MicrobesOnline: an integrated portal for comparative and functional genomics

Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.United States. Dept. of Energy (Genomics: GTL program (grant DE-AC02-05CH11231)

Exocyclic Carbons Adjacent to the N6 of Adenine are Targets for Oxidation by the Escherichia coli Adaptive Response Protein AlkB

The DNA and RNA repair protein AlkB removes alkyl groups from nucleic acids by a unique iron- and α-ketoglutarate-dependent oxidation strategy. When alkylated adenines are used as AlkB targets, earlier work suggests that the initial target of oxidation can be the alkyl carbon adjacent to N1. Such may be the case with ethano-adenine (EA), a DNA adduct formed by an important anticancer drug, BCNU, whereby an initial oxidation would occur at the carbon adjacent to N1. In a previous study, several intermediates were observed suggesting a pathway involving adduct restructuring to a form that would not hinder replication, which would match biological data showing that AlkB almost completely reverses EA toxicity in vivo. The present study uses more sensitive spectroscopic methodology to reveal the complete conversion of EA to adenine; the nature of observed additional putative intermediates indicates that AlkB conducts a second oxidation event in order to release the two-carbon unit completely. The second oxidation event occurs at the exocyclic carbon adjacent to the N[superscript 6] atom of adenine. The observation of oxidation of a carbon at N[superscript 6] in EA prompted us to evaluate N[superscript 6]-methyladenine (m6A), an important epigenetic signal for DNA replication and many other cellular processes, as an AlkB substrate in DNA. Here we show that m6A is indeed a substrate for AlkB and that it is converted to adenine via its 6-hydroxymethyl derivative. The observation that AlkB can demethylate m6A in vitro suggests a role for AlkB in regulation of important cellular functions in vivo.National Institutes of Health (U.S.) (Grant number CA080024)National Institutes of Health (U.S.) (Grant number CA26731)National Institutes of Health (U.S.) (Grant number ES02109

All-particle primary energy spectrum in the 3-200 PeV energy range

We present all-particle primary cosmic-ray energy spectrum in the 3-200 PeV energy range obtained by a multi-parametric event-by-event evaluation of the primary energy. The results are obtained on the basis of an expanded EAS data set detected at mountain level (700 g/cm^2) by the GAMMA experiment. The energy evaluation method has been developed using the EAS simulation with the SIBYLL interaction model taking into account the response of GAMMA detectors and reconstruction uncertainties of EAS parameters. Nearly unbiased (<5%) energy estimations regardless of a primary nuclear mass with an accuracy of about 15-10% in the 3-200 PeV energy range respectively are attained. An irregularity ('bump') in the spectrum is observed at primary energies of ~74 PeV. This bump exceeds a smooth power-law fit to the data by about 4 standard deviations. Not rejecting stochastic nature of the bump completely, we examined the systematic uncertainties of our methods and conclude that they cannot be responsible for the observed feature.Comment: Accepted by J.Phys.G: Nucl.Part.Phy

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the ‘Dicty annotation marathon’, a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations

БАЛАНС ВЗАИМОДЕЙСТВИЯ ЭФФЕКТОРНЫХ И РЕГУЛЯТОРНЫХ КЛЕТОК ПАМЯТИ КАК ОСНОВА ВЫРАБОТКИ УСТОЙЧИВОЙ ИММУННОЙ ТОЛЕРАНТНОСТИ ПРИ ПЕРЕСАДКЕ ОРГАНОВ (АНАЛИЗ ПРОБЛЕМЫ НА ПРИМЕРЕ ТРАНСПЛАНТАЦИИ ПЕЧЕНИ)

In this article the main mechanisms and methods of immune tolerance producing under influence of different antigenic loads in organism were considered. It was shown that the state of steady tolerance was produced by making the balance of effectory and regulatory cell interactions into innate and adaptive immunities. But because of a high risk of transplant rejection at different methods of tolerance producing it is necessary to work out safe diagnostic and prognostic methods for controlling of an individual level and power tolerance stability. В статье представлен анализ механизмов и способов выработки иммунной толерантности в организме при воздействии антигенных нагрузок различной природы. Показано, что состояние устойчивой толерантности достигается путем воссоздания баланса взаимодей- ствия эффекторных и регуляторных клеток во врожденной и адаптивной иммунной системе. Однако из- за высокого риска отторжения трансплантата при разных способах выработки толерантности возникает необходимость разработки надежных диагностических и прогностических методов контроля уровня и степени индивидуальной устойчивости толерантности.

