Boron concentrations and isotope ratios of authigenic carbonates from the Oregon margin

Boron contents and boron, carbon and oxygen stable isotopes were determined for authigenic carbonates recovered from Ocean Drilling Program Leg 146, Oregon margin. Carbonate precipitates are the most widespread authigenic phase in the shallow accretionary wedge and carry chemical information about long-term variations in pore fluid origin and flow paths in the Cascadia subduction zone. Drilling the first ridge (toe area including the frontal thrust) and the second ridge (or Hydrate Ridge) of the prism demonstrated different fluid regimes, with higher B contents in the authigenic precipitates at the toe. The delta11B of 18 authigenic precipitates analysed ranges from 13.9 per mil to as high as 39.8 per mil, extending the upper range of previously reported carbonate delta11B values considerably. When related to the delta11B ratio of their parent solutions, these data are characteristic of fluid-related processes in accretionary prisms. Together with delta13C and delta18O, delta11B ratios of the carbonate concretions, nodules and crusts allow one to distinguish between precipitation influenced by (i) seawater, (ii) fluid reservoirs at different depth levels within the accretionary prism and (iii) cage water from dissociated gas hydrates, the latter possibly indicating a fluctuation of the bottom simulating reflector during most recent Earth's history. From this first systematic boron study on authigenic precipitates from an accretionary prism it is suggested that B contents of such carbonate crusts and concretions exceed those reported for other marine carbonates. Given the abundance of such precipitates at convergent margins, they represent a significant B sink in geochemical cycling. Isotopic compositions of the parent fluids to the carbonates mirror B chemistry of modern pore waters from convergent margins. The precipitates carry information of different subduction-related fluid processes over a certain period of time, and hence are a crucial tracer in the investigation of palaeo-fluid flow.

(Table 3) Carbon and oxygen isotopic data of carbonates from Core SLR 37-1, HYC 25-1 and an aragonite crust from station DR 35-1

An area of massive barite precipitations was studied at a tectonic horst in 1500 m water depth in the Derugin Basin, Sea of Okhotsk. Seafloor observations and dredge samples showed irregular, block- to column-shaped barite build-ups up to 10 m high which were scattered over the seafloor along an observation track 3.5 km long. High methane concentrations in the water column show that methane expulsion and probably carbonate precipitation is a recently active process. Small fields of chemoautotrophic clams (Calyptogena sp., Acharax sp.) at the seafloor provide additional evidence for active fluid venting. The white to yellow barites show a very porous and often layered internal fabric, and are typically covered by dark-brown Mn-rich sediment; electron microprobe spectroscopy measurements of barite sub-samples show a Ba substitution of up to 10.5 mol% of Sr. Rare idiomorphic pyrite crystals (1%) in the barite fabric imply the presence of H2S. This was confirmed by clusters of living chemoautotrophic tube worms (1 mm in diameter) found in pores and channels within the barite. Microscopic examination showed that micritic aragonite and Mg-calcite aggregates or crusts are common authigenic precipitations within the barite fabric. Equivalent micritic carbonates and barite carbonate cemented worm tubes were recovered from sediment cores taken in the vicinity of the barite build-up area. Negative ?13C values of these carbonates (>?43.5? PDB) indicate methane as major carbon source; ?18O values between 4.04 and 5.88? PDB correspond to formation temperatures, which are certainly below 5°C. One core also contained shells of Calyptogena sp. at different core depths with 14C-ages ranging from 20 680 to >49 080 yr. Pore water analyses revealed that fluids also contain high amounts of Ba; they also show decreasing SO42- concentrations and a parallel increase of H2S with depth. Additionally, S and O isotope data of barite sulfate (?34S: 21.0-38.6? CDT; ?18O: 9.0-17.6? SMOW) strongly point to biological sulfate reduction processes. The isotope ranges of both S and O can be exclusively explained as the result of a mixture of residual sulfate after a biological sulfate reduction and isotopic fractionation with 'normal' seawater sulfate. While massive barite deposits are commonly assumed to be of hydrothermal origin, the assemblage of cheomautotrophic clams, methane-derived carbonates, and non-thermally equilibrated barite sulfate strongly implies that these barites have formed at ambient bottom water temperatures and form the features of a Giant Cold Seep setting that has been active for at least 49 000 yr.

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.

Gas discharges for continental Spain: geochemical and isotopic features

In this work the results of a geochemical and isotopic survey of 37 gas discharges was carried out in continental Spain are presented and discussed. On the basis of the gas chemical composition, four different areas can be distinguished, as follows: 1) Selva-Emborda (SE) region; 2) Guadalentin Valley (GV); 3) Campo de Calatrava (CC) and 3) the inner part of Spain (IS). The SE, GV and CC areas are characterized by CO2-rich gases, while IS has N2 as main gas compound. The CO2-rich gases can be distinguished at their turn on the basis on the helium and carbon isotopic composition. The SE and CC areas have a strong mantle signature (up to 3 Ra). Nevertheless, the carbon isotopic composition of CC is within the mantle range and that of SE is slightly more negative (down to -8‰ PDB). The GV gases have a lower mantle signature (61 Ra) with respect to SE and CC and more negative carbon isotopes (6-10‰ PDB). It is worth to mention that the SE, GV and CC areas are related to the youngest volcanic activity in continental Spain, for example the Garrotxa Volcanic Field in Catalonia records the latest event dated at 10,000 years, and the isotopic features, particularly those of helium, are suggesting the presence of magmatic bodies still cooling at depth. The N2-rich gases, i.e. those from the IS area, has an atmospheric origin, as highlighted by the N2/Ar ratio that ranges between those of air and ASW (Air Saturated Water). The isotopic composition of carbon is distinctly negative (down to -21‰ PDB) and that of helium is typically crustal (0.02-0.08 Ra), confirming that these gas discharges are related to a relatively shallow source.

