Public support for the deployment of next generation access networks-Common themes, methodological caveats and further research

Next generation telecommunications infrastructures are considered as a principal example of a new technology for sustainable economic growth. From their deployment it is expected that a wealth of innovations – hopefully converted into economic growth – new sources of employment and improved quality of life will result. In line with these prospects, public administrations at supranational, national, regional and local levels have encouraged the development of these new infrastructures. Moreover, in times of economic crisis, public assistance to deploy such networks encompasses the promise of placing a weak economy on the road to prosperity. However, such arguments and political claims clearly require rigorous assessment. In particular, any such assessment must adequately address the appropriate form of modelling that best captures key elements for identifiable progress from next generation access networks (NGAN).

Using online presence to improve online collaborative learning

Social software tools have become an integral part of students? personal lives and their primary communication medium. Likewise, these tools are increasingly entering the enterprise world (within the recent trend known as Enterprise 2.0) and becoming a part of everyday work routines. Aiming to keep the pace with the job requirements and also to position learning as an integral part of students? life, the field of education is challenged to embrace social software. Personal Learning Environments (PLEs) emerged as a concept that makes use of social software to facilitate collaboration, knowledge sharing, group formation around common interests, active participation and reflective thinking in online learning settings. Furthermore, social software allows for establishing and maintaining one?s presence in the online world. By being aware of a student's online presence, a PLE is better able to personalize the learning settings, e.g., through recommendation of content to use or people to collaborate with. Aiming to explore the potentials of online presence for the provision of recommendations in PLEs, in the scope of the OP4L project, we have develop a software solution that is based on a synergy of Semantic Web technologies, online presence and socially-oriented learning theories. In this paper we present the current results of this research work.

Proyectar dibujando: Una aproximación fenomenológica al estado naciente del proyecto. Un estudio entre dos culturas arquitectónicas

La acción del dibujar intenta presentarse en este texto como lenguaje mudo, práctica común general y práctica común en el campo arquitectónico en concreto; y también como acción, apertura, exploración (no representación) en el estado naciente del proyecto. La tesis se presenta como un estudio basado en la experiencia directa, la observación in situ (Practice Based Design Doctórate) intentando reflexionar no desde sus productos alcanzados al dibujar, sino desde la propia acción, enfatizando la dinamicidad del cuerpo como productor de gestos dinámicos. El trabajo busca describir la acción del trazar como apertura, exploración (no representación) en el estado naciente del proyecto. Es el cruce entre la acción experienciada y el pensamiento crítico respecto al hacer con aproximaciones a la artesanía (Sennett, 2010), al placer del dibujar (Nancy, 2013) y la aventura de conformar (Badiou, 2006). La experiencia en el dibujar que este estudio recoge es la desarrollada por la autora en el contexto pedagógico del D.I.G.A. de la E.T.S.A. de Madrid en concreto en las asignaturas “Dibujo Avanzado e Interpretación Gráfica (DAII) I y II” y “Dibujo del Natural” ambas impartidas por el profesor Antonio Verd Herrero y en la participación en los trabajos del Grupo de Investigación y de Innovación Educativa denominado: “Hypermedia” dirigidos por el profesor Javier Seguí, en el periodo que va del año 2007 a la actualidad. La colección de acontecimientos que surgió de esta experiencia y se formó de aproximaciones sucesivas presenta algunos rasgos característicos de la acción del dibujar. Los acontecimientos abordan la acción del dibujar desde una experiencia muda, un tipo de lenguaje, escritura y comunicación común, intercultural pero a la vez impersonal, desde su relación con la escritura, la palabra, el movimiento, el gesto y su imagen. El dibujar se presenta como modo de exploración en la investigación proyectual basada en la arbitrariedad que requiere voluntad, compromiso, ir en contra para participar en cualquier transformación de los límites (físicos, nacionales, sociales, de género, religión, sentido). El dibujar no representativo se presenta como técnica imaginaria radical, “terapia” configural con capacidad para la experimentación con uno mismo (Sloderdijk, 2003), un modo de comunicación intercultural que, sin embargo, siempre recurre al lenguaje verbal, leída e interpretada para cobrar sentido. ABSTRACT The action of drawing is intended to be presented in this text as a mute language, a common practice in general and a common practice in the field of architecture specifically; and also as an action, opening, exploration (not representation) at the birth stage of a project. The thesis forms a study based on a direct observation in an in situ experience (Practice Based Design Doctórate), which intends to reflect not on the products produced by drawing, but on the action itself, emphasizing on the dynamics of the body as a generator of dynamic gestures. The work is the intersection of experienced action and critical thinking related with the making with an approach to a path on craftsmanship (Sennett, 2010), the pleasure in drawing (Nancy, 2013) and the adventure of compromise/ conciliation (Badiou, 2006). The experience in drawing was collected and developed for this study by the author in the context of D.I.G.A. at the E.T.S.A. of Madrid and in particular at the courses of “Advanced Drawing and Graphic Interpretation” (DAII) I y II” and “Life drawing”, together with the active participation and the work of the investigation and Innovation Educational Group “Hypermedia”, coordinated by professor Javier Seguí, during the period starting the year 2007 until the present (2013). The collection of the events derives from a process of successive attempts to approach some characteristic aspects of the action of drawing. The events approach the action of drawing as a mute experience, a kind of language, common communication, writing, gesture and image. Drawing is presented as a way of exploration for a project's investigation, based on arbitrarily and on the asking “what if”. At the same time this process requires will, compromise, opposition in order to participate in a transformation of any kind of limits (physical, national, social, genre, religion, sense). This thesis aims to present non-representative drawing as a radical imaginary technique, a configurational ‘therapy’ with the capacity to experiment with oneself (Sloderdijk, 2003). It can also be considered as a way of intercultural communication which always uses the verbal, readable and interpreted language in order to charge sense.

