bluuebunny/crossref_metadata_2025 huggingface dataset:
A System for Visualizing and Analyzing Near-Optimal Protein Sequence Alignments
Authors: Smoot Michael E. , Bass Ellen J. , Guerlain Stephanie A. , Pearson William R.
Published: July 2005

System modeling and analysis is an imperfect art and as a consequence there are problems where alternative solutions may exist. Information visualization is often used to enhance system modeling and analysis efforts by taking advantage of human perceptual capabilities. Our research uses visual representations of alternative solutions as a way to aid understanding and foster insight into problems, their solutions, and the underlying algorithms. Specifically, our system visualizes large sets of near-optimal protein sequence alignments. Prior efforts focused on the visualization of near-optimal alignments, using an animation metaphor for providing context to detailed displays. This paper discusses novel extensions: (1) a new overview display, the enhanced path graph; (2) the integration of the detail-oriented (animation) and overview-oriented (path graph) displays; and (3) additional human-computer interaction capabilities for filtering, highlighting, and mixed-initiative interaction that allow researchers to combine their expertise with algorithmic output to gain insight into the sequence alignment algorithms and the problem domain. Two case studies illustrate the effectiveness of this system.
The electronic structure of vanadium carbide, VC
Authors: Kalemos Apostolos , Dunning Thom H. , Mavridis Aristides
Published: July 2005

Within an energy range of 2.4 eV, we have explored 29 of the 36 states of the diatomic molecule VC that arise from the atoms in their ground state, V(4s23d3;F4)+C(2s22p2;P3). We use multireference methods with large atomic natural orbital basis sets. The ground state is of Δ2 symmetry with the first two excited states, Δ4 and Σ+2, located 4.2 and 7.0kcal∕mol above the X state. All the states examined in this work are relatively strongly bound and show significant charge transfer from V to C. The binding energy of the XΔ2 state is estimated to be 95.3kcal∕mol in good agreement with the experimental value.
Orientation-dependent potential of mean force for protein folding
Authors: Mukherjee Arnab , Bhimalapuram Prabhakar , Bagchi Biman
Published: July 2005

We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model, the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other sites through an orientation-dependent interaction potential which we construct in the following fashion. First, the site–site potential of mean force (PMF) between heavy atoms is calculated [following F. Melo and E. Feytsman, J. Mol. Biol. 267, 207 (1997)] from statistics of their distance separation obtained from crystal structures. These site–site potentials are then used to calculate the distance and the orientation-dependent potential between side chains of all the amino acid residues (AAR). The distance and orientation dependencies show several interesting results. For example, we find that the PMF between two hydrophobic AARs, such as phenylalanine, is strongly attractive at short distances (after the obvious repulsive region at very short separation) and is characterized by a deep minimum, for specific orientations. For the interaction between two hydrophilic AARs, such a deep minimum is absent and in addition, the potential interestingly reveals the combined effect of polar (charge) and hydrophobic interactions among some of these AARs. The effectiveness of our potential has been tested by calculating the Z-scores for a large set of proteins. The calculated Z-scores show high negative values for most of them, signifying the success of the potential to identify the native structure from among a large number of its decoy states.
Existence of solitary waves for a simplified two fluid system of equations in plasma
Authors: Guo Boling , Huang Daiwen
Published: July 2005

In this paper, we consider a simplified two fluid system of equations in plasma under some conditions. The existence, uniqueness, and the behavior of solitary waves at infinity for the system are proved by ordinary differential equations methods.
Interdimensional degeneracies in van der Waals clusters and quantum Monte Carlo computation of rovibrational states
Authors: Nightingale M. P. , Moodley Mervlyn
Published: July 2005

Quantum Monte Carlo estimates of the spectrum of rotationally invariant states of noble gas clusters suggest interdimensional degeneracy in N−1 and N+1 spatial dimensions. We derive this property by mapping the Schrödinger eigenvalue problem onto an eigenvalue equation in which D appears as a continuous variable. We discuss implications for quantum Monte Carlo and dimensional scaling methods.
Size dependence of refractive index of Si nanoclusters embedded in SiO2
Authors: Moreno J. A. , Garrido B. , Pellegrino P. , Garcia C. , Arbiol J. , Morante J. R. , Marie P. , Gourbilleau F. , Rizk R.
Published: July 2005

The complex refractive index of SiO2 layers containing Si nanoclusters (Si-nc) has been measured by spectroscopic ellipsometry in the range from 1.5 to 5.0 eV. It has been correlated with the amount of Si excess accurately measured by x-ray photoelectron spectroscopy and the nanocluster size determined by energy-filtered transmission electron microscopy. The Si-nc embedded in SiO2 have been produced by a fourfold Si+ ion implantation, providing uniform Si excess aimed at a reliable ellipsometric modeling. The complex refractive index of the Si-nc phase has been calculated by the application of the Bruggeman effective-medium approximation to the composite media. The characteristic resonances of the refractive index and extinction coefficient of bulk Si vanish out in Si-nc. In agreement with theoretical simulations, a significant reduction of the refractive index of Si-nc is observed, in comparison with bulk and amorphous silicon. The knowledge of the optical properties of these composite layers is crucial for the realization of Si-based waveguides and light-emitting devices.
Self-consistent solution for a collisionless plasma slab in motion across a magnetic field
Authors: Echim Marius M. , Lemaire Joseph F. , Roth Michel
Published: July 2005

