Proximal genomic localization of STAT1 binding and regulated transcriptional activity

BACKGROUND: Signal transducer and activator of transcription (STAT) proteins are key regulators of gene expression in response to the interferon (IFN) family of anti-viral and anti-microbial cytokines. We have examined the genomic relationship between STAT1 binding and regulated transcription using multiple tiling microarray and chromatin immunoprecipitation microarray (ChIP-chip) experiments from public repositories. RESULTS: In response to IFN-γ, STAT1 bound proximally to regions of the genome that exhibit regulated transcriptional activity. This finding was consistent between different tiling microarray platforms, and between different measures of transcriptional activity, including differential binding of RNA polymerase II, and differential mRNA transcription. Re-analysis of tiling microarray data from a recent study of IFN-γ-induced STAT1 ChIP-chip and mRNA expression revealed that STAT1 binding is tightly associated with localized mRNA transcription in response to IFN-γ. Close relationships were also apparent between STAT1 binding, STAT2 binding, and mRNA transcription in response to IFN-α. Furthermore, we found that sites of STAT1 binding within the Encyclopedia of DNA Elements (ENCODE) region are precisely correlated with sites of either enhanced or diminished binding by the RNA polymerase II complex. CONCLUSION: Together, our results indicate that STAT1 binds proximally to regions of the genome that exhibit regulated transcriptional activity. This finding establishes a generalized basis for the positioning of STAT1 binding sites within the genome, and supports a role for STAT1 in the direct recruitment of the RNA polymerase II complex to the promoters of IFN-γ-responsive genes

AFC-1 Transmutation Fuels Post-Irradiation Hot Cell Examination 4-8 at.% - Final Report (Irradiation Experiments AFC-1B, -1F and -1Æ)

The AFC-1B, AFC-1F and AFC-1Æ irradiation tests are part of a series of test irradiations designed to evaluate the feasibility of the use of actinide bearing fuel forms in advanced fuel cycles for the transmutation of transuranic elements from nuclear waste. The tests were irradiated in the Idaho National Laboratory’s (INL) Advanced Test Reactor (ATR) to an intermediate burnup of 4 to 8 at% (2.7 - 6.8 x 1020 fiss/cm3). The tests contain metallic and nitride fuel forms with non-fertile (i.e., no uranium) and low-fertile (i.e., uranium bearing) compositions. Results of postirradiation hot cell examinations of AFC-1 irradiation tests are reported for eleven metallic alloy transmutation fuel rodlets and five nitride transmutation fuel rodlets. Non-destructive examinations included visual examination, dimensional inspection, gamma scan analysis, and neutron radiography. Detailed examinations, including fission gas puncture and analysis, metallography / ceramography and isotopics and burnup analyses, were performed on five metallic alloy and three nitride transmutation fuels. Fuel performance of both metallic alloy and nitride fuel forms was best correlated with fission density as a burnup metric rather than at.% depletion. The actinide bearing transmutation metallic alloy compositions exhibit irradiation performance very similar to U-xPu-10Zr fuel at equivalent fission densities. The irradiation performance of nitride transmutation fuels was comparable to limited data published on mixed nitride systems

A Mouse Model of Harlequin Ichthyosis Delineates a Key Role for Abca12 in Lipid Homeostasis

Harlequin Ichthyosis (HI) is a severe and often lethal hyperkeratotic skin disease caused by mutations in the ABCA12 transport protein. In keratinocytes, ABCA12 is thought to regulate the transfer of lipids into small intracellular trafficking vesicles known as lamellar bodies. However, the nature and scope of this regulation remains unclear. As part of an original recessive mouse ENU mutagenesis screen, we have identified and characterised an animal model of HI and showed that it displays many of the hallmarks of the disease including hyperkeratosis, loss of barrier function, and defects in lipid homeostasis. We have used this model to follow disease progression in utero and present evidence that loss of Abca12 function leads to premature differentiation of basal keratinocytes. A comprehensive analysis of lipid levels in mutant epidermis demonstrated profound defects in lipid homeostasis, illustrating for the first time the extent to which Abca12 plays a pivotal role in maintaining lipid balance in the skin. To further investigate the scope of Abca12's activity, we have utilised cells from the mutant mouse to ascribe direct transport functions to the protein and, in doing so, we demonstrate activities independent of its role in lamellar body function. These cells have severely impaired lipid efflux leading to intracellular accumulation of neutral lipids. Furthermore, we identify Abca12 as a mediator of Abca1-regulated cellular cholesterol efflux, a finding that may have significant implications for other diseases of lipid metabolism and homeostasis, including atherosclerosis