Stoichiometry in Context: Inquiry-Guided Problems of Chemistry for Encouraging Critical Thinking in Engineering Students

This paper focuses on examples of educational tools concerning the learning of chemistry for engineering students through different daily life cases. These tools were developed during the past few years for enhancing the active role of students. They refer to cases about mineral water, medicaments, dentifrices and informative panels about solar power, where an adequate quantitative treatment through stoichiometry calculations allows the interpretation of data and values announced by manufacturers. These cases were developed in the context of an inquiry-guided instruction model. By bringing tangible chemistry examples into the classroom we provide an opportunity for engineering students to apply this science to familiar products in hopes that they will appreciate chemistry more, will be motivated to study concepts in greater detail, and will connect the relevance of chemistry to everyday life.

Influencia de un programa de ejercicio aeróbico en la calidad de vida de pacientes afectadas por cáncer de mama = Influence of an aerobic exercise program on breast cancer patients’ quality of life

INTRODUCCIÓN Actualmente las supervivientes de cáncer de mama viven durante más tiempo. Sin embargo, los tratamientos utilizados presentan importantes efectos secundarios que afectan y marcan su calidad de vida. Numerosos estudios han mostrado que el ejercicio es una herramienta apta, segura y efectiva reduciendo algunos de estos efectos secundarios y, en suma, mejorando la calidad de vida de estas pacientes, aspecto que presenta al ejercicio físico como una intervención integral para ellas. Por el contrario, se ha observado que las supervivientes de cáncer de mama reducen la cantidad de ejercicio que realizan después de dichos tratamientos. Por ello, el objetivo de este proyecto es examinar los efectos de un programa integral de ejercicio en la calidad de vida y la cantidad de ejercicio físico que realizan las pacientes con cáncer de mama en su tiempo, tras finalizar sus tratamientos. MATERIAL Y MÉTODOS Se diseñó un Ensayo Clínico Aleatorizado. Noventa pacientes diagnosticadas de cáncer de mama en estadios tempranos que habían terminado sus tratamientos de radioterapia y quimioterapia recientemente, fueron reclutadas por la Universidad Politécnica de Madrid, desde enero de 2013 hasta junio de 2014. Las pacientes fueron aleatorizadas tras las mediciones iniciales al grupo control (tratamientos habituales) o grupo intervención, durante tres meses. La intervención consistió en 24 clases de ejercicio combinando práctica aeróbica y de fuerza con el fin de reducir los efectos secundarios de dichos tratamientos. La calidad de vida, la cantidad de ejercicio físico realizado en tiempo de ocio, VO2max, la fuerza, la movilidad articular del hombro, la fatiga, la depresión y la ansiedad fueron medidos al inicio y después de los tres meses en todos los pacientes. RESULTADOS Un total de 89 pacientes con una media de 49.06±8.75 de edad fueron finalmente analizadas. El grupo intervención (n=44) mostraron significativamente mejores resultados en calidad de vida (p=0.0001; d=0.85), cantidad de ejercicio en tiempo de ocio (p=0.0001; d=2.77), en variables de la composición corporal, en variables físicas y en variables psicológicas comparado con el grupo control (n=45). Además, se observó una correlación significativa entre la calidad de vida y el ejercicio