A collaborative filtering approach to mitigate the new user cold start problem.

The new user cold start issue represents a serious problem in recommender systems as it can lead to the loss of new users who decide to stop using the system due to the lack of accuracy in the recommenda- tions received in that first stage in which they have not yet cast a significant number of votes with which to feed the recommender system?s collaborative filtering core. For this reason it is particularly important to design new similarity metrics which provide greater precision in the results offered to users who have cast few votes. This paper presents a new similarity measure perfected using optimization based on neu- ral learning, which exceeds the best results obtained with current metrics. The metric has been tested on the Netflix and Movielens databases, obtaining important improvements in the measures of accuracy, precision and recall when applied to new user cold start situations. The paper includes the mathematical formalization describing how to obtain the main quality measures of a recommender system using leave- one-out cross validation.

Use and abuse of audivisual media in the college classroom. Slides show and web pages

The multimedia development that has taken place within the university classrooms in recent years has caused a revolution at psychological level within the collectivity of students and teachers inside and outside the classrooms. The slide show applications have become a key supporting element for university professors, who, in many cases, rely blindly in the use of them for teaching. Additionally, ill-conceived slides, poorly structured and with a vast amount of multimedia content, can be the basis of a faulty communication between teacher and student, which is overwhelmed by the appearance and presentation, neglecting their content. The same applies to web pages. This paper focuses on the study and analysis of the impact caused in the process of teaching and learning by the slide show presentations and web pages, and its positive and negative influence on the student’s learning process, paying particular attention to the consequences on the level of attention within the classroom, and on the study outside the classroom. The study is performed by means of a qualitative analysis of student surveys conducted during the last 8 school Civil Engineering School at the Polytechnic University of Madrid. It presents some of the weaknesses of multimedia material, including the difficulties for students to study them, because of the many distractions they face and the need for incentives web pages offer, or the insignificant content and shallowness of the studies due to wrongly formulated presentations.

