Low-dose studies of bystander cell killing with targeted soft X rays

The Gray Cancer Institute ultrasoft X-ray microprobe was used to quantify the bystander response of individual V79 cells exposed to a focused carbon K-shell (278 eV) X-ray beam. The ultrasoft X-ray microprobe is designed to precisely assess the biological response of individual cells irradiated in vitro with a very fine beam of low-energy photons. Characteristic C-K X rays are generated by a focused beam of 10 keV electrons striking a graphite target. Circular diffraction gratings (i.e. zone plates) are then employed to focus the X-ray beam into a spot with a radius of 0.25 mum at the sample position. Using this microbeam technology, the correlation between the irradiated cells and their nonirradiated neighbors can be examined critically. The survival response of V79 cells irradiated with a C-K X-ray beam was measured in the 0-2-Gy dose range. The response when all cells were irradiated was compared to that obtained when only a single cell was exposed. The cell survival data exhibit a linear-quadratic response when all cells were targeted (with evidence for hyper-sensitivity at low doses). When only a single cell was targeted within the population, 10% cell killing was measured. In contrast to the binary bystander behavior reported by many other investigations, the effect detected was initially dependent on dose (200 mGy). In the low-dose region (

Performance of clay samples reinforced with vertical granular columns

This paper reports an experimental study in which samples of soft kaolin clay (100 mm in diameter and 200 mm in height) were reinforced with vertical columns of sand and tested under triaxial conditions. Samples were reinforced with either a single column of sand of 32 mm diameter or three columns of sand, each of 20 mm diameter. The replacement method was used to form the columns. The columns were installed in the clay to depths of 120 and 200 mm. Tests were also carried out on samples that were not reinforced with sand columns. The samples were compressed under both drained and undrained conditions. It was found that the undrained shear strength of samples containing full-depth columns was greatly improved compared with that of the unreinforced samples. In the fully drained tests, the sample installed with a single column of 32 mm diameter exhibited better performance than the sample with three columns of 20 mm diameter, although the area replacement ratio in the case of the three 20 mm diameter columns was higher than that of the single 32 mm diameter column. However, the undrained strength of the composite material was not particularly affected by the number of columns.

Tracking biological invasions in space and time: elucidating the invasive history of the green alga Codium fragile using old DNA

With the advent of 'ancient DNA' studies on preserved material of extant and extinct species, museums and herbaria now represent an important although still underutilized resource in molecular ecology. The ability to obtain sequence data from archived specimens can reveal the recent history of cryptic species and introductions. We have analysed extant and herbarium samples of the highly invasive green alga Codium fragile, many over 100 years old, to identify cryptic accessions of the invasive strain known as C. fragile ssp. tomentosoides, which can be identified by a unique haplotype. Molecular characterization of specimens previously identified as native in various regions shows that the invasive tomentosoides strain has been colonizing new habitats across the world for longer than records indicate, in some cases nearly 100 years before it was noticed. It can now be found in the ranges of all the other native haplotypes detected, several of which correspond to recognized subspecies. Within regions in the southern hemisphere there was a greater diversity of haplotypes than in the northern hemisphere, probably as a result of dispersal by the Antarctic Circumpolar Current. The findings of this study highlight the importance of herbaria in preserving contemporaneous records of invasions as they occur, especially when invasive taxa are cryptic.

Quasi-isochoric ion beam heating using dynamic confinement in spherical geometry for X-ray scattering experiments in WDM regime

Extreme states of matter such as Warm Dense Matter “WDM” and Dense Strongly Coupled Plasmas “DSCP” play a key role in many high energy density experiments, however creating WDM and DSCP in a manner that can be quantified is not readily feasible. In this paper, isochoric heating of matter by intense heavy ion beams in spherical symmetry is investigated for WDM and DSCP research: The heating times are long (100 ns), the samples are macroscopically large (mm-size) and the symmetry is advantageous for diagnostic purposes. A dynamic confinement scheme in spherical symmetry is proposed which allows even ion beam heating times that are long on the hydrodynamic time scale of the target response. A particular selection of low Z-target tamper and x-ray probe radiation parameters allows to identify the x-ray scattering from the target material and use it for independent charge state measurements Z* of the material under study.

Ordered arrays of lead zirconium titanate nanorings

Periodic arrays of nanorings of morphotropic phase boundary lead zirconium titanate ( PZT) have been successfully fabricated using a novel self-assembly technique: close-packed monolayers of latex nanospheres were deposited onto Pt-coated silicon substrates, and then plasma cleaned to form ordered arrays of isolated nanospheres, not in contact with each other. Subsequent pulsed laser deposition of PZT, high angle argon ion etching and thermal annealing created the arrays of isolated nanorings, with diameters of similar to 100 nm and wall thicknesses of similar to 10 nm. Energy dispersive x-ray analysis confirms that the rings are compositionally morphotropic phase boundary PZT, and high resolution transmission electron microscopy imaging of lattice fringes demonstrates some periodicities consistent with perovskite rather than pyrochlore material. The dimensions of these nanorings, and the expected 'soft' behaviour of the ferroelectric material from which they are made, means that they offer the most likely opportunity to date for observing whether or not vortex arrangements of electrical dipoles, analogous to those seen in ferromagnetic nanostructures, actually exist.

