Supplements to article: A novel transcription complex that selectively modulates apoptosis of breast cancer cells through regulation of FASTKD2

The materials provided here are supplemental tables and figures to an article to be published in 'Molecular and Cellular Biology.'(This refers to the article.) We previously reported that expression of NRIF3 (Nuclear Receptor Interacting Factor-3) rapidly and selectively leads to apoptosis of breast cancer cells. DIF-1 (a.k.a IRF-2BP2), the cellular target of NRIF3, was identified as a transcriptional repressor and DIF-1 knockdown leads to apoptosis of breast cancer cells but not other cell types. Here, we identify IRF2BP1 (Interferon Regulatory Factor-2 Binding Protein 1) and EAP1 (Enhanced At Puberty 1) as important components of the DIF-1 complex mediating both complex stability and transcriptional repression. This interaction of DIF-1, IRF2BP1, and EAP1 occurs through the conserved C4 zinc-fingers of these proteins. Microarray studies were carried out in breast cancer cell lines engineered to conditionally and rapidly increase the levels of the Death Domain region of NRIF3 (DD1). The DIF-1 complex was found to repress FASTKD2, a putative pro-apoptotic gene, in breast cancer cells and to bind to the FASTKD2 gene by chromatin immunoprecipitation. FASTKD2 knockdown prevents apoptosis of breast cancer cells from NRIF3 expression or DIF-1 knockdown while expression of FASTKD2 leads to apoptosis of both breast and non-breast cancer cells. Thus, regulation of FASTKD2 by NRIF3 and the DIF-1 complex acts as a novel death switch that selectively modulates apoptosis in breast cancer

Dissipative dynamics of vortex lines in superfluid 4^{4}He

We propose a Hamiltonian model that describes the interaction between a vortex line in superfluid $^{4}$He and the gas of elementary excitations. An equation of irreversible motion for the density operator of the vortex, regarded as a macroscopic quantum particle with a finite mass, is derived in the frame of Generalized Master Equations. This enables us to cast the effect of the coupling as a drag force with one reactive and one dissipative component, in agreement with the assumption of the phenomenological theories of vortex mutual friction in the two fluid model.Comment: 16 pages, no figures, to be published in PR

Nuclear receptor coactivator/coregulator NCoA6(NRC) is a pleiotropic coregulator involved in transcription, cell survival, growth and development

NCoA6 (also referred to as NRC, ASC-2, TRBP, PRIP and RAP250) was originally isolated as a ligand-dependent nuclear receptor interacting protein. However, NCoA6 is a multifunctional coregulator or coactivator necessary for transcriptional activation of a wide spectrum of target genes. The NCoA6 gene is amplified and overexpressed in breast, colon and lung cancers. NCoA6 is a 250 kDa protein which harbors a potent N-terminal activation domain, AD1; and a second, centrally-located activation domain, AD2, which is necessary for nuclear receptor signaling. The intrinsic activation potential of NCoA6 is regulated by its C-terminal STL regulatory domain. Near AD2 is an LxxLL-1 motif which interacts with a wide spectrum of ligand-bound NRs with high-affinity. A second LxxLL motif (LxxLL-2) located towards the C-terminal region is more restricted in its NR specificity. The potential role of NCoA6 as a co-integrator is suggested by its ability to enhance transcriptional activation of a wide variety of transcription factors and from its in vivo association with a number of known cofactors including CBP/p300. NCoA6 has been shown to associate with at least three distinct coactivator complexes containing Set methyltransferases as core polypeptides. The composition of these complexes suggests that NCoA6 may play a fundamental role in transcriptional activation by modulating chromatin structure through histone methylation. Knockout studies in mice suggest that NCoA6 is an essential coactivator. NCoA6-/- embryos die between 8.5-12.5 dpc from general growth retardation coupled with developmental defects in the heart, liver, brain and placenta. NCoA6-/- MEFs grow at a reduced rate compared to WT MEFs and spontaneously undergo apoptosis, indicating the importance of NCoA6 as a prosurvival and anti-apoptotic gene. Studies with NCoA6+/- and conditional knockout mice suggest that NCoA6 is a pleiotropic coregulator involved in growth, development, wound healing and maintenance of energy homeostasis

Finite temperature molecular dynamics study of unstable stacking fault free energies in silicon

We calculate the free energies of unstable stacking fault (USF) configurations on the glide and shuffle slip planes in silicon as a function of temperature, using the recently developed Environment Dependent Interatomic Potential (EDIP). We employ the molecular dynamics (MD) adiabatic switching method with appropriate periodic boundary conditions and restrictions to atomic motion that guarantee stability and include volume relaxation of the USF configurations perpendicular to the slip plane. Our MD results using the EDIP model agree fairly well with earlier first-principles estimates for the transition from shuffle to glide plane dominance as a function of temperature. We use these results to make contact to brittle-ductile transition models.Comment: 6 pages revtex, 4 figs, 16 refs, to appear in Phys. Rev.

