Lipidic cubic phases: A novel concept for the crystallization of membrane proteins

Understanding the mechanisms of action of membrane proteins requires the elucidation of their structures to high resolution. The critical step in accomplishing this by x-ray crystallography is the routine availability of well-ordered three-dimensional crystals. We have devised a novel, rational approach to meet this goal using quasisolid lipidic cubic phases. This membrane system, consisting of lipid, water, and protein in appropriate proportions, forms a structured, transparent, and complex three-dimensional lipidic array, which is pervaded by an intercommunicating aqueous channel system. Such matrices provide nucleation sites (“seeding”) and support growth by lateral diffusion of protein molecules in the membrane (“feeding”). Bacteriorhodopsin crystals were obtained from bicontinuous cubic phases, but not from micellar systems, implying a critical role of the continuity of the diffusion space (the bilayer) on crystal growth. Hexagonal bacteriorhodopsin crystals diffracted to 3.7 Å resolution, with a space group P63, and unit cell dimensions of a = b = 62 Å, c = 108 Å; α = β = 90° and γ = 120°.

Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells

Fluorescein-labeled oligodeoxynucleotides (oligos) were introduced into cultured rat myoblasts, and their molecular movements inside the nucleus were studied by fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). FCS revealed that a large fraction of both intranuclear oligo(dT) (43%) and oligo(dA) (77%) moves rapidly with a diffusion coefficient of 4 × 10−7 cm2/s. Interestingly, this rate of intranuclear oligo movement is similar to their diffusion rates measured in aqueous solution. In addition, we detected a large fraction (45%) of the intranuclear oligo(dT), but not oligo(dA), diffusing at slower rates (≤1 × 10−7 cm2/s). The amount of this slower-moving oligo(dT) was greatly reduced if the oligo(dT) was prehybridized in solution with (unlabeled) oligo(dA) prior to introduction to cells, presumably because the oligo(dT) was then unavailable for subsequent hybridization to endogenous poly(A) RNA. The FCS-measured diffusion rate for much of the slower oligo(dT) population approximated the diffusion rate in aqueous solution of oligo(dT) hybridized to a large polyadenylated RNA (1.0 × 10−7 cm2/s). Moreover, this intranuclear movement rate falls within the range of calculated diffusion rates for an average-sized heterogeneous nuclear ribonucleoprotein particle in aqueous solution. A subfraction of oligo(dT) (15%) moved over 10-fold more slowly, suggesting it was bound to very large macromolecular complexes. Average diffusion coefficients obtained from FRAP experiments were in agreement with the FCS data. These results demonstrate that oligos can move about within the nucleus at rates comparable to those in aqueous solution and further suggest that this is true for large ribonucleoprotein complexes as well.

Mechanisms underlying losses of heterozygosity in human colorectal cancers

Losses of heterozygosity are the most common molecular genetic alteration observed in human cancers. However, there have been few systematic studies to understand the mechanism(s) responsible for losses of heterozygosity in such tumors. Here we report a detailed investigation of the five chromosomes lost most frequently in human colorectal cancers. A total of 10,216 determinations were made with 88 microsatellite markers, revealing 245 chromosomal loss events. The mechanisms of loss were remarkably chromosome-specific. Some chromosomes displayed complete loss such as that predicted to result from mitotic nondisjunction. However, more than half of the losses were associated with losses of only part of a chromosome rather than a whole chromosome. Surprisingly, these losses were due largely to structural alterations rather than to mitotic recombination, break-induced replication, or gene conversion, suggesting novel mechanisms for the generation of much of the aneuploidy in this common tumor type.

Role of tumor–host interactions in interstitial diffusion of macromolecules: Cranial vs. subcutaneous tumors

The large size of many novel therapeutics impairs their transport through the tumor extracellular matrix and thus limits their therapeutic effectiveness. We propose that extracellular matrix composition, structure, and distribution determine the transport properties in tumors. Furthermore, because the characteristics of the extracellular matrix largely depend on the tumor–host interactions, we postulate that diffusion of macromolecules will vary with tumor type as well as anatomical location. Diffusion coefficients of macromolecules and liposomes in tumors growing in cranial windows (CWs) and dorsal chambers (DCs) were measured by fluorescence recovery after photobleaching. For the same tumor types, diffusion of large molecules was significantly faster in CW than in DC tumors. The greater diffusional hindrance in DC tumors was correlated with higher levels of collagen type I and its organization into fibrils. For molecules with diameters comparable to the interfibrillar space the diffusion was 5- to 10-fold slower in DC than in CW tumors. The slower diffusion in DC tumors was associated with a higher density of host stromal cells that synthesize and organize collagen type I. Our results point to the necessity of developing site-specific drug carriers to improve the delivery of molecular medicine to solid tumors.

