PATSTAT revisited

This study provides a comprehensive summary of and guidance for using the EPO Worldwide Patent Statistical Database (PATSTAT), one of the most widely used patent databases for researchers. We highlight the three most important issues that PATSTAT users must consider when performing patent data analyses and suggest ways to deal with those issues. Although PATSTAT is chosen in this study, the issues that we discuss are also applicable to other patent databases.

What best transfers knowledge? : capital, goods, and innovative labor in East Asia

This paper compares three knowledge carriers—trade, foreign direct investment (FDI), and inventors—as knowledge mediums, and investigates their effects on knowledge flow in East Asia from 1996 to 2010. Using patent citations as a proxy for knowledge flow, this paper shows that FDI and inventor mobility have positive effects on increasing patent citations in East Asia when the technological portfolios of two countries are less similar. While trade shows statistical significance, the effect is inconsistent according to the regression models.

Descriptive analysis of the knowledge network formation in East Asia

This paper shows descriptively how the knowledge network in East Asia has been formed. In addition, the correlation between the knowledge network and economic growth is also examined. Evidence is provided to show that plugging into the knowledge network of developed countries could be a key for increasing innovativeness in a country.

Caracterización molecular del mutante riso 1508 de cebada : modificaciones transcripcionales y posttranscripcionales en el desarrollo de la semilla

