Oxygen photo-adsorption related quenching of photoluminescence in group-III nitride nanocolumns

GaN and InGaN nanocolumns of various compositions are studied by room-temperature photoluminescence (PL) under different ambient conditions. GaN nanocolumns exhibit a reversible quenching upon exposure to air under constant UV excitation, following a t−1/2 time dependence and resulting in a total reduction of intensity by 85–90%, as compared to PL measured in vacuum, with no spectral change. This effect is not observed when exposing the samples to pure nitrogen. We attribute this effect to photoabsorption and photodesorption of oxygen that modifies the surface potential bending. InGaN nanocolumns, under the same experimental conditions do not show the same quenching features: The high-energy part of the broad PL line is not modified by exposure to air, whereas a lower-energy part, which does quench by 80–90%, can now be distinguished. We discuss the different behaviors in terms of carrier localization and possible composition or strain gradients in the InGaN nanocolumns.

Hydrogeochemistry of surface and spring waters in the surroundings of the CO2 injection site at Hontomín–Huermeces (Burgos, Spain)

In this paper the very first geochemical and isotopic data related to surface and spring waters and dissolved gases in the area of Hontomín–Huermeces (Burgos, Spain) are presented and discussed. Hontomín–Huermeces has been selected as a pilot site for the injection of pure (>99%) CO2. Injection and monitoring wells are planned to be drilled close to 6 oil wells completed in the 1980s for which detailed stratigraphical logs are available, indicating the presence of a confined saline aquifer at the depth of about 1500 m into which less than 100,000 tons of iquid CO2 will be injected, possibly starting in 2013. The chemical and features of the spring waters suggest that they are related to a shallow hydrogeological system as the concentration of the Total Dissolved Solids approaches 800 mg/L with a Ca2+(Mg2+)-HCO3− composition, similar to that of the surface waters. This is also supported by the oxygen and hydrogen isotopic ratios that have values lying between those of the Global and the Mediterranean Meteoric Water Lines. Some spring waters close to the oil wells are haracterized by relatively high concentrations of NO3− (up to 123 mg/L), unequivocally suggesting an anthropogenic source that adds to the main water–rock interaction processes. The latter can be referred to Ca-Mg-carbonate and, at a minor extent, Al-silicate dissolution, being the outcropping sedimentary rocks characterized by Palaeozoic to Quaternary rocks. Anomalous concentrations of Cl−, SO42−, As, B and Ba were measured in two springs discharging a few hundred meters from the oil wells and in the Rio Ubierna. These contents are significantly higher than those of the whole set of the studied waters and are possibly indicative of mixing processes, although at very low extent, between deep and shallow aquifers. No evidence of deep-seated gases interacting with the Hontomín–Huermeces waters was recognized in the chemistry of the disolved gases. This is likely due to the fact that they are mainly characterized by an atmospheric source as highlighted by the high contents of N2, O2 and Ar and by N2/Ar ratios that approach that of ASW (Air Saturated Water) and possibly masking any contribution related to a deep source. Nevertheless, significant concentrations (up to 63% by vol.) of isotopically negative CO2 (<−17.7‰ V-PDB) were found in some water samples, likely related to a biogenic source. The geochemical and isotopic data of this work are of particular importance when a monitoring program will be established to verify whether CO2 leakages, induced by the injection of this greenhouse gas, may be affecting the quality of the waters in the shallow hydrological circuits at Hontomín–Huermeces. In this respect, carbonate chemistry, the isotopic carbon of dissolved CO2 and TDIC (Total Dissolved Inorganic Carbon) and selected trace elements can be considered as useful parameters to trace the migration of the injected CO2 into near-surface environments.

