Template Synthesis of Three-Dimensional Cubic Ordered Mesoporous Carbon With Tunable Pore Sizes

Three-dimensional cubic ordered mesoporous carbons with tunable pore sizes have been synthesized by using cubic Ia3d mesoporous KIT-6 silica as the hard template and boric acid as the pore expanding agent. The prepared ordered mesoporous carbons were characterized by powder X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption–desorption analysis. The results show that the pore sizes of the prepared ordered mesoporous carbons with three-dimensional cubic structure can be regulated in the range of 3.9–9.4 nm. A simplified model was proposed to analyze the tailored pore sizes of the prepared ordered mesoporous carbons on the basis of the structural parameters of the silica template

RNA polymerase II stalling promotes nucleosome occlusion and pTEFb recruitment to drive immortalization by Epstein-Barr virus

Epstein-Barr virus (EBV) immortalizes resting B-cells and is a key etiologic agent in the development of numerous cancers. The essential EBV-encoded protein EBNA 2 activates the viral C promoter (Cp) producing a message of ~120 kb that is differentially spliced to encode all EBNAs required for immortalization. We have previously shown that EBNA 2-activated transcription is dependent on the activity of the RNA polymerase II (pol II) C-terminal domain (CTD) kinase pTEFb (CDK9/cyclin T1). We now demonstrate that Cp, in contrast to two shorter EBNA 2-activated viral genes (LMP 1 and 2A), displays high levels of promoter-proximally stalled pol II despite being constitutively active. Consistent with pol II stalling, we detect considerable pausing complex (NELF/DSIF) association with Cp. Significantly, we observe substantial Cp-specific pTEFb recruitment that stimulates high-level pol II CTD serine 2 phosphorylation at distal regions (up to +75 kb), promoting elongation. We reveal that Cp-specific pol II accumulation is directed by DNA sequences unfavourable for nucleosome assembly that increase TBP access and pol II recruitment. Stalled pol II then maintains Cp nucleosome depletion. Our data indicate that pTEFb is recruited to Cp by the bromodomain protein Brd4, with polymerase stalling facilitating stable association of pTEFb. The Brd4 inhibitor JQ1 and the pTEFb inhibitors DRB and Flavopiridol significantly reduce Cp, but not LMP1 transcript production indicating that Brd4 and pTEFb are required for Cp transcription. Taken together our data indicate that pol II stalling at Cp promotes transcription of essential immortalizing genes during EBV infection by (i) preventing promoter-proximal nucleosome assembly and ii) necessitating the recruitment of pTEFb thereby maintaining serine 2 CTD phosphorylation at distal regions

Phonon-assisted radiofrequency absorption by gold nanoparticles resulting in hyperthermia

It is suggested that in gold nanoparticles (GNPs) of about 5 nm sizes used in the radiofrequency (RF) hyperthermia, an absorption of the RF photon by the Fermi electron occurs with involvement of the longitudinal acoustic vibrational mode (LAVM), the dominating one in the distribution of vibrational density of states (VDOS). This physical mechanism helps to explain two observed phenomena: the size dependence of the heating rate (HR) in GNPs and reduced heat production in aggregated GNPs. The argumentation proceeds within the one-electron approximation, taking into account the discretenesses of energies and momenta of both electrons and LAVMs. The heating of GNPs is thought to consist of two consecutive processes: first, the Fermi electron absorbs simultaneously the RF photon and the LAVM available in the GNP; hereafter the excited electron gets relaxed within the GNP's boundary, exciting a LAVM with the energy higher than that of the previously absorbed LAVM. GNPs containing the Ta and/or Fe impurities are proposed for the RF hyperthermia as promising heaters with enhanced HRs, and GNPs with rare-earth impurity atoms are also brought into consideration. It is shown why the maximum HR values should be expected in GNPs with about 5-7 nm size.Comment: proceedings at the NATO Advanced Research workshop FANEM-2015 (Minsk, May 25-27, 2015). To be published in the final form in: "Fundamental and Applied NanoElectroMagnetics" (Springer Science + Business Media B.V.

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming

Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors

The C-Terminal Domain of the Novel Essential Protein Gcp Is Critical for Interaction with Another Essential Protein YeaZ of Staphylococcus aureus

Previous studies have demonstrated that the novel protein Gcp is essential for the viability of various bacterial species including Staphylococcus aureus; however, the reason why it is required for bacterial growth remains unclear. In order to explore the potential mechanisms of this essentiality, we performed RT-PCR analysis and revealed that the gcp gene (sa1854) was co-transcribed with sa1855, yeaZ (sa1856) and sa1857 genes, indicating these genes are located in the same operon. Furthermore, we demonstrated that Gcp interacts with YeaZ using a yeast two-hybrid (Y2H) system and in vitro pull down assays. To characterize the Gcp-YeaZ interaction, we performed alanine scanning mutagenesis on the residues of C-terminal segment of Gcp. We found that the mutations of the C-terminal Y317-F322 region abolished the interaction of Gcp and YeaZ, and the mutations of the D324-N329 and S332-Y336 regions alleviated Gcp binding to YeaZ. More importantly, we demonstrated that these key regions of Gcp are also necessary for the bacterial survival since these mutated Gcp could not complement the depletion of endogenous Gcp. Taken together, our data suggest that the interaction of Gcp and YeaZ may contribute to the essentiality of Gcp for S. aureus survival. Our findings provide new insights into the potential mechanisms and biological functions of this novel essential protein