The problem of the dynamics of a plasma slab moving across a magnetic field is treated in the framework of the kinetic theory. A velocity distribution function (VDF) is found for each plasma species, electrons and protons, in terms of the constants of motion defined by the geometry of the problem. The zero- and first-order moments of the VDF are introduced into the right-hand side term of Maxwell’s equations to compute the electric and magnetic vector potentials and corresponding fields. The solutions are found numerically. We obtain a region of plasma convection—the slab proper—where the plasma moves with a uniform velocity, Vx=V0=(E×B∕B2)x. At the core margins two plasma “wings” are formed, each being the result of a pair of interpenetrated boundary layers with different transition lengths. Inside these wings, the plasma velocity is not uniform, Vx≠(E×B∕B2)x. It decreases from the maximum value obtained in the core to a minimum value in the central region of the wings where a flow reversal is found with the plasma convecting in the opposite direction to the core motion. There is also an asymmetry of the velocity gradient at the borders of the core, which results in a corresponding asymmetry in the thickness of the wings. Furthermore, it is found that the reversed plasma flow in the thinner wing is larger than that in the broader wing. For a fixed direction of the magnetic field the two plasma wings interchange position with respect to the center of the slab when the plasma bulk velocity reverses sign.
Superconductivity suppression in Fe-implanted thin Al films
Authors: Jalkanen P. , Touboltsev V. , Koivisto H. , Suominen P. , Suppula T. , Arutyunov K. Yu. , Räisänen J.
Published: July 2005

At present, ion implantation into metallic systems is given increasing attention, aiming at achieving properties and functionalities of technologically valuable materials not easily available via conventional techniques. In our experiments thin Al films were implanted with Fe ions in order to find out how the superconductive properties of the metal can be modified at will. The purpose was twofold, viz., first, to study the basic physics of superconductivity in low-dimensional metallic structures doped with impurities. The second purpose was to apply ion implantation for the suppression of undesired superconductivity in aluminum widely used for fabrication of micro- and nanodevices operated at low temperatures. In many applications transition to the superconductive state is detrimental for the device’s functionality, for instance, those based on Coulomb blockage (CB) effect (e.g., in CB thermometry).
Heat transport in turbulent Rayleigh-Bénard convection: Effect of finite top- and bottom-plate conductivities
Authors: Brown Eric , Nikolaenko Alexei , Funfschilling Denis , Ahlers Guenter
Published: July 2005

We describe three apparatus, known as the large, medium, and small apparatus, used for high-precision measurements of the Nusselt number N as a function of the Rayleigh number R for cylindrical samples of fluid and present results illustrating the influence of the finite conductivity of the top and bottom plates on the heat transport in the fluid. We used water samples at a mean temperature of 40°C (Prandtl number σ=4.4). The samples in the large apparatus had a diameter D of 49.69cm and heights L≃116.33, 74.42, 50.61, and 16.52cm. For the medium apparatus we had D=24.81cm, and L=90.20 and 24.76cm. The small apparatus contained a sample with D=9.21cm and L=9.52cm. For each aspect ratio Γ≡D∕L the data covered a range of a little over a decade of R. The maximum R≃1×1012 with Nusselt number N≃600 was reached for Γ=0.43. Measurements were made with both aluminum (conductivity λp=161W∕mK) and copper (λp=391W∕mK) top and bottom plates of nominally identical size and shape. For the large and medium apparatus the results with aluminum plates fall below those obtained with copper plates, thus confirming qualitatively the prediction by [Verzicco, “Effects of nonperfect thermal sources in turbulent thermal convection,” Phys. Fluids 16, 1965 (2004)] that plates of finite conductivity diminish the heat transport in the fluid. The Nusselt number N∞ for plates with infinite conductivity was estimated by fitting simultaneously aluminum- and copper-plate data sets to an effective power law for N∞ multiplied by a correction factor f(X)=1−exp[−(aX)b] that depends on the ratio X of the thermal resistance of the fluid to that of the plates, as suggested by Verzicco. Within their uncertainties the parameters a and b were independent of Γ for the large apparatus and showed a small Γ dependence for the medium apparatus. The correction was larger for the large, smaller for the medium, and negligible for the small apparatus.
Microscale application of column theory for high resolution force and displacement sensing
Authors: Samuel B. A. , Desai A. V. , Haque M. A.
Published: July 2005

We present the design, fabrication, and experimental validation of a device which exploits the amplification of displacement and attenuation of structural stiffness in the post-buckling deformation of slender columns to obtain pico-Newton force and nanometer displacement resolution, even under an optical microscope. The extremely small size, purely mechanical sensing scheme and vacuum compatibility of the instrument makes it compatible with existing visualization tools of nanotechnology. The instrument has a wide variety of potential applications ranging from electro-mechanical characterization of one dimensional solids to single biological cells.
Improvement of current gain of C-doped GaAsSb-base heterojunction bipolar transistors by using an InAlP emitter
Authors: Oda Yasuhiro , Yokoyama Haruki , Kurishima Kenji , Kobayashi Takashi , Watanabe Noriyuki , Uchida Masahiro
Published: July 2005