Surface InGaAs nanostructures for sensing applications

El desarrollo de sensores está ganando cada vez mayor importancia debido a la concienciación ciudadana sobre el medio ambiente haciendo que su desarrollo sea muy elevado en todas las disciplinas, entre las que cabe destacar, la medicina, la biología y la química. A pesar de la existencia de estos dispositivos, este área está aún por mejorar, ya que muchos de los materiales propuestos hasta el momento e incluso los ya comercializados muestran importantes carencias de funcionamiento, eficiencia e integrabilidad entre otros. Para la mejora de estos dispositivos, se han propuesto diversas aproximaciones basadas en nanosistemas. Quizá, uno de las más prometedoras son las nanoestructuras de punto cuántico, y en particular los semiconductores III-V basados en la consolidada tecnología de los arseniuros, las cuáles ofrecen excelentes propiedades para su uso como sensores. Además, estudios recientes demuestran su gran carácter sensitivo al medio ambiente, la posibilidad de funcionalizar la superficie para la fabricación de sensores interdisciplinares y posibilididad de mejorar notablemente su eficiencia. A lo largo de esta tesis, nos centramos en la investigación de SQD de In0.5Ga0.5As sobre substratos de GaAs(001) para el desarrollo de sensores de humedad. La tesis abarca desde el diseño, crecimiento y caracterización de las muestras hasta la el posterior procesado y caracterización de los dispositivos finales. La optimización de los parámetros de crecimiento es fundamental para conseguir una nanoestructura con las propiedades operacionales idóneas para un fin determinado. Como es bien sabido en la literatura, los parámetros de crecimiento (temperatura de crecimiento, relación de flujos del elemento del grupo V y del grupo I II (V/III), velocidad de crecimiento y tratamiento térmico después de la formación de la capa activa) afectan directamente a las propiedades estructurales, y por tanto, operacionales de los puntos cuánticos (QD). En esta tesis, se realiza un estudio de las condiciones de crecimiento para el uso de In0.5Ga0.5As SQDs como sensores. Para los parámetros relacionados con la temperatura de crecimiento de los QDs y la relación de flujos V / I I I se utilizan los estudios previamente realizados por el grupo. Mientras que este estudio se centrará en la importancia de la velocidad de crecimiento y en el tratamiento térmico justo después de la nucleación de los QDs. Para ello, se establece la temperatura de creciemiento de los QDs en 430°C y la relación de flujos V/III en 20. Como resultado, los valores más adecuados que se obtienen para la velocidad de crecimiento y el tratamiento térmico posterior a la formación de los puntos son, respectivamente, 0.07ML/s y la realización de una bajada y subida brusca de la temperatura del substrato de 100°C con respecto a la temperatura de crecimiento de los QDs. El crecimiento a una velocidad lo suficientemente alta que permita la migración de los átomos por la superficie, pero a su vez lo suficientemente baja para que se lleve a cabo la nucleación de los QDs; en combinación con el tratamiento brusco de temperatura que hace que se conserve la forma y composición de los QDs, da lugar a unos SQDs con un alto grado de homogeneidad y alta densidad superficial. Además, la caracterización posterior indica que estas nanoestructuras de gran calidad cristalina presentan unas propiedades ópticas excelentes incluso a temperatura ambiente. Una de las características por la cual los SQD de Ino.5Gao.5As se consideran candidatos prometedores para el desarrollo de sensores es el papel decisivo que juega la superficie por el mero hecho de estar en contacto directo con las partículas del ambiente y, por tanto, por ser capaces de interactuar con sus moléculas. Así pues, con el fin de demostrar la idoneidad de este sistema para dicha finalidad, se evalúa el impacto ambiental en las propiedades ópticas y eléctricas de las muestras. En un primer lugar, se analiza el efecto que tiene el medio en las propiedades ópticas. Para dicha evaluación se compara la variación de las propiedades de emisión de una capa de puntos enterrada y una superficial en distintas condiciones externas. El resultado que se obtiene es muy claro, los puntos enterrados no experimentan un cambio óptico apreciable cuando se varían las condiciones del entorno; mientras que, la emisión de los SQDs se modifica significativamente con las condiciones del medio. Por una parte, la intensidad de emisión de los puntos superficiales desaparece en condiciones de vacío y decrece notablemente en atmósferas secas de gases puros (N2, O2). Por otra parte, la fotoluminiscencia se conserva en ambientes húmedos. Adicionalmente, se observa que la anchura a media altura y la longitud de onda de emisión no se ven afectadas por los cambios en el medio, lo que indica, que las propiedades estructurales de los puntos se conservan al variar la atmósfera. Estos resultados apuntan directamente a los procesos que tienen lugar en la superficie entre estados confinados y superficiales como responsables principales de este comportamiento. Así