bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural convection in a differentially heated horizontal cylinder: Effects of Prandtl number on flow structure and instability
Authors: Xin Shihe , Le Quéré Patrick , Daube Olivier
Published: July 2002

Natural convection in a differentially heated horizontal cylinder is investigated numerically and analytically. Particular attention is paid to the structure of steady convection, the nature of the transients and the onset of unsteadiness for a range of Prandtl numbers extending from 0.7 to infinity. The numerical algorithm integrates the 2-D Navier-Stokes equations in velocity-pressure formulation with a Chebyshev-Fourier spatial approximation. A gradual shift from the conduction to the boundary layer regime is observed for increasing Rayleigh number and the steady flow structure becomes rapidly independent of Pr. Whereas classical scalings are obtained for the azimuthal velocity and the thermal boundary layer thickness, the dynamic boundary layer thickness is found to be independent of the Prandtl number. A simplified semi-analytical model derived from projecting the governing equations on the lowest Fourier modes is proposed, which explains this property. Its solutions are in good quantitative agreement with the full nonlinear solutions in particular for large Prandtl numbers. For large enough Rayleigh values, the transients are found to be dominated by internal waves and the approach to steady state is achieved in an oscillatory manner by decay of internal wave motion. In the steady boundary layer regime, the average Nusselt number classically scales like Ra1/4 and a correlation valid over the range of Prandtl numbers considered is 0.28Ra1/4. The onset of unsteadiness is investigated either by direct numerical integration or by linear stability analysis which combines Newton’s iterations to determine the unstable steady states and Arnoldi’s method to compute the eigenvalues of largest real part of the linearized evolution operator about a steady state. It is thus found that the steady state solution undergoes a Hopf bifurcation and that depending on the Prandtl number the most unstable eigenvector may break or keep the symmetry of the base flow. The critical Rayleigh number is found to achieve an asymptotic value for large enough Prandtl number. The location of the hottest point is also shown to have a very large effect on the critical value. Finally, time integration of the unsteady nonlinear equations indicates that the Hopf bifurcation seems of supercritical type for values of the Prandtl number up to 9 and possibly subcritical for larger Pr values.
The generation of the first visible wind waves
Authors: Caulliez G. , Ricci N. , Dupont R.
Published: July 2002

In this paper we report the results of the first laboratory study on the relationship between the initial growth of the short wind waves and the simultaneous development of the wind-induced drift current. The phenomenon of the first visible ripples appearing “suddenly” on the water surface and forming V-shaped streaks aligned with the wind is explained. We show that the laminar–turbulent transition of the near surface water flow causes an explosive growth of the initial wind-generated ripples. The grown ripples become visible and thus mark the surface of the well-localized V-shaped turbulent zones forming the streaks.
Surface current equilibria from a geometric point of view
Authors: Kaiser R. , Salat A.
Published: July 2002

In this paper the inverse problem of the existence of surface current magnetohydrodynamic (MHD) equilibria in toroidal geometry with vanishing magnetic field inside is addressed. Inverse means that the plasma–vacuum interface rather than the external wall or conductors is given, and the latter remain to be determined. This makes a reformulation of the problem possible in geometric terms: what toroidal surfaces with analytic parametrization allow a simple analytic covering by geodesics? If such a covering by geodesics (field lines) exists, their orthogonal trajectories (current lines) also form a simple covering, and are described by a function satisfying a nonlinear partial differential equation of the Hamilton–Jacobi type, whose coefficients are combinations of the metric elements of the surface. All known equilibria—equilibria with zero and infinite rotational transform and the symmetric ones in the case of finite rotational transform—turn out to be solutions of separable cases of that equation, and allow a unified description if the toroidal surface is parametrized in the moving trihedral associated with a closed curve. Analogously to volume current equilibria, the only continuous symmetries compatible with separability are plane, helical, and axial symmetry. In the nonseparable case numerical evidence is presented for cases with chaotic behavior of geodesics, thus restricting possible equilibria for these surfaces. For weak deviation from axisymmetry, Kolmogorov–Arnold–Moser (KAM)-type behavior is observed, i.e., destruction of geodesic coverings with a low rational rotational transform and preservation of those with irrational rotational transform. A previous attempt to establish three-dimensional surface current equilibria on the basis of the KAM theorem is rejected as incomplete, and a complete proof of the existence of equilibria in the weakly nonaxisymmetric case, based on the twist theorem for mappings, is given. Finally, for a certain class of strong deviations from axisymmetry, an analytic criterion is formulated that rules out equilibria for these surfaces.
Magnetohydrodynamics of dusty plasmas
Authors: Shukla P. K. , Rahman H. U.
Published: July 2002

A set of magnetohydrodynamic (MHD) equations for multi-component dusty plasmas has been derived, by assuming that the characteristic wave frequency is much smaller than the ion gyrofrequency. The dusty plasma MHD equations admit a linear dispersion relation which exhibits a coupling between dust-Alfvén, dust-magnetosonic, and dust-whistler waves. The dust inertia is found to play a major role in the wave dynamics.
Structure of the plasma-wall interaction in an oblique magnetic field
Authors: Ahedo E.
Published: July 2002

