3,420 research outputs found
Nuclear factor I genomic binding associates with chromatin boundaries
No full textBACKGROUND: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequencing (ChIP-Seq), we performed a genome-wide mapping of NFI DNA binding sites in primary mouse embryonic fibroblasts. RESULTS: We found that in vivo and in vitro NFI DNA binding specificities are indistinguishable, as in vivo ChIP-Seq NFI binding sites matched predictions based on previously established position weight matrix models of its in vitro binding specificity. Combining ChIP-Seq with mRNA profiling data, we found that NFI preferentially associates with highly expressed genes that it up-regulates, while binding sites were under-represented at expressed but unregulated genes. Genomic binding also correlated with markers of transcribed genes such as histone modifications H3K4me3 and H3K36me3, even outside of annotated transcribed loci, implying NFI in the control of the deposition of these modifications. Positional correlation between + and - strand ChIP-Seq tags revealed that, in contrast to other transcription factors, NFI associates with a nucleosomal length of cleavage-resistant DNA, suggesting an interaction with positioned nucleosomes. In addition, NFI binding prominently occurred at boundaries displaying discontinuities in histone modifications specific of expressed and silent chromatin, such as loci submitted to parental allele-specific imprinted expression. CONCLUSIONS: Our data thus suggest that NFI nucleosomal interaction may contribute to the partitioning of distinct chromatin domains and to epigenetic gene expression regulation. NFI ChIP-Seq and input control DNA data were deposited at Gene Expression Omnibus (GEO) repository under accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts are on GEO accession number GSE15871
The North is another country. by Nicolas Rothwell
No full texttag=1 data=The North is another country. by Nicolas Rothwell
tag=2 data=Rothwell, Nicolas
tag=3 data=Australian Magazine,
tag=6 data=16/17 November 1996
tag=7 data=20-33.
tag=8 data=NT%TOURISM
tag=10 data=Worse, better, stranger, wilder, but above all different from the rest of the country. Continuing his journey of discovery across Australia's Top half the author stops over in Darwin to hear all the truths and whispers about the North.
tag=11 data=1996/2/8
tag=12 data=96/0316
tag=13 data=CABWorse, better, stranger, wilder, but above all different from the rest of the country. Continuing his journey of discovery across Australia's Top half the author stops over in Darwin to hear all the truths and whispers about the North
Grace S. Fong, Herself an Author : Gender, Agency, and Writing in Late Imperial China, 2008
No full textZufferey Nicolas. Grace S. Fong, Herself an Author : Gender, Agency, and Writing in Late Imperial China, 2008. In: Études chinoises, n°28, 2009. Numéro spécial sur le droit chinois. pp. 243-247
New Necklaces: 400 Designs in Contemporary Jewellery
No full textAfter the successful New Rings and New Earrings, New Necklaces is the third book curated by jeweller and author Nicolas Estrada, from classic forms and materials to the most daring, experimental and surprising ideas, each of the 500 necklaces included in this book has something that makes it unique and relates strongly to today's social, cultural and artistic reality. With prefaces by German jeweller Julia Wild and Leo Caballero, owner of the Barcelona gallery Klimt 02, specialised in contemporary jewellers
How Did I Get to Princess Margaret? (And How Did I Get Her to the World Wide Web?)
No full textThe paper explores the growing use of
tools from the arts and humanities for investigation
and dissemination of social science research.
Emerging spaces for knowledge transfer, such as
the World Wide Web, are explored as outlets for
"performative social science". Questions of ethnics
and questions of evaluation which emerge from
performative social science and the use of new
technologies are discussed. Contemporary thinking
in aesthetics is explored to answer questions
of evaluation. The use of the Internet for productions
is proposed as supporting the collective
elaboration of meaning supported by Relational
Aesthetics.
One solution to the ethical problem of performing
the narrations of others is the use of the writer's
own story as autoethnography. The author queries
autoethnography's tendency to tell "sad" stories and
proposes an amusing story, exemplified by "The
One about Princess Margaret" (see Appendix).
