bluuebunny/crossref_metadata_2025 huggingface dataset:
Traveling waves on vertical films: Numerical analysis using the finite element method
Authors: Salamon Todd R. , Armstrong Robert C. , Brown Robert A.
Published: July 2002

Finite-amplitude waves propagating at constant speed down an inclined fluid layer are computed by finite element analysis of the Navier–Stokes equations written in a reference frame translating at the wave speed. The velocity and pressure fields, free-surface shape and wave speed are computed simultaneously as functions of the Reynolds number Re and the wave number μ. The finite element results are compared with predictions of long-wave, asymptotic theories and boundary-layer approximations for the form and nonlinear transitions of finite-amplitude waves that evolve from the flat film state. Comparisons between the finite element calculations and the long-wave predictions for fixed μ and increasing Re agree well for small-amplitude waves. However, for larger-amplitude waves the long-wave results diverge qualitatively from the finite element predictions; the long-wave theories predict limit points in the solution families that do not exist in the finite element solutions. Comparisons between the finite element predictions, previous numerical simulations and experimental results for the shape and speed of periodic and solitary-like waves are in good agreement. Nonlinear interactions are demonstrated between multiple waves in a periodic wave train that cause secondary bifurcations to families of waves that differ from those that evolve from the neutral stability curve. These predictions for fixed Re and decreasing μ are in quantitative agreement with the results of long-wave approximations for small-amplitude waves. Comparisons with the predictions of boundary-layer approximations show sensitivity of the solution structure to the value of the Weber number We.
Particle behavior in the turbulent boundary layer. I. Motion, deposition, and entrainment
Authors: Kaftori D. , Hetsroni G. , Banerjee S.
Published: July 2002

The motion of solid particles near the wall in a turbulent boundary layer was investigated experimentally in a water flume by flow visualization techniques and by LDA. The particles were of polystyrene (specific density ∼1.05) with diameters ranging from 100 to 900 μm. Results show that particle motion, as well as entrainment and deposition processes, are controlled by the action of coherent wall structures, which appear to be funnel vortices. The behavior of the particles is consistent with the motion and effects of such vortices. The vortices appear to cause the formation of particle streaks near the wall, to create suitable conditions for particle entrainment, and to assist in particle deposition by conveying them from the outer flow to the wall region.
Transition experiments in a boundary layer with embedded streamwise vortices
Authors: Bakchinov A. A. , Grek G. R. , Klingmann B. G. B. , Kozlov V. V.
Published: July 2002

The stability of a flat plate boundary layer modulated by stationary streamwise vortices was studied experimentally in the T-324 low speed wind tunnel in Novosibirsk. Vortices were generated inside the boundary layer by means of roughness elements arranged in a regular array along the spanwise (z-) direction. Transition is not caused directly by these structures, but by the growth of small amplitude traveling waves riding on top of the steady vortices. This situation is analogous to the transition process in Görtler and cross-flows. The waves were found to amplify up to a stage where higher harmonics are generated, leading to turbulent breakdown and disintegration of the spanwise boundary layer structure. For strong modulations, the observed instability is quite powerful, and can be excited ‘‘naturally’’ by small uncontrollable background disturbances. Controlled oscillations were then introduced by means of a vibrating ribbon, allowing a detailed investigation of the wave characteristics. The instability seems to be associated with the spanwise gradients of the mean flow, ∂U/∂z, and at all z-positions, the maximum wave amplitude was found at a wall-normal position where the mean velocity is equal to the phase velocity of the wave, U(y)=c, i.e., at the local critical layer. Unstable waves were observed at frequencies well above those for which Tollmien–Schlichting (TS) waves amplify in the Blasius boundary layer. Excitation at lower frequencies and milder basic flow modulations showed that TS-type waves may also develop. The relation between TS-type waves and the observed high-frequency instability is discussed in the light of previous authors’ findings.
Nonlinear sound–vortex interactions in an inviscid isentropic fluid: A two-fluid model
Authors: Nazarenko Sergey V. , Zabusky Norman J. , Scheidegger Thomas
Published: July 2002

A new two-fluid model is developed to describe the nonlinear interaction of acoustic waves and vortices. Analytical and computational results are presented for a sound pulse interacting with and being modified by a vortex. A novel numerical method based on a particle-in-cell discretization of the acoustic field is developed and used to study the nonlinear scattering of sound by a cylindrical vortex. Equations for the sound wave packet propagating in an axially symmetric mean flow are integrated analytically. Nonlinear modification of the vortex flow by the high-frequency sound is found to be mediated by growing pressure disturbances generated by the radiative forcing on the high gradient regions of the acoustic pulse. The total energy of the vortex mean flow grows monotonically, as the acoustic component loses its energy. The changes in the kinetic and internal energies of the vortex are greater than the changes in its total energy, although these changes are reversible in lowest order of the nonlinear vortex–acoustic interaction.
On a critical case of internal solitary waves in a two-layer fluid
Authors: Choi J. W. , Shen M. C.
Published: July 2002

This Brief Communication answers an unsettled question pointed out by Peters and Stoker [Commun. Pure Appl. Math 13, 115 (1960)] with regard to a critical case of a two-layer fluid flow with a free surface supported by a horizontal rigid bottom. In the critical case the coefficient of the nonlinear term in the Korteweg–deVries (KdV) equation vanishes and the KdV theory models only a parallel flow. By using higher-order asymptotic expansion, an extended and a modified KdV equation are derived and internal solitary waves and transition waves in the critical case are found.
Instability of thermocapillary convection in liquid bridges
Authors: Carotenuto L. , Castagnolo D. , Albanese C. , Monti R.
Published: July 2002

