Molecular cloning and characterization of an amidase from Arabidopsis thaliana capable of converting indole-3-acetamide into the plant growth hormone, indole-3-acetic acid

Acylamidohydrolases from higher plants have not been characterized or cloned so far. AtAMI1 is the first member of this enzyme family from a higher plant and was identified in the genome of Arabidopsis thaliana based on sequence homology with the catalytic-domain sequence of bacterial acylamidohydrolases, particularly those that exhibit indole-3-acetamide amidohydrolase activity. AtAMI1 polypeptide and mRNA are present in leaf tissues, as shown by immunoblotting and RT-PCR, respectively. AtAMI1 was expressed from its cDNA in enzymatically active form and exhibits substrate specificity for indole-3-acetamide, but also some activity against l-asparagine. The recombinant enzyme was characterized further. The results show that higher plants have acylamidohydrolases with properties similar to the enzymes of certain plant-associated bacteria such as Agrobacterium-, Pseudomonas- and Rhodococcus-species, in which these enzymes serve to synthesize the plant growth hormone, indole-3-acetic acid, utilized by the bacteria to colonize their host plants. As indole-3-acetamide is a native metabolite in Arabidopsis thaliana, it can no longer be ruled out that one pathway for the biosynthesis of indole-3-acetic acid involves indole-3-acetamide-hydrolysis by AtAMI1.

Low-thickness high-quality aluminum nitride films for super high frequency solidly mounted resonators

We investigate the sputter growth of very thin aluminum nitride (AlN) films on iridium electrodes for electroacoustic devices operating in the super high frequency range. Superior crystal quality and low stress films with thicknesses as low as 160 nm are achieved after a radio frequency plasma treatment of the iridium electrode followed by a two-step alternating current reactive magnetron sputtering of an aluminum target, which promotes better conditions for the nucleation of well textured AlN films in the very first stages of growth. Solidly mounted resonators tuned around 8 GHz with effective electromechanical coupling factors of 5.8% and quality factors Q up to 900 are achieved.

