preAssemble: a tool for automatic sequencer trace data processing

BACKGROUND: Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages – Phred and Staden are used by preAssemble to perform sequence quality processing. RESULTS: The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. CONCLUSION: preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing

Oligomerization of Dicyclopentadiene Fraction Using Monosubstituted Titanium Chloride as a Catalyst

The purpose of this study is to investigate the dicyclopentadiene fraction of liquid pyrolysis product oligomerization with the use of the modified catalytic system based on titanium alkoxides. The choice of reaction catalyst is specified by searching the ways of obtaining petroleum resins with the improved performance characteristics and the possibility of low-temperature polymerization. The use of monosubstituted titanium chloride as a catalyst allows obtaining light resins, films on the base of which are smooth, glossy and have good technical characteristics: adhesion 1 point, resilience 10 cm

О НЕОБХОДИМОСТИ СВОЕВРЕМЕННОЙ ДИАГНОСТИКИ ТУБЕРКУЛЕЗА У ДЕТЕЙ РАННЕГО ВОЗРАСТА

The topicality of this work consists in the fact that even at the present time one of the significant problems in pediatrics remains tuberculosis in infancy and toddlerhood. And today, in spite of successful preventive work at all levels, theproportion of young children in the structure of tuberculosis in children and adolescents prevails. Such patients require aspecial approach to treatment and prevention of the disease. Timely diagnosis often leads to a quick and complete cure.Актуальность данной работы состоит в том, что и в настоящее время одной из значимых проблем в педиатрии остается туберкулез у детей раннего возраста. И сегодня, несмотря на успешную профилактическую работуна всех уровнях, доля детей раннего возраста в структуре туберкулеза у детей и подростков преобладает. Такиепациенты нуждаются в особом подходе к лечению и профилактике заболевания. Своевременная диагностиказачастую приводит к быстрому и полному излечению

Functional Evolution of Clustered Aquaporin Genes Reveals Insights into the Oceanic Success of Teleost Eggs

Aquaporin-mediated oocyte hydration is considered important for the evolution of pelagic eggs and the radiative success of marine teleosts. However, the molecular regulatory mechanisms controlling this vital process are not fully understood. Here, we analyzed >400 piscine genomes to uncover a previously unknown teleost-specific aquaporin-1 cluster (TSA1C) comprised of tandemly arranged aqp1aa-aqp1ab2-aqp1ab1 genes. Functional evolutionary analysis of the TSA1C reveals a ∼300-million-year history of downstream aqp1ab-type gene loss, neofunctionalization, and subfunctionalization, but with marine species that spawn highly hydrated pelagic eggs almost exclusively retaining at least one of the downstream paralogs. Unexpectedly, one-third of the modern marine euacanthomorph teleosts selectively retain both aqp1ab-type channels and co-evolved protein kinase-mediated phosphorylation sites in the intracellular subdomains together with teleost-specific Ywhaz-like (14-3-3ζ-like) binding proteins for co-operative membrane trafficking regulation. To understand the selective evolutionary advantages of these mechanisms, we show that a two-step regulated channel shunt avoids competitive occupancy of the same plasma membrane space in the oocyte and accelerates hydration. These data suggest that the evolution of the adaptive molecular regulatory features of the TSA1C facilitated the rise of pelagic eggs and their subsequent geodispersal in the oceanic currents.info:eu-repo/semantics/publishedVersio

Convergent phenotypes but non-convergent genomes in simple social insect societies

Dissertação de Mestrado na área de especialização em Ciências Jurídico-Forenses apresentada à Faculdade de Direito da Universidade de Coimbr