bluuebunny/crossref_metadata_2025 huggingface dataset:
The UBL domain of PLIC‐1 regulates aggresome formation
Authors: Heir Renu , Ablasou Celine , Dumontier Emilie , Elliott Meghan , Fagotto‐Kaufmann Christine , Bedford Fiona K
Published: November 2006

Defects in protein folding and the proteasomal pathway have been linked with many neurodegenerative diseases. PLIC‐1 (protein linking IAP to the cytoskeleton) is a ubiquitin‐like protein that binds to the ubiquitin‐interacting motif (UIM) of the proteasomal subunit S5a. Here, we show that PLIC‐1 also binds to the UIM proteins ataxin 3—a deubiquitinating enzyme—HSJ1a—a co‐chaperone—and EPS15 (epidermal growth factor substrate 15)—an endocytic protein. Using a polyglutamine (polyQ) disease model, we found that both endogenous PLIC‐1 and EPS15 localize to perinuclear aggresomes, and that polyQ enhances their in vivo interaction. We show that knockdown of PLIC‐1 and EPS15 by RNA interference reduces aggresome formation. In addition, PLIC‐1ΔUBL functions as a dominant‐negative mutant, blocking both polyQ transport to aggresomes and the association of EPS15 with dispersed aggregates. We also show that PLIC‐1 is upregulated by arsenite‐induced protein misfolding. These results indicate a role for PLIC‐1 in the protein aggregation‐stress pathway, and we propose a novel function for the ubiquitin‐like (UBL) domain—by means of UBL–UIM interactions—in transport to aggresomes.
Epigenetic regulation of transcription in intermediate heterochromatin
Authors: Habu Yoshiki , Mathieu Olivier , Tariq Muhammad , Probst Aline V , Smathajitt Chotika , Zhu Tong , Paszkowski Jerzy
Published: November 2006

Constitutive heterochromatin is a compact, transcriptionally inert structure formed in gene‐poor and repeat‐ and transposon‐rich regions. In Arabidopsis, constitutive heterochromatin is characterized by hypermethylated DNA and histone H3 dimethylated at lysine (K) 9 (H3K9me2) together with depletion of histone H3 dimethylated at lysine 4 (H3K4me2). Here, we describe loci with intermediate properties of heterochromatin in which transcription downregulation is inherited in a manner similar to constitutive heterochromatin, although the loci are associated with opposing histone marks—H3K4me2 and H3K9me2. In the ddm1 (decrease in DNA methylation 1) mutants, their transcriptional activation is accompanied by the expected shift in the H3 modifications—depletion of H3K9me2 and enrichment in H3K4me2. In mom1 (Morpheus' molecule 1) mutants, however, a marked increase in transcription is not accompanied by detectable changes in the levels of H3K4me2 and H3K9me2. Therefore, transcriptional regulation in the intermediate heterochromatin involves two distinct epigenetic mechanisms. Interestingly, silent transgenic inserts seem to acquire properties characteristic of the intermediate heterochromatin.
Chemokine sequestration by atypical chemokine receptors
Authors: Hansell C.A.H. , Simpson C.V. , Nibbs R.J.B.
Published: November 2006

Leucocyte migration is essential for robust immune and inflammatory responses, and plays a critical role in many human diseases. Chemokines, a family of small secreted protein chemoattractants, are of fundamental importance in this process, directing leucocyte trafficking by signalling through heptahelical G-protein-coupled receptors expressed by the migrating cells. However, several mammalian chemokine receptors, including D6 and CCX-CKR (ChemoCentryx chemokine receptor), do not fit existing models of chemokine receptor function, and do not even appear to signal in response to chemokine binding. Instead, these ‘atypical’ chemokine receptors are biochemically specialized for chemokine sequestration, acting to regulate chemokine bioavailability and thereby influence responses through signalling-competent chemokine receptors. This is of critical importance in vivo, as mice lacking D6 show exaggerated cutaneous inflammatory responses and an increased susceptibility to the development of skin cancer. CCX-CKR, on the other hand, is predicted to modulate homoeostatic lymphocyte and dendritic cell trafficking, key migratory events in acquired immune responses that are directed by CCX-CKR-binding chemokines. Thus studies on ‘atypical’ chemokine receptors are revealing functional and biochemical diversity within the chemokine receptor family and providing insights into novel mechanisms of chemokine regulation.
STAT3-mediated anti-inflammatory signalling
Authors: Murray P.J.
Published: November 2006

IL-1O (interleukin-10) negatively regulates inflammation through a mechanism that blocks the expression of pro-inflammatory genes encoding cytokines, chemokines, cell-surface molecules and other molecules required for the full activation of the innate and adaptive immune responses. The signalling pathway used by the IL-10 receptor to generate the anti-inflammatory response requires STAT3 (signal transducer and activator of transcription 3) and is indirect. Thus STAT3 activates other genes whose task is to selectively control transcription of inflammatory targets. Here, I summarize current knowledge of the key features of IL-10 signalling and make predictions concerning the mechanism of IL-10 at the level of inflammatory genes. Understanding IL-10 signalling should be a gateway to the development of broadly acting anti-inflammatory agents.
Patterns of exposure to glucocorticoid receptor ligand
Authors: Lightman S.L.
Published: November 2006