Ultra high frequency thin film saw devices

Durante los ��ltimos a��os el flujo de datos en la transmisi��n que tiene lugar en los sistemas de comunicaci��n ha aumentado considerablemente de forma que d��a a d��a se requieren m��s aplicaciones trabajando en un rango de frecuencias muy alto (3-30 GHz). Muchos de estos sistemas de comunicaci��n incluyen dispositivos de onda ac��stica superficial (SAW) y por tanto se hace necesario el aumento de frecuencia a la que ��stos trabajan. Pero este incremento de frecuencia de los dispositivos SAW no s��lo es utilizado en los sistemas de comunicaci��n, varios tipos de sensores, por ejemplo, aumentan su sensibilidad cuando la frecuencia a la que trabajan tambi��n lo hace. Tradicionalmente los dispositivos SAW se han fabricado sobre cuarzo, LiNbO3 y LiTaO3 principalmente. Sin embargo la principal limitaci��n de estos materiales es su velocidad SAW. Adem��s, debido a la alta temperatura a la que se depositan no pueden ser integrados en la tecnolog��a de fabricaci��n CMOS. El uso de la tecnolog��a de capa delgada, en la que un material piezoel��ctrico es depositado sobre un substrato, se est�� utilizando en las ��ltimas d��cadas para incrementar la velocidad SAW de la estructura y poder obtener dispositivos trabajando en el rango de frecuencias requerido en la actualidad. Por otra parte, esta tecnolog��a podr��a ser integrada en el proceso de fabricaci��n CMOS. Durante esta tesis nos hemos centrado en la fabricaci��n de dispositivos SAW trabajando a muy alta frecuencia. Para ello, utilizando la tecnolog��a de capa delgada, hemos utilizado la estructura nitruro de aluminio (AlN) sobre diamante que permite conseguir velocidades SAW del sustrato que no se pueden alcanzar con otros materiales. El dep��sito de AlN se realiz�� mediante sputtering reactivo. Durante esta tesis se han realizado diferentes experimentos para optimizar dicho dep��sito de forma que se han obtenido los par��metros ��ptimos para los cuales se pueden obtener capas de AlN de alta calidad sobre cualquier tipo de sustrato. Adem��s todo el proceso se realiz�� a baja temperatura para que el procesado de estos dispositivos pueda ser compatible con la tecnolog��a CMOS. Una vez optimizada la estructura AlN/diamante, mediante litograf��a por haz de electrones se fabricaron resonadores SAW de tama��o nanom��trico que sumado a la alta velocidad resultante de la combinaci��n AlN/diamante nos ha permitido obtener dispositivos trabajando en el rango de 10-28 GHz con un alto factor de calidad y rechazo fuera de la banda. Est��s frecuencias y prestaciones no han sido alcanzadas por el momento en resonadores de este tipo. Por otra parte, se han utilizado estos dispositivos para fabricar sensores de presi��n de alta sensibilidad. Estos dispositivos son afectados altamente por los cambios de temperatura. Se realiz�� tambi��n un exhaustivo estudio de c��mo se comportan en temperatura estos resonadores, entre -250��C y 250��C (rango de temperaturas no estudiado hasta el momento) diferenci��ndose dos regiones una a muy baja temperatura en la que el dispositivo muestra un coeficiente de retraso en frecuencia (TCF) relativamente bajo y otra a partir de los -100��C en la que el TCF es similar al observado en la bibliograf��a. Por tanto, durante esta tesis se ha optimizado el dep��sito de AlN sobre diamante para que sea compatible con la tecnolog��a CMOS y permita el procesado de dispositivos trabajando a muy alta frecuencia con altas prestaciones para comunicaciones y sensores. ABSTRACT The increasing volume of information in data transmission systems results in a growing demand of applications working in the super-high-frequency band (3���30 GHz). Most of these systems work with surface acoustic wave (SAW) devices and thus there is a necessity of increasing their resonance frequency. Moreover, sensor application includes this kind of devices. The sensitivity of them is proportional with its frequency. Traditionally, quartz, LiNbO3 and LiTaO3 have been used in the fabrication of SAW devices. These materials suffer from a variety of limitations and in particular they have low SAW velocity as well as being incompatible with the CMOS technology. In order to overcome these problems, thin film technology, where a piezoelectric material is deposited on top of a substrate, has been used during the last decades. The piezoelectric/substrate structure allows to reach the frequencies required nowadays and could be compatible with the mass electronic production CMOS technology. This thesis work focuses on the fabrication of SAW devices working in the super-high-frequency range. Thin film technology has been used in order to get it, especially aluminum nitride (AlN) deposited by reactive sputtering on diamond has been used to increase the SAW velocity. Different experiments were carried out to optimize the parameters for the deposit of high quality AlN on any kind of substrates. In addition, the system was optimized under low temperature and thus this process is CMOS compatible. Once the AlN/diamond was optimized, thanks to the used e-beam lithography, nanometric SAW resonators were fabricated. The combination of the structure and the size of the devices allow the fabrication of devices working in the range of 10-28 GHz with a high quality factor and out of band rejection. These high performances and frequencies have not been reached so far for this kind of devices. Moreover, these devices have been used as high sensitivity pressure sensors. They are affected by temperature changes and thus a wide temperature range (-250��C to 250��C) study was done. From this study two regions were observed. At very low temperature, the temperature coefficient of frequency (TCF) is low. From -100��C upwards the TCF is similar to the one appearing in the literature. Therefore, during this thesis work, the sputtering of AlN on diamond substrates was optimized for the CMOS compatible fabrication of high frequency and high performance SAW devices for communication and sensor application.

Insect growth regulators as potential insecticides to control olive fruit fly (Bactrocera oleae Rossi): insect toxicity bioassays and molecular docking approach

Olive fruit fly, Bactrocera oleae (Rossi), is a key pest in olive orchards, causing serious economic damage. To date, the pest has already developed resistance to the insecticides commonly applied to control it. Thus, in searching for new products for an accurate resistance management programme, targeting the ecdysone receptor (EcR)might provide alternative compounds for use in such programmes. RESULTS: Residual contact and oral exposure in the laboratory of B. oleae adults to the dibenzoylhydrazine-based compounds methoxyfenozide, tebufenozide and RH-5849 showed different results. Methoxyfenozide and tebufenozide did not provoke anynegative effectsontheadults,but RH-5849 killed98-100%of the treated insects15 days after treatment. Theligand-binding domain (LBD) of the EcR of B. oleae (BoEcR-LBD) was sequenced, and a homology protein model was constructed. Owing to a restricted extent of the ligand-binding cavity of the BoEcR-LBD, docking experiments with the three tested insecticides showed a severe steric clash in the case of methoxyfenozide and tebufenozide, while this was not the case with RH-5849. CONCLUSION: IGR molecules similar to the RH-5849 molecule, and different from methoxyfenozide and tebufenozide, might have potential in controlling this pest.

