bluuebunny/crossref_metadata_2025 huggingface dataset:
Particle acceleration by a wave in a strong magnetic field: Regular and stochastic motion
Authors: Karimabadi H. , Akimoto K. , Omidi N. , Menyuk C. R.
Published: July 2002

A general theory for the acceleration of a charged particle by a coherent wave of arbitrary polarization, propagation angle, and phase velocity in the presence of a uniform and strong magnetic field is presented. It is shown that the Hamiltonian surfaces are topologically open for waves with parallel phase velocity, ω/k∥, equal to or larger than the speed of light. The trapping width is found to be a strong function of the index of refraction (N), and for N=1 the trapping width increases as a function of the harmonic number. Particular emphasis is put on waves with N∥ ≡ck∥/ ω=1, and it is demonstrated that the physics of such waves is the relativistic counterpart of the nonrelativistic particle acceleration by a perpendicularly propagating wave. It is found that even at small wave amplitudes particles can be accelerated coherently to very large energies (relativistic factor γ>8) in the presence of such waves. The autoresonance acceleration mechanism [Sov. Phys. JETP 16, 629 (1963); Phys. Rev. A 135, 381 (1964)] is shown to be a special case of particle acceleration by waves with N∥ =1. A detailed analysis of the dispersion properties of these waves in a cold plasma is given. Finally, a novel mechanism for coherently accelerating particles to unlimited energies is presented. This new mechanism requires waves with N∥ ≲1 and wave amplitudes large enough so that the zeroth-order particle motion is the trapping due to the wave (‘‘weak’’ magnetic field limit) rather than the Larmor gyration which was the case for the autoresonance mechanism. This new mechanism is somewhat similar to the surfatron mechanism [Phys. Rev. Lett. 51, 392 (1983)] but can operate even if the wave amplitude is smaller than the magnetic field as a result of the oblique propagation angle of the wave.
Nonlinear Trivelpiece–Gould waves: Recurrence, harmonic cascade, and sidebands
Authors: Cabral J. A. C. , Lapão L. M. , Mendonça J. T.
Published: July 2002

A theoretical and experimental study of Trivelpiece–Gould waves propagating in a magnetized plasma column is presented in this paper. In the experiments, these waves are excited by a radio frequency (rf) source, which also serves to create the plasma. Observation of nonlinear effects includes space and time recurrence effects, a wave spectrum containing a large number (up to 25) harmonics, and low-frequency sidebands. The theoretical model explains the recurrence effects as a consequence of multiple nonlinear interactions between the fundamental wave and its harmonics. A good agreement is found between theory and the experiments.
On the forced flow of salty water in a loop
Authors: Dewar W. K. , Huang R. X.
Published: July 2002

The buoyancy-driven flow of salty water in a loop is computed. This problem belongs to the general class of the convective behavior of solutal fluids, a specific example of which is the oceanic thermohaline circulation. The two cases of freshwater flux forcing and so-called virtual salt flux forcing are compared and contrasted. The former is an exact statement of the saline forcing of the ocean by the atmosphere, while the latter is an approximation used in many climate models. Analytical solutions appropriate to both cases are presented for broad parameter ranges and ultimately encapsulated in the form of bifurcation maps. These allow for comparisons between the behaviors predicted for the two cases. Furthermore, the solutions are supported by means of numerical experimentation. It is found that a simple loop model, forced by a steady flux, can possess multiple solutions, either stationary solutions and limit cycles or distinctly different limit cycles. This result is closely related to climate models. In addition, this study transcends climate applications and applies to the more general classical problem of convection in a loop.

The novel aspect here is the application of freshwater flux to a salty fluid. The effect on density of this forcing is different from that due to the application of heat to a thermally sensitive fluid. Surprising and counter-intuitive behaviors have been found which reflect these differences. As an example, in the limit where diffusion is weak relative to freshwater flux, a δ-function-like salinity profile appears if freshwater flux conditions are used. Models using a virtual salt flux approximation, or a relaxation condition, yield a low mode solution for these parameters. In contrast, the virtual salt flux equations can be obtained from the freshwater-forced equations by a systematic expansion in one limit where diffusion dominates freshwater flux. Numerical experiments are used to examine the comparisons between virtual salt flux and freshwater-forced solutions, with the result that virtual salt flux generally yields accurate results when diffusion is strong.
Elimination of cross talk in optical directional couplers
Authors: Haus H. A. , Whitaker N. A.
Published: July 2002

Waveguide directional couplers may suffer from incomplete isolation between channels due to unequal excitation of symmetric and antisymmetric coupler modes. This letter shows that tapering may be used to eliminate cross talk while maintaining negligible radiation and reflection loss.
Bistability and switching in thin-film waveguides with liquid-crystal cladding
Authors: Valera J. D. , Svensson B. , Seaton C. T. , Stegeman G. I.
Published: July 2002

The transmission of guided waves through a thin-film waveguide with an oriented liquid-crystal cladding of K18 exhibits, near the liquid-crystal nematic–isotropic phase transition, a number of all-optical operations, such as switching and bistability.
Laser-driven chemical reaction for etching LiNbO3
Authors: Ashby C. I. H. , Brannon P. J.
Published: July 2002

