bluuebunny/crossref_metadata_2025 huggingface dataset:
High performance acrylic polymers for chemically amplified photoresist applications
Authors: Allen Robert D. , Wallraff Gregory M. , Hinsberg William D. , Simpson Logan L.
Published: July 2002

Chemically amplified resists have recently achieved importance as materials useful for high density microlithographic applications requiring submicron imaging. In an effort to extend the chemical amplification concept to applications requiring thick film resists, we have developed a family of acrylic polymers which provide high performance, aqueous developing positive resists when formulated with the appropriate photo-acid generators. The polymers were prepared from methyl methacrylate (MMA), t-butyl methacrylate (TBMA) and methacrylic acid (MAA), each of which serves a separate function in the formed terpolymer. An unusual degree of control over the aqueous development kinetics can be achieved by manipulation of the terpolymer composition. The lithographic properties of resist formulations based on these polymers have been examined employing optical exposure at wavelengths from 248 to 514 nm, and e-beam exposure.
Improved method for fractal analysis using scanning probe microscopy
Authors: Miller S. , Reifenberger R.
Published: July 2002

The variation method of fractal analysis is used to determine the fractal dimension of a surface imaged with a scanning tunneling microscope. Using this technique, an estimate of the experimental uncertainty in the fractal dimension is obtained. The utility of this variation method is demonstrated by investigating the fractal behavior of a fractured carbon surface.
Effect of compressive and tensile strain on misfit dislocation injection in SiGe epitaxial layers
Authors: Wegscheider Werner , Cerva Hans
Published: July 2002

The relaxation behavior of short-period Si/Ge superlattices and SixGe1−x alloy layers under compressive and tensile strain field is compared experimentally by means of transmission electron microscopy as well as theoretically on the basis of a half-loop dislocation nucleation model. It was found that misfit dislocations in tensily strained layers grown on Ge(001) substrates are imperfect and of the 90° Shockley type provided some critical misfit fc is exceeded. Subsequent nucleation and glide of these partial dislocations on adjacent {111} glide planes leads to the formation of stacking faults and microtwins. In the low misfit regime (f<fc), the nucleation of 60° perfect dislocations is energetically favorable. In contrast, misfit dislocations in layers which experience a compressive strain field within the (001) growth plane are generally of the 60° type. In this case the critical thickness for coherent growth is found to be substantially enlarged with respect to the inverse strain situation where microtwin formation occurs.
High frequency reactive ion etching of silylated photoresist
Authors: Kalpakjian Kent M. , Lieberman M. A. , Oldham W. G.
Published: July 2002

The effects of high frequency operation on the reactive ion etching (RIE) of silylated photoresist are investigated. Using a simple parallel plate discharge model, the frequency scalings of dc bias, ion density, and sheath width are predicted to be ω−1.5, ω2, and ω−1.125, respectively. Measurements on the RIE system reveal dependencies of ω−1.48, ω1.85, and ω−1.00, respectively, in the 13.5–100 MHz range. The high frequency discharge is applied to the etching of silylated Plasmask 200G photoresist as part of the DESIRE (diffusion enhanced silylated resist) process flow. Increasing the drive frequency is shown to increase the unsilylated:silylated etch selectivity and reduce the postetch grass residues. Statistical design of experiments (SDE) is also employed to fully characterize the resist etch process. An L934 table is designed with plasma power, pressure, oxygen flow, and frequency as the controlled factors. Measured responses are etch rate, etch uniformity, selectivity, dc bias, residue size, residue density, linewidth, and etch profile angle. Main effects plots are tabulated from the design matrix revealing which factors have the greatest effect on each of the responses. Through the use of SDE, a significant reduction in postetch residues is observed for the high frequency RIE etch of Plasmask 200G resist.
Field emission from p-type polycrystalline diamond films
Authors: Hong D. , Aslam M.
Published: July 2002

Vapor-deposited-diamond field emitters are fabricated using diamond film technology compatible with integrated circuit processing. The field emission data from p-type polycrystalline diamond films are presented. Field emission current in the range of 15 μA was detected at an electric field intensity of <20 MV/m at a pressure of 10−7 Torr. A current of approximately 50 nA was observed at a pressure up to 10−2 Torr in H2 environment.
Dry development of photosensitive polyimides for high resolution and aspect ratio applications
Authors: Muñoz J. , Domínguez C.
Published: July 2002

A plasma developing process for photosensitive polyimide layers has been investigated as an alternative to wet development. Silylation of photoimageable polyimide by applying an organosilicon compound and subsequent ultraviolet exposure using a g-line mask aligner equipment lead, as a consequence, to copolymerization of photoactive functional groups of silylating agents and sensitizer groups of the polyimide-based photoresists. Development of the photoresist layer is carried out by means of oxygen-containing plasma. Interaction of oxygen plasma with a silylated surface of polyimide leads to the formation of a silicon oxide layer that acts as a barrier giving large differences in the etching rates of the photoresist covered and not covered with organosilane. The influence of O2 plasma etching process parameters on the etching selectivity is studied. The photochemical silylation process and the dry developing method have been characterized by scanning electron microscopy and Fourier transform infrared spectroscopy.
Reactive ion etching of silicon oxynitride formed by plasma-enhanced chemical vapor deposition
Authors: Ueno Kazuyoshi , Kikkawa Takamaro , Tokashiki Ken
Published: July 2002

