Biogeochemical processes in anoxic sediment from Lake Plußsee, Germany

In anoxic environments, volatile methylated sulfides like methanethiol (MT) and dimethyl sulfide (DMS) link the pools of inorganic and organic carbon with the sulfur cycle. However, direct formation of methylated sulfides from reduction of dissolved inorganic carbon has previously not been demonstrated. When studying the effect of temperature on hydrogenotrophic microbial activity, we observed formation of DMS in anoxic sediment of Lake Plußsee at 55 °C. Subsequent experiments strongly suggested that the formation of DMS involves fixation of bicarbonate via a reductive pathway in analogy to methanogenesis and engages methylation of MT. DMS formation was enhanced by addition of bicarbonate and further increased when both bicarbonate and H2 were supplemented. Inhibition of DMS formation by 2-bromoethanesulfonate points to the involvement of methanogens. Compared to the accumulation of DMS, MT showed the opposite trend but there was no apparent 1:1 stoichiometric ratio between both compounds. Both DMS and MT had negative d13C values of -62 per mil and -55 per mil, respectively. Labeling with NaH**13CO3 showed more rapid incorporation of bicarbonate into DMS than into MT. The stable carbon isotopic evidence implies that bicarbonate was fixed via a reductive pathway of methanogenesis, and the generated methyl coenzyme M became the methyl donor for MT methylation. Neither DMS nor MT accumulation were stimulated by addition of the methyl-group donors methanol and syringic acid or by the methyl-group acceptor hydrogen sulphide. The source of MT was further investigated in a H2**35S labeling experiment, which demonstrated a microbially-mediated process of hydrogen sulfide methylation to MT that accounted for only <10% of the accumulation rates of DMS. Therefore, the major source of the 13C-depleted MT was neither bicarbonate nor methoxylated aromatic compounds. Other possibilities for isotopically depleted MT, such as other organic precursors like methionine, are discussed. This DMS-forming pathway may be relevant for anoxic environments such as hydrothermally influenced sediments and fluids and sulfate-methane transition zones in marine sediments.

Disruption of abscisic acid signaling constitutively activates Arabidopsis resistance to the necrotrophic fungus Plectosphaerella cucumerina.

Plant resistance to necrotrophic fungi is regulated by a complex set of signaling pathways that includes those mediated by the hormones salicylic acid (SA), ethylene (ET), jasmonic acid (JA), and abscisic acid (ABA). The role of ABA in plant resistance remains controversial, as positive and negative regulatory functions have been described depending on the plant-pathogen interaction analyzed. Here, we show that ABA signaling negatively regulates Arabidopsis (Arabidopsis thaliana) resistance to the necrotrophic fungus Plectosphaerella cucumerina. Arabidopsis plants impaired in ABA biosynthesis, such as the aba1-6 mutant, or in ABA signaling, like the quadruple pyr/pyl mutant (pyr1pyl1pyl2pyl4), were more resistant to P. cucumerina than wild-type plants. In contrast, the hab1-1abi1-2abi2-2 mutant impaired in three phosphatases that negatively regulate ABA signaling displayed an enhanced susceptibility phenotype to this fungus. Comparative transcriptomic analyses of aba1-6 and wild-type plants revealed that the ABA pathway negatively regulates defense genes, many of which are controlled by the SA, JA, or ET pathway. In line with these data, we found that aba1-6 resistance to P. cucumerina was partially compromised when the SA, JA, or ET pathway was disrupted in this mutant. Additionally, in the aba1-6 plants, some genes encoding cell wall-related proteins were misregulated. Fourier transform infrared spectroscopy and biochemical analyses of cell walls from aba1-6 and wild-type plants revealed significant differences in their Fourier transform infrared spectratypes and uronic acid and cellulose contents. All these data suggest that ABA signaling has a complex function in Arabidopsis basal resistance, negatively regulating SA/JA/ET-mediated resistance to necrotrophic fungi.

