Analysis of the Organic Hydroperoxide Response of Chromobacterium violaceum Reveals That OhrR Is a Cys-Based Redox Sensor Regulated by Thioredoxin

Organic hydroperoxides are oxidants generated during bacterial-host interactions. Here, we demonstrate that the peroxidase OhrA and its negative regulator OhrR comprise a major pathway for sensing and detoxifying organic hydroperoxides in the opportunistic pathogen Chromobacterium violaceum. Initially, we found that an ohrA mutant was hypersensitive to organic hydroperoxides and that it displayed a low efficiency for decomposing these molecules. Expression of ohrA and ohrR was specifically induced by organic hydroperoxides. These genes were expressed as monocistronic transcripts and also as a bicistronic ohrR-ohrA mRNA, generating the abundantly detected ohrA mRNA and the barely detected ohrR transcript. The bicistronic transcript appears to be processed. OhrR repressed both the ohrA and ohrR genes by binding directly to inverted repeat sequences within their promoters in a redox-dependent manner. Site-directed mutagenesis of each of the four OhrR cysteine residues indicated that the conserved Cys21 is critical to organic hydroperoxide sensing, whereas Cys126 is required for disulfide bond formation. Taken together, these phenotypic, genetic and biochemical data indicate that the response of C. violaceum to organic hydroperoxides is mediated by OhrA and OhrR. Finally, we demonstrated that oxidized OhrR, inactivated by intermolecular disulfide bond formation, is specifically regenerated via thiol-disulfide exchange by thioredoxin (but not other thiol reducing agents such as glutaredoxin, glutathione and lipoamide), providing a physiological reducing system for this thiol-based redox switch.

Environmental assessment of residues generated after consecutive acid-base pretreatment of sugarcane bagasse by advanced oxidative process

Abstract Background Biofuels produced from sugarcane bagasse (SB) have shown promising results as a suitable alternative of gasoline. Biofuels provide unique, strategic, environmental and socio-economic benefits. However, production of biofuels from SB has negative impact on environment due to the use of harsh chemicals during pretreatment. Consecutive sulfuric acid-sodium hydroxide pretreatment of SB is an effective process which eventually ameliorates the accessibility of cellulase towards cellulose for the sugars production. Alkaline hydrolysate of SB is black liquor containing high amount of dissolved lignin. Results This work evaluates the environmental impact of residues generated during the consecutive acid-base pretreatment of SB. Advanced oxidative process (AOP) was used based on photo-Fenton reaction mechanism (Fenton Reagent/UV). Experiments were performed in batch mode following factorial design L9 (Taguchi orthogonal array design of experiments), considering the three operation variables: temperature (°C), pH, Fenton Reagent (Fe2+/H2O2) + ultraviolet. Reduction of total phenolics (TP) and total organic carbon (TOC) were responsive variables. Among the tested conditions, experiment 7 (temperature, 35°C; pH, 2.5; Fenton reagent, 144 ml H2O2+153 ml Fe2+; UV, 16W) revealed the maximum reduction in TP (98.65%) and TOC (95.73%). Parameters such as chemical oxygen demand (COD), biochemical oxygen demand (BOD), BOD/COD ratio, color intensity and turbidity also showed a significant change in AOP mediated lignin solution than the native alkaline hydrolysate. Conclusion AOP based on Fenton Reagent/UV reaction mechanism showed efficient removal of TP and TOC from sugarcane bagasse alkaline hydrolysate (lignin solution). To the best of our knowledge, this is the first report on statistical optimization of the removal of TP and TOC from sugarcane bagasse alkaline hydrolysate employing Fenton reagent mediated AOP process.

Water-soluble organic compounds in air particulate matter analyzed by HPLC-DAD-MS and HPLC-MS/MS: abundance, sources and transformation of carboxylic acids, nitrophenols and nitrated proteins

