Total V9 rDNA information organized at the OTU level

The present data set provides a tab separated text file compressed in a zip archive. The file includes metadata for each TaraOceans V9 rDNA OTU including the following fields: md5sum = identifier of the representative (most abundant) sequence of the swarm; cid = identifier of the OTU; totab = total abundance of barcodes in this OTU; TARA_xxx = number of occurrences of barcodes in this OTU in each of the 334 samples;rtotab = total abundance of the representative barcode; pid = percentage identity of the representative barcode to the closest reference sequence from V9_PR2; lineage = taxonomic path assigned to the representative barcode ; refs = best hit reference sequence(s) with respect to the representative barcode ; taxogroup = high-taxonomic level assignation of the representative barcode. The file also includes three categories of functional annotations: (1) Chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast ; NA, undetermined. (2) Symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) Symbiont (host): photo, the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis); photo_falc, same as photo, but facultative relationship; photo_klep, the host species maintains chloroplasts from microalgal prey(s) to survive; photo_klep_falc, same as photo_klep, but facultative; Nfix, the host species must interact with a mutualistic symbiont providing N2 fixation to survive; Nfix_falc, same as Nfix, but facultative; no, the species is not involved in any mutualistic symbioses; NA, undetermined.

Environmental context of selected samples from the Tara Oceans Expedition (2009-2013)

The present data set provides contextual environmental data for samples from the Tara Oceans Expedition (2009-2013) that were selected for publication in a special issue of the SCIENCE journal (see related references below). The data set provides calculated averages of mesaurements made at the sampling location and depth, calculated averages from climatologies (AMODIS, VGPM) and satellite products.

Photosynthetically Active Radiation (PAR) measurements from a Biospherical Instrument Inc. QCR-2150 surface PAR sensor mounted on a sensor mast during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with a Biospherical Instrument Inc. QCR-2150 surface PAR sensor mounted on a sensor mast at the stern of the ship (ca. 8m above deck) and time synchronized with the CTD recording unit. The sensor consists of a cosine collector and was also utilized to correct the CTD PAR sensor data. The dark was computed as the lowest 0.01% voltage of the signal that was found to be very stable (0.00965V) for all the legs except for the 2nd leg of the polar circle where there was no complete night (the manufacturer dark was 0.0097V). The manufacturer calibration slope from 12/ 2012 was used to transform the data to scientific units.

Properties of seawater and particulate matter (fluorescence) from a WETLabs Eco-FL sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with a WETLabs Eco-FL sensor mounted on the flowthrough system between June 4th, 2011 and March 30th, 2012. Data was recorded approximately every 10s. Two issues affected the data: 1. Periods when the water 0.2µm filtered water were used as blanks and 2. Periods where fluorescence was affected by non-photochemical quenching (NPQ, chlorophyll fluorescence is reduced when cells are exposed to light, e.g. Falkowski and Raven, 1997). Median data and their standard deviation were binned to 5min bins with period of light/dark indicated by an added variable (so that NPQ affected data could be neglected if the user so chooses). Data was first calibrated using HPLC data collected on the Tara (there were 36 data within 30min of each other). Fewer were available when there was no evident NPQ and the resulting scale factor was 0.0106 mg Chl m-3/count. To increase the calibration match-ups we used the AC-S data which provided a robust estimate of Chlorophyll (e.g. Boss et al., 2013). Scale factor computed over a much larger range of values than HPLC was 0.0088 mg Chl m-3/count (compared to 0.0079 mg Chl m-3/count based on manufacturer). In the archived data the fluorometer data is merged with the TSG, raw data is provided as well as manufacturer calibration constants, blank computed from filtered measurements and chlorophyll calibrated using the AC-S. For a full description of the processing of the Eco-FL please see Taillandier, 2015.

Properties of seawater (pH total scale) from a Satlantic SeaFET instrument mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous pH measurements made during 2013 expedition with a Satlantic SeaFET instrument that was connected to the flowthrough system. Data calibration was performed according to Bresnahan et al. (2014) (using spectrophotometric pH measurements on discrete samples (Clayton and Byrne 1993). pH_internal values were taken to calibrate the data (rather than pH_external) because of the better calibration coefficient (there was no trend associated with it). The equations of Clayton and Byrne (1993) was used to compute pH from the measured absorbance values at the temperature of measurement. The data was converted to in situ temperature using the "CO2-sys" program which can be downloaded from http://cdiac.ornl.gov/ftp/co2sys/.