It is well known that thermocapillary convection arises in liquid bridges when the support discs are heated differentially and uniformly. Upon increasing the temperature difference, the convective flow shows a transition from an axisymmetric to an oscillatory regime. This phenomenon has been investigated both experimentally and theoretically, but prior experimental results exhibit some discrepancies with respect to the predictions of stability analyses. The present paper discusses experimental results obtained under microgravity conditions, comparing them with previous experimental observations made on ground and in space and with recent theoretical models of the instability. The results agree with the description of oscillations in terms of superposition of hydrothermal waves. Finally, a possible mechanism for a “pulsating” instability is proposed, together with a new scaling law for the oscillation frequencies at onset; this law, which correlates the critical frequency to the fluid properties, the geometrical parameters and the critical temperature difference, agrees with all the available experimental data.
Field-aligned coordinates for nonlinear simulations of tokamak turbulence
Authors: Beer M. A. , Cowley S. C. , Hammett G. W.
Published: July 2002

Turbulence in tokamaks is characterized by long parallel wavelengths and short perpendicular wavelengths. A coordinate system for nonlinear fluid, gyrokinetic ‘‘Vlasov,’’ or particle simulations is presented that exploits the elongated nature of the turbulence by resolving the minimum necessary simulation volume: a long thin twisting flux tube. It is very similar to the ballooning representation, although periodicity constraints can be incorporated in a manner that allows E×B nonlinearities to be evaluated efficiently with fast Fourier transforms (FFT’s). If the parallel correlation length is very long, however, enforcing periodicity can introduce artificial correlations, so periodicity should not necessarily be enforced in the poloidal angle at θ=±π. This method is applied to high resolution three-dimensional simulations of toroidal ion temperature gradient (ITG) driven turbulence, which predict fluctuation spectra and ion heat transport similar to experimental measurements.
A general critique of inertial-electrostatic confinement fusion systems
Authors: Rider Todd H.
Published: July 2002

The suitability of various implementations of inertial-electrostatic confinement (IEC) systems for use as D–T, D–D, D–3He, 3He–3He, p–11B, and p–6Li reactors has been examined, and several fundamental flaws in the concept have been discovered. Bremsstrahlung losses for all of these fuels have been calculated in a general fashion which applies not only to IEC systems but also to most other fusion schemes; these calculations indicate that bremsstrahlung losses will be prohibitively large for 3He–3He, p–11B, and p–6Li reactors and will be a considerable fraction of the fusion power for D–3He and D–D reactors. Further calculations show that it does not appear possible for the dense central region of a reactor-grade IEC device to maintain significantly non-Maxwellian ion distributions or to keep two different ion species at significantly different temperatures, in contradiction with earlier claims made about such systems. Since the ions form a Maxwellian distribution with a mean energy not very much smaller than the electrostatic well depth, ions in the energetic tail of the distribution will be lost at rates greatly in excess of the fusion rate. Even by using one of the best electron confinement systems proposed for such devices, a polyhedral cusp magnetic field, and by making exceedingly optimistic assumptions about the performance of that confinement system, the electron losses from the machine prove to be intolerable for all fuels except perhaps DT. In order for IEC systems to be used as fusion reactors, it will be necessary to find methods to circumvent these problems.
Triton burnup in plasma focus plasmas
Authors: Brzosko Jan S. , Brzosko Jan R. , Robouch Benjamin V. , Ingrosso Luigi
Published: July 2002

Pure deuterium plasma discharge from plasma focus breeds 1.01 MeV tritons via the D(d,p)T fusion branch, which has the same cross section as the D(d,n)3He (En=2.45 MeV) fusion branch. Tritons are trapped in and collide with the background deuterium plasma, producing 14.1 MeV neutrons via the D(t,n)4He reaction. The paper presents published in preliminary form as well as unpublished experimental data and theoretical studies of the neutron yield ratio R=Yn(14.1 MeV)/Yn(2.45 MeV). The experimental data were obtained from 1 MJ Frascati plasma focus operated at W=490 kJ with pure deuterium plasma (in the early 1980s). Neutrons were monitored using the nuclear activation method and nuclear emulsions. The present theoretical analysis of the experimental data is based on an exact adaptation of the binary encounter theory developed by Gryzinski. It is found that the experimentally defined value 1⋅10−3<R<3⋅10−3 can be explained theoretically only if one considers that tritium burnup occurs in the plasma domains of very high density (n≳1021 cm−3), high temperature (kT≳1 keV), and short trapping time (t0≤20 ns). These domains are known as efficient traps of MeV ions but are not the main source of D(d,n)3He fusion.
Analysis of the beam bunching produced by a free electron laser
Authors: Gardelle J. , Labrouche J. , Marchese G. , Rullier J. L. , Villate D. , Donohue J. T.
Published: July 2002

A high-power microwave Free Electron Laser (FEL) experiment has been performed to study the inherent electron beam bunching that occurs in the FEL interaction. An induction linac delivered a 1 kA, 2.2 MeV electron beam to a FEL amplifier. In the process of amplifying the input signal of frequency 35 GHz to power levels of the order of 10 MW, the electron beam was bunched by the ponderomotive force. In this paper we describe the FEL experiment and the optical technique that was used to observe the bunches. Their properties as functions of the basic FEL parameters are discussed.
Implosion dynamics of long-pulse wire array Z pinches
Authors: Douglas M. R. , Deeney C. , Spielman R. B. , Coverdale C. A. , Roderick N. F. , Peterson D. L.
Published: July 2002