Wasserlösliche organische Verbindungen (WSOCs) sind Hauptbestandteile atmosphärischer Aerosole, die bis zu ~ 50% und mehr der organischen Aerosolfraktion ausmachen. Sie können die optischen Eigenschaften sowie die Hygroskopizität von Aerosolpartikeln und damit deren Auswirkungen auf das Klima beeinflussen. Darüber hinaus können sie zur Toxizität und Allergenität atmosphärischer Aerosole beitragen.In dieser Studie wurde Hochleistungsflüssigchromatographie gekoppelt mit optischen Diodenarraydetektion und Massenspektrometrie (HPLC-DAD-MS und HPLC-MS/MS) angewandt, um WSOCs zu analysieren, die für verschiedene Aerosolquellen und -prozesse charakteristisch sind. Niedermolekulare Carbonsäuren und Nitrophenole wurden als Indikatoren für die Verbrennung fossiler Brennstoffe und die Entstehung sowie Alterung sekundärer organischer Aerosole (SOA) aus biogenen Vorläufern untersucht. Protein-Makromoleküle wurden mit Blick auf den Einfluss von Luftverschmutzung und Nitrierungsreaktionen auf die Allergenität primärer biologischer Aerosolpartikel – wie Pollen und Pilzsporen – untersucht.rnFilterproben von Grob- und Feinstaubwurden über ein Jahr hinweg gesammelt und auf folgende WSOCs untersucht: die Pinen-Oxidationsprodukte Pinsäure, Pinonsäure und 3-Methyl-1,2,3-Butantricarbonsäure (3-MBTCA) sowie eine Vielzahl anderer Dicarbonsäuren und Nitrophenole. Saisonale Schwankungen und andere charakteristische Merkmale werden mit Blick auf Aerosolquellen und -senken im Vergleich zu Daten anderen Studien und Regionen diskutiert. Die Verhätlnisse von Adipinsäure und Phthalsäure zu Azelainsäure deuten darauf hin, dass die untersuchten Aerosolproben hauptsächlich durch biogene Quellen beeinflusst werden. Eine ausgeprägte Arrhenius-artige Korrelation wurde zwischen der 3-MBTCA-¬Konzentration und der inversen Temperatur beobachtet (R2 = 0.79, Ea = 126±10 kJ mol-1, Temperaturbereich 275–300 K). Modellrechnungen zeigen, dass die Temperaturabhängigkeit auf eine Steigerung der photochemischen Produktionsraten von 3-MBTCA durch erhöhte OH-Radikal-Konzentrationen bei erhöhten Temperaturen zurückgeführt werden kann. Im Vergleich zur chemischen Reaktionskinetik scheint der Einfluss von Gas-Partikel-Partitionierungseffekten nur eine untergeordnete Rolle zu spielen. Die Ergebnisse zeigen, dass die OH-initiierte Oxidation von Pinosäure der geschwindigkeitsbestimmende Schritt der Bildung von 3-MBTCA ist. 3-MBTCA erscheint somit als Indikator für die chemische Alterung von biogener sekundärer organischer Aerosole (SOA) durch OH-Radikale geeignet. Eine Arrhenius-artige Temperaturabhängigkeit wurde auch für Pinäure beobachtet und kann durch die Temperaturabhängigkeit der biogenen Pinen-Emissionen als geschwindigkeitsbestimmender Schritt der Pinsäure-Bildung erklärt werden (R2 = 0.60, Ea = 84±9 kJ mol-1).rn rnFür die Untersuchung von Proteinnitrierungreaktionen wurde nitrierte Protein¬standards durch Flüssigphasenreaktion von Rinderserumalbumin (BSA) und Ovalbumin (OVA) mit Tetranitromethan (TNM) synthetisiert.Proteinnitrierung erfolgt vorrangig an den Resten der aromatischen Aminosäure Tyrosin auf, und mittels UV-Vis-Photometrie wurde der Proteinnnitrierungsgrad (ND) bestimmt. Dieser ist definiert als Verhältnis der mittleren Anzahl von Nitrotyrosinresten zur Tyrosinrest-Gesamtzahl in den Proteinmolekülen. BSA und OVA zeigten verschiedene Relationen zwischen ND und TNM/Tyrosin-Verhältnis im Reaktionsgemisch, was vermutlich auf Unterschiede in den Löslichkeiten und den molekularen Strukturen der beiden Proteine zurück zu führen ist.rnDie Nitrierung von BSA und OVA durch Exposition mit einem Gasgemisch aus Stickstoffdioxid (NO2) und Ozon (O3) wurde mit einer neu entwickelten HPLC-DAD-¬Analysemethode untersucht. Diese einfache und robuste Methode erlaubt die Bestimmung des ND ohne Hydrolyse oder Verdau der untersuchten Proteine und ernöglicht somit eine effiziente Untersuchung der Kinetik von Protein¬nitrierungs-Reaktionen. Für eine detaillierte Produktstudien wurden die nitrierten Proteine enzymatisch verdaut, und die erhaltenen Oligopeptide wurden mittels HPLC-MS/MS und Datenbankabgleich mit hoher Sequenzübereinstimmung analysiert. Die Nitrierungsgrade individueller Nitrotyrosin-Reste (NDY) korrelierten gut mit dem Gesamt-Proteinnitrierungsgrad (ND), und unterschiedliche Verhältnisse von NDY zu ND geben Aufschluss über die Regioselektivität der Reaktion. Die Nitrierungmuster von BSA und OVA nach Beahndlung mit TNM deuten darauf hin, dass die Nachbarschaft eines negativ geladenen Aminosäurerestes die Tyrosinnitrierung fördert. Die Behandlung von BSA durch NO2 und O3 führte zu anderend Nitrierungemustern als die Behandlung mit TNM, was darauf hindeutet, dass die Regioselektivität der Nitrierung vom Nitrierungsmittel abhängt. Es zeigt sich jedoch, dass Tyrosinreste in Loop-Strukturen bevorzugt und unabhängig vom Reagens nitriert werden.Die Methoden und Ergebnisse dieser Studie bilden eine Grundlage für weitere, detaillierte Untersuchungen der Reaktionskinetik sowie der Produkte und Mechanismen von Proteinnitrierungreaktionen. Sie sollen helfen, die Zusammenhänge zwischen verkehrsbedingten Luftschadstoffen wie Stickoxiden und Ozon und der Allergenität von Luftstaub aufzuklären.rn

Nutritive Value of the Crop Residues from bt-Corn Hybrids and Their Effects on Performance of Grazing Beef Cows