A variation in the reactive ion etch (RIE) rate of silicon oxynitride ( SiOxNy) films deposited by plasma-enhanced chemical vapor deposition was studied by CHF3 RIE, CHF3+carbon mono-oxide (CO) RIE and CF4 RIE. The source gas flow rate ratio (R=N2O/SiH4) during the SiOxNyfilm deposition was varied to obtain a film of different atomic composition. Etch rates decreased in the order of CF4 RIE, CHF3 RIE, and CHF3+CO RIE, and the etch selectivity of SiO2 over SiOxNy increased in the same order also. The fluorocarbon ( CFx) film deposited during a RIE process was analyzed by x-ray photoelectron spectroscopy measurements. Etch rates are found to be correlated to both thickness and atomic composition of the CFx film. Carbon-rich fluorocarbon films are found to be more resistive against RIE.
Statistical analysis of field emitter emissivity: Application to flat displays
Authors: Levine J. D.
Published: July 2002

A new type of field emitter diagnostics has been developed, which takes into account a normal distribution of microtip sharpness. Substantial curvature in the Fowler–Nordheim plot is predicted at very low voltages and currents. From this curvature it is possible to calculate the mean and standard deviation of tip sharpness as well as other parameters relating to the voltage dependence of microtip sharpness. Thirteen Fowler–Nordheim plots are made with three anode voltages and six field emitter display (FED) panels fabricated at Pixel/LETI. Each of the FEDs has about 200 million Spindt-type microtips. Comparison between theory and experiment shows good agreement. The ratio of standard deviation to mean tip sharpness is about 10% for all panels tested. Noise-free measurements are made with very low average currents in the range of 10−16–10−11 A/tip.
Elastic deformations of tip and sample during atomic force microscope measurements
Authors: Heuberger Manfred , Dietler Giovanni , Schlapbach Louis
Published: July 2002

Two established models, based on continuum mechanics, are discussed to describe the elastic deformation of the tip and the sample in the atomic force microscope. We present arguments why the elastic deformation of a surface is more rigorously described by Sneddon mechanics rather than by the habitually used Hertzian mechanics. The results presented here show that elastic deformations are an important issue for measurements with the atomic force microscope. We demonstrate how elastic deformations impose limits to the capability of the atomic force microscope to image at true atomic resolution and how elastic deformations can be used to measure local elastic properties of a sample. Against the commonly accepted assumption of a ‘‘rigid’’ tip, we show that the elastic deformation of the tip can become a significant factor, when imaging hard samples. With few exceptions, the atomic force microscope has not been operated at true atomic resolution so far and more complex contrast mechanisms, with multiple atom interaction, must be considered.
A new high-performance surface-micromachined tunneling accelerometer fabricated using nanolithography
Authors: Kubena R. L. , Atkinson G. M. , Robinson W. P. , Stratton F. P.
Published: July 2002

We have fabricated a new class of high-performance tunneling accelerometers using surface micromachining. The accelerometer structures are fabricated on the surface of a single silicon wafer and consist of a single cantilevered beam with electrostatic deflection electrodes and a sub-100-nm-diam tunneling tip underneath. The noise level resolutions in air of 100- and 250-μm-long cantilever devices are 8.3×10−4 and 8.5×10−5 g/Hz1/2 at 500 Hz, respectively. The devices are operated in a force rebalance feedback mode using a low noise automatic servo-control circuit, providing a dynamic range of over 104 g. This new accelerometer technology provides devices with extremely high sensitivity, high bandwidth, and wide dynamic range, in an ultracompact, low-cost package that is easily integrated with silicon control electronics.
Interface roughness effects on transport in tunnel structures
Authors: Ting D. Z.-Y. , McGill T. C.
Published: July 2002

Direct simulations of interface roughness effects on transport properties of tunnel structures are performed using the planar supercell stack method. The method allows for the inclusion of realistic three-dimensional rough interfacial geometries in transport calculations. For double barrier resonant tunneling structures, we used our method to analyze the effect of roughness at each of the four interfaces, and to test for sensitivity of transport properties to island size and height. Our simulations yields the following conclusions: (1) We find that scattering of off-resonance states into on-resonance states provides the dominant contribution to interface roughness assisted tunneling. Analyses of scattering strength sensitivity to interface layer configurations reveals preferential scattering into Δk∥≊2π/λ states, where λ is the island size. (2) We find that roughness at interfaces adjacent to the quantum well can cause lateral localization of wave functions, which increases with island size and depth. Lateral localization can result in the broadening and shifting of transmission resonances, and the introduction of preferential transmission paths. In structures with wide and tall islands, it is possible to find localization over ‘‘islands’’ as well as localization over ‘‘oceans.’’ (3) The leading rough interface is the strongest off-resonance scatterer, while rough interfaces adjacent to quantum well are the strongest on-resonance scatterers. The trailing interface is the weakest scatterer.
Negative electron affinity of cesiated p-GaN(0001) surfaces
Authors: Eyckeler M. , Mönch W. , Kampen T. U. , Dimitrov R. , Ambacher O. , Stutzmann M.
Published: July 2002

