A novel cassette method for probe evaluation in the designed biochips

A critical step in biochip design is the selection of probes with identical hybridisation characteristics. In this article we describe a novel method for evaluating DNA hybridisation probes, allowing the fine-tuning of biochips, that uses cassettes with multiple probes. Each cassette contains probes in equimolar proportions so that their hybridisation performance can be assessed in a single reaction. The model used to demonstrate this method was a series of probes developed to detect TORCH pathogens. DNA probes were designed for Toxoplasma gondii, Chlamidia trachomatis, Rubella, Cytomegalovirus, and Herpes virus and these were used to construct the DNA cassettes. Five cassettes were constructed to detect TORCH pathogens using a variety of genes coding for membrane proteins, viral matrix protein, an early expressed viral protein, viral DNA polymerase and the repetitive gene B1 of Toxoplasma gondii. All of these probes, except that for the B1 gene, exhibited similar profiles under the same hybridisation conditions. The failure of the B1 gene probe to hybridise was not due to a position effect, and this indicated that the probe was unsuitable for inclusion in the biochip. The redesigned probe for the B1 gene exhibited identical hybridisation properties to the other probes, suitable for inclusion in a biochip

Electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii with a DNA-biosensor

The steady rise of observations of harmful or toxic algal blooms throughout the world in the past decades constitute a menace for coastal ecosystems and human interests. As a consequence, a number of programs have been launched to monitor the occurrence of harmful and toxic algae. However, the identification is currently done by microscopic examination, which requires a broad taxonomic knowledge, expensive equipment and is very time consuming. In order to facilitate the identification of toxic algae, an inexpensive and easy-to-handle DNA-biosensor has been adapted for the electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii. The detection of the toxic algae is based on a sandwich hybridisation, which is carried out on a disposable sensor chip. A set of two probes for the species specific identification of A. ostenfeldii was developed. The specificity of the probes could be shown in dot-blot hybridisation and with the DNA-biosensor. The sensitivity of the DNA-biosensor was optimised with respect to hybridisation temperature and NaCl-concentration and a significant increase of the sensitivity of the DNA-biosensor could be obtained by a fragmentation of the rRNA prior to the hybridisation and by adding a helper oligonucleotide, which binds in close proximity to the probes to the hybridisation

Hybridisation for versatile decision-making in game opponent AI

Hybridisation for versatile decision-making in game opponent A

Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle

Eukaryotic ultraphytoplankton (<5 μm) are an important component of phytoplankton populations, Dot blot hybridisation analysis using class level 16S rRNA gene probes as well as clone libraries were used to investigate the diversity of these ultraphytoplankton during a 15 mo period (2003 to 2004) in the Gulf of Naples. Hybridisation data showed the presence of 3 main classes, Cryptophyceae, Chrysophyceae and Prymnesiophyceae, along with lower signals from the Pelagophyceae. Clone libraries also contained these 4 classes as well as sequences from the Dictyochophyceae, Bacillariophyceae and Prasinophyceae. However, the Prymnesiophyceae gave the dominant hybridisation signal and constituted the majority of each clone library. Their diversity, with a total of 190 sequences belonging to 114 operational taxonomic units (OTUs), probably allows them to dominate the ultraphytoplankton throughout the whole year under differing environmental conditions. Over 100 of these OTUs were unique to different libraries, suggesting a succession of different taxa during the year. The Cryptophyceae were present most of the year with 1 OTU, corresponding to a Plagioselmis prolonga strain from the Gulf of Naples, being the dominant taxon (28 % of sequences). A striking result was the high hybridisation signal from the Chrysophyceae, which showed a preference for the summer months. The Pelagophyceae were present between December and March. Most (80 %) of the sequences found in the clone libraries were not identical to available 16S rRNA gene sequences, indicating a high amount of hidden diversity for these algal classes. However, sequences from Prasinophyceae Clade II (Mamiellales) were not detected in the clone libraries