Properties of seawater and particulate matter from a FRRF instrument, operating in a flow-through mode on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with a FRRF instrument, operating in a flow-through mode during the 2009-2012 part of the expedition. It operates by exciting chlorophyll fluorescence using a series of short flashes of controlled energy and time intervals (Kolber et al, 1998). The fluorescence transients produced by this excitation signal were analysed in real-time to provide estimates of abundance of photosynthetic pigments, the photosynthetic yields (Fv/Fm), the functional absorption cross section (a proxy for efficiency of photosynthetic energy acquisition), the kinetics of photosynthetic electron transport between Photosystem II and Photosystem I, and the size of the PQ pool. These parameters were measured at excitation wavelength of 445 nm, 470nm, 505 nm, and 535 nm, allowing to assess the presence and the photosynthetic performance of different phytoplankton taxa based on the spectral composition of their light harvesting pigments. The FRRF-derived photosynthetic characteristics were used to calculate the initial slope, the half saturation, and the maximum level of Photosynthesis vs Irradiance relationship. FRRF data were acquired continuously, at 1-minute time intervals.

Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol.

Properties of seawater (partial pressure of carbon dioxide (pCO2)) from a ProOceanus CO2-Pro sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements of partial pressure of carbon dioxide (pCO2), using a ProOceanus CO2-Pro instrument mounted on the flowthrough system. This automatic sensor is fitted with an equilibrator made of gas permeable silicone membrane and an internal detection loop with a non-dispersive infrared detector of PPSystems SBA-4 CO2 analyzer. A zero-CO2 baseline is provided for the subsequent measurements circulating the internal gas through a CO2 absorption chamber containing soda lime or Ascarite. The frequency of this automatic zero point calibration was set to be 24 hours. All data recorded during zeroing processes were discarded with the 15-minute data after each calibration. The output of CO2-Pro is the mole fraction of CO2 in the measured water and the pCO2 is obtained using the measured total pressure of the internal wet gas. The fugacity of CO2 (fCO2) in the surface seawater, whose difference with the atmospheric CO2 fugacity is proportional to the air-sea CO2 fluxes, is obtained by correcting the pCO2 for non-ideal CO2 gas concentration according to Weiss (1974). The fCO2 computed using CO2-Pro measurements was corrected to the sea surface condition by considering the temperature effect on fCO2 (Takahashi et al., 1993). The surface seawater observations that were initially estimated with a 15 seconds frequency were averaged every 5-min cycle. The performance of CO2-Pro was adjusted by comparing the sensor outputs against the thermodynamic carbonate calculation of pCO2 using the carbonic system constants of Millero et al. (2006) from the determinations of total inorganic carbon (CT ) and total alkalinity (AT ) in discrete samples collected at sea surface. AT was determined using an automated open cell potentiometric titration (Haraldsson et al. 1997). CT was determined with an automated coulometric titration (Johnson et al. 1985; 1987), using the MIDSOMMA system (Mintrop, 2005). fCO2 data are flagged according to the WOCE guidelines following Pierrot et al. (2009) identifying recommended values and questionable measurements giving additional information about the reasons of the questionability.

Registry of all samples from the Tara Oceans Expedition (2009-2013)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. Data sets in this collection provide methodological and environmental context to all samples collected during the Tara Oceans Expedition (2009-2013).