The first laser-driven chemical reaction for etching ionic solids based on the fusion of salts in the molten phase is reported here for the reaction of LiNbO3 with KF. The process involves spatially localized melting of LiNbO3 by high-power-density laser pulses with photon energies in excess of the band gap of LiNbO3. While molten, LiNbO3 undergoes reaction with KF to form niobium oxyfluoride anions by fusion of the salts. The resulting solid is highly water soluble. The insolubility of LiNbO3 permits subsequent removal of only the irradiated area by rinsing in water. This laser-driven chemical etching process shows great potential for applications which require either smooth surface morphology or very rapid etching rates.
Undercooling of pure metals in a containerless, microgravity environment
Authors: Hofmeister W. H. , Robinson M. B. , Bayuzick R. J.
Published: July 2002

The 105-m drop tube at NASA/Marshall Space Flight Center has been used in a series of undercooling experiments on pure metals. Ti, Zr, Nb, Mo, Rh, Hf, Ta, and Pt were undercooled 17–20% of the melting temperature in a containerless, microgravity environment. Ir and Ru were undercooled to 13% Tm. Sample sizes ranged from 175 to 880 mg.
Holocarboxylase synthetase is an obligate participant in biotin-mediated regulation of its own expression and of biotin-dependent carboxylases mRNA levels in human cells
Authors: Solórzano-Vargas R. Sergio , Pacheco-Alvarez Diana , León-Del-Río Alfonso
Published: July 2002

Holocarboxylase synthetase (HCS) catalyzes the covalent attachment of biotin to five biotin-dependent carboxylases in human cells. Multiple carboxylase deficiency (MCD) is a life-threatening disease characterized by the lack of carboxylase activities because of deficiency of HCS activity. Here, we report the obligatory participation of HCS in the biotin-dependent stimulation of the level of HCS mRNA and those of acetyl-CoA carboxylase and the α subunit of propionyl-CoA carboxylase in human cells. Fibroblasts from patients with MCD are unable to increase HCS mRNA in response to biotin unless the vitamin concentration is raised 100-fold, in keeping with mutations that cause a reduced affinity for biotin by the mutant enzyme. The outcome is deficient synthesis of biotinyl-5′-AMP, the active form of the vitamin in the biotinylation reaction. HCS and carboxylase mRNA levels in normal and MCD fibroblasts and HepG2 cells can be restored by the addition of the cGMP analogue, 8-Br-cGMP, and can be abolished by the addition of inhibitors of the soluble form of guanylate cyclase. We propose a regulatory role for biotin in the control of HCS and carboxylase mRNA levels through a signaling cascade that requires HCS, guanylate cyclase, and cGMP-dependent protein kinase.
Sorting and directed transport of membrane proteins during development of hippocampal neurons in culture
Authors: Silverman M. A. , Kaech S. , Jareb M. , Burack M. A. , Vogt L. , Sonderegger P. , Banker G.
Published: July 2002

Hippocampal neurons in culture develop morphological polarity in a sequential pattern; axons form before dendrites. Molecular differences, particularly those of membrane proteins, underlie the functional polarity of these domains, yet little is known about the temporal relationship between membrane protein polarization and morphological polarization. We took advantage of viral expression systems to determine when during development the polarization of membrane proteins arises. All markers were unpolarized in neurons before axonogenesis. In neurons with a morphologically distinguishable axon, even on the first day in culture, both axonal and dendritic proteins were polarized. The degree of polarization at these early stages was somewhat less than in mature cells and varied from cell to cell. The cellular mechanism responsible for the polarization of the dendritic marker protein transferrin receptor (TfR) in mature cells centers on directed transport to the dendritic domain. To examine the relationship between cell surface polarization and transport, we assessed the selectivity of transport by live cell imaging. TfR-green fluorescent protein-containing vesicles were already preferentially transported into dendrites at 2 days, the earliest time point we could measure. The selectivity of transport also varied somewhat among cells, and the amount of TfR-green fluorescent protein fluorescence on intracellular structures within the axon correlated with the amount of cell surface expression. This observation implies that selective microtubule-based transport is the primary mechanism that underlies the polarization of TfR on the cell surface. By 5 days in culture, the extent of polarization on the cell surface and the selectivity of transport reached mature levels.
Afipia felisinduces uptake by macrophages directly into a nonendocytic compartment
Authors: Lührmann Anja , Streker Karin , Schüttfort Anja , Daniels Justin J. D. , Haas Albert
Published: July 2002

Afipia felisis a Gram-negative bacterium that causes some cases of human Cat Scratch Disease.A. feliscan survive and multiply in several mammalian cell types, including macrophages, but the precise intracellular compartmentalization ofA. felis-containing phagosomes is unknown. Here, we demonstrate that, in murine macrophages, mostA. felis-containing phagosomes exclude lysosomal tracer loaded into macrophage lysosomes before, as well as endocytic tracer loaded after, establishment of an infection. EstablishedAfipia-containing phagosomes possess neither early endosomal marker proteins [early endosome antigen 1 (EEA1), Rab5, transferrin receptor, trytophane aspartate containing coat protein (TACO)] nor late endosomal or lysosomal proteins [cathepsin D, β-glucuronidase, vacuolar proton-pumping ATPase, rab7, mannose-6-phosphate receptor, vesicle-associated membrane protein 8, lysosome-associated membrane proteins LAMP-1 and LAMP-2]. Those bacteria that will be found in a nonendosomal compartment enter the macrophage via an EEA1-negative compartment, which remains negative for LAMP-1. The smaller subpopulation of afipiae whose phagosomes will be part of the endocytic system enters into an EEA1-positive compartment, which also subsequently acquires LAMP-1. Killing ofAfipiaor opsonization with immune antibodies leads to a strong increase in the percentage ofA. felis-containing phagosomes that interact with the endocytic system. We conclude that most phagosomes containingA. felisare disconnected from the endosome–lysosome continuum, that their unusual compartmentalization is decided at uptake, and that this compartmentalization requires bacterial viability.
Inversion of stereospecificity of vanillyl-alcohol oxidase
Authors: van den Heuvel Robert H. H. , Fraaije Marco W. , Ferrer Miriam , Mattevi Andrea , van Berkel Willem J. H.
Published: July 2002

