Heavy metal and petroleum product concentrations in waters at the Obskaya 1 drill site

During recent years, the basins of the Kara Sea (Kamennomysskaya, Obskaya, and Chugor'yakhinskaya structures) in the Russian Federation have been considered as promising regions for oil and gas exploration and, simultaneously, as possible paths of relatively cheap pipeline and tanker transportation of hydrocarbons projected for recovery. On the other hand, exploration operations, recovery, and transportation of gas pose a considerable risk of accidents and environmental pollution, which causes a justified concern about the future state of the ecological system of the Gulf of Ob and the adjoining parts of the Kara Sea. Therefore, regular combined environmental investigations (monitoring) are the most important factor for estimating the current state and forecasting the dynamics of the development of estuary systems. The program of investigations (schedule, station network, and measured parameters) is standardized in accordance with the international practice of such work and accounts for the experience of monitoring studies of Russian and foreign researchers. Two measurement sessions were performed during ecological investigations in the region of exploration drilling: at the beginning at final stage of drilling operations and borehole testing; in addition, natural parameters were determined in various parts of the Ob estuary before the beginning of investigations. Hydrophysical and hydrochemical characteristics of the water medium were determined and bottom sediments and water were analyzed for various pollutants (petroleum products, heavy metals, and radionuclides). The forms of heavy-metal occurrence in river and sea waters were determined by the method of continuous multistep filtration, which is based on water component fractionation on membrane filters of various pore sizes. These investigations revealed environmental pollution by chemical substances during the initial stage of drilling operations, when remains of fuels, oils, and solutions could be spilled, and part of the chemical pollutants could enter the environment. Owing to horizontal and vertical turbulent diffusion, wave mixing, and the effect of the general direction of currents in the Ob estuary from south to north, areas are formed with elevated concentrations of the analyzed elements and compounds. However, the concentration levels of chemical pollutants are practically no higher than the maximum admissible concentrations, and their substantial dissipation to the average regional background contents can be expected in the near future. Our investigations allowed us to determine in detail the parameters of anthropogenic pollution in the regions affected by hydrocarbon exploration drilling in the Obskii and Kamennomysskii prospects in the Gulf of Ob and estimate their influence on the ecological state of the basin of the Ob River and the Kara Sea on the whole.

Composition and structural formulas of ODP Site 200-1224 Eocene ferrobasalt minerals

The ~46-m.y.-old igneous basement cored during Leg 200 in the North Pacific represents one of the few cross sections of Pacific oceanic crust with a total penetration into basalt of >100 m. The rocks, emplaced during the Eocene at a fast-spreading rate (~14 cm/yr; full rate) are strongly differentiated tholeiitic basalts (ferrobasalts) with 7-4.5 wt% MgO, relatively high TiO2 (2-3.5 wt%), and total iron as Fe2O3 (9.1-16.8 wt%). The differentiated character of these lavas is related to unusually large amounts of crystallization differentiation of plagioclase, clinopyroxene, and olivine. The lithostratigraphy of the basement (cored to ~170 meters below seafloor) is divided into three units. The deepest unit (lithologic Unit 3), is a succession of lava flows of no more that a few meters thickness each. The intermediate unit (lithologic Unit 2) is represented by intermixed thin flows and pillows, whereas the shallowest unit (lithologic Unit 1), comprises two massive flows. The rocks range from aphyric to sparsely clinopyroxene-plagioclase-phyric (phenocryst content = <3 vol%) and from holocrystalline to hypohyaline. Chilled margins of pillow fragments show holohyaline to sparsely vitrophyric textures. Site 1224 oxide minerals present a type of alteration not previously seen, where titanomagnetite is only partially destroyed and the pure magnetite component is partially removed from the mineral, leaving, in the most extreme case, a nearly pure ulvöspinel residuum. As a result of this dissolution, iron, mainly in the oxidized state, is added to the circulating solvent fluids. This means that a considerable metal source can result from low-temperature reactions throughout the upper ocean crust. The coarsest-grained lithologic Unit 1 rocks have interstitial myrmekitic intergrowths of quartz and sodic plagioclase (~An12), roughly similar in mineralogy and bulk composition to tonalite/trondhjemite veinlets in abyssal gabbros from the southwest Indian Ocean and Hess Deep, eastern equatorial Pacific. Based on idiomorphic relationships and projections into the simplified Q-Ab-Or-H2O granite ternary system, the myrmekitic intergrowths formed at the same time as, or just after, the oxide minerals coprecipitated and at low water vapor pressure (~0.5 kbar). Their compositions correspond to SiO2-oligoclase intergrowths that are considerably less potassic than dacitic glasses that erupt, although rarely, along the East Pacific Rise or that have been produced experimentally by partial melting of gabbro. Based on the crystallization history and comparison to experimental data, the original interstitial siliceous liquids resulted from late-stage immiscible separation of siliceous and iron-rich liquids. The rare andesitic lavas found along the East Pacific Rise may be hybrid rocks formed by mixing of these immiscible siliceous melts with basaltic magma.