mismo, se ha llevado a cabo un análisis más detallado de la influencia de la calidad y composición de la atmósfera en las propiedades ópticas de los puntos cuánticos superficiales. Para ello, se utilizan distintas sustancias con diferente polaridad, composición atómica y masa molecular. Como resultado se observa que las moléculas de menor polaridad y más pesadas causan una mayor variación en la intensidad de emisión. Además, se demuestra que el oxígeno juega un papel decisivo en las propiedades ópticas. En presencia de moléculas que contienen oxígeno, la intensidad de fotoluminiscencia disminuye menos que en atmósferas constituidas por especies que no contienen oxígeno. Las emisión que se observa respecto a la señal en aire es del 90% y del 77%, respectivamente, en atmósferas con presencia o ausencia de moléculas de oxígeno. El deterioro de la señal de emisión se atribuye a la presencia de defectos, enlaces insaturados y, en general, estados localizados en la superficie. Estos estados actúan como centros de recombinación no radiativa y, consecuentemente, se produce un empeoramiento de las propiedades ópticas de los SQDs. Por tanto, la eliminación o reducción de la densidad de estos estados superficiales haría posible una mejora de la intensidad de emisión. De estos experimentos de fotoluminiscencia, se deduce que las interacciones entre las moléculas presentes en la atmósfera y la superficie de la muestra modifican la superficie. Esta alteración superficial se traduce en un cambio significativo en las propiedades de emisión. Este comportamiento se atribuye a la posible adsorción de moléculas sobre la superficie pasivando los centros no radiativos, y como consecuencia, mejorando las propiedades ópticas. Además, los resultados demuestran que las moléculas que contienen oxígeno con mayor polaridad y más ligeras son adsorbidas con mayor facilidad, lo que hace que la intensidad óptica sufra variaciones despreciables con respecto a la emisión en aire. Con el fin de desarrollar sensores, las muestras se procesan y los dispositivos se caracterizan eléctricamente. El procesado consiste en dos contactos cuadrados de una aleación de Ti/Au. Durante el procesado, lo más importante a tener en cuenta es no realizar ningún ataque o limpieza que pueda dañar la superficie y deteriorar las propiedades de las nanostructuras. En este apartado, se realiza un análisis completo de una serie de tres muestras: GaAs (bulk), un pozo cuántico superficial (SQW) de Ino.5Gao.5As y SQDs de Ino.5Gao.5As. Para ello, a cada una de las muestras se le realizan medidas de I-V en distintas condiciones ambientales. En primer lugar, siguiendo los resultados obtenidos ópticamente, se lleva a cabo una comparación de la respuesta eléctrica en vacío y aire. A pesar de que todas las muestras presentan un carácter más resistivo en vacío que en aire, se observa una mayor influencia sobre la muestra de SQD. En vacío, la resistencia de los SQDs decrece un 99% respecto de su valor en aire, mientras que la variación de la muestras de GaAs e Ino.5Gao.5As SQW muestran una reducción, respectivamente, del 31% y del 20%. En segundo lugar, se realiza una evaluación aproximada del posible efecto de la humedad en la resistencia superficial de las muestras mediante la exhalación humana. Como resultado se obtiene, que tras la exhalación, la resistencia disminuye bruscamente y recupera su valor inicial cuando dicho proceso concluye. Este resultado preliminar indica que la humedad es un factor crítico en las propiedades eléctricas de los puntos cuánticos superficiales. Para la determinación del papel de la humedad en la respuesta eléctrica, se somete a las muestras de SQD y SQW a ambientes con humedad relativa (RH, de la siglas del inglés) controlada y se analiza el efecto sobre la conductividad superficial. Tras la variación de la RH desde 0% hasta el 70%, se observa que la muestra SQW no cambia su comportamiento eléctrico al variar la humedad del ambiente. Sin embargo, la respuesta de la muestra SQD define dos regiones bien diferenciadas, una de alta sensibilidad para valores por debajo del 50% de RH, en la que la resistencia disminuye hasta en un orden de magnitud y otra, de baja sensibilidad (>50%), donde el cambio de la resistencia es menor. Este resultado resalta la especial relevancia no sólo de la composición sino también de la morfología de la nanostructura superficial en el carácter sensitivo de la muestra. Por último, se analiza la influencia de la iluminación en la sensibilidad de la muestra. Nuevamente, se somete a las muestras SQD y SQW a una irradiación de luz de distinta energía y potencia a la vez que se varía controladamente la humedad ambiental. Una vez más, se observa que la muestra SQW no presenta ninguna variación apreciable con las alteraciones del entorno. Su resistencia superficial permanece prácticamente inalterable tanto al modificar la potencia de la luz incidente como al variar la energía de la irradiación. Por el contrario, en la muestra de SQD se obtiene una reducción la resistencia superficial de un orden de magnitud al pasar de condiciones de oscuridad a iluminación. Con