Translational control of SEPT9 isoforms is perturbed in disease

A common feature of the mammalian septin gene family is complex genomic architecture with multiple alternate splice variants. Septin 9 has 18 distinct transcripts encoding 15 polypeptides, with two transcripts (SEPT9_v4 and v4*) encoding the same polypeptide. We have previously reported that the ratio of these distinct transcripts is altered in neoplasia, with the v4 transcript being the usual form in normal cells but v4* becoming predominant in tumours. This led us to ask what the functional differences between these two transcripts might be. The 5'-UTRs of v4 and v4* have distinct 5' ends encoded by exons 1 beta (v4) and 1 zeta and 2 (v4*) and a common 3' region and initiating ATG encoded within exon 3. Here we show that the two mRNAs are translated with different efficiencies and that cellular stress can alter this. A putative internal ribosome entry site can be identified in the common region of the v4 and v4* 5'-UTRs and translation is modulated by an upstream open-reading frame in the unique region of the v4 5'-UTR. Germline mutations in hereditary neuralgic amyotrophy (HNA) map to the region which is common to the two UTRs. These mutations dramatically enhance the translational efficiency of the v4 5'-UTR, leading to elevated SEPT9_v4 protein under hypoxic conditions. Our data provide a mechanistic insight into how the HNA mutations can alter the fine control of SEPT9_v4 protein and its regulation under physiologically relevant conditions and are consistent with the episodic and stress-induced nature of the clinical features of HNA.

Phase transitions in epitaxial Ba0.5Sr0.5TiO3 thin films

Ba0.5Sr0.5TiO3 (BST) thin-film capacitor structures with various thicknesses, (50-1200 nm) and different strain conditions (on lanthanum strontium cobalt oxide La0.5Sr0.5CoO3 and strontium ruthenate SrRuO3 buffer layers) were made using pulsed laser deposition, and characterized by x-ray diffraction. The out-of-plane lattice parameter was followed as a function of temperature within the 100-300 K temperature interval. The phase sequence (cubic-tetragonal-orthorhombic-rhombohedral) known to exist in the bulk analog is shown to be strongly affected by both the stress conditions imposed by the buffer layer and the thickness of the BST film itself. Thus, no phase transition was found for the in-plane compressed BST films. On the stress-free BST films, on the contrary, more phase transitions were observed. It appeared that the complexity of structural phase transitions increased as the film thickness in this system was reduced.

Optimisation of radiotherapy for carcinoma of the parotid gland: a comparison of conventional, three-dimensional conformal, and intensity-modulated techniques

Background and purpose: To compare external beam radiotherapy techniques for parotid gland tumours using conventional radiotherapy (RT), three-dimensional conformal radiotherapy (3DCRT), and intensity-modulated radiotherapy (IMRT). To optimise the IMRT techniques, and to produce an IMRT class solution.Materials and methods: The planning target volume (PTV), contra-lateral parotid gland, oral cavity, brain-stem, brain and cochlea were outlined on CT planning scans of six patients with parotid gland tumours. Optimised conventional RT and 3DCRT plans were created and compared with inverse-planned IMRT dose distributions using dose-volume histograms. The aim was to reduce the radiation dose to organs at risk and improve the PTV dose distribution. A beam-direction optimisation algorithm was used to improve the dose distribution of the IMRT plans, and a class solution for parotid gland IMRT was investigated.Results: 3DCRT plans produced an equivalent PTV irradiation and reduced the dose to the cochlea, oral cavity, brain, and other normal tissues compared with conventional RT. IMRT further reduced the radiation dose to the cochlea and oral cavity compared with 3DCRT. For nine- and seven-field IMRT techniques, there was an increase in low-dose radiation to non-target tissue and the contra-lateral parotid gland. IMRT plans produced using three to five optimised intensity-modulated beam directions maintained the advantages of the more complex IMRT plans, and reduced the contra-lateral parotid gland dose to acceptable levels. Three- and four-field non-coplanar beam arrangements increased the volume of brain irradiated, and increased PTV dose inhomogeneity. A four-field class solution consisting of paired ipsilateral coplanar anterior and posterior oblique beams (15, 45, 145 and 170o from the anterior plane) was developed which maintained the benefits without the complexity of individual patient optimisation.Conclusions: For patients with parotid gland tumours, reduction in the radiation dose to critical normal tissues was demonstrated with 3DCRT compared with conventional RT. IMRT produced a further reduction in the dose to the cochlea and oral cavity. With nine and seven fields, the dose to the contra-lateral parotid gland was increased, but this was avoided by optimisation of the beam directions. The benefits of IMRT were maintained with three or four fields when the beam angles were optimised, but were also achieved using a four-field class solution. Clinical trials are required to confirm the clinical benefits of these improved dose distributions.

