Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

Background: Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome. Results: In this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG’s annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG. Conclusions: The methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is currently being finished.

Re-establishment of Drosera spiralis (Droseraceae), and a new circumscription of D. graminifolia

Drosera graminifolia and D. spiralis have long been considered conspecific, but new morphological and ecological data support the recognition of these taxa as distinct species. Both species are here described and illustrated, including observations on ecology, habitat, and conservation status, together with a distribution map, line drawings, photographs, and a table containing the distinctive characters.

Re-treatment of previous non-responders and relapsers to interferon plus ribavirin with peginterferon alfa-2a (40KD), ribavirin +/- amantadine in patients with chronic hepatitis C: randomized multicentre clinical trial

Introduction. A large number of patients with chronic hepatitis C have not been cured with interferon-based therapy. Therefore, we evaluated the efficacy of amantadine combined with the standard of care (pegylated interferon plus ribavirin) in patients who had not responded to or had relapsed after 24 weeks of treatment with conventional interferon plus ribavirin. Material and methods. Patients stratified by previous response (i.e., non-response or relapse) were randomized to 48 weeks of open-label treatment with peginterferon alfa-2a (401(D) 180 pg/week plus ribavirin 1,000/1,200 mg/day plus amantadine 200 mg/day (triple therapy), or the standard of care (peginterferon alfa-2a [40KD] plus ribavirin). Results. The primary outcome was sustained virological response (SVR), defined as undetectable hepatitis C virus RNA in serum (< 50 IU/mL) at end of follow-up (week 72). Among patients with a previous non-response, 12/53 (22.6%; 95% confidence interval [CI] 12.3-36.2%) randomized to triple therapy achieved an SVR compared with 16/52 (30.8%; 95% CI 18.7-45.1%) randomized to the standard of care. Among patients with a previous relapse 22/39 (56.4%; 95% CI 39.6-72.2%) randomized to triple therapy achieved an SVR compared with 23/38 (60.5%; 95% CI 43.4-76.0%) randomized to the standard of care. Undetectable HCV RNA (< 50 IU/mL) at week 12 had a high positive predictive value for SVR. A substantial proportion of non-responders and relapsers to conventional interferon plus ribavirin achieve an SVR when re-treated with peginterferon alfa-2a (40KD) plus ribavirin. Conclusion. Amantadine does not enhance SVR rates in previously treated patients with chronic hepatitis C and cannot be recommended in this setting.

The Enhanced Tool-Kit of Two Groups of Wild Bearded Capuchin Monkeys in the Caatinga: Tool Making, Associative Use, and Secondary Tools

The use of stones to crack open encapsulated fruit is widespread among wild bearded capuchin monkeys (Cebus libidinosus) inhabiting savanna-like environments. Some populations in Serra da Capivara National Park (Piaui, Brazil), though, exhibit a seemingly broader toolkit, using wooden sticks as probes, and employing stone tools for a variety of purposes. Over the course of 701.5 hr of visual contact of two wild capuchin groups we recorded 677 tool use episodes. Five hundred and seventeen of these involved the use of stones, and 160 involved the use of sticks (or other plant parts) as probes to access water, arthropods, or the contents of insects` nests. Stones were mostly used as ""hammers""-not only to open fruit or seeds, or smash other food items, but also to break dead wood, conglomerate rock, or cement in search of arthropods, to dislodge bigger stones, and to pulverize embedded quartz pebbles (licking, sniffing, or rubbing the body with the powder produced). Stones also were used in a ""hammer-like"" fashion to loosen the soil for digging out roots and arthropods, and sometimes as ""hoes"" to pull the loosened soil. In a few cases, we observed the re-utilization of stone tools for different purposes (N = 3), or the combined use of two tools-stones and sticks (N = 4) or two stones (N = 5), as sequential or associative tools. On three occasions, the monkeys used smaller stones to loosen bigger quartz pebbles embedded in conglomerate rock, which were subsequently used as tools. These could be considered the first reports of secondary tool use by wild capuchin monkeys. Am. J. Primatol. 71:242-251, 2009. (c) 2008 Wiley-Liss, Inc.

Black carbon affects the cycling of non-black carbon in soil

Black carbon (BC) is an important fraction of many soils worldwide and plays an important role in global C biogeochemistry. However, few studies have examined how it influences the mineralization of added organic matter (AOM) and its incorporation into soil physical fractions and whether BC decomposition is increased by AOM. BC-rich Anthrosols and BC-poor adjacent soils from the Central Amazon (Brazil) were incubated for 532 days either with or without addition of (13)C-isotopically different plant residue. Total C mineralization from the BC-rich Anthrosols with AOM was 25.5% (P < 0.05) lower than with mineralization from the BC-poor adjacent soils. The AOM contributed to a significantly (P < 0.05) higher proportion to the total C mineralized in the BC-rich Anthrosols (91-92%) than the BC-poor adjacent soils (69-80%). The AOM was incorporated more rapidly in BC-rich than BC-poor soils from the separated free light fraction through the intra-aggregate light fraction into the stable organo-mineral fraction and up to 340% more AOM was found in the organo-mineral fraction. This more rapid stabilization was observed despite a significantly (P < 0.05) lower metabolic quotient for BC-rich Anthrosols. The microbial biomass (MB) was up to 125% greater (P < 0.05) in BC-rich Anthrosols than BC-poor adjacent soils. To account for increased MB adsorption onto BC during fumigation extraction, a correction factor was developed via addition of a (13)C-enriched microbial culture. The recovery was found to be 21-41 % lower (P < 0.05) for BC-rich than BC-poor soils due to re-adsorption of MB onto BC. Mineralization of native soil C was enhanced to a significantly greater degree in BC-poor adjacent soils compared to BC-rich Anthrosols as a result of AOM. No positive priming by way of cometabolism due to AOM could be found for aged BC in the soils. (C) 2009 Elsevier Ltd. All rights reserved.

TAXONOMIC STATUS OF CHIRONIUS MULTIVENTRIS AND CHIRONIUS COCHRANAE (SERPENTES)

Recently four subspecies of Chironius multiventris were recognized as valid distinct species: C. in. foveatus, C. in. multiventris, C. in. cochranae, and C. m. septentrionalis. Although C. foveatus and C. septentrionalis clearly deserve specific status, a re-evaluation of the characters pointed in the literature as diagnostic of C. multiventris and C. cochranae does not support their recognition as valid distinct taxa. Additionally, our analysis of the scutellation pattern, continuous characters, and hemipenial morphology of 34 specimens, and of the available data in literature, shows that there are no significant differences between them. We therefore suggest that C. cochranae should be synonymized with C. multiventris.

Compulsive features in behavioural addictions: the case of pathological gambling

Aims To describe, in the context of DSM-V, how a focus on addiction and compulsion is emerging in the consideration of pathological gambling (PG). Methods A systematic literature review of evidence for the proposed re-classification of PG as an addiction. Results Findings include: (i) phenomenological models of addiction highlighting a motivational shift from impulsivity to compulsivity associated with a protracted withdrawal syndrome and blurring of the ego-syntonic/ego-dystonic dichotomy; (ii) common neurotransmitter (dopamine, serotonin) contributions to PG and substance use disorders (SUDs); (iii) neuroimaging support for shared neurocircuitries between behavioural and substance addictions and differences between obsessivecompulsive disorder (OCD), impulse control disorders (ICDs) and SUDs; (iv) genetic findings more closely related to endophenotypic constructs such as compulsivity and impulsivity than to psychiatric disorders; (v) psychological measures such as harm avoidance identifying a closer association between SUDs and PG than with OCD; (vi) community and pharmacotherapeutic trials data supporting a closer association between SUDs and PG than with OCD. Adapted behavioural therapies, such as exposure therapy, appear applicable to OCD, PG or SUDs, suggesting some commonalities across disorders. Conclusions PG shares more similarities with SUDs than with OCD. Similar to the investigation of impulsivity, studies of compulsivity hold promising insights concerning the course, differential diagnosis and treatment of PG, SUDs, and OCD.

Periapical Tissue Response After Use of Intermediate Restorative Material, Gutta-Percha, Reinforced Zinc Oxide Cement, and Mineral Trioxide Aggregate as Retrograde Root-End Filling Materials: A Histologic Study in Dogs

Purpose: To investigate the periapical tissue response of 4 different retrograde root-filling materials, ie, intermediate restorative material, thermoplasticized gutta-percha, reinforced zinc oxide cement (Super-EBA), and mineral trioxide aggregate (MTA), in conjunction with an ultrasonic root-end preparation technique in an animal model. Materials and Methods: Vital roots of the third and fourth right mandibular premolars in 6 healthy mongrel dogs were apicectomized and sealed with 1 of the materials using a standardized surgical procedure. After 120 days, the animals were sacrificed and the specimens were analyzed radiologically, histologically, and scanning electron microscopically. The Fisher exact test was performed on the 2 outcome values. Results: Twenty-three sections were analyzed histologically. Evaluation showed better re-establishment of the periapical tissues and generally lower inflammatory infiltration in the sections from teeth treated with the intermediate restorative material and the MTA. New root cement on the resected dentin surfaces was seen on all sections regardless of the used material. New hard tissue formation, directly on the surface of the material, was seen only in the MTA sections. There was no statistical difference in outcome among the tested materials. Conclusions: The results from this dog model favor the intermediate restorative material and MTA as retrograde fillings when evaluating the bone defect regeneration. MTA has the most favorable periapical tissue response when comparing the biocompatibility of the materials tested. (C) 2012 American Association of Oral and Maxillofacial Surgeons J Oral Maxillofac Surg 70:2041-2047, 2012

