High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Background: High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results: We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions: This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity >= 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.

Immunological Basis for the Gender Differences in Murine Paracoccidioides brasiliensis Infection

This study aimed to investigate the immunological mechanisms involved in the gender distinct incidence of paracoccidioidomycosis (pcm), an endemic systemic mycosis in Latin America, which is at least 10 times more frequent in men than in women. Then, we compared the immune response of male and female mice to Paracoccidioides brasiliensis infection, as well as the influence in the gender differences exerted by paracoccin, a P. brasiliensis component with carbohydrate recognition property. High production of Th1 cytokines and T-bet expression have been detected in the paracoccin stimulated cultures of spleen cells from infected female mice. In contrast, in similar experimental conditions, cells from infected males produced higher levels of the Th2 cytokines and expressed GATA-3. Macrophages from male and female mice when stimulated with paracoccin displayed similar phagocytic capability, while fungicidal activity was two times more efficiently performed by macrophages from female mice, a fact that was associated with 50% higher levels of nitric oxide production. In order to evaluate the role of sexual hormones in the observed gender distinction, we have utilized mice that have been submitted to gonadectomy followed by inverse hormonal reconstitution. Spleen cells derived from castrated males reconstituted with estradiol have produced higher levels of IFN-gamma (1291+/-15 pg/mL) and lower levels of IL-10 (494+/-38 pg/mL), than normal male in response to paracoccin stimulus. In contrast, spleen cells from castrated female mice that had been treated with testosterone produced more IL-10 (1284+/-36 pg/mL) and less IFN-gamma (587614 pg/mL) than cells from normal female. In conclusion, our results reveal that the sexual hormones had a profound effect on the biology of immune cells, and estradiol favours protective responses to P. brasiliensis infection. In addition, fungal components, such as paracoccin, may provide additional support to the gender dimorphic immunity that marks P. brasiliensis infection.

Detection of high-velocity material from the wind-wind collision zone of Eta Carinae across the 2009.0 periastron passage

We report near-infrared spectroscopic observations of the Eta Carinae massive binary system during 2008-2009 using the CRIRES spectrograph mounted on the 8m UT 1 Very Large Telescope (VLT Antu). We detect a strong, broad absorption wing in He I lambda 10833 extending up to -1900 km s(-1) across the 2009.0 spectroscopic event. Analysis of archival Hubble Space Telescope/Space Telescope Imaging Spectrograph ultraviolet and optical data identifies a similar high-velocity absorption (up to -2100 km s(-1)) in the ultraviolet resonance lines of Si IV lambda lambda 1394, 1403 across the 2003.5 event. Ultraviolet resonance lines from low-ionization species, such as Si II lambda lambda 1527, 1533 and CII lambda lambda 1334, 1335, show absorption only up to -1200 km s(-1), indicating that the absorption with velocities -1200 to -2100 km s(-1) originates in a region markedly more rapidly moving and more ionized than the nominal wind of the primary star. Seeing-limited observations obtained at the 1.6m OPD/LNA telescope during the last four spectroscopic cycles of Eta Carinae (1989-2009) also show high-velocity absorption in He I lambda 10833 during periastron. Based on the large OPD/LNA dataset, we determine that material with velocities more negative than -900 km s(-1) is present in the phase range 0.976 <= phi <= 1.023 of the spectroscopic cycle, but absent in spectra taken at phi <= 0.947 and phi >= 1.049. Therefore, we constrain the duration of the high-velocity absorption to be 95 to 206 days (or 0.047 to 0.102 in phase). We propose that the high-velocity absorption component originates in shocked gas in the wind-wind collision zone, at distances of 15 to 45 AU in the line-of-sight to the primary star. With the aid of three-dimensional hydrodynamical simulations of the wind-wind collision zone, we find that the dense high-velocity gas is along the line-of-sight to the primary star only if the binary system is oriented in the sky such that the companion is behind the primary star during periastron, corresponding to a longitude of periastron of omega similar to 240 degrees-270 degrees. We study a possible tilt of the orbital plane relative to the Homunculus equatorial plane and conclude that our data are broadly consistent with orbital inclinations in the range i = 40 degrees-60 degrees.

Beyond the Fragmentation Threshold Hypothesis: Regime Shifts in Biodiversity Across Fragmented Landscapes

Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andren proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions - that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework, providing a powerful tool for analysing the potential effectiveness of management interventions.

