Locating and sequencing of the E3 and neighbouring regions in bovine advenovirus type 2

Adenoviruses are nonenveloped icosahedral shaped particles. The double stranded DNA viral genome is divided into 5 major early transcription units, designated E1 A, E1 B, and E2 to E4, which are expressed in a regulated manner soon after infection. The gene products of the early region 3 (E3), shown to be nonessential for viral replication in vitro, are believed to be involved in counteracting host immunosurveillance. In order to sequence the E3 region of Bovine adenovirus type 2 (BAV2) it was necessary to determine the restriction map for the plasmid pEA48. A physical restriction endonuclease map for BamHl, Clal, Eco RI, Hindlll, Kpnl, Pstt, Sail, and Xbal was constructed. The DNA insert in pEA48 was determined to be viral in origin using Southern hybridization. A human adenovirus type 5 recombinant plasmid, containing partial DNA fragments of the two transcription units L4 and L5 that lie just outside the E3, was used to localize this region. The recombinant plasmid pEA was subcloned to facilitate sequencing. The DNA sequences between 74.8 and 90.5 map units containing the E3, the hexon associated protein (pVIII), and the fibre gene were determined. Homology comparison revealed that the genes for the hexon associated pV11I and the fibre protein are conserved. The last 70 amino acids of the BAV2 pV11I were the most conserved, showing a similarity of 87 percent with Ad2 pV1I1. A comparison between the predicted amino acid sequences of BAV2 and Ad40, Ad41 , Ad2 and AdS, revealed that they have an identical secondary structure consisting of a tail, a shaft and a knob. The shaft is composed of 22, 15 amino acid motifs, with periodic glycines and hydrophobic residues. The E3 region was found to consist of about 2.3 Kbp and to encode four proteins that were greater than 60 amino acids. However, these four open reading frames did not show significant homology to any other known adenovirus DNA or protein sequence.

The cloning and reconstitution of a bovine adenovirus type 2 E3 deletion mutant and the sequencing and analysis of the early 4 region

Recombinant Adenoviruses (Ads) have been shown to have potential applications in three areas: gene therapy, high level protein expression and recombinant vaccines.' At least three different locations within the Ad genome can be deleted and subsequently used for the insertion of foreign sequences. These include the Early 3 (E3), Early 1 (E1) and Early 4 (E4) regions. Viral vectors of this type have been well studied in Human Ads 2 and 5, however one has not yet been constructed for Bovine Adenovirus Type 2 (BAV2). The E3 region is located between 76.6 and 86 m.u. on the r-strand and is transcribed in a rightward direction. The gene products of the Early 3 region (E3) have been shown to be non-essential for viral replication, in vitro, but are required for host immunosurveillance. This study represents the cloning and reconstitution of a BAV2 E3 deletion mutant. A deletion of 1800bp was made within the E3 region of BAV2 and the thymidine kinase gene was subsequently inserted in the deleted area . . The plasmid pdlE3-4tk1 (23.4Kbp) was constructed and used to to facilitate homologous recombination with the wild type BAV2 to produce a mutant. Southern Blotting and Hybridization results suggest the presence of a BAV2 E3 deletion mutant with thymidine kinase sequences present. The E4 region of Human Adenovirus types 2 and 5 is located at the extreme right end of the genome (91.3 map units - 99.1 map units) and is transcribed in a leftward direction giving rise to a complicated set of differentially spliced mRNAs. Essentially there are 7 open reading frames (ORFs) encoding for at least 7 polypeptides. The gene products encoded by the E4 region have been shown to be essential for the expression of late viral genes, host cell shutoff and normal viral growth. We have cloned and sequenced the right end segment between 90.5 map units and 100 map units of the BAV2 genome. The results show several open reading frames which encode polypeptides exhibiting homology to three polypeptides encoded by the E4 region of human adenovirus type 2. These include the 14kDa protein encoded by ORF1, the 34kDa protein encoded by ORF6 and the 13kDa protein encoded by ORF3. The nucleotide sequence, restriction enzyme map, and ORF map of the E4 region could be very useful in future molecular manipulation of this region and could possibly explain the slow growth rate of BAV2 in MDBK cells.