realizado en tiempo de ocio en el grupo intervención (r= 0.58; p=0.001), que no fue patente en el grupo control. Se observaron cambios significativos en el grupo de intervención relativos a la composición corporal, con aumento de la masa muscular (p=0.001) y reducción de la masa grasa (p=0.0001). Tanto las variables físicas como psicológicas también mostraron diferencias significativas a favor al grupo de intervención en las comparaciones entre grupos. CONCLUSIONES Según estos resultados, un programa de ejercicio físico específico es una intervención integral que mejora los hábitos y la calidad de vida de las supervivientes de cáncer de mama, lo que reduce determinados efectos secundarios de los tratamientos y aumenta la salud física y psicológica general de estas mujeres. Este tipo de intervenciones pude ser una herramienta barata y efectiva para ofrecer a los pacientes, integrada en los tratamientos habituales. ABSTRACT INTRODUCTION It is well known that breast cancer survivors are living longer. However, breast cancer treatments present serious side effects, which could affect breast cancer survivors’ (BCS) health and quality of life (QoL). Exercise has been presented as a feasible, safe and effective tool in reducing some of these side effects and to improve survivors’ QoL, acting as an integrative treatment for them, although it has been observed that BCS reduce their leisure time exercise (LTE) levels. Therefore, the aim of this study was to examine the effects of an integrative exercise program in QoL and LTE in BCS after the completion of their adjuvant treatment. MATERIAL AND METHODS A randomized controlled trial (RCT) was designed. Ninety patients diagnosed with an early stage of breast cancer and who recently finished chemotherapy and radiotherapy treatments were recruited by the Technical University of Madrid from January 2013 to June 2014. Patients were randomized after baseline assessments to the intervention group (IG) or to the control group (CG) (usual care) for three months. The Intervention consisted in 24 supervised exercise classes, combining aerobic and resistance exercises in order to reduce the most common side effects of the treatments. QoL, LTE, body composition, VO2max, strength, shoulder range of motion, fatigue, depression and self-esteem were measured in all the patients at baseline and after three months. RESULTS A total of 89 patients aged 49.06±8.75 years were finally assessed. IG (n=44) showed significant better results in QoL (p=0.0001; d=0.85), LTE (p=0.0001; d=2.77), in body composition, in the physical variable and in psychological outcomes, compared with the CG (n=45). In addition, a correlation between QoL and LTE (r= 0.58; p=0.001) was found in the IG, while CG did not show this correlation. Significant changes in body composition were observed in the group comparisons, especially in lean mass (p=0.001) and body fat mass (p= 0.0001). Positive changes were also observed in the physical and psychological variables in comparisons between groups. CONCLUSIONS These results suggest that this exercise program may be an integrative intervention, which is able to improve QoL and LTE levels in breast cancer survivors, reducing breast cancer side effects of treatments and improving their physical and psychological general health. Exercise may be an effective and inexpensive strategy to be included in patients integrative care.

Engineering Computational Emotion - A Reference Model for Emotion in Artificial Systems