Three Mechanisms for the Calcium Alleviation of Mineral Toxicities

Ca2+ in rooting medium is essential for root elongation, even in the absence of added toxicants. In the presence of rhizotoxic levels of Al3+, H+, or Na+ (or other cationic toxicants), supplementation of the medium with higher levels of Ca2+ alleviates growth inhibition. Experiments to determine the mechanisms of alleviation entailed measurements of root elongation in wheat (Triticum aestivum L. cv Scout 66) seedlings in controlled medium. A Gouy-Chapman-Stern model was used to compute the electrical potentials and the activities of ions at the root-cell plasma membrane surfaces. Analysis of root elongation relative to the computed surface activities of ions revealed three separate mechanisms of Ca2+ alleviation. Mechanism I is the displacement of cell-surface toxicant by the Ca2+-induced reduction in cell-surface negativity. Mechanism II is the restoration of Ca2+ at the cell surface if the surface Ca2+ has been reduced by the toxicant to growth-limiting levels. Mechanism III is the collective ameliorative effect of Ca2+ beyond mechanisms I and II, and may involve Ca2+-toxicant interactions at the cell surface other than the displacement interactions of mechanisms I and II. Mechanism I operated in the alleviation of all of the tested toxicities; mechanism II was generally a minor component of alleviation; and mechanism III was toxicant specific and operated strongly in the alleviation of Na+ toxicity, moderately in the alleviation of H+ toxicity, and not at all in the alleviation of Al3+ toxicity.

Instability of repetitive DNA sequences: The role of replication in multiple mechanisms

Rearrangements between tandem sequence homologies of various lengths are a major source of genomic change and can be deleterious to the organism. These rearrangements can result in either deletion or duplication of genetic material flanked by direct sequence repeats. Molecular genetic analysis of repetitive sequence instability in Escherichia coli has provided several clues to the underlying mechanisms of these rearrangements. We present evidence for three mechanisms of RecA-independent sequence rearrangements: simple replication slippage, sister-chromosome exchange-associated slippage, and single-strand annealing. We discuss the constraints of these mechanisms and contrast their properties with RecA-dependent homologous recombination. Replication plays a critical role in the two slipped misalignment mechanisms, and difficulties in replication appear to trigger rearrangements via all these mechanisms.

The biology of vision of Drosophila.

Phototransduction systems in vertebrates and invertebrates share a great deal of similarity in overall strategy but differ significantly in the underlying molecular machinery. Both are rhodopsin-based G protein-coupled signaling cascades displaying exquisite sensitivity and broad dynamic range. However, light activation of vertebrate photoreceptors leads to activation of a cGMP-phosphodiesterase effector and the generation of a hyperpolarizing response. In contrast, activation of invertebrate photoreceptors, like Drosophila, leads to stimulation of phospholipase C and the generation of a depolarizing receptor potential. The comparative study of these two systems of phototransduction offers the opportunity to understand how similar biological problems may be solved by different molecular mechanisms of signal transduction. The study of this process in Drosophila, a system ideally suited to genetic and molecular manipulation, allows us to dissect the function and regulation of such a complex signaling cascade in its normal cellular environment. In this manuscript I review some of our recent findings and the strategies used to dissect this process.

Directed selection of recombinant human monoclonal antibodies to herpes simplex virus glycoproteins from phage display libraries.

Human monoclonal antibodies have considerable potential in the prophylaxis and treatment of viral disease. However, only a few such antibodies suitable for clinical use have been produced to date. We have previously shown that large panels of human recombinant monoclonal antibodies against a plethora of infectious agents, including herpes simplex virus types 1 and 2, can be established from phage display libraries. Here we demonstrate that facile cloning of recombinant Fab fragments against specific viral proteins in their native conformation can be accomplished by panning phage display libraries against viral glycoproteins "captured" from infected cell extracts by specific monoclonal antibodies immobilized on ELISA plates. We have tested this strategy by isolating six neutralizing recombinant antibodies specific for herpes simplex glycoprotein gD or gB, some of which are against conformationally sensitive epitopes. By using defined monoclonal antibodies for the antigen-capture step, this method can be used for the isolation of antibodies to specific regions and epitopes within the target viral protein. For instance, monoclonal antibodies to a nonneutralizing epitope can be used in the capture step to clone antibodies to neutralizing epitopes, or antibodies to a neutralizing epitope can be used to clone antibodies to a different neutralizing epitope. Furthermore, by using capturing antibodies to more immunodominant epitopes, one can direct the cloning to less immunogenic ones. This method should be of value in generating antibodies to be used both in the prophylaxis and treatment of viral infections and in the characterization of the mechanisms of antibody protective actions at the molecular level.

