De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

<p>Abstract</p> <p>Background</p> <p>Arthropods are the most diverse animal phylum, but their genomic resources are relatively few. While the genome of the branchiopod <it>Daphnia pulex </it>is now available, no other large-scale crustacean genomic resources are available for comparison. In particular, genomic resources are lacking for the most tractable laboratory model of crustacean development, the amphipod <it>Parhyale hawaiensis</it>. Insight into shared and divergent characters of crustacean genomes will facilitate interpretation of future developmental, biomedical, and ecological research using crustacean models.</p> <p>Results</p> <p>To generate a transcriptome enriched for maternally provided and zygotically transcribed developmental genes, we created cDNA from ovaries and embryos of <it>P. hawaiensis</it>. Using 454 pyrosequencing, we sequenced over 1.1 billion bases of this cDNA, and assembled them <it>de novo </it>to create, to our knowledge, the second largest crustacean genomic resource to date. We found an unusually high proportion of C2H2 zinc finger-containing transcripts, as has also been reported for the genome of the pea aphid <it>Acyrthosiphon pisum</it>. Consistent with previous reports, we detected trans-spliced transcripts, but found that they did not noticeably impact transcriptome assembly. Our assembly products yielded 19,067 unique BLAST hits against <b>nr </b>(E-value cutoff e-10). These included over 400 predicted transcripts with significant similarity to <it>D. pulex </it>sequences but not to sequences of any other animal. Annotation of several hundred genes revealed <it>P. hawaiensis </it>homologues of genes involved in development, gametogenesis, and a majority of the members of six major conserved metazoan signaling pathways.</p> <p>Conclusions</p> <p>The amphipod <it>P. hawaiensis </it>has higher transcript complexity than known insect transcriptomes, and trans-splicing does not appear to be a major contributor to this complexity. We discuss the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models such as <it>D. pulex </it>and <it>P. hawaiensis</it>, as well as the need for development of further substantial crustacean genomic resources.</p

Applying QCA with Fuzzy Logic to Generate a Refined set of Factors for Information Systems Adoption: The Case of Public Ecuadorian Organization, an Example of IS Adoption in Emerging Economies

Information Systems (IS) research continues to contribute to a long list of technology adoption factors from many studies conducted outside the Latin American (LAT) nations. These investigations fail to appropriate the context of IS adoption in LAT. This fail is mainly due to the geographical scope of existing studies. Those aimed at North America for example, are out of context regarding a diverse technological approach when applied to LAT. Further, uncertainty and an inability to predict outcomes of technology adoption, create variances in results because the local contexts are not considered. The reasons for this are unclear from existing studies. To detailed explore this problem further, a Qualitative Comparative Analysis (QCA) was applied to LAT economies, expecting to assess a refined set of drivers from existing technology adoption studies. A Fuzzy Logic process was used to refine these drivers. The research found that fourteen themes are candidates for future study purposes. The drivers provide LAT stakeholders, as well as actors from other emerging economies, with a contextual frame that can be the basis for adopting technology more meaningfully within these nation

Systems of Pruning on Jigacho (Vasconcellea stipulata Badillo) under Greenhouse Conditions

[EN] Vasconcellea stipulata Badillo is a fruit tree native of the temperate areas of the Andes valleys, found between 2000 and 2600 m above sea level. The good organoleptic qualities and few seeds of its fruit, compared with those of other Caricas, give it a high potential in markets. The development of this crop would allow the economic development of small-scale farmers and contribute to the preservation of genetic resources native to the Andean region. However, there are few studies concerning its appropriate cultivation. The aim of this study was to analyze the effect of different pruning techniques under greenhouse conditions. Trees were pruned to one, two, or three axes, or not pruned (control). The experiment was performed in a tunnel greenhouse with polyethylene cover, located 2950 m above sea level in Querochaca (Ecuador),with an annual rainfall of 465mmand an average annual temperature of 12.9 8C. The duration of each stage of development was recorded. The number of flower clusters, number of flowers, production, incidence of diseases, and weight and size of fruit were recorded. Cuttings took over 90 days for getting before being transplanted into the greenhouse. Flowering began 283 days (40 weeks) after transplantation; fruit set began at 30 days after flowering (44 weeks after transplant); and the fruit started to mature 170 days after fruit set (69 weeks after transplant). The plants pruned to three axes had the greatest number of flowers and fruits and the greatest production, with an average 54 fruits per tree. Pruning had no effect on fruit dimensions.The participation of Borja Velazquez Marti in this work was possible by the funding from the Ecuadorian Government through PROMETEO program, leaded by the Secretaria Nacional de Educacion Superior, Ciencia y Tecnologia (SENESCYT).Velázquez Martí, B.; Castillo, M.; Rodriguez, F.; López- Cortés, I.; Alcivar, S. (2017). Systems of Pruning on Jigacho (Vasconcellea stipulata Badillo) under Greenhouse Conditions. HortScience. 52(8):1060-1064. doi:10.21273/HORTSCI12058-17S1060106452