Vanillyl-alcohol oxidase (VAO) is the prototype of a newly recognized family of structurally related oxidoreductases sharing a conserved FAD-binding domain. The active site of VAO is formed by a cavity where the enzyme is able to catalyze many reactions with phenolic substrates. Among these reactions is the stereospecific hydroxylation of 4-ethylphenol-forming (
R
)-1-(4′-hydroxyphenyl)ethanol. During this conversion, Asp-170 is probably critical for the hydration of the initially formed
p
-quinone methide intermediate. By site-directed mutagenesis, the putative active site base has been relocated to the opposite face of the active site cavity. In this way, a change in stereospecificity has been achieved. Like native VAO, the single mutants T457E, D170A, and D170S preferentially converted 4-ethylphenol to the (
R
)-enantiomer of 1-(4′-hydroxyphenyl)ethanol. The double mutants D170A/T457E and D170S/T457E exhibited an inverted stereospecificity with 4-ethylphenol. Particularly, D170S/T457E was strongly (
S
)-selective, with an enantiomeric excess of 80%. The crystal structure of D170S/T457E, in complex with trifluoromethylphenol, showed a highly conserved mode of ligand binding and revealed that the distinctive catalytic properties of this mutant are not caused by major structural changes.
Why multiple small subunits (Y2 and Y4) for yeast ribonucleotide reductase? Toward understanding the role of Y4
Authors: Ge Jie , Perlstein Deborah L. , Nguyen Hiep-Hoa , Bar Galit , Griffin Robert G. , Stubbe JoAnne
Published: July 2002

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides. Class I RNRs are composed of two homodimeric subunits: R1 and R2. R1 is directly involved in the reduction, and R2 contains the diferric-tyrosyl radical (Y⋅) cofactor essential for the initiation of reduction.
Saccharomyces cerevisiae
has two RNRs; Y1 and Y3 correspond to R1, whereas Y2 and Y4 correspond to R2. Y4 is essential for diferric-Y⋅ formation in Y2 from apoY2, Fe
2+
, and O
2
. The actual function of Y4 is controversial. Y2 and Y4 have been further characterized in an effort to understand their respective roles in nucleotide reduction. (His)
6
-Y2, Y4, and (His)
6
-Y4 are homodimers, isolated largely in apo form. Their CD spectra reveal that they are predominantly helical. The concentrations of Y2 and Y4
in vivo
are 0.5–2.3 μM, as determined by Western analysis. Incubation of Y2 and Y4 under physiological conditions generates apo Y2Y4 heterodimer, which can form a diferric-Y⋅ when incubated with Fe
2+
and O
2
. Holo Y2Y4 heterodimer contains 0.6–0.8 Y⋅ and has a specific activity of 0.8–1.3 μmol⋅min⋅mg. Titration of Y2 with Y4 in the presence of Fe
2+
and O
2
gives maximal activity with one equivalent of Y4 per Y2. Models for the function of Y4 based on these data and the accompanying structure will be discussed.
Analysis of
Schizosaccharomyces pombe
Mediator reveals a set of essential subunits conserved between yeast and metazoan cells
Authors: Spåhr Henrik , Samuelsen Camilla O. , Baraznenok Vera , Ernest Isabelle , Huylebroeck Danny , Remacle Jacques E. , Samuelsson Tore , Kieselbach Thomas , Holmberg Steen , Gustafsson Claes M.
Published: July 2002

With the identification of eight new polypeptides, we here complete the subunit characterization of the
Schizosaccharomyces pombe
RNA polymerase II holoenzyme. The complex contains homologs to all 10 essential gene products present in the
Saccharomyces cerevisiae
Mediator, but lacks clear homologs to any of the 10
S. cerevisiae
components encoded by nonessential genes.
S. pombe
Mediator instead contains three unique components (Pmc2, -3, and -6), which lack homologs in other cell types. Presently,
pmc2

+

and
pmc3

+

have been shown to be nonessential genes. The data suggest that
S. pombe
and
S. cerevisiae
share an essential protein module, which associates with nonessential speciesspecific subunits. In support of this view, sequence analysis of the conserved yeast Mediator components Med4 and Med8 reveals sequence homology to the metazoan Mediator components Trap36 and Arc32. Therefore, 8 of 10 essential genes conserved between
S. pombe
and
S. cerevisiae
also have a metazoan homolog, indicating that an evolutionary conserved Mediator core is present in all eukaryotic cells. Our data suggest a closer functional relationship between yeast and metazoan Mediator than previously anticipated.
Dynamic expression of multiple scavenger receptor cysteine-rich genes in coelomocytes of the purple sea urchin
Authors: Pancer Zeev
Published: July 2002

