bluuebunny/crossref_metadata_2025 huggingface dataset:
Laboratory studies of magnetic vortices. I. Directional radiation of whistler waves based on helicity injection
Authors: Stenzel R. L. , Urrutia J. M.
Published: July 2002

A novel principle for the directional excitation of whistler waves is demonstrated in a laboratory experiment. It is based on helicity conservation of electron magnetohydrodynamic fields in plasmas. Whistler wave packets propagating in opposite directions to a static magnetic field have opposite signs of helicity. Injection of helicity of one sign produces radiation in one direction. This is accomplished with an antenna consisting of a loop linked through a torus. Directionality of 20 dB is readily achieved. The direction of radiation is electronically reversible. Transmission between two antennas is unidirectional, hence nonreciprocal. Possible applications include secure communication, direction finding, and efficient power deposition in radio frequency (rf) heating.
Single-mode, Rayleigh-Taylor growth-rate measurements on the OMEGA laser system
Authors: Knauer J. P. , Betti R. , Bradley D. K. , Boehly T. R. , Collins T. J. B. , Goncharov V. N. , McKenty P. W. , Meyerhofer D. D. , Smalyuk V. A. , Verdon C. P. , Glendinning S. G. , Kalantar D. H. , Watt R. G.
Published: July 2002

The results from a series of single-mode, Rayleigh–Taylor (RT) instability growth experiments performed on the OMEGA laser system [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)] using planar targets are reported. Planar targets with imposed mass perturbations were accelerated using five or six 351 nm laser beams overlapped with total intensities up to 2.5×1014 W/cm2. Experiments were performed with both 3 ns ramp and 3 ns flat-topped temporal pulse shapes. The use of distributed phase plates and smoothing by spectral dispersion resulted in a laser-irradiation nonuniformity of 4%–7% over a 600 μm diam region defined by the 90% intensity contour. The temporal growth of the modulation in optical depth was measured using throughfoil radiography and was detected with an x-ray framing camera for CH targets. Two-dimensional (2-D) hydrodynamic simulations (ORCHID) [R. L. McCrory and C. P. Verdon, in Inertial Confinement Fusion (Editrice Compositori, Bologna, 1989), pp. 83–124] of the growth of 20, 31, and 60 μm wavelength perturbations were in good agreement with the experimental data when the experimental details, including noise, were included. The amplitude of the simulation optical depth is in good agreement with the experimental optical depth; therefore, great care must be taken when the growth rates are compared to dispersion formulas. Since the foil’s initial condition just before it is accelerated is not that of a uniformly compressed foil, the optical density measurement does not accurately reflect the amplitude of the ablation surface but is affected by the initial nonuniform density profile.
The origin of primeval magnetic fields: Self-consistent simulation of magnetic field generation and amplification
Authors: Wiechen H. , Birk G. T. , Lesch H.
Published: July 2002

A self-consistent numerical model of self-generation and amplification of magnetic fields in weakly ionized protogalactic matter is presented. This model is based on three-dimensional two-fluid simulations of the dynamics expected for protogalactic plasma–neutral gas clouds characterized by shear flow. Due to the friction between the ionized and neutral gas components self-generated magnetic fields of seed field order, i.e., 10−17 G are created on time scales of 105 yr. Moreover, unstable Kelvin–Helmholtz modes are excited yielding a significant amplification of the field.
Generalized Langmuir waves in magnetized kinetic plasmas
Authors: Willes A. J. , Cairns Iver H.
Published: July 2002

The properties of unmagnetized Langmuir waves and cold plasma magnetoionic waves (x, o, z and whistler) are well known. However, the connections between these modes in a magnetized kinetic plasma have not been explored in detail. Here, wave properties are investigated by numerically solving the dispersion equation derived from the Vlasov equations both with and without a beam instability present. For ωp>Ωe, it is shown that the generalized Langmuir mode at oblique propagation angles has magnetic z-mode characteristics at low wave numbers and thermal Langmuir mode characteristics at high wave numbers. For ωp<Ωe, it is shown that the (oblique) Langmuir mode instead connects to the whistler mode at low wave numbers. The transition from the Langmuir/z mode to the Langmuir/whistler mode near ωp=Ωe is rapid. In addition, the effects on wave dispersion and polarization after adding a beam are investigated. Applications of this theory to magnetized Langmuir waves in Earth’s foreshock and the solar wind, to waves observed near the plasma frequency in the auroral regions, and to solar type III bursts are discussed.
A reciprocity theorem for charge collection
Authors: Donolato C.
Published: July 2002

It is shown that the current collected by a p-n junction in presence of a unit point generation of carriers at a point P is the same (apart from the dimensions) as the excess minority-carrier density at P due to a unit density of carriers at the junction edge. Use of this reciprocity relation may simplify the calculation of beam induced currents in semiconductor devices. The practical meaning of this property is illustrated in the case of a light-emitting diode containing defects.
Evidence of a charge induced contribution to the sputtering yield of insulating and semiconducting materials
Authors: Eccles A. J. , van den Berg J. A. , Brown A. , Vickerman J. C.
Published: July 2002