Coupled consolidation of a solid, infinite cylinder using a Terzaghi formulation

Axisymmetric consolidation is a classical boundary value problem for geotechnical engineers. Under some circumstances an analysis in which the changes in pore pressure, effective stress and displacement can be uncoupled from each other is sufficient, leading to a Terzaghi formulation of the axisymmetric consolidation equation in terms of the pore pressure. However, representation of the Mandel-Cryer effect usually requires more complex, coupled, Biot formulations. A new coupled formulation for the plane strain, axisymmetric consolidation problem is presented for small, linear elastic deformations. A single, easily evaluated parameter couples changes in pore pressure to changes in effective stress, and the resulting differential equation for pore pressure dissipation is very similar to Terzaghi’s classic formulation. The governing equations are then solved using finite differences and the consolidation of a solid infinite cylinder analysed, calculating the variation with time and with radius of the excess pore pressure and the radial displacement. Comparison with a previously published semi-analytical solution indicates that the formulation successfully embodies the Mandel-Cryer effect.

Two functionally linked amino acids in the stem 2 region of measles virus haemagglutinin determine infectivity and virulence in the rodent central nervous system.

Rodent brain-adapted measles virus (MV) strains, such as CAM/RB and recombinant MVs based on the Edmonston strain containing the haemagglutinin (H) of CAM/RB, cause acute encephalitis after intracerebral infection of newborn rodents. We have demonstrated that rodent neurovirulence is modulated by two mutations at amino acid positions 195 and 200 in the H protein, one of these positions (200) being a potential glycosylation site. In order to analyse the effects of specific amino acids at these positions, we introduced a range of individual and combined mutations into the open reading frame of the H gene to generate a number of eukaryotic expression plasmids. The functionality of the mutant H proteins was assessed in transfected cells and by generating recombinant viruses. Interestingly, viruses caused acute encephalitis only if the amino acid Ser at position 200 was coupled with Gly at position 195, whereas viruses with single or combined mutations at these positions, including glycosylation at position 200, were attenuated. Neurovirulence was associated with virus spread and induction of neuronal apoptosis, whereas attenuated viruses failed to infect brain cells. Similar results were obtained by using primary brain-cell cultures. Our findings indicate that a structural alteration in the stem 2 region of the H protein at position 195 or 200 interferes with infectivity of rodent neurons, and suggest that the interaction of the viral attachment protein with cellular receptors on neurons is affected.

An exploratory non-LTE model atmosphere analysis of B-type supergiants in the Small Magellanic Cloud

A preliminary differential non-LTE model atmosphere analysis of moderate resolution (R ~ 5 000) and signal-to-noise ratio spectra of 48 Small Magellanic Cloud B-type supergiants is presented. Standard techniques are adopted, viz. plane-parallel geometry and radiative and hydrostatic equilibrium. Spectroscopic atmospheric parameters (T_eff, log g and v_turb), luminosities and chemical abundances (He, C, N, O, Mg and Si) are estimated. These are compared with those deduced for a comparable sample of Galactic supergiants. The SMC targets appear to have similar atmospheric parameters, luminosities and helium abundances to the Galactic sample. Their magnesium and silicon underabundances are compatible with those found for main sequence SMC objects and there is no evidence for any large variation in their oxygen abundances. By contrast both their carbon and nitrogen lines strengths are inconsistent with single abundances, while their nitrogen to carbon abundance ratios appear to vary by at least as much and probably more than that found in the Galactic sample.

