18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired-end (PE; 2 9 150 bp) technology. To critically evaluate the method's performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual-based diet analysis methods. The high sensitivity and semi-quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR-based results. This molecular approach provides an alternative cost and time effective tool for food-web analysis.

Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels.

In this paper, we demonstrate for the first time that insulative dielectrophoresis can induce size-dependent trajectories of DNA macromolecules. We experimentally use lambda (48.5 kbp) and T4GT7 (165.6 kbp) DNA molecules flowing continuously around a sharp corner inside fluidic channels with a depth of 0.4 mum. Numerical simulation of the electrokinetic force distribution inside the channels is in qualitative agreement with our experimentally observed trajectories. We discuss a possible physical mechanism for the DNA polarization and dielectrophoresis inside confining channels, based on the observed dielectrophoresis responses due to different DNA sizes and various electric fields applied between the inlet and the outlet. The proposed physical mechanism indicates that further extensive investigations, both theoretically and experimentally, would be very useful to better elucidate the forces involved at DNA dielectrophoresis. When applied for size-based sorting of DNA molecules, our sorting method offers two major advantages compared to earlier attempts with insulative dielectrophoresis: Its continuous operation allows for high-throughput analysis, and it only requires electric field strengths as low as approximately 10 Vcm.

Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks(1-3), the extent to which genetic epistasis reflects biologically meaningful interactions remains unclear(4-6). We have addressed this question through in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant and, unexpectedly, often occurs between reactions without overlapping functions. We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Hierarchical electrohydrodynamic structures for surface-enhanced Raman scattering.

Surface enhanced Raman scattering (SERS) is a well-established spectroscopic technique that requires nanoscale metal structures to achieve high signal sensitivity. While most SERS substrates are manufactured by conventional lithographic methods, the development of a cost-effective approach to create nanostructured surfaces is a much sought-after goal in the SERS community. Here, a method is established to create controlled, self-organized, hierarchical nanostructures using electrohydrodynamic (HEHD) instabilities. The created structures are readily fine-tuned, which is an important requirement for optimizing SERS to obtain the highest enhancements. HEHD pattern formation enables the fabrication of multiscale 3D structured arrays as SERS-active platforms. Importantly, each of the HEHD-patterned individual structural units yield a considerable SERS enhancement. This enables each single unit to function as an isolated sensor. Each of the formed structures can be effectively tuned and tailored to provide high SERS enhancement, while arising from different HEHD morphologies. The HEHD fabrication of sub-micrometer architectures is straightforward and robust, providing an elegant route for high-throughput biological and chemical sensing.

Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

Gamma-ray spectroscopy at TRIUMF-ISAC

The 8π spectrometer at TRIUMF-ISAC consists of 20 Compton-suppressed germanium detectors and various auxiliary devices. The Ge array, once used for studies of nuclei at high angular momentum, has been transformed into the world's most powerful device dedicated to radioactive-decay studies. Many improvements in the spectrometer have been made, including a high-throughput data acquisition system, installation of a moving tape collector, incorporation of an array of 20 plastic scintillators for β-particle tagging, 5 Si(Li) detectors for conversion electrons, and 10 BaF2 detectors for fast-lifetime measurements. Experiments can be performed where data from all detectors are collected simultaneously, resulting in a very detailed view of the nucleus through radioactive decay. A number of experimental programmes have been launched that take advantage of the versatility of the spectrometer, and the intense beams available at TRIUMF-ISAC. © 2006 American Institute of Physics.

Theoretical and experimental analysis of pneumatic balloon microactuators

This paper presents a theoretical and experimental analysis of a biologically inspired balloon-type pneumatic microactuator. The operation principle of pneumatic balloon actuators (PBA's) is based on an asymmetric deflection of two PDMS layers with different thicknesses or different Young's moduli that are bonded together. A new analytical 2D model that describes the complex behavior of these actuators is presented and validated using both 3D FEM models and measurements. The actuators have dimensions ranging from 11 mm × 2 mm × 0.24 mm to 4 mm × 1 mm × 0.12 mm. Their fabrication is based on micromolding of PDMS, and can therefore easily be fabricated in high throughput. Measurements showed that the analytical model provides a qualitative description of the actuator behavior, and showed that the larger actuators are capable of delivering a 7 mm stroke at a supply pressure of 70 kPa and a force of max 22 mN at a supply pressure of 105 kPa. © 2011 Elsevier B.V. All rights reserved.

