Novel Nonbiologic Therapies for Ulcerative Colitis

An extensive array of compounds has been studied for the treatment of ulcerative colitis (UC). The most frequently used nonbiologic drugs for the oral and intravenous treatment of ulcerative colitis include 5-aminosalicylate (5-ASA) drugs (mesalamine and derivatives), sulfasalazine, and other azo-bonded molecules of 5-ASA, steroids, calcineurin inhibitors (cyclosporine, tacrolimus, and sirolimus), thiopurines (azathioprine, 6-mercaptopurine), and methotrexate, which are already presented in other sections of this book and are thus not considered in this chapter. The therapies presented in this section should be considered as potential alternatives, mostly for mild-to-moderate ulcerative colitis (UC). They are substances mostly used without FDA indications, such as heparin, nicotine, rosiglitazone, and N-acetylcysteine as well as “natural” compounds suggested to have anti-inflammatory or reparative properties, such as aloe vera, curcumin, short-chain fatty acids, and Bowman-Birk inhibitor

Mechanism of silica -induced apoptosis in human alveolar macrophages

The mechanisms involved in the development of pulmonary silicosis have not been well defined, however most current evidence implicates a central role for alveolar macrophages in this process. We propose that the fibrotic potential of a particulate depends upon its ability to cause apoptosis in alveolar macrophage (AM). The overall goal of this study was to determine the mechanism of silica-induced apoptosis of AM. Human AM were treated with fibrogenic, poorly fibrogenic and nonfibrogenic model particulates, such as, silica, amorphous silica and titanium dioxide, respectively (equal surface area). Treatment with silica resulted in apoptosis in human AM as observed by morphology, DNA fragmentation and Cell Death ELISA assays. In contrast, amorphous silica and titanium dioxide demonstrated no significant apoptotic potential. To elucidate the possible mechanism by which silica causes apoptosis, we investigated the role of the scavenger receptor (SR) in silica-induced apoptosis. Cells were pretreated with and without SR ligand binding inhibitors, polyinosinic acid (Poly I), fucoidan and high density lipoprotein (HDL), prior to silica treatment. Pretreatment with Poly I and fucoidan resulted in significant inhibition of silica-induced apoptosis suggesting that silica-induced AM apoptosis is mediated via the SR. Further, we examined the involvement of interleukin converting enzyme (ICE) family of proteases in silica-mediated apoptosis. Silica activated ICE, Ich-1L, cpp32 beta and cleavage of PARP. Taken together, these results suggested that (1) fibrogenic particulates, such as, silica caused apoptosis of alveolar macrophages, (2) this apoptotic potential of fibrogenic particulates may be a critical factor in initiating an inflammatory response resulting in fibrosis, (3) silica-induced apoptosis of alveolar macrophages may be due to the interaction of silica particulates with the SR, and (4) silica-induced apoptosis involves the activation of the ICE family of proteases. An understanding of the molecular events involved in fibrogenic particulate-induced apoptosis may provide a useful insight into the mechanism involved in particulate-induced fibrosis. ^

Utilización del cultivo plurianual de pataca (Helianthus tuberosus L.) para la producción de hidratos de carbono fermentables a partir de los tallos