The effect of flexoelectricity on the dielectric properties of inhomogeneously strained ferroelectric thin films

Recent experimental measurements of large flexoelectric coefficients in ferroelectric ceramics suggest that strain gradients can affect the polarization and permittivity behaviour of inhomogeneously strained ferroelectrics. Here we present a phenomenological model of the effect of flexoelectricity on the dielectric constant, polarization, Curie temperature (T-C), temperature of maximum dielectric constant (T-m) and temperature of the onset of reversible polarization (T-ferro) for ferroelectric thin films subject to substrate-induced epitaxial strains that are allowed to relax with thickness, and the qualitative and quantitative predictions of the model are compared with experimental results for (Ba0.5Sr0.5)TiO3 thin films on SrRuO3 electrodes. It is shown that flexoelectricity can play an important role in decreasing the maximum dielectric constant of ferroelectric thin films under inhomogeneous in-plane strain, regardless of the sign of the strain gradient.

Existence of multibreathers in one-dimensional Debye crystals

The existence of highly localized multisite oscillatory structures (discrete multibreathers) in a nonlinear Klein-Gordon chain which is characterized by an inverse dispersion law is proven and their linear stability is investigated. The results are applied in the description of vertical (transverse, off-plane) dust grain motion in dusty plasma crystals, by taking into account the lattice discreteness and the sheath electric and/or magnetic field nonlinearity. Explicit values from experimental plasma discharge experiments are considered. The possibility for the occurrence of multibreathers associated with vertical charged dust grain motion in strongly coupled dusty plasmas (dust crystals) is thus established. From a fundamental point of view, this study aims at providing a rigorous investigation of the existence of intrinsic localized modes in Debye crystals and/or dusty plasma crystals and, in fact, suggesting those lattices as model systems for the study of fundamental crystal properties.

Spatial structures of plasma parameters in a magnetic neutral loop discharge

Spatial structures of plasma parameters in a radio-frequency inductively coupled magnetic neutral loop discharge are investigated under various parameter variations using spatially resolved Langmuir probe measurements. A strong coupling between the plasma production region, in the neutral loop (NL) plane, and the axially remote substrate region is observed. The two regions are connected through the separatrices and therefore, spatial profiles in the substrate region are strongly influenced by the plasma production region and the structure of the separatrices. The electron temperature in the plasma production region peaks in the centre of the NL while the maximum in electron density is shifted radially inwards due to diffusion. Details of the structures in both regions, the production region and the substrate region, are determined through the position of the NL and the gradient of the inhomogeneous magnetic field around the NL confinement region. Parameter combinations are found providing higher plasma densities and better uniformity than in common inductively coupled plasmas without applying an additional magnetic field. The uniformity can be further improved using temporal variations of the magnetic field structure.

A planar inductively coupled radio-frequency magnetic neutral loop discharge

A planar inductively coupled radio-frequency (rf) magnetic neutral loop discharge has been designed. It provides diagnostic access to both the main plasma production region as well as a remote plane for applications. Three coaxial coils are arranged to generate a specially designed inhomogeneous magnetic field structure with vanishing field along a ring in the discharge-the so-called neutral loop (NL). The plasma is generated by applying an oscillating rf electric field along the NL, induced through a four-turn, planar antenna operated at 13.56 MHz. Electron density and temperature measurements are performed under various parameter variations. Collisionless electron heating in the NL region allows plasma operation at comparatively low pressures, down to 10(-2) Pa, with a degree of ionization in the order of several per cent. Conventional plasma operation in inductive mode without applying the magnetic field is less efficient, in particular in the low pressure regime where the plasma cannot be sustained without magnetic fields.

