Effect of SWI/SNF chromatin remodeling complex on HIV-1 Tat activated transcription

BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) is the etiologic agent of acquired immunodeficiency virus (AIDS). Following entry into the host cell, the viral RNA is reverse transcribed into DNA and subsequently integrated into the host genome as a chromatin template. The integrated proviral DNA, along with the specific chromatinized environment in which integration takes place allows for the coordinated regulation of viral transcription and replication. While the specific roles of and interplay between viral and host proteins have not been fully elucidated, numerous reports indicate that HIV-1 retains the ability for self-regulation via the pleiotropic effects of its viral proteins. Though viral transcription is fully dependent upon host cellular factors and the state of host activation, recent findings indicate a complex interplay between viral proteins and host transcription regulatory machineries including histone deacetylases (HDACs), histone acetyltransferases (HATs), cyclin dependent kinases (CDKs), and histone methyltransferases (HMTs). RESULTS: Here, we describe the effect of Tat activated transcription at the G(1)/S border of the cell cycle and analyze the interaction of modified Tat with the chromatin remodeling complex, SWI/SNF. HIV-1 LTR DNA reconstituted into nucleosomes can be activated in vitro using various Tat expressing extracts. Optimally activated transcription was observed at the G(1)/S border of the cell cycle both in vitro and in vivo, where chromatin remodeling complex, SWI/SNF, was present on the immobilized LTR DNA. Using a number of in vitro binding as well as in vivo chromatin immunoprecipitation (ChIP) assays, we detected the presence of both BRG1 and acetylated Tat in the same complex. Finally, we demonstrate that activated transcription resulted in partial or complete removal of the nucleosome from the start site of the LTR as evidenced by a restriction enzyme accessibility assay. CONCLUSION: We propose a model where unmodified Tat is involved in binding to the CBP/p300 and cdk9/cyclin T(1 )complexes facilitating transcription initiation. Acetylated Tat dissociates from the TAR RNA structure and recruits bromodomain-binding chromatin modifying complexes such as p/CAF and SWI/SNF to possibly facilitate transcription elongation

Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation

Background DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DNA methylation and histone deacetylation. Treatment with 5-aza-2'-deoxycytidine (5-aza-dC) to inhibit DNA methylation with and/or Trichostatin A (TSA) to inhibit histone deacetylation should allow us to identify genes that are regulated epigenetically in hepatoma cells. Results 5-aza-dC had a much larger effect on gene expression in HepG2 cells than did TSA, as measured using Affymetrix® HG-U133 Plus 2.0 microarrays. The expression of 1504 probe sets was affected by 5-aza-dC (at p < 0.01), 535 probe sets by TSA, and 1929 probe sets by the combination of 5-aza-dC and TSA. 5-aza-dC treatment turned on the expression of 211 probe sets that were not detectably expressed in its absence. Expression of imprinted genes regulated by DNA methylation, such as H19 and NNAT, was turned on or greatly increased in response to 5-aza-dC. Genes involved in liver processes such as xenobiotic metabolism (CYP3A4, CYP3A5, and CYP3A7) and steroid biosynthesis (CYP17A1 and CYP19A1), and genes encoding CCAAT element-binding proteins (C/EBPα, C/EBPβ, and C/EBPγ) were affected by 5-aza-dC or the combination. Many of the genes that fall within these groups are also expressed in the developing fetal liver and adult liver. Quantitative real-time RT-PCR assays confirmed selected gene expression changes seen in microarray analyses. Conclusion Epigenetics play a role in regulating the expression of several genes involved in essential liver processes such as xenobiotic metabolism and steroid biosynthesis in HepG2 cells. Many genes whose expression is normally silenced in these hepatoma cells were re-expressed by 5-aza-dC treatment. DNA methylation may be a factor in restricting the expression of fetal genes during liver development and in shutting down expression in hepatoma cells

New Directions in Degenerate Dipolar Molecules via Collective Association

We survey results on the creation of heteronuclear Fermi molecules by tuning a degenerate Bose-Fermi mixture into the neighborhood of an association resonance, either photoassociation or Feshbach, as well as the subsequent prospects for Cooper-like pairing between atoms and molecules. In the simplest case of only one molecular state, corresponding to either a Feshbach resonance or one-color photoassociation, the system displays Rabi oscillations and rapid adiabatic passage between a Bose-Fermi mixture of atoms and fermionic molecules. For two-color photoassociation, the system admits stimulated Raman adiabatic passage (STIRAP) from a Bose-Fermi mixture of atoms to stable Fermi molecules, even in the presence of particle-particle interactions. By tailoring the STIRAP sequence it is possible to deliberately convert only a fraction of the initial atoms, leaving a finite fraction of bosons behind to induce atom-molecule Cooper pairing via density fluctuations; unfortunately, this enhancement is insufficient to achieve a superfluid transition with present ultracold technology. We therefore propose the use of an association resonance that converts atoms and diatomic molecules (dimers) into triatomic molecules (trimers), which leads to a crossover from a Bose-Einstein condensate of trimers to atom-dimer Cooper pairs. Because heteronuclear dimers may possess a permanent electric dipole moment, this overall system presents an opportunity to investigate novel microscopic physics.Comment: 10 pages, 5 figures, 77+ references, submitted to Euro. Phys. J. topical issue on "Ultracold Polar Molecules: Formation and Collisions

