A New Cell-Selective Three-Dimensional Microincubator Based on Silicon Photonic Crystals

In this work, we show that vertical, high aspect-ratio (HAR) photonic crystals (PhCs), consisting of periodic arrays of 5 µm wide gaps with depth of 50 µm separated by 3 µm thick silicon walls, fabricated by electrochemical micromachining, can be used as three-dimensional microincubators, allowing cell lines to be selectively grown into the gaps. Silicon micromachined dice incorporating regions with different surface profiles, namely flat silicon and deeply etched PhC, were used as microincubators for culturing adherent cell lines with different morphology and adhesion properties. We extensively investigated and compared the proliferative behavior on HAR PhCs of eight human cell models, with different origins, such as the epithelial (SW613-B3; HeLa; SW480; HCT116; HT29) and the mesenchymal (MRC-5V1; CF; HT1080). We also verified the contribution of cell sedimentation into the silicon gaps. Fluorescence microscopy analysis highlights that only cell lines that exhibit, in the tested culture condition, the behavior typical of the mesenchymal phenotype are able to penetrate into the gaps of the PhC, extending their body deeply in the narrow gaps between adjacent silicon walls, and to grow adherent to the vertical surfaces of silicon. Results reported in this work, confirmed in various experiments, strongly support our statement that such three-dimensional microstructures have selection capabilities with regard to the cell lines that can actively populate the narrow gaps. Cells with a mesenchymal phenotype could be exploited in the next future as bioreceptors, in combination with HAR PhC optical transducers, e.g., for label-free optical detection of cellular activities involving changes in cell adhesion and/or morphology (e.g., apoptosis) in a three-dimensional microenvironment.     

DNA Tetrominoes: The Construction of DNA Nanostructures Using Self-Organised Heterogeneous Deoxyribonucleic Acids Shapes

The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner.     

Fabrication,Densification, and Replica Molding of 3D Carbon Nanotube Microstructures

The introduction of new materials and processes to microfabrication has, in large part, enabled many important advances in microsystems, lab-on-a-chip devices, and their applications. In particular, capabilities for cost-effective fabrication of polymer microstructures were transformed by the advent of soft lithography and other micromolding techniques ^{1, 2}, and this led a revolution in applications of microfabrication to biomedical engineering and biology. Nevertheless, it remains challenging to fabricate microstructures with well-defined nanoscale surface textures, and to fabricate arbitrary 3D shapes at the micro-scale. Robustness of master molds and maintenance of shape integrity is especially important to achieve high fidelity replication of complex structures and preserving their nanoscale surface texture. The combination of hierarchical textures, and heterogeneous shapes, is a profound challenge to existing microfabrication methods that largely rely upon top-down etching using fixed mask templates. On the other hand, the bottom-up synthesis of nanostructures such as nanotubes and nanowires can offer new capabilities to microfabrication, in particular by taking advantage of the collective self-organization of nanostructures, and local control of their growth behavior with respect to microfabricated patterns. Our goal is to introduce vertically aligned carbon nanotubes (CNTs), which we refer to as CNT "forests", as a new microfabrication material. We present details of a suite of related methods recently developed by our group: fabrication of CNT forest microstructures by thermal CVD from lithographically patterned catalyst thin films; self-directed elastocapillary densification of CNT microstructures; and replica molding of polymer microstructures using CNT composite master molds. In particular, our work shows that self-directed capillary densification ("capillary forming"), which is performed by condensation of a solvent onto the substrate with CNT microstructures, significantly increases the packing density of CNTs. This process enables directed transformation of vertical CNT microstructures into straight, inclined, and twisted shapes, which have robust mechanical properties exceeding those of typical microfabrication polymers. This in turn enables formation of nanocomposite CNT master molds by capillary-driven infiltration of polymers. The replica structures exhibit the anisotropic nanoscale texture of the aligned CNTs, and can have walls with sub-micron thickness and aspect ratios exceeding 50:1. Integration of CNT microstructures in fabrication offers further opportunity to exploit the electrical and thermal properties of CNTs, and diverse capabilities for chemical and biochemical functionalization ³.     

