We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.
Interleukin 4 (IL-4) can suppress delayed-type hypersensitivity reactions (DTHRs), including organ-specific autoimmune diseases in mice and humans. Despite the broadly documented antiinflammatory effect of IL-4, the underlying mode of action remains incompletely understood, as IL-4 also promotes IL-12 production by dendritic cells (DCs) and IFN-γ-producing T H 1 cells in vivo. Studying the impact of IL-4 on the polarization of human and mouse DCs, we found that IL-4 exerts opposing effects on the production of
Deguelin exhibits potent apoptotic and antiangiogenic activities in a variety of transformed cells and cancer cells. Deguelin also exhibits potent tumor suppressive effects in xenograft tumor models for many human cancers. Our initial studies confirmed that deguelin disrupts ATP binding to HSP90 and consequently induces destabilization of its client proteins such as HIF-1α. Interestingly, a fluorescence probe assay revealed that deguelin and its analogues do not compete with ATP binding to the N-terminus of HSP90, unlike most HSP90 inhibitors. To determine the key parts of deguelin that contribute to its potent HSP90 inhibition, as well as its antiproliferative and antiangiogenic activities, we have established a structure-activity relationship (SAR) of deguelin. In the course of these studies, we identified a series of novel and potent HSP90 inhibitors. In particular, analogues 54 and 69, the B- and C-ring-truncated compounds, exhibited excellent antiproliferative activities with IC(50) of 140 and 490 nM in the H1299 cell line, respectively, and antiangiogenic activities in zebrafish embryos in a dose dependent manner (0.25-1.25 μM).
Heat shock protein (Hsp)70 is a molecular chaperone that maintains protein homoeostasis during cellular stress through two opposing mechanisms: protein refolding and degradation. However, the mechanisms by which Hsp70 balances these opposing functions under stress conditions remain unknown. Here, we demonstrate that Hsp70 preferentially facilitates protein refolding after stress, gradually switching to protein degradation via a mechanism dependent on ARD1-mediated Hsp70 acetylation. During the early stress response, Hsp70 is immediately acetylated by ARD1 at K77, and the acetylated Hsp70 binds to the co-chaperone Hop to allow protein refolding. Thereafter, Hsp70 is deacetylated and binds to the ubiquitin ligase protein CHIP to complete protein degradation during later stages. This switch is required for the maintenance of protein homoeostasis and ultimately rescues cells from stress-induced cell death in vitro and in vivo. Therefore, ARD1-mediated Hsp70 acetylation is a regulatory mechanism that temporally balances protein refolding/degradation in response to stress.
The N-acetyltransferase arrest defective 1 (ARD1) is an important regulator of cell growth and differentiation that has emerged recently as a critical molecule in cancer progression. However, the regulation of the enzymatic and biological activities of human ARD1 (hARD1) in cancer is presently poorly understood. Here, we report that hARD1 undergoes autoacetylation and that this modification is essential for its functional activation. Using liquid chromatography-tandem mass spectrometry and site-directed mutational analyses, we identified K136 residue as an autoacetylation target site. K136R mutation abolished the ability of hARD1 to promote cancer cell growth in vitro and tumor xenograft growth in vivo. Mechanistic investigations revealed that hARD1 autoacetylation stimulated cyclin D1 expression through activation of the transcription factors β-catenin and activator protein-1. Our results show that hARD1 autoacetylation is critical for its activation and its ability to stimulate cancer cell proliferation and tumorigenesis. Cancer Res; 70(11); 4422-32. ©2010 AACR.
Different aspects of stress response of Lactobacillus acidophilus were investigated. First, the sublethal and lethal levels of bile, heat, and NaCl stresses were determined. They were 0.05% and 0.5% (bile), 53 degrees C and 60 degrees C (heat), and 2% and 18% (NaCl), respectively. To evaluate the effect of each stress at log phase, log-phase cultures were challenged directly with the lethal level of each stress (control) and were compared to log-phase cultures that were pre-exposed to the sublethal level prior to the exposure at the lethal level (test). Some, if not most, of the cells were killed in the control cultures against each of the three stresses. However, in the test cultures, the number of cells that had survived increased significantly. It appears that L. acidophilus is capable of displaying adaptive response to stress. The adaptive response to one stress was also shown to provide cross-protection against different stresses tested. The effect of each stress on stationary-phase cultures was also investigated. In contrast to log-phase culture, stationary-phase culture was inherently resistant to stress.
We report the growth of high-quality nonpolar (m-plane) and semipolar (r-plane) multiple quantum well (MQW) nanowires (NWs) for high internal quantum efficiency light emitting diodes (LEDs) without polarization. Highly aligned and uniform In(x)Ga(1-x)N/GaN MQW layers are grown coaxially on the {1-100} sidewalls of hexagonal c-axis n-GaN NWs on Si(111) substrates by a pulsed flow metal-organic chemical vapor deposition (MOCVD) technique. The photoluminescence (PL) measurements reveal that the wavelength and intensity of an MQW structure with various pairs (2-20) are very stable and possess composition-dependent emission ranging from 369 to 600 nm. The cathodoluminescence (CL) spectrum of individual In(x)Ga(1-x)N/GaN MQW NW is dominated by band-edge emission at 369 and 440 nm with a relatively homogeneous profile of parallel alignment. High-resolution transmission electron microscopy (HR-TEM) studies of coaxial InxGa1-xN/GaN MQW NWs measured along the [0001] and [2-1-10] zone axes reveal that the grown NWs are uniform with six nonpolar m-plane facets without any dislocations and stacking faults. The p-GaN/In(x)Ga(1-x)N/GaN MQW/n-GaN NW coaxial LEDs show a current rectification with a sharp onset voltage at 2.65 V in the forward bias. The linear enhancement of power output could be attributed to the elimination of piezoelectric fields in the In(x)Ga(1-x)N/GaN MQW active region. The superior performance of coaxial NW LEDs is observed in comparison with that of thin film LEDs. Overall, the feasibility of obtaining low defect and strain free m-plane coaxial NWs using pulsed MOCVD can be utilized for the realization of high-power LEDs without an efficiency droop. These kinds of coaxial NWs are viable high surface area MQW structures which can be used to enhance the efficiency of LEDs.
Heterostructures of compositionally and electronically variant two-dimensional (2D) atomic layers are viable building blocks for ultrathin optoelectronic devices. We show that the composition of interfacial transition region between semiconducting WSe2 atomic layer channels and metallic NbSe2 contact layers can be engineered through interfacial doping with Nb atoms. WxNb1-xSe2 interfacial regions considerably lower the potential barrier height of the junction, significantly improving the performance of the corresponding WSe2-based field-effect transistor devices. The creation of such alloyed 2D junctions between dissimilar atomic layer domains could be the most important factor in controlling the electronic properties of 2D junctions and the design and fabrication of 2D atomic layer devices.
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