Coelomocytes, the heterogeneous population of sea urchin putative immune cells, were found to express a complex set of transcripts featuring scavenger receptor cysteine-rich (SRCR) repeats. SRCR domains define a metazoan superfamily of proteins, many of which are implicated in development and regulation of the immune system of vertebrates. Coelomocytes transcribe multiple SRCR genes from among a multigene family encoding an estimated number of 1,200 SRCR domains in specific patterns particular to each individual. Transcription levels for given SRCR genes may range from pronounced to undetectable, yet all tested animals harbor the genomic loci encoding these genes. Analysis of several SRCR genes revealed multiple loci corresponding to each type. In the case of one SRCR type, a cluster of at least three genes was detected within a 133-kb bacterial artificial chromosome insert, and conserved as well as unique regions were identified in sequences of three genomic clones derived from a single animal. Array hybridizations with repeated samples of coelomocyte messages revealed substantial alterations in levels of expression of many SRCR genes, with fluctuations of up to 10-fold in 1 week and up to 30-fold over a period of 3 months. This report is the first demonstration of genomic and transcriptional complexity in molecules expressed by invertebrate coelomocytes. The mechanisms controlling SRCR gene expression and the functional significance of this dynamic system await elucidation.
Efficient and specific ribozyme-mediated reduction of bovine alpha-lactalbumin expression in double transgenic mice.
Authors: L'Huillier P J , Soulier S , Stinnakre M G , Lepourry L , Davis S R , Mercier J C , Vilotte J L
Published: July 2002

Transgenic mice carrying a bovine alpha-lactalbumin (alpha-lac) specific ribozyme gene under the transcriptional control of the mouse mammary tumor virus long terminal repeat were generated and cross-bred with animals that highly express a bovine alpha-lac transgene (0.4 mg of alpha-lac/ml(-1) of milk). The ribozyme contains the hammerhead catalytic domain, flanked by 12-nt sequences complementary to the 3' untranslated region of bovine alpha-lac transcript. High-level expression of the ribozyme gene was detected by Northern blot analysis in the mammary gland of 7-8 day lactating transgenic mice, from 3 of 12 lines analyzed. Heterozygous expression of the ribozyme resulted in a reduction in the levels of the target mRNA to 78, 58, and 50% of that observed in the nonribozyme transgenic littermate controls for three independent lines. The ribozyme-mediated reduction in the levels of the bovine protein paralleled that observed for the mRNA, and was positively correlated with the level of expression of the ribozyme. In nonribozyme expressing transgenic mice, the level of bovine alpha-lac mRNA and protein was not affected. The specificity of this activity is demonstrated by the absence of a reduction in the levels of the endogenous murine alpha-lac mRNA or protein. These results demonstrate the feasibility of ribozyme-mediated down-regulation of highly-expressed transcripts in transgenic animals.
Low lead levels stunt neuronal growth in a reversible manner.
Authors: Cline H T , Witte S , Jones K W
Published: July 2002

The developing brain is particularly susceptible to lead toxicity; however, the cellular effects of lead on neuronal development are not well understood. The effect of exposure to nanomolar concentrations of lead on several parameters of the developing retinotectal system of frog tadpoles was tested. Lead severely reduced the area and branchtip number of retinal ganglion cell axon arborizations within the optic tectum at submicromolar concentrations. These effects of lead on neuronal growth are more dramatic and occur at lower exposure levels than previously reported. Lead exposure did not interfere with the development of retinotectal topography. The deficient neuronal growth does not appear to be secondary to impaired synaptic transmission, because concentrations of lead that stunted neuronal growth were lower than those required to block synaptic transmission. Subsequent treatment of lead-exposed animals with the chelating agent 2,3-dimercaptosuccinic acid completely reversed the effect of lead on neuronal growth. These studies indicate that impaired neuronal growth may be responsible in part for lead-induced cognitive deficits and that chelator treatment counteracts this effect.
High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex.
Authors: Lagrange T , Kim T K , Orphanides G , Ebright Y W , Ebright R H , Reinberg D
Published: July 2002

We have used a novel site-specific protein-DNA photocrosslinking procedure to define the positions of polypeptide chains relative to promoter DNA in binary, ternary, and quaternary complexes containing human TATA-binding protein, human or yeast transcription factor IIA (TFIIA), human transcription factor IIB (TFIIB), and promoter DNA. The results indicate that TFIIA and TFIIB make more extensive interactions with promoter DNA than previously anticipated. TATA-binding protein, TFIIA, and TFIIB surround promoter DNA for two turns of DNA helix and thus may form a "cylindrical clamp" effectively topologically linked to promoter DNA. Our results have implications for the energetics, DNA-sequence-specificity, and pathway of assembly of eukaryotic transcription complexes.
The natural killer cell receptor Ly-49A recognizes a peptide-induced conformational determinant on its major histocompatibility complex class I ligand.
Authors: Orihuela M , Margulies D H , Yokoyama W M
Published: July 2002

Natural killer (NK) cells are inhibited from killing cellular targets by major histocompatibility complex (MHC) class I molecules. In the mouse, this can be mediated by the Ly-49A NK cell receptor that specifically binds the H-2Dd MHC class I molecule, then inhibits NK cell activity. Previous experiments have indicated that Ly-49A recognizes the alpha 1/alpha 2 domains of MHC class I and that no specific MHC-bound peptide appeared to be involved. We demonstrate here that alanine-substituted peptides, having only the minimal anchor motifs, stabilized H-2Dd expression and provided resistance to H-2Dd-transfected, transporter associated with processing (TAP)-deficient cells from lysis by Ly-49A+ NK cells. Peptide-induced resistance was blocked only by an mAb that binds a conformational determinant on H-2Dd. Moreover, stabilization of "empty" H-2Dd heavy chains by exogenous beta 2-microglobulin did not confer resistance. In contrast to data for MHC class I-restricted T cells that are specific for peptides displayed MHC molecules, these data indicate that NK cells are specific for a peptide-induced conformational determinant, independent of specific peptide. This fundamental distinction between NK cells and T cells further implies that NK cells are sensitive only to global changes in MHC class I conformation or expression, rather than to specific pathogen-encoded peptides. This is consistent with the "missing self" hypothesis, which postulates that NK cells survey tissues for normal expression of MHC class I.
Nucleotide binding-promoted conformational changes release a nonnative polypeptide from the Escherichia coli chaperonin GroEL.
Authors: Lin Z , Eisenstein E
Published: July 2002