Statistical Representations of a Dashboard to Monitor Educational Videogames in Natural Language

This paper explains how Natural Language (NL) processing by computers, through smart programs as a way of Machine Learning (ML), can represent large sets of quantitative data as written statements. The study recognized the need to improve the implemented web platform using a dashboard in which we collected a set of extensive data to measure assessment factors of using children’s educational games. In this case, applying NL is a strategy to give assessments, build, and display more precise written statements to enhance the understanding of children’s gaming behavior.We propose the development of a new tool to assess the use of written explanations rather than a statistical representation of feedback information for the comprehension of parents and teachers with a lack of primary level knowledge in statistics. Applying fuzzy logic theory, we present verbatim explanations of children’s behavior playing educational videogames as NL interpretation instead of statistical representations. An educational series of digital game applications for mobile devices, identified as MIDI (Spanish acronym of “Interactive Didactic Multimedia for Children”) linked to a dashboard in the cloud, is evaluated using the dashboard metrics. MIDI games tested in local primary schools helps to evaluate the results of using the proposed tool. The guiding results allow analyzing the degrees of playability and usability factors obtained from the data produced when children play a MIDI game. The results obtained are presented in a comprehensive guiding evaluation report applying NL for parents and teachers. These guiding evaluations are useful to enhance children’s learning understanding related to the school curricula applied to ludic digital games

BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage.

The BRCA2 tumor suppressor protects genome integrity by promoting homologous recombination-based repair of DNA breaks, stability of stalled DNA replication forks and DNA damage-induced cell cycle checkpoints. BRCA2 deficient cells display the radio-resistant DNA synthesis (RDS) phenotype, however the mechanism has remained elusive. Here we show that cells without BRCA2 are unable to sufficiently restrain DNA replication fork progression after DNA damage, and the underrestrained fork progression is due primarily to Primase-Polymerase (PRIMPOL)-mediated repriming of DNA synthesis downstream of lesions, leaving behind single-stranded DNA gaps. Moreover, we find that BRCA2 associates with the essential DNA replication factor MCM10 and this association suppresses PRIMPOL-mediated repriming and ssDNA gap formation, while having no impact on the stability of stalled replication forks. Our findings establish an important function for BRCA2, provide insights into replication fork control during the DNA damage response, and may have implications in tumor suppression and therapy response

Death-effector domain-containing protein DEDD is an inhibitor of mitotic Cdk1/cyclin B1

Accumulating evidence has shown that many molecules, including some cyclin-dependent kinases (Cdks) and cyclins, as well as the death-effector domain (DED)-containing FADD, function for both apoptosis and cell cycle. Here we identified that DEDD, which also possesses the DED domain, acts as a novel inhibitor of the mitotic Cdk1/cyclin B1 complex. DEDD associates with mitotic Cdk1/cyclin B1 complexes via direct binding to cyclin B1 and reduces their function. In agreement, kinase activity of nuclear Cdk1/cyclin B1 in DEDD-null (DEDD(−/−)) embryonic fibroblasts is increased compared with that in DEDD(+/+) cells, which results in accelerated mitotic progression, thus exhibiting a shortened G(2)/M stage. Interestingly, DEDD(−/−) cells also demonstrated decreased G(1) duration, which perhaps enhanced the overall reduction in rRNA amounts and cell volume, primarily caused by the rapid termination of rRNA synthesis before cell division. Likewise, DEDD(−/−) mice show decreased body and organ weights relative to DEDD(+/+) mice. Thus, DEDD is an impeder of cell mitosis, and its absence critically influences cell and body size via modulation of rRNA synthesis