The adsorption of cesium on clean n- and p-GaN(0001)-1×1 surfaces at 150 K was investigated using x-ray photoemission spectroscopy, photoemission spectroscopy with monochromatized He I radiation ultraviolet photoelectron spectroscopy (UPS) and a Kelvin probe (contact potential difference, CPD). The CPD measurements gave work functions of 3.88±0.15 and 3.6±0.15 eV for clean n- and p-GaN(0001) surfaces, respectively. The widths of UPS energy distribution curves yield an ionization energy of 6.8±0.15 eV. Thus, depletion and inversion layers exist at clean surfaces of n- and p-GaN(0001) surfaces, respectively. As a function of Cs coverage, the work function displays the well-known behavior in that it first decreases, passes through a minimum, and eventually reaches a value of 2.1 eV, the work function of metallic cesium. In the submonolayer coverage regime, the ionization energy decreases by 2.3±0.15 eV. At clean p-GaN(0001) surfaces the vacuum level lies by only 0.3 eV above the conduction-band minimum in the bulk. Already minute amounts of Cs suffice to produce negative electron affinity. The Schottky barrier height of metallic Cs films on n-GaN(0001) is determined as 0.2±0.15 eV. This value is in good agreement with what is predicted by the MIGS and electronegativity model.
Simulation of diamond-film field emission microtetrodes
Authors: Zeng Baoqing , Yang Zhonghai
Published: July 2002

Using the particle-in-cell simulation code MAGIC, a vacuum microelectronics tetrode with a planar emitter has been simulated. The electron beam streamlines have been evaluated, which show that the upper gate focuses the electron beam. The current distribution between gate and anode has been calculated and the effect of the lower gate voltage and the emitter size on emitted current and gate capture current has been investigated. Simulation results are presented for a single vertical diamond-film field-emission tetrode with the anode biased at 300 V and spaced 50 μm from the cathode. Simulation results indicated that the radius of the electron beam at the anode is about 20 μm for a microtriode, but only about 6 μm for the microtetrode. The results show that gate capture current should not be negligible in most cases, and can be ignored only if the emitter radius is less than half of the gate aperture radius. Then the percentage of gate capture current to emitted current is less than 0.1%.
Activity-Dependent Transfer of Brain-Derived Neurotrophic Factor to Postsynaptic Neurons
Authors: Kohara Keigo , Kitamura Akihiko , Morishima Mieko , Tsumoto Tadaharu
Published: July 2002

Neurotrophins such as brain-derived neurotrophic factor (BDNF) are thought to be transferred from post- to presynaptic neurons and to be involved in the formation and plasticity of neural circuits. However, direct evidence for a transneuronal transfer of BDNF and its relation to neuronal activity remains elusive. We simultaneously injected complementary DNAs of green fluorescent protein (GFP)–tagged BDNF and red fluorescence protein into the nucleus of single neurons and visualized expression, localization, and transport of BDNF in living neurons. Fluorescent puncta representing BDNF moved in axons in the anterograde direction, though some moved retrogradely, and transferred to postsynaptic neurons in an activity-dependent manner.
The Art of the Probable: System Control in the Adaptive Immune System
Authors: Germain Ronald N.
Published: July 2002

The immune system provides very effective host defense against infectious agents. Although many details are known about the cells and molecules involved, a broader “systems engineering” view of this complex system is just beginning to emerge. Here the argument is put forward that stochastic events, potent amplification mechanisms, feedback controls, and heterogeneity arising from spatially dispersed cell interactions give rise to many of the gross properties of the immune system. A better appreciation of these underlying features will not only add to our basic understanding of how immunity develops or goes awry, but also illuminate new directions for manipulating the system in prophylactic and therapeutic settings.
Factors Controlling Long- and Short-Term Sequestration of Atmospheric CO
2
in a Mid-latitude Forest
Authors: Barford Carol C. , Wofsy Steven C. , Goulden Michael L. , Munger J. William , Pyle Elizabeth Hammond , Urbanski Shawn P. , Hutyra Lucy , Saleska Scott R. , Fitzjarrald David , Moore Kathleen
Published: July 2002

Net uptake of carbon dioxide (CO
2
) measured by eddy covariance in a 60- to 80-year-old forest averaged 2.0 ± 0.4 megagrams of carbon per hectare per year during 1993 to 2000, with interannual variations exceeding 50%. Biometry indicated storage of 1.6 ± 0.4 megagrams of carbon per hectare per year over 8 years, 60% in live biomass and the balance in coarse woody debris and soils, confirming eddy-covariance results. Weather and seasonal climate (e.g., variations in growing-season length or cloudiness) regulated seasonal and interannual fluctuations of carbon uptake. Legacies of prior disturbance and management, especially stand age and composition, controlled carbon uptake on the decadal time scale, implying that eastern forests could be managed for sequestration of carbon.
Genome-Wide Distribution of ORC and MCM Proteins in
S. cerevisiae
: High-Resolution Mapping of Replication Origins
Authors: Wyrick John J. , Aparicio Jennifer G. , Chen Ting , Barnett John D. , Jennings Ezra G. , Young Richard A. , Bell Stephen P. , Aparicio Oscar M.
Published: July 2002

DNA replication origins are fundamental to chromosome organization and duplication, but understanding of these elements is limited because only a small fraction of these sites have been identified in eukaryotic genomes. Origin Recognition Complex (ORC) and minichromosome maintenance (MCM) proteins form prereplicative complexes at origins of replication. Using these proteins as molecular landmarks for origins, we identified ORC- and MCM-bound sites throughout the yeast genome. Four hundred twenty-nine sites in the yeast genome were predicted to contain replication origins, and ∼80% of the loci identified on chromosome X demonstrated origin function. A substantial fraction of the predicted origins are associated with repetitive DNA sequences, including subtelomeric elements (X and Y') and transposable element–associated sequences (long terminal repeats). These findings identify the global set of yeast replication origins and open avenues of investigation into the role(s) ORC and MCM proteins play in chromosomal architecture and dynamics.
Electrically Driven Single-Photon Source
Authors: Yuan Zhiliang , Kardynal Beata E. , Stevenson R. Mark , Shields Andrew J. , Lobo Charlene J. , Cooper Ken , Beattie Neil S. , Ritchie David A. , Pepper Michael
Published: July 2002