La semilla es el principal órgano reproductivo de las plantas espermatofitas, permitiendo la dispersión de las poblaciones y asegurando su supervivencia gracias a su tolerancia a la desecación y a su capacidad para germinar bajo condiciones ambientales óptimas. El rendimiento y valor económico de los cereales, que constituyen la primera cosecha mundial, depende, en buena medida, de la eficacia con que se acumulan en la semilla sustancias de reserva: proteínas, carbohidratos y lípidos. El principal carbohidrato acumulado en la semilla de cebada es el almidón y la fracción mayoritaria de proteínas es la de las prolaminas (solubles en etanol al 70%); estas proteínas tienen muy bajo contenido en lisina, un aminoácido esencial en la dieta de animales monogástricos. Con el fin de mejorar el valor nutricional de la semilla de cebada, se han obtenido diferentes mutantes con un mayor contenido en este aminoácido. Riso 1508 es un mutante de cebada rico en lisina cuya mutación lys3a, de efectos pleiotrópicos, segrega como un único gen mendeliano. Entre otros, presenta una reducción drástica de la expresión de algunos genes que codifican proteínas de reserva de tipo prolamina, en concreto, presenta reducida la expresión de los genes que codifican B-, C- y ϒ-Hordeínas y del inhibidor de tripsina CMe, pero no tiene alterada la expresión del gen que codifica las D-Hordeínas. Este último gen carece en su promotor del motivo GLM (5’‐(G/A)TGA(G/C)TCA(T/C)‐3’), que es reconocido por factores transcripcionales bZIP. En este trabajo, el mutante de cebada Riso 1508 se ha utilizado como herramienta para profundizar en el conocimiento de la regulación génica en semillas durante las fases de la maduración y la germinación. Para ello, en una primera aproximación, se llevó a cabo un análisis transcriptómico comparando el genotipo mutante con el silvestre durante la maduración de la semilla. Además de confirmar variaciones en los genes que codifican proteínas de reserva, este análisis indicó que también estaban afectados los genes relacionados con metabolismo de carbohidratos. Por ello se decidió caracterizar la familia multigénica de sacarosas sintasa (SUSy) en cebada. Se anotaron dos nuevos genes, HvSs3 y HvSs4, cuya expresión se comparó con la de los genes HvSs1 y HvSs2, previamente descritos en el laboratorio. La expresión de los cuatro genes en tejidos diferentes y su respuesta a estreses abióticos se analizó mediante RT-qPCR. HvSs1 y HvSs2 se expresaron preferencialmente durante el desarrollo del endospermo, y HvSs1 también fue un tránscrito abundante durante la germinación. HvSs1 se indujo en hojas en condiciones de anoxia y HvSs3 por estrés hídrico, y ambos genes se indujeron por tratamientos de frío. La localización subcelular de las cuatro isoformas no fue sólo citoplásmica, sino que también se localizaron en zonas próximas a retículo endoplásmico y en la cara interna de la membrana plasmática; además, se observó una co-localización de HvSS1 con el marcador de mitocondrias. Estos datos sugieren un papel distinto aunque parcialmente solapante de las cuatro Sacarosa Sintasas de cebada, descritas hasta la fecha. Las cinéticas de expresión de los genes que codifican los TFs más importantes implicados en la regulación génica durante el desarrollo del endospermo de cebada, se analizaron por RT-qPCR en ambos genotipos, demostrando que los TFs de la clase DOF aparecieron desregulados durante todo el proceso en Riso 1508 comparado con el cv. Bomi, aunque también se observaron diferencias significativas en algunos de los que codifican bZIPs. Estudios previos indicaban que el ortólogo de BLZ2 en maíz, O2, se regula post-traduccionalmente mediante un mecanismo de fosforilación/defosforilación reversible, y que la forma defosforilada es la fisiológicamente activa. En este trabajo se demostró que BLZ2 está sujeto a este tipo de regulación y que la proteín-fosfatasa HvPP2C2 está implicada en el proceso. La interacción de HvPP2C2 y BLZ2 tiene lugar en el núcleo celular únicamente en presencia de 100 μM ABA. En el mutante Riso 1508, BLZ2 se encuentra en un estado hiperfosforilado tanto durante la maduración como durante la germinación de la semilla, lo que dificultaría la unión de BLZ2 a las secuencias GLM en los promotores de los genes que codifican B-, C-,y ϒ- Hordeínas y CMe. Summary The seed is the main reproductive organ of spermatophyte plants allowing the spread of populations and ensuring their survival through its desiccation tolerance and because of their ability to germinate under optimum environmental conditions. Yield and economic value of cereal crops, that constitute the first world crop, depend largely on the efficiency with which they accumulate in the seed reserve substances: proteins, carbohydrates and lipids. The main carbohydrate accumulated in the barley seed is starch and the major protein fraction is that of prolamins (soluble in 70% ethanol); these proteins have a very low lysine content, an essential amino-acid for the diet of monogastric animals. In order to improve the nutritional value of the barley seed, different mutants have been obtained with a higher content of this amino-acid. Riso 1508 is one lysine-rich mutant whose mutation (lys3a) segregates as a single Mendelian gene with pleiotropic effects, such as a drastic reduction of genes encoding the trypsin inhibitor CMe and the B-, C-and ϒ-hordeins, but has not altered the expression of the gene encoding the D-hordeins. This latter gene lacks in its promotor the GLM motif (5’‐(G/A)TGA(G/C)TCA(T/C)‐3’), that is recognised by bZIP transcription factors In this work we have used the barley mutant Riso 1508 as a tool for better understanding gene regulation in seeds during the maturation and germination phases. To this aim, a transcriptomic analysis was performed comparing wild and mutant genotypes during seed maturation. Besides confirming variations in the expression of genes encoding reserve proteins, this analysis indicated that some genes related with carbohydrate metabolism were also affected. It was therefore decided to characterize the multigene family of sucrose synthases (SUSy) in barley. Two new genes were annotated, HvSs3 and HvSs4, and its expression was compared with that of genes HvSs1 and HvSs2, previously described in our laboratory. The expression of the four genes in different tissues and in response to abiotic stresses was analyzed by RTqPCR. HvSs1 and HvSs2 were preferentially expressed during the development of the endosperm, and the HvSs1 transcript was also abundant upon germination. HvSs1 was induced in leaves by anoxic conditions, HvSs3 by water stress, and both genes were induced by cold treatments. The subcellular localization of all four isoforms was not only cytoplasmic, but they could be found along the endoplasmic reticulum and at the inner side of the cell membrane; HvSS1, was also associated with the mitochondrial marker. These data suggest a distinct but partially overlapping roles for the barley sucrose synthases, described so far. The expression kinetics of the genes encoding the most important TFs involved in gene regulation during barley endosperm development was analyzed by RT-qPCR in both genotypes. These data show that the genes encoding DOF TFs were mis-regulated throughout the process in Riso 1508, although significant differences were also found among some of those encoding bZIPs. Previous studies indicated that the BLZ2 orthologue in maize, O2, was post-translationally regulated by reversible phosphorylation/dephosphorylation and that the dephosphorylated protein is the physiologically active form. In this work we demostrate that BLZ2 is under a similar regulation and that the proteinphosphatase HvPP2C2 is implicated in the process. The interaction between HvPP2C2 and BLZ2 takes place in the cell nucleus only in the presence of 100 μM ABA. In the Riso 1508 mutant, BLZ2 is found in a hyperphosphorylated state in the maturation phase and upon seed germination; because of this, the BLZ2 binding to the GLM promoter sequences of genes encoding B-, C- y ϒ- Hordeins and CMe would be decreased in the mutant.