The influence of the magnetic field strength B and angle of incidence ψ on the one-dimensional (1-D) structure of a weakly collisional plasma near a charged wall is investigated. The models of Chodura [Phys. Fluids 25, 1628 (1982)] and Riemann [Phys. Plasmas 1, 552 (1994)] are recovered as particular cases: intermediate-B and weak-B cases, respectively, of the model presented here, and are compared with a third, strong-B case, where the space-charge sheath is partially magnetized. A triple structure comprising (collisional) presheath, Chodura layer, and sheath, exists only for the intermediate-B case. For weaker and stronger ranges of B, the Chodura layer disappears immersed into the presheath and the sheath, respectively, recovering a classical double-structure. In the Chodura model the importance of the collisional presheath to characterize completely the perturbation region is discussed. For the weak-B case: results for the whole range of angles of incidence are presented and compared; for grazing incidence and a near-collisionless plasma, an approximate analytical solution is derived; and, the asymptotic convergence to the triple-structure is shown. For the strong-B case, the analysis includes: (i) an involved derivation of the local behavior around the entrance point to the sheath, and (ii), for a certain range of ψ, to cross, with a regular solution, an internal singular point of the sheath equations. The similarities between the entrance conditions to the different plasma regions are pointed out.
Reduction of laser self-focusing in plasma by polarization smoothing
Authors: Lefebvre E. , Berger R. L. , Langdon A. B. , MacGowan B. J. , Rothenberg J. E. , Williams E. A.
Published: July 2002

Dramatic reductions in the filamentation of an intense speckled laser beam in a hot, high-density plasma are reported in simulations of polarization smoothing (PS), which consists of irradiating the plasma with two superimposed, orthogonally polarized and uncorrelated speckle patterns. PS instantaneously smooths the spatial beam structure, and thus can be more effective than temporal smoothing techniques. Even greater reduction in filamentation, offering improved prospects for inertial fusion, results from combining these two methods.
Stable Josephson reference voltages between 0.1 and 1.3 V for high-precision voltage standards
Authors: Niemeyer J. , Grimm L. , Meier W. , Hinken J. H. , Vollmer E.
Published: July 2002

A new series array of 1440 Josephson tunnel junctions has been developed and tested as a reference voltage standard. It yields microwave induced quantized voltage steps up to 1.3 V. The steps are usually stable for more than 5 h with a microwave driving frequency of either 70 or 90 GHz. A high-resolution comparison of a constant voltage step at the 1-V level with the electromotive force of a saturated Weston cell is described. The comparison shows that the step voltage is constant to within ±1 nV over the full step width.
Influence of low-energy electron irradiation on the adhesion of gold films on a silicon substrate
Authors: Dallaporta H. , Cros A.
Published: July 2002

Gold-silicon interfaces have been studied under ultrahigh vacuum conditions. The interface growth, its characterization by Auger electron spectroscopy, and its irradiation by low-energy (1–3 keV) electrons have all been carried out in situ. We have estimated the adhesion of the gold layer by the peeling test. The adhesion is good when Au is deposited on a clean Si substrate and poor when a native oxide (thickness ∼10–15 Å) is present at the interface. We show that the electron irradiation decomposes the oxide partially and this produces a drastic increase of the adhesion. The oxide decomposition is not thermally induced and is attributed to electronic effects. We suggest that the formation of Au–Si bonds at the interface is at the origin of the adhesion enhancement.
Friction and wear measurements of sputtered MoSx films amorphized by ion bombardment
Authors: Mikkelsen Niels Jo/rgen , Chevallier Jacques , So/rensen Gunnar , Straede Christen A.
Published: July 2002

The present study presents an experimental evidence for amorphization of rf sputtered MoSx films by ion bombardment. Even at low doses (3×1015 ions/cm2) of 400 keV argon ions a complete amorphization was confirmed by x-ray diffraction analysis and transmission electron microscopy. As a result of the ion bombardment the film density increased 100% to almost the bulk value for MoS2. The friction coefficient for ion beam amorphized MoSx was measured to be 0.04 in agreement with the values reported for crystalline films but disagreeing considerably with the friction coefficient of 0.4 previously reported for amorphous films.
Peptide hybrids containing α- and β-amino acids: Structure of a decapeptide β-hairpin with two facing β-phenylalanine residues
Authors: Karle Isabella L. , Gopi Hosahudya N. , Balaram Padmanabhan
Published: July 2002

A β-hairpin conformation has been characterized in crystals of the decapeptidet-butoxycarbonyl-Leu-Val-βPhe-Val-DPro-Gly-Leu-βPhe-Val-Val-methyl ester [βPhe; (S)-β3homophenylalanine] by x-ray diffraction. The polypeptide chain reversal is nucleated by the centrally positionedDPro-Gly segment, which adopts a type-I′ β-turn conformation. Four intramolecular cross-strand hydrogen bonds stabilize the peptide fold. The βPhe(3) and βPhe(8) residues occupy facing positions on the hairpin, with the side chains projecting on opposite faces of the β-sheet. At the site of insertion of β-residues, the polarity of the peptide units along each strand reverses, as compared with the α-peptide segments. In this analog, a small segment of a polar sheet is observed, where adjacent CO and NH groups line up in opposite directions in each strand. In the crystal, an extended β-sheet is formed by hydrogen bonding between strands of antiparallel pairs of β-hairpins. The crystallographic parameters for C65H102N10O13⋅ 3H2O are: space group P212121; a = 19.059(8) Å, b = 19.470(2) Å, c = 21.077(2) Å; Z = 4; agreement factorR1= 9.12% for 3,984 data observed >4σ(F) and a resolution of 0.90 Å.
Generation of ultra-intense single-cycle laser pulses by using photon deceleration
Authors: Tsung F. S. , Ren C. , Silva L. O. , Mori W. B. , Katsouleas T.
Published: July 2002