The Escherichia coli chaperonins GroEL and GroES facilitate the refolding of polypeptide chains in an ATP hydrolysis-dependent reaction. The elementary steps in the binding and release of polypeptide substrates to GroEL were investigated in surface plasmon resonance studies to measure the rates of binding and dissociation of a normative variant of subtilisin. The rate constants determined for GroEL association with and dissociation from this variant yielded a micromolar dissociation constant, in agreement with independent calorimetric estimates. The rate of GroEL dissociation from the nonnative chain was increased significantly in the presence of 5'-adenylylimidodiphosphate (AMP-PNP), ADP, and ATP, yielding maximal values between 0.04 and 0.22 s(-1). The sigmoidal dependence of the dissociation rate on the concentration of AMP-PNP and ADP indicated that polypeptide dissociation is limited by a concerted conformational change that occurs after nucleotide binding. The dependence of the rate of release on ATP exhibited two sigmoidal transitions attributable to nucleotide binding to the distal and proximal toroid of a GroEL-polypeptide chain complex. The addition of GroES resulted in a marked increase in the rate of nonnative polypeptide release from GroEL, indicating that the cochaperonin binds more rapidly than the dissociation of polypeptides. These data demonstrate the importance of nucleotide binding-promoted concerted conformational changes for the release of chains from GroEL, which correlate with the sigmoidal hydrolysis of ATP by the chaperonin. The implications of these findings are discussed in terms of a working hypothesis for a single cycle of chaperonin action.
Human semaphorins A(V) and IV reside in the 3p21.3 small cell lung cancer deletion region and demonstrate distinct expression patterns.
Authors: Sekido Y , Bader S , Latif F , Chen J Y , Duh F M , Wei M H , Albanesi J P , Lee C C , Lerman M I , Minna J D
Published: July 2002

Semaphorins and collapsins make up a family of conserved genes that encode nerve growth cone guidance signals. We have identified two additional members of the human semaphorin family [human semaphorin A(V) and human semaphorin IV] in chromosome region 3p21.3, where several small cell lung cancer (SCLC) cell lines exhibit homozygous deletions indicative of a tumor suppressor gene. Human semaphorin A(V) has 86% amino acid homology with murine semaphorin A, whereas semaphorin IV is most closely related to murine semaphorin E, with 50% homology. These semaphorin genes are approximately 70 kb apart flanking two GTP-binding protein genes, GNAI-2 and GNAT-1. In contrast, other human semaphorin gene sequences (human semaphorin III and homologues of murine semaphorins B and C) are not located on chromosome 3. Human semaphorin A(V) is translated in vitro into a 90-kDa protein, which accumulates at the endoplasmic reticulum. The human semaphorin A(V) (3.4-kb mRNA) and IV (3.9- and 2.9-kb mRNAs) genes are expressed abundantly but differentially in a variety of human neural and nonneural tissues. Human semaphorin A(V) was expressed in only 1 out of 23 SCLCs and 7 out of 16 non-SCLCs, whereas semaphorin IV was expressed in 19 out of 23 SCLCs and 13 out of 16 non-SCLCs. Mutational analysis in semaphorin A(V) revealed mutations (germ line in one case) in 3 of 40 lung cancers. Our data suggest the need to determine the function of human semaphorins A(V) and IV in nonneural tissues and their role in the pathogenesis of lung cancer.
Rapid evolution of sex-related genes in
Chlamydomonas
Authors: Ferris Patrick J. , Pavlovic Christopher , Fabry Stefan , Goodenough Ursula W.
Published: July 2002

Biological speciation ultimately results in prezygotic isolation—the inability of incipient species to mate with one another–but little is understood about the selection pressures and genetic changes that generate this outcome. The genus
Chlamydomonas
comprises numerous species of unicellular green algae, including numerous geographic isolates of the species
C. reinhardtii
. This diverse collection has allowed us to analyze the evolution of two sex-related genes: the
mid
gene of
C. reinhardtii
, which determines whether a gamete is mating-type
plus
or
minus
, and the
fus1
gene, which dictates a cell surface glycoprotein utilized by
C. reinhardtii plus
gametes to recognize
minus
gametes. Low stringency Southern analyses failed to detect any
fus1
homologs in other
Chlamydomonas
species and detected only one
mid
homolog, documenting that both genes have diverged extensively during the evolution of the lineage. The one
mid
homolog was found in
C. incerta
, the species in culture that is most closely related to
C. reinhardtii
. Its
mid
gene carries numerous nonsynonymous and synonymous codon changes compared with the
C. reinhardtii mid
gene. In contrast, very high sequence conservation of both the
mid
and
fus1
sequences is found in natural isolates of
C. reinhardtii
, indicating that the genes are not free to drift within a species but do diverge dramatically between species. Striking divergence of sex determination and mate recognition genes also has been encountered in a number of other eukaryotic phyla, suggesting that unique, and as yet unidentified, selection pressures act on these classes of genes during the speciation process.
Bacterial nodulation protein NodZ is a chitin oligosaccharide fucosyltransferase which can also recognize related substrates of animal origin
Authors: Quinto Carmen , Wijfjes André H. M. , Bloemberg Guido V. , Blok-Tip Leonore , López-Lara Isabel M. , Lugtenberg Ben J. J. , Thomas-Oates Jane E. , Spaink Herman P.
Published: July 2002