Emotion is generally argued to be an influence on the behavior of life systems, largely concerning flexibility and adaptivity. The way in which life systems acts in response to a particular situations of the environment, has revealed the decisive and crucial importance of this feature in the success of behaviors. And this source of inspiration has influenced the way of thinking artificial systems. During the last decades, artificial systems have undergone such an evolution that each day more are integrated in our daily life. They have become greater in complexity, and the subsequent effects are related to an increased demand of systems that ensure resilience, robustness, availability, security or safety among others. All of them questions that raise quite a fundamental challenges in control design. This thesis has been developed under the framework of the Autonomous System project, a.k.a the ASys-Project. Short-term objectives of immediate application are focused on to design improved systems, and the approaching of intelligence in control strategies. Besides this, long-term objectives underlying ASys-Project concentrate on high order capabilities such as cognition, awareness and autonomy. This thesis is placed within the general fields of Engineery and Emotion science, and provides a theoretical foundation for engineering and designing computational emotion for artificial systems. The starting question that has grounded this thesis aims the problem of emotion--based autonomy. And how to feedback systems with valuable meaning has conformed the general objective. Both the starting question and the general objective, have underlaid the study of emotion, the influence on systems behavior, the key foundations that justify this feature in life systems, how emotion is integrated within the normal operation, and how this entire problem of emotion can be explained in artificial systems. By assuming essential differences concerning structure, purpose and operation between life and artificial systems, the essential motivation has been the exploration of what emotion solves in nature to afterwards analyze analogies for man--made systems. This work provides a reference model in which a collection of entities, relationships, models, functions and informational artifacts, are all interacting to provide the system with non-explicit knowledge under the form of emotion-like relevances. This solution aims to provide a reference model under which to design solutions for emotional operation, but related to the real needs of artificial systems. The proposal consists of a multi-purpose architecture that implement two broad modules in order to attend: (a) the range of processes related to the environment affectation, and (b) the range or processes related to the emotion perception-like and the higher levels of reasoning. This has required an intense and critical analysis beyond the state of the art around the most relevant theories of emotion and technical systems, in order to obtain the required support for those foundations that sustain each model. The problem has been interpreted and is described on the basis of AGSys, an agent assumed with the minimum rationality as to provide the capability to perform emotional assessment. AGSys is a conceptualization of a Model-based Cognitive agent that embodies an inner agent ESys, the responsible of performing the emotional operation inside of AGSys. The solution consists of multiple computational modules working federated, and aimed at conforming a mutual feedback loop between AGSys and ESys. Throughout this solution, the environment and the effects that might influence over the system are described as different problems. While AGSys operates as a common system within the external environment, ESys is designed to operate within a conceptualized inner environment. And this inner environment is built on the basis of those relevances that might occur inside of AGSys in the interaction with the external environment. This allows for a high-quality separate reasoning concerning mission goals defined in AGSys, and emotional goals defined in ESys. This way, it is provided a possible path for high-level reasoning under the influence of goals congruence. High-level reasoning model uses knowledge about emotional goals stability, letting this way new directions in which mission goals might be assessed under the situational state of this stability. This high-level reasoning is grounded by the work of MEP, a model of emotion perception that is thought as an analogy of a well-known theory in emotion science. The work of this model is described under the operation of a recursive-like process labeled as R-Loop, together with a system of emotional goals that are assumed as individual agents. This way, AGSys integrates knowledge that concerns the relation between a perceived object, and the effect which this perception induces on the situational state of the emotional goals. This knowledge enables a high-order system of information that provides the sustain for a high-level reasoning. The extent to which this reasoning might be approached is just delineated and assumed as future work. This thesis has been studied beyond a long range of fields of knowledge. This knowledge can be structured into two main objectives: (a) the fields of psychology, cognitive science, neurology and biological sciences in order to obtain understanding concerning the problem of the emotional phenomena, and (b) a large amount of computer science branches such as Autonomic Computing (AC), Self-adaptive software, Self-X systems, Model Integrated Computing (MIC) or the paradigm of models@runtime among others, in order to obtain knowledge about tools for designing each part of the solution. The final approach has been mainly performed on the basis of the entire acquired knowledge, and described under the fields of Artificial Intelligence, Model-Based Systems (MBS), and additional mathematical formalizations to provide punctual understanding in those cases that it has been required. This approach describes a reference model to feedback systems with valuable meaning, allowing for reasoning with regard to (a) the relationship between the environment and the relevance of the effects on the system, and (b) dynamical evaluations concerning the inner situational state of the system as a result of those effects. And this reasoning provides a framework of distinguishable states of AGSys derived from its own circumstances, that can be assumed as artificial emotion.