Hormones are characteristically secreted in distinct pulses. Corticosterone (in rodents) and cortisol (in human) show profound circadian and ultradian rhythmicity which results in rapid changes in ligand concentration in the circulating blood. The pattern of ultradian glucocorticoid levels shows genetic modulation, can change according to the physiological and pathological status of the animal and can be programmed by neonatal events. Since the tissue response to changes in circulating glucocorticoid levels can be very rapid, changes in ultradian rhythm could allow tissue-specific regulation of glucocorticoid signalling without major changes in mean plasma hormone levels.
Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis
Authors: Ehlting J. , Provart N.J. , Werck-Reichhart D.
Published: November 2006

Cytochrome P450 mono-oxygenases play prominent roles in a diverse set of metabolic pathways, but the function of most of these enzymes remains obscure. A bottleneck in the functional genomics of this superfamily constitutes hypothesis generation to identify potential substrates (or substrate classes) individual P450s may act on. We used publicly available large-scale expression data to perform co-expression analysis comparing the expression matrix of each P450 with those from more than 4000 selected genes across thousands of microarrays. Based on functional annotations of co-expressed genes from a diverse set of databases, co-expressed pathways were thus identified for each P450. Using this approach, most P450s with known functions were placed into their respective pathways, thereby proofing the concept. As examples, pathway mapping results identifying novel P450s potentially acting on flower-specific monoterpenes and root-specific triterpenes are described. Co-expression results for all Arabidopsis P450s will be presented as a web resource on the ‘CYPedia’ web pages (http://ibmp.u-strasbg.fr/~CYPedia/).
Dwarfism and cytochrome P450-mediated C-6 oxidation of plant steroid hormones
Authors: Bishop G. , Nomura T. , Yokota T. , Montoya T. , Castle J. , Harrison K. , Kushiro T. , Kamiya Y. , Yamaguchi S. , Bancos S. , Szatmári A.-M. , Szekeres M.
Published: November 2006

BRs (brassinosteroids) are plant steroid hormones that are essential for normal plant development. The dramatic dwarfism exhibited by mutants in the CYP (cytochrome P450) enzymes involved in BR biosynthesis indicates a role for these hormones in plant growth and development. Since the mid-1990s, collaborative research has been geared towards developing a better understanding of the CYP85 class of CYPs involved in BR biosynthesis in both Arabidopsis and tomato. Some of the most recent observations include the fact that certain CYP85 CYPs catalyse the synthesis of the most bioactive BR, BL (brassinolide). Current evidence suggests that evolution of this function may have occurred independently in different dicotyledonous species. Interestingly, BL accumulates in tomato fruits, highlighting a key role for this hormone in fruit development. At the same time as developing a better understanding of the enzymatic function of these CYPs, we have also carried out experiments towards characterizing where and when these genes are expressed and mechanisms of their regulation. As expected for a hormone involved in growth and development, biosynthetic gene promoter activity is associated with young rapidly growing cells and with fruit development.
CYP74C3 and CYP74A1, plant cytochrome P450 enzymes whose activity is regulated by detergent micelle association, and proposed new rules for the classification of CYP74 enzymes
Authors: Hughes R.K. , Belfield E.J. , Casey R.
Published: November 2006

CYP74C3 (cytochrome P450 subfamily 74C3), an HPL (hydroperoxide lyase) from Medicago truncatula (barrel medic), and CYP74A1, an AOS (allene oxide synthase) from Arabidopsis thaliana, are key membrane-associated P450 enzymes in plant oxylipin metabolism. Both recombinant detergent-free enzymes are monomeric proteins with dual specificity and very low enzyme activity that can be massively activated with detergent. This effect is a result of the formation of a complex between the protein monomer and a single detergent micelle and, in the case of CYP74A1, has a major effect on the substrate specificity of the enzyme. Association with a detergent micelle without an effect on protein oligomeric state represents a new mechanism of activation for membrane-associated P450 enzymes. This may represent a second unifying feature of CYP74 enzymes, in addition to their known differences in reaction mechanism, which separates them functionally from more classical P450 enzymes. Highly concentrated and monodispersed samples of detergent-free CYP74C3 and CYP74A1 proteins should be suitable for structural resolution. On the basis of recent evidence for incorrect assignment of CYP74 function, using the current rules for CYP74 classification based on sequence relatedness, we propose an alternative based on substrate and product specificity for debate and discussion.
Mitochondrial translocation of p53 underlies the selective death of hippocampal CA1 neurons after global cerebral ischaemia
Authors: Endo H. , Saito A. , Chan P.H.
Published: November 2006

p53, a tumour suppressor, is involved in DNA repair and cell death processes and mediates apoptosis in response to death stimuli by transcriptional activation of pro-apoptotic genes and by transcription-independent mechanisms. In the latter process, p53 induces permeabilization of the outer mitochondrial membrane by forming an inhibitory complex with a protective Bcl-2 family protein, resulting in cytochrome c release in several cell line systems. However, it is unclear how the mitochondrial p53 pathway mediates neuronal apoptosis after cerebral ischaemia. We examined interaction between the mitochondrial p53 pathway and vulnerable hippocampal CA1 neurons using a tGCI (transient global cerebral ischaemia) rat model. We showed mitochondrial translocation of p53 and its binding to Bcl-XL. Mitochondrial p53 translocation, interaction between p53 and Bcl-XL, and cytochrome c release from mitochondria and subsequent CA1 neuronal death were prevented by pifithrin-α, a p53-specific inhibitor. These results suggest that the mitochondrial p53 pathway plays a role in delayed CA1 neuronal death after tGCI.
NF-κB signalling in cerebral ischaemia
Authors: Schwaninger M. , Inta I. , Herrmann O.
Published: November 2006

