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Deoxynucleotide Set, 10 mM (Individual dNTPs for routine PCR; 0.5 mL each); For routine PCR amplifications; Buy online from Sigma-Aldrich.

Deoxynucleotide Set, 10 mM Individual dNTPs for routine PCR; 0.5 mL each | Sigma-Aldrich

Individual dNTPs for routine PCR; 0.5 mL each

Deoxynucleotide Set, 10 mM Individual dNTPs for routine PCR; 0.5 mL each

Deoxynucleotide Set, 10 mM

Genetic (RAPD) diversity in two Armadillidium vulgare populations

We describe here a method to identify the position of retroviral insertion sites and simultaneously to quantify the absolute abundance of each clone, i.e., the number of cells having the provirus inserted at a given place in the host genome. The method is based on random shearing of the host cell DNA, followed by a linker-mediated PCR to amplify the genomic regions flanking the proviruses, and high-throughput sequencing of the amplicons. The quantification of the abundance of each infected clone allowed us to develop two new metrics: i. the oligoclonality index, which quantifies the nonuniformity of the distribution of clone abundance, and ii. an estimator of the total number of clones in the body of the host. These new tools are valuable for the study of retroviral infections and can also be adapted for the tracking of gene-edited cells.

High-Throughput Mapping and Clonal Quantification of Retroviral Integration Sites.

Chapter 8 - DNA Sequencing

Recent studies on genome-wide localization of transcription factor (TF) binding to DNA have shown that a large proportion of identified sequences do not contain consensus motifs predicted by databases of transcription factor binding sites, such as TRANSFAC. The main limitation of these databases is that they are based on a literature search of published examples of binding; consequently the data are not from a systematic survey and may be subject to sampling biases if investigators focused on particular motifs. Thus, there is an urgent need for systematic profiling of vertebrate transcription factor binding to DNA. We have developed a high-throughput platform for the quantitative analysis of protein-DNA interactions based on microarray technology.

Quantitative profiling of protein-DNA binding on microarrays.

With the completion of the human and mouse genome sequences and the development of high-throughput knockout mouse technologies, there is now a need for equally high-throughput methods for the production of mice for phenotypic studies. In response to this challenge, we recently developed a new method termed VelociMouse for the production of F0-generation mice that are fully derived from gene-targeted ES cells. In the version of the VelociMouse method described here, laser ablation of a portion of the zona pellucid (zp) of a normal eight-cell-stage embryo facilitates ES cell injection. Upon gestation in a surrogate mother, the injected embryos produce F0 mice that carry no detectable host embryo contribution (<0.1%). The fully ES cell-derived mice are normal, healthy, and fertile and exhibit 100% germline transmission for optimal breeding efficiency. The VelociMouse method accommodates both inbred or hybrid ES cells and either inbred or outbred eight-cell host embryos. Because the F0 mice produced are suitable for direct phenotyping studies, the VelociMouse method, coupled with high-throughput ES cell targeting technologies, such as VelociGene, offers an accelerated path to new drug target discovery and validation and a revolutionary approach to realize the full value of large-scale functional genomic efforts, such as the NIH Knockout Mouse Project ( 1 ) and the European Conditional Mouse Mutagenesis Project( 9 ).

VelociMouse: fully ES cell-derived F0-generation mice obtained from the injection of ES cells into eight-cell-stage embryos.

Induction of the antiviral interferon response is initiated upon recognition of viral RNA structures by the RIG-I or Mda-5 DEX(D/H) helicases. A complex signaling cascade then converges at the mitochondrial adapter MAVS, culminating in the activation of the IRF and NF-kappaB transcription factors and the induction of interferon gene expression. We have previously shown that MAVS recruits IkappaB kinase epsilon (IKKepsilon) but not TBK-1 to the mitochondria following viral infection. Here we map the interaction of MAVS and IKKepsilon to the C-terminal region of MAVS and demonstrate that this interaction is ubiquitin dependent. MAVS is ubiquitinated following Sendai virus infection, and K63-linked ubiquitination of lysine 500 (K500) of MAVS mediates recruitment of IKKepsilon to the mitochondria. Real-time PCR analysis reveals that a K500R mutant of MAVS increases the mRNA level of several interferon-stimulated genes and correlates with increased NF-kappaB activation. Thus, recruitment of IKKepsilon to the mitochondria upon MAVS K500 ubiquitination plays a modulatory role in the cascade leading to NF-kappaB activation and expression of inflammatory and antiviral genes. These results provide further support for the differential role of IKKepsilon and TBK-1 in the RIG-I/Mda5 pathway.

Ubiquitin-regulated recruitment of IkappaB kinase epsilon to the MAVS interferon signaling adapter.

Thymic stromal lymphopoietin (TSLP) is a cytokine released by human lung epithelium in response to external insult. Considered as a master switch in T helper 2 lymphocyte (Th2) mediated responses, TSLP is believed to play a key role in allergic diseases including asthma. The aim of this study was to use a phenotypic approach to identify new biological and chemical starting points for inhibition of TSLP production in human bronchial epithelial cells (NHBE), with the objective of reducing Th2-mediated airway inflammation. To this end, a phenotypic screen was performed using poly I:C / IL-4 stimulated NHBE cells interrogated with a 44,974 compound library. As a result, 85 hits which downregulated TSLP protein and mRNA levels were identified and a representative subset of 7 hits was selected for further characterization. These molecules inhibited the activity of several members of the MAPK, PI3K and tyrosine kinase families and some of them have been reported as modulators of cellular phenotypic endpoints like cell-cell contacts, microtubule polymerization and caspase activation. Characterization of the biological profile of the hits suggested that mTOR could be a key activity involved in the regulation of TSLP production in NHBE cells. Among other targeted kinases, inhibition of p38 MAPK and JAK kinases showed different degrees of correlation with TSLP downregulation, while Syk kinase did not seem to be related. Overall, inhibition of TSLP production by the selected hits, rather than resulting from inhibition of single isolated targets, appeared to be due to a combination of activities with different levels of relevance. Finally, a hit expansion exercise yielded additional active compounds that could be amenable to further optimization, providing an opportunity to dissociate TSLP inhibition from other non-desired activities. This study illustrates the potential of phenotypic drug discovery to complement target based approaches by providing new chemistry and biology leads.

Application of a phenotypic drug discovery strategy to identify biological and chemical starting points for inhibition of TSLP production in lung epithelial cells.

Creating Transgenic Mice using CRISPR-Cas9 Genome Editing

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Individual dNTPs for routine PCR; 0.5 mL each

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