One non bt-corn hybrid (Pioneer 3489) and three btcorn hyrids (Pioneer 34RO7, Novartis NX6236, and Novartis N64-Z4) were planted in replicated 7.1-acre fields. After grain harvest, fields were stocked with 3 mature cows in midgestation to be strip-grazed as four paddocks over 126 days. Six similar cows were allotted to replicated drylots. All cows were fed hay as necessary to maintain a condition score of 5 on a 9-point scale. Cows were condition-scored biweekly and weighed monthly. Forage yield and weathering losses were determined by sampling one 4-m2 location per grazed or ungrazed paddock in each field with a minimum total of 2 locations of grazed or ungrazed forage per field. To measure forage selection during grazing, samples of grazed forage were collected from the rumen of one fistulated steer that grazed for 2 hours after ruminal evacuation. Non-bt-corn hybrids had greater (P<.05) infestation of corn borers in the upper stalk, lower stalk and ear shank than bt-corn hybrids. However, there were no differences in grain yields or dropped grain between hybrids. Crop residue dry matter, organic matter and in vitro digestible dry matter yields at the initiation of grazing did not differ between corn hybrids. Dry matter, organic matter and in vitro digestible dry matter losses tended (P<.10) to be greater from the NX6236 and N64-Z4 hybrids than from the 3489 and 34RO7 hybrids and were greater (P<.05) from grazed than non-grazed areas of the fields. At the initiation of grazing, dry matter concentrations of the crop residues from the NX6236 and N64-Z4 hybrids tended to be lower than those from the 3489 and 34RO7 hybrids. Crop residues from the NX6236 and N64-74 hybrids had lower concentrations of acid detergent fiber (P<.05) and acid detergent lignin (P=.07) and higher concentrations of in vitro digestible organic matter than the 3489 and 34RO7 hybrids. Over the grazing season, corn hybrid did not affect mean rates of change in forage composition. The concentration of in vitro digestible organic matter in forage selected by steers after two weeks of grazing did not differ. However, steers grazing corn crop residues consumed forage with higher (P<.05) concentrations of neutral detergent fiber, acid detergent fiber, and acid detergent insoluble nitrogen than steers fed hay. The acid detergent fiber concentration of forage selected by steers grazing the 3489 and N64-Z4 hybrids was lower (P < .05) than concentrations from the 34RO7 and NX6236 hybrids. In order to maintain similar body condition score changes, cows grazing crop residues from the 3489, 34RO7, NX6236, and N64-Z4 hybrids required 650, 628, 625, and 541 kg hay DM/cow compared with a hay requirement of 1447 kg hay DM/cow for cows maintained in a drylot.

Use of Stockpiled Berseem Clover as a Supplement for Grazed Corn Crop Residues

In the fall of 1994, mature Charolais cross cows in midgestation were allotted to duplicate 15 acre fields containing corn crop residues or a 2-to-1 mixture of corn crop residues and berseem clover planted in 3 strips at an allowance of 2.5 acres/cow for a 140 day wintering season. Similar cows were allotted duplicate drylots. All cows were fed hay as necessary to maintain a body condition score of 5. Cows grazing corn crop residues with or without berseem clover required 2596 pounds less hay per cow than cows maintained in a drylot. There was no difference in the amounts of hay required by cows grazing corn crop residues alone or with berseem clover. Initial organic matter yield of berseem clover was nearly that of corn crop residues and did not decrease as rapidly as corn crop residues. Berseem clover had a higher organic matter digestibility than corn crop residues at the initiation of grazing. Organic matter digestibility of berseem clover, however, decreased more rapidly than corn crop residues because of weathering during the winter.

Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues--synthesis and biochemical characterization.

Modified nucleoside triphosphates (dA(Hs)TP, dU(POH)TP, and dC(Val)TP) bearing imidazole, hydroxyl, and carboxylic acid residues connected to the purine and pyrimidine bases through alkyne linkers were prepared. These modified dN*TPs were excellent substrates for various DNA polymerases in primer extension reactions. Moreover, the combined use of terminal deoxynucleotidyl transferase (TdT) and the modified dNTPs led to efficient tailing reactions that rival those of natural counterparts. Finally, the triphosphates were tolerated by polymerases under PCR conditions, and the ensuing modified oligonucleotides served as templates for the regeneration of unmodified DNA. Thus, these modified dN*TPs are fully compatible with in vitro selection methods and can be used to develop artificial peptidases based on DNA.

(Table 2) Organic residue at DSDP Hole 76-534A

The kind, sedimentation rate, and diagenesis of organic particles delivered to the North Atlantic seafloor during the Middle Jurassic-Early Cretaceous were responsible for the presence of carbonaceous sediments in Hole 534A. Organic-rich black clays formed from the rapid supply of organic matter; this organic matter was composed of either abundant, well-preserved, and poorly sorted particles of land plants deposited in clays and silty clays within terrigenous turbiditic sequences (tracheal facies) or abundant amorphous debris (xenomorphic facies) generated through the digestive tracts of marine zooplankton and sedimented as fecal pellets. Evidence for the fecal-pellet origin of xenomorphic debris is illustrated. Black clays were also produced in sediments containing less organic matter as a result of the black color of carbonized particles composing all or most of the residues (micrinitic facies). Slowly sedimented hematitic Aptian clays contain very little carbonized, organic debris that survived diagenetic oxidation. In the red calcareous clay sequence of the Late Jurassic, larger amounts of this oxidized debris turned several clay layers black or blackish red. Carbonized debris also dominates the residues recovered in interbedded black and green Albian clays. Carbonization of organic matter in these sediments either turned them black or provided the diagenetic environment for reduced iron. Carbonized debris is also appreciable in burrow-mottled black-green Kimmeridgian clay. The study of Hole 534A organic matter indicates that during the middle Callovian there was a rapid supply of terrigenous organic matter, followed by a late Callovian episode of rapidly supplied xenomorphic debris deposited as fecal pellets. The Late Jurassic-Berriasian was a time of slower sedimentation of organic matter, primarily of a marine dinoflagellate flora in a poorly preserved xenomorphic facies variously affected by diagenetic oxidation. Several intervals of carbonized tracheal tissue in the Oxfordian and Kimmeridgian suggest episodes of oxidized terrigenous matter. The same sequence of Callovian organic events is evident in much of the Early Cretaceous

