bluuebunny/crossref_metadata_2025 huggingface dataset:
The frequency and damping of ion acoustic waves in hydrocarbon (CH) and two-ion-species plasmas
Authors: Williams E. A. , Berger R. L. , Drake R. P. , Rubenchik A. M. , Bauer B. S. , Meyerhofer D. D. , Gaeris A. C. , Johnston T. W.
Published: July 2002

The kinetic theory of ion-acoustic waves in multi-ion-species plasmas is discussed. Particular application is made to hydrocarbon (CH) plasmas, which are widely used in laser–plasma experiments. The mode frequencies and Landau damping of the two, dominant, ion-acoustic modes in CH plasmas are calculated by numerical solution of the kinetic dispersion relation. In addition, some useful results are obtained analytically from expansions of the kinetic dispersion relation and from fluid models. However, these results disagree with the numerical results in domains of particular practical interest. When ion temperatures exceed two-tenths of the electron temperature, the least damped mode is the one with the smaller phase velocity, and this mode is then found to dominate the ponderomotive response of the CH plasma.
Viscous dissipation of sound in strongly compressed plasmas
Authors: Atrazhev V. M. , Iakubov I. T.
Published: July 2002

Theoretical investigation is made into ion sound propagation and damping in strongly coupled plasmas near the Wigner crystallization of the ion subsystem. Sound velocity grows with the strengthening of the coupling, and sound decay is due to ion viscosity. The transition from the collisional mechanism of viscosity to the vacancial one proceeds along the Wigner crystallization of the ion subsystem. As a result, a sharp increase in viscosity occurs. Viscoelastic sound replaces hydrodynamic viscous sound. The damping of the viscoelastic sound is determined by Landau damping in the electron subsystem.
Frequency dependent effects in helicon plasmas
Authors: Keiter Paul A. , Scime Earl E. , Balkey Matthew M.
Published: July 2002

Variations in the plasma parameters of a large volume, helicon source as a function of applied rf power (0–2 kW), driving frequency (8–18 MHz), magnetic field (0–1.4 kG) and fill pressure (2–10 mTorr) have been studied. The transitions between the capacitive, inductive, and resonant helicon mode are consistent with previous experiments. Our data indicate that the transition to the helicon mode occurs at a unique magnetic field, independent of the driving frequency. Based on the helicon wave dispersion relation, from which helicon wavelengths can be calculated, the observed variations in plasma density as a function of driving frequency suggest that the wavelength of the helicon wave is a weak function of driving frequency. Calculation of the electron energies which correspond to the phase velocity of the driving wave (i.e., Landau damping) suggest that either Landau damping cannot be responsible for the efficient ionization of helicon sources, or that the helicon portion of the discharge does not extend over the entire radius of the apparatus.
Coupled Langmuir and ion-acoustic waves in two-electron temperature plasmas
Authors: Rao N. N. , Shukla P. K.
Published: July 2002

The nonlinear propagation of coupled Langmuir and ion-acoustic waves in a two-electron temperature plasma is shown to be governed by a generalized Schrödinger–Boussinesq system, which for uni-directional propagation reduces to the coupled Schrödinger–Korteweg-de Vries (K-dV) system. For stationary propagation of the coupled waves, the Schrödinger–Boussinesq (or K-dV) system leads to a generic Hamiltonian which is shown to be integrable in the sub- as well as supersonic regimes of the Mach number. Different classes of exact analytical solutions of the stationary Schrödinger–Boussinesq system are explicitly obtained. Two-electron temperature plasmas are shown to admit a new class of coupled Langmuir–ion-acoustic solitons which propagate with supersonic speeds but are accompanied by density rarefactions. We also derive exact governing equations valid for large amplitude waves, and obtain their approximate solutions. Existence conditions for large amplitude localized solutions in the quasi-neutral limit are derived. A comparison between different types of governing equations and their analytical solutions is carried out.
The covariant transport of electromagnetic fields and its relation to magnetohydrodynamics
Authors: Hornig G.
Published: July 2002

Ohm’s law in ideal magnetohydrodynamics (MHD) leads to an induction equation which can be interpreted in terms of magnetic flux being transported by the plasma flow. It is shown that this frozen-in condition is the non-relativistic limit of a corresponding relativistic condition for the electromagnetic field tensor. Several invariants for this type of transport are analyzed. The relativistic formulation also includes a broader class of transporting flows, which may differ from the plasma flow. A classification and interpretation of these transporting flows is given and it is shown that the corresponding evolutions of the electromagnetic field also includes cases of non-ideal MHD evolution. Thus it is possible to find invariants in non-ideal MHD similar to the magnetic flux for ideal plasma flows.
Steady state multipactor and dependence on material properties
Authors: Kishek R. A. , Lau Y. Y. , Chernin D.
Published: July 2002

The interaction of multipactor discharge and an rf circuit is analyzed with the use of a simple model, in which the multipactor electrons are in the form of a single sheet that is released from the surface with a monoenergetic velocity. An explicit formula is derived for the saturation level of multipactor current in steady state. This formula is given in terms of the secondary electron yield properties of the multipactoring surfaces and the level of the external rf drive. It is valid when the quality factor Q of the rf circuit is higher than 10, in which case the space charge effects do not contribute significantly to the saturation level. When it occurs, the steady state multipactor may consume tens of percents of the external rf power that is needed to sustain the gap voltage. Numerical computations determine the accessibility to steady state from the transient buildup. In particular, they suggest various conditions for the multipactor to exhibit in a burst mode or in a steady state mode. The dynamic linkage of the rf circuit and material properties allows the construction of the susceptibility diagram for various materials, within the limitations imposed by the present model.
Beyond the Brillouin limit with the Penning Fusion Experiment
Authors: Barnes D. C. , Mitchell T. B. , Schauer M. M.
Published: July 2002

