Registry of samples and environmental context from the Ocean Sampling Day 2014

The Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world's oceans which took place (for the first time) on the summer solstice (June 21st) in the year 2014. These cumulative samples, related in time, space and environmental parameters, provide insights into fundamental rules describing microbial diversity and function and contribute to the blue economy through the identification of novel, ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments to follow in the coming decade. The present data set includes a description of each sample collected during the Ocean Sampling Day 2014 and provides contextual environmental data measured concurrently with the collection of water samples for genomic analyses.

La ciudad progresiva: una lectura de los asentamientos humanos de Lima

La presente tesis busca aquellos aspectos de la ciudad informal, espontánea o popular, que podrían enriquecer el estudio y las miradas sobre las ciudades contemporáneas y dar ideas sobre una nueva forma de planificación, más versátil, capaz de evolucionar en el tiempo, más habitable y más adaptada a este momento histórico, partiendo desde una mirada de la ciudad de Lima, hasta develar, mediante el análisis de la evolución de sus tejidos y unidades de vivienda, una nueva idea de ciudad. La ciudad progresiva, es el corolario de una lectura que hace referencia por un lado, al vínculo entre la casa y la ciudad, y por otro, a la evolución y cambio de Lima y sus asentamientos. ABSTRACT This thesis seeks those aspects of the informal, spontaneous or popular city, which could enrich the study and overviews on contemporary cities and provide insights into a new way of planning, more versatile and able to evolve over time, more livable and more adapted to this historic moment, starting from a viewpoint of the city of Lima, to reveal, by analyzing the evolution of their tissues and housing units, a new idea of the city. The progressive city, is the corollary of a reading that refers on the one hand, the link between the house and the city, and secondly, to the evolution and change of Lima and its settlements.