Electroluminescence from a single quantum dot within the intrinsic region of a p-i-n junction is shown to act as an electrically driven single-photon source. At low injection currents, the dot electroluminescence spectrum reveals a single sharp line due to exciton recombination, while another line due to the biexciton emerges at higher currents. The second-order correlation function of the diode displays anti-bunching under a continuous drive current. Single-photon emission is stimulated by subnanosecond voltage pulses. These results suggest that semiconductor technology can be used to mass-produce a single-photon source for applications in quantum information technology.
Effect of
p53
Status on Tumor Response to Antiangiogenic Therapy
Authors: Yu Joanne L. , Rak Janusz W. , Coomber Brenda L. , Hicklin Daniel J. , Kerbel Robert S.
Published: July 2002

The
p53
tumor suppressor gene is inactivated in the majority of human cancers. Tumor cells deficient in p53 display a diminished rate of apoptosis under hypoxic conditions, a circumstance that might reduce their reliance on vascular supply, and hence their responsiveness to antiangiogenic therapy. Here, we report that mice bearing tumors derived from
p53
−/−
HCT116 human colorectal cancer cells were less responsive to antiangiogenic combination therapy than mice bearing isogenic
p53
+/+
tumors. Thus, although antiangiogenic therapy targets genetically stable endothelial cells in the tumor vasculature, genetic alterations that decrease the vascular dependence of tumor cells can influence the therapeutic response of tumors to this therapy.
Cerebellum Activation Associated with Performance Change but Not Motor Learning
Authors: Seidler R. D. , Purushotham A. , Kim S.-G. , Uğurbil K. , Willingham D. , Ashe J.
Published: July 2002

The issue of whether the cerebellum contributes to motor skill learning is controversial, principally because of the difficulty of separating the effects of motor learning from changes in performance. We performed a functional magnetic resonance imaging investigation during an implicit, motor sequence-learning task that was designed to separate these two processes. During the sequence-encoding phase, human participants performed a concurrent distractor task that served to suppress the performance changes associated with learning. Upon removal of the distractor, participants showed evidence of having learned. No cerebellar activation was associated with the learning phase, despite extensive involvement of other cortical and subcortical regions. There was, however, significant cerebellar activation during the expression of learning; thus, the cerebellum does not contribute to learning of the motor skill itself but is engaged primarily in the modification of performance.
Tat-SF1: Cofactor for Stimulation of Transcriptional Elongation by HIV-1 Tat
Authors: Zhou Qiang , Sharp Phillip A.
Published: July 2002

Tat may stimulate transcriptional elongation by recruitment of a complex containing Tat-SF1 and a kinase to the human immunodeficiency virus-type 1 (HIV-1) promoter through a Tat-TAR interaction. A complementary DNA for the cellular activity, Tat-SF1, has been isolated. This factor is required for Tat trans-activation and is a substrate of an associated cellular kinase. Cotransfection with the complementary DNA for Tat-SF1 specifically modulates Tat activation. Tat-SF1 contains two RNA recognition motifs and a highly acidic carboxyl-terminal half. It is distantly related to EWS and FUS/TLS, members of a family of putative transcription factors with RNA recognition motifs that are associated with sarcomas.
Induction of Autoimmune Diabetes by Oral Administration of Autoantigen
Authors: Blanas Effrossini , Carbone Francis R. , Allison Janette , Miller Jacques F. A. P. , Heath William R.
Published: July 2002

An antigen administered orally can induce immunological tolerance to a subsequent challenge with the same antigen. Evidence has been provided for the efficacy of this approach in the treatment of human autoimmune diseases such as rheumatoid arthritis and multiple sclerosis. However, oral administration of autoantigen in mice was found to induce a cytotoxic T lymphocyte response that could lead to the onset of autoimmune diabetes. Thus, feeding autoantigen can cause autoimmunity, which suggests that caution should be used when applying this approach to the treatment of human autoimmune diseases.
Initiation of Plant Disease Resistance by Physical Interaction of AvrPto and Pto Kinase
Authors: Tang Xiaoyan , Frederick Reid D. , Zhou Jianmin , Halterman Dennis A. , Jia Yulin , Martin Gregory B.
Published: July 2002

Resistance to bacterial speck disease in tomato occurs when the Pto kinase in the plant responds to expression of the avirulence gene
avrPto
in the
Pseudomonas
pathogen. Transient expression of an
avrPto
transgene in plant cells containing
Pto
elicited a defense response. In the yeast two-hybrid system, the Pto kinase physically interacted with AvrPto. Alterations of AvrPto or Pto that disrupted the interaction in yeast also abolished disease resistance in plants. The physical interaction of AvrPto and Pto provides an explanation of gene-for-gene specificity in bacterial speck disease resistance.
Preattentive Filling-in of Visual Surfaces in Parietal Extinction
Authors: Mattingley Jason B. , Davis Greg , Driver Jon
Published: July 2002