Several years ago, it was proposed that a dense non-neutral plasma could be produced in a Penning trap. Nonneutral plasmas have excellent confinement, and such a dense plasma might produce simultaneously high density and good confinement. Recently, this theoretical conjecture has been demonstrated in a small (3 mm radius) electron experiment, PFX (Penning Fusion Experiment). Densities up to 35 times the Brillouin density (limiting number density in a static trap) have been inferred from the observed strong (100:1) spherical focusing. Electrons are injected at low energy from a single pole of the sphere. A surprising observation is the self-organization of the system into a spherical state, which occurs precisely when the trap parameters are adjusted to produce a spherical well. This organization is caused by a bootstrapping mechanism which produces a hysteresis. Observations of energy-scattered electrons confirm the existence of a dense spherical focus.
Parametric interaction of self-localized upper hybrid states in quantized plasma density irregularities
Authors: Istomin Ya. N. , Leyser T. B.
Published: July 2002

A theoretical model of the interaction between slow transport and rapid ponderomotive processes of upper hybrid (UH) oscillations driven by a homogeneous pump electric field is presented. The self-localization of UH oscillations in quantized plasma density depletions due to a thermal nonlinearity is described. The threshold for the parametric decay of the primary localized UH state into a secondary UH state and lower hybrid waves is calculated, as well as the amplitudes of the nonlinearly stabilized UH states. These self-localized UH states constitute a complex response of the plasma to the imposed energy flux, which may be an important source of electromagnetic radiation, such as the electromagnetic emissions stimulated in high frequency pumping of the ionospheric plasma.
Drift mode growth rates and associated transport
Authors: Redd Aaron J. , Kritz Arnold H. , Bateman Glenn , Rewoldt Gregory , Tang W. M.
Published: July 2002

Drift mode linear growth rates and quasilinear transport are investigated using the FULL kinetic stability code [Rewoldt et al., Phys. Plasmas 5, 1815 (1998)] and a version of the Weiland transport model [Strand et al., Nucl. Fusion 38, 545 (1998)]. It is shown that the drift mode growth rates (as well as the marginal stability temperature gradient) obtained using the FULL code are dependent on the accuracy of the equilibrium employed. In particular, when an approximate equilibrium model is utilized by the FULL code, the results can differ significantly from those obtained using a more accurate numerical equilibrium. Also investigated are the effects of including full electron physics. It is shown, using both the FULL code and the Weiland model, that the nonadiabatic (e.g., trapped) electron response produces a significant increase in the linear growth rate of the ion-temperature-gradient (ITG) driven branch of the drift instability. Other consequences of the nonadiabatic electron response include a reduction in the marginal temperature gradient for the onset of the ITG mode and an additional contribution to transport due to the excitation of the Trapped Electron Mode (TEM). Physical explanations are given for the sensitivity of the mode growth rates to the equilibrium and the nonadiabatic electron response. Finally, linear growth rates for the ITG mode computed using the FULL code are compared with growth rates obtained using the Weiland model.
The unstable eigenmodes of a neutral sheet
Authors: Daughton William
Published: July 2002

The linear stability of a Harris current sheet is examined using the Vlasov description for both ions and electrons. Orbit integrals are treated numerically using the exact particle orbits and including the global structure of the perturbation inside the integral. Both electromagnetic and electrostatic contributions to the field perturbation are retained and the eigenvalue problem for the system of integro-differential equations is solved using a Hermite expansion of the eigenfunction. For the tearing mode, results are in excellent agreement with established theory. For the recently discovered kink mode, results are consistent with kinetic simulations at low mass ratio mi/me⩽16. However, in the limit of realistic electron mass, the growth rate of the kink mode is substantially reduced in contrast to results from kinetic simulations. It is demonstrated that a background population may dramatically alter the growth rate of the kink mode at realistic values of the mass ratio. This result may have relevance to the stability of the Earth’s geomagnetic tail.
Tunneling microscopy of graphite in air
Authors: Park Sang-Il , Quate C. F.
Published: July 2002

Images of graphite have been recorded with a scanning tunneling microscope operating in air at ambient pressure. The results, which are in agreement with theory and previous experiments in vacuum, confirm that with a surface such as graphite the tunneling microscopy in air can be used to examine the geometry of the surface with a resolution that is less than 2 Å.
Deep level transient spectroscopy signature analysis of D
X centers in AlGaAs and GaAsP
Authors: Criado J. , Gomez A. , Muñoz E. , Calleja E.
Published: July 2002

The characterization of deep levels generated by donor dopants (DX centers) requires reliable deep level transient spectroscopy (DLTS) data. Because in AlGaAs and GaAsP the electron thermal emission from DX centers produces strong nonexponential capacitance transients, blind DLTS analysis may lead to erroneous trap parameter determinations. In this work the DLTS sampling conditions to be used for proper DX center characterization are examined. It is concluded that, only under constant tb/ta windowing ratios, self-consistent trap parameters are obtained.
Study of nonstoichiometry in undoped semi-insulating GaAs using precise lattice parameter measurements
Authors: Nakajima Masato , Sato Takashi , Inada Tomoki , Fukuda Tsuguo , Ishida Koichi
Published: July 2002