La invención en la obra de Julio Lafuente: entre la utopía y la construcción

La obra de Julio Lafuente es extraordinariamente abundante y heterogenea, de un experimentalismo tan admirable en casos particulares como difícilmente caracterizable en su conjunto. El inventario ha revelado la existencia de más de 360 proyectos, de los que cerca de 200 están construidos, e incluye obras de arquitectura, urbanismo, escenografía y mobiliario, muchas de ellas reconocidas internacionalmente y profusamente publicadas entre 1950 y 1980. Es decir, nos encontramos ante un panorama de producción, divulgación y reconocimiento de su obra en el pasado reciente que contrasta con el actual desconocimiento de la misma. Situación que esta tesis doctoral pretende revertir. La investigación se articula en dos partes. La primera de ellas constituye el núcleo argumental y se compone de cuatro capítulos que permiten comprender el carácter de la obra de Julio Lafuente: su biografía profesional, una panorámica contextualizada de su obra, el estudio en profundidad de dos obras escogidas y la revisión transversal de los aspectos más relevantes en su arquitectura. Este primer volumen incluye dos capítulos adicionales: una bibliografía exhaustiva de sus obras y la traducción de publicaciones específicas coetáneas, recogidas en un anexo. La segunda parte consiste en una catalogación de la obra de Julio Lafuente, inexistente hasta la fecha, desarrollada por la autora en paralelo a su participación en la realización del Archivo de Julio Lafuente en Roma, lo que ha facilitado el acceso directo a la documentación original. Una revisión panorámica de diversas obras de Lafuente en relación con otras obras y corrientes de pensamiento coetáneas ha permitido comprender la pertenencia inequívoca de la obra de Julio Lafuente a su contexto: fundamentalmente, la Italia del período comprendido entre 1950 y 1980, un contexto del que se nutre y al que contribuye sin descanso. La mayor parte de la abundante obra arquitectónica de Lafuente se dedica al desarrollo de edificios de vivienda, normalmente construidos en los ensanches de Roma. En el conjunto de esta prolija trayectoria sobresalen, sin embargo, algunos logros extraordinarios que han permitido apoyar el desarrollo argumental de la investigación. Entre ellos, se han escogido para su estudio en profundidad dos obras —el hotel en la roca (1967), en Gozo (Malta) y el hipódromo de Tor di Valle (1959), en Roma—, que constituyen sendos casos singulares en los que Lafuente alcanza las cotas más altas de coherencia, significación y calidad arquitectónica, y que caracterizan el marco en el que se desarrolla la investigación: entre la utopía y la construcción. Al mismo tiempo, se trata de dos obras complementarias que llevan al extremo algunos de los aspectos a los que Julio Lafuente presta más atención en el conjunto de su obra, como la relación con el lugar, la invención estructural o el cuidado de los detalles constructivos. Estos rasgos se han revisado de un modo transversal en el último capítulo, incidiendo en algunos casos particulares que, a modo de metonimia, han permitido tomar la parte por el todo. La investigación confirma el compromiso de la obra de Lafuente con la lógica constructiva, si bien la componente idealizada se reconoce, aunque en un tono menor respecto al empeño constructivo, en una gran parte su arquitectura. Esta tendencia a la idealización es, posiblemente, una de las razones que ha llevado a quienes hasta hoy han escrito sobre su obra, a especular con las ideas de invención y utopía en la arquitectura de Julio Lafuente. El catálogo inédito de la obra de Julio Lafuente constituye la segunda parte de la tesis doctoral y permite realizar consultas posteriores que puedan dar continuidad a la investigación aquí iniciada. ABSTRACT The architectural work of Julio Lafuente is extraordinary wide and heterogeneous, of so admirable experimentalism in particular cases as difficult to be characterized as a whole. The inventory of his work has revealed the existence of more than 360 projects, of which about 200 are built, including works of architecture, urban planning, scenery and furniture, many of which were internationally recognized and widely published between 1950 and 1980. This overview of production, spread and recognition of his work in the recent past hugely contrasts with the current lack of knowledge of it. Situation that this PhD thesis aims to reverse. The thesis is divided into two parts. The first part is the core argument and comprises four sections that provide insights into the nature of the work of Julio Lafuente: professional biography, a contextualized view of his work, in-depth study of two selected works and cross review of the most relevant aspects in his architecture. This volume includes an exhaustive bibliography and translation of contemporaneous specific publications, incorporated in an annex. The second part consists of a catalog of the work of Julio Lafuente, non-existent to date, developed in parallel with the participation of the author in the making process of the Archive of Julio Lafuente in Rome, which has provided access to the original documentation. Research develops a wide-ranging approach to the architecture of Julio Lafuente in its context. To this purpose, various of his works have been reviewed in relation to other contemporary works, which have revealed a direct attachment of Lafuente’s work to its context: mainly Italy, for the period between 1950 and 1980. Most of his wide architectural work is related to housing projects, usually built in the extensions of Rome. In this broad regular work, however, highlight some outstanding achievements which have given support to the research argumental line. Among them, two works have been selected for an in-depth study: the hotel in the Maltese rock of Gozo (1967) and the Tor di Valle racecourse building (1959) in Rome. Both are individual cases in which Lafuente reaches the highest levels of coherence, significance and architectural quality, and both characterize the frame in which this research takes place: between utopia and construction. These selected projects are two complementary works that embody some of the aspects to which Julio Lafuente pays more attention, such as the experiencing of place, the structural invention or concern for construction details, among others. These features have been reviewed through a transversal regard in the last chapter, focusing on some particular cases, in the way in which metonymy is used, allowing to take the part for the whole. Research confirms that the work of Julio Lafuente stands out for its commitment to construction logic, while the idealized component is recognized, although in a minor key with respect to constructive engagement, in most of his architecture from the beginning to his latest proposals. This tendency to idealization is probably one of the reasons that has often led to those who have written about him, to speculate on the ideas of invention and utopia in the work of Julio Lafuente. The unpublished catalog of the work of Julio Lafuente, which constitutes the second part of the thesis, presents the architectural work of Julio Lafuente and allows further research that could continue the one started here.

Developmental emergence of different forms of neuromodulation in Aplysia sensory neurons

The capacity for neuromodulation and biophysical plasticity is a defining feature of most mature neuronal cell types. In several cases, modulation at the level of the individual neuron has been causally linked to changes in the functional output of a neuronal circuit and subsequent adaptive changes in the organism’s behavioral responses. Understanding how such capacity for neuromodulation develops therefore may provide insights into the mechanisms both of neuronal development and learning and memory. We have examined the development of multiple forms of neuromodulation triggered by a common neurotransmitter, serotonin, in the pleural sensory neurons of Aplysia californica. We have found that multiple signaling cascades within a single neuron develop sequentially, with some being expressed only very late in development. In addition, our data suggest a model in which, within a single neuromodulatory pathway, the elements of the signaling cascade are developmentally expressed in a “retrograde” manner with the ionic channel that is modulated appearing early in development, functional elements in the second messenger cascade appearing later, and finally, coupling of the second messenger cascade to the serotonin receptor appearing quite late. These studies provide the characterization of the development of neuromodulation at the level of an identified cell type and offer insights into the potential roles of neuromodulatory processes in development and adult plasticity.

