RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov

MAP4 Mechanism that Stabilizes Mitochondrial Permeability Transition in Hypoxia: Microtubule Enhancement and DYNLT1 Interaction with VDAC1

Mitochondrial membrane permeability has received considerable attention recently because of its key role in apoptosis and necrosis induced by physiological events such as hypoxia. The manner in which mitochondria interact with other molecules to regulate mitochondrial permeability and cell destiny remains elusive. Previously we verified that hypoxia-induced phosphorylation of microtubule-associated protein 4 (MAP4) could lead to microtubules (MTs) disruption. In this study, we established the hypoxic (1% O2) cell models of rat cardiomyocytes, H9c2 and HeLa cells to further test MAP4 function. We demonstrated that increase in the pool of MAP4 could promote the stabilization of MT networks by increasing the synthesis and polymerization of tubulin in hypoxia. Results showed MAP4 overexpression could enhance cell viability and ATP content under hypoxic conditions. Subsequently we employed a yeast two-hybrid system to tag a protein interacting with mitochondria, dynein light chain Tctex-type 1 (DYNLT1), by hVDAC1 bait. We confirmed that DYNLT1 had protein-protein interactions with voltage-dependent anion channel 1 (VDAC1) using co-immunoprecipitation; and immunofluorescence technique showed that DYNLT1 was closely associated with MTs and VDAC1. Furthermore, DYNLT1 interactions with MAP4 were explored using a knockdown technique. We thus propose two possible mechanisms triggered by MAP4: (1) stabilization of MT networks, (2) DYNLT1 modulation, which is connected with VDAC1, and inhibition of hypoxia-induced mitochondrial permeabilization

Генетическая модель болезни двигательного нейрона у мышей линии B6SjL-tg: новые данные о динамике двигательных нарушений и иммуногистохимических проявлений нейродегенеративного процесса

Introduction. Over the past several decades, the study of mutations associated with motor neuron disease has led to the development of a number of transgenic animal models of motor neuron disease. One of the causes of the familial form of this disorder is mutations in the gene encoding Cu/Zn superoxide dismutase 1. The B6SJL-Tg (SOD1*G93A) mouse strain expresses a mutant form of human superoxide dismutase 1. Aim of study. To assess motor functions, dynamics of survival, and morphological changes in the spinal cord of transgenic B6SJL-Tg (SOD1*G93A) mice. Material and methods. In total, 31 animals have been studied. Starting from the age of 22 weeks, once every two weeks, the “open field” and “beam walking” motor tests were performed. The morphological changes in the spinal cord were evaluated at intermediate (26–35 weeks) and late stages (40–45 weeks). Neuronal proteins NeuN and PGP9.5, gliofibrillar protein, cyclonucleotide phosphatase (a marker of oligodendroglia) and a marker protein of microglia IBA1 were detected by immunohistochemistry; antibodies MTC02 to the outer membrane protein were used to detect mitochondria. Results. Motor problems appeared at the age of 24–26 weeks and steadily progressed; one could see consistent paresis of the hindlimbs, then the forelimbs, which was accompanied by general hypotrophy of the animals. There was a greater variability in the timing of symptom onset and life expectancy in males compared to females. The neurodegenerative process with damage to motor neurons was accompanied by the activation of micro- and astroglia. A sharp decrease in immunoreactivity to the mitochondrial marker MTC02 was found. Conclusion. The obtained results demonstrate new details of the development of a complex of motor and pathomorphological changes characteristic of motor neuron disease in B6SJL-Tg (SOD1*G93A) mice. Clarification of the fine dynamics of the neurodegenerative process in these animals is of great importance for monitoring the course of the disease during preclinical trials of new drugs and methods of gene therapy.Введение. За последние несколько десятилетий изучение мутаций, связанных с болезнью двигательного нейрона, привело к разработке ряда трансгенных моделей этого заболевания на животных. Одной из известных причин семейной формы болезни двигательного нейрона являются мутации в гене, кодирующем Cu / Zn-супероксиддисмутазу 1 (SOD1). Линия мышей B6SJL-Tg (SOD1*G93A) экспрессирует мутантную форму данного гена и может рассматриваться как анимальная модель болезни двигательного нейрона. Цель исследования – оценить двигательные функции, динамику выживаемости и морфологические изменения в спинном мозге трансгенных мышей B6SJL-Tg (SOD1*G93A). Материалы и методы. В исследование было взято 31 животное с указанной мутацией, которым начиная с возраста 22 нед, раз в 2 нед проводили двигательные тесты «открытое поле» и «сужающаяся дорожка». Морфологические изменения в спинном мозге оценивали на промежуточных (26–35 нед) и поздних стадиях (40–45 нед). Иммуногистохимически выявляли нейрональные белки NeuN и PGP9.5, глиофибриллярный белок, циклонуклеотидфосфатазу (маркер олигодендроглии) и маркерный белок микроглии IBA1, для выявления митохондрий использовали антитела MTC02 к белку наружной мембраны. Результаты. Двигательные нарушения появлялись в возрасте 24–26 нед и неуклонно прогрессировали, наблюдался восходящий парез задних, затем передних конечностей, что сопровождалось общей гипотрофией животных. Отмечена бóльшая вариабельность в сроках появления симптомов и продолжительности жизни самцов по сравнению с самками. Нейродегенеративный процесс с поражением двигательных нейронов сопровождался активацией микро- и астроглии. Обнаружено резкое снижение иммунореактивности к митохондриальному маркеру MTC02. Заключение. Полученные результаты демонстрируют особенности развития у мышей B6SJL-Tg (SOD1*G93A) комплекса двигательных и патоморфологических изменений, характерных для болезни двигательного нейрона. Уточнение тонкой динамики нейродегенеративного процесса у модельных животных имеет значение для мониторинга течения болезни при проведении доклинических испытаний новых лекарственных препаратов и методов генной терапии