Electron microscopy of RecA-DNA complexes: Two different states, their functional significance and relation to the solved crystal structure

Seven different electron microscopy techniques habe been employed to study the RecA protein of E. coli. This review provides a summary of the conclusions that have been drawn from these studies, and attempts to relate these observations to models for the role of RecA protein in homologous recombination.

L'estudi dels incendis en el món mediterrani

This article discusses briefly the evolution of fire in the Mediterranean biome and reviews afterwards the main research themes that geographers, ecologists and botanists have developed around forest fires issues in the Mediterranean

Impact of recombination on genetic variability within Staphylococcus aureus clonal complexes.

The population structure of Staphylococcus aureus is generally described as highly clonal and is consequently subdivided into several clonal complexes (CCs). Recent data suggested that recombination might occur more frequently within than among CCs. To test this hypothesis as well as to understand how genetic diversity is created in S. aureus, we analyzed a collection of 182 isolates with MLST and five highly variable core adhesion (ADH) genes. As expected the polymorphism of ADH genes was higher than MLST genes. However both categories of genes showed low within CCs diversity with a dominant haplotype and its single nucleotide variants. Several recombination events were detected but none involved intra-CC recombination. This did not confirm the hypothesis of higher recombination within CCs. Nevertheless, molecular analyses of variance indicated that these few recombination events have a significant impact on the genetic diversity within CCs. In addition, although most ADH genes were under purifying selection, signs of positive selection associated with a recombinant group were detected. These data highlight the importance of recombination on the evolution of the highly clonal S. aureus and suggest that recombination when combined with demographic mechanisms as well as selection might favor the rapid creation of new clonal complexes.

Isolated integrin beta3 subunit cytoplasmic domains require membrane anchorage and the NPXY motif to recruit to adhesion complexes but do not discriminate between beta1- and beta3-positive complexes.

Integrin adhesion receptors consist of non-covalently linked alpha and beta subunits each of which contains a large extracellular domain, a single transmembrane domain and a short cytoplasmic tail. Engaged integrins recruit to focal structures globally termed adhesion complexes. The cytoplasmic domain of the beta subunit is essential for this clustering. beta1 and beta3 integrins can recruit at distinct cellular locations (i.e. fibrillar adhesions vs focal adhesions, respectively) but it is not clear whether individual beta subunit cytoplasmic and transmembrane domains are by themselves sufficient to drive orthotopic targeting to the cognate adhesion complex. To address this question, we expressed full-length beta3 transmembrane anchored cytoplasmic domains and truncated beta3 cytoplasmic domains as GFP-fusion constructs and monitored their localization in endothelial cells. Membrane-anchored full-length beta3 cytoplasmic domain and a beta3 mutant lacking the NXXY motif recruited to adhesion complexes, while beta3 mutants lacking the NPXY and NXXY motifs or the transmembrane domain did not. Replacing the natural beta subunit transmembrane domain with an unrelated (i.e. HLA-A2 alpha chain) transmembrane domain significantly reduced recruitment to adhesion complexes. Transmembrane anchored beta3 and cytoplasmic domain constructs, however, recruited without discrimination to beta1- and beta3-rich adhesions complexes. These findings demonstrate that membrane anchorage and the NPXY (but not the NXXY) motif are necessary for beta3 cytoplasmic domain recruitment to adhesion complexes and that the natural transmembrane domain actively contributes to this recruitment. The beta3 transmembrane and cytoplasmic domains alone are insufficient for orthotopic recruitment to cognate adhesion complexes.

Interplay between T cell receptor binding kinetics and the level of cognate peptide presented by major histocompatibility complexes governs CD8+ T cell responsiveness.

