Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel

Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S-trnI-trnA-23S-5S, rbcL-rbcS and rpl12-rps31-rpl9 regions and the mitochondrial cox2–3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128 000 bp and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20 000 bp) in the Hurd Deep, an enigmatic trench in the English Channel.

Single- and multiphoton detachment of K

Single- and multiphoton detachment rates have been calculated for K- using the R-matrix Floquet approach. Single-photon detachment rates, obtained at a laser field peak intensity of 10(9) W cm(-2), are discussed and compared with other theoretical work. Two-photon detachment rates at the same intensity have also been obtained, and similarities with results from earlier calculations for Li- and Na- are discussed. Three-photon rates are also presented at this laser intensity, and are compared and contrasted with those arising in the single-photon case, since both involve resonance structure with P-1(o) symmetry. The influence of resonances such as the 5s(2) S-1(e) doubly excited state and excitations of the residual atom are also considered.

High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications.

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine–adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3'-5')-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554–1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis–syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield.

Dynamic resonances and tunnelling in the multiphoton ionization of argon

We present results of wavepacket simulations for multiphoton ionization in argon. A single active electron model is applied to estimate the single-electron ionization rates and photoelectron energy distributions for lambda = 390 nm light with intensities up to I = 2 x 10(14) W cm(-2). The multiphoton ionization rates are compared with R-matrix Floquet calculations and found to be in very good agreement. The photoelectron energy distribution is used to study the nature of ionization at the higher intensities. Our results are consistent with recent calculations and experiments which show the imprint of the tunnelling process in the multiphoton regime. For few-cycle intense pulses, we find that the strong modulation of intensity and increased bandwidth leads to dynamic mixing of the 3d and 5s resonances.

Metals in the Exosphere of the Highly Irradiated Planet WASP-12b

We present near-UV transmission spectroscopy of the highly irradiated transiting exoplanet WASP-12b, obtained with the Cosmic Origins Spectrograph on the Hubble Space Telescope. The spectra cover three distinct wavelength ranges: NUVA (2539-2580 Å), NUVB (2655-2696 Å), and NUVC (2770-2811 Å). Three independent methods all reveal enhanced transit depths attributable to absorption by resonance lines of metals in the exosphere of WASP-12b. Light curves of total counts in the NUVA and NUVC wavelength ranges show a detection at a 2.5s level. We detect extra absorption in the Mg II ??2800 resonance line cores at the 2.8s level. The NUVA, NUVB, and NUVC light curves imply effective radii of 2.69 ± 0.24 R J , 2.18 ± 0.18 R J , and 2.66 ± 0.22 R J respectively, suggesting the planet is surrounded by an absorbing cloud which overfills the Roche lobe. We detect enhanced transit depths at the wavelengths of resonance lines of neutral sodium, tin, and manganese, and at singly ionized ytterbium, scandium, manganese, aluminum, vanadium, and magnesium. We also find the statistically expected number of anomalous transit depths at wavelengths not associated with any known resonance line. Our data are limited by photon noise, but taken as a whole the results are strong evidence for an extended absorbing exosphere surrounding the planet. The NUVA data exhibit an early ingress, contrary to model expectations; we speculate this could be due to the presence of a disk of previously stripped material.

Biosynthetic Chlorination of the Piperazate Residue in Kutzneride Biosynthesis by KthP

Kutznerides 2 and 8 of the cyclic hexadepsipeptide family of antifungal natural products from the soil actinomycete Kutzneria sp. 744 contain two sets of chlorinated residues, a 6,7-dichlorohexahydropyrroloindole moiety derived from dichlorotryptophan and a 5-chloropiperazate moiety, as well as a methylcyclopropylglycine residue that may arise from isoleucine via a cryptic chlorination pathway. Previous studies identified KtzD, KtzQ and KtzR as three halogenases in the kutzneride pathway but left no candidate for installing the CS chlorine on piperazate. On the basis of analysis of the complete genome sequence of Kutzneria, we now identify a fourth halogenase in the pathway whose gene is separated from the defined kutzneride cluster by 12 open reading frames. KthP (kutzneride halogenase for piperazate) is a mononuclear nonheme iron halogenase that acts on the piperazyl ring tethered by a thioester linkage to the holo forms of thiolation domains. MS analysis of the protein-bound product confirmed chlorination of the piperazate framework from the (3S)- but not the (3R)-piperazyl-S-pantetheinyl thiolation proteins. After thioesterase-mediated release, nuclear magnetic resonance was used to assign the free imino acid as (3S,5S)-5-chloropiperazate, distinct from the 3S,5R stereoisomer reported in the mature kutznerides. These results demonstrate that a fourth halogenase, KthP, is active in the kutzneride biosynthetic pathway and suggest further processing of the (3S,5S)-5-chloropiperazate during subsequent incorporation into the kutzneride depsipeptide frameworks.

