Amplification and cloning of cDNAS of cytochrome P4501A1 and metallothionein genes from Sparus aurata Linnaeus, 1758 and Liza aurata (Risso, 1810) by Race-PCR

The biotransformation of xenobiotics found in marine ecosystems is catalysed by inducible systems, a property that makes them useful as early-warning biomarkers of environmental pollution. We have focused our study on cytochrome P4501A1 (CYP 1A1) as a phase I response against organic aromatic xenobiotics, and metallothionein (MT), which reflects pollution by transition metals. The high homology existing between the sequences of both genes, already cloned in different fish species, enabled us to design degenerate oligos to amplify by RT-PCR specific sequences of CYP 1A1 and MT genes in two teleost fish species of the Spanish South Atlantic littoral, the gilthead seabream, Sparus aurata Linnaeus, 1758, and the grey mullet, Liza aurata (Risso 1810). To this end, the expression of both genes was previously induced by intraperitoneal injection with Aroclor 1254 (CYP 1A1) and CdCl2 (MT). The specific sequences for both genes amplified by RT-PCR with degenerate oligos were subsequently used to design new, specific oligos to obtain by Race-PCR (Rapid Amplification of cDNA Ends) the complete cDNAs coding for both genes in both fish species, which were subsequently cloned and sequenced. The coding sequences and the corresponding proteins were compared with those already obtained in other fish species. We are currently developing homologous probes for mRNA quantification using molecular biology techniques in both fish species, to be employed as molecular biomarkers of pollution in the Spanish South Atlantic littoral.La biotransformación de xenobióticos presentes en ecosistemas marinos está catalizada por varios sistemas inducibles, lo que permite su uso como biomarcadores de alerta temprana de contaminación ambiental. Este estudio se ha centrado en el citocromo P4501A1 (CYP 1A1), como respuesta de fase I contra xenobióticos orgánicos aromáticos, y la metalotioneína (MT), que refleja la contaminación por metales de transición. La alta homología existente entre las secuencias de ambos genes previamente clonados en diferentes especies de peces permitió diseñar oligos degenerados para amplificar por RT-PCR secuencias específicas de los genes CYP 1A1 y MT en dos especies de peces teleósteos del litoral suratlántico español, la dorada Sparus aurata Linnaeus, 1758 y la lisa Liza aurata (Risso, 1810). Para ello, la expresión de ambos genes se indujo por inyección intraperitoneal con Aroclor 1254 (CYP 1A1) y CdCl2 (MT). Las secuencias específicas de ambos genes, amplificadas por RT-PCR con tales oligos, se usaron posteriormente para diseñar nuevos oligos específicos; éstos se usaron para amplificar por Race-PCR (Rapid Amplification of cDNA Ends) los cDNAs completos que codifican tales genes en ambas especies de peces, que fueron posteriormente clonados y secuenciados. Las secuencias codificantes y las proteínas correspondientes se han comparado con las obtenidas en otras especies de peces. Actualmente se desarrollan sondas homólogas para cuantificar por métodos de biología molecular los mRNAs específicos en ambos peces, para su uso como biomarcadores moleculares de contaminación en el litoral suratlántico español.Instituto Español de Oceanografí

Cost-aware multi data-center bulk transfers in the cloud from a customer-side perspective

Many cloud applications (e.g., data backup and replication, video distribution) require dissemination of large volumes of data from a source data-center to multiple geographically distributed data-centers. Given the high costs of wide-area bandwidth, the overall cost of inter-data-center communication is a major concern in such scenarios. While previous works have focused on optimizing the costs of bulk transfer, most of them use the charging models of Internet service providers, typically based on the 95th percentile of bandwidth consumption. However, public Cloud Service Providers (CSP) follow very different models to charge their customers. First, the cost for transmission is flat and depends on the location of the source and receiver data-centers. Second, CSPs offer discounts once customer transfers exceed certain volume thresholds per data-center. We present a systematic framework, CloudMPcast, that exploits these two aspects of cloud pricing schemes. CloudMPcast constructs overlay distribution trees for bulk-data transfer that both optimizes dollar costs of distribution, and ensures end-to-end data transfer times are not affected. CloudMPCast monitors TCP throughputs between data-centers and only proposes alternative trees that respect original transfer times. After an extensive measurement study, the cost savings range from 10 to 60 percent for both Azure and EC2 infrastructures, which potentially translates to millions of dollars a year assuming realistic demandsThis material is based upon work supported in part by the National Science Foundation (NSF) under Award No.1162333, . J. L. Garc ıa-Dorado is thankful for the financial support of the Jos e Castillejo Program (CAS12/00057

