bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman-scattering elucidation of the giant isotope effect in hydrogen-ion blistering of silicon
Authors: Moutanabbir O. , Terreault B.
Published: October 2004

In this work, we investigate the origin of a giant isotope effect discovered in the blistering of hydrogen-ion-implanted and annealed silicon. Si(001) samples were implanted or coimplanted with 5 keV of H and/or D ions to total fluences of 2×1016 and 6×1016 ion/cm2. The lower fluence is sufficient for blistering by pure H, but the higher one is required for the maximum blister coverage whenever D is involved. On these samples, we carried out Raman-scattering investigations of the evolution of Si-H/D complexes upon a stepwise thermal annealing from 200 to 550 °C. We have identified the critical chemical transformations characterizing the hydrogen-deuterium-induced blistering of silicon. The puzzling dependence on ion mass appears to be mainly connected with the nature of the radiation damage. We have found that H is more efficient in “preparing the ground” for blistering by nucleating platelets parallel to the surface, essentially due to its ability to agglomerate in the multihydride monovacancy complexes that evolve into hydrogenated extended internal surfaces. By contrast, D is preferentially trapped in the surprisingly stable monodeuteride multivacancies.
Calculations of static and dynamic polarizabilities of excited states by means of density functional theory
Authors: Jansik Branislav , Jonsson Dan , Sałek Pawel , Ågren Hans
Published: October 2004

We present density functional theory and calculations for excited state second order, static or dynamic, properties. The excited state properties are identified from a double residue of a cubic response function. The performance of various functionals, including the generalized gradient approximation and fractional exact Hartree-Fock exchange, is compared to coupled cluster calculations. Applications on excited state polarizabilities of s-tetrazine and pyrimidine show a good agreement with ab initio correlated, coupled cluster, results.
Nucleation in cylindrical capillaries
Authors: Husowitz B. , Talanquer V.
Published: October 2004

We use a local density functional theory in the square gradient approximation to explore the properties of critical nuclei for the liquid-vapor transition of van der Waals fluids in cylindrical capillaries. The proposed model allows us to investigate the effect of pore size, surface field, and supersaturation on the behavior of the system. Our calculations predict the existence of at least three different pathways for the nucleation of droplets and bubbles in these confined fluids: axisymmetric annular bumps and lenses, and asymmetric droplets. The morphological transition between these different structures is driven by the existence of states of zero compressibility in the capillary. We show that the classical capillarity theory provides surprisingly accurate predictions for the work of formation of critical nuclei in cylindrical pores when line tension contributions to the free energy are taken into account.
Spectral implementation of some quantum algorithms by one- and two-dimensional nuclear magnetic resonance
Authors: Das Ranabir , Kumar Anil
Published: October 2004

Quantum information processing has been effectively demonstrated on a small number of qubits by nuclear magnetic resonance. An important subroutine in any computing is the readout of the output. “Spectral implementation” originally suggested by Z. L. Madi, R. Bruschweiler, and R. R. Ernst [J. Chem. Phys. 109, 10603 (1999)], provides an elegant method of readout with the use of an extra “observer” qubit. At the end of computation, detection of the observer qubit provides the output via the multiplet structure of its spectrum. In spectral implementation by two-dimensional experiment the observer qubit retains the memory of input state during computation, thereby providing correlated information on input and output, in the same spectrum. Spectral implementation of Grover’s search algorithm, approximate quantum counting, a modified version of Berstein-Vazirani problem, and Hogg’s algorithm are demonstrated here in three- and four-qubit systems.
Simulations of stable pores in membranes: System size dependence and line tension
Authors: Tolpekina T. V. , den Otter W. K. , Briels W. J.
Published: October 2004

Amphiphilic bilayers with a pore were simulated using a coarse grained model. By stretching the bilayer to 70% beyond its equilibrium surface area, we established the phase diagram of pores, identifying regions where pores are stable, metastable, or unstable. A simple theoretical model is proposed to explain the phase diagram, and to calculate the critical and equilibrium relative stretches. Interestingly, these are found to scale with the inverse cubic root of the number of amphiphiles in the bilayer, thus explaining the order of magnitude difference between the simulated and the measured values. Three different methods are used to calculate a line tension coefficient of (3.5–4.0)×10−11 J/m, in good agreement with experimental data.
Laser pulse control of ultrafast heterogeneous electron transfer: A computational study
Authors: Wang Luxia , May Volkhard
Published: October 2004

Laser pulse control of the photoinduced 90 fs charge injection from perylene into the conduction band of TiO2 is studied theoretically. The approach accounts for the electronic-ground state of the dye, the first excited state, the ionized state formed after charge injection, and the continuum of the electronic states in the conduction band, all defined vs a single reaction coordinate. To address different control tasks optimal control theory is combined with a full quantum dynamical description of the electron-vibrational motion accompanying the charge injection process. First it is proved in which way the charge injection time can be changed by tailored laser pulses. In a second step a pump-dump scheme from the perylene ground state to the first excited electronic state and back to the ground state is discussed. Because of the strong coupling of the excited perylene state to the band continuum of TiO2 this control task is more suited to an experimental test than the direct control of the charge injection.
Spectroscopic identification of the CO-H2O 2-1 cluster trapped in an argon matrix
Authors: Abe Hisashi , Yamada Koichi M. T.
Published: October 2004

