A high speed data acquisition system

Digital systems pervade the world around us. The interface between analogue data sources and these digital systems is the realm of analogue to digital converters (ADCs) that acquire digital snap-shots of data for further processing. Some applications require high sampling rates or high resolution data (or both). In addition to this, certain applications require the capture of large amounts of data. A good example of an application requiring a high sampling rate and high resolution data, is a digital spectrum analyser used to analyse large bands of a spectrum and offer precise results. Radar systems such as synthetic aperture radars use post-processing techniques on large quantities of data. A developing field requiring versatile data capture systems is that of software defined radio (SDR). It is a collection of hardware and software technologies that enable reconfigurable system architectures for wireless networks and user terminals. This document gives details on a project to build a high speed, high resolution data acquisition system that is capable of performing to some of the most stringent requirements. Specifically, this thesis documents the design, implementation and testing of firmware implemented in an FPGA in a commercial data capture card as part of the system. This firmware would facilitate the real-time transfer of captured data to RAM in a host PC

Alien Registration- Martens, Andrew (Mattawamkeag, Penobscot County)

https://digitalmaine.com/alien_docs/8276/thumbnail.jp

Paths to Fisheries Subsidies Reform: Creating Sustainable Fisheries Through Trade and Economics

The world depends on the oceans for food and livelihood. More than a billion people worldwide depend on fish as a source of protein, including some of the poorest populations on earth. According to the United Nations Food and Agriculture Organization (FAO), the world must produce 70 percent more food to meet coming hunger needs.Fishing activities support coastal communities and hundreds of millions of people who depend on fishing for all or part of their income. Of the world's fishers, more than 95 percent engage in small-scale and artisanal activity and catch nearly the same amount of fish for human consumption as the highly capitalized industrial sector. Small-scale and artisanal fishing produces a greater return than industrial operations by unit of input, investment in catch, and number of people employed.Today, overfishing and other destructive fishing practices have severely decreased the world's fish populations. The FAO estimates that 90 percent of marine fisheries worldwide are now overexploited, fully exploited, significantly depleted, or recovering from overexploitation

Improving the sustainability of global meat and milk production

Global demand for meat and dairy products has increased dramatically in recent decades and, through a combination of global population growth, increased lifespan and improved economic prosperity in the developing world will inevitably continue to increase. The predicted increases in livestock production will put a potentially unsustainable burden on global resources, including land for production of crops required for animal feed and fresh water. Furthermore, animal production itself is associated with greenhouse gas production, which may speed up global warming and thereby impact on our ability to produce food. There is, therefore, an urgent need to find methods to improve the sustainability of livestock production. This review will consider various options for improving the sustainability of livestock production with particular emphasis on finding ways to replace conventional crops as sources of animal feeds. Alternatives, such as currently under-utilized crops (grown on marginal land) and insects, reared on substrates not suitable for direct consumption by farm animals, represent possible solutions. Coupled with a moderation of excessive meat consumption in wealthier countries, such strategies may secure the long-term sustainability of meat and milk production and mitigate against the adverse health effects of excessive intake

Synonymous codons affect polysome spacing, protein production and protein folding stress: studies of bacterial translation using ribosome profiling

The acquisition of protein secondary and tertiary structure depends on the primary sequence of amino acids. However, predicting a protein's folded structure is difficult even with the knowledge of its sequence. It has been suggested that, in addition to encoding the amino acid sequence, genes also encode kinetic information which regulates the ribosome's translation rate. This information might guide nascent protein folding during translation. With the advent of ribosome profiling, a high-throughput sequencing technique which quantifies ribosome density on mRNA, it is now possible to investigate this hypothesis in greater detail. Here, a new way to analyze ribosome profiling data is presented, confirming that ribosome profiling detects ribosome pauses at slow codons. This method is able to precisely determine the locations of the ribosome aminoacyl and peptidyl transfer sites within the ribosome footprint. Next, a simulation tool which models the progression of ribosomes along an mRNA is used to explore the effects of translation initiation and elongation rates on protein expression. This tool can be used to generate testable predictions for how changing the translation rate should affect various experimental observables, including ribosome density. New experimental data, collected from the bacterium Escherichia coli, demonstrate that the sequence of the Firefly (Photinus pyralis) Luciferase mRNA affects its ribosome occupancy. Importantly, ribosome occupancy is differentially influenced by synonymous codons. These data also show that Luc expression is controlled by the 15 codons immediately downstream of the start codon and that greater Luciferase expression levels progressively activate the heat shock response. However, this response appears to saturate, suggesting that the overexpression of foreign proteins in E. coli readily overwhelms the endogenous chaperone system. This result demonstrates that expression level, rather than translation kinetics, determines the yield of folded Luciferase protein in E. coli