La pataca (Helianthus tuberosus L.) es una especie de cultivo con un alto potencial en la producción de hidratos de carbono de reserva en forma de polifructanos, especialmente inulina, que se acumulan temporalmente en los tallos en forma de polisacáridos para translocarse posteriormente a los tubérculos, donde son almacenados. Aunque tradicionalmente el producto de interés del cultivo son los tubérculos, que acumulan gran cantidad de hidratos de carbono fermentables (HCF) cuando se recogen al final del ciclo de desarrollo, en este trabajo se pretende evaluar el potencial de la pataca como productor de HCF a partir de los tallos cosechados en el momento de máximo contenido en HCF, mediante un sistema de cultivo plurianual. Se han realizado los siguientes estudios: i) Determinación del momento óptimo de cosecha en ensayos con 12 clones ii) Potencial del cultivo plurianual de la pataca en términos de producción anual de biomasa aérea y de HCF en cosechas sucesivas, iii) Ensayos de conservación de la biomasa aérea, iv) Estimación de los costes de las dos modalidades de cultivo de pataca para producción de HCF y v) Estimación de la sostenibilidad energética de la producción de bioetanol mediante la utilización de los subproductos. Para la determinación del momento óptimo de la cosecha de la biomasa aérea se ensayaron 12 clones de diferente precocidad en Madrid; 4 tempranos (Huertos de Moya, C-17, Columbia y D-19) y 8 tardíos (Boniches, China, K-8, Salmantina, Nahodka, C-13, INIA y Violeta de Rennes). El máximo contenido en HCF tuvo lugar en el estado fenológico de botón floral-flor que además coincidió con la máxima producción de biomasa aérea. De acuerdo con los resultados obtenidos, la cosecha de los clones tempranos se debería realizar en el mes de julio y en los clones tardíos en septiembre, siendo éstos últimos más productivos. La producción media más representativa entre los 12 clones, obtenida en el estado fenológico de botón floral fue de 23,40 t ms/ha (clon INIA), con un contenido medio en HCF de 30,30 % lo que supondría una producción potencial media de 7,06 t HCF/ha. La producción máxima en HCF se obtuvo en el clon Boniches con 7,61 t/ha y 22,81 t ms/ha de biomasa aérea. En el sistema de cultivo plurianual la cantidad de tallos por unidad de superficie aumenta cada año debido a la cantidad de tubérculos que van quedando en el terreno, sobre todo a partir del 3er año, lo que produce la disminución del peso unitario de los tallos, con el consiguiente riesgo de encamado. El aclareo de los tallos nacidos a principios de primavera mediante herbicidas tipo Glifosato o mediante una labor de rotocultor rebaja la densidad final de tallos y mejora los rendimientos del cultivo. En las experiencias de conservación de la biomasa aérea se obtuvo una buena conservación por un período de 6 meses de los HCF contenidos en los tallos secos empacados y almacenados bajo cubierta. Considerando que el rendimiento práctico de la fermentación alcohólica es de 0,5 l de etanol por cada kg de azúcar, la producción potencial de etanol para una cosecha de tallos de 7,06 t de HCF/ha sería de 3.530 l/ha. El bagazo producido en la extracción de los HCF de la biomasa aérea supondría 11,91 t/ha lo que utilizado para fines térmicos supone más de 3 veces la energía primaria requerida en el proceso de producción de etanol, considerando un poder calorífico inferior de 3.832,6 kcal/kg. Para una producción de HCF a partir de la biomasa aérea de 7,06 t/ha y en tubérculos al final del ciclo de 12,11 t/ha, los costes de producción estimados para cada uno de ellos fueron de 184,69 €/t para los HCF procedentes de la biomasa aérea y 311,30 €/t para los de tubérculos. Como resultado de este trabajo se puede concluir que la producción de HCF a partir de la biomasa aérea de pataca en cultivo plurianual, es viable desde un punto de vista técnico, con reducción de los costes de producción respecto al sistema tradicional de cosecha de tubérculos. Entre las ventajas técnicas de esta modalidad de cultivo, cabe destacar: la reducción de operaciones de cultivo, la facilidad y menor coste de la cosecha, y la posibilidad de conservación de los HCF en la biomasa cosechada sin mermas durante varios meses. Estas ventajas, compensan con creces el menor rendimiento por unidad de superficie que se obtiene con este sistema de cultivo frente al de cosecha de los tubérculos. Jerusalem artichoke (Helianthus tuberosus L.) (JA) is a crop with a high potential for the production of carbohydrates in the form of polyfructans, especially inulin, which are temporarily accumulated in the stems in the form of polysaccharides. Subsequently they are translocated to the tubers, where they are finally accumulated. In this work the potential of Jerusalem artichoke for fermentable carbohydrates from stems that are harvested at their peak of carbohydrates accumulation is assessed as compared to the traditional cultivation system that aims at the production of tubers harvested at the end of the growth cycle. Tubers are storage organs of polyfructans, namely fermentable carbohydrates. Studies addressed in this work were: i) Determination of the optimum period of time for stem harvesting as a function of clone precocity in a 12-clone field experiment; ii) Study of the potential of JA poly-annual crop regarding the annual yield of aerial biomass and fermentable carbohydrates (HCF) over the years; iii) Tests of storage of the aerial biomass, iv) Comparative analysis of the two JA cultivation systems for HCF production: the poly-annual system for aerial biomass harvesting versus the annual cultivation system for tubers and v) Estimation of the energy sustainability of the bioethanol production by using by-products of the production chain. In order to determine the best period of time for aerial biomass harvesting twelve JA clones of different precocity were tested in Madrid: four early clones (Huertos de Moya, C-17, Columbia and D-19) and eight late clones (Boniches, China, K-8 , Salmantina, Nahodka, C-13, INIA and Violeta de Rennes). Best time was between the phenological stages of floral buds (closed capitula) and blossom (opened capitula), period in which the peak of biomass production coincides with the peak of HCF accumulation in the stems. According to the results, the early clones should be harvested in July and the late ones in September, being the late clones more productive. The clone named INIA was the one that exhibited more steady yields in biomass over the 12 clones experimented. The average potential biomass production of this clone was 23.40 t dm/ha when harvested at the floral buds phenological stage; mean HCF content is 30.30%, representing 7.06 t HCF/ha yield. However, the highest HCF production was obtained for the clone Boniches, 7.61 t HCF/ha from a production of 22.81 t aerial biomass/ha. In the poly-annual cultivation system the number of stems per unit area increases over the years due to the increase in the number of tubers that are left under ground; this effect is particularly important after the 3rd year of the poly-annual crop and results in a decrease of the stems unit weight and a risk of lodging. Thinning of JA shoots in early spring, by means of an herbicide treatment based on glyphosate or by means of one pass with a rotary tiller, results in a decrease of the crop stem density and in higher crop yields. Tests of biomass storing showed that the method of keeping dried stems packed and stored under cover results in a good preservation of HCF for a period of six months at least. Assuming that the fermentation yield is 0.5 L ethanol per kg sugars and a HCF stem production of 7.06 t HCF/ha, the potential for bioethanol is estimated at 3530 L/ha. The use of bagasse -by-product of the process of HCF extraction from the JA stems- for thermal purposes would represent over 3 times the primary energy required for the industrial ethanol production process, assuming 11.91 t/ha bagasse and 3832.6 kcal/kg heating value. HCF production costs of 7.06 t HCF/ha yield from aerial biomass and HCF production costs of 12.11 t HCF/ha from tubers were estimated at 184.69 €/t HCF and 311.30 €/t HCF, respectively. It can be concluded that the production of HCF from JA stems, following a poly-annual cultivation system, can be feasible from a technical standpoint and lead to lower production costs as compared to the traditional annual cultivation system for the production of HCF from tubers. Among the technical advantages of the poly-annual cultivation system it is worth mentioning the reduction in crop operations, the ease and efficiency of harvesting operations and the possibility of HCF preservation without incurring in HCF losses during the storage period, which can last several months. These advantages might compensate the lower yield of HCF per unit area that is obtained in the poly-annual crop system, which aims at stems harvesting, versus the annual one, which involves tubers harvesting.

