected by the host) and the luminescence features of trivalent lanthanide ions (high luminescence quantum yield, narrow bandwidth, long-lived emission, large Stokes shifts, ligand-dependent luminescence sensitization). Promising applications may be envisaged, such as light-emitting devices, active waveguides in the visible and near-IR spectral regions, active coatings, and bio-medical actuators and sensors, opening up exciting directions in materials science and related technologies with significant implications in the integration, miniaturization, and multifunctionalization of devices. This review provides an overview of the latest advances in Ln(3+)-containing siloxane-based hybrids, with emphasis on the different possible synthetic strategies, photoluminescence features, empirical determination.

Allium cepa test in environmental monitoring: a review on its application.

Abstract: Higher plants are recognized as excellent genetic models to detect environmental mutagens and are frequently used in monitoring studies. Among the plant species, Alium cepa has been used to evaluate DNA damages, such as chromosome aberrations and disturbances in the mitotic cycle. Employing the A. cepa as a test system to detect mutagens dates back to the 40s. It has been used to this day to assess a great number of chemical agents, which contributes to its increasing application in environmental monitoring. The A. cepa is characterized as a low cost test. It is easily handled and has advantages over other short-term tests that require previous preparations of tested samples, as well as the addition of exogenous metabolic system. Higher plants, even showing low concentrations of oxidase enzymes and a limitation in the substrate specification in relation to other organism groups, present consistent results that may serve as a warning to other biological systems, since the target is DNA, common to all organisms. The A. cepa test also enables the evaluation of different endpoints. Among the endpoints, chromosome aberrations have been the most used one to detect genotoxicity along the years. The mitotic index and some nuclear abnormalities are used to evaluate citotoxicity and analyze micronucleus to verify mutagenicity of different chemicals. Moreover, the A. cepa test system provides important information to evaluate action mechanisms of an agent about its effects on the genetic material (clastogenic and/or aneugenic effects). In the face of all the advantages that the A. cepa test system offers, it has been widely used to assess the impacts caused by xenobiotics, characterizing an important tool for environmental monitoring studies, where satisfactory results have been reported.

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

Abstract: The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Basic notions of heart rate variability and its clinical applicability

Abstract: Autonomic nervous system (ANS) plays an important role in the regulation of the physiological processes of the human organism during normal and pathological conditions. Among the techniques used in its evaluation, the heart rate variability (HRV) has arising as a simple and non-invasive measure of the autonomic impulses, representing one of the most promising quantitative markers of the autonomic balance. The HRV describes the oscillations in the interval between consecutive heart beats (RR interval), as well as the oscillations between consecutive instantaneous heart rates. It is a measure that can be used to assess the ANS modulation under physiological conditions, such as wakefulness and sleep conditions, different body positions, physical training and also pathological conditions. Changes in the HRV patterns provide a sensible and advanced indicator of health involvements. Higher HRV is a signal of good adaptation and characterizes a health person with efficient autonomic mechanisms, while lower HRV is frequently an indicator of abnormal and insufficient adaptation of the autonomic nervous system, provoking poor patient's physiological function. Because of its importance as a marker that reflects the ANS activity on the sinus node and as a clinical instrument to assess and identify health involvements, this study reviews conceptual aspects of the HRV, measurement devices, filtering methods, indexes used in the HRV analyses, limitations in the use and clinical applications of the HRV.

Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions

Abstract: Quantitative data from gene expression experiments are often normalized by transcription levels of reference or housekeeping genes. An inherent assumption for their use is that the expression of these genes is highly uniform in living organisms during various phases of development, in different cell types and under diverse environmental conditions. To date, the validation of reference genes in plants has received very little attention and suitable reference genes have not been defined for a great number of crop species including Coffea arabica. The aim of the research reported herein was to compare the relative expression of a set of potential reference genes across different types of tissue/organ samples of coffee. We also validated the expression profiles of the selected reference genes at various stages of development and under a specific biotic stress. The expression levels of five frequently used housekeeping genes (reference genes), namely alcohol dehydrogenase (adh), 14-3-3, polyubiquitin (poly), β-actin (actin) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) was assessed by quantitative real-time RT-PCR over a set of five tissue/organ samples (root, stem, leaf, flower, and fruits) of Coffea arabica plants. In addition to these commonly used internal controls, three other genes encoding a cysteine proteinase (cys), a caffeine synthase (ccs) and the 60S ribosomal protein L7 (rpl7) were also tested. Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. The obtained results revealed significantly variable expression levels of all reference genes analyzed, with the exception of gapdh, which showed no significant changes in expression among the investigated experimental conditions. Our data suggests that the expression of housekeeping genes is not completely stable in coffee. Based on our results, gapdh, followed by 14-3-3 and rpl7 were found to be homogeneously expressed and are therefore adequate for normalization purposes, showing equivalent transcript levels in different tissue/organ samples. Gapdh is therefore the recommended reference gene for measuring gene expression in Coffea arabica. Its use will enable more accurate and reliable normalization of tissue/organ-specific gene expression studies in this important cherry crop plant.

Molecular phylogeny of advanced snakes (Serpentes, Caenophidia) with an emphasis on South American Xenodontines: a revised classification and descriptions of new taxa

Abstract: Este trabalho apresenta uma analise filogenetica molecular das serpentes avancadas (Caenophidia), realizada com base na analise de sequencias de dois genes mitocondriais (rRNA 12S e 16S) e de um gene nuclear (c-mos; 1681 pares de bases no total) e com 131 taxons terminais, amostrados a partir das principais linhagens de Caenophidia, com enfase nos xenodontineos neotropicais. A analise de parcimonia dos dados mediante otimizacao direta resultou em uma arvore filogenetica bem resolvida que, por um lado, corrobora alguns dos clados identificados em analises anteriores e por outro, estabelece novas hipoteses sobre a composicao de outros grupos e do relacionamento entre eles. Os principais resultados obtidos salientam: (1) a alocacao de Achrochordus, xenodermatideos e pareatideos como grupos externos sucessivos de todos os demais cenofidios (incluindo viperideos, elapideos, atractaspidideos e todos os grupos de "colubrideos"); (2) que, em relacao ao ultimo grupo, viperideos e homalopsideos podem ser considerados como clados irmaos dos demais; (3) a existencia, dentro do grande grupo dos cenofidia, dos seguintes sub-grupos: psamophiideos afro-asiaticos (incluindo o genero Mimophis, de Madagascar), Elapidae (incluindo os hidrophiineos, mas excluindo Homoroselaps, associado aos atractaspidideos), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae e Xenodontinae. A analise sugere algumas alteracoes de cunho taxonomico dentro dos xenodontineos, incluindo realocacoes genericas para Alsophis elegans, Liophis amarali e modificacoes substanciais em relacao a Xenodontini e a radiacao dos xenodontineos das Antilhas. Tambem e a aqui apresentada uma revisao da classificacao de Caenophidia, baseada inicialmente nas analises moleculares, mas provendo diagnoses morfologicas para muitos dos clados incluidos, realcando os grupos que ainda merecem atencao especial no futuro. Sao aqui nomeados originalmente dois grandes clados dentro de Caenophidia, uma nova subfamilia dentro de Dipsadidae e, dentro de Xenodontinae, cinco novas tribos e seis novos generos, sendo ainda dois generos revalidados. Os generos Xenoxybelis e Pseudablabes sao considerados sinonimos de Philodryas; Erythrolamprus, sinonimo de Liophis; Lystrophis e Waglerophis, sinonimos de Xenodon.

Flavonoids with gastroprotective activity.

Abstract: Peptic ulcers are a common disorder of the entire gastrointestinal tract that occurs mainly in the stomach and the proximal duodenum. This disease is multifactorial and its treatment faces great difficulties due to the limited effectiveness and severe side effects of the currently available drugs. The use of natural products for the prevention and treatment of different pathologies is continuously expanding throughout the world. This is particularly true with regards to flavonoids, which represent a highly diverse class of secondary metabolites with potentially beneficial human health effects that is widely distributed in the plant kingdom and currently consumed in large amounts in the diet. They display several pharmacological properties in the gastroprotective area, acting as anti-secretory, cytoprotective and antioxidant agents. Besides their action as gastroprotectives, flavonoids also act in healing of gastric ulcers and additionally these polyphenolic compounds can be new alternatives for suppression or modulation of peptic ulcers associated with H. pylori. In this review, we have summarized the literature on ninety-five flavonoids with varying degrees of antiulcerogenic activity, confirming that flavonoids have a therapeutic potential for the more effective treatment of peptic ulcers.