Water chemistry at Hontomín-Huermeces (Burgos, Spain): insights for a pre-, intra- and post-CO2 injection geochemical monitoring.

In this study, 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 was 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 1980’s. Stratigraphical logs indicate the presence of a confined saline aquifer at the depth of about 1,500 m into which less than 100,000 tons of liquid CO2 will be injected, possibly starting in 2013. The chemical and isotopic features of the spring waters suggest the occurrence of a shallow aquifer having a Ca2+(Mg2+)-HCO3- composition, relatively low salinity (Total Dissolved Solids _800 mg/L) and a meteoric isotopic signature. Some spring waters close to the oil wells are characterized by relatively high concentrations of NO3- (up to 123 mg/L), unequivocally indicating anthropogenic contamination 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 hundreds meters from the oil wells and in the Rio Ubierna, possibly indicative of mixing processes, although at very low extent, between deep and shallow aquifers. Gases dissolved in spring waters show relatively high concentrations of atmospheric species, such as N2, O2 and Ar, and isotopically negative CO2 (<-17.7 h V-PDB), likely related to a biogenic source, possibly masking any contribution related to a deep source. The geochemical and isotopic data of this study 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 affect the quality of the waters of the shallow Hontomín-Huermeces hydrological circuit. 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.

Estrategias de monitorización de CO2 y otros gases en los estudios de análogos naturales

