Discrimination of the closely related A and D genomes of the hexaploid oat Avena sativa L.

A satellite DNA sequence, As120a, specific to the A-genome chromosomes in the hexaploid oat, Avena sativa L., was isolated by subcloning a fragment with internal tandem repeats from a plasmid, pAs120, that had been obtained from an Avena strigosa (As genome) genomic library. Southern and in situ hybridization showed that sequences with homology to sequences within pAs120 were dispersed throughout the genome of diploid (A and C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) Avena species. In contrast, sequences homologous to As120a were found in two A-genome species (A. strigosa and Avena longiglumis) and in the hexaploid A. sativa whereas this sequence was little amplified in the tetraploid Avena murphyi and was absent in the remaining A- and C-genome diploid species. In situ hybridization of pAs120a to hexaploid oat species revealed the distribution of elements of the As120a repeated family over both arms of 14 of 42 chromosomes of this species. By using double in situ hybridization with pAs120a and a C genome-specific probe, three sets of 14 chromosomes were revealed corresponding to the A, C, and D genomes of the hexaploid species. Simultaneous in situ hybridizations with pAs120a and ribosomal probes were used to assign the SAT chromosomes of hexaploid species to their correct genomes. This work reports a sequence able to distinguish between the closely related A and D genomes of hexaploid oats. This sequence offers new opportunities to analyze the relationships of Avena species and to explore the possible evolution of various polyploid oat species.

Subtraction hybridization identifies a transformation progression-associated gene PEG-3 with sequence homology to a growth arrest and DNA damage-inducible gene

Cancer is a progressive multigenic disorder characterized by defined changes in the transformed phenotype that culminates in metastatic disease. Determining the molecular basis of progression should lead to new opportunities for improved diagnostic and therapeutic modalities. Through the use of subtraction hybridization, a gene associated with transformation progression in virus- and oncogene-transformed rat embryo cells, progression elevated gene-3 (PEG-3), has been cloned. PEG-3 shares significant nucleotide and amino acid sequence homology with the hamster growth arrest and DNA damage-inducible gene gadd34 and a homologous murine gene, MyD116, that is induced during induction of terminal differentiation by interleukin-6 in murine myeloid leukemia cells. PEG-3 expression is elevated in rodent cells displaying a progressed-transformed phenotype and in rodent cells transformed by various oncogenes, including Ha-ras, v-src, mutant type 5 adenovirus (Ad5), and human papilloma virus type 18. The PEG-3 gene is transcriptionally activated in rodent cells, as is gadd34 and MyD116, after treatment with DNA damaging agents, including methyl methanesulfonate and γ-irradiation. In contrast, only PEG-3 is transcriptionally active in rodent cells displaying a progressed phenotype. Although transfection of PEG-3 into normal and Ad5-transformed cells only marginally suppresses colony formation, stable overexpression of PEG-3 in Ad5-transformed rat embryo cells elicits the progression phenotype. These results indicate that PEG-3 is a new member of the gadd and MyD gene family with similar yet distinct properties and this gene may directly contribute to the transformation progression phenotype. Moreover, these studies support the hypothesis that constitutive expression of a DNA damage response may mediate cancer progression.

