Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North+East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST=0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST=0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and sub-group levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

Continuous and High-Level In Vivo Delivery of Endostatin From Recombinant Cells Encapsulated in TheraCyte (R) Immunoisolation Devices

Endostatin (ES) is a potent inhibitor of angiogenesis and tumor growth. Continuous ES delivery of ES improves the efficacy and potency of the antitumoral therapy. The TheraCyte (R) system is a polytetrafluoroethylene (PTFE) semipermeable membrane macroencapsulation system for implantation of genetically engineered cells specially designed for the in vivo delivery of therapeutic proteins, such as ES, which circumvents the problem of limited half-life and variation in circulating levels. In order to enable neovascularization at the tissues adjacent to the devices prior to ES secretion by the cells inside them, we designed a scheme in which empty TheraCyte (R) devices were preimplanted SC into immunodeficient mice. Only after healing (17 days later) were Chinese hamster ovary cells expressing ES injected into the preimplanted devices. In another model for device implantation, the cells expressing ES where loaded into the immunoisolation devices prior to implantation into the animals, and the TheraCyte (R) were then immediately implanted SC into the mice. Throughout the 2-month study, constant high ES levels of up to 3.7 mu g/ml were detected in the plasma of the mice preimplanted with the devices, while lower but also constant levels of ES (up to 2.1 mu g/ml plasma) were detected in the mice that had received devices preloaded with the ES-expressing cells. Immunohistochemistry using anti-ES antibody showed reaction within the device and outside it, demonstrating that ES, secreted by the confined recombinant cells, permeated through the membrane and reached the surrounding tissues.

Strain variation in ppGpp concentration and RpoS levels in laboratory strains of Escherichia coli K-12

Laboratory strains and natural isolates of Escherichia coli differ in their level of stress resistance due to strain variation in the level of the sigma factor sigma(S) (or RpoS), the transcriptional master controller of the general stress response. We found that the high level of RpoS in one laboratory strain (MC4100) was partially dependent on an elevated basal level of ppGpp, an alarmone responding to stress and starvation. The elevated ppGpp was caused by two mutations in spoT, a gene associated with ppGpp synthesis and degradation. The nature of the spoT allele influenced the level of ppGpp in both MC4100 and another commonly used K-12 strain, MG1655. Introduction of the spoT mutation into MG1655 also resulted in an increased level of RpoS, but the amount of RpoS was lower in MG1655 than in MC4100 with either the wild-type or mutant spoT allele. In both MC4100 and MG1655, high ppGpp concentration increased RpoS levels, which in turn reduced growth with poor carbon sources like acetate. The growth inhibition resulting from elevated ppGpp was relieved by rpoS mutations. The extent of the growth inhibition by ppGpp, as well as the magnitude of the relief by rpoS mutations, differed between MG1655 and MC4100. These results together suggest that spoT mutations represent one of several polymorphisms influencing the strain variation of RpoS levels. Stress resistance was higher in strains with the spoT mutation, which is consistent with the conclusion that microevolution affecting either or both ppGpp and RpoS can reset the balance between self-protection and nutritional capability, the SPANC balance, in individual strains of E coli.

Global minimization using an Augmented Lagrangian method with variable lower-level constraints

A novel global optimization method based on an Augmented Lagrangian framework is introduced for continuous constrained nonlinear optimization problems. At each outer iteration k the method requires the epsilon(k)-global minimization of the Augmented Lagrangian with simple constraints, where epsilon(k) -> epsilon. Global convergence to an epsilon-global minimizer of the original problem is proved. The subproblems are solved using the alpha BB method. Numerical experiments are presented.

Predicting and characterizing new molecular species at a high-level theoretical approach: HSeCl, HClSe, and SeCl

New molecular species HSeCl, HClSe, and SeCl were investigated at a high level of theory, CCSD(T), with a series of correlation consistent basis sets with extrapolation to the CBS limit. Account has been taken for valence-only and core-valence correlation effects, and of anharmonic effects on the vibrational frequencies. HSeCl is 43.25 kcal mol (1) more stable than HClSe. A barrier (Delta G(#)) of 47.20 kcal mol (1) separates these species. Internuclear distances are generally overestimated by 0.008 angstrom in the valence-only correlation calculations. Inclusion of anharmonicity leads to much improved vibrational frequencies. For SeCl, we estimate Delta H(f) (0 K) = 23.96 and Delta H(f) (298.15 K) = 24.64 kcal mol (1); for HSeCl, we had 4.20 and 4.97 kcal mol (1), respectively. (C) 2010 Elsevier B.V. All rights reserved.