respecto a la potencia y energía de la luz incidente, se observa que a pesar de que la muestra no experimenta variaciones notables con la potencia de la irradiación, esta sufre cambios significativos con la energía de la luz incidente. Cuando se ilumina con energías por encima de la energía de la banda prohibida (gap) del GaAs (Eg ~1.42 eV ) se produce una reducción de la resistencia de un orden de magnitud en atmósferas húmedas, mientras que en atmósferas secas la conductividad superficial permanece prácticamente constante. Sin embargo, al inicidir con luz de energía menor que Eg, el efecto que se produce en la respuesta eléctrica es despreciable. Esto se atribuye principalmente a la densidad de portadores fotoactivados durante la irradiación. El volumen de portadores excita dos depende de la energía de la luz incidente. De este modo, cuando la luz que incide tiene energía menor que el gap, el volumen de portadores generados es pequeño y no contribuye a la conductividad superficial. Por el contrario, cuando la energía de la luz incidente es alta (Eg), el volumen de portadores activados es elevado y éstos contribuyen significantemente a la conductividad superficial. La combinación de ambos agentes, luz y humedad, favorece el proceso de adsorción de moléculas y, por tanto, contribuye a la reducción de la densidad de estados superficiales, dando lugar a una modificación de la estructura electrónica y consecuentemente favoreciendo o dificultando el transporte de portadores. ABSTRACT Uncapped three-dimensional (3D) nanostructures have been generally grown to assess their structural quality. However, the tremendous growing importance of the impact of the environment on life has become such nanosystems in very promising candidates for the development of sensing devices. Their direct exposure to changes in the local surrounding may influence their physical properties being a perfect sign of the atmosphere quality. The goal of this thesis is the research of Ino.5Gao.5As surface quantum dots (SQDs) on GaAs(001), covering from their growth to device fabrication, for sensing applications. The achievement of this goal relies on the design, growth and sample characterization, along with device fabrication and characterization. The first issue of the thesis is devoted to analyze the main growth parameters affecting the physical properties of the Ino.5Gao.5As SQDs. It is well known that the growing conditions (growth temperature , deposition rate, V/III flux ratio and treatment after active layer growth) directly affect the physical properties of the epilayer. In this part, taking advantage of the previous results in the group regarding Ino.5Gao.5As QD growth temperature and V/III ratio, the effect of the growth rate and the temperature treatment after QDs growth nucleation is evaluated. Setting the QDs growth temperature at 430°C and the V/III flux ratio to ~20, it is found that the most appropriate conditions rely on growing the QDs at 0.07ML/s and just after QD nucleation, rapidly dropping and again raising 100°C the substrate temperature with respect to the temperature of QD growth. The combination of growing at a fast enough growth rate to promote molecule migration but sufficiently slow to allow QD nucleation, together with the sharp variation of the temperature preserving their shape and composition yield to high density, homogeneous Ino.5Gao.5As SQDs. Besides, it is also demonstrated that this high quality SQDs show excellent optical properties even at room temperature (RT). One of the characteristics by which In0.5Ga0.5As/GaAs SQDs are considered promising candidates for sensing applications is the crucial role that surface plays when interacting with the gases constituting the atmosphere. Therefore, in an attempt to develop sensing devices, the influence of the environment on the physical properties of the samples is evaluated. By comparing the resulting photoluminescence (PL) of SQDs with buried QDs (BQDs), it is found that BQDs do not exhibit any significant variation when changing the environmental conditions whereas, the external conditions greatly act on the SQDs optical properties. On one hand, it is evidenced that PL intensity of SQDs sharply quenches under vacuum and clearly decreases under dry-pure gases atmospheres (N2, O2). On the other hand, it is shown that, in water containing atmospheres, the SQDs PL intensity is maintained with respect to that in air. Moreover, it is found that neither the full width at half maximun nor the emission wavelength manifest any noticeable change indicating that the QDs are not structurally altered by the external atmosphere. These results decisively point to the processes taking place at the surface such as coupling between confined and surface states, to be responsible of this extraordinary behavior. A further analysis of the impact of the atmosphere composition on the optical characteristics is conducted. A sample containing one uncapped In0.5Ga0.5As QDs layer is exposed to different environments. Several solvents presenting different polarity, atomic composition and molecular mass, are used to change the