Identification of a core promoter and a novel isoform of the human TSCI gene transcript and structural comparison with mouse homolog

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder with loci on chromosome 9q34.12 (TSC1) and chromosome 16p13.3 (TSC2). Genes for both loci have been isolated and characterized. The promoters of both genes have not been characterized so far and little is known about the regulation of these genes. This study reports the characterization of the human TSC1 promoter region for the first time. We have identified a novel alternative isoform in the 5' untranslated region (UTR) of the TSC1 gene transcript involving exon 1. Alternative isoforms in the 5' UTR of the mouse Tsc1 gene transcript involving exon I and exon 2 have also been identified. We have identified three upstream open reading frames (uORFs) in the 5' UTR of the TSC1/Tsc1 gene. A comparative study of the 5' UTR of TSC1/Tsc1 gene has revealed that there is a high degree of similarity not only in the sequence but also in the splicing pattern of both human and mouse TSC1 genes. We have used PCR methodology to isolate approximately 1.6 kb genomic DNA 5' to the TSC1 cDNA. This sequence has directed a high level of expression of luciferase activity in both HeLa and HepG2 cells. Successive 5' and 3' deletion analysis has suggested that a -587 bp region, from position +77 to -510 from the transcription start site (TSS), contains the promoter activity. Interestingly, this region contains no consensus TATA box or CAAT box. However, a 521-bp fragment surrounding the TSS exhibits the characteristics of a CpG island which overlaps with the promoter region. The identification of the TSC1 promoter region will help in designing a suitable strategy to identify mutations in this region in patients who do not show any mutations in the coding regions. It will also help to study the regulation of the TSC1 gene and its role in tumorigenesis. (C) 2003 Elsevier B.V. All rights reserved.

Analysis of Serpentine folded-waveguide slow-wave structures by elliptical conformal transformation

Analysis of the serpentine folded-waveguide slow-wave structure was carried out using elliptical conformal transformation, for the dispersion and interaction impedance characteristics of the structure. The results obtained from the present analysis were compared with those from 3D electromagnetic simulation using MAFIA.

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

Onset of sphalerite to wurtzite transformation in ZnS nanoparticles

In this work, the incubation period for the onset of sphalerite to wurtzite transformation in isolated ZnS nanoparticles 2 to 7 nm in size was determined via the in situ isothermal annealing of as-synthesized sphalerite nanoparticles in a transmission electron microscope (TEM). Nanoparticles sitting on the TEM grid were well separated from each other in order to minimize particle sintering during the annealing operation. The phase transformation onset was observed at 300 degrees C, 350 degrees C, and 400 degrees C after 90, 10, and 4 min, respectively. These time-temperature data for the phase transformation onset were then used to calculate the activation energy for the nucleation of the wurtzite phase in 2 to 7 nm sphalerite particles. The activation energy determined was 24 Kcal/mol. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3622625]

Characterization of phase transformation behaviour and microstructural development of electroless Ni-B coating

Phase transformation behaviour of amorphous electroless Ni-B coating with a targeted composition of Ni-6wt% B is characterized in conjunction with microstructural development and hardness. Microscopic observations of the as-deposited coating display a novel microstructure which is already phase separated at multiple length scales. Spherical colonies of similar to 5 mu m consist of 2-3 mu m nodular regions which are surrounded by similar to 2-3 mu m region that contains fine bands ranging from 10 to 70 nm in width. The appearance of three crystalline phases in this binary system at different stages of heat treatment and the concomitant variation in hardness are shown to arise from nanoscale fluctuations in the as-deposited boron content from 4 to 8 wt%. High temperature annealing reveals continuous crystallization up to 430 degrees C, overlapping with the domain of B loss due to diffusion into the substrate. The implications of such a microstructure for optimal heat treatment procedures are discussed. (C) 2011 Elsevier B.V. All rights reserved.

Evolution of crystallinity of free gold agglomerates and shape transformation

We report the shape evolution of free gold agglomerates with different morphologies that transform to ellipsoidal and then to spherical shapes during the heating cycle. The shape transformation is associated with a structural transition from polycrystalline to single crystalline. The structural transition temperature is shown to be dependent on the final size of the particles and not on the initial morphologies of the agglomerates. It is also shown that the transition occurs well below the melting temperature which is in contrast with the melt-freeze process reported in the literature.

Bacterial transformation using micro-shock waves

Shock waves are one of the most competent mechanisms of energy dissipation observed in nature. We have developed a novel device to generate controlled micro-shock waves using an explosive-coated polymer tube. In this study, we harnessed these controlled micro-shock waves to develop a unique bacterial transformation method. The conditions were optimized for the maximum transformation efficiency in Escherichia coli. The maximum transformation efficiency was obtained when we used a 30 cm length polymer tube, 100 mu m thick metal foil, 200 mM CaCl(2), 1 ng/mu l plasmid DNA concentration, and 1 x 10(9) cell density. The highest transformation efficiency achieved (1 x 10(-5) transformants/cell) was at least 10 times greater than the previously reported ultrasound-mediated transformation (1 x 10(-6) transformants/cell). This method was also successfully employed for the efficient and reproducible transformation of Pseudomonas aeruginosa and Salmonella typhimurium. This novel method of transformation was shown to be as efficient as electroporation with the added advantage of better recovery of cells, reduced cost (40 times cheaper than a commercial electroporator), and growth phase independent transformation. (C) 2011 Elsevier Inc. All rights reserved.