Modeling the evolution of item rating networks using time-domain preferential attachment

The understanding of the structure and dynamics of the intricate network of connections among people that consumes products through Internet appears as an extremely useful asset in order to study emergent properties related to social behavior. This knowledge could be useful, for example, to improve the performance of personal recommendation algorithms. In this contribution, we analyzed five-year records of movie-rating transactions provided by Netflix, a movie rental platform where users rate movies from an online catalog. This dataset can be studied as a bipartite user-item network whose structure evolves in time. Even though several topological properties from subsets of this bipartite network have been reported with a model that combines random and preferential attachment mechanisms [Beguerisse D��az et al., 2010], there are still many aspects worth to be explored, as they are connected to relevant phenomena underlying the evolution of the network. In this work, we test the hypothesis that bursty human behavior is essential in order to describe how a bipartite user-item network evolves in time. To that end, we propose a novel model that combines, for user nodes, a network growth prescription based on a preferential attachment mechanism acting not only in the topological domain (i.e. based on node degrees) but also in time domain. In the case of items, the model mixes degree preferential attachment and random selection. With these ingredients, the model is not only able to reproduce the asymptotic degree distribution, but also shows an excellent agreement with the Netflix data in several time-dependent topological properties.

Tailoring the magnetic anisotropy and domain patterns of sputtered TbFeGa alloys

We report the magnetic anisotropy and domain configuration of cosputtered TbFeGa alloys. The layers were deposited from two targets with compositions TbFe2 and Fe3Ga, respectively. The structural and magnetic properties do not only depend on the composition but also on the growth conditions. Alloys with the same composition but deposited using a DC or a pulsed power source in the TbFe2 target exhibit a different magnetic anisotropy. The perpendicular magnetic anisotropy, the size and topology of domain patterns can be tailored by changing the evaporation parameters of TbFe2. The width of the stripe domain increases from 235 to 835 nm when using the DC source in the TbFe2. We correlate this effect with Tb enrichment of the TbxFe1���x phases present in the samples.

Self assembled and ordered group III nitride nanocolumnar structures for light emitting applications