atmosphere composition. It is revealed that low polarity and heavy molecules cause a greater variation on the PL intensity. Besides, oxygen is demonstrated to play a decisive role on the PL response. Results indicate that in presence of oxygen-containing molecules, the PL intensity experiments a less reduction than that suffered in presence of nonoxygen-containing molecules, 90% compared to 77% signal respect to the emission in air. In agreement with these results, it is demonstrated that high polarity and lighter molecules containing oxygen are more easily adsorbed, and consequently, PL intensity is less affected. The presence of defects, unsaturated bonds and in general localized states in the surface are proposed to act as nonradiative recombination centers deteriorating the PL emission of the sample. Therefore, suppression or reduction of the density of such states may lead to an increase or, at least, conservation of the PL signal. This research denotes that the interaction between sample surface and molecules in the atmosphere modifies the surface characteristics altering thus the optical properties. This is attributed to the likely adsoption of some molecules onto the surface passivating the nonradiative recombination centers, and consequently, not deteriorating the PL emission. Aiming for sensors development, samples are processed and electrically characterized under different external conditions. Samples are processed with two square (Ti/Au) contacts. During the processing, especial attention must be paid to the surface treatment. Any process that may damage the surface such as plasma etching or annealing must be avoided to preserve the features of the surface nanostructures. A set of three samples: a GaAs (bulk), In0.5Ga0.5As SQDs and In0.5Ga0.5As surface quantum well (SQW) are subjected to a throughout evaluation. I-V characteristics are measured following the results from the optical characterization. Firstly, the three samples are exposed to vacuum and air. Despite the three samples exhibit a more resistive character in vacuum than in air, it is revealed a much more clear influence of the pressure atmosphere in the SQDs sample. The sheet resistance (Rsh) of SQDs decreases a 99% from its response value under vacuum to its value in air, whereas Rsh of GaAs and In0.5Ga0.5As SQW reduces its value a 31% and a 20%, respectively. Secondly, a rough analysis of the effect of the human breath on the electrical response evidences the enormous influence of moisture (human breath is composed by several components but the one that overwhelms all the rest is the high concentration of water vapor) on the I-V characteristics. Following this result, In0.5Ga0.5As SQDs and In0.5Ga0.5As SQW are subjected to different controlled relative humidity (RH) environments (from 0% to 70%) and electrically characterized. It is found that SQW shows a nearly negligible Rsh variation when increasing the RH in the surroundings. However, the response of SQDs to changes in the RH defines two regions. Below 50%, high sensitive zone, Rsh of SQD decreases by more than one order of magnitude, while above 50% the dependence of Rsh on the RH becomes weaker. These results remark the role of the surface and denote the existence of a finite number of surface states. Nevertheless, most significantly, they highlight the importance not only of the material but also of the morphology. Finally, the impact of the illumination is determined by means of irradiating the In0.5Ga0.5As SQDs and In0.5Ga0.5As SQW samples with different energy and power sources. Once again, SQW does not exhibit any correlation between the surface conductivity and the external conditions. Rsh remains nearly unalterable independently of the energy and power of the incident light. Conversely, Rsh of SQD experiences a decay of one order of magnitude from dark-to-photo conditions. This is attributed to the less density of surface states of SQW compared to that of SQDs. Additionally, a different response of Rsh of SQD with the energy of the impinging light is found. Illuminating with high energy light results in a Rsh reduction of one order of mag nitude under humid atmospheres, whereas it remains nearly unchanged under dry environments. On the contrary, light with energy below the bulk energy bandgap (Eg), shows a negligible effect on the electrical properties regardless the local moisture. This is related to the density of photocarriers generated while lighting up. Illuminating with excitation energy below Eg affects a small absorption volume and thus, a low density of photocarriers may be activated leading to an insignificant contribution to the conductivity. Nonetheless, irradiating with energy above the Eg can excite a high density of photocarriers and greatly improve the surface conductivity. These results demonstrate that both illumination and humidity are therefore needed for sensing. The combination of these two agents improves the surface passivation by means of molecule adsorption reducing the density of surface states, thus modifying the electronic structures, and consequently, promoting the carrier motion.