Large conduction band edge discontinuity (ΔEc) at the emitter/base interface in InP∕GaAs0.51Sb0.49∕InP heterojunction bipolar transistor (HBT) is one of the possible reasons that the recombination process in the emitter/base depletion region dominates the characteristics of this HBT. We fabricate an InAlP emitter∕GaAs0.51Sb0.49base∕InP collector HBT for reducing the ΔEc at the emitter/base interface. It is demonstrated that a HBT with an InAlP emitter shows a relatively lower recombination current than one with an InP emitter, resulting in the higher current gain. It is also found that the decrease of recombination current depends on the Al content of InAlP emitter. Additionally, the ideality factor of the emitter-base current is smallest at the Al content of 0.15 in the InAlP emitter. These results indicate that using an InAlP emitter is effective for improving the current gain of GaAsSb-base HBTs.
Effect of Sulfate on Selenium Uptake and Chemical Speciation in Convolvulus arvensis L.
Authors: Cruz-Jímenez Gustavo , Peralta-Videa Jose R. , de la Rosa Guadalupe , Meitzner George , Parsons Jason G. , Gardea-Torresdey Jorge L.
Published: July 2005

Environmental Context. Selenium (Se) is one of the most serious problems confronted in agricultural soils derived from Se-containing rocks. This metalloid, an essential nutrient for animals and humans, may be toxic at relatively low concentrations. Se removal from soil and water using plants is a promising alternative to traditional chemical or electrochemical techniques. However, very few plant species are able to accumulate Se at high concentrations. Since Se and sulfur (S) have similar chemical properties, sulfate (SO42−) in the plant growth media may interfere in the process of Se uptake by plants. Thus, plant species able to uptake more Se than S when both elements are present are desired for Se phytoremediation purposes.
Abstract. Hydroponic experiments were performed to study several aspects of Se uptake by C. arvensis plants. Ten day old seedlings were exposed for eight days to different combinations of selenate (SeO42−), sulfate (SO42−), and selenite (SeO32−). The results showed that in C. arvensis, SO42− had a negative effect (P < 0.05) on SeO42− uptake. However, a positive interaction produced a significant increase in SO42− uptake when SeO42− was at high concentration in the media. X-ray absorption spectroscopy studies showed that C. arvensis plants converted more than 70% of the supplied SeO32− into organoselenium compounds. However, only approximately 50% of the supplied SeO42− was converted into organoselenium species while the residual 50% remained in the inorganic form. Analysis using LC-XANES fittings confirmed that the S metabolic pathway was affected by the presence of Se. The main Se compounds that resembled those Se species identified in C. arvensis were Se-cystine, Se-cysteine, SeO32−, and SeO42−, whereas for S the main compounds were cysteine, cystine, oxidized glutathione, reduced glutathione, and SO42−. The results of these studies indicated that C. arvensis could be considered as a possible option for the restoration of soil moderately contaminated with selenium even in the presence of sulfate.
Comment on 'Measuring Marine Iron(III) Complexes by CLE-AdSV'
Authors: Hunter Keith A.
Published: July 2005

Environmental Context. Town and Leeuwen’s paper (Environ. Chem. 2005, 2, 80) challenges interpretations of the role of organic matter binding iron in the ocean. This challenge is based on the theory behind a commonly used electrochemical technique, CLE-AdSV. Consistent experimental measurements for iron and other metals and the use of other techniques suggests that their interpretation of iron(III) being non-bioavailable is incorrect and, rather, the use of CLE-AdSV needs to be modified.
Temperature influences growth and maturation of fruit on 'Hayward' kiwifruit vines
Authors: Snelgar William P. , Hall Alistair J. , Ferguson A. Ross , Blattmann Peter
Published: July 2005

The responses of fruit and shoot growth of ‘Hayward’ kiwifruit vines to changes of temperature were determined during spring, summer or autumn. Mature vines were warmed 2–5°C above ambient temperatures by enclosing them in temperature-controlled tunnel houses for 34–89 d. Increasing temperature during spring advanced the date of flowering by 17 d and increased the rate of shoot elongation by 6 mm d–1 °C–1. The fruit on these early-flowering vines were larger and had a higher dry matter concentration than control fruit during the first part of the season. Increasing temperature during summer increased the rate of shoot elongation but reduced fruit growth, accumulation of dry matter in fruit and fruit firmness. In contrast, increasing temperature during late autumn increased fruit growth but reduced the soluble solids concentration (SSC) of fruit and thus, delayed commercial maturity. When fruit growth data for summer and autumn were combined the variation in fruit growth with temperature could be described by a single quadratic curve. Maximum fruit growth occurred at 17°C and temperatures above or below this optimum reduced fruit growth. Consequently, during summer when ambient temperatures averaged 17°C, warming vines decreased fruit growth, while during late autumn, when ambient temperatures had fallen to 13°C, warming vines increased fruit growth. Warming vines during summer reduced both the SSC of ripe fruit and the vitamin C concentration. Warming vines during autumn increased SSC but reduced the vitamin C concentration.
Inhibition of IFN-α signaling by a PKC- and protein tyrosine phosphatase SHP-2-dependent pathway
Authors: Du Zhimei , Shen Yuhong , Yang Wentian , Mecklenbrauker Ingrid , Neel Benjamin G. , Ivashkiv Lionel B.
Published: July 2005