SPC3, a synthetic peptide derived from the V3 domain of human immunodeficiency virus type 1 (HIV-1) gp120, inhibits HIV-1 entry into CD4+ and CD4- cells by two distinct mechanisms.

The third variable region (V3 loop) of gp120, the HIV-1 surface envelope glycoprotein, plays a key role in HIV-1 infection and pathogenesis. Recently, we reported that a synthetic multibranched peptide (SPC3) containing eight V3-loop consensus motifs (GPGRAF) inhibited HIV-1 infection in both CD4+ and CD4- susceptible cells. In the present study, we investigated the mechanisms of action of SPC3 in these cell types--i.e., CD4+ lymphocytes and CD4- epithelial cells expressing galactosylceramide (GalCer), an alternative receptor for HIV-1 gp120. We found that SPC3 was a potent inhibitor of HIV-1 infection in CD4+ lymphocytes when added 1 h after initial exposure of the cells to HIV-1, whereas it had no inhibitory effect when present only before and/or during the incubation with HIV-1. These data suggested that SPC3 did not inhibit the binding of HIV-1 to CD4+ lymphocytes but interfered with a post-binding step necessary for virus entry. In agreement with this hypothesis, SPC3 treatment after HIV-1 exposure dramatically reduced the number of infected cells without altering gp120-CD4 interaction or viral gene expression. In contrast, SPC3 blocked HIV-1 entry into CD4-/GalCer+ human colon epithelial cells when present in competition with HIV-1 but had no effect when added after infection. Accordingly, SPC3 was found to inhibit the binding of gp120 to the GalCer receptor. Thus, the data suggest that SPC3 affects HIV-1 infection by two distinct mechanisms: (i) prevention of GalCer-mediated HIV-1 attachment to the surface of CD4-/GalCer+ cells and (ii) post-binding inhibition of HIV-1 entry into CD4+ lymphocytes.

Agents et modèles de l'adaptation publicitaire en agence de communication marketing

