Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Attachment, marital interaction, and relationship satisfaction: A diary study

The relations among measures of attachment, spouse behavior, and marital satisfaction were assessed in a broad sample of 193 married couples, using both questionnaire and diary methods. Insecure attachment was associated with less favorable reports of spouse behavior, as assessed by diary checklists. Marital satisfaction was predicted by attachment treasures and reports of spouse behavior. The relation between attachment security and marital satisfaction was moderated, but not mediated, by reported spouse behavior. Specifically, insecure individuals' evaluations of their relationships were more reactive to recent spouse behavior, an effect that was especially marked for fearful participants and for those in longer-term marriages. Some gender differences in patterns of prediction were obtained. The results are discussed in terms of the working models associated with attachment styles, and the processes by which relationship satisfaction may be eroded over time.

Control of ovulation with a GnRH agonist after superstimulation of follicular growth in buffalo: fertilization and embryo recovery

The potential to use a GnRH agonist bioimplant and injection of exogenous LH to control the time of ovulation in a multiple ovulation and embryo transfer (MOET) protocol was examined in buffalo. Mixed-parity buffalo (Bubalus bubalis; 4-15-year-old; 529 13 kg LW) were randomly assigned to one of five groups (n = 6): Group 1, conventional MOET protocol; Group 2, conventional MOET with 12 It delay in injection of PGF(2alpha); Group 3, implanted with GnRH agonist to block the pre-ovulatory surge release of LH; Group 4, implanted with GnRH agonist and injected with exogenous LH (Lutropin(R), 25 mg) 24 h after 4 days of superstimulation with FSH; Group 5, implanted with GnRH agonist and injected with LH 36 h after superstimulation with FSH. Ovarian follicular growth in all buffaloes was stimulated by treatment with FSH (Folltropin-V(R), 200 mg) administered over 4 days, and was monitored by ovarian ultrasonography. At the time of estrus, the number of follicles greater than or equal to8 mm. was greater (P < 0.05) for buffaloes in Group 2 (12.8) than for buffaloes in Groups 1 (8.5), 3 (7.3), 4 (6.1) and 5 (6.8), which did not differ. All buffaloes were mated by AI after spontaneous (Groups 1-3) or induced (Groups 4 and 5) ovulation. The respective number of buffalo that ovulated, number of corpora lutea, ovulation rate (%), and embryos + oocytes recovered were: Group 1 (2, 1.8 +/- 1.6, 18.0 +/- 13.6, 0.2 +/- 0.2); Group 2 (4, 6.1 +/- 2.9, 40.5 +/- 17.5, 3.7 +/- 2.1); Group 3 (0, 0, 0, 0); Group 4 (6, 4.3 +/- 1.2, 69.3 +/- 14.2, 2.0 +/- 0.9); and Group 5 (1, 2.5 +/- 2.5, 15.5 +/- 15.5, 2.1 +/- 2.1). All buffaloes in Group 4 ovulated after injection of LH and had a relatively high ovulation rate (69%) and embryo recovery (46%). It has been shown that the GnRH agonist-LH protocol can be used to improve the efficiency of MOET in buffalo. (C) 2002 Elsevier Science Inc. All rights reserved.

The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta : thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes

To help understand the mechanisms of gene rearrangement in the mitochondrial (mt) genomes of hemipteroid insects, we sequenced the mt genome of the plague thrips, Thrips imaginis (Thysanoptera). This genome is circular, 15,407 by long, and has many unusual features, including (1) rRNA genes inverted and distant from one another, (2) an extra gene for tRNA-Ser, (3) a tRNA-Val lacking a D-arm, (4) two pseudo-tRNA genes, (5) duplicate control regions, and (6) translocations and/or inversions of 24 of the 37 genes. The mechanism of rRNA gene transcription in T. imaginis may be different from that of other arthropods since the two rRNA genes have inverted and are distant from one another. Further, the rRNA genes are not adjacent or even close to either of the two control regions. Tandem duplication and deletion is a plausible model for the evolution of duplicate control regions and for the gene translocations, but intramitochondrial recombination may account for the gene inversions in T. imaginis. All the 18 genes between control regions #1 and #2 have translocated and/or inverted, whereas only six of the 20 genes outside this region have translocated and/or inverted. Moreover, the extra tRNA gene and the two pseudo-tRNA genes are either in this region or immediately adjacent to one of the control regions. These observations suggest that tandem duplication and deletion may be facilitated by the duplicate control regions and may have occurred a number of times in the lineage leading to T. imaginis. T. imaginis shares two novel gene boundaries with a lepidopsocid species from another order of hemipteroid insects, the Psocoptera. The evidence available suggests that these shared gene boundaries evolved by convergence and thus are not informative for the interordinal phylogeny of hemipteroid insects. We discuss the potential of hemipteroid insects as a model system for studies of the evolution of animal rut genomes and outline some fundamental questions that may be addressed with this system.

The essential role of democracy in the Bush Doctrine: the invasions of Iraq and Afghanistan

Everyone knows that democracy played a role in the Bush Doctrine. What not everyone knows is that this role was essential for the doctrine to be put into operation under which the Iraq invasion was prepared and launched. We argue moreover that, even if aggressive, the Bush doctrine is compatible with the American Liberal Tradition. To demonstrate these arguments we analyze the links between democracy, security, and the US national interests as expressed in the pillars of the American foreign policy since the end of Cold War. The consequential belief of the Bush Administration on the positive effect of exporting democracy by the use of force to Afghanistan and Iraq to fight terrorism will be remarked. It will be shown, however, that in the first years of the Bush Administration, among the justifications for the military interventions in the two countries, security reasons prevailed over democratic concerns, although the latter was significantly present since the early hours after September 11. It was only when it became clear that WMDs did not exist in Iraq that the exporting of democracy as the ultimate weapon to fight terrorism grew remarkably and prevailed over security reasons to invade those rogue states. The paper uses quantitative and qualitative content analysis of the speeches of President Bush and his Secretaries of State and Defense.

Bone mineral density of rat femurs after hindlimb unloading and different physical rehabilitation programs

Bone weakening can occur due to the absence of load on the skeleton or even short periods of decreased physical activity. Therefore, musculoskeletal diseases that involve temporary immobilization by casts, inactivity or tension increases the risk of fractures. Physical activity is the most studied procedure both to prevent damage and to restore bone structure. The present study aimed at evaluating, by bone densitometry on rat femurs, the influence of hindlimb unloading and later running activity on treadmill or free movement. Sixty-four Wistar rats were used, aged 65 days with a mean corporal mass of 316.11g, randomly divided into eight experimental groups: group 1, the suspended control with seven animals under hindlimb unloading regimen for 28 days, then euthanized; groups 2 and 3, the trained suspended comprising of 7 and five animals, respectively, subjected to hindlimb unloading for 28 days, followed by treadmill exercise for 28 days (group 2) or 56 days (group 3), then euthanized; groups 4 and 5, designated free suspended, comprised of 7 animals each under hindlimb unloading regimen for 28 days followed by free activity in cages for 28 days (group 4) or 56 days (group 5), then euthanized; groups 6, 7 and 8, negative controls, each with 8 animals allowed to free activity in cages and euthanized at the ages of 93, 121 and 149 days, respectively. Bone mineral density (BMD) of the left femur was analyzed by bone densitometry. Unloading by tail-suspension decreased BMD while treadmill training and free activity in cages promoted its recovery in a similar way and over time.