First results on label-free detection of DNA and protein molecules using a novel integrated sensor technology based on gravimetric detection principles

A novel integrated bio-sensor technology based on thin-film bulk acoustic wave resonators on silicon is presented and the feasibility of detecting DNA and protein molecules proofed. The detection principle of these sensors is label-free and relies on a resonance frequency shift caused by mass loading of an acoustic resonator, a principle very well known from quartz crystal micro balances. Integrated ZnO bulk acoustic wave resonators with resonance frequencies around 2 GHz have been fabricated, employing an acoustic mirror for isolation from the silicon substrate. DNA oligos have been thiol-coupled to the gold electrode by on-wafer dispensing. In a further step, samples have either been hybridised or alternatively a protein has been coupled to the receptor. The measurement results show the new bio-sensor being capable of both, detecting proteins as well as the DNA hybridisation without using a label. Due to the substantially higher oscillation frequency, these sensors already show much higher sensitivity and resolution comparable to quartz crystal micro balances. The potential for these sensors and sensors arrays as well as technological challenges will be discussed in detail.     

REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query

Genes occupy ~3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes.     

Surface-Enhanced Resonance Raman Scattering (SERRS) Using Au Nanohole Arrays on Optical Fiber Tips

Circular and bow tie-shaped Au nanoholes arrays were fabricated on gold films deposited on the tips of single-mode optical fibers. The nanostructures were milled using focused ion beam with a high quality control of their shapes and sizes. The optical fiber devices were used for surface-enhanced resonance Raman scattering (SERRS) measurements in both back- and forward-scattering geometries, yielding promising performance in both detection arrangements. The effect of the hole shape on the SERRS performance was explored with the bow tie nanostructures presenting a better SERRS performance than the circular holes arrays. The results present here are another step towards the development of optical fiber tips modified with plasmonic nanostructures for SERRS applications.

Recombinational telomere elongation promoted by DNA circles

Yeast mutants lacking telomerase are capable of maintaining telomeres by an alternate mechanism that depends on homologous recombination. We show here, by using Kluyveromyces lactis cells containing two types of telomeric repeats, that recombinational telomere elongation generates a repeating pattern common in most or all telomeres in survivors that retain both repeat types. We propose that these patterns arise from small circles of telomeric DNA being used as templates for rolling-circle gene conversion and that the sequence from the lengthened telomere is spread to other telomeres by additional, more typical gene conversion events. Consistent with this, artificially constructed circles of DNA containing telomeric repeats form long tandem arrays at telomeres when transformed into K. lactis cells. Mixing experiments done with two species of telomeric circles indicated that all of the integrated copies of the transforming sequence arise from a single original circular molecule.     

Design,Surface Treatment,Cellular Plating,and Culturing of Modular Neuronal Networks Composed of Functionally Inter-connected Circuits

The brain operates through the coordinated activation and the dynamic communication of neuronal assemblies. A major open question is how a vast repertoire of dynamical motifs, which underlie most diverse brain functions, can emerge out of a fixed topological and modular organization of brain circuits. Compared to in vivo studies of neuronal circuits which present intrinsic experimental difficulties, in vitro preparations offer a much larger possibility to manipulate and probe the structural, dynamical and chemical properties of experimental neuronal systems. This work describes an in vitro experimental methodology which allows growing of modular networks composed by spatially distinct, functionally interconnected neuronal assemblies. The protocol allows controlling the two-dimensional (2D) architecture of the neuronal network at different levels of topological complexity.A desired network patterning can be achieved both on regular cover slips and substrate embedded micro electrode arrays. Micromachined structures are embossed on a silicon wafer and used to create biocompatible polymeric stencils, which incorporate the negative features of the desired network architecture. The stencils are placed on the culturing substrates during the surface coating procedure with a molecular layer for promoting cellular adhesion. After removal of the stencils, neurons are plated and they spontaneously redirected to the coated areas. By decreasing the inter-compartment distance, it is possible to obtain either isolated or interconnected neuronal circuits. To promote cell survival, cells are co-cultured with a supporting neuronal network which is located at the periphery of the culture dish. Electrophysiological and optical recordings of the activity of modular networks obtained respectively by using substrate embedded micro electrode arrays and calcium imaging are presented. While each module shows spontaneous global synchronizations, the occurrence of inter-module synchronization is regulated by the density of connection among the circuits.     