Through a rational design approach, we generated a panel of HLA-A*0201/NY-ESO-1(157-165)-specific T cell receptors (TCR) with increasing affinities of up to 150-fold from the wild-type TCR. Using these TCR variants which extend just beyond the natural affinity range, along with an extreme supraphysiologic one having 1400-fold enhanced affinity, and a low-binding one, we sought to determine the effect of TCR binding properties along with cognate peptide concentration on CD8(+) T cell responsiveness. Major histocompatibility complexes (MHC) expressed on the surface of various antigen presenting cells were peptide-pulsed and used to stimulate human CD8(+) T cells expressing the different TCR via lentiviral transduction. At intermediate peptide concentration we measured maximum cytokine/chemokine secretion, cytotoxicity, and Ca(2+) flux for CD8(+) T cells expressing TCR within a dissociation constant (K(D)) range of ∼1-5 μM. Under these same conditions there was a gradual attenuation in activity for supraphysiologic affinity TCR with K(D) < ∼1 μM, irrespective of CD8 co-engagement and of half-life (t(1/2) = ln 2/k(off)) values. With increased peptide concentration, however, the activity levels of CD8(+) T cells expressing supraphysiologic affinity TCR were gradually restored. Together our data support the productive hit rate model of T cell activation arguing that it is not the absolute number of TCR/pMHC complexes formed at equilibrium, but rather their productive turnover, that controls levels of biological activity. Our findings have important implications for various immunotherapies under development such as adoptive cell transfer of TCR-engineered CD8(+) T cells, as well as for peptide vaccination strategies.

Variación estacional del fitoplancton en el Área del Callao durante El Niño 1987 (10-200 mn)

Se analizó la distribución espacio temporal de la abundancia fitoplanctónica, asociándola con la temperatura, salinidad, nutrientes y clorofila "a" en el perfil Callao 12 ºS, durante el año 1987. Se determinó la estructura de las asociaciones del fitoplancton mediante la composición específica, la riqueza específica (S), diversidad (H') y la dominancia ( D ) . La variación anual fitoplanctónica presentó un comportamiento similar al ciclo anual de producción del mar peruano, con dos picos de abundancia; el primero en primavera y el segundo en verano. Los eventos de surgencias que enriquecen de nutrientes las aguas del área del Callao son los responsables de que en esta zona se hayan registrado las concentraciones más altas de fitoplancton. Las diatomeas, los cocolitofóridos y los fitoflagelados fueron los componentes dominantes en los muestreos; siendo los dinoflagelados y los silicoflagelados ligeramente abundantes en el verano. La composición específica arrojó un total de 172 especies, comprendidos en 91 diatomeas, 52 dinoflagelados, 21 cocolitofóridos, 6 fitoflagelados y 2 silicoflagelados . Las especies Thalassiosira mínima, Skeletonema costatum, Nitzschia bicapitata, Nitzschia closterium, Navícula sp ., Guinardia delicatula, Gymnodinium splendens, Emiliania huxleyi y Eutreptiella gimnastica, fueron características de la temporada de la Primavera y Verano, mientras que Planktoniella sol, Rhizosolenia bergonii, Gymnodinium sp. y Nonada sp. lo fueron para la temporada del Otoño e Invierno. La variación de la diversidad específica y la dominancia estuvo relacionada por la influencia del fenómeno El Niño, así tenemos que durante la época de El Niño hasta el invierno de 1987 se observaron valores altos de diversidad y baja dominancia en la zona costera indicando una comunidad fitoplanctónica de etapa avanzada de la sucesión ecológica . El evento "El Niño" 1987, provocó una notable caída de la abundancia fitoplanctónica, desde Noviembre de 1986 hasta Marzo de 1987. Los indicios de recuperación del fitoplancton se observaron a partir de setiembre de 1987, habiéndose recuperado parcialmente en Primavera del mismo año. Durante el período 1987, Emiliania huxleyi, Caloiosolenia murrayi y el grupo de los Fitoflagelados fueron los taxas predominantes.

Selectively expanding subsets of T cells in mice by injection of interleukin-2/antibody complexes: implications for transplantation tolerance.

