Amino acids in the interstitial waters from ODP Hole 113-695A

Site 695 lies on the southeast margin of the South Orkney microcontinent on the northern margin of the Weddell Sea, at 62°23.48'S, 43°27.10'W in 1305 m water depth. The inorganic properties of interstitial waters at this site, including sulfate reduction, biogenic methane production, and high concentrations of ammonia and phosphate, imply high microbial activity. However, no clear relationship between amino acid composition and concentration and the type of microbial activity (e.g., sulfate reduction or methane production) can be identified. The THAA (total hydrolyzable amino acids) values range between 2.45 and 17.31 µmol/L, averaging 7.14 µmol/L. The mean concentrations and relative abundance values of acidic, basic, neutral, aromatic, and sulfur-containing amino acids are 1.34 (18%), 1.09 (15%), 3.93 (54%), 0.50 (8%), and 0.02 (0%) µmol/L, respectively. Glycine is the most abundant amino acid residue, with serine, glutamic acid, and ornithine next. The DFAA (dissolved free amino acids) values range from 0.10 to 12.73 µmol/L, averaging 4.07 µmol/L. The acidic, basic, neutral, aromatic, and sulfurcontaining amino acids are on average 0.21, 0.79, 2.56, 0.41, and 0.01 µmol/L, respectively. The relative abundances of acidic, basic, neutral, and aromatic amino acids average 4%, 18%, 58%, and 15%, respectively. Predominance of DFAA over DCAA (dissolved combined amino acids) in interstitial waters of Lithologic Units I and II is contrary to the predominance of DCAA over DFAA in other interstitial waters and seawater. The comparison of amino acid compositions between DCAA and siliceous plankton suggests that the DCAA in interstitial waters originally comes from amino acids derived from siliceous plankton. However, other sources which are much enriched in glutamic acid contribute to the DCAA composition.

Surface InGaAs nanostructures for sensing applications

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

Methionine residues as endogenous antioxidants in proteins

Cysteine and methionine are the two sulfur-containing residues normally found in proteins. Cysteine residues function in the catalytic cycle of many enzymes, and they can form disulfide bonds that contribute to protein structure. In contrast, the specific functions of methionine residues are not known. We propose that methionine residues constitute an important antioxidant defense mechanism. A variety of oxidants react readily with methionine to form methionine sulfoxide, and surface exposed methionine residues create an extremely high concentration of reactant, available as an efficient oxidant scavenger. Reduction back to methionine by methionine sulfoxide reductases would allow the antioxidant system to function catalytically. The effect of hydrogen peroxide exposure upon glutamine synthetase from Escherichia coli was studied as an in vitro model system. Eight of the 16 methionine residues could be oxidized with little effect on catalytic activity of the enzyme. The oxidizable methionine residues were found to be relatively surface exposed, whereas the intact residues were generally buried within the core of the protein. Furthermore, the susceptible residues were physically arranged in an array that guarded the entrance to the active site.

The role of phosphoglycans in Leishmania–sand fly interactions

Leishmania promastigotes synthesize an abundance of phosphoglycans, either attached to the cell surface through phosphatidylinositol anchors (lipophosphoglycan, LPG) or secreted as protein-containing glycoconjugates. These phosphoglycans are thought to promote the survival of the parasite within both its vertebrate and invertebrate hosts. The relative contributions of different phosphoglycan-containing molecules in Leishmania–sand fly interactions were tested by using mutants specifically deficient in either total phosphoglycans or LPG alone. Leishmania donovani promastigotes deficient in both LPG and protein-linked phosphoglycans because of loss of LPG2 (encoding the Golgi GDP-Man transporter) failed to survive the hydrolytic environment within the early blood-fed midgut. In contrast, L. donovani and Leishmania major mutants deficient solely in LPG expression because of loss of LPG1 (involved in biosynthesis of the core oligosaccharide LPG domain) had only a slight reduction in the survival and growth of promastigotes within the early blood-fed midgut. The ability of the LPG1-deficient promastigotes to persist in the midgut after blood meal excretion was completely lost, and this defect was correlated with their inability to bind to midgut epithelial cells in vitro. For both mutants, when phosphoglycan expression was restored to wild-type levels by reintroduction of LPG1 or LPG2 (as appropriate), then the wild-type phenotype was also restored. We conclude, first, that LPG is not essential for survival in the early blood-fed midgut but, along with other secreted phosphoglycan-containing glycoconjugates, can protect promastigotes from the digestive enzymes in the gut and, second, that LPG is required to mediate midgut attachment and to maintain infection in the fly during excretion of the digested blood meal.