Cadena de valor de papas nativas (Solanum andigenum sp.) en la provincia de Jauja, Perú

La Asamblea General de la ONU, a solicitud del gobierno peruano, declara en el año 2008 el Año Internacional de la Papa, (AIP). Desde el año 2005, el gobierno peruano ha puesto en marcha estrategias en torno a la importancia de la papa, como la declaración del 30 de Mayo como el Día Nacional de la Papa. El año 2014 es declarado por la FAO, (Food and Agriculture Organization of the United Nations), Año Internacional de la Agricultura Familiar, con un enfoque compartido por esta Tesis Doctoral en el apoyo a la familia campesina peruana. El gobierno peruano utiliza las cadenas de valor como una estrategia de promoción de desarrollo sostenible, que ha permitido contribuir a la inclusión social y económica de productores pobres de zonas alto andinas, como las localizadas en la mancomunidad municipal del Yacus, (MMY), provincia de Jauja, departamento de Junín. Esta estrategia, en la que el mercado incorpora a los pequeños agricultores de las zonas altas de los Andes, (que disponen de recursos económicos muy bajos), en procesos productivos rentables, implica una serie de cambios a realizar, como la transformación de los patrones de producción tradicional hacia aquellos productos o servicios que tienen demanda en el mercado, o la variación de la mentalidad del agricultor pequeño hacia una concepción empresarial de su producción. (Fabián, 2013). Por otra parte, la sostenibilidad de las cadenas de valor depende del eslabón más débil, lo que obliga a conocer la situación de todos los eslabones para poder integrar y reforzar la cadena. Se requiere un sistema de transparencia adecuado que facilite el flujo de la información entre los distintos eslabones. (Briz et al., 2012). Además, el establecimiento de la cadena de valor debe hacerse con cuidado, ya que la eficacia y supervivencia de las empresas están cada vez más ligadas a la cadena de valor a la que pertenece y a la coordinación de la misma. (Briz, 2011). En esta situación, adquiere importancia el estudio de la cadena de valor de la papa nativa, para una vez establecidas sus características, poder determinar la viabilidad o no de una cadena de valor de este producto que repercuta parte de la riqueza generada en los pequeños agricultores alto andinos, e incluso, de su extensión hasta España. Existen estudios sobre las papas nativas, realizadas por diferentes universidades de distintos países, e incluso, de diferentes continentes. Sin embargo, la mayoría de los estudios se centran en la mejora de la producción de la papa nativa. La novedad de la investigación realizada en la presente Tesis Doctoral radica en el estudio de la viabilidad de la comercialización de la papa nativa, mediante el establecimiento de una cadena de valor que se inicie en la provincia de Jauja, Perú, y finalice tanto en los mercados peruanos de las regiones de Junín y Lima, como en España. El objetivo planteado en esta investigación es la mejora de las condiciones económicas y sociales de las comunidades agrícolas de la provincia de Jauja en el Perú, así como fomentar su desarrollo tecnológico e industrial, mediante el fomento de la cadena de valor de la papa nativa y sus derivados. Se establecen como objetivos específicos la caracterización de los eslabones de la cadena de valor de la papa nativa y sus derivados en la provincia de Jauja del Perú y en España, de manera que se determine el valor agregado en los mismos; el fortalecimiento de las organizaciones de productores de papas nativas para la comercialización de sus producciones y para el fomento de la cultura empresarial; y el desarrollo de una cadena de comercialización papas nativas y sus derivados con origen en la Provincia de Jauja, Perú, y que finalice en España, con la venta al consumidor español. Para alcanzar estos objetivos la metodología utilizada es la cadena de valor agroalimentaria, utilizando como herramientas de análisis el análisis DAFO de la cadena de valor de la papa nativa. Las fuentes de información primarias utilizadas proceden en parte del proyecto de cooperación de UPM, “Mejora de la cadena de valor de la patata andina como impulso al desarrollo rural. Caso de tres Comunidades Campesinas en la Provincia de Jauja del Perú”, en el que participó el doctorando, y en parte proceden de la batería de encuestas específicamente diseñadas para los diferentes eslabones de la cadena de valor de la papa nativa. Las fuentes de información secundarias proceden de artículos académicos publicados, de artículos publicados por revistas especializadas del sector y de informes realizados por diferentes instituciones gubernamentales, tanto españolas como peruanas. Las conclusiones de la investigación son las siguientes. La creación de la mancomunidad del Yacus ha beneficiado a los pequeños agricultores. Estos consiguen mejores condiciones de venta y mejores precios para sus productos, lo que repercute en la mejora de sus condiciones de vida. Estas mejoras en las condiciones de venta de los productos se deben a su pertenencia a una cadena de valor de papa nativa que está funcionando de forma eficaz. Las empresas consideradas para constituir la cadena de valor han mostrado interés por formar parte de ella: los campesinos para obtener mejores precios por sus productos y unas mejores condiciones de venta; los distribuidores para asegurarse una calidad determinada de unas variedades fijas de papa nativa; la industria transformadora por disponer de un suministro de producto adecuado al derivado de papa nativa correspondiente, (hojuelas, tunta, etc.); las empresas exportadoras para tener suministro garantizado de los productos que ellos requieren en los volúmenes adecuados. Es una situación ventajosa para todas las empresas participantes. A pesar de trabajar con un producto tradicional, la cadena de valor de la papa nativa presenta innovación en los productos comercializados, tanto en la papa nativa fresca como en sus derivados, en los formatos de los productos, en la red de distribución, en las instituciones peruanas y en el consumidor final. Se percibe una demanda de papa nativa y de sus productos derivados en aquellos países donde existen comunidades de latinoamericanos que han emigrado de sus países de origen. España está entre los países que han acogido a un importante número de personas de origen latinoamericano. A pesar de la fuerte crisis económica sufrida por España, que ha llevado consigo la vuelta a sus países de origen de parte de su comunidad latinoamericana, el tamaño de esta población sigue siendo importante. Esta población demanda productos originarios de sus propios países, y los consumirían de forma frecuente si los precios son adecuados a su capacidad de consumo. El precio de venta de la papa nativa y sus derivados en España es de gran importancia. La importación de estos productos desde Perú hace que este eleve a niveles que le resta competitividad, en especial en la papa fresca. Se aconseja la búsqueda de empresas que puedan adaptar la producción de la papa fresca de forma local, y mantener para los derivados la exportación directa a España. Las