Accesibilidad y mejora de un sistema Web e implementación de RSS para avisos

El presente Trabajo de Fin de Grado se enmarca dentro del sistema web de la asignaturade Procesadores de Lenguajes perteneciente al departamento de Lenguajes y Sistemas Informáticos e Ingeniería de Software de la Escuela Técnica Superior de Ingenieros Informáticos de la Universidad Politécnica de Madrid. Este Trabajo consta de varias líneas de desarrollo, que se engloban dentro de dicho marco y surgen de la necesidad de mejorar el sistema para hacer que éste sea accesible a todo tipo de usuarios, y a la vez se mantenga actualizado según las tecnologías más recientes. En primer lugar, el presente Trabajo se centra en estudiar la accesibilidad de la web de la asignatura de Procesadores de Lenguajes siguiendo las Pautas de Accesibilidad al Contenido en la Web (Web Content Accessibility Guidelines, WCAG) en su segunda versión (2.0). Para ello, se ha llevado a cabo un informe detallado que recoge los resultados de este estudio sobre los criterios de aceptación de las WCAG, y posteriormente se han implementado los cambios necesarios para solucionar los criterios erróneos detectados. De esta manera se puede asegurar que la web es accesible para personas con distintos tipos de discapacidad. Así mismo, y siguiendo el criterio de conseguir una web más accesible, se ha adaptado el sistema a tecnologías más recientes. En el momento de empezar el Trabajo, el sistema web contaba con una serie de páginas estáticas (XHTML 1.1 + CSS 2.1) y una serie de páginas dinámicas (XHTML 1.1 + CSS 2.1 + PHP + MySQL). Estas páginas han sido actualizadas a sus versiones más recientes (HTML 5 y CSS 3). La web cuenta también con un sistema de creación de grupos de prácticas que facilita su gestión tanto a profesores como a alumnos, además de facilitar el alta de los estudiantes de la asignatura. El sistema posee además un módulo de administración para que el personal docente pueda gestionarlo. Sobre este sistema web implantado en la actualidad, se ha realizado una batería de pruebas para garantizar su correcto funcionamiento, y se han corregido todos los errores detectados durante dicho proceso. Al mismo tiempo, se han implementado nuevas funcionalidades que han ido surgiendo desde la creación del sistema hasta el momento presente. Por último, se ha desarrollado un sistema de avisos RSS que permite a los alumnos de la asignatura permanecer al corriente de los avisos y noticias publicados en el tablón de anuncios de la web. Este sistema de avisos RSS servirá también para otros sitios web del Centro que utilicen el tablón de avisos multipropósito y podrá ser visualizado tanto en inglés como en español. ---ABSTRACT---The present final year project is set within the framework of the subject “Procesadores de Lenguajes”, that belongs to the “Computer Languages and Systems and Software Engineering” department of the Escuela Técnica Superior de Ingenieros Informáticos of the Polytechnic University of Madrid. This study is divided in several angles of development that are included inside the abovementioned framework. They all emerge from the necessity of upgrading the system in order to make it accessible to everybody and the same time bringing it up to date to the latest technologies. First of all, it is focused on the study of the accessibility of the web site of the subject Procesadores de Lenguajes, following the second version of the Web Content Accessibility Guidelines (WCAG 2.0). In order to do this, an in-depth report containing the results of the study on the acceptance criteria of the WCAG has been developed. Right afterwards, necessary changes were implemented to correct the erroneous criteria detected. Similarly, and following the criteria of achieving a more accessible web site, the system has been adapted to updated technologies. At the start point, the web system consisted in a series of static pages (XHTML 1.1 + CSS 2.1) and a series of dynamic ones (XHTML 1.1 + CSS 2.1 + PHP + MySQL). These pages have been updated to their latest versions (HTML 5 and CSS 3). The web site has a system for the creation of working groups that makes their management easier, both for the teachers and for the students, as well as the registration process. The teaching staff can also manage the system through the administration module. Over the current web system, sets of several tests have taken place in order to guarantee its correct functioning and all the errors that appeared have been corrected. Likewise, new functionalities have been implemented, and those have been arising since the creation of the system till the present time. Finally, an RSS alert system has been developed, allowing students to keep updated on the news and alerts published in the website noticeboard. This RSS alert system will be shared with other websites of the School using the multipurpose noticeboard, and will be available both in Spanish and English.

Teoría y práctica de la restauración de la Mezquita-Catedral de Córdoba durante el siglo XX