Indigenous Populations of Three Closely Related Lysobacter spp. in Agricultural Soils Using Real-Time PCR

Previous research had shown that three closely related species of Lysobacter, i.e., Lysobacter antibioticus, Lysobacter capsici, and Lysobacter gummosus, were present in different Rhizoctonia-suppressive soils. However, the population dynamics of these three Lysobacter spp. in different habitats remains unknown. Therefore, a specific primer–probe combination was designed for the combined quantification of these three Lysobacter spp. using TaqMan. Strains of the three target species were efficiently detected with TaqMan, whereas related non-target strains of Lysobacter enzymogenes and Xanthomonas campestris were not or only weakly amplified. Indigenous Lysobacter populations were analyzed in soils of 10 organic farms in the Netherlands during three subsequent years with TaqMan. These soils differed in soil characteristics and crop rotation. Additionally, Lysobacter populations in rhizosphere and bulk soil of different crops on one of these farms were studied. In acid sandy soils low Lysobacter populations were present, whereas pH neutral clay soils contained high populations (respectively, <4.0–5.87 and 6.22–6.95 log gene copy numbers g−1 soil). Clay content, pH and C/N ratio, but not organic matter content in soil, correlated with higher Lysobacter populations. Unexpectedly, different crops did not significantly influence population size of the three Lysobacter spp. and their populations were barely higher in rhizosphere than in bulk soil

Effects of estrogens and bladder inflammation on mitogen-activated protein kinases in lumbosacral dorsal root ganglia from adult female rats

BACKGROUND: Interstitial cystitis is a chronic condition associated with bladder inflammation and, like a number of other chronic pain states, symptoms associated with interstitial cystitis are more common in females and fluctuate during the menstrual cycle. The aim of this study was to determine if estrogens could directly modulate signalling pathways within bladder sensory neurons, such as extracellular signal-related kinase (ERK) and p38 mitogen-activated protein (MAP) kinases. These signalling pathways have been implicated in neuronal plasticity underlying development of inflammatory somatic pain but have not been as extensively investigated in visceral nociceptors. We have focused on lumbosacral dorsal root ganglion (DRG) neurons projecting to pelvic viscera (L1, L2, L6, S1) of adult female Sprague-Dawley rats and performed both in vitro and in vivo manipulations to compare the effects of short- and long-term changes in estrogen levels on MAPK expression and activation. We have also investigated if prolonged estrogen deprivation influences the effects of lower urinary tract inflammation on MAPK signalling. RESULTS: In studies of isolated DRG neurons in short-term (overnight) culture, we found that estradiol and estrogen receptor (ER) agonists rapidly stimulated ER-dependent p38 phosphorylation relative to total p38. Examination of DRGs following chronic estrogen deprivation in vivo (ovariectomy) showed a parallel increase in total and phosphorylated p38 (relative to beta-tubulin). We also observed an increase in ERK1 phosphorylation (relative to total ERK1), but no change in ERK1 expression (relative to beta-tubulin). We observed no change in ERK2 expression or phosphorylation. Although ovariectomy increased the level of phosphorylated ERK1 (vs. total ERK1), cyclophosphamide-induced lower urinary tract inflammation did not cause a net increase of either ERK1 or ERK2, or their phosphorylation. Inflammation did, however, cause an increase in p38 protein levels, relative to beta-tubulin. Prior ovariectomy did not alter the response to inflammation. CONCLUSIONS: These results provide new insights into the complex effects of estrogens on bladder nociceptor signalling. The diversity of estrogen actions in these ganglia raises the possibility of developing new ways to modulate their function in pelvic hyperactivity or pain states

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/

Structural Characterization of Mesoporous Silica Nanofibers Synthesized Within Porous Alumina Membranes

Mesoporous silica nanofibers were synthesized within the pores of the anodic aluminum oxide template using a simple sol–gel method. Transmission electron microscopy investigation indicated that the concentration of the structure-directing agent (EO20PO70EO20) had a significant impact on the mesostructure of mesoporous silica nanofibers. Samples with alignment of nanochannels along the axis of mesoporous silica nanofibers could be formed under the P123 concentration of 0.15 mg/mL. When the P123 concentration increased to 0.3 mg/mL, samples with a circular lamellar mesostructure could be obtained. The mechanism for the effect of the P123 concentration on the mesostructure of mesoporous silica nanofibres was proposed and discussed

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined