Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells

Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES) cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species

That 80s Show [The Curatorial Incubator : v.4]

"Vtape was born in 1980, so it seemed fitting to invite young curators to study, research and otherwise reflect on video from this decade of our nascence. Thus developed the idea of the Curatorial Incubator v.4 : That 80s Show. [...] The only catch was that the curators had to have been born in 1980 or later. This would, we assumed, result in a new look at video from this decade. After all, our curators were children when these videos were made. Removed from the first hand experience of the lived-in discourses present in the 80s, each has distilled a look back that is intense and unexpected. Here we see the familiar topics of that decade -- censorship, AIDS, the dialogue around artist-as-performer, and the role of technology in video -- take on new life and vitality." -- p. 3

BIOLOGICAL FEATURES OF SARS-CoV-2 AND CURRENT APPROACHES TO ANTIVIRAL THERAPY AND VACCINATION: A REVIEW

Since the first description of patients with pneumonia of unknown origin in Wuhan in December 2019, unprecedented efforts of the international scientific community led to the identification and molecular characterization of its etiological agent, e.g. SARS-CoV-2. The global pandemic of COVID-19 represents an outstanding challenge for the scientists and medical professionals worldwide. In this review, we discuss the most important aspects of SARS-CoV-2 biology and virology including antiviral and immunomodulatory treatment strategies as well as vaccine development

Analysis of donor-derived cell-free DNA with 3 year outcomes in heart transplant recipients

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Deficiency of annexins A5 and A6 induces complex changes in the transcriptome of growth plate cartilage but does not inhibit the induction of mineralization

Initiation of mineralization during endochondral ossification is a multistep process and has been assumed to correlate with specific interactions of annexins A5 and A6 and collagens. However, skeletal development appears to be normal in mice deficient for either A5 or A6, and the highly conserved structures led to the assumption that A5 and A6 may fulfill redundant functions. We have now generated mice deficient of both proteins. These mice were viable and fertile and showed no obvious abnormalities. Assessment of skeletal elements using histologic, ultrastructural, and peripheral quantitative computed tomographic methods revealed that mineralization and development of the skeleton were not significantly affected in mutant mice. Otherwise, global gene expression analysis showed subtle changes at the transcriptome level of genes involved in cell growth and intermediate metabolism. These results indicate that annexins A5 and A6 may not represent the essential annexins that promote mineralization in vivo

Enabling consistency in pluripotent stem cell-derived products for research and development and clinical applications through material standards

There is a need for physical standards (reference materials) to ensure both reproducibility and consistency in the production of somatic cell types from human pluripotent stem cell (hPSC) sources. We have outlined the need for reference materials (RMs) in relation to the unique properties and concerns surrounding hPSC-derived products and suggest in-house approaches to RM generation relevant to basic research, drug screening, and therapeutic applications. hPSCs have an unparalleled potential as a source of somatic cells for drug screening, disease modeling, and therapeutic application. Undefined variation and product variability after differentiation to the lineage or cell type of interest impede efficient translation and can obscure the evaluation of clinical safety and efficacy. Moreover, in the absence of a consistent population, data generated from in vitro studies could be unreliable and irreproducible. Efforts to devise approaches and tools that facilitate improved consistency of hPSC-derived products, both as development tools and therapeutic products, will aid translation. Standards exist in both written and physical form; however, because many unknown factors persist in the field, premature written standards could inhibit rather than promote innovation and translation. We focused on the derivation of physical standard RMs. We outline the need for RMs and assess the approaches to in-house RM generation for hPSC-derived products, a critical tool for the analysis and control of product variation that can be applied by researchers and developers. We then explore potential routes for the generation of RMs, including both cellular and noncellular materials and novel methods that might provide valuable tools to measure and account for variation. Multiparametric techniques to identify "signatures" for therapeutically relevant cell types, such as neurons and cardiomyocytes that can be derived from hPSCs, would be of significant utility, although physical RMs will be required for clinical purposes

Validation of a clinical-grade assay to measure donor-derived cell-free DNA in solid organ transplant recipients

[Abstract] The use of circulating cell-free DNA (cfDNA) as a biomarker in transplant recipients offers advantages over invasive tissue biopsy as a quantitative measure for detection of transplant rejection and immunosuppression optimization. However, the fraction of donor-derived cfDNA (dd-cfDNA) in transplant recipient plasma is low and challenging to quantify. Previously reported methods to measure dd-cfDNA require donor and recipient genotyping, which is impractical in clinical settings and adds cost. We developed a targeted next-generation sequencing assay that uses 266 single-nucleotide polymorphisms to accurately quantify dd-cfDNA in transplant recipients without separate genotyping. Analytical performance of the assay was characterized and validated using 1117 samples comprising the National Institute for Standards and Technology Genome in a Bottle human reference genome, independently validated reference materials, and clinical samples. The assay quantifies the fraction of dd-cfDNA in both unrelated and related donor-recipient pairs. The dd-cfDNA assay can reliably measure dd-cfDNA (limit of blank, 0.10%; limit of detection, 0.16%; limit of quantification, 0.20%) across the linear quantifiable range (0.2% to 16%) with across-run CVs of 6.8%. Precision was also evaluated for independently processed clinical sample replicates and is similar to across-run precision. Application of the assay to clinical samples from heart transplant recipients demonstrated increased levels of dd-cfDNA in patients with biopsy-confirmed rejection and decreased levels of dd-cfDNA after successful rejection treatment. This noninvasive clinical-grade sequencing assay can be completed within 3 days, providing the practical turnaround time preferred for transplanted organ surveillance

Влияние моделей обратного тока насыщения диода на выходные характеристики двух-диодной модели солнечной батареи в среде Matlab Simulink

В работе проводилось моделирование солнечной батареи в программном обеспечении MATLAB Simulink. Изучались выходные параметры солнечной батареи в зависимости от модели обратного тока насыщения диода. Полученными результатами являются вольт-амперные и вольт-ваттные характеристики, показывающие влияние модели обратного тока насыщения диода на выходные параметры солнечной батареи.The work was carried out modeling of the solar battery in the software MATLAB Simulink. The output parameters of the solar battery were studied depending on the model of the reverse current saturation of the diode. The results are current-voltage and voltage-watt characteristics, showing the influence of the model of the inverse diode saturation current on the output parameters of the solar battery

Extracting sequence features to predict protein–DNA interactions: a comparative study

Predicting how and where proteins, especially transcription factors (TFs), interact with DNA is an important problem in biology. We present here a systematic study of predictive modeling approaches to the TF–DNA binding problem, which have been frequently shown to be more efficient than those methods only based on position-specific weight matrices (PWMs). In these approaches, a statistical relationship between genomic sequences and gene expression or ChIP-binding intensities is inferred through a regression framework; and influential sequence features are identified by variable selection. We examine a few state-of-the-art learning methods including stepwise linear regression, multivariate adaptive regression splines, neural networks, support vector machines, boosting and Bayesian additive regression trees (BART). These methods are applied to both simulated datasets and two whole-genome ChIP-chip datasets on the TFs Oct4 and Sox2, respectively, in human embryonic stem cells. We find that, with proper learning methods, predictive modeling approaches can significantly improve the predictive power and identify more biologically interesting features, such as TF–TF interactions, than the PWM approach. In particular, BART and boosting show the best and the most robust overall performance among all the methods