El objetivo de este trabajo es un estudio profundo del crecimiento selectivo de nanoestructuras de InGaN por epitaxia de haces moleculares asistido por plasma, concentrandose en el potencial de estas estructuras como bloques constituyentes en LEDs de nueva generaci��n. Varias aproximaciones al problema son discutidas; desde estructuras axiales InGaN/GaN, a estructuras core-shell, o nanoestructuras crecidas en sustratos con orientaciones menos convencionales (semi polar y no polar). La primera secci��n revisa los aspectos b��sicos del crecimiento auto-ensamblado de nanocolumnas de GaN en sustratos de Si(111). Su morfolog��a y propiedades ��pticas son comparadas con las de capas compactas de GaN sobre Si(111). En el caso de las columnas auto-ensambladas de InGaN sobre Si(111), se presentan resultados sobre el efecto de la temperatura de crecimiento en la incorporaci��n de In. Por ��ltimo, se discute la inclusi��n de nanodiscos de InGaN en las nanocolumnas de GaN. La segunda secci��n revisa los mecanismos b��sicos del crecimiento ordenado de nanoestructuras basadas en GaN, sobre templates de GaN/zafiro. Aumentando la relaci��n III/V localmente, se observan cambios morfol��gicos; desde islas piramidales, a nanocolumnas de GaN terminadas en planos semipolares, y finalmente, a nanocolumnas finalizadas en planos c polares. Al crecer nanodiscos de InGaN insertados en las nanocolumnas de GaN, las diferentes morfologias mencionadas dan lugar a diferentes propiedades ��pticas de los nanodiscos, debido al diferente car��cter (semi polar o polar) de los planos cristalinos involucrados. La tercera secci��n recoge experimentos acerca de los efectos que la temperatura de crecimiento y la raz��n In/Ga tienen en la morfolog��a y emisi��n de nanocolumnas ordenadas de InGaN crecidas sobre templates GaN/zafiro. En el rango de temperaturas entre 650 y 750 C, la incorporacion de In puede modificarse bien por la temperatura de crecimiento, o por la raz��n In/Ga. Controlar estos factores permite la optimizaci��n de la longitud de onda de emisi��n de las nanocolumnas de InGaN. En el caso particular de la generaci��n de luz blanca, se han seguidos dos aproximaciones. En la primera, se obtiene emisi��n amarilla-blanca a temperatura ambiente de nanoestructuras donde la regi��n de InGaN consiste en un gradiente de composiciones de In, que se ha obtenido a partir de un gradiente de temperatura durante el crecimiento. En la segunda, el apilamiento de segmentos emitiendo en azul, verde y rojo, consiguiendo la integraci��n monol��tica de estas estructuras en cada una de las nanocolumnas individuales, da lugar a emisores ordenados con un amplio espectro de emisi��n. En esta ��ltima aproximaci��n, la forma espectral puede controlarse con la longitud (duraci��n del crecimiento) de cada uno de los segmentos de InGaN. M��s adelante, se presenta el crecimiento ordenado, por epitaxia de haces moleculares, de arrays de nanocolumnas que son diodos InGaN/GaN cada una de ellas, emitiendo en azul (441 nm), verde (502 nm) y amarillo (568 nm). La zona activa del dispositivo consiste en una secci��n de InGaN, de composici��n constante nominalmente y longitud entre 250 y 500 nm, y libre de defectos extendidos en contraste con capas compactas de InGaN de similares composiciones y espesores. Los espectros de electroluminiscencia muestran un muy peque��o desplazamiento al azul al aumentar la corriente inyectada (desplazamiento casi inexistente en el caso del dispositivo amarillo), y emisiones ligeramente m��s anchas que en el caso del estado del arte en pozos cu��nticos de InGaN. A continuaci��n, se presenta y discute el crecimiento ordenado de nanocolumnas de In(Ga)N/GaN en sustratos de Si(111). Nanocolumnas ordenadas emitiendo desde el ultravioleta (3.2 eV) al infrarrojo (0.78 eV) se crecieron sobre sustratos de Si(111) utilizando una capa compacta (���buffer���) de GaN. La morfolog��a y eficiencia de emisi��n de las nanocolumnas emitiendo en el rango espectral verde pueden ser mejoradas ajustando las relaciones In/Ga y III/N, y una eficiencia cu��ntica interna del 30% se deriva de las medidas de fotoluminiscencia en nanocolumnas optimizadas. En la siguiente secci��n de este trabajo se presenta en detalle el mecanismo tras el crecimiento ordenado de nanocolumnas de InGaN/GaN emitiendo en el verde, y sus propiedades ��pticas. Nanocolumnas de InGaN/GaN con secciones largas de InGaN (330-830 nm) se crecieron tanto en sustratos GaN/zafiro como GaN/Si(111). Se encuentra que la morfolog��a y la distribuci��n espacial del In dentro de las nanocolumnas dependen de las relaciones III/N e In/Ga locales en el frente de crecimiento de las nanocolumnas. La dispersi��n en el contenido de In entre diferentes nanocolumnas dentro de la misma muestra es despreciable, como indica las casi identicas formas espectrales de la catodoluminiscencia de una sola nanocolumna y del conjunto de ellas. Para las nanocolumnas de InGaN/GaN crecidas sobre GaN/Si(111) y emitiendo en el rango espectral verde, la eficiencia cu��ntica interna aumenta hasta el 30% al disminuir la temperatura de crecimiento y aumentar el nitr��geno activo. Este comportamiento se debe probablemente a la formaci��n de estados altamente localizados, como indica la particular evoluci��n de la energ��a de fotoluminiscencia con la temperatura (ausencia de ���s-shape���) en muestras con una alta eficiencia cu��ntica interna. Por otro lado, no se ha encontrado la misma dependencia entre condiciones de crecimiento y efiencia cu��ntica interna en las nanoestructuras InGaN/GaN crecidas en GaN/zafiro, donde la m��xima eficiencia encontrada ha sido de 3.7%. Como alternativa a las nanoestructuras axiales de InGaN/GaN, la secci��n 4 presenta resultados sobre el crecimiento y caracterizaci��n de estructuras core-shell de InGaN/GaN, re-crecidas sobre arrays de micropilares de GaN fabricados por ataque de un template GaN/zafiro (aproximaci��n top-down). El crecimiento de InGaN/GaN es conformal, con componentes axiales y radiales en el crecimiento, que dan lugar a la estructuras core-shell con claras facetas hexagonales. El crecimiento radial (shell) se ve confirmado por medidas de catodoluminiscencia con resoluci��n espacial efectuadas en un microscopio electr��nico de barrido, asi como por medidas de microscop��a de transmisi��n de electrones. M��s adelante, el crecimiento de micro-pilares core-shell de InGaN se realiz�� en pilares GaN (cores) crecidos selectivamente por epitaxia de metal-org��nicos en fase vapor. Con el crecimiento de InGaN se forman estructuras core-shell con emisi��n alrededor de 3 eV. Medidas de catodoluminiscencia resuelta espacialmente indican un aumento en el contenido de indio del shell en direcci��n a la parte superior del pilar, que se manifiesta en un desplazamiento de la emisi��n de 3.2 eV en la parte inferior, a 3.0 eV en la parte superior del shell. Este desplazamiento est�� relacionado con variaciones locales de la raz��n III/V en las facetas laterales. Finalmente, se demuestra la fabricaci��n de una estructura pin basada en estos pilares core-shell. Medidas de electroluminiscencia resuelta espacialmente, realizadas en pilares individuales, confirman que la electroluminiscencia proveniente del shell de InGaN (diodo lateral) est�� alrededor de 3.0 eV, mientras que la emisi��n desde la parte superior del pilar (diodo axial) est�� alrededor de 2.3 eV. Para finalizar, se presentan resultados sobre el crecimiento