Topological Constraints on the Dynamics of Vortex Formation in a Two-Dimensional Quantum Fluid

We present experimental and theoretical results on formation of quantum vortices in a laser beam propagating in a nonlinear medium. Topological constrains richer than the mere conservation of vorticity impose an elaborate dynamical behavior to the formation and annihilation of vortex-antivortex pairs. We identify two such mechanisms, both described by the same fold-Hopf bifurcation. One of them is particularly efficient although it is not observed in the context of liquid helium films or stationary systems because it relies on the compressible nature of the fluid of light we consider and on the nonstationarity of its flow.

Oscillating Solitons and ac Josephson Effect in Ferromagnetic Bose-Bose Mixtures

Close to the demixing transition, the degree of freedom associated with relative density fluctuations of a two-component Bose-Einstein condensate is described by a nondissipative Landau-Lifshitz equation. In the quasi-one-dimensional weakly immiscible case, this mapping surprisingly predicts that a dark-bright soliton should oscillate when subject to a constant force favoring separation of the two components. We propose a realistic experimental implementation of this phenomenon which we interpret as a spin-Josephson effect in the presence of a movable barrier.

Quantitative Analysis of Shock Wave Dynamics in a Fluid of Light

We report on the formation of a dispersive shock wave in a nonlinear optical medium. We monitor the evolution of the shock by tuning the incoming beam power. The experimental observations for the position and intensity of the solitonic edge of the shock, as well as the location of the nonlinear oscillations are well described by recent developments of Whitham modulation theory. Our work constitutes a detailed and accurate benchmark for this approach. It opens exciting possibilities to engineer specific configurations of optical shock wave for studying wave-mean flow interaction.

Departing from Thermality of Analogue Hawking Radiation in a Bose-Einstein Condensate

We study the quantum fluctuations in a one-dimensional Bose-Einstein condensate realizing an analogous acoustic black hole. The taking into account of evanescent channels and of zero modes makes it possible to accurately reproduce recent experimental measurements of the density correlation function. We discuss the determination of Hawking temperature and show that in our model the analogous radiation presents some significant departure from thermality.

Long-time evolution of pulses in the Korteweg-de Vries equation in the absence of solitons reexamined: Whitham method

We consider the long-time evolution of pulses in the Korteweg-de Vries equation theory for initial distributions which produce no soliton but instead lead to the formation of a dispersive shock wave and of a rarefaction wave. An approach based on Whitham modulation theory makes it possible to obtain an analytic description of the structure and to describe its self-similar behavior near the soliton edge of the shock. The results are compared with numerical simulations.

Solution of the Riemann problem for polarization waves in a two-component Bose-Einstein condensate

We provide a classification of the possible flows of two-component Bose-Einstein condensates evolving from initially discontinuous profiles. We consider the situation where the dynamics can be reduced to the consideration of a single polarization mode (also denoted as "magnetic excitation") obeying a system of equations equivalent to the Landau-Lifshitz equation for an easy-plane ferromagnet. We present the full set of one-phase periodic solutions. The corresponding Whitham modulation equations are obtained together with formulas connecting their solutions with the Riemann invariants of the modulation equations. The problem is not genuinely nonlinear, and this results in a non-single-valued mapping of the solutions of the Whitham equations with physical wave patterns as well as the appearance of interesting elements-contact dispersive shock waves-that are absent in more standard, genuinely nonlinear situations. Our analytic results are confirmed by numerical simulations.

Evolution of initial discontinuities in the Riemann problem for the Kaup-Boussinesq equation with positive dispersion

We consider the space-time evolution of initial discontinuities of depth and flow velocity for an integrable version of the shallow water Boussinesq system introduced by Kaup. We focus on a specific version of this "Kaup-Boussinesq model" for which a flat water surface is modulationally stable, we speak below of "positive dispersion" model. This model also appears as an approximation to the equations governing the dynamics of polarisation waves in two-component Bose-Einstein condensates. We describe its periodic solutions and the corresponding Whitham modulation equations. The self-similar, one-phase wave structures are composed of different building blocks, which are studied in detail. This makes it possible to establish a classification of all the possible wave configurations evolving from initial discontinuities. The analytic results are confirmed by numerical simulations.

Dipole oscillations of a Bose-Einstein condensate in the presence of defects and disorder

We consider dipole oscillations of a trapped dilute Bose-Einstein condensate in the presence of a scattering potential consisting either in a localized defect or in an extended disordered potential. In both cases the breaking of superfluidity and the damping of the oscillations are shown to be related to the appearance of a nonlinear dissipative flow. At supersonic velocities the flow becomes asymptotically dissipationless.