“Una Casa Entre el Greco y el Siroco” Crítica de la Malaparte

El título de esta tesis, utiliza primero una expresión periodística muy conocida sobre esta obra, que expresa muy bien su característica contradictoria, paradójica, siempre entre opuestos, frecuentemente utilizadas por los textos que sobre esta obra se han escrito. La segunda expresión define a esta tesis, incluida en el grupo de investigación sobre el objetivo común de la Crítica Arquitectónica. La casa Malaparte, olvidada durante largo tiempo y venerada en otros momentos, fue elegida por referéndum en 1979 por la revista “Modo (Cien proyectos para recordar)” como la obra más representativa de la arquitectura italiana del siglo XX. Un icono de modernidad en 1979 y paradójicamente no en su momento, ya que difícilmente se podría encuadrar en las tipologías de vivienda moderna de los años treinta. El objetivo de esta tesis es la racionalización del valor de esta obra, admitida de alguna manera en los “manuales de arquitectura moderna”, proponiendo para ello el reconocimiento de sus singularidades y regularidades como elementos de investigación del valor sustantivo de la arquitectura, el polinomio indisociable: contexto, forma, función, construcción. Tenemos datos, textos, hermenéutica. Nuestro método no puede ser otro que la crítica de los datos y texto y la crítica poética. Nuestra tesis, se inserta en este conjunto de crítica arquitectónica, vinculada al método llamado por el Catedrático Dr. Antonio Miranda Regojo “Mírregan-Todorov” que emplearemos como referencia y método para mostrar lo que más nos interesa, la calidad de la arquitectura, su ser, que paradójicamente, difiere de su descripción, de su momento histórico, en fin de todo aquello que en realidad solo la describe, la analiza y la interpreta. Nuestra variación propuesta al modelo de referencia, consta del siguiente desarrollo: 1. Crítica de “La Crítica”. 2. Crítica poética. 3. Conclusiones El primer capítulo, propone “La Crítica”, entendida como ese valor colectivo depositado por los textos escritos sobre la obra contrastado con nuestras observaciones personales respecto de cada uno de ellos. Las críticas seleccionadas muestran una nube de alternativas relativas a la descripción, análisis e interpretación que sobre la obra se han producido. Este capítulo, constituye una compilación de textos ordenada cronológicamente, que introduce al conocimiento de la obra. Recoge las primeras referencias, los artículos, los libros, las películas y anuncios así como alguno de los textos académicos que se han escrito sobre esta obra. 15 Los artículos seleccionados son los siguientes: Aldo Morbelli 1942. A. Alieri M.Clerici F.Palpacelli y G.Vaccaro 1966. Francesco Venezia con G.Petrusch 1973 Vieri Quilici.1977/1981 G.K.Koenig, 1979 John Hejduk 1980 Audrey Batey 1980. Manfredo Tafuri 1981. Francesco Venezia 1983. Joe Bostik 1989. Vittorio Savi, 1989. Marida Talamona 1989. W. Arets, W. Van der Bergh. 1989. Franco Purinni 1991. Marida Talamona 1997. Bruce Chatwin 1997. Los libros seleccionados han sido: Marida Talamona. Casa Malaparte, Milano 1990. Sergio Attanasio. Curzio Malaparte “Casa come me” Punta del Massullo, tel. 160 Capri. Nápoles 1990 Gianni Petenna. CasaMalaparte, Capri, 1999 Michael McDonough. A house like me. Edit.Clarkson Potter,New York 1999 Mario Ferrari. Adalberto Libera “Casa Malaparte en Capri1938-1942” 2008 Las películas seleccionadas: Il Cristo proibito, 1956 Le Mèpris, 1963 La Pelle, 1981 Anuncio de Hugo Boss 2010 16 Los textos académicos recogidos son: Angela delGaudio. Casa Malaparte. Interventi e restauri. 2003 Nicoletta Setola. Casa Malaparte. Il cantiere le tecnologie i materiali. 2004 Gloria Paz Saravia Ortiz. La casa Malaparte de A.libera. 2007 En el capítulo segundo “Crítica poética” se circunscribe, según la definición utilizada, a lo que en particular tiene como nivel de verdad, por la idoneidad de su construcción, tipología e iconología en relación al lugar (entidad propia, identidad auténtica). Existen algunos estudios que proponen a la casa Malaparte comprendida en la poética común de la obra de su arquitecto, Adalberto Libera. Nuestra posición nada tiene que ver con “la manera de hacer de un autor” se inclina a investigar obras enlazadas por estructuras comunes, reflejo y consecuencia especialmente de la propia arquitectura, nos interesa la poética de la arquitectura, no la de un autor. Realizamos tres ensayos, el primero trata de investigar el “Lugar” contexto de la obra, proponiendo el reconocimiento de un sistema lugar-arquitectura, (Conjunto de reglas o principios sobre una materia racionalmente enlazados entre sí) del que formulamos una serie de definiciones como características de esta relación: la analogía, la simpatía, la emulación, la signatura, la nematología y la sinexión. Concluyendo que la relación encontrada en la Malaparte podría explicarse de esta manera: ninguna mimesis, admite cierta analogía, un camuflaje solo geométrico, sin emulación de “tipismo” alguno, con emulación del modelo continuo de la “caja” desde el ataúd a la humilde vivienda , con “simpatía” como una obra contemporánea, con una fuerte signatura sobre el lugar, en correspondencia a lugar señalado por la historia y a la indeterminación iconológica que propone su arquitectura, (fetiche, simulacro) con una relación “nematológica” a través de su implantación y con una vinculación especial de “sinexión” entre la superficie del lugar y el acomodo de esta arquitectura. Continuamos con la relación propia de la obra y el lugar, concluyendo como la casa Malaparte propone el espacio sobre su cubierta, a modo de patio, de recinto. La obra demuestra que no es únicamente la sustancia material quien protagoniza la acción de “recintar”. El vértigo constituye la materia infranqueable del perímetro. En la Malaparte es el plano arquitectónico, (elevado) el recinto descubierto, el plano que posibilita la máxima relación con el exterior en esta arquitectura. En su interior el paisaje deja de ser fondo y el habitante se incorpora al escenario, se incorpora al paisaje. Te encuentras midiendo, relacionando distancias desde las espículas de pino, rocas, acantilados, barcos, islas, mar hasta la costa de Amalfi. Esta posición sobre el paisaje, es comparada con