Transition phenomena in a radio-frequency inductively coupled plasma

Changes of the electron dynamics during the mode transition (E- to H-mode) in a hydrogen radio-frequency (rf) inductively coupled plasma are investigated using space and phase resolved optical emission spectroscopy. The E- mode is characterized through relatively weak optical emission which is strongly modulated on a nanosecond time scale during the rf-cycle, with one pronounced maximum per cycle. The modulation in H-mode, with twice the rf-frequency, is significantly weaker while the emission intensities are about two orders of magnitude higher. In particular the transition between these two modes is studied under variations of rf-power input and gas pressure. Characteristic spatio-temporal structures are observed and can be understood in the frame of a simple model combining both coupling mechanisms in the transition regime.

Iron abundances from optical FeIII absorption lines in B-type stellar spectra

The role of optical FeIII absorption lines in B-type stars as iron abundance diagnostics is considered. To date, ultraviolet Fe lines have been widely used in B-type stars, although line blending can severely hinder their diagnostic power. Using optical spectra, covering a wavelength range ~3560-9200Å, a sample of Galactic B-type main-sequence and supergiant stars of spectral types B0.5 to B7 are investigated. A comparison of the observed FeIII spectra of supergiants, and those predicted from the model atmosphere codes TLUSTY [plane-parallel, non-local thermodynamic equilibrium (LTE)], with spectra generated using SYNSPEC (LTE), and CMFGEN (spherical, non-LTE), reveal that non-LTE effects appear small. In addition, a sample of main-sequence and supergiant objects, observed with the Fiber-fed Extended Range Optical Spectrograph (FEROS), reveal LTE abundance estimates consistent with the Galactic environment and previous optical studies. Based on the present study, we list a number of FeIII transitions which we recommend for estimating the iron abundance from early B-type stellar spectra.

The mouse and human IGSF6 (DORA) genes map to the inflammatory bowel disease 1 locus and are embedded in an intron of a gene of unknown function.

We have previously characterized IGSF6 (DORA), a novel member of the immunoglobulin superfamily (IGSF) from human and rat expressed in dendritic and myeloid cells. Using a probe from the open reading frame of the rat cDNA, we isolated a cosmid which contains the entire mouse gene. By comparative analysis and reverse transcriptase polymerase chain reaction, we defined the intron/exon structure and the mRNA of the mouse gene and, with respect to human BAC clones, the human gene. The genes span 10 kb (mouse) and 12 kb (human), with six exons arranged in a manner similar to other members of the IGSF. All intron/exon boundaries follow the GT-AG rule. Expression of the mouse Igsf6 gene is restricted to cells of the immune system, particularly macrophages. Northern blot revealed a single mRNA of 2.5 kb, in contrast to the human gene which is expressed as two mRNAs of 1 and 2.5 kb. The human and mouse genes were localized to a locus associated with inflammatory bowel disease. Analysis of the flanking regions of the Igsf6 gene revealed the presence of an unrelated gene, transcribed from the opposite strand of the DNA and oriented such that the Igsf6 gene is encoded entirely within an intron. An identical organization is seen in human. This gene of unknown function is transcribed and processed, contains homologues in Caenorhabditis elegans and prokaryotes, and is expressed in most organs in the mouse.

Cloning of the (Thr6)-phyllokinin precursor from Phyllomedusa sauvagei skin confirms a non-consensus tyrosine 0-sulfation motif.

Nine bradykinin-related peptides were identified in Phyllomedusa sauvagei skin secretion using QTOF MS/MS fragmentation sequencing. The major peptides were (Thr6)-bradykinin, (Hyp3, Thr6)-bradykinin, (Thr6)-phyllokinin and (Hyp3, Thr6)-phyllokinin. The phyllokinins occurred in both sulfated and non-sulfated forms. All (Thr6)-substituted bradykinins/phyllokinins could be generated from a common precursor by differential post-translational processing and modification. The open-reading frame of the cloned precursor cDNA consisted of 62 amino acid residues with a single bradykinin/phyllokinin coding sequence located at the C-terminus. Structural features included a Glu-Arg processing site at the N-terminus of the bradykinin/phyllokinin domain and the absence of an acidic amino acid residue adjacent to the C-terminal Tyr residue in the phyllokinins. However, the neutral amino acid residue (Ile) at position -1 and the basic amino acid residue (Arg) at position -2 from the Tyr residue, constitute a sulfation motif previously identified only in a protochordean.