Texts, images and sounds in the urban environment, c.1100– c.1500

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Therapeutic Monoclonal Antibodies to Prevent Tuberculosis Infection

Mycobacteria tuberculosis (Mtb) is a major cause of human morbidity and mortality. Transmission occurs through inhalation of aerosolized Mtb and the initial infection is believed to occur primarily in the alveolar macrophage, although Mtb can infect other cells residing in the lung including dendritic cells, pneumocytes and M cells. Several molecules derived from Mtb are involved in the attachment of the organism to host receptors (opsonic and non-opsonic), which have been reasonably well elucidated. However, a complete understanding of how Mtb attaches to the host and the relative importance of each mechanism on the outcome of infection remains elusive. We hypothesize that protection from infection is possible by blocking the critical initial surface interactions of the organism with the host cell using specific monoclonal antibodies (mAbs). To develop effective mAbs, the outermost layers of Mtb, the capsule and outer membrane, were isolated and characterized by protein gel and LC/MS/MS. Approximately 1000 different proteins were identified in the isolations, of which ~25% were unique to one of the two fractions. The capsule or outer membrane preparations were used as antigens to immunize CD1 mice for up to 12 weeks to generate antibodies via traditional hybridoma generation. Antibodies were screened, selected and characterized by their ability to bind whole cell Mtb by ELISA, demonstration of unique heavy chain variable region sequence and binding specificity by Western Blot. Of approximately 1500 screened hybridomas, 30 lead mAbs have been isolated with specificity to various targets. Preliminary results suggest several of the lead mAb candidates are able to prevent Mtb-induced macrophage cell death in vitro. Future studies will attempt to confirm efficacy in vivo after aerosolized infection in mice with mAb-coated Mtb or parenteral administration of mAb(s). Targets of functional mAbs will be determined and these antigens could serve as viable candidates for vaccine development

Genetic and Computational Identification of a Conserved Bacterial Metabolic Module

We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the α-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined an operon encoding an ABC-family myo-inositol transmembrane transporter, and (3) identified a novel myo-inositol regulator protein and cis-acting regulatory motif that control expression of genes in this metabolic module. Despite being encoded from non-contiguous loci on the C. crescentus chromosome, these myo-inositol catabolic enzymes and transporter proteins form a tightly linked functional group in a computationally inferred network of protein associations. Primary sequence comparison was not sufficient to confidently extend annotation of all components of this novel metabolic module to related bacterial genera. Consequently, we implemented the Graemlin multiple-network alignment algorithm to generate cross-species predictions of genes involved in myo-inositol transport and catabolism in other α-proteobacteria. Although the chromosomal organization of genes in this functional module varied between species, the upstream regions of genes in this aligned network were enriched for the same palindromic cis-regulatory motif identified experimentally in C. crescentus. Transposon disruption of the operon encoding the computationally predicted ABC myo-inositol transporter of Sinorhizobium meliloti abolished growth on myo-inositol as the sole carbon source, confirming our cross-genera functional prediction. Thus, we have defined regulatory, transport, and catabolic genes and a cis-acting regulatory sequence that form a conserved module required for myo-inositol metabolism in select α-proteobacteria. Moreover, this study describes a forward validation of gene-network alignment, and illustrates a strategy for reliably transferring pathway-level annotation across bacterial species.</p

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

Advances in sequencing technology allow researchers to map genome-wide changes in DNA methylation in development and disease. However, there is a lack of experimental tools to site-specifically manipulate DNA methylation to discern the functional consequences. We developed a CRISPR/Cas9 DNA methyltransferase 3A (DNMT3A) fusion to induce DNA methylation at specific loci in the genome. We induced DNA methylation at up to 50% of alleles for targeted CpG dinucleotides. DNA methylation levels peaked within 50 bp of the short guide RNA (sgRNA) binding site and between pairs of sgRNAs. We used our approach to target methylation across the entire CpG island at the CDKN2A promoter, three CpG dinucleotides at the ARF promoter, and the CpG island within the Cdkn1a promoter to decrease expression of the target gene. These tools permit mechanistic studies of DNA methylation and its role in guiding molecular processes that determine cellular fate