Saccharomyces cerevisiae NineTeen Complex (NTC)-associated Factor Bud31/Ycr063w Assembles on Precatalytic Spliceosomes and Improves First and Second Step Pre-mRNA Splicing Efficiency

Pre-mRNA splicing occurs in spliceosomes whose assembly and activation are critical for splice site selection and catalysis. The highly conserved NineTeen complex protein complex stabilizes various snRNA and protein interactions early in the spliceosome assembly pathway. Among several NineTeen complex-associated proteins is the nonessential protein Bud31/Ycr063w, which is also a component of the Cef1p subcomplex. A role for Bud31 in pre-mRNA splicing is implicated by virtue of its association with splicing factors, but its specific functions and spliceosome interactions are uncharacterized. Here, using in vitro splicing assays with extracts from a strain lacking Bud31, we illustrate its role in efficient progression to the first catalytic step and its requirement for the second catalytic step in reactions at higher temperatures. Immunoprecipitation of functional epitope-tagged Bud31 from in vitro reactions showed that its earliest association is with precatalytic B complex and that the interaction continues in catalytically active complexes with stably bound U2, U5, and U6 small nuclear ribonucleoproteins. In complementary experiments, wherein precatalytic spliceosomes are selected from splicing reactions, we detect the occurrence of Bud31. Cross-linking of proteins to pre-mRNAs with a site-specific 4-thio uridine residue at the -3 position of exon 1 was tested in reactions with WT and bud31 null extracts. The data suggest an altered interaction between a similar to 25-kDa protein and this exonic residue of pre-mRNAs in the arrested bud31 null spliceosomes. These results demonstrate the early spliceosomal association of Bud31 and provide plausible functions for this factor in stabilizing protein interactions with the pre-mRNA.

Electrical Treeing and the Associated PD Characteristics in LDPE Nanocomposites

Treeing in low density polyethylene (LDPE) filled with alumina nanocomposite as well as unfilled LDPE samples stressed with 50 Hz ac voltage has been studied. The tree inception voltage was monitored for various samples with different nano-filler loadings and it is seen that there is an increase in tree inception voltage with filler loading in LDPE. Treeing pattern and tree growth duration for unfilled and nano-filled LDPE samples have also been studied. Different tree growth patterns as well as a slower tree growth with increase in filler loading in LDPE nanocomposites were observed. The observed slow propagation of tree growth with filler loading is attributed to the changes in the polymer crystalline morphology induced by the presence of nano-particles and the greater ability of the nanoparticles to resist discharge growth. SEM studies carried out to determine the morphology of unfilled and nano-filled LDPE showed an increase in lamellae packing in LDPE nanocomposites and this increased lamellar density leads to a reduction in the tree propagation rate. Partial discharge activities were also monitored during the electrical tree growth in both the unfilled and the nano-filled LDPE samples and were found to be significantly different. PD magnitude and the number of PD pulses per cycle were found to be lower with electrical tree growth duration in LDPE nanocomposites as compared to unfilled LDPE. The same trend was seen with increased filler loading also.

Radial infall of two compact objects: 2.5-post-Newtonian linear momentum flux and associated recoil

The loss rate of linear momentum from a binary system composed of compact objects (radially falling towards each other under mutual gravitational influence) has been investigated using the multipolar post-Minkowskian approach. The 2.5PN accurate analytical formula for the linear momentum flux is provided, in terms of the separation of the two objects, in harmonic coordinates, both for a finite and an infinite initial separation. The 2.5PN formulas for the linear momentum flux are finally used to estimate the recoil velocity accumulated during a premerger phase of the binary evolution.

Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (similar to 80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

Equal channel angular pressing processing routes and associated structure modification: a differential scanning calorimetry and X-ray line profile analysis

The effectiveness of different routes of equal channel angular pressing (A, B-c, and C) is studied for commercially pure copper. The stored energy and the activation energy of recrystallization for the deformed samples were quantified using differential scanning calorimetry and X-ray diffraction line profile analysis. Results of the study revealed that the dislocation density and the stored energy are higher in the case of route B-c deformed sample. The activation energy for recrystallization is lower for route B-c. (C) 2012 International Centre for Diffraction Data doi:10.1017/S0885715612000310]

Exploiting coherence for the simultaneous discovery of latent facets and associated sentiments

Facet-based sentiment analysis involves discovering the latent facets, sentiments and their associations. Traditional facet-based sentiment analysis algorithms typically perform the various tasks in sequence, and fail to take advantage of the mutual reinforcement of the tasks. Additionally,inferring sentiment levels typically requires domain knowledge or human intervention. In this paper, we propose aseries of probabilistic models that jointly discover latent facets and sentiment topics, and also order the sentiment topics with respect to a multi-point scale, in a language and domain independent manner. This is achieved by simultaneously capturing both short-range syntactic structure and long range semantic dependencies between the sentiment and facet words. The models further incorporate coherence in reviews, where reviewers dwell on one facet or sentiment level before moving on, for more accurate facet and sentiment discovery. For reviews which are supplemented with ratings, our models automatically order the latent sentiment topics, without requiring seed-words or domain-knowledge. To the best of our knowledge, our work is the first attempt to combine the notions of syntactic and semantic dependencies in the domain of review mining. Further, the concept of facet and sentiment coherence has not been explored earlier either. Extensive experimental results on real world review data show that the proposed models outperform various state of the art baselines for facet-based sentiment analysis.