Cytokine signaling by the Jak–STAT pathway is subject to complex negative regulation that limits the amplitude and duration of signal transduction. Inhibition of signaling also mediates negative crosstalk, whereby factors with opposing biological activities crossinhibit each other's function. Here, we investigated a rapidly inducible mechanism that inhibited Jak–STAT activation by IFN-α, a cytokine that is important for antiviral responses, growth control, and modulation of immune responses. IFN-α-induced signaling and gene activation were inhibited by ligation of Fc receptors and Toll-like receptors 7 and 8 in a PKCβ-dependent manner. Neither PKCβ nor PKCδ influenced responses of cells treated with IFN-α alone. Inhibition of IFN-α signaling correlated with suppression of IFN-α-dependent antiviral responses. PKC-mediated inhibition did not requirede novogene expression but involved the recruitment of PKCβ to the IFN-α receptor and interaction with protein tyrosine phosphatase SHP-2, resulting in augmented phosphatase activity. PKC-mediated inhibition of IFN-α signaling was abolished in SHP-2-deficient cells, demonstrating a pivotal role for SHP-2 in this inhibitory pathway. Together, our data describe a rapidly inducible, direct mechanism of inhibition of Jak–STAT signaling mediated by a PKCβ–SHP-2 signaling pathway.
Restriction mapping in nanofluidic devices
Authors: Riehn Robert , Lu Manchun , Wang Yan-Mei , Lim Shuang Fang , Cox Edward C. , Austin Robert H.
Published: July 2005

We have performed restriction mapping of DNA molecules using restriction endonucleases in nanochannels with diameters of 100-200 nm. The location of the restriction reaction within the device is controlled by electrophoresis and diffusion of Mg
2+
and EDTA. We have successfully used the restriction enzymes SmaI, SacI, and PacI, and have been able to measure the positions of restriction sites with a precision of ≈1.5 kbp in 1 min using single DNA molecules.
Interaction between the Shuttling mRNA Export Factor Gle1 and the Nucleoporin hCG1: A Conserved Mechanism in the Export of Hsp70 mRNA
Authors: Kendirgi Frederic , Rexer Deborah J. , Alcázar-Román Abel R. , Onishko Halina M. , Wente Susan R.
Published: July 2005

Translocation of messenger RNAs through the nuclear pore complex (NPC) requires coordinated physical interactions between stable NPC components, shuttling transport factors, and mRNA-binding proteins. In budding yeast (y) and human (h) cells, Gle1 is an essential mRNA export factor. Nucleocytoplasmic shuttling of hGle1 is required for mRNA export; however, the mechanism by which hGle1 associates with the NPC is unknown. We have previously shown that the interaction of hGle1 with the nucleoporin hNup155 is necessary but not sufficient for targeting hGle1 to NPCs. Here, we report that the unique C-terminal 43 amino acid region of the hGle1B isoform mediates binding to the C-terminal non-FG region of the nucleoporin hCG1/NPL1. Moreover, hNup155, hGle1B, and hCG1 formed a heterotrimeric complex in vitro. This suggested that these two nucleoporins were required for the NPC localization of hGle1. Using an siRNA-based approach, decreased levels of hCG1 resulted in hGle1 accumulation in cytoplasmic foci. This was coincident with inhibition of heat shock-induced production of Hsp70 protein and export of the Hsp70 mRNA in HeLa cells. Because this closely parallels the role of the hCG1 orthologue yNup42/Rip1, we speculate that hGle1-hCG1 function in the mRNA export mechanism is highly conserved.
Calcium-activated RAF/MEK/ERK Signaling Pathway Mediates p53-dependent Apoptosis and Is Abrogated by αB-Crystallin through Inhibition of RAS Activation
Authors: Li David Wan-Cheng , Liu Jin-Ping , Mao Ying-Wei , Xiang Hua , Wang Juan , Ma Wei-Ya , Dong Zigang , Pike Helen M. , Brown Rhoderick E. , Reed John C.
Published: July 2005

The ocular lens is the only organ that does not develop spontaneous tumor. The molecular mechanism for this phenomenon remains unknown. Through examination of the signaling pathways mediating stress-induced apoptosis, here we presented evidence to show that different from most other tissues in which the extracellular signal-regulated kinases (ERKs) pathway is generally implicated in mediation of survival signals activated by different factors, the RAF/MEK/ERK signaling pathway alone plays a key role in stress-activated apoptosis of lens epithelial cells. Treatment of N/N1003A cells with calcimycin, a calcium mobilizer, activates the RAF/MEK/ERK pathway through RAS, which is indispensable for the induced apoptosis because inhibition of this pathway by either pharmacological drug or dominant negative mutants greatly attenuates the induced apoptosis. Calcimycin also activates p38 kinase and JNK2, which are not involved in calcium-induced apoptosis. Downstream of ERK activation, p53 is essential. Activation of RAF/MEK/ERK pathway by calcimycin leads to distinct up-regulation of p53. Moreover, overexpression of p53 enhances calcimycin-induced apoptosis, whereas inhibition of p53 expression attenuates calcimycin-induced apoptosis. Up-regulation of p53 directly promotes Bax expression, which changes the integrity of mitochondria, leading to release of cytochrome c, activation of caspase-3 and eventually execution of apoptosis. Overexpression of αB-crystallin, a member of the small heat-shock protein family, blocks activation of RAS to inhibit ERK1/2 activation, and greatly attenuates calcimycin-induced apoptosis. Together, our results provide 1) a partial explanation for the lack of spontaneous tumor in the lens, 2) a novel signaling pathway for calcium-induced apoptosis, and 3) a novel antiapoptotic mechanism for αB-crystallin.
Interactions between Mad1p and the Nuclear Transport Machinery in the YeastSaccharomyces cerevisiae
Authors: Scott Robert J. , Lusk C. Patrick , Dilworth David J. , Aitchison John D. , Wozniak Richard W.
Published: July 2005