Observation of single top-quark production

Abstract: We report observation of the electroweak production of single top quarks in pp collisions at s=1.96 TeV based on 2.3 fb(-1) of data collected by the D0 detector at the Fermilab Tevatron Collider. Using events containing an isolated electron or muon and missing transverse energy, together with jets originating from the fragmentation of b quarks, we measure a cross section of sigma(pp -> tb+X,tqb+X)=3.94 +/- 0.88 pb. The probability to measure a cross section at this value or higher in the absence of signal is 2.5x10(-7), corresponding to a 5.0 standard deviation significance for the observation.

Pectin and Pectinases: Production, Characterization and Industrial Application of Microbial Pectinolytic Enzymes

Abstract: Departamento de Bioquimica e Microbiologia Instituto de Biociencias Universidade Estadual Paulista, UNESP, Avenida 24A, 1515, CEP 13506-900 Rio Claro, SP

Prevalence of dementia in Latin America: a collaborative study of population-based cohorts.

Abstract: Background: Dementia is becoming a major public health problem in Latin America (LA), yet epidemiological information on dementia remains scarce in this region. This study analyzes data from epidemiological studies on the prevalence of dementia in LA and compares the prevalence of dementia and its causes across countries in LA and attempts to clarify differences from those of developed regions of the world. Methods: A database search for population studies on rates of dementia in LA was performed. Abstracts were also included in the search. Authors of the publications were invited to participate in this collaborative study by sharing missing or more recent data analysis with the group. Results: Eight studies from six countries were included. The global prevalence of dementia in the elderly (≥65 years) was 7.1% (95% CI: 6.8-7.4), mirroring the rates of developed countries. However, prevalence in relatively young subjects (65-69 years) was higher in LA studies The rate of illiteracy among the elderly was 9.3% and the prevalence of dementia in illiterates was two times higher than in literates. Alzheimer's disease was the most common cause of dementia. Conclusions: Compared with studies from developed countries, the global prevalence of dementia in LA proved similar, although a higher prevalence of dementia in relatively young subjects was evidenced, which may be related to the association between low educational level and lower cognitive reserve, causing earlier emergence of clinical signs of dementia in the LA elderly population.

Electron transport in dye-sensitized solar cells based on ZnO nanotubes: evidence for highly efficient charge collection and exceptionally rapid dynamics.

Abstract: Dye-sensitized solar cells based on ordered arrays of polycrystalline ZnO nanotubes, 64 μm in length, are shown to exhibit efficient electron collection over the entire photoanode array length. Electrochemical impedance spectroscopy, open-circuit photovoltage decay analysis, and incident-photon-to-current efficiency spectra are used to quantify charge transport and lifetimes. Despite the relatively thick photoanode, the charge extraction time is found to be faster than observed in traditional TiO2 nanoparticle photoanodes. If the extraction dynamics are interpreted as diffusive, effective electron diffusion coefficients of up to 0.4 cm2 s−1 are obtained, making these pseudo-1D photoanodes the fastest reported for an operating DSC to date. Rapid electron collection is of practical significance because it should enable alternative redox shuttles, which display relatively fast electron-interception dynamics, to be employed without significant loss of photocurrent.

The effects of canal preparation and filling on the incidence of dentinal defects

Abstract: Aim To evaluate ex vivo the incidence of defects in root dentine before and after root canal preparation and filling. Methodology Eighty extracted mandibular premolars were divided equally in four groups. Group 1 was left unprepared. All other root canals were prepared using Gates Glidden drills and System GT files up to size-40, 0.06 taper at the working length. Group 2 was not filled while the canals of the other groups were filled with gutta-percha and AH26, either with a master cone and passive insertion of secondary gutta percha points (group 3) or lateral compaction (group 4). Roots were then sectioned horizontally 3, 6, and 9 mm from the apex and observed under a microscope. The presence of dentinal defects (fractures, craze lines or incomplete cracks) was noted and the differences between the groups were analysed with the Fisher’s exact test. Results No defects were observed in the roots with unprepared canals. The overall difference between the groups was significant (P < 0.05). Canal preparation alone created significantly more defects than unprepared canals (P < 0.05). The total number of defects after lateral compaction was significantly larger than after noncompaction canal filling. Conclusion Root canal preparation and filling of extracted teeth created dentine defects such as fractures, craze lines and incomplete cracks.