Structural Changes in Asparagus Production and Exports from Peru

Asparagus is the star product among non-traditional agricultural exports (NTAXs) in Peru. The export of preserved asparagus has expanded since the end of the 1980s. Although there was some stagnation in the mid-1990s, exports of fresh asparagus have expanded rapidly since the end of the 1990s. Now, the export of both preserved and fresh asparagus constitute the second most important agricultural export in Peru after coffee. Besides the change in demand on the international market, the important factor behind the shift from preserved to fresh asparagus is the change in the supply structure of asparagus. In the case of preserved asparagus, Peruvian exports expanded because of Peru’s competitiveness, which originated from favorable production factors, such as climate, soil and labor. However, because of the growing presence of Chinese products on the international market, Peru’s products lost their competitiveness. In the case of fresh asparagus, the investment of agricultural corporations in production and their innovation in integrating different economic processes from the point of production to the time of export built a successful supply structure that is suited for the export of fresh agricultural produce.

Structural properties of InAlN single layers nearly latice-matched to GaN grown by plasma assisted molecular beal epitaxy

The high lattice mismatch between III-nitride binaries (InN, GaN and AlN) remains a key problem to grow high quality III-nitride heterostructures. Recent interest has been focused on the growth of high-quality InAlN layers, with approximately 18% of indium incorporation, in-plane lattice-matched (LM) to GaN. While a lot of work has been done by metal-organic vapour phase epitaxy (MOVPE) by Carlin and co-workers, its growth by molecular beam epitaxy (MBE) is still in infancy

Conceptual design of the liquid metal laboratory of the TECHNOFUSION facility

The application of liquid metal technology in fusion devices requires R&D related to many phenomena: interaction between liquid metals and structural material as corrosion, erosion and passivation techniques; magneto-hydrodynamics; free surface fluid-dynamics and any other physical aspect that will be needed for their safe reliable operation. In particular, there is a significant shortage of experimental facilities dedicated to the development of the lithium technology. In the framework of the TECHNOFUSION project, an experimental laboratory devoted to the lithium technology development is proposed, in order to shed some light in the path to IFMIF and the design of chamber's first wall and divertors. The conceptual design foresee a development in two stages, the first one consisting on a material testing loop. The second stage proposes the construction of a mock-up of the IFMIF target that will allow to assess the behaviour of a free-surface lithium target under vacuum conditions. In this paper, such conceptual design is addressed.

Dual role of HupF in the biosynthesis of [NiFe] hydrogenase in Rhizobium leguminosarum

Background: [NiFe] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use H2 as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. Biosynthesis of [NiFe] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. The endosymbiotic bacterium Rhizobium leguminosarum requires the products of eighteen genes (hupSLCDEFGHIJKhypABFCDEX) to synthesize an active hydrogenase. hupF and hupK genes are found only in hydrogenase clusters from bacteria expressing hydrogenase in the presence of oxygen. Results: HupF is a HypC paralogue with a similar predicted structure, except for the C-terminal domain present only in HupF. Deletion of hupF results in the inability to process the hydrogenase large subunit HupL, and also in reduced stability of this subunit when cells are exposed to high oxygen tensions. A ?hupF mutant was fully complemented for hydrogenase activity by a C-terminal deletion derivative under symbiotic, ultra low-oxygen tensions, but only partial complementation was observed in free living cells under higher oxygen tensions (1% or 3%). Co-purification experiments using StrepTag-labelled HupF derivatives and mass spectrometry analysis indicate the existence of a major complex involving HupL and HupF, and a less abundant HupF-HupK complex. Conclusions: The results indicate that HupF has a dual role during hydrogenase biosynthesis: it is required for hydrogenase large subunit processing and it also acts as a chaperone to stabilize HupL when hydrogenase is synthesized in the presence of oxygen.