Nonstoichiometry in undoped semi-insulating GaAs grown by the liquid-encapsulated Czochralski technique has been evaluated by absolute lattice parameter measurements using the Bond method. The lattice parameter increases with increasing As atom fraction in the initial melt. The observed range of lattice parameters and the variation along the growth direction suggest that the solidus curve in the phase diagram extends to the As-rich side than to the Ga-rich side, and the congruent point is located on the stoichiometric point or the slightly As-rich side.
Determination of gap state density in polycrystalline silicon by field-effect conductance
Authors: Fortunato G. , Migliorato P.
Published: July 2002

We have obtained the density of states (DOS) in polycrystalline silicon from the analysis of the field-effect conductance. The DOS exhibits a U-shaped distribution with an exponential band tail. The method is very sensitive and accounts for the effect of film morphology and differences in device processing (e.g., post-hydrogenation).
Interactions between bombardment-induced defects in GaAs
Authors: Makram-Ebeid Sherif , Boher Pierre , Lannoo Michel
Published: July 2002

Interdefect electron hopping is shown to play an important role in the physical manifestations of radiation induced defects in GaAs. In fast electron irradiated n-GaAs, we are led to attribute the observed high-temperature deep level transient spectroscopy (DLTS) peaks to defect pairs each including an antisite AsGa related midgap level defect together with a VAs vacancy related shallower level defect. In contrast with recent publications, we show that one can consistently interpret DLTS, electrical conductivity, and electron paramagnetic resonance experimental data in terms of the same irradiation induced defects.
Nonlinear optical properties of an azo dye attached polymer
Authors: Matsumoto Shiro , Kubodera Ken-ichi , Kurihara Takashi , Kaino Toshikuni
Published: July 2002

Copolymers of azo dye substituted acrylic monomer and methylmethacrylate are synthesized and their third-order nonlinear optical susceptibility χ(3) is evaluated using the third harmonic generation Maker fringe method. The χ(3) is 1.26×10−12 esu at 25.9 mol % azo dye monomer content in the copolymer. It is also shown that there is a linear relationship between χ(3) and the monomer content.
Preparation of superconducting thin films of calcium strontium bismuth copper oxides by coevaporation
Authors: Rice C. E. , Levi A. F. J. , Fleming R. M. , Marsh P. , Baldwin K. W. , Anzlowar M. , White A. E. , Short K. T. , Nakahara S. , Stormer H. L.
Published: July 2002

Superconducting films of Ca-Sr-Bi-Cu oxides have been prepared by coevaporation of CaF2, SrF2, Bi, and Cu, followed by post-oxidation in wet O2. The films were characterized by four-probe resistivity measurements, Rutherford backscattering, transmission electron microscopy, x-ray diffraction, and Hall measurements. Zero resistance was achieved at ∼80 K, although evidence of traces of superconductivity at higher temperatures was seen in resistivity and Hall data. The critical current at 4.2 K was 1.0×106 A cm−2. The films were epitaxial on 〈100〉 and 〈110〉 SrTiO3 substrates. The electrical and structural properties of the films were insensitive to film composition over a wide range of stoichiometries.
PDK1 regulates growth through Akt and S6K in
Drosophila
Authors: Rintelen Felix , Stocker Hugo , Thomas George , Hafen Ernst
Published: July 2002

The insulin/insulin-like growth factor-1 signaling pathway
promotes growth in invertebrates and vertebrates by increasing the
levels of phosphatidylinositol 3,4,5-triphosphate through the
activation of p110 phosphatidylinositol 3-kinase. Two key effectors of
this pathway are the phosphoinositide-dependent protein kinase 1 (PDK1)
and Akt/PKB. Although genetic analysis in
Caenorhabditis elegans
has implicated
Akt as the only relevant PDK1 substrate, cell culture studies have
suggested that PDK1 has additional targets. Here we show that, in
Drosophila,
dPDK1 controls cellular and organism growth
by activating dAkt and S6 kinase, dS6K. Furthermore,
dPDK1
genetically interacts with
dRSK
but
not with
dPKN
, encoding two substrates of PDK1
in
vitro
. Thus, the results suggest that dPDK1 is required for
dRSK but not dPKN activation and that it regulates insulin-mediated
growth through two main effector branches, dAkt and dS6K.
Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast
Authors: Conconi Antonio , Bespalov Vyacheslav A. , Smerdon Michael J.
Published: July 2002

Nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers (CPDs) was measured in the individual strands of transcriptionally active and inactive ribosomal genes of yeast. Ribosomal genes (rDNA) are present in multiple copies, but only a fraction of them is actively transcribed. Restriction enzyme digestion was used to specifically release the transcriptionally active fraction from yeast nuclei, and selective psoralen crosslinking was used to distinguish between active and inactive rDNA chromatin. Removal of CPDs was followed in both rDNA populations, and the data clearly show that strand-specific repair occurs in transcriptionally active rDNA while being absent in the inactive rDNA fraction. Thus, transcription-coupled repair occurs in RNA polymerase I-transcribed genes in yeast. Moreover, the nontranscribed strand of active rDNA is repaired faster than either strand of inactive rDNA, implying that NER has preferred access to the active, non-nucleosomal rDNA chromatin. Finally, restriction enzyme accessibility to active rDNA varies during NER, suggesting that there is a change in ribosomal gene chromatin structure during or soon after CPD removal.
Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye
Authors: Oakley Todd H. , Cunningham Clifford W.
Published: July 2002