The solution structure of the Zα domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA

Double-stranded RNA deaminase I (ADAR1) contains the Z-DNA binding domain Zα. Here we report the solution structure of free Zα and map the interaction surface with Z-DNA, confirming roles previously assigned to residues by mutagenesis. Comparison with the crystal structure of the (Zα)2/Z-DNA complex shows that most Z-DNA contacting residues in free Zα are prepositioned to bind Z-DNA, thus minimizing the entropic cost of binding. Comparison with homologous (α+β)helix–turn–helix/B-DNA complexes suggests that binding of Zα to B-DNA is disfavored by steric hindrance, but does not eliminate the possibility that related domains may bind to both B- and Z-DNA.

Functionality of major histocompatibility complex class II molecules in mice doubly deficient for invariant chain and H-2M complexes

By combining two previously generated null mutations, Ii° and M°, we produced mice lacking the invariant chain and H-2M complexes, both required for normal cell-surface expression of major histocompatibility complex class II molecules loaded with the usual diverse array of peptides. As expected, the maturation and transport of class II molecules, their expression at the cell surface, and their capacity to present antigens were quite similar for cells from Ii°M° double-mutant mice and from animals carrying just the Ii° mutation. More surprising were certain features of the CD4+ T cell repertoire selected in Ii°M° mice: many fewer cells were selected than in Ii+M° animals, and these had been purged of self-reactive specificities, unlike their counterparts in Ii+M° animals. These findings suggest (i) that the peptides carried by class II molecules on stromal cells lacking H-2M complexes may almost all derive from invariant chain and (ii) that H-2M complexes edit the peptide array displayed on thymic stromal cells in the absence of invariant chain, showing that it can edit, in vivo, peptides other than CLIP.

Fluorescence and photobleaching dynamics of single light-harvesting complexes

Single light-harvesting complexes LH-2 from Rhodopseudomonas acidophila were immobilized on various charged surfaces under physiological conditions. Polarized light experiments showed that the complexes were situated on the surface as nearly upright cylinders. Their fluorescence lifetimes and photobleaching properties were obtained by using a confocal fluorescence microscope with picosecond time resolution. Initially all molecules fluoresced with a lifetime of 1 ± 0.2 ns, similar to the bulk value. The photobleaching of one bacteriochlorophyll molecule from the 18-member assembly caused the fluorescence to switch off completely, because of trapping of the mobile excitations by energy transfer. This process was linear in light intensity. On continued irradiation the fluorescence often reappeared, but all molecules did not show the same behavior. Some LH-2 complexes displayed a variation of their quantum yields that was attributed to photoinduced confinement of the excited states and thereby a diminution of the superradiance. Others showed much shorter lifetimes caused by excitation energy traps that are only ≈3% efficient. On repeated excitation some molecules entered a noisy state where the fluorescence switched on and off with a correlation time of ≈0.1 s. About 490 molecules were examined.

Soluble complexes of regulated upon activation, normal T cells expressed and secreted (RANTES) and glycosaminoglycans suppress HIV-1 infection but do not induce Ca2+ signaling

Chemokines comprise a family of low-molecular-weight proteins that elicit a variety of biological responses including chemotaxis, intracellular Ca2+ mobilization, and activation of tyrosine kinase signaling cascades. A subset of chemokines, including regulated upon activation, normal T cell expressed and secreted (RANTES), macrophage inflammatory protein-1α (MIP-1α), and MIP-1β, also suppress infection by HIV-1. All of these activities are contingent on interactions between chemokines and cognate seven-transmembrane spanning, G protein-coupled receptors. However, these activities are strongly inhibited by glycanase treatment of receptor-expressing cells, indicating an additional dependence on surface glycosaminoglycans (GAG). To further investigate this dependence, we examined whether soluble GAG could reconstitute the biological activities of RANTES on glycanase-treated cells. Complexes formed between RANTES and a number of soluble GAG failed to induce intracellular Ca2+ mobilization on either glycanase-treated or untreated peripheral blood mononuclear cells and were unable to stimulate chemotaxis. In contrast, the same complexes demonstrated suppressive activity against macrophage tropic HIV-1. Complexes composed of 125I-labeled RANTES demonstrated saturable binding to glycanase-treated peripheral blood mononuclear cells, and such binding could be reversed partially by an anti-CCR5 antibody. These results suggest that soluble chemokine–GAG complexes represent seven-transmembrane ligands that do not activate receptors yet suppress HIV infection. Such complexes may be considered as therapeutic formulations for the treatment of HIV-1 infection.