Utilización de bloqueadores metabólicos y optimización de las condiciones de aplicación para la reducción del grado alcohólico en vinos elaborados a partir de uva procedente de zonas cálidas

El presente trabajo de Tesis describe la posibilidad de modular la fermentación alcohólica utilizando bloqueadores metabólicos como furfural, o-vainillina, ácido cinámico, glicolaldehído, p-benzoquinona y cobre; para controlar la producción de etanol. El redireccionamiento de la ruta glicolítica en Saccharomyces cerevisiae favorece el descenso del grado alcohólico gracias al aumento de la producción de metabolitos secundarios de interés enológico. La primera parte de la Tesis presenta una revisión bibliográfica sobre estudios previos en los que se ha evaluado el efecto de los diferentes bloqueadores metabólicos en la producción de etanol durante la fermentación alcohólica. La segunda parte muestra los resultados experimentales de producción de etanol obtenidos con los bloqueadores metabólicos, observándose una amplia variabilidad en su efecto en función de la naturaleza química de cada bloqueador y de la naturaleza del medio fermentativo utilizado. Finalmente, la tercera parte del trabajo muestra el efecto de los bloqueadores metabólicos sobre los parámetros colorimétricos y la producción de metabolitos secundarios, observándose un importante efecto en la producción de glicerina y en algunos de los compuestos volátiles fermentativos. La principal aplicación de esta tecnología basada en la utilización de bloqueadores metabólicos sería la elaboración de vinos con una menor graduación alcohólica a partir de uva procedente de zonas cálidas. ABSTRACT This thesis describes the possibility of modulating the alcoholic fermentation using metabolic blockers such as furfural, o-vanillin, cinnamic acid, glycolaldehyde, p-benzoquinone and copper. The controlled production of ethanol by redirecting of the glycolytic pathway in Saccharomyces cerevisiae, is achieved through diverting some of the carbohydrates away from alcohol production into the formation of glycolytic intermediates of interest to the winemaking industry. The first part of this work shows a literature review on previous studies about the effect of different metabolic blockers in order to reduce the ethanol production during alcoholic fermentation. The second part deals about the experimental results of ethanol production obtained with the metabolic blockers, showing a wide variation in the inhibitory effect depending on the chemical nature of each blocker and the nature of the fermentation medium used. Finally, the third part discussed about the effect of the metabolic blockers on colorimetric parameters and production of secondary metabolites, showing a significant effect on the production of glycerol and in some of the volatile fermentative compounds. The main application of this technology based on the use of metabolic blockers could lie in the preparation of reduced-alcohol wines from grapes grown in hot climate regions.

Analysis of advanced European nuclear fuel cycle scenarios including transmutation and economic estimates

Four European fuel cycle scenarios involving transmutation options (in coherence with PATEROS and CPESFR EU projects) have been addressed from a point of view of resources utilization and economic estimates. Scenarios include: (i) the current fleet using Light Water Reactor (LWR) technology and open fuel cycle, (ii) full replacement of the initial fleet with Fast Reactors (FR) burning U?Pu MOX fuel, (iii) closed fuel cycle with Minor Actinide (MA) transmutation in a fraction of the FR fleet, and (iv) closed fuel cycle with MA transmutation in dedicated Accelerator Driven Systems (ADS). All scenarios consider an intermediate period of GEN-III+ LWR deployment and they extend for 200 years, looking for long term equilibrium mass flow achievement. The simulations were made using the TR_EVOL code, capable to assess the management of the nuclear mass streams in the scenario as well as economics for the estimation of the levelized cost of electricity (LCOE) and other costs. Results reveal that all scenarios are feasible according to nuclear resources demand (natural and depleted U, and Pu). Additionally, we have found as expected that the FR scenario reduces considerably the Pu inventory in repositories compared to the reference scenario. The elimination of the LWR MA legacy requires a maximum of 55% fraction (i.e., a peak value of 44 FR units) of the FR fleet dedicated to transmutation (MA in MOX fuel, homogeneous transmutation) or an average of 28 units of ADS plants (i.e., a peak value of 51 ADS units). Regarding the economic analysis, the main usefulness of the provided economic results is for relative comparison of scenarios and breakdown of LCOE contributors rather than provision of absolute values, as technological readiness levels are low for most of the advanced fuel cycle stages. The obtained estimations show an increase of LCOE ? averaged over the whole period ? with respect to the reference open cycle scenario of 20% for Pu management scenario and around 35% for both transmutation scenarios. The main contribution to LCOE is the capital costs of new facilities, quantified between 60% and 69% depending on the scenario. An uncertainty analysis is provided around assumed low and high values of processes and technologies.