Following the recent observation in this laboratory of a charge induced damage effect in insulators under inert gas ion bombardment, the influence of the charge state of the beam (ion or atom) on the sputtering yield of insulating and semiconducting materials has been investigated. A series of sputter measurements has been carried out on Au, Ta2O5, Si, GaAs, and glass using calibrated ion and atom fluxes. For this purpose a recently developed gun capable of producing raster-scanned, microfocused energetic ion or atom beams was employed. While for the conductor Au, as expected, no effect was seen, for the remaining materials sputter yield increases of up to 150% were observed under ion bombardment which implies the existence of a substantial electronic sputtering effect in insulators and semiconductors due to low-energy ion bombardment.
Effective saturable absorber for KrF lasers
Authors: Bigio Irving J. , Thomas Scott J.
Published: July 2002

We report what we believe is the first demonstration of an effective and scalable saturable absorber for KrF lasers. Our measurements show that a 10-cm path length of ozone (O3) at a partial pressure ∼1 Torr will attenuate a flux of less than 50 mJ/cm2 by a factor ∼50 (∼2% transmission), while allowing transmission of ∼90% for energy densities above 1 J/cm2.
Two-photon excitation of molecular hydrogen and stimulated emission in the vacuum ultraviolet
Authors: Döbele H. F. , Hörl M. , Röwekamp M.
Published: July 2002

Narrow-bandwidth 193-nm radiation is generated by stimulated Raman scattering and amplified in ArF to ≊100 mJ in a ≊5-ns pulse. Two-photon excitation of H2 results in 23 vacuum-ultraviolet lines down to 117 nm.
Damage calculation and measurement for GaAs amorphized by Si implantation
Authors: Opyd W. G. , Gibbons J. F. , Bravman J. C. , Parker M. A.
Published: July 2002

Extended defects in GaAs are investigated following epitaxial regrowth of amorphous layers. GaAs surface layers were amorphized by Si+ implants at liquid-nitrogen temperature. Anneals were performed for 4 s to 30 min from 150 to 885 °C. Rutherford backscattering spectrometry and transmission electron microscopy were used to evaluate the results of annealing. Complete solid-state epitaxy occurs rapidly at low temperature. Stacking faults and microtwins surrounded by dislocation networks extend to the surface following regrowth. The dislocations anneal at varying rates over intermediate temperature ranges (200–700 °C), and the microtwins climb out at higher temperatures (>700 °C). Defect depth profiles are correlated with damage and stoichiometric imbalances computed by the Boltzmann transport equation approach to ion-implant modeling.
High current density hollow cathode electron beam source
Authors: Rocca J. J. , Szapiro B. , Verhey T.
Published: July 2002

An electron beam with current density greater than 30 A/cm2 and total current of 92 A has been generated in 5 μs pulses by accelerating the electrons from a glow discharge in a narrow gap between two grids. The ratio of the extracted electron beam current to discharge current is approximately 1. The gun also operates in a dc mode.
Cr- and Cu-polyimide interface: Chemistry and structure
Authors: White R. C. , Haight R. , Silverman B. D. , Ho P. S.
Published: July 2002

High-resolution x-ray and ultraviolet photoemission spectroscopies have been applied to study the initial formation of the Cr- and Cu-polyimide interfaces. A model for the growth modes of these two interfaces is proposed based on comparison of experimental results with trends derived from quantum-chemical calculations.
Influence of implant induced vacancies and interstitials on boron diffusion in silicon
Authors: Solmi S. , Angelucci R. , Cembali F. , Servidori M. , Anderle M.
Published: July 2002

A dependence of boron anomalous diffusion on defect depth position has been observed after furnace and electron beam annealing of samples damaged with 28Si ions implanted at different energies. This behavior was correlated with the vacancy and interstitial excesses, produced under bombardment in the surface region and in depth, respectively. The spatial separation of these point defects was evidenced by the analysis of the intensity profiles obtained by double-crystal x-ray diffraction.
Precipitation of impurities in GaAs amorphized by ion implantation
Authors: Opyd W. G. , Gibbons J. F. , Mardinly A. J.
Published: July 2002

Impurities in a GaAs layer that had been amorphized by ion implantation were observed to precipitate upon annealing. Photoluminescence spectra indicated that the resulting high electrical resistivity could be attributed to the formation of neutral impurity complexes rather than a compensation mechanism. Impurities studied were implanted Si and Se. Transmission electron microscopy and x-ray microanalysis were used to identify impurity precipitates and related stacking fault tetrahedra. These results correlate with similar examples of poor activation for impurities in GaAs grown by low-temperature molecular beam epitaxy.
A poxvirus-like type IB topoisomerase family in bacteria
Authors: Krogh Berit Olsen , Shuman Stewart
Published: July 2002

We report that diverse species of bacteria encode a type IB DNA topoisomerase that resembles vaccinia virus topoisomerase.
Deinococcus radiodurans
topoisomerase IB (DraTopIB), an exemplary member of this family, relaxes supercoiled DNA in the absence of a divalent cation or ATP. DraTopIB has a compact size (346 aa) and is a monomer in solution. Mutational analysis shows that the active site of DraTopIB is composed of the same constellation of catalytic side chains as the vaccinia enzyme. Sequence comparisons and limited proteolysis suggest that their folds are conserved. These findings imply an intimate evolutionary relationship between the poxvirus and bacterial type IB enzymes, and they engender a scheme for the evolution of topoisomerase IB and tyrosine recombinases from a common ancestral strand transferase in the bacterial domain. Remarkably, bacteria that possess topoisomerase IB appear to lack DNA topoisomerase III.
Constitutive expression of a single antimicrobial peptide can restore wild-type resistance to infection in immunodeficient
Drosophila
mutants
Authors: Tzou Phoebe , Reichhart Jean-Marc , Lemaitre Bruno
Published: July 2002