preferencias de los consumidores peruanos y españoles en cuanto a formatos y marcas se refieren no son coincidentes. De las encuestas realizadas, se concluye que no puede seguirse la misma estrategia de marketing en ambos países, debiéndose diferenciar los formatos de los paquetes de la papa nativa y de sus derivados en España y en Perú, para así lograr llegar a los consumidores potenciales de ambos países. ABSTRACT At the request of the Peruvian government, the UN General Assembly declared the International Year of the Potato in 2008. Since 2005, the Peruvian government has implemented strategies around the importance of the potato, as the declaration of the 30th of May as the National Day of the Potato. FAO (Food and Agriculture Organization of the United Nations) has declared 2014 as the International Year of Family Farming, with an approach shared by this Ph.D. dissertation about the Peruvian peasant family. The Peruvian government uses value chains as a strategy to promote sustainable development, which has allowed to contribute to the social and economic inclusion of poor farmers in the high Andean regions as those located in the municipal commonwealth of Yacus (MMY) province of Jauja, department of Junín. This strategy, which incorporates small farmers in the high Andean regions, (who have very low income), to the market with profitable production processes, implies a number of changes that should take place, such as changing patterns of traditional production to those products or services that are in demand in the market, or changes in the mentality of the small farmer into a concept of production business. (Fabián, 2013). Moreover, the sustainability of value chains depends on the weakest link, which demands a knowledge of the status of all the links, in order to integrate and strengthen the chain. It is required an adequate transparency to facilitate the flow of information between the various actors. (Briz et al., 2012). Furthermore, the establishment of the value chain should be done carefully, since the effectiveness and the survival of the businesses are increasingly linked to the value chain where the firm is included and to its coordination. (Briz, 2011). In this situation, it becomes important to study the value chain of the native potato, once we establish its features, to be able to determine the feasibility or not of a value chain of this product, which has an impact of the generated wealth in small farms of the high Andean regions, and even the extension of this value chain to Spain. There are studies on native potatoes, made by different universities in several countries and even in more than one continent. However, most studies focus on improving the production of native potato. The originality of the research conducted in this Ph.D. dissertation is the study of the feasibility of commercialization of native potato, by the creation of a value chain that starts in the province of Jauja, Perú, and ends both in Peruvian markets in the region of Lima, and in Spain. The main goal of this research is to improve the economic and social conditions of farming communities in the province of Jauja in Perú, while promoting its technological and industrial development, by the establishment of a value chain of the native potato and derivatives. The specific objectives of the research are the characterization of the links in the value chain of the native potato and its derivatives in the province of Jauja, (Perú) and in Spain, in order to determine the added value; the strengthening of organizations of native potato producers, to commercialize their products and the promotion of enterprise culture; and the development of a chain to market native potato and its derivatives, with its origin in the province of Jauja, (Perú), and its end in Spain, with the sale to the Spanish consumer. In order to achieve these objectives, the used methodology is the agrifood value chain, using as a tool to analysis it the SWOT analysis of the value chain of the native potato. The primary sources of information used in the research come partly from UPM cooperation project, "Improving the value chain of Andean potato as a boost to rural development. Case Three Rural Communities in the Province of Jauja, (Perú)", in which the Ph.D. student was involved, and partly from the surveys, which were specifically designed for the different links of the value chain of the native potato. The secondary sources of information come from academic articles, from articles published by magazines of the industry, and from reports of several government institutions, both Spanish and Peruvian. The conclusions of the research are as follows. The creation of the commonwealth of Yacus has benefited small farmers. They get better sales conditions and better prices for their products, which results in the improvement of their living conditions. These improvements are due to a value chain of native potato which is working effectively. All the firms invited to constitute the value chain have shown interest in being part of it: the farmers to get better prices for their products and better sale conditions; the distributors to ensure a certain quality of fixed varieties of native potato, the processing industry in order to have an adequate supply of product to the corresponding derivative of native potato (chips, “tunta”, etc.); exporting firms to have a guaranteed supply of the products that they require with the right volumes. It's a win-win situation for all participating companies. Despite being a traditional product, the value chain of the native potato presents innovation in marketed products, (both fresh native potato and its derivatives), in the formats of products, in the distribution network, in Peruvian institutions and in relation with the consumer. There is a perceived demand of native potato and its products in countries where communities of Latin Americans have settled down. Spain is among the countries that have received a significant number of people from Latin America. Despite the strong economic crisis suffered by Spain, which has lead to a return to their home countries of part of the Latin American community, the size of this population is still considerable. This population demands products from their own countries, and they frequently consume them if the prices are suitable to their standard of living. The selling price of the native potato and its derivatives in Spain is of great importance. The import of these products from Perú makes the prices rise to levels that reduce competitiveness, especially in fresh native potatoes. It is advised to look for companies which can adapt the fresh potato production in our country, and keep direct export to Spain for the derivatives products. The preferences of Peruvian and Spanish consumers in terms of formats and brands are not the same. The surveys concluded that the same marketing strategy cannot be followed in both countries. Packet formats of native potato and its derivatives should be differentiated in Spain and Perú, in order to reach the potential consumers of both countries.