Purification and Characterization of NADP+-Linked Isocitrate Dehydrogenase from Scots Pine1 : Evidence for Different Physiological Roles of the Enzyme in Primary Development

NADP+-isocitrate dehydrogenase (NADP+-IDH; EC 1.1.1.42) is involved in the supply of 2-oxoglutarate for ammonia assimilation and glutamate synthesis in higher plants through the glutamine synthetase/glutamate synthase (GS/GOGAT) cycle. Only one NADP+-IDH form of cytosolic localization was detected in green cotyledons of pine (Pinus spp.) seedlings. The pine enzyme was purified and exhibited molecular and kinetic properties similar to those described for NADP+-IDH from angiosperm, with a higher catalytic efficiency (105 m−1 s−1) than the deduced efficiencies for GS and GOGAT in higher plants. A polyclonal antiserum was raised against pine NADP+-IDH and used to assess protein expression in the seedlings. Steady-state levels of NADP+-IDH were coordinated with GS during seed germination and were associated with GS/GOGAT enzymes during chloroplast biogenesis, suggesting that NADP+-IDH is involved in the provision of carbon skeletons for the synthesis of nitrogen-containing molecules. However, a noncoordinated pattern of NADP+-IDH and GS/GOGAT was observed in advanced stages of cotyledon development and in the hypocotyl. A detailed analysis in hypocotyl sections revealed that NADP+-IDH abundance was inversely correlated with the presence of GS, GOGAT, and ribulose-1,5-bisphosphate carboxylase/oxygenase but was associated with the differentiation of the organ. These results cannot be explained by the accepted role of the enzyme in nitrogen assimilation and strongly suggest that NADP+-IDH may have other, as-yet-unknown, biological functions.

Refinery Nonconventional Feedstocks: Influence of the Coprocessing of Vacuum Gas Oil and Low Density Polyethylene in Fluid Catalytic Cracking Unit on Full Range Gasoline Composition

Gasoline coming from refinery fluid catalytic cracking (FCC) unit is a major contributor to the total commercial grade gasoline pool. The contents of the FCC gasoline are primarily paraffins, naphthenes, olefins, aromatics, and undesirables such as sulfur and sulfur containing compounds in low quantities. The proportions of these components in the FCC gasoline invariable determine its quality as well as the performance of the associated downstream units. The increasing demand for cleaner and lighter fuels significantly influences the need not only for novel processing technologies but also for alternative refinery and petrochemical feedstocks. Current and future clean gasoline requirements include increased isoparaffins contents, reduced olefin contents, reduced aromatics, reduced benzene, and reduced sulfur contents. The present study is aimed at investigating the effect of processing an unconventional refinery feedstock, composed of blend of vacuum gas oil (VGO) and low density polyethylene (LDPE) on FCC full range gasoline yields and compositional spectrum including its paraffins, isoparaffins, olefins, napthenes, and aromatics contents distribution within a range of operating variables of temperature (500–700 °C) and catalyst-feed oil ratio (CFR 5–10) using spent equilibrium FCC Y-zeolite based catalyst in a FCC pilot plant operated at the University of Alicante’s Research Institute of Chemical Process Engineering (RICPE). The coprocessing of the oil-polymer blend led to the production of gasoline with very similar yields and compositions as those obtained from the base oil, albeit, in some cases, the contribution of the feed polymer content as well as the processing variables on the gasoline compositional spectrum were appreciated. Carbon content analysis showed a higher fraction of the C9–C12 compounds at all catalyst rates employed and for both feedstocks. The gasoline’s paraffinicity, olefinicity, and degrees of branching of the paraffins and olefins were also affected in various degrees by the scale of operating severity. In the majority of the cases, the gasoline aromatics tended toward the decrease as the reactor temperature was increased. While the paraffins and iso-paraffins gasoline contents were relatively stable at around 5 % wt, the olefin contents on the other hand generally increased with increase in the FCC reactor temperature.

Molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit

Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 angstrom) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.

