Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency

BACKGROUND: Transcription regulatory regions in higher eukaryotes are often represented by cis-regulatory modules (CRM) and are responsible for the formation of specific spatial and temporal gene expression patterns. These extended, ~1 KB, regions are found far from coding sequences and cannot be extracted from genome on the basis of their relative position to the coding regions. RESULTS: To explore the feasibility of CRM extraction from a genome, we generated an original training set, containing annotated sequence data for most of the known developmental CRMs from Drosophila. Based on this set of experimental data, we developed a strategy for statistical extraction of cis-regulatory modules from the genome, using exhaustive analysis of local word frequency (LWF). To assess the performance of our analysis, we measured the correlation between predictions generated by the LWF algorithm and the distribution of conserved non-coding regions in a number of Drosophila developmental genes. CONCLUSIONS: In most of the cases tested, we observed high correlation (up to 0.6–0.8, measured on the entire gene locus) between the two independent techniques. We discuss computational strategies available for extraction of Drosophila CRMs and possible extensions of these methods

REPRESENTATION OF THE GLOBAL INNOVATIVE INFORMATION AND COMMUNICATION SPACE IN THE MODERN CINEMA (BASED ON MATERIALS OF TRAILERS TEXTS)

The article deals with the special features of trailers’ texts representing the idea of formation of a global innovative information and communication space as one of the modern society’s trends. The author also analyzes the revealed semantic fields of actualization of the researched phenomenon in the language of movie advertising

DEVELOPING OF THINKING PROCESS OF MEDICAL STUDENTS IN THE TEACHING SPECIAL TERMINOLOGY IN LATIN AND FOREIGN LANGUAGES

Цель. Статья посвящена актуальной теме развития познавательных компетенций и мыслительных способностей студентов медицинского вуза. Предметом анализа выступает развитие мышления первокурсников Оренбургского государственного медицинского университета в ходе обучения латинскому и иностранному языкам. Авторы ставят целью раскрыть продуктивные приемы развития мышления в процессе освоения студентами-медиками специальной терминологии.Метод или методология проведения работы. Основу исследования образуют общенаучные методы наблюдения, классификации, обобщения и сравнения, а также методы анкетирования и тестирования, описательно-аналитический метод.Результаты. Наиболее популярными приемами развития мышления, применяемыми в рамках преподавания дисциплин «Латинский язык» и «Иностранный язык», выступают «Мозаика проблем», «Фишбон», «Инсерт». Результаты мониторинга подтверждают продуктивность применения системы рассмотренных приемов, способствующих выработке у студентов медицинского вуза профессионально значимых качеств. Билингвальная направленность обучения в медицинском вузе способствует совершенствованию у студентов ряда мыслительных процессов. Эффективная структурная организация практических занятий по латинскому и иностранному языкам, способствующая актуализации мыслительных процессов, включает этапы вызова, осмысления и рефлексии.Область применения результатов. Результаты исследования могут быть применены при обучении студентов-медиков латинскому языку, профессионально-ориентированной межкультурной коммуникации, в спецкурсах лингвистики, психологии, методики преподавания иностранного языка.Purpose. The article is devoted to the topical theme of developing of cognitive competence and thinking abilities of medical students. The subject of analysis is the developing of thinking process of the first-year students of the Orenburg State Medical University in the teaching of Latin and foreign languages. The authors aim to reveal productive methods of thinking development in the process of mastering special terminology by medical students.Methodology. The basis of the research is the general scientific methods of observing, classifying, summarizing and comparing, as well as the methods of questioning and testing, and the descriptive-analytical method.Results. The most popular methods of thinking development, which are applied in the teaching of the disciplines “Latin” and “Foreign Language”, are “The Mosaic of Problems”, “Fishbone”, “Insert”. The monitoring results confirm the effectiveness of the application of the considered methods system, which contribute, to the development of professionally significant qualities in students of a medical higher school. The bilingual orientation of teaching in a medical higher school contributes to the improvement of a number of the students thinking abilities. Effective structural organization of practical classes in Latin and foreign languages, which contributes to the actualization of thought processes, includes stages of challenge, comprehension and reflection.Practical implications. The results of the study can be applied in the sphere of teaching medical students the Latin language, professionally oriented intercultural communication, as well as in special courses of linguistics, psychology, methodology of teaching foreign languages

Novel methylotrophic bacteria isolated from the River Thames (London, UK)

Enrichment and elective culture for methylotrophs from sediment of the River Thames in central London yielded a diversity of pure cultures representing several genera of Gram-negative and Gram-positive bacteria, which were mainly of organisms not generally regarded as typically methylotrophic. Substrates leading to successful isolations included methanol, monomethylamine, dimethylamine, trimethylamine, methanesulfonate and dimethylsulfone. Several isolates were studied in detail and shown by their biochemical and morphological properties and 16S rRNA gene sequencing to be Sphingomonas melonis strain ET35, Mycobacterium fluoranthenivorans strain DSQ3, Rhodococcus erythropolis strain DSQ4, Brevibacterium casei strain MSQ5, Klebsiella oxytoca strains MMA/F and MMA/1, Pseudomonas mendocina strain TSQ4, and Flavobacterium sp. strains MSA/1 and MMA/2. The results show that facultative methylotrophy is present across a wide range of Bacteria, suggesting that turnover of diverse C1-compounds is of much greater microbiological and environmental significance than is generally thought. The origins of the genes encoding the enzymes of methylotrophy in diverse heterotrophs need further study, and could further our understanding of the phylogeny and antiquity of methylotrophic systems

Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository

The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3–V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant – nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation

Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping

The idea of identifying or characterizing an RNA molecule based on a mass spectrum of specifically generated RNA fragments has been used in various forms for well over a decade. We have developed software—named RRM for ‘RNA mass mapping’—which can search whole prokaryotic genomes or RNA FASTA sequence databases to identify the origin of a given RNA based on a mass spectrum of RNA fragments. As input, the program uses the masses of specific RNase cleavage of the RNA under investigation. RNase T1 digestion is used here as a demonstration of the usability of the method for RNA identification. The concept for identification is that the masses of the digestion products constitute a specific fingerprint, which characterize the given RNA. The search algorithm is based on the same principles as those used in peptide mass fingerprinting, but has here been extended to work for both RNA sequence databases and for genome searches. A simple and powerful probability model for ranking RNA matches is proposed. We demonstrate viability of the entire setup by identifying the DNA template of a series of RNAs of biological and of in vitro transcriptional origin in complete microbial genomes and by identifying authentic 16S ribosomal RNAs in a ‘small ribosomal subunit RNA’ database. Thus, we present a new tool for a rapid identification of unknown RNAs using only a few picomoles of starting material

DiRE: identifying distant regulatory elements of co-expressed genes

Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors and silencers. We have developed a web server named DiRE, based on the Enhancer Identification (EI) method, for predicting distant regulatory elements in higher eukaryotic genomes, namely for determining their chromosomal location and functional characteristics. The server uses gene co-expression data, comparative genomics and profiles of transcription factor binding sites (TFBSs) to determine TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is its ability to detect REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs and it also scores the association of individual transcription factors (TFs) with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. The DiRE web server is freely available at http://dire.dcode.org

Some (bacilli) like it hot: Genomics of Geobacillus species

Copyright © 2014 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.What are Geobacillus?BBSR