Amplification and cloning of cDNAS of cytochrome P4501A1 and metallothionein genes from Sparus aurata Linnaeus, 1758 and Liza aurata (Risso, 1810) by Race-PCR

The biotransformation of xenobiotics found in marine ecosystems is catalysed by inducible systems, a property that makes them useful as early-warning biomarkers of environmental pollution. We have focused our study on cytochrome P4501A1 (CYP 1A1) as a phase I response against organic aromatic xenobiotics, and metallothionein (MT), which reflects pollution by transition metals. The high homology existing between the sequences of both genes, already cloned in different fish species, enabled us to design degenerate oligos to amplify by RT-PCR specific sequences of CYP 1A1 and MT genes in two teleost fish species of the Spanish South Atlantic littoral, the gilthead seabream, Sparus aurata Linnaeus, 1758, and the grey mullet, Liza aurata (Risso 1810). To this end, the expression of both genes was previously induced by intraperitoneal injection with Aroclor 1254 (CYP 1A1) and CdCl2 (MT). The specific sequences for both genes amplified by RT-PCR with degenerate oligos were subsequently used to design new, specific oligos to obtain by Race-PCR (Rapid Amplification of cDNA Ends) the complete cDNAs coding for both genes in both fish species, which were subsequently cloned and sequenced. The coding sequences and the corresponding proteins were compared with those already obtained in other fish species. We are currently developing homologous probes for mRNA quantification using molecular biology techniques in both fish species, to be employed as molecular biomarkers of pollution in the Spanish South Atlantic littoralLa biotransformación de xenobióticos presentes en ecosistemas marinos está catalizada por varios sistemas inducibles, lo que permite su uso como biomarcadores de alerta temprana de contaminación ambiental. Este estudio se ha centrado en el citocromo P4501A1 (CYP 1A1), como respuesta de fase I contra xenobióticos orgánicos aromáticos, y la metalotioneína (MT), que refleja la contaminación por metales de transición. La alta homología existente entre las secuencias de ambos genes previamente clonados en diferentes especies de peces permitió diseñar oligos degenerados para amplificar por RT-PCR secuencias específicas de los genes CYP 1A1 y MT en dos especies de peces teleósteos del litoral suratlántico español, la dorada Sparus aurata Linnaeus, 1758 y la lisa Liza aurata (Risso, 1810). Para ello, la expresión de ambos genes se indujo por inyección intraperitoneal con Aroclor 1254 (CYP 1A1) y CdCl2 (MT). Las secuencias específicas de ambos genes, amplificadas por RT-PCR con tales oligos, se usaron posteriormente para diseñar nuevos oligos específicos; éstos se usaron para amplificar por Race-PCR (Rapid Amplification of cDNA Ends) los cDNAs completos que codifican tales genes en ambas especies de peces, que fueron posteriormente clonados y secuenciados. Las secuencias codificantes y las proteínas correspondientes se han comparado con las obtenidas en otras especies de peces. Actualmente se desarrollan sondas homólogas para cuantificar por métodos de biología molecular los mRNAs específicos en ambos peces, para su uso como biomarcadores moleculares de contaminación en el litoral suratlántico españo

Software público, libre, abierto, gratuito, privativo y comercial para la innovación y mejora de la calidad en la docencia, investigación, gestión y asistencia