Lithology and organic geochemistry at DSDP Hole 77-535

Analyses of extractable organic matter from selected core samples obtained at DSDP Site 535 in the eastern Gulf of Mexico show that the asphalt (or tar) and adjacent oil stains in Lower Cretaceous fractured limestones have a common origin and are not derived from the surrounding organic-matter-rich limestones. Organic matter indigenous to those surrounding limestones was shown to be thermally immature and incapable of yielding the hydrocarbon mixture discovered. In contrast, the oil-stained and asphaltic material appears to be a post-migration alteration product of a mature oil that has migrated from source rocks deeper in the section, or from stratigraphically equivalent but compositionally different source-facies down-dip from the drill site. Further, hydrocarbons of the altered petroleum residues were shown to be similar to Sunniland-type oils found in Lower Cretaceous rocks of South Florida. The results suggest that shallowwater, platform-type source-rock facies similar to those that generated Sunniland-type oils, or deeper-water facies having comparable oil-generating material, are present in this deep-water (> 3000 m) environment. These findings have important implications for the petroleum potential in the eastern Gulf of Mexico and for certain types of deep-sea sediments.

Organic matter from black shales collected in DSDP Holes 41-367 and 41-368

It is shown that microscopic algae dominate in source material of organic matter of black shales, and admixture of residues of organisms and terrestrial humic material is contained. The main direction of source material transformation during syngenesis and sedimentogenesis is associated with jellofication resulting to formation of organic matter of significantly sapropelic type. Low reflectance of vitrinite and alginite from organic matter refer to the primary and secondary lignite stages of its carbonification. Significantly sapropel type of organic matter and low stage of carbonification are reliable criteria for assigning black shales to the category of potential oil source strata.

Crop rotation and residues influence N2O emission and N efficiency rather than tillage under a rainfed Mediterranean agroecosystem

Conservation tillage and crop rotation have spread during the last decades because promotes several positive effects (increase of soil organic content, reduction of soil erosion, and enhancement of carbon sequestration) (Six et al., 2004). However, these benefits could be partly counterbalanced by negative effects on the release of nitrous oxide (N2O) (Linn and Doran, 1984). There is a lack of data on long-term tillage system study, particularly in Mediterranean agro-ecosystems. The aim of this study was to evaluate the effects of long-term (>17 year) tillage systems (no tillage (NT), minimum tillage (MT) and conventional tillage (CT)); and crop rotation (wheat (W)-vetch (V)-barley (B)) versus wheat monoculture (M) on N2O emissions. Additionally, Yield-scaled N2O emissions (YSNE) and N uptake efficiency (NUpE) were assessed for each treatment.

Agricultural use of organic wastes as source of nitrogen and phosphorus: risks and opportunities