One of the characteristics of the host defense of insects is the rapid synthesis of a variety of potent antibacterial and antifungal peptides. To date, seven types of inducible antimicrobial peptides (AMPs) have been characterized in
Drosophila
. The importance of these peptides in host defense is supported by the observation that flies deficient for the Toll or Immune deficiency (Imd) pathway, which affects AMP gene expression, are extremely susceptible to microbial infection. Here we have developed a genetic approach to address the functional relevance of a defined antifungal or antibacterial peptide in the host defense of
Drosophila
adults. We have expressed AMP genes via the control of the UAS/GAL4 system in
imd
;
spätzle
double mutants that do not express any known endogenous AMP gene. Our results clearly show that constitutive expression of a single peptide in some cases is sufficient to rescue
imd
;
spätzle
susceptibility to microbial infection, highlighting the important role of AMPs in
Drosophila
adult host defense.
A DAF-1-binding protein BRA-1 is a negative regulator of DAF-7 TGF-β signaling
Authors: Morita Kiyokazu , Shimizu Miho , Shibuya Hiroshi , Ueno Naoto
Published: July 2002

We have identified homologs of a human BMP receptor-associated
molecule BRAM1 in
Caenorhabditis
elegans
. One of them, BRA-1, has been found to bind DAF-1, the
type I receptor in the DAF-7 transforming growth factor-β pathway
through the conserved C-terminal region. As analyzed using a
BRA-1∷GFP (green fluorescent protein) fusion gene product, the
bra-1
gene is expressed in amphid neurons such as ASK,
ASI, and ASG, where
daf-1
is also expressed. A
loss-of-function mutation in
bra-1
exhibits robust
suppression of the Daf-c phenotype caused by the DAF-7 pathway
mutations. We propose that BRA-1 represents a novel class of
receptor-associated molecules that negatively regulate transforming
growth factor-β pathways.
Dynamical principles in biological processes: A model of charge migration in proteins and DNA
Authors: Schlag E. W. , Yang D.-Y. , Sheu S.-Y. , Selzle H. L. , Lin S. H. , Rentzepis P. M.
Published: July 2002

The generalized master equations (GMEs) that contain multiple time scales have been derived quantum mechanically. The GME method has then been applied to a model of charge migration in proteins that invokes the hole hopping between local amino acid sites driven by the torsional motions of the floppy backbones. This model is then applied to analyze the experimental results for sequence-dependent long-range hole transport in DNA reported by Meggerset al.[Meggers, E., Michel-Beyerle, M. E., & Giese, B. (1998)J. Am. Chem. Soc.120, 12950–12955]. The model has also been applied to analyze the experimental results of femtosecond dynamics of DNA-mediated electron transfer reported by Zewail and co-workers [Wan, C., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J. K. & Zewail, A. H. (1999)Proc. Natl. Acad. Sci. USA96, 6014–6019]. The initial events in the dynamics of protein folding have begun to attract attention. The GME obtained in this paper will be applicable to this problem.
Kinetic and thermodynamic control of protein adsorption
Authors: Satulovsky J. , Carignano M. A. , Szleifer I.
Published: July 2002

Control of nonspecific protein adsorption is very important for the design of biocompatible and biomimetic materials as well as drug carriers. Grafted polymer layers can be used to prevent protein adsorption. We have studied the molecular factors that determine the equilibrium and kinetic control of protein adsorption by grafted polymer layers. We find that polymers that are not attracted to the surface are very effective for kinetic control but not very good for equilibrium reduction of protein adsorption. Polymers with attractions to the surface show exactly the opposite behavior. The implications for molecular design of biocompatible materials also are discussed in this paper.
Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II
Authors: Carty Sherry M. , Goldstrohm Aaron C. , Suñé Carles , Garcia-Blanco Mariano A. , Greenleaf Arno L.
Published: July 2002

An approach for purifying nuclear proteins that bind directly to the hyperphosphorylated C-terminal repeat domain (CTD) of RNA polymerase II was developed and used to identify one human phosphoCTD-associating protein as CA150. CA150 is a nuclear factor implicated in transcription elongation. Because the hyperphosphorylated CTD is a feature of actively transcribing RNA polymerase II (Pol II), phosphoCTD (PCTD) binding places CA150 in a location appropriate for performing a role in transcription elongation-related events. Several recombinant segments of CA150 bound the PCTD. Predominant binding is mediated by the portion of CA150 containing six FF domains, compact modules of previously unknown function. In fact, small recombinant proteins containing the fifth FF domain bound the PCTD. PCTD binding is the first specific function assigned to an FF domain. As FF domains are found in a variety of nuclear proteins, it is likely that some of these proteins are also PCTD-associating proteins. Thus FF domains appear to be compact protein-interaction modules that, like WW domains, can be evolutionarily shuffled to organize nuclear function.
An unsuspected autoregulatory pathway involving apocytochrome TorC and sensor TorS in
Escherichia coli
Authors: Gon Stéphanie , Jourlin-Castelli Cécile , Théraulaz Laurence , Méjean Vincent
Published: July 2002