Structural and spectroscopic properties of the diazocarbene radical (CNN) and its ions CNN(+) and CNN(-): a high-level theoretical investigation

The diazocarbene radical, CNN, and the ions CNN(+) and CNN(-) were investigated at a high level of theory. Very accurate structural parameters for the states X(3)Sigma(-) and A(3)Pi of CNN, and X(2)Pi of both CNN(+) and CNN(-) were obtained with the UCCSD(T) method using correlated-consistent basis functions with extrapolations to the complete basis set limit, with valence only and also with all electrons correlated. Harmonic and anharmonic frequencies were obtained for all species and the Renner parameter and average frequencies evaluated for the Pi states. At the UCCSD(T)/CBS(T-5) level of theory, Delta(f)H(0 K) = 138.89 kcal/mol and Delta(f)H(298 K) = 139.65 kcal/mol were obtained for diazocarbene; for the ionization potential and the electron affinity of CNN, 10.969 eV (252.95 kcal/mol), and 1.743 eV (40.19 kcal/mol), respectively, are predicted. Geometry optimization was also carried out with the CASSCF/MRCI/CBS(T-5) approach for the states X(3)Sigma(-) A(3)Pi, and a(1)Delta of CNN, and with the CASSCF/MRSDCI/aug-cc-pVTZ approach for the states b(1)Sigma(+), c(1)Pi, d(1)Sigma(-), and B(3)Sigma(-), and excitation energies (T(e)) evaluated. Vertical energies were calculated for 15 electronic states, thus improving on the accuracy of the five transitions already described, and allowing for a reliable overview of a manifold of other states, which is expected to guide future spectroscopic experiments. This study corroborates the experimental assignment for the vertical transition X (3)Sigma(-) <- E (3)Pi.

Classification of Parkinson’s Disease using MultiPass Lvq,Logistic Model Tree,K-Star for Audio Data set : Classification of Parkinson Disease using Audio Dataset

Parkinson's disease (PD) is a degenerative illness whose cardinal symptoms include rigidity, tremor, and slowness of movement. In addition to its widely recognized effects PD can have a profound effect on speech and voice.The speech symptoms most commonly demonstrated by patients with PD are reduced vocal loudness, monopitch, disruptions of voice quality, and abnormally fast rate of speech. This cluster of speech symptoms is often termed Hypokinetic Dysarthria.The disease can be difficult to diagnose accurately, especially in its early stages, due to this reason, automatic techniques based on Artificial Intelligence should increase the diagnosing accuracy and to help the doctors make better decisions. The aim of the thesis work is to predict the PD based on the audio files collected from various patients.Audio files are preprocessed in order to attain the features.The preprocessed data contains 23 attributes and 195 instances. On an average there are six voice recordings per person, By using data compression technique such as Discrete Cosine Transform (DCT) number of instances can be minimized, after data compression, attribute selection is done using several WEKA build in methods such as ChiSquared, GainRatio, Infogain after identifying the important attributes, we evaluate attributes one by one by using stepwise regression.Based on the selected attributes we process in WEKA by using cost sensitive classifier with various algorithms like MultiPass LVQ, Logistic Model Tree(LMT), K-Star.The classified results shows on an average 80%.By using this features 95% approximate classification of PD is acheived.This shows that using the audio dataset, PD could be predicted with a higher level of accuracy.

