ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles

<p>Abstract</p> <p>Background</p> <p>Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organisms. For the common carp, an environmental model of aquacultural interest, large numbers of ESTs remained unidentified using BLAST sequence alignment. We have used the expression profiles from large-scale microarray experiments to suggest gene identities.</p> <p>Results</p> <p>Expression profiles from ~700 cDNA microarrays describing responses of 7 major tissues to multiple environmental stressors were used to define a co-expression landscape. This was based on the Pearsons correlation coefficient relating each gene with all other genes, from which a network description provided clusters of highly correlated genes as 'mountains'. We show that these contain genes with known identities and genes with unknown identities, and that the correlation constitutes evidence of identity in the latter. This procedure has suggested identities to 522 of 2701 unknown carp ESTs sequences. We also discriminate several common carp genes and gene isoforms that were not discriminated by BLAST sequence alignment alone. Precision in identification was substantially improved by use of data from multiple tissues and treatments.</p> <p>Conclusion</p> <p>The detailed analysis of co-expression landscapes is a sensitive technique for suggesting an identity for the large number of BLAST unidentified cDNAs generated in EST projects. It is capable of detecting even subtle changes in expression profiles, and thereby of distinguishing genes with a common BLAST identity into different identities. It benefits from the use of multiple treatments or contrasts, and from the large-scale microarray data.</p

SCOTT: A Martian Moon Exploration Excursion Vehicle FDR

In recent years, the development of space exploration and technologies has been brought to attention with a focus on the planet Mars. With this, many companies have set out to develop space vehicles for space and surface excursions of Mars and Mars’s moons, Phobos and Deimos. With Mars being a location for human civilization to inhabit, a look into the best solutions for travel to Mars has been developed. The solution of focus that has been developed and presented by NASA (National Aeronautics and Space Administration) is to imply an incremental exploration approach. In this solution, a focus is brought to developing bases on Mars’s moons Phobos and Deimos. To first begin this process of building bases on the moons of Mars, frequent missions to the surfaces of both moons are required. With the goal of building bases on the surfaces of Phobos and Deimos, NASA has set out in search of space technologies to fulfill the task at hand. The technologies in need for NASA’s plans are a surface rover, as well as a transporter for the rover. Presented in this document are developments for the space rover and transporter for the rover. With an already existing model for the surface rover designed by NASA, the surface rover presented in this paper will take similar aspects from this rover as well as presenting innovative technologies the rover shall acquire. As for the transporter, innovative ideas and technologies are presented to solve various issues when embarking on such travels to the surfaces of both moons. A few concerns focused on this paper when considering the surface rover are traction from the rover, living space, payload capabilities, and maneuverability of the rover while on the surface. A few concerns regarding the rover transporter are propulsion systems, docking systems, and safety of the rover while being joined in transportation. The value of the solutions presented in this document range from simple solutions for safety hazards, to solutions for the complete exploration by humans of Mars and the moons of Mars. When considering the expansion of human civilization, each step in progressing the technologies to make humans multiplanetary is of the utmost importance. Presented in this document are solutions focused on the excursions of both Phobos and Deimos but are not limited to the singular goals given by NASA

Rapid cell extraction in aqueous two-phase microdroplet systems

Distinguishing specific cells is an essential technique in cell research and clinical diagnostics. We report a novel method to passively isolate and extract cells in a microfluidic device. We utilise a droplet-based microfluidic system to generate an aqueous two phase system in which aqueous droplets consist of two phases in the form of a double emulsion. Specifically, we generate PEG droplets that completely encapsulate DEX droplets within a microfluidic channel. Target cells can be introduced directly into the droplets and driven to partition to the more favourable phase, whilst still being contained within the aqueous droplet. Human T lymphoma cells, with diameters in the range of 10–15 μm, are chosen as a model cell line to demonstrate the partitioning

Filter Bank Multi-Sub-Band Transmission for Optical Systems with Mode Multiplexing

Mode-multiplexed optical transmission is subject to mode coupling and potentially large differential mode delays. In most recent implementations, these effects are compensated for at the receiver by complex adaptive multiple-input multiple-output (MIMO) equalizers. Although frequency-domain MIMO equalization requires a moderate complexity compared to time-domain equalization, the long required fast Fourier transforms may face implementation issues. In this paper, we evaluate an alternative transceiver architecture based on sub-band partitioning, implemented by filter banks, which enables concurrent time-domain equalization. Single-carrier (SC) and multi-sub-band (MSB) mode division multiplexing transmission are simulated using frequency-domain equalization and time-domain equalization, respectively. Their performance is compared in terms of static transmission performance, channel tracking capability, phase noise tolerance, and computational complexity. The results indicate that compared with an equivalent SC solution, the MSB architecture provides a high degree of parallelism at the cost of a penalty of 0.7-1.3 dB for a laser linewidth of 25-100 kHz and a moderate increase in complexity

OLIA: An open-source digital lock-in amplifier

The Open Lock-In Amplifier (OLIA) is a microcontroller-based digital lock-in amplifier built from a small number of inexpensive and easily sourced electronic components. Despite its small credit card-sized form-factor and low build-cost of around US$35, OLIA is a capable instrument that offers many features associated with far costlier commercial devices. Key features include dual-phase lock-in detection at multiple harmonic frequencies up to 50 kHz, internal and external reference modes, adjustable levels of input gain, a choice between low-pass filtering and synchronous filtering, noise estimation, and a comprehensive programming interface for remote software control. OLIA comes with an optional optical breakout board that allows noise-tolerant optical detection down to the 40-pW level. OLIA and its breakout board are released here as open hardware, with technical diagrams, full parts-lists, and source-code for the firmware

Oriented Cell Growth on Self-Assembled Bacteriophage M13 Thin Films

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions

Farmers Markets and the Local Food System: The Case of Gettysburg, Pennsylvania

In order to examine and obtain a better understanding of the local food system within Adams County, Pennsylvania, this study explores the characteristics and perspectives of the customers and vendors at the farmers markets in Gettysburg, Pennsylvania. Survey findings from the Gettysburg Farmers Market and the three Adams County Farmers Markets include customer demographic information, perspectives and shopping behavior as well as vendor product information, farm size and location and preference for market management. Introductory background information on the Farm Bill and the influence of agricultural practices on the environment, human health and nutrition and the relationship between farmers markets and the local economy are offered in order to emphasize the value of a well-managed local food system. Conclusions provide evidence that lower income and lower education levels are not sufficiently represented at all the markets and food stamp programs are being underutilized. This study suggests employing additional marketing to target underrepresented demographic groups, public transportation to potentially inaccessible market locations and increased advertisement and encouragement of food stamp programs at all markets in order to expand the customer base and increase access to healthy, local foods for less advantaged citizens. The results from this study are intended to offer evidence that will promote and facilitate market management, strengthen customer/vendor relationships and encourage better ties between the local community and local food systems at the farmers markets within Gettysburg in Adams County, Pennsylvania

Inducible systemic RNA silencing in Caenorhabditis elegans

Introduction of double-stranded RNA (dsRNA) can elicit a gene-specific RNA interference response in a variety of organisms and cell types. In many cases, this response has a systemic character in that silencing of gene expression is observed in cells distal from the site of dsRNA delivery. The molecular mechanisms underlying the mobile nature of RNA silencing are unknown. For example, although cellular entry of dsRNA is possible, cellular exit of dsRNA from normal animal cells has not been directly observed. We provide evidence that transgenic strains of Caenorhabditis elegans transcribing dsRNA from a tissue-specific promoter do not exhibit comprehensive systemic RNA interference phenotypes. In these same animals, modifications of environmental conditions can result in more robust systemic RNA silencing. Additionally, we find that genetic mutations can influence the systemic character of RNA silencing in C. elegans and can separate mechanisms underlying systemic RNA silencing into tissue-specific components. These data suggest that trafficking of RNA silencing signals in C. elegans is regulated by specific physiological and genetic factors