Replication and mutation on neutral networks

Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely defined base pairing pattern to every sequence. The mapping is non-invertible since many sequences fold into the same minimum free energy (secondary) structure or shape. The pre-images of this map, called neutral networks, are uniquely associated with the shapes and vice versa. Random graph theory is used to construct networks in sequence space which are suitable models for neutral networks. The theory of molecular quasispecies has been applied to replication and mutation on single-peak fitness landscapes. This concept is extended by considering evolution on degenerate multi-peak landscapes which originate from neutral networks by assuming that one particular shape is fitter than all the others. On such a single-shape landscape the superior fitness value is assigned to all sequences belonging to the master shape. All other shapes are lumped together and their fitness values are averaged in a way that is reminiscent of mean field theory. Replication and mutation on neutral networks are modeled by phenomenological rate equations as well as by a stochastic birth-and-death model. In analogy to the error threshold in sequence space the phenotypic error threshold separates two scenarios: (i) a stationary (fittest) master shape surrounded by closely related shapes and (ii) populations drifting through shape space by a diffusion-like process. The error classes of the quasispecies model are replaced by distance classes between the master shape and the other structures. Analytical results are derived for single-shape landscapes, in particular, simple expressions are obtained for the mean fraction of master shapes in a population and for phenotypic error thresholds. The analytical results are complemented by data obtained from computer simulation of the underlying stochastic processes. The predictions of the phenomenological approach on the single-shape landscape are very well reproduced by replication and mutation kinetics of tRNA(phe). Simulation of the stochastic process at a resolution of individual distance classes yields data which are in excellent agreement with the results derived from the birth-and-death model.     

Controlled Synthesis and Energy Applications of One‐Dimensional Conducting Polymer Nanostructures: An Overview

The past decade has witnessed increasing attention in the synthesis, properties, and applications of one‐dimensional (1D) conducting polymer nanostructures. This overview first summarizes the synthetic strategies for various 1D nanostructures of conjugated polypyrrole (PPy), polyaniline (PANI), polythiophene (PTh), poly(p‐phenylenevinylene) (PPV) and derivatives thereof. By using template‐directed or template‐free methods, nanoscale rods, wires/fibers, belts/ribbons, tubes, arrays, or composites have been successfully synthesized. With their unique structures and advantageous characteristics (e.g., high conductivity, high carrier mobility, good electrochemical activity, large specific surface area, short and direct path for charge/ion transportation, good mechanical properties), 1D conducting polymer nanostructures are demonstrated to be very useful for energy applications. Next, their applications in solar cells, fuel cells, rechargeable lithium batteries, and electrochemical supercapacitors are highlighted, with a strong emphasis on recent literature examples. Finally, this review ends with a summary and some perspectives on the challenges and opportunities in this emerging area of research.     

Recent Development of Ni/Fe‐Based Micro/Nanostructures toward Photo/Electrochemical Water Oxidation

The oxygen evolution reaction (OER), as an important process involved in water splitting and rechargeable metal–air batteries, has drawn increasing attention in the context of clean energy generation and efficient energy storage. This review concerns the progress and new discoveries in the field of Ni/Fe‐based micro/nanostructures toward electrochemical and photo‐electrochemical (PEC) water oxidation during last few years. First, toward the design and construction of new electrocatalysis, different types of current Ni/Fe‐based compounds for OER are summarized. The mechanism studies of the active phases and positions of Ni/Fe‐based micro/nanostructures are further introduced to understand the properties of catalytic active sites, which could facilitate further improving the performance of Ni/Fe‐based OER electrocatalysts. Second, splitting water using sunlight with low overpotential is another important target in making solar‐to‐hydrogen micro/nanodevices, and thus attention is then focused on the development of several important Ni/Fe‐based PEC catalysts. Third, the recent theoretical calculations on the OER mechanism during water splitting and insights into electronic structures are analyzed; finally, the future trends and perspectives are also discussed briefly.     