Timekeeping strategies operate independently from spatial and accuracy demands in beat-interception movements

The prevailing paradigm for researching sensorimotor synchronisation in humans involves finger tapping and temporal accuracy measures. However, many successful sensorimotor synchronisation actions require not only to be 'in time', but also to be in a predefined spatial position. Reaching this spatial position in many everyday actions often exceeds the average amplitude of a finger movement. The aim of this study is to address how people coordinate their movement to be in the right place at the right time when the scale of the movement varies. Does the scale of the movement and accuracy demands of the movement change the ability to accurately synchronise? To address these questions, a sensorimotor synchronisation task with three different inter-beat intervals, two different movement amplitudes and two different target widths was used. Our experiment demonstrated that people use different timing strategies-employing either a movement strategy (varying movement time) or a waiting strategy (keeping movement time constant) for large-scale movements. Those two strategies were found to be equally successful in terms of temporal accuracy and variability (spread of errors). With longer interval durations (2.5 and 3.5 s), variability of sensorimotor synchronisation performance increased (measured as the spread of errors). Analysing the data using the Vorberg and Wing (Handbook of perception and action. Academic Press, New York, pp 181-262, 1996) model shows a need to develop further existing timing models of sensorimotor synchronisation so that they could apply to large-scale movements, where different movement strategies naturally emerge.

Seasonal variation in month of diagnosis in children with type 1 diabetes registered in 23 EURODIAB centres during 1989-2008

Objectives: To investigate seasonal variation in month of diagnosis in children with type 1 diabetes registered in EURODIAB centres during 1989-2008.
Methods: 23 population-based registers recorded date of diagnosis in new cases of clinically diagnosed type 1 diabetes in children aged under 15 years. Completeness of ascertainment was assessed through capture-recapture methodology and was high in most centres. A general test for seasonal variation (11df) and Edward's test for sinusoidal (sine wave) variation (2df) were employed. Time series methods were also used to investigate if meteorological data were predictive of monthly counts after taking account of seasonality and long term trends.
Results: Significant seasonal variation was apparent in all but two small centres, with an excess of cases apparent in the winter quarter. Significant sinusoidal pattern was also evident in all but two small centres with peaks in December (14 centres), January (5 centres) or February (2 centres). Relative amplitude varied from ±11% to ±39% (median ±18%). There was no relationship across the centres between relative amplitude and incidence level. However there was evidence of significant deviation from the sinusoidal pattern in the majority of centres. Pooling results over centres, there was significant seasonal variation in each age-group at diagnosis, but with significantly less variation in those aged under 5 years. Boys showed marginally greater seasonal variation than girls. There were no differences in seasonal pattern between four sub-periods of the 20 year period. In most centres monthly counts of cases were not associated with deviations from normal monthly average temperature or sunshine hours; short term meteorological variations do not explain numbers of cases diagnosed.
Conclusions: Seasonality with a winter excess is apparent in all age-groups and both sexes, but girls and the under 5s show less marked variation. The seasonal pattern changed little in the 20 year period.

Optimizing geometric accuracy of four dimensional CT scans acquired using the wall and couch mounted Varian Real-Time Position Management camera systems

Objective:

The aim of this study was to identify sources of anatomical misrepresentation due to the location of camera mounting, tumour motion velocity and image processing artefacts in order to optimise the 4DCT scan protocol and improve geometrical-temporal accuracy.

A phantom with an imaging insert was driven with a sinusoidal superior-inferior motion of varying amplitude and period for 4DCT scanning. The length of a high density cube within the insert was measured using treatment planning software to determine the accuracy of its spatial representation. Scan parameters were varied including the tube rotation period and the cine time between reconstructed images. A CT image quality phantom was used to measure various image quality signatures under the scan parameters tested.

No significant difference in spatial accuracy was found for 4DCT scans carried out using the wall mounted or couch mounted camera for sinusoidal target motion. Greater spatial accuracy was found for 4DCT scans carried out using a tube rotation speed of 0.5s rather than 1.0s. The reduction in image quality when using a faster rotation speed was not enough to require an increase in patient dose.

4DCT accuracy may be increased by optimising scan parameters, including choosing faster tube rotation speeds. Peak misidentification in the recorded breathing trace leads to spatial artefacts and this risk can be reduced by using a couch mounted infrared camera.

This study explicitly shows that 4DCT scan accuracy is improved by scanning with a faster CT tube rotation speed.