The public free software (now renamed as open software) is the basis of the open source software (OSS) project. This initiative promotes the use of open standards and platform-independent accessibility. Many OSS products are free or low cost, which allows their deployment even in the absence of large economic resources (developing countries, schools, etc.). Besides, their source code can be modified, adapted and optimized by anyone, since it is public. Nevertheless, the OSS may also have drawbacks. Thus, its development may not be as orderly and hierarchical as the privative software is, and may not have an appropriate funding. This may jeopardize the ease of use and coherence of the final product, increasing the transition, training and technical support costs. Besides, it must be taken into account that there is also commercial open software, as well as free privative software. In any case, the excellence of the software may be independent of such variables. Thus, the best strategy is the coexistence and free competition of all kinds of software. This will allow a quality improvement and an innovation enhancement, which will benefit the education, research, management and assistance at the university in particular and at the whole society in general.El software público libre es el fundamento del movimiento de software de fuente abierta (OSS). Éste puede facilitar el uso de estándares abiertos, con accesibilidad independiente de plataforma informática. El bajo coste o gratuidad de muchos productos OSS permite su implantación cuando los recursos económicos son escasos (países en desarrollo, escuelas, etc.). Además, su código se puede modificar, adaptar y mejorar por cualquiera, ya que es público. No obstante, el OSS también puede presentar inconvenientes. Así, su desarrollo puede no ser tan ordenado y jerárquico como el del software privativo y puede no tener una financiación apropiada. De este modo, puede verse comprometida la facilidad de uso y coherencia del producto final. Ello puede incrementar los costes de transición, entrenamiento y soporte técnico. Por otra parte, conviene recordar que existe software libre comercial y software privativo gratuito. En cualquier caso, la excelencia del software puede ser independiente de dichas variables. Por tanto, la mejor estrategia es la coexistencia y libre competencia de todo tipo de software. Así se puede conseguir una mejora de calidad y una potenciación de la innovación, que beneficie a la docencia, investigación, gestión y asistencia universitarias en particular, así como a la sociedad en general

Varietal Tracing of Virgin Olive Oils Based on Plastid DNA Variation Profiling

Olive oil traceability remains a challenge nowadays. DNA analysis is the preferred approach to an effective varietal identification, without any environmental influence. Specifically, olive organelle genomics is the most promising approach for setting up a suitable set of markers as they would not interfere with the pollinator variety DNA traces. Unfortunately, plastid DNA (cpDNA) variation of the cultivated olive has been reported to be low. This feature could be a limitation for the use of cpDNA polymorphisms in forensic analyses or oil traceability, but rare cpDNA haplotypes may be useful as they can help to efficiently discriminate some varieties. Recently, the sequencing of olive plastid genomes has allowed the generation of novel markers. In this study, the performance of cpDNA markers on olive oil matrices, and their applicability on commercial Protected Designation of Origin (PDO) oils were assessed. By using a combination of nine plastid loci (including multi-state microsatellites and short indels), it is possible to fingerprint six haplotypes (in 17 Spanish olive varieties), which can discriminate high-value commercialized cultivars with PDO. In particular, a rare haplotype was detected in genotypes used to produce a regional high-value commercial oil. We conclude that plastid haplotypes can help oil traceability in commercial PDO oils and set up an experimental methodology suitable for organelle polymorphism detection in the complex olive oil matrices

MOBFLOW: Movilidad para los procesos de negocio de la organización

Este artículo presenta la plataforma MobFlow (Mobile Flow); un sistema que permite particionar, distribuir, y ejecutar en entornos móviles, procesos de negocio descritos a través del estándar BPEL. También, MobFlow realiza el monitoreo de la ejecución de los procesos de negocio de la organización, los cuales son consumidos en tiempo real en los dispositivos móviles de los empleados. Además de exponer los módulos que componen la plataforma, el artículo presenta la implementación de un prototipo que valida la arquitectura propuesta, y un caso de estudio práctico de un proceso de ventas, que expone el funcionamiento de la plataforma

Methodology proposal for the location of microsatellites in the equine genome

We present a relatively simple methodology for the detection of microsatellite sequences in partial genetic libraries in plasmids, consisting mainly in a new DNA extraction protocol and the use of a probe (TG)7T to locate different types of microsatellites.Se presenta una metodología relativamente sencilla para la detección de secuencias microsatélites a partir de genotecas parciales en plásmidos, que consiste fundamentalmente en un nuevo protocolo de extracción de DNA y el empleo de una sonda (TG)7T para localizar diferentes tipos de microsatélites

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing-Review

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals

MC64-Cluster: Many-Core CPU Cluster Architecture and Performance Analysis in B-Tree Searches

The MC64-Cluster computer platform was designed, based on many-core CPU microprocessors: Tile64. MC64-Cluster architecture was outlined in terms of both hardware and software, including commands available to manage jobs and provided application programming interfaces to communicate and synchronize tiles, making this system easy to use. Massively, concurrent-searches of keys in B-trees, which are used in many applications, including bioinformatics, were used. Remarkable performance improvements were obtained when the cluster resources were combined with those available in host machine (hybrid or heterogeneous environments). These results were even more outstanding when analyzed in terms of performance-per-watt, highlighting their green-computing advantages. Together with the cluster architecture, they represent the main contributions of this work. To our knowledge, this is the first cluster implementation of this kind being developed