Unilateral brain damage frequently produces “extinction,” in which patients can detect brief single visual stimuli on either side but are unaware of a contralesional stimulus if presented concurrently with an ipsilesional stimulus. Explanations for extinction have invoked deficits in initial processes that operate before the focusing of visual attention or in later attentive stages of vision. Preattentive vision was preserved in a parietally damaged patient, whose extinction was less severe when bilateral stimuli formed a common surface, even if this required visual filling-in to yield illusory Kanizsa figures or completion of partially occluded figures. These results show that parietal extinction arises only after substantial processing has generated visual surfaces, supporting recent claims that visual attention is surface-based.
Calcium Waves in Retinal Glial Cells
Authors: Newman Eric A. , Zahs Kathleen R.
Published: July 2002

Calcium signals were recorded from glial cells in acutely isolated rat retina to determine whether Ca
2+
waves occur in glial cells of intact central nervous system tissue. Chemical (adenosine triphosphate), electrical, and mechanical stimulation of astrocytes initiated increases in the intracellular concentration of Ca
2+
that propagated at ∼23 micrometers per second through astrocytes and Müller cells as intercellular waves. The Ca
2+
waves persisted in the absence of extracellular Ca
2+
but were largely abolished by thapsigargin and intracellular heparin, indicating that Ca
2+
was released from intracellular stores. The waves did not evoke changes in cell membrane potential but traveled synchronously in astrocytes and Müller cells, suggesting a functional linkage between these two types of glial cells. Such glial Ca
2+
waves may constitute an extraneuronal signaling pathway in the central nervous system.
Soft-Landing of Polyatomic Ions at Fluorinated Self-Assembled Monolayer Surfaces
Authors: Miller S. A. , Luo H. , Pachuta S. J. , Cooks R. G.
Published: July 2002

A method of preparing modified surfaces, referred to as soft-landing, is described in which intact polyatomic ions are deposited from the gas phase into a monolayer fluorocarbon surface at room temperature. The ions are trapped in the fluorocarbon matrix for many hours. They are released, intact, upon sputtering at low or high energy or by thermal desorption, and their molecular compositions are confirmed by isotopic labeling and high-resolution mass measurements. The method is demonstrated for various silyl and pyridinium cations. Capture at the surface is favored when the ions bear bulky substituents that facilitate steric trapping in the matrix.
An Elicitor of Plant Volatiles from Beet Armyworm Oral Secretion
Authors: Alborn H. T. , Turlings T. C. J. , Jones T. H. , Stenhagen G. , Loughrin J. H. , Tumlinson J. H.
Published: July 2002

The compound
N
-(17-hydroxylinolenoyl)-
l
-glutamine (named here volicitin) was isolated from oral secretions of beet armyworm caterpillars. When applied to damaged leaves of corn seedlings, volicitin induces the seedlings to emit volatile compounds that attract parasitic wasps, natural enemies of the caterpillars. Mechanical damage of the leaves, without application of this compound, did not trigger release of the same blend of volatiles. Volicitin is a key component in a chain of chemical signals and biochemical processes that regulate tritrophic interactions among plants, insect herbivores, and natural enemies of the herbivores.
Scanning Confocal Optical Microscopy and Magnetic Resonance on Single Defect Centers
Authors: Gruber A. , Dräbenstedt A. , Tietz C. , Fleury L. , Wrachtrup J. , Borczyskowski C. von
Published: July 2002

The fluorescence of individual nitrogen-vacancy defect centers in diamond was observed with room-temperature scanning confocal optical microscopy. The centers were photostable, showing no detectable change in their fluorescence emission spectrum as a function of time. Magnetic resonance on single centers at room temperature was shown to be feasible. The magnetic resonance spectra revealed marked changes in zero-field splitting parameters among different centers. These changes were attributed to strain-induced differences in the symmetry of the centers.
Protein Transport by Purified Yeast Sec Complex and Kar2p Without Membranes
Authors: Matlack Kent E. S. , Plath Kathrin , Misselwitz Benjamin , Rapoport Tom A.
Published: July 2002

Posttranslational protein translocation across the endoplasmic reticulum membrane of yeast requires a seven-component transmembrane complex (the Sec complex) in collaboration with the lumenal Kar2 protein (Kar2p). A translocation substrate was initially bound to the cytosolic face of the purified Sec complex in a signal-sequence–dependent but Kar2p- and nucleotide-independent manner. In a subsequent reaction, in which Kar2p interacted with the lumenal face of the Sec complex and hydrolyzed adenosine triphosphate, the substrate moved through a channel formed by the Sec complex and was released at the lumenal end. Movement through the channel occurred in detergent solution in the absence of a lipid bilayer.
Conversion by Peyer's Patch Lymphocytes of Human Enterocytes into M Cells that Transport Bacteria
Authors: Kernéis Sophie , Bogdanova Anna , Kraehenbuhl Jean-Pierre , Pringault Eric
Published: July 2002

The epithelium that lines the gut is impermeable to macromolecules and microorganisms, except in Peyer's patches (PPs), where the lymphoid follicle-associated epithelium (FAE) contains M cells that transport antigens and microorganisms. A cultured system that reproduces the main characteristics of FAE and M cells was established by cultivation of PP lymphocytes with the differentiated human intestinal cell line Caco-2. Lymphocytes settled into the epithelial monolayer, inducing reorganization of the brush border and a temperature-dependent transport of particles and
Vibrio cholerae
. This model system could prove useful for intestinal physiology, vaccine research, and drug delivery studies.
X-ray Structure of Bacteriorhodopsin at 2.5 Angstroms from Microcrystals Grown in Lipidic Cubic Phases
Authors: Pebay-Peyroula Eva , Rummel Gabriele , Rosenbusch Jurg P. , Landau Ehud M.
Published: July 2002