Propidium monoazide (PMA) and ethidium bromide monoazide(EMA) improve DNA array and high-throughput sequencing ofporcine reproductive and respiratory syndrome virus identification

Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.

Microsatellites from Fosterella christophii (Bromeliaceae) by de novo transcriptome sequencing on the Pacific Biosciences RS platform

• Premise of the study: Microsatellite markers were developed in Fosterella christophii (Bromeliaceae) to investigate the genetic diversity and population structure within the F. micrantha group, comprising F. christophii, F. micrantha, and F. villosula. • Methods and Results: Full-length cDNAs were isolated from F. christophii and sequenced on a Pacific Biosciences RS platform. A total of 1590 high-quality consensus isoforms were assembled into 971 unigenes containing 421 perfect microsatellites. Thirty primer sets were designed, of which 13 revealed a high level of polymorphism in three populations of F. christophii, with four to nine alleles per locus. Each of these 13 loci cross-amplified in the closely related species F. micrantha and F. villosula, with one to six and one to 11 alleles per locus, respectively. • Conclusions: The new markers are promising tools to study the population genetics of F. christophii and to discover species boundaries within the F. micrantha group.

Curriculum sequencing for an e-learning system based on learning styles

This work shows the use of adaptation techniques involved in an e-learning system that considers students' learning styles and students' knowledge states. The mentioned e-learning system is built on a multiagent framework designed to examine opportunities to improve the teaching and to motivate the students to learn what they want in a user-friendly and assisted environment

"Whole-Exome Sequencing Enables Rapid Determination of Xeroderma Pigmentosum Molecular Etiology"

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder haracterized by extreme sensitivity to actinic pigmentation changes in the skin and increased incidence of skin cancer. In some cases, patients are affected by neurological alterations. XP is caused by mutations in 8 distinct genes (XPA through XPG and XPV). The XP-V (variant) subtype of the disease results from mutations in a gene (XPV, also named POLH) which encodes for Polg, a member of the Y-DNA polymerase family. Although the presence and severity of skin and neurological dysfunctions differ between XP subtypes, there are overlapping clinical features among subtypes such that the sub-type cannot be deduced from the clinical features. In this study, in order to overcome this drawback, we undertook whole-exome sequencing in two XP sibs and their father. We identified a novel homozygous nonsense mutation (c.897T.G, p.Y299X) in POLH which causes the disease. Our results demonstrate that next generation sequencing is a powerful approach to rapid determination of XP genetic etiology.

Secuenciamiento de actividades educativas orientado a la reutilización y la auto-organización en tutoría inteligente. ' 'Sequencing of learning activities oriented towards reuse and auto-organization for intelligent tutoring systems' '.

Se pretende la elaboración una plataforma capaz de implementar sistemas de tutoría inteligente, orientada al problema de la adaptación del secuenciamiento; la creación de una herramienta o método que defina secuenciamientos adaptativos de material educativo; el desarrollo, empleando la herramienta anterior, de uno o más tutores y adaptar las técnicas de inteligencia de enjambre al campo de los cursos impartidos a través de Internet, Elearning.. En primer lugar se analiza el estado de la cuestión, destacando los aspectos novedosos. A continuación se presentan las aportaciones de la investigación. Por último, se exponen las conclusiones y las líneas de investigación abiertas. También se incluyen apéndices con información adicional que puede ser relevante para algunos lectores. Se investiga el uso de técnicas de inteligencia de enjambre para obtener sistemas educativos robustos y con capacidad de autoorganización. Las lecciones aprendidas de los sistemas cristalizan en la creación de un módulo para SIT.. Las principales contribuciones son: el diseño de una plataforma para el desarrollo de Sistemas de Tutoría Inteligentes (ITS); se presenta una herramienta para la adaptación de secuencias de unidades de aprendizaje, grafos de secuenciamiento (Sequencing Graphs, SG) y se analizan las iniciativas actuales relacionadas con las técnicas de enjambre en educación. Estas técnicas tienen un interés especial para los sistemas de elearning dada su complejidad. .