The infrared spectra of the carbon monoxide-water cluster as well as the CO monomer and dimer in an argon matrix at cryogenic temperatures have been reinvestigated on the basis of the isotope substitution experiment with CO12 and CO12. Lines due to the CO-H2O 2-1 cluster in the matrix have been unambiguously identified in the CO and OH stretching regions. The isotope effect on the vibrational frequency of the cluster is observed in the CO stretching vibration but neither in the symmetric nor antisymmetric OH stretching vibrations. Each of the two vibrational lines due to the two CO vibrations of the CO-H2O 2-1 cluster is examined by comparing the expected spectral features at a CO12/13CO ratio on a simulation with those observed experimentally. The migration of the trapped molecules (CO and H2O) in the matrix is discussed, in which the observed spectral change with the deposition temperature from 14 K to 30 K is explained.
Tacticity effects on the barriers to rotation of the ester methyl group in poly (methyl methacrylate): A deuteron magnetic resonance study
Authors: Cereghetti P. M. , Kind R. , Higgins J. S.
Published: October 2004

In isotactic poly(methyl methacrylate) (PMMA), we investigate the dynamics of the ester methyl groups by means of deuteron magnetic resonance (DMR) in a deuterated sample. We find that the motion of the CD3-group affects the deuteron spin-lattice relaxation as well as the DMR line shape in a characteristic way. Quadrupolar order spin lattice relaxation measurements between T=291 K and T=70 K reveal a broad temperature dependent probability distribution of autocorrelation times τc for the 2π/3 reorientation. This broad distribution corresponds to a temperature independent Gaussian distribution of activation energies ρ(Ea) with variance σEa=13.8±0.5 meV (1.33 kJ/mol). The line shape transition between T=70 K and T=23 K is explained with the freezing in of the methyl group reorientation. By comparing our results in an 88% isotactic sample with results obtained from a 50% syndiotactic, 30% atactic, and 20% isotactic sample of a previous investigation, we demonstrate the higher local order of the 88% isotactic sample, which corresponds to a ratio of 1.6 in the relative width σEa/Ea of the Ea distribution. We show that different stereospecific forms of PMMA can be easily distinguished by the characteristics of their line shape transition between T=70 K and T=23 K.
Self-consistent mode-coupling theory for the viscosity of rodlike polyelectrolyte solutions
Authors: Miyazaki Kunimasa , Bagchi Biman , Yethiraj Arun
Published: October 2004

A self-consistent mode-coupling theory is presented for the viscosity of solutions of charged rodlike polymers. The static structure factor used in the theory is obtained from polymer integral equation theory; the Debye-Hückel approximation is inadequate even at low concentrations. The theory predicts a nonmonotonic dependence of the reduced excess viscosity ηR on concentration from the behavior of the static structure factor in polyelectrolyte solutions. The theory predicts that the peak in ηR occurs at concentrations slightly lower than the overlap threshold concentration, c*. The peak height increases dramatically with increasing molecular weight and decreases with increased concentrations of added salt. The position of the peak, as a function of concentration divided by c*, is independent of salt concentration or molecular weight. The predictions can be tested experimentally.
Electronic spectra of iron monohydride in the infrared near 1.35 and 1.58 μm
Authors: Balfour Walter J. , Brown John M. , Wallace Lloyd
Published: October 2004

The complex, many-line spectrum of FeH, lying in the infrared region between 5500 and 7500 cm−1, has been shown to consist of two separate electronic transitions: E 4Π-X 4Δ and E 4Π-A 4Π. High resolution Fourier transform spectra from thermal emission have been rotationally analyzed in detail. Lambda doubling in both the E 4Π and A 4Π states is considerable. The experimentally determined energies and bond lengths of the newly characterized states are in good agreement with theoretical predictions.
Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study
Authors: Mielke Steven P. , Fink William H. , Krishnan V. V. , Grønbech-Jensen Niels , Benham Craig J.
Published: October 2004

The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this paper, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of hydrodynamic beads interacting through potentials of linearly elastic stretching, bending, and twisting, as well as excluded volume. The chain, linear when relaxed, is looped to form two open but topologically constrained subdomains. This permits the dynamic introduction of torsional stress via a centrally applied torque. We simulate by Brownian dynamics the 100 μs response of a 477-base pair B-DNA template to the localized torque generated by the prokaryotic transcription ensemble. Following a sharp rise at early times, the distributed twist assumes a nearly constant value in both subdomains, and a succession of supercoiling deformations occurs as superhelical stress is increasingly partitioned to writhe. The magnitude of writhe surpasses that of twist before also leveling off when the structure reaches mechanical equilibrium with the torsional load. Superhelicity is simultaneously right handed in one subdomain and left handed in the other, as predicted by the “transcription-induced twin-supercoiled-domain” model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, 7024 (1987)]. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA.
Calculated optical and magnetic properties of hexafluorouranate (V) anion: UF6−
Authors: Arratia-Pérez Ramiro , Hernandez-Acevedo Lucia , Malli Gulzari L.
Published: October 2004