Expression of the peroxisome proliferator-activated receptor γ (PPARγ) in human atherosclerosis and regulation in macrophages by colony stimulating factors and oxidized low density lipoprotein

The peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-dependent transcription factor that has been demonstrated to regulate fat cell development and glucose homeostasis. PPARγ is also expressed in a subset of macrophages and negatively regulates the expression of several proinflammatory genes in response to natural and synthetic ligands. We here demonstrate that PPARγ is expressed in macrophage foam cells of human atherosclerotic lesions, in a pattern that is highly correlated with that of oxidation-specific epitopes. Oxidized low density lipoprotein (oxLDL) and macrophage colony-stimulating factor, which are known to be present in atherosclerotic lesions, stimulated PPARγ expression in primary macrophages and monocytic cell lines. PPARγ mRNA expression was also induced in primary macrophages and THP-1 monocytic leukemia cells by the phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA). Inhibition of protein kinase C blocked the induction of PPARγ expression by TPA, but not by oxLDL, suggesting that more than one signaling pathway regulates PPARγ expression in macrophages. TPA induced the expression of PPARγ in RAW 264.7 macrophages by increasing transcription from the PPARγ1 and PPARγ3 promoters. In concert, these observations provide insights into the regulation of PPARγ expression in activated macrophages and raise the possibility that PPARγ ligands may influence the progression of atherosclerosis.

Complex gangliosides are essential in spermatogenesis of mice: Possible roles in the transport of testosterone

Mice, homozygous for disrupted ganglioside GM2/GD2 synthase (EC 2.4.1.94) gene and lacking all complex gangliosides, do not display any major neurologic abnormalities. Further examination of these mutant mice, however, revealed that the males were sterile and aspermatogenic. In the seminiferous tubules of the mutant mice, a number of multinuclear giant cells and vacuolated Sertoli cells were observed. The levels of testosterone in the serum of these mice were very low, although testosterone production equaled that produced in wild-type mice. Testosterone was found to be accumulated in interstitial Leydig cells, and intratesticularly injected testosterone was poorly drained in seminiferous fluid in the mutant mice. These results suggested that complex gangliosides are essential in the transport of testosterone to the seminiferous tubules and bloodstream from Leydig cells. Our results provide insights into roles of gangliosides in vivo.

Attenuated sensitivity to neuroactive steroids in γ-aminobutyrate type A receptor delta subunit knockout mice

γ-Aminobutyric acid (GABA) type A receptors mediate fast inhibitory synaptic transmission and have been implicated in responses to sedative/hypnotic agents (including neuroactive steroids), anxiety, and learning and memory. Using gene targeting technology, we generated a strain of mice deficient in the δ subunit of the GABA type A receptors. In vivo testing of various behavioral responses revealed a strikingly selective attenuation of responses to neuroactive steroids, but not to other modulatory drugs. Electrophysiological recordings from hippocampal slices revealed a significantly faster miniature inhibitory postsynaptic current decay time in null mice, with no change in miniature inhibitory postsynaptic current amplitude or frequency. Learning and memory assessed with fear conditioning were normal. These results begin to illuminate the novel contributions of the δ subunit to GABA pharmacology and sedative/hypnotic responses and behavior and provide insights into the physiology of neurosteroids.

Evidence for rapid disappearance of initially expanded HIV-specific CD8+ T cell clones during primary HIV infection

Down-regulation of the initial burst of viremia during primary HIV infection is thought to be mediated predominantly by HIV-specific cytotoxic T lymphocytes, and the appearance of this response is associated with major perturbations of the T cell receptor repertoire. Changes in the T cell receptor repertoire of virus-specific cytotoxic T lymphocytes were analyzed in patients with primary infection to understand the failure of the cellular immune response to control viral spread and replication. This analysis demonstrated that a significant number of HIV-specific T cell clones involved in the primary immune response rapidly disappeared. The disappearance was not the result of mutations in the virus epitopes recognized by these clones. Evidence is provided that phenomena such as high-dose tolerance or clonal exhaustion might be involved in the disappearance of these monoclonally expanded HIV-specific cytotoxic T cell clones. These findings should provide insights into how HIV, and possibly other viruses, elude the host immune response during primary infection.

Characterization of human cardiac Na+ channel mutations in the congenital long QT syndrome

The congenital long QT syndrome (LQTS) is an inherited disorder characterized by a prolonged cardiac action potential. This delay in cellular repolarization can lead to potentially fatal arrhythmias. One form of LQTS (LQT3) has been linked to the human cardiac voltage-gated sodium channel gene (SCN5A). Three distinct mutations have been identified in the sodium channel gene. The biophysical and functional characteristics of each of these mutant channels were determined by heterologous expression of a recombinant human heart sodium channel in a mammalian cell line. Each mutation caused a sustained, non-inactivating sodium current amounting to a few percent of the peak inward sodium current, observable during long (>50 msec) depolarizations. The voltage dependence and rate of inactivation were altered, and the rate of recovery from inactivation was changed compared with wild-type channels. These mutations in diverse regions of the ion channel protein, all produced a common defect in channel gating that can cause the long QT phenotype. The sustained inward current caused by these mutations will prolong the action potential. Furthermore, they may create conditions that promote arrhythmias due to prolonged depolarization and the altered recovery from inactivation. These results provide insights for successful intervention in the disease.

The α-helical FXXΦΦ motif in p53: TAF interaction and discrimination by MDM2

Transcriptional activation domains share little sequence homology and generally lack folded structures in the absence of their targets, aspects that have rendered activation domains difficult to characterize. Here, a combination of biochemical and nuclear magnetic resonance experiments demonstrates that the activation domain of the tumor suppressor p53 has an FXXΦΦ motif (F, Phe; X, any amino acids; Φ, hydrophobic residues) that folds into an α-helix upon binding to one of its targets, hTAFII31 (a human TFIID TATA box-binding protein-associated factor). MDM2, the cellular attenuator of p53, discriminates the FXXΦΦ motif of p53 from those of NF-κB p65 and VP16 and specifically inhibits p53 activity. Our studies support the notion that the FXXΦΦ sequence is a general α-helical recognition motif for hTAFII31 and provide insights into the mechanistic basis for regulation of p53 function.

Pleiotropic Alterations in Lipid Metabolism in Yeast sac1 Mutants: Relationship to “Bypass Sec14p” and Inositol Auxotrophy

SacIp dysfunction results in bypass of the requirement for phosphatidylinositol transfer protein (Sec14p) function in yeast Golgi processes. This effect is accompanied by alterations in inositol phospholipid metabolism and inositol auxotrophy. Elucidation of how sac1 mutants effect “bypass Sec14p” will provide insights into Sec14p function in vivo. We now report that, in addition to a dramatic accumulation of phosphatidylinositol-4-phosphate, sac1 mutants also exhibit a specific acceleration of phosphatidylcholine biosynthesis via the CDP-choline pathway. This phosphatidylcholine metabolic phenotype is sensitive to the two physiological challenges that abolish bypass Sec14p in sac1 strains; i.e. phospholipase D inactivation and expression of bacterial diacylglycerol (DAG) kinase. Moreover, we demonstrate that accumulation of phosphatidylinositol-4-phosphate in sac1 mutants is insufficient to effect bypass Sec14p. These data support a model in which phospholipase D activity contributes to generation of DAG that, in turn, effects bypass Sec14p. A significant fate for this DAG is consumption by the CDP-choline pathway. Finally, we determine that CDP-choline pathway activity contributes to the inositol auxotrophy of sac1 strains in a novel manner that does not involve obvious defects in transcriptional expression of the INO1 gene.