Eyes often take a central role in discussions of evolution, with debate focused on how often such complex organs might have evolved. One such debate is whether arthropod compound eyes are the product of single or multiple origins. Here we use molecular phylogeny to address this long-standing debate and find results favoring the multiple-origins hypothesis. Our analyses of DNA sequences encoding rRNA unequivocally indicate that myodocopids—the only Ostracoda (Crustacea) with compound eyes—are nested phylogenetically within several groups that lack compound eyes. With our well-supported phylogeny, standard maximum likelihood (ML) character reconstruction methods significantly reconstruct ancestral ostracods as lacking compound eyes. We also introduce a likelihood sensitivity analysis, and show that the single-origin hypothesis is not significantly favored unless we assume a highly asymmetric model of evolution (one favoring eye loss more than 30:1 over gain). These results illustrate exactly why arthropod compound eye evolution has remained controversial, because one of two seemingly very unlikely evolutionary histories must be true. Either compound eyes with detailed similarities evolved multiple times in different arthropod groups or compound eyes have been lost in a seemingly inordinate number of arthropod lineages.
The B cell-restricted adaptor BASH is required for normal development and antigen receptor-mediated activation of B cells
Authors: Hayashi Katsuhiko , Nittono Ryo , Okamoto Noriaki , Tsuji Sachiyo , Hara Yasushi , Goitsuka Ryo , Kitamura Daisuke
Published: July 2002

B cell antigen receptor signals development, activation, proliferation, or apoptosis of B cells depending on their condition, and its proper signaling is critical for activation and homeostasis of the immune system. The B cell-restricted adaptor protein BASH (also termed BLNK/SLP-65) is rapidly phosphorylated by the tyrosine kinase Syk after BCR ligation and binds to various signaling proteins. BASH structurally resembles SLP-76, which is essential for T cell development and T cell receptor signaling. To evaluate the role for BASH in B cell development and functionin vivo, we disrupted BASH alleles in embryonic stem cells by means of homologous recombination and used these cells to complement lymphocyte-incompetent blastocysts from RAG2-deficient mice. In the resultant chimeric mice, T cell development was apparently normal, but B cell development was impaired, and a normally rare population of large preB cells expressing preB cell receptor dominated in the bone marrow in place of small preB cells, although they were mostly noncycling. In addition, the mature B cell populations in the periphery and the bone marrow profoundly decreased in size, as did B-1 cells in the peritoneal cavity, and serum Ig was severely reduced. The BASH-deficient B cells scarcely proliferated or up-regulated B7-2 in response to BCR ligation and poorly proliferated upon CD40 ligation or lipopolysaccharide stimulation. This phenotype indicates that BASH is critical for preB cell receptor signaling inducing proliferation of large preB cells and the following differentiation, for peripheral B cell maturation, and for BCR signaling inducing activation/proliferation of B cells.
Covalent modification of proteins by cocaine
Authors: Deng Shi-Xian , Bharat Narine , Fischman Marian C. , Landry Donald W.
Published: July 2002

Cocaine covalently modifies proteins through a reaction in which the methyl ester of cocaine acylates the ɛ-amino group of lysine residues. This reaction is highly specificin vitro, because no other amino acid reacts with cocaine, and only cocaine's methyl ester reacts with the lysine side chain. Covalently modified proteins were present in the plasma of rats and human subjects chronically exposed to cocaine. Modified endogenous proteins are immunogenic, and specific antibodies were elicited in mouse and detected in the plasma of human subjects. Covalent modification of proteins could explain cocaine's autoimmune effects and provide a new biochemical approach to cocaine's long-term actions.
Integrins regulate the apoptotic response to DNA damage through modulation of p53
Authors: Lewis Jean McArthur , Truong Tony Nguyen , Schwartz Martin Alexander
Published: July 2002

p53 mediates apoptosis of cells after DNA damage including tumor cells after radiation or chemotherapy. Survival of isolated cancer cells after therapy leads to recurrence of therapy-resistant tumors. We now show that for some melanoma, sarcoma, or fibroblastic cell types that survive without integrin-mediated adhesion, apoptosis in response to DNA damage requires cell adhesion. This effect correlates with rapid changes in levels of p14/p19 Arf and its downstream component, p53. Killing of nonadherent cells is increased by treatment with antiintegrin antibodies or by increasing levels of p53 or Arf. Consistent with low p53 levels, suspended cells show chromosomal instability after irradiation. Thus, loss of normal adhesion in susceptible tumor cells during genotoxic stress may play a role in therapy resistance and promote survival of cells with aberrant DNA.
Recognition of triple-helical DNA structures by transposon Tn7
Authors: Rao Jason E. , Miller Paul S. , Craig Nancy L.
Published: July 2002

We have found that the bacterial transposon Tn7can recognize and preferentially insert adjacent to triple-helical nucleic acid structures. Both synthetic intermolecular triplexes, formed through the pairing of a short triplex-forming oligonucleotide on a plasmid DNA, and naturally occurring mirror repeat sequences known to form intramolecular triplexes or H-form DNA are preferential targets for Tn7insertionin vitro. This target site selectivity depends upon the recognition of the triplex region by a Tn7-encoded ATP-using protein, TnsC, which controls Tn7target site selection: the interaction of TnsC with the triplex region results in recruitment and activation of the Tn7transposase. Recognition of a nucleic acid structural motif provides both new information into the factors that influence Tn7's target site selection and broadens its targeting capabilities.
Structural basis for Hif-1α/CBP recognition in the cellular hypoxic response
Authors: Dames Sonja A. , Martinez-Yamout Maria , De Guzman Roberto N. , Dyson H. Jane , Wright Peter E.
Published: July 2002