La Universidad Politécnica de Madrid (UPM) y la Università degli Studi di Firenze (UniFi), bajo la coordinación técnica de AMPHOS21, participan desde 2009 en el proyecto de investigación “Estrategias de Monitorización de CO2 y otros gases en el estudio de Análogos Naturales”, financiado por la Fundación Ciudad de la Energía (CIUDEN) en el marco del Proyecto Compostilla OXYCFB300 (http://www.compostillaproject.eu), del Programa “European Energy Program for Recovery - EEPR”. El objetivo principal del proyecto fue el desarrollo y puesta a punto de metodologías de monitorización superficiales para su aplicación en el seguimiento y control de los emplazamientos donde se realice el almacenamiento geológico de CO2, analizando técnicas que permitan detectar y cuantificar las posibles fugas de CO2 a la atmósfera. Los trabajos se realizaron tanto en análogos naturales (españoles e italianos) como en la Planta de Desarrollo Tecnológico de Almacenamiento de CO2 de Hontomín. Las técnicas analizadas se centran en la medición de gases y aguas superficiales (de escorrentía y manantiales). En cuanto a la medición de gases se analizó el flujo de CO2 que emana desde el suelo a la atmósfera y la aplicabilidad de trazadores naturales (como el radón) para la detección e identificación de las fugas de CO2. En cuanto al análisis químico de las aguas se analizaron los datos geoquímicos e isotópicos y los gases disueltos en las aguas de los alrededores de la PDT de Hontomín, con objeto de determinar qué parámetros son los más apropiados para la detección de una posible migración del CO2 inyectado, o de la salmuera, a los ambientes superficiales. Las medidas de flujo de CO2 se realizaron con la técnica de la cámara de acúmulo. A pesar de ser una técnica desarrollada y aplicada en diferentes ámbitos científicos se estimó necesario adaptar un protocolo de medida y de análisis de datos a las características específicas de los proyectos de captura y almacenamiento de CO2 (CAC). Donde los flujos de CO2 esperados son bajos y en caso de producirse una fuga habrá que detectar pequeñas variaciones en los valores flujo con un “ruido” en la señal alto, debido a actividad biológica en el suelo. La medida de flujo de CO2 mediante la técnica de la cámara de acúmulo se puede realizar sin limpiar la superficie donde se coloca la cámara o limpiando y esperando al reequilibrio del flujo después de la distorsión al sistema. Sin embargo, los resultados obtenidos después de limpiar y esperar muestran menor dispersión, lo que nos indica que este procedimiento es el mejor para la monitorización de los complejos de almacenamiento geológico de CO2. El protocolo de medida resultante, utilizado para la obtención de la línea base de flujo de CO2 en Hontomín, sigue los siguiente pasos: a) con una espátula se prepara el punto de medición limpiando y retirando el recubrimiento vegetal o la primera capa compacta de suelo, b) se espera un tiempo para la realización de la medida de flujo, facilitando el reequilibrio del flujo del gas tras la alteración provocada en el suelo y c) se realiza la medida de flujo de CO2. Una vez realizada la medición de flujo de CO2, y detectada si existen zonas de anomalías, se debe estimar la cantidad de CO2 que se está escapando a la atmósfera (emanación total), con el objetivo de cuantificar la posible fuga. Existen un amplio rango de metodologías para realizar dicha estimación, siendo necesario entender cuáles son las más apropiadas para obtener el valor más representativo del sistema. En esta tesis se comparan seis técnicas estadísticas: media aritmética, estimador insegado de la media (aplicando la función de Sichel), remuestreo con reemplazamiento (bootstrap), separación en diferentes poblaciones mediante métodos gráficos y métodos basados en criterios de máxima verosimilitud, y la simulación Gaussiana secuencial. Para este análisis se realizaron ocho campañas de muestreo, tanto en la Planta de Desarrollo Tecnológico de Hontomón como en análogos naturales (italianos y españoles). Los resultados muestran que la simulación Gaussiana secuencial suele ser el método más preciso para realizar el cálculo, sin embargo, existen ocasiones donde otros métodos son más apropiados. Como consecuencia, se desarrolla un procedimiento de actuación para seleccionar el método que proporcione el mejor estimador. Este procedimiento consiste, en primer lugar, en realizar un análisis variográfico. Si existe una autocorrelación entre los datos, modelizada mediante el variograma, la mejor técnica para calcular la emanación total y su intervalo de confianza es la simulación Gaussiana secuencial (sGs). Si los datos son independientes se debe comprobar la distribución muestral, aplicando la media aritmética o el estimador insesgado de la media (Sichel) para datos normales o lognormales respectivamente. Cuando los datos no son normales o corresponden a una mezcla de poblaciones la mejor técnica de estimación es la de remuestreo con reemplazamiento (bootstrap). Siguiendo este procedimiento el máximo valor del intervalo de confianza estuvo en el orden del ±20/25%, con la mayoría de valores comprendidos entre ±3,5% y ±8%. La identificación de las diferentes poblaciones muestrales en los datos de flujo de CO2 puede ayudar a interpretar los resultados obtenidos, toda vez que esta distribución se ve afectada por la presencia de varios procesos geoquímicos como, por ejemplo, una fuente geológica o biológica del CO2. Así pues, este análisis puede ser una herramienta útil en el programa de monitorización, donde el principal objetivo es demostrar que no hay fugas desde el reservorio a la atmósfera y, si ocurren, detectarlas y cuantificarlas. Los resultados obtenidos muestran que el mejor proceso para realizar la separación de poblaciones está basado en criterios de máxima verosimilitud. Los procedimientos gráficos, aunque existen pautas para realizarlos, tienen un cierto grado de subjetividad en la interpretación de manera que los resultados son menos reproducibles. Durante el desarrollo de la tesis se analizó, en análogos naturales, la relación existente entre el CO2 y los isótopos del radón (222Rn y 220Rn), detectándose en todas las zonas de emisión de CO2 una relación positiva entre los valores de concentración de 222Rn en aire del suelo y el flujo de CO2. Comparando la concentración de 220Rn con el flujo de CO2 la relación no es tan clara, mientras que en algunos casos aumenta en otros se detecta una disminución, hecho que parece estar relacionado con la profundidad de origen del radón. Estos resultados confirmarían la posible aplicación de los isótopos del radón como trazadores del origen de los gases y su aplicación en la detección de fugas. Con respecto a la determinación de la línea base de flujo CO2 en la PDT de Hontomín, se realizaron mediciones con la cámara de acúmulo en las proximidades de los sondeos petrolíferos, perforados en los ochenta y denominados H-1, H-2, H-3 y H-4, en la zona donde se instalarán el sondeo de inyección (H-I) y el de monitorización (H-A) y en las proximidades de la falla sur. Desde noviembre de 2009 a abril de 2011 se realizaron siete campañas de muestreo, adquiriéndose más de 4.000 registros de flujo de CO2 con los que se determinó la línea base y su variación estacional. Los valores obtenidos fueron bajos (valores medios entre 5 y 13 g•m-2•d-1), detectándose pocos valores anómalos, principalmente en las proximidades del sondeo H-2. Sin embargo, estos valores no se pudieron asociar a una fuente profunda del CO2 y seguramente estuvieran más relacionados con procesos biológicos, como la respiración del suelo. No se detectaron valores anómalos cerca del sistema de fracturación (falla Ubierna), toda vez que en esta zona los valores de flujo son tan bajos como en el resto de puntos de muestreo. En este sentido, los valores de flujo de CO2 aparentemente están controlados por la actividad biológica, corroborado al obtenerse los menores valores durante los meses de otoño-invierno e ir aumentando en los periodos cálidos. Se calcularon dos grupos de valores de referencia, el primer grupo (UCL50) es 5 g•m-2•d-1 en las zonas no aradas en los meses de otoño-invierno y 3,5 y 12 g•m-2•d-1 en primavera-verano para zonas aradas y no aradas, respectivamente. El segundo grupo (UCL99) corresponde a 26 g•m-2•d- 1 durante los meses de otoño-invierno en las zonas no aradas y 34 y 42 g•m-2•d-1 para los meses de primavera-verano en zonas aradas y no aradas, respectivamente. Flujos mayores a estos valores de referencia podrían ser indicativos de una posible fuga durante la inyección y posterior a la misma. Los primeros datos geoquímicos e isotópicos de las aguas superficiales (de escorrentía y de manantiales) en el área de Hontomín–Huermeces fueron analizados. Los datos sugieren que las aguas estudiadas están relacionadas con aguas meteóricas con un circuito hidrogeológico superficial, caracterizadas por valores de TDS relativamente bajos (menor a 800 mg/L) y una fácie hidrogeoquímica de Ca2+(Mg2+)-HCO3 −. Algunas aguas de manantiales se caracterizan por concentraciones elevadas de NO3 − (concentraciones de hasta 123 mg/l), lo que sugiere una contaminación antropogénica. Se obtuvieron concentraciones anómalas de of Cl−, SO4 2−, As, B y Ba en dos manantiales cercanos a los sondeos petrolíferos y en el rio Ubierna, estos componentes son probablemente indicadores de una posible mezcla entre los acuíferos profundos y superficiales. El estudio de