la casa Kaufman de F.L.Wrigth. El segundo ensayo investiga el proyecto de la obra. Distinguimos entre proyecto-forma, proyecto-origen, proyecto programa, proyecto-acción y proyectos-signo. Encontramos que no existe proyecto-forma que explique la casa Malaparte, tenemos proyectoorigen, proyecto-programa y proyectos-signo suficientes para racionalizar esta obra. Nos encontramos con un proyecto-acción, en permanente discusión, debatido hasta la saciedad, con la finalidad de habitar aquella roca, cuyas proposiciones se contrastan en la obra, ampliando el proceso de proyecto a la propia acción de construir, proyecto y construcción no estan disociados. Los proyectos “signo” de esta obra, nos permiten relacionar la permanencia de un programa, una organización, una comunicación y distribución que entendemos continua y conducida por Malaparte. Lo realmente importante previsto y controlable por aquel: programa y distribución. Nos permitimos afirmar que lo significante continuo es un proyecto–programa limitado a una forma necesaria iniciada por Libera, como una semilla. Su forma es el resultado de un procedimiento, arraigado y condicionado a un terreno. Un proceso que consiste en establecer unas alturas tipo sobre un programa distribuido en planta, y limitado con una construcción racional, tipológica sobre muros de carga, capaz de soportar cualquier programa habitacional, que proporciona inevitablemente un resultado seguro. El tercer ensayo propone una “novela” sobre la manera de construcción de la obra, que nos permite explicar la gran escalera de la Malaparte. Encontramos que la construcción de la Malaparte, también forma parte de un sistema. Este sistema es capaz de generar forma, sin recurrir a las mascaras fijadas por la tradición o las modas, manteniendo su libertad de expresión sin concesiones. Consideramos que en el camino de acceso a la obra que hubo que ejecutarse para tal fin están las claves para la comprensión de su escalera. La escalera de la Malaparte la comprendemos desde la propia accesibilidad a la obra. Su trazado abocinado, su forma “strombata”, es consecuencia para nosotros de sus límites físicos, su elevación, resultado de las cotas que responden a los niveles de los planos de trabajo, incluida la terraza –patio. Su expresión geométrica sería visible desde la ejecución de las obras; no es posterior al paralelepípedo inicial, sino previa. Su función de acceso a la terraza no es la principal, excluida desde el proyecto administrativo de Libera, al texto escrito de Malaparte sobre su casa (ninguna escalera exterior). Sus funciones principales subyacentes que quedan envueltas son primeramente abastecer la obra, en segundo lugar como cubierta de la escalera interior que tuvo que salir de su posición centrada en el paralelepípedo inicial, al extremo exterior de este. La solución a estas necesidades acuciantes, mostrarían su función paradigmática en un tercer lugar, su solución como cubierta peldañeada, como fachada remontable, que se produce desde nuestra visión del exterior, la gran escalera de acceso al lugar principal y el hecho único y genial de la Malaparte. Las conclusiones finales de esta tesis están referidas en primer lugar al Texto escrito sobre la obra y en segundo lugar a la obra misma: La Casa es entendida en los textos analizados, como objeto que soporta simultáneamente la idea romántica de emoción-inspiración y la contemporánea de invitación a su conocimiento. Producto de su singular abstracción explicamos su transformación en lo que constatamos dos vías extremas: una como artefacto, trasto inútil y pretencioso que explica las críticas extremas de Koening y Durante. Habría que demoler la Malaparte, y por la otra se produce su transformación en “objeto artístico” (inspiraciónemoción– conocimiento) que hay que venerar. Este trinomio deviene en interpretación y de aquí su provocación hacia la literatura, el cine y la imagen sobre la obra. Ambos extremos podrían originarse por no comprender, por no llegar a explicar cómo este objeto es también casa, casa con patio, habitación, refugio, arquitectura con toda su contingencia que con coherencia, razón y libertad de expresión produce aquel objeto, con la única intencionalidad acuciante de ser construido y habitado. El gran valor “literario-artístico” de la Malaparte recogido en sus textos, debemos admitir pues que tiene su origen en la interpretación de lo arquitectónico, que no es evidente, que entendemos no puede deducirse de su mera imagen, del mismo modo que la escultura asociada a un capitel corintio, que algunos pretenden disociar del apoyo constructivo de un pie derecho, como la solución del tímpano- escultura de una portada barroca, que pretendemos separar de la eficacia del dintel, como la cúpula solución a la cubierta del Panteón de Agripa, que estudiamos aparte como un problema de ingeniería, estos aspectos múltiples, complejos y no evidentes producen la fragmentación de lo arquitectónico, y permiten sus interpretaciones independientes, desguazando la arquitectura en trozos muy visibles que algunos llamaron “arte” y sistemas mas ocultos que otros llamaron “ingeniería y técnica”. Contemplar lo humano con fantasía es también nuestra conclusión deductiva de lo que nos permite la Malaparte, su identidad propia y peculiar deducida del Texto. Una arquitectura que permite examinar lo humano con fantasía, también un gran valor común, literario y arquitectónico que no queremos disociar. Si nos afirmamos en la autonomía de la arquitectura, sin renunciar al Texto, su identidad no es más que materialidad, ni menos que la metáfora del habitar diverso del hombre en la tierra. Ambos discursos permanecerán siempre abiertos para poetas y arquitectos. La Malaparte puede explicarse desde el lugar, de su proyecto y su construcción. Podríamos limitarnos aun más, solamente de su realidad congelada actual lograríamos inferir su valor como arquitectura que ha resuelto el problema; cubriendo, superponiendo con rigurosa limpieza, orden y geometría, al caos de accidentalidad y esfuerzo, un resultado despejado, de la materialidad y la técnica, esto es en definitiva el poder de lo arquitectónico, realizado no como máscara superpuesta, sino como resultado coherente, piel viva sobre huesos y músculos necesarios.