In acute stroke, neuronal apoptosis and inflammation are considered to be important mechanisms on the road to tissue loss and neurological deficit. Both apoptosis and inflammation depend on gene transcription. We have identified a signalling pathway that regulates transcription of genes involved in apoptosis and inflammation. In a mouse model of focal cerebral ischaemia, there is an induction of the cytokine TWEAK (tumour necrosis factor-like weak inducer of apoptosis) and its membrane receptor Fn14. TWEAK promotes neuronal cell death and activates the transcription factor NF-κB (nuclear factor κB) through the upstream kinase IKK [IκB (inhibitory κB) kinase]. In vivo, IKK is activated in neurons. Neuron-specific deletion of the subunit IKK2 or inhibition of IKK activity reduced the infarct size and neuronal cell loss. A pharmacological inhibitor of IKK also showed neuroprotective properties. IKK-dependent ischaemic brain damage is likely to be mediated by NF-κB, because neuron-specific inhibition of NF-κB through transgenic expression of the NF-κB superrepressor was found to reduce the infarct size. In summary, there is evidence that IKK/NF-κB signalling contributes to ischaemic brain damage and may provide suitable drug targets for the treatment of stroke.
Mining for survival genes
Authors: Dawson V.L. , Dawson T.M.
Published: November 2006

Many stressful, but not lethal, stimuli activate endogenous protective mechanisms that significantly decrease the degree of injury to subsequent injurious stimuli. This protective mechanism is termed preconditioning and tolerance. It occurs across organ systems including the brain and nervous system. Preconditioning has been investigated in cell and animal models and recently been shown to potentially occur in human brain. Learning more about these powerful endogenous neuroprotective mechanisms could help identify new approaches to treat patients with stroke and other central nervous system disorders or injury. Cell and animal models are helping us to better understand the network response of gene and protein expression that activates the neuroprotective response.
The ALIAS (ALbumin In Acute Stroke) Phase III randomized multicentre clinical trial: design and progress report
Authors: Ginsberg M.D. , Palesch Y.Y. , Hill M.D. ,   for the ALIAS Trialists
Published: November 2006

High-dose human ALB (albumin) therapy is highly neuroprotective in animal models of ischaemic stroke. A recently completed 82-subject pilot-phase dose-escalation trial has shown that ALB is safe, with strong preliminary suggestions of possible efficacy. We are now proceeding to a large randomized, double-blinded, placebo-controlled multicentre trial funded by the NIH (National Institutes of Health), the ALIAS (Albumin In Acute Stroke) Phase III Trial, which is designed to ascertain definitively whether high-dose ALB therapy confers neuroprotection in subjects with acute ischaemic stroke treated within 5 h of stroke onset. The primary efficacy outcome measure is a favourable outcome, defined as an NIHSS (NIH Stroke Scale) score of 0–1 or a modified Rankin Scale score of 0–1 at 3 months post-randomization. Separate randomization (1:1) to ALB or placebo therapy will be carried out in two cohorts of 900 subjects each, one that receives standard-of-care thrombolytic therapy and the other that does not. Approx. 60 North American clinical sites will participate. Subject enrolment is expected to commence in July 2006.
G-CSF and neuroprotection: a therapeutic perspective in cerebral ischaemia
Authors: Lu C.-Z. , Xiao B.-G.
Published: November 2006

In several experimental studies of cerebral ischaemia, G-CSF (granulocyte colony-stimulating factor) exerted neuroprotective effects through different mechanisms, including mobilization of haemopoietic stem cells, anti-apoptosis, neuronal differentiation, angiogenesis and anti-inflammation. Hence, G-CSF not only inhibits neuron death, but also generates ‘new’ neural tissue formation. A small pilot trial reports on the safety and feasibility of G-CSF therapy in stroke patients. According to this evidence, we can speculate that G-CSF, being used either alone or in combination with another agent, should have a dual activity beneficial both to acute neuronal protection and long-term plasticity after cerebral ischaemia, thus proposing that G-CSF is an ideal new drug for stroke and neurodegenerative diseases.
PPAR: a new pharmacological target for neuroprotection in stroke and neurodegenerative diseases
Authors: Bordet R. , Ouk T. , Petrault O. , Gelé P. , Gautier S. , Laprais M. , Deplanque D. , Duriez P. , Staels B. , Fruchart J.C. , Bastide M.
Published: November 2006

PPARs (peroxisome-proliferator-activated receptors) are ligand-activated transcriptional factor receptors belonging to the so-called nuclear receptor family. The three isoforms of PPAR (α, β/δ and γ) are involved in regulation of lipid or glucose metabolism. Beyond metabolic effects, PPARα and PPARγ activation also induces anti-inflammatory and antioxidant effects in different organs. These pleiotropic effects explain why PPARα or PPARγ activation has been tested as a neuroprotective agent in cerebral ischaemia. Fibrates and other non-fibrate PPARα activators as well as thiazolidinediones and other non-thiazolidinedione PPARγ agonists have been demonstrated to induce both preventive and acute neuroprotection. This neuroprotective effect involves both cerebral and vascular mechanisms. PPAR activation induces a decrease in neuronal death by prevention of oxidative or inflammatory mechanisms implicated in cerebral injury. PPARα activation induces also a vascular protection as demonstrated by prevention of post-ischaemic endothelial dysfunction. These vascular effects result from a decrease in oxidative stress and prevention of adhesion proteins, such as vascular cell adhesion molecule 1 or intercellular cell-adhesion molecule 1. Moreover, PPAR activation might be able to induce neurorepair and endothelium regeneration. Beyond neuroprotection in cerebral ischaemia, PPARs are also pertinent pharmacological targets to induce neuroprotection in chronic neurodegenerative diseases.
Oestrogen and stroke: the potential for harm as well as benefit
Authors: Macrae I.M. , Carswell H.V.
Published: November 2006