RECONHECENDO-SE SEM-RELIGIÃO NAS PERIFERIAS DA CIDADE: LIBERDADE COMPARTILHADA COMO RESISTÊNCIA

Reconhecendo, a partir da constatação empírica, a multiplicidade de escolhas de crenças no Mundo e em particular na periferia urbana paulistana, reconhecemos, também, a emergência criativa de novas possibilidades de crer e não crer. Tal amplitude não apenas aponta para o crer (segundo as ofertas de um sem número de religiões) e o não crer (ateu e agnóstico), mas para uma escolha que poderia vir a ser silenciada e esquecida, neste binômio arcaico e obsoleto, quando alguém se dá à liberdade crer sem ter religião. Reconhecer interessadamente os sem-religião nas periferias urbanas paulistanas é dar-se conta das violências a que estes indivíduos estão submetidos: violência econômica, violência da cidadania (vulnerabilidade) e proveniente da armas (grupos x Estado). Tanto quanto a violência do esquecimento e silenciamento. A concomitância espaço-temporal dos sem-religião nas periferias, levou-nos buscar referências em teorias de secularização e de laicidade, e, a partir destas, traçar uma história do poder violento, cuja pretensão é a inelutabilidade, enquanto suas fissuras são abertas em espaços de resistências. A história da legitimação do poder que se quer único, soberano, de caráter universal, enquanto fragmenta a sociedade em indivíduos atomizados, fragilizando vínculos horizontais, e a dos surgimentos de resistências não violentas questionadoras da totalidade trágica, ao reconhecer a liberdade de ser com autonomia, enquanto se volta para a produção de partilha de bens comuns. Propomos reconhecer a igual liberdade de ser (expressa na crença da filiação divina) e de partilhar o bem comum em reconhecimentos mútuos (expressa pela ação social), uma expressão de resistência não violenta ao poder que requer a igual abdicação da liberdade pela via da fragmentação individualizante e submissão inquestionável à ordem totalizante. Os sem-religião nas periferias urbanas, nossos contemporâneos, partilhariam uma tal resistência, ao longo da história, com as melissas gregas, os profetas messiânicos hebreus, os hereges cristãos e os ateus modernos, cuja pretensão não é o poder, mas a partilha igual da liberdade e dos bens comuns. Estes laicos, de fato, seriam agentes de resistências de reconhecimento mútuos, em espaços de multiplicidade crescente, ao poder violento real na história.

Antiviral agent blocks breathing of the common cold virus

A dynamic capsid is critical to the events that shape the viral life cycle; events such as cell attachment, cell entry, and nucleic acid release demand a highly mobile viral surface. Protein mass mapping of the common cold virus, human rhinovirus 14 (HRV14), revealed both viral structural dynamics and the inhibition of such dynamics with an antiviral agent, WIN 52084. Viral capsid digestion fragments resulting from proteolytic time-course experiments provided structural information in good agreement with the HRV14 three-dimensional crystal structure. As expected, initial digestion fragments included peptides from the capsid protein VP1. This observation was expected because VP1 is the most external viral protein. Initial digestion fragments also included peptides belonging to VP4, the most internal capsid protein. The mass spectral results together with x-ray crystallography data provide information consistent with a “breathing” model of the viral capsid. Whereas the crystal structure of HRV14 shows VP4 to be the most internal capsid protein, mass spectral results show VP4 fragments to be among the first digestion fragments observed. Taken together this information demonstrates that VP4 is transiently exposed to the viral surface via viral breathing. Comparative digests of HRV14 in the presence and absence of WIN 52084 revealed a dramatic inhibition of digestion. These results indicate that the binding of the antiviral agent not only causes local conformational changes in the drug binding pocket but actually stabilizes the entire viral capsid against enzymatic degradation. Viral capsid mass mapping provides a fast and sensitive method for probing viral structural dynamics as well as providing a means for investigating antiviral drug efficacy.

Late-onset minor and major depression: early evidence for common neuroanatomical substrates detected by using MRI

The purpose of our study was to examine the neuroanatomical correlates of late-onset minor and major depression and to compare them with similar measures obtained from nondepressed controls. Our study groups were comprised of 18 patients with late-onset minor depression, 35 patients diagnosed with late-onset major depression, and 30 nondepressed controls. All subjects were scanned by using a 1.5-tesla MRI scanner. Absolute whole brain volume and normalized measures of prefrontal and temporal lobe volumes were obtained and used for comparison among groups. Our findings indicate that patients with minor depression present with specific neuroanatomical abnormalities that are comparable with the major depression group but significantly different from the controls. Normalized prefrontal lobe volumes show a significant linear trend with severity of depression, with volumes decreasing with illness severity. Whole brain volumes did not differ significantly among groups. These findings have broad implications for the biology of late-life depression and suggest that there may be common neurobiological substrates that underlie all clinically significant forms of late-onset mood disturbances.