El nitrógeno (N) y el fósforo (P) son nutrientes esenciales en la producción de cultivos. El desarrollo de los fertilizantes de síntesis durante el siglo XX permitió una intensificación de la agricultura y un aumento de las producciones pero a su vez el gran input de nutrientes ha resultado en algunos casos en sistemas poco eficientes incrementando las pérdidas de estos nutrientes al medio ambiente. En el caso del P, este problema se agrava debido a la escasez de reservas de roca fosfórica necesaria para la fabricación de fertilizantes fosfatados. La utilización de residuos orgánicos en agricultura como fuente de N y P es una buena opción de manejo que permite valorizar la gran cantidad de residuos que se generan. Sin embargo, es importante conocer los procesos que se producen en el suelo tras la aplicación de los mismos, ya que influyen en la disponibilidad de nutrientes que pueden ser utilizados por el cultivo así como en las pérdidas de nutrientes de los agrosistemas que pueden ocasionar problemas de contaminación. Aunque la dinámica del N en el suelo ha sido más estudiada que la del P, los problemas importantes de contaminación por nitratos en zonas vulnerables hacen necesaria la evaluación de aquellas prácticas de manejo que pudieran agravar esta situación, y en el caso de los residuos orgánicos, la evaluación de la respuesta agronómica y medioambiental de la aplicación de materiales con un alto contenido en N (como los residuos procedentes de la industria vinícola y alcoholera). En cuanto al P, debido a la mayor complejidad de su ciclo y de las reacciones que ocurren en el suelo, hay un mayor desconocimiento de los factores que influyen en su dinámica en los sistemas suelo-planta, lo que supone nuevas oportunidades de estudio en la evaluación del uso agrícola de los residuos orgánicos. Teniendo en cuenta los conocimientos previos sobre cada nutriente así como las necesidades específicas en el estudio de los mismos, en esta Tesis se han evaluado: (1) el efecto de la aplicación de residuos procedentes de la industria vinícola y alcoholera en la dinámica del N desde el punto de vista agronómico y medioambiental en una zona vulnerable a la contaminación por nitratos; y (2) los factores que influyen en la disponibilidad de P en el suelo tras la aplicación de residuos orgánicos. Para ello se han llevado a cabo incubaciones de laboratorio así como ensayos de campo que permitieran evaluar la dinámica de estos nutrientes en condiciones reales. Las incubaciones de suelo en condiciones controladas de humedad y temperatura para determinar el N mineralizado se utilizan habitualmente para estimar la disponibilidad de N para el cultivo así como el riesgo medioambiental. Por ello se llevó a cabo una incubación en laboratorio para conocer la velocidad de mineralización de N de un compost obtenido a partir de residuos de la industria vinícola y alcoholera, ampliamente distribuida en Castilla-La Mancha, región con problemas importantes de contaminación de acuíferos por nitratos. Se probaron tres dosis crecientes de compost correspondientes a 230, 460 y 690 kg de N total por hectárea que se mezclaron con un suelo franco arcillo arenoso de la zona. La evolución del N mineral en el suelo a lo largo del tiempo se ajustó a un modelo de regresión no lineal, obteniendo valores bajos de N potencialmente mineralizable y bajas contantes de mineralización, lo que indica que se trata de un material resistente a la mineralización y con una lenta liberación de N en el suelo, mineralizándose tan solo 1.61, 1.33 y 1.21% del N total aplicado con cada dosis creciente de compost (para un periodo de seis meses). Por otra parte, la mineralización de N tras la aplicación de este material también se evaluó en condiciones de campo, mediante la elaboración de un balance de N durante dos ciclos de cultivo (2011 y 2012) de melón bajo riego por goteo, cultivo y manejo agrícola muy característicos de la zona de estudio. Las constantes de mineralización obtenidas en el laboratorio se ajustaron a las temperaturas reales en campo para predecir el N mineralizado en campo durante el ciclo de cultivo del melón, sin embargo este modelo generalmente sobreestimaba el N mineralizado observado en campo, por la influencia de otros factores no tenidos en cuenta para obtener esta predicción, como el N acumulado en el suelo, el efecto de la planta o las fluctuaciones de temperatura y humedad. Tanto el ajuste de los datos del laboratorio al modelo de mineralización como las predicciones del mismo fueron mejores cuando se consideraba el efecto de la mezcla suelo-compost que cuando se aislaba el N mineralizado del compost, mostrando la importancia del efecto del suelo en la mineralización del N procedente de residuos orgánicos. Dado que esta zona de estudio ha sido declarada vulnerable a la contaminación por nitratos y cuenta con diferentes unidades hidrológicas protegidas, en el mismo ensayo de campo con melón bajo riego por goteo se evaluó el riesgo de contaminación por nitratos tras la aplicación de diferentes dosis de compost bajo dos regímenes de riego, riego ajustado a las necesidades del cultivo (90 ó 100% de la evapotranspiración del cultivo (ETc)) o riego excedentario (120% ETc). A lo largo del ciclo de cultivo se estimó semanalmente el drenaje mediante la realización de un balance hídrico, así como se tomaron muestras de la solución de suelo y se determinó su concentración de nitratos. Para evaluar el riesgo de contaminación de las aguas subterráneas asociado con estas prácticas, se utilizaron algunos índices medioambientales para determinar la variación en la calidad del agua potable (Índice de Impacto (II)) y en la concentración de nitratos del acuífero (Índice de Impacto Ambiental (EII)). Para combinar parámetros medioambientales con parámetros de producción, se calculó la eficiencia de manejo. Se observó que la aplicación de compost bajo un régimen de riego ajustado no aumentaba el riesgo de contaminación de las aguas subterráneas incluso con la aplicación de la dosis más alta. Sin embargo, la aplicación de grandes cantidades de compost combinada con un riego excedentario supuso un incremento en el N lixiviado a lo largo del ciclo de cultivo, mientras que no se obtuvieron mayores producciones con respecto al riego ajustado. La aplicación de residuos de la industria vinícola y alcoholera como fuente de P fue evaluada en suelos calizos caracterizados por una alta capacidad de retención de P, lo cual en algunos casos limita la disponibilidad de este nutriente. Para ello se llevó a cabo otro ensayo de incubación con dos suelos de diferente textura, con diferente contenido de carbonato cálcico, hierro y con dos niveles de P disponible; a los que se aplicaron diferentes materiales procedentes de estas industrias (con y sin compostaje previo) aportando diferentes cantidades de P. A lo largo del tiempo se analizó el P disponible del suelo (P Olsen) así como el pH y el carbono orgánico disuelto. Al final de la incubación, con el fin de estudiar los cambios producidos por los diferentes residuos en el estado del P del suelo se llevó a cabo un fraccionamiento del P inorgánico del suelo, el cual se separó en P soluble y débilmente enlazado (NaOH-NaCl-P), P soluble en reductores u ocluido en los óxidos de Fe (CBD-P) y P poco soluble precipitado como Ca-P (HCl-P); y se determinó la capacidad de retención de P así como el grado de saturación de este elemento en el suelo. En este ensayo se observó que, dada la naturaleza caliza de los suelos, la influencia de la cantidad de P aplicado con los residuos en el P disponible sólo se producía al comienzo del periodo de incubación, mientras que al final del ensayo