Lipidic cubic phases provide a continuous three-dimensional bilayer matrix that facilitates nucleation and growth of bacteriorhodopsin microcrystals. The crystals diffract x-rays isotropically to 2.0 angstroms. The structure of this light-driven proton pump was solved at a resolution of 2.5 angstroms by molecular replacement, using previous results from electron crystallographic studies as a model. The earlier structure was generally confirmed, but several differences were found, including loop conformations and side chain residues. Eight water molecules are now identified experimentally in the proton pathway. These findings reveal the constituents of the proton translocation pathway in the ground state.
Predictive Genetic Testing: From Basic Research to Clinical Practice
Authors: Holtzman Neil A. , Murphy Patricia D. , Watson Michael S. , Barr Patricia A.
Published: July 2002

As increasing numbers of genes are identified and associated with human diseases, researchers are considering how to bring their discoveries from the research bench to the clinic. Holtzman, Murphy, Watson, and Barr, who were part of a Task Force on Genetic Testing sponsored by the National Institutes of Health and U.S. Department of Energy, discuss policies for regulating the development of genetic tests so that the full potential of gene discovery to help the general population can be realized.
Requirement for CD44 in Activated T Cell Extravasation into an Inflammatory Site
Authors: DeGrendele Heather C. , Estess Pila , Siegelman Mark H.
Published: July 2002

Leukocytes extravasate from the blood into inflammatory sites through complementary ligand interactions between leukocytes and endothelial cells. Activation of T cells increases their binding to hyaluronate (HA) and enables CD44-mediated primary adhesion (rolling). This rolling could be induced in vivo in murine V
β
8
+
T cells in response to specific superantigen stimulation; it was initially found in lymph nodes, then in peripheral blood, and finally within the peritoneum, the original inflamed site. The migration of V
β
8
+
cells into the peritoneal cavity was dependent on CD44 and HA, as shown by inhibition studies. Thus, CD44-HA interactions can target lymphocytes to specific extralymphoid effector sites.
Activation of the Cardiac Calcium Release Channel (Ryanodine Receptor) by Poly-S-Nitrosylation
Authors: Xu Le , Eu Jerry P. , Meissner Gerhard , Stamler Jonathan S.
Published: July 2002

Several ion channels are reportedly redox responsive, but the molecular basis for the changes in activity is not known. The mechanism of nitric oxide action on the cardiac calcium release channel (ryanodine receptor) (CRC) in canines was explored. This tetrameric channel contains ∼84 free thiols and is S-nitrosylated in vivo. S-Nitrosylation of up to 12 sites (3 per CRC subunit) led to progressive channel activation that was reversed by denitrosylation. In contrast, oxidation of 20 to 24 thiols per CRC (5 or 6 per subunit) had no effect on channel function. Oxidation of additional thiols (or of another class of thiols) produced irreversible activation. The CRC thus appears to be regulated by poly-S-nitrosylation (multiple covalent attachments), whereas oxidation can lead to loss of control. These results reveal that ion channels can differentiate nitrosative from oxidative signals and indicate that the CRC is regulated by posttranslational chemical modification(s) of sulfurs.
Helicobacter pylori
Adhesin Binding Fucosylated Histo-Blood Group Antigens Revealed by Retagging
Authors: Ilver Dag , Arnqvist Anna , Ögren Johan , Frick Inga-Maria , Kersulyte Dangeruta , Incecik Engin T. , Berg Douglas E. , Covacci Antonello , Engstrand Lars , Borén Thomas
Published: July 2002

The bacterium
Helicobacter pylori
is the causative agent for peptic ulcer disease. Bacterial adherence to the human gastric epithelial lining is mediated by the fucosylated Lewis b (Le
b
) histo-blood group antigen. The Le
b
-binding adhesin, BabA, was purified by receptor activity–directed affinity tagging. The bacterial Le
b
-binding phenotype was associated with the presence of the
cag
pathogenicity island among clinical isolates of
H. pylori
. A vaccine strategy based on the BabA adhesin might serve as a means to target the virulent type I strains of
H. pylori.
A Transmembrane Form of the Prion Protein in Neurodegenerative Disease
Authors: Hegde Ramanujan S. , Mastrianni James A. , Scott Michael R. , DeFea Kathryn A. , Tremblay Patrick , Torchia Marilyn , DeArmond Stephen J. , Prusiner Stanley B. , Lingappa Vishwanath R.
Published: July 2002

At the endoplasmic reticulum membrane, the prion protein (PrP) can be synthesized in several topological forms. The role of these different forms was explored with transgenic mice expressing PrP mutations that alter the relative ratios of the topological forms. Expression of a particular transmembrane form (termed
Ctm
PrP) produced neurodegenerative changes in mice similar to those of some genetic prion diseases. Brains from these mice contained
Ctm
PrP but not PrP
Sc
, the PrP isoform responsible for transmission of prion diseases. Furthermore, in one heritable prion disease of humans, brain tissue contained
Ctm
PrP but not PrP
Sc
. Thus, aberrant regulation of protein biogenesis and topology at the endoplasmic reticulum can result in neurodegeneration.
Molecular Mimicry by Herpes Simplex Virus-Type 1: Autoimmune Disease After Viral Infection
Authors: Zhao Zi-Shan , Granucci Francesca , Yeh Lily , Schaffer Priscilla A. , Cantor Harvey
Published: July 2002