The
nodZ
gene, which is present in various soil bacteria such as
Bradyrhizobium japonicum
,
Azorhizobium caulinodans
, and
Rhizobium loti
, is involved in the addition of a fucosyl residue to the reducing
N
-acetylglucosamine residue of lipochitin oligosaccharide (LCO) signal molecules. Using an
Escherichia coli
strain that produces large quantities of the NodZ protein of
B. japonicum
, we have purified the NodZ protein to homogeneity. The purified NodZ protein appears to be active in an
in vitro
transfucosylation assay in which GDP-β-fucose and LCOs or chitin oligosaccharides are used as substrates. The products of the
in vitro
reaction using chitin oligosaccharides as substrate were studied by using mass spectrometry, linkage analysis, and composition analysis. The data show that one fucose residue is added to C6 of the reducing-terminal
N
-acetylglucosamine residue. The substrate specificity of NodZ protein was analyzed in further detail, using radiolabeled GDP-β-fucose as the donor. The results show that chitin oligosaccharides are much better substrates than LCOs, suggesting that in
Rhizobium
NodZ fucosylates chitin oligosaccharides prior to their acylation. The free glycan core pentasaccharides of N-linked glycoproteins are also substrates for NodZ. Therefore, the NodZ enzyme seems to have an activity equivalent to that of the enzyme involved in the addition of the C6-linked fucosyl substituent in the glycan core of N-linked glycoproteins in eukaryotes. Oligosaccharides that contain only one
N
-acetylglucosamine at the reducing terminus are also substrates for NodZ, although in this case very high concentrations of such oligosaccharides are needed. An example is the leukocyte antigen Lewis-X, which can be converted by NodZ to a novel fucosylated derivative that could be used for binding studies with E-selectin.
Interaction of the DNA modifying proteins VirD1 and VirD2 of
Agrobacterium tumefaciens
: Analysis by subcellular localization in mammalian cells
Authors: Relić Biserka , Andjelković Mirjana , Rossi Luca , Nagamine Yoshikuni , Hohn Barbara
Published: July 2002

Interaction between
Agrobacterium tumefaciens
and plants provides a unique example of interkingdom gene transfer.
Agrobacterium
, a plant pathogen, is capable to stably transform the plant cell with a segment of its own DNA called T-DNA (transferred DNA). This process depends, among others, on the specialized bacterial virulence proteins VirD1 and VirD2 that excise the T-DNA from its adjacent sequences. Subsequent to transfer to the plant cell, the virulence protein VirD2, through its nuclear localization signal (NLS), is believed to guide the T-DNA to the nucleus. The T-DNA then is integrated into the plant genome. Although both of these proteins are essential for bacterial virulence, physical interaction of them has not been analyzed so far. We studied associations between these proteins by expressing them in mammalian cells and by testing for intracellular localization and colocalization. When expressed in human cells [HeLa, human embryo kidney (HEK) 293], the VirD2 protein homogeneously distributed over the nucleoplasm. The presence of any of two NLSs, on the N and C termini of VirD2, was sufficient for its efficient nuclear localization whereas deletion of both NLSs rendered the protein cytoplasmic. However, this double NLS mutant was translocated to the nucleus in the presence of wild-type VirD2 protein, implying VirD2–VirD2 interaction. The VirD1 protein, by itself localized in the cytoplasm, moved to the nucleus when coexpressed with the VirD2 protein, suggesting VirD1–VirD2 interaction. This interaction was confirmed by coimmunoprecipitation tests. Of interest, both proteins coimported to the nucleus showed a similar, peculiar sublocalization. The data are discussed in terms of functions of the VirD proteins. In addition, coimport of proteins into nuclei is suggested as a useful system in studying individual protein–protein interactions.
Structural requirements for antigen presentation by mouse CD1
Authors: Burdin Nicolas , Brossay Laurent , Degano Massimo , Iijima Hiroshi , Gui Ming , Wilson Ian A. , Kronenberg Mitchell
Published: July 2002

The structural basis for the T cell response to glycolipid antigens (Ags) remains poorly understood. T lymphocytes autoreactive for mouse CD1 (mCD1.1) or reactive for the glycosphingolipid αgalactosylceramide (α-GalCer) presented by mCD1.1 have been described previously. In this paper it is shown that mutations at the top of the α helices and in the bottom of the Ag-binding groove can disrupt both mCD1.1 autoreactivity and α-GalCer recognition. The locations of the positions that affect T cell responses indicate that recognition of mCD1.1 is not likely to be unconventional or superantigen-like. Furthermore, the effects of the bottom of the pocket mutation suggest that the autoreactive response could require an autologous ligand, and they indicate that α-GalCer binds to the groove of mCD1.1, most likely with the shorter 18-carbon hydrophobic chain in the A′ pocket. Natural killer T cell hybridomas with identical T cell antigen receptor (TCR) α chains and different β chains respond differently to α-GalCer presented by mCD1.1 mutants. This finding indicates a role for TCR β in defining natural killer T cell specificity, despite the more restricted diversity of the α chains in these cells. Overall, the data are consistent with a mode of lipoglycan recognition similar to that proposed for glycopeptides, in which the TCR α and β chains survey a surface composed of both mCD1.1 and the carbohydrate portion of α-GalCer.
United They Stood, Divided They Fell: Nationalism and the Yugoslav School of Basketball, 1968–2000
Authors: Perica Vjekoslav
Published: July 2002