The cellular response to low tissue oxygen concentrations is mediated by the hypoxia-inducible transcription factor HIF-1. Under hypoxic conditions, HIF-1 activates transcription of critical adaptive genes by recruitment of the general coactivators CBP/p300 through interactions with its α-subunit (Hif-1α). Disruption of the Hif-1α/p300 interaction has been linked to attenuation of tumor growth. To delineate the structural basis for this interaction, we have determined the solution structure of the complex between the carboxy-terminal activation domain (CAD) of Hif-1α and the zinc-binding TAZ1 (CH1) motif of cyclic-AMP response element binding protein (CREB) binding protein (CBP). Despite the overall similarity of the TAZ1 structure to that of the TAZ2 (part of the CH3) domain of CBP, differences occur in the packing of helices that can account for differences in specificity. The unbound CAD is intrinsically disordered and remains relatively extended upon binding, wrapping almost entirely around the TAZ1 domain in a groove through much of its surface. Three short helices are formed upon binding, stabilized by intermolecular interactions. The Asn-803 side chain, which functions as a hypoxic switch, is located on the second of these helices and is buried in the molecular interface. The third helix of the Hif-1α CAD docks in a deep hydrophobic groove in TAZ1, providing extensive intermolecular hydrophobic interactions that contribute to the stability of the complex. The structure of this complex provides new insights into the mechanism through which Hif-1α recruits CBP/p300 in response to hypoxia.
CFTR is a pattern recognition molecule that extracts
Pseudomonas aeruginosa
LPS from the outer membrane into epithelial cells and activates NF-κB translocation
Authors: Schroeder Torsten H. , Lee Martin M. , Yacono Patrick W. , Cannon Carolyn L. , Gerçeker A. Alev , Golan David E. , Pier Gerald B.
Published: July 2002

Immune cells are activated during cellular responses to antigen by two described mechanisms: (
i
) direct uptake of antigen and (
ii
) extraction and internalization of membrane components from antigen-presenting cells. Although endocytosis of microbial antigens by pattern recognition molecules (PRM) also activates innate immunity, it is not known whether this involves extraction and internalization of microbial surface components. Epithelial cells on mucosal surfaces use a variety of receptors that are distinct from the classical endocytic PRM to bind and internalize intact microorganisms. Nonclassical receptor molecules theoretically could act as a type of endocytic PRM if these molecules could recognize, bind, extract, and internalize a pathogen-associated molecule and initiate cell signaling. We report here that the interaction between the cystic fibrosis transmembrane conductance regulator (CFTR) and the outer core oligosaccharide of the lipopolysaccharide (LPS) in the outer membrane of
Pseudomonas aeruginosa
satisfies all of these conditions.
P. aeruginosa
LPS was specifically recognized and bound by CFTR, extracted from the organism's surface, and endocytosed by epithelial cells, leading to a rapid (5- to 15-min) and dynamic translocation of nuclear transcription factor NF-κB. Inhibition of epithelial cell internalization of
P. aeruginosa
LPS prevented NF-κB activation. Cellular activation depended on expression of wild-type CFTR, because both cultured ΔF508
CFTR
human airway epithelial cells and lung epithelial cells of transgenic-CF mice failed to endocytose LPS and translocate NF-κB. CFTR serves as a critical endocytic PRM in the lung epithelium, coordinating the effective innate immune response to
P. aeruginosa
infection.
SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness
Authors: Yeiser Bethany , Pepper Evan D. , Goodman Myron F. , Finkel Steven E.
Published: July 2002

Escherichia coli
encodes three SOS-induced DNA polymerases: pol II, pol IV, and pol V. We show here that each of these polymerases confers a competitive fitness advantage during the stationary phase of the bacterial life cycle, in the absence of external DNA-damaging agents known to induce the SOS response. When grown individually, wild-type and SOS pol mutants exhibit indistinguishable temporal growth and death patterns. In contrast, when grown in competition with wild-type
E. coli
, mutants lacking one or more SOS polymerase suffer a severe reduction in fitness. These mutants also fail to express the “growth advantage in stationary phase” phenotype as do wild-type strains, instead expressing two additional new types of “growth advantage in stationary phase” phenotype. These polymerases contribute to survival by providing essential functions to ensure replication of the chromosome and by generating genetic diversity.
Subjective surfaces: A method for completing missing boundaries
Authors: Sarti Alessandro , Malladi Ravi , Sethian James A.
Published: July 2002

We present a model and algorithm for segmentation of images with missing boundaries. In many situations, the human visual system fills in missing gaps in edges and boundaries, building and completing information that is not present. This presents a considerable challenge in computer vision, since most algorithms attempt to exploit existing data. Completion models, which postulate how to construct missing data, are popular but are often trained and specific to particular images. In this paper, we take the following perspective: We consider a reference point within an image as given and then develop an algorithm that tries to build missing information on the basis of the given point of view and the available information as boundary data to the algorithm. We test the algorithm on some standard images, including the classical triangle of Kanizsa and low signal/noise ratio medical images.
Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes
Authors: Cousyn C. , De Meester L. , Colbourne J. K. , Brendonck L. , Verschuren D. , Volckaert F.
Published: July 2002