Viral infection is sometimes associated with the initiation or exacerbation of autoimmune disease, although the underlying mechanisms remain unclear. One proposed mechanism is that viral determinants that mimic host antigens trigger self-reactive T cell clones to destroy host tissue. An epitope expressed by a coat protein of herpes simplex virus–type 1 (HSV-1) KOS strain has now been shown to be recognized by autoreactive T cells that target corneal antigens in a murine model of autoimmune herpes stromal keratitis. Mutant HSV-1 viruses that lacked this epitope did not induce autoimmune disease. Thus, expression of molecular mimics can influence the development of autoimmune disease after viral infection.
Activity-Dependent Cortical Target Selection by Thalamic Axons
Authors: Catalano Susan M. , Shatz Carla J.
Published: July 2002

Connections in the developing nervous system are thought to be formed initially by an activity-independent process of axon pathfinding and target selection and subsequently refined by neural activity. Blockade of sodium action potentials by intracranial infusion of tetrodotoxin in cats during the early period when axons from the lateral geniculate nucleus (LGN) were in the process of selecting visual cortex as their target altered the pattern and precision of this thalamocortical projection. The majority of LGN neurons, rather than projecting to visual cortex, elaborated a significant projection within the subplate of cortical areas normally bypassed. Those axons that did project to their correct target were topographically disorganized. Thus, neural activity is required for initial targeting decisions made by thalamic axons as they traverse the subplate.
Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life
Authors: Huber Claudia , Wächtershäuser Günter
Published: July 2002

In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H
2
S (or CH
3
SH) as a catalyst and condensation agent at 100°C and pH 7 to 10 under anaerobic, aqueous conditions. These results demonstrate that amino acids can be activated under geochemically relevant conditions. They support a thermophilic origin of life and an early appearance of peptides in the evolution of a primordial metabolism.
Activation of the ATM Kinase by Ionizing Radiation and Phosphorylation of p53
Authors: Canman Christine E. , Lim Dae-Sik , Cimprich Karlene A. , Taya Yoichi , Tamai Katsuyuki , Sakaguchi Kazuyasu , Appella Ettore , Kastan Michael B. , Siliciano Janet D.
Published: July 2002

The p53 tumor suppressor protein is activated and phosphorylated on serine-15 in response to various DNA damaging agents. The gene product mutated in ataxia telangiectasia, ATM, acts upstream of p53 in a signal transduction pathway initiated by ionizing radiation. Immunoprecipitated ATM had intrinsic protein kinase activity and phosphorylated p53 on serine-15 in a manganese-dependent manner. Ionizing radiation, but not ultraviolet radiation, rapidly enhanced this p53-directed kinase activity of endogenous ATM. These observations, along with the fact that phosphorylation of p53 on serine-15 in response to ionizing radiation is reduced in ataxia telangiectasia cells, suggest that ATM is a protein kinase that phosphorylates p53 in vivo.
Direct Observations of Structural Phase Transitions in Planar Crystallized Ion Plasmas
Authors: Mitchell T. B. , Bollinger J. J. , Dubin D. H. E. , Huang X.-P. , Itano W. M. , Baughman R. H.
Published: July 2002

Laser-cooled
9
Be
+
ions confined in two-dimensionally extended lattice planes were directly observed, and the images were used to characterize the structural phases of the ions. Five different stable crystalline phases were observed, and the energetically favored structure could be sensitively tuned by changing the areal density of the confined ions. The experimental results are in good agreement with theoretical predictions for the planar (infinite in two dimensions) one-component plasma. Qualitatively similar structural phase transitions occur, or are predicted to occur, in other experimentally realizable planar systems.
Behavioral State Modulation of Auditory Activity in a Vocal Motor System
Authors: Dave Amish S. , Yu Albert C. , Margoliash Daniel
Published: July 2002

Neurons of the song motor control nucleus robustus archistriatalis (RA) exhibited far weaker auditory responses in awake than in anesthetized zebra finches. Remarkably, sleep induced complex patterns of bursts in ongoing activity and uncovered vigorous auditory responses of RA neurons. Local injections of norepinephrine suggested that the changes in response strength occur through neuromodulatory control of the sensorimotor nucleus HVc, which projects to RA. Thus, motor access to auditory feedback, which zebra finches require for song learning and maintenance, may be regulated through neuromodulation. During sleep, the descending motor system may gain access to sensorimotor song memories represented as bursting patterns of activity.
Female × Male Interactions in
Drosophila
Sperm Competition
Authors: Clark Andrew G. , Begun David J. , Prout Timothy
Published: July 2002

In several organisms, the success of a male's sperm in multiply inseminated females depends on the male's genotype. In
Drosophila
, the female also plays a role in determining which sperm are successful. Pairwise tests among six isogenic lines of
Drosophila melanogaster
were performed to determine whether there is a genotype-specific interaction in the success of sperm. The success of a particular male's sperm was found to depend on the genotype of the female with which he mates, providing evidence for an interaction with profound evolutionary consequences.
"Dip-Pen" Nanolithography
Authors: Piner Richard D. , Zhu Jin , Xu Feng , Hong Seunghun , Mirkin Chad A.
Published: July 2002