Superfluidity versus Anderson localization in a dilute Bose gas

We consider the motion of a quasi-one-dimensional beam of Bose-Einstein condensed particles in a disordered region of finite extent. Interaction effects lead to the appearance of two distinct regions of stationary flow. One is subsonic and corresponds to superfluid motion. The other one is supersonic and dissipative and shows Anderson localization. We compute analytically the interaction-dependent localization length. We also explain the disappearance of the supersonic stationary flow for large disordered samples.

Diffractive corrections in the trace formula for polygonal billiards

We derive contributions to the trace formula for the spectral density accounting for the role of diffractive orbits in two-dimensional polygonal billiards. In polygons, diffraction typically occurs at the boundary of a family of trajectories. In this case the first diffractive correction to the contribution of the family to the periodic orbit expansion is of order of that of an isolated orbit, and gives the first sqrt[Planck's over 2pi] correction to the leading semiclassical term. Keller's geometrical theory of diffraction is inadequate for treating these corrections and we develop an alternative approximation based on Kirchhoff's theory. Numerical checks show that our procedure allows reduction of the typical semiclassical error by about two orders of magnitude. The method permits treatment of the related problem of flux-line diffraction with the same degree of accuracy.

Genetic variation of Porphyromonas gingivalis genes encoding gingipains, cysteine proteinases with arginine or lysine specificity

Porphyromonas gingivalis hemagglutinating cysteine proteinases (gingipains) are considered as important virulence factors in the development of adult periodontitis. Using Southern blot analysis it was determined that genes of three distinct but related gingipains (gingipain-R1, gingipain-R2 and gingipain-K) were present in all tested strains including HG66, ATCC 33277, W50, E-20-1, EM-3, 381, A7436, and IKG5, with a region encoding a part of the hemagglutinin domain of gingipain-R1 and gingipain-K showing considerable variability. In contrast, the loci encoding gingipain-R1 (rgp1) and gingipain-R2 (rgp2) were strongly conserved excluding the concurrent occurrence of other gingipain-R-like genes such as cpgR and agp. Significantly, no evidence could be found to support the expression of a gene coding for the putative proteinase porphypain, an enzyme suggested to have both gingipain-R and gingipain-K activity.

Maspin is an intracellular serpin that partitions into secretory vesicles and is present at the cell surface

The tumor suppressor maspin (mammary serpin) was originally identified as a component of human mammary epithelial cells that is downregulated as mammary tumor cells progress from the benign to the invasive and metastatic states. Maspin inhibits cellular invasion, motility, and proliferation, but its mechanism of action is currently unknown. Because the cellular machinery responsible for these processes is cytoplasmic, we have reexamined the tissue distribution and subcellular localization of maspin. We find that maspin, or a maspin-like protein, is present in many human organs, in which it localizes to epithelia. In cultured human mammary myoepithelial cells, maspin is predominantly a soluble cytoplasmic protein that associates with secretory vesicles and is present at the cell surface. In vitro assays show that the vesicle association is due to the existence of an uncleaved facultative secretion signal that allows small amounts of maspin to partition into the endoplasmic reticulum. These results demonstrate that maspin is more widespread than previously believed. The subcellular localization studies indicate that soluble intracellular and vesicle-associated maspin probably play an important role in controlling the invasion, motility, and proliferation of cells expressing it, whereas extracellular maspin may also regulate these processes in adjacent cells.