Characterising emergent semantics in Twitter lists

Twitter lists organise Twitter users into multiple, often overlapping, sets. We believe that these lists capture some form of emergent semantics, which may be useful to characterise. In this paper we describe an approach for such characterisation, which consists of deriving semantic relations between lists and users by analyzing the cooccurrence of keywords in list names. We use the vector space model and Latent Dirichlet Allocation to obtain similar keywords according to co-occurrence patterns. These results are then compared to similarity measures relying on WordNet and to existing Linked Data sets. Results show that co-occurrence of keywords based on members of the lists produce more synonyms and more correlated results to that of WordNet similarity measures.

Time-motion analysis on Chinese male field hockey players

The aim of the study was to evaluate the match work-rate of Chinese field hockey players by analyzing the distance covered at different intensities pooled by specific positions during different periods of matches. Thirty-eight players from twenty-four male field hockey matches at the 11th Chinese National Games were filmed and analyzed.

“O CRISTO AFOGADO: UMA NÃO-CRISTOLOGIA” RELIGIÃO, LITERATURA E PÓS-COLONIALISMO

O objetivo dessa tese é aprofundar, a partir do discurso pós-colonial, uma crise na perspectiva teológica da libertação. Esta promoveu, na década de 1970, uma reviravolta nos estudos teológicos no terceiro mundo. Para tanto, leremos um conto de Gabriel García Márquez chamado “El ahogado más hermosodel mundo” (1968) analizando e avaliando as estratégias políticas e culturais ali inscritas. Para levar a frente tal avaliação é preciso ampliar o escopo de uma visão que divide o mundo em secular/religioso, ou em ideias/práticas religiosas e não religiosas, para dar passo a uma visão unificada que compreende a mundanalidade, tanto do que é catalogado como ‘religioso’ quanto do que se pretende ‘não religioso’. A teologia/ciências da religião, como discurso científico sobre a economia das trocas que lidam com visões, compreensões e práticas de mundo marcadas pelo reconhecimento do mistério que lhes é inerente, possuem um papel fundamental na compreensão, explicitação, articulação e disponibilização de tais forças culturais. A percepção de existirem elementos no conto que se relacionam com os símbolos sobre Jesus/Cristo nos ofereceu um vetor de análise; entretanto, não nos deixamos limitar pelos grilhões disciplinares que essa simbologia implica. Ao mesmo tempo, esse vínculo, compreendido desde a relação imperial/colonial inerente aos discursos e imagens sobre Jesus-Cristo, embora sem centralizar a análise, não poderia ficar intocado. Partimos para a construção de uma estrutura teórica que explicitasse os valores, gestos, e horizontes mundanos do conto, cristológicos e não-cristológicos, contribuindo assim para uma desestabilização dos quadros tradicionais a partir dos quais se concebem a teologia e as ciências da religião, a obra de García Márquez como literatura, e a geografia imperial/colonial que postula o realismo ficcional de territórios como “América Latina”. Abrimos, assim, um espaço de significação que lê o conto como uma “não-cristologia”, deslocando o aprisionamento disciplinar e classificatório dos elementos envolvidos na análise. O discurso crítico de Edward Said, Homi Bhabha e GayatriSpivak soma-se à prática teórica de teólogas críticas feministas da Ásia, da África e da América Latina para formular o cenário político emancipatório que denominaremos teologia crítica secular.