Organisms producing resting stages provide unique opportunities for reconstructing the genetic history of natural populations. Diapausing seeds and eggs often are preserved in large numbers, representing entire populations captured in an evolutionary inert state for decades and even centuries. Starting from a natural resting egg bank of the waterfleaDaphnia,we compare the evolutionary rates of change in an adaptive quantitative trait with those in selectively neutral DNA markers, thus effectively testing whether the observed genetic changes in the quantitative trait are driven by natural selection. The population studied experienced variable and well documented levels of fish predation over the past 30 years and shows correlated genetic changes in phototactic behavior, a predator-avoidance trait that is related to diel vertical migration. The changes mainly involve an increased plasticity response upon exposure to predator kairomone, the direction of the changes being in agreement with the hypothesis of adaptive evolution. Genetic differentiation through time was an order of magnitude higher for the studied behavioral trait than for neutral markers (DNA microsatellites), providing strong evidence that natural selection was the driving force behind the observed, rapid, evolutionary changes.
Neuronal correlates of sensory discrimination in the somatosensory cortex
Authors: Hernández Adrián , Zainos Antonio , Romo Ranulfo
Published: July 2002

Monkeys are able to discriminate the difference in frequency between two periodic mechanical vibrations applied sequentially to the fingertips. It has been proposed that this ability is mediated by the periodicity of the responses in the quickly adapting (QA) neurons of the primary somatosensory cortex (S1), instead of the average firing rates. We recorded from QA neurons of S1 while monkeys performed the vibrotactile discrimination task. We found that the periodic mechanical vibrations can be represented both in the periodicity and in the firing rate responses to varying degrees across the QA neuronal population. We then computed neurometric functions by using both the periodicity and the firing rate and sought to determine which of these two measures is associated with the psychophysical performance. We found that neurometric thresholds based on the firing rate are very similar to the animal's psychometric thresholds whereas neurometric thresholds based on periodicity are far lower than those thresholds. These results indicate that an observer could solve this task with a precision similar to that of the monkey, based only on the firing rate produced during the stimulus periods.
A macrophage receptor for apolipoprotein B48: Cloning, expression, and atherosclerosis
Authors: Brown Matthew L. , Ramprasad M. P. , Umeda Patrick K. , Tanaka Akira , Kobayashi Yasushi , Watanabe Teruo , Shimoyamada Hiroaki , Kuo Wen-Lin , Li Ran , Song Ruiling , Bradley William A. , Gianturco Sandra H.
Published: July 2002

We have cloned a human macrophage receptor that binds to apolipoprotein (apo)B48 of dietary triglyceride (TG)-rich lipoproteins. TG-rich lipoprotein uptake by the apoB48R rapidly converts macrophages and apoB48R-transfected Chinese hamster ovary cells
in vitro
into lipid-filled foam cells, as seen in atherosclerotic lesions. The apoB48R cDNA (3,744 bp) encodes a protein with no known homologs. Its ≈3.8-kb mRNA is expressed primarily by reticuloendothelial cells: monocytes, macrophages, and endothelial cells. Immunohistochemistry shows the apoB48R is in human atherosclerotic lesion foam cells. Normally, the apoB48R may provide essential lipids to reticuloendothelial cells. If overwhelmed, foam cell formation, endothelial dysfunction, and atherothrombogenesis may ensue, a mechanism for cardiovascular disease risk of elevated TG.
Nonnucleoside reverse transcriptase inhibitors are chemical enhancers of dimerization of the HIV type 1 reverse transcriptase
Authors: Tachedjian Gilda , Orlova Marianna , Sarafianos Stefan G. , Arnold Edward , Goff Stephen P.
Published: July 2002

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are allosteric inhibitors of the HIV type 1 (HIV-1) reverse transcriptase (RT). Yeast grown in the presence of many of these drugs exhibited dramatically increased association of the p66 and p51 subunits of the HIV-1 RT as reported by a yeast two-hybrid assay. The enhancement required drug binding by RT; introduction of a drug-resistance mutation into the p66 construct negated the enhancement effect. The drugs could also induce heterodimerization of dimerization defective mutants. Coimmunoprecipitation of RT subunits from yeast lysates confirmed the induction of heterodimer formation by the drugs.
In vitro
-binding studies indicate that NNRTIs can bind tightly to p66 but not p51 and then mediate subsequent heterodimerization. This study demonstrates an unexpected effect of NNRTIs on the assembly of RT subunits.
Evidence that subcellular localization of a bacterial membrane protein is achieved by diffusion and capture
Authors: Rudner David Z. , Pan Qi , Losick Richard M.
Published: July 2002

Bacteria lack an endoplasmic reticulum, a Golgi apparatus, and transport vesicles and yet are capable of sorting and delivering integral membrane proteins to particular sites within the cell with high precision. What is the pathway by which membrane proteins reach their proper subcellular destination in bacteria? We have addressed this question by using green fluorescent protein (GFP) fused to a polytopic membrane protein (SpoIVFB) that is involved in the process of sporulation in the bacterium
Bacillus subtilis
. SpoIVFB-GFP localizes to a region of the sporulating cell known as the outer forespore membrane, which is distinct from the cytoplasmic membrane. Experiments are presented that rule out a mechanism in which SpoIVFB-GFP localizes to all membranes but is selectively eliminated from the cytoplasmic membrane by proteolytic degradation and argue against a model in which SpoIVFB-GFP is selectively inserted into the outer forespore membrane. Instead, the results are most easily compatible with a model in which SpoIVFB-GFP achieves proper localization by insertion into the cytoplasmic membrane followed by diffusion to, and capture in, the outer forespore membrane. The possibility that diffusion and capture is a general feature of protein localization in bacteria is discussed.
BDNF but not NT-4 is required for normal flexion reflex plasticity and function
Authors: Heppenstall Paul A. , Lewin Gary R.
Published: July 2002