Epidemiological studies point to a beneficial influence of the female reproductive hormones on stroke risk in that women have a lower incidence of stroke prior to the menopause compared with men, but this difference weakens with age and stroke risk in women rises after the menopause. However, recent Women's Health Initiative trials in post-menopausal women report an increased stroke risk on hormone replacement therapy. An influence of gender is also apparent on stroke outcome in animal models: female rats exposed to transient MCA (middle cerebral artery) occlusion sustain less brain damage than age-matched males, with loss of protection following ovariectomy. The major hormone thought to be responsible for beneficial influences on stroke incidence and outcome is oestrogen, and a large preclinical literature now exists where exogenously administered oestrogen has been studied in male and ovariectomized female rats using a range of stroke models and outcome measures. Most of these studies administer oestrogen prior to the stroke, use a model of transient ischaemia followed by reperfusion and report a significant oestrogen-induced neuroprotection. However, in some studies where the MCA is permanently occluded, oestrogen pre-treatment in ovariectomized female rats has been shown to significantly exacerbate ischaemic damage. Therefore preclinical results demonstrate harmful as well as beneficial influences of oestrogen on the ischaemic brain, highlighting the need for further study to elucidate the mechanisms responsible for both detrimental and beneficial influences. Ultimately, this could lead to the development of new classes of oestrogenic compounds with improved risk/benefit profiles, designed to selectively activate pathways inducing only the beneficial effects of oestrogen in vivo.
Fully retarded van der Waals interaction between dielectric nanoclusters
Authors: Kim Hye-Young , Sofo Jorge O. , Velegol Darrell , Cole Milton W.
Published: November 2006

The van der Waals (dispersion) interaction between an atom and a cluster or between two clusters at large separation is calculated by considering each cluster as a point particle, characterized by a polarizability tensor. For the extreme limit of very large separation, the fully retarded regime, one needs to know just the static polarizability in order to determine the interaction. This polarizability is evaluated by including all many-body (MB) intracluster atomic interactions self-consistently. The results of these calculations are compared with those obtained from various alternative methods. One is to consider each cluster as a collection of many atoms and evaluate the sum of two-body interatomic interactions, a common assumption. An alternative method is to include three-body atomic interactions as a MB correction term in the total energy. A comparison of these results reveals that the contribution of the higher-than-three-body MB interactions is always attractive and non-negligible even at such a large separation, in contrast to common assumptions. The procedure employed is quite general and is applicable, in principle, to any shape or size of dielectric cluster. We present numerical results for clusters composed of atoms with polarizability consistent with silica, for which the higher-than-three-body MB correction term can be as high as 42% of the atomic pairwise sum. This result is quite sensitive to the anisotropy and orientation of the cluster, in contrast to the result found in the additive case. We also present a power law expansion of the total van der Waals interaction as a series of n-body interaction terms.
Calculation of reactive flux correlation functions for systems in a condensed phase environment: A multilayer multiconfiguration time-dependent Hartree approach
Authors: Wang Haobin , Skinner David E. , Thoss Michael
Published: November 2006

A numerically exact quantum mechanical approach is proposed to evaluate thermal rate constants for systems in a model condensed phase environment. Employing the reactive flux correlation function formalism, the approach efficiently combines the multilayer multiconfiguration time-dependent Hartree theory with an importance sampling scheme for thermal distribution of the initial states. The performance of the method is illustrated by applications to two models of condensed phase dynamics: the donor-acceptor electron transfer model also known as the spin-boson model and a model for proton transfer reactions in the condensed phase.
Size and shape control of GaAs nanowires grown by metalorganic vapor phase epitaxy using tertiarybutylarsine
Authors: Paiano P. , Prete P. , Lovergine N. , Mancini A. M.
Published: November 2006

Au-catalyzed self-assembly of GaAs nanowires on (1¯1¯1¯)B GaAs by metalorganic vapor phase epitaxy is reported between 375 and 500°C, using tertiarybutylarsine and trimethylgallium in H2. The nanowires are [1¯1¯1¯]B aligned and kink-free. Below 425°C the nanowires have narrow base diameter distributions, closely matching the size (∼60nm) of the Au nanoparticles at their tip (no tapering). Above 425°C the nanowires show a hexagonal-based pyramidal shape with base edges normal to the ⟨2¯11⟩ in-plane substrate directions and base diameters which increase exponentially with temperature, indicating a kinetics limited growth along the nanowire sidewalls. Activation energies in the range of ∼20–23kcal∕mol were estimated for growth along both the sidewalls and the [1¯1¯1¯]B direction.
Investigation of liquid∕solid interface waves with laser excitation and photoelastic effect detection
Authors: Han Qingbang , Qian Menglu , Wang Hao
Published: November 2006

Theoretical and experimental investigations on transparent liquid (water)∕solid (aluminum or steel) interface waves generated by laser pulse and detected with photoelastic effect are reported. When the detection beam of a laser interferometer is skimmed over the water∕solid interface and conjoined with the interface wave propagated in water, an extra optical phase shift is produced. The output signal from the interferometer is proportional to the acoustic pressure in water. The characteristic equation of the liquid∕solid interface wave is derived from elastic wave theory, and the transient response of acoustic pressure in water is simulated by means of inverse Laplace and Hankel transforms. The experimental results of acoustic velocity and wave form for all interface waves are in good agreement with theoretical predictions. They show that the optical detecting method based on photoelastic effect is very powerful for the research of liquid∕solid interface waves.
Fabrication of highly efficient and stable doped red organic light-emitting device using 2-methyl-9,10-di(2-napthyl)anthracene and tris(8-hydroxyquinolinato)aluminum as cohost materials
Authors: Lee Young Gu , Lee Ho-Nyeon , Kang Sung Kee , Oh Tae Sik , Lee Soonil , Koh Ken Ha
Published: November 2006

The authors fabricated red organic light-emitting devices using DCJTB as red dopant, and blue-emitting MADN and green-emitting Alq3 as cohost materials for emission layers. The luminance efficiency of 2% DCJTB-doped Alq3(20%)∕MADN(80%) device was 5.42cd∕A at 20mA∕cm2, while that of equivalently doped Alq3 single-host device was 1.79cd∕A, and remained over 5.2cd∕A up to 200mA∕cm2. At the benchmark luminance of 7680cd∕m2, the power efficiency of DCJTB-doped Alq3∕MADN device was 4.1 times better than that of Alq3 single-host device. Moreover, the half-decay lifetime of DCJTB-doped Alq3∕MADN device measured at an initial luminance of 1000cd∕m2 was 14000h.
Young’s moduli of ZnO nanoplates: Ab initio determinations
Authors: Zhang Lixin , Huang Hanchen
Published: November 2006

The elastic constants of ZnO nanostructures control their elastic energy and thereby are important to their function in converting strain energy to electricity. This letter presents the size dependence of Young’s moduli of ZnO nanoplates, according to density-functional-theory-based ab initio calculations. Our results show that Young’s moduli of (0001)∕(0001¯), (11¯00), and (112¯0) nanoplates increase as size decreases. For (0001)∕(0001¯) nanoplate, Young’s moduli vary discontinuously with size, due to a phase transformation from wurtzite to graphitic structure. Further, our analyses show that the increase of moduli is due to surface stiffening and bulk nonlinear elasticity.
Determination of interlayer composition at buried interfaces using soft x-ray resonant reflectivity
Authors: Nayak Maheswar , Lodha G. S. , Sinha A. K. , Nandedkar R. V. , Shivashankar S. A.
Published: November 2006

The authors report determination of interlayer composition with subnanometer sensitivity at the buried interfaces using soft x-ray resonant reflectivity technique. Near the absorption edge, fine structure features of energy-dependent atomic scattering factor are sensitive to the composition, and can be exploited for determination of composition at the buried interfaces. This technique is demonstrated for a Mo–Si multilayer system using soft x-ray resonant reflectivity measurement.
Influence of annealing on stimulated emission in ZnO nanorods
Authors: Kwok W. M. , Djurišić Aleksandra B. , Leung Yu Hang , Li D. , Tam K. H. , Phillips D. L. , Chan W. K.
Published: November 2006

Vertically aligned ZnO nanorod arrays with rod lengths in the range of 200–1500nm were fabricated by a hydrothermal method. No stimulated emission was observed in as grown nanorods. Annealing of the rods in forming gas and oxygen significantly affected their optical properties and enabled the achievement of stimulated emission. The lowest lasing threshold and defect emission as well as the longest spontaneous emission decay times were obtained for nanorods annealed in oxygen flow. This indicates that interstitial oxygen, which is commonly assumed to be the cause of yellow-green defect emission, is not the dominant defect in hydrothermally grown nanorods.
Prompt gamma measurements for locating the dose falloff region in the proton therapy
Authors: Min Chul-Hee , Kim Chan Hyeong , Youn Min-Young , Kim Jong-Won
Published: November 2006

The location of the distal falloff in the proton therapy is an important but often uncertain parameter as different tissue elements are traversed by the beam. A multilayered collimator system has been constructed as a practical means to locate the dose ends by measuring prompt gammas. The collimator is designed to moderate and capture fast neutrons and to prevent unwanted gammas from reaching the scintillation detector. The system has been studied using Monte Carlo technique and has been tested in the beam energy range of 100–200MeV. Measurements clearly indicated correlations between the gamma distributions and the distal falloff regions.
Hot-carrier effects in p-channel polycrystalline silicon thin film transistors
Authors: Mariucci L. , Valletta A. , Gaucci P. , Fortunato G. , Templier F.
Published: November 2006

The effects of hot carriers on the electrical characteristics of polycrystalline silicon p-channel thin film transistors have been analyzed, combining experimental data and numerical simulations. The transfer characteristics showed minor variations upon application of prolonged bias stress, while the output characteristics presented a reduction of kink effect. These results have been explained by using a self-consistent model based on the trapping of injected hot electrons. The authors’ charge injection model provided a precise evaluation of the extension of the trapped charge regions, at both front and back interfaces. By using such trapped charge distributions, it was possible to reproduce the output characteristics variations as well as the minor on-current increase observed in the transfer characteristics after bias stress.
Femtosecond pulse distortion at surface plasmon resonances in a plasmonic crystal: Effect of surface plasmon lifetime
Authors: Vengurlekar A. S. , Gopal A. Venu , Ishihara T.
Published: November 2006