los gases disueltos en las aguas también evidencia el circuito superficial de las aguas. Estando, por lo general, dominado por la componente atmosférica (N2, O2 y Ar). Sin embargo, en algunos casos el gas predominante fue el CO2 (con concentraciones que llegan al 63% v/v), aunque los valores isotópicos del carbono (<-17,7 ‰) muestran que lo más probable es que esté relacionado con un origen biológico. Los datos geoquímicos e isotópicos de las aguas superficiales obtenidos en la zona de Hontomín se pueden considerar como el valor de fondo con el que comparar durante la fase operacional, la clausura y posterior a la clausura. En este sentido, la composición de los elementos mayoritarios y traza, la composición isotópica del carbono del CO2 disuelto y del TDIC (Carbono inorgánico disuelto) y algunos elementos traza se pueden considerar como parámetros adecuados para detectar la migración del CO2 a los ambientes superficiales. ABSTRACT Since 2009, a group made up of Universidad Politécnica de Madrid (UPM; Spain) and Università degli Studi Firenze (UniFi; Italy) has been taking part in a joint project called “Strategies for Monitoring CO2 and other Gases in Natural analogues”. The group was coordinated by AMPHOS XXI, a private company established in Barcelona. The Project was financially supported by Fundación Ciudad de la Energía (CIUDEN; Spain) as a part of the EC-funded OXYCFB300 project (European Energy Program for Recovery -EEPR-; www.compostillaproject.eu). The main objectives of the project were aimed to develop and optimize analytical methodologies to be applied at the surface to Monitor and Verify the feasibility of geologically stored carbon dioxide. These techniques were oriented to detect and quantify possible CO2 leakages to the atmosphere. Several investigations were made in natural analogues from Spain and Italy and in the Tecnchnological Development Plant for CO2 injection al Hontomín (Burgos, Spain). The studying techniques were mainly focused on the measurements of diffuse soil gases and surface and shallow waters. The soil-gas measurements included the determination of CO2 flux and the application to natural trace gases (e.g. radon) that may help to detect any CO2 leakage. As far as the water chemistry is concerned, geochemical and isotopic data related to surface and spring waters and dissolved gases in the area of the PDT of Hontomín were analyzed to determine the most suitable parameters to trace the migration of the injected CO2 into the near-surface environments. The accumulation chamber method was used to measure the diffuse emission of CO2 at the soil-atmosphere interface. Although this technique has widely been applied in different scientific areas, it was considered of the utmost importance to adapt the optimum methodology for measuring the CO2 soil flux and estimating the total CO2 output to the specific features of the site where CO2 is to be stored shortly. During the pre-injection phase CO2 fluxes are expected to be relatively low where in the intra- and post-injection phases, if leakages are to be occurring, small variation in CO2 flux might be detected when the CO2 “noise” is overcoming the biological activity of the soil (soil respiration). CO2 flux measurements by the accumulation chamber method could be performed without vegetation clearance or after vegetation clearance. However, the results obtained after clearance show less dispersion and this suggests that this procedure appears to be more suitable for monitoring CO2 Storage sites. The measurement protocol, applied for the determination of the CO2 flux baseline at Hontomín, has included the following steps: a) cleaning and removal of both the vegetal cover and top 2 cm of soil, b) waiting to reduce flux perturbation due to the soil removal and c) measuring the CO2 flux. Once completing the CO2 flux measurements and detected whether there were anomalies zones, the total CO2 output was estimated to quantify the amount of CO2 released to the atmosphere in each of the studied areas. There is a wide range of methodologies for the estimation of the CO2 output, which were applied to understand which one was the most representative. In this study six statistical methods are presented: arithmetic mean, minimum variances unbiased estimator, bootstrap resample, partitioning of data into different populations with a graphical and a maximum likelihood procedures, and sequential Gaussian simulation. Eight campaigns were carried out in the Hontomín CO2 Storage Technology Development Plant and in natural CO2 analogues. The results show that sequential Gaussian simulation is the most accurate method to estimate the total CO2 output and the confidential interval. Nevertheless, a variety of statistic methods were also used. As a consequence, an application procedure for selecting the most realistic method was developed. The first step to estimate the total emanation rate was the variogram analysis. If the relation among the data can be explained with the variogram, the best technique to calculate the total CO2 output and its confidence interval is the sequential Gaussian simulation method (sGs). If the data are independent, their distribution is to be analyzed. For normal and log-normal distribution the proper methods are the arithmetic mean and minimum variances unbiased estimator, respectively. If the data are not normal (log-normal) or are a mixture of different populations the best approach is the bootstrap resampling. According to these steps, the maximum confidence interval was about ±20/25%, with most of values between ±3.5% and ±8%. Partitioning of CO2 flux data into different populations may help to interpret the data as their distribution can be affected by different geochemical processes, e.g. geological or biological sources of CO2. Consequently, it may be an important tool in a monitoring CCS program, where the main goal is to demonstrate that there are not leakages from the reservoir to the atmosphere and, if occurring, to be able to detect and quantify it. Results show that the partitioning of populations is better performed by maximum likelihood criteria, since graphical procedures have a degree of subjectivity in the interpretation and results may not be reproducible. The relationship between CO2 flux and radon isotopes (222Rn and 220Rn) was studied in natural analogues. In all emissions zones, a positive relation between 222Rn and CO2 was observed. However, the relationship between activity of 220Rn and CO2 flux is not clear. In some cases the 220Rn activity indeed increased with the CO2 flux in other measurements a decrease was recognized. We can speculate that this effect was possibly related to the route (deep or shallow) of the radon source. These results may confirm the possible use of the radon isotopes as tracers for the gas origin and their application in the detection of leakages. With respect to the CO2 flux baseline at the TDP of Hontomín, soil flux measurements in the vicinity of oil boreholes, drilled in the eighties and named H-1 to H-4, and injection and monitoring wells were performed using an accumulation chamber. Seven surveys were carried out from November 2009 to summer 2011. More than 4,000 measurements were used to determine the baseline flux of CO2 and its seasonal variations. The measured values were relatively low (from 5 to 13 g•m-2•day-1) and few outliers were identified, mainly located close to the H-2 oil well. Nevertheless, these values cannot be associated to a deep source of CO2, being more likely related to biological processes, i.e. soil respiration. No anomalies were recognized close to the deep fault system (Ubierna Fault) detected by geophysical investigations. There, the CO2 flux is indeed as low as other measurement stations. CO2 fluxes appear to be controlled by the biological activity since the lowest values were recorded during autumn-winter seasons and they tend to increase in warm periods. Two reference CO2 flux values (UCL50 of 5 g•m-2•d-1 for non-ploughed areas in autumn-winter seasons and 3.5 and 12 g•m-2•d-1 for in ploughed and non-ploughed areas, respectively, in spring-summer time, and UCL99 of 26 g•m-2•d-1 for autumn-winter in not-ploughed areas and 34 and 42 g•m-2•d-1 for spring-summer in ploughed and not-ploughed areas, respectively, were calculated. Fluxes higher than these reference values could be indicative of possible leakage during the operational and post-closure stages of the storage project. The 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. 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. Some spring waters are characterized by relatively high concentrations of NO3 − (up to 123 mg/L), unequivocally suggesting an anthropogenic source. Anomalous concentrations of Cl−, SO4 2−, 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 possibly indicative of mixing processes between deep and shallow aquifers. The chemistry of the dissolved gases also evidences the shallow circuits of the Hontomín– Huermeces, mainly characterized by an atmospheric source as highlighted by the contents of N2, O2, Ar and their relative ratios. 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 the surface and spring waters in the surroundings of Hontomín can be considered as background values when intra- and post-injection monitoring programs will be carried out. In this respect, main and minor solutes, 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.