Analysis of the meiotic segregation in intergeneric hybrids of tilapias

Tilapia species exhibit a large ecological diversity and an important propensity to interspecific hybridisation. This has been shown in the wild and used in aquaculture. However, despite its important evolutionary implications, few studies have focused on the analysis of hybrid genomes and their meiotic segregation. Intergeneric hybrids between Oreochromis niloticus and Sarotherodon melanotheron, two species highly differentiated genetically, ecologically, and behaviourally, were produced experimentally. The meiotic segregation of these hybrids was analysed in reciprocal second generation hybrid (F2) and backcross families and compared to the meiosis of both parental species, using a panel of 30 microsatellite markers. Hybrid meioses showed segregation in accordance to Mendelian expectations, independent from sex and the direction of crosses. In addition, we observed a conservation of linkage associations between markers, which suggests a relatively similar genome structure between the two parental species and the apparent lack of postzygotic incompatibility, despite their important divergence. These results provide genomics insights into the relative ease of hybridisation within cichlid species when prezygotic barriers are disrupted. Overall our results support the hypothesis that hybridisation may have played an important role in the evolution and diversification of cichlids

Kondo hybridisation and the origin of metallic states at the (001) surface of SmB6

SmB6, a well-known Kondo insulator, has been proposed to be an ideal topological insulator with states of topological character located in a clean, bulk electronic gap, namely the Kondo hybridisation gap. Seeing as the Kondo gap arises from many body electronic correlations, this would place SmB6 at the head of a new material class: topological Kondo insulators. Here, for the first time, we show that the k-space characteristics of the Kondo hybridisation process is the key to unravelling the origin of the two types of metallic states observed directly by ARPES in the electronic band structure of SmB6(001). One group of these states is essentially of bulk origin, and cuts the Fermi level due to the position of the chemical potential 20 meV above the lowest lying 5d-4f hybridisation zone. The other metallic state is more enigmatic, being weak in intensity, but represents a good candidate for a topological surface state. However, before this claim can be substantiated by an unequivocal measurement of its massless dispersion relation, our data raises the bar in terms of the ARPES resolution required, as we show there to be a strong renormalisation of the hybridisation gaps by a factor 2-3 compared to theory, following from the knowledge of the true position of the chemical potential and a careful comparison with the predictions from recent LDA+Gutzwiler calculations. All in all, these key pieces of evidence act as triangulation markers, providing a detailed description of the electronic landscape in SmB6, pointing the way for future, ultrahigh resolution ARPES experiments to achieve a direct measurement of the Dirac cones in the first topological Kondo insulator.Comment: 9 pages, 4 Figures and supplementary material (including Movies and CORPES13 "best prize" poster

Strong 3p -T1u Hybridization in Ar@C60

Multilayers of fullerenes with and without endohedral Ar units, C60 and Ar@C60, were investigated by photoemission and density functional theory. The stoichiometry and the endohedral nature of Ar is checked by x-ray photoelectron spectroscopy and x-ray photoelectron diffraction. Valence band ultraviolet photoemission spectra show a strong hybridisation of the Ar 3p valence shell with the 6T1u molecular orbital of C60. A hybridisation gap of 1.6 +/- 0.2 eV is found. This is in agreement with density functional theory (DFT) that predicts 1.47 eV, and indicates Ar@C60 to be a noble gas compound with a strong coupling between Ar and the C60 cage. No giant Ar photoemission cross section as predicted for the gas phase in [Phys. Rev. Lett. 99, 243003 (2007)] was found

How much hybridisation does machine translation need?

This is the peer reviewed version of the following article: [Costa-jussà, M. R. (2015), How much hybridization does machine translation Need?. J Assn Inf Sci Tec, 66: 2160–2165. doi:10.1002/asi.23517], which has been published in final form at [10.1002/asi.23517]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Rule-based and corpus-based machine translation (MT)have coexisted for more than 20 years. Recently, bound-aries between the two paradigms have narrowed andhybrid approaches are gaining interest from bothacademia and businesses. However, since hybridapproaches involve the multidisciplinary interaction oflinguists, computer scientists, engineers, and informa-tion specialists, understandably a number of issuesexist.While statistical methods currently dominate researchwork in MT, most commercial MT systems are techni-cally hybrid systems. The research community shouldinvestigate the bene¿ts and questions surrounding thehybridization of MT systems more actively. This paperdiscusses various issues related to hybrid MT includingits origins, architectures, achievements, and frustra-tions experienced in the community. It can be said thatboth rule-based and corpus- based MT systems havebene¿ted from hybridization when effectively integrated.In fact, many of the current rule/corpus-based MTapproaches are already hybridized since they do includestatistics/rules at some point.Peer ReviewedPostprint (author's final draft