Single cell analyses of ES cells reveal alternative pluripotent cell states and molecular mechanisms that control self-renewal

Analyses of gene expression in single mouse embryonic stem cells (mESCs) cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM). In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN) reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP) data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB) suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal

Разработка алгоритма построения факторного поля процесса сушки торфа в паровых трубчатых сушилках

У статті виділено сукупність досліджуваних факторів роботи парової трубчастої сушарки, що включає 33 фактори. Зменшення кількості ознак дозволить скоротити кількість проведених дослідів до прийнятної виробництвом кількості, підвищити швидкість виконання алгоритмів, зменшити загальну похибку моделі та спростити задачу математичного моделювання. Для досягнення цієї мети розроблено методику стиснення факторного поля для вирішення завдання управління парової трубчастої сушарки за допомогою проведення експертного оцінювання та застосування нейронних мереж, що дозволило виділити основні показники процесу сушіння.The paper identified a set of causal factors of steam tubular dryers, which includes 33 factors. Reducing the number of features will reduce the number of experiments carried out to an acceptable production quantities increase the speed of the algorithms reduce the overall accuracy of the models and simplify the task of mathematical modeling. Design the method for determining the field of factors of drying process of peat in the steam tube dryers. The method that reduced the field of factors for solving the control problem of the steam tube dryer by using a peer evaluation and application of neural networks was designed for those purpose that allowed identify the main characteristics of the drying process.В статье выделены совокупность исследуемых факторов работы паровой трубчатой сушилки, что включает 33 факторы. Уменьшение количества признаков позволит сократить количество проводимых опытов до приемлемого производством количества, повысить скорость выполнения алгоритмов, уменьшить общую погрешность модели и упростить задачу математического моделирования. Для достижения этой цели разработана методика сжатия факторного поля для решения задачи управления паровой трубчатой сушилки с помощью проведения экспертного оценивания и применения нейронных сетей, что позволило выделить основные показатели процесса сушки

Построение нейронных сетей модели процесса сушки торфа в паровых сушилках в энергосберегающих режимах

В статті розглянуто основні особливості побудови енергоефективної системи управління процесом сушіння торфу. Визначено значення оптимальних керуючих параметрів процесу сушіння торфу в парових трубчатих сушарках для певних значень збурюючих впливів, що дозволяють отримати сушенку необхідної якості за мінімальної затрати енергії. Система управління, в якій для певних значень збурюючих впливів визначаються оптимальні значення керуючих впливів, реалізована в моделі нейронної мережі. Для представницького навчання мережі проведено генерування випадкових чисел збурюючих впливів та знаходження оптимальних значень керуючих параметрів за згенерованих впливів на процес. Знайдено оптимальну структуру, алгоритм навчання та функції активації нейронної мережі типу персептрон.The article reviews the main features of energy efficient operation of peat’s drying process. The optimal control parameters of drying peat steam tube dryers for certain values of perturbations that can get drying peat of required quality at the lowest cost energy It was determined. The operation system in which for certain values of perturbation influences can be determined the optimal values of control actions was implemented in the neural network model. It was necessary to generate random amount of perturbations and find the optimal values of control parameters for generated effects in the process for a good network training. It was found optimal structure, learning algorithm and activation function of neural network for model of drying process in peat tube steam dryer.В статье рассмотрены основные особенности построения энергоэффективной системы управления процессом сушки торфа. Определены значения оптимальных управляющих параметров процесса сушки торфа в паровых трубчатых сушилках при определенных значениях возмущающих воздействий, позволяющие получить сушенку необходимого качества при минимальных затратах энергии. Система управления, в которой для определенных значений возмущающих воздействий определяются оптимальные значения управляющих воздействий, реализована в модели нейронной сети. Для хорошего обучения сети было проведено генерирование случайных чисел возмущающих воздействий и нахождение оптимальных значений управляющих параметров при сгенерированных значениях возмущающих воздействий. Была найдена оптимальная структура, алгоритм обучения и функции активации нейронной сети типа персептрон

Abstract P-22: Enhanced Crosslinking and Immunoprecipitation (Eclip) Data Reveal Interactions of RNA Binding Proteins with the Human Ribosome