A scheme to generate single-cycle laser pulses is presented based
on photon deceleration in underdense plasmas. This robust and
tunable process is ideally suited for lasers above critical power
because it takes advantage of the relativistic self-focusing of these
lasers and the nonlinear features of the plasma wake. The mechanism is
demonstrated by particle-in-cell simulations in three and 2½
dimensions, resulting in pulse shortening up to a factor of 4, thus
making it feasible to generate few-femtosecond single-cycle pulses in
the optical to IR domain with intensities
I
>
10
20
W/cm
2
by using present-day laser
technology.
Selective pressure of a quinoxaline nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) on HIV-1 replication results in the emergence of nucleoside RT-inhibitor-specific (RT Leu-74-->Val or Ile and Val-75-->Leu or Ile) HIV-1 mutants.
Authors: Kleim J P , Rösner M , Winkler I , Paessens A , Kirsch R , Hsiou Y , Arnold E , Riess G
Published: July 2002

The quinoxaline nonnucleoside RT inhibitor (NNRTI) (S)-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3,4- dihydroquinoxaline-2(1H)-thione (HBY 097) was used to select for drug-resistant HIV-1 variants in vitro. The viruses first developed mutations affecting the NNRTI-binding pocket, and five of six strains displayed the RT G190-->E substitution, which is characteristic for HIV-1 resistance against quinoxalines. In one variant, a new mutant (G190-->Q) most likely evolved from preexisting G190-->E mutants. The negative charge introduced by the G190-->E substitution was maintained at that site of the pocket by simultaneous selection for V179-->D together with G190-->Q. After continued exposure to the drug, mutations at positions so far known to be specific for resistance against nucleoside RT inhibitors (NRTIs) (L74-->V/I and V75-->L/I) were consistently detected in all cultures. The inhibitory activities of the cellular conversion product of 2',3'-dideoxyinosine (ddI, didanosine), 2',3'-dideoxyadenosine (ddA) and of 2',3'-didehydro-3'-deoxythymidine (d4T, stavudine) against these late-passage viruses were shown to be enhanced with the L74-->V/I RT mutant virus as compared with the wild-type (wt) HIV-1MN isolate. Clonal analysis proved linkage of the codon 74 and codon 75 mutations to the NNRTI-specific mutations in all RT gene fragments. The nonnucleoside- and nucleoside-resistance mutation sites are separated by approximately 35 A. We propose that the two sites "communicate" through the template-primer which is situated in the DNA-binding cleft between these two sites. Quinoxalines cause high selective pressure on HIV-1 replication in vitro; however, the implication of these findings for the treatment of HIV-1 infection has yet to be determined.
Limited up-regulation of DNA methyltransferase in human colon cancer reflecting increased cell proliferation.
Authors: Lee P J , Washer L L , Law D J , Boland C R , Horon I L , Feinberg A P
Published: July 2002

Epigenetic alterations in the genome of tumor cells have attracted considerable attention since the discovery of widespread alterations in DNA methylation of colorectal cancers over 10 years ago. However, the mechanism of these changes has remained obscure. el-Deiry and coworkers [el-Deiry, W. S., Nelkin, B. D., Celano, P., Yen, R. C., Falco, J. P., Hamilton, S. R. & Baylin, S. B. (1991) Proc. Natl. Acad. Sci. USA 88, 3470-3474], using a quantitative reverse transcription-PCR assay, reported 15-fold increased expression of DNA methyltransferase (MTase) in colon cancer, compared with matched normal colon mucosa, and a 200-fold increase in MTase mRNA levels compared with mucosa of unaffected patients. These authors suggested that increases in MTase mRNA levels play a direct pathogenetic role in colon carcinogenesis. To test this hypothesis, we developed a sensitive quantitative RNase protection assay of MTase, linear over three orders of magnitude. Using this assay on 12 colorectal carcinomas and matched normal mucosal specimens, we observed a 1.8- to 2.5-fold increase in MTase mRNA levels in colon carcinoma compared with levels in normal mucosa from the same patients. There was no significant difference between the normal mucosa of affected and unaffected patients. Furthermore, when the assay was normalized to histone H4 expression, a measure of S-phase-specific expression, the moderate increase in tumor MTase mRNA levels was no longer observed. These data are in contrast to the previously reported results, and they indicate that changes in MTase mRNA levels in colon cancer are nonspecific and compatible with other markers of cell proliferation.
Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection.
Authors: Mishra R K , Le Tinévez R , Toulmé J J
Published: July 2002

Using an in vitro selection approach, we have isolated oligonucleotides that can bind to a DNA hairpin structure. Complex formation of these oligonucleotides with the target hairpin involves some type of triple-stranded structure with noncanonical interaction, as indicated by bandshift assays and footprinting studies. The selected oligomers can block restriction endonuclease cleavage of the target hairpin in a sequence-specific manner. We demonstrate that in vitro selection can extend the antisense approach to functional targeting of secondary structure motifs. This could provide a basis for interfering with regulatory processes mediated by a variety of nucleic acid structures.
Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation.
Authors: McPhee F , Good A C , Kuntz I D , Craik C S
Published: July 2002