X=Y-ZH COMPOUNDS AS POTENTIAL 1,3-DIPOLES .43. METAL-ION CATALYZED ASYMMETRIC 1,3-DIPOLAR CYCLOADDITION REACTIONS OF IMINES AND MENTHYL ACRYLATE

Metallo-azomethine ylides, generated from imines by the action of amine bases in combination with LiBr or AgOAc, undergo cycloaddition with both 1R, 2S, 5R- and 1S, 2R, 5S-menthyl acrylate at room temperature to give homochiral pyrrolidines in excellent yield. The stronger the base the faster the cycloaddition and the greater the yield with: 2-t-butyl-1,1,3,3-tetramethylguanidine > DBU > NEt(3) X-Ray crystal structures of representative cycloadducts establish that the absolute configuration of the newly established pyrrolidine stereocentres is independent of the metal salt and the size of the pyrrolidineC(2)-substituent for a series of aryl and aliphatic imines.

Mitochondrial DNA Damage Following Isolated Muscle Exercise: A Preliminary Investigation Into HO-1 Gene Expression

PURPOSE: This preliminary investigation was designed to test the hypothesis that high intensity single-leg exercise can cause extensive cell DNA damage, which subsequently may affect the expression of the HO-1 gene. METHODS: Six (n=6) apparently healthy male participants (age 27 + 7 yrs, stature 174 + 12 cm, body mass 79 + 4 kg and BMI 24 + 4 kg/m2) completed 100 isolated and continuous maximal concentric contractions (minimum force = 200 N, speed of contraction = 60°/sec) of the rectus femoris muscle. Using a spring-loaded and reusable Magnum biopsy gun with a 16-gauge core disposable biopsy needle, skeletal muscle micro biopsy tissue samples were extracted at rest and following exercise. mRNA gene expression was determined via two-step quantitative real-time PCR using GAPDH as a reference gene. RESULTS: The average muscle force production was 379 + 179 N. High intensity exercise increased mitochondrial 8-OHdG concentration (P < 0.05 vs. rest) with a concomitant decrease in total antioxidant capacity (P < 0.05 vs. rest). Exercise also increased protein oxidation as quantified by protein carbonyl concentration (P < 0.05 vs. rest). HO-1 expression increased (> 2-fold change vs. rest) following exercise, and it is postulated that this change was not significant due to low subject numbers (P > 0.05). CONCLUSION: These preliminary findings tentatively suggest that maximal concentric muscle contractions can cause intracellular DNA damage with no apparent disruption to the expression of the antioxidant stress protein HO-1. Moreover, it is likely that cell oxidant stress is required to activate the signal transduction cascade related to the expression of HO-1. A large-scale study incorporating a greater subject number is warranted to fully elucidate this relationship.

The effects of Chronic Lycopene Supplementation on Exercise-Induced Oxidative Stress and Glucose Homeostasis.

Lycopene can exert antioxidant effects against peripheral and cellular oxidative stress and may be associated with reduced diabetic risk. Conversely, exercise-induced free radicals are thought to underpin many of the desirable whole-body adaptations following training and the use of antioxidants within the exercise model remains debatable. PURPOSE: To investigate the effect of lycopene supplementation on oxidative stress and glucose homeostasis following acute aerobic exercise. METHOD: Twenty-eight (n=28) apparently healthy male volunteers were recruited (age 24 ± 4 years; weight 78 ± 10 kg; height 178 ± 8 cm; 2max 40 ± 7 ml·kg-1 ·min-1 ) in a randomised, single blind, placebo-controlled study. Participants were required to attend the Laboratory on two occasions: prior to and following 6 weeks of supplementation of either 10mg lycopene (LG; n=15) or placebo (PG; n=13) followed by a bout of acute exercise for one hour at 65% 2max. Exogenous glucose oxidation was then measured on an isotope ratio mass spectrometer in a sub-group of participants (n=14) following exercise, by administration of a standard oral glucose tolerance test (OGTT; 75g glucose). Venous blood samples were drawn for measurement of oxidative stress parameters, plasma glucose and insulin. RESULTS: Plasma lycopene increased in LG only (0.01 ± 0.004 vs.0.02 ± 0.007 µmol/L; P <0.05) following supplementation and remained elevated post exercise compared to PG (0.01 ± 0.004 vs. 0.02 ± 0.009 µmol/L; P <0.05). There were no changes in other markers of oxidative stress (SOD, LOOHs, F2 ISP and Alkoxyl radical) either between or within the trials, (P >0.05, respectively). A main effect for an increase in insulin was observed two hours post OGTT in the sub-groups (Pooled data, P <0.05) but trends in the HOMA scores were evident with a 57% increase for LG (2.20 ± 1.84 vs. 5.14 ± 2.5; P >0.05) and an 11% decrease for PG (2.17 ± 1.06 vs. 1.94 ± 1.53; P >0.05). No change in plasma glucose was detected at any point, or after the OGTT (P >0.05). CONCLUSION: In healthy males, lycopene supplementation had no effect on post exercise levels of ROS or markers of lipid peroxidation, despite an increase in plasma lycopene. However, lycopene supplementation may affect post exercise insulin sensitivity in response to glucose consumption, but further parallel research is required.