Abnormal photoresponses and light-induced apoptosis in rods lacking rhodopsin kinase

Phosphorylation is thought to be an essential first step in the prompt deactivation of photoexcited rhodopsin. In vitro, the phosphorylation can be catalyzed either by rhodopsin kinase (RK) or by protein kinase C (PKC). To investigate the specific role of RK, we inactivated both alleles of the RK gene in mice. This eliminated the light-dependent phosphorylation of rhodopsin and caused the single-photon response to become larger and longer lasting than normal. These results demonstrate that RK is required for normal rhodopsin deactivation. When the photon responses of RK−/− rods did finally turn off, they did so abruptly and stochastically, revealing a first-order backup mechanism for rhodopsin deactivation. The rod outer segments of RK−/− mice raised in 12-hr cyclic illumination were 50% shorter than those of normal (RK+/+) rods or rods from RK−/− mice raised in constant darkness. One day of constant light caused the rods in the RK−/− mouse retina to undergo apoptotic degeneration. Mice lacking RK provide a valuable model for the study of Oguchi disease, a human RK deficiency that causes congenital stationary night blindness.

Direct adenovirus-mediated gene transfer of interleukin 1 and tumor necrosis factor α soluble receptors to rabbit knees with experimental arthritis has local and distal anti-arthritic effects

Adenoviral vectors were used to deliver genes encoding a soluble interleukin 1 (IL-1)-type I receptor-IgG fusion protein and/or a soluble type I tumor necrosis factor α (TNFα) receptor-IgG fusion protein directly to the knees of rabbits with antigen-induced arthritis. When tested individually, knees receiving the soluble IL-1 receptor had significantly reduced cartilage matrix degradation and white blood cell infiltration into the joint space. Delivery of the soluble TNFα receptor was less effective, having only a moderate effect on white blood cell infiltration and no effect on cartilage breakdown. When both soluble receptors were used together, there was a greater inhibition of white blood cell infiltration and cartilage breakdown with a considerable reduction of synovitis. Interestingly, anti-arthritic effects were also seen in contralateral control knees receiving only a marker gene, suggesting that sustained local inhibition of disease activity in one joint may confer an anti-arthritic effect on other joints. These results suggest that local intra-articular gene transfer could be used to treat systemic polyarticular arthritides.

Activity and nature of p21WAF1 complexes during the cell cycle

Elevated levels of the p21WAF1 (p21) cyclin-dependent kinase inhibitor induce growth arrest. We have characterized a panel of monoclonal antibodies against human p21 in an effort to understand the dynamic regulatory interactions between this and other cellular proteins during the cell cycle. The use of these reagents has allowed us to address several important, yet unresolved, issues concerning the biological activity of p21, including the potential kinase activity of complexes that associate with this cyclin-dependent kinase inhibitor. We have found that the kinase activity of cyclin A/Cdk2 associated with p21 is significantly lower than that of cyclin A/Cdk2 free of p21, suggesting that p21 abolishes its activity in vivo, and the use of multiple antibodies has enabled us to begin the study of the molecular architecture of p21 complexes in vivo. In addition, we found that human fibroblasts released from a quiescent state display abundant amounts of p21 devoid of associated proteins (“free” p21), the levels of which decrease as cells approach S phase. Cyclin A levels increase as the amount of monomeric p21 decreases, resulting in an excess of cyclin A/Cdk2 complexes that are not bound to, or inactivated by, p21. Our data strengthen the notion that the G1-to-S phase transition in human fibroblasts occurs when the concentration of cyclin A/Cdk2 surpasses that of p21.

Microbes as engines of ecosystem function : When does community structure enhance predictions of ecosystem processes?

