The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule

IRE1 couples endoplasmic reticulum unfolded protein load to RNA cleavage events that culminate in the sequence-specific splicing of the Xbp1 mRNA and in the regulated degradation of diverse membrane-bound mRNAs. We report on the identification of a small molecule inhibitor that attains its selectivity by forming an unusually stable Schiff base with lysine 907 in the IRE1 endonuclease domain, explained by solvent inaccessibility of the imine bond in the enzyme-inhibitor complex. The inhibitor (abbreviated 4μ8C) blocks substrate access to the active site of IRE1 and selectively inactivates both Xbp1 splicing and IRE1-mediated mRNA degradation. Surprisingly, inhibition of IRE1 endonuclease activity does not sensitize cells to the consequences of acute endoplasmic reticulum stress, but rather interferes with the expansion of secretory capacity. Thus, the chemical reactivity and sterics of a unique residue in the endonuclease active site of IRE1 can be exploited by selective inhibitors to interfere with protein secretion in pathological settings.

Selective regulation of p38β protein and signaling by integrin-linked kinase mediates bladder cancer cell migration

Integrin-linked kinase (ILK) and p38MAPK are protein kinases that transduce extracellular signals regulating cell migration and actin cytoskeletal organization. ILK-dependent regulation of p38MAPK is critical for mammalian kidney development and in smooth muscle cell migration, however, specific p38 isoforms has not been previously examined in ILK-regulated responses. Signaling by ILK and p38MAPK is often dysregulated in bladder cancer, and here we report a strong positive correlation between protein levels of ILK and p38β, which is the predominant isoform found in bladder cancer cells, as well as in patient-matched normal bladder and tumor samples. Knockdown by RNA interference of either p38β or ILK disrupts serum-induced, Rac1-dependent migration and actin cytoskeletal organization in bladder cancer cells. Surprisingly, ILK knockdown causes the selective reduction in p38β cellular protein level, without inhibiting p38β messenger RNA (mRNA) expression. The loss of p38β protein in ILK-depleted cells is partially rescued by the 26S proteasomal inhibitor MG132. Using co-precipitation and bimolecular fluorescent complementation assays, we find that ILK selectively forms cytoplasmic complexes with p38β. In situ proximity ligation assays further demonstrate that serum-stimulated assembly of endogenous ILK–p38β complexes is sensitive to QLT-0267, a small molecule ILK kinase inhibitor. Finally, inhibition of ILK reduces the amplitude and period of serum-induced activation of heat shock protein 27 (Hsp27), a target of p38β implicated in actin cytoskeletal reorganization. Our work identifies Hsp27 as a novel target of ILK–p38β signaling complexes, playing a key role in bladder cancer cell migration.

Selective combination of visual and thermal imaging for resilient localization in adverse conditions : day and night, smoke and fire

Long-term autonomy in robotics requires perception systems that are resilient to unusual but realistic conditions that will eventually occur during extended missions. For example, unmanned ground vehicles (UGVs) need to be capable of operating safely in adverse and low-visibility conditions, such as at night or in the presence of smoke. The key to a resilient UGV perception system lies in the use of multiple sensor modalities, e.g., operating at different frequencies of the electromagnetic spectrum, to compensate for the limitations of a single sensor type. In this paper, visual and infrared imaging are combined in a Visual-SLAM algorithm to achieve localization. We propose to evaluate the quality of data provided by each sensor modality prior to data combination. This evaluation is used to discard low-quality data, i.e., data most likely to induce large localization errors. In this way, perceptual failures are anticipated and mitigated. An extensive experimental evaluation is conducted on data sets collected with a UGV in a range of environments and adverse conditions, including the presence of smoke (obstructing the visual camera), fire, extreme heat (saturating the infrared camera), low-light conditions (dusk), and at night with sudden variations of artificial light. A total of 240 trajectory estimates are obtained using five different variations of data sources and data combination strategies in the localization method. In particular, the proposed approach for selective data combination is compared to methods using a single sensor type or combining both modalities without preselection. We show that the proposed framework allows for camera-based localization resilient to a large range of low-visibility conditions.