Is the raised volume rapid thoracic compression technique ready for use in clinical trials in infants with cystic fibrosis?

The European Cystic Fibrosis Society Clinical Trial Network (ECFS-CTN) has established a Standardization Committee to undertake a rigorous evaluation of promising outcome measures with regard to use in multicentre clinical trials in cystic fibrosis (CF). The aim of this article is to present a review of literature on clinimetric properties of the infant raised-volume rapid thoracic compression (RVRTC) technique in the context of CF, to summarise the consensus amongst the group on feasibility and answer key questions regarding the promotion of this technique to surrogate endpoint status.

METHODS: A literature search (from 1985 onwards) identified 20 papers that met inclusion criteria of RVRTC use in infants with CF. Data were extracted and tabulated regarding repeatability, validity, correlation with other outcome measures, responsiveness and reference values. A working group discussed the tables and answered 4 key questions.

RESULTS: Overall, RVRTC in particular forced expiratory volume in 0.5s, showed good clinimetric properties despite presence of individual variability. Few studies showed a relationship between RVRTC and inflammation and infection, and to date, data remains limited regarding the responsiveness of RVRTC after an intervention. Concerns were raised regarding feasibility in multi-centre studies and availability of reference values.

CONCLUSION: The ECFS-CTN Working Group considers that RVRTC cannot be used as a primary outcome in clinical trials in infants with CF before universal standardization of this measurement is achieved and implementation of inter-institutional networking is in place. We advise its use currently in phase I/II trials and as a secondary endpoint in phase III studies. We emphasise the need for (1) more short-term variability and longitudinal 'natural history' studies, and (2) robust reference values for commercially available devices.

Electron-impact excitation of Ar 2+

Context: Emission from Ar III is seen in planetary nebulae, in H II regions, and from laboratory plasmas. The analysis of such spectra requires accurate electron impact excitation data. Aims: The aim of this work is to improve the electron impact excitation data available for Ar2+, for application in studies of planetary nebulae and laboratory plasma spectra. The effects of the new data on diagnostic line ratios are also studied. Methods: Electron-impact excitation collision strengths have been calculated using the R-Matrix Intermediate-Coupling Frame-Transformation method and the R-Matrix Breit-Pauli method. Excitation cross sections are calculated between all levels of the configurations 3s^23p^4, 3s3p^5, 3p^6, 3p^53d, and 3s^23p^3nl (3d ≤ nl ≤ 5s). Maxwellian effective collision strengths are generated from the collision strength data. Results: Good agreement is found in the collision strengths calculated using the two R-Matrix methods. The collision strengths are compared with literature values for transitions within the 3s^23p4 configuration. The new data has a small effect on Te values obtained from the I(λ7135 Å+ λ7751 Å)/ I(λ5192 Å) line ratio, and a larger effect on the Ne values obtained from the I(λ7135 Å)/I(λ9 μm) line ratio. The final effective collision strength data is archived online.

Single-photon single ionization of W+ ions: experiment and theory

Experimental and theoretical results are reported for photoionization of Ta-like (W+) tungsten ions. Absolute cross sections were measured in the energy range 16–245 eV employing the photon–ion merged-beam setup at the advanced light source in Berkeley. Detailed photon-energy scans at 100 meV bandwidth were performed in the 16–108 eV range. In addition, the cross section was scanned at 50 meV resolution in regions where fine resonance structures could be observed. Theoretical results were obtained from a Dirac–Coulomb R-matrix approach. Photoionization cross section calculations were performed for singly ionized atomic tungsten ions in their 5s²5p⁶5d⁴(⁵D)6s ⁶Dj.  J = 1/2, ground level and the associated excited metastable levels with J = 3/2, 5/2, 7/2 and 9/2. Since the ion beams used in the experiments must be expected to contain long-lived excited states also from excited configurations, additional cross-section calculations were performed for the second-lowest term, 5d⁵⁶Sj, J = 5/2, and for the 4F term, 5d³6s^{2 4}Fj, with J = 3/2, 5/2, 7/2 and 9/2. Given the complexity of the electronic structure of W+ the calculations reproduce the main features of the experimental cross section quite well.