Feasibility of Intralaminar, Lateral Mass, or Pedicle Axis Vertebra Screws in Children Under 10 Years of Age: A Tomographic Study

BACKGROUND: There are several techniques for screw insertion in upper cervical spine surgery, and the use of the 3.5-mm screw is usually the standard. However, there is no consensus regarding the feasibility of using these screws in the pediatric population. OBJECTIVE: To determine the measurement of the lamina angle, lamina and pedicle length and thickness, and lateral mass length of the topographic axial view of the axis vertebra of 2- to 10-year-old children to guide the use of surgical screws. METHODS: Seventy-five computed tomography scans from 24- to 120-month-old patients were studied. Measurements were taken in an axial view of C2 and correlated with 2 age groups and both sexes. Statistical analysis was performed with the Student t test. RESULTS: In the 24- to 48-month age group, only 5.5% of the lamina and 8.3% of the pedicles had thicknesses < 3.5 mm. In the 49- to 120-month age group, there were no lamina thickness values < 3.5 mm, and 1.2% of pedicle thicknesses were < 3.5 mm. Both age groups had no lamina and pedicle lengths < 12 mm and no lateral mass lengths > 12 mm. CONCLUSION: In the majority of cases, the use of 3.5-mm lamina and pedicle screws in children is feasible. A base value of 45 degrees for the spinolaminar angle can be adopted as a reference for insertion of screws in the C2 lamina. This information can be particularly useful for decision making during preoperative planning for C1-C2 or craniocervical arthrodesis in children.

Consolidation of Bi-2223 superconducting powders by spark plasma sintering

The spark plasma sintering (SPS) technique, by using a compacting pressure of 50 MPa, was used to consolidate pre-reacted powders of Bi1.65Pb0.35Sr2Ca2Cu3O10+delta (Bi-2223). The influence of the consolidation temperature, T-D, on the structural and electrical properties has been investigated and compared with those of a reference sample synthesized by the traditional solid-state reaction method and subjected to the same compacting pressure. From the X-ray diffraction patterns, performed in both powder and pellet samples, we have found that the dominant phase is the Bi-2223 in all samples but traces of the Bi2Sr2CaCu2O8+x (Bi-2212) were identified. Their relative density were similar to 85% of the theoretical density and the temperature dependence of the electrical resistivity, rho(T), indicated that increasing T-D results in samples with low oxygen content because the SPS is performed in vacuum. Features of the rho(T) data, as the occurrence of normal-state semiconductor-like behavior of rho(T) and the double resistive superconducting transition, are consistent with samples comprised of grains with shell-core morphology in which the shell is oxygen deficient. The SPS samples also exhibited superconducting critical current density at 77 K, J(c)(77K), between 2 and 10A/cm(2), values much smaller than similar to 22A/cm(2) measured in the reference sample. Reoxygenation of the SPS samples, post-annealed in air at different temperatures and times, was found to improve their microstructural and transport properties. Besides the suppression of the Bragg peaks belonging to the Bi-2212 phase, the superconducting properties of the post-annealed samples and particularly J(c)(77K) were comparable or better than those corresponding to the reference sample. Post-annealed samples at 750 degrees C for 5min exhibited J(c)(77K) similar to 130A/cm(2) even when uniaxially pressed at only 50 MPa. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4768257]

The eagle and the starlings: Galileo's argument for the autonomy of science-how pertinent is it today?

After Galileo's argument for the autonomy of science is analysed and adapted to take into account later developments of scientific practices, we conclude that, in the final analysis, it is not compelling. Nevertheless, Galileo's argument still provides a useful point of reference, for aspects of it can be interpreted to anticipate central components of the often acclaimed ideal of science as value free, so that appraising it contributes to the larger purpose of exploring how well that ideal stands up today. Finally, we will argue that residue from Galileo's struggle with the Church remains with us, making it difficult to identify the conditions that would need to be put into place today for any robust sense of the autonomy of science to be defensible. (C) 2011 Elsevier Ltd. All rights reserved.