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.

Amelioration of a degraded acid soil from SW Spain by no-tillage and Ca-amendment

En los suelos, el exceso de acidez lleva asociado deficiencias en ciertos nutrientes y una alta disponibilidad de aluminio, tóxico para los cultivos propios del ambiente mediterráneo. Su laboreo, provoca la pérdida de materia orgánica (MO), deteriora su estructura y reduce la actividad biológica, provocando en última instancia una menor calidad del suelo. Es de esperar pues que cuando se labran suelos ácidos, sus problemáticas particulares tiendan a agravarse. En nuestra zona de estudio, la “raña” de Cañamero (Extremadura, España), predominan los suelos muy ácidos y degradados por un laboreo inadecuado. Las rañas constituyen amplias plataformas casi horizontales, con unos suelos muy viejos (Palexerults), que se caracterizan por tener el complejo de cambio dominado por el aluminio, y un pH ácido que decrece en profundidad. Poseen un potente horizonte Bt rico en arcillas caoliníticas, que propicia que en periodos con exceso de lluvia, se generen capas colgadas de agua cercanas a la superficie. En torno a los años 1940’s estos suelos, que previamente sostenían un alcornocal, o su matorral de sustitución, se pusieron en cultivo. El laboreo aceleró la mineralización de la materia orgánica, agravó los problemas derivados del exceso de acidez y condujo al abandono de los campos cultivados por falta de productividad. Para recuperar la calidad de estos suelos degradados y obtener unos rendimientos compatibles con su uso agrícola es necesario, por un lado, aplicar enmiendas que eleven el pH y reduzcan la toxicidad del aluminio y, por otro, favorecer el incremento en el contenido en MO. En 2005 se implantó en esta raña un ensayo de campo para estudiar la influencia del no laboreo y de la utilización de una enmienda cálcica en parámetros relacionados con la calidad del suelo en un cultivo forrajero. El diseño experimental fue en parcelas divididas con cuatro repeticiones donde el factor principal fue el tipo de laboreo, no laboreo (NL) frente a laboreo convencional (LC), y el factor secundario el uso o no de una enmienda cálcica. La enmienda consistió básicamente en una mezcla de espuma de azucarería y yeso rojo y se incorporó al comienzo del ensayo hasta los 7 cm de profundidad. Desde el comienzo del ensayo el NL influyó positivamente en el contenido de carbono orgánico total (COT) y particulado (COP), mientras que la enmienda tuvo una ligera influencia al principio del ensayo en ambos pero su efecto positivo se desvaneció con el paso del tiempo. Los mayores contenidos en COT y POC se observaron cuando se combinó el NL con la enmienda. La enmienda incrementó con rapidez el pH, y el Ca, y disminuyó el contenido en aluminio hasta una profundidad de 50 cm, incluso en NL, y mejoró ligeramente la agregación del suelo. El NL por sí solo, gracias al aumento en POC, TOC y las proteínas del suelo relacionadas con la glomalina (PSRG), que son capaces de formar compuestos estables no tóxicos con el aluminio, también contribuyó a la reducción de la toxicidad de aluminio en la capa más superficial. Cuando en las campañas con exceso de precipitaciones se generaron capas colgadas de agua próximas a la superficie, el NL generó unas condiciones más favorables para la germinación y desarrollo del cultivo, resultando en una producción más alta que el LC. A ello contribuyó la mayor capacidad de almacenamiento de agua y la mayor transmisividad de esta hacia abajo, en la capa más superficial (0-5 cm) que propició una menor saturación por agua que el LC. Respecto a los parámetros relacionados con la agregación, el NL aumentó los macroagregados hasta los 10 cm de profundidad y favoreció la acumulación de CO y N en todas las fracciones de tamaño de agregados. Sin embargo, la recuperación del grado de macroagregación tras el cese del laboreo resulta lenta en comparación con otros suelos, posiblemente debido al bajo contenido en arcilla en el horizonte Ap. En comparación con el NL, la enmienda mostró también un efecto positivo, aunque muy ligero, en la agregación del suelo. En contradicción con otros estudios en suelos ácidos, nuestros resultados indican la existencia de una jerarquía de agregados, y destacan el papel importante de la MO en la mejora de la agregación. Tanto el NL como la enmienda favorecieron por separado varias propiedades químicas, físicas y biológicas del suelo, pero, en general, encontramos los mayores beneficios con su uso combinado. Además, a largo plazo el efecto positivo de NL en las propiedades del suelo fue en aumento, mientras que el efecto beneficioso de la enmienda se limitó básicamente a las propiedades químicas y se desvaneció en pocos años. Destacamos que las condiciones meteorológicas a lo largo del ensayo beneficiaron la producción de biomasa en NL, y en consecuencia las propiedades relacionadas con la materia orgánica, por lo que son un factor a tener en cuenta a la hora de evaluar los efectos de la enmienda y el laboreo sobre las propiedades del suelo, especialmente en zonas donde esas condiciones son muy variables entre una campaña y otra. Los resultados de este estudio han puesto de manifiesto que el NL no ha mermado la eficacia de la enmienda caliza, posiblemente gracias a la alta solubilidad de la enmienda aplicada, es más, el manejo con NL y enmienda es el que ha favorecido en mayor medida ciertos