VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes

Abstract Motivation Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data. Results We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated. Availability and implementation VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence

MOTIVATION: The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. RESULTS: We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. AVAILABILITY AND IMPLEMENTATION: BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/

Accurate characterization of Escherichia coli tRNA modifications with a simple method of deep sequencing library preparation

International audienceIn conventional RNA high-throughput sequencing, modified bases prevent a large fraction of tRNA transcripts to be converted into cDNA libraries. Recent proposals aiming at resolving this issue take advantage of the interference of base modifications with RT enzymes to detect and identify them by establishing signals from aborted cDNA transcripts. Because some modifications, such as methyl groups, do almost not allow RT bypassing, demethylation and highly processive RT enzymes have been used to overcome these obstacles. Working with Escherichia coli as a model system, we show that with a conventional (albeit still engineered) RT enzyme and key optimizations in library preparation, all RT-impairing modifications can be highlighted along the entire tRNA length without demethylation procedure. This is achieved by combining deep-sequencing samples, which allows to establish aborted transcription signal of higher accuracy and reproducibility, with the potential for differentiating tiny differences in the state of modification of all cellular tRNAs. In addition, our protocol provides estimates of the relative tRNA abundance

Transcriptional regulation of congocidine (netropsin) biosynthesis and resistance

International audienceThe production of specialized metabolites by Streptomyces bacteria is usually temporally regulated. This regulation is complex and frequently involves both global and pathway-specific mechanisms. Streptomyces ambofaciens ATCC23877 produces several specialized metabolites, including spiramycins, stambomycins, kinamycins and congocidine. The production of the first three molecules has been shown to be controlled by one or several cluster-situated transcriptional regulators. However, nothing is known regarding the regulation of congocidine biosynthesis. Congocidine (netropsin) belongs to the family of pyrrolamide metabolites, which also includes distamycin and anthelvencins. Most pyrrolamides bind into the minor groove of DNA, specifically in A/T rich regions, which gives them numerous biological activities, such as antimicrobial and antitumoral activities. We previously reported the isolation and characterization of the pyrrolamide biosynthetic gene clusters of congocidine (cgc) in S. ambofaciens ATCC23877, of distamycin (dst) in Streptomyces netropsis DSM40846 and of anthelvencins (ant) in Streptomyces venezuelae ATCC14583. The three gene clusters contain a gene encoding a putative transcriptional regulator, cgc1, dst1 and ant1 respectively. Cgc1, Dst1 and Ant1 present a high percentage of amino acid sequence similarity. We demonstrate here that Cgc1, an atypical orphan response regulator, activates the transcription of all cgc genes in the stationary phase of S. ambofaciens growth. We also show that the cgc cluster is constituted of eight main transcriptional units. Finally, we show that congocidine induces the expression of the transcriptional regulator Cgc1 and of the operon containing the resistance genes (cgc20 and cgc21, coding for an ABC transporter), and propose a model for the transcriptional regulation of the cgc gene cluster

The neoliberal model of global development, critical social philosophy of education and the world system perspective of democratic institutionalization. Part the first. The neoliberal of global development and its consequence as world problems of an educa

Стаття присвячена дослідженню процесів сучасної світової системи освіти в умовах глобалізації. Розглядаються тенденції освіти та моделі інститутів глобалізованого суспільства сучасності в контексті особливості взаємовідношення освіти і соціуму, людини і держав. Здійснюється дослідження і системний аналіз неоліберальних реформ на рівні суспільства загалом і освіти зокрема. Досліджуються змістовні, структурні і функціональні характеристики концепції «критичної соціальної філософії освіти» в контексті інституційних тенденцій суспільної практики, а також форми і можливості її методологічного застосування. Стверджується, що глобалізація і технологічна революція повинні бути використані для радикальної перебудови та реконструкції освіти для її служіння демократії та прогресивних соціальних змін. Усвідомлення уроків глобального розвитку є необхідним як для теоретичного осмислення сьогоднішніх перспектив світової прогресивної політики загалом та у сфері освіти зокрема, так і для практичних спроб змінити наш світ в інтересах суспільної більшості.The article deals with the processes of the modern world system of education in the context of globalization. Examines trends in educational institutions and models of globalizing society in the context of our particular relationship of education and society, man and the state, and processes. Ongoing research and systems analysis of neoliberal reforms on the level of society in general and education in particular. Examines substantive, structural and functional characteristics of the concept of "critical social philosophy of education" in the context of institutional tendencies of social life, as well as forms and possibilities of its methodological application. Argues that globalization and the technological revolution to be used for a radical restructuring and reconstruction of education for his service to democracy and progressive social change. Awareness lessons of the global development is necessary for a theoretical understanding of today's global outlook for progressive politics in general and in education in particular, and for the practical attempts to change our world for the public majority