Meis1 and pKnox1 bind DNA cooperatively with Pbx1 utilizing an interaction surface disrupted in oncoprotein E2a-Pbx1

E2a-Pbx1 is a chimeric transcription factor oncoprotein produced by the t(1;19) translocation in human pre-B cell leukemia. Class I Hox proteins bind DNA cooperatively with both Pbx proteins and oncoprotein E2a-Pbx1, suggesting that leukemogenesis by E2a-Pbx1 and Hox proteins may alter transcription of cellular genes regulated by Pbx–Hox motifs. Likewise, in murine myeloid leukemia, transcriptional coactivation of Meis1 with HoxA7/A9 suggests that Meis1–HoxA7/9 heterodimers may evoke aberrant gene transcription. Here, we demonstrate that both Meis1 and its relative, pKnox1, dimerize with Pbx1 on the same TGATTGAC motif selected by dimers of Pbx proteins and unidentified partner(s) in nuclear extracts, including those from t(1;19) pre-B cells. Outside their homeodomains, Meis1 and pKnox1 were highly conserved only in two motifs required for cooperativity with Pbx1. Like the unidentified endogenous partner(s), both Meis1 and pKnox1 failed to dimerize significantly with E2a-Pbx1. The Meis1/pKnox1-interaction domain in Pbx1 resided predominantly in a conserved N-terminal Pbx domain deleted in E2a-Pbx1. Thus, the leukemic potential of E2a-Pbx1 may require abrogation of its interaction with members of the Meis and pKnox families of transcription factors, permitting selective targeting of genes regulated by Pbx–Hox complexes. In addition, because most motifs bound by Pbx–Meis1/pKnox1 were not bound by Pbx1–Hox complexes, the leukemic potential of Meis1 in myeloid leukemias may involve shifting Pbx proteins from promoters containing Pbx–Hox motifs to those containing Pbx–Meis motifs.

Formation and Turnover of NSF- and SNAP-containing “Fusion” Complexes Occur on Undocked, Clathrin-coated Vesicle–derived Membranes

Specificity of vesicular transport is determined by pair-wise interaction between receptors (SNAP receptors or SNAREs) associated with a transport vesicle and its target membrane. Two additional factors, N-ethylmaleimide-sensitive fusion protein (NSF) and soluble NSF attachment protein (SNAP) are ubiquitous components of vesicular transport pathways. However, the precise role they play is not known. On the basis that NSF and SNAP can be recruited to preformed SNARE complexes, it has been proposed that NSF- and SNAP-containing complexes are formed after SNARE-dependent docking of transport vesicles. This would enable ATPase-dependent complex disassembly to be coupled directly to membrane fusion. Alternatively, binding and release of NSF/SNAP may occur before vesicle docking, and perhaps be involved in the activation of SNAREs. To gain more information about the point at which so-called 20S complexes form during the transport vesicle cycle, we have examined NSF/SNAP/SNARE complex turnover on clathrin-coated vesicle–derived membranes in situ. This has been achieved under conditions in which the extent of membrane docking can be precisely monitored. We demonstrate by UV-dependent cross-linking experiments, coupled to laser light-scattering analysis of membranes, that complexes containing NSF, SNAP, and SNAREs will form and dissociate on the surface of undocked transport vesicles.

Congruent Docking of Dimeric Kinesin and ncd into Three-dimensional Electron Cryomicroscopy Maps of Microtubule–Motor ADP Complexes

We present a new map showing dimeric kinesin bound to microtubules in the presence of ADP that was obtained by electron cryomicroscopy and image reconstruction. The directly bound monomer (first head) shows a different conformation from one in the more tightly bound empty state. This change in the first head is amplified as a movement of the second (tethered) head, which tilts upward. The atomic coordinates of kinesin·ADP dock into our map so that the tethered head associates with the bound head as in the kinesin dimer structure seen by x-ray crystallography. The new docking orientation avoids problems associated with previous predictions; it puts residues implicated by proteolysis-protection and mutagenesis studies near the microtubule but does not lead to steric interference between the coiled-coil tail and the microtubule surface. The observed conformational changes in the tightly bound states would probably bring some important residues closer to tubulin. As expected from the homology with kinesin, the atomic coordinates of nonclaret disjunctional protein (ncd)·ADP dock in the same orientation into the attached head in a map of microtubules decorated with dimeric ncd·ADP. Our results support the idea that the observed direct interaction between the two heads is important at some stages of the mechanism by which kinesin moves processively along microtubules.