Measurements of temporal profile of a femtosecond laser pulse propagating through a one-dimensional metallic plasmonic crystal show that the pulses are severely distorted when they excite surface plasmon (SP) resonances. Significant differences in the nature of the distortion are found for the SP states at the two edges of the SP band gap, reflecting sharp contrasts in their lifetime.
Heat dissipation in carbon nanotube transistors
Authors: Ouyang Yijian , Guo Jing
Published: November 2006

Heat dissipation and its effect on current in carbon nanotube (CNT) Schottky barrier field-effect transistors are studied by solving nonequilibrium Green’s function transport equation self-consistently with a heat transport equation. Temperature rise in the semiconducting CNT channel is significantly smaller than its metallic counterpart because (i) the percentage of total power dissipated in the semiconducting CNT channel is smaller, and (ii) the heat dissipation reaches peak values at two ends of the channel. The simulation indicates that in the bias regime of interest to nanoelectronic applications, the effect of heating on the transistor I-V characteristics is small.
Improved characteristics of 660nm AlGaInP red laser diodes by precise control of the V/III ratio in metal-organic vapor phase epitaxy
Authors: Ohgoh Tsuyoshi , Mukai Atsushi , Mukaiyama Akihiro , Asano Hideki , Hayakawa Toshiro
Published: November 2006

The effects of the group V/III ratio during low-pressure metal-organic vapor phase epitaxy on laser performance have been investigated for GaInP∕AlGaInP laser diodes. The quality of GaInP is found to be better at a V/III ratio much lower than an optimal V/III ratio for AlGaInP. GaInP∕AlGaInP laser diodes with the emission wavelength of 660nm were grown at a low V/III ratio for GaInP quantum wells and at a high V/III ratio for AlGaInP waveguide and clad layers. As a result, device characteristics, particularly operating lifetime, are much improved as compared with those of devices grown with a constant high V/III ratio.
Electron tunneling in a metal-protein-metal junction investigated by scanning tunneling and conductive atomic force spectroscopies
Authors: Andolfi Laura , Bizzarri Anna Rita , Cannistraro Salvatore
Published: November 2006

The electron tunneling across a redox protein covalently bound to Au(111) electrode is investigated by both scanning tunneling and conductive atomic force spectroscopies. Although the current-voltage curves, detected by the two techniques, refer to different tunneling junctions, they are analyzed within the same transport model. By evaluating the electron transmission probability of each element constituting the tunneling junctions, the electron transport properties of the protein macromolecule are singled out. These results represent an advancement in understanding current flow through protein macromolecule in tunneling experiments, also in the perspectives of applications in nanobioelectronics.
The protective role of silicon in theArabidopsis–powdery mildew pathosystem
Authors: Fauteux François , Chain Florian , Belzile François , Menzies James G. , Bélanger Richard R.
Published: November 2006

The role and essentiality of silicon (Si) in plant biology have been debated for >150 years despite numerous reports describing its beneficial properties. To obtain unique insights regarding the effect of Si on plants, we performed a complete transcriptome analysis of both control and powdery mildew-stressedArabidopsisplants, with or without Si application, using a 44K microarray. Surprisingly, the expression of all but two genes was unaffected by Si in control plants, a result contradicting reports of a possible direct effect of Si as a fertilizer. In contrast, inoculation of plants, treated or not with Si, altered the expression of a set of nearly 4,000 genes. After functional categorization, many of the up-regulated genes were defense-related, whereas a large proportion of down-regulated genes were involved in primary metabolism. Regulated defense genes included R genes, stress-related transcription factors, genes involved in signal transduction, the biosynthesis of stress hormones (SA, JA, ethylene), and the metabolism of reactive oxygen species. In inoculated plants treated with Si, the magnitude of down-regulation was attenuated by >25%, an indication of stress alleviation. Our results demonstrate that Si treatment had no effect on the metabolism of unstressed plants, suggesting a nonessential role for the element but that it has beneficial properties attributable to modulation of a more efficient response to pathogen stress.
Special Topics Issue of Microcirculation: Ion Channels and Pulmonary Vascular Function
Authors: TOWNSLEY MARY I.
Published: November 2006

Unique features of the pulmonary circulation impact its function in health and disease, not the least of which is the existence of developmentally distinct, functionally heterogeneous extra‐alveolar and septal capillary networks. The impact of ion channel expression and regulation in lung vascular smooth muscle or endothelium in these vascular compartments provides a focus for this special topics issue. Reviews and original contributions from experts in the field discuss two broad groups of ion channels, drawing on studies utilizing biophysical and molecular approaches in heterologous expression systems, in vitro approaches in pulmonary vascular smooth muscle and endothelial cells, and physiologic studies in animal models of chronic pulmonary hypertension. First, channels involved in membrane depolarization and related alterations in vascular tone, and shear sensing or exocytosis by endothelium are discussed: voltage‐gated potassium channels, ATP‐regulated potassium channels and L‐ and T‐ type voltage‐gated calcium channels. The second series of reviews discusses the role of calcium influx pathways provided by transient receptor potential channels in regulation of pulmonary vascular tone or vascular remodeling, and endothelial barrier function. Understanding the role of ion channels in pulmonary vascular pathophysiology may be critical to development of new therapeutic strategies.
KATP Channels Are an Important Component of the Shear‐Sensing Mechanism in the Pulmonary Microvasculature
Authors: CHATTERJEE S. , LEVITAN I. , WEI Z. , FISHER A. B.
Published: November 2006

Objective: To investigate the role of a KATP channel in sensing shear, specifically its cessation, in the endothelial cells of the pulmonary microvasculature.