Shape and size of jatropha beans (Jatropha curcas L.) during drying at different temperatures

This study was carried out to study the physical properties of the jatropha beans over the drying under six air conditions, based on measurements of roundness, sphericity, volume, superficial area, projected area and surface/volume ratio. Jatropha beans with moisture content around 0.61 (decimal d.b.) were subjected to thin-layer drying in oven with forced-air circulation under six temperature conditions (36, 45, 60, 75, 90 and 105 °C) and relative humidity of 31.7; 19.6; 9.4; 4.8; 2.6 and 1.5% respectively, until reaching the moisture content of 0.11 ± 0.006 (decimal d. b.). The results showed that the necessary time for jatropha beans to reach the moisture content of 0.11 ± 0.006 (decimal d.b.) were 1.5; 2.25; 3.0; 4.75; 6.75 and 12.0 h for the drying temperatures of 105, 90, 75, 60, 45 and 36 °C, respectively; and the reduction in the moisture content as well as the drying conditions promoted changes in the shape and reduced the size of the jatropha beans.

Indirect effect of neem oil on Podisus nigrispinus (Hemiptera, Pentatomidae): biology and predatory capacity

This study evaluated the effects on the development and predatory capacity of Podisus nigrispinus fed on Spodoptera frugiperda that have ingested different concentrations of neem oil. The predatory capacity of Podisus nigrispinus was assessed, separating nymphs (fourth instar) and adults (males and females). The treatments consisted of S. frugiperda larvae reared in neem oil aqueous solutions (0.077, 0.359 and 0.599%), deltamethrin EC 25 (0.100%) and control arranged in a completely randomized design, with ten replicates. Insects were offered three larval densities (one, three and six), in the third or fourth instars. The predated larvae were examined at 24 and 48 hours after the beginning of the experiment. Biological parameters of Podisus nigrispinus were evaluated in groups of ten second-instar nymphs transferred to pots, in five replicates. Insects were offered 2-6 third and/or fourth-instar larvae reared in the same neem oil concentrations in a completely randomized design. The following parameters were evaluated: duration of each nymph stage (days), nymph mortality (%), weight of fifth-instar nymphs (mg), sex ratio, weight of males and females (mg) and longevity of unfed adults (days). The predatory capacity of nymphs and adults of Podisus nigrispinus was influenced by the neem oil at the concentrations of 0.359% and 0.599% in the highest density. The concentration of 0.359% lengthened the nymphal stage and the concentration of 0.599% reduced the weight of males.

Morphological and phytochemical characterization of Piper hispidinervum DC. and Piper aduncum L. populations in the state of Acre

Because of the increasing demand of the industry for the production of essential oils, studies highlight the genetic variability of Piper hispidinervum and P. aduncum species according to their patterns of spatial distribution, showing the Amazon region as the source of superior genetic material in the production of safrole and dillapiole. Thus, the objective this study was to characterize the morphology and the phytochemistry of Piper hispidinervum and P. aduncum populations in the Active Germplasm Bank of Embrapa Acre to generate subsidies for the genetic improvement of these species. The results showed that the average values for leaf width and length were 141.67 and 48.04 mm, and petioles length and diameter measurements were 2.83 and 1.78 mm for P. hispidinervum and 189.22; 67.74; 6.03 and 2.22 mm for P. aduncum respectively. The average height and canopy volume measurements were 2.39 m and 6.30 m3 and 2.70 m and 7.78 m3 respectively for each species. For P. hispidinervum, the population with higher performance indried yield and content of safrole was population 02, with 3.9%, and the population 04 showed 94.3% safrole content, both with genetic material from the region of Acrelândia and Plácido de Castro. To P. aduncum, the populations with better performance were 207, 208 and 209, forming a homogeneous group with dried yield average of 3.8% and dillapiol content of 84-85%. Such populations are indicated for selection in breeding program of these species due to better performance.