Background: The ribosome is a protein-synthesizing molecular machine composed of four ribosomal RNAs (rRNAs) and dozens of ribosomal proteins. In mammals, the ribosome has a complicated structure with an additional outer layer of rRNA, including large tentacle-like extensions. A number of RNA binding proteins (RBPs) interact with this layer to assist ribosome biogenesis, nuclear export and decay, or to modulate translation. Plenty of methods have been developed in the last decade in order to study such protein-RNA interactions, including RNA pulldown and crosslinking-immunoprecipitation (CLIP) assays. Methods: In the current study, using publicly available data of the enhanced CLIP (eCLIP) experiments for 223 proteins studied in the ENCODE project, we found a number of RBPs that bind rRNAs in human cells. To locate their binding sites in rRNAs, we used a newly developed computational protocol for mapping and evaluation of the eCLIP data with the respect to the repetitive sequences. Results: For two proteins with known ribosomal localization, uS3/RPS3 and uS17/RPS11, the identified sites were in good agreement with structural data, thus validating our approach. Then, we identified rRNA contacts of overall 22 RBPs involved in rRNA processing and ribosome maturation (DDX21, DDX51, DDX52, NIP7, SBDS, UTP18, UTP3, WDR3, and WDR43), translational control during stress (SERBP1, G3BP1, SND1), IRES activity (PCBP1/hnRNPE1), and other translation-related functions. In many cases, the identified proteins interact with the rRNA expansion segments (ES) of the human ribosome pointing to their important role in protein synthesis. Conclusion: Our study identifies a number of RBPs as interacting partners of the human ribosome and sheds light on the role of rRNA expansion segments in translation

A GO catalogue of human DNA-binding transcription factors

To control gene transcription, DNA-binding transcription factors recognise specific sequence motifs in gene regulatory regions. A complete and reliable GO annotation of all DNA-binding transcription factors is key to investigating the delicate balance of gene regulation in response to environmental and developmental stimuli. The need for such information is demonstrated by the many lists of transcription factors that have been produced over the past decade. The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) Consortium brought together experts in the field of transcription with the aim of providing high quality and interoperable gene regulatory data. The Gene Ontology (GO) Consortium provides strict definitions for gene product function, including factors that regulate transcription. The collaboration between the GREEKC and GO Consortia has enabled the application of those definitions to produce a new curated catalogue of over 1400 human DNA-binding transcription factors, that can be accessed at https://www.ebi.ac.uk/QuickGO/targetset/dbTF. This catalogue has facilitated an improvement in the GO annotation of human DNA-binding transcription factors and led to the GO annotation of almost sixty thousand DNA-binding transcription factors in over a hundred species. Thus, this work will aid researchers investigating the regulation of transcription in both biomedical and basic science

A GO catalogue of human DNA-binding transcription factors

DNA-binding transcription factors recognise genomic addresses, specific sequence motifs in gene regulatory regions, to control gene transcription. A complete and reliable catalogue of all DNA-binding transcription factors is key to investigating the delicate balance of gene regulation in response to environmental and developmental stimuli. The need for such a catalogue of proteins is demonstrated by the many lists of DNA-binding transcription factors that have been produced over the past decade. The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) Consortium brought together experts in the field of transcription with the aim of providing high quality and interoperable gene regulatory data. The Gene Ontology (GO) Consortium provides strict definitions for gene product function, including factors that regulate transcription. The collaboration between the GREEKC and GO Consortia has enabled the application of those definitions to produce a new curated catalogue of human DNA-binding transcription factors, that can be accessed at https://www.ebi.ac.uk/QuickGO/targetset/dbTF. In addition, this curation effort has led to the GO annotation of almost sixty thousand DNA-binding transcription factors in over a hundred species. Thus, this work will aid researchers investigating the regulation of transcription in both biomedical and basic science

EpiFactors : a comprehensive database of human epigenetic factors and complexes

Altres ajuts: Russian Fund For Basic Research(RFFI)grant 14-04-0018 i grant 15-34-20423, Ake Olsson's foundation, Swedish Cancer foundation, Swedish Childhood cancer foundation, Dynasty Foundation Fellowship, RIKEN Omics Science Center, RIKEN Preventive Medicine and Diagnosis Innovation Program i RIKEN Center for Life Science Technologies.Abstract: Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones affect gene expression and genome stability via proteins that recognize and act upon such modifications. Many enzymes that catalyse epigenetic modifications or are critical for enzymatic complexes have been discovered, and this is encouraging investigators to study the role of these proteins in diverse normal and pathological processes. Rapidly growing knowledge in the area has resulted in the need for a resource that compiles, organizes and presents curated information to the researchers in an easily accessible and user-friendly form. Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. For 789 of these genes, we include expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

PMCID: PMC3710212This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range