Functional roles of HypC and HupK in the biosynthesis of [NiFe] hydrogenase in Rhizobium leguminosarum.

Some rhizobia induce a hydrogen (H2)-uptake system with a [NiFe] hydrogenase along with nitrogenase to recover part of the energy lost as H2. Biosynthesis of NiFe hydrogenases is a process that ocurrs in the cytoplasm, where a number of auxiliary proteins (products of hup and hyp genes) are required to synthesize and insert the metal cofactors into the enzyme structural units. Although HypC is expressed in all hydrogenase systems, HupF and HupK are found only in bacteria that express the hydrogenase in the presence of oxygen (O2). Co-purification experiments have demonstrated HypC-HupK and HypC-HupL interactions. Results have shown that some conserved residues from HypC and HupK play a protective role of hydrogenase against the presence of O2.

Evaluation of damping properties of structural glass panes under impact loading

The latest technology and architectural trends have significantly improved the use of a large variety of glass products in construction which, in function of their own characteristocs, allow to design and calculate structural glass elements under safety conditions. This paper presents the evaluation and analysis of the damping properties of rectangular laminated glass plates of 1.938 m x 0.876 m with different thickness depending on the number of PVB interlayers arranged. By means of numerical simulation and experimental verification, using modal analysis, natural frequencies and damping of the glass plates were calculated, both under free boundary conditions and operational conditions for the impact test equipment used in the experimental program, as the European standard UNE-EN 12600:2003 specifies.

Muro cortina modular con marco de baja transmitancia térmica integrado en el vidrio aislante a través de adhesivos estructurales = Unitised curtain wall with low thermal transmittance frame integrated within the insulating glass unit through structural adhesives

Los muros cortina modulares están constituidos por paneles prefabricados que se fijan al edificio a través de anclajes a lo largo del borde del forjado. El proceso de prefabricación garantiza buena calidad y control de los acabados y el proceso de instalación es rápido y no requiere andamiaje. Por estas razones su uso está muy extendido en torres. Sin embargo, el diseño de los marcos de aluminio podría ser más eficiente si se aprovechara la rigidez de los vidrios para reducir la profundidad estructural de los montantes. Asimismo, se podrían reducir los puentes térmicos en las juntas si se sustituyeran los marcos por materiales de menor conductividad térmica que el aluminio. Esta investigación persigue desarrollar un muro cortina alternativo que reduzca la profundidad estructural, reduzca la transmisión térmica en las juntas y permita un acabado enrasado al interior, sin que sobresalgan los montantes. La idea consiste en conectar un marco de material compuesto de fibra de vidrio a lo largo del borde del vidrio aislante a través de adhesivos estructurales para así movilizar una acción estructural compuesta entre los dos vidrios y lograr una baja transmitancia térmica. El marco ha de estar integrado en la profundidad del vidrio aislante. En una primera fase se han efectuado cálculos estructurales y térmicos preliminares para evaluar las prestaciones a un nivel esquemático. Además, se han realizado ensayos a flexión en materiales compuestos de fibra de vidrio y ensayos a cortante en las conexiones adhesivas entre vidrio y material compuesto. Con la información obtenida se ha seleccionado el material del marco y del adhesivo y se han efectuado cambios sobre el diseño original. Los análisis numéricos finales demuestran una reducción de la profundidad estructural de un 80% y una reducción de la transmisión térmica de un 6% en comparación con un sistema convencional tomado como referencia. El sistema propuesto permite obtener acabados enrasados. ABSTRACT Unitised curtain wall systems consist of pre manufactured cladding panels which can be fitted to the building via pre fixed brackets along the edge of the floor slab. They are universally used for high rise buildings because the factory controlled assembly of units ensures high quality and allows fast installation without external access. However, its frame is structurally over-dimensioned because it is designed to carry the full structural load, failing to take advantage of potential composite contribution of glass. Subsequently, it is unnecessarily deep, occupying valuable space, and protrudes to the inside, causing visual disruption. Moreover, it is generally made of high thermal conductivity metal alloys, contributing to substantial thermal transmission at joints. This research aims to develop a novel frame-integrated unitised curtain wall system that will reduce thermal transmission at joints, reduce structural depth significantly and allow an inside flush finish. The idea is to adhesively bond a Fibre Reinforced Polymer (FRP) frame to the edge of the Insulated Glass Unit (IGU), thereby achieving composite structural behaviour and low thermal transmittance. The frame is to fit within the glazing cavity depth. Preliminary analytical structural and numerical thermal calculations are carried out to assess the performance of an initial schematic design. 4-point bending tests on GFRP and single-lap shear tests on bonded connections between GFRP and glass are performed to inform the frame and adhesive material selection process and to characterise these materials. Based on the preliminary calculations and experimental tests, some changes are put into effect to improve the performance of the system and mitigate potential issues. Structural and thermal numerical analysis carried out on the final detail design confirm a reduction of the structural depth to almost one fifth and a reduction of thermal transmission of 6% compared to a benchmark conventional system. A flush glazed appearance both to the inside and the outside are provided while keeping the full functionality of a unitised system.