Governing step of metastasis visualized in vitro

Metastasis is the ultimate life-threatening stage of cancer. The lack of accurate model systems thwarted studies of the metastatic cell’s basic biology. To follow continuously the succeeding stages of metastatic colony growth, we heritably labeled cells from the human lung adenocarcinoma cell line ANIP 973 with green fluorescent protein (GFP) by transfection with GFP cDNA. Labeled cells were then injected intravenously into nude mice, where, by 7 days, they formed brilliantly fluorescing metastatic colonies on mouse lung [Chishima, T., Miyagi, Y., Wang, X., Yang, M., Tan, Y., Shimada, H., Moossa, A. R. & Hoffman, R. M. (1997) Clin. Exp. Metastasis 15, 547–552]. The seeded lung tissue was then excised and incubated in the three-dimensional sponge-gel-matrix-supported histoculture that maintained the critical features of progressive in vivo tumor colonization while allowing continuous access for measurement and manipulation. Tumor progression was continuously visualized by GFP fluorescence in the same individual cultures over a 52-day period, during which the tumors spread throughout the lung. Histoculture tumor colonization was selective for lung cancer cells to grow on lung tissue, because no growth occurred on histocultured mouse liver tissue, which was also observed in vivo. The ability to support selective organ colonization in histoculture and visualize tumor progression by GFP fluorescence allows the in vitro study of the governing processes of metastasis [Kuo, T.-H., Kubota, T., Watanbe, M., Furukawa, T., Teramoto, T., Ishibiki, K., Kitajima, M., Moossa, A. R., Penman, S. & Hoffman, R. M. (1995) Proc. Natl. Acad. Sci. USA 92, 12085–12089]. The results presented here provide significant, new opportunities to understand and to develop treatments that prevent and possibly reverse metastasis.

Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis

The availability of complete genome sequences and mRNA expression data for all genes creates new opportunities and challenges for identifying DNA sequence motifs that control gene expression. An algorithm, “MobyDick,” is presented that decomposes a set of DNA sequences into the most probable dictionary of motifs or words. This method is applicable to any set of DNA sequences: for example, all upstream regions in a genome or all genes expressed under certain conditions. Identification of words is based on a probabilistic segmentation model in which the significance of longer words is deduced from the frequency of shorter ones of various lengths, eliminating the need for a separate set of reference data to define probabilities. We have built a dictionary with 1,200 words for the 6,000 upstream regulatory regions in the yeast genome; the 500 most significant words (some with as few as 10 copies in all of the upstream regions) match 114 of 443 experimentally determined sites (a significance level of 18 standard deviations). When analyzing all of the genes up-regulated during sporulation as a group, we find many motifs in addition to the few previously identified by analyzing the subclusters individually to the expression subclusters. Applying MobyDick to the genes derepressed when the general repressor Tup1 is deleted, we find known as well as putative binding sites for its regulatory partners.

Creating a Web-accessible, point-of-care, team-based information system (PoinTIS): the librarian as publisher*

The Internet has created new opportunities for librarians to develop information systems that are readily accessible at the point of care. This paper describes the multiyear process used to justify, fund, design, develop, promote, and evaluate a rehabilitation prototype of a point-of-care, team-based information system (PoinTIS) and train health care providers to use this prototype for their spinal cord injury and traumatic brain injury patient care and education activities. PoinTIS is a successful model for librarians in the twenty-first century to serve as publishers of information created or used by their parent organizations and to respond to the opportunities for information dissemination provided by recent technological advances.

Transcriptional and posttranslational plasticity and the generation of inflammatory pain

Inflammatory pain manifests as spontaneous pain and pain hypersensitivity. Spontaneous pain reflects direct activation of specific receptors on nociceptor terminals by inflammatory mediators. Pain hypersensitivity is the consequence of early posttranslational changes, both in the peripheral terminals of the nociceptor and in dorsal horn neurons, as well as later transcription-dependent changes in effector genes, again in primary sensory and dorsal horn neurons. This inflammatory neuroplasticity is the consequence of a combination of activity-dependent changes in the neurons and specific signal molecules initiating particular signal-transduction pathways. These pathways phosphorylate membrane proteins, changing their function, and activate transcription factors, altering gene expression. Two distinct aspects of sensory neuron function are changed as a result of these processes, basal sensitivity, or the capacity of peripheral stimuli to evoke pain, and stimulus-evoked hypersensitivity, the capacity of certain inputs to generate prolonged alterations in the sensitivity of the system. Posttranslational changes largely alter basal sensitivity. Transcriptional changes both potentiate the system and alter neuronal phenotype. Potentiation occurs as a result of the up-regulation in the dorsal root ganglion of centrally acting neuromodulators and simultaneously in the dorsal horn of their receptors. This means that the response to subsequent inputs is augmented, particularly those that induce stimulus-induced hypersensitivity. Alterations in phenotype includes the acquisition by A fibers of neurochemical features typical of C fibers, enabling these fibers to induce stimulus-evoked hypersensitivity, something only C fiber inputs normally can do. Elucidation of the molecular mechanisms responsible provides new opportunities for therapeutic approaches to managing inflammatory pain.