Trimethylamine
N
-oxide (TMAO) respiration is carried
out mainly by the Tor system in
Escherichia coli
. This
system is encoded by the
torCAD
operon and comprises a
periplasmic TMAO reductase (TorA) and a
c
-type
cytochrome (TorC), which shuttles electrons to TorA. Expression of the
tor
operon is positively controlled by the
TorS/TorR phosphorelay system in response to TMAO availability
and negatively regulated by apocytochrome TorC. Interaction studies
showed that, when immature, TorC can no longer bind TorA efficiently
but can bind the periplasmic detector region of sensor TorS. ApoTorC
negative autoregulation and TMAO induction are thus mediated by the
same sensor protein. As apocytochromes related to TorC could not
down-regulate the
tor
operon, we concluded that this
negative control is highly specific. Moreover, the N-terminal half of
apoTorC played no role in this control but the immature C-terminal
domain of TorC strongly down-regulated the
tor
operon
and interacted with the TorS detector region. This sophisticated
autoregulatory pathway thus involves the C-terminal domain of apoTorC
and allows optimal TorC biogenesis by preventing from saturation the
c
-type cytochrome maturation machinery.
Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns
Authors: Fedorov Alexei , Cao Xiaohong , Saxonov Serge , de Souza Sandro J. , Roy Scott W. , Gilbert Walter
Published: July 2002

Do introns delineate elements of protein tertiary structure? This issue is crucial to the debate about the role and origin of introns. We present an analysis of the full set of proteins with known three-dimensional structures that have homologs with intron positions recorded in GenBank. A computer program was generated that maps on a reference sequence the positions of all introns in homologous genes. We have applied this program to a set of 665 nonredundant protein sequences with defined three-dimensional structures in the Protein Data Bank (PDB), which yielded 8,217 introns in 407 proteins. For the subset of proteins corresponding to ancient conserved regions (ACR), we find that there is a correlation of phase-zero introns with the boundary regions of modules and no correlation for the phase-one and phase-two positions. However, for a subset of proteins without prokaryotic counterparts (131 non-ACR proteins), a set of presumably modern proteins (or proteins that have diverged extremely far from any ancestral form), we do not find any correlation of phase-zero intron positions with three-dimensional structure. Furthermore, we find an anticorrelation of phase-one intron positions with module boundaries: they actually have a preference for the interior of modules. This finding is explicable as a preference for phase-one introns to lie in glycines, between G|G sequences, the preference for glycines being anticorrelated with the three-dimensional modules. We interpret this anticorrelation as a sign that a number of phase-one introns, and hence many modern introns, have been inserted into G|G “protosplice” sequences.
Synthesis of an organoinsulin molecule that can be activated by antibody catalysis
Authors: Worrall Dorothy S. , McDunn Jonathan E. , List Benjamin , Reichart Donna , Hevener Andrea , Gustafson Thomas , Barbas Carlos F. , Lerner Richard A. , Olefsky Jerrold M.
Published: July 2002

We have developed a methodology of prodrug delivery by using a modified insulin species whose biological activity potentially can be regulated
in vivo
. Native insulin was derivatized with aldol-terminated chemical modifications that can be selectively removed by the catalytic aldolase antibody 38C2 under physiologic conditions. The derivatized organoinsulin (insulin
D
) was defective with respect to receptor binding and stimulation of glucose transport. The affinity of insulin
D
for the insulin receptor was reduced by 90% in binding studies using intact cells. The ability of insulin
D
to stimulate glucose transport was reduced by 96% in 3T3-L1 adipocytes and by 55% in conscious rats. Incubation of insulin
D
with the catalytic aldolase antibody 38C2 cleaved all of the aldol-terminated modifications, restoring native insulin. Treatment of insulin
D
with 38C2 also restored insulin
D
's receptor binding and glucose transport-stimulating activities
in vitro
, as well as its ability to lower glucose levels in animals
in vivo
. We propose that these results are the foundation for an
in vivo
regulated system of insulin activation using the prohormone insulin
D
and catalytic antibody 38C2 with potential therapeutic application.
Adeno-associated viral vector-mediated vascular endothelial growth factor gene transfer induces neovascular formation in ischemic heart
Authors: Su Hua , Lu Ronghua , Kan Yuet Wai
Published: July 2002

Vascular endothelial growth factor (VEGF) plays important roles in
physiological and pathological angiogenesis. Recent studies have
demonstrated that direct injection of VEGF protein, plasmid DNA, or an
adenoviral vector encoding the
VEGF
gene into ischemic
myocardium or limb can induce collateral blood vessel formation and
improve perfusion of the ischemic areas. However, these approaches have
limitations ranging from a short-lasting effect to angioma formation.
In this study, we investigated the feasibility of using
adeno-associated viral (AAV) vectors to deliver
VEGF
genes to mouse myocardium. A cytomegalovirus promoter was used to drive
genes for a human VEGF isoform, VEGF
165
, and LacZ. A mouse
myocardial ischemic model was generated by ligation of the anterior
descending coronary artery. Approximately 10
11
copies of
the AAV-VEGF vector mixed with 10
10
copies of AAV-LacZ were
injected to one site of normal myocardium and a total of
10
11
copies of AAV-VEGF were injected to multiple sites of
myocardium around the ischemic region. LacZ gene expression was
observed up to 3 months after the vector inoculation. After AAV-VEGF
inoculation, neoangiogenesis was observed in the ischemic heart model
but not in normal heart tissue. An inflammatory-cell infiltration was
not observed in the AAV-VEGF- and AAV-LacZ-inoculated hearts, and
angioma-like structure was not observed. These results indicated that
injection of the AAV vector directly to myocardium could mediate
efficient gene transfer and transgene expression and that VEGF gene
delivered by AAV vector can induce angiogenesis in ischemic myocardium.
X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis.
Authors: Messerschmidt A , Wever R
Published: July 2002