Strain engineering of selective chemical adsorption on monolayer MoS2

Nanomaterials are prone to influence by chemical adsorption because of their large surface to volume ratios. This enables sensitive detection of adsorbed chemical species which, in turn, can tune the property of the host material. Recent studies discovered that single and multi-layer molybdenum disulfide (MoS2) films are ultra-sensitive to several important environmental molecules. Here we report new findings from ab inito calculations that reveal substantially enhanced adsorption of NO and NH3 on strained monolayer MoS2 with significant impact on the properties of the adsorbates and the MoS2 layer. The magnetic moment of adsorbed NO can be tuned between 0 and 1 μB; strain also induces an electronic phase transition between half-metal and metal. Adsorption of NH3 weakens the MoS2 layer considerably, which explains the large discrepancy between the experimentally measured strength and breaking strain of MoS2 films and previous theoretical predictions. On the other hand, adsorption of NO2, CO, and CO2 is insensitive to the strain condition in the MoS2 layer. This contrasting behavior allows sensitive strain engineering of selective chemical adsorption on MoS2 with effective tuning of mechanical, electronic, and magnetic properties. These results suggest new design strategies for constructing MoS2-based ultrahigh-sensitivity nanoscale sensors and electromechanical devices.

Efficient selective identity-based encryption without random oracles

We construct two efficient Identity-Based Encryption (IBE) systems that admit selective-identity security reductions without random oracles in groups equipped with a bilinear map. Selective-identity secure IBE is a slightly weaker security model than the standard security model for IBE. In this model the adversary must commit ahead of time to the identity that it intends to attack, whereas in an adaptive-identity attack the adversary is allowed to choose this identity adaptively. Our first system—BB1—is based on the well studied decisional bilinear Diffie–Hellman assumption, and extends naturally to systems with hierarchical identities, or HIBE. Our second system—BB2—is based on a stronger assumption which we call the Bilinear Diffie–Hellman Inversion assumption and provides another approach to building IBE systems. Our first system, BB1, is very versatile and well suited for practical applications: the basic hierarchical construction can be efficiently secured against chosen-ciphertext attacks, and further extended to support efficient non-interactive threshold decryption, among others, all without using random oracles. Both systems, BB1 and BB2, can be modified generically to provide “full” IBE security (i.e., against adaptive-identity attacks), either using random oracles, or in the standard model at the expense of a non-polynomial but easy-to-compensate security reduction.

Tethering for Selective Synthesis of 2,2′-Biphenols : the Acetal Method

2,2'-Biphenols are a large and diverse group of compounds with exceptional properties both as ligands and bioactive agents. Traditional methods for their synthesis by oxidative dimerisation are often problematic and lead to mixtures of ortho- and para-connected regioisomers. To compound these issues, an intermolecular dimerisation strategy is often inappropriate for the synthesis of heterodimers. The ‘acetal method’ provides a solution for these problems: stepwise tethering of two monomeric phenols enables heterodimer synthesis, enforces ortho regioselectivity and allows relatively facile and selective intramolecular reactions to take place. The resulting dibenzo[1,3]dioxepines have been analysed by quantum chemical calculations to obtain information about the activation barrier for ring flip between the enantiomers. Hydrolytic removal of the dioxepine acetal unit revealed the 2,2′-biphenol target.

An MMP13-selective inhibitor delays primary tumor growth and the onset of tumor-associated osteolytic lesions in experimental models of breast cancer

We investigated the effects of the matrix metalloproteinase 13 (MMP13)-selective inhibitor, 5-(4-{4-[4-(4-fluorophenyl)-1,3-oxazol-2-yl]phenoxy}phenoxy)-5-(2-methoxyethyl) pyrimidine-2,4,6(1H,3H,5H)-trione (Cmpd-1), on the primary tumor growth and breast cancer-associated bone remodeling using xenograft and syngeneic mouse models. We used human breast cancer MDA-MB-231 cells inoculated into the mammary fat pad and left ventricle of BALB/c Nu/Nu mice, respectively, and spontaneously metastasizing 4T1.2-Luc mouse mammary cells inoculated into mammary fat pad of BALB/c mice. In a prevention setting, treatment with Cmpd-1 markedly delayed the growth of primary tumors in both models, and reduced the onset and severity of osteolytic lesions in the MDA-MB-231 intracardiac model. Intervention treatment with Cmpd-1 on established MDA-MB-231 primary tumors also significantly inhibited subsequent growth. In contrast, no effects of Cmpd-1 were observed on soft organ metastatic burden following intracardiac or mammary fat pad inoculations of MDA-MB-231 and 4T1.2-Luc cells respectively. MMP13 immunostaining of clinical primary breast tumors and experimental mice tumors revealed intra-tumoral and stromal expression in most tumors, and vasculature expression in all. MMP13 was also detected in osteoblasts in clinical samples of breast-to-bone metastases. The data suggest that MMP13-selective inhibitors, which lack musculoskeletal side effects, may have therapeutic potential both in primary breast cancer and cancer-induced bone osteolysis.