el incremento en el P disponible del suelo se igualaba independientemente del P aplicado con cada residuo, aumentando el P retenido en la fracción menos soluble con el aumento del P aplicado. Por el contrario, la aplicación de materiales orgánicos menos estabilizados y con un menor contenido en P, produjo un aumento en las formas de P más lábiles debido a una disolución del P retenido en la fracción menos lábil, lo cual demostró la influencia de la materia orgánica en los procesos que controlan el P disponible en el suelo. La aplicación de residuos aumentó el grado de saturación de P de los suelos, sin embargo los valores obtenidos no superaron los límites establecidos que indican un riesgo de contaminación de las aguas. La influencia de la aplicación de residuos orgánicos en las formas de P inorgánico y orgánico del suelo se estudió además en un suelo ácido de textura areno francosa tras la aplicación en campo a largo plazo de estiércol vacuno y de compost obtenido a partir de biorresiduos, así como la aplicación combinada de compost y un fertilizante mineral (superfosfato tripe), en una rotación de cultivos. En muestras de suelo recogidas 14 años después del establecimiento del experimento en campo, se determinó el P soluble y disponible, la capacidad de adsorción de P, el grado de saturación de P así como diferentes actividades enzimáticas (actividad deshidrogenasa, fosfatasa ácida y fosfatasa alcalina). Las diferentes formas de P orgánico en el suelo se estudiaron mediante una técnica de adición de enzimas con diferentes substratos específicos a extractos de suelo de NaOH-EDTA, midiendo el P hidrolizado durante un periodo de incubación por colorimetría. Las enzimas utilizadas fueron la fosfatasa ácida, la nucleasa y la fitasa las cuales permitieron identificar monoésteres hidrolizables (monoester-like P), diésteres (DNA-like P) e inositol hexaquifosfato (Ins6P-like P). La aplicación a largo plazo de residuos orgánicos aumentó el P disponible del suelo proporcionalmente al P aplicado con cada tipo de fertilización, suponiendo un mayor riesgo de pérdidas de P dado el alto grado de saturación de este suelo. La aplicación de residuos orgánicos aumentó el P orgánico del suelo resistente a la hidrólisis enzimática, sin embargo no influyó en las diferentes formas de P hidrolizable por las enzimas en comparación con las observadas en el suelo sin enmendar. Además, las diferentes formas de P orgánico aplicadas con los residuos orgánicos no se correspondieron con las analizadas en el suelo lo cual demostró que éstas son el resultado de diferentes procesos en el suelo mediados por las plantas, los microorganismos u otros procesos abióticos. En este estudio se encontró una correlación entre el Ins6P-like P y la actividad microbiana (actividad deshidrogenasa) del suelo, lo cual refuerza esta afirmación. Por último, la aplicación de residuos orgánicos como fuente de N y P en la agricultura se evaluó agronómicamente en un escenario real. Se estableció un experimento de campo para evaluar el compost procedente de residuos de bodegas y alcoholeras en el mismo cultivo de melón utilizado en el estudio de la mineralización y lixiviación de N. En este experimento se estudió la aplicación de tres dosis de compost: 1, 2 y 3 kg de compost por metro lineal de plantación correspondientes a 7, 13 y 20 t de compost por hectárea respectivamente; y se estudió el efecto sobre el crecimiento de las plantas, la acumulación de N y P en la planta, así como la producción y calidad del cultivo. La aplicación del compost produjo un ligero incremento en la biomasa vegetal acompañado por una mejora significativa de la producción con respecto a las parcelas no enmendadas, obteniéndose la máxima producción con la aplicación de 2 kg de compost por metro lineal. Aunque los efectos potenciales del N y P fueron parcialmente enmascarados por otras entradas de estos nutrientes en el sistema (alta concentración de nitratos en el agua de riego y ácido fosfórico suministrado por fertirrigación), se observó una mayor acumulación de P uno de los años de estudio que resultó en un aumento en el número de frutos en las parcelas enmendadas. Además, la mayor acumulación de N y P disponible en el suelo al final del ciclo de cultivo indicó el potencial uso de estos materiales como fuente de estos nutrientes. ABSTRACT Nitrogen (N) and phosphorus (P) are essential nutrients in crop production. The development of synthetic fertilizers during the 20th century allowed an intensification of the agriculture increasing crop yields but in turn the great input of nutrients has resulted in some cases in inefficient systems with higher losses to the environment. Regarding P, the scarcity of phosphate rock reserves necessary for the production of phosphate fertilizers aggravates this problem. The use of organic wastes in agriculture as a source of N and P is a good option of management that allows to value the large amount of wastes generated. However, it is important to understand the processes occurring in the soil after application of these materials, as they affect the availability of nutrients that can be used by the crop and the nutrient losses from agricultural systems that can cause problems of contamination. Although soil N dynamic has been more studied than P, the important concern of nitrate pollution in Nitrate Vulnerable Zones requires the evaluation of those management practices that could aggravate this situation, and in the case of organic wastes, the evaluation of the agronomic and environmental response after application of materials with a high N content (such as wastes from winery and distillery industries). On the other hand, due to the complexity of soil P cycle and the reactions that occur in soil, there is less knowledge about the factors that can influence its dynamics in the soil-plant system, which means new opportunities of study regarding the evaluation of the agricultural use of organic wastes. Taking into account the previous knowledge of each nutrient and the specific needs of study, in this Thesis we have evaluated: (1) the effect of the application of wastes from the winery and distillery industries on N dynamics from the agronomic and environmental viewpoint in a vulnerable zone; and (2) the factors that influence P availability in soils after the application of organic wastes. With this purposes, incubations were carried out in laboratory conditions as well as field trials that allow to assess the dynamic of these nutrients in real conditions. Soil incubations under controlled moisture and temperature conditions to determine N mineralization are commonly used to estimate N availability for crops together with the environmental risk. Therefore, a laboratory incubation was conducted in order to determine the N mineralization rate of a compost made from wastes generated in the winery and distillery industries, widely distributed in Castilla-La Mancha, a region with significant problems of aquifers contamination by nitrates. Three increasing doses of compost corresponding to 230, 460 and 690 kg of total N per hectare were mixed with a sandy clay loam soil collected in this area. The evolution of mineral N in soil over time was adjusted to a nonlinear regression model, obtaining low values of potentially mineralizable N and low constants of mineralization, indicating that it is a material resistant to mineralization with a slow release of N, with only 1.61, 1.33 and 1.21% of total N applied being mineralized with each increasing dose of compost (for a period of six months). Furthermore, N mineralization after the application of this material was also evaluated in field conditions