G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

Dynamic state estimation for identifying earthquake support motions in instrumented structures

The problem of identification of multi-component and (or) spatially varying earthquake support motions based on measured responses in instrumented structures is considered. The governing equations of motion are cast in the state space form and a time domain solution to the input identification problem is developed based on the Kalman and particle filtering methods. The method allows for noise in measured responses, imperfections in mathematical model for the structure, and possible nonlinear behavior of the structure. The unknown support motions are treated as hypothetical additional system states and a prior model for these motions are taken to be given in terms of white noise processes. For linear systems, the solution is developed within the Kalman filtering framework while, for nonlinear systems, the Monte Carlo simulation based particle filtering tools are employed. In the latter case, the question of controlling sampling variance based on the idea of Rao-Blackwellization is also explored. Illustrative examples include identification of multi-component and spatially varying support motions in linear/nonlinear structures.

High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio

Four-dimensional fluorescence microscopy-which records 3D image information as a function of time-provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light-efficient way of imaging, obtaining high-quality reconstructions requires deconvolution to remove optical aberrations. Unfortunately, most deconvolution methods perform very poorly at low signal-to-noise ratios, thereby requiring moderate photon doses to obtain acceptable resolution. We present a unique deconvolution method that combines an entropy-based regularization function with kernels that can exploit general spatial characteristics of the fluorescence image to push the required dose to extreme low levels, resulting in an enabling technology for high-resolution in vivo biological imaging.

Patterned growth and differentiation of neural cells on polymer derived carbon substrates with micro/nano structures in vitro

The growth of neuroblastoma (N2a) and Schwann cells has been explored on polymer derived carbon substrates of varying micro and nanoscale geometries: resorcinol-formaldehyde (RE) gel derived carbon films and electrospun nanofibrous (similar to 200 nm diameter) mat and SU-8 (a negative photoresist) derived carbon micro-patterns. MTT assay and complementary lactate dehydrogenase (LDH) assay established cytocompatibility of RE derived carbon films and fibers over a period of 6 days in culture. The role of length scale of surface patterns in eliciting lineage-specific adaptive response along, across and on the interspacing between adjacent micropatterns (i.e., ``on'', ``across'' and ``off'') has been assayed. Textural features were found to affect 3',5'-cyclic AMP sodium salt-induced neurite outgrowth, over a wide range of length scales: from similar to 200 nm (carbon fibers) to similar to 60 mu m (carbon patterns). Despite their innate randomness, carbon nanofibers promoted preferential differentiation of N2a cells into neuronal lineage, similar to ordered micro-patterns. Our results, for the first time, conclusively demonstrate the potential of RE-gel and SU-8 derived carbon substrates as nerve tissue engineering platforms for guided proliferation and differentiation of neural cells in vitro. (C) 2013 Elsevier Ltd. All rights reserved.

Graphene-MoS2 hybrid structures for multifunctional photoresponsive memory devices

Combining the electronic properties of graphene(1,2) and molybdenum disulphide (MoS2)(3-6) in hybrid heterostructures offers the possibility to create devices with various functionalities. Electronic logic and memory devices have already been constructed from graphene-MoS2 hybrids(7,8), but they do not make use of the photosensitivity of MoS2, which arises from its optical-range bandgap(9). Here, we demonstrate that graphene-on-MoS2 binary heterostructures display remarkable dual optoelectronic functionality, including highly sensitive photodetection and gate-tunable persistent photoconductivity. The responsivity of the hybrids was found to be nearly 1 x 10(10) A W-1 at 130 K and 5 x 10(8) A W-1 at room temperature, making them the most sensitive graphene-based photodetectors. When subjected to time-dependent photoillumination, the hybrids could also function as a rewritable optoelectronic switch or memory, where the persistent state shows almost no relaxation or decay within experimental timescales, indicating near-perfect charge retention. These effects can be quantitatively explained by gate-tunable charge exchange between the graphene and MoS2 layers, and may lead to new graphene-based optoelectronic devices that are naturally scalable for large-area applications at room temperature.