A direct-write “dip-pen” nanolithography (DPN) has been developed to deliver collections of molecules in a positive printing mode. An atomic force microscope (AFM) tip is used to write alkanethiols with 30-nanometer linewidth resolution on a gold thin film in a manner analogous to that of a dip pen. Molecules are delivered from the AFM tip to a solid substrate of interest via capillary transport, making DPN a potentially useful tool for creating and functionalizing nanoscale devices.
Adhesive and Mammalian Transglutaminase Substrate Properties of
Candida albicans
Hwp1
Authors: Staab Janet F. , Bradway Steven D. , Fidel Paul L. , Sundstrom Paula
Published: July 2002

The pathogenesis of candidiasis involves invasion of host tissues by filamentous forms of the opportunistic yeast
Candida albicans
. Morphology-specific gene products may confer proinvasive properties. A hypha-specific surface protein, Hwp1, with similarities to mammalian small proline-rich proteins was shown to serve as a substrate for mammalian transglutaminases.
Candida albicans
strains lacking Hwp1 were unable to form stable attachments to human buccal epithelial cells and had a reduced capacity to cause systemic candidiasis in mice. This represents a paradigm for microbial adhesion that implicates essential host enzymes.
Functional Selection of Adaptive Auditory Space Map by GABA
A
-Mediated Inhibition
Authors: Zheng Weimin , Knudsen Eric I.
Published: July 2002

The external nucleus of the inferior colliculus in the barn owl contains an auditory map of space that is based on the tuning of neurons for interaural differences in the timing of sound. In juvenile owls, this region of the brain can acquire alternative maps of interaural time difference as a result of abnormal experience. It has been found that, in an external nucleus that is expressing a learned, abnormal map, the circuitry underlying the normal map still exists but is functionally inactivated by inhibition mediated by γ-aminobutyric acid type A (GABA
A
) receptors. This inactivation results from disproportionately strong inhibition of specific input channels to the network. Thus, experience-driven changes in patterns of inhibition, as well as adjustments in patterns of excitation, can contribute critically to adaptive plasticity in the central nervous system.
Supercurrents Through Single-Walled Carbon Nanotubes
Authors: Kasumov A. Yu. , Deblock R. , Kociak M. , Reulet B. , Bouchiat H. , Khodos I. I. , Gorbatov Yu. B. , Volkov V. T. , Journet C. , Burghard M.
Published: July 2002

Proximity-induced superconductivity in single-walled carbon nanotubes below 1 kelvin, both in a single tube 1 nanometer in diameter and in crystalline ropes containing about 100 nanotubes, was observed. The samples were suspended between two superconducting electrodes, permitting structural study in a transmission electron microscope. When the resistance of the nanotube junction is sufficiently low, it becomes superconducting and can carry high supercurrents. The temperature and magnetic field dependence of the critical current of such junctions exhibits unusual features related to their strong one-dimensional character.
Role of Bacterial Intimin in Colonic Hyperplasia and Inflammation
Authors: Higgins Lisa M. , Frankel Gad , Connerton Ian , Gonçalves Nathalie S. , Dougan Gordon , MacDonald Thomas T.
Published: July 2002

Enteropathogenic
Escherichia coli
(EPEC) cells adhere to gut epithelial cells through intimin α: the ligand for a bacterially derived epithelial transmembrane protein called the translocated intimin receptor.
Citrobacter rodentium
colonizes the mouse colon in a similar fashion and uses a different intimin: intimin β. Intimin α was found to costimulate submitogenic signals through the T cell receptor. Dead intimin β
+
C. rodentium
, intimin α–transfected
C. rodentium
or
E. coli
strain K12, and EPEC induced mucosal hyperplasia identical to that caused by
C. rodentium
live infection, as well as a massive T helper cell–type 1 immune response in the colonic mucosa. Mutation of cysteine-937 of intimin to alanine reduced costimulatory activity in vitro and prevented immunopathology in vivo. The mucosal changes elicited by
C. rodentium
were interferon-γ–dependent. Immunopathology induced by intimin enables the bacteria to promote conditions that are favorable for increased microbial colonization.
Quantitative Assessment of Reactive Surface Area of Phlogopite During Acid Dissolution
Authors: Rufe Eric , Hochella Michael F.
Published: July 2002

The reactive surface area of a dissolving sheet silicate, phlogopite, was quantitatively assessed in experiments performed in the fluid cell of an atomic force microscope at room temperature and pH values of 2 and 5.7. Additional assessment was provided by surface chemical analysis and electron diffraction. Dissolution rates of phlogopite {
hk
0} edges are in the range of 10
−10
moles per square meters per second, two orders of magnitude faster than bulk rates for this mineral. The basal {001} surfaces also show distinct reactivity, although it is short-lived before they become relatively inert. These basal surfaces are shown to leach, hydrate, and expand to an amorphous silica-enriched film.
Brownian Ratchets: Molecular Separations in Lipid Bilayers Supported on Patterned Arrays
Authors: van Oudenaarden Alexander , Boxer Steven G.
Published: July 2002

Brownian ratchets use a time-varying asymmetric potential that can be applied to separate diffusing particles or molecules. A new type of Brownian ratchet, a geometrical Brownian ratchet, has been realized. Charged, fluorescently labeled phospholipids in a two-dimensional fluid bilayer were driven in one direction by an electric field through a two-dimensional periodic array of asymmetric barriers to lateral diffusion fabricated from titanium oxide on silica. Diffusion spreads the phospholipid molecules in the orthogonal direction, and the asymmetric barriers rectify the Brownian motion, causing a directional transport of molecules. The geometrical ratchet can be used as a continuous molecular sieve to separate mixtures of membrane-associated molecules that differ in electrophoretic mobility and diffusion coefficient.