Both Yugoslav wars and Yugoslav basketball were conspicuous in Western media in the 1990s. While CNN transmitted scenes of horror from battlefields of Bosnia and Kosovo, several dozen professional athletes of Yugoslav background could be seen in action on U. S. sport channels. Yugoslavs, by far the most numerous among foreign players in the strongest basketball league in the world—the American professional basketball league (NBA)—sparked the audience's curiosity about their background and the peculiar Yugoslav style of basketball. The literature concerning the Yugoslav crisis and Balkan wars noted sporadic outbursts of ethnic hatred in sport arenas, but did not provide any detailed information on the otherwise important role of sport in Yugoslav history and society. Not even highly competent volumes such as Beyond Yugoslavia, which highlighted the country's culture, arts, religion, economy, and military, paid attention to what Yugoslavs called “the most important secondary issue in the world”—sport. Yet sport reveals not merely the pastimes of the Yugoslav peoples, but also the varieties of nationalism in the former Yugoslavia, including probably the most neglected of all local nationalisms: the official communist-era patriotic ideology of interethnic “brotherhood and unity.” The goal of this article is to highlight this type of nationalism manifested via state-directed sport using as a case study the most successful basketball program outside the United States.
Feminist Scholarship in Education: The state of the art?
Authors: Ivinson Gabrielle
Published: July 2002

The Realities of Teachers' Work: never a dull moment: Sandra Acker

The Feminist Teacher Anthology: pedagogies and classroom strategies: Gail Cohee, Elizabeth Daumer, Theresa Kemp, Paula Krebs, Sue Lafky & Sandra Runzo, Foreword by Bernice Sandler

Power Plays: primary school children's constructions of gender, power and adult work Becky Francis
Progress from GCSE to A and AS Level: Institutional and gender differences, and trends over time
Authors: Yang Min , Woodhouse Geoffrey
Published: July 2002

Abstract The authors study the relationship between results obtained in examinations for the General Certificate of Education at Advanced and Advanced Supplementary (A/AS) level and those obtained by the same students two years earlier in examinations for the General Certificate of Secondary Education (GCSE). They used comprehensive data on four cohorts examined between 1994 and 1997 to build a multilevel, longitudinal model of student progress. It was found that progress differs between males and females, and between students of different ages, and that the average GCSE performance of the students in an establishment is a significant predictor of individual progress. Once establishments are matched on this measure, and students are matched on their own GCSE performance, the effects of most establishment types are substantially reduced: in particular, the average progress of students in maintained grammar schools does not differ significantly from that of students in maintained comprehensive schools. Less stability over time was found in the usual residual estimates of the relative effectiveness of institutions than has been found in earlier studies.
PP-Attachment Disambiguation for Swedish: Combining Unsupervised and Supervised Training Data
Authors: Kokkinakis Dimitrios
Published: July 2002

Structural ambiguity, particularly attachment of prepositional phrases, is a serious type of global ambiguity in Natural Language. The disambiguation becomes crucial when a syntactic analyzer must make the correct decision among at least two equally grammatical parse-trees for the same sentence. This paper attempts to find answers to the problem of how attachment ambiguity can be resolved by utilizing Machine Learning (ML) techniques. ML is founded on the assumption that the performance in cognitive tasks is based on the similarity of new situations (testing) to stored representations of earlier experiences (training). Therefore, a large amount of training data is an important prerequisite for providing a solution to the problem. A combination of unsupervised and restricted supervised acquisition of such data will be reported. Training is performed both on a subset of the content of the Gothenburg Lexical Database (GLDB), and on instances of large corpora annotated with coarse-grained semantic information. Testing is performed on corpora instances using a range of different algorithms and metrics. The application language is written Swedish.
Alcohol marketing on the internet: new challenges for harm reduction
Authors: CARROLL TOM E. , DONOVAN ROBERT J.
Published: July 2002

While much has been made of the problems of regulating alcohol and other drug promotion in the traditional media of print, radio and newspapers, the ‘new media’ and in particular the world wide web, provides new fertile ground for alcohol advertisers. In this Harm Reduction Digest Tom Carroll and Rob Donovan apply the voluntary standards of the Alcohol Beverages Advertising Code to six websites for alcohol products available in Australia. They conclude that the internet provides an opportunity for alcohol marketing targeted at underage consumers, that some alcohol‐related web pages would be in breach of the Code if it applied to the internet, and suggest that web marketing practices of alcohol beverage companies should be monitored and a code of practice developed to regulate alcohol promotion on the web.
Pergolide Mesylate for Cocaine Abuse: A Controlled Preliminary Trial
Authors: Levin Frances R. , McDowell David , Evans Suzette M. , Brooks Daniel , Spano Christina , Nunes Edward V.
Published: July 2002