Efeito da vitamina K da dieta na anticoagulação oral crônica : evidências prospectivas observacionais e randomizadas

Base Teórica. Embora vários relatos de casos tenham sugerido uma associação entre a ingesta de vitamina K e a instabilidade da anticoagulação oral, o impacto clínico de diferentes quantidades de vitamina K dietética na anticoagulação oral crônica nunca foi prospectivamente estabelecido. Métodos. Características clínicas e estimativas semi-quantitativas sobre a ingesta de vitamina K foram avaliadas, prospectivamente, em 230 visitas ambulatoriais de pacientes anticoagulados em um hospital público universitário (protocolo observacional). Treze pacientes ambulatoriais anticoagulados cronicamente e estáveis foram arrolados em um ensaio clínico randomizado cruzado de intervenção dietética de 4 dias com aumento e diminuição de 5 vezes da sua ingesta habitual de vitamina K (protocolo experimental randomizado). Resultados. Protocolo observacional: Na análise univariada, identificamos uma associação estatisticamente significativa, progressiva e inversa entre um escore global de ingesta de vitamina K e diferentes níveis de anticoagulação. Na análise multivariada, a ingesta de vitamina K dietética foi independentemente associada com níveis subterapêuticos e anticoagulação excessiva (ambos valores de p =0,04), após ajuste para escolaridade, renda, uso de novos fármacos, aderência à anticoagulação oral e intercorrências clínicas. Protocolo randomizado: Após a dieta restrita em vitamina K, observamos um aumento significativo nos valores do INR (de 2,6 ± 0,5 para 3,3 ± 1,0, p=0,03; do início para o dia 7) enquanto, após a dieta enriquecida, identificamos uma diminuição significativa e mais precoce no INR (de 3,2 ± 0,9 para 2,8 ± 0,7, p=0,005; do início para o dia 4). O efeito da ingesta de vitamina K sobre a variação do INR foi particularmente influenciada pela ingesta média habitual da vitamina. Conclusões. Nossos dados prospectivos reforçam o conceito de que a interação vitamina K e fármacos cumarínicos é de fato real e clinicamente relevante, devendo ser reconhecida como um fator importante e independente que interfere com a estabilidade da anticoagulação oral crônica.

Non-durable consumption and real-estate prices in Brazil: panel-data analysis at the state level

Housing is an important component of wealth for a typical household in many countries. The objective of this paper is to investigate the effect of real-estate price variation on welfare, trying to close a gap between the welfare literature in Brazil and that in the U.S., the U.K., and other developed countries. Our first motivation relates to the fact that real estate is probably more important here than elsewhere as a proportion of wealth, which potentially makes the impact of a price change bigger here. Our second motivation relates to the fact that real-estate prices boomed in Brazil in the last five years. Prime real estate in Rio de Janeiro and São Paulo have tripled in value in that period, and a smaller but generalized increase has been observed throughout the country. Third, we have also seen a recent consumption boom in Brazil in the last five years. Indeed, the recent rise of some of the poor to middle-income status is well documented not only for Brazil but for other emerging countries as well. Regarding consumption and real-estate prices in Brazil, one cannot imply causality from correlation, but one can do causal inference with an appropriate structural model and proper inference, or with a proper inference in a reduced-form setup. Our last motivation is related to the complete absence of studies of this kind in Brazil, which makes ours a pioneering study. We assemble a panel-data set for the determinants of non-durable consumption growth by Brazilian states, merging the techniques and ideas in Campbell and Cocco (2007) and in Case, Quigley and Shiller (2005). With appropriate controls, and panel-data methods, we investigate whether house-price variation has a positive effect on non-durable consumption. The results show a non-negligible significant impact of the change in the price of real estate on welfare consumption), although smaller then what Campbell and Cocco have found. Our findings support the view that the channel through which house prices affect consumption is a financial one.

Influence of genetic type and level of concentrate in the finishing diet on carcass and meat quality traits in beef heifers

Carcass and meat quality traits of thirty-six feedlot beef heifers from different genetic groups (GG) fed at two concentrate levels (CL) were evaluated using 12- Nellore (NE), 12 - 1/2Angus x 1/2Nellore (AN) and 12 - 1/2Simmental x 1/2Nellore (SN) animals. Six heifers of each GG were randomly assigned into one of two treatments: concentrate at 0.8% or 1.2% of body weight (BW). Heifers fed concentrate at 0.8% of BW had greater (P<0.05) dressing percentage. None of the proximate analysis components of the beef were affected (P>0.05) by either CL or GG. Heifers from the AN group had higher (P<0.05) carcass weights, 12th rib fat thickness and lower dressing percentage (P<0.05) compared to the other groups. NE heifers had greater WBSF values (P<0.05) than the other genetic groups. Data suggest that the concentrate level can be reduced without compromising meat quality traits. (C) 2011 Elsevier Ltd. All rights reserved.