L’industrie de la publicité doit se renouveler sans cesse pour suivre la réalité en constante évolution des entreprises et de leurs consommateurs, afin de produire des messages qui toucheront, séduiront, puis convaincront les publics visés. Différents facteurs socioéconomiques, politiques mais également technologiques incitent les annonceurs à orchestrer de vastes campagnes multilingues et multiculturelles, où est présentée une idée unique, conforme à l’identité de la marque, qui sera adaptée dans différents marchés. Il s’agit d’une stratégie très différente de celle de la création de campagnes propres à chaque culture, par des agences locales. Le choix de l’adaptation, motivé par des raisons économiques bien sûr, mais également stratégiques, entraîne une évolution de la perception de l’acte traduisant et de ses acteurs au sein du milieu du marketing et de la publicité. Alors que nous assistons à un rapprochement des industries du marketing et de la traduction, principalement dans les marchés secondaires comme le Québec, ce projet doctoral propose une réflexion traductologique sur la place que peut occuper l’adaptation dans une stratégie en publicité marketing, et sur les différentes fonctions que peut remplir un traducteur intégré à une équipe de spécialistes de la communication. Par ailleurs, de la réception du mandat d’adaptation à l’agence de marketing jusqu’à la diffusion du message dans la culture cible, nous explorons dans notre travail les différentes avenues que peut prendre le processus d’adaptation publicitaire. Cette thèse par articles comprend six publications en traductologie, publiées ou acceptées par des comités scientifiques, qui étudient la question de l’adaptation publicitaire sous un angle traductologique, mais ce travail multidisciplinaire s’inspire aussi des contributions des experts des études sur l’adaptation, la culture ainsi que la communication publicitaire. D’abord, le premier chapitre définit les notions de traduction, d’adaptation et d’appropriation auxquelles nous référerons tout au long de la thèse, et les situe dans le contexte de la communication promotionnelle internationale, notamment. Le deuxième chapitre dresse un portrait pratique et théorique de l’adaptation publicitaire, et porte sur les relations de travail entre le traducteur et les autres professionnels de l’agence. Nous y énumérons notamment les raisons de la progression du marché mondial de l’adaptation, comparativement à celui des multiples créations locales. Ensuite, le chapitre 3 définit les défis variés de l’adaptation publicitaire, et en présente une classification inspirée par la taxonomie de la théorie fonctionnaliste en traductologie, formée de quatre problèmes et deux difficultés traductionnels. Le chapitre 4 présente une réflexion sur les mécanismes intellectuels de l’adaptation publicitaire et sur les différentes lectures que le traducteur doit faire du texte source pour produire un message efficace, respectivement la lecture analytique (rationnelle et raisonnée), puis la lecture empathique, où il anticipe la réaction émotive des cibles. Le cinquième chapitre se concentre sur un aspect de la traduction audiovisuelle presque exclusive à l’industrie publicitaire : la double version, où le traducteur traduit non pas des dialogues apposés à l’image originale, mais plutôt le scénario dans son entièreté, afin de produire un nouveau message vidéo avec des acteurs appartenant à la culture cible. Enfin, notre sixième chapitre est une étude de cas menée en agence de publicité, qui analyse la pratique professionnelle de traducteurs dans leur environnement de travail, les mandats qui leur sont confiés ainsi que les ressources dont ils disposent. Ensemble, ces six chapitres visent à mieux faire connaître la démarche intellectuelle de l’adaptation publicitaire, à comprendre comment différents facteurs influencent le rôle du traducteur au sein d’une agence, à déterminer comment mieux préparer les professionnels de demain à exceller dans le marché très prometteur du marketing international, et à contribuer à l’avancement de la réflexion traductologique par l’étude d’un type de traduction spécialisée qui se démarque par ses pratiques et ses défis aussi intéressants qu’uniques.

Germany on Russia. Yes to links, no to rapprochement. OSW Point of View Number 39, March 2014

The German media have been correctly describing the atmosphere between the Chancellor's Office and the Kremlin as the chilliest in years. Various factors have laid bare the fact that the strategic partnership between Germany and Russia is at best currently undergoing a 'technical pause’: the underwhelming outcomes of the German-Russian intergovernmental consultations in the autumn of 2012 and of Chancellor Merkel's meeting with President Putin during the Hanover fair in the spring of 2013, as well as the way in which the EU dealt with the Cyprus debt issue and, finally, the support that Germany has extended to the anti-presidential protests in Ukraine. Meanwhile, the priorities of Germany's foreign and economic policy have changed considerably, not only as a result of the eurozone crisis, but also, even more importantly, because the attention of German business and politics has been shifting to the so-called neue Gestaltungsmächte, or new regional powers. German politicians increasingly believe that Russia should not be offered new methods or mechanisms of co-operation. Firstly, because the existing ones have not been fully utilised, and secondly, because Germany at this stage seems to have no idea of what the long-term strategy of co-operation with Putin's Russia should be.

Agents et modèles de l'adaptation publicitaire en agence de communication marketing