In addition to its role in nucleocytoplasmic transport, the nuclear pore complex (NPC) acts as a docking site for proteins whose apparent primary cellular functions are unrelated to nuclear transport, including Mad1p and Mad2p, two proteins of the spindle assembly checkpoint (SAC) machinery. To understand this relationship, we have mapped domains of yeast Saccharomyces cerevisiae Mad1p that interact with the nuclear transport machinery, including further defining its interactions with the NPC. We showed that a Kap95p/Kap60p-dependent nuclear localization signal, positioned in the C-terminal third of Mad1p, is required for its efficient targeting to the NPC. At the NPC, Mad1p interacts with Nup53p and a presumed Nup60p/Mlp1p/Mlp2p complex through two coiled coil regions within its N terminus. When the SAC is activated, a portion of Mad1p is recruited to kinetochores through an interaction that is mediated by the C-terminal region of Mad1p and requires energy. We showed using photobleaching analysis that in nocodazole-arrested cells Mad1p rapidly cycles between the Mlp proteins and kinetochores. Our further analysis also showed that only the C terminus of Mad1p is required for SAC function and that the NPC, through Nup53p, may act to regulate the duration of the SAC response.
Stochastic Simulation of Neurofilament Transport in Axons: The “Stop-and-Go” Hypothesis
Authors: Brown Anthony , Wang Lei , Jung Peter
Published: July 2005

According to the “stop-and-go” hypothesis of slow axonal transport, cytoskeletal and cytosolic proteins are transported along axons at fast rates but the average velocity is slow because the movements are infrequent and bidirectional. To test whether this hypothesis can explain the kinetics of slow axonal transport in vivo, we have developed a stochastic model of neurofilament transport in axons. We propose that neurofilaments move in both anterograde and retrograde directions along cytoskeletal tracks, alternating between short bouts of rapid movement and short “on-track” pauses, and that they can also temporarily disengage from these tracks, resulting in more prolonged “off-track” pauses. We derive the kinetic parameters of the model from a detailed analysis of the moving and pausing behavior of single neurofilaments in axons of cultured neurons. We show that the model can match the shape, velocity, and spreading of the neurofilament transport waves obtained by radioisotopic pulse labeling in vivo. The model predicts that axonal neurofilaments spend ∼8% of their time on track and ∼97% of their time pausing during their journey along the axon.
Regression-based quantitative trait loci mapping: robust, efficient and effective
Authors: Knott Sara A
Published: July 2005

Regression has always been an important tool for quantitative geneticists. The use of maximum likelihood (ML) has been advocated for the detection of quantitative trait loci (QTL) through linkage with molecular markers, and this approach can be very effective. However, linear regression models have also been proposed which perform similarly to ML, while retaining the many beneficial features of regression and, hence, can be more tractable and versatile than ML in some circumstances. Here, the use of linear regression to detect QTL in structured outbred populations is reviewed and its perceived shortfalls are revisited. It is argued that the approach is valuable now and will remain so in the future.
Approximating the coalescent with recombination
Authors: McVean Gilean A.T , Cardin Niall J
Published: July 2005

The coalescent with recombination describes the distribution of genealogical histories and resulting patterns of genetic variation in samples of DNA sequences from natural populations. However, using the model as the basis for inference is currently severely restricted by the computational challenge of estimating the likelihood. We discuss why the coalescent with recombination is so challenging to work with and explore whether simpler models, under which inference is more tractable, may prove useful for genealogy-based inference. We introduce a simplification of the coalescent process in which coalescence between lineages with no overlapping ancestral material is banned. The resulting process has a simple Markovian structure when generating genealogies sequentially along a sequence, yet has very similar properties to the full model, both in terms of describing patterns of genetic variation and as the basis for statistical inference.
Animal breeding and disease
Authors: Nicholas Frank W
Published: July 2005

Single-locus disorders in domesticated animals were among the first Mendelian traits to be documented after the rediscovery of Mendelism, and to be included in early linkage maps. The use of linkage maps and (increasingly) comparative genomics has been central to the identification of the causative gene for single-locus disorders of considerable practical importance. The ‘score-card’ in domestic animals is now more than 100 disorders for which the molecular lesion has been identified and hence for which a DNA test is available. Because of the limited lifespan of any such test, a cost-effective and hence popular means of protecting the intellectual property inherent in a DNA test is not to publish the discovery. While understandable, this practice creates a disconcerting precedent. For multifactorial disorders that are scored on an all-or-none basis or into many classes, the effectiveness of control schemes could be greatly enhanced by selection on estimated breeding values for liability. Genetic variation for resistance to pathogens and parasites is ubiquitous. Selection for resistance can therefore be successful. Because of the technical and welfare challenges inherent in the requirement to expose animals to pathogens or parasites in order to be able to select for resistance, there is a very active search for DNA markers for resistance. The first practical fruits of this research were seen in 2002, with the launch of a national scrapie control programme in the UK.
Effect of static growth and different levels of environmental oxygen on toxA and ptxR expression in the Pseudomonas aeruginosa strain PAO1
Authors: Gaines Jennifer M. , Carty Nancy L. , Colmer-Hamood Jane A. , Hamood Abdul N.
Published: July 2005