Fas-mediated apoptosis in human prostatic carcinoma cell lines

Of six prostatic carcinoma cell lines examined (ALVA31, DU145, JCA1, LNCaP, ND1, and PC3) by flow cytometric analysis, all were found to be positive for Fas antigen. Furthermore, of the prostate tissue specimens studied (six cases), all revealed Fas expression in benign and malignant epithelial cells. The agonistic anti-Fas monoclonal antibody (IPO-4) induced apoptosis in only two of six cell lines investigated, PC3 and ALVA31. PCR analysis indicated that all cell lines expressed normal transmembrane and death domains of Fas antigen. Using Western blot analysis, we found abundant expression of p53 in the cytoplasm of two Fas-resistant cell lines, DU145 and ND1, and did not find p53 in two Fas-sensitive cell lines, PC3 and ALVA31. Western blot and PCR analysis did not show consistent differences between cell lines examined in the expression of Bcl-2, Bcl-X(L), Bcl-X(S), and Bak. In contrast, Bax protein was not detected in two Fas-resistant cell lines, DU145 and ND1. We also showed that three Fas-resistant cell lines, DU145, ND1, and JCA1, expressed CD40, whereas the two Fas-sensitive cell lines, PC3 and ALVA31, were CD40 negative. Fas-sensitive cell lines were transfected with the cDNA encoding CD40, and the CD40-positive transfectant became more resistant to growth inhibition mediated by treatment with TNF-alpha and anti-Fas monoclonal antibody. Treatment with cycloheximide converted the phenotype of resistant cell lines from Fas resistant to Fas sensitive. Moreover, anti-Fas treatment of both resistant and sensitive cell lines induced rapid tyrosine phosphorylation or dephosphorylation of multiple proteins. These results suggest that the apoptotic machinery involved in DNA fragmentation is already in place in Fas-resistant cell lines, and thus, Fas-mediated apoptosis could be a target for therapeutic intervention.

Molecular cloning and characterization of Porphyromonas gingivalis lysine-specific gingipain. A new member of an emerging family of pathogenic bacterial cysteine proteinases

The proteinases of Porphyromonas gingivalis are key virulence factors in the etiology and progression of periodontal disease. Previous work in our laboratories resulted in the purification of arginine- and lysine-specific cysteine proteinases, designated gingipains, that consist of several tightly associated protein subunits. Recent characterization of arginine-specific gingipain-1 (gingipain R1; RGP-1) revealed that the sequence is unique and that the protein subunits are initially translated as a polyprotein encoding a proteinase domain and multiple adhesin domains (Pavloff, N., Potempa, J., Pike, R. N., Prochazka, V., Kiefer, M. C., Travis, J., and Barr, P. J. (1995) J. Biol. Chem. 270, 1007-1010). We now show that the lysine-specific gingipain (gingipain K; KGP) is also biosynthesized as a polyprotein precursor that contains a proteinase domain that is 22% homologous to the proteinase domain of RGP-1 and multiple adhesin domains. This precursor is similarly processed at distinct sites to yield active KGP. The key catalytic residues in the proteinase domain of KGP are identical to those found in RGP-1, but there are significant differences elsewhere within this domain that likely contribute to the altered substrate specificity of KGP. Independent expression of the proteinase domain in insect cells has shown that KGP does not require the presence of the adhesin domains for correct folding to confer proteolytic activity.

Porphyromonas gingivalis: a proteinase/gene accounting audit

Analysis of the available data on the Porphyromonas gingivalis proteinase system suggests that at most three different genes encode arginine-X- and lysine-X-specific cysteine proteinases. These are synthesized as polyproteins containing a prepropeptide, a catalytic domain and a hemagglutinin domain. Post-translational processing of each precursor is responsible for the variety of proteinase forms that are seen.

Molecular cloning and structural characterization of the Arg-gingipain proteinase of Porphyromonas gingivalis. Biosynthesis as a proteinase-adhesin polyprotein

The identification of proteinases of Porphyromonas gingivalis that act as virulence factors in periodontal disease has important implications in the study of host-pathogen interactions as well as in the discovery of potential therapeutic and immunoprophylactic agents. We have cloned and characterized a gene that encodes the 50-kDa cysteine proteinase gingipain or Arg-gingipain-1 (RGP-1) described previously (Chen, Z., Potempa, J., Polanowski, A., Wikstrom, M., and Travis, J. (1992) J. Biol. Chem. 267, 18896-18901). Analysis of the amino acid sequence of RGP-1 deduced from the cloned DNA sequence showed that the biosynthesis of this proteinase involves processing of a polyprotein that contains multiple adhesin molecules located at its carboxyl terminus. This finding corroborates previous evidence (Pike R., McGraw, W., Potempa, J., and Travis, J. (1994) J. Biol. Chem. 269, 406-411) that RGP-1 is closely associated with adhesin molecules, and that high molecular weight forms of the proteinase are involved in the binding of erythrocytes.