Recent improvements in Z-pinch wire array load design at Sandia National Laboratories have led to a substantial increase in pinch performance as measured by radiated powers of up to 280 TW in 4 ns and 1.8 MJ of total radiated energy. Next generation, higher-current machines will allow for larger mass arrays and comparable or higher velocity implosions to be reached, possibly extending these results. As the current is pushed above 20 MA, a conventional machine design based on a 100 ns implosion time results in higher voltages, hence higher cost and power flow risk. Another approach, which shifts the risk to the load configuration, is to increase the implosion time to minimize the voltage. This approach is being investigated in a series of experimental campaigns on the Saturn [C. Deeney et al., Phys. Plasmas 6, 3576 (1999)] and Z [R. B. Spielman et al., Phys. Plasmas 5, 2105 (1998)] machines. In this paper, both experimental and two-dimensional computational modeling of the first long implosion time Z experiments will be presented. The experimental data shows broader pulses, lower powers, and larger pinch diameters compared to the corresponding short pulse data. By employing a nested array configuration, the pinch diameter was reduced by 50% with a corresponding increase in power of >30%. Numerical simulations suggest that load velocity is the dominating mechanism behind these results.
Determination of heterojunction band offsets by capacitance-voltage profiling through nonabrupt isotype heterojunctions
Authors: Kroemer Herbert
Published: July 2002

It is shown that the capacitance-voltage (C-V) profiling technique to obtain heterojunction (HJ) band offsets is grading independent, that is, the band offset values obtained by it are the values for the limit of zero compositional grading, even in nonabrupt junctions. The result explains the good agreement of old data taken on nonabrupt HJ’s grown by liquid phase epitaxy (LPE) with more recent data on abrupt junctions. It suggests that LPE grown HJ’s may be used more freely than was previously thought to determine those offsets, making C-V profiling the most versatile technique for the determination of HJ band offsets.
Epitaxial relations in CaxSr1−xF2 films grown on GaAs {111} and Ge(111) substrates
Authors: Tsutsui Kazuo , Ishiwara Hiroshi , Asano Tanemasa , Furukawa Seijiro
Published: July 2002

Epitaxial relations in CaxSr1−xF2 (0≤x≤1) films grown on GaAs(111), (1̄1̄1̄), and Ge(111) substrates were investigated by He+ ion channeling analysis and transmission electron microscopy. Though the lattice constants of GaAs and Ge are nearly the same, the relations were found to be completely different. That is, the lattice-matched fluoride film on GaAs exhibited an orientation identical to that of the substrate (type A orientation), whereas the orientation of the film on Ge was rotated by 180° about the surface normal 〈111〉 axis (type B orientation). It was also found that the type A growth of the Cax Sr1−x F2 films is maintained in the whole range of x on the As face of GaAs, while the growth types are partially or totally inverted in the lattice-mismatched fluoride films grown on the Ga face of GaAs and on Ge.
Microstructure and formation mechanism of porous silicon
Authors: Beale M. I. J. , Chew N. G. , Uren M. J. , Cullis A. G. , Benjamin J. D.
Published: July 2002

A systematic study is presented of the effects of silicon dopant type, resistivity, current density, and hydrofluoric acid concentration on the formation and properties of porous silicon. Cross-section transmission electron microscopy revealed the presence of two distinct microstructures. The structure formed is determined by the doping level with the transition occurring near degeneracy. A model of the anodisation process is presented which is based on the semiconducting properties of the material and which explains the formation of the two different types of porous structure observed.
Crystal orientation dependence of silicon doping in molecular beam epitaxial AlGaAs/GaAs heterostructures
Authors: Wang W. I. , Mendez E. E. , Kuan T. S. , Esaki L.
Published: July 2002

Results on crystal orientation dependence of n- and p-type Si doping in molecular beam epitaxial GaAs are presented. High electron and hole mobilities in AlGaAs/GaAs heterostructures on high index planes are demonstrated for the first time. The doping results should prove useful for various transistor structures and complementary circuits. Also, due to the differences in the band structure for different orientations, quantum well heterostructures are likely to exhibit many interesting phenomena which are strongly orientation dependent.
3C-SiC p-n junction diodes
Authors: Furukawa K. , Uemoto A. , Shigeta M. , Suzuki A. , Nakajima S.
Published: July 2002

3C-SiC p-n junction diodes are prepared on Si substrates by chemical vapor deposition growth with appropriate impurity doping, and their current-voltage (I-V) and capacitance-voltage (C-V) characteristics are studied. I-V curves show good rectifying characteristics with a value of 3.3 for the ideal factor n and a reverse leakage current less than 10 μA at −5 V. The junction area is approximately 0.8 mm2. The built-in voltage is around 1.4 V by C-V measurements.
Large area, uniform silicon-on-insulator using a buried layer of oxidized porous silicon
Authors: Benjamin J. D. , Keen J. M. , Cullis A. G. , Innes B. , Chew N. G.
Published: July 2002

We describe a process for the formation of silicon-on-insulator structures by selective anodization of a buried p-type layer to form porous silicon which is then oxidized. A buried n-type layer ensures that the flow of the anodizing current, and hence the formation of the porous silicon layer, is directed laterally rather than downwards. By this means we have produced defect-free, 200-nm-thick and 40-μm-wide silicon strips extending across the full width of device wafers and resting on 800 nm of silicon dioxide. This approach, which shows considerable promise for further enhancement, gives continuous large areas of high quality isolated silicon with minimal wafer warpage compared with most existing silicon-on-silicon dioxide technologies.
Detection of surface director reorientation in a nematic liquid crystal
Authors: Welford K. R. , Sambles J. R.
Published: July 2002