Within certain infection sites, such as the lung of cystic fibrosis patients,Pseudomonas aeruginosagrows statically under either decreased oxygen tension or anaerobic conditions, a situation that is likely to influence the production of virulence factors. The goal of this study was to determine the effect of static growth under microaerobic (decreased oxygen) and anaerobic conditions on the expression of theP. aeruginosaexotoxin A (ETA) genetoxAand its positive regulatorptxR. UsingtoxA–lacZandptxR–lacZfusion plasmids, the level oftoxAandptxRexpression was measured throughout the growth cycle of strain PAO1, which was grown in either iron-deficient or iron-sufficient medium under four different conditions: 20 %-SH (aerobic, shaking), 20 %-ST (aerobic, static), 10 %-ST (microaerobic, static) and 0 %-ST (anaerobic, static). In iron-deficient medium,toxAexpression was higher under 20 %-ST and 10 %-ST than under 20 %-SH. However, the highest level oftoxAexpression occurred under 0 %-ST. Analysis of ETA protein using sandwich ELISA revealed that at time points between 8 and 24 h of the growth curve, PAO1 produced higher levels of ETA under 0 %-ST than under 20 %-SH. In iron-sufficient medium,toxAexpression was significantly repressed under all conditions. Additional analyses using PAO1 strains that carrylacZfusions with thetoxAregulatory genesregAandpvdSrevealed that the expression ofregAandpvdSis reduced rather than increased at 0 %-ST.ptxRexpression under different conditions paralleled that oftoxAexpression, except that it was repressed by iron under 20 %-SH only. Between 6 and 24 h of growth, and under all conditions, the level of dissolved oxygen (DO) within the PAO1 cultures was sharply reduced. These results suggest that (1) the combined effect of static growth and anaerobic conditions produce a significant increase intoxAandptxRexpression in PAO1; (2) this effect appears to be unique totoxAandptxR, since the level ofregAandpvdSexpression was reduced under the same conditions; (3) neither static growth nor anaerobic conditions interfere with the repression oftoxAexpression by iron, although static growth deregulatesptxRexpression with respect to iron; and (4) the enhanced expression oftoxAandptxRis not related to the reduced levels of DO in PAO1 cultures.
Immunogenic membrane-associated proteins of Mycobacterium tuberculosis revealed by proteomics
Authors: Sinha Sudhir , Kosalai K. , Arora Shalini , Namane Abdelkader , Sharma Pawan , Gaikwad Anil N. , Brodin Priscille , Cole Stewart T.
Published: July 2005

Membrane-associated proteins ofMycobacterium tuberculosisoffer a challenge, as well as an opportunity, in the quest for better therapeutic and prophylactic interventions against tuberculosis. The authors have previously reported that extraction with the detergent Triton X-114 (TX-114) is a useful step in proteomic analysis of mycobacterial cell membranes, and detergent-soluble membrane proteins of mycobacteria are potent stimulators of human T cells. In this study 1-D and 2-D gel electrophoresis-based protocols were used for the analysis of proteins in the TX-114 extract ofM. tuberculosismembranes. Peptide mass mapping (using MALDI-TOF-MS, matrix assisted laser desorption/ionization time of flight mass spectrometry) of 116 samples led to the identification of 105 proteins, 9 of which were new to theM. tuberculosisproteome. Functional orthologues of 73 of these proteins were also present inMycobacterium leprae, suggesting their relative importance. Bioinformatics predicted that as many as 73 % of the proteins had a hydrophobic disposition. 1-D gel electrophoresis revealed more hydrophobic/transmembrane and basic proteins than 2-D gel electrophoresis. Identified proteins fell into the following major categories: protein synthesis, cell wall biogenesis/architecture and conserved hypotheticals/unknowns. To identify immunodominant proteins of the detergent phase (DP), 14 low-molecular-mass fractions prepared by continuous-elution gel electrophoresis were subjected to T cell activation assays using blood samples from BCG-vaccinated healthy donors from a tuberculosis endemic area. Analysis of the responses (cell proliferation and IFN-γproduction) showed that the immunodominance of certain DP fractions was most probably due to ribosomal proteins, which is consistent with both their specificity for mycobacteria and their abundance. Other membrane-associated proteins, including transmembrane proteins/lipoproteins and ESAT-6, did not appear to contribute significantly to the observed T cell responses.
DNA methylation in Yersinia enterocolitica: role of the DNA adenine methyltransferase in mismatch repair and regulation of virulence factors
Authors: Fälker Stefan , Schmidt M. Alexander , Heusipp Gerhard
Published: July 2005

DNA adenine methyltransferase (Dam) plays an important role in physiological processes of Gram-negative bacteria such as mismatch repair and replication. In addition, Dam regulates the expression of virulence genes in various species. The authors cloned thedamgene ofYersinia enterocoliticaand showed that Dam is essential for viability. Dam overproduction inY. enterocoliticaresulted in an increased frequency of spontaneous mutation and decreased resistance to 2-aminopurine; however, these effects were only marginal compared to the effect of overproduction ofEscherichia coli-derived Dam inY. enterocolitica, implying different roles or activities of Dam in mismatch repair of the two species. These differences in Dam function are not the cause for the essentiality of Dam inY. enterocolitica, as Dam ofE. colican complement adamdefect inY. enterocolitica. Instead, Dam seems to interfere with expression of essential genes. Furthermore, Dam mediates virulence ofY. enterocolitica. Dam overproduction results in increased tissue culture invasion ofY. enterocolitica, while the expression of specificallyin vivo-expressed genes is not altered.
Utilization of geraniol is dependent on molybdenum in Pseudomonas aeruginosa: evidence for different metabolic routes for oxidation of geraniol and citronellol
Authors: Höschle Birgit , Jendrossek Dieter
Published: July 2005