ordenado de GaN, con y sin inserciones de InGaN, en templates semi polares (GaN(11-22)/zafiro) y no polares (GaN(11-20)/zafiro). Tras el crecimiento ordenado, gran parte de los defectos presentes en los templates originales se ven reducidos, manifest��ndose en una gran mejora de las propiedades ��pticas. En el caso de crecimiento selectivo sobre templates con orientaci��n GaN(11-22), no polar, la formaci��n de nanoestructuras con una particular morfolog��a (baja relaci��n entre crecimiento perpedicular frente a paralelo al plano) permite, a partir de la coalescencia de estas nanoestructuras, la fabricaci��n de pseudo-templates no polares de GaN de alta calidad. ABSTRACT The aim of this work is to gain insight into the selective area growth of InGaN nanostructures by plasma assisted molecular beam epitaxy, focusing on their potential as building blocks for next generation LEDs. Several nanocolumn-based approaches such as standard axial InGaN/GaN structures, InGaN/GaN core-shell structures, or InGaN/GaN nanostructures grown on semi- and non-polar substrates are discussed. The first section reviews the basics of the self-assembled growth of GaN nanocolumns on Si(111). Morphology differences and optical properties are compared to those of GaN layer grown directly on Si(111). The effects of the growth temperature on the In incorporation in self-assembled InGaN nanocolumns grown on Si(111) is described. The second section reviews the basic growth mechanisms of selectively grown GaNbased nanostructures on c-plane GaN/sapphire templates. By increasing the local III/V ratio morphological changes from pyramidal islands, to GaN nanocolumns with top semi-polar planes, and further to GaN nanocolumns with top polar c-planes are observed. When growing InGaN nano-disks embedded into the GaN nanocolumns, the different morphologies mentioned lead to different optical properties, due to the semipolar and polar nature of the crystal planes involved. The third section reports on the effect of the growth temperature and In/Ga ratio on the morphology and light emission characteristics of ordered InGaN nanocolumns grown on c-plane GaN/sapphire templates. Within the growth temperature range of 650 to 750oC the In incorporation can be modified either by the growth temperature, or the In/Ga ratio. Control of these factors allows the optimization of the InGaN nanocolumns light emission wavelength. In order to achieve white light emission two approaches are used. First yellow-white light emission can be obtained at room temperature from nanostructures where the InGaN region is composition-graded by using temperature gradients during growth. In a second approach the stacking of red, green and blue emitting segments was used to achieve the monolithic integration of these structures in one single InGaN nanocolumn leading to ordered broad spectrum emitters. With this approach, the spectral shape can be controlled by changing the thickness of the respective InGaN segments. Furthermore the growth of ordered arrays of InGaN/GaN nanocolumnar light emitting diodes by molecular beam epitaxy, emitting in the blue (441 nm), green (502 nm), and yellow (568 nm) spectral range is reported. The device active region, consisting of a nanocolumnar InGaN section of nominally constant composition and 250 to 500 nm length, is free of extended defects, which is in strong contrast to InGaN layers (planar) of similar composition and thickness. Electroluminescence spectra show a very small blue shift with increasing current, (almost negligible in the yellow device) and line widths slightly broader than those of state-of-the-art InGaN quantum wells. Next the selective area growth of In(Ga)N/GaN nanocolumns on Si(111) substrates is discussed. Ordered In(Ga)N/GaN nanocolumns emitting from ultraviolet (3.2 eV) to infrared (0.78 eV) were then grown on top of GaN-buffered Si substrates. The morphology and the emission efficiency of the In(Ga)N/GaN nanocolumns emitting in the green could be substantially improved by tuning the In/Ga and total III/N ratios, where an estimated internal quantum efficiency of 30 % was derived from photoluminescence data. In the next section, this work presents a study on the selective area growth mechanisms of green-emitting InGaN/GaN nanocolumns and their optical properties. InGaN/GaN nanocolumns with long InGaN sections (330-830nm) were grown on GaN/sapphire and GaN-buffered Si(111). The nanocolumn���s morphology and spatial indium distribution is found to depend on the local group (III)/N and In/Ga ratios at the nanocolumn���s top. A negligible spread of the average indium incorporation among different nanostructures is found as indicated by similar shapes of the cathodoluminescence spectra taken from single nanocolumns and ensembles of nanocolumns. For InGaN/GaN nanocolumns grown on GaN-buffered Si(111), all emitting in the green spectral range, the internal quantum efficiency increases up to 30% when decreasing growth temperature and increasing active nitrogen. This behavior is likely due to the formation of highly localized states, as indicated by the absence of a complete s-shape behavior of the PL peak position with temperature (up to room temperature) in samples with high internal quantum efficiency. On the other hand, no dependence of the internal quantum efficiency on the growth conditions is found for InGaN/GaN nanostructures grown on GaN/sapphire, where the maximum achieved efficiency is 3.7%. As alternative to axial InGaN/GaN nanostructures, section 4 reports on the growth and characterization of InGaN/GaN core-shell structures on an ordered array of top-down patterned GaN microrods etched from a GaN/sapphire template. Growth of InGaN/GaN is conformal, with axial and radial growth components leading to core-shell structures with clear hexagonal facets. The radial InGaN growth (shell) is confirmed by spatially resolved cathodoluminescence performed in a scanning electron microscopy as well as in scanning transmission electron microscopy. Furthermore the growth of InGaN core-shell micro pillars using an ordered array of GaN cores grown by metal organic vapor phase epitaxy as a template is demonstrated. Upon InGaN overgrowth core-shell structures with emission at around 3.0 eV are formed. With spatially resolved cathodoluminescence, an increasing In content towards the pillar top is found to be present in the InGaN shell, as indicated by a shift of CL peak position from 3.2 eV at the shell bottom to 3.0 eV at the shell top. This shift is related to variations of the local III/V ratio at the side facets. Further, the successful fabrication of a core-shell pin diode structure is demonstrated. Spatially resolved electroluminescence measurements performed on individual micro LEDs, confirm emission from the InGaN shell (lateral diode) at around 3.0 eV, as well as from the pillar top facet (axial diode) at around 2.3 eV. Finally, this work reports on the selective area growth of GaN, with and without InGaN insertion, on semi-polar (11-22) and non-polar (11-20) templates. Upon SAG the high defect density present in the GaN templates is strongly reduced as indicated by TEM and a dramatic improvement of the optical properties. In case of SAG on non-polar (11-22) templates the formation of nanostructures with a low aspect ratio took place allowing for the fabrication of high-quality, non-polar GaN pseudo-templates by coalescence of the nanostructures.