La Mezquita-Catedral de Córdoba es un edificio vivo. Un edificio que ha sido transformado sucesivamente por hombres de razas, culturas y religiones distintas durante sus más de 1.200 años de vida y que, a pesar de ello, no ha dejado de estar en uso ni uno solo de esos días de esa larga vida. De esta forma, el edificio se muestra ante el visitante como un complejo objeto arquitectónico, resultado de una continua transformación. La capacidad de la transformación de los edificios es algo inherente a su propia condición arquitectónica, no es un hecho exclusivo de la Mezquita-Catedral. Sin embargo, en este edificio esa transformación se produce con una gran intensidad y sin pérdida de su autenticidad. Tradicionalmente, los edificios se han adaptado a los nuevos requerimientos de cada época en un proceso que ha buscado en el propio edificio las leyes o principios que habían de regir la intervención. De esta forma, tanto las sucesivas ampliaciones de la Mezquita de Abd al-Rahman I como las siguientes intervenciones cristianas debieron asumir lo preexistente como material de trabajo. Así, los arquitectos del califa al-Hakam II dialogaron con sus antecesores complejizando el espacio que recibieron, así como los Hernán Ruiz consiguieron un nuevo organismo resultante de la introducción de su arquitectura luminosa en la trama hispanomusulmana. El siglo XIX confirmó el deseo por descubrir las huellas de un pasado esplendoroso que la intervención barroca había silenciado bajo un tratamiento homogéneo del espacio. La recuperación de esas huellas supuso, hace exactamente dos siglos, el inicio de la última gran etapa en la transformación del edificio, la de la restauración. La fábrica es considerada como objeto a conservar y los esfuerzos desde ese momento se centraron en la recuperación de la arquitectura omeya latente. De este modo, la práctica de la restauración como disciplina se encontró absolutamente influenciada por la Arqueología como única fuente de conocimiento. Las intervenciones buscaban lo original como modo de recuperar espacial y formalmente aquel pasado, concentrándose en los lugares del edificio considerados como esenciales. La declaración del edificio como monumento nacional en 1882 propició que el Estado se hiciera cargo de su mantenimiento y conservación, sustituyendo en esa tarea a los Obispos y Cabildos del siglo XIX, que tuvieron un entendimiento muy avanzado para su época. La llegada del arquitecto Velázquez Bosco en las últimas décadas del siglo XIX supuso un cambio trascendental en la historia del edificio, puesto que recibió un edificio con importantes deterioros y consiguió poner las bases del edificio que hoy contemplamos. El empeño por la recuperación material y espacial devolvió a la Mezquita-Catedral buena parte de su imagen original, reproduciendo con exactitud los modelos hallados en las exploraciones arqueológicas. La llegada de Antonio Flórez tras la muerte de Velázquez Bosco supuso la traslación al edificio del debate disciplinar que se desarrolló en las dos primeras décadas del siglo XX. Flórez procuró un nuevo entendimiento de la intervención, considerando la conservación como actuación prioritaria. En 1926 el Estado reformó la manera en que se atendía al patrimonio con la creación de un sistema de zonas y unos arquitectos a cargo de ellas. La existencia de un nuevo marco legislativo apuntaló esa nueva visión conservativa, avalada por la Carta de Atenas de 1931. Este modelo restauración científica huía de la intervención en estilo y valoraba la necesidad de intervenir de la manera más escueta posible y con un lenguaje diferenciado, basándose en los datos que ofrecía la Arqueología. Por tanto, se continuaba con la valoración del edificio como documento histórico, buscando en este caso una imagen diferenciada de la intervención frente a la actitud mimética de Velázquez. Resulta destacable la manera en la que el historiador Manuel Gómez-Moreno influyó en varias generaciones de arquitectos, arqueólogos e historiadores, tanto en el entendimiento científico de la restauración como en la propia estructura administrativa. La labor desarrollada en el edificio por José Mª Rodríguez Cano primero y Félix Hernández a continuación estuvo influida de manera teórica por el método de Gómez-Moreno, aunque en muchos aspectos su labor no representó una gran diferencia con lo hecho por Velázquez Bosco. La búsqueda de lo original volvió a ser recurrente, pero la carga económica del mantenimiento de un edificio tan extenso conllevó la no realización de muchos de los proyectos más ambiciosos. Esta obsesiva búsqueda de la imagen original del edificio tuvo su última y anacrónica etapa con la intervención de la Dirección General de Arquitectura en los 70. Sin embargo, el agotamiento del modelo científico ya había propiciado un nuevo escenario a nivel europeo, que cristalizó en la Carta de Venecia de 1964 y en una nueva definición del objeto a preservar, más allá del valor como documento histórico. Esta nueva posición teórica tuvo su traslación al modelo restaurador español en el último cuarto de siglo XX, coincidiendo con la Transición. El arquitecto Dionisio Hernández Gil defendió una interpretación distinta a la de los arqueólogos y de los historiadores, que había prevalecido durante todo el siglo. En opinión de Hernández Gil, los problemas de intervención debían enfocarse fundamentalmente como problemas de Arquitectura, abandonando la idea de que solamente podían ser resueltos por especialistas. Esta convicción teórica fue defendida desde la nueva Administración y deparó la utilización de unos criterios de intervención particularizados, provenientes del análisis multifocal de cada situación y no sólo desde el valor de los edificios como documentos históricos. Y este cambio tuvo su traslación a la Mezquita-Catedral con la práctica de Gabriel Ruiz Cabrero y Gabriel Rebollo. En consecuencia con esa nueva perspectiva, aceptaron el edificio que recibieron, sustituyendo la búsqueda de aquella página original por la aceptación de cada una de las páginas de su historia y el respeto a las técnicas constructivas del pasado. La búsqueda de soluciones específicas desde el propio objeto arquitectónico significó la renovada atención a la potente estructura formal-constructiva como origen de toda reflexión. Considerar la Mezquita-Catedral en primer lugar como Arquitectura implicaba la atención a todo tipo de factores además de los históricos, como medio para preservar su autenticidad. Esta tesis pretende demostrar que la práctica de la restauración realizada en la Mezquita-Catedral a lo largo del siglo XX ha evolucionado desde la búsqueda de lo original hasta la búsqueda de lo auténtico, como