El análogo natural de almacenamiento y escape de Co2 de la cuenca de Gañuelas-Mazarrón : implicaciones para el comportamiento y la seguridad de un almacenamiento de Co2 en estaso supercrítico

El aumento de la temperatura media de la Tierra durante el pasado siglo en casi 1 ºC; la subida del nivel medio del mar; la disminución del volumen de hielo y nieve terrestres; la fuerte variabilidad del clima y los episodios climáticos extremos que se vienen sucediendo durante las ultimas décadas; y el aumento de las epidemias y enfermedades infecciosas son solo algunas de las evidencias del cambio climático actual, causado, principalmente, por la acumulación de gases de efecto invernadero en la atmósfera por actividades antropogénicas. La problemática y preocupación creciente surgida a raíz de estos fenómenos, motivo que, en 1997, se adoptara el denominado “Protocolo de Kyoto” (Japón), por el que los países firmantes adoptaron diferentes medidas destinadas a controlar y reducir las emisiones de los citados gases. Entre estas medidas cabe destacar las tecnologías CAC, enfocadas a la captura, transporte y almacenamiento de CO2. En este contexto se aprobó, en octubre de 2008, el Proyecto Singular Estratégico “Tecnologías avanzadas de generación, captura y almacenamiento de CO2” (PSE-120000-2008-6), cofinanciado por el Ministerio de Ciencia e Innovación y el FEDER, el cual abordaba, en su Subproyecto “Almacenamiento Geológico de CO2” (PSS-120000-2008-31), el estudio detallado, entre otros, del Análogo Natural de Almacenamiento y Escape de CO2 de la cuenca de Ganuelas-Mazarrón (Murcia). Es precisamente en el marco de dicho Proyecto en el que se ha realizado este trabajo, cuyo objetivo final ha sido el de predecir el comportamiento y evaluar la seguridad, a corto, medio y largo plazo, de un Almacenamiento Geológico Profundo de CO2 (AGP-CO2), mediante el estudio integral del citado análogo natural. Este estudio ha comprendido: i) la contextualización geológica e hidrogeológica de la cuenca, así como la investigación geofísica de la misma; ii) la toma de muestras de aguas de algunos acuíferos seleccionados con el fin de realizar su estudio hidrogeoquímico e isotópico; iii) la caracterización mineralógica, petrográfica, geoquímica e isotópica de los travertinos precipitados a partir de las aguas de algunos de los sondeos de la cuenca; y iv) la medida y caracterización química e isotópica de los gases libres y disueltos detectados en la cuenca, con especial atención al CO2 y 222Rn. Esta información, desarrollada en capítulos independientes, ha permitido realizar un modelo conceptual de funcionamiento del sistema natural que constituye la cuenca de Ganuelas-Mazarrón, así como establecer las analogías entre este y un AGP-CO2, con posibles escapes naturales y/o antropogénicos. La aplicación de toda esta información ha servido, por un lado, para predecir el comportamiento y evaluar la seguridad, a corto, medio y largo plazo, de un AGP-CO2 y, por otro, proponer una metodología general aplicable al estudio de posibles emplazamientos de AGP-CO2 desde la perspectiva de los reservorios naturales de CO2. Los resultados más importantes indican que la cuenca de Ganuelas-Mazarrón se trata de una cubeta o fosa tectónica delimitada por fallas normales, con importantes saltos verticales, que hunden al substrato rocoso (Complejo Nevado-Filabride), y rellenas, generalmente, por materiales volcánicos-subvolcánicos ácidos. Además, esta cuenca se encuentra rellena por formaciones menos resistivas que son, de muro a techo, las margas miocenas, predominantes y casi exclusivas de la cuenca, y los conglomerados y gravas pliocuaternarias. El acuífero salino profundo y enriquecido en CO2, puesto de manifiesto por la xx exploración geotérmica realizada en dicha cuenca durante la década de los 80 y objeto principal de este estudio, se encuentra a techo de los materiales del Complejo Nevado-Filabride, a una profundidad que podría superar los 800 m, según los datos de la investigación mediante sondeos y geofísica. Por ello, no se descarta la posibilidad de que el CO2 se encuentre en estado supe critico, por lo que la citada cuenca reuniría las características principales de un almacenamiento geológico natural y profundo de CO2, o análogo natural de un AGP-CO2 en un acuífero salino profundo. La sobreexplotación de los acuíferos mas someros de la cuenca, con fines agrícolas, origino, por el descenso de sus niveles piezométricos y de la presión hidrostática, el ascenso de las aguas profundas, salinas y enriquecidas en CO2, las cuales son las responsables de la contaminación de dichos acuíferos. El estudio hidrogeoquímico de las aguas de los acuíferos investigados muestra una gran variedad de hidrofacies, incluso en aquellos de litología similar. La alta salinidad de estas aguas las hace inservibles tanto para el consumo humano como para fines agrícolas. Además, el carácter ligeramente ácido de la mayoría de estas aguas determina que tengan gran capacidad para disolver y transportar, hacia la superficie, elementos pesados y/o tóxicos, entre los que destaca el U, elemento abundante en las rocas volcánicas ácidas de la cuenca, con contenidos de hasta 14 ppm, y en forma de uraninita submicroscópica. El estudio isotópico ha permitido discernir el origen, entre otros, del C del DIC de las aguas (δ13C-DIC), explicándose como una mezcla de dos componentes principales: uno, procedente de la descomposición térmica de las calizas y mármoles del substrato y, otro, de origen edáfico, sin descartar una aportación menor de C de origen mantélico. El estudio de los travertinos que se están formando a la salida de las aguas de algunos sondeos, por la desgasificación rápida de CO2 y el consiguiente aumento de pH, ha permitido destacar este fenómeno, por analogía, como alerta de escapes de CO2 desde un AGP-CO2. El análisis de los gases disueltos y libres, con especial atención al CO2 y al 222Rn asociado, indican que el C del CO2, tanto disuelto como en fase libre, tiene un origen similar al del DIC, confirmándose la menor contribución de CO2 de origen mantélico, dada la relación R/Ra del He existente en estos gases. El 222Rn sería el generado por el decaimiento radiactivo del U, particularmente abundante en las rocas volcánicas de la cuenca, y/o por el 226Ra procedente del U o del existente en los yesos mesinienses de la cuenca. Además, el CO2 actúa como carrier del 222Rn, hecho evidenciado en las anomalías positivas de ambos gases a ~ 1 m de profundidad y relacionadas principalmente con perturbaciones naturales (fallas y contactos) y antropogénicas (sondeos). La signatura isotópica del C a partir del DIC, de los carbonatos (travertinos), y del CO2 disuelto y libre, sugiere que esta señal puede usarse como un excelente trazador de los escapes de CO2 desde un AGPCO2, en el cual se inyectara un CO2 procedente, generalmente, de la combustión de combustibles fósiles, con un δ13C(V-PDB) de ~ -30 ‰. Estos resultados han permitido construir un modelo conceptual de funcionamiento del sistema natural de la cuenca de Ganuelas-Mazarrón como análogo natural de un AGP-CO2, y establecer las relaciones entre ambos. Así, las analogías mas importantes, en cuanto a los elementos del sistema, serian la existencia de: i) un acuífero salino profundo enriquecido en CO2, que seria análoga a la formación almacén de un AGPxxi CO2; ii) una formación sedimentaria margosa que, con una potencia superior a 500 m, se correspondería con la formación sello de un AGP-CO2; y iii) acuíferos mas someros con aguas dulces y aptas para el consumo humano, rocas volcánicas ricas en U y fallas que se encuentran selladas por yesos y/o margas; elementos que también podrían concurrir en un emplazamiento de un AGP-CO2. Por otro lado, los procesos análogos mas importantes identificados serian: i) la inyección ascendente del CO2, que seria análoga a la inyección de CO2 de origen antropogénico, pero este con una signatura isotópica δ13C(V-PDB) de ~ -30 ‰; ii) la disolución de CO2 y 222Rn en las aguas del acuífero profundo, lo que seria análogo a la disolución de dichos gases en la formación almacén de un AGP-CO2; iii) la contaminación de los acuíferos mas someros por el ascenso de las aguas sobresaturadas en CO2, proceso que seria análogo a la contaminación que se produciría en los acuíferos existentes por encima de un AGP-CO2, siempre que este se perturbara natural (reactivación de fallas) o artificialmente (sondeos); iv) la desgasificación (CO2 y gases asociados, entre los que destaca el 222Rn) del acuífero salino profundo a través de sondeos, proceso análogo al que pudiera ocurrir en un AGP-CO2 perturbado; y v) la formación rápida de travertinos, proceso análogo indicativo de que el AGP-CO2 ha perdido su estanqueidad. La identificación de las analogías más importantes ha permitido, además, analizar y evaluar, de manera aproximada, el comportamiento y la seguridad, a corto, medio y largo plazo, de un AGP-CO2 emplazado en un contexto geológico similar al sistema natural estudiado. Para ello se ha seguido la metodología basada en el análisis e identificación de los FEPs (Features, Events and Processes), los cuales se han combinado entre sí para generar y analizar diferentes escenarios de evolución del sistema (scenario analysis). Estos escenarios de evolución identificados en el sistema natural perturbado, relacionados con la perforación de sondeos, sobreexplotación de acuíferos, precipitación rápida de travertinos, etc., serian análogos a los que podrían ocurrir en un AGP-CO2 que también fuera perturbado antropogénicamente, por lo que resulta totalmente necesario evitar la perturbación artificial de la formación sello del AGPCO2. Por último, con toda la información obtenida se ha propuesto una metodología de estudio que pueda aplicarse al estudio de posibles emplazamientos de un AGP-CO2 desde la perspectiva de los reservorios naturales de CO2, sean estancos o no. Esta metodología comprende varias fases de estudio, que