Our ab initio all-electron Dirac-Fock and the corresponding nonrelativistic limit calculations performed at four U-F bond distances yield for octahedral UF6− the optimized U-F bond distance of 2.091 and 2.088 Å, respectively. We have also performed Dirac scattered wave calculations at the optimized U-F bond distances using the first-order pertubational procedure to obtain the Zeeman and hyperfine magnetic tensors for the octahedral anion UF6−. The calculated isotropic Zeeman tensor of Δg=−2.87 is in fairly good agreement with the value of Δg=−2.78±0.10 obtained in electron spin resonance experiments on the H3O+UF6− adduct and the unpaired electron-spin spends ∼2.5% of its time on the fluorine 2p3/2 spinors. The calculated relativistic transition energies of the near-IR and visible absorption bands are also in good agreement with the experimental results. The octahedral uranium hexafluoride anion has a simple crystal field f1 configuration; however, relativistic four-component wave functions are necessary to interpret correctly the available magnetic data, while a relativistic treatment taking into account double group symmetrized basis functions should suffice for the interpretation of the optical data.
Accurate calculation of core-electron binding energies: Multireference perturbation treatment
Authors: Shirai Soichi , Yamamoto Satoru , Hyodo Shi-aki
Published: October 2004

Multireference perturbation theory (MRPT) with multiconfigurational self-consistent field (MCSCF) reference functions is applied to the calculations of core-electron binding energies (CEBEs) of atoms and molecules. Orbital relaxations in a core-ionized state and electron correlation are both taken into account in a conventional MCSCF-MRPT procedure. In the MCSCF calculation, the target core ionized state is directly optimized as an excited state and this treatment can completely prevent a variational collapse. Multireference Møller-Plesset perturbation theory and multiconfigurational self-consistent field reference quasidegenerated perturbation theory were used to treat electron correlation. The present method quite accurately reproduced the 1s CEBEs of CH4, NH3, H2O, and FH; the average deviation from the experimental data is 0.11 eV using Ahlrichs’ VTZ basis set. The C 1s and O 1s CEBEs of formic acid and acetic acid were calculated and the results are consistent with the bonding characters of the atoms in these molecules. The present procedure can also be applied to CEBEs of higher angular momentum orbitals by including spin-orbit coupling. The calculated CEBEs of Ar 2p, HCl 2p, Kr 3d, and HBr 3d are in reasonable agreement with the available experimental values. In the calculation of the 3d CEBEs, a relativistic correction significantly improves the agreements. The effect of polarization functions is also discussed.
Self-directed growth of benzonitrile line on H-terminated Si(001) surface
Authors: Lee Jung-Yup , Cho Jun-Hyung
Published: October 2004

Using first-principles density-functional calculations we predict a self-directed growth of benzonitrile molecular line on a H-terminated Si(001) surface. The C≡N bond of benzonitrile reacts with a single Si dangling bond which can be generated by the removal of a H atom, forming one Si–N bond and one C radical. Subsequently, the produced C radical can be stabilized by abstracting a H atom from a neighboring Si dimer, creating another H-empty site. This H-abstraction process whose activation barrier is 0.65 eV sets off a chain reaction to grow one-dimensional benzonitrile line along the Si dimer row. Our calculated energy profile for formation of the benzonitrile line shows its relatively easier formation compared with previously reported styrene and vinylferrocene lines.
Structure and rheological behavior of casein micelle suspensions during ultrafiltration process
Authors: Pignon F. , Belina G. , Narayanan T. , Paubel X. , Magnin A. , Gésan-Guiziou G.
Published: October 2004

The stability and mechanism underlying the formation of deposits of casein micelles during ultrafiltration process were investigated by small-angle and ultra small-angle x-ray scattering (SAXS and USAXS). The casein micelle dispersions consisted of phospho-caseinate model powders and the measurements probed length scales ranging from 1 to 2000 nm. Rheometric and frontal filtration measurements were combined with SAXS to establish the relationship between the rheological behavior of deposits (shear and/or compression) and the corresponding microstructure. The results revealed two characteristic length scales for the equilibrium structure with radius of gyrations Rg, about 100 and 5.6 nm pertaining to the globular micelles and their non-globular internal structure, respectively. The SAXS measurements further indicated that the increase of temperature from 20 to 70 °C or the decrease of pH from 6.6 to 6 lead to agglomeration of the globular micelles. In situ scattering measurements showed that the decrease of permeation flows is directly related to the deformation and compression of the micelles in the immediate vicinity of the membrane.
Ions in water: The microscopic structure of a concentrated HCl solution
Authors: Botti A. , Bruni F. , Imberti S. , Ricci M. A. , Soper A. K.
Published: October 2004

A neutron diffraction experiment with isotopic H/D substitution on a concentrated HCl/H2O solution is presented. The full set of partial structure factors is extracted, by combining the diffraction data with a Monte Carlo simulation. This allows us to investigate both the changes of the water structure in the presence of ions and their solvation shell, overcoming the limitations of standard diffraction experiments. It is found that the interaction with the solutes affects the tetrahedral network of hydrogen bonded water molecules, in a manner similar to the application of an external pressure to pure water, although HCl seems less effective than other solutes, such as NaOH, at the same concentration. Consistent with experimental and theoretical data, the number of water molecules in the solution is not sufficient to completely dissociate the acid molecule. As a consequence, both dissociated H+ and Cl− ions and undissociated HCl molecules coexist in the sample, and this mixture is correctly reproduced in the simulation box. In particular, the hydrated H+ ions, forming a H3O+ complex, participate in three strong and short hydrogen bonds, while a well-defined hydration shell is found around the chlorine ion. These results are not consistent with the findings of early diffraction experiments on the same system and could only be obtained by combining high quality experimental data with a proper computer simulation.
Melting points and thermal expansivities of proton-disordered hexagonal ice with several model potentials
Authors: Koyama Yuji , Tanaka Hideki , Gao Guangtu , Zeng X. C.
Published: October 2004