A small, controlled study was conducted to assess whether pergolide mesylate has clinical promise as a treatment for cocaine abuse prior to embarking on a larger, randomized, double‐blind, controlled trial. Fourteen individuals were placed on placebo for 2 weeks, followed by a 24‐week single‐blind study in which they were placed on pergolide for 12 weeks, followed by placebo for 12 weeks. Another 14 patients received single‐blind placebo for two weeks and then were randomized into a 24‐week double‐blind, placebo‐controlled, multiple baseline design. Initially, patients enrolled in the study were placed on risperidone (n = 9) or placebo (n = 5). During the first 12 weeks, retention was worse for those receiving pergolide compared to risperidone or placebo. Neither risperidone nor pergolide were more efficacious in reducing cocaine use than placebo. Although earlier open studies found pergolide to show promise as a treatment for cocaine abuse, this study did not support these earlier findings. Comparing an agent to both an active control and placebo group may better predict whether a promising new agent will have clinical utility compared to the standard open trial.
Cortical metabolite alterations in abstinent cocaine and cocaine/alcohol‐dependent subjects: proton magnetic resonance spectroscopic imaging
Authors: MEYERHOFF D. J. , BLOOMER C. , SCHUFF N. , EZEKIEL F. , NORMAN D. , CLARK W. , WEINER M. W. , FEIN G.
Published: July 2002

Chronic abuse of cocaine or alcohol is associated with structural, neuropathological and cognitive impairments that have been documented extensively. Little is known, however, about neurobiochemical changes in chronic substance abusers.We performed MRI and multi‐slice brain proton magnetic resonance spectroscopic imaging (MRSI) to assess neuronal viability (via N‐acetylaspartate (NAA)) and white matter metabolite status in 22 4‐months‐abstinent individuals dependent on crack cocaine only and on both crack cocaine and alcohol. Compared to 11 non‐dependent controls we found (1) significantly lower NAA measures in the dorsolateral prefrontal cortex of the combined cocaine‐dependent groups; (2) comparable spatial distribution and magnitude of these NAA effects for both cocaine‐dependent groups; (3) higher choline‐containing metabolites in frontal white matter of individuals dependent on both cocaine and alcohol; (4) absence of brain atrophy in both abstinent cocaine‐dependent samples; and (5) partial recovery from prefrontal cortical NAA loss, primarily with abstinence from alcohol. The MRSI findings suggest preferential neuronal damage to the frontal cortex of both cocaine‐dependent samples and gliosis in frontal white matter of individuals dependent on both alcohol and cocaine, conditions that persist for more than 4 months of abstinence.
Bilingual Children In Language Units: Does Having ‘Well‐Informed’ Parents Make A Difference?
Authors: Crutchley Alison
Published: July 2002

Findings from a large‐cohort study of children with speech and language impairments in language units attached to primary schools across England have suggested that the 11% of the cohort who were bilingual form a subgroup with distinct characteristics. In particular, bilingual children's language difficulties seemed to be more complex and possibly more severe than those of their monolingual peers. It was suggested that these findings might reflect differences in the way that the bilingual children were identified and assessed for speech and language difficulties. Parents of the bilingual children in the original study were interviewed to explore the kind of experiences they had with the identification and assessment process. Differences were found between the bilingual parents and a group of monolingual parents who were also interviewed. Moreover, differences were found between two subgroups of the bilingual parents: those who were ‘more informed’ and ‘less informed’ about the process. These differences were found to be related to several other factors, including attitudes to language use within the family and the nature of the parents' relationship with the language unit.
Differential Glycosylation of Tractin and LeechCAM, Two Novel Ig Superfamily Members, Regulates Neurite Extension and Fascicle Formation
Authors: Huang Yueqiao , Jellies John , Johansen Kristen M. , Johansen Jørgen
Published: July 2002

By immunoaffinity purification with the mAb Lan3-2, we have identified two novel Ig superfamily members, Tractin and LeechCAM. LeechCAM is an NCAM/FasII/ApCAM homologue, whereas Tractin is a cleaved protein with several unique features that include a PG/YG repeat domain that may be part of or interact with the extracellular matrix. Tractin and LeechCAM are widely expressed neural proteins that are differentially glycosylated in sets and subsets of peripheral sensory neurons that form specific fascicles in the central nervous system. In vivo antibody perturbation of the Lan3-2 glycoepitope demonstrates that it can selectively regulate extension of neurites and filopodia. Thus, these experiments provide evidence that differential glycosylation can confer functional diversity and specificity to widely expressed neural proteins.
Stromal Processing Peptidase Binds Transit Peptides and Initiates Their Atp-Dependent Turnover in Chloroplasts
Authors: Richter Stefan , Lamppa Gayle K.
Published: July 2002

A stromal processing peptidase (SPP) cleaves a broad range of precursors targeted to the chloroplast, yielding proteins for numerous biosynthetic pathways in different compartments. SPP contains a signature zinc-binding motif, His-X-X-Glu-His, that places it in a metallopeptidase family which includes the mitochondrial processing peptidase. Here, we have investigated the mechanism of cleavage by SPP, a late, yet key event in the import pathway. Recombinant SPP removed the transit peptide from a variety of precursors in a single endoproteolytic step. Whereas the mature protein was immediately released, the transit peptide remained bound to SPP. SPP converted the transit peptide to a subfragment form that it no longer recognized. We conclude that SPP contains a specific binding site for the transit peptide and additional proteolysis by SPP triggers its release. A stable interaction between SPP and an intact transit peptide was directly demonstrated using a newly developed binding assay. Unlike recombinant SPP, a chloroplast extract rapidly degraded both the transit peptide and subfragment. A new degradative activity, distinguishable from SPP, was identified that is ATP- and metal-dependent. Our results indicate a regulated sequence of events as SPP functions during precursor import, and demonstrate a previously unrecognized ATP-requirement for transit peptide turnover.