comprendería la caracterización geológico-estructural del sitio y de sus componentes (agua, roca y gases), la identificación de las analogías entre un sistema natural de almacenamiento de CO2 y un modelo conceptual de un AGP-CO2, y el establecimiento de las implicaciones para el comportamiento y la seguridad de un AGP-CO2. ABSTRACT The accumulation of the anthropogenic greenhouse gases in the atmosphere is the main responsible for: i) the increase in the average temperature of the Earth over the past century by almost 1 °C; ii) the rise in the mean sea level; iii) the drop of the ice volume and terrestrial snow; iv) the strong climate variability and extreme weather events that have been happening over the last decades; and v) the spread of epidemics and infectious diseases. All of these events are just some of the evidence of current climate change. The problems and growing concern related to these phenomena, prompted the adoption of the so-called "Kyoto Protocol" (Japan) in 1997, in which the signatory countries established different measurements to control and reduce the emissions of the greenhouse gases. These measurements include the CCS technologies, focused on the capture, transport and storage of CO2. Within this context, it was approved, in October 2008, the Strategic Singular Project "Tecnologías avanzadas de generación, captura y almacenamiento de CO2" (PSE-120000-2008-6), supported by the Ministry of Science and Innovation and the FEDER funds. This Project, by means of the Subproject "Geological Storage of CO2" (PSS- 120000-2008-31), was focused on the detailed study of the Natural Analogue of CO2 Storage and Leakage located in the Ganuelas-Mazarron Tertiary basin (Murcia), among other Spanish Natural Analogues. This research work has been performed in the framework of this Subproject, being its final objective to predict the behaviour and evaluate the safety, at short, medium and long-term, of a CO2 Deep Geological Storage (CO2-DGS) by means of a comprehensive study of the abovementioned Natural Analogue. This study comprises: i) the geological and hydrogeological context of the basin and its geophysical research; ii) the water sampling of the selected aquifers to establish their hydrogeochemical and isotopic features; iii) the mineralogical, petrographic, geochemical and isotopic characterisation of the travertines formed from upwelling groundwater of several hydrogeological and geothermal wells; and iv) the measurement of the free and dissolved gases detected in the basin, as well as their chemical and isotopic characterisation, mainly regarding CO2 and 222Rn. This information, summarised in separate chapters in the text, has enabled to build a conceptual model of the studied natural system and to establish the analogies between both the studied natural system and a CO2-DGS, with possible natural and/or anthropogenic escapes. All this information has served, firstly, to predict the behaviour and to evaluate the safety, at short, medium and long-term, of a CO2-DGS and, secondly, to propose a general methodology to study suitable sites for a CO2-DGS, taking into account the lessons learned from this CO2 natural reservoir. The main results indicate that the Ganuelas-Mazarron basin is a graben bounded by normal faults with significant vertical movements, which move down the metamorphic substrate (Nevado-Filabride Complex), and filled with acid volcanic-subvolcanic rocks. Furthermore, this basin is filled with two sedimentary formations: i) the Miocene marls, which are predominant and almost exclusive in the basin; xxiv and ii) the Plio-Quaternary conglomerates and gravels. A deep saline CO2-rich aquifer was evidenced in this basin as a result of the geothermal exploration wells performed during the 80s, located just at the top of the Nevado-Filabride Complex and at a depth that could exceed 800 m, according to the geophysical exploration performed. This saline CO2-rich aquifer is precisely the main object of this study. Therefore, it is not discarded the possibility that the CO2 in this aquifer be in supercritical state. Consequently, the aforementioned basin gathers the main characteristics of a natural and deep CO2 geological storage, or natural analogue of a CO2-DGS in a deep saline aquifer. The overexploitation of the shallow aquifers in this basin for agriculture purposes caused the drop of the groundwater levels and hydrostatic pressures, and, as a result, the ascent of the deep saline and CO2-rich groundwater, which is the responsible for the contamination of the shallow and fresh aquifers. The hydrogeochemical features of groundwater from the investigated aquifers show the presence of very different hydrofacies, even in those with similar lithology. The high salinity of this groundwater prevents the human and agricultural uses. In addition, the slightly acidic character of most of these waters determines their capacity to dissolve and transport towards the surface heavy and/or toxic elements, among which U is highlighted. This element is abundant in the acidic volcanic rocks of the basin, with concentrations up to 14 ppm, mainly as sub-microscopic uraninite crystals. The isotopic study of this groundwater, particularly the isotopic signature of C from DIC (δ13C-DIC), suggests that dissolved C can be explained considering a mixture of C from two main different sources: i) from the thermal decomposition of limestones and marbles forming the substrate; and ii) from edaphic origin. However, a minor contribution of C from mantle degassing cannot be discarded. The study of travertines being formed from upwelling groundwater of several hydrogeological and geothermal wells, as a result of the fast CO2 degassing and the pH increase, has allowed highlighting this phenomenon, by analogy, as an alert for the CO2 leakages from a CO2-DGS. The analysis of the dissolved and free gases, with special attention to CO2 and 222Rn, indicates that the C from the dissolved and free CO2 has a similar origin to that of the DIC. The R/Ra ratio of He corroborates the minor contribution of CO2 from the mantle degassing. Furthermore, 222Rn is generated by the radioactive decay of U, particularly abundant in the volcanic rocks of the basin, and/or by 226Ra from the U or from the Messinian gypsum in the basin. Moreover, CO2 acts as a carrier of the 222Rn, a fact evidenced by the positive anomalies of both gases at ~ 1 m depth and mainly related to natural (faults and contacts) and anthropogenic (wells) perturbations. The isotopic signature of C from DIC, carbonates (travertines), and dissolved and free CO2, suggests that this parameter can be used as an excellent tracer of CO2 escapes from a CO2-DGS, in which CO2 usually from the combustion of fossil fuels, with δ13C(V-PDB) of ~ -30 ‰, will be injected. All of these results have allowed to build a conceptual model of the behaviour of the natural system studied as a natural analogue of a CO2-DGS, as well as to establish the relationships between both natural xxv and artificial systems. Thus, the most important analogies, regarding the elements of the system, would be the presence of: i) a deep saline CO2-rich aquifer, which would be analogous to the storage formation of a CO2-DGS; ii) a marly sedimentary formation with a thickness greater than 500 m, which would correspond to the sealing formation of a CO2-DGS; and iii) shallow aquifers with fresh waters suitable for human consumption, U-rich volcanic rocks, and faults that are sealed by gypsums and/or marls; geological elements that could also be present in a CO2-DGS. On the other hand, the most important analogous processes identified are: i) the upward injection of CO2, which would be analogous to the downward injection of the anthropogenic CO2, this last with a δ13C(V-PDB) of ~ -30 ‰; ii) the dissolution of CO2 and 222Rn in groundwater of the deep aquifer, which would be analogous to the dissolution of these gases in the storage formation of a CO2-DGS; iii) the contamination of the shallow aquifers by the uprising of CO2-oversaturated groundwater, an analogous process to the contamination that would occur in shallow aquifers located above a CO2-DGS, whenever it was naturally (reactivation of faults) or artificially (wells) perturbed; iv) the degassing (CO2 and associated gases, among which 222Rn is remarkable) of the deep saline aquifer through wells, process which could be similar in a perturbed CO2- DGS; v) the rapid formation of travertines, indicating that the CO2-DGS has lost its seal capacity. The identification of the most important analogies has also allowed analysing and evaluating, approximately, the behaviour and safety in the short, medium and long term, of a CO2-DGS hosted in a similar geological context of the natural system studied. For that, it has been followed the methodology based on the analysis and identification of FEPs (Features, Events and Processes) that have been combined together in order to generate and analyse different scenarios of the system evolution (scenario analysis). These identified scenarios in the perturbed natural system, related to boreholes, overexploitation of aquifers, rapid precipitation of travertines, etc., would be similar to those that might occur in a CO2-DGS anthropogenically perturbed, so that it is absolutely necessary to avoid the artificial perturbation of the seal formation of a CO2-DGS. Finally, a useful methodology for the study of possible sites for a CO2-DGS is suggested based on the information obtained from this investigation, taking into account the lessons learned from this CO2 natural reservoir. This methodology comprises several phases of study, including the geological and structural characterisation of the site and its components (water, rock and gases), the identification of the analogies between a CO2 storage natural system and a conceptual model of a CO2-DGS, and the implications regarding the behaviour and safety of a CO2-DGS.