The chloroperoxidase (EC 1.11.1.-) from the fungus Curvularia inaequalis belongs to a class of vanadium enzymes that oxidize halides in the presence of hydrogen peroxide to the corresponding hypohalous acids. The 2.1 A crystal structure (R = 20%) of an azide chloroperoxidase complex reveals the geometry of the catalytic vanadium center. Azide coordinates directly to the metal center, resulting in a structure with azide, three nonprotein oxygens, and a histidine as ligands. In the native state vanadium will be bound as hydrogen vanadate(V) in a trigonal bipyramidal coordination with the metal coordinated to three oxygens in the equatorial plane, to the OH group at one apical position, and to the epsilon 2 nitrogen of a histidine at the other apical position. The protein fold is mainly alpha-helical with two four-helix bundles as main structural motifs and an overall structure different from other structures. The helices pack together to a compact molecule, which explains the high stability of the protein. An amino acid sequence comparison with vanadium-containing bromoperoxidase from the seaweed Ascophyllum nodosum shows high similarities in the regions of the metal binding site, with all hydrogen vanadate(V) interacting residues conserved except for lysine-353, which is an asparagine.
Regulation of the retinoblastoma protein-related protein p107 by G1 cyclin-associated kinases.
Authors: Xiao Z X , Ginsberg D , Ewen M , Livingston D M
Published: July 2002

p107 is a retinoblastoma protein-related phosphoprotein that, when overproduced, displays a growth inhibitory function. It interacts with and modulates the activity of the transcription factor, E2F-4. In addition, p107 physically associates with cyclin E-CDK2 and cyclin A-CDK2 complexes in late G1 and at G1/S, respectively, an indication that cyclin-dependent kinase complexes may regulate, contribute to, and/or benefit from p107 function during the cell cycle. Our results show that p107 phosphorylation begins in mid G1 and proceeds through late G1 and S and that cyclin D-associated kinase(s) contributes to this process. In addition, E2F-4 binds selectively to hypophosphorylated p107, and G1 cyclin-dependent p107 phosphorylation leads to the dissociation of p107-E2F-4 complexes as well as inactivation of p107 G1 blocking function.
Small viscosity asymptotics for the inertial range of local structure and for the wall region of wall-bounded turbulent shear flow.
Authors: Barenblatt G I , Chorin A J
Published: July 2002

The small viscosity asymptotics of the inertial range of local structure and of the wall region in wallbounded turbulent shear flow are compared. The comparison leads to a sharpening of the dichotomy between Reynolds number dependent scaling (power-type) laws and the universal Reynolds number independent logarithmic law in wall turbulence. It further leads to a quantitative prediction of an essential difference between them, which is confirmed by the results of a recent experimental investigation. These results lend support to recent work on the zero viscosity limit of the inertial range in turbulence.
Targeted gene correction of episomal DNA in mammalian cells mediated by a chimeric RNA.DNA oligonucleotide.
Authors: Yoon K , Cole-Strauss A , Kmiec E B
Published: July 2002

An experimental strategy to facilitate correction of single-base mutations of episomal targets in mammalian cells has been developed. The method utilizes a chimeric oligonucleotide composed of a contiguous stretch of RNA and DNA residues in a duplex conformation with double hairpin caps on the ends. The RNA/DNA sequence is designed to align with the sequence of the mutant locus and to contain the desired nucleotide change. Activity of the chimeric molecule in targeted correction was tested in a model system in which the aim was to correct a point mutation in the gene encoding the human liver/bone/kidney alkaline phosphatase. When the chimeric molecule was introduced into cells containing the mutant gene on an extrachromosomal plasmid, correction of the point mutation was accomplished with a frequency approaching 30%. These results extend the usefulness of the oligonucleotide-based gene targeting approaches by increasing specific targeting frequency. This strategy should enable the design of antiviral agents.
Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides
Authors: Maulitz Andreas H. , Lightstone Felice C. , Zheng Ya-Jun , Bruice Thomas C.
Published: July 2002

The SN2 displacements of chloride ion from CH3Cl, C2H5Cl, and C2H4Cl2by acetate and hydroxide ions have been investigated, usingab initiomolecular orbital theory at the HF/6–31+G(d), MP2/6–31+G(d), and MP4/6–31+G(d) levels of theory. The central barriers (calculated from the initial ion–molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH3Cl, C2H5Cl, and C2H4Cl2have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH3Cl, C2H5Cl, and C2H4Cl2. A self-consistent reaction field solvation model was used to examine the SN2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined byab initiocalculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic SN2 displacement of halogen.
Analysis of the role of the Spitzenkörper in fungal morphogenesis by computer simulation of apical branching in
Aspergillus niger
Authors: Reynaga-Peña Cristina G. , Gierz Gerhard , Bartnicki-Garcia Salomon
Published: July 2002