Contaminantes orgánicos (PAHs) derivados de la escombrera de la Central Térmica de Aliaga (Teruel)

The aim of this study was to determine if the soils, waters and plants from the Aliaga dump contained polycyclic aromatic hydrocarbons (PAHs) and their quantification.The results showed that PAHs concentrations in soils are in general higher than the reference levels from the Spanish legislation. Waters and plants contained PAHs but in low concentrations. The possible actions for remediation (photodegradation and bioremediation) seem to be unviable here because of the large volume of materials involved, although its use as an additive for the cement industry and derivatives can be considered. It is proposed that fluorantene in waters, and phenanthrene and benzo[ghi]perilene in soils be considered as pollutants as well as to study the incorporation of PAHs to plants. Key-words: Polycyclic aromatic hydrocarbons, soil, plant and water contamination, fly- ash, power plant. RESUMEN: El objetivo de este estudio fue determinar y cuantificar los hidrocarburos policíclicos aromáticos (PAHs) en los suelos, plantas y aguas de la Escombrera de Aliaga. La concentración de PAHs en las cenizas supera, en general, los valores establecidos en la legislación española.Las aguas y plantas contienen PAHs, aunque en concentraciones bajas. La remoción de los materiales para someterlos a fotodegradación y biorremediación es inviable debido al gran volumen de la escombrera, aunque se plantea su uso como aditivo en la fabricación de productos derivados del cemento. Se propone incluir el fenantreno y benzo[ghi]perileno en la normativa de suelos, así como el naftaleno en la de aguas y la elaboración de una legislación sobre la incorporación de estos compuestos a las plantas.

Coilin Can Form a Complex with the U7 Small Nuclear Ribonucleoprotein

Coiled bodies (CBs) in the amphibian oocyte nucleus are spherical structures up to 10 μm or more in diameter, much larger than their somatic counterparts, which rarely exceed 1 μm. Oocyte CBs may have smaller granules attached to their surface or embedded within them, which are identical in structure and composition to the many hundreds of B-snurposomes found free in the nucleoplasm. The matrix of the CBs contains the diagnostic protein p80-coilin, which is colocalized with the U7 small nuclear ribonucleoprotein (snRNP), whereas the attached and embedded B-snurposomes contain splicing snRNPs. A few of the 50–100 CBs in the oocyte nucleus are attached to lampbrush chromosomes at the histone gene loci. By coimmunoprecipitation we show that coilin and the U7 snRNP can form a weak but specific complex in the nucleoplasm, which is dependent on the special U7 Sm-binding site. Under the same conditions coilin does not associate with the U1 and U2 snRNPs. Coilin is a nucleic acid-binding protein, as shown by its interaction with single-stranded DNA and with poly r(U) and poly r(G). We suggest that an important function of coilin is to form a transient complex with the U7 snRNP and accompany it to the CBs. In the case of CBs attached to chromosomes at the histone gene loci, the U7 snRNP is thus brought close to the actual site of histone pre-mRNA transcription.