Ire1α-Regulated Rate of mRNA Translation is Required for Acquisition of Identity and Polarity in Upper Layer Cortical Neurons

Evolutionary expansion of the neocortex is associated with the increase in upper layer neurons. Here, we present Inositol-Requiring Enzyme 1α, Ire1α, as an essential determinant of upper layer fate, neuronal polarization and cortical lamination. We demonstrate a non-canonical function of Ire1α in the regulation of global translation rates in the developing neocortex through its dynamic interaction with the ribosome and regulation of eIF4A1 and eEF-2 expression. Inactivation of Ire1α engenders lower protein synthesis rates associated with stalled ribosomes and decreased number of translation start sites. We show unique sensitivity of upper layer fate to translation rates. Whereas eEF-2 is required for cortical lamination, eIF4A1 regulates acquisition of upper layer fate downstream of Ire1α in a mechanism of translational control dependent on 5’UTR-embedded structural elements in fate determinant genes. Our data unveil developmental regulation of ribosome dynamics as post-transcriptional mechanisms orchestrating neuronal diversity establishment and assembly of cortical layers

Recurrent neck abscesses due to cervical tuberculous lymphadenopathy in an elderly woman post-splenectomy: a case report

<p>Abstract</p> <p>Introduction</p> <p>There are approximately 7000 new cases of tuberculosis every year in the UK, the majority of which are pulmonary. Approximately 5% affect the lymph nodes in immunocompetent patients. Scrofula is an old term used to describe lymph nodes of the neck infected with tuberculosis</p> <p>Case presentation</p> <p>In the elderly population, growing neck lumps are always treated as red flags until a diagnosis is confirmed. Here, the case of an 89-year-old Caucasian woman is presented. She was reluctant to seek medical help as she feared the cause was sinister and did not want surgical intervention.</p> <p>Conclusion</p> <p>It is difficult to culture tuberculosis from superficial swabs, resulting in a high proportion of false negative results. Where there is a high degree of clinical suspicion for tuberculosis, it is important to consider a biopsy with culture. Patients over the age of 65 have waning immunity and are therefore a vulnerable group for acute infections as well as the re-activation of indolent organisms. Post-splenectomy patients are at a major disadvantage during sepsis and when a cellular immune response is required, such as when faced with a <it>Mycobacterium tuberculosis </it>infection. Scrofula is treated with a similar regime as pulmonary tuberculosis and has a near 100% success rate.</p

Parkinsonism caused by adverse drug reactions: a case series

<p>Abstract</p> <p>Introduction</p> <p>Parkinsonism puts a high direct cost burden on both patient and caregiver. Several reports of drug-induced parkinsonism have been published, but to the best of our knowledge, there has not been any report of quinine or halothane inducing parkinsonism.</p> <p>Case presentation</p> <p>We describe two cases of parkinsonism possibly caused by adverse drug reaction to quinine in a 29-year-old black Nigerian woman and to halothane in a 36-year-old black Hausa (Nigerian) man who received it as general anaesthesia for appendicectomy in our teaching hospital.</p> <p>Conclusion</p> <p>These are two unusual cases of parkinsonism caused by adverse drug reactions to high-dose quinine and to halothane as general anaesthesia. We consider that these two cases are important in bringing this potential side-effect to the attention of both pharmacologists and primary care physicians as these are two of the most commonly used medications in our clinics. We conclude that parkinsonism should be included among the adverse drug reactions to high-dose quinine and halothane general anaesthetic.</p

Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia

Abstract In addition to being causally linked to the formation of multiple tumor types, tobacco use has been associated with decreased efficacy of anticancer treatment and reduced survival time. A detailed understanding of the cellular mechanisms that are affected by tobacco smoke (TS) should facilitate the development of improved preventive and therapeutic strategies. We have investigated the effects of a TS extract on the transcriptome of MSK-Leuk1 cells, a cellular model of oral leukoplakia. Using Affymetrix HGU133 Plus 2 arrays, 411 differentially expressed probe sets were identified. The observed transcriptome changes were grouped according to functional information and translated into molecular interaction network maps and signaling pathways. Pathways related to cellular proliferation, inflammation, apoptosis, and tissue injury seemed to be perturbed. Analysis of networks connecting the affected genes identified specific modulated molecular interactions, hubs, and key transcription regulators. Thus, TS was found to induce several epidermal growth factor receptor (EGFR) ligands forming an EGFR-centered molecular interaction network, as well as several aryl hydrocarbon receptor-dependent genes, including the xenobiotic metabolizing enzymes CYP1A1 and CYP1B1. Notably, the latter findings in vitro are consistent with our parallel finding that CYP1A1 and CYP1B1 levels were increased in oral mucosa of smokers. Collectively, these results offer insights into the mechanisms underlying the procarcinogenic effects of TS and raise the possibility that inhibitors of EGFR or aryl hydrocarbon receptor signaling will prevent or delay the development of TS-related tumors. Moreover, the inductive effects of TS on xenobiotic metabolizing enzymes may help explain the reduced efficacy of chemotherapy, and suggest targets for chemopreventive agents in smokers