Dimerization of human immunodeficiency virus type 1 protease (HIV-1 PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disruption of the dimer interface inhibits this activity as does formation of heterodimers between wild-type and defective monomers. A structure-based approach was used to identify amino acid substitutions at the dimer interface of HIV-1 PR that facilitate preferential association of heterodimers and inhibit self-association of the defective monomers. Expression of the designed PR monomers inhibits activity of wild-type HIV-1 PR and viral infectivity when assayed in an ex vivo model system. These results show that it is possible to design PR monomers as macromolecular inhibitors that may provide an alternative to small molecule inhibitors for the treatment of HIV infection.
Alterations of the outer membrane composition in
Escherichia coli
lacking the histone-like protein HU
Authors: Painbeni Eric , Caroff Martine , Rouviere-Yaniv Josette
Published: July 2002

Escherichia coli
cells lacking the histone-like protein HU form filaments and have an abnormal number of anucleate cells. Furthermore, their phenotype resembles that of
rfa
mutants, the well-characterized deep-rough phenotype, as they show an enhanced permeability that renders them hypersensitive to chloramphenicol, novobiocin, and detergents. We show that, unlike
rfa
mutants,
hupAB
mutants do not have a truncated lipopolysaccharide but do have an abnormal abundance of OmpF porin in their outer membrane. While the complete absence of HU does not abolish the osmoregulation of OmpF protein synthesis, the steady-state level of
micF
RNA, the negative regulator of OmpF, decreases in bacteria lacking HU, increasing the basal level of this membrane protein. These findings demonstrate a novel link between a bacterial chromosomal protein and the outer membrane composition.
Specific requirement of putrescine for the mitogenic action of juvenile hormone on adult insect neuroblasts
Authors: Cayre Myriam , Strambi Colette , Charpin Pierre , Augier Roger , Strambi Alain
Published: July 2002

Persistent neurogenesis in an adult insect brain was recently shown to be stimulated by juvenile hormone (JH). This morphogenetic hormone was also shown to act on polyamine biosynthesis. To analyze the possible involvement of polyamines in the neurogenic action of JH, two series of experiments were carried out with adult female crickets,
Acheta domesticus
: (
i
) inhibition of the first key enzyme in polyamine biosynthesis, ornithine decarboxylase, with α-difluoromethylornithine (α-DFMO), and examination of the effects of this treatment on the neuroblast proliferation response to JH; and (
ii
) examination of the effects of putrescine supplementation on the mitotic index of JH-deprived and α-DFMO-treated females. In control females, α-DFMO treatment, as well as JH deprivation, greatly reduced neuroblast proliferation. Putrescine supplementation in α-DFMO-treated insects overcame the effects of α-DFMO, and allowed for detection of putrescine in the neural tissue and stimulation of brain neurogenesis. In JH-deprived females, α-DFMO treatment completely prevented the stimulatory action of JH on neuroblast proliferation and on brain putrescine levels. By contrast, putrescine feeding of JH-deprived animals was able to mimic the stimulatory effect of JH: brain putrescine levels increased and neuroblast proliferation was restored. To our knowledge, this report demonstrates for the first time that
in vivo
administration of putrescine can mimic the effects of a morphogenetic hormone on adult neuroblast proliferation, and shows the importance of polyamines, especially putrescine, in the transduction of JH message in neural tissue.
The amphiphysin-like protein 1 (ALP1) interacts functionally with the cABL tyrosine kinase and may play a role in cytoskeletal regulation
Authors: Kadlec Lisa , Pendergast Ann Marie
Published: July 2002

cABL is a protooncogene, activated in a subset of human leukemias, whose protein product is a nonreceptor tyrosine kinase of unknown function. cABL has a complex structure that includes several domains and motifs found in proteins implicated in signal transduction pathways. An approach to elucidate cABL function is to identify proteins that interact directly with cABL and that may serve as regulators or effectors of its activity. To this end, a protein-interaction screen of a phage expression library was undertaken to identify proteins that interact with specific domains of cABL. An SH3-domain-containing protein has been identified that interacts with sequences in the cABL carboxyl terminus. The cDNA encoding ALP1 (
a
mphiphysin-
l
ike
p
rotein 1) was isolated from a 16-day mouse embryo. ALP1 has high homology to BIN1, a recently cloned myc-interacting protein, and also shows significant homology to amphiphysin, a neuronal protein cloned from human and chicken. The amino terminus has homology to two yeast proteins, Rvs167 and Rvs161, which are involved in cell entry into stationary phase and cytoskeletal organization. ALP1 binds cABL
in vitro
and
in vivo
. Expression of ALP1 results in morphological transformation of NIH 3T3 fibroblasts in a cABL-dependent manner. The properties of ALP1 suggest that it may be involved in possible cytoskeletal functions of the cABL kinase. Additionally, these results provide further evidence for the importance of the cABL carboxyl terminus and its binding proteins in the regulation of cABL function.
Effects of muscarinic blockade in perirhinal cortex during visual recognition
Authors: Tang Yi , Mishkin Mortimer , Aigner Thomas G.
Published: July 2002