Tissue inhibitor of metalloproteinases-3 (TIMP-3) is an extracellular matrix-associated protein with a distinctive pattern of expression in mouse cells and tissues

We have isolated cDNA clones corresponding to a novel mouse metalloproteinase inhibitor. Five overlapping cDNA clones contain most of the information for a prominent 4.5-kilobase transcript that was detected in RNA from mouse fibroblasts and adult tissues. Sequence analysis revealed an open reading frame (ORF) for a protein of 212 amino acids that is 80% identical to chicken inhibitor of metalloproteinases-3 (ChIMP-3). The 3'-untranslated sequence also showed remarkable conservation with the chicken gene. The ORF directed the expression of a 24-kDa protein in COS-1 cells that localized to the extracellular matrix (ECM). On the basis of these similarities we propose to identify the new gene as murine tissue inhibitor of metalloproteinases-3 (TIMP-3). Mouse C3H 10T1/2 fibroblasts produced a 24-kDa metalloproteinase inhibitor that also localized to the ECM and was recognized by a polyclonal antibody to ChIMP-3. Like TIMP-1, TIMP-3 was highly inducible in mouse C3H 10T1/2 fibroblasts by phorbol ester (PMA), epidermal growth factor (EGF), and transforming growth factor-beta 1, but nuclear run-on assays showed that the on/off transcription kinetics were faster for TIMP-3 than TIMP-1. A major difference in vitro was the stimulation of expression of TIMP-3 by dexamethasone which inhibits EGF- and PMA-induced TIMP-1 transcription. Also, TIMP-3 showed a distinctive pattern of expression in adult tissues with abundant transcripts detected in kidney, lung, and brain but only low levels detected in bone, a prominent location of TIMP-1 transcripts. We propose that TIMP-3 functions in a tissue-specific fashion as part of an acute response to remodeling stimuli.

A new inhibitor of metalloproteinases from chicken: ChIMP-3. A third member of the TIMP family

We report cDNA cloning and primary structure of a new metalloproteinase inhibitor (ChIMP-3) produced by chicken embryo fibroblasts. ChIMP-3, formerly called the 21-kDa protein, is one of five ChIMPs (Chicken Inhibitor of MetalloProteinases). In this paper, we report that of the three most abundant ChIMPs, ChIMP-3 and ChIMP-a are extracellular matrix components, whereas ChIMP-2 is found in the media conditioned by the cells. Treatment of ChIMP-3 and ChIMP-a with N-glycosidase-F indicates that ChIMP-a is N-glycosylated whereas ChIMP-3 is not. The deduced amino acid sequence of ChIMP-3 predicts a protein whose properties are consistent with experimental measurements. Analysis of sequence alignments with the two previously described members of the TIMP (tissue inhibitor of metalloproteinases) family, TIMP-1 and TIMP-2, from various species indicates that ChIMP-3 is a related but distinct protein. This conclusion is supported by lack of significant binding with anti-TIMP-1 and anti-TIMP-2 antibodies. Based on these data, its unusual solubility properties, and its exclusive location in the matrix, we propose that ChIMP-3 is a new member of this family of metalloproteinase inhibitors, a TIMP-3.

Sequence analysis of the large and small subunits of human ribonucleotide reductase

We have isolated and sequenced overlapping cDNA clones from a breast carcinoma cDNA library containing the entire coding region of both the R1 and R2 subunits of the human ribonucleotide reductase gene. The coding region of the human R1 subunit comprises 2376 nucleotides and predicts a polypeptide of 792 amino acids (calculated molecular mass 90,081). The sequence of this subunit is almost identical to the equivalent mouse ribonucleotide reductase subunit with 97.7% homology between the mouse and human R1 subunit amino acid sequences. The coding region of the human R2 subunit of ribonucleotide reductase comprises 1170 nucleotides and predicts a polypeptide of 389 amino acids (calculated molecular mass 44,883), which is one amino acid shorter than the equivalent mouse subunit. The human and mouse R2 subunits display considerable homology in their carboxy-terminal amino acid sequences, with 96.3% homology downstream of amino acid 68 of the human and mouse R2 proteins. However, the amino-terminal portions of these two proteins are more divergent in sequence, with only 69.2% homology in the first 68 amino acids.

Simultaneous overexpression of avian pp60c-src and polyomavirus middle T antigen in mammalian cells

Recombinant adenoviruses bearing the avian c-src gene and polyomavirus middle-T-antigen gene were isolated and used to simultaneously overexpress both proteins in human 293 cells. Cells overexpressing both proteins had greater middle-T-antigen-associated tyrosine kinase activity than cells overexpressing only middle T antigen. By contrast, the intrinsic pp60c-src tyrosine kinase activity was not greater in cells overexpressing both proteins than in cells overexpressing only pp60c-src. This system of simultaneous overexpression provides a means of obtaining large quantities of pp60c-src, middle T antigen, and the complex between them.