Solitons in Seiberg-Witten Theory and D-branes in the Derived Category

We analyze the "geometric engineering" limit of a type II string on a suitable Calabi-Yau threefold to obtain an N=2 pure SU(2) gauge theory. The derived category picture together with Pi-stability of B-branes beautifully reproduces the known spectrum of BPS solitons in this case in a very explicit way. Much of the analysis is particularly easy since it can be reduced to questions about the derived category of CP1.Comment: 20 pages, LaTex2

The behaviour of dark matter associated with 4 bright cluster galaxies in the 10kpc core of Abell 3827

Galaxy cluster Abell 3827 hosts the stellar remnants of four almost equally bright elliptical galaxies within a core of radius 10kpc. Such corrugation of the stellar distribution is very rare, and suggests recent formation by several simultaneous mergers. We map the distribution of associated dark matter, using new Hubble Space Telescope imaging and VLT/MUSE integral field spectroscopy of a gravitationally lensed system threaded through the cluster core. We find that each of the central galaxies retains a dark matter halo, but that (at least) one of these is spatially offset from its stars. The best-constrained offset is 1.62+/-0.48kpc, where the 68% confidence limit includes both statistical error and systematic biases in mass modelling. Such offsets are not seen in field galaxies, but are predicted during the long infall to a cluster, if dark matter self-interactions generate an extra drag force. With such a small physical separation, it is difficult to definitively rule out astrophysical effects operating exclusively in dense cluster core environments - but if interpreted solely as evidence for self-interacting dark matter, this offset implies a cross-section sigma/m=(1.7+/-0.7)x10^{-4}cm^2/g x (t/10^9yrs)^{-2}, where t is the infall duration.Comment: 15 pages, 9 figure

Suppressors of cytokine signaling: Relevance to gastrointestinal function and disease

AbstractBackground & Aims: The suppressor of cytokine signaling (SOCS) proteins are a family of Src homology 2 domain-containing proteins. Currently, there are 8 members of the SOCS family, of which a number have been implicated strongly in the negative regulation of cytokine signal transduction pathways. Methods: This review focuses on recent discoveries about 4 SOCS family members, SOCS-1, -2, and -3, and cytokine-inducible SH2-domain containing (CIS), and provides more limited information about other SOCS family members. Results: A large number of cytokines and growth factors are now known to induce SOCS proteins. In turn, SOCS inhibit the actions of a growing number of cytokines and growth factors in vitro or in vivo. SOCS proteins exert their inhibitory effects at the level of activation of janus kinases (JAKs) or by competing with transcription factors for binding sites on activated cytokine receptors. SOCS proteins also may mediate the ubiquitination and subsequent degradation of the SOCS protein and its bound signaling complex. Genetic modification of SOCS genes in mice has revealed crucial roles in the negative regulation of a number of important physiologic parameters including interferon γ activity, growth, blood cell production, and placental development. Conclusions: Information about SOCS action in gastrointestinal function and disease is only just emerging, but available data indicate a role in growth of gastrointestinal tissues, inflammatory bowel disease, and cancer.GASTROENTEROLOGY 2002;123:2064-208

Complete Genome Sequences of Paenibacillus Larvae Phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana

We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA

Cord compression defined by MRI is the driving factor behind the decision to operate in Degenerative Cervical Myelopathy despite poor correlation with disease severity.

OBJECTIVES:The mainstay treatment for Degenerative Cervical Myelopathy (DCM) is surgical decompression. Not all cases, however, are suitable for surgery. Recent international guidelines advise surgery for moderate to severe disease as well as progressive mild disease. The goal of this study was to examine the factors in current practice that drive the decision to operate in DCM. STUDY DESIGN:Retrospective cohort study. METHODS:1 year of cervical spine MRI scans (N = 1123) were reviewed to identify patients with DCM with sufficient clinical documentation (N = 39). Variables at surgical assessment were recorded: age, sex, clinical signs and symptoms of DCM, disease severity, and quantitative MRI measures of cord compression. Bivariate correlations were used to compare each variable with the decision to offer the patient an operation. Subsequent multivariable analysis incorporated all significant bivariate correlations. RESULTS:Of the 39 patients identified, 25 (64%) were offered an operation. The decision to operate was significantly associated with narrower non-pathological canal and cord diameters as well as cord compression ratio, explaining 50% of the variance. In a multivariable model, only cord compression ratio was significant (p = 0.017). Examination findings, symptoms, functional disability, disease severity, disease progression, and demographic factors were all non-significant. CONCLUSIONS:Cord compression emerged as the main factor in surgical decision-making prior to the publication of recent guidelines. Newly identified predictors of post-operative outcome were not significantly associated with decision to operate