Ecological approaches and the development of “truly integrated” pest management

Recent predictions of growth in human populations and food supply suggest that there will be a need to substantially increase food production in the near future. One possible approach to meeting this demand, at least in part, is the control of pests and diseases, which currently cause a 30–40% loss in available crop production. In recent years, strategies for controlling pests and diseases have tended to focus on short-term, single-technology interventions, particularly chemical pesticides. This model frequently applies even where so-called integrated pest management strategies are used because in reality, these often are dominated by single technologies (e.g., biocontrol, host plant resistance, or biopesticides) that are used as replacements for chemicals. Very little attention is given to the interaction or compatibility of the different technologies used. Unfortunately, evidence suggests that such approaches rarely yield satisfactory results and are unlikely to provide sustainable pest control solutions for the future. Drawing on two case histories, this paper demonstrates that by increasing our basic understanding of how individual pest control technologies act and interact, new opportunities for improving pest control can be revealed. This approach stresses the need to break away from the existing single-technology, pesticide-dominated paradigm and to adopt a more ecological approach built around a fundamental understanding of population biology at the local farm level and the true integration of renewable technologies such as host plant resistance and natural biological control, which are available to even the most resource-poor farmers.

Molecular cloning of violaxanthin de-epoxidase from romaine lettuce and expression in Escherichia coli.

Plants need to avoid or dissipate excess light energy to protect photosystem II (PSII) from photoinhibitory damage. Higher plants have a conserved system that dissipates excess energy as heat in the light-harvesting complexes of PSII that depends on the transthylakoid delta pH and violaxanthin de-epoxidase (VDE) activity. To our knowledge, we report the first cloning of a cDNA encoding VDE and expression of functional enzyme in Escherichia coli. VDE is nuclear encoded and has a transit peptide with characteristic features of other lumen-localized proteins. The cDNA encodes a putative polypeptide of 473 aa with a calculated molecular mass of 54,447 Da. Cleavage of the transit peptide results in a mature putative polypeptide of 348 aa with a calculated molecular mass of 39,929 Da, close to the apparent mass of the purified enzyme (43 kDa). The protein has three interesting domains including (i) a cysteine-rich region, (ii) a lipocalin signature, and (iii) a highly charged region. The E. coli expressed enzyme de-epoxidizes violaxanthin sequentially to antheraxanthin and zeaxanthin, and is inhibited by dithiothreitol, similar to VDE purified from chloroplasts. This confirms that the cDNA encodes an authentic VDE of a higher plant and is unequivocal evidence that the same enzyme catalyzes the two-step mono de-epoxidation reaction. The cloning of VDE opens new opportunities for examining the function and evolution of the xanthophyll cycle, and possibly enhancing light-stress tolerance of plants.

Acciones públicas de sensibilización de género: el esfuerzo de la administración regional y local en comunicación publicitaria (1999-2007)

El artículo analiza las iniciativas de comunicación relacionadas con la igualdad de oportunidades entre mujeres y hombres. El objetivo es analizar con enfoque de género las acciones realizadas por parte de las instituciones públicas regionales y locales para sensibilizar y promover la conciliación entre la vida familiar y laboral de seis comunidades autónomas (Andalucía, Cataluña, Comunidad Valenciana, Galicia, Madrid y País Vasco) y de sus capitales, desde 1999 (cuando se aprueba la ley de conciliación) hasta 2007 (se aprueba la ley de igualdad). La información sobre publicidad convencional fue proporcionada por Infoadex. Para la recogida de otro tipo de iniciativas a través de medios menos convencionales se acudió a cuatro fuentes institucionales: 1) Ayuntamientos de las capitales, como fuente estrictamente local, 2) Diputaciones de la capital de la Comunidad Autónoma, como fuente provincial, 3) Direcciones Generales de la Mujer o instituciones análogas como fuente de información a nivel regional o autonómico y, por último, 4) otras concejalías vinculadas al tema de la corresponsabilidad, cuyo radio de acción también es autonómico. Los resultados, aunque con diferencias entre regiones, reflejan carencias en la cobertura de las acciones que llevan a cuestionar la falta de estrategia política en términos de comunicación, pese a la introducción sistemática de estos objetivos en la agenda internacional (ONU y UE) y del gobierno español. En consecuencia, las campañas publicitarias e iniciativas recogidas contribuyen a la visibilización del problema y al empoderamiento, pero no tanto al objetivo de la paridad.