Mini-Tn5-induced mutants with defects in utilization of linear terpenes such as citronellol, geraniol, citronellate and/or geranylate were isolated from Pseudomonas aeruginosa. One mutant was unable to utilize geraniol but showed wild-type growth with the three other acyclic terpenes tested. The Tn5 insertion site of the mutant was determined by DNA sequencing. Comparison with the P. aeruginosa genome sequence revealed that PA3028, an ORF with high similarity on the amino acid level to molybdenum cofactor biosynthesis protein A2 (encoded by moeA2), was the target of mini-Tn5 in the mutant. Disruption of moeA2 in P. aeruginosa PAO1 wild-type by insertion mutagenesis resulted in the same geraniol-minus phenotype. The ability to utilize geraniol was restored to the mutant by conjugative transfer of PCR-cloned wild-type moeA2 on a broad-host-range plasmid. Growth of P. aeruginosa PAO1 on geraniol and geranial, but not on citronellol, citronellate or geranylate, was inhibited by the presence of 10 mM tungstate, a molybdenum-specific inhibitor. Inhibition by tungstate was prevented by addition of molybdate. The results indicate that at least one step in the oxidation of geraniol to geranic acid (geranial oxidation) is a molybdenum-dependent reaction in P. aeruginosa and is different from the molybdenum-independent oxidation of citronellol to citronellate.
Porins limit the intracellular persistence of Mycobacterium smegmatis
Authors: Sharbati-Tehrani Soroush , Stephan Joachim , Holland Gudrun , Appel Bernd , Niederweis Michael , Lewin Astrid
Published: July 2005

The genus Mycobacterium comprises highly pathogenic as well as opportunistic or apathogenic species exhibiting a great variability with respect to their ability to persist or multiply within monocytic host cells. The impact of the permeability of the mycobacterial outer membrane on intracellular persistence was studied. For this purpose, a Mycobacterium smegmatis mutant with a deletion of the major porin gene mspA and a second mutant lacking mspA and the homologous porin gene mspC were used. Deletion of mspA together with mspC significantly enhanced intracellular persistence in murine bone marrow macrophages, the mouse macrophage cell line J774A.1 and Acanthamoeba castellanii. Complementation of mspA in the porin mutant strains resulted in restoration of the wild-type phenotype with respect to intracellular persistence. This is the first report to show that the deletion of porins of mycobacteria results in improved persistence in eukaryotic cells, demonstrating that the intracellular persistence of M. smegmatis depends upon the permeability of the outer membrane.
Lacrimal caruncle primary basal cell carcinoma: case report and review
Authors: Mencía‐Gutiérrez Enrique , Gutiérrez‐Díaz Esperanza , Pérez‐Martín María E.
Published: July 2005

Background:  Basal cell carcinoma (BCC) is a common malignant skin neoplasm. The surface of the caruncle contains sebaceous glands, hair follicles, and lacrimal and sweat gland elements. Consequently, the caruncle may spawn any neoplasm that occurs in the conjunctiva, skin, or lacrimal gland. We report a patient with a primary BCC located on the lacrimal caruncle.

Methods:  An 80‐year‐old man with a 5‐month history of a gradually enlarging left caruncular neoplasm was seen. The lesion was nodular and irregularly brown‐black colored, with no involvement of adjacent conjunctiva or skin. He had a history of sun exposure, but no personal or family history of other malignant neoplasms.

Results:  The mass was excised completely. Histopathologic examination revealed a BCC originating in the basal layer of the conjunctival epithelium. No tumor recurrence has been noted after 7 years of follow‐up. Primary BCC of the caruncle is unusual, and only four cases have been described in the PubMed. BCC should be considered in the differential diagnosis of caruncle and adjacent skin lesions.
Epstein–Barr virus‐associated B‐cell lymphoma in the setting of iatrogenic immune dysregulation presenting initially in the skin
Authors: Verma Shannon , Frambach Gwyn E. , Seilstad Kay H. , Nuovo Gerard , Porcu Pierluigi , Magro Cynthia M.
Published: July 2005

Background:  Epstein–Barr virus (EBV) has been implicated in B‐cell lymphoma associated with iatrogenic immune dysregulation, primarily in the context of extracutaneous lymphoma.

Methods:  We describe six patients, five transplant recipients receiving cyclosporine and one patient with rheumatoid arthritis receiving methotrexate, who developed cutaneous presentations of EBV‐associated B‐cell lymphoma. Human herpesvirus 8 (HHV8) and EBV thymidine kinase (vTK) expression were also explored.

Results:  The cases comprised plasmablastic lymphoma (one case), plasmacytic marginal zone lymphoma (two cases), and diffuse large B‐cell lymphoma (three cases). There was a monoclonal gammopathy in one and concurrent extracutaneous disease in two of the six patients. EBV‐associated latent small nuclear RNA was detected in all cases with coexpression of HHV8 in one of the five cases and of vTK in three of the six cases. Three patients responded to a reduction in the immunosuppressive regimen and antiviral therapy. Recurrent disease developed in two, with one patient succumbing to multiorgan dissemination.

Conclusions:  EBV‐associated cutaneous B‐cell lymphoma is characterized by a long interval between the initiation of immunosuppression and the development of lymphoma. Although previous reports have reported an indolent clinical course, an aggressive clinical course may occur. HHV8 and lytic phase EBV antigens are detected in some cases, possibly suggesting a pathogenetic role.
Modulation of murine experimental asthma by Ascaris suum components
Authors: Itami D. M. , Oshiro T. M. , Araujo C. A. , Perini A. , Martins M. A. , Macedo M. S. , Macedo‐Soares M. F.
Published: July 2005

Background
We have recently isolated two distinct components from Ascaris suum adult worms with different effects on the immune system: the allergenic protein of A. suum (APAS‐3), which induces IgE antibody production, and suppressive protein of A. suum (PAS‐1), which inhibits humoral and cellular immune responses induced by unrelated antigens. In this study, we investigated the immunomodulatory effect of PAS‐1 on a murine model of asthma induced by APAS‐3.