Methods: Endothelial cells isolated from the pulmonary microvasculature of wild‐type and KATP channel knockout (KIR6.2−/−) mice were either statically cultured (non‐flow‐adapted) or kept under flow (flow‐adapted) and the KIR currents in these cells were monitored by whole‐cell patch‐clamp technique during flow and its cessation. Membrane potential changes, generation of reactive oxygen species (ROS), and Ca2+ influx with flow cessation were evaluated by the use of fluorescent dyes. Lungs isolated from wild‐type mice were imaged to visualize ROS generation in the subpleural endothelium.

Results: By patch‐clamp analysis, reduction in the KIR current with cessation of flow occurred only in wild‐type cells that were flow‐adapted and not in flow‐adapted KIR6.2−/− cells. Similar observations were made using changes in bisoxonol fluorescence as an index of cell membrane potential. Generation of ROS and Ca2+ influx that follow membrane depolarization were significantly lower in statically cultured and in KIR6.2−/− cells as compared to flow‐adapted wild‐type cells. Imaging of subpleural endothelial cells of the whole lung showed that the KATP antagonist glyburide caused the production of ROS in the absence of flow cessation.

Conclusions: The responses to stop of flow (viz. membrane depolarization, KIR currents, ROS, Ca2+) were significantly altered with knockout of KATP channels, which indicates that this channel is an important component of the pulmonary endothelial response to abrupt loss of shear stress.
T‐type Calcium Channels in Pulmonary Vascular Endothelium
Authors: ZHOU CHUN , WU SONGWEI
Published: November 2006

The expression of low‐voltage‐gated T‐type calcium channel α1G‐subunit (Cav3.1) has recently been revealed in pulmonary microvascular endothelial cells (PMVECs). In endothelial cells, changes in membrane potential may be caused by a variety of physiological or pathophysiological vascular stimuli. Thus, the characteristic low‐voltage range of activation, transient kinetics of inactivation, and conducting continuous Ca2+ entry in a range of low membrane potentials of this channel may confer its temporal and spatial control of cytosolic Ca2 + important for a variety of cellular processes in vascular endothelial cells. The goal of this review is to provide a succinct description of the endothelial cell T‐type calcium channel, including its molecular characteristics, biophysical and pharmacological profiles, and involvement in certain endothelial cell functions.
Ca2+Channels and Chronic Hypoxia
Authors: SHIMODA LARISSA A. , WANG JIAN , SYLVESTER J. T.
Published: November 2006

Many chronic lung diseases are associated with prolonged exposure to alveolar hypoxia, resulting in the development of pulmonary hypertension. While the exact mechanisms underlying the pathogenesis of hypoxic pulmonary hypertension remain poorly understood, a key role for changes in Ca2+homeostasis has emerged. Intracellular Ca2+concentration controls a variety of pulmonary vascular cell functions, including contraction, gene expression, growth, barrier function and synthesis of vasoactive substances. Several studies indicate that prolonged exposure to hypoxia causes alterations in the expression and activity of several Ca2+handling pathways in pulmonary arterial smooth muscle cells. In contrast, the effect of chronic hypoxia on Ca2+homeostasis in pulmonary arterial endothelial cells is relatively unexplored. In this review, we discuss data from our laboratory and others describing the effects of prolonged hypoxia on pulmonary vascular smooth muscle and endothelial cell Ca2+homeostasis and the various Ca2+channels and handling pathways involved in these responses. We will also highlight future directions of investigation that might improve our understanding of the response of pulmonary vascular cells to chronic hypoxia.
Marinobacter koreensis sp. nov., isolated from sea sand in Korea
Authors: Kim Byung-Yong , Weon Hang-Yeon , Yoo Seung-Hee , Kim Jong-Shik , Kwon Soon-Wo , Stackebrandt Erko , Go Seung-Joo
Published: November 2006

A marine, Gram-negative, aerobic, motile, straight-rod-shaped, moderately halophilic bacterium, designated strain DD-M3T, was isolated from sea sand in Pohang, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that the strain fell within the evolutionary radiation encompassed by the genus Marinobacter. The levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of recognized Marinobacter species ranged from 94.2 to 97.6 %, the highest values being with Marinobacter flavimaris SW-145T (97.6 %) and Marinobacter lipolyticus SM19T (96.8 %). The values for DNA–DNA relatedness between isolate DD-M3T and the type strains of the most closely related species, M. flavimaris and M. lipolyticus, were 41 and 36 %, respectively. Strain DD-M3T was characterized as having Q-9 as the predominant respiratory quinone and 16 : 0, summed feature 3 and 18 : 1ω9c as the main fatty acids. The DNA G+C content was 54.1 mol%. On the basis of its phenotypic and genotypic characteristics, DD-M3T represents a novel species of the genus Marinobacter, for which the name Marinobacter koreensis sp. nov. is proposed, with DD-M3T (=KACC 11513T=DSM 17924T) as the type strain.
Nesterenkonia jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood
Authors: Yoon Jung-Hoon , Jung Seo-Youn , Kim Wonyong , Nam Sun-Woo , Oh Tae-Kwang
Published: November 2006