Profile Simulation and Fabrication of Gold Nanostructures by Separated Nanospheres with Oblique Deposition and Perpendicular Etching

This paper investigates in detail the profiles of the nanostructures fabricated by nanosphere lithography through oblique deposition and perpendicular etching. 2D or 3D nanostructures can be achieved by this cost-effective method. Because the optical response of a particular nanoparticle depends on its size and shape, this angle deposition method can produce various shapes of nanostructures, which are suitable for localized surface plasmon resonance biosensor applications. The nanostructure profiles under various deposition and etching conditions are simulated in our work. The calculated 3D profiles are verified by the 3D nanostructures fabricated in our experiments, and the calculated 2D profiles are in good agreement with the fabricated nanocrescents reported by another research group. This paper gives a full theoretical solution of the obtainable nanostructure shapes by nanosphere lithography utilizing oblique deposition and perpendicular etching.     

Influence of Substrate on Plasmon-Induced Absorption Enhancements

A set of periodic plasmonic nanostructures is designed and fabricated as a means to investigate light absorption in single-crystal silicon thin-film structures with silicon-on-insulator (SOI) wafers as a model system. It is shown both computationally and experimentally that plasmon-induced absorption enhancement is remarkably higher for such devices than for thick or semi-infinite structures or for the thin-film amorphous silicon solar cells reported in the literature. Experimental photocurrent enhancements of the orders of 12 and 20 are demonstrated for non-optimized 2200-nm-thick photoconductive and 300-nm-thick photovoltaic test structures, respectively. Theoretical absorption enhancements as high as 80 are predicted to be achievable for the similar structures. The features of the spectral enhancements observed are attributed to several interacting resonance phenomena: not just to the favourable scattering of light by the periodic plasmonic nanoparticle arrays into the SOI device layer and coupling to the waveguide modes interacting with the plasmonic array but also to the Fabry-Pérot type interferences in the layered structure. We show that the latter effect gives a significant contribution to the spectral features of the enhancements, although frequently ignored in the discussions of previous reports.

     

Hyperacute rejection by anti-Gal IgG1, IgG2a, and IgG2b is dependent on complement and Fc-gamma receptors

We have previously reported that anti-Gal-alpha1,3Gal (Gal) IgG3 mAbs mediate a classical complement-dependent hyperacute rejection (HAR), while anti-Gal IgG1 mAbs mediate HAR that is dependent on complement, the Fc-gamma receptors FcgammaRII/III (CD32/CD16), and NK cells. IgG2a and IgG2b subclasses can activate complement and have FcgammaR binding properties in vitro. Whether these IgG subclasses can mediate HAR in vivo and the mechanisms by which they would do so are not known. In this study, we isolated spontaneous IgG switch mutants from an anti-Gal IgG1 hybridoma. In vitro complement-mediated hemolytic assays with mouse complement indicate that both anti-Gal IgG2a and IgG2b mAbs were more potent compared with the parent anti-Gal IgG1. In vivo administration of anti-Gal IgG2a and IgG2b mAbs into Gal-/- mice induced HAR of rat cardiac xenografts. HAR induced by anti-Gal IgG2a and IgG2b was dependent on complement activation and the presence of NK cells. Using FcgammaRIII-deficient (Gal-/-CD16-/-) recipients, we observed that HAR mediated by different anti-Gal IgG subclasses was variably dependent on FcgammaRIII, with IgG1>IgG2b>IgG2a=IgG3. Using FcgammaRI-deficient (Gal-/-CD64-/-) recipients, we observed that HAR mediated by anti-Gal IgG1, IgG2a, and IgG2b, but not by anti-Gal IgG3, was dependent on FcgammaRI. Collectively, these studies demonstrate the necessity and sufficiency of complement in IgG3-mediated HAR and the necessity of both complement and FcgammaR, especially FcgammaRI, in IgG1-, IgG2a-, and IgG2b-mediated HAR.     