Validation of a mouse xenograft model system for gene expression analysis of human acute lymphoblastic leukaemia

<p>Abstract</p> <p>Background</p> <p>Pre-clinical models that effectively recapitulate human disease are critical for expanding our knowledge of cancer biology and drug resistance mechanisms. For haematological malignancies, the non-obese diabetic/severe combined immunodeficient (NOD/SCID) mouse is one of the most successful models to study paediatric acute lymphoblastic leukaemia (ALL). However, for this model to be effective for studying engraftment and therapy responses at the whole genome level, careful molecular characterisation is essential.</p> <p>Results</p> <p>Here, we sought to validate species-specific gene expression profiling in the high engraftment continuous ALL NOD/SCID xenograft. Using the human Affymetrix whole transcript platform we analysed transcriptional profiles from engrafted tissues without prior cell separation of mouse cells and found it to return highly reproducible profiles in xenografts from individual mice. The model was further tested with experimental mixtures of human and mouse cells, demonstrating that the presence of mouse cells does not significantly skew expression profiles when xenografts contain 90% or more human cells. In addition, we present a novel <it>in silico </it>and experimental masking approach to identify probes and transcript clusters susceptible to cross-species hybridisation.</p> <p>Conclusions</p> <p>We demonstrate species-specific transcriptional profiles can be obtained from xenografts when high levels of engraftment are achieved or with the application of transcript cluster masks. Importantly, this masking approach can be applied and adapted to other xenograft models where human tissue infiltration is lower. This model provides a powerful platform for identifying genes and pathways associated with ALL disease progression and response to therapy <it>in vivo</it>.</p

Model validation for a noninvasive arterial stenosis detection problem

Copyright @ 2013 American Institute of Mathematical SciencesA current thrust in medical research is the development of a non-invasive method for detection, localization, and characterization of an arterial stenosis (a blockage or partial blockage in an artery). A method has been proposed to detect shear waves in the chest cavity which have been generated by disturbances in the blood flow resulting from a stenosis. In order to develop this methodology further, we use both one-dimensional pressure and shear wave experimental data from novel acoustic phantoms to validate corresponding viscoelastic mathematical models, which were developed in a concept paper [8] and refined herein. We estimate model parameters which give a good fit (in a sense to be precisely defined) to the experimental data, and use asymptotic error theory to provide confidence intervals for parameter estimates. Finally, since a robust error model is necessary for accurate parameter estimates and confidence analysis, we include a comparison of absolute and relative models for measurement error.The National Institute of Allergy and Infectious Diseases, the Air Force Office of Scientific Research, the Deopartment of Education and the Engineering and Physical Sciences Research Council (EPSRC)

Standard survey methods for estimating colony losses and explanatory risk factors in Apis mellifera

This chapter addresses survey methodology and questionnaire design for the collection of data pertaining to estimation of honey bee colony loss rates and identification of risk factors for colony loss. Sources of error in surveys are described. Advantages and disadvantages of different random and non-random sampling strategies and different modes of data collection are presented to enable the researcher to make an informed choice. We discuss survey and questionnaire methodology in some detail, for the purpose of raising awareness of issues to be considered during the survey design stage in order to minimise error and bias in the results. Aspects of survey design are illustrated using surveys in Scotland. Part of a standardized questionnaire is given as a further example, developed by the COLOSS working group for Monitoring and Diagnosis. Approaches to data analysis are described, focussing on estimation of loss rates. Dutch monitoring data from 2012 were used for an example of a statistical analysis with the public domain R software. We demonstrate the estimation of the overall proportion of losses and corresponding confidence interval using a quasi-binomial model to account for extra-binomial variation. We also illustrate generalized linear model fitting when incorporating a single risk factor, and derivation of relevant confidence intervals