Comparison of different methods for the determination of total organic carbon and humic substances in Brazilian soils

ABSTRACTAiming to compare three different methods for the determination of organic carbon (OC) in the soil and fractions of humic substances, seventeen Brazilian soil samples of different classes and textures were evaluated. Amounts of OC in the soil samples and the humic fractions were measured by the dichromate-oxidation method, with and without external heating in a digestion block at 130 °C for 30 min; by the loss-on-ignition method at 450 °C during 5 h and at 600 °C during 6 h; and by the dry combustion method. Dry combustion was used as reference in order to measure the efficiency of the other methods. Soil OC measured by the dichromate-oxidation method with external heating had the highest efficiency and the best results comparing to the reference method. When external heating was not used, the mean recovery efficiency dropped to 71%. The amount of OC was overestimated by the loss-on-ignition methods. Regression equations obtained between total OC contents of the reference method and those of the other methods showed relatively good adjustment, but all intercepts were different from zero (p < 0.01), which suggests that more accuracy can be obtained using not one single correction factor, but considering also the intercept. The Walkley-Black method underestimated the OC contents of the humic fractions, which was associated with the partial oxidation of the humin fraction. Better results were obtained when external heating was used. For the organic matter fractions, the OC in the humic and fulvic acid fractions can be determined without external heating if the reference method is not available, but the humin fraction requires the external heating.

Identification of tsunami-induced deposits using numerical modeling and rock magnetism techniques: A study case of the 1755 Lisbon tsunami in Algarve, Portugal

Storm- and tsunami-deposits are generated by similar depositional mechanisms making their discrimination hard to establish using classic sedimentologic methods. Here we propose an original approach to identify tsunami-induced deposits by combining numerical simulation and rock magnetism. To test our method, we investigate the tsunami deposit of the Boca do Rio estuary generated by the 1755 earthquake in Lisbon which is well described in the literature. We first test the 1755 tsunami scenario using a numerical inundation model to provide physical parameters for the tsunami wave. Then we use concentration (MS. SIRM) and grain size (chi(ARM), ARM, B1/2, ARM/SIRM) sensitive magnetic proxies coupled with SEM microscopy to unravel the magnetic mineralogy of the tsunami-induced deposit and its associated depositional mechanisms. In order to study the connection between the tsunami deposit and the different sedimentologic units present in the estuary, magnetic data were processed by multivariate statistical analyses. Our numerical simulation show a large inundation of the estuary with flow depths varying from 0.5 to 6 m and run up of similar to 7 m. Magnetic data show a dominance of paramagnetic minerals (quartz) mixed with lesser amount of ferromagnetic minerals, namely titanomagnetite and titanohematite both of a detrital origin and reworked from the underlying units. Multivariate statistical analyses indicate a better connection between the tsunami-induced deposit and a mixture of Units C and D. All these results point to a scenario where the energy released by the tsunami wave was strong enough to overtop and erode important amount of sand from the littoral dune and mixed it with reworked materials from underlying layers at least 1 m in depth. The method tested here represents an original and promising tool to identify tsunami-induced deposits in similar embayed beach environments.

Identification of tsunami-induced deposits using numerical modeling and rock magnetism techniques: A study case of the 1755 Lisbon tsunami in Algarve, Portugal

Storm- and tsunami-deposits are generated by similar depositional mechanisms making their discrimination hard to establish using classic sedimentologic methods. Here we propose an original approach to identify tsunami-induced deposits by combining numerical simulation and rock magnetism. To test our method, we investigate the tsunami deposit of the Boca do Rio estuary generated by the 1755 earthquake in Lisbon which is well described in the literature. We first test the 1755 tsunami scenario using a numerical inundation model to provide physical parameters for the tsunami wave. Then we use concentration (MS. SIRM) and grain size (chi(ARM), ARM, B1/2, ARM/SIRM) sensitive magnetic proxies coupled with SEM microscopy to unravel the magnetic mineralogy of the tsunami-induced deposit and its associated depositional mechanisms. In order to study the connection between the tsunami deposit and the different sedimentologic units present in the estuary, magnetic data were processed by multivariate statistical analyses. Our numerical simulation show a large inundation of the estuary with flow depths varying from 0.5 to 6 m and run up of similar to 7 m. Magnetic data show a dominance of paramagnetic minerals (quartz) mixed with lesser amount of ferromagnetic minerals, namely titanomagnetite and titanohematite both of a detrital origin and reworked from the underlying units. Multivariate statistical analyses indicate a better connection between the tsunami-induced deposit and a mixture of Units C and D. All these results point to a scenario where the energy released by the tsunami wave was strong enough to overtop and erode important amount of sand from the littoral dune and mixed it with reworked materials from underlying layers at least 1 m in depth. The method tested here represents an original and promising tool to identify tsunami-induced deposits in similar embayed beach environments.