Alpha-selenoconotoxins, a new class of potent alpha(7) neuronal nicotinic receptor antagonists

Disulfide bonds are important structural motifs that play an essential role in maintaining the conformational stability of many bioactive peptides. Of particular importance are the conotoxins, which selectively target a wide range of ion channels that are implicated in numerous disease states. Despite the enormous potential of conotoxins as therapeutics, their multiple disulfide bond frameworks are inherently unstable under reducing conditions. Reduction or scrambling by thiol-containing molecules such as glutathione or serum albumin in intracellular or extracellular environments such as blood plasma can decrease their effectiveness as drugs. To address this issue, we describe a new class of selenoconotoxins where cysteine residues are replaced by selenocysteine to form isosteric and non-reducible diselenide bonds. Three isoforms of alpha-conotoxin ImI were synthesized by t-butoxycarbonyl chemistry with systematic replacement of one([ Sec(2,8)] ImI or [Sec(3,12)] ImI), or both([Sec(2,3,8,12)] ImI) disulfide bonds with a diselenide bond. Each analogue demonstrated remarkable stability to reduction or scrambling under a range of chemical and biological reducing conditions. Three-dimensional structural characterization by NMR and CD spectroscopy indicates conformational preferences that are very similar to those of native ImI, suggesting fully isomorphic structures. Additionally, full bioactivity was retained at the alpha(7) nicotinic acetylcholine receptor, with each seleno-analogue exhibiting a dose-response curve that overlaps with wild-type ImI, thus further supporting an isomorphic structure. These results demonstrate that selenoconotoxins can be used as highly stable scaffolds for the design of new drugs.

Factors affecting the nodulation and growth of tropical woody legume seedlings

This study surveys the occurrence of nodulation in woody legume species in Panamá and Costa Rica, describes nodule and root characteristics, and researches host-bacteria specificity, nodulation potential of soils, and the effects of light, added nitrogen, and rhizobia and VA mycorrhizal fungi inoculation on seedling growth. I examined 83 species in 37 genera and found 80% to be nodulated. Percent nodulated species in the Caesalpinioideae, Mimosoideae, and Papilionoideae was 17, 95, and 86, respectively, with no correlation between nodule morphology and tribal classification. Nodules formed mainly at root branch points which supports epidermal breaks as an important rhizobia infection route. More non-nodulated than nodulated species had root hairs. Several species emitted volatile sulfur-containing compounds, including the toxic compound ethylmercaptan, from roots, germinating seeds, and other tissues. These emissions may have an allelopathic action against pathogens, predators, or other plants. In contrast to the general non-specificity of most legumes for rhizobia, Mimosa pigra L. was highly specific and only nodulated in flooded soils. This species' specificity, combined with a limited occurrence of its root nodule bacteria may limit its natural distribution, but its spread as an invasive weed is facilitated when fill material from rivers is deposited in other areas. ^ An experimental light level of 1.5% of full sun completely inhibited seedling nodulation, as do similar naturally low levels in forest understory. In the forest, trees and seedlings were not nodulated. in some soils with suspected high N content. For six experimental species, added N progressively increased seedling growth while decreasing nodule biomass; at the highest level of added N nodulation was completely suppressed. Species and individuals showed variation in nodule biomass at high N applications which may indicate an opportunity for genetic selection for optimal N acquisition. Rhizobia inoculation had a small positive effect on seedling shoot growth, but VA mycorrhiza inoculation overwhelmingly increased seedling size, biomass, and leaf mineral concentration. In lowland tropical forest, VA mycorrhizal colonization appears indispensable for legume nodulation because of the fungus' ability to supply P in deficient soils. This requirement makes the legume-rhizobia-mycorrhiza association obligately tripartite. ^

Generation and screening of natural product-like compounds for antibiotic discovery