Regulation of lipid biosynthesis, sliding motility, and biofilm formation by a membrane-anchored nucleoid-associated protein of mycobacterium tuberculosis

Bacteria use a number of small basic proteins for organization and compaction of their genomes. By their interaction with DNA, these nucleoid-associated proteins (NAPs) also influence gene expression. Rv3852, a NAP of Mycobacterium tuberculosis, is conserved among the pathogenic and slow-growing species of mycobacteria. Here, we show that the protein predominantly localizes in the cell membrane and that the carboxy-terminal region with the propensity to form a transmembrane helix is necessary for its membrane localization. The protein is involved in genome organization, and its ectopic expression in Mycobacterium smegmatis resulted in altered nucleoid morphology, defects in biofilm formation, sliding motility, and change in apolar lipid profile. We demonstrate its crucial role in regulating the expression of KasA, KasB, and GroEL1 proteins, which are in turn involved in controlling the surface phenotypes in mycobacteria.

A novel adeno-associated virus serotype (AAV)-8 capsid mutant improves human coagulation factor IX expression in vivo

Recombinant AAV-8 vectors have shown significant promise for hepatic gene therapy of hemophilia B. However, the theme of AAV vector dose dependent immunotoxicity seen with AAV2 vectors earlier seem to re-emerge with AAV8 vectors as well. It is therefore important to develop novel AAV8 vectors that provide enhanced gene expression at significantly less vector doses. We hypothesized that AAV8 during its intracellular trafficking, are targeted for destruction in the cytoplasm by the host-cellular kinase/ubiquitination/proteasomal degradation machinery and modification of specific serine/threonine kinase or ubiquitination targets on AAV8 capsid (Fig.1A) may improve its transduction efficiency. To test this, point mutations at specific serine (S)/threonine (T) > alanine (A) or lysine (K)>arginine (R) residues were generated on AAV8 capsid. scAAV8-EGFP vectors containing the wild-type (WT) and each one of the 5 S/T/K-mutant(S276A, S501A, S671A, T251A and K137R) capsids were evaluated for their liver transduction efficiency at a dose of 5 X 1010 vgs/ animal in C57BL/6 mice in vivo. The best performing mutant was found to be the K137R vector in terms of either the gene expression (46-fold) or the vector copy numbers in the hepatocytes (22-fold) compared to WT-AAV8 (Fig.1B). The K137R-AAV8 vector that showed significantly decreased ubiquitination of the viral capsid had reduced activation of markers of innate immune response [IL-6, IL-12, tumor necrosis factor α, Kupffer cells and TLR-9]. In addition, animals injected with the K137R mutant also demonstrated decreased (2-fold) levels of cross-neutralizing antibodies when compared to animals that received the WT-AAV8 vector. To study further the utility of the novel AAV8-K137R mutant in a therapeutic setting, we delivered human coagulation factor IX (h.FIX) under the control of liver specific promoters (LP1 or hAAT) at two different doses (2.5x10^10 and 1x10^11 vgs per mouse) in 8-12 weeks old male C57BL/6 mice. As can be seen in Fig.1C/D, the circulating levels of h.FIX were higher in all the K137R-AAV8 treated groups as compared to the WT-AAV8 treated groups either at 2 weeks (62% vs 37% for hAAT constructs and 47% vs 21% for LP1 constructs) or 4 weeks (78% vs 56% for hAAT constructs and 64% vs 30% for LP1 constructs) post hepatic gene transfer. These studies demonstrate the feasibility of the use of this novel vector for potential gene therapy of hemophilia B.

Spatial memory deficits in maternal iron deficiency paradigms are associated with altered glucocorticoid levels

``The goal of this study was to examine the effect of maternal iron deficiency on the developing hippocampus in order to define a developmental window for this effect, and to see whether iron deficiency causes changes in glucocorticoid levels. The study was carried out using pre-natal, post-natal, and pre + post-natal iron deficiency paradigm. Iron deficient pregnant dams and their pups displayed elevated corticosterone which, in turn, differentially affected glucocorticoid receptor (GR) expression in the CA1 and the dentate gyrus. Brain Derived Neurotrophic Factor (BDNF) was reduced in the hippocampi of pups following elevated corticosterone levels. Reduced neurogenesis at P7 was seen in pups born to iron deficient mothers, and these pups had reduced numbers of hippocampal pyramidal and granule cells as adults. Hippocampal subdivision volumes also were altered. The structural and molecular defects in the pups were correlated with radial arm maze performance; reference memory function was especially affected. Pups from dams that were iron deficient throughout pregnancy and lactation displayed the complete spectrum of defects, while pups from dams that were iron deficient only during pregnancy or during lactation displayed subsets of defects. These findings show that maternal iron deficiency is associated with altered levels of corticosterone and GR expression, and with spatial memory deficits in their pups.'' (C) 2013 Elsevier Inc. All rights reserved.