The biological activity of interleukin (IL)-2 and other cytokines in vivo can be augmented by binding to certain anti-cytokine monoclonal antibodies (mAb). Here, we review evidence on how IL-2/anti-IL-2 mAb complexes can be used to cause selective stimulation and expansion of certain T-cell subsets. With some anti-IL-2 mAbs, injection of IL-2/mAb complexes leads to expansion of CD8 T effector cells but not CD4 T regulatory cells (Tregs); these complexes exert less adverse side effects than soluble IL-2 and display powerful antitumor activity. Other IL-2/mAb complexes have minimal effects on CD8 T cells but cause marked expansion of Tregs. Preconditioning mice with these complexes leads to permanent acceptance of MHC-disparate pancreatic islets in the absence of immunosuppression.

Produção de grãos e absorção de Cu, Fe, Mn e Zn pelo milho em solo adubado com lodo de esgoto, com e sem calcário

O lodo de esgoto (LE), apesar do seu reconhecido valor como fertilizante, ainda é motivo de preocupação quando usado na agricultura, em virtude do potencial de absorção excessiva de metais pesados pelas plantas e entrada na cadeia alimentar. Para avaliar o efeito da adição de 0, 20, 40, 60 e 80 Mg ha-1 (com base no material seco) de LE, aplicado de forma única ou parcelada em 2, 3 e 4 anos nas doses de 40, 60 e 80 Mg ha-1, respectivamente, com e sem calcário, na produção de grãos e massa seca da parte aérea e na absorção de Cu, Fe, Mn e Zn pelo milho, foi realizado, em Cordeirópolis (SP), um experimento em condições de campo, utilizando um Latossolo Vermelho distrófico típico, no período de 1983 a 1987. Foi utilizado o experimento em faixas ("split block") com quatro repetições. A maior dose de LE adicionou ao solo, em kg ha-1, 63, 3040, 25 e 152 de Cu, Fe, Mn e Zn, respectivamente. A produção de grãos e de massa seca da parte aérea aumentou linearmente com a adição de LE nos anos estudados. O LE aumentou significativamente as concentrações de Zn nas folhas e na parte aérea e provocou a redução nas concentrações de Fe e Mn, mas não alterou as de Cu. As concentrações dos metais nos grãos não foram influenciadas de forma significativa pela adição de LE, estando mesmo nas maiores doses, dentro dos níveis aceitáveis, sem causar restrição ao consumo humano. A absorção de Zn, Fe e Mn pelo milho foi significativamente reduzida pela adição de calcário. O Zn foi o metal que mais teve reduzida sua concentração na parte aérea pela adição de calcário. O parcelamento das doses de lodo de 40 a 80 Mg ha-1 provocou, de modo geral, aumento das quantidades absorvidas de metais pelo milho, sendo o Fe e o Zn os elementos que mais se acumularam na planta em resposta a esse parcelamento.

Soluble MHC-peptide complexes containing long rigid linkers abolish CTL-mediated cytotoxicity.

Soluble MHC-peptide (pMHC) complexes induce intracellular calcium mobilization, diverse phosphorylation events, and death of CD8+ CTL, given that they are at least dimeric and co-engage CD8. By testing dimeric, tetrameric, and octameric pMHC complexes containing spacers of different lengths, we show that their ability to activate CTL decreases as the distance between their subunit MHC complexes increases. Remarkably, pMHC complexes containing long rigid polyproline spacers (&gt; or =80 A) inhibit target cell killing by cloned S14 CTL in a dose- and valence-dependent manner. Long octameric pMHC complexes abolished target cell lysis, even very strong lysis, at nanomolar concentrations. By contrast, an altered peptide ligand antagonist was only weakly inhibitory and only at high concentrations. Long D(b)-gp33 complexes strongly and specifically inhibited the D(b)-restricted lymphocytic choriomeningitis virus CTL response in vitro and in vivo. We show that complications related to transfer of peptide from soluble to cell-associated MHC molecules can be circumvented by using covalent pMHC complexes. Long pMHC complexes efficiently inhibited CTL target cell conjugate formation by interfering with TCR-mediated activation of LFA-1. Such reagents provide a new and powerful means to inhibit Ag-specific CTL responses and hence should be useful to blunt autoimmune disorders such as diabetes type I.