Molecular characteristics of fibroblast growth factor���fibroblast growth factor receptor���heparin-like glycosaminoglycan complex

Fibroblast growth factor (FGF) family plays key roles in development, wound healing, and angiogenesis. Understanding of the molecular nature of interactions of FGFs with their receptors (FGFRs) has been seriously limited by the absence of structural information on FGFR or FGF���FGFR complex. In this study, based on an exhaustive analysis of the primary sequences of the FGF family, we determined that the residues that constitute the primary receptor-binding site of FGF-2 are conserved throughout the FGF family, whereas those of the secondary receptor binding site of FGF-2 are not. We propose that the FGF���FGFR interaction mediated by the ���conserved��� primary site interactions is likely to be similar if not identical for the entire FGF family, whereas the ���variable��� secondary sites, on both FGF as well as FGFR mediates specificity of a given FGF to a given FGFR isoform. Furthermore, as the pro-inflammatory cytokine interleukin 1 (IL-1) and FGF-2 share the same structural scaffold, we find that the spatial orientation of the primary receptor-binding site of FGF-2 coincides structurally with the IL-1�� receptor-binding site when the two molecules are superimposed. The structural similarities between the IL-1 and the FGF system provided a framework to elucidate molecular principles of FGF���FGFR interactions. In the FGF���FGFR model proposed here, the two domains of a single FGFR wrap around a single FGF-2 molecule such that one domain of FGFR binds to the primary receptor-binding site of the FGF molecule, while the second domain of the same FGFR binds to the secondary receptor-binding site of the same FGF molecule. Finally, the proposed model is able to accommodate not only heparin-like glycosaminoglycan (HLGAG) interactions with FGF and FGFR but also FGF dimerization or oligomerization mediated by HLGAG.

Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association

Nrd1 is an essential yeast protein of unknown function that has an RNA recognition motif (RRM) in its carboxyl half and a putative RNA polymerase II-binding domain, the CTD-binding motif, at its amino terminus. Nrd1 mediates a severe reduction in pre-mRNA production from a reporter gene bearing an exogenous sequence element in its intron. The effect of the inserted element is highly sequence-specific and is accompanied by the appearance of 3���-truncated transcripts. We have proposed that Nrd1 binds to the exogenous sequence element in the nascent pre-mRNA during transcription, aided by the CTD-binding motif, and directs 3���-end formation a short distance downstream. Here we show that highly purified Nrd1 carboxyl half binds tightly to the RNA element in vitro with sequence specificity that correlates with the efficiency of cis-element-directed down-regulation in vivo. A large deletion in the CTD-binding motif blocks down-regulation but does not affect the essential function of Nrd1. Furthermore, a nonsense mutant allele that produces truncated Nrd1 protein lacking the RRM has a dominant-negative effect on down-regulation but not on cell growth. Viability of this and several other nonsense alleles of Nrd1 appears to require translational readthrough, which in one case is extremely efficient. Thus the CTD-binding motif of Nrd1 is important for pre-mRNA down-regulation but is not required for the essential function of Nrd1. In contrast, the RNA-binding activity of Nrd1 appears to be required both for down-regulation and for its essential function.

soc-2 encodes a leucine-rich repeat protein implicated in fibroblast growth factor receptor signaling

Activation of fibroblast growth factor (FGF) receptors elicits diverse cellular responses including growth, mitogenesis, migration, and differentiation. The intracellular signaling pathways that mediate these important processes are not well understood. In Caenorhabditis elegans, suppressors of clr-1 identify genes, termed soc genes, that potentially mediate or activate signaling through the EGL-15 FGF receptor. We demonstrate that three soc genes, soc-1, soc-2, and sem-5, suppress the activity of an activated form of the EGL-15 FGF receptor, consistent with the soc genes functioning downstream of EGL-15. We show that soc-2 encodes a protein composed almost entirely of leucine-rich repeats, a domain implicated in protein���protein interactions. We identified a putative human homolog, SHOC-2, which is 54% identical to SOC-2. We find that shoc-2 maps to 10q25, shoc-2 mRNA is expressed in all tissues assayed, and SHOC-2 protein is cytoplasmically localized. Within the leucine-rich repeats of both SOC-2 and SHOC-2 are two YXNX motifs that are potential tyrosine-phosphorylated docking sites for the SEM-5/GRB2 Src homology 2 domain. However, phosphorylation of these residues is not required for SOC-2 function in vivo, and SHOC-2 is not observed to be tyrosine phosphorylated in response to FGF stimulation. We conclude that this genetic system has allowed for the identification of a conserved gene implicated in mediating FGF receptor signaling in C. elegans.

Antibody-mediated inhibition of the growth of larvae from an insect causing cutaneous myiasis in a���mammalian���host

Many insects feed on blood or tissue from mammalian hosts. One potential strategy for the control of these insects is to vaccinate the host with antigens derived from the insect. The larvae of the fly Lucilia cuprina feed on ovine tissue and tissue fluids causing a cutaneous myiasis associated with considerable host morbidity and mortality. A candidate vaccine antigen, peritrophin 95, was purified from the peritrophic membrane, which lines the gut of these larvae. Serum from sheep vaccinated with peritrophin 95 inhibited growth of first-instar L. cuprina larvae that fed on this serum. Growth inhibition was probably caused by antibody-mediated blockage of the normally semipermeable peritrophic membrane and the subsequent development of an impervious layer of undefined composition on the gut lumen side of the peritrophic membrane that restricted access of nutrients to the larvae. The amino acid sequence of peritrophin 95 was determined by cloning the DNA complementary to its mRNA. The deduced amino acid sequence codes for a secreted protein containing a distinct Cys-rich domain of 317 amino acids followed by a mucin-like domain of 139 amino acids. The Cys-rich domain may be involved in binding chitin. This report describes a novel immunological strategy for the potential control of L. cuprina larvae that may have general application to the control of other insect pests.