Drosophila coracle, a Member of the Protein 4.1 Superfamily, Has Essential Structural Functions in the Septate Junctions and Developmental Functions in Embryonic and Adult Epithelial Cells

Although extensively studied biochemically, members of the Protein 4.1 superfamily have not been as well characterized genetically. Studies of coracle, a Drosophila Protein 4.1 homologue, provide an opportunity to examine the genetic functions of this gene family. coracle was originally identified as a dominant suppressor of EgfrElp, a hypermorphic form of the Drosophila Epidermal growth factor receptor gene. In this article, we present a phenotypic analysis of coracle, one of the first for a member of the Protein 4.1 superfamily. Screens for new coracle alleles confirm the null coracle phenotype of embryonic lethality and failure in dorsal closure, and they identify additional defects in the embryonic epidermis and salivary glands. Hypomorphic coracle alleles reveal functions in many imaginal tissues. Analysis of coracle mutant cells indicates that Coracle is a necessary structural component of the septate junction required for the maintenance of the transepithelial barrier but is not necessary for apical–basal polarity, epithelial integrity, or cytoskeletal integrity. In addition, coracle phenotypes suggest a specific role in cell signaling events. Finally, complementation analysis provides information regarding the functional organization of Coracle and possibly other Protein 4.1 superfamily members. These studies provide insights into a range of in vivo functions for coracle in developing embryos and adults.

Localization of non-Mhc collagen-induced arthritis susceptibility loci in DBA/1j mice

One approach to understanding common human diseases is to determine the genetic defects responsible for similar diseases in animal models and place those defective genes in their corresponding biochemical pathways. Our laboratory is working with an animal model for human rheumatoid arthritis called collagen-induced arthritis (CIA). We are particularly interested in determining the location of disease-predisposing loci. To that end, we performed experiments to localize susceptibility loci for CIA in an F2 cross between the highly susceptible mouse strain DBA/1j and the highly resistant mouse strain SWR/j. Specifically, a quantitative trait locus analysis was performed to localize regions of the mouse genome responsible for susceptibility/severity to CIA. One susceptibility locus, Cia1 in the major histocompatibility locus, had been identified previously. Two additional loci were detected in our analysis that contribute to CIA severity (Cia2, Cia3) on chromosomes 2 and 6. A third locus was detected that contributes to the age of onset of the disease. This locus (Cia4) was located on chromosome 2 and was linked to the same region as Cia2. Determining the identity of these loci may provide insights into the etiology of human rheumatoid arthritis.

Solution structure and peptide binding studies of the C-terminal Src homology 3-like domain of the diphtheria toxin repressor protein

The diphtheria toxin repressor (DtxR) is the best-characterized member of a family of homologous proteins that regulate iron uptake and virulence gene expression in the Gram-positive bacteria. DtxR contains two domains that are separated by a short, unstructured linker. The N-terminal domain is structurally well-defined and is responsible for Fe2+ binding, dimerization, and DNA binding. The C-terminal domain adopts a fold similar to eukaryotic Src homology 3 domains, but the functional role of the C-terminal domain in repressor activity is unknown. The solution structure of the C-terminal domain, consisting of residues N130-L226 plus a 13-residue N-terminal extension, has been determined by using NMR spectroscopy. Residues before A147 are highly mobile and adopt a random coil conformation, but residues A147-L226 form a single structured domain consisting of five β-strands and three helices arranged into a partially orthogonal, two-sheet β-barrel, similar to the structure observed in the crystalline Co2+ complex of full-length DtxR. Chemical shift perturbation studies demonstrate that a proline-rich peptide corresponding to residues R125-G139 of intact DtxR binds to the C-terminal domain in a pocket formed by residues in β-strands 2, 3, and 5, and helix 3. Binding of the proline-rich peptide by the C-terminal domain of DtxR presents an example of peptide binding by a prokaryotic Src homology 3-like protein. The results of this study, combined with previous x-ray studies of intact DtxR, provide insights into a possible biological function of the C-terminal domain in regulating repressor activity.

Fundamental patterns underlying gene expression profiles: Simplicity from complexity

Analysis of previously published sets of DNA microarray gene expression data by singular value decomposition has uncovered underlying patterns or “characteristic modes” in their temporal profiles. These patterns contribute unequally to the structure of the expression profiles. Moreover, the essential features of a given set of expression profiles are captured using just a small number of characteristic modes. This leads to the striking conclusion that the transcriptional response of a genome is orchestrated in a few fundamental patterns of gene expression change. These patterns are both simple and robust, dominating the alterations in expression of genes throughout the genome. Moreover, the characteristic modes of gene expression change in response to environmental perturbations are similar in such distant organisms as yeast and human cells. This analysis reveals simple regularities in the seemingly complex transcriptional transitions of diverse cells to new states, and these provide insights into the operation of the underlying genetic networks.