The surface plasmon polariton is used to investigate the nematic director reorientation close to the director aligning layer. This has resulted in the determination of the surface anchoring energy and the realization that surface effects are significant even when surface anchoring is strong. A consequence of this is that existing data for the physical parameters of the nematic material may suffer systematic errors.
Alternatives to arsine: The atmospheric pressure organometallic chemical vapor deposition growth of GaAs using triethylarsenic
Authors: Speckman D. M. , Wendt J. P.
Published: July 2002

Studies on the homoepitaxial growth of unintentionally doped GaAs by atmospheric pressure organometallic chemical vapor deposition using triethylarsenic and trimethylgallium have been carried out, and the effects of growth temperature, V/III ratio, and flow rate on film characteristics are reported. Mirrorlike epitaxial layers of n-type GaAs were obtained at substrate temperatures of 540–650 °C and at V/III ratios of 6.7–11. The carrier concentrations for these films were approximately 1016–1017 cm−3, and from secondary ion mass spectroscopic analysis, the predominant epilayer impurities were determined to be both carbon and silicon.
Indium phosphide shallow homojunction solar cells made by metalorganic chemical vapor deposition
Authors: Spitzer M. B. , Keavney C. J. , Vernon S. M. , Haven V. E.
Published: July 2002

The fabrication of highly efficient indium phosphide solar cells is described. The cells are formed by metalorganic chemical vapor deposition. A shallow homojunction design is discussed and total area air mass zero efficiency of 17.9% is reported; air mass 1.5 efficiency is 20.4%. Electrical characterization identifying loss mechanisms is made, and areas for possible improvement are summarized.
Schottky and field-effect transistor fabrication on InP and GaInAs
Authors: Loualiche S. , L’Haridon H. , Le Corre A. , Lecrosnier D. , Salvi M. , Favennec P. N.
Published: July 2002

Schottky contacts with barrier heights of 0.76 eV on n-type InP and 0.65 eV on n-type GaInAs are realized by a new surface treatment. These contacts are used as a gate for the fabrication of field-effect transistors (FET) on these materials. Extrinsic transconductances of 100 and 7.5 mS/mm are measured on GaInAs and InP FET’s, respectively. These values are obtained without optimization of the ohmic contacts of the devices and without a gate recess.
Small angle relaxation of highly deformed nematic liquid crystals
Authors: Wu Shin-Tson , Wu Chiung-Sheng
Published: July 2002

Transient phase response associated with a small angle relaxation from highly deformed nematic liquid crystal (LC) directors is analyzed experimentally and numerically. Qualitative agreement between computer simulations and experimental results is obtained. Based on these results, decay time of a fast LC modulator employing the transient nematic effect is derived. This decay time is found to be fast (with potential to achieve ∼50 μs), insensitive to LC thickness, but proportional to (λ/Δn0)2, λ being the wavelength and Δn0 the corresponding birefringence.
One ring or two? Determination of ring number in carotenoids by lycopene ɛ-cyclases
Authors: Cunningham Francis X. , Gantt Elisabeth
Published: July 2002

Carotenoids in the photosynthetic membranes of plants typically
contain two β-rings (e.g., β-carotene and zeaxanthin) or one ɛ-
and one β-ring (e.g., lutein). Carotenoids with two ɛ-rings are
uncommon. We reported earlier that the
Arabidopsis
thaliana
lycopene ɛ-cyclase (LCYe) adds one ɛ-ring to the
symmetrical linear substrate lycopene, whereas the structurally related
lycopene β-cyclase (LCYb) adds two β-rings. Here we describe a cDNA
encoding LCYe in romaine lettuce (
Lactuca sativa
var.
romaine), one of the few plant species known to accumulate substantial
quantities of a carotenoid with two ɛ-rings: lactucaxanthin. The
product of the lettuce cDNA, similar in sequence to the
Arabidopsis
LCYe (77% amino acid identity), efficiently
converted lycopene into the bicyclic ɛ-carotene in a heterologous
Escherichia coli
system. Regions of the lettuce and
Arabidopsis
ɛ-cyclases involved in the determination
of ring number were mapped by analysis of chimeric ɛ-cyclases
constructed by using an inverse PCR approach. A single amino acid was
found to act as a molecular switch: lettuce LCYe mutant H457L added
only one ɛ-ring to lycopene, whereas the complementary
Arabidopsis
LCYe mutant, L448H, added two ɛ-rings. An
R residue in this position also yields a bi-ɛ-cyclase for both the
lettuce and
Arabidopsis
enzymes. Construction and
analysis of chimera of related enzymes with differing catalytic
activities provide an informative approach that may be of particular
utility for studying membrane-associated enzymes that cannot easily be
crystallized or modeled to existing crystal structures.
A robust inducible-repressible promoter greatly facilitates gene knockouts, conditional expression, and overexpression of homologous and heterologous genes in
Tetrahymena
thermophila
Authors: Shang Yuhua , Song Xiaoyuan , Bowen Josephine , Corstanje Robert , Gao Yan , Gaertig Jacek , Gorovsky Martin A.
Published: July 2002