The constancy of global regulation across a species: the concentrations of ppGpp and RpoS are strain-specific in Escherichia coli

Background: Sigma factors and the alarmone ppGpp control the allocation of RNA polymerase to promoters under stressful conditions. Both ppGpp and the sigma factor sigma(S) (RpoS) are potentially subject to variability across the species Escherichia coli. To find out the extent of strain variation we measured the level of RpoS and ppGpp using 31 E. coli strains from the ECOR collection and one reference K-12 strain. Results: Nine ECORs had highly deleterious mutations in rpoS, 12 had RpoS protein up to 7-fold above that of the reference strain MG1655 and the remainder had comparable or lower levels. Strain variation was also evident in ppGpp accumulation under carbon starvation and spoT mutations were present in several low-ppGpp strains. Three relationships between RpoS and ppGpp levels were found: isolates with zero RpoS but various ppGpp levels, strains where RpoS levels were proportional to ppGpp and a third unexpected class in which RpoS was present but not proportional to ppGpp concentration. High-RpoS and high-ppGpp strains accumulated rpoS mutations under nutrient limitation, providing a source of polymorphisms. Conclusions: The ppGpp and sigma(S) variance means that the expression of genes involved in translation, stress and other traits affected by ppGpp and/or RpoS are likely to be strain-specific and suggest that influential components of regulatory networks are frequently reset by microevolution. Different strains of E. coli have different relationships between ppGpp and RpoS levels and only some exhibit a proportionality between increasing ppGpp and RpoS levels as demonstrated for E. coli K-12.

Density-functional description of superconducting and magnetic proximity effects across a tunneling barrier

A density-functional formalism for superconductivity and magnetism is presented. The resulting relations unify previously derived Kohn-Sham equations for superconductors and for noncollinear magnetism. The formalism, which discriminates Cooper-pair singlets from triplets, is applied to two quantum liquids coupled by tunneling through a barrier. An exact expression is derived, relating the eigenstates and eigenvalues of the Kohn-Sham equations, unperturbed by tunneling, on one side of the barrier to the proximity-induced ordering potential on the other.

Increasing trends of sleep complaints in the city of Sao Paulo, Brazil

Objective: The aim of this study was to compare the prevalence of sleep habits and complaints and to estimate the secular trends through three population-based surveys carried out in 1987, 1995, and 2007 in the general adult population of the city of Sao Paulo, Brazil. Methods: Surveys were performed using the same three-stage cluster-sampling technique in three consecutive decades to obtain representative samples of the inhabitants of Sao Paulo with respect to gender, age (20-80 years), and socio-economic status. Sample sizes were 1000 volunteers in 1987 and 1995 surveys and 1101 in a 2007 survey. In each survey, the UNIFESP Sleep Questionnaire was administered face-to-face in each household selected. Results: For 1987, 1995, and 2007, respectively, difficulty initiating sleep (weighted frequency %; 95% CI) [(13.9; 11.9-16.2), (19.15; 16.8-21.6), and (25.0; 22.5-27.8)], difficulty maintaining sleep [(15.8; 13.7-18.2), (27.6; 24.9-30.4), and (36.5; 33.5-39.5)], and early morning awakening [(10.6; 8.8-12.7), (14.2; 12.2-16.5), and (26.7; 24-29.6)] increased in the general population over time, mostly in women. Habitual snoring was the most commonly reported complaint across decades and was more prevalent in men. There was no statistically significant difference in snoring complaints between 1987 (21.5; 19.1-24.2) and 1995 (19.0; 16.7-21.6), but a significant increase was noted in 2007 (41.7; 38.6-44.8). Nightmares, bruxism, leg cramps, and somnambulism complaints were significantly higher in 2007 compared to 1987 and 1995. All were more frequent in women. Conclusions: This is the first study comparing sleep complaints in probabilistic population-based samples from the same metropolitan area, using the same methodology across three consecutive decades. Clear trends of increasing sleep complaints were observed, which increased faster between 1995 and 2007 than from 1987 to 1995. These secular trends should be considered a relevant public health issue and support the need for development of health care and educational strategies to supply the population`s increased need for information on sleep disorders and their consequences. (C) 2010 Elsevier B.V. All rights reserved.