Evaluación teórico experimental de la influencia de espumas de relleno metálicas como elementos de absorción de energía en perfiles tubulares de pequeño espesor. Su aplicación a vehículos para el transporte colectivo de personas

Los accidentes con implicación de autocares en los que se producen vuelcos ponen de manifiesto la especial agresividad de los mismos, como lo confirman las estadísticas. Como medida para mejorar la seguridad de los Vehículos de Grandes Dimensiones para el Transporte de Pasajeros (V.G.D.T.P.) frente a vuelco fue aprobado por las Naciones Unidas el Reglamento Nº 66 de Ginebra. Este reglamento establece los requisitos mínimos que las estructuras de los vehículos de grandes dimensiones deben cumplir con respecto a vuelco. El reglamento 66 ha supuesto un paso adelante muy importante en relación con la seguridad de los autocares, puesto que especifica por primera vez requerimientos estructurales a este tipo de vehículos, y en general ha supuesto una mejora del vehículo . Por otro lado, a consecuencia de la obligatoriedad de instalación de cinturones de seguridad, existe una unión entre pasajeros y vehículo, pero como no se trata de una unión rígida, hay que contemplar el porcentaje de la masa de los ocupantes que influye en la absorción de energía de la estructura. Además la retención de los ocupantes con cinturones de seguridad influye en la energía a absorber por la estructura del vehículo en dos aspectos, por un lado aumenta la masa del vehículo y en el otro se incrementa la altura el centro de gravedad. Esta situación a conducido a elaborar por parte de las Naciones Unidas la revisión 01 del Reglamento 66, en el que se considera que el 50 % de la masa total de los pasajeros posee una unión rígida con la estructura del vehículo, y por lo tanto debe ser tenida en cuenta si el vehículo posee sistemas de retención. En la situación actual, con limitaciones de peso del vehículo y peso por eje, los elementos de confort, seguridad y espacio para maleteros contribuyen a aumentar el peso del vehículo. Esto unido a la dificultad de introducción de cambios radicales en la concepción actual de fabricación de este tipo de vehículos por suponer unas pérdidas importantes para los fabricantes existentes, tanto en su conocimiento del producto como en su metodología de proceso, conlleva la necesidad cada vez más agobiante de analizar y evaluar otras alternativas estructurales que sin suponer grandes revoluciones a los productos actualmente en fabricación los complementen permitiendo adaptarse a los nuevos requerimientos en seguridad. Recientes desarrollos en la relación costo-beneficio de los procesos para la producción de materiales celulares metálicos de baja densidad, tales como las espumas metálicas, los posiciona como una alternativa de especial interés para la aplicación como elementos de absorción de energía para reforzar estructuras. El relleno con espumas metálicas puede ser más eficiente en términos de optimización de peso comparado con el aumento de espesor de los perfiles estructurales, dado que la absorción de energía se produce en una fracción relativamente pequeña de los perfiles, en las denominadas rótulas plásticas. La aplicación de espumas de relleno metálicas en estructuras de vehículos se está empezando a emplear en determinadas zonas de los vehículos de turismo, siendo totalmente novedosa cualquier intento de aplicación en estructuras de autobuses y autocares. Conforme a lo expuesto, y con el objeto de resolver estos problemas, se ha elaborado el presente trabajo de tesis doctoral, cuyos objetivos son: -Desarrollar un modelo matemático, que permita simular el ensayo de vuelco, considerando la influencia de los ocupantes retenidos con cinturones de seguridad para evaluar su influencia en la absorción de energía de la estructura. -Validar el modelo matemático de vuelco de la estructura mediante ensayos de secciones representativas de la estructura del vehículo y mediante el ensayo de un vehículo completo. -Realizar un estudio de las propiedades de las espumas metálicas que permitan incorporarlas como elemento de absorción de energía en el relleno de componentes de la superestructura de autobuses y autocares. -Desarrollar un modelo matemático para evaluar el aporte del relleno de espuma metálica en la absorción de energía ante solicitaciones por flexión estática y dinámica en componentes de la superestructura de autobuses o autocares. -Realizar un programa de ensayos a flexión estáticos y dinámicos para validar el modelo matemático del aporte del relleno de espuma metálica sobre componentes de la superestructura de autobuses y autocares. . -Incorporar al modelo matemático