The Cd
2+
-inducible metallothionein (
MTT1
) gene was cloned from
Tetrahymena thermophila
. Northern blot analysis showed that
MTT1
mRNA is not detectable in the absence of Cd
2+
, is induced within 10 min of its addition, is expressed in proportion to its concentration, and rapidly disappears upon its withdrawal. Similarly, when the
neo1
gene coding region flanked by the
MTT1
gene noncoding sequences was used to disrupt the
MTT1
locus, no transformants were observed in the absence of Cd
2+
, and the number of transformants was proportional to increased Cd
2+
concentration. The
neo3
cassette, in which the
MTT1
promoter replaced the histone gene
HHF1
promoter of the previously used
neo2
cassette
,
transformed cells at much higher frequencies than
neo2
and produced germ-line knockouts where
neo2
had failed. Rescuing the progeny of a mating of γ-tubulin gene,
GTU1,
knockout heterokaryons with a
GTU1
gene inserted into the
MTT1
locus yielded >75 times more transformants than rescuing with the wild-type
GTU1
gene itself. When cells rescued with the
MTT1-GTU1
chimeric gene were transferred to medium lacking Cd
2+
, they stopped growing and had phenotypic changes indistinguishable from cells containing only disrupted
GTU1
genes. Thus, it is now possible to create conditional lethal mutants and study the terminal phenotypes of null mutations for essential genes by replacing the endogenous gene with one under the control of the
MTT1
promoter. The
MTT1
promoter also resulted in ≈30 times more overexpression of the IAG48[G1] surface antigen gene of the ciliate fish parasite
Ichthyophthirius multifiliis
than the highly expressed
BTU1
promoter, accounting for ≈1% of the total cell protein. Thus, the
MTT1
promoter should enable routine over-expression of endogenous and foreign genes in
Tetrahymena
.
The lipofuscin component A2E selectively inhibits phagolysosomal degradation of photoreceptor phospholipid by the retinal pigment epithelium
Authors: Finnemann Silvia C. , Leung Lawrence W. , Rodriguez-Boulan Enrique
Published: July 2002

Daily phagocytosis of spent photoreceptor outer segments is a critical maintenance function performed by the retinal pigment epithelium (RPE) to preserve vision. Aging RPE accumulates lipofuscin, which includes
N
-retinylidene-
N
-retinylethanolamine (A2E) as the major autofluorescent component. We studied the effect of physiological levels of A2E in RPE cultures on their ability to phagocytose outer segments. A2E localized to lysosomes in cultured RPE as well as in human RPE
in situ
. A2E-loaded RPE cells in culture bound and internalized identical numbers of outer segments as control RPE indicating that A2E does not alter early steps of phagocytosis. A2E-loaded RPE degraded outer segment proteins efficiently but, strikingly, failed to completely digest phospholipids within 24 h. Because of the circadian rhythm of RPE phagocytosis in the eye, a delay in lipid degradation would likely result in a build up of undigested material in RPE that could contribute to the development of age-related macular degeneration.
Crystal structure and electron transfer kinetics of CueO, a multicopper oxidase required for copper homeostasis in
Escherichia coli
Authors: Roberts Sue A. , Weichsel Andrzej , Grass Gregor , Thakali Keshari , Hazzard James T. , Tollin Gordon , Rensing Christopher , Montfort William R.
Published: July 2002

CueO (YacK), a multicopper oxidase, is part of the copper-regulatory
cue
operon in
Escherichia coli
. The crystal structure of CueO has been determined to 1.4-Å resolution by using multiple anomalous dispersion phasing and an automated building procedure that yielded a nearly complete model without manual intervention. This is the highest resolution multicopper oxidase structure yet determined and provides a particularly clear view of the four coppers at the catalytic center. The overall structure is similar to those of laccase and ascorbate oxidase, but contains an extra 42-residue insert in domain 3 that includes 14 methionines, nine of which lie in a helix that covers the entrance to the type I (T1, blue) copper site. The trinuclear copper cluster has a conformation not previously seen: the Cu-O-Cu binuclear species is nearly linear (Cu-O-Cu bond angle = 170°) and the third (type II) copper lies only 3.1 Å from the bridging oxygen. CueO activity was maximal at pH 6.5 and in the presence of >100 μM Cu(II). Measurements of intermolecular and intramolecular electron transfer with laser flash photolysis in the absence of Cu(II) show that, in addition to the normal reduction of the T1 copper, which occurs with a slow rate (
k =
4 × 10
7
M
−1
⋅s
−1
), a second electron transfer process occurs to an unknown site, possibly the trinuclear cluster, with
k =
9 × 10
7
M
−1
⋅s
−1
, followed by a slow intramolecular electron transfer to T1 copper (
k
∼10 s
−1
). These results suggest the methionine-rich helix blocks access to the T1 site in the absence of excess copper.
The use of mRNA display to select high-affinity protein-binding peptides
Authors: Wilson David S. , Keefe Anthony D. , Szostak Jack W.
Published: July 2002

We report the use of “mRNA display,” an
in
vitro
selection technique, to identify peptide aptamers to a
protein target. mRNA display allows for the preparation of polypeptide
libraries with far greater complexity than is possible with phage
display. Starting with a library of ≈10
13
random
peptides, 20 different aptamers to streptavidin were obtained, with
dissociation constants as low as 5 nM. These aptamers function without
the aid of disulfide bridges or engineered scaffolds, yet possess
affinities comparable to those for monoclonal antibody–antigen
complexes. The aptamers bind streptavidin with three to four orders of
magnitude higher affinity than those isolated previously by phage
display from lower complexity libraries of shorter random peptides.
Like previously isolated peptides, they contain an HPQ consensus motif.
This study shows that, given sufficient length and diversity,
high-affinity aptamers can be obtained even from random nonconstrained
peptide libraries. By engineering structural constraints into these
ultrahigh complexity peptide libraries, it may be possible to produce
binding agents with subnanomolar binding constants.
A self-assembled, redox-responsive receptor for the selective extraction of LiCl from water
Authors: Piotrowski Holger , Severin Kay
Published: July 2002