The conclusion is reached that the free and open
environment of the Internet sidelines the usual
tediousness of academic publishing and begins to
explore new answers to questions posed about
the evaluation and ethics of performative social
science
Identification of author profiles through social networks
No full textThe aim of this paper is to compile dictionaries of slang words, abbreviations, contractions, and emoticons to help the pre-processing of texts published in social networks. The use of these dictionaries is intended to improve the results of the tasks related to data obtained from these platforms. Therefore, a hypothesis was evaluated in the task of identifying author profiles (author profiling).Silva, JesúsMaria Santodomingo, Nicolas EliasRomero, LigiaJorge, MarisolHerrera, MaritzaPineda Lezama, Omar Bonerg
Study of DNA repair and recombination mechanisms in Chinese hamster ovary cells
No full textThe CRISPR nuclease systems greatly facilitate targeted genome modifications in mammalian cells. The outcome of genome editing depends on the involved DNA double strand break (DSB) repair pathways. While the classical non-homologous end-joining and the poorly defined alternative end-joining (alt-EJ) DSB repair pathways can cause imprecise repair and thus gene inactivations, the homologous recombination (HR) pathway often introduces precise modifications. Although CRISPR is highly efficient at inactivating single genes, it is inefficient at introducing precise genome modifications. Moreover, its efficiency at inactivating multi-locus DNA sequences such as highly repetitive endogenous viral elements also remains limited.
This thesis addressed these limitations by better characterizing DSB repair pathways in Chinese hamster ovary (CHO) cells - the most widely used production cell host for therapeutic proteins. In this thesis, I first aimed at identifying rate-limiting factors to improve HR-mediated genome editing. Second, I strove for studying approaches to inactivate repetitive endogenous retroviruses (ERV) presumably releasing viral particles into the CHO supernatant.
To identify factors limiting HR, we established two chromosomal CHO assays that measure HR activity based on the correction of a GFP loss-of-function mutation. By using knockdown and overexpression studies, we found that efficient HR-mediated genome editing depended on certain alt-EJ activities. Furthermore, we observed that alt-EJ contribution to HR correlates with the nuclease type and the location of the DSB site relative to the GFP mutation. These observations suggest that alt-EJ and HR repair pathways tightly interact and challenges the common perception of alt-EJ opposing HR. Finally, among the tested repair factors, high Mre11 nuclease and Pari anti-recombinase as well as low Rad51 recombinase levels were the most rate-limiting factors for HR in CHO cells. Counteracting these bottlenecks improved HR efficiency by 75%.
To inactivate repetitive ERVs, we transiently expressed a CRISPR-Cas9 nuclease that targets the gag gene of a specific transcriptionally active ERV group. Clones bearing a loss-of-function mutation in one particular ERV locus and corresponding mRNA produced considerably fewer particles loaded with viral RNA genomes. These findings indicated that a single ERV locus is responsible for the release of most, if not all, viral particles from CHO cells. Notably, ERV mutagenesis did not compromise cell growth, cell size or therapeutic protein production. In sum, this work provided novel strategies to improve HR-mediated genome editing and to inhibit viral particle release from CHO cells
Nikolski de Nicolas Dickner. - américanité, archéologie, intertextualité
No full textAuthor treats different dimensions of space in Nicolas Dickner's novel Nikolski. He analyses the way in which the novel ties links between space and family and, furthermore, outlines the role stratification plays in the novel
Statistical and experimental analysis of quantitative PCR
No full textQuantitative PCR (qPCR) is a powerful technique that is now commonly used in many research and clinical laboratories. Although it allows precise quantification of specific DNA sequences, it is often not used at its full potential. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, their relative performances have not been evaluated systematically, and they often remain poorly validated statistically and/or experimentally. Highly sophisticated mathematical models have also been proposed to decipher the PCR intimate process, but most of them were never validated. Often poor knowledge of the underlying mechanisms lead to inaccurate results and misinterpretation. Our first objective has been to measure by qPCR chromatin accessibility that was probed by a DNA adenine methylase. Results showed that 2-fold variations in relative accessibility could be assessed. However, the variability of the measures lead us to question the reproducibility of the qPCR. Placing our work in a robust statistical frame work, we proceeded with the evaluation of the parameters influencing PCR efficiency. Performance of known methods were also evaluated in terms of sensitivity, precision and robustness; and compared with various improved models, based on individual or averaged efficiency values. Our results show that when accurate quantification is required, single reaction efficiencies need to be measured and averaged for a given sample and primer. Furthermore, we show that well designed primers can hold the assumption of equal efficiency and therefore that the ∆Ct model is valid for measurement of 5-fold induction of a gene expression, at the least. Finally, we tried, as much as we could, to produce an exhaustive list of pitfalls qPCR users could stumble upon and proposed solutions. Our results allow the precise evaluation of minute amount of DNA, with a predictable and realistic number of measures
Assessment of a cell therapy approach for Duchenne muscular dystrophy using mesoangioblasts and non-viral vectors
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