High-resolution video microscopy, image analysis, and computer simulation were used to study the role of the Spitzenkörper (Spk) in apical branching of
ramosa-1
, a temperature-sensitive mutant of
Aspergillus niger
. A shift to the restrictive temperature led to a cytoplasmic contraction that destabilized the Spk, causing its disappearance. After a short transition period, new Spk appeared where the two incipient apical branches emerged. Changes in cell shape, growth rate, and Spk position were recorded and transferred to the
fungus simulator
program to test the hypothesis that the Spk functions as a vesicle supply center (VSC). The simulation faithfully duplicated the elongation of the main hypha and the two apical branches. Elongating hyphae exhibited the growth pattern described by the hyphoid equation. During the transition phase, when no Spk was visible, the growth pattern was nonhyphoid, with consecutive periods of isometric and asymmetric expansion; the apex became enlarged and blunt before the apical branches emerged. Video microscopy images suggested that the branch Spk were formed anew by gradual condensation of vesicle clouds. Simulation exercises where the VSC was split into two new VSCs failed to produce realistic shapes, thus supporting the notion that the branch Spk did not originate by division of the original Spk. The best computer simulation of apical branching morphogenesis included simulations of the ontogeny of branch Spk via condensation of vesicle clouds. This study supports the hypothesis that the Spk plays a major role in hyphal morphogenesis by operating as a VSC—i.e., by regulating the traffic of wall-building vesicles in the manner predicted by the hyphoid model.
The atypical codon usage of the plant
psbA
gene may be the remnant of an ancestral bias
Authors: Morton Brian R. , Levin Justine A.
Published: July 2002

The
psbA
gene of the chloroplast genome has a codon usage that is unusual for plant chloroplast genes. In the present study the evolutionary status of this codon usage is tested by reconstructing putative ancestral
psbA
sequences to determine the pattern of change in codon bias during angiosperm divergence. It is shown that the codon biases of the ancestral genes are much stronger than all extant flowering plant
psbA
genes. This is related to previous work that demonstrated a significant increase in synonymous substitution in
psbA
relative to other chloroplast genes. It is suggested, based on the two lines of evidence, that the codon bias of this gene currently is not being maintained by selection. Rather, the atypical codon bias simply may be a remnant of an ancestral codon bias that now is being degraded by the mutation bias of the chloroplast genome, in other words, that the
psbA
gene is not at equilibrium. A model for the evolution of selective pressure on the codon usage of plant chloroplast genes is discussed.
Molecular basis of cooperative DNA bending and oriented heterodimer binding in the NFAT1—Fos–Jun—ARRE2 complex
Authors: Diebold Ronald J. , Rajaram Nirmala , Leonard David A. , Kerppola Tom K.
Published: July 2002

Cooperative DNA binding by transcription factors that bind to separate recognition sites is likely to require bending of intervening sequences and the appropriate orientation of transcription factor binding. We investigated DNA bending in complexes formed by the basic region–leucine zipper domains of Fos and Jun with the DNA binding region of nuclear factor of activated T cells 1 (NFAT1) at composite regulatory elements using gel electrophoretic phasing analysis. The NFAT1—Fos–Jun complex induced a bend at the ARRE2 site that was distinct from the sum of the bends induced by NFAT1 and Fos–Jun separately. We designate this difference DNA bending cooperativity. The bending cooperativity was directed toward the interaction interface between Fos–Jun and NFAT1. We also examined the influence of NFAT1 on the orientation of Fos–Jun heterodimer binding using a novel fluorescence resonance energy transfer assay. The interaction with NFAT1 could reverse the orientation of Fos–Jun heterodimer binding to the ARRE2 site. The principal determinants of both cooperative DNA bending and oriented heterodimer binding were localized to three amino acid residues at the amino-terminal ends of the leucine zippers of Fos and Jun. Consequently, interactions between transcription factors can remodel promoters by altering DNA bending and the orientation of heterodimer binding.
An activity in rat tissues that modifies nitrotyrosine-containing proteins
Authors: Kamisaki Yoshinori , Wada Kouichirou , Bian Ka , Balabanli Barbaros , Davis Karen , Martin Emil , Behbod Fariba , Lee Yu-Chen , Murad Ferid
Published: July 2002

Homogenates from rat spleen and lung could modify nitrotyrosine-containing BSA. With incubation, nitrotyrosine-containing BSA lost its epitope to a monoclonal antibody that selectively recognized nitrotyrosine-containing proteins. In the presence of protease inhibitors, the loss of the nitrotyrosine epitope occurred without protein degradation and hydrolysis. This activity was found in supernatant but not particulate fractions of spleen homogenates. The factor was heat labile, was sensitive to trypsin treatment, and was retained after passage through a membrane with a 10-kDa retention. The activity was time- and protein-concentration dependent. The activity increased about 2-fold in spleen extracts with endotoxin (bacterial lipopolysaccharide) treatment of animals, suggesting that the activity is inducible or regulatable. Other nitrotyrosine-containing proteins also served as substrates, while free nitrotyrosine and some endogenous nitrotyrosine-containing proteins in tissue extracts were poor substrates. Although the product and possible cofactors for this reaction have not yet been identified, this activity may be a “nitrotyrosine denitrase” that reverses protein nitration and, thus, decreases peroxynitrite toxicity. This activity was not observed in homogenates from rat liver or kidney, suggesting that there may also be some tissue specificity for the apparent denitrase activity.
Charge-dependent translocation ofBordetella pertussisadenylate cyclase toxin into eukaryotic cells: Implication for thein vivodelivery of CD8+T cell epitopes into antigen-presenting cells
Authors: Karimova G. , Fayolle C. , Gmira S. , Ullmann A. , Leclerc C. , Ladant D.
Published: July 2002