Peer reviewed

RGS-r, a retinal specific RGS protein, binds an intermediate conformation of transducin and enhances recycling

G proteins regulate intracellular signaling by coupling a cycle of guanine nucleotide binding and hydrolysis to transient changes of cellular functions. The mechanisms that control the recycling of transducin, the “pace-setting” G protein that regulates mammalian phototransduction, are unclear. We show that a novel retinal specific RGS-motif protein specifically binds to an intermediate conformation involved in GTP hydrolysis by transducin and accelerates phosphate release and the recycling of transducin. This specific interaction further rationalizes the kinetics of the phototransduction cascade and provides a general hypothesis to explain the mechanism of interaction of RGS proteins with other G proteins.

The Vibrio cholerae genome contains two unique circular chromosomes

Vibrio cholerae, the etiologic agent of the diarrheal disease cholera, is a Gram-negative bacterium that belongs to the γ subdivision of the family Proteobacteriaceae. The physical map of the genome has been reported, and the genome has been described as a single 3.2-Mb chromosome [Majumder, R., et al. (1996) J. Bacteriol. 178, 1105–1112]. By using pulsed-field gel electrophoresis of genomic DNA immobilized in agarose plugs and digested with the restriction enzymes I-CeuI, SfiI, and NotI, we have also constructed the physical map of V. cholerae. Our analysis estimates the size of the genome at 4.0 Mb, 25% larger than the physical map reported by others. Our most notable finding is, however, that the V. cholerae chromosome appears to be not the single chromosome reported but two unique and separate circular megareplicons.

Ribozyme-mediated high resistance against potato spindle tuber viroid in transgenic potatoes

A hammerhead ribozyme [R(-)] targeting the minus strand RNA of potato spindle tuber viroid (PSTVd) and a mutated nonfunctional ribozyme [mR(-)] were designed, cloned, and transcribed. As predicted, both monomer and dimer transcripts of the active R(-) ribozyme gene could cleave the PSTVd minus strand dimer RNA into three fragments of 77, 338, and 359 bases in vitro at 25 and 50°C. The tandem dimer genes of R(-) and mR(-) were subcloned separately into the plant expression vector pROK2. Transgenic potato plants (cultivar Desirée) were generated by Agrobacterium tumefaciens-mediated transformation. Twenty-three of 34 independent transgenic plant lines expressing the active ribozyme R(-) resulted in having high levels of resistance to PSTVd, being free of PSTVd accumulation after challenge inoculation with PSTVd, but the remaining lines showed weaker levels of resistance to PSTVd with low levels of PSTVd accumulation. In contrast, 59 of 60 independent transgenic lines expressing the mutated ribozyme mR(-) were susceptible to PSTVd inoculation and had levels of PSTVd accumulation similar to that of the control plants transformed with the empty vector. The resistance against PSTVd replication was stably inherited to the vegetative progenies.

Retinoic acid alters the intracellular trafficking of the mannose-6-phosphate/insulin-like growth factor II receptor and lysosomal enzymes

Previously, we showed that retinoic acid (RA) binds to the mannose-6-phosphate/insulin-like growth factor II receptor (M6P/IGF2R) with high affinity, suggesting that M6P/IGF2R may be a receptor for RA. Here, we show that RA, after 2–3 h of incubation with cultured neonatal-rat cardiac fibroblasts, dramatically alters the intracellular distribution of M6P/IGF2R as well as that of cathepsin B (a lysosomal protease bearing M6P). Immunofluorescence techniques indicate that this change in intracellular distribution is characterized by a shift of the proteins from the perinuclear area to cytoplasmic vesicles. The effect of RA was neither blocked by an RA nuclear receptor antagonist (AGN193109) nor mimicked by a selective RA nuclear-receptor agonist (TTNPB). Furthermore, the RA-induced translocation of cathepsin B was not observed in M6P/IGF2R-deficient P388D1 cells but occurred in stably transfected P388D1 cells expressing the receptor, suggesting that the effect of RA might be the result of direct interaction with M6P/IGF2R, rather than the result of binding to the nuclear receptors. These observations not only support the idea that M6P/IGF2R mediates an RA-response pathway but also indicate a role for RA in control of intracellular trafficking of lysosomal enzymes. Therefore, our observations may have important implications for the understanding of the diverse biological effects of retinoids.