Stimulus recognition in monkeys is severely impaired by destruction or dysfunction of the perirhinal cortex and also by systemic administration of the cholinergic-muscarinic receptor blocker, scopolamine. These two effects are shown here to be linked: Stimulus recognition was found to be significantly impaired after bilateral microinjection of scopolamine directly into the perirhinal cortex, but not after equivalent injections into the laterally adjacent visual area TE or into the dentate gyrus of the overlying hippocampal formation. The results suggest that the formation of stimulus memories depends critically on cholinergic-muscarinic activation of the perirhinal area, providing a new clue to how stimulus representations are stored.
Highly purified CD25−resting T cells cannot be infectedde novowith HIV-1
Authors: Chou Chin-Sheng , Ramilo Octavio , Vitetta Ellen S.
Published: July 2002

Previous studies have demonstrated that the expression of CD25 can distinguish CD25−latently infected cells from CD25+cells actively producing virus. Our studies were designed to characterize the nature and stability of the viral genome in CD25−quiescent HIV-1-infected cells and to determine whether these cells could be infectedde novowith HIV-1. Our results show that: (i) When unfractionated peripheral blood mononuclear cells are first infected with HIV-1 and the CD25−cells then isolated, the latter contain only incomplete DNA transcripts and no full-length DNA or 2-LTR circles. Phytohemagglutinin activation of these CD25−cells results in the generation of full-length viral DNA and p24 production. (ii) When CD25−CD4+cells are first purified from peripheral blood mononuclear cells and then incubated with HIV-1, viral DNA cannot be detected, suggesting that these purified cells cannot be infected. Furthermore, CD25−adherent cells do not facilitate the infection of CD4+CD25−T cells when they were present at the time of incubation with HIV-1. Taken together, these studies suggest either that (i) the CD25−cells containing incomplete DNA transcripts are derived from infected-activated CD25+cells, which subsequently become CD25−or (ii) the presence of CD25+cells is required for the infection of CD25−cellsin vitro.
A direct comparison of helix propensity in proteins and peptides
Authors: Myers Jeffrey K. , Pace C. Nick , Scholtz J. Martin
Published: July 2002

α-Helical secondary structure occurs widely in globular proteins and its formation is a key step in their folding. As a consequence, understanding the energetics of helix formation is crucial to understanding protein folding and stability. We have measured the helix propensities of the nonpolar amino acids for an α-helix in an intact protein, ribonuclease T
1
, and for a 17-residue peptide with a sequence identical to that of the α-helix in the protein. The helix propensities are in excellent agreement. This shows that when compared in the same sequence context, the helix propensities of the nonpolar amino acids are identical in helical peptides and intact proteins, and that conclusions based on studies of the helix-to-coil transitions of peptides may, in favorable cases, be directly applicable to proteins. Our helix propensities based on ribonuclease T
1
are in good agreement with those from similar studies of barnase and T4 lysozyme. In contrast, our helix propensities differ substantially from those derived from studies of alanine-stabilized or salt bridge-stabilized model α-helical peptides.
The exocyclic groups of DNA modulate the affinity and positioning of the histone octamer
Authors: Buttinelli Memmo , Minnock Andrew , Panetta Gianna , Waring Michael , Travers Andrew
Published: July 2002

To investigate the nature of the chemical determinants in DNA required for nonspecific binding and bending by proteins we have created a novel DNA in which inosine–5-methylcytosine and 2,6-diaminopurine–uracil base pairs are substituted for normal base pairs in a defined DNA sequence. This procedure completely switches the patterns of the base pair H bonding and attachment of exocyclic groups. We show that this DNA binds a histone octamer more tightly than normal DNA but, surprisingly, does not alter the orientation of the sequence on the surface of the protein. However, in general, the addition or removal of DNA exocyclic groups reduces or increases, respectively, the affinity for the histone octamer. The average incremental change in binding energy for a single exocyclic group is ≈40 J/mol. The orientation of the DNA in core nucleosomes also is sensitive to the number and nature of the exocyclic groups present. Notably, substitution with the naturally occurring cytosine analogue, 5-methylcytosine, shifts the preferred rotational position by 3 bp, whereas incorporating 2,6-diaminopurine shifts it 2 bp in the opposite direction. These manipulations potentially would alter the accessibility of a protein recognition sequence on the surface of the histone octamer. We propose that exocyclic groups impose steric constraints on protein-induced DNA wrapping and are also important in determining the orientation of DNA on a protein surface. In addition, we consider the implications of the selection of A-T and G-C base pairs in natural DNA.
Cytotoxic agents directed to peptide hormone receptors: Defining the requirements for a successful drug
Authors: Czerwinski Grzegorz , Tarasova Nadya I. , Michejda Christopher J.
Published: July 2002

In principle, cell surface receptors that are overexpressed in tumor tissue could serve as targets for anticancer drugs attached to receptor ligands. The purpose of this paper is to identify the necessary elements for a successful receptor-targeted drug. We used the gastrin/cholecystokinin type B receptor as a model delivery system, and we report on the synthesis, trafficking, and
in vitro
and
in vivo
evaluation of heptagastrin, the C-terminal heptapeptide of gastrin, linked via an appropriate linker to a potently cytotoxic ellipticine derivative, 1-[3-[
N
-(3-aminopropyl)-
N
-methylamino]propyl]amino-9-methoxy-5,11-dimethyl-6H-pyrido[4,3-b]carbazole. These data, and previous work from our laboratory, show that the drug-complexed ligand is sorted to lysosomes whereas the receptor is recycled to the plasma membrane. The lysosomal processing of the ligand/drug construct depends on the linker between the ligand sequence and the cytotoxic moiety. We show that heptagastrin linked to ellipticine via a succinoyl-substituted pentapeptide, AlaLeuAlaLeuAla, is at least 10
3
more toxic to cholecystokinin type B receptor-positive NIH/3T3 cells than to isogenic NIH/3T3 cells lacking the receptor. The conjugated drug eradicated all receptor-positive tumor cells
in vivo
without producing any general toxicity. The data indicate that the density of the cell surface receptor, the properties of the cytotoxic moiety, and the correct processing of the drug-conjugated ligand in lysosomes are crucial to the effectiveness of a receptor-targeted drug.
A strategy for genome-wide gene analysis: Integrated procedure for gene identification
Authors: Wang San Ming , Rowley Janet D.
Published: July 2002

