The bromodomain-containing protein Ibd1 links multiple chromatin related protein complexes to highly expressed genes in Tetrahymena thermophila

Background: The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1. Results: Using affinity purification coupled to mass spectrometry (AP-MS) we identified members of a SWI/SNF complex (SWI/SNFTt) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt, Swi1Tt, Swi3Tt, Snf12Tt, Brg1Tt, two proteins with potential chromatin interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals. SWI/SNFTt subunits localize exclusively to the transcriptionally active macronucleus (MAC) during growth and development, consistent with a role in transcription. While Tetrahymena Brg1 does not contain a BRD, our AP-MS results identified a BRD-containing SWI/SNFTt component, Ibd1 that associates with SWI/SNFTt during growth but not development. AP-MS analysis of epitope-tagged Ibd1 revealed it to be a subunit of several additional protein complexes, including putative SWRTt, and SAGATt complexes as well as a putative H3K4-specific histone methyl transferase complex. Recombinant Ibd1 recognizes acetyl-lysine marks on histones correlated with active transcription. Consistent with our AP-MS and histone array data suggesting a role in regulation of gene expression, ChIP-Seq analysis of Ibd1 indicated that it primarily binds near promoters and within gene bodies of highly expressed genes during growth. Conclusions: Our results suggest that through recognizing specific histones marks, Ibd1 targets active chromatin regions of highly expressed genes in Tetrahymena where it subsequently might coordinate the recruitment of several chromatin remodeling complexes to regulate the transcriptional landscape of vegetatively growing Tetrahymena cells.Comment: Published on BMC Epigenetics & Chromati

Oppression and Racism Toward Black American in “12 Years a Slave” Movie

The study deals with those oppressions faced by Black American in “12 Years aSlave” movie and what resistances they showed toward those oppressions. Theobjectives of the study are to describe the oppressions faced by the two maincharacters – Platt and Patsey and to explain the resistances they shown in “12Years a Slave” Movie. This research focuses the study merely on oppressionfaced by two main characters; they were Salomon Northup or Platt and Patsey.This research was conducted by using descriptive qualitative design and limitedon two of main characters. The data analysis result was found five kinds ofoppression faced by black American in this film, those were: powerlessness,exploitation, marginalization, culture imperialism and violence. The resistancesshown by American toward those oppressions were revolt, radicalism, asking forhelp and religion or spirituality. The issue of racism with oppression had been thecrucial issue since long time ago which could not be denied that until nowadaysthe issue of racism is still happening though without oppression. The stigma ofBlack was being inferior and white was being superior had driven mind into thedestruction of race relationship between Black and White. However, in this filmwe could see how badly the oppression faced by black American and how theystruggled for fighting toward those oppressions

A status update on the determination of ΛMS‾Nf=3{\Lambda}_{\overline{\rm MS}}^{N_{\rm f}=3} by the ALPHA collaboration

The ALPHA collaboration aims to determine $\alpha_s(m_Z)$ with a total error below the percent level. A further step towards this goal can be taken by combining results from the recent simulations of 2+1-flavour QCD by the CLS initiative with a number of tools developed over the years: renormalized couplings in finite volume schemes, recursive finite size techniques, two-loop renormalized perturbation theory and the (improved) gradient flow on the lattice. We sketch the strategy, which involves both the standard SF coupling in the high energy regime and a gradient flow coupling at low energies. This implies the need for matching both schemes at an intermediate switching scale, $L_{\rm swi}$, which we choose roughly in the range 2-4 GeV. In this contribution we present a preliminary result for this matching procedure, and we then focus on our almost final results for the scale evolution of the SF coupling from $L_{\rm swi}$ towards the perturbative regime, where we extract the $N_{\rm f} = 3$ ${\Lambda}$-parameter, ${\Lambda}_{\overline{\rm MS}}^{N_{\rm f}=3}$, in units of $L_{\rm swi}$ . Connecting $L_{\rm swi}$ and thus the ${\Lambda}$-parameter to a hadronic scale such as $F_K$ requires 2 further ingredients: first, the connection of $L_{\rm swi}$ to $L_{\rm max}$ using a few steps with the step-scaling function of the gradient flow coupling, and, second, the continuum extrapolation of $L_{\rm max} F_K$.Comment: 7 pages, 4 figures, Proceedings of the 33rd International Symposium on Lattice Field Theory (Lattice 2015), 14-18 July 2015, Kobe, Japa

SWI-Prolog and the Web

Where Prolog is commonly seen as a component in a Web application that is either embedded or communicates using a proprietary protocol, we propose an architecture where Prolog communicates to other components in a Web application using the standard HTTP protocol. By avoiding embedding in external Web servers development and deployment become much easier. To support this architecture, in addition to the transfer protocol, we must also support parsing, representing and generating the key Web document types such as HTML, XML and RDF. This paper motivates the design decisions in the libraries and extensions to Prolog for handling Web documents and protocols. The design has been guided by the requirement to handle large documents efficiently. The described libraries support a wide range of Web applications ranging from HTML and XML documents to Semantic Web RDF processing. To appear in Theory and Practice of Logic Programming (TPLP)Comment: 31 pages, 24 figures and 2 tables. To appear in Theory and Practice of Logic Programming (TPLP

SWI/SNF regulates a transcriptional programme that induces senescence to prevent liver cancer

Oncogene-induced senescence (OIS) is a potent tumour suppressor mechanism. To identify senescence regulators relevant to cancer, we screened an shRNA library targeting genes deleted in hepatocellular carcinoma (HCC). Here, we describe how knockdown of the SWI/SNF component ARID1B prevents OIS and cooperates with RAS to induce liver tumours. ARID1B controls p16INK4a and p21CIP1a transcription but also regulates DNA damage, oxidative stress and p53 induction, suggesting that SWI/SNF uses additional mechanisms to regulate senescence. To systematically identify SWI/SNF targets regulating senescence, we carried out a focused shRNA screen. We discovered several new senescence regulators including ENTPD7, an enzyme that hydrolyses nucleotides. ENTPD7 affects oxidative stress, DNA damage and senescence. Importantly, expression of ENTPD7 or inhibition of nucleotide synthesis in ARID1B-depleted cells results in re-establishment of senescence. Our results identify novel mechanisms by which epigenetic regulators can affect tumor progression and suggest that pro-senescence therapies could be employed against SWI/SNF-mutated cancers

Classroom Interactions, Instructional Activities And Learning Affordances Of An Undergraduate Technical Writing Classroom: A Sociocultural Study

This thesis is the result of an academic venture to explore writing practices in the Malaysian higher education. The study assumes a sociocultural view and approaches writing practices as the teaching, learning, and doing of writing. Tesis ini dihasilkan menerusi satu usaha akademik untuk menerokai amalan menulis di institusi pengajian tinggi di Malaysia. Kajian ini berdasarkan pandangan sosiobudaya dan mengambil pendekatan terhadap amalan menulis sebagai pengajaran, pembelajaran dan perlakuan penulisan