Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies

Phylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations are reviewed. Sampling of genes, genomes and species are considered. Although increased higher-level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.

Holocene environmental changes in the lower Thames Valley, London, UK: implications for our understanding of the history of Taxus woodland

A radiocarbon-dated multiproxy palaeoenvironmental record from the Lower Thames Valley at Hornchurch Marshes has provided a reconstruction of the timing and nature of vegetation succession against a background of Holocene climate change, relative sea level movement and human activities. The investigation recorded widespread peat formation between c. 6300 and 3900 cal. yr BP (marine ‘regression’), succeeded by evidence for marine incursion. The multiproxy analyses of these sediments, comprising pollen, Coleoptera, diatoms, and plant and wood macrofossils, have indicated significant changes in both the wetland and dryland environment, including the establishment of Alnus (Alder) carr woodland, and the decline of both Ulmus (Elm; c. 5740 cal. yr BP) and Tilia (Lime; c. 5600 cal. yr BP, and 4160–3710 cal. yr BP). The beetle faunas from the peat also suggest a thermal climate similar to that of the present day. At c. 4900 cal. yr BP, Taxus (L.; Yew) woodland colonised the peatland forming a plant community that has no known modern analogue in the UK. The precise reason, or reasons, for this event remain unclear, although changes in peatland hydrology seem most likely. The growth of Taxus on peatland not only has considerable importance for our knowledge of the vegetation history of southeast England, and NW Europe generally, but also has wider implications for the interpretation of Holocene palaeobotanical records. At c. 3900 cal. yr BP, Taxus declined on the peatland surface during a period of major hydrological change (marine incursion), an event also strongly associated with the decline of dryland woodland taxa, including Tilia and Quercus, and the appearance of anthropogenic indicators.

Mechanism of the Escherichia coli DNA T:G-mismatch endonuclease (Vsr protein) probed with thiophosphate-containing oligodeoxynucleotides

The mechanism of the Escherichia coli DNA T:G mismatch endonuclease (Vsr) has been investigated using oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric phosphorothioates and a 3'-phosphorothiolate. Binding and kinetic data with the phosphorothioates/phosphorothiolate indicate that the two magnesium ions, which constitute essential co-factors, are required to stabilise the extra negative charge developed on the phosphate as the transition state is formed. Additionally one of the magnesium ions serves to activate the leaving group (the non-bridging 3'-oxygen atom of the scissile phosphate) during the hydrolysis reaction. Stereochemical analysis, using the R-p phosphorothioate isomer, indicates that Vsr carries out a hydrolytic reaction with inversion of stereochemistry at phosphorus, compatible with an in-line attack of water and a pentacovalent transition state with trigonal bipyramidal geometry. In conjunction with structures of Vsr bound to its products, these data allow the reconstruction of the enzyme-substrate complex and a comprehensive description of the hydrolysis mechanism. (c) 2005 Elsevier Ltd. All rights reserved.

Initialisation and predictability of the AMOC over the last 50 years in a climate model

The mechanisms involved in Atlantic meridional overturning circulation (AMOC) decadal variability and predictability over the last 50 years are analysed in the IPSL–CM5A–LR model using historical and initialised simulations. The initialisation procedure only uses nudging towards sea surface temperature anomalies with a physically based restoring coefficient. When compared to two independent AMOC reconstructions, both the historical and nudged ensemble simulations exhibit skill at reproducing AMOC variations from 1977 onwards, and in particular two maxima occurring respectively around 1978 and 1997. We argue that one source of skill is related to the large Mount Agung volcanic eruption starting in 1963, which reset an internal 20-year variability cycle in the North Atlantic in the model. This cycle involves the East Greenland Current intensity, and advection of active tracers along the subpolar gyre, which leads to an AMOC maximum around 15 years after the Mount Agung eruption. The 1997 maximum occurs approximately 20 years after the former one. The nudged simulations better reproduce this second maximum than the historical simulations. This is due to the initialisation of a cooling of the convection sites in the 1980s under the effect of a persistent North Atlantic oscillation (NAO) positive phase, a feature not captured in the historical simulations. Hence we argue that the 20-year cycle excited by the 1963 Mount Agung eruption together with the NAO forcing both contributed to the 1990s AMOC maximum. These results support the existence of a 20-year cycle in the North Atlantic in the observations. Hindcasts following the CMIP5 protocol are launched from a nudged simulation every 5 years for the 1960–2005 period. They exhibit significant correlation skill score as compared to an independent reconstruction of the AMOC from 4-year lead-time average. This encouraging result is accompanied by increased correlation skills in reproducing the observed 2-m air temperature in the bordering regions of the North Atlantic as compared to non-initialized simulations. To a lesser extent, predicted precipitation tends to correlate with the nudged simulation in the tropical Atlantic. We argue that this skill is due to the initialisation and predictability of the AMOC in the present prediction system. The mechanisms evidenced here support the idea of volcanic eruptions as a pacemaker for internal variability of the AMOC. Together with the existence of a 20-year cycle in the North Atlantic they propose a novel and complementary explanation for the AMOC variations over the last 50 years.

Palaeomagnetism, rock magnetism and AMS of the Cabo Magmatic Province, NE Brazil, and the opening of South Atlantic

P>Reconstruction of the South Atlantic opening has long been a matter of debate and several models have been proposed. One problem in tracing properly the Atlantic history arises from the existence of a long interval without geomagnetic reversals, the Cretaceous Normal Superchron, for which ages are difficult to assign. Palaeomagnetism may help in addressing this issue if high-quality palaeomagnetic poles are available for the two drifting continental blocks, and if precise absolute ages are available. In this work we have investigated the Cabo Magmatic Province, northeastern Brazil, recently dated at 102 +/- 1 Ma (zircon fission tracks, Ar39/Ar40). All volcanic and plutonic rocks showed stable thermal and AF demagnetization patterns, and exhibit primary magnetic signatures. AMS data also support a primary origin for the magnetic fabric and is interpreted to be contemporaneous of the rock formation. The obtained pole is located at 335.9 degrees E/87.9 degrees S (N = 24; A(95) = 2.5; K = 138) and satisfies modern quality criteria, resulting in a reference pole for South America at similar to 100 Ma. This new pole also gives an insight to test and discuss the kinematic models currently proposed for the South Atlantic opening during mid-Cretaceous.

Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory

The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs ""radio-hybrid"" measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request. (C) 2011 Elsevier B.V. All rights reserved.

Histoarchitectural Features of the Hepatopancreas of the Amazon River Prawn Macrobrachium amazonicum

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Influence of the elevation of the left ventricular diastolic pressure on the values of the first temporal derivative of the ventricular pressure (dP/dt)

PURPOSE: To assess the effects of the elevation of the left ventricular end-diastolic pressure (LVEDP) on the value of the 1st temporal derivative of the ventricular pressure (dP/dt). METHODS: Nineteen anesthetized dogs were studied. The dogs were mechanically ventilated and underwent thoracotomy with parasympathetic nervous system block. The LVEDP was controlled with the use of a perfusion circuit connected to the left atrium and adjusted to the height of a reservoir. The elevation of the LVEDP was achieved by a sudden increase in the height of a reservoir filled with blood. Continuous recordings of the electrocardiogram, the aortic and ventricular pressures and the dP/dt were performed. RESULTS: Elevation of the LVEDP did not result in any variation of the heart rate (167±16.0bpm, before the procedure; 167±15.5bpm, after the procedure). All the other variables assessed, including systolic blood pressure (128±18.3mmHg and 150±21.5mmHg), diastolic blood pressure (98±16.9mmHg and 115±19.8mmHg), LVEDP (5.5±2.49 and 9.3±3.60mmHg), and dP/dt (4,855 ± 1,082 mmHg/s and 5,149±1,242mmHg/s) showed significant increases following the expansion of the ventricular cavity. Although the elevation of the dP/dt was statistically significant, 6 dogs curiously showed a decrease in the values of dP/dt. CONCLUSION: Sudden elevation of the LVEDP resulted in increased values of dP/dt; however, in some dogs, this response was not uniform.

Reconstruction of Skull Defects: Currently Available Materials

The restoration and recovery of a compromised skull continues to be a challenge to craniofacial surgeons and neurosurgeons. Different operative techniques and implant materials are being used to reconstruct the rigid framework of the skull. However, no currently available materials satisfy all of these criteria. According to this premise, the aim of this study was to report on the currently available materials for the reconstruction of the cranial vault and to describe their main characteristics, advantages, and disadvantages. Although the use of the materials discussed in this study is clearly positive for the reconstruction of skull defects and cranioplasties, there is a need for more complex studies and research into developing these materials to achieve all the ideal prerequisites stipulated by the scientific community and to evaluate their properties and aesthetic and functional results in the long term.

Evaluation of the Smear Layer and Hybrid Layer in Noncarious and Carious Dentin Prepared by Air Abrasion System and Diamond Tips

Purpose: To analyze the smear layer and the hybrid layer in noncarious and carious dentin prepared by different cutting instruments and restored with composite resin. Study design: Cavities were randomly prepared in 160 specimens (noncarious and artificial carious dentin) by high-speed diamond tips (KG Sorensen 1013), air abrasion system (Prepstart, Danville Engineering), ultrasonic tip (CVDentus 8.3231-1), and ultrasonic tip associated with ultrasonic cavitation by water for 10 s. Half of the cavities in each group were conditioned with 37% phosphoric acid for 15 s. The amount of smear layer and dentinal tubules present were analyzed using scanning electron microscopy and graded from 0 to 3. Cavities were prepared in another 20 noncarious specimens and 20 carious specimens and restored with adhesive composite resin system. The restorations were hemisected longitudinally and analyzed using scanning electron microscopy to evaluate the hybrid layer and resinous prolongation characteristics, using scores ranging from 1 to 6. Results: The data were statistically analyzed using Kruskal-Wallis and Dunn tests at 5% of significance level. There was evidence that the most efficient smear layer removal was the acid etching in the noncarious dentin and the water ultrasonic cavitation in the carious dentin. The hybrid layer formed on the noncarious and carious dentin prepared by the ultrasonic tip was more regular than in the specimens prepared by high-speed diamond tip, with many resinous prolongations. Conclusion: The ultrasonic tip seems to be a promising tool for carious dentin cavity preparation. Microsc. Res. Tech. 73:597-605, 2010. (C) 2009 Wiley-Liss, Inc.

Measurement of the t(t)over-bar production cross section in pp collisions at root s=7 TeV using the kinematic properties of events with leptons and jets

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Congenital deformity of the paw in a captive tiger: case report

Background: The aim of this report was to describe the clinical signs, diagnostic approach, treatment and outcome in the case of a tiger with a deformity of the paw.Case presentation: A 1.5-year-old tiger (Panthera tigris) was presented with lameness of the left thoracic limb. A deformity involving the first and second metacarpal bones, and a soft tissue separation between the second and third metacarpal bones of the left front paw were observed. The second digit constantly struck the ground during locomotion. Based on the physical and radiographic evaluations, a diagnosis of ectrodactyly was made. A soft tissue reconstruction of the cleft with excision of both the second digit and distal portion of the second metacarpal bone was performed. Marked improvement of the locomotion was observed after surgical treatment, although the tiger showed a low degree of lameness probably associated with the discrepancy in length between the thoracic limbs.Conclusion: This report shows a rare deformity in an exotic feline that it is compatible to ectrodactyly. Reconstructive surgery of the cleft resulted in significant improvement of limb function.

Indicators of the risk mechanics for Class-I and Class-II amalgam and composite resin restorations

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

Structure, histochemistry and seasonal variations of the male reproductive accessory glands in the Pallas

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

Plasmacytoma in the oral cavity: a case report

The plasma cell neoplasms may present in soft tissue as extramedullary plasmacytoma (EMP), in bone as a solitary plasmacytoma of bone (SPB), or as part of the multifocal disseminated disease multiple myeloma (MM). The EMP is rare, comprising around 3% of all plasma cell neoplasm. The majority (80%) occurs in the head and neck region. In this study we report a case of a man, 70 years old, melanoderm, with a lesion of the oral cavity. Upon physical examination, a lesion was found that extended throughout the posterior upper alveolar ridge, as far as the maxillary tuber on the left side, extending towards the palate. Radiographic examination, complementary laboratory exams were performed. Based on the conclusive symptoms of plasmacytoma, the patient was referred to the hematology service for treatment with local radiotherapy. The patient responded satisfactorily to the treatment, and after 15 months, all clinical symptoms of the lesion in the oral cavity had disappeared.