Substrate-induced conformational change in a trimeric ornithine transcarbamoylase

The crystal structure of Escherichia coli ornithine transcarbamoylase (OTCase, EC 2.1.3.3) complexed with the bisubstrate analog N-(phosphonacetyl)-l-ornithine (PALO) has been determined at 2.8-Å resolution. This research on the structure of a transcarbamoylase catalytic trimer with a substrate analog bound provides new insights into the linkages between substrate binding, protein–protein interactions, and conformational change. The structure was solved by molecular replacement with the Pseudomonas aeruginosa catabolic OTCase catalytic trimer (Villeret, V., Tricot, C., Stalon, V. & Dideberg, O. (1995) Proc. Natl. Acad. Sci. USA 92, 10762–10766; Protein Data Bank reference pdb 1otc) as the model and refined to a crystallographic R value of 21.3%. Each polypeptide chain folds into two domains, a carbamoyl phosphate binding domain and an l-ornithine binding domain. The bound inhibitor interacts with the side chains and/or backbone atoms of Lys-53, Ser-55, Thr-56, Arg-57, Thr-58, Arg-106, His-133, Asn-167, Asp-231, Met-236, Leu-274, Arg-319 as well as Gln-82 and Lys-86 from an adjacent chain. Comparison with the unligated P. aeruginosa catabolic OTCase structure indicates that binding of the substrate analog results in closure of the two domains of each chain. As in E. coli aspartate transcarbamoylase, the 240s loop undergoes the largest conformational change upon substrate binding. The clinical implications for human OTCase deficiency are discussed.

Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements

The parasitic bacterium Mycoplasma genitalium has a small, reduced genome with close to a basic set of genes. As a first step toward determining the families of protein domains that form the products of these genes, we have used the multiple sequence programs psi-blast and geanfammer to match the sequences of the 467 gene products of M. genitalium to the sequences of the domains that form proteins of known structure [Protein Data Bank (PDB) sequences]. PDB sequences (274) match all of 106 M. genitalium sequences and some parts of another 85; thus, 41% of its total sequences are matched in all or part. The evolutionary relationships of the PDB domains that match M. genitalium are described in the structural classification of proteins (SCOP) database. Using this information, we show that the domains in the matched M. genitalium sequences come from 114 superfamilies and that 58% of them have arisen by gene duplication. This level of duplication is more than twice that found by using pairwise sequence comparisons. The PDB domain matches also describe the domain structure of the matched sequences: just over a quarter contain one domain and the rest have combinations of two or more domains.

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K

The conformational space annealing (CSA) method for global optimization has been applied to the 10-55 fragment of the B-domain of staphylococcal protein A (protein A) and to a 75-residue protein, apo calbindin D9K (PDB ID code 1CLB), by using the UNRES off-lattice united-residue force field. Although the potential was not calibrated with these two proteins, the native-like structures were found among the low-energy conformations, without the use of threading or secondary-structure predictions. This is because the CSA method can find many distinct families of low-energy conformations. Starting from random conformations, the CSA method found that there are two families of low-energy conformations for each of the two proteins, the native-like fold and its mirror image. The CSA method converged to the same low-energy folds in all cases studied, as opposed to other optimization methods. It appears that the CSA method with the UNRES force field, which is based on the thermodynamic hypothesis, can be used in prediction of protein structures in real time.

tmRDB (tmRNA database)

The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html. Mirror sites are located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Institute of Biological Sciences, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/). The tmRDB provides information and citation links about tmRNA, a molecule that combines functions of tRNA and mRNA in trans-translation. tmRNA is likely to be present in all bacteria and has been found in algae chloroplasts, the cyanelle of Cyanophora paradoxa and the mitochondrion of the flagellate Reclinomonas americana. This release adds 26 new sequences and corresponding predicted tmRNA-encoded tag peptides for a total of 86 tmRNAs, ordered alphabetically and phylogenetically. Secondary structures and three-dimensional models in PDB format for representative molecules are being made available. tmRNA alignments prove individual base pairs and are generated manually assisted by computational tools. The alignments with their corresponding structural annotation can be obtained in various formats, including a new column format designed to improve and simplify computational usability of the data.

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins

The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam and ProDom. Links to the InterPro graphical interface allow users to see at a glance whether proteins from the cluster share particular functional sites. CluSTr also provides cross-references to HSSP and PDB. The database is available for querying and browsing at http://www.ebi.ac.uk/clustr.

CKAAPs DB: a conserved key amino acid positions database

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) Proteins, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly­peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families.

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure–structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure–structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.