We have developed a technique called the Integrated Procedure for Gene Identification that modifies and integrates parts from several existing techniques to increase the efficiency for genome-wide gene identification. The procedure has the following features: (
i
) Only the 3′ portion of the expressed templates is used to ensure a match to 3′ expressed sequence tag (EST) sequences; (
ii
) the 3′ portion of the cDNA is poly dA/poly dT minus, which maintains complete representation of the expressed copies, particularly the rare copies, which otherwise would be lost heavily because of random poly dA/poly dT hybridization in the subtraction reaction; (
iii
) redundancy is decreased substantially by the subtraction reaction to reduce the effort for sequencing analysis; (
iv
) the nonsubtracted templates that largely contain the rare copies are amplified selectively with suppression PCR and are sequenced directly or through serial analysis of gene expression (SAGE); and (
v
) the identified sequences are matched to databases to determine whether they are cloned genes, ESTs, or novel sequences. Using this procedure in a model system, we showed that the redundant copies were largely removed, and the rates of EST matches and the novel sequence identification were significantly increased. Most of the plasmids containing the matched EST are readily available from the IMAGE consortium. This technique can be used to index genome-wide expressed genes and to identify differentially expressed genes in different cells. Compared with the existing techniques, this procedure is relatively efficient, simple, less expensive, and labor intensive. It is especially useful for standard molecular laboratories to perform genome-wide studies.
Singular value decomposition with self-modeling applied to determine bacteriorhodopsin intermediate spectra: Analysis of simulated data
Authors: Zimányi László , Kulcsár Ágnes , Lanyi Janos K. , Sears Donald F. , Saltiel Jack
Published: July 2002

An
a priori
model-independent method for the
determination of accurate spectra of photocycle intermediates is
developed. The method, singular value decomposition with self-modeling
(SVD-SM), is tested on simulated difference spectra designed to mimic
the photocycle of the Asp-96 → Asn mutant of
bacteriorhodopsin. Stoichiometric constraints,
valid until the onset of the recovery of bleached
bacteriorhodopsin at the end of the photocycle,
guide the self-modeling procedure. The difference spectra of the
intermediates are determined in eigenvector space by confining the
search for their coordinates to a stoichiometric plane. In the absence
of random noise, SVD-SM recovers the intermediate spectra and their
time evolution nearly exactly. The recovery of input spectra and
kinetics is excellent although somewhat less exact when realistic
random noise is included in the input spectra. The difference between
recovered and input kinetics is now visually discernible, but the same
reaction scheme with nearly identical rate constants to those assumed
in the simulation fits the output kinetics well. SVD-SM relegates the
selection of a photocycle model to the late stage of the analysis. It
thus avoids derivation of erroneous model-specific spectra that result
from global model-fitting approaches that assume a model at the outset.
Identification of the proton pathway in bacterial reaction centers: Replacement of Asp-M17 and Asp-L210 with Asn reduces the proton transfer rate in the presence of Cd
2+
Authors: Paddock M. L. , Feher G. , Okamura M. Y.
Published: July 2002

The reaction center (RC) from
Rhodobacter sphaeroides
converts light into chemical energy through the reduction and protonation of a bound quinone molecule Q
B
(the secondary quinone electron acceptor). We investigated the proton transfer pathway by measuring the proton-coupled electron transfer,
k
AB
(2)
[Q
A
⨪Q
B
⨪ + H
+
→ Q
A
(Q
B
H)
−
] in native and mutant RCs in the absence and presence of Cd
2+
. Previous work has shown that the binding of Cd
2+
decreases
k
AB
(2)
in native RCs ≈100-fold. The preceding paper shows that bound Cd
2+
binds to Asp-H124, His-H126, and His-H128. This region represents the entry point for protons. In this work we investigated the proton transfer pathway connecting the entry point with Q
B
⨪ by searching for mutations that greatly affect
k
AB
(2)
(≳10-fold) in the presence of Cd
2+
, where
k
AB
(2)
is limited by the proton transfer rate (
k
H
). Upon mutation of Asp-L210 or Asp-M17 to Asn,
k
H
decreased from ≈60 s
−1
to ≈7 s
−1
, which shows the important role that Asp-L210 and Asp-M17 play in the proton transfer chain. By comparing the rate of proton transfer in the mutants (
k
H
≈ 7 s
−1
) with that in native RCs in the absence of Cd
2+
(
k
H
≥ 10
4
s
−1
), we conclude that alternate proton transfer pathways, which have been postulated, are at least 10
3
-fold less effective.
Quantitative assessment of
Hox
complex expression in the indirect development of the polychaete annelid
Chaetopterus
sp.
Authors: Peterson Kevin J. , Irvine Steven Q. , Cameron R. Andrew , Davidson Eric H.
Published: July 2002

A prediction from the set-aside theory of bilaterian origins is that pattern formation processes such as those controlled by the
Hox
cluster genes are required specifically for adult body plan formation. This prediction can be tested in animals that use maximal indirect development, in which the embryonic formation of the larva and the postembryonic formation of the adult body plan are temporally and spatially distinct. To this end, we quantitatively measured the amount of transcripts for five
Hox
genes in embryos of a lophotrochozoan, the polychaete annelid
Chaetopterus
sp. The polychaete
Hox
complex is shown not to be expressed during embryogenesis, but transcripts of all measured
Hox
complex genes are detected at significant levels during the initial stages of adult body plan formation. Temporal colinearity in the sequence of their activation is observed, so that activation follows the 3′–5′ arrangement of the genes. Moreover,
Hox
gene expression is spatially localized to the region of teloblastic set-aside cells of the later-stage embryos. This study shows that an indirectly developing lophotrochozoan shares with an indirectly developing deuterostome, the sea urchin, a common mode of
Hox
complex utilization: construction of the larva, whether a trochophore or dipleurula, does not involve
Hox
cluster expression, but in both forms the complex is expressed in the set-aside cells from which the adult body plan derives.
Effects of testosterone propionate and nandrolone decanoate on body composition and lipoprotein concentrations in the rat
Authors: Lewanowitsch T. , Irvine R. J.
Published: July 2002

Anabolic–androgenic steroids (AAS) are used illicitly by athletes, bodybuilders and polydrug users. Cardiovascular complications are associated with their use and adverse lipoprotein alterations have been implicated as a contributing factor. In this experiment male and female rats were administered testosterone propionate, nandrolone decanoate or vehicle (peanut oil), 1 mg/kg/day s.c. for 14 days. Only the testosterone‐treated females experienced a significant increase in total body weight gain compared to peanut oil controls. No changes in food and water intake or excretion were noted between these two groups. Total body water increased in the testosterone‐treated female rats. Changes in lipoprotein profiles in female testosterone rats over the treatment period indicated a significant decrease in high‐density lipoproteins (HDL) compared to peanut oil‐treated animals.This study indicates that the treatment protocol used may serve as a model to further investigate the mechanisms underlying the effects of AAS.
Influence of concomitant drugs on methadone elimination half‐life in patients under a maintenance treatment
Authors: Lucas A. C. S. , Bermejo A. M. , Tabernero M. J. , FernÁNdez P. , CÁMpora P.
Published: July 2002

Methadone elimination half‐life was determined in 18 patients under maintenance treatments and found to range from 2.05 to 49.6 h. A study of potential correlations between this parameter and the presence of concomitant drugs, inhibitors or inducers of cytochrome P450, revealed an increase or decrease of methadone elimination half‐life, respectively. Twenty‐four‐hour urinary excretion of methadone was determined in three patients, who were found to release 22.3–49.8% of the dose taken. The amount excreted varied with the chemical form (unaltered drug or its main metabolite) in the three cases. No statistically significant correlation was found between urine pH and the elimination half‐life (p < 0.50).
Combined effects of nicotine and alcohol on subjective, behavioral and physiological responses in humans
Authors: PERKINS KENNETH A.
Published: July 2002

Nicotine and alcohol have each been widely studied in humans, but there has been relatively little attention paid to their combined effects. This is surprising, given the high frequency with which they are consumed together. The limited literature on these combined effects is murky, partly because of failure to recognize that alcohol can have contrasting subjective mood effects depending on whether blood alcohol level is ascending or descending. However, in general, nicotine and alcohol (when blood alcohol level is descending) tend to have contrasting effects on mood (“stimulating” vs. “sedating”, respectively), behavioral performance (slightly improving vs. impairing, respectively), and selected physiological responses (e.g. increased beta EEG vs. increased α EEG, respectively), but similar effects on other physiological responses (e.g. heart rate). Thus, when consumed together, mood, performance, and EEG responses are often intermediate between those due to alcohol alone or nicotine alone. Responses influenced in the same direction by either, such as cardiovascular effects, are exacerbated beyond effects due to either alone. Since mood and behavioral effects are likely to reinforce drug use, the attenuating influence of nicotine on alcohol's sedative effects could explain the frequently observed increase in smoking after alcohol consumption. At the same time, nicotine plus alcohol may exacerbate some physiological responses (e.g. cardiovascular) that can impact negatively on health. Limitations of this research and possible mechanisms of interaction between nicotine and alcohol are briefly noted. The need to consider the modulating influences of environmental and baseline‐relevant factors is also emphasized.
Ethanol‐induced osmolality changes and lymphocyte proliferation
Authors: GREIG J. E. , KEAST D. , PALMER T. N.
Published: July 2002