L’industrie de la publicité doit se renouveler sans cesse pour suivre la réalité en constante évolution des entreprises et de leurs consommateurs, afin de produire des messages qui toucheront, séduiront, puis convaincront les publics visés. Différents facteurs socioéconomiques, politiques mais également technologiques incitent les annonceurs à orchestrer de vastes campagnes multilingues et multiculturelles, où est présentée une idée unique, conforme à l’identité de la marque, qui sera adaptée dans différents marchés. Il s’agit d’une stratégie très différente de celle de la création de campagnes propres à chaque culture, par des agences locales. Le choix de l’adaptation, motivé par des raisons économiques bien sûr, mais également stratégiques, entraîne une évolution de la perception de l’acte traduisant et de ses acteurs au sein du milieu du marketing et de la publicité. Alors que nous assistons à un rapprochement des industries du marketing et de la traduction, principalement dans les marchés secondaires comme le Québec, ce projet doctoral propose une réflexion traductologique sur la place que peut occuper l’adaptation dans une stratégie en publicité marketing, et sur les différentes fonctions que peut remplir un traducteur intégré à une équipe de spécialistes de la communication. Par ailleurs, de la réception du mandat d’adaptation à l’agence de marketing jusqu’à la diffusion du message dans la culture cible, nous explorons dans notre travail les différentes avenues que peut prendre le processus d’adaptation publicitaire. Cette thèse par articles comprend six publications en traductologie, publiées ou acceptées par des comités scientifiques, qui étudient la question de l’adaptation publicitaire sous un angle traductologique, mais ce travail multidisciplinaire s’inspire aussi des contributions des experts des études sur l’adaptation, la culture ainsi que la communication publicitaire. D’abord, le premier chapitre définit les notions de traduction, d’adaptation et d’appropriation auxquelles nous référerons tout au long de la thèse, et les situe dans le contexte de la communication promotionnelle internationale, notamment. Le deuxième chapitre dresse un portrait pratique et théorique de l’adaptation publicitaire, et porte sur les relations de travail entre le traducteur et les autres professionnels de l’agence. Nous y énumérons notamment les raisons de la progression du marché mondial de l’adaptation, comparativement à celui des multiples créations locales. Ensuite, le chapitre 3 définit les défis variés de l’adaptation publicitaire, et en présente une classification inspirée par la taxonomie de la théorie fonctionnaliste en traductologie, formée de quatre problèmes et deux difficultés traductionnels. Le chapitre 4 présente une réflexion sur les mécanismes intellectuels de l’adaptation publicitaire et sur les différentes lectures que le traducteur doit faire du texte source pour produire un message efficace, respectivement la lecture analytique (rationnelle et raisonnée), puis la lecture empathique, où il anticipe la réaction émotive des cibles. Le cinquième chapitre se concentre sur un aspect de la traduction audiovisuelle presque exclusive à l’industrie publicitaire : la double version, où le traducteur traduit non pas des dialogues apposés à l’image originale, mais plutôt le scénario dans son entièreté, afin de produire un nouveau message vidéo avec des acteurs appartenant à la culture cible. Enfin, notre sixième chapitre est une étude de cas menée en agence de publicité, qui analyse la pratique professionnelle de traducteurs dans leur environnement de travail, les mandats qui leur sont confiés ainsi que les ressources dont ils disposent. Ensemble, ces six chapitres visent à mieux faire connaître la démarche intellectuelle de l’adaptation publicitaire, à comprendre comment différents facteurs influencent le rôle du traducteur au sein d’une agence, à déterminer comment mieux préparer les professionnels de demain à exceller dans le marché très prometteur du marketing international, et à contribuer à l’avancement de la réflexion traductologique par l’étude d’un type de traduction spécialisée qui se démarque par ses pratiques et ses défis aussi intéressants qu’uniques.

Maintenance of coelomic fluid pH in sea urchins exposed to elevated CO2: the role of body cavity epithelia and stereom dissolution

Experimental ocean acidification leads to a shift in resource allocation and to an increased [HCO3-] within the perivisceral coelomic fluid (PCF) in the Baltic green sea urchin Strongylocentrotus droebachiensis. We investigated putative mechanisms of this pH compensation reaction by evaluating epithelial barrier function and the magnitude of skeleton (stereom) dissolution. In addition, we measured ossicle growth and skeletal stability. Ussing chamber measurements revealed that the intestine formed a barrier for HCO3- and was selective for cation diffusion. In contrast, the peritoneal epithelium was leaky and only formed a barrier for macromolecules. The ossicles of 6 week high CO2-acclimatised sea urchins revealed minor carbonate dissolution, reduced growth but unchanged stability. On the other hand, spines dissolved more severely and were more fragile following acclimatisation to high CO2. Our results indicate that epithelia lining the PCF space contribute to its acid-base regulation. The intestine prevents HCO3- diffusion and thus buffer leakage. In contrast, the leaky peritoneal epithelium allows buffer generation via carbonate dissolution from the surrounding skeletal ossicles. Long-term extracellular acid-base balance must be mediated by active processes, as sea urchins can maintain relatively high extracellular [HCO3-]. The intestinal epithelia are good candidate tissues for this active net import of HCO3- into the PCF. Spines appear to be more vulnerable to ocean acidification which might significantly impact resistance to predation pressure and thus influence fitness of this keystone species.

The Renaissance of Performance Funding for Higher Education: Policy Adoption, Implementation, and Impacts

Thesis (Ph.D.)--University of Washington, 2016-06

Elucidating the cis-regulatory landscape of retinal development and regeneration

Thesis (Ph.D.)--University of Washington, 2016-04