Laser annealing of sputtered silicon for wafer-bonding applications

Sputtered silicon is investigated as a bonding layer for transfer of pre-processed silicon layers to various insulating substrates. Although the material appears suitable for low temperature processing, previous work has shown that gas trapped in the pores of the sputtered material is released at temperatures above 350 degrees C and further increases of temperature lead to destruction of any bonded interface. Pre-annealing at 1000 degrees C before bonding drives out gas and/or seals the surface, but for device applications where processing temperatures must be kept below about 300 degrees C, this technique cannot be used. In the current work, we have investigated the effect of excimer laser-annealing to heat the sputtered silicon surface to high temperature whilst minimising heating of the underlying substrate. Temperature profile simulations are presented and the results of RBS, TEM and AFM used to characterise the annealed layers. The results verify that gases are present in the sub-surface layers and suggest that while sealing of the surface is important for suppression of the out-diffusion of gases, immediate surface gas removal may also play a role. The laser-annealing technique appears to be an effective method of treating sputtered silicon, yielding a low roughness surface suitable for wafer bonding, thermal splitting and layer transfer.

The iron abundance of the Magellanic Bridge

High-resolution Hubble Space Telescope ultraviolet spectra for five B-type stars in the Magellanic Bridge and in the Large (LMC) and Small (SMC) Magellanic Clouds have been analysed to estimate their iron abundances. Those for the Clouds are lower than estimates obtained from late-type stars or the optical lines in B-type stars by approximately 0.5 dex. This may be due to systematic errors possibly arising from non-local thermodynamic equilibrium (non-LTE) effects or from errors in the atomic data, as similar low Fe abundances have previously been reported from the analysis of the ultraviolet spectra of Galactic early-type stars. The iron abundance estimates for all three Bridge targets appear to be significantly lower than those found for the SMC and LMC by approximately -0.5 and -0.8 dex, respectively, and these differential results should not be affected by any systematic errors present in the absolute abundance estimates. These differential iron abundance estimates are consistent with the underabundances for C, N, O, Mg and Si of approximately -1.1 dex relative to our Galaxy previously found in our Bridge targets. The implications of these very low metal abundances for the Magellanic Bridge are discussed in terms of metal deficient material being stripped from the SMC.

Rapid identification of precursor cDNAs encoding five structural classes of antimicrobial peptides from pickerel frog (Rana palustris) skin secretion by single step “shotgun” cloning.

The skin secretion of the North American pickerel frog (Rana palustris) has long been known to have pronounced noxious/toxic properties and to be highly effective in defence against predators and against other sympatric amphibians. As it consists largely of a complex mixture of peptides, it has been subjected to systematic peptidomic study but there has been little focus on molecular cloning of peptide-encoding cDNAs and by deduction, the biosynthetic precursors that they encode. Here, we demonstrate that the cDNAs encoding the five major structural families of antimicrobial peptides can be elucidated by a single step “shotgun” cloning approach using a cDNA library constructed from the source material of the peptidomic studies—the defensive skin secretion itself. Using a degenerate primer pool designed to a highly conserved nucleic acid sequence 5' to the initiation codon of known antimicrobial peptide precursor transcripts, we amplified cDNA sequences representing five major classes of antimicrobial peptides, such as esculentins, brevinins, ranatuerins, palustrins and temporins. Bioinformatic comparisons of precursor open-reading frames and nucleic acid sequences revealed high degrees of structural similarities between analogous peptides of R. palustris and the Chinese bamboo odorous frog, Rana versabilis. This approach thus constitutes a robust technique that can be used either alone or ideally, in parallel with peptidomic analysis of skin secretion, to rapidly extract primary structural information on amphibian skin secretion peptides and their biosynthetic precursors.

Elements of the granular gland peptidome and transcriptome persist in air-dried skin of the South American orange-legged leaf frog, Phyllomedusa hypocondrialis.

The defensive strategy of amphibians against predator attack relies heavily on the secretion of noxious/toxic chemical cocktails from specialized skin granular glands. Bioactive peptides constitute a major component of secretions in many species and the most complex are produced by neotropical leaf frogs of the sub-family Phyllomedusinae. We recently reported that these skin secretions contain elements of both the granular gland peptidome and transcriptome and that polyadenylated mRNAs constituting the latter are protected from degradation by interactions with endogenous amphipathic peptides. This thus permits parallel amino acid sequencing of peptides and nucleic acid sequencing of cloned precursor transcripts from single lyophilized samples of secretion. Here we report that the protection afforded is sufficiently robust to permit transcriptome studies by cloning of full-length polyadenylated peptide precursor encoding mRNAs from libraries constructed using ambient temperature air-dried skin from recently deceased specimens as source material. The technique was sufficiently sensitive to permit the identification of cDNAs encoding antimicrobial peptides constituted by six different isoforms of phylloseptin and two dermaseptins. Also, for the first time, establishment of the nucleic acid and amino acid sequence of the precursor encoding the phyllomedusine frog skin bradykinin-related peptide, phyllokinin, from cloned cDNA, was achieved. These data unequivocally demonstrate that the granular gland transcriptome persists in air-dried amphibian skin—a finding that may have fundamental implications in the study of archived materials but also in the wider field of molecular biology.

Nanoscale ferroelectrics machined from single crystals

This paper summarises some of the most recent work that has been done on nanoscale ferroelectrics as a result of a joint collaborative research effort involving groups in Queen's University Belfast, the University of Cambridge and the University of St. Andrews. Attempts have been made to observe fundamental effects of reduced size, and increasing morphological complexity, on ferroelectric behaviour by studying the functional response and domain characteristics in nanoscale single crystal material, whose size and morphology have been defined by Focused Ion Beam (FIB) patterning. This approach to nanoshape fabrication has allowed the following broad statements to be made: (i) in single crystal BaTiO3 sheets, permittivity and phase transition behaviour is not altered from that of bulk material down to a thickness of similar to 75 nm; (ii) in single crystal BaTiO3 sheets and nanowires changes in observed domain morphologies are consistent with large scale continuum modeling.