Bozena Kaminska

Nanohole-array-based device for 2D snapshot multispectral imaging

We present a two-dimensional (2D) snapshot multispectral imager that utilizes the optical transmission characteristics of nanohole arrays (NHAs) in a gold film to resolve a mixture of input colors into multiple spectral bands. The multispectral device consists of blocks of NHAs, wherein each NHA has a unique periodicity that results in transmission resonances and minima in the visible and near-infrared regions. The multispectral device was illuminated over a wide spectral range, and the transmission was spectrally unmixed using a least-squares estimation algorithm. A NHA-based multispectral imaging system was built and tested in both reflection and transmission modes. The NHA-based multispectral imager was capable of extracting 2D multispectral images representative of four independent bands within the spectral range of 662u2005nm to 832u2005nm for a variety of targets. The multispectral device can potentially be integrated into a variety of imaging sensor systems.

Rapid fabrication of nano-structured quartz stamps

Replication of surface nano-structures from a master stamp allows large-area volume production that is otherwise cost prohibitive through conventional direct-write methods, such as electron beam lithography and focused ion beam milling. However, the creation of a master stamp containing sophisticated patterns still requires significant time on such direct-write tools. We demonstrate a method for reducing this tool time by patterning smaller nano-structures, and then enlarging them to the desired size through isotropic etching. We can create circular structures of any arrangement and size, down to the patterning limits of the direct-write tools. Subsequent metal mask deposition, lift-off, and anisotropic etching transforms the circular patterns to out-of-plane pillar structures for the final stamp. A 1xa0cm(2) area filled with a pattern of 200xa0nm diameter nano-holes spaced 520xa0nm apart, requires only 21xa0h to complete using our process, compared to 75xa0h using conventional fabrication. We demonstrate the utility and practicality of the quartz stamps through polymer embossing and replication. Embossed polymer nano-hole arrays are coated with a Cr/Au (5/100xa0nm) film to create surface plasmon resonance structures. Extraordinary optical transmission spectra from the metallized arrays show the expected spectral features when compared to focused ion beam milled structures.

ER stress and autophagy contribute to CsA-induced death of malignant glioma cells.

Cyclosporine A (CsA), which revolutionized transplantology due to its ability to block the activation of lymphocytes and other immune system cells, triggers autophagy in malignant glioma cell lines via stimulation of endoplasmic reticulum (ER) stress. We also found that autophagy serves as a protective mechanism against CsA toxicity.

Short peptides interfering with signaling pathways as new therapeutic tools for cancer treatment

Short peptides have many advantages, such as low molecular weight, selectivity for a specific target, organelles or cells with minimal toxicity. We describe properties of short peptides, which interfere with communication networks in tumor cells and within microenvironment of malignant gliomas, the most common brain tumors. We focus on ligand/receptor axes and intracellular signaling pathways critical for gliomagenesis that could be targeted with interfering peptides. We review structures and efficacy of organelle-specific and cell-penetrating peptides and describe diverse chemical modifications increasing proteolytic stability and protecting synthetic peptides against degradation. We report results of application of short peptides in glioma therapy clinical trials, their rises and falls. The most advanced examples of therapeutics such as short interfering peptides combined with cell-penetrating peptides that show good effectiveness in disease models are presented. It is foreseen that identification of peptides with better clinical properties may improve their success rates in clinical trials.

Rapid production of structural color images with optical data storage capabilities

In this paper, we present novel methods to produce structural color image for any given color picture using a pixelated generic stamp named nanosubstrate. The nanosubstrate is composed of prefabricated arrays of red, green and blue subpixels. Each subpixel has nano-gratings and/or sub-wavelength structures which give structural colors through light diffraction. Micro-patterning techniques were implemented to produce the color images from the nanosubstrate by selective activation of subpixels. The nano-grating structures can be nanohole arrays, which after replication are converted to nanopillar arrays or vice versa. It has been demonstrated that visible and invisible data can be easily stored using these fabrication methods and the information can be easily read. Therefore the techniques can be employed to produce personalized and customized color images for applications in optical document security and publicity, and can also be complemented by combined optical data storage capabilities.

Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems.