Neurotrophins can directly modulate the function of diverse types of central nervous system synapses. Brain-derived neurotrophic factor (BDNF) might be released by nociceptors onto spinal neurons and mediate central sensitization associated with chronic pain. We have studied the role of BDNF and neurotrophin-4 (NT-4), both ligands of the trkB tyrosine kinase receptor, in synaptic transmission and reflex plasticity in the mouse spinal cord. We used an
in vitro
spinal cord preparation to measure monosynaptic and polysynaptic reflexes evoked by primary afferents in BDNF- and NT-4-deficient mice.
In situ
hybridization studies show that both these neurotrophins are synthesized by sensory neurons, and NT-4, but not BDNF, also is expressed by spinal neurons. BDNF null mutants display selective deficits in the ventral root potential (VRP) evoked by stimulating nociceptive primary afferents whereas the non-nociceptive portion of the VRP remained unaltered. In addition, activity-dependent plasticity of the VRP evoked by repetitive (1 Hz) stimulation of nociceptive primary afferents (termed wind-up) was substantially reduced in BDNF-deficient mice. This plasticity also was reduced in a reversible manner by the protein kinase inhibitor K252a. Although the trkB ligand NT-4 is normally present, reflex properties in NT-4 null mutant mice were normal. Pharmacological studies also indicated that spinal
N
-methyl-
d
-aspartate receptor function was unaltered in BDNF-deficient mice. Using immunocytochemistry for markers of nociceptive neurons we found no evidence that their number or connectivity was substantially altered in BDNF-deficient mice. Our data therefore are consistent with a direct role for presynaptic BDNF release from sensory neurons in the modulation of pain-related neurotransmission.
Noninvasive neuroelectronic interfacing with synaptically connected snail neurons immobilized on a semiconductor chip
Authors: Zeck Günther , Fromherz Peter
Published: July 2002

A hybrid circuit of a semiconductor chip and synaptically connected neurons was implemented and characterized. Individual nerve cells from the snail
Lymnaea stagnalis
were immobilized on a silicon chip by microscopic picket fences of polyimide. The cells formed a network with electrical synapses after outgrowth in brain conditioned medium. Pairs of neurons were electronically interfaced for noninvasive stimulation and recording. Voltage pulses were applied to a capacitive stimulator on the chip to excite the attached neuron. Signals were transmitted in the neuronal net and elicited an action potential in a second neuron. The postsynaptic excitation modulated the current of a transistor on the chip. The implementation of the silicon-neuron-neuron-silicon circuit constitutes a proof-of-principle experiment for the development of neuroelectronic systems to be used in studies on neuronal signal processing, neurocomputation, and neuroprosthetics.
N-terminal transcriptional activation domain of LZIP comprises two LxxLL motifs and the Host Cell Factor-1 binding motif
Authors: Luciano Randy L. , Wilson Angus C.
Published: July 2002

Host Cell Factor-1 (HCF-1, C1) was first identified as a cellular
target for the herpes simplex virus transcriptional activator VP16.
Association between HCF and VP16 leads to the assembly of a
multiprotein enhancer complex that stimulates viral immediate-early
gene transcription. HCF-1 is expressed in all cells and is required for
progression through G
1
phase of the cell cycle. In addition
to VP16, HCF-1 associates with a cellular bZIP protein known as LZIP
(or Luman). Both LZIP and VP16 contain a four-amino acid HCF-binding
motif, recognized by the N-terminal β-propeller domain of HCF-1.
Herein, we show that the N-terminal 92 amino acids of LZIP contain a
potent transcriptional activation domain composed of three elements:
the HCF-binding motif and two LxxLL motifs. LxxLL motifs are found in a
number of transcriptional coactivators and mediate protein–protein
interactions, notably recognition of the nuclear hormone receptors.
LZIP is an example of a sequence-specific DNA-binding protein that uses
LxxLL motifs within its activation domain to stimulate transcription.
The LxxLL motifs are not required for association with the HCF-1
β-propeller and instead interact with other regions in HCF-1 or
recruit additional cofactors.
An alternative pathway to β-carotene formation in plant chromoplasts discovered by map-based cloning of
Beta
and
old-gold
color mutations in tomato
Authors: Ronen Gil , Carmel-Goren Lea , Zamir Dani , Hirschberg Joseph
Published: July 2002