A method of free energy calculation is proposed, which enables to cover a wide range of pressure and temperature. The free energies of proton-disordered hexagonal ice (ice Ih) and liquid water are calculated for the TIP4P [J. Chem. Phys. 79, 926 (1983)] model and the TIP5P [J. Chem. Phys. 112, 8910 (2000)] model. From the calculated free energy curves, we determine the melting point of the proton-disordered hexagonal ice at 0.1 MPa (atmospheric pressure), 50 MPa, 100 MPa, and 200 MPa. The melting temperatures at atmospheric pressure for the TIP4P ice and the TIP5P ice are found to be about Tm=229 K and Tm=268 K, respectively. The melting temperatures decrease as the pressure is increased, a feature consistent with the pressure dependence of the melting point for realistic proton-disordered hexagonal ice. We also calculate the thermal expansivity of the model ices. Negative thermal expansivity is observed at the low temperature region for the TIP4P ice, but not for the TIP5P ice at the ambient pressure.
Bound state spectroscopy of NH–He
Authors: Kerenskaya Galina , Schnupf Udo , Heaven Michael C. , van der Avoird Ad
Published: October 2004

The NH–He van der Waals complex was characterized via laser excitation of bands associated with the NH A 3Π–X 3Σ− transition. It was demonstrated that the ground state supports a bound level with a rotational constant of B″=0.334(2) cm−1. These results are in agreement with the predictions of recent high-level theoretical calculations. Spin–orbit predissociation of the excited complex was observed, and the spectra yield insights regarding the NH(A)+He potential energy surfaces.
Forecast and control of epidemics in a globalized world
Authors: Hufnagel L. , Brockmann D. , Geisel T.
Published: October 2004

The rapid worldwide spread of severe acute respiratory syndrome demonstrated the potential threat an infectious disease poses in a closely interconnected and interdependent world. Here we introduce a probabilistic model that describes the worldwide spread of infectious diseases and demonstrate that a forecast of the geographical spread of epidemics is indeed possible. This model combines a stochastic local infection dynamics among individuals with stochastic transport in a worldwide network, taking into account national and international civil aviation traffic. Our simulations of the severe acute respiratory syndrome outbreak are in surprisingly good agreement with published case reports. We show that the high degree of predictability is caused by the strong heterogeneity of the network. Our model can be used to predict the worldwide spread of future infectious diseases and to identify endangered regions in advance. The performance of different control strategies is analyzed, and our simulations show that a quick and focused reaction is essential to inhibiting the global spread of epidemics.
Crystal structure of γ-glutamylcysteine synthetase: Insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis
Authors: Hibi Takao , Nii Hiroshi , Nakatsu Toru , Kimura Akira , Kato Hiroaki , Hiratake Jun , Oda Jun'ichi
Published: October 2004

γ-Glutamylcysteine synthetase (γGCS), a rate-limiting enzyme in glutathione biosynthesis, plays a central role in glutathione homeostasis and is a target for development of potential therapeutic agents against parasites and cancer. We have determined the crystal structures of
Escherichia coli
γGCS unliganded and complexed with a sulfoximine-based transition-state analog inhibitor at resolutions of 2.5 and 2.1 Å, respectively. In the crystal structure of the complex, the bound inhibitor is phosphorylated at the sulfoximido nitrogen and is coordinated to three Mg
2+
ions. The cysteine-binding site was identified; it is formed inductively at the transition state. In the unliganded structure, an open space exists around the representative cysteine-binding site and is probably responsible for the competitive binding of glutathione. Upon inhibitor binding, the side chains of Tyr-241 and Tyr-300 turn, forming a hydrogen-bonding triad with the carboxyl group of the inhibitor's cysteine moiety, allowing this moiety to fit tightly into the cysteine-binding site with concomitant accommodation of its side chain into a shallow pocket. This movement is caused by a conformational change of a switch loop (residues 240–249). Based on this crystal structure, the cysteine-binding sites of mammalian and parasitic γGCSs were predicted by multiple sequence alignment, although no significant sequence identity exists between the
E. coli
γGCS and its eukaryotic homologues. The identification of this cysteine-binding site provides important information for the rational design of novel γGCS inhibitors.
Melanin acts as a potent UVB photosensitizer to cause an atypical mode of cell death in murine skin
Authors: Takeuchi Seiji , Zhang Wengeng , Wakamatsu Kazumasa , Ito Shosuke , Hearing Vincent J. , Kraemer Kenneth H. , Brash Douglas E.
Published: October 2004