Metal Sulfide Hollow Nanostructures for Electrochemical Energy Storage

Metal sulfide hollow nanostructures (MSHNs) have received intensive attention as electrode materials for electrical energy storage (EES) systems due to their unique structural features and rich chemistry. Here, we summarize recent research progress in the rational design and synthesis of various metal sulfide hollow micro‐/nanostructures with controlled shape, composition and structural complexity, and their applications to lithium ion batteries (LIBs) and hybrid supercapacitors (HSCs). The current understanding of hollow structure control, including single‐shelled, yolk‐shelled, multi‐shelled MSHNs, and their hybrid micro‐/nanostructures with carbon (amorphous carbon nanocoating, graphene and hollow carbon), is focused on. The importance of proper structural and compositional control on the enhanced electrochemical properties of MSHNs is emphasized. A relationship between structural and compositional engineering with improved electrochemical activity of MSHNs is sought, in order to shed some light on future electrode design trends for next‐generation EES technologies.     

Microcontact printing of axon guidance molecules for generation of graded patterns

Microcontact printing (microCP) of proteins has been successfully used for patterning surfaces in various contexts. Here we describe a simple 'lift-off' method to print precise patterns of axon guidance molecules, which are used as substrate for growing chick retinal ganglion cell (RGC) axons. Briefly, the etched pattern of a silicon master is transferred to a protein-coated silicone cuboid (made from polydimethylsiloxane, PDMS), which is then used as a stamp on a glass coverslip. RGC explants are placed adjacent to the pattern and cultured overnight. Fluorescent labeling of the printed proteins allows the quantitative analysis of the interaction of axons and growth cones with single protein dots and of the overall outgrowth and guidance rate in variously designed patterns. Patterned substrates can be produced in 3-4 h and are stable for up to one week at 4 degrees C; the entire protocol can be completed in 3 d.     

Creation of low-copy integrated transgenic lines in Caenorhabditis elegans

In Caenorhabditis elegans, transgenic lines are typically created by injecting DNA into the hermaphrodite germline to form multicopy extrachromosomal DNA arrays. This technique is a reliable means of expressing transgenes in C. elegans, but its use has limitations. Because extrachromosomal arrays are semistable, only a fraction of the animals in a transgenic extrachromosomal array line are transformed. In addition, because extrachromosomal arrays can contain hundreds of copies of the transforming DNA, transgenes may be overexpressed, misexpressed, or silenced. We have developed an alternative method for C. elegans transformation, using microparticle bombardment, that produces single- and low-copy chromosomal insertions. Using this method, we find that it is possible to create integrated transgenic lines that reproducibly express GFP reporter constructs without the variations in expression level and pattern frequently exhibited by extrachromosomal array lines. In addition, we find that low-copy integrated lines can also be used to express transgenes in the C. elegans germline, where conventional extrachromosomal arrays typically fail to express due to germline silencing.     

Fabrication and Characterization of Large, Perfectly Periodic Arrays of Metallic Nanocups

Fabrication of plasmonic resonance devices composed of large arrays of highly ordered gold nanocups is presented. The nanostructures are generated from periodic photoresist templates created by interference lithography and subsequent reflow, deposition, and dislodging. The nanocups are hemispherical in shape and arranged in both rectangular and hexagonal arrays with periods of ~500?nm. Their ability to support surface plasmonic resonances is manifested experimentally by reflectance spectroscopy. Theoretical modeling to ascertain the plasmonic spectra of these nanostructures is performed. The computed spectra of the rectangular structure are in qualitative agreement with the measurements. A weaker correlation observed for the hexagonal structure is explained by its more intricate symmetry which complicates the spectral response.     

Influences of Nanostructure Arrays on Light Absorption in Amorphous Silicon Thin-Film Solar Cells

By means of finite-difference time-domain (FDTD) numerical method, we investigate the possibility to enhance the light absorption in solar cells by employing different nanostructures. The solar cells are made of 100-nm-thick amorphous silicon (α-Si). The impacts of gold nanohole arrays, dielectric nanosphere arrays, and gold nanoparticle arrays on the light absorption are simulated, compared, and analyzed. The results show that gold nanohole arrays functioning as the back reflective layer, dielectric nanosphere arrays, and gold nanoparticle arrays can significantly enhance the light absorption for the solar cells, and the former two can increase the short-circuit current by more than 40 %, showing a great potential to improve the utilization efficiency of solar energy.