Gender Differences in Life Expectancy and Disability-Free Life Expectancy Among Older Adults in Sao Paulo, Brazil

Background: Research on life expectancy has demonstrated the negative impact of disability on the health of older adults and its differential effects on women as evidenced by their higher disabled life expectancy (DLE). The goal of the present study was to investigate gender differences in total life expectancy (TLE), disability-free life expectancy (DFLE), and DLE; examine gender differences on personal care assistance among older adults in Sao Paulo, Brazil; and discuss the implications for public policies. Methods: The sample was drawn from two waves (2000, 2006) of the dataset of Salud, Bienestar, y Envejecimiento, a large longitudinal study conducted in Sao Paulo (n = 2,143). The study assessed disability using the activities of daily living (ADL). The interpolation of Markov Chain method was used to estimate gender differences in TLE, DLE, and DFLE. Findings: TLE at age 60 years was approximately 5 years longer for women than men. Women aged 60 years were expected to live 28% of their remaining lives twice the percentage for men with at least one ADL disability. These women also lived more years (M = 0.71, SE = 0.42) with three or more ADL disabilities than men (M = 0.82, SE = 0.16). In terms of personal care assistance, women received more years of assistance than men. Conclusion: Among older adults in Sao Paulo, women lived longer lives but experienced a higher and more severe disability burden than men. In addition, although women received more years of personal assistance than men, women experienced more unmet care assistance needs. Copyright (C) 2011 by the Jacobs Institute of Women`s Health. Published by Elsevier. Inc.

Categories of manual asymmetry and their variation with advancing age

Manual asymmetries were analyzed in 18- to 63-year-old right-handers in different motor tasks. This analysis aimed at describing the asymmetry profile for each task and assessing their stability across ages. For this purpose, performance of the right and left hands were analyzed in the following aspects: simple reaction time, rate of sequential finger movements, maximum grip force, accuracy in anticipatory timing, rate of repetitive tapping, and rate of drawing movements. In addition, stability of manual preference across ages was assessed through the Edinburgh inventory (Oldfield, 1971). The results indicated different profiles of manual asymmetry, with identification of three categories across tasks: symmetric performance (asymmetry indices close to zero), inconsistent asymmetry (asymmetry indices variable in magnitude and direction), and consistent asymmetry (asymmetry indices favoring a single hand). The different profiles observed in the young adults were stable across ages with two exceptions: decreased lateral asymmetry for maximum grip force and increased asymmetry for sequential drawing in older individuals. These results indicate that manual asymmetries are task specific. Such task specificity is interpreted to be the result of different sensorimotor requirements imposed by each motor task in association with motor experiences accumulated over the lifetime. Analysis of manual preference showed that strength of preference for the right hand was greater in older individuals. (C) 2008 Elsevier Masson Srl. All rights reserved.

Tracking 10-year competitive winning performance of judo athletes across age groups

Little information is available concerning early specialization and competitive success in judo across the early training years. Thus, the present objective was to verify the stability of individual competitive performance of a state-level championship for judo athletes who had been previously successful. For this, 406 athletes from six age groups (9 to 20+ years old) of each sex were followed for 10 years. Using recorded data from the Sao Paulo State Judo Federation beginning in 1999, the scores and standings for these judo players were analyzed. The proportion of medal winners during this period was not constant, differing from the grand mean in all groups of both 204 males and 202 females. At the end of this period, only 7% of the male and 5% of the female athletes had maintained their competitive levels. Successful competitive performance in early judo competition was not associated with success later in adulthood.

The Effects of Host, Geographic Origin, and Gender on the Thermal Requirements of Diaphorina citri (Hemiptera: Psyllidae)

Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the vector of the bacteria that causes citrus greening and is considered one of the world`s most important citrus diseases. We examined how host, geographic region, and gender affect the thermal requirements of D. citri. The insects were reared in climatic chambers at constant temperatures of 18, 20, 22, 25, 28, 30, and 32 1 degrees C, 70 +/- 10% RH, and a 14 h photophase. Host plants for D. citri included orange (Citrus sinensis [Rutaceae]) varieties Pera and Natal, the rootstock, Rungpur lime (C. limonia [Rutaceae]) and the natural host, Orange jessamine (Murraya paniculata [Rutaceae]). To study the influence of geographic origin on thermal requirements, we studied D. citri populations from Piracicaba, SP (warmer region) and Itapetininga, SP (cooler region). The duration and survival of the development stages and the duration of the total development (egg-adult) did not differ significantly on the different hosts, but it did vary with temperature. Nymphs of D. citri created on the different hosts have the same thermal requirements. The thermal requirements for this species collected from the two climate regions were identical; males and females also had the same thermal requirements.