Bordetella pertussissecretes a calmodulin-activated adenylate cyclase toxin, CyaA, that is able to deliver its N-terminal catalytic domain (400-aa residues) into the cytosol of eukaryotic target cells, directly through the cytoplasmic membrane. We have previously shown that CyaA can be used as a vehicle to deliver T cell epitopes, inserted within the catalytic domain of the toxin, into antigen-presenting cells and can trigger specific class I-restricted CD8+cytotoxic T cell responsesin vivo. Here, we constructed a series of recombinant toxins harboring at the same insertion site various peptide sequences of 11–25 amino acids, corresponding to defined CD8+T cell epitopes and differing in the charge of the inserted sequence. We show that inserted peptide sequences containing net negative charges (−1 or −2) decreased or completely blocked (charge of −4) the internalization of the toxin into target cellsin vitroand abolished the induction of cytotoxic T cell responsesin vivo. The blocking of translocation due to the inserted acidic sequences can be relieved by appropriate mutations in the flanking region of CyaA that counterbalance the inserted charges. Our data indicate that (i) the electrostatic charge of the peptides inserted within the catalytic domain of CyaA is critical for its translocation into eukaryotic cells and (ii) the delivery of T cell epitopes into the cytosol of antigen-presenting cells by recombinant CyaA toxins is essential for thein vivostimulation of specific cytotoxic T cells. These findings will help to engineer improved recombinant CyaA vectors able to stimulate more efficiently cellular immunity.
Heterogeneous gene expression from the inactive X chromosome: An X-linked gene that escapes X inactivation in some human cell lines but is inactivated in others
Authors: Carrel Laura , Willard Huntington F.
Published: July 2002

In mammalian females, most genes on one X chromosome are transcriptionally silenced as a result of X chromosome inactivation. Whereas it is well established that some X-linked genes “escape” X inactivation and are expressed from both active (Xa) and inactive (Xi) X chromosomes, most models for the chromosomal control of X-linked gene expression assume that the X inactivation status of a given gene is constant among different females within a population. In this report, we test the expression of human X-linked genes in primary cell lines from females with complete nonrandom X inactivation, by using transcribed polymorphisms to distinguish Xa and Xi expression. Six X-linked genes used to document this assay system showed monoallelic expression in all informative cell lines, consistent with X inactivation. However, a novel pattern of expression was observed for another gene,REP1; monoallelic expression, indicating inactivation, was detected in some lines, whereas biallelic expression, indicating escape from inactivation, was detected in others. Furthermore, levels of Xi expression varied among cell lines that expressedREP1. The cellular basis of Xi expression was examined by expression assays in single cells. These data indicate thatREP1is expressed from the Xi in all cells, but that the level of expression relative to Xa levels is reduced. These findings suggest that Xi gene expression is under a previously unsuspected level of genetic or epigenetic control, likely involving local or regional changes in chromatin organization that determine whether a gene escapes or is subject to X inactivation.
Calcium-independent activation of endothelial nitric oxide synthase by ceramide
Authors: Igarashi Junsuke , Thatte Hemant S. , Prabhakar Prakash , Golan David E. , Michel Thomas
Published: July 2002

The endothelial isoform of NO synthase (eNOS) is targeted to sphingolipid-enriched signal-transducing microdomains in the plasma membrane termed caveolae. Among the caveolae-targeted sphingolipids are the ceramides, a class of acylated sphingosine compounds that have been implicated in diverse cellular responses. We have explored the role of ceramide analogues in eNOS signaling in cultured bovine aortic endothelial cells (BAEC). Addition of the ceramide analogue
N-
acetylsphingosine (C
2
-ceramide; 5 μM) to intact BAEC leads to a significant increase in NO synthase activity (assayed by using the fluorescent indicator 4,5-diaminofluorescein) and translocation of eNOS from the endothelial cell membrane to intracellular sites (measured by using quantitative immunofluorescence techniques); the biologically inactive ceramide
N-
acetyldihydrosphingosine is entirely without effect. C
2
-ceramide-induced eNOS activation and translocation are unaffected by the intracellular calcium chelator 1,2-bis-
o
-aminophenoxyethane-
N,N,N
′
,N
′-tetraacetic acid (BAPTA). Using the calcium-specific fluorescent indicator fluo-3, we also found that C
2
-ceramide activation of eNOS is unaccompanied by a drug-induced increase in intracellular calcium. These findings stand in sharp contrast to the mechanism by which bradykinin, estradiol, and other mediators acutely activate eNOS, in which a rapid, agonist-promoted increase in intracellular calcium is required. Finally, we show that treatment of BAEC with bradykinin causes a significant increase in cellular ceramide content; the response to bradykinin has an EC
50
of 3 nM and is blocked by the bradykinin B
2
-receptor antagonist HOE140. Bradykinin-induced ceramide generation could represent a mechanism for longer-term regulation of eNOS activity. Our results suggest that ceramide functions independently of Ca
2+
-regulated pathways to promote activation and translocation of eNOS, and that this lipid mediator may represent a physiological regulator of eNOS in vascular endothelial cells.
Poly(ADP-ribose) polymerase is a mediator of necrotic cell death by ATP depletion
Authors: Ha Hyo Chol , Snyder Solomon H.
Published: July 2002