tRNA Nuclear Export in Saccharomyces cerevisiae: In Situ Hybridization Analysis

To understand the factors specifically affecting tRNA nuclear export, we adapted in situ hybridization procedures to locate endogenous levels of individual tRNA families in wild-type and mutant yeast cells. Our studies of tRNAs encoded by genes lacking introns show that nucleoporin Nup116p affects both poly(A) RNA and tRNA export, whereas Nup159p affects only poly(A) RNA export. Los1p is similar to exportin-t, which facilitates vertebrate tRNA export. A los1 deletion mutation affects tRNA but not poly(A) RNA export. The data support the notion that Los1p and exportin-t are functional homologues. Because LOS1 is nonessential, tRNA export in vertebrate and yeast cells likely involves factors in addition to exportin-t. Mutation of RNA1, which encodes RanGAP, causes nuclear accumulation of tRNAs and poly(A) RNA. Many yeast mutants, including those with the rna1-1 mutation, affect both pre-tRNA splicing and RNA export. Our studies of the location of intron-containing pre-tRNAs in the rna1-1 mutant rule out the possibility that this results from tRNA export occurring before splicing. Our results also argue against inappropriate subnuclear compartmentalization causing defects in pre-tRNA splicing. Rather, the data support “feedback” of nucleus/cytosol exchange to the pre-tRNA splicing machinery.

Analysis of microsatellite mutations in the mitochondrial DNA of Saccharomyces cerevisiae

In the nuclear genome of Saccharomyces cerevisiae, simple, repetitive DNA sequences (microsatellites) mutate at rates much higher than nonrepetitive sequences. Most of these mutations are deletions or additions of repeat units. The yeast mitochondrial genome also contains many microsatellites. To examine the stability of these sequences, we constructed a reporter gene (arg8m) containing out-of-frame insertions of either poly(AT) or poly(GT) tracts within the coding sequence. Yeast strains with this reporter gene inserted within the mitochondrial genome were constructed. Using these strains, we showed that poly(GT) tracts were considerably less stable than poly(AT) tracts and that alterations usually involved deletions rather than additions of repeat units. In contrast, in the nuclear genome, poly(GT) and poly(AT) tracts had similar stabilities, and alterations usually involved additions rather than deletions. Poly(GT) tracts were more stable in the mitochondria of diploid cells than in haploids. In addition, an msh1 mutation destabilized poly(GT) tracts in the mitochondrial genome.

In vivo analysis of the 3′ untranslated region of the hepatitis C virus after in vitro mutagenesis of an infectious cDNA clone

Large sections of the 3′ untranslated region (UTR) of hepatitis C virus (HCV) were deleted from an infectious cDNA clone, and the RNA transcripts from seven deletion mutants were tested sequentially for infectivity in a chimpanzee. Mutants lacking all or part of the 3′ terminal conserved region or the poly(U–UC) region were unable to infect the chimpanzee, indicating that both regions are critical for infectivity in vivo. However, the third region, the variable region, was able to tolerate a deletion that destroyed the two putative stem–loop structures within this region. Mutant VR-24 containing a deletion of the proximal 24 nt of the variable region of the 3′ UTR was viable in the chimpanzee and seemed to replicate as well as the undeleted parent virus. The chimpanzee became viremic 1 week after inoculation with mutant VR-24, and the HCV genome titer increased over time during the early acute infection. Therefore, the poly(U–UC) region and the conserved region, but not the variable region, of the 3′ UTR seem to be critical for in vivo infectivity of HCV.

Evidence for regulation of protein synthesis at the elongation step by CDK1/cyclin B phosphorylation

Eukaryotic elongation factor 1 (eEF-1) contains the guanine nucleotide exchange factor eEF-1B that loads the G protein eEF-1A with GTP after each cycle of elongation during protein synthesis. Two features of eEF-1B have not yet been elucidated: (i) the presence of the unique valyl-tRNA synthetase; (ii) the significance of target sites for the cell cycle protein kinase CDK1/cyclin B. The roles of these two features were addressed by elongation measurements in vitro using cell-free extracts. A poly(GUA) template RNA was generated to support both poly(valine) and poly(serine) synthesis and poly(phenylalanine) synthesis was driven by a poly(uridylic acid) template. Elongation rates were in the order phenylalanine > valine > serine. Addition of CDK1/cyclin B decreased the elongation rate for valine whereas the rate for serine and phenylalanine elongation was increased. This effect was correlated with phosphorylation of the eEF-1δ and eEF-1γ subunits of eEF-1B. Our results demonstrate specific regulation of elongation by CDK1/cyclin B phosphorylation.

A maize cytokinin gene encoding an O-glucosyltransferase specific to cis-zeatin

Zeatin is a naturally occurring cytokinin. Biosynthesis and metabolism studies of zeatin have been directed mostly at the trans isomer, although cis-zeatin and its riboside occur as major components in some plant species. It is not known whether parallel regulatory pathways exist for the two isomers. Based on the sequence of the gene ZOG1 encoding a trans-zeatin O-glucosyltransferase from Phaseolus (EC 2.4.1.203), a cis-zeatin-specific O-glucosyltransferase was isolated from maize. This gene, cisZOG1, contains an ORF of 1,401 nucleotides encoding a protein of 51.1 kDa with 41% identity to the Phaseolus ZOG1 protein. Unexpectedly, the maize enzyme recognizes as substrates cis-zeatin and UDP-glucose but not cis-ribosylzeatin, trans-zeatin, or trans-ribosylzeatin. This finding indicates the existence of cis-specific regulatory elements in plants and suggests that cis-zeatin and derivatives may be more important in cytokinin homeostasis than currently recognized.