Determinação de Fe, Zn, Cu e Mn extraídos do solo por diferentes extratores e dosados por espectrofotometria de emissão ótica em plasma induzido e espectrofotometria de absorção atômica

Para aumentar a precisão nas análises químicas de fertilidade do solo e dosar simultaneamente vários elementos, alguns laboratórios vêm optando pelo uso da técnica da espectrofotometria de emissão ótica em plasma induzido (ICP), em detrimento da técnica da espectrofotometria de absorção atômica (EAA), hoje comumente utilizada nos laboratórios de análise de solos. Este trabalho, além de comparar as duas técnicas de dosagem quanto à precisão, à reprodutibilidade e à magnitude dos teores dos micronutrientes Fe, Zn, Cu e Mn, extraídos por Mehlich-1, Mehlich-3 e DTPA-TEA, objetivou, também, selecionar os comprimentos de onda que apresentam menores interferências espectrais no ICP. Foram utilizadas 36 amostras (0 a 0,2 m) de solos coletadas nos Estados de Minas Gerais e Bahia, com ampla variação nos teores de micronutrientes, sendo selecionados três solos para definir os comprimentos de onda do ICP e avaliar a precisão e a reprodutibilidade dos métodos de dosagem. Os comprimentos de onda com menores interferências espectrais no ICP foram: 259,939 nm para Fe em Mehlich-1 e DTPA-TEA e 234,349 nm em Mehlich-3; 213,857 nm para Zn e 324,752 nm para Cu nos três extratores; e 259,372 nm para Mn em Mehlich-1 e DTPA-TEA e 260,568 nm em Mehlich-3. Tanto o ICP quanto o EAA foram precisos e reprodutíveis nas dosagens de Fe e Mn, sendo o ICP, em virtude do seu menor limite de detecção, mais preciso e reprodutível nas dosagens de Zn e Cu. Os métodos de dosagem diferiram estatisticamente (p < 0,01) pelo teste de identidade aplicado, para as dosagens de Fe, Zn, Cu e Mn, utilizando Mehlich-1, Mehlich-3 e DTPA-TEA, comprometendo assim a interpretação dos resultados gerados pelo ICP, com base nos níveis críticos gerados a partir do EAA.

Efeito da adição de fontes de matéria orgânica como amenizantes do efeito tóxico de B, Zn, Cu, Mn e Pb no cultivo de Brassica juncea

Atividades humanas como mineração, siderurgia e aplicação de fertilizantes tornam a poluição por metais sério problema ambiental na atualidade. A fitorremediação - uso de plantas e da microbiota, associada ou não a adições de amenizantes de solo, para extrair, seqüestrar e, ou, reduzir a toxicidade dos poluentes - tem sido descrita como uma tecnologia efetiva, não-destrutiva, econômica e socialmente aceita para remediar solos poluídos. O objetivo deste trabalho foi avaliar a eficiência da mostarda na remoção de Zn, Cu, Mn, Pb e B de um solo contaminado e o efeito da adição de materiais orgânicos na redução da disponibilidade de metais pesados e B para essa planta. O trabalho foi realizado em casa de vegetação, com delineamento inteiramente casualizado em esquema fatorial 3 x 5 com quatro repetições, utilizando 0, 7, 14, 21 e 28 g kg-1 de C no solo. Os materiais orgânicos utilizados foram: solomax, turfa e concentrado húmico mineral (CHM). A adição de turfa e concentrado húmico mineral reduziu os teores de Zn, Cu, Pb e B extraíveis do solo e na parte aérea da mostarda; contudo, essa redução não foi suficiente para impedir os efeitos fitotóxicos dos elementos. A adição dos materiais orgânicos promoveu aumento nos teores de Mn no solo, entretanto apenas o solomax proporcionou aumento na concentração do elemento na parte aérea das plantas. Os efeitos da turfa e do CHM sobre a disponibilidade de Zn, Cu, Mn, Pb e B no solo, a concentração na parte aérea e o crescimento das plantas indicaram o potencial desses materiais como agentes amenizantes de toxicidade e do solomax como auxiliar em programas de fitoextração induzida.

The central Sesia-Lanzo zone (Western Italian Alps) - New field observations and lithostratigraphic subdivisions

An extensive study of the central part of the Sesia Lanzo Zone has been undertaken to identify pre-Alpine protoliths and to reconstruct the lithologic and tectonic setting of this part of the Western Alps. Three main complexes have been defined: 1) the Polymetamorphic Basement Complex, corresponding to the lower unit of the Sesia Lanzo Zone after COMPAGNONI et al. (1977), is further subdivided into the three following units: a) an Internal Unit characterized by eo-Alpine high pressure (HP) assemblages (DAL PIAZ et al., 1972) (Eclogitic Micaschists); b) an Intermediate Unit where HP parageneses are partially re-equilibrated under greenschist conditions and c) an External Unit where the main foliation is defined by a greenschist paragenesis (Gneiss Minuti auct.). 2) the Monometamorphic Cover Complex, subdivided into the followings: a) the Bonze Unit, composed of sheared metagabbros, eclogitized metabasalts with MORB geochemical affinity and related metasediments (micaschists, quartzites and Mn-cherts) and b) the Scalaro Unit, containing predominantly metasediments of supposed Permo-Triassic age (yellow dolomitic marbles, calcschists and conglomeratic limestones, micaschists and quartzites with thin levels of basic rocks with within plate basalts [WPB] geochimical affinity). Multiple lithostratigraphic sequences for the Monometamorphic Cover Complex are proposed. The contact between the Bonze and Scalaro Units is defined by repetitions of dolomitic marbles and metabasalts; the ages of the metasediments have been assigned solely by analogy with other sediments of the Western Alps, due to the absence of fossils. The Monometamorphic Cover Complex can be considered as the autochthonous cover of the Sesia Lanzo Zone because of the primary contacts with the basement and because of the presence of preAlpine HT basement blocks in the cover sequences. 3) The pre-Alpine high temperature (HT) Basement Complex (or `'Seconda Zona Diorito-Kinzigitica''), comprises HT Hercynian rocks like kinzigites, amphibolites, granulites and calcite marbles; this Complex is always located between the Internal and the External Units and can be followed continuously for several kilometers south of the Gressoney Valley to the Orco Valley. A schematic evolution for the Sesia Lanzo Zone is proposed; based on available data together with new geochronological data, this study shows that the internal and external parts of the polymetamorphic basement of the Sesia Zone experienced different cooling histories .

NS4B Self-Interaction through Conserved C-Terminal Elements Is Required for the Establishment of Functional Hepatitis C Virus Replication Complexes.

Hepatitis C virus (HCV) is an important human pathogen, persistently infecting more than 170 million individuals worldwide. Studies of the HCV life cycle have become possible with the development of cell culture systems supporting the replication of viral RNA and the production of infectious virus. However, the exact functions of individual proteins, especially of nonstructural protein 4B (NS4B), remain poorly understood. NS4B triggers the formation of specific, vesicular membrane rearrangements, referred to as membranous webs, which have been reported to represent sites of HCV RNA replication. However, the mechanism of vesicle induction is not known. In this study, a panel of 15 mutants carrying substitutions in the highly conserved NS4B C-terminal domain was generated. Five mutations had only a minor effect on replication, but two of them enhanced assembly and release of infectious virus. Ten mutants were replication defective and used for selection of pseudoreversions. Most of the pseudoreversions also localized to the highly conserved NS4B C-terminal domain and were found to restore replication competence upon insertion into the corresponding primary mutant. Importantly, pseudoreversions restoring replication competence also restored heterotypic NS4B self-interaction, which was disrupted by the primary mutation. Finally, electron microscopy analyses of membrane alterations induced by NS4B mutants revealed striking morphological abnormalities, which were restored to wild-type morphology by the corresponding pseudoreversion. These findings demonstrate the important role of the C-terminal domain in NS4B self-interaction and the formation of functional HCV replication complexes.