There is considerable interest in synthetic ionophores with high affinity and selectivity for Li
+
. But so far, compounds that selectively bind Li
+
in the presence of other alkali and alkaline earth metal ions are rare and current approaches toward this goal are often accompanied with substantial synthetic efforts. Here we describe a trinuclear ruthenium metallamacrocyclic complex (1) that was obtained by self-assembly of ruthenium halfsandwich complexes and 3-hydroxy-2-pyridone ligands. This complex was shown to be an extremely potent receptor for LiCl with an affinity high enough to extract LiCl from water. The selectivity of this receptor is exceptional: even in the presence of a large excess of Na
+
, K
+
, Cs
+
, Ca
2+
, and Mg
2+
, Li
+
was extracted exclusively. The Li
+
/Na
+
selectivity ratio was determined to be higher than 1,000:1. Compared with other synthetic ionophores, the receptor 1 offers two additional advantages: (
i
) the synthesis can be accomplished in one step by using simple starting materials; and (
ii
) the presence of lithium ions can be detected electrochemically. Complex 1 is therefore a very attractive candidate for the construction of a Li
+
-specific chemosensor.
Partial shell-filled core-shell tecto(dendrimers): A strategy to surface differentiated nano-clefts and cusps
Authors: Tomalia Donald A. , Brothers Herbert M. , Piehler Lars T. , Durst H. Dupont , Swanson Douglas R.
Published: July 2002

Poly(amidoamine) (PAMAM) dendrimer shell reagents possessing either nucleophilic (i.e., primary amines) or electrophilic (i.e., carboxymethyl esters) functional groups have been covalently assembled around appropriate electrophilic or nucleophilic dendrimer core reagents to produce partial shell filled/core-shell tecto(dendrimers). Partial shell-filled products with saturation levels ranging from 28% to 66% were obtained. These metastable, remarkably monodispersed assemblies possess functionally differentiated nano-cusps and clefts that exhibit “autoreactive” behavior. Pacification of these autoreactive products with appropriate alkanolamine reagents produced robust, nonreactive, “hydroxy-amine-differentiated” surfaces that exhibit very active self-assembly properties. Based on the monodispersity, dimensional scaling, and electrophoretic similarities of PAMAM dendrimers to globular proteins, these assemblies may be viewed as crude biomimetics of classical core shell-type protein aggregates. These dimensionally larger, but analogous PAMAM core-shell tecto(dendrimer) architectures extend and complete a similar pattern of autoreactivity and pacification that was observed earlier for traditional mono PAMAM dendrimer core-shell modules possessing unsaturated shell levels.
Early Cretaceous lineages of monocot flowering plants
Authors: Bremer Kåre
Published: July 2002

The phylogeny of flowering plants is now rapidly being disclosed by analysis of DNA sequence data, and currently, many Cretaceous fossils of flowering plants are being described. Combining molecular phylogenies with reference fossils of known minimum age makes it possible to date the nodes of the phylogenetic tree. The dating may be done by counting inferred changes in sequenced genes along the branches of the phylogeny and calculating change rates by using the reference fossils. Plastid DNA
rbcL
sequences and eight reference fossils indicate that ≈14 of the extant monocot lineages may have diverged from each other during the Early Cretaceous >100 million years B.P. The lineages are very different in size and geographical distribution and provide perspective on flowering plant evolution.
Leukocyte ABCA1 controls susceptibility to atherosclerosis and macrophage recruitment into tissues
Authors: Van Eck Miranda , Bos I. Sophie T. , Kaminski Wolfgang E. , Orsó Evelyn , Rothe Gregor , Twisk Jaap , Böttcher Alfred , Van Amersfoort Edwin S. , Christiansen-Weber Trudy A. , Fung-Leung Wai-Ping , Van Berkel Theo J. C. , Schmitz Gerd
Published: July 2002

The ATP-binding cassette transporter 1 (ABCA1) has recently been identified as a key regulator of high-density lipoprotein (HDL) metabolism, which is defective in familial HDL-deficiency syndromes such as Tangier disease. ABCA1 functions as a facilitator of cellular cholesterol and phospholipid efflux, and its expression is induced during cholesterol uptake in macrophages. To assess the role of macrophage ABCA1 in atherosclerosis, we generated low-density lipoprotein (LDL) receptor knockout (LDLr
−/−
) mice that are selectively deficient in leukocyte ABCA1 (ABCA1
−/−
) by using bone marrow transfer (ABCA1
−/−
→ LDLr
−/−
). Here we demonstrate that ABCA1
−/−
→ LDLr
−/−
chimeras develop significantly larger and more advanced atherosclerotic lesions compared with chimeric LDLr
−/−
mice with functional ABCA1 in hematopoietic cells. Targeted disruption of leukocyte ABCA1 function did not affect plasma HDL cholesterol levels. The amount of macrophages in liver and spleen and peripheral blood leukocyte counts is increased in the ABCA1
−/−
→ LDLr
−/−
chimeras. Our results provide evidence that leukocyte ABCA1 plays a critical role in the protection against atherosclerosis, and we identify ABCA1 as a leukocyte factor that controls the recruitment of inflammatory cells.
Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination
Authors: Sutton Mark D. , Walker Graham C.
Published: July 2002

Two important and timely questions with respect to DNA replication, DNA recombination, and DNA repair are: (
i
) what controls which DNA polymerase gains access to a particular primer-terminus, and (
ii
) what determines whether a DNA polymerase hands off its DNA substrate to either a different DNA polymerase or to a different protein(s) for the completion of the specific biological process? These questions have taken on added importance in light of the fact that the number of known template-dependent DNA polymerases in both eukaryotes and in prokaryotes has grown tremendously in the past two years. Most notably, the current list now includes a completely new family of enzymes that are capable of replicating imperfect DNA templates. This UmuC-DinB-Rad30-Rev1 superfamily of DNA polymerases has members in all three kingdoms of life. Members of this family have recently received a great deal of attention due to the roles they play in translesion DNA synthesis (TLS), the potentially mutagenic replication over DNA lesions that act as potent blocks to continued replication catalyzed by replicative DNA polymerases. Here, we have attempted to summarize our current understanding of the regulation of action of DNA polymerases with respect to their roles in DNA replication, TLS, DNA repair, DNA recombination, and cell cycle progression. In particular, we discuss these issues in the context of the Gram-negative bacterium,
Escherichia coli
, that contains a DNA polymerase (Pol V) known to participate in most, if not all, of these processes.
A quantitative model for membrane fusion based on low-energy intermediates
Authors: Kuzmin Peter I. , Zimmerberg Joshua , Chizmadzhev Yuri A. , Cohen Fredric S.
Published: July 2002

The energetics of a fusion pathway is considered, starting from the contact site where two apposed membranes each locally protrude (as “nipples”) toward each other. The equilibrium distance between the tips of the two nipples is determined by a balance of physical forces: repulsion caused by hydration and attraction generated by fusion proteins. The energy to create the initial stalk, caused by bending of cis monolayer leaflets, is much less when the stalk forms between nipples rather than parallel flat membranes. The stalk cannot, however, expand by bending deformations alone, because this would necessitate the creation of a hydrophobic void of prohibitively high energy. But small movements of the lipids out of the plane of their monolayers allow transformation of the stalk into a modified stalk. This intermediate, not previously considered, is a low-energy structure that can reconfigure into a fusion pore via an additional intermediate, the prepore. The lipids of this latter structure are oriented as in a fusion pore, but the bilayer is locally compressed. All membrane rearrangements occur in a discrete local region without creation of an extended hemifusion diaphragm. Importantly, all steps of the proposed pathway are energetically feasible.
Altered myelopoiesis and the development of acute myeloid leukemia in transgenic mice overexpressing cyclin A1
Authors: Liao Ching , Wang Xiang Yuan , Wei Hong Quan , Li Sherry Q. , Merghoub Taha , Pandolfi Pier Paolo , Wolgemuth Debra J.
Published: July 2002

A mammalian A-type cyclin, cyclin A1, is highly expressed in testes
of both human and mouse and targeted mutagenesis in the mouse has
revealed the unique requirement for cyclin A1 in the progression of
male germ cells through the meiotic cell cycle. While very low levels
of cyclin A1 have been reported in the human hematopoietic system and
brain, the sites of elevated levels of expression of human cyclin A1
were several leukemia cell lines and blood samples from patients with
hematopoietic malignances, notably acute myeloid leukemia. To evaluate
whether cyclin A1 is directly involved with the development of myeloid
leukemia, mouse cyclin A1 protein was overexpressed in the myeloid
lineage of transgenic mice under the direction of the human cathepsin G
(hCG) promoter. The resulting transgenic mice exhibited an increased
proportion of immature myeloid cells in the peripheral blood, bone
marrow, and spleen. The abnormal myelopoiesis developed within the
first few months after birth and progressed to overt acute myeloid
leukemia at a low frequency (≈15%) over the course of 7–14 months.
Both the abnormalities in myelopoiesis and the leukemic state could be
transplanted to irradiated SCID (severe combined immunodeficient) mice.
The observations suggest that cyclin A1 overexpression results in
abnormal myelopoiesis and is necessary, but not sufficient in the
cooperative events inducing the transformed phenotype. The data further
support an important role of cyclin A1 in hematopoiesis and the
etiology of myeloid leukemia.
A framework for sustainability science: A renovated IPAT identity
Authors: Waggoner P. E. , Ausubel J. H.
Published: July 2002

Learning actors' leverage for change along the journey to sustainability requires quantifying the component forces of environmental impact and integrating them. Population, income, consumers' behavior, and producers' efficiency jointly force impact. Here, we renovate the “IPAT Identity” to identify actors with the forces. Forcing impact I are P for population, A for income as gross domestic product (GDP) per capita, C for intensity of use as a good per GDP, and T for efficiency ratios as impact per good. In the “ImPACT Identity,” parents modify P, workers modify A, consumers modify C, and producers modify T. Because annual percentage changes in component forces add to a change in national impact, actors' leverage is reflected transparently in consistent units of annual percentage changes that can be compared from force to force. Examples from energy and food, farming and manufacturing, and steel and water show that declining C, called dematerialization, can temper the sustainability challenge of growth (P × A), and that innovation or efficient technology that lowers T can counter rising consumption (P × A × C). Income elasticity can accommodate connections between income and other forces. From rates of change of forces, the identity can forecast impacts. Alternatively, by identifying the necessary change in forces to cause a projected impact, ImPACT can assay the likelihood and practicability of environmental targets and timetables. An annual 2–3% progress in consumption and technology over many decades and sectors provides a benchmark for sustainability.
Phenserine regulates translation of β-amyloid precursor protein mRNA by a putative interleukin-1 responsive element, a target for drug development
Authors: Shaw Karen T. Y. , Utsuki Tadanobu , Rogers Jack , Yu Qian-Sheng , Sambamurti Kumar , Brossi Arnold , Ge Yuan-Wen , Lahiri Debomoy K. , Greig Nigel H.
Published: July 2002

The reduction in levels of the potentially toxic amyloid-β peptide (Aβ) has emerged as one of the most important therapeutic goals in Alzheimer's disease. Key targets for this goal are factors that affect the expression and processing of the Aβ precursor protein (βAPP). Earlier reports from our laboratory have shown that a novel cholinesterase inhibitor, phenserine, reduces βAPP levels
in vivo
. Herein, we studied the mechanism of phenserine's actions to define the regulatory elements in βAPP processing. Phenserine treatment resulted in decreased secretion of soluble βAPP and Aβ into the conditioned media of human neuroblastoma cells without cellular toxicity. The regulation of βAPP protein expression by phenserine was posttranscriptional as it suppressed βAPP protein expression without altering βAPP mRNA levels. However, phenserine's action was neither mediated through classical receptor signaling pathways, involving extracellular signal-regulated kinase or phosphatidylinositol 3-kinase activation, nor was it associated with the anticholinesterase activity of the drug. Furthermore, phenserine reduced expression of a chloramphenicol acetyltransferase reporter fused to the 5′-mRNA leader sequence of βAPP without altering expression of a control chloramphenicol acetyltransferase reporter. These studies suggest that phenserine reduces Aβ levels by regulating βAPP translation via the recently described iron regulatory element in the 5′-untranslated region of βAPP mRNA, which has been shown previously to be up-regulated in the presence of interleukin-1. This study identifies an approach for the regulation of βAPP expression that can result in a substantial reduction in the level of Aβ.
Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning
Authors: Hu R.-M. , Han Z.-G. , Song H.-D. , Peng Y.-D. , Huang Q.-H. , Ren S.-X. , Gu Y.-J. , Huang C.-H. , Li Y.-B. , Jiang C.-L. , Fu G. , Zhang Q.-H. , Gu B.-W. , Dai M. , Mao Y.-F. , Gao G.-F. , Rong R. , Ye M. , Zhou J. , Xu S.-H. , Gu J. , Shi J.-X. , Jin W.-R. , Zhang C.-K. , Wu T.-M. , Huang G.-Y. , Chen Z. , Chen M.-D. , Chen J.-L.
Published: July 2002

The primary neuroendocrine interface, hypothalamus and pituitary, together with adrenals, constitute the major axis responsible for the maintenance of homeostasis and the response to the perturbations in the environment. The gene expression profiling in the human hypothalamus-pituitary-adrenal axis was catalogued by generating a large amount of expressed sequence tags (ESTs), followed by bioinformatics analysis (
http://www.chgc.sh.cn/
database). Totally, 25,973 sequences of good quality were obtained from 31,130 clones (83.4%) from cDNA libraries of the hypothalamus, pituitary, and adrenal glands. After eliminating 5,347 sequences corresponding to repetitive elements and mtDNA, 20,626 ESTs could be assembled into 9,175 clusters (3,979, 3,074, and 4,116 clusters in hypothalamus, pituitary, and adrenal glands, respectively) when overlapping ESTs were integrated. Of these clusters, 2,777 (30.3%) corresponded to known genes, 4,165 (44.8%) to dbESTs, and 2,233 (24.3%) to novel ESTs. The gene expression profiles reflected well the functional characteristics of the three levels in the hypothalamus-pituitary-adrenal axis, because most of the 20 genes with highest expression showed statistical difference in terms of tissue distribution, including a group of tissue-specific functional markers. Meanwhile, some findings were made with regard to the physiology of the axis, and 200 full-length cDNAs of novel genes were cloned and sequenced. All of these data may contribute to the understanding of the neuroendocrine regulation of human life.
Nutritional regulation of the fatty acid synthase promoter
in vivo
: Sterol regulatory element binding protein functions through an upstream region containing a sterol regulatory element
Authors: Latasa Maria-Jesus , Moon Yang Soo , Kim Kee-Hong , Sul Hei Sook
Published: July 2002

The transcription of fatty acid synthase (FAS), a central enzyme in
de novo
lipogenesis, is dramatically induced by fasting/refeeding and insulin. We reported that upstream stimulatory factor binding to the −65 E-box is required for induction of the FAS transcription by insulin in 3T3-L1 adipocytes. On the other hand, we recently found that two upstream 5′ regions are required for induction
in vivo
by fasting/refeeding and insulin; one at −278 to −131 albeit at a low level, and the other at −444 to −278 with an E-box at −332 where upstream stimulatory factor functions for maximal induction. Here, we generated double transgenic mice carrying the chloramphenicol acetyltransferase reporter driven by the various 5′ deletions of the FAS promoter region and a truncated active form of the sterol regulatory element (SRE) binding protein (SREBP)-1a. We found that SREBP participates in the nutritional regulation of the FAS promoter and that the region between −278 and −131 bp is required for SREBP function. We demonstrate that SREBP binds the −150 canonical SRE present between −278 and −131, and SREBP can function through the −150 SRE in cultured cells. These
in vivo
and
in vitro
results indicate that SREBP is involved in the nutritional induction of the FAS promoter via the −278/−131 region and that the −150 SRE is the target sequence.