Different Modes of Transactivation of Bacteriophage Mu Late Promoters by Transcription Factor C

Transactivator protein C is required for the expression of bacteriophage Mu late genes from lys, I, P and mom promoters during lytic life cycle of the phage. The mechanism of transcription activation of mom gene by C protein is well understood. C activates transcription at Pmom by initial unwinding of the promoter DNA, thereby facilitating RNA polymerase (RNAP) recruitment. Subsequently, C interacts with the (sic) subunit of RNAP to enhance promoter clearance. The mechanism by which C activates other late genes of the phage is not known. We carried out promoter-polymerase interaction studies with all the late gene promoters to determine the individual step of C mediated activation. Unlike at P-mom, at the other three promoters, RNAP recruitment and closed complex formation are not C dependent. Instead, the action of C at P-lys, P-I, and P-P is during the isomerization from closed complex to open complex with no apparent effect at other steps of initiation pathway. The mechanism of transcription activation of mom and other late promoters by their common activator is different. This distinction in the mode of activation (promoter recruitment and escape versus isomerization) by the same activator at different promoters appears to be important for optimized expression of each of the late genes.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Crystallographic studies of the extracytoplasmic function sigma factor sigma(J) from Mycobacterium tuberculosis

Mycobacterium tuberculosis has multiple sigma factors which enable the bacterium to reprogram its transcriptional machinery under diverse environmental conditions. sigma(J), an extracytoplasmic function sigma factor, is upregulated in late stationary phase cultures and during human macrophage infection. sigma(J) governs the cellular response to hydrogen peroxide-mediated oxidative stress. sigma(J) differs from other canonical sigma factors owing to the presence of a SnoaL_2 domain at the C-terminus. sigma(J) crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 133.85, c = 75.08 angstrom. Diffraction data were collected to 2.16 angstrom resolution on the BM14 beamline at the European Synchrotron Radiation Facility (ESRF).

Glioblastoma-derived Macrophage Colony-stimulating Factor (MCSF) Induces Microglial Release of Insulin-like Growth Factor-binding Protein 1 (IGFBP1) to Promote Angiogenesis

Glioblastoma (grade IV glioma/GBM) is the most common primary adult malignant brain tumor with poor prognosis. To characterize molecular determinants of tumor-stroma interaction in GBM, we profiled 48 serum cytokines and identified macrophage colony-stimulating factor (MCSF) as one of the elevated cytokines in sera from GBM patients. Both MCSF transcript and protein were up-regulated in GBM tissue samples through a spleen tyrosine kinase (SYK)-dependent activation of the PI3K-NF kappa B pathway. Ectopic overexpression and silencing experiments revealed that glioma-secreted MCSF has no role in autocrine functions and M2 polarization of macrophages. In contrast, silencing expression of MCSF in glioma cells prevented tube formation of human umbilical vein endothelial cells elicited by the supernatant from monocytes/microglial cells treated with conditioned medium from glioma cells. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture showed that glioma-derived MCSF induces changes in microglial secretome and identified insulin-like growth factor-binding protein 1 (IGFBP1) as one of the MCSF-regulated proteins secreted by microglia. Silencing IGFBP1 expression in microglial cells or its neutralization by an antibody reduced the ability of supernatants derived from microglial cells treated with glioma cell-conditioned medium to induce angiogenesis. In conclusion, this study shows up-regulation of MCSF in GBM via a SYK-PI3K-NF kappa B-dependent mechanism and identifies IGFBP1 released by microglial cells as a novel mediator of MCSF-induced angiogenesis, of potential interest for developing targeted therapy to prevent GBM progression.

Ac2PIM-responsive miR-150 and miR-143 Target Receptor-interacting Protein Kinase 2 and Transforming Growth Factor Beta-activated Kinase 1 to Suppress NOD2-induced Immunomodulators

Specific and coordinated regulation of innate immune receptor-driven signaling networks often determines the net outcome of the immune responses. Here, we investigated the cross-regulation of toll-like receptor (TLR)2 and nucleotide-binding oligomerization domain (NOD)2 pathways mediated by Ac2PIM, a tetra-acylated form of mycobacterial cell wall component and muramyl dipeptide (MDP), a peptidoglycan derivative respectively. While Ac2PIM treatment of macrophages compromised their ability to induce NOD2-dependent immunomodulators like cyclooxygenase (COX)-2, suppressor of cytokine signaling (SOCS)-3, and matrix metalloproteinase (MMP)-9, no change in the NOD2-responsive NO, TNF-alpha, VEGF-A, and IL-12 levels was observed. Further, genome-wide microRNA expression profiling identified Ac2PIM-responsive miR-150 and miR-143 to target NOD2 signaling adaptors, RIP2 and TAK1, respectively. Interestingly, Ac2PIM was found to activate the SRC-FAK-PYK2-CREB cascade via TLR2 to recruit CBP/P300 at the promoters of miR-150 and miR-143 and epigenetically induce their expression. Loss-of-function studies utilizing specific miRNA inhibitors establish that Ac2PIM, via the miRNAs, abrogate NOD2-induced PI3K-PKC delta-MAPK pathway to suppress beta-catenin-mediated expression of COX-2, SOCS-3, and MMP-9. Our investigation has thus underscored the negative regulatory role of Ac2PIM-TLR2 signaling on NOD2 pathway which could broaden our understanding on vaccine potential or adjuvant utilities of Ac2PIM and/or MDP.