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[a]- pyrene diol epoxide adducts at the 6-amino group of adenine

DNA topoisomerase I (top1) is the target of potent anticancer agents, including camptothecins and DNA intercalators, which reversibly stabilize (trap) top1 catalytic intermediates (cleavage complexes). The aim of the present study was to define the structural relationship between the site(s) of covalently bound intercalating agents, whose solution conformations in DNA are known, and the site(s) of top1 cleavage. Two diastereomeric pairs of oligonucleotide 22-mers, derived from a sequence used to determine the crystal structure of top1–DNA complexes, were synthesized. One pair contained either a trans-opened 10R- or 10S-benzo[a]pyrene 7,8-diol 9,10-epoxide adduct at the N6-amino group of a central 2′-deoxyadenosine residue in the scissile strand, and the other pair contained the same two adducts in the nonscissile strand. These adducts were derived from the (+)-(7R,8S,9S,10R)- and (−)-(7S,8R,9R,10S)-7,8-diol 9,10-epoxides in which the benzylic 7-hydroxyl group and the epoxide oxygen are trans. On the basis of analogy with known solution conformations of duplex oligonucleotides containing these adducts, we conclude that top1 cleavage complexes are trapped when the hydrocarbon adduct is intercalated between the base pairs flanking a preexisting top1 cleavage site, or between the base pairs immediately downstream (3′ relative to the scissile strand) from this site. We propose a model with the +1 base rotated out of the duplex, and in which the intercalated adduct prevents religation of the corresponding nucleotide at the 5′ end of the cleaved DNA. These results suggest mechanisms whereby intercalating agents interfere with the normal function of human top1.

Oxygen isotope ratios of PO4: An inorganic indicator of enzymatic activity and P metabolism and a new biomarker in the search for life

The distinctive relations between biological activity and isotopic effect recorded in biomarkers (e.g., carbon and sulfur isotope ratios) have allowed scientists to suggest that life originated on this planet nearly 3.8 billion years ago. The existence of life on other planets may be similarly identified by geochemical biomarkers, including the oxygen isotope ratio of phosphate (δ18Op) presented here. At low near-surface temperatures, the exchange of oxygen isotopes between phosphate and water requires enzymatic catalysis. Because enzymes are indicative of cellular activity, the demonstration of enzyme-catalyzed PO4–H2O exchange is indicative of the presence of life. Results of laboratory experiments are presented that clearly show that δ18OP values of inorganic phosphate can be used to detect enzymatic activity and microbial metabolism of phosphate. Applications of δ18Op as a biomarker are presented for two Earth environments relevant to the search for extraterrestrial life: a shallow groundwater reservoir and a marine hydrothermal vent system. With the development of in situ analytical techniques and future planned sample return strategies, δ18Op may provide an important biosignature of the presence of life in extraterrestrial systems such as that on Mars.

Direct Binding of Occupied Urokinase Receptor (uPAR) to LDL Receptor-related Protein Is Required for Endocytosis of uPAR and Regulation of Cell Surface Urokinase Activity

Low-density lipoprotein receptor-related protein (LRP) mediates internalization of urokinase:plasminogen activator inhibitor complexes (uPA:PAI-1) and the urokinase receptor (uPAR). Here we investigated whether direct interaction between uPAR, a glycosyl-phosphatidylinositol–anchored protein, and LRP, a transmembrane receptor, is required for clearance of uPA:PAI-1, regeneration of unoccupied uPAR, activation of plasminogen, and the ability of HT1080 cells to invade extracellular matrix. We found that in the absence of uPA:PAI-1, uPAR is randomly distributed along the plasma membrane, whereas uPA:PAI-1 promotes formation of uPAR-LRP complexes and initiates redistribution of occupied uPAR to clathrin-coated pits. uPAR-LRP complexes are endocytosed via clathrin-coated vesicles and traffic together to early endosomes (EE) because they can be coimmunoprecipitated from immunoisolated EE, and internalization is blocked by depletion of intracellular K+. Direct binding of domain 3 (D3) of uPAR to LRP is required for clearance of uPA-PAI-1–occupied uPAR because internalization is blocked by incubation with recombinant D3. Moreover, uPA-dependent plasmin generation and the ability of HT1080 cells to migrate through Matrigel-coated invasion chambers are also inhibited in the presence of D3. These results demonstrate that GPI-anchored uPAR is endocytosed by piggybacking on LRP and that direct binding of occupied uPAR to LRP is essential for internalization of occupied uPAR, regeneration of unoccupied uPAR, plasmin generation, and invasion and migration through extracellular matrix.