Melanin protects the skin against DNA damage induced by direct absorption of sunlight's UV radiation. Yet, irradiating melanin
in vitro
or in cultured cells also generates active oxygen species such as superoxide, which can indirectly induce oxidative base lesions and DNA strand breaks. This photosensitization is greater for pheomelanin (yellow and red melanin) than for eumelanin (brown and black). The
in vivo
photosensitizing ability of melanin is unknown. We used congenic mice of black, yellow, and albino coat colors to investigate the induction of DNA lesions and apoptosis after exposure to predominantly UVB (280–320 nm) or UVA (320–400 nm) radiation. Cyclobutane pyrimidine dimers induced by direct UVB absorption were equal in all three strains, as was apoptosis measured as sunburn cells or as keratinocytes containing active caspase-3. However, terminal deoxynucleotidyltransferase-mediated dUTP nick end-labeling (TUNEL)-positive cells were ≈3-fold more frequent in black and yellow mice after UVB or UVA irradiation than in albino. In epidermal sheets, TUNEL-positive cells lined the upper portion of the hair follicle, consistent with UV-induced photosensitization by melanin in the hair shaft. Because the concentration of eumelanin in black mice was three times that of pheomelanin in yellow mice, pheomelanin had 3-fold greater specific activity. We conclude that UV-irradiated melanin, particularly pheomelanin, photosensitizes adjacent cells to caspase-3 independent apoptosis, and this occurs at a frequency greater than the apoptosis induced by direct DNA absorption of UV. Melanin-induced apoptosis may contribute to the increased sensitivity of individuals with blonde and red hair to sunburn and skin cancer.
Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor
Authors: Vannini Alessandro , Volpari Cinzia , Filocamo Gessica , Casavola Elena Caroli , Brunetti Mirko , Renzoni Debora , Chakravarty Prasun , Paolini Chantal , De Francesco Raffaele , Gallinari Paola , Steinkühler Christian , Di Marco Stefania
Published: October 2004

Histone deacetylases (HDACs) are a family of enzymes involved in the regulation of gene expression, DNA repair, and stress response. These processes often are altered in tumors, and HDAC inhibitors have had pronounced antitumor activity with promising results in clinical trials. Here, we report the crystal structure of human HDAC8 in complex with a hydroxamic acid inhibitor. Such a structure of a eukaryotic zinc-dependent HDAC has not be described previously. Similar to bacterial HDAC-like protein, HDAC8 folds in a single α/β domain. The inhibitor and the zinc-binding sites are similar in both proteins. However, significant differences are observed in the length and structure of the loops surrounding the active site, including the presence of two potassium ions in HDAC8 structure, one of which interacts with key catalytic residues. CD data suggest a direct role of potassium in the fold stabilization of HDAC8. Knockdown of HDAC8 by RNA interference inhibits growth of human lung, colon, and cervical cancer cell lines, highlighting the importance of this HDAC subtype for tumor cell proliferation. Our findings open the way for the design and development of selective inhibitors of HDAC8 as possible antitumor agents.
Upstream binding factor association induces large-scale chromatin decondensation
Authors: Chen Danyang , Belmont Andrew S. , Huang Sui
Published: October 2004

The function of upstream binding factor (UBF), an essential component of the RNA polymerase (pol) I preinitiation complex, is unclear. Recently, UBF was found distributed throughout ribosomal gene repeats rather than being restricted to promoter regions. This observation has led to the speculation that one role of UBF binding may be to induce chromatin remodeling. To directly evaluate the impact of UBF on chromatin structure, we used an
in vivo
assay in which UBF is targeted via a lac repressor fusion protein to a heterochromatic, amplified chromosome region containing lac operator repeats. We show that the association of UBF with this locus induces large-scale chromatin decondensation. This process does not appear to involve common remodeling complexes, including SWI/SNF and histone acetyltransferases, and is independent of histone H3 lysine 9 acetylation. However, UBF recruits the pol I-specific, TATA box-binding protein containing complex SL1 and pol I subunits. Our results suggest a working hypothesis in which the dynamic association of UBF with ribosomal DNA clusters recruits the pol I transcription machinery and maintains these loci in a transcriptionally competent configuration. These studies also provide an
in vivo
model simulating ribosomal DNA transactivation outside the nucleolus, allowing temporal and spatial analyses of chromatin remodeling and assembly of the pol I transcription machinery.
Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease
Authors: Kirino Yohei , Yasukawa Takehiro , Ohta Shigeo , Akira Shigeo , Ishihara Kaisuke , Watanabe Kimitsuna , Suzuki Tsutomu
Published: October 2004

Point mutations in the mitochondrial (mt) tRNA
Leu(UUR)
gene are responsible for mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), a subgroup of mitochondrial encephalomyopathic diseases. We previously showed that mt tRNA
Leu(UUR)
with an A3243G or T3271C mutation derived from patients with MELAS are deficient in a normal taurine-containing modification (τm
5
U; 5-taurinomethyluridine) at the anticodon wobble position. To examine decoding disorder of the mutant tRNA due to the wobble modification deficiency independent of the pathogenic point mutation itself, we used a molecular surgery technique to construct an mt tRNA
Leu(UUR)
molecule lacking the taurine modification but without the pathogenic mutation. This “operated” mt tRNA
Leu(UUR)
without the taurine modification showed severely reduced UUG translation but no decrease in UUA translation. We thus concluded that the UUG codon–specific translational defect of the mutant mt tRNAs
Leu(UUR)
is the primary cause of MELAS at the molecular level. This result could explain the complex I deficiency observed clinically in MELAS.
The host response to smallpox: Analysis of the gene expression program in peripheral blood cells in a nonhuman primate model
Authors: Rubins Kathleen H. , Hensley Lisa E. , Jahrling Peter B. , Whitney Adeline R. , Geisbert Thomas W. , Huggins John W. , Owen Art , LeDuc James W. , Brown Patrick O. , Relman David A.
Published: October 2004