Apoptotic and necrotic cell death are well characterized and are influenced by intracellular ATP levels. Poly(ADP-ribose) polymerase (PARP), a nuclear enzyme activated by DNA strand breaks, physiologically participates in DNA repair. Overactivation of PARP after cellular insults can lead to cell death caused by depletion of the enzyme’s substrate β-nicotinamide adenine dinucleotide and of ATP. In this study, we have differentially elicited apoptosis or necrosis in mouse fibroblasts. Fibroblasts from PARP-deficient (PARP
−/−
) mice are protected from necrotic cell death and ATP depletion but not from apoptotic death. These findings, together with cell death patterns in PARP
−/−
animals receiving other types of insults, indicate that PARP activation is an active trigger of necrosis, whereas other mechanisms mediate apoptosis.
Drob-1, a
Drosophila
member of the Bcl-2/CED-9 family that promotes cell death
Authors: Igaki Tatsushi , Kanuka Hirotaka , Inohara Naohiro , Sawamoto Kazunobu , Núñez Gabriel , Okano Hideyuki , Miura Masayuki
Published: July 2002

The Bcl-2/CED-9 family of proteins, which includes both antiapoptotic and proapoptotic members, plays key regulating roles in programmed cell death. We report here the identification and characterization of Drob-1, the first
Drosophila
member of the Bcl-2/CED-9 family to be isolated. Drob-1 contains four conserved Bcl-2 homology domains (BH1, BH2, BH3, and BH4) and a C-terminal hydrophobic domain. Ectopic expression of Drob-1 in the developing
Drosophila
eye resulted in a rough-eye phenotype. Furthermore, when overexpressed in
Drosophila
S2 cells, Drob-1 induced apoptosis accompanied by elevated caspase activity. This Drob-1-induced cell death, however, could not be antagonized by baculovirus p35, a broad-spectrum caspase inhibitor. Drob-1 was localized to the intracytoplasmic membranes, predominantly to the mitochondrial membranes, and a mutant Drob-1 lacking the hydrophobic C terminus lost both its mitochondrial localization and its proapoptotic activity. These results suggest that Drob-1 promotes cell death by inducing both caspase-dependent and -independent pathways at the mitochondria. Our identification of Drob-1 and further genetic analysis should provide increased understanding of the universal mechanisms by which the Bcl-2/CED-9 family members and other related proteins regulate apoptosis.
Bien‐ětre et contraintes d'adolescents: Une comparaison entre adolescents de familles monoparentales et de families biparentales
Authors: Bodmer Nancy M. , Grob Alexander
Published: July 2002

Dans ce travail nous analysons les relations entre deux types de famille (monoparentales et biparentales), les contraintes familiales et extra‐familiales, les stratégies de résolution de problèmes et le bien‐ětre d'adolescents. L'enquěte est composée de 418 adolescents âgés de 12 à 18 ans (367 adolescents de familles biparentales; 51 de familles monoparentales). Les adolescents de familles monoparentales ressentent plus de contraintes familiales que les adolescents de familles biparentales; les deux groupes d'adolescents ont les měmes stratégies de résolution de problèmes et ressentent le měme degré de bien‐ětre. Seuls les adolescents de familles monoparentales profitent d'une stratégie active de résolution de problèmes, car seul leur bien‐ětre est rehaussé quand ils choisissent une telle stratégie. Par contre, une stratégie émotionnelle de résolution de problèmes n'affecte que le bien‐ětre des adolescents de familles biparentales.
Intellectual as Hustler: Researching against the grain of the market
Authors: Smyth John , Hattam Robert
Published: July 2002

In many respects, universities around the world are living through a period of quite extraordinary turmoil as their role and purposes are under serious challenge. In this paper we explore the latest attempt in Australia to push universities even further in the direction of becoming marketised, and we examine what this means in terms of the loss of public space for academics as public intellectuals. In this, we draw some fragments from our own autobiographical experiences in trying to assert what a ‘counter public’ might look like around university research. We find the notion of ‘hustler’ to be a sufficiently playful metaphor around which to begin to frame what happens to knowledge as it is increasingly treated as another commodity.
Continuity and Change in Special School Provision: Some perspectives on local education authority policy‐making
Authors: Croll Paul , Moses Diana
Published: July 2002

The article considers aspects of local authority policy‐making with regard to segregated special school provision for children with special educational needs and the resilience of a separate special school sector, despite a policy climate favouring inclusion. Statistical evidence shows a small but steady trend to more inclusive provsion but very considerable variation between local education authorities (LEAs). The notion of ‘the dominance of structure over ideology’ is used to explore LEA decision‐making processes but is shown to have limited explanatory power. The data suggest that the use of incremental policy development has not resulted in significant long‐term change and that a fundamental policy initiative has been a necessary, though not sufficient, condition of reform. Other factors facilitating reform included a small size of LEA and a preparedness to confront opposition. Strong commitment by key individuals was more important than an overall climate of opinion in securing greater inclusion.