A Computational Method based on Radio Frequency Technologies for the Analysis of Accessibility of Disabled People in Sustainable Cities

The sustainability strategy in urban spaces arises from reflecting on how to achieve a more habitable city and is materialized in a series of sustainable transformations aimed at humanizing different environments so that they can be used and enjoyed by everyone without exception and regardless of their ability. Modern communication technologies allow new opportunities to analyze efficiency in the use of urban spaces from several points of view: adequacy of facilities, usability, and social integration capabilities. The research presented in this paper proposes a method to perform an analysis of movement accessibility in sustainable cities based on radio frequency technologies and the ubiquitous computing possibilities of the new Internet of Things paradigm. The proposal can be deployed in both indoor and outdoor environments to check specific locations of a city. Finally, a case study in a controlled context has been simulated to validate the proposal as a pre-deployment step in urban environments.

Pinos autóctonos y conservación de bosques en Andalucía

La evolución del arbolado en la Península Ibérica pasó por numerosos episodios que le condujeron a una situación grave de deforestación. Tras varios intentos de reforestación en épocas distintas, finalmente la apuesta definitiva se produciría con la creación del Patrimonio Forestal del Estado y el Plan Nacional de Repoblación Forestal de España de 1939. La sustitución del PFE por el ICONA en 1971, supuso un nuevo contexto, en el que se puso en duda tanto la actuación repobladora, como las especies utilizadas, principalmente del género Pinus. Este trabajo trata de poner en valor la información que aportan distintas corrientes científicas, la botánica, la biogeografía, paleobotánica y los datos de otros estudios realizados en numerosos yacimientos arqueológicos en Andalucía, especialmente en la zona oriental. Estos trabajos ponen de manifiesto la presencia de especies del género Pinus en distintos periodos geológicos, con avances y retrocesos del binomio Pinus-Quercus, durante períodos más o menos extensos. La repoblación forestal supuso un avance a una de esas situaciones, que dió como resultado el marco de nuevas intervenciones de manejo del bosque por la Administración Andaluza, siendo las exigencias de conservación prioritarias en la gestión de los espacios forestales, muchos de ellos declarados Espacios Protegidos. Se trata pues, de poner en valor aquellas actuaciones que dieron lugar a la nueva situación en la que se apuesta por la conservación y en la que juegan un papel importante la genética y la productividad de las especies utilizadas en las intervenciones forestales.

Trade policy issues in the Wider Europe – that led to war and not yet to peace. CEPS Working Document No. 398, July 2014

This paper looks at the trade policy landscape of the EU and the wider Europe, with a focus on issues arising from the signature on 27 June 2014 of Deep and Comprehensive Free Trade Agreements (DCFTAs) between the EU and three East European countries (Georgia, Moldova and Ukraine), and actual or prospective issues relating to the customs union of Belarus, Russia and Kazakhstan (BRK), and the Eurasian Economic Union whose founding treaty was signed on 29 May 2014. The huge expansion of intercontinental free trade area negotiations currently underway, in which the EU is an active participant alongside much of the Americas and Asia, stands in contrast with Russia’s choice to restrict itself to the Eurasian Economic Union, which is only a marginal extension of its own economy. Alone among the major economies in the world, Russia does not seek to integrate economically with any major economic bloc, which should be a matter of serious concern for Moscow. Within the wider Europe, the EU’s DCFTAs with Ukraine, Moldova and Georgia are a major new development, but Russia now threatens trade sanctions against Ukraine in particular, the economic case for which seems unfounded and whose unilateral application would also impair the customs union. The Belarus-Russia-Kazakhstan customs union itself poses several issues of compatibility with the rules of the WTO, which in turn are viewed by the EU as an impediment to discussing possible free trade scenarios with the customs union, although currently there are far more fundamental political impediments to any consideration of such ideas. Nonetheless, this paper looks at various long-term scenarios, if only as a reminder that there could be much better alternatives to the present context of conflict around Ukraine.