reflejo de una visión basada en lo arqueológico frente a una renovada visión arquitectónica más completa, que incluye a la anterior. La consideración de la intervención en este edificio como otra página más de su historia y no como la última, significa la reedición de un mecanismo recurrente en la vida del edificio y un nuevo impulso en ese proceso de continua transformación. ABSTRACT The Mosque-Cathedral of Cordoba is a living building. A building transformed by men of different races, cultures and religions during more than 1.200 years old and that, nevertheless, it has continued to be in use all days in that long life. Thus, the building shows to the visitor as a complex architectural object, the result of continuous transformation. This transformation capacity of the buildings is inherent in their own architectural condition, it’s not an exclusive fact of the Mosque-Cathedral. However, in this building that transformation happens with a great intensity, without losing their authenticity. Traditionally, buildings have been adapted to the new requirements of times in a process that looked for laws or principles in order to guide the intervention. Thus, both the successive enlargements of the Mosque of Abd al-Rahman and Christian interventions must assume the preexistence as a working material. So, the architects of the caliph al-Hakam II spoke to their predecessors, complexing the receiving space, as well as Hernan Ruiz got a new organism as result the introduction of his luminous architecture into hispanic-muslim weft. The nineteenth century confirmed the desire to discover the traces of a glorious past that Baroque intervention had silenced, under a uniform space treatment. Exactly two centuries ago, the recovery of these traces meant the start of the last major phase in the transformation of the building: the restoration. The building was considered subject to conserve and since then, efforts focused on the recovery of latent Umayyad architecture. Thus, the practice of restoration as a discipline was absolutely influenced by Archaeology as the only source of knowledge. Interventions were seeking the original as the way to recover that past in a space and formal way, concentrating on essential sites of the building. The statement as a national monument in 1882 prompted the State take charge of its maintenance and preservation, replacing to the nineteenth century Bishops and Cabildos, which had a very advanced understanding for that time. The arrival of the architect Velazquez Bosco in the last decades of the nineteenth century involved a momentous change in the history of the building, since he received a building with significant damage and he achieved the foundations of the building that we can see today. Efforts to a material and space recover returned the Mosque-Cathedral to its original image, accurately reproducing the models found in archaeological explorations. The arrival of Antonio Florez after Velazquez’s death involved the translation of discipline debate, which was developed in the first two decades of the twentieth century. Florez tried a new understanding of the intervention, considering conservation as a priority action. In 1926, the State reformed the way in which heritage was attended, creating a zones system with a few architects in charge of them. The existence of a new legislative framework, underpinned this new conservative vision, supported by the Athens Charter of 1931. This scientific restoration model fleeing from intervention in style and it appreciated the need to intervene in the most concise way, with a distinct language based on the data offered by Archaeology. Therefore, it continued with the appraisement of the building as a historical document, seeking in this case a differentiated image of intervention, against Velazquez mimetic attitude. It is remarkable the way in which the historian Manuel Gomez-Moreno influenced several generations of architects, archaeologists and historians, both in the scientific understanding of the restoration and the administrative structure. The work of Jose Maria Rodriguez Cano first and then Felix Hernandez was theoretically influenced by the Gomez-Moreno’s method, although in many respects their work did not represent a great difference to Velazquez Bosco. The search of the original returned to recur, but the economic charge of maintaining such a large building led to the non-realization of many of the most ambitious projects. This obsessive search for the original image of the building had its last and anachronistic stage with the intervention of the Department of Architecture at 70’s. However, the exhaustion of the scientific model had already led to a new scenario at European level, which crystallized in the Venice Charter of 1964 and a new definition of the object to be preserved beyond the value as a historical document. This new theoretical position had its translation to Spanish restaurateur model in the last quarter of the twentieth century, coinciding with the Transition. The architect Dionisio Hernandez Gil defended a different interpretation from archaeologists and historians, that had prevailed throughout the century. According to Hernandez Gil, the problems of intervention should focus primarily as architectural issues, abandoning the idea that they could only be determined by specialist. This theoretical conviction was defended from the new administration and led to the use of particularized criteria, from a multifocal analysis of each situation. And this change had its translation to the Mosque with the practice of Gabriel Ruiz Cabrero and Gabriel Rebollo. Consistent with this new perspective, they accepted the receiving building, replacing the search on original page for acceptance of all historical pages and respecting the constructive techniques of the past. The search for specific solutions from the architectural object meant the renewed attention to the powerful formal-constructive structure as the origin of all thought. Consider the Mosque-Cathedral as Architecture, involved the attention to all kinds of factors in addition to the historical, as a means to preserve its authenticity. This thesis aims to demonstrate that the practice of restoration in the Mosque-Cathedral throughout the twentieth century has evolved from the search of the original to the search for the authentic, reflecting a vision based on the archaeological against a renewed more complete architectural vision, including the above. Consideration of intervention in this building as another page in its history and not the last one, means the reissue of an own mechanism and a new impetus in that continuous transformation process.