parámetros de calidad del suelo. Por el contrario el LC sí parece anular los beneficios de la enmienda en relación con las propiedades relacionadas con la MO. Por tanto, cabe concluir que la combinación de NL y la enmienda es una práctica adecuada para mejorar las propiedades químicas y físicas de suelos ácidos degradados por el laboreo. ABSTRACT Excessive acidity in soils is associated with deficiencies in certain nutrients and high concentrations of available aluminum, which is toxic for most Mediterranean crops. Tilling these soils results in the loss of soil organic matter (SOM), damages soil structure and reduces biological activity, ultimately degrading soil quality. It is expected, therefore, that when acid soils are tilled, their particular problems will tend to get worse. In our study area, the "Cañamero’s Raña” (Extremadura, Spain), acid soils degraded by an inappropriate tillage prevail. Rañas are large and flat platforms with very old soils (Palexerults), which are characterized by an exchange complex dominated by aluminum and an acid pH which decreases with depth. These soils have a strong Bt horizon rich in kaolinite clays, which encourages the formation of perched water-tables near the soil surface during periods of excessive rain. During the first third of the 20th century, these soils, that previously supported cork oak or its scrub replacement, were cultivated. Tillage accelerated the mineralization of the SOM, aggravating the problems of excessive acidity, which finally led to the abandonment of the land due to low productivity. To recover the quality of these degraded soils and to obtain consistent yields it is necessary, first, to apply amendments to raise the pH and reduce aluminum toxicity, and second to encourage the accumulation of SOM. In 2005 a field trial was established in the Raña to study the influence of no-tillage and the use of a Ca-amendment on soil quality related parameters in a forage crop agrosystem. The experimental design was a split-plot with four replicates where the main factor was tillage type, no-tillage (NT) versus traditional tillage (TT) and the secondary factor was the use or not of a Ca-amendment. The Ca-amendment was a mixture of sugar foam and red gypsum that was incorporated into the top 7 cm of the soil. Since the beginning of the experiment, NT had a positive influence on total and particulate organic carbon (TOC and POC, respectively), while the Ca-amendment had a small positive influence at the beginning of the study but its effect diminished with time. The highest TOC and POC contents were observed when NT and the Ca-amendment were combined. The Ca-amendment, even under NT, rapidly increased pH and Ca, and decreased the aluminum content to a depth of 50 cm, as well as improving soil aggregation slightly. NT, due to the increased POC, TOC and Glomalin-related soil proteins (GRSP), which can form stable non-toxic compounds with aluminum, also contributed to the reduction of aluminum toxicity in the upper layer. When perched water-tables near the soil surface were formed in campaigns with excessive rainfall, NT provided more favorable conditions for germination and crop development, resulting in higher yields compared with TT. This was directly related to the higher water storage capacity and the greater transmissivity of the water downwards from the upper layers, which led to lower water saturation under NT compared with TT. With regards to the aggregation-related parameters, NT increased macroaggregation to a depth of 10 cm and favored the accumulation of OC and N in all aggregate size fractions. However, the degree of recovery of macroaggregation after tillage ceased was slow compared with other soils, possibly due to the low clay content in the Ap horizon. Compared with NT, the Ca-amendment had a slight positive effect on soil aggregation. In contrast to other studies in acid soils, our results indicate the existence of an aggregate hierarchy, and highlight the important role of SOM in improving aggregation. Both NT and the Ca-amendment separately favored various chemical, physical and biological soil properties, but in general we found the greatest benefits when the two treatments were combined. In addition, the positive effect of NT on soil properties increased with time, while the beneficial effect of the Ca-amendment, which was limited to the chemical properties, vanished after a few years. It is important to note that the meteorological conditions throughout the experiment benefited biomass production under NT and, as a consequence, organic matter related properties. This suggests that meteorological conditions are a factor to consider when evaluating the effects of Ca-amendments and tillage on soil properties, especially in areas where such conditions vary significantly from one campaign to another. The results of this study show that NT did not diminish the effectiveness of the Ca-amendment, possibly due to the high solubility of the selected amendment. Moreover, the combination of NT and the Ca-amendment was actually the management that favored certain soil quality parameters the most. By contrast, TT seemed to nullify the benefits of the Ca-amendment with regards to the OM related properties. In conclusion, the combination of NT and the application of a Ca-amendment is an advisable practice for improving the chemical and physical properties of acid soils degraded by tillage.