Transnistrian Conflict after 20 years: A Report by an International Expert Group. OSW Report, October 2011

The present report is the result of an initiative put forward in 2010 by the Soros Foundation Moldova (East East: Partnership Beyond Borders Program) with the aim of attracting new foreign expertise to provide a fresh look at the ‘frozen conflict’ in the Republic of Moldova. The initiative was informed by the conviction that the political shifts in and around Moldova that have occurred since 2009 are creating new opportunities to resolve the conflict. The idea was to convene a joint group of international and Moldovan experts who, after conducting a fact-finding field trip to Chisinau and Tiraspol and conducting extensive discussions, would draw up a report with their analysis of the situation and their political recommendations.

The WTO and Female Labor Rights in Developing Countries. IES WORKING PAPER 3/2008

The impacts of WTO on women’s labour rights in the developing countries have been raised to the international agenda by various nongovernmental organizations. On the one hand it is assumed that international trade policies are gender neutral. On the other hand a number of authors hold the view that the negative impacts of WTO policies are more pronounced on female than male workers. This paper takes a critical look at these claims. It argues that the impact of the WTO system, the driving force of trade liberalization, on women’s labour rights in the developing countries is a complicated issue, because the effects have been both negative and positive. In support of this claim, this paper first briefly reviews the international framework for the protection of women’s labour rights. Next, the WTO agreements and policies are analysed insofar as they are relevant for the protection of women’s labour rights. The analysis covers, for example, the use of the trade policy review mechanism and restrictions of trade on grounds of violation of public morals.. Finally, a case study is conducted on the situation of female workers in Bangladesh and Pakistan, countries that have recently undergone a liberalization of trade in the textiles and clothing sectors. It is concluded that the increase of international trade in the developing countries has created many work opportunities for women, helped them to become more independent and allowed them to participate in the society more actively. However, it is at the same time posited that in order to comply with its own objectives of raising standards of living and full employment, the WTO should engage itself in active policies to overcome the negative aspects of trade on female workers in the developing countries.

The consequences for Russia of the nuclear deal with Iran. OSW COMMENTARY NUMBER 177/03.08.2015

The five permanent members of the UN Security Council (the USA, the United Kingdom, China, France and Russia) plus Germany and the European Union signed a deal with Iran on 14 July in Vienna (a Plan of Action with five appendices, henceforth referred to as the Vienna Agreement). Under this agreement, Iran undertook to restrict its nuclear programme and to bring it under international scrutiny for 15 years in exchange for a gradual lifting of international sanctions (both those imposed between 2006 and 2010 by the UN Security Council and the unilateral US and EU sanctions). Even though Russia has officially reacted positively to this deal, the consequences it will have are rather ambiguous from Moscow’s point of view. Iran looks set to become stronger and will possibly normalise its relations with the West, and especially the United States. This, in political terms, is a disadvantage for Russia. The Kremlin’s ability to use its policy towards Iran as a bargaining chip in contacts with Washington will be reduced significantly. In turn, the benefits will include improving the perception of Russia in the West and the opening up of new opportunities for the geopolitical game in the region, both with Iran and its opponents in the Arab world. Similarly, in economic terms, the possible lifting of sanctions will offer Russia new opportunities to achieve immediate benefits owing to co-operation in the nuclear and military-technical areas. In the short term, the lifting of sanctions will not pose any threat to Russia’s position on the global energy markets. However, in the long term, the end of Iran’s international isolation may bring negative consequences for Russia, such as the dominant position of Western and/or Chinese companies in the Iranian upstream sector, rising exports of Iranian oil and gas to EU and Asian markets (which are essential for Russia) and the downward pressure on oil and gas prices.