Avec l’apparition de plus en plus de souches de bactérie résistante aux antibiotiques, le développement de nouveaux antibiotiques est devenu une important problématique pour les agences de santé. C’est pour cela que la création de nouvelles plateformes pour accélérer la découverte de médicaments est devenu un besoin urgent. Dans les dernières décennies, la recherche était principalement orientée sur la modification de molécules préexistantes, la méta-analyse d’organismes produisant des molécules activent et l’analyse de librairies moléculaires pour trouver des molécules synthétiques activent, ce qui s’est avéré relativement inefficace. Notre but était donc de développer de nouvelles molécules avec des effets thérapeutiques de façon plus efficace à une fraction du prix et du temps comparé à ce qui se fait actuellement. Comme structure de base, nous avons utilisé des métabolites secondaires qui pouvaient altérer le fonctionnement des protéines ou l’interaction entre deux protéines. Pour générer ces molécules, j’ai concentré mes efforts sur les terpènes, une classe de métabolites secondaires qui possède un large éventail d’activités biologiques incluant des activités antibactériennes. Nous avons développé un système de chromosome artificiel de levure (YAC) qui permet à la fois l’assemblage directionnel et combinatoire de gènes qui permet la création de voies de biosynthèse artificielles. Comme preuve de concept, j’ai développé des YACs qui contiennent les gènes pour l’expression des enzymes impliquées dans la biosynthèse de la -carotène et de l’albaflavenone et produit ces molécules avec un haut rendement. Finalement, Des YACs produits à partir de librairies de gènes ont permis de créer une grande diversité de molécules.

Generation and screening of natural product-like compounds for antibiotic discovery

Avec l’apparition de plus en plus de souches de bactérie résistante aux antibiotiques, le développement de nouveaux antibiotiques est devenu une important problématique pour les agences de santé. C’est pour cela que la création de nouvelles plateformes pour accélérer la découverte de médicaments est devenu un besoin urgent. Dans les dernières décennies, la recherche était principalement orientée sur la modification de molécules préexistantes, la méta-analyse d’organismes produisant des molécules activent et l’analyse de librairies moléculaires pour trouver des molécules synthétiques activent, ce qui s’est avéré relativement inefficace. Notre but était donc de développer de nouvelles molécules avec des effets thérapeutiques de façon plus efficace à une fraction du prix et du temps comparé à ce qui se fait actuellement. Comme structure de base, nous avons utilisé des métabolites secondaires qui pouvaient altérer le fonctionnement des protéines ou l’interaction entre deux protéines. Pour générer ces molécules, j’ai concentré mes efforts sur les terpènes, une classe de métabolites secondaires qui possède un large éventail d’activités biologiques incluant des activités antibactériennes. Nous avons développé un système de chromosome artificiel de levure (YAC) qui permet à la fois l’assemblage directionnel et combinatoire de gènes qui permet la création de voies de biosynthèse artificielles. Comme preuve de concept, j’ai développé des YACs qui contiennent les gènes pour l’expression des enzymes impliquées dans la biosynthèse de la -carotène et de l’albaflavenone et produit ces molécules avec un haut rendement. Finalement, Des YACs produits à partir de librairies de gènes ont permis de créer une grande diversité de molécules.

First report on Meloidogyne chitwoodi hatching inhibition activity of essential oils and essential oils fractions

The Columbia root-knot nematode (CRKN), Meloidogyne chitwoodi, is an EPPO A2 type quarantine pest since 1998. This nematode causes severe damage in economically important crops such as potato and tomato, making agricultural products unacceptable for the fresh market and food processing. Commonly used nematicidal synthetic chemicals are often environmentally unsafe. Essential oils (EOs) may constitute safer alternatives against RKN. EOs, isolated from 56 plant samples, were tested against CRKN hatching, in direct contact bioassays. Some of the most successful EOs were fractionated and the hydrocarbon molecules (HM) and oxygen-containing molecules (OCM) fractions tested separately. 24 EOs displayed very strong hatching inhibitions (≥90 %) at 2 µL mL−1 and were further tested at lower concentrations. Dysphaniaambrosioides, Filipendula ulmaria, Ruta graveolens, Satureja montana and Thymbra capitata EOs revealed the lowest EC50 values (<0.15 µL mL−1). The main compounds of these EOs, namely 2-undecanone, ascaridol, carvacrol, isoascaridol, methyl salicylate, p-cymene and/or γ-terpinene, were putatively considered responsible for CRKN hatching inhibition. S. montana and T. capitata OCM fractions showed hatching inhibitions higher than HM fractions. The comparison of EO and corresponding fractions EC50 values suggests interactions between OCM and HM fractions against CRKN hatching. These species EOs showed to be potential environmentally friendly CRKN hatching inhibitors; nonetheless, bioactivity should be considered globally, since its HM and OCM fractions may contribute, diversely, to the full anti-hatching activity.