CLARP, a death effector domain-containing protein interacts with caspase-8 and regulates apoptosis

We have identified and characterized CLARP, a caspase-like apoptosis-regulatory protein. Sequence analysis revealed that human CLARP contains two amino-terminal death effector domains fused to a carboxyl-terminal caspase-like domain. The structure and amino acid sequence of CLARP resemble those of caspase-8, caspase-10, and DCP2, a Drosophila melanogaster protein identified in this study. Unlike caspase-8, caspase-10, and DCP2, however, two important residues predicted to be involved in catalysis were lost in the caspase-like domain of CLARP. Analysis with fluorogenic substrates for caspase activity confirmed that CLARP is catalytically inactive. CLARP was found to interact with caspase-8 but not with FADD/MORT-1, an upstream death effector domain-containing protein of the Fas and tumor necrosis factor receptor 1 signaling pathway. Expression of CLARP induced apoptosis, which was blocked by the viral caspase inhibitor p35, dominant negative mutant caspase-8, and the synthetic caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp-(OMe)-fluoromethylketone (zVAD-fmk). Moreover, CLARP augmented the killing ability of caspase-8 and FADD/MORT-1 in mammalian cells. The human clarp gene maps to 2q33. Thus, CLARP represents a regulator of the upstream caspase-8, which may play a role in apoptosis during tissue development and homeostasis.