Purification and characterization of proteins with associated tyrosine protein kinase activity from human B lymphocytes

Burkitt lymphoma cells and their counterpart of normal origin contain proteins with associated tyrosine protein, kinase activity. These proteins were isolated by affinity chromatography and Fast Pressure Liquid Chromatography. Proteins with enzyme activity had an app. M. W. of 47 KDa. This protein in extracts of Burkitt lymphoma cells differed by overall charge and phosphorylation from the 47 KDa protein isolated from B lymphocytes of normal origin. Before and after purification the 47 KDa protein of Burkitt lymphoma cells reacted with an antibody directed against the dodecapeptide Arg-Arg-Leu-Ile-Glu-Asp-Asn-Glu-Tyr-Thr-Ala-Arg (conserved region of pp60src), the 47 KDa protein from B cells of normal origin did not; the same protein from both cell lines reacted with anti-pp60src antibody. These results suggest that a tyrosine protein kinase, related to the products of the src family of oncogenes, is modified in Burkitt lymphoma cells.

Differentiation of Burkitt lymphoma cells by hexamethylenbisacetamide

Hexamethylenbisacetamide (HMBA) can induce the Burkitt lymphoma Raji cells to enter the differentiation process as evidenced by the decrease of HLA-DR antigens. This event is preceded by a decrease of c-myc expression and of the phosphorylation of cellular proteins, due to either a decrease of tyrosine protein kinase activity or an increase of tyrosine phosphatase activity. These three events form a sequence and are part of the genetic program for differentiation and growth though they may not be causally related.

Viral products in cells infected with vesicular stomatitis virus and superinfected with Rous sarcoma virus

In cells infected with Vesicular Stomatitis virus (VSV) ts 1026 and superinfected with Rous Sarcoma virus (RSV) synthesis of vsrc mRNA and RSV env mRNA decreases. In these cells post-translational processing of RSV precursor proteins is impaired and small amounts of VSV antigens are detected.

Integration and expression of provirus in human cells transformed by avian sarcoma virus

Previously, human diploid fibroblasts from some donors infected in vitro by avian sarcoma virus (ASV) were transformed and found, by electron microscopy, to produce small numbers of virus particles that were infectious by bioassay; also, a line of human osteosarcoma cells infected with ASV developed additional characteristics of transformation and released a small number of infectious virus particles. In this study the complete proviral sequence was shown to be integrated in the genome of these cells. The env-related proteins gp85 and gp37 and the gag-related proteins pr76, pr60, and p19 can be detected in cytoplasmic extracts of ASV-infected human cells. Comparable amounts of pp60v-src were found in human and avian cells infected with ASV. The associated kinase activity in infected human cells was dramatically increased as compared to that of uninfected controls; the enzyme had the same cation and substrate requirements as those from ASV-transformed avian cells. Replicating particles from infected human cells were purified and were significantly modified compared to those from avian hosts as shown by a) higher specific gravity, b) the presence of RSV gag-related but not env-related antigens, and c) the fact that the virus-associated reverse transcriptase preferred the divalent cations Mn2+ and Fe2+ over Mg2+.

Binding of proteins, including pp60src, to activated CH-sepharose 4B

Activated CH-Sepharose 4B and protein A Sepharose CL-4B can bind, selectively and non-specifically, polypeptides from chick embryo cells. The major polypeptides bound have apparent molecular masses of 57-60 kDa and 47-49 kDa and cannot be eluted by extensive washing with buffers containing detergents. One of the 57-60 kDa polypeptides was identified by immunoblotting as the transforming protein of Rous Sarcoma Virus (RSV), pp60src. This polypeptide could be removed from the solid phase immunoabsorbent with 60% dimethylsulfoxide, but not with 2% SDS, 5% beta-mercaptoethanol, 1 M NaCl or 0.1% Tween 20.

Isolation of proteins with kinase activity and related to pp60 src from human cells

A protein kinase activity (PK) was associated with immunoprecipitates between polypeptides of human lymphoblastoid cells of malignant origin (Raji cell line) or of their normal counterparts ( Priess cell line) and antibodies directed against avian pp60 src or against the carboxyterminal hexapeptide of pp60 src. Therefore, these human cells and Rous Sarcoma Virus (RSV) transformed avian cells share antigenic determinants of pp60 src and, in particular, its carboxyterminal sequence, as well as one of its functions, a protein kinase activity. The protein kinase from Raji cells phosphorylated predominantly tyrosine residues, that from Priess cells threonine residues.