de vuelco de la estructura, los resultados obtenidos sobre componentes con relleno de espuma metálica, para evaluar el aporte en la absorción de energía. -Validar el modelo de vuelco de la estructura del autobús o autocar con relleno de espuma metálica, mediante ensayos de secciones de carrocería. ABSTRACT Accidents involving buses in which rollovers occur reveal the special aggressiveness thereof, as the statistics prove. As a measure to improve the safety of large vehicles for the transport of passengers to rollover, Regulation 66 of Geneva was approved by the United Nations. This regulation establishes the minimum requirements that structures of large vehicles must comply with respect to rollovers. The regulation 66 has been a major step forward in relation to the safety of coaches, since it specifies structural requirements to such vehicles and has been an improvement for the vehicle. In turn, as a result of compulsory installation of safety belts, there is contact between passengers and vehicle, but as it is not a rigid connection we must contemplate the percentage of the mass of the occupants that impacts on the energy absorption of the structure. Thus, the passengers’ restraining modifies the energy to absorb by the vehicle in two different aspects: On the one hand, it increases the vehicle weight and on the other the height of the center of gravity. This circumstance has taken the United Nations to elaborate Revision 01 of Regulation 66, in which it is considered that the 50 percent of passengers’ mass has a rigid joint together with the vehicle structure and, therefore, the passengers’ mass mentioned above should be highly considered if the vehicle has seat belts. In the present situation, in which limitations in vehicle weight and weight in axles are stricter, elements of comfort, safety and space for baggage are contributing to increase the weight of the vehicle. This coupled with the difficulty of introducing radical changes in the current conception of manufacturing such vehicles pose significant losses for existing manufacturers, both in product knowledge and process methodology, entails the overwhelming need to analyze and evaluate other structural alternatives without assuming relevant modifications on the products manufactured currently allowing them to adapt to the new safety requirements. Recent developments in cost-benefit processes for the production of metallic foams of low density, such as metal foams, place them as an alternative of special interest to be used as energy absorbers to strengthen structures. The filling with metal foams can be more efficient in terms of weight optimization compared with increasing thickness of the structural beams, since the energy absorption occurs in a relatively small fraction of the beams, called plastic hinges. The application of metal filling foams in vehicle structures is beginning to be used in certain areas of passenger cars, being an innovative opportunity in structures for application in buses and coaches. According to the mentioned before, and in order to come forward with a solution, this doctoral thesis has been prepared and its objectives are: - Develop a mathematical model to simulate the rollover test, considering the influence of the occupants held with seat belts to assess their influence on energy absorption structure. - Validate the mathematical model of the structure rollover by testing representative sections of the vehicle structure and by testing a complete vehicle. - Conduct a study of the properties of metal foams as possible incorporation of energy absorbing element in the filler component of the superstructure of buses and coaches. - Elaborate a mathematical model to assess the contribution of the metal foam filling in absorbing energy for static and dynamic bending loads on the components of buses or coaches superstructure. - Conduct a static and dynamic bending test program to validate the mathematical model of contribution of metal foam filling on components of the superstructure of buses and coaches bending. - To incorporate into the mathematical model of structure rollover, the results obtained on components filled with metal foam, to evaluate the contribution to the energy absorption. - Validate the rollover model structure of the bus or coach filled with metal foam through tests of bay sections. The objectives in this thesis have been achieved successfully. The contribution calculation model with metal foam filling in the vehicle structure has revealed that the filling with metal foam is more efficient than increasing thickness of the beams, as demonstrated in the experimental validation of bay sections.