Revision of the genera Interrhodeus, Pennarhodeus and Poropodalius (Acari: Rhodacaridae)

The genera Interrhodeus Karg, Pennarhodeus Karg and Poropodalius Karg are redescribed on the basis of one species of Interrhodeus, four species of Pennarhodeus and five species of Poropodalius, including the type species of each genus. All species are redescribed on the basis of the type specimens, and keys for the separation of the species of the latter two genera are provided. Re-examination of these species shows that these three genera are correctly placed in the family Rhodacaridae.

Scrupocellaria (Bryozoa: Cheilostomata) from the Queensland coast, with the description of three new species

Among the Scrupocellaria species previously reported from Queensland, three are here redescribed - S. cervicornis, S. curvata and S. diadema; two other species, S. frondis and S. sinuosa, are recorded from the area for the first time; three new species, S. hamata n. sp., S. prolata n. sp. and S. peltata n. sp., are also described, and the remainder are discussed. The need for the re-examination of specimens assigned to this genus is highlighted. The geographic range of some Scrupocellaria species is far more limited than once thought.

High precision astrometry mission for the detection and characterization of nearby habitable planetary systems with the Nearby Earth Astrometric Telescope (NEAT)

A complete census of planetary systems around a volume-limited sample of solar-type stars (FGK dwarfs) in the Solar neighborhood (d a parts per thousand currency signaEuro parts per thousand 15 pc) with uniform sensitivity down to Earth-mass planets within their Habitable Zones out to several AUs would be a major milestone in extrasolar planets astrophysics. This fundamental goal can be achieved with a mission concept such as NEAT-the Nearby Earth Astrometric Telescope. NEAT is designed to carry out space-borne extremely-high-precision astrometric measurements at the 0.05 mu as (1 sigma) accuracy level, sufficient to detect dynamical effects due to orbiting planets of mass even lower than Earth's around the nearest stars. Such a survey mission would provide the actual planetary masses and the full orbital geometry for all the components of the detected planetary systems down to the Earth-mass limit. The NEAT performance limits can be achieved by carrying out differential astrometry between the targets and a set of suitable reference stars in the field. The NEAT instrument design consists of an off-axis parabola single-mirror telescope (D = 1 m), a detector with a large field of view located 40 m away from the telescope and made of 8 small movable CCDs located around a fixed central CCD, and an interferometric calibration system monitoring dynamical Young's fringes originating from metrology fibers located at the primary mirror. The mission profile is driven by the fact that the two main modules of the payload, the telescope and the focal plane, must be located 40 m away leading to the choice of a formation flying option as the reference mission, and of a deployable boom option as an alternative choice. The proposed mission architecture relies on the use of two satellites, of about 700 kg each, operating at L2 for 5 years, flying in formation and offering a capability of more than 20,000 reconfigurations. The two satellites will be launched in a stacked configuration using a Soyuz ST launch vehicle. The NEAT primary science program will encompass an astrometric survey of our 200 closest F-, G- and K-type stellar neighbors, with an average of 50 visits each distributed over the nominal mission duration. The main survey operation will use approximately 70% of the mission lifetime. The remaining 30% of NEAT observing time might be allocated, for example, to improve the characterization of the architecture of selected planetary systems around nearby targets of specific interest (low-mass stars, young stars, etc.) discovered by Gaia, ground-based high-precision radial-velocity surveys, and other programs. With its exquisite, surgical astrometric precision, NEAT holds the promise to provide the first thorough census for Earth-mass planets around stars in the immediate vicinity of our Sun.

Description of the Pupa and Redescription of the Imagines of Geyeria decussata and their Association with Bromeliads in Southern Brazil (Lepidoptera: Castniidae)

ALBERTONI F F [Fed Univ, Florianopolis, Brazil], MORAES S S [Mus Zool USP, Sao Paulo, Brazil], STEINER J [Fed Univ. Florianopolis, Brazil] & ZILLIKENS A [Univ Tubingen, Germany]: Description of the Pupa and Redescription of the Imagines of Geyeria decussata and their Association with Bromeliads in Southern Brazil (Lepidoptera: Castniidae). - Entomol Gener 34 (1-2): 061-074: Stuttgart 2012-09. - [Article] Bromeliads can serve as a resource for numerous arthropods, especially insects. Caterpillars of the moth Geyeria decussata (Godart 1824) were recorded in the leaf rosettes of the bromeliads Wittrockia superba, Vriesea philippocoburgii and Aechmea nudicaulis. The larvae were feeding on the leaf bases, eventually killing the plants. In addition to life history data a description of the pupa and a re-description of the imagines are provided here. These findings constitute new records of larval hosts for this species and confirm a close association of castniid moths and bromeliads.