The effects of sequence context on DNA curvature.

Recent experiments have exposed significant discrepancies between experimental data and predictive models for DNA structure. These results strongly suggest that DNA structural parameters incorporated in the models are not always sufficient to account for the influence of sequence context and of specific ion effects. In an attempt to evaluate these two effects, we have investigated repetitive DNA sequences with the sequence motif GAGAG.CTCTC located in different helical phasing arrangements with respect to poly(A) tracts and GGGCCC.GGGCCC sequence motifs. Methods used are ligase-mediated cyclization and gel mobility experiments along with DNase I cutting and chemical probe studies. The results provide new evidence for curvature in poly(A) tracts. They also show that the sequence context in which bending and flexible sequence elements are found is an important aspect of sequence-dependent DNA conformation. Although dinucleotide models generally have good predictive power, this work demonstrates that in some instances sequence elements larger than the dinucleotide must be taken into account, and hence it provides a starting point for the appropriate modification and refinement of existing structural models for DNA.

The octadecanoic pathway: signal molecules for the regulation of secondary pathways.

Plant defense against microbial pathogens and herbivores relies heavily on the induction of defense proteins and low molecular weight antibiotics. The signals between perception of the aggression, gene activation, and the subsequent biosynthesis of secondary compounds are assumed to be pentacylic oxylipin derivatives. The rapid, but transient, synthesis of cis-jasmonic acid was demonstrated after insect attack on a food plant and by microbial elicitor addition to plant suspension cultures. This effect is highly specific and not caused by a number of environmental stresses such as light, heavy metals, or cold or heat shock. Elicitation of Eschscholtzia cell cultures also led to a rapid alkalinization of the growth medium prior to jasmonate formation. Inhibition of this alkalinization process by the protein kinase inhibitor staurosporine also inhibited jasmonate formation. The induction of specific enzymes in the benzo[c]phenanthridine alkaloid pathway leading to the antimicrobial sanguinarine was induced to a qualitatively and quantitatively similar extent by fungal elicitor, methyl jasmonate, and its linolenic acid-derived precursor 12-oxophytodienoic acid. It is herein proposed that a second oxylipid cascade may exist in plants starting from linoleic acid via 15,16-dihydro-12-oxophytodienoic acid to 9,10-dihydrojasmonate. Experiments with synthetic trihomojasmonate demonstrated that beta-oxidation is not a prerequisite for biological activity and that 12-oxophytodienoic acid and derivatives are most likely fully active as signal transducers. Octadecanoic acid-derived compounds are essential elements in modulating the synthesis of antibiotic compounds and are thus integral to plant defense.