Smallpox has played an unparalleled role in human history and remains a significant potential threat to public health. Despite the historical significance of this disease, we know little about the underlying pathophysiology or the virulence mechanisms of the causative agent, variola virus. To improve our understanding of variola pathogenesis and variola-host interactions, we examined the molecular and cellular features of hemorrhagic smallpox in cynomolgus macaques. We used cDNA microarrays to analyze host gene expression patterns in sequential blood samples from each of 22 infected animals. Variola infection elicited striking and temporally coordinated patterns of gene expression in peripheral blood. Of particular interest were features that appear to represent an IFN response, cell proliferation, immunoglobulin gene expression, viral dose-dependent gene expression patterns, and viral modulation of the host immune response. The virtual absence of a tumor necrosis factor α/NF-κB-activated transcriptional program in the face of an overwhelming systemic infection suggests that variola gene products may ablate this response. These results provide a detailed picture of the host transcriptional response during smallpox infection, and may help guide the development of diagnostic, therapeutic, and prophylactic strategies.
IL-15/IL-15Rα-mediated avidity maturation of memory CD8+T cells
Authors: Oh SangKon , Perera Liyanage P. , Burke Donald S. , Waldmann Thomas A. , Berzofsky Jay A.
Published: October 2004

T cell avidity is critical to viral clearance, but mechanisms of CD8+T cell avidity maturation are poorly understood. Here, we find that IL-15 mediates two mechanisms of avidity maturation. (i) By selection at the population level, IL-15 promotes greater survival of high- compared with low-avidity cytotoxic T lymphocytes (CTLs). High-avidity CTLs express higher levels of IL-15Rα and persist longer by homeostatic proliferation. (ii) At the individual cell level, IL-15 induces higher levels of surface coreceptor CD8αβ, increasing functional avidity. IL-15 during priming selects or induces higher-avidity CTLs. Conversely, high-avidity CTLs are diminished in IL-15Rα knockout mice. These results provide an explanation of CD8+T cell avidity maturation and may contribute to the design of novel vaccines.
Cell division and cell survival in the absence of survivin
Authors: Yang Dun , Welm Alana , Bishop J. Michael
Published: October 2004

The survivin protein contains structural features of the inhibitor of apoptosis protein family. Previous studies have suggested that survivin is essential for cell survival because it counteracts an otherwise constitutive propensity to apoptosis during mitosis. In addition, survivin appears to be a component of the chromosomal passenger protein complex that participates in multiple facets of cell division. Here we report that euploid human cells do not die in the absence of survivin. Instead, depletion of survivin caused defects in cell division, followed by an arrest of DNA synthesis due to activation of a checkpoint involving the tumor suppressor protein p53. During anaphase mitosis in survivin-deficient cells, sister chromatids disjoined normally, but one or more of the sister chromatids frequently lagged behind the main mass of segregating chromosomes, probably because of merotelic kinetochore attachments. Survivin-deficient cells initiated but failed to complete cytokinesis, apparently because the spindle midzone and midbody microtublues were absent during late mitosis. The abnormalities of both chromosome segregation and cytokinesis could be attributed to a defect in the chromosomal passenger protein complex, with a consequent mislocalization of the kinesin-like motor protein MKLP-1 playing a more immediate role in the microtubule abnormalities. Depletion of another chromosomal passenger protein, aurora-B, recapitulated the survivin RNA interference phenotypes. We conclude that survivin can be essential for the proliferation of normal human cells by virtue of its contributions to accurate sister chromatid segregation and assembly/stabilization of microtubules in late mitosis. However, the protein is not inevitably required for the survival of normal cells.
Transforming growth factor β-induced cell cycle arrest of human hematopoietic cells requires p57KIP2 up-regulation
Authors: Scandura Joseph M. , Boccuni Piernicola , Massagué Joan , Nimer Stephen D.
Published: October 2004

Transforming growth factor β (TGFβ) is one of few known negative regulators of hematopoiesis, yet the mechanisms by which it affects cell cycle arrest and stem cell quiescence are poorly understood. Induction of the cyclin-dependent kinase inhibitors, p15INK4b (p15) and p21WAF1 (p21) is important for TGFβ-mediated cytostasis in epithelial cells but not in hematopoietic cells. Using primary human hematopoietic cells and microarray analysis, we identified p57KIP2 (p57) as the only cyclin-dependent kinase inhibitor induced by TGFβ. Up-regulation of p57 mRNA and protein occurs before TGFβ-induced G
1
cell cycle arrest, requires transcription, and is mediated via a highly conserved region of the proximal p57 promoter. The up-regulation of p57 is essential for TGFβ-induced cell cycle arrest in these cells, because two different small interfering RNAs that prevent p57 up-regulation block the cytostatic effects of TGFβ on human hematopoietic cells. Reduction of basal p57 expression by this approach also allows hematopoietic cells to proliferate more readily in the absence of TGFβ. p57 is a putative tumor suppressor gene whose expression is frequently silenced by promoter hypermethylation in hematologic malignancies. Our studies identify a molecular pathway by which TGFβ mediates its cytostatic effects on human hematopoietic cells and suggests an explanation for the frequent silencing of p57 expression.
Retinal Endothelial Angiogenic Activity: Effects of Hypoxia and Glial (Müller) Cells
Authors: YAFAI YOUSEF , IANDIEV IANORS , WIEDEMANN PETER , REICHENBACH ANDREAS , EICHLER WOLFRAM
Published: October 2004

Objective: To explore the impact of retinal glial (Müller) cells on survival and neovascularization‐related activities of cultured retinal endothelial cells under normoxic and hypoxic conditions.