Dynamic stress intensity factor of a functionally graded material under antiplane shear loading

The dynamic response of a finite crack in an unbounded Functionally Graded Material (FGM) subjected to an antiplane shear loading is studied in this paper. The variation of the shear modulus of the functionally graded material is modeled by a quadratic increase along the direction perpendicular to the crack surface. The dynamic stress intensity factor is extracted from the asymptotic expansion of the stresses around the crack tip in the Laplace transform plane and obtained in the time domain by a numerical Laplace inversion technique. The influence of graded material property on the dynamic intensity factor is investigated. It is observed that the magnitude of dynamic stress intensity factor for a finite crack in such a functionally graded material is less than in the homogeneous material with a property identical to that of the FGM crack plane.

A bulk acoustic mode single-crystal silicon microresonator with a high-quality factor

This paper details a bulk acoustic mode resonator fabricated in single-crystal silicon with a quality factor of 15 000 in air, and over a million below 10 mTorr at a resonant frequency of 2.18 MHz. The resonator is a square plate that is excited in the square-extensional mode and has been fabricated in a commercial foundry silicon-on-insulator (SOI) MEMS process through MEMSCAP. This paper also presents a simple method of extracting resonator parameters from raw measurements heavily buried in electrical feedthrough. Its accuracy has been demonstrated through a comparison between extracted motional resistance values measured at different voltage biases and those predicted from an analytical model. Finally, a method of substantially cancelling electrical feedthrough through system-level electronic implementation is also introduced. © 2008 IOP Publishing Ltd.

5.4-MHz single-crystal silicon wine glass mode disk resonator with quality factor of 2 million

This paper reports the design and electrical characterization of a micromechanical disk resonator fabricated in single crystal silicon using a foundry SOI micromachining process. The microresonator has been selectively excited in the radial extensional and the wine glass modes by reversing the polarity of the DC bias voltage applied on selected drive electrodes around the resonant structure. The quality factor of the resonator vibrating in the radial contour mode was 8000 at a resonant frequency of 6.34 MHz at pressure below 10 mTorr vacuum. The highest measured quality factor of the resonator in the wine glass resonant mode was 1.9 × 106 using a DC bias voltage of 20 V at about the same pressure in vacuum; the resonant frequency was 5.43 MHz and the lowest motional resistance measured was approximately 17 kΩ using a DC bias voltage of 60 V applied across 2.7 μm actuation gaps. This corresponds to a resonant frequency-quality factor (f-Q) product of 1.02 × 1013, among the highest reported for single crystal silicon microresonators, and on par with the best quartz crystal resonators. The quality factor for the wine glass mode in air was approximately 10,000. © 2009 Elsevier B.V. All rights reserved.

Square wine glass mode resonator with quality factor of 4 million

We report on the experimental characterization of a single crystal silicon square-plate microresonator. The resonator is excited in the square wine glass (SWG) mode at a mechanical resonance frequency of 2.065 MHz. The resonator displays quality factor of 9660 in air and an ultra-high quality factor of Q = 4.05 × 106 in 12 mtorr vacuum. The SWG mode may be described as a square plate that contracts along one axis in the fabrication plane, while simultaneously extending along an orthogonal axis in the same plane. The resonant structure is addressed in a 2-terminal configuration by utilizing equal and opposite drive polarities on surrounding capacitor electrodes, thereby decreasing the motional resistance of the resonator. The resonant micromechanical device has been fabricated in a commercial silicon-on-insulator process through the MEMSCAP foundry utilising a minimum electrostatic gap of 2 μm. © 2008 IEEE.

Stress intensity factor histories of a steadily propagating crack under 3-D combined mode traction

Elastodynamic stress intensity factor histories of an unbounded solid containing a semi-infinite plane crack that propagates at a constant velocity under 3-D time-independent combined mode loading are considered. The fundamental solution, which is the response of point loading, is obtained. Then, stress intensity factor histories of a general loading system are written out in terms of superposition integrals. The methods used here are the Laplace transform methods in conjunction with the Wiener-Hopf technique.