A Gram-positive, non-motile, slightly halophilic actinomycete, strain JG-241T, was isolated from jeotgal, a traditional Korean fermented seafood, and its taxonomic position was investigated by using a polyphasic approach. Strain JG-241Tgrew optimally at 25–30 °C and in the presence of 2–5 % (w/v) NaCl. The physiological and biochemical properties of strain JG-241Twere distinguishable from those of recognizedNesterenkoniaspecies. Strain JG-241Thad a peptidoglycan type based onl-lys–gly–d-Asp. It contained MK-7, MK-8 and MK-9 as the predominant menaquinones and anteiso-C15 : 0and anteiso-C17 : 0as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The DNA G+C content was 68.0 mol%. Comparative 16S rRNA gene sequence analysis showed that strain JG-241Tfalls within the radiation of the cluster comprisingNesterenkoniaspecies. Similarity values between the 16S rRNA gene sequence of strain JG-241Tand those of the type strains ofNesterenkoniaspecies ranged from 96.7 to 99.7 %. DNA–DNA relatedness data and repetitive extragenic palindromic DNA-PCR genomic fingerprinting patterns showed that strain JG-241Tdiffers genetically from recognizedNesterenkoniaspecies. On the basis of its phenotypic properties and phylogenetic and genetic distinctiveness, strain JG-241Trepresents a novel species of the genusNesterenkonia, for which the nameNesterenkonia jeotgalisp. nov. is proposed. The type strain is JG-241T(=KCTC 19053T=JCM 12610T).
Confirmation of Thiomonas delicata (formerly Thiobacillus delicatus) as a distinct species of the genus Thiomonas Moreira and Amils 1997 with comments on some species currently assigned to the genus
Authors: Katayama Yoko , Uchino Yoshihito , Wood Ann P. , Kelly Donovan P.
Published: November 2006

The transfer of Thiobacillus delicatus to the genus Thiomonas as a distinct species, Thiomonas delicata (type strain NBRC 14566T), is confirmed by its morphological and physiological properties, DNA–DNA hybridization and the grouping of its 16S rRNA gene sequence with those of other species of the genus. An emended formal description of Thiomonas delicata is given. The status of Thiomonas cuprina DSM 5495T as a member of the genus is reconsidered.
Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov.
Authors: Hatayama Kouta , Shoun Hirofumi , Ueda Yasuichi , Nakamura Akira
Published: November 2006

Two thermophilic strains, designated 607T and 606b, were isolated from a compost pile in Japan. The novel strains were Gram-positive, aerobic, spore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains 607T and 606b were closely related to Bacillus naganoensis (94.0–94.1 % similarity) and separated from clusters of the related genera Bacillus (<91.9 %) and Sporolactobacillus (91.0–92.5 %). In addition, some chemotaxonomic and physiological characteristics of strains 607T and 606b differed from those of B. naganoensis and the two related genera. Several differences in physiological characteristics and 16S–23S rRNA gene internal transcribed spacer region nucleotide sequences were observed between strains 607T and 606b; however, DNA–DNA hybridization indicated that these two strains belonged to the same species. From these results, it is proposed that strains 607T and 606b represent the type species of a new genus, Tuberibacillus calidus gen. nov., sp. nov., with strain 607T (=JCM 13397T=DSM 17572T) as the type strain. In addition, the results of phylogenetic analyses, as well as chemotaxonomic and physiological characterization, indicated that B. naganoensis and Bacillus laevolacticus did not belong to the genus Bacillus. Based on these results, it is proposed that B. naganoensis and B. laevolacticus should be transferred to Pullulanibacillus naganoensis gen. nov., comb. nov. and Sporolactobacillus laevolacticus comb. nov., respectively.
Proposal of Parvimonas gen. nov. and Quatrionicoccus gen. nov. as replacements for the illegitimate, prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002, respectively
Authors: Tindall B. J. , Euzéby J. P.
Published: November 2006

The prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002 are illegitimate* because they are later homonyms of the names Micromonas Manton and Parke 1960 (alga) and Quadricoccus Fott 1948 (alga). [Principle 2, Rule 51b(4) of the Bacteriological Code (1990 Revision)]. Such names have no claim to be correct names (Principle 6) and, therefore, replacement generic names must be proposed (Rule 54).
Lysobacter enzymogenes subsp. enzymogenes Christensen and Cook 1978, L. enzymogenes subsp. cookii Christensen 1978 and Streptococcus casseliflavus (Mundt and Graham 1968) Vaughan et al. 1978 should have been cited in the Approved Lists of Bacterial Names. Request for an Opinion
Authors: Tindall B. J. , Euzéby J. P.
Published: November 2006

Lysobacter enzymogenes subsp. enzymogenes Christensen and Cook 1978, L. enzymogenes subsp. cookii Christensen 1978 and Streptococcus casseliflavus (Mundt and Graham 1968) Vaughan et al. 1978 were inadvertently omitted from the Approved Lists of Bacterial Names. According to Rule 24a, Note 1, the authors request that these names be considered as included in these Lists.