A common polymorphism associated with antibiotic-induced cardiac arrhythmia

Drug-induced long QT syndrome (LQTS) is a prevalent disorder of uncertain etiology that predisposes to sudden death. KCNE2 encodes MinK-related peptide 1 (MiRP1), a subunit of the cardiac potassium channel IKr that has been associated previously with inherited LQTS. Here, we examine KCNE2 in 98 patients with drug-induced LQTS, identifying three individuals with sporadic mutations and a patient with sulfamethoxazole-associated LQTS who carried a single-nucleotide polymorphism (SNP) found in ≈1.6% of the general population. While mutant channels showed diminished potassium flux at baseline and wild-type drug sensitivity, channels with the SNP were normal at baseline but inhibited by sulfamethoxazole at therapeutic levels that did not affect wild-type channels. We conclude that allelic variants of MiRP1 contribute to a significant fraction of cases of drug-induced LQTS through multiple mechanisms and that common sequence variations that increase the risk of life-threatening drug reactions can be clinically silent before drug exposure.

Functional expression of the Wilson disease protein reveals mislocalization and impaired copper-dependent trafficking of the common H1069Q mutation

Wilson disease is an autosomal recessive disorder of hepatic copper metabolism caused by mutations in a gene encoding a copper-transporting P-type ATPase. To elucidate the function of the Wilson protein, wild-type and mutant Wilson cDNAs were expressed in a Menkes copper transporter-deficient mottled fibroblast cell line defective in copper export. Expression of the wild-type cDNA demonstrated trans-Golgi network localization and copper-dependent trafficking of the Wilson protein identical to previous observations for the endogenously expressed protein in hepatocytes. Furthermore, expression of the Wilson cDNA rescued the mottled phenotype as evidenced by a reduction in copper accumulation and restoration of cell viability. In contrast, expression of an H1069Q mutant Wilson cDNA did not rescue the mottled phenotype, and immunofluorescence studies showed that this mutant Wilson protein was localized in the endoplasmic reticulum. Consistent with these findings, pulse–chase analysis demonstrated a 5-fold decrease in the half-life of the H1069Q mutant as compared with the wild-type protein. Maintenance of these transfected cell lines at 28°C resulted in localization of the H1069Q protein in the trans-Golgi network, suggesting that a temperature-sensitive defect in protein folding followed by degradation constitutes the molecular basis of Wilson disease in patients harboring the H1069Q mutation. Taken together, these studies describe a tractable expression system for elucidating the function and localization of the copper-transporting ATPases in mammalian cells and provide compelling evidence that the Wilson protein can functionally substitute for the Menkes protein, supporting the concept that these proteins use common biochemical mechanisms to effect cellular copper homeostasis.

Programmed cell death: a way of life for plants.

Cell death in higher plants has been widely observed in predictable patterns throughout development and in response to pathogenic infection. Genetic, biochemical, and morphological evidence suggests that these cell deaths occur as active processes and can be defined formally as examples of programmed cell death (PCD). Intriguingly, plants have at least two types of PCD, an observation that is also true of PCD in animals [Schwartz, L. M., Smith, W.W., Jones, M. E. E. & Osborne, B. A. (1993) Proc. Natl. Acad. Sci. USA 90, 980-984]. Thus, in plants, PCD resembles either a common form of PCD seen in animals called apoptosis or it resembles a morphologically distinct form of cell death. The ubiquitous occurrence and necessity of PCD for plant development and defense suggest that the underlying mechanisms of regulation and execution of these processes merit further examination.

A minimal gene set for cellular life derived by comparison of complete bacterial genomes.