СОВРЕМЕННАЯ ТАКТИКА ИММУНОСУПРЕССИВНОЙ ТЕРАПИИ КАК СПОСОБ ФОРМИРОВАНИЯ ТОЛЕРОГЕННОЙ СТРАТЕГИИ ОРГАНИЗМА (НА ПРИМЕРЕ ТРАНСПЛАНТАЦИИ ПЕЧЕНИ)

In this article the necessity of working out of individual therapeutical immunosuppressive tactics was consi- dered. The authors believe that doses and schemes of used drugs must not prevent the immunity regulation. Immunosuppressive drugs must induce native mechanisms of immune tolerance and reparative regeneration for preventing of fibrotic processes in grafts (liver). For optimal effect of drug immunosuppression after clinical liver transplantation it was suggested to reveal tole- rogenic recipient’s groups and also to work out and use informative diagnostic and prognostic methods for value of individual level and power tolerance stability of recipients. В статье обсуждается необходимость разработки индивидуальной тактики медикаментозной иммуно- супрессии при трансплантации органов (печени). Авторы полагают, что препараты, их дозы и схемы применения не должны препятствовать регуляции иммунитета. Их назначение – тормозить образование эффекторных клеток и клеток памяти, а также способствовать индукции естественных механизмов толе- рантности и репаративной регенерации, тормозящих процессы фиброзирования органов (печени). Для оптимизации медикаментозной иммуносупрессии при трансплантации печени в клинике авторы предлагают выявлять толерогенные группы реципиентов, а также разрабатывать и применять инфор- мативные диагностические и прогностические методы для оценки уровня и степени индивидуальной толерогенной устойчивости реципиентов.

Разработка технологии получения наночастиц на основе PLGA и дипропоксибактериопурпуринимида. Оценка физико-химических и биологических свойств полученной системы доставки

The article describes the process of developing a technology for producing nanoparticles based on a copolymer of lactic and glycolic acids (PLGA) containing dipropoxybacteriopurpurinimide (DPBPI) for photodynamic therapy of malignant tumors of various origins. Technological parameters for optimizing the method in order to obtain nanoparticles with specified characteristics are presented in this paper. As a result, the nanoparticles sample with an average particle diameter of 222.6±2.8 nm; ξ-potential 26.3±4.61 mV; polydispersity index 0.144; the total content of DPBPI in PLGA-DPBPI nanoparticles 13.6% were obtained. In accordance with the developed technique, the batch of PLGA-DPBPI nanoparticles was developed for further biological studies. In vitro experiments on A549 human non-small cell lung carcinoma for DPBPI, delivered as a part of PLGA-DPBPI nanoparticles, and an EL cremophor-based emulsion (CrEL-DPBPI) showed a similar intracellular distribution (concentrated in vesicular cell structures and diffusely distributed in cytoplasm), as well as high photo induced activity and the absence of dark cytotoxicity in case of PLGA-DPBPI nanoparticles. The study of the PLGA-DPBPI nanoparticles specific activity in vivo on the S37 mouse soft tissue sarcoma model showed the selective accumulation of DPBPI in tumor tissue and the almost complete elimination of DPBPI from the body within 48 hours, as well as significant antitumor efficacy in PDT.В статье описан процесс разработки технологии получения наночастиц на основе сополимера молочной и гликолевой кислот (PLGA), включающих дипропоксибактериопурпуринимид (DPBPI) и предназначенных для фотодинамической терапии (ФДТ) злокачественных новообразований различного генеза. В работе подобраны технологические параметры, позволяющие оптимизировать метод получения наночастиц с заданными характеристиками, в результате был получен образец сферических частиц, обладающая средним диаметром частиц 222,6±2,8 нм; ξ-потенциалом –26,3±4,61 мВ; индексом полидисперсности 0,144; общее содержание DPBPI в частицах PLGA-DPBPI составило13,6%. В соответствии с разработанной методикой была осуществлена наработка партии наночастиц PLGA-DPBPI для дальнейших биологических исследований. В экспериментах in vitro на клетках немелкоклеточной карциномы легкого человека А549 для DPBPI, доставленного в клетки с помощью наночастиц PLGA-DPBPI, и эмульсии на основе кремофора EL (CrEL-DPBPI) было показано сходное внутриклеточное распределение (концентрирование в везикулярных клеточных структурах и диффузное распределение в цитоплазме), а также была показана высокая фотоиндуцированная активность и отсутствие темновой цитотоксичности в случае использования частиц PLGA-DPBPI. Изучение специфической активности наночастиц PLGA-DPBPI in vivo на модели саркомы мягких тканей мыши S37 показало селективное накопление DPBPI в опухолевой ткани и практически полное выведение DPBPI из организма в течение 48 ч, а также выраженную противоопухолевую эффективность при ФДТ