Methods
BALB/c mice were immunized twice with APAS‐3 or APAS‐3 plus PAS‐1 by the intraperitoneal and subcutaneous route (on days 0 and 7) and challenged twice with the same antigens intranasally (days 14 and 21). Two days after the last challenge, the allergic airway inflammation was evaluated by cellular migration, eosinophil peroxidase (EPO) activity, cytokine and chemokine production and pulmonary mechanical parameters.

Results
The allergenic properties of APAS‐3 were confirmed by the stimulation of anaphylactic IgE and IgG1 antibody production and eosinophilic airway inflammation and hyper‐responsiveness. On the other hand, PAS‐1‐treated mice showed a marked suppression of cellular migration and EPO activity that correlated well with a significant reduction in the levels of IL‐4, IL‐5, eotaxin and RANTES in the bronchoalveolar lavage (BAL) fluid. In contrast, considerable amounts of IL‐10 were observed in the BAL fluid of PAS‐1‐treated mice. Airway hyper‐responsiveness was obtained in APAS‐3‐immunized mice, but the conductance of the respiratory system was restored to normal values in the presence of PAS‐1.

Conclusion
These results indicate that A. suum allergenic protein APAS‐3 induces a T helper 2‐type immune response and, consequently, eosinophilic airway inflammation and hyper‐responsiveness. Moreover, the modulatory protein PAS‐1 has a marked suppressive effect on this response, and the inhibition of cytokine (IL‐4, IL‐5) and chemokine (eotaxin and RANTES) release, probably because of the presence of IL‐10, may contribute to this effect.
Airway generation‐specific differences in the spatial distribution of immune cells and cytokines in allergen‐challenged rhesus monkeys
Authors: Miller L. A. , Hurst S. D. , Coffman R. L. , Tyler N. K. , Stovall M. Y. , Chou D. L. , Putney L. F. , Gershwin L. J. , Schelegle E. S. , Plopper C. G. , Hyde D. M.
Published: July 2005

Background
Accumulation of immune cell populations and their cytokine products within tracheobronchial airways contributes to the pathogenesis of allergic asthma. It has been postulated that peripheral regions of the lung play a more significant role than proximal airways with regard to inflammatory events and airflow obstruction.

Objective
To determine whether immune cell populations and associated cytokines are uniformly distributed throughout the conducting airway tree in a non‐human primate model of allergic asthma.

Methods
We used a stereologic approach with a stratified sampling scheme to measure the volume density of immune cells within the epithelium and interstitium of trachea and 4–5 intrapulmonary airway generations from house dust mite (HDM) (Dermatophagoides farinae)‐challenged adult monkeys. In conjunction with immune cell distribution profiles, mRNA levels for 21 cytokines/chemokines and three chemokine receptors were evaluated at four different airway generations from microdissected lungs.

Results
In HDM‐challenged monkeys, the volume of CD1a+ dendritic cells, CD4+ T helper lymphocytes, CD25+ cells, IgE+ cells, eosinophils, and proliferating cells were significantly increased within airways. All five immune cell types accumulated within airways in unique patterns of distribution, suggesting compartmentalized responses with regard to trafficking. Although cytokine mRNA levels were elevated throughout the conducting airway tree of HDM‐challenged animals, the distal airways (terminal and respiratory bronchioles) exhibited the most pronounced up‐regulation.

Conclusion
These findings demonstrate that key effector immune cell populations and cytokines associated with asthma differentially accumulate within distinct regions and compartments of tracheobronchial airways from allergen‐challenged primates.
High fractional concentration of nitric oxide in exhaled air despite steroid treatment in asthmatic children
Authors: Pijnenburg M. W. H. , Bakker E. M. , Lever S. , Hop W. C. , De Jongste J. C.
Published: July 2005

Background
The fractional concentration of nitric oxide in exhaled air (FENO) is elevated in atopic asthma and typically responds to treatment with inhaled corticosteroids (ICS). However, some patients have persistently high FENO levels despite treatment.

Objective
We studied how optimizing the inhalation technique and increasing ICS doses would affect FENO in stable atopic asthmatic children who had elevated FENO while using ICS.

Methods
In 41 stable asthmatic children who were treated with ICS (median daily dose 800 μg budesonide equivalent, range 100–1600 μg) and maintained FENO20 p.p.b., we optimized the inhalation technique by thorough instruction and measured FENO 2 weeks later. Then, if FENO remained 20 p.p.b., we increased the ICS dose and reassessed FENO 2 weeks later.

Results
Improving the inhalation technique did not reduce FENO. Increasing ICS from a daily median dose of 800 to 1200 μg budesonide had no significant effect on FENO. FENO correlated positively with symptom scores in the following 2 and 4 weeks (P=0.001, 0.002) and β2‐agonist use the 2 and 4 weeks following FENO measurement (P=0.02, 0.004).

Conclusion
We conclude that common steps in asthma treatment, i.e. inhalation instruction and increasing ICS dose, were both ineffective in reducing FENO in atopic asthmatic children with elevated FENO values despite treatment with ICS. This implies that FENO cannot simply be incorporated in current treatment guidelines.