The six-minute walk test and body weight-walk distance product in healthy Brazilian subjects

Abstract: We assessed the 6-min walk distance (6MWD) and body weight x distance product (6MWw) in healthy Brazilian subjects and compared measured 6MWD with values predicted in five reference equations developed for other populations. Anthropometry, spirometry, reported physical activity, and two walk tests in a 30-m corridor were evaluated in 134 subjects (73 females, 13-84 years). Mean 6MWD and 6MWw were significantly greater in males than in females (622 ± 80 m, 46,322 ± 10,539 kg.m vs 551 ± 71 m, 36,356 ± 8,289 kg.m, P < 0.05). Four equations significantly overestimated measured 6MWD (range, 32 ± 71 to 137 ± 74 m; P < 0.001), and one significantly underestimated it (-36 ± 86 m; P < 0.001). 6MWD significantly correlated with age (r = -0.39), height (r = 0.44), body mass index (r = -0.24), and reported physical activity (r = 0.25). 6MWw significantly correlated with age (r = -0.21), height (r = 0.66) and reported physical activity (r = 0.25). The reference equation devised for walk distance was 6MWD

Heat Exchange from the Toucan Bill Reveals a Controllable Vascular Thermal Radiator

Abstract: The toco toucan (Ramphastos toco), the largest member of the toucan family, possesses the largest beak relative to body size of all birds. This exaggerated feature has received various interpretations, from serving as a sexual ornament to being a refined adaptation for feeding. However, it is also a significant surface area for heat exchange. Here we show the remarkable capacity of the toco toucan to regulate heat distribution by modifying blood flow, using the bill as a transient thermal radiator. Our results indicate that the toucan's bill is, relative to its size, one of the largest thermal windows in the animal kingdom, rivaling elephants' ears in its ability to radiate body heat.

Macrophage activation syndrome in juvenile systemic lupus erythematosus: a multinational multicenter study of thirty-eight patients.

Abstract: Objective To describe the clinical and laboratory features of macrophage activation syndrome as a complication of juvenile systemic lupus erythematosus (SLE). Methods Cases of juvenile SLE–associated macrophage activation syndrome were provided by investigators belonging to 3 pediatric rheumatology networks or were found in the literature. Patients who had evidence of macrophage hemophagocytosis on bone marrow aspiration were considered to have definite macrophage activation syndrome, and those who did not have such evidence were considered to have probable macrophage activation syndrome. Clinical and laboratory findings in patients with macrophage activation syndrome were contrasted with those of 2 control groups composed of patients with active juvenile SLE without macrophage activation syndrome. The ability of each feature to discriminate macrophage activation syndrome from active disease was evaluated by calculating sensitivity, specificity, and area under the receiver operating characteristic curve. Results The study included 38 patients (20 with definite macrophage activation syndrome and 18 with probable macrophage activation syndrome). Patients with definite and probable macrophage activation syndrome were comparable with regard to all clinical and laboratory features of the syndrome, except for a greater frequency of lymphadenopathy, leukopenia, and thrombocytopenia in patients with definite macrophage activation syndrome. Overall, clinical features had better specificity than sensitivity, except for fever, which was highly sensitive but had low specificity. Among laboratory features, the best sensitivity and specificity was achieved using hyperferritinemia, followed by increased levels of lactate dehydrogenase, hypertriglyceridemia, and hypofibrinogenemia. Based on the results of statistical analysis, preliminary diagnostic guidelines for macrophage activation syndrome in juvenile SLE were developed. Conclusion Our findings indicate that the occurrence of unexplained fever and cytopenia, when associated with hyperferritinemia, in a patient with juvenile SLE should raise the suspicion of macrophage activation syndrome. We propose preliminary guidelines for this syndrome in juvenile SLE to facilitate timely diagnosis and correct classification of patients.