Patterns of Activity Sequencing in the Teaching of English as a Foreing Language and Their Effects on Learning : a Quasi-Experimental Study.'Patrones de secuenciación de actividades en la enseñanza del inglés como lengua extranjera y su incidencia en el aprendizaje : estudio cuasi-experimental.

Contrastar el modelo denominado CPM (basado en el desarrollo de los procesos comunicativos) con el modelo de secuenciación de actividades P-P-P (presentación-práctica-producción) que es el utilizado con mayor frecuencia en los libros de texto para la enseñanza de los idiomas, para medir la eficacia diferencial en el aprendizaje lingüístico del inglés como lengua extranjera.. Estudio llevado a cabo en la Escuela Oficial de Idiomas de Murcia con una muestra inicial de 51 sujetos que se redujo a 34 nativos de lengua española de edades comprendidas entre los 16 y 41 años formada mayoritariamente por mujeres. Estudio cuasi-experimental de análisis de medidas repetidas con grupo experimental y grupo de control (factor intersujetos). La variable dependiente es la eficacia de la intervención objeto de estudio o intervención CPM. La variable independiente es el grupo, que consta de dos partes, el que sigue el programa establecido en el centro de enseñanza, versión P-P-P y el grupo experimental (EG) que recibe instrucción basada en el CPM. La aplicación duró 4 meses (enero-mayo 2003) y el total de sesiones fue de 35 para cada uno de los dos grupos. Se utilizó el examen estandarizado internacional Cambridge First Certificate in English (FCE) en su parte: Use of English.. La secuenciación de actividades en general y la basada en el CPM en particular merecen un justo reconocimiento en el ámbito de la investigación en enseñanza de lenguas extranjeras debido no solo a las puntuaciones obtenidas en la investigación sino también a su fundamentación teórica basada en un modelo cognitivo de adquisición de conocimientos ampliamente aplicado en SLA y a su flexibilidad en cuanto a las vías de aprendizaje propuestas, su atención al concepto script y su afinidad con los enfoques didácticos actuales (integración de destrezas, relevancia e interés para el alumno, variedad en la instrucción)..

Multivariate Statistical Process Control and Case-Based Reasoning for situation assessment of Sequencing Batch Reactors

ABSRACT This thesis focuses on the monitoring, fault detection and diagnosis of Wastewater Treatment Plants (WWTP), which are important fields of research for a wide range of engineering disciplines. The main objective is to evaluate and apply a novel artificial intelligent methodology based on situation assessment for monitoring and diagnosis of Sequencing Batch Reactor (SBR) operation. To this end, Multivariate Statistical Process Control (MSPC) in combination with Case-Based Reasoning (CBR) methodology was developed, which was evaluated on three different SBR (pilot and lab-scales) plants and validated on BSM1 plant layout.

The automatic layout model in the sequencing of construction activities of multi-objective diaphragm wall unit by using self-learning neural network

Foundation construction process has been an important key point in a successful construction engineering. The frequency of using diaphragm wall construction method among many deep excavation construction methods in Taiwan is the highest in the world. The traditional view of managing diaphragm wall unit in the sequencing of construction activities is to establish each phase of the sequencing of construction activities by heuristics. However, it conflicts final phase of engineering construction with unit construction and effects planning construction time. In order to avoid this kind of situation, we use management of science in the study of diaphragm wall unit construction to formulate multi-objective combinational optimization problem. Because the characteristic (belong to NP-Complete problem) of problem mathematic model is multi-objective and combining explosive, it is advised that using the 2-type Self-Learning Neural Network (SLNN) to solve the N=12, 24, 36 of diaphragm wall unit in the sequencing of construction activities program problem. In order to compare the liability of the results, this study will use random researching method in comparison with the SLNN. It is found that the testing result of SLNN is superior to random researching method in whether solution-quality or Solving-efficiency.