While there have been reports on the in vitro effects of ethanol on mitogen‐stimulated lymphocyte proliferation, little attention has been paid to whether these effects are mediated by the ethanol molecule per se or the associated hyperosmolality. There is controversy whether ethanol at high concentrations inhibits or has no effect on mitogen‐stimulated proliferation of T cells. In this study we sought to distinguish between effects due to ethanol and those related to increased osmolality. Rat splenocytes were cultured in vitro in hypertonic (320 mOsm) or isotonic (320 mOsm) ethanol solutions (up to 400 mg/dL), or in corresponding hypertonic solutions without ethanol. Proliferative responses to the B cell mitogen lipopolysaccharide and the T cell mitogen concanavalin A were measured by mitochondrial dimethylthiazole diphenyl tetrazolium metabolism and [3H]‐thymidine incorporation into DNA. B cell response was not significantly affected by ethanol under any conditions. By contrast, T cell proliferative responses were significantly inhibited by isotonic ethanol solutions or hypertonic solutions in the absence of ethanol, but not by hypertonic ethanol solutions. These results indicate that, while high osmolality is normally inhibitory to lymphocyte function, the increase in osmolality caused by ethanol is protective against the otherwise detrimental effects of ethanol.
Developing a scale to measure parental attitudes towards preschool speech and language therapy services
Authors: Glogowska Margaret , Campbell Rona , Peters Tim J. , Roulstone Sue , Enderby Pam
Published: July 2002

In the past decade, there has been growing recognition of the need to involve clients in decisions about the healthcare they receive and in the evaluation of services offered. In health services research, survey and scaling methods have become important tools for research into ‘consumer views’ and the perspectives of people receiving healthcare. In spite of the increase in recent years in the participation of parents in their children's Speech and Language Therapy (SLT), there has been little attempt to investigate parents' perceptions and opinions of the services they receive. Moreover, there has been no previous attempt to derive a scale to measure these attitudes. The paper reports a study that explored the attitudes to therapy of 81 parents whose preschool children were receiving SLT intervention. Factor analysis of 12 items on a questionnaire revealed three issues salient in parental attitudes to therapy: practical help, emotional support and the perceived effectiveness of the service. The validity of these factors was supported by other findings from the questionnaire. The properties of the resulting scales are discussed and the ways in which they might be further refined and developed for use in SLT are suggested.
Conformation Changes in Brain Calcineurin in Diabetic Rats with or without Treatment with Vanadyl Sulfate
Authors: Li Hong , Wei Qun
Published: July 2002

Recent studies have shown that vanadium salts are able to reduce blood glucose in diabetics and overcome, to some degree, insulin resistance. This paradigm has been followed to monitor the effects of diabetes and vanadyl treatment on brain calcineurin (CN), an important protein phosphatase. Male rats were rendered diabetic by a single injection of streptozotocin (STZ), resulting in an elevation of blood glucose from 108 ±13 to > 400 mg/dl. Diabetic animals were given vanadyl sulfate trihydrate (0.5 mg/dl.) in their drinking water for 3 weeks, which led to a fall in blood glucose to 156 ±53 mg/ml. Brain CN activity (units/mg brain protein) in diabetic rats was 77% that of control animals, whereas vanadyl‐treated diabetic animals were characterized by CN activities like that of controls. CN was purified from brains of control animals, STZ‐induced diabetic animals, and STZ‐induced diabetic animals receiving vanadyl, then spin‐labeled with 3‐maleimide‐proxyl and studied via electron spin resonance spectroscopy. The rotational correlation time of CN from control animals and vanadyl‐treated diabetic animals was 6.4 ×10 ‐11 s ‐1, whereas that from STZ‐induced‐diabetic animals was 8 ×10 ‐11 s ‐1 . Thus, STZ‐induced diabetes in rats results in an increase in the rotational correlation time of brain CN relative to control animals, yet vanadyl treatment of STZ‐induced diabetic animals reduced the rotational correlation time to that of control. These data suggest that diabetes can lead to apparent conformational changes in brain CN; also, CN conformation in diabetic rats was restored by vanadyl treatment.
A Nuclear Export Signal in Kap95p Is Required for Both Recycling the Import Factor and Interaction with the Nucleoporin GLFG Repeat Regions of Nup116p and Nup100p
Authors: Iovine M. Kathryn , Wente Susan R.
Published: July 2002

During nuclear import, cytosolic transport factors move through the nuclear pore complex (NPC) to the nuclear compartment. Kap95p is required during import for docking the nuclear localization signal-receptor and ligand to the NPC. Recycling of this factor back to the cytoplasm is necessary for continued rounds of import; however, the mechanism for Kap95p recycling is unknown. We have determined that recycling of Kap95p requires a nuclear export signal (NES). A region containing the NES in Kap95p was sufficient to mediate active nuclear export in a microinjection assay. Moreover, the NES was necessary for function. Mutation of the NES in Kap95p resulted in a temperaturesensitive import mutant, and immunofluorescence microscopy experiments showed that the mutated Kap95p was not recycled but instead localized in the nucleus and at the nuclear envelope. Srp1p, the yeast nuclear localization signal-receptor, also accumulated in the nuclei of the arrested kap95 mutant cells. Wild-type and NES-mutated Kap95p both bound Gsp1p (the yeast Ran/TC4 homologue), Srp1p, and the FXFG repeat region of the nucleoporin Nup1p. In contrast, the NES mutation abolished Kap95p interaction with the GLFG repeat regions from the nucleoporins Nup116p and Nup100p. In vivo interaction was demonstrated by isolation of Kap95p from yeast nuclear lysates in either protein A–tagged Nup116p or protein A–tagged Nup100p complexes. The protein A–tagged Nup116p complex also specifically contained Gle2p. These results support a model in which a step in the recycling of Kap95p is mediated by interaction of an NES with GLFG regions. Analysis of genetic interactions suggests Nup116p has a primary role in Kap95p recycling, with Nup100p compensating in the absence of Nup116p. This finding highlights an important role for a subfamily of GLFG nucleoporins in nuclear export processes.