Medida del consumo de energía en la descodificación de vídeos

Este proyecto se encuentra adscrito a la línea de investigación de optimización de consumo en terminales multimedia móviles que el Grupo de Diseño Electrónico y Microelectrónico (GDEM) de la UPM (Universidad Politécnica de Madrid) está llevando a cabo. Los sistemas empotrados móviles (Smartphone, Tablet,...) están alimentados con baterías. En este tipo de sistemas, una de las aplicaciones que más rápidamente consume energía es la descodificación de secuencias de vídeo. En este trabajo, queremos medir el consumo de energía de distintos descodificadores de vídeo para distintas secuencias, con el objetivo de entender mejor cómo se consume esta energía y poder encontrar diferentes métodos que lo reduzcan. Para ello comenzaremos describiendo nuestro entorno de trabajo, tanto el hardware como el software utilizado. Respeto al hardware cabe destacar el uso de una PandaBoard y un Smart Power de Odroid, entre otros muchos elementos utilizados, los cuales serán debidamente explicados en las siguientes páginas de este proyecto. Mientras que para el software destaca el uso de dos tipos de descodificadores uno CBP y otro PHP, los cuales serán descritos en profundidad en los siguientes capítulos de este documento. Este entorno de trabajo nos servirá para el estudio de las diferentes secuencias de vídeo, cuya codificación ha sido llevada en paralelo con otro proyecto que se está realizando en el grupo de GDEM de la UPM, y cuyo objetivo es el estudio de la calidad subjetiva durante la descodificación del mismo conjunto de secuencias de vídeo. Todas estas secuencias de vídeo han sido codificadas con diferentes parámetros de calidad y diversas estructuras de imágenes, para obtener así un banco de pruebas lo más amplio posible. Gracias a la obtención de estas secuencias de vídeo y utilizando nuestro entorno de trabajo, pasaremos a estudiar el consumo de energía que se produce al descodificar una a una todas las posibles secuencias de vídeo, dependiendo todo esto de su estructura de imágenes, su calidad y por supuesto, el descodificador utilizado en cada caso. Para terminar, se mostrará una comparativa entre los diferentes resultados obtenidos y se hará una discusión de estos, obteniendo en este caso, un resumen de los datos más significativos, así como las conclusiones más importantes obtenidas durante todo este trabajo. Al término de este proyecto y en unión con el estudio que se está llevando a cabo en paralelo sobre la calidad subjetiva, queda como línea futura de investigación encontrar el compromiso entre el consumo de energía de diferentes secuencias de vídeo y la calidad subjetiva de dichas secuencias. ABSTRACT. This project is assigned to the research line on consumption optimization in mobile multimedia terminals carried out by the Group of Electronic Design and Microelectronics (GDEM) of the Polytechnic University of Madrid (UPM). Embedded mobile systems (smartphones, tablets...) are powered by batteries. In such systems, one of the applications that more rapidly consumes power is the decoding of video streams. In this work, we measure the power consumption of different video decoders for different streams, in order to better understand how this energy is consumed and to find different methods to reduce it. To this end, we start by describing our working environment, both hardware and software used. As for the hardware, it is worth mentioning the use of PandaBoard and Smart Power Odroid, among many other elements, which will be duly explained in the following pages of this project. As for the software, we highlight the use of two types of decoders, CBP and PHP, which will be described in detail in the following chapters of this document. This working environment will help us to study different video streams, whose coding has been perfor-med in parallel under another project that is being carried out in the GDEM group of the UPM, and whose objective is the study of subjective quality for decoding the same set of video streams. All these video streams have been encoded with different quality parameters and image structures in order to obtain the widest set of samples. Thanks to the production of these video streams and the use of our working environment, we study the power consumption that occurs when decoding one by one all possible video streams, depending on the image structure, their quality and, of course, the decoder used in each case. Finally, we show a comparison between the different results and a discussion of these, obtaining a sum-mary of the most significant data and the main conclusions obtained during this project. Upon completion of this project and in conjunction with the project on the study of subjective quality that is being carried out in parallel, a future line of research could consist in finding the compromise between power consumption of different video streams and the subjective quality of these.