Identification of genes required for Drosophila eye development using a phenotypic enhancer-trap

A novel method of P-element mutagenesis is described for the isolation of mutants affecting the development of the Drosophila compound eye. It exploits the interaction between the Bride of Sevenless (Boss) ligand and the Sevenless (Sev) receptor tyrosine kinase that triggers the formation of the UV-sensitive photoreceptor neuron, R7. Transposition of a boss cDNA transgene, in an otherwise boss mutant background, was used as a “phenotypic trap” in live flies to identify enhancers expressed during a narrow time window in eye development. Using a rapid behavioral screen, more than 400,000 flies were tested for restoration of R7. Some 1,800 R7-containing flies were identified. Among these, 21 independent insertions with expression of the boss reporter gene in the R8 cell were identified by a external eye morphology and staining with an antibody against Boss. Among 900 lines with expression of the boss reporter gene in multiple cells assessed for homozygous mutant phenotypes, insertions in the marbles, glass, gap1, and fasciclin II genes were isolated. This phenotypic enhancer-trap facilitates (i) the isolation of enhancer-traps with a specific expression pattern, and (ii) the recovery of mutants disrupting development of specific tissues. Because the temporal and tissue specificity of the phenotypic trap is dependent on the choice of the marker used, this approach can be extended to other tissues and developmental stages.

Genetic Dissection of Endocytic Trafficking in Drosophila Using a Horseradish Peroxidase-Bride of Sevenless Chimera: hook Is Required for Normal Maturation of Multivesicular Endosomes

Mutations in the hook gene alter intracellular trafficking of internalized ligands in Drosophila. To dissect this defect in more detail, we developed a new approach to visualize the pathway taken by the Bride of Sevenless (Boss) ligand after its internalization into R7 cells. A chimeric protein consisting of HRP fused to Boss (HRP-Boss) was expressed in R8 cells. This chimera was fully functional: it rescued the boss mutant phenotype, and its trafficking was indistinguishable from that of the wild-type Boss protein. The HRP activity of the chimera was used to follow HRP-Boss trafficking on the ultrastructural level through early and late endosomes in R7 cells. In both wild-type and hook mutant eye disks, HRP-Boss was internalized into R7 cells. In wild-type tissue, Boss accumulated in mature multivesicular bodies (MVBs) within R7 cells; such accumulation was not observed in hook eye disks, however. Quantitative electron microscopy revealed a loss of mature MVBs in hook mutant tissue compared with wild type, whereas more than twice as many multilammelar late endosomes were detected. Our genetic analysis indicates that Hook is required late in endocytic trafficking to negatively regulate delivery from mature MVBs to multilammelar late endosomes and lysosomes.