The recently sequenced genome of the parasitic bacterium Mycoplasma genitalium contains only 468 identified protein-coding genes that have been dubbed a minimal gene complement [Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., et al. (1995) Science 270, 397-403]. Although the M. genitalium gene complement is indeed the smallest among known cellular life forms, there is no evidence that it is the minimal self-sufficient gene set. To derive such a set, we compared the 468 predicted M. genitalium protein sequences with the 1703 protein sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae. M. genitalium and H. influenzae belong to two ancient bacterial lineages, i.e., Gram-positive and Gram-negative bacteria, respectively. Therefore, the genes that are conserved in these two bacteria are almost certainly essential for cellular function. It is this category of genes that is most likely to approximate the minimal gene set. We found that 240 M. genitalium genes have orthologs among the genes of H. influenzae. This collection of genes falls short of comprising the minimal set as some enzymes responsible for intermediate steps in essential pathways are missing. The apparent reason for this is the phenomenon that we call nonorthologous gene displacement when the same function is fulfilled by nonorthologous proteins in two organisms. We identified 22 nonorthologous displacements and supplemented the set of orthologs with the respective M. genitalium genes. After examining the resulting list of 262 genes for possible functional redundancy and for the presence of apparently parasite-specific genes, 6 genes were removed. We suggest that the remaining 256 genes are close to the minimal gene set that is necessary and sufficient to sustain the existence of a modern-type cell. Most of the proteins encoded by the genes from the minimal set have eukaryotic or archaeal homologs but seven key proteins of DNA replication do not. We speculate that the last common ancestor of the three primary kingdoms had an RNA genome. Possibilities are explored to further reduce the minimal set to model a primitive cell that might have existed at a very early stage of life evolution.

Hematopoietic and lung abnormalities in mice with a null mutation of the common beta subunit of the receptors for granulocyte-macrophage colony-stimulating factor and interleukins 3 and 5.

Gene targeting was used to create mice with a null mutation of the gene encoding the common beta subunit (beta C) of the granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin 3 (IL-3; multi-CSF), and interleukin 5 (IL-5) receptor complexes (beta C-/- mice). High-affinity binding of GM-CSF was abolished in beta C-/- bone marrow cells, while cells from heterozygous animals (beta C+/- mice) showed an intermediate number of high-affinity receptors. Binding of IL-3 was unaffected, confirming that the IL-3-specific beta chain remained intact. Eosinophil numbers in peripheral blood and bone marrow of beta C-/- animals were reduced, while other hematological parameters were normal. In clonal cultures of beta C-/- bone marrow cells, even high concentrations of GM-CSF and IL-5 failed to stimulate colony formation, but the cells exhibited normal quantitative responsiveness to stimulation by IL-3 and other growth factors. beta C-/- mice exhibited normal development and survived to young adult life, although they developed pulmonary peribronchovascular lymphoid infiltrates and areas resembling alveolar proteinosis. There was no detectable difference in the systemic clearance and distribution of GM-CSF between beta C-/- and wild-type littermates. The data establish that beta C is normally limiting for high-affinity binding of GM-CSF and demonstrate that systemic clearance of GM-CSF is not mediated via such high-affinity receptor complexes.

Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications.

Universal trees based on sequences of single gene homologs cannot be rooted. Iwabe et al. [Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S. & Miyata, T. (1989) Proc. Natl. Acad. Sci. USA 86, 9355-9359] circumvented this problem by using ancient gene duplications that predated the last common ancestor of all living things. Their separate, reciprocally rooted gene trees for elongation factors and ATPase subunits showed Bacteria (eubacteria) as branching first from the universal tree with Archaea (archaebacteria) and Eucarya (eukaryotes) as sister groups. Given its topical importance to evolutionary biology and concerns about the appropriateness of the ATPase data set, an evaluation of the universal tree root using other ancient gene duplications is essential. In this study, we derive a rooting for the universal tree using aminoacyl-tRNA synthetase genes, an extensive multigene family whose divergence likely preceded that of prokaryotes and eukaryotes. An approximately 1600-bp conserved region was sequenced from the isoleucyl-tRNA synthetases of several species representing deep evolutionary branches of eukaryotes (Nosema locustae), Bacteria (Aquifex pyrophilus and Thermotoga maritima) and Archaea (Pyrococcus furiosus and Sulfolobus acidocaldarius). In addition, a new valyl-tRNA synthetase was characterized from the protist Trichomonas vaginalis. Different phylogenetic methods were used to generate trees of isoleucyl-tRNA synthetases rooted by valyl- and leucyl-tRNA synthetases. All isoleucyl-tRNA synthetase trees showed Archaea and Eucarya as sister groups, providing strong confirmation for the universal tree rooting reported by Iwabe et al. As well, there was strong support for the monophyly (sensu Hennig) of Archaea. The valyl-tRNA synthetase gene from Tr. vaginalis clustered with other eukaryotic ValRS genes, which may have been transferred from the mitochondrial genome to the nuclear genome, suggesting that this amitochondrial trichomonad once harbored an endosymbiotic bacterium.