BackgroundIt is often desirable to separate effects of different regulators on gene expression, or to identify effects of the same regulator across several systems. Here, we focus on the rat brain following stroke or seizures, and demonstrate how the two tasks can be approached simultaneously.ResultsWe applied SVD to time-series gene expression datasets from the rat experimental models of stroke and seizures. We demonstrate conservation of two eigensystems, reflecting inflammation and/or apoptosis (eigensystem 2) and neuronal synaptic activity (eigensystem 3), between the stroke and seizures. We analyzed cis-regulation of gene expression in the subspaces of the conserved eigensystems. Bayesian networks analysis was performed separately for either experimental model, with cross-system validation of the highest-ranking features. In this way, we correctly re-discovered the role of AP1 in the regulation of apoptosis, and the involvement of Creb and Egr in the regulation of synaptic activity-related genes.We identified a novel antagonistic effect of the motif recognized by the nuclear matrix attachment region-binding protein Satb1 on AP1-driven transcriptional activation, suggesting a link between chromatin loop structure and gene activation by AP1. The effects of motifs binding Satb1 and Creb on gene expression in brain conform to the assumption of the linear response model of gene regulation. Our data also suggest that numerous enhancers of neuronal-specific genes are important for their responsiveness to the synaptic activity.ConclusionEigensystems conserved between stroke and seizures separate effects of inflammation/apoptosis and neuronal synaptic activity, exerted by different transcription factors, on gene expression in rat brain.

Authentication and process control system based on optical variable nanostructures

A new authentication and security system together with a nano-key concept using optical variable nanostructures (OVNs) are introduced. The three proposed designs are 1) the passive authentication, 2) the active authentication, and 3) the nano-key authentication. The passive authentication is obtained by insertion of an OVN image divided between multiple layers of the fabrication process. Authentic fabrication process is validated when the proper alignment (reconstructed image, for example) at the end of fabrication is achieved. The active and the nano-key authentication systems are implemented to directly interact with the active CMOS circuitry. A simple proof-of-concept for all introduced OVN-based authentication options are presented along with the optical images of the resulting authentication patterns.

Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival

In order to find clinically useful prognostic markers for glioma patients’ survival, we employed Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID) algorithm on DNA methylation (HumanMethylation450 platform) and RNA-seq datasets from The Cancer Genome Atlas (TCGA) for 88 patients observed until death. The input features were ranked according to their importance in predicting patients’ longer (400+ days) or shorter (≤400 days) survival without prior classification of the patients. Interestingly, out of the 65 most important features found, 63 are methylation sites, and only two mRNAs. Moreover, 61 out of the 63 methylation sites are among those detected by the 450u2009k array technology, while being absent in the HumanMethylation27. The most important methylation feature (cg15072976) overlaps with the RE1 Silencing Transcription Factor (REST) binding site, and was confirmed to intersect with the REST binding motif in human U87 glioma cells. Six additional methylation sites from the top 63 overlap with REST sites. We found that the methylation status of the cg15072976 site affects transcription factor binding in U87 cells in gel shift assay. The cg15072976 methylation status discriminates ≤400 and 400+ patients in an independent dataset from TCGA and shows positive association with survival time as evidenced by Kaplan-Meier plots.

Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal

The massive increase in computational power over the recent years and wider applicationsof machine learning methods, coincidental or not, were paralleled by remarkable advances inhigh-throughput DNA sequencing technologies.[...].

Role of cooling rate in selective synthesis of graphene and carbon nanotube on Fe foil using hot filament chemical vapor deposition

In this study, graphene sheets and carbon nanotubes (CNTs) were selectively grown on Fe foil at a relatively low growth temperature and varying cooling rates using a hot filament chemical vapor deposition (HFCVD) apparatus with C2H2 as the precursor. The results of the scanning electron microscopy and Raman spectroscopy revealed that the increase of the cooling rate from 7 to 10 or 20 °C/min provoked a structure transition from CNT to graphene. The optimum crystal quality of the graphene sheets (IG/ID ~1.1) was achieved at the cooling rate of 20 °C/min. According to the AFM analysis, the thickness of the stacked graphene sheets was found to be ~2.9-3.8 nm containing ~8-11 monolayers. The XRD profiles suggest the coexistence of graphene, graphene oxide, and Fe3C structures on Fe foil.