by carrying out a N balance during two growing seasons (2011 and 2012) of a melon crop under drip irrigation, a crop and management very characteristic of the area of study. The mineralization constants obtained in the laboratory were adjusted to the actual temperatures observed in the field to predict N mineralized during each growing season, however, this model generally overestimated the N mineralization observed in the field, because of the influence of other factors not taken into account for this prediction, as N accumulated in soil, the plant effect or the fluctuations of temperature and moisture. The fitting of the laboratory data to the model as well as the predictions of N mineralized in the field were better when considering N mineralized from the soil-compost mixture rather than when N mineralized from compost was isolated, underlining the important role of the soil on N mineralization from organic wastes. Since the area of study was declared vulnerable to nitrate pollution and is situated between different protected hydrological units, the risk of nitrate pollution after application of different doses compost was evaluated in the same field trial with melon under two irrigation regimes, irrigation adjusted to the crop needs (90 or 100% of the crop evapotranspiration (ETc)) or excedentary irrigation (120% ETc). Drainage was estimated weekly throughout the growing season by conducting a water balance, samples of the soil solution were taken and the concentration of nitrates was determined. To assess the risk of groundwater contamination associated with these practices, some environmental indices were used to determine the variation in the quality of drinking water (Impact Index (II)) and the nitrates concentration in the groundwater (Environmental Impact Index (EII)). To combine environmental parameters together with yield parameters, the Management Efficiency was calculated. It was observed that the application of compost under irrigation adjusted to the plant needs did not represent a higher risk of groundwater contamination even with the application of the highest doses. However, the application of large amounts of compost combined with an irrigation surplus represented an increase of N leaching during the growing season compared with the unamended plots, while no additional yield with respect to the adjusted irrigation strategy is obtained. The application of wastes derived from the winery and distillery industry as source of P was evaluated in calcareous soils characterized by a high P retention capacity, which in some cases limits the availability of this nutrient. Another incubation experiment was carried out using two soils with different texture, different calcium carbonate and iron contents and two levels of available P; to which different materials from these industries (with and without composting) were applied providing different amounts of P. Soil available P (Olsen P), pH and dissolved organic carbon were analyzed along time. At the end of the incubation, in order to study the changes in soil P status caused by the different residues, a fractionation of soil inorganic P was carried out, which was separated into soluble and weakly bound P (NaOH-NaCl- P), reductant soluble P or occluded in Fe oxides (CBD-P) and P precipitated as poorly soluble Ca-P (HCl-P); and the P retention capacity and degree of P saturation were determined as well. Given the calcareous nature of the soils, the influence of the amount of P applied with the organic wastes in soil available P only occurred at the beginning of the incubation period, while at the end of the trial the increase in soil available P equalled independently of the amount of P applied with each residue, increasing the P retained in the least soluble fraction when increasing P applied. Conversely, the application of less stabilized materials with a lower content of P resulted in an increase in the most labile P forms due to dissolution of P retained in the less labile fraction, demonstrating the influence of organic matter addition on soil P processes that control P availability in soil. As expected, the application of organic wastes increased the degree of P saturation in the soils, however the values obtained did not exceed the limits considered to pose a risk of water pollution. The influence of the application of organic wastes on inorganic and organic soil P forms was also studied in an acid loamy sand soil after long-term field application of cattle manure and biowaste compost and the combined application of compost and mineral fertilizer (triple superphosphate) in a crop rotation. Soil samples were collected 14 years after the establishment of the field experiment, and analyzed for soluble and available P, P sorption capacity, degree of P saturation and enzymatic activities (dehydrogenase, acid phosphatase and alkaline phosphatase). The different forms of organic P in soil were determined by using an enzyme addition technique, based on adding enzymes with different substrate specificities to NaOH-EDTA soil extracts, measuring the hydrolyzed P colorimetrically after an incubation period. The enzymes used were acid phosphatase, nuclease and phytase which allowed to identify hydrolyzable monoesters (monoester-like P) diesters (DNA-like P) and inositol hexakisphosphate (Ins6P-like P). The long-term application of organic wastes increased soil available P proportionally to the P applied with each type of fertilizer, assuming a higher risk of P losses given the high degree of P saturation of this soil. The application of organic wastes increased soil organic P resistant to enzymatic hydrolysis, but no influence was observed regarding the different forms of enzyme hydrolyzable organic P compared to those observed in the non-amended soil. Furthermore, the different forms of organic P applied with the organic wastes did not correspond to those analyzed in the soil which showed that these forms in soil are a result of multifaceted P turnover processes in soil affected by plants, microorganisms and abiotic factors. In this study, a correlation between Ins6P-like P and the microbial activity (dehydrogenase activity) of soil was found, which reinforces this claim. Finally, the application of organic wastes as a source of N and P in agriculture was evaluated agronomically in a real field scenario. A field experiment was established to evaluate the application of compost made from wine-distillery wastes in the same melon crop used in the experiments of N mineralization and leaching. In this experiment the application of three doses of compost were studied: 1 , 2 and 3 kg of compost per linear meter of plantation corresponding to 7, 13 and 20 tonnes of compost per hectare respectively; and the effect on plant growth, N and P accumulation in the plant as well as crop yield and quality was studied. The application of compost produced a slight increase in plant biomass accompanied by a significant improvement in crop yield with respect to the unamended plots, obtaining the maximum yield with the application of 2 kg of compost per linear meter. Although the potential effects of N and P were partially masked by other inputs of these nutrients in the system (high concentration of nitrates in the irrigation water and phosphoric acid supplied by fertigation), an effect of P was observed the first year of study resulting in a greater plant P accumulation and in an increase in the number of fruits in the amended plots. In addition, the higher accumulation of available N and P in the topsoil at the end of the growing season indicated the potential use of this material as source of these nutrients.