The cysteine-rich frizzled domain of Frzb-1 is required and sufficient for modulation of Wnt���signaling

Convincing evidence has accumulated to identify the Frizzled proteins as receptors for the Wnt growth factors. In parallel, a number of secreted frizzled-like proteins with a conserved N-terminal frizzled motif have been identified. One of these proteins, Frzb-1, binds Wnt-1 and Xwnt-8 proteins and antagonizes Xwnt-8 signaling in Xenopus embryos. Here we report that Frzb-1 blocks Wnt-1 induced cytosolic accumulation of ��-catenin, a key component of the Wnt signaling pathway, in human embryonic kidney cells. Structure/function analysis reveals that complete removal of the frizzled domain of Frzb-1 abolishes the Wnt-1/Frzb-1 protein interaction and the inhibition of Wnt-1 mediated axis duplication in Xenopus embryos. In contrast, removal of the C-terminal portion of the molecule preserves both Frzb-Wnt binding and functional inhibition of Wnt signaling. Partial deletions of the Frzb-1 cysteine-rich domain maintain Wnt-1 interaction, but functional inhibition is lost. Taken together, these findings support the conclusion that the frizzled domain is necessary and sufficient for both activities. Interestingly, Frzb-1 does not block Wnt-5A signaling in a Xenopus functional assay, even though Wnt-5A coimmunoprecipitates with Frzb-1, suggesting that coimmunoprecipitation does not necessarily imply inhibition of Wnt function.

Domain-specific gene disruption reveals critical regulation of neuregulin signaling by its cytoplasmic tail

Neuregulins are a multi-isoform family of growth factors that activate members of the erbB family of receptor tyrosine kinases. The membrane-anchored isoforms contain the receptor-activating ligand in their extracellular domain, a single membrane-spanning region, and a long cytoplasmic tail. To evaluate the potential biological role of the intracellular domain of the membrane-anchored neuregulin isoforms, we used a domain-specific gene disruption approach to produce a mouse line in which only the region of the neuregulin gene encoding almost the entire intracellular domain was disrupted. Consistent with previous reports in which all neuregulin isoforms were disrupted, the resulting homozygous neuregulin mutants died at E10.5 of circulatory failure and displayed defects in neural and cardiac development. To further understand these in vivo observations, we evaluated a similarly truncated neuregulin construct after transient expression in COS-7 cells. This cytoplasmic tail-deleted mutant, unlike wild-type neuregulin isoforms, was resistant to proteolytic release of its extracellular-domain ligand, a process required for erbB receptor activation. Thus, proteolytic processing of the membrane-bound neuregulin isoforms involved in cranial ganglia and heart embryogenesis is likely developmentally regulated and is critically controlled by their intracellular domain. This observation indicates that erbB receptor activation by membrane-bound neuregulins most likely involves a unique temporally and spatially regulated ���inside-out��� signaling process that is critical for processing and release of the extracellular-domain ligand.

Specificity in transforming growth factor ��-induced transcription of the plasminogen activator inhibitor-1 gene: Interactions of promoter DNA, transcription factor ��E3, and Smad proteins

Transforming growth factor �� (TGF-��) regulates a broad range of biological processes, including cell growth, development, differentiation, and immunity. TGF-�� signals through its cell surface receptor serine kinases that phosphorylate Smad2 or Smad3 proteins. Because Smad3 and its partner Smad4 bind to only 4-bp Smad binding elements (SBEs) in DNA, a central question is how specificity of TGF-��-induced transcription is achieved. We show that Smad3 selectively binds to two of the three SBEs in PE2.1, a TGF-��-inducible fragment of the plasminogen activator inhibitor-1 promoter, to mediate TGF-��-induced transcription; moreover, a precise 3-bp spacer between one SBE and the E-box, a binding site for transcription factor ��E3 (TFE3), is essential for TGF-��-induced transcription. Whereas an isolated Smad3 MH1 domain binds to TFE3, TGF-�� receptor-mediated phosphorylation of full-length Smad3 enhances its binding to TFE3. Together, these studies elucidate an important mechanism for specificity in TGF-��-induced transcription of the plasminogen activator inhibitor-1 gene.