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.

RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates

Sequence-selective transcription by bacterial RNA polymerase (RNAP) requires σ factor that participates in both promoter recognition and DNA melting. RNAP lacking σ (core enzyme) will initiate RNA synthesis from duplex ends, nicks, gaps, and single-stranded regions. We have used DNA templates containing short regions of heteroduplex (bubbles) to compare initiation in the presence and absence of various σ factors. Using bubble templates containing the σD-dependent flagellin promoter, with or without its associated upstream promoter (UP) element, we demonstrate that UP element stimulation occurs efficiently even in the absence of σ. This supports a model in which the UP element acts primarily through the α subunit of core enzyme to increase the initial association of RNAP with the promoter. Core and holoenzyme do differ substantially in the template positions chosen for initiation: σD restricts initiation to sites 8–9 nucleotides downstream of the conserved −10 element. Remarkably, σA also has a dramatic effect on start-site selection even though the σA holoenzyme is inactive on the corresponding homoduplexes. The start sites chosen by the σA holoenzyme are located 8 nucleotides downstream of sequences on the nontemplate strand that resemble the conserved −10 hexamer recognized by σA. Thus, σA appears to recognize the −10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, σ also localizes the transcription start site.

Functional Domains of Rep2, a Transcriptional Activator Subunit for Res2–Cdc10, Controlling the Cell Cycle “Start”

In the fission yeast Schizosaccharomyces pombe, passage from G1 to S-phase requires the execution of the transcriptional factor complex that consists of the Cdc10 and Res1/2 molecules. This complex activates the MluI cell cycle box cis-element contained in genes essential for S-phase onset and progression. The rep2+ gene, isolated as a multicopy suppressor of a temperature-sensitive cdc10 mutant, has been postulated to encode a putative transcriptional activator subunit for the Res2–Cdc10 complex. To identify the rep2+ function and molecularly define its domain organization, we reconstituted the Res2–Cdc10 complex-dependent transcriptional activation in Saccharomyces cerevisiae. Reconstitution experiments, deletion analyses using one and two hybrid systems, and in vivo Res2 coimmunoprecipitation assays show that the Res2–Cdc10 complex itself can recognize but cannot activate MluI cell cycle box without Rep2, and that consistent with its postulated function, Rep2 contains 45-amino acid Res2 binding and 22-amino acid transcriptional activation domains in the middle and C terminus of the molecule, respectively. The functional essentiality of these domains is also demonstrated by their requirement for rescue of the cold-sensitive rep2 deletion mutant of fission yeast.

PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites

PromEC is an updated compilation of Escherichia coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E.coli chromosome, as well as the actual sequences in the promoter region. The database was updated as of July 2000 and includes 472 entries. PromEC is accessible at http://bioinfo.md.huji.ac.il/marg/promec

The Sda1 Protein Is Required for Passage through Start

We have used affinity chromatography to identify proteins that interact with Nap1, a protein previously shown to play a role in mitosis. Our studies demonstrate that a highly conserved protein called Sda1 binds to Nap1 both in vitro and in vivo. Loss of Sda1 function causes cells to arrest uniformly as unbudded cells that do not increase significantly in size. Cells arrested by loss of Sda1 function have a 1N DNA content, fail to produce the G1 cyclin Cln2, and remain responsive to mating pheromone, indicating that they arrest in G1 before Start. Expression of CLN2 from a heterologous promoter in temperature-sensitive sda1 cells induces bud emergence and polarization of the actin cytoskeleton, but does not induce cell division, indicating that the sda1 cell cycle arrest phenotype is not due simply to a failure to produce the G1 cyclins. The Sda1 protein is absent from cells arrested in G0 and is expressed before Start when cells reenter the cell cycle, further suggesting that Sda1 functions before Start. Taken together, these findings reveal that Sda1 plays a critical role in G1 events. In addition, these findings suggest that Nap1 is likely to function during G1. Consistent with this, we have found that Nap1 is required for viability in cells lacking the redundant G1 cyclins Cln1 and Cln2. In contrast to a previous study, we have found no evidence that Sda1 is required for the assembly or function of the actin cytoskeleton. Further characterization of Sda1 is likely to provide important clues to the poorly understood mechanisms that control passage through G1.

The cyclin-dependent kinase inhibitor p40SIC1 imposes the requirement for Cln G1 cyclin function at Start.

In yeast, commitment to cell division (Start) is catalyzed by activation of the Cdc28 protein kinase in late G1 phase by the Cln1, Cln2, and Cln3 G1 cyclins. The Clns are essential, rate-limiting activators of Start because cells lacking Cln function (referred to as cln-) arrest at Start and because CLN dosage modulates the timing of Start. At or shortly after Start, the development of B-type cyclin Clb-Cdc28 kinase activity and initiation of DNA replication requires the destruction of p40SIC1, a specific inhibitor of the Clb-Cdc28 kinases. I report here that cln cells are rendered viable by deletion of SIC1. Conversely, in cln1 cln2 cells, which have low CLN activity, modest increases in SIC1 gene dosage cause inviability. Deletion of SIC1 does not cause a general bypass of Start since (cln-)sic1 cells remain sensitive to mating pheromone-induced arrest. Far1, a pheromone-activated inhibitor of Cln-Cdc28 kinases, is dispensable for arrest of (cln-)sic1 cells by pheromone, implying the existence of an alternate Far1-independent arrest pathway. These observations define a pheromone-sensitive activity able to catalyze Start only in the absence of p40SIC1. The existence of this activity means that the B-type cyclin inhibitor p40SIC1 imposes the requirement for Cln function at Start.

How photons start vision.

Recent studies have elucidated how the absorption of a photon in a rod or cone cell leads to the generation of the amplified neural signal that is transmitted to higher-order visual neurons. Photoexcited visual pigment activates the GTP-binding protein transducin, which in turn stimulates cGMP phosphodiesterase. This enzyme hydrolyzes cGMP, allowing cGMP-gated cationic channels in the surface membrane to close, hyperpolarize the cell, and modulate transmitter release at the synaptic terminal. The kinetics of reactions in the cGMP cascade limit the temporal resolution of the visual system as a whole, while statistical fluctuations in the reactions limit the reliability of detection of dim light. Much interest now focuses on the processes that terminate the light response and dynamically regulate amplification in the cascade, causing the single photon response to be reproducible and allowing the cell to adapt in background light. A light-induced fall in the internal free Ca2+ concentration coordinates negative feedback control of amplification. The fall in Ca2+ stimulates resynthesis of cGMP, antagonizes rhodopsin's catalytic activity, and increases the affinity of the light-regulated cationic channel for cGMP. We are using physiological methods to study the molecular mechanisms that terminate the flash response and mediate adaptation. One approach is to observe transduction in truncated, dialyzed photoreceptor cells whose internal Ca2+ and nucleotide concentrations are under experimental control and to which exogenous proteins can be added. Another approach is to observe transduction in transgenic mouse rods in which specific proteins within the cascade are altered or deleted.