Probing p300/CBP associated Factor (PCAF)-dependent pathways with a small molecule inhibitor

PCAF (KAT2B) belongs to the GNAT family of lysine acetyltransferases (KAT) and specifically acetylates the histone H3K9 residue and several nonhistone proteins. PCAF is also a transcriptional coactivator. Due to the lack of a PCAF KAT-specific small molecule inhibitor, the exclusive role of the acetyltransferase activity of PCAF is not well understood. Here, we report that a natural compound of the hydroxybenzoquinone class, embelin, specifically inhibits H3Lys9 acetylation in mice and inhibits recombinant PCAF-mediated acetylation with near complete specificity in vitro. Furthermore, using embelin, we have identified the gene networks that are regulated by PCAF during muscle differentiation, further highlighting the broader regulatory functions of PCAF in muscle differentiation in addition to the regulation via MyoD acetylation.

The Modified Selenenyl Amide, M-hydroxy Ebselen, Attenuates Diabetic Nephropathy and Diabetes-Associated Atherosclerosis in ApoE/GPx1 Double Knockout Mice

Seleno-organic glutathione peroxidase (GPx) mimetics, including ebselen (Eb), have been tested in in vitro studies for their ability to scavenge reactive oxygen and nitrogen species, including hydrogen peroxide and peroxynitrite. In this study, we investigated the efficacies of two Eb analogues, m-hydroxy ebselen (ME) and ethanol-ebselen (EtE) and compared these with Eb in cell based assays. We found that ME is superior in attenuating the activation of hydrogen peroxide-induced pro-inflammatory mediators, ERK and P38 in human aortic endothelial cells. Consequently, we investigated the effects of ME in an in vivo model of diabetes, the ApoE/GPx1 double knockout (dKO) mouse. We found that ME attenuates plaque formation in the aorta and lesion deposition within the aortic sinus of diabetic dKO mice. Oxidative stress as assessed by 8-OHdG in urine and nitrotyrosine immunostaining in the aortic sinus and kidney tubules, was reduced by ME in diabetic dKO mice. ME also attenuated diabetes-associated renal injury which included tubulointerstitial fibrosis and glomerulosclerosis. Furthermore, the bioactivity of the pro-fibrotic cytokine transforming growth factor-beta (TGF-beta) as assessed by phospho-Smad2/3 immunostaining was attenuated after treatment with ME. TGF-beta-stimulated increases in collagen I and IV gene expression and protein levels were attenuated by ME in rat kidney tubular cells. However, in contrast to the superior activity of ME in in vitro and cell based assays, ME did not further augment the attenuation of diabetes-associated atherosclerosis and renal injury in our in vivo model when compared with Eb. In conclusion, this study strengthens the notion that bolstering GPx-like activity using synthetic mimetics may be a useful therapeutic strategy in lessening the burden of diabetic complications. However, these studies highlight the importance of in vivo analyses to test the efficacies of novel Eb analogues, as in vitro and cell based assays are only partly predictive of the in vivo situation.

Fractional Hilbert transform extensions and associated analytic signal construction

The analytic signal (AS) was proposed by Gabor as a complex signal corresponding to a given real signal. The AS has a one-sided spectrum and gives rise to meaningful spectral averages. The Hilbert transform (HT) is a key component in Gabor's AS construction. We generalize the construction methodology by employing the fractional Hilbert transform (FrHT), without going through the standard fractional Fourier transform (FrFT) route. We discuss some properties of the fractional Hilbert operator and show how decomposition of the operator in terms of the identity and the standard Hilbert operators enables the construction of a family of analytic signals. We show that these analytic signals also satisfy Bedrosian-type properties and that their time-frequency localization properties are unaltered. We also propose a generalized-phase AS (GPAS) using a generalized-phase Hilbert transform (GPHT). We show that the GPHT shares many properties of the FrHT, in particular, selective highlighting of singularities, and a connection with Lie groups. We also investigate the duality between analyticity and causality concepts to arrive at a representation of causal signals in terms of the FrHT and GPHT. On the application front, we develop a secure multi-key single-sideband (SSB) modulation scheme and analyze its performance in noise and sensitivity to security key perturbations. (C) 2013 Elsevier B.V. All rights reserved.