Cloning of a gene (RIG-G) associated with retinoic acid-induced differentiation of acute promyelocytic leukemia cells and representing a new member of a family of interferon-stimulated genes

In a cell line (NB4) derived from a patient with acute promyelocytic leukemia, all-trans-retinoic acid (ATRA) and interferon (IFN) induce the expression of a novel gene we call RIG-G (for retinoic acid-induced gene G). This gene codes for a 58-kDa protein containing 490 amino acids with several potential sites for post-translational modification. In untreated NB4 cells, the expression of RIG-G is undetectable. ATRA treatment induces the transcriptional expression of RIG-G relatively late (12–24 hr) in a protein synthesis-dependent manner, whereas IFN-α induces its expression early (30 min to 3 hr). Database search has revealed a high-level homology between RIG-G and several IFN-stimulated genes in human (ISG54K, ISG56K, and IFN-inducible and retinoic acid-inducible 58K gene) and some other species, defining a well conserved gene family. The gene is composed of two exons and has been mapped by fluorescence in situ hybridization to chromosome 10q24, where two other human IFN-stimulated gene members are localized. A synergistic induction of RIG-G expression in NB4 cells by combined treatment with ATRA and IFNs suggests that a collaboration exists between their respective signaling pathways.

Oncogenic stimulation recruits cyclin-dependent kinase in the cell cycle start in rat fibroblast

The rat fibroblast NRK cells are transformed reversibly by a combination of growth factors. When stimulated with serum, NRK cells rely on cyclin-dependent kinase 4 (Cdk4) for their S phase entry. However, when stimulated with serum containing oncogenic growth factors, they come to rely on either Cdk4 or Cdk6, and their S phase entry cannot be blocked unless both Cdk4 and Cdk6 are immunodepleted. Such change of dependence does not occur in the NRK cell mutants defective in an oncogenic signal pathway and, therefore, deficient in anchorage-independent cell cycle start ability, correlating Cdk6 dependence with this remarkable, cancer-associated phenotype. However, both Cdk4 and Cdk6 are activated upon serum stimulation, and neither the amounts of Cdk6, Cdk4, cyclin D1, and cyclin-dependent kinase inhibitors nor the activities or subcellular localization of Cdk6 and Cdk4 are significantly influenced by oncogenic stimulation. Thus, oncogenic stimulation invokes Cdk6 to participate in a critical step of the cell cycle start in a rat fibroblast, but by a mechanism seemingly unrelated to the regulation of the kinase. Given that many hematopoietic cells employ predominantly Cdk6 for the cell cycle start and perform anchorage-independent growth by nature, our results raise the possibility that the oncogenic stimulation-induced anchorage-independent cell cycle start of NRK is elicited by a mechanism similar to the one used for hematopoietic cell proliferation.

The mycosubtilin synthetase of Bacillus subtilis ATCC6633: A multifunctional hybrid between a peptide synthetase, an amino transferase, and a fatty acid synthase

Bacillus subtilis strain ATCC6633 has been identified as a producer of mycosubtilin, a potent antifungal peptide antibiotic. Mycosubtilin, which belongs to the iturin family of lipopeptide antibiotics, is characterized by a β-amino fatty acid moiety linked to the circular heptapeptide Asn-Tyr-Asn-Gln-Pro-Ser-Asn, with the second, third, and sixth position present in the D-configuration. The gene cluster from B. subtilis ATCC6633 specifying the biosynthesis of mycosubtilin was identified. The putative operon spans 38 kb and consists of four ORFs, designated fenF, mycA, mycB, and mycC, with strong homologies to the family of peptide synthetases. Biochemical characterization showed that MycB specifically adenylates tyrosine, as expected for mycosubtilin synthetase, and insertional mutagenesis of the operon resulted in a mycosubtilin-negative phenotype. The mycosubtilin synthetase reveals features unique for peptide synthetases as well as for fatty acid synthases: (i) The mycosubtilin synthase subunit A (MycA) combines functional domains derived from peptide synthetases, amino transferases, and fatty acid synthases. MycA represents the first example of a natural hybrid between these enzyme families. (ii) The organization of the synthetase subunits deviates from that commonly found in peptide synthetases. On the basis of the described characteristics of the mycosubtilin synthetase, we present a model for the biosynthesis of iturin lipopeptide antibiotics. Comparison of the sequences flanking the mycosubtilin operon of B. subtilis ATCC6633, with the complete genome sequence of B. subtilis strain 168 indicates that the fengycin and mycosubtilin lipopeptide synthetase operons are exchanged between the two B. subtilis strains.

Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens

The endogenous plant hormones salicylic acid (SA) and jasmonic acid (JA), whose levels increase on pathogen infection, activate separate sets of genes encoding antimicrobial proteins in Arabidopsis thaliana. The pathogen-inducible genes PR-1, PR-2, and PR-5 require SA signaling for activation, whereas the plant defensin gene PDF1.2, along with a PR-3 and PR-4 gene, are induced by pathogens via an SA-independent and JA-dependent pathway. An Arabidopsis mutant, coi1, that is affected in the JA-response pathway shows enhanced susceptibility to infection by the fungal pathogens Alternaria brassicicola and Botrytis cinerea but not to Peronospora parasitica, and vice versa for two Arabidopsis genotypes (npr1 and NahG) with a defect in their SA response. Resistance to P. parasitica was boosted by external application of the SA-mimicking compound 2,6-dichloroisonicotinic acid [Delaney, T., et al. (1994) Science 266, 1247–1250] but not by methyl jasmonate (MeJA), whereas treatment with MeJA but not 2,6-dichloroisonicotinic acid elevated resistance to Alternaria brassicicola. The protective effect of MeJA against A. brassicicola was the result of an endogenous defense response activated in planta and not a direct effect of MeJA on the pathogen, as no protection to A. brassicicola was observed in the coi1 mutant treated with MeJA. These data point to the existence of at least two separate hormone-dependent defense pathways in Arabidopsis that contribute to resistance against distinct microbial pathogens.

A novel multifunctional O-methyltransferase implicated in a dual methylation pathway associated with lignin biosynthesis in loblolly pine

S-adenosyl-l-methionine (SAM)-dependent O-methyltransferases (OMTs) catalyze the methylation of hydroxycinnamic acid derivatives for the synthesis of methylated plant polyphenolics, including lignin. The distinction in the extent of methylation of lignins in angiosperms and gymnosperms, mediated by substrate-specific OMTs, represents one of the fundamental differences in lignin biosynthesis between these two classes of plants. In angiosperms, two types of structurally and functionally distinct lignin pathway OMTs, caffeic acid 3-O-methyltransferases (CAOMTs) and caffeoyl CoA 3-O-methyltransferases (CCoAOMTs), have been reported and extensively studied. However, little is known about lignin pathway OMTs in gymnosperms. We report here the first cloning of a loblolly pine (Pinus taeda) xylem cDNA encoding a multifunctional enzyme, SAM:hydroxycinnamic Acids/hydroxycinnamoyl CoA Esters OMT (AEOMT). The deduced protein sequence of AEOMT is partially similar to, but clearly distinguishable from, that of CAOMTs and does not exhibit any significant similarity with CCoAOMT protein sequences. However, functionally, yeast-expressed AEOMT enzyme catalyzed the methylation of CAOMT substrates, caffeic and 5-hydroxyferulic acids, as well as CCoAOMT substrates, caffeoyl CoA and 5-hydroxyferuloyl CoA esters, with similar specific activities and was completely inactive with substrates associated with flavonoid synthesis. The lignin-related substrates were also efficiently methylated in crude extracts of loblolly pine secondary xylem. Our results support the notion that, in the context of amino acid sequence and biochemical function, AEOMT represents a novel SAM-dependent OMT, with both CAOMT and CCoAOMT activities and thus the potential to mediate a dual methylation pathway in lignin biosynthesis in loblolly pine xylem.

Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins

The immunosuppressant rapamycin inhibits Tor1p and Tor2p (target of rapamycin proteins), ultimately resulting in cellular responses characteristic of nutrient deprivation through a mechanism involving translational arrest. We measured the immediate transcriptional response of yeast grown in rich media and treated with rapamycin to investigate the direct effects of Tor proteins on nutrient-sensitive signaling pathways. The results suggest that Tor proteins directly modulate the glucose activation and nitrogen discrimination pathways and the pathways that respond to the diauxic shift (including glycolysis and the citric acid cycle). Tor proteins do not directly modulate the general amino acid control, nitrogen starvation, or sporulation (in diploid cells) pathways. Poor nitrogen quality activates the nitrogen discrimination pathway, which is controlled by the complex of the transcriptional repressor Ure2p and activator Gln3p. Inhibiting Tor proteins with rapamycin increases the electrophoretic mobility of Ure2p. The work presented here illustrates the coordinated use of genome-based and biochemical approaches to delineate a cellular pathway modulated by the protein target of a small molecule.

The anaphase inhibitor of Saccharomyces cerevisiae Pds1p is a target of the DNA damage checkpoint pathway

Inhibition of DNA replication and physical DNA damage induce checkpoint responses that arrest cell cycle progression at two different stages. In Saccharomyces cerevisiae, the execution of both checkpoint responses requires the Mec1 and Rad53 proteins. This observation led to the suggestion that these checkpoint responses are mediated through a common signal transduction pathway. However, because the checkpoint-induced arrests occur at different cell cycle stages, the downstream effectors mediating these arrests are likely to be distinct. We have previously shown that the S. cerevisiae protein Pds1p is an anaphase inhibitor and is essential for cell cycle arrest in mitosis in the presence DNA damage. Herein we show that DNA damage, but not inhibition of DNA replication, induces the phosphorylation of Pds1p. Analyses of Pds1p phosphorylation in different checkpoint mutants reveal that in the presence of DNA damage, Pds1p is phosphorylated in a Mec1p- and Rad9p-dependent but Rad53p-independent manner. Our data place Pds1p and Rad53p on parallel branches of the DNA damage checkpoint pathway. We suggest that Pds1p is a downstream target of the DNA damage checkpoint pathway and that it is involved in implementing the DNA damage checkpoint arrest specifically in mitosis.

Regulation of G2/M Progression by the STE Mitogen-activated Protein Kinase Pathway in Budding Yeast Filamentous Growth

Inoculation of diploid budding yeast onto nitrogen-poor agar media stimulates a MAPK pathway to promote filamentous growth. Characteristics of filamentous cells include a specific pattern of gene expression, elongated cell shape, polar budding pattern, persistent attachment to the mother cell, and a distinct cell cycle characterized by cell size control at G2/M. Although a requirement for MAPK signaling in filamentous gene expression is well established, the role of this pathway in the regulation of morphogenesis and the cell cycle remains obscure. We find that ectopic activation of the MAPK signal pathway induces a cell cycle shift to G2/M coordinately with other changes characteristic of filamentous growth. These effects are abrogated by overexpression of the yeast mitotic cyclins Clb1 and Clb2. In turn, yeast deficient for Clb2 or carrying cdc28-1N, an allele of CDK defective for mitotic functions, display enhanced filamentous differentiation and supersensitivity to the MAPK signal. Importantly, activation of Swe1-mediated inhibitory phosphorylation of Thr-18 and/or Tyr-19 of Cdc28 is not required for the MAPK pathway to affect the G2/M delay. Mutants expressing a nonphosphorylatable mutant Cdc28 or deficient for Swe1 exhibit low-nitrogen-dependent filamentous growth and are further induced by an ectopic MAPK signal. We infer that the MAPK pathway promotes filamentous growth by a novel mechanism that inhibits mitotic cyclin/CDK complexes and thereby modulates cell shape, budding pattern, and cell-cell connections.