Identification of tsunami-induced deposits using numerical modeling and rock magnetism techniques: Astudy case of the 1755 Lisbon tsunami in Algarve, Portugal (vol 182, pg 187, 2010)

Storm- and tsunami-deposits are generated by similar depositional mechanisms making their discrimination hard to establish using classic sedimentologic methods. Here we propose an original approach to identify tsunami-induced deposits by combining numerical simulation and rock magnetism. To test our method, we investigate the tsunami deposit of the Boca do Rio estuary generated by the 1755 earthquake in Lisbon which is well described in the literature. We first test the 1755 tsunami scenario using a numerical inundation model to provide physical parameters for the tsunami wave. Then we use concentration (MS. SIRM) and grain size (chi(ARM), ARM, B1/2, ARM/SIRM) sensitive magnetic proxies coupled with SEM microscopy to unravel the magnetic mineralogy of the tsunami-induced deposit and its associated depositional mechanisms. In order to study the connection between the tsunami deposit and the different sedimentologic units present in the estuary, magnetic data were processed by multivariate statistical analyses. Our numerical simulation show a large inundation of the estuary with flow depths varying from 0.5 to 6 m and run up of similar to 7 m. Magnetic data show a dominance of paramagnetic minerals (quartz) mixed with lesser amount of ferromagnetic minerals, namely titanomagnetite and titanohematite both of a detrital origin and reworked from the underlying units. Multivariate statistical analyses indicate a better connection between the tsunami-induced deposit and a mixture of Units C and D. All these results point to a scenario where the energy released by the tsunami wave was strong enough to overtop and erode important amount of sand from the littoral dune and mixed it with reworked materials from underlying layers at least 1 m in depth. The method tested here represents an original and promising tool to identify tsunami-induced deposits in similar embayed beach environments.

Information and communication technologies in education – a web-based intelligent tutoring system on teaching and learning electrical project

Electrical activity is extremely broad and distinct, requiring by one hand, a deep knowledge on rules, regulations, materials, equipments, technical solutions and technologies and assistance in several areas, as electrical equipment, telecommunications, security and efficiency and rational use of energy, on the other hand, also requires other skills, depending on the specific projects to be implemented, being this knowledge a characteristic that belongs to the professionals with relevant experience, in terms of complexity and specific projects that were made.

Voltammetric oxidation of drugs of abuse III. Heroin and metabolites

The oxidative behavior of heroin in aqueous solution is reported. In order to identify its oxidation peaks, several metabolites, 6-monoacetylmorphine, 3-monoacetylmorphine and norheroin, were synthesized and their electrochemical behavior studied using differential pulse voltammetry. The anodic waves observed for heroin correspond to the oxidation of the tertiary amine group and its follow-up product (secondary amine), and to the oxidation of the phenolic group obtained from hydrolysis, at alkaline pHs, of the 3-acetyl group. The results enabled a new oxidative mechanism for heroin to be proposed in which a secondary amine, norheroin, and an aldehyde are obtained. The voltammetric behavior of 6-monoacetylmorphine and morphine was found to be similar demonstrating that the presence of an acetyl substituent on the 6-hydroxy group does not have a relevant influence on the peak potential of the wave resulting from oxidation of the 3-phenolic group.