On-chip switching of a silicon nitride micro-ring resonator based on digital microfluidics platform.

We demonstrate the switching of a silicon nitride micro ring resonator (MRR) by using digital microfluidics (DMF). Our platform allows driving micro-droplets on-chip, providing control over the effective refractive index at the vicinity of the resonator and thus facilitating the manipulation of the transmission spectrum of the MRR. The device is fabricated using a process that is compatible with high-throughput silicon fabrication techniques with buried highly doped silicon electrodes. This platform can be extended towards controlling arrays of micro optical devices using minute amounts of liquid droplets. Such an integration of DMF and optical resonators on chip can be used in variety of applications, ranging from biosensing and kinetics to tunable filtering on chip.

Band gap opening of graphene after UV/ozone and oxygen plasma treatments

Graphene grown by Chemical Vapor Deposition (CVD) on nickel subsrate is oxidized by means of oxygen plasma and UV/Ozone treatments to introduce bandgap opening in graphene. The degree of band gap opening is proportional to the degree of oxidation on the graphene. This result is analyzed and confirmed by Scanning Tunnelling Microscopy/Spectroscopy and Raman spectroscopy measurements. Compared to conventional wet-oxidation methods, oxygen plasma and UV/Ozone treatments do not require harsh chemicals to perform, allow faster oxidation rates, and enable site-specific oxidation. These features make oxygen plasma and UV/Ozone treatments ideal candidates to be implemented in high-throughput fabrication of graphene-based microelectronics. © 2011 Materials Research Society.

A Simplified Soft-output QRD-M MIMO Detector

In this paper, a low-complexity soft-output QRD-M detection algorithm is proposed for high-throughput Multiple-input multiple-output (MIMO) systems. By employing novel expansion on demand and distributed sorting scheme, the proposed algorithm can reduce 70% and 85% foundational operations for 16-QAM and 64-QAM respectively compared to the conventional QRD-M algorithm. Furthermore, the proposed algorithm can yield soft information to improve the bit error rate (BER) performance. Simulation results show that the proposed algorithm can achieve a near-NIL detection performance with less foundational operations

Selective and lithography-independent fabrication of 20 nm nano-gap electrodes and nano-channels for nanoelectrofluidics applications

A new method has been developed to selectively fabricate nano-gap electrodes and nano-channels by conventional lithography. Based on a sacrificial spacer process, we have successfully obtained sub-100-nm nano-gap electrodes and nano-channels and further reduced the dimensions to 20 nm by shrinking the sacrificial spacer size. Our method shows good selectivity between nano-gap electrodes and nano-channels due to different sacrificial spacer etch conditions. There is no length limit for the nano-gap electrode and the nano-channel. The method reported in this paper also allows for wafer scale fabrication, high throughput, low cost, and good compatibility with modern semiconductor technology.

Multi-wafer 3C-SiC heteroepitaxial growth on Si(100) substrates

Epitaxial growth of semiconductor films in multiple-wafer mode is under vigorous development in order to improve yield output to meet the industry increasing demands. Here we report on results of the heteroepitaxial growth of multi-wafer 3C-SiC films on Si(100) substrates by employing a home-made horizontal hot wall low pressure chemical vapour deposition (HWLPCVD) system which was designed to be have a high-throughput, multi-wafer (3x2-inch) capacity. 3C-SiC film properties of the intra-wafer and the wafer-to-wafer including crystalline morphologies, structures and electronics are characterized systematically. The undoped and the moderate NH3 doped n-type 3C-SiC films with specular surface are grown in the HWLPCVD, thereafter uniformities of intra-wafer thickness and sheet resistance of the 3C-SiC films are obtained to be 6%similar to 7% and 6.7%similar to 8%, respectively, and within a run, the deviations of wafer-to-wafer thickness and sheet resistance are less than 1% and 0.8%, respectively.