Chemical Signals in the Stingless Bee, Frieseomelitta varia, Indicate Caste, Gender, Age, and Reproductive Status

Chemical compounds on the cuticle are a rich source of information used during interactions among social insects. Despite the multitude of studies on these substances and their function in ants, wasps, and honeybees, little is known about this subject in stingless bees (Hymenoptera: Apidae, Meliponini). We studied the chemical composition of the cuticle of the stingless bee, Frieseomelitta varia, by gas chromatography-mass spectrometry (GC-MS), to investigate potential chemical variation among castes, gender, age, and reproductive status. We found differences in the cuticular hydrocarbon composition among workers, males, and queens, recording both qualitative and quantitative differences among individuals of different ages and gender. The cuticle of physogastric queens presented a chemical profile that was distinct from all other groups in the analysis, with high relative abundances of alkenes and alkadienes with 27, 29, and 31 carbon atoms. We discuss the possibility that these compounds signal a queen`s presence to the colony, thereby initiating all vital worker-queen interactions.

Gender-specific vascular effects elicited by chronic ethanol consumption in rats: a role for inducible nitric oxide synthase

Background and purpose: Epidemiological data suggest that the risk of ethanol-associated cardiovascular disease is greater in men than in women. This study investigates the mechanisms underlying gender-specific vascular effects elicited by chronic ethanol consumption in rats. Experimental approach: Vascular reactivity experiments using standard muscle bath procedures were performed on isolated thoracic aortae from rats. mRNA and protein for inducible NO synthase (iNOS) and for endothelial NOS (eNOS) was assessed by RT-PCR or western blotting, respectively. Key results: In male rats, chronic ethanol consumption enhanced phenylephrine-induced contraction in both endothelium-intact and denuded aortic rings. However, in female rats, chronic ethanol consumption enhanced phenylephrine-induced contraction only in endothelium denuded aortic rings. After pre-incubation of endothelium-intact rings with L-NAME, both male and female ethanol-treated rats showed larger phenylephrine-induced contractions in aortic rings, compared to the control group. Acetylcholine-induced relaxation was not affected by ethanol consumption. The effects of ethanol on responses to phenylephrine were similar in ovariectomized (OVX) and intact (non-OVX) female rats. In the presence of aminoguanidine, but not 7-nitroindazole, the contractions to phenylephrine in rings from ethanol-treated female rats were greater than that found in control tissues in the presence of the inhibitors. mRNA levels for eNOS and iNOS were not altered by ethanol consumption. Ethanol intake reduced eNOS protein levels and increased iNOS protein levels in aorta from female rats. Conclusions and implications: Gender differences in the vascular effects elicited by chronic ethanol consumption were not related to ovarian hormones but seemed to involve the upregulation of iNOS.

Incorporating demand-side aspects into regional policy: variations in the importance of private investment decision factors across regions

Most regional programs focus on the supply side of regions, emphasizing the attraction conditions offered, such as infrastructure, labor skills, tax incentives, etc. This study analyzes one aspect of the demand side, that is, how investment decisions of private firms are made by asking the question: ""Do corporations decide the same way on investments in different parts of the territory?"" The paper analyzes the investments of 373 large Brazilian firms during 1996-2004. Based on the investment decisions of these firms, the role of sales, cash-flow, external financing, and working capital is investigated through regression analysis. The regional influence is captured by explanatory variables representing regional and firm characteristics, and by interaction dummies between the region and the main investment determinants. The results indicate significant differences across regions in the importance of investment determinants. This information is important for regional development policy, because different mechanisms should be used in different regions to foster private investments.

ON THE DIFFERENCES BETWEEN THE MARGINAL PRODUCT OF CAPITAL ACROSS COUNTRIES

We extended the standard neoclassical model of investment for the case of an open economy. Our model shows that risk premium not only creates a wedge between the marginal product of capital across countries but also reduces an economy`s savings rate. A riskier market thus presents a lower income per capita, ceteris paribus. Our empirical analysis, from 1950 to 2003, lends support to the conclusion that both risk and the correction for output price to investment ratio help to explain the differentials.