CIITA stimulation of transcription factor binding to major histocompatibility complex class II and associated promoters in vivo

CIITA is a master transactivator of the major histocompatibility complex class II genes, which are involved in antigen presentation. Defects in CIITA result in fatal immunodeficiencies. CIITA activation is also the control point for the induction of major histocompatibility complex class II and associated genes by interferon-γ, but CIITA does not bind directly to DNA. Expression of CIITA in G3A cells, which lack endogenous CIITA, followed by in vivo genomic footprinting, now reveals that CIITA is required for the assembly of transcription factor complexes on the promoters of this gene family, including DRA, Ii, and DMB. CIITA-dependent promoter assembly occurs in interferon-γ-inducible cell types, but not in B lymphocytes. Dissection of the CIITA protein indicates that transactivation and promoter loading are inseparable and reveal a requirement for a GTP binding motif. These findings suggest that CIITA may be a new class of transactivator.

Changes in Phosphoinositide Metabolism with Days in Culture Affect Signal Transduction Pathways in Galdieria sulphuraria1

The metabolism of phosphatidylinositol-4,5-bisphosphate (PIP2) changed during the culture period of the thermoacidophilic red alga Galdieria sulphuraria. Seven days after inoculation, the amount of PIP2 in the cells was 910 ± 100 pmol g−1 fresh weight; by 12 d, PIP2 levels increased to 1200 ± 150 pmol g−1 fresh weight. In vitro assays indicated that phosphatidylinositol monophosphate (PIP) kinase specific activity increased from 75 to 230 pmol min−1 mg−1 protein between d 7 and 12. When G. sulphuraria cells were osmostimulated, transient increases of up to 4-fold could be observed in inositol-1,4,5-trisphosphate (IP3) levels within 90 s, regardless of the age of the cells. In d-12 cells, the increase in IP3 was preceded by a transient increase of up to 5-fold in specific PIP kinase activity, whereas no such increase was detected after osmostimulation of d-7 cells. The increase in PIP kinase activity before IP3 signaling in d-12 cells indicates that there is an additional pathway for regulation of phosphoinositide metabolism after stimulation other than an initial activation of phospholipase C. Also, the rapid activation of PIP2 biosynthesis in cells with already-high PIP2 levels suggests that the PIP2 present was not available for signal transduction. By comparing the response of the cells at d 7 and 12, we have identified two potentially distinct pools of PIP2.

Overexpression of the LAR (leukocyte antigen-related) protein-tyrosine phosphatase in muscle causes insulin resistance

Previous reports indicate that the expression and/or activity of the protein-tyrosine phosphatase (PTP) LAR are increased in insulin-responsive tissues of obese, insulin-resistant humans and rodents, but it is not known whether these alterations contribute to the pathogenesis of insulin resistance. To address this question, we generated transgenic mice that overexpress human LAR, specifically in muscle, to levels comparable to those reported in insulin-resistant humans. In LAR-transgenic mice, fasting plasma insulin was increased 2.5-fold compared with wild-type controls, whereas fasting glucose was normal. Whole-body glucose disposal and glucose uptake into muscle in vivo were reduced by 39–50%. Insulin injection resulted in normal tyrosyl phosphorylation of the insulin receptor and insulin receptor substrate 1 (IRS-1) in muscle of transgenic mice. However, phosphorylation of IRS-2 was reduced by 62%, PI3′ kinase activity associated with phosphotyrosine, IRS-1, or IRS-2 was reduced by 34–57%, and association of p85α with both IRS proteins was reduced by 39–52%. Thus, overexpression of LAR in muscle causes whole-body insulin resistance, most likely due to dephosphorylation of specific regulatory phosphotyrosines on IRS proteins. Our data suggest that increased expression and/or activity of LAR or related PTPs in insulin target tissues of obese humans may contribute to the pathogenesis of insulin resistance.