Methods: Bovine retinal endothelial cells (BRECs) were cultured under normoxia or hypoxia (0.5% O2) either alone, together with the human Müller cell line MIO‐M1, or in normoxia‐ or hypoxia‐conditioned media of MIO‐M1 cells. Cell number, proliferation, apoptotic cell death, and migration of BRECs were determined.

Results: Exposure of BRECs to hypoxia for 24 h decreased the number of adherent cells and the proliferation rate, but increased apoptosis and cell migration. Increased apoptosis and decreased proliferation of the BRECs occurred also in the presence of conditioned media of MIO‐M1 cells. Under normoxic conditions, co‐culture with MIO‐M1 cells resulted in increased proliferation, but decreased apoptosis and migration rates of BRECs. Under hypoxic conditions, the Müller cells released elevated amounts of VEGF but their presence decreased proliferation, apoptosis and the migration rates of BRECs.

Conclusions: Hypoxia inhibits the proliferation of retinal endothelial cells. Müller cells release soluble mediators that enhance this hypoxia‐mediated effect but, under certain conditions (i.e., in co‐culture), may protect retinal endothelial cells from apoptosis, thus supporting their survival. Altogether the findings indicate that the key signal necessary to trigger retinal endothelial proliferation under hypoxia remains to be determined.
Ethanol Binging Enhances Hepatic Microvascular Responses to Acetaminophen in Mice
Authors: ITO YOSHIYA , ABRIL EDWARD R. , BETHEA NANCY W. , MCCUSKEY ROBERT S.
Published: October 2004

Objective: Chronic alcoholism has been considered to be a risk for acetaminophen (APAP) hepatotoxicity, but little is known about the effect of binge alcohol drinking on APAP‐induced liver injury. The present study was conducted to examine the effect of ethanol binging on APAP‐induced hepatic microcirculatory dysfunction.

Methods: Male C57Bl/6 mice received 3 weekly ethanol binges (4 g/kg every 12 h × 5 doses/ week) or water binges. At 12 h after the last gavage, APAP (300 mg/kg) was given by oral gavage. In one group of mice, gadolinium chloride (GdCl3, 10 mg/kg) was intraperitoneally administered 2 and 1 days before the start of each weekly ethanol binge.

Results: Ethanol binging enhanced APAP‐induced liver injury as indicated by ALT levels. Intravital microscopic study showed that APAP further increased the area occupied by infiltrated erythrocytes into the extrasinusoidal space as well as Kupffer cell phagocytic activity in ethanol‐binged mice when compared with water‐binged mice, while no significant differences in sinusoidal perfusion and leukocyte adhesion were observed. ALT levels after APAP were exacerbated in ethanol‐binged mice treated with GdCl3, but APAP‐induced hepatic microcirculatory dysfunction was not changed significantly.

Conclusions: These results suggest that ethanol binging increases APAP‐induced liver injury by exacerbating infiltration of the Disse space with blood cells. Kupffer cells exert a protective role in the liver against APAP intoxication following ethanol binging.
Spermidine/spermine N1-acetyltransferase specifically binds to the integrin α9 subunit cytoplasmic domain and enhances cell migration
Authors: Chen Chun , Young Bradford A. , Coleman Catherine S. , Pegg Anthony E. , Sheppard Dean
Published: October 2004

The integrin α9β1 is expressed on migrating cells, such as leukocytes, and binds to multiple ligands that are present at sites of tissue injury and inflammation. α9β1, like the structurally related integrin α4β1, mediates accelerated cell migration, an effect that depends on the α9 cytoplasmic domain. α4β1 enhances migration through reversible binding to the adapter protein, paxillin, but α9β1-dependent migration is paxillin independent. Using yeast two-hybrid screening, we identified the polyamine catabolizing enzyme spermidine/spermine N1-acetyltransferase (SSAT) as a specific binding partner of the α9 cytoplasmic domain. Overexpression of SSAT increased α9β1-mediated migration, and small interfering RNA knockdown of SSAT inhibited this migration without affecting cell adhesion or migration that was mediated by other integrin cytoplasmic domains. The enzyme activity of SSAT is critical for this effect, because a catalytically inactive version did not enhance migration. We conclude that SSAT directly binds to the α9 cytoplasmic domain and mediates α9-dependent enhancement of cell migration, presumably by localized effects on acetylation of polyamines or of unidentified substrates.
COPII-dependent export of cystic fibrosis transmembrane conductance regulator from the ER uses a di-acidic exit code
Authors: Wang Xiaodong , Matteson Jeanne , An Yu , Moyer Bryan , Yoo Jin-San , Bannykh Sergei , Wilson Ian A. , Riordan John R. , Balch William E.
Published: October 2004