Oxide Semiconductors For Organic Opto-electronic Devices

Development of transparent oxide semiconductors (TOS) from Earth-abundant materials is of great interest for cost-effective thin film device applications, such as solar cells, light emitting diodes (LEDs), touch-sensitive displays, electronic paper, and transparent thin film transistors. The need of inexpensive or high performance electrode might be even greater for organic photovoltaic (OPV), with the goal to harvest renewable energy with inexpensive, lightweight, and cost competitive materials. The natural abundance of zinc and the wide bandgap ($sim$3.3 eV) of its oxide make it an ideal candidate. In this dissertation, I have introduced various concepts on the modulations of various surface, interface and bulk opto-electronic properties of ZnO based semiconductor for charge transport, charge selectivity and optimal device performance. I have categorized transparent semiconductors into two sub groups depending upon their role in a device. Electrodes, usually 200 to 500 nm thick, optimized for good transparency and transporting the charges to the external circuit. Here, the electrical conductivity in parallel direction to thin film, i.e bulk conductivity is important. And contacts, usually 5 to 50 nm thick, are optimized in case of solar cells for providing charge selectivity and asymmetry to manipulate the built in field inside the device for charge separation and collection. Whereas in Organic LEDs (OLEDs), contacts provide optimum energy level alignment at organic oxide interface for improved charge injections. For an optimal solar cell performance, transparent electrodes are designed with maximum transparency in the region of interest to maximize the light to pass through to the absorber layer for photo-generation, plus they are designed for minimum sheet resistance for efficient charge collection and transport. As such there is need for material with high conductivity and transparency. Doping ZnO with some common elements such as B, Al, Ga, In, Ge, Si, and F result in n-type doping with increase in carriers resulting in high conductivity electrode, with better or comparable opto-electronic properties compared to current industry-standard indium tin oxide (ITO). Furthermore, improvement in mobility due to improvement on crystallographic structure also provide alternative path for high conductivity ZnO TCOs. Implementing these two aspects, various studies were done on gallium doped zinc oxide (GZO) transparent electrode, a very promising indium free electrode. The dynamics of the superimposed RF and DC power sputtering was utilized to improve the microstructure during the thin films growth, resulting in GZO electrode with conductivity greater than 4000 S/cm and transparency greater than 90 %. Similarly, various studies on research and development of Indium Zinc Tin Oxide and Indium Zinc Oxide thin films which can be applied to flexible substrates for next generation solar cells application is presented. In these new TCO systems, understanding the role of crystallographic structure ranging from poly-crystalline to amorphous phase and the influence on the charge transport and optical transparency as well as important surface passivation and surface charge transport properties. Implementation of these electrode based on ZnO on opto-electronics devices such as OLED and OPV is complicated due to chemical interaction over time with the organic layer or with ambient. The problem of inefficient charge collection/injection due to poor understanding of interface and/or bulk property of oxide electrode exists at several oxide-organic interfaces. The surface conductivity, the work function, the formation of dipoles and the band-bending at the interfacial sites can positively or negatively impact the device performance. Detailed characterization of the surface composition both before and after various chemicals treatment of various oxide electrode can therefore provide insight into optimization of device performance. Some of the work related to controlling the interfacial chemistry associated with charge transport of transparent electrodes are discussed. Thus, the role of various pre-treatment on poly-crystalline GZO electrode and amorphous indium zinc oxide (IZO) electrode is compared and contrasted. From the study, we have found that removal of defects and self passivating defects caused by accumulation of hydroxides in the surface of both poly-crystalline GZO and amorphous IZO, are critical for improving the surface conductivity and charge transport. Further insight on how these insulating and self-passivating defects cause charge accumulation and recombination in an device is discussed. With recent rapid development of bulk-heterojunction organic photovoltaics active materials, devices employing ZnO and ZnO based electrode provide air stable and cost-competitive alternatives to traditional inorganic photovoltaics. The organic light emitting diodes (OLEDs) have already been commercialized, thus to follow in the footsteps of this technology, OPV devices need further improvement in power conversion efficiency and stable materials resulting in long device lifetimes. Use of low work function metals such as Ca/Al in standard geometry do provide good electrode for electron collection, but serious problems using low work-function metal electrodes originates from the formation of non-conductive metal oxide due to oxidation resulting in rapid device failure. Hence, using low work-function, air stable, conductive metal oxides such as ZnO as electrons collecting electrode and high work-function, air stable metals such as silver for harvesting holes, has been on the rise. Devices with degenerately doped ZnO functioning as transparent conductive electrode, or as charge selective layer in a polymer/fullerene based heterojunction, present useful device structures for investigating the functional mechanisms within OPV devices and a possible pathway towards improved air-stable high efficiency devices. Furthermore, analysis of the physical properties of the ZnO layers with varying thickness, crystallographic structure, surface chemistry and grain size deposited via various techniques such as atomic layer deposition, sputtering and solution-processed ZnO with their respective OPV device performance is discussed. We find similarity and differences in electrode property for good charge injection in OLEDs and good charge collection in OPV devices very insightful in understanding physics behind device failures and successes. In general, self-passivating surface of amorphous TCOs IZO, ZTO and IZTO forms insulating layer that hinders the charge collection. Similarly, we find modulation of the carrier concentration and the mobility in electron transport layer, namely zinc oxide thin films, very important for optimizing device performance.

Formação de ligação carbono-carbono através de compostos orgânicos de telúrio

Diversas classes de compostos orgânicos de telúrio foram exploradas neste trabalho. Inicialmente foi estudada a transmetalação entre teluretos alílicos e dibutil cianocupratos de lítio de ordem superior, levando aos respectivos cianocupratos alílicos de lítio. Estes, por sua vez, foram acoplados com triflatos vinílicos, importantes intermediários sintéticos preparados previamente a partir de teluretos vinílicos, levando a sistemas altamente insaturados em ótimos rendimentos (Esquema 1). (Ver no arquivo em PDF) Em seguida, foi explorada a reatividade de teluretos aromáticos frente a reagentes organometálicos. Cianocupratos arílicos, gerados a partir da transmetalação entre teluretos aromáticos com cianocupratos de lítio de ordem superior, foram adicionados a cetonas α,β -insaturadas, levando aos produtos de adição 1,4 em bons rendimentos (Esquema 2). (Ver no arquivo em PDF) Teluretos vinílicos funcionalizados de configuração Z também foram alvo de estudo visando a formação de ligação carbono-carbono. Reações de substituição entre estes teluretos e cianocupratos de lítio de ordem inferior levaram a cetonas e ésteres α,β- insaturados com estereoquímica defInida em ótimos rendimentos (Esquema 3). (Ver no arquivo em PDF) De agosto/20OJ a março/2004, a aluna realizou um estágio sanduíche na University of California, Santa Barbara, sob a orientação do Prof. Bruce H. Lipshutz, onde realizou estudos sobre a ciclização de Bergman, visando a síntese do fragmentobiarílico A-B da vancornicina. Diversas condições para a ciclização foram estudadas com um composto modelo (Esquema 4) (Ver no arquivo em PDF) e parte da síntese total do fragmento da vancomlcma, onde a ciclização seria a etapa-chave, foi realizada com sucesso (Esquema 5). (Ver no arquivo em PDF)