Size and temperature dependent stability and phase transformation in single-crystal zirconium nanowire

A novel size dependent FCC (face-centered-cubic) -> HCP (hexagonally-closed-pack) phase transformation and stability of an initial FCC zirconium nanowire are studied. FCC zirconium nanowires with cross-sectional dimensions < 20 are found unstable in nature, and they undergo a FCC -> HCP phase transformation, which is driven by tensile surface stress induced high internal compressive stresses. FCC nanowire with cross-sectional dimensions > 20 , in which surface stresses are not enough to drive the phase transformation, show meta-stability. In such a case, an external kinetic energy in the form of thermal heating is required to overcome the energy barrier and achieve FCC -> HCP phase transformation. The FCC-HCP transition pathway is also studied using Nudged Elastic Band (NEB) method, to further confirm the size dependent stability/metastability of Zr nanowires. We also show size dependent critical temperature, which is required for complete phase transformation of a metastable-FCC nanowire.

Direct detection of Salmonella without pre-enrichment in milk, ice-cream and fruit juice by PCR against hilA gene

A novel PCR based assay was devised to specifically detect contamination of any Salmonella serovar in milk, fruit juice and ice-cream without pre-enrichment. This method utilizes primers against hilA gene which is conserved in all Salmonella serovars and absent from the close relatives of Salmonella. An optimized protocol, in terms time and money, is provided for the reduction of PCR contaminants from milk, ice-cream and juice through the use of routine laboratory chemicals. The simplicity, efficiency (time taken 3-4 h) and sensitivity (to about 5-10 CFU/ml) of this technique confers a unique advantage over other previously used time consuming detection techniques. This technique does not involve pre-enrichment of the samples or extensive sample processing, which was a pre-requisite in most of the other reported studies. Hence, this assay can be ideal for adoption, after further fine tuning, by food quality control for timely detection of Salmonella contamination as well as other food-borne pathogens (with species specific primers) in food especially milk, ice-cream and fruit juice. (C) 2011 Elsevier Ltd. All rights reserved.

Nanostructuration via solid state transformation as a strategy for improving the thermoelectric efficiency of PbTe alloys

The approach taken in this paper in order to modify the scattering features of electrons and phonons and improve the figure of merit (ZT) of thermoelectric PbTe is to alter the microstructure at constant chemistry. A lamellar pattern of PbTe/GeTe at the nano- and microscale was produced in Pb(0.36)Ge(0.64)Te alloy by the diffusional decomposition of a supersaturated solid solution. The mechanism of nanostructuration is most likely a discontinuous spinodal decomposition. A simple model relating the interface velocity to the observed lamellar spacing is proposed. The effects of nanostructuration in Pb(0.36)Ge(0.64)Te alloy on the electrical and thermal conductivity, thermopower and ZT were investigated. It was shown that nanostructuration through the formation of a lamellar pattern of PbTe/GeTe is unlikely to provide a significant improvement due to the occurrence of discontinuous coarsening. However, the present study allows an analysis of possible strategies to improve thermoelectric materials via optimal design of the microstructure and optimized heat treatment. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Why Is Less Cationic Lipid Required To Prepare Lipoplexes from Plasmid DNA than Linear DNA in Gene Therapy?

The most important objective of the present study was to explain why cationic lipid (CL)-mediated delivery of plasmid DNA (pDNA) is better than that of linear DNA in gene therapy, a question that, until now, has remained unanswered. Herein for the first time we experimentally show that for different types of CLs, pDNA, in contrast to linear DNA, is compacted with a large amount of its counterions, yielding a lower effective negative charge. This feature has been confirmed through a number of physicochemical and biochemical investigations. This is significant for both in vitro and in vivo transfection studies. For an effective DNA transfection, the lower the amount of the CL, the lower is the cytotoxicity. The study also points out that it is absolutely necessary to consider both effective charge ratios between CL and pDNA and effective pDNA charges, which can be determined from physicochemical experiments.

Usefulness of in Situ Single Crystal to Single Crystal Transformation (SCSC) Studies in Understanding the Temperature-Dependent Dimensionality Cross-over and Structural Reorganization in Copper-Containing Metal-Organic Frameworks (MOFs)

Two copper-containing compounds [Cu(3)(mu(3)-OH)(2)-(H(2)O)(2){(SO(3))-C(6)H(3)-(COO)(2)}(CH(3)COO)] , I, and [Cu(5)(mu(3)-OH)(2)(H(2)O)(6){(NO(2))-C(6)H(3)-(COO)(2)}(4)]center dot 5H(2)O, II, were prepared using sulphoisophthalic and nitroisophthalic acids. The removal of the coordinated water molecules in the compounds was investigated using in situ single crystal to single crystal (SCSC) transformation studies, temperature-dependent powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). The efficacy of SCSC transformation studies were established by the observation of dimensionality cross-over from a two-dimensional (I) to a three-dimensional structure, Cu(6)(mu(3)-OH)(4){(SO(3))-C(6)H(3)-(COO)(2)}(2)(CH(3)COO)(2), Ia, during the removal of the coordinated water molecules. Compound H exhibited a structural reorganization forming Cu(5)(mu(2)-OH)(2){(NO(2))C(6)H(3)-(COO)(2))(4)], Ha, possessing trimeric (Cu(3)O(12)) and dimeric (Cu(2)O(8)) copper clusters. The PXRD studies indicate that the three-dimensional structure (Ia) is transient and unstable, reverting back to the more stable two-dimensional structure (I) on cooling to room temperature. Compound Ha appears to be more stable at room temperature. The rehydration/dehydration studies using a modified TGA setup suggest complete rehydration of the water molecules, indicating that the water molecules in both compounds are labile. A possible model for the observed changes in the structures has been proposed. Magnetic studies indicate changes in the exchanges between the copper centers in Ha, whereas no such behavior was observed in Ia.