Translocação orgânica, produtividade e rendimento de óleo essencial de Mentha piperita L. cultivada em solução nutritiva com variação dos níveis de N, P, K e Mg

O estudo objetivou avaliar translocação orgânica, índices fisiológicos da análise de crescimento e rendimento do óleo essencial de Mentha piperita L. cultivada em solução nutritiva com variação dos níveis de N, P, K e Mg. Assim, foram avaliados os quatro tratamentos contendo 50% N, P, K, 25% Mg; 50% N, P, K, Mg; 65%N, 50%P, 25%K, 100% Mg e 100% N, P, K, Mg. A translocação orgânica foi avaliada por meio da determinação da razão de massa foliar (RMF) e da distribuição de massa seca para os diferentes órgãos. Os índices fisiológicos razão de área foliar (RAF), área foliar específica (AFE), taxa assimilatória líquida (TAL) e taxa de crescimento relativo (TCR) derivadas que compõem a análise de crescimento foram estimados pelo programa ANACRES, após ajuste exponencial quadrático da área foliar e massa seca de lâminas foliares e total da planta em relação ao tempo. O rendimento do óleo essencial, em porcentagem, foi calculado após extração da parte aérea por hidrodestilação. As plantas submetidas ao tratamento com nível completo de nutrientes (100%N/P/K/Mg) exportaram com menor eficiência o material orgânico a partir da folha e a RMF mostrou queda mais lenta, devido à retenção desse material por mais tempo no local de sua produção. Além disso, não apresentaram melhor produtividade e as curvas da TAL e TCR mostraram quedas mais lentas. As plantas submetidas ao tratamento com 65%N/50%P/25%K/100%Mg revelaram adequada exportação de matéria orgânica da folha para caule e pecíolos, conforme demonstra a RMF e a distribuição de massa seca para esses órgãos. Revelaram ainda a RAF mais elevada no inicio do desenvolvimento e mais baixa aos 94 DAT, indicando sombreamento das folhas como resultado de seu crescimento. A AFE dessas plantas mostrou menor variação durante o ciclo, refletindo espessura mais constante de suas folhas. A TAL e a TCR apresentaram curvas decrescentes, com quedas bem acentuadas em relação às demais plantas. Todos esses índices indicam melhor produtividade das plantas submetidas ao tratamento 65%N/50%P/25%K/100%Mg, que também apresentaram rendimento de óleo essencial, em média, maior durante o ciclo. Conclui-se que a redução de 35% de N, 50% de P, 75% de K (65%N/50%P/25%K/100%Mg) é indicada para o cultivo e extração de óleo essencial de M. piperita.

Mucociliary clearance and its relation with the level of physical activity in daily life in healthy smokers and nonsmokers

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

Evaluation of strain, dietary energy level and stocking density on broiler feathering

This study evaluated the effects of strain, stocking density and dietary energy level on the feathering of broiler chickens. Four trials were carried out between September 2000 and April 2002. There were 10,685 broiler chicks from the strains Ross 308, Cobb 500, Hybro PG, Hubbard, MPK, and Isa Vedette. The bids were reared at stocking densities varying between 10 and 16 birds/m² and were given diets containing different metabolizable energy levels. Broiler feathering was evaluated either by atrributing scores from 1 to 10 to feather covering along the thigh and back (visual inspection), or by determining the percentage weight of the feathers at 28 and 42 days of age. Increasing rearing densities resulted in poorer feathering, mainly if 12 or 13 birds/m² were compared with 16 birds/m². The strains showed different feathering; it was better in Cobb 500 and MPK birds, whereas Hubbard birds showed poorer feathering, mostly along the back. The energy level in the diet has also affected feathering scores. Medium energy level resulted in better feathering along the back at 28 days, and the low level, in better feathering along the thigh at 35 days of age. Finally, feather scores were better in females than in males.