Mechanistic Insights into a Non-Classical Diffusion Pathway for the Formation of Hollow Intermetallics: A Route to Multicomponent Hollow Structures

Hollow nanostructures are used for various applications including catalysis, sensing, and drug delivery. Methods based on the Kirkendall effect have been the most successful for obtaining hollow nanostructures of various multicomponent systems. The classical Kirkendall effect relies on the presence of a faster diffusing species in the core; the resultant imbalance in flux results in the formation of hollow structures. Here, an alternate non-Kirkendall mechanism that is operative for the formation of hollow single crystalline particles of intermetallic PtBi is demonstrated. The synthesis method involves sequential reduction of Pt and Bi salts in ethylene glycol under microwave irradiation. Detailed analysis of the reaction at various stages indicates that the formation of the intermetallic PtBi hollow nanoparticles occurs in steps. The mechanistic details are elucidated using control experiments. The use of microwave results in a very rapid synthesis of intermetallics PtBi that exhibits excellent electrocatalytic activity for formic acid oxidation reaction. The method presented can be extended to various multicomponent systems and is independent of the intrinsic diffusivities of the species involved.

Role of dicarboxylate linkers in Mn-III-salicylaldoximate based extended structures: synthesis, structures, and magnetic behavior

Four new oxo-centered Mn-III-salicylaldoximate triangle-based extended complexes (Mn6O2)-O-III(salox)(6)(EtOH)(4)(phda)](n)(saloxH(2))(n)(2H(2)O)(n) (1), (Mn6O2)-O-III(salox)(6)(MeOH)(5)(5-I-isoph)](n)(3MeOH)(n) (2), (Mn6O2)-O-III(salox)(6)(MeOH)(4)(H2O) (5-N-3-isoph)](n)(4MeOH)(n) (3) and (Mn3NaO)-Na-III(salox)(3)(MeOH)(4)(5-NO2-isoph)](n)(MeOH)(n) (H2O)(n) (4) salox=salicylaldoximate, phda=1,3-phenylenediacetate, isoph=isophthalate] have been synthesized under similar reaction conditions. Single crystal X-ray structures show that in 1, only one type of Mn-6 cluster is arranged in 1D, whereas in 2 and 3 there are two types of clusters, differing in the way the triangle units are joined and assembled. In complex4, however, the basic building structure is heteronuclear and based on Mn-3 units extended in 2D. Susceptibility measurements (dc and ac) over a wide range of temperatures and fields show that the complexes1, 2, and 3 behave as single molecule magnets (SMMs) with S=4ground state, while 4 is dominantly antiferromagnetic with a ground spin state S=2. Density functional theory calculations have been performed on model complexes to provide a qualitative theoretical interpretation for their overall magnetic behavior.

New Structural Topologies in a Series of 3d Metal Complexes with Isomeric Phenylenediacetates and 1,3,5-Tris(1-imidazolyl)benzene Ligand: Syntheses, Structures, and Magnetic and Luminescence Properties

In this article we present the syntheses, characterizations, magnetic and luminescence properties of five 3d-metal complexes, Co(tib)(1,2-phda)](n)center dot(H2O)(n) (1), Co-3(tib)(2)(1,3-phda)(3)(H2O)](n)center dot(H2O)(2n) (2), Co-5(tib)(3)(1,4-phda)(5)(H2O)(3)](n)center dot(H2O)(7n) (3), Zn-3(tib)(2)(1,3-phda)(3)](n)center dot(H2O)(4n) (4), and Mn(tib)(2)(H2O)(2)](n)center dot(1,4-phdaH)(2n)center dot(H2O)(4n) (5), obtained from the use of isomeric phenylenediacetates (phda) and the neutral 1,3,5-tris(1-imidazolyl)benzene (tib) ligand. Single crystal X-ray structures showed that 1 constitutes 3,5-connected 2-nodal nets with a double-layered two-dimensional (2D) structure, while 2 forms an interpenetrated 2D network (3,4-connected 3-nodal net). Complex 3 has a complicated three-dimensional structure with 10-nodal 3,4,5-connected nets. Complex 4, although it resembles 2 in stoichiometry and basic building structures, forms a very different overall 2D assembly. In complex 5 the dicarboxylic acid, upon losing only one of the acidic protons, does not take part in coordination; instead it forms a complicated hydrogen bonding network with water molecules. Magnetic susceptibility measurements over a wide range of temperatures revealed that the metal ions exchange very poorly through the tib ligand, but for the Co(II) complexes the effects of nonquenched orbital contributions are prominent. The 3d(10) metal complex 4 showed strong luminescence with lambda(max) = 415 nm (lambda(ex) = 360 nm).

Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop

Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.

Lamb Wave Propagation in Laminated Composite Structures

Damage detection using guided Lamb waves is an important tool in Structural health Monitoring. In this paper, we outline a method of obtaining Lamb wave modes in composite structures using two dimensional Spectral Finite Elements. Using this approach, Lamb wave dispersion curves are obtained for laminated composite structures with different fibre orientation. These propagating Lamb wave modes are pictorially captured using tone burst signal.