Conversion of agonist site to metal-ion chelator site in the β2-adrenergic receptor

Previously metal-ion sites have been used as structural and functional probes in seven transmembrane receptors (7TM), but as yet all the engineered sites have been inactivating. Based on presumed agonist interaction points in transmembrane III (TM-III) and -VII of the β2-adrenergic receptor, in this paper we construct an activating metal-ion site between the amine-binding Asp-113 in TM-III—or a His residue introduced at this position—and a Cys residue substituted for Asn-312 in TM-VII. No increase in constitutive activity was observed in the mutant receptors. Signal transduction was activated in the mutant receptors not by normal catecholamine ligands but instead either by free zinc ions or by zinc or copper ions in complex with small hydrophobic metal-ion chelators. Chelation of the metal ions by small hydrophobic chelators such as phenanthroline or bipyridine protected the cells from the toxic effect of, for example Cu2+, and in several cases increased the affinity of the ions for the agonistic site. Wash-out experiments and structure–activity analysis indicated, that the high-affinity chelators and the metal ions bind and activate the mutant receptor as metal ion guided ligand complexes. Because of the well-understood binding geometry of the small metal ions, an important distance constraint has here been imposed between TM-III and -VII in the active, signaling conformation of 7TM receptors. It is suggested that atoxic metal-ion chelator complexes could possibly in the future be used as generic, pharmacologic tools to switch 7TM receptors with engineered metal-ion sites on or off at will.

Design and characterization of α-melanotropin peptide analogs cyclized through rhenium and technetium metal coordination

α-Melanocyte stimulating hormone (α-MSH) analogs, cyclized through site-specific rhenium (Re) and technetium (Tc) metal coordination, were structurally characterized and analyzed for their abilities to bind α-MSH receptors present on melanoma cells and in tumor-bearing mice. Results from receptor-binding assays conducted with B16 F1 murine melanoma cells indicated that receptor-binding affinity was reduced to approximately 1% of its original levels after Re incorporation into the cyclic Cys4,10, d-Phe7–α-MSH4-13 analog. Structural analysis of the Re–peptide complex showed that the disulfide bond of the original peptide was replaced by thiolate–metal–thiolate cyclization. A comparison of the metal-bound and metal-free structures indicated that metal complexation dramatically altered the structure of the receptor-binding core sequence. Redesign of the metal binding site resulted in a second-generation Re–peptide complex (ReCCMSH) that displayed a receptor-binding affinity of 2.9 nM, 25-fold higher than the initial Re–α-MSH analog. Characterization of the second-generation Re–peptide complex indicated that the peptide was still cyclized through Re coordination, but the structure of the receptor-binding sequence was no longer constrained. The corresponding 99mTc- and 188ReCCMSH complexes were synthesized and shown to be stable in phosphate-buffered saline and to challenges from diethylenetriaminepentaacetic acid (DTPA) and free cysteine. In vivo, the 99mTcCCMSH complex exhibited significant tumor uptake and retention and was effective in imaging melanoma in a murine-tumor model system. Cyclization of α-MSH analogs via 99mTc and 188Re yields chemically stable and biologically active molecules with potential melanoma-imaging and therapeutic properties.

Structural origins of the exonuclease resistance of a zwitterionic RNA

Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2′-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1°C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3′ ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3′-5′ exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-Å resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 Å and compared with the structure of the complex between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest that interference of the positively charged 2′-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.

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.