Multidrug resistance proteins QacA and QacB from Staphylococcus aureus: membrane topology and identification of residues involved in substrate specificity.

The closely related multidrug efflux pumps QacA and QacB, from the bacterial pathogen Staphylococcus aureus, both confer resistance to various toxic organic cations but differ in that QacB mediates lower levels of resistance to divalent cations. Cloning and nucleotide sequencing of the qacB gene revealed that qacB differs from qacA by only seven nucleotide substitutions. Random hydroxylamine mutagenesis of qacB was undertaken, selecting for variants that conferred increased resistance to divalent cations. Both QacA and the QacB mutants capable of conferring resistance to divalent cations contain an acidic residue at either amino acid 322 or 323, whereas QacB contains uncharged residues in these positions. Site-directed mutagenesis of qacA confirmed the importance of an acidic residue within this region of QacA in conferring resistance to divalent cations. Membrane topological analysis using alkaline phosphatase and beta-galactosidase fusions indicated that the QacA protein contains 14 transmembrane segments. Thus, QacA represents the first membrane transport protein shown to contain 14 transmembrane segments, and confirms that the major facilitator superfamily contains a family of proteins with 14 transmembrane segments.

Cloning the expression of a mammalian gene involved in the reduction of methionine sulfoxide residues in proteins.

An enzyme that reduces methionine sulfoxide [Met(O)] residues in proteins [peptide Met(O) reductase (MsrA), EC 1.8.4.6; originally identified in Escherichia coli] was purified from bovine liver, and the cDNA encoding this enzyme was cloned and sequenced. The mammalian homologue of E. coli msrA (also called pmsR) cDNA encodes a protein of 255 amino acids with a calculated molecular mass of 25,846 Da. This protein has 61% identity with the E. coli MsrA throughout a region encompassing a 199-amino acid overlap. The protein has been overexpressed in E. coli and purified to homogeneity. The mammalian recombinant MsrA can use as substrate, proteins containing Met(O) as well as other organic compounds that contain an alkyl sulfoxide group such as N-acetylMet(O), Met(O), and dimethyl sulfoxide. Northern analysis of rat tissue extracts showed that rat msrA mRNA is present in a variety of organs with the highest level found in kidney. This is consistent with the observation that kidney extracts also contained the highest level of enzyme activity.

Decomposition of nitrogen-15 labeled hoop pine harvest residues in subtropical Australia

Information on decomposition of harvest residues may assist in the maintenance of soil fertility in second rotation (2R) hoop pine plantations (Araucaria cunninghamii Aiton ex A. Cunn.) of subtropical Australia. The experiment was undertaken to determine the dynamics of residue decomposition and fate of residue-derived N. We used N-15-labeled hoop pine foliage, branch, and stem material in microplots, over a 30-mo period following harvesting. We examined the decomposition of each component both singly and combined, and used C-13 cross-polarization and magic-angle spinning nuclear magnetic resonance (C-13 CPMAS NMR) to chart C transformations in decomposing foliage. Residue-derived N-15 was immobilized in the 0- to 5-cm soil layer, with approximately 40% N-15 recovery in the soil from the combined residues by the end of the 30-mo period. Total recovery of N-15 in residues and soil varied between 60 and 80% for the combined-residue microplots, with 20 to 40% of the residue N-15 apparently lost. When residues were combined within microplots the rate of foliage decomposition decreased by 30% while the rate of branch and stem decomposition increased by 50 and 40% compared with rates for these components when decomposed separately. Residue decomposition studies should include a combined-residue treatment. Based on C-15 CPMAS NMR spectra for decomposing foliage, we obtained good correlations for methoxyl C, aryl C, carbohydrate C and phenolic C with residue mass, N-15 enrichment, and total N. The ratio of carbohydrate C to methoxyl C may be useful as an indicator of harvest residue decomposition in hoop pine plantations.

Organic Matter Dynamics in the Wet Tropics Under Different Sugarcane Residue Management Regimes

Retention of sugarcane leaves and tops on the soil surface after harvesting has almost completely replaced pre- and post-harvest burning of crop residues in the Australian sugar industry. Since its introduction around 25 years ago, residue retention has increased soil organic matter to improve soil fertility as well as improve harvest flexibility and reduce erosion. However, in the wet tropics residue retention also poses potential problems of prolonged waterlogging, and late-season release of nitrogen which can reduce sugar content of the crop. The objective of this project is to examine the management of sugarcane residues in the wet tropics using a systems approach. Subsidiary objectives are (a) to improve understanding of nitrogen cycling in Australian sugarcane soils in the wet tropics, and (b) to identify ways to manage crop residues to retain their advantages and limit their disadvantages. Project objectives will be addressed using several approaches. Historic farm production data recorded by sugar mills in the wet tropics will be analysed to determine the effect of residue burning or retention on crop yield and sugar content. The impact of climate on soil processes will be highlighed by development of an index of nitrogen mineralisation using the Agricultural Production Systems Simulator (APSIM) model. Increased understanding of nitrogen cycling in Australian sugarcane soils and management of crop residues will be gained through a field experiment recently established in the Australian wet tropics. From this experiment the decomposition and nitrogen dynamics of residues placed on the soil surface and incorporated will be compared. The effect of differences in temperature, soil water content and pH will be further examined on these soils under glasshouse conditions. Preliminary results show a high ammonium to nitrate ratio in tropics soils, which may be due to low rates of nitrification that increase the retention of nitrogen in a form (ammonium) that is less subject to leaching. Further results will be presented at Congress.