Selective involvement of TIMP-2 in the second activational cleavage of pro-MMP-2 : refinement of the pro-MMP-2 activation mechanism

A tissue inhibitor of metalloproteinases-2 (TIMP-2)-independent mechanism for generating the first activational cleavage of pro-matrix metalloproteinase-2 (MMP-2) was identified in membrane type-1 MMP (MT1-MMP)-transfected MCF-7 cells and confirmed in TIMP-2-deficient fibroblasts. In contrast, the second MMP-2-activational step was found to be TIMP-2 dependent in both systems. MMP-2 hemopexin C-terminal domain was found to be critical for the first step processing, confirming a need for membrane tethering. We propose that the intermediate species of MMP-2 forms the well-established trimolecular complex (MT1-MMP/TIMP-2/MMP-2) for further TIMP-2-dependent autocatalytic cleavage to the fully active species. This alternate mechanism may supplement the traditional TIMP-2-mediated first step mechanism.

Selective neuronal differentiation of neural stem cells induced by nanosecond microplasma agitation

An essential step for therapeutic and research applications of stem cells is their ability to differentiate into specific cell types. Neuronal cells are of great interest for medical treatment of neurodegenerative diseases and traumatic injuries of central nervous system (CNS), but efforts to produce these cells have been met with only modest success. In an attempt of finding new approaches, atmospheric-pressure room-temperature microplasma jets (MPJs) are shown to effectively direct in vitro differentiation of neural stem cells (NSCs) predominantly into neuronal lineage. Murine neural stem cells (C17.2-NSCs) treated with MPJs exhibit rapid proliferation and differentiation with longer neurites and cell bodies eventually forming neuronal networks. MPJs regulate ~. 75% of NSCs to differentiate into neurons, which is a higher efficiency compared to common protein- and growth factors-based differentiation. NSCs exposure to quantized and transient (~. 150. ns) micro-plasma bullets up-regulates expression of different cell lineage markers as β-Tubulin III (for neurons) and O4 (for oligodendrocytes), while the expression of GFAP (for astrocytes) remains unchanged, as evidenced by quantitative PCR, immunofluorescence microscopy and Western Blot assay. It is shown that the plasma-increased nitric oxide (NO) production is a factor in the fate choice and differentiation of NSCs followed by axonal growth. The differentiated NSC cells matured and produced mostly cholinergic and motor neuronal progeny. It is also demonstrated that exposure of primary rat NSCs to the microplasma leads to quite similar differentiation effects. This suggests that the observed effect may potentially be generic and applicable to other types of neural progenitor cells. The application of this new in vitro strategy to selectively differentiate NSCs into neurons represents a step towards reproducible and efficient production of the desired NSC derivatives. © 2013.

Size- and orientation-selective Si nanowire growth : thermokinetic effects of naeoscale plasma chemistry

A multiscale, multiphase thermokinetic model is used to show the effective control of the growth orientation of thin Si NWs for nanoelectronic devices enabled by nanoscale plasma chemistry. It is shown that very thin Si NWs with [110] growth direction can nucleate at much lower process temperatures and pressures compared to thermal chemical vapor deposition where [111]-directed Si NWs are predominantly grown. These findings explain a host of experimental results and offer the possibility of energy- and matter-efficient, size- and orientation-controlled growth of [110] Si NWs for next-generation nanodevices.