Non-Destructive Evaluation of Defects and Damage in Composite Materials and Structures

The mechanical behaviour of composite materials differs from that of conventional structural materials owing to their heterogeneous and anisotropic nature. Different types of defects and anomalies get induced in these materials during the fabrication process. Further, during their service life, the components made of composite materials develop different types of damage. The performance and life of such components is governed by the combined effect of all these defects and damage. While porosity, voids, inclusions etc., are some defects those can get induced during the fabrication of composites, matrix cracks, interface debonds, delaminations and fiber breakage are major types of service induced damage which are of concern. During the service life of components made of composites, one type of damage can grow and initiate another type of damage. For example, matrix cracks can gradually grow to the interface and initiate debonds. Interface debonds in a particular plane can lead to delaminations. Consequently, the combined effect of different types of distributed damage causes the failure of the component. A set of non-destructive evaluation (NDE) methods is well established for testing conventional metallic materials. Some of them can also be utilized for composite materials as they are, and in some cases with a little different approach or modification. Ultrasonics, Radiography, Thermography, Fiber Optics, Acoustic Emision Techniques etc., to name a few. Detection, evaluation and characterization of different types of defects and damage encountered in composite materials and structures using different NDE tools is discussed briefly in this paper.

Note on high aspect-ratio SU-8 micromechanical structures using mask-less direct laser writing

We report high aspect-ratio micromechanical structures made of SU-8 polymer, which is a negative photoresist. Mask-less direct writing with 405 nm laser is used to pattern spin-cast SU-8 films of thickness of more than 600 um. As compared with X-ray lithography, which helps pattern material to give aspect ratios of 1:50 or higher, laser writing is a less expensive and more accessible alternative. In this work, aspect ratios up to 1:30 were obtained on narrow pillars and cantilever structures. Deep vertical patterning was achieved in multiple exposures of the surface with varying dosages given at periodic intervals of sufficient duration. It was found that a time lag between successive exposures at the same location helps the material recover from the transient changes that occur during exposure to the laser. This gives vertical sidewalls to the resulting structures. The time-lags and dosages were determined by conducting several trials. The micromechanical structures obtained with laser writing are compared with those obtained with traditional UV lithography as well as e-beam lithography. Laser writing gives not only high aspect ratios but also narrow gaps whereas e-beam can only give narrow gaps over very small depths. Unlike traditional UV lithography, laser writing does not need a mask. Furthermore, there is no adjustment for varying the dosage in traditional UV lithography. A drawback of this method compared to UV lithography is that the writing time increases. Some test structures as well as a compliant microgripper are fabricated.

Target reliability-based optimisation for internal seismic stability of reinforced soil structures

In this paper, an approach for target component and system reliability-based design optimisation (RBDO) to evaluate safety for the internal seismic stability of geosynthetic-reinforced soil (GRS) structures is presented. Three modes of failure are considered: tension failure of the bottom-most layer of reinforcement, pullout failure of the topmost layer of reinforcement, and total pullout failure of all reinforcement layers. The analysis is performed by treating backfill properties, geometric and strength properties of reinforcement as random variables. The optimum number of reinforcement layers and optimum pullout length needed to maintain stability against tension failure, pullout failure and total pullout failure for different coefficients of variation of friction angle of the backfill, design strength of the reinforcement and horizontal seismic acceleration coefficients by targeting various system reliability indices are proposed. The results provide guidelines for the total length of reinforcement required, considering the variability of backfill as well as seismic coefficients. One illustrative example is presented to explain the evaluation of reliability for internal stability of reinforced soil structures using the proposed approach. In the second illustration (the stability of five walls), the Kushiro wall subjected to the Kushiro-Oki earthquake, the Seiken wall subjected to the Chiba-ken Toho-Oki earthquake, the Ta Kung wall subjected to the Ji-Ji earthquake, and the Gould and Valencia walls subjected to Northridge earthquake are re-examined.

Spontaneous assembly of iridium nanochain-like structures: surface enhanced Raman scattering activity using visible light

A facile, environmentally friendly approach to synthesize branched Ir nanochain-like structures under mild conditions, using polyfunctional capping molecules in an aqueous medium is reported; the nanostructures exhibit a surface plasmon resonance peak (SPR) in the visible region and serve as an active substrate for surface enhanced Raman scattering studies.