Cystic fibrosis (CF) is a childhood hereditary disease in which the most common mutant form of the CF transmembrane conductance regulator (CFTR) ΔF508 fails to exit the endoplasmic reticulum (ER). Export of wild-type CFTR from the ER requires the coat complex II (COPII) machinery, as it is sensitive to Sar1 mutants that disrupt normal coat assembly and disassembly. In contrast, COPII is not used to deliver CFTR to ER-associated degradation. We find that exit of wild-type CFTR from the ER is blocked by mutation of a consensus di-acidic ER exit motif present in the first nucleotide binding domain. Mutation of the code disrupts interaction with the COPII coat selection complex Sec23/Sec24. We propose that the di-acidic exit code plays a key role in linking CFTR to the COPII coat machinery and is the primary defect responsible for CF in ΔF508-expressing patients.
Rap1 promotes cell spreading by localizing Rac guanine nucleotide exchange factors
Authors: Arthur William T. , Quilliam Lawrence A. , Cooper Jonathan A.
Published: October 2004

The Ras-related GTPase Rap1 stimulates integrin-mediated adhesion and spreading in various mammalian cell types. Here, we demonstrate that Rap1 regulates cell spreading by localizing guanine nucleotide exchange factors (GEFs) that act via the Rho family GTPase Rac1. Rap1a activates Rac1 and requires Rac1 to enhance spreading, whereas Rac1 induces spreading independently of Rap1. Active Rap1a binds to a subset of Rac GEFs, including VAV2 and Tiam1 but not others such as SWAP-70 or COOL-1. Overexpressed VAV2 and Tiam1 specifically require Rap1 to promote spreading, even though Rac1 is activated independently of Rap1. Rap1 is necessary for the accumulation of VAV2 in membrane protrusions at the cell periphery. In addition, if VAV2 is artificially localized to the cell edge with the subcellular targeting domain of Rap1a, it increases cell spreading independently of Rap1. These results lead us to propose that Rap1 promotes cell spreading by localizing a subset of Rac GEFs to sites of active lamellipodia extension.
Adherens junction-dependent and -independent steps in the establishment of epithelial cell polarity in Drosophila
Authors: Harris Tony J.C. , Peifer Mark
Published: October 2004

Adherens junctions (AJs) are thought to be key landmarks for establishing epithelial cell polarity, but the origin of epithelial polarity in Drosophila remains unclear. Thus, we examined epithelial polarity establishment during early Drosophila development. We found apical accumulation of both Drosophila E-Cadherin (DE-Cad) and the apical cue Bazooka (Baz) as cells first form. Mutant analyses revealed that apical Baz accumulations can be established in the absence of AJs, whereas assembly of apical DE-Cad complexes requires Baz. Thus, Baz acts upstream of AJs during epithelial polarity establishment. During gastrulation the absence of AJs results in widespread cell dissociation and depolarization. Some epithelial structures are retained, however. These structures maintain apical Baz, accumulate apical Crumbs, and organize polarized cytoskeletons, but display abnormal cell morphology and fail to segregate the basolateral cue Discs large from the apical domain. Thus, although epithelial polarity develops in the absence of AJs, AJs play specific roles in maintaining epithelial architecture and segregating basolateral cues.
Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response
Authors: Lu Phoebe D. , Harding Heather P. , Ron David
Published: October 2004

Stress-induced eukaryotic translation initiation factor 2 (eIF2) α phosphorylation paradoxically increases translation of the metazoan activating transcription factor 4 (ATF4), activating the integrated stress response (ISR), a pro-survival gene expression program. Previous studies implicated the 5′ end of the ATF4 mRNA, with its two conserved upstream ORFs (uORFs), in this translational regulation. Here, we report on mutation analysis of the ATF4 mRNA which revealed that scanning ribosomes initiate translation efficiently at both uORFs and ribosomes that had translated uORF1 efficiently reinitiate translation at downstream AUGs. In unstressed cells, low levels of eIF2α phosphorylation favor early capacitation of such reinitiating ribosomes directing them to the inhibitory uORF2, which precludes subsequent translation of ATF4 and represses the ISR. In stressed cells high levels of eIF2α phosphorylation delays ribosome capacitation and favors reinitiation at ATF4 over the inhibitory uORF2. These features are common to regulated translation of GCN4 in yeast. The metazoan ISR thus resembles the yeast general control response both in its target genes and its mechanistic details.
The Cytomegalovirus m155 Gene Product Subverts Natural Killer Cell Antiviral Protection by Disruption of H60–NKG2D Interactions
Authors: Lodoen Melissa B. , Abenes Gerardo , Umamoto Sean , Houchins Jeffrey P. , Liu Fenyong , Lanier Lewis L.
Published: October 2004

Natural killer (NK) cells are an important early mediator of host immunity to murine cytomegalovirus (MCMV) infection. However, MCMV has evolved mechanisms to elude recognition and clearance by NK cells. We have identified an MCMV immune evasion protein that impairs NKG2D-mediated NK cell antiviral activity. Infection of BALB/c 3T3 cells with the Smith strain of MCMV resulted in strong down-regulation of H60, a high affinity ligand for NKG2D, from the surface of virus-infected cells. The MCMV m155 protein specifically down-regulated H60 without affecting expression of the other known NKG2D ligands, RAE-1 and MULT-1. Treatment with the proteasome inhibitors lactacystin or epoxomicin reversed m155 down-regulation of H60. An MCMV mutant virus lacking m155 was severely attenuated in BALB/c mice; however, treatment with neutralizing anti-NKG2D monoclonal antibody or with NK-depleting anti-asialo GM1 antisera restored virulence of the mutant virus. Thus, down-regulation of H60 by m155 is a powerful mechanism of inhibiting NKG2D-mediated antiviral function.