Nanoscale plasma chemistry enables fast, size-selective nanotube nucleation

The possibility of fast, narrow-size/chirality nucleation of thin single-walled carbon nanotubes (SWCNTs) at low, device-tolerant process temperatures in a plasma-enhanced chemical vapor deposition (CVD) is demonstrated using multiphase, multiscale numerical experiments. These effects are due to the unique nanoscale reactive plasma chemistry (NRPC) on the surfaces and within Au catalyst nanoparticles. The computed three-dimensional process parameter maps link the nanotube incubation times and the relative differences between the incubation times of SWCNTs of different sizes/chiralities to the main plasma- and precursor gas-specific parameters and explain recent experimental observations. It is shown that the unique NRPC leads not only to much faster nucleation of thin nanotubes at much lower process temperatures, but also to better selectivity between the incubation times of SWCNTs with different sizes and chiralities, compared to thermal CVD. These results are used to propose a time-programmed kinetic approach based on fast-responding plasmas which control the size-selective, narrow-chirality nucleation and growth of thin SWCNTs. This approach is generic and can be used for other nanostructure and materials systems.

Energy and matter-efficient size-selective growth of thin quantum wires in a plasma

It is shown that plasmas can minimize the adverse Gibbs-Thompson effect in thin quantum wire growth. The model of Si nanowirenucleation includes the unprecedented combination of the plasma sheath, ion- and radical-induced species creation and heating effects on the surface and within an Au catalyst nanoparticle. Compared to neutral gas thermal processes, much thinner, size-selective wires can nucleate at the same temperature and pressure while much lower energy and matter budget is needed to grow same-size wires. This explains the experimental observations and may lead to energy- and matter-efficient synthesis of a broader range of one-dimensional quantum structures.

Plasma-aided hydrogenation and Al-doping : increasing the conductivity and optical transparency of ZnO transparent conducting oxide

Plasma-assisted magnetron sputtering with varying ambient conditions has been utilised to deposit Al-doped ZnO (AZO) transparent conductive thin films directly onto a glass substrate at a low substrate temperature of 400 °C. The effects of hydrogen addition on electrical, optical and structural properties of the deposited AZO films have been investigated using X-ray diffractometry (XRD), scanning electron microscopy (SEM), Hall effect measurements and UV–vis optical transmission spectroscopy. The results indicate that hydrogen addition has a remarkable effect on the film transparency and conductivity with the greatest effects observed with a hydrogen flux of approximately 3 sccm. It has been demonstrated that the conductivity and the average transmittance in the visible range can increase simultaneously contrary to the effects observed by other authors. In addition, hydrogen incorporation further leads to the absorption edge shifting to a shorter wavelength due to the Burstein–Moss effect. These results are of particular relevance to the development of the next generation of optoelectronic and photovoltaic devices based on highly transparent conducting oxides with controllable electronic and optical properties.

Hydrogen in plasma-nanofabrication : selective control of nanostructure heating and passivation

The possibility of independent control of the surface fluxes of energy and hydrogen-containing radicals, thus enabling selective control of the nanostructure heating and passivation, is demonstrated. In situ energy flux measurements reveal that even a small addition of H2 to low-pressure Ar plasmas leads to a dramatic increase in the energy deposition through H recombination on the surface. The heat release is quenched by a sequential addition of a hydrocarbon precursor while the surface passivation remains effective. Such selective control offers an effective mechanism for deterministic control of the growth shape, crystallinity, and density of nanostructures in plasma-aided nanofabrication. © 2010 American Institute of Physics.

Si quantum dots embedded in an amorphous SiC matrix : nanophase control by non-equilibrium plasma hydrogenation

Nanophase nc-Si/a-SiC films that contain Si quantum dots (QDs) embedded in an amorphous SiC matrix were deposited on single-crystal silicon substrates using inductively coupled plasma-assisted chemical vapor deposition from the reactive silane and methane precursor gases diluted with hydrogen at a substrate temperature of 200 °C. The effect of the hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen-to-silane plus methane gases), ranging from 0 to 10.0, on the morphological, structural, and compositional properties of the deposited films, is extensively and systematically studied by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared absorption spectroscopy, and X-ray photoelectron spectroscopy. Effective nanophase segregation at a low hydrogen dilution ratio of 4.0 leads to the formation of highly uniform Si QDs embedded in the amorphous SiC matrix. It is also shown that with the increase of X, the crystallinity degree and the crystallite size increase while the carbon content and the growth rate decrease. The obtained experimental results are explained in terms of the effect of hydrogen dilution on the nucleation and growth processes of the Si QDs in the high-density plasmas. These results are highly relevant to the development of next-generation photovoltaic solar cells, light-emitting diodes, thin-film transistors, and other applications.