Molecular modeling of peptide-MHC class I complexes : applications to peptide based immunotherapy

Summary The specific CD8+ T cell immune response against tumors relies on the recognition by the T cell receptor (TCR) on cytotoxic T lymphocytes (CTL) of antigenic peptides bound to the class I major histocompatibility complex (MHC) molecule. Such tumor associated antigenic peptides are the focus of tumor immunotherapy with peptide vaccines. The strategy for obtaining an improved immune response often involves the design of modified tumor associated antigenic peptides. Such modifications aim at creating higher affinity and/or degradation resistant peptides and require precise structures of the peptide-MHC class I complex. In addition, the modified peptide must be cross-recognized by CTLs specific for the parental peptide, i.e. preserve the structure of the epitope. Detailed structural information on the modified peptide in complex with MHC is necessary for such predictions. In this thesis, the main focus is the development of theoretical in silico methods for prediction of both structure and cross-reactivity of peptide-MHC class I complexes. Applications of these methods in the context of immunotherapy are also presented. First, a theoretical method for structure prediction of peptide-MHC class I complexes is developed and validated. The approach is based on a molecular dynamics protocol to sample the conformational space of the peptide in its MHC environment. The sampled conformers are evaluated using conformational free energy calculations. The method, which is evaluated for its ability to reproduce 41 X-ray crystallographic structures of different peptide-MHC class I complexes, shows an overall prediction success of 83%. Importantly, in the clinically highly relevant subset of peptide-HLAA*0201 complexes, the prediction success is 100%. Based on these structure predictions, a theoretical approach for prediction of cross-reactivity is developed and validated. This method involves the generation of quantitative structure-activity relationships using three-dimensional molecular descriptors and a genetic neural network. The generated relationships are highly predictive as proved by high cross-validated correlation coefficients (0.78-0.79). Together, the here developed theoretical methods open the door for efficient rational design of improved peptides to be used in immunotherapy. Résumé La réponse immunitaire spécifique contre des tumeurs dépend de la reconnaissance par les récepteurs des cellules T CD8+ de peptides antigéniques présentés par les complexes majeurs d'histocompatibilité (CMH) de classe I. Ces peptides sont utilisés comme cible dans l'immunothérapie par vaccins peptidiques. Afin d'augmenter la réponse immunitaire, les peptides sont modifiés de façon à améliorer l'affinité et/ou la résistance à la dégradation. Ceci nécessite de connaître la structure tridimensionnelle des complexes peptide-CMH. De plus, les peptides modifiés doivent être reconnus par des cellules T spécifiques du peptide natif. La structure de l'épitope doit donc être préservée et des structures détaillées des complexes peptide-CMH sont nécessaires. Dans cette thèse, le thème central est le développement des méthodes computationnelles de prédiction des structures des complexes peptide-CMH classe I et de la reconnaissance croisée. Des applications de ces méthodes de prédiction à l'immunothérapie sont également présentées. Premièrement, une méthode théorique de prédiction des structures des complexes peptide-CMH classe I est développée et validée. Cette méthode est basée sur un échantillonnage de l'espace conformationnel du peptide dans le contexte du récepteur CMH classe I par dynamique moléculaire. Les conformations sont évaluées par leurs énergies libres conformationnelles. La méthode est validée par sa capacité à reproduire 41 structures des complexes peptide-CMH classe I obtenues par cristallographie aux rayons X. Le succès prédictif général est de 83%. Pour le sous-groupe HLA-A*0201 de complexes de grande importance pour l'immunothérapie, ce succès est de 100%. Deuxièmement, à partir de ces structures prédites in silico, une méthode théorique de prédiction de la reconnaissance croisée est développée et validée. Celle-ci consiste à générer des relations structure-activité quantitatives en utilisant des descripteurs moléculaires tridimensionnels et un réseau de neurones couplé à un algorithme génétique. Les relations générées montrent une capacité de prédiction remarquable avec des valeurs de coefficients de corrélation de validation croisée élevées (0.78-0.79). Les méthodes théoriques développées dans le cadre de cette thèse ouvrent la voie du design de vaccins peptidiques améliorés.