Carotenoid pigments in plants fulfill indispensable functions
in photosynthesis. Carotenoids that accumulate as secondary metabolites
in chromoplasts provide distinct coloration to flowers and fruits. In
this work we investigated the genetic mechanisms that regulate
accumulation of carotenoids as secondary metabolites during ripening of
tomato fruits. We analyzed two mutations that affect fruit pigmentation
in tomato (
Lycopersicon esculentum
):
Beta
(
B
), a single dominant gene that increases β-carotene
in the fruit, and
old-gold
(
og
), a
recessive mutation that abolishes β-carotene and increases lycopene.
Using a map-based cloning approach we cloned the genes
B
and
og
. Molecular analysis revealed that
B
encodes a novel type of lycopene β-cyclase, an
enzyme that converts lycopene to β-carotene. The amino acid sequence
of B is similar to capsanthin-capsorubin synthase, an enzyme that
produces red xanthophylls in fruits of pepper (
Capsicum
annum
). Our results prove that β-carotene is synthesized
de novo
during tomato fruit development by the B
lycopene cyclase. In wild-type tomatoes
B
is expressed
at low levels during the breaker stage of ripening, whereas in the
Beta
mutant its transcription is dramatically increased.
Null mutations in the gene
B
are responsible for the
phenotype in
og
, indicating that
og
is an
allele of
B
. These results confirm that developmentally
regulated transcription is the major mechanism that governs lycopene
accumulation in ripening fruits. The cloned
B
genes can
be used in various genetic manipulations toward altering pigmentation
and enhancing nutritional value of plant foods.
Multiple conformations of PEVK proteins detected by single-molecule techniques
Authors: Li Hongbin , Oberhauser Andres F. , Redick Sambra D. , Carrion-Vazquez Mariano , Erickson Harold P. , Fernandez Julio M.
Published: July 2002

An important component of muscle elasticity is the PEVK region of titin, so named because of the preponderance of these amino acids. However, the PEVK region, similar to other elastomeric proteins, is thought to form a random coil and therefore its structure cannot be determined by standard techniques. Here we combine single-molecule electron microscopy and atomic force microscopy to examine the conformations of the human cardiac titin PEVK region. In contrast to a simple random coil, we have found that cardiac PEVK shows a wide range of elastic conformations with end-to-end distances ranging from 9 to 24 nm and persistence lengths from 0.4 to 2.5 nm. Individual PEVK molecules retained their distinctive elastic conformations through many stretch-relaxation cycles, consistent with the view that these PEVK conformers cannot be interconverted by force. The multiple elastic conformations of cardiac PEVK may result from varying degrees of proline isomerization. The single-molecule techniques demonstrated here may help elucidate the conformation of other proteins that lack a well-defined structure.
Creating multiple-crossover DNA libraries independent of sequence identity
Authors: Lutz Stefan , Ostermeier Marc , Moore Gregory L. , Maranas Costas D. , Benkovic Stephen J.
Published: July 2002

We have developed, experimentally implemented, and modeled
in silico
a methodology named SCRATCHY that enables the
combinatorial engineering of target proteins, independent of sequence
identity. The approach combines two methods for recombining genes:
incremental truncation for the creation of hybrid enzymes and DNA
shuffling. First, incremental truncation for the creation of hybrid
enzymes is used to create a comprehensive set of fusions between
fragments of genes in a DNA homology-independent fashion. This
artificial family is then subjected to a DNA-shuffling step to augment
the number of crossovers. SCRATCHY libraries were created from the
glycinamide-ribonucleotide formyltransferase (GART) genes from
Escherichia coli
(
purN
) and human
(
hGART
). The developed modeling framework
e
SCRATCHY provides insight into the effect of sequence
identity and fragmentation length on crossover statistics and draws
contrast with DNA shuffling. Sequence analysis of the naive shuffled
library identified members with up to three crossovers, and modeling
predictions are in good agreement with the experimental findings.
Subsequent
in vivo
selection in an auxotrophic
E.
coli
host yielded functional hybrid enzymes containing multiple
crossovers.
Accumulation of cholera toxin and GM1 ganglioside in the early endosome of Niemann–Pick C1-deficient cells
Authors: Sugimoto Yuko , Ninomiya Haruaki , Ohsaki Yuki , Higaki Katsumi , Davies Joanna P. , Ioannou Yiannis A. , Ohno Kousaku
Published: July 2002

We investigated intracellular trafficking of GM1 ganglioside in Niemann–Pick C1 (NPC1)-deficient Chinese hamster ovary cells [NPC1(−) cells] by using cholera toxin (CT) as a probe. Both the holotoxin and the B subunit (CTB) accumulated in GM1-enriched intracellular vesicles of NPC1(−) cells. CTB-labeled vesicles contained the early endosome marker Rab5 but not lysosome-associated membrane protein 2 and were not labeled with either Texas red–transferrin or Lysotracker, indicating that they represent early endosomes. Similarly, CT accumulated in intracellular vesicles of human NPC fibroblasts that contained both Rab5 and early endosomal antigen 1. CTB accumulation in NPC1(−) cells was abolished by expression of wild-type NPC1 but not by mutant proteins with a mutation either in the NPC domain or the sterol-sensing domain. A part of these mutant NPC1 proteins expressed in NPC1(−) cells was localized on CTB-labeled vesicles. U18666A treatment of “knock in” cells [NPC1(−) cells that stably expressed wild-type NPC1] caused CTB accumulation similar to that in NPC1(−) cells, and a part of wild-type NPC1was localized on CTB-labeled vesicles in drug-treated cells. Finally, CT tracer experiments in NPC1(−) cells revealed retarded excretion of internalized toxin into the culture medium and an increase in the intracellular release of A subunits. In accordance with the latter result, CT was more effective in stimulating cAMP formation in NPC1(−) than in wild-type cells. These results suggest that transport of CT/GM1 complexes from the early endosome to the plasma membrane depends on the function of NPC1, whereas transport to the Golgi apparatus/endoplasmic reticulum does not.