The Russian consensus on the diagnosis and treatment of chronic pancreatitis: Enzyme replacement therapy

The Russian consensus on the diagnosis and treatment of chronic pancreatitis has been prepared on the initiative of the Russian Pancreatology Club to clarify and consolidate the opinions of Russian specialists (gastroenterologists, surgeons, and pediatricians) on the most significant problems of diagnosis and treatment of chronic pancreatitis. This article continues a series of publications explaining the most significant interdisciplinary consensus statements and deals with enzyme replacement therapy

Network analysis of human glaucomatous optic nerve head astrocytes

<p>Abstract</p> <p>Background</p> <p>Astrocyte activation is a characteristic response to injury in the central nervous system, and can be either neurotoxic or neuroprotective, while the regulation of both roles remains elusive.</p> <p>Methods</p> <p>To decipher the regulatory elements controlling astrocyte-mediated neurotoxicity in glaucoma, we conducted a systems-level functional analysis of gene expression, proteomic and genetic data associated with reactive optic nerve head astrocytes (ONHAs).</p> <p>Results</p> <p>Our reconstruction of the molecular interactions affected by glaucoma revealed multi-domain biological networks controlling activation of ONHAs at the level of intercellular stimuli, intracellular signaling and core effectors. The analysis revealed that synergistic action of the transcription factors AP-1, vitamin D receptor and Nuclear Factor-kappaB in cross-activation of multiple pathways, including inflammatory cytokines, complement, clusterin, ephrins, and multiple metabolic pathways. We found that the products of over two thirds of genes linked to glaucoma by genetic analysis can be functionally interconnected into one epistatic network via experimentally-validated interactions. Finally, we built and analyzed an integrative disease pathology network from a combined set of genes revealed in genetic studies, genes differentially expressed in glaucoma and closely connected genes/proteins in the interactome.</p> <p>Conclusion</p> <p>Our results suggest several key biological network modules that are involved in regulating neurotoxicity of reactive astrocytes in glaucoma, and comprise potential targets for cell-based therapy.</p

Russian consensus on exoand endocrine pancreatic insufficiency after surgical treatment

The Russian consensus on exo - and endocrine pancreatic insufficiency after surgical treatment was prepared on the initiative of the Russian "Pancreatic Club" on the Delphi method. His goal was to clarify and consolidate the opinions of specialists on the most relevant issues of diagnosis and treatment of exo - and endocrine insufficiency after surgical interventions on the pancreas. An interdisciplinary approach is provided by the participation of leading gastroenterologists and surgeons