Monitoring and control of a marine ecosystem in an aquarium

Research has shown that marine ecosystems are not only complex but also extremely difficult to replicate. Reef aquarists aim to replicate these marine ecosystems within aquariums in their homes, for the aesthetic beauty of such coral reef tanks. To assist aquarists in the task of maintaining environmental parameters in their tanks, a number of control and monitoring systems have been created through the advancement of embedded systems. The project, that this thesis is based on, involves the development of a control and monitoring system for a marine ecosystem sustained within an aquarium. The aim for the system was to control and monitor water parameters not yet considered by existing systems, in turn improving the stability of the ecosystem and reducing maintenance of the aquarium. As a part of this report, significant research was undertaken to assess existing systems and further understand the important water parameters necessary for marine ecosystems. The main focus of this thesis was to outline the approach, design and implementation of the control and monitoring system. This includes details on the systems selected features including: Control and monitoring of pH, Dissolved Oxygen, Temperature and Salinity. Control of realistic lighting. Control and monitoring of system parameters, water levels, pumps and other equipment. HMI interface for easy monitoring. To facilitate these features a PiLeven microcontroller has been programmed as a master device and performs all control and monitoring functions along with the communication to slave sensors. Additionally a Raspberry Pi microprocessor was utilised as the computer interface enabling the programming of the microcontroller and HMI for monitoring. At the completion of this thesis all aspects of the control and monitoring system are considered complete aside from the control of the pH and Salinity. Despite this the control and monitoring system was effectively implemented and is ready to house a marine ecosystem

Effect of Post-extraction Algal Residue Supplementation on the Therumen Microbiome of Steers Consuming Low-quality Forage

The rumen microbiome is a dynamic environment consisting of bacteria, protist, and fungi responsible for fiber degradation. Advances in molecular techniques have enabled description of bacterial microbiome via pyrosequencing. Cattle consuming low-quality forage are often supplemented with protein to increase forage intake and digestion, but effect on the rumen bacterial community is unknown. Thus, increasing post-extraction algal residue (PEAR) and cottonseed meal (CSM) supplementation was provided to steers consuming oat straw to observe the rumen microbiome within the liquid and solid fraction. Weighted UniFrac analysis indicated different fraction-associated communities with greater similarity across treatments in the solid fraction. Bacteroidetes was the predominant phyla detected in all samples (>65%). Within Bacteroidetes, Prevotella was the most abundant genus. In the liquid fraction, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae increased with PEAR provision (P < 0.05). Similar proportions of bacteria between unsupplemented control and CSM supplemented steers indicate factors other than N supply may impact ruminal bacteria populations. A second experiment evaluated the effect of supplemental CSM or dried distillers’ grain (DDG) for Brahman steers consuming rice straw. Total digestible OM intake and total tract OM digestion increased linearly with additional CSM and DDG provision (P < 0.01). Provision of CSM increased ruminal ammonia linearly (P < 0.01), but DDG supplementation resulted in a quadratic response (P = 0.02). Overall, protein supplementation may increase LQF utilization via changes in the rumen microbiome

Influence of nutrition on the muscle transcriptome and ruminal microbiome in cattle

Beef cattle nutrition research has historically focused on formulating diets to address nutrient requirements of cattle for given level of animal performance. While predictive models account for many factors that may affect nutrient requirements, additional physiological effects can alter the animal's ability to utilize dietary nutrients. Several of these factors include the ruminal microbiome composition and epithelial tissue function, and nutrient provision in utero. The objective of this dissertation was to evaluate the effects of nutrition on these physiological effects to determine their potential to influence nutrient utilization. Supplemental sources of fat, such as condensed distillers solubles (CDS), are often added to the diets of growing cattle to increase the energy density of the diet, but these products may negatively impact rumen bacteria at high inclusion levels. Five ruminally-fistulated steers were used in a 5 × 5 Latin square design to determine the effects of increasing dietary fat and sulfur from (CDS) on the ruminal microbiome. Alpha-diversity and species richness decreased (linear; P 0.10) of feeding increasing dietary fat from CDS on fibroylytic phyla Fibrobacteres in either fraction. Rapid consumption of a highly digestible diet causes rapid fermentation and may lead to the onset of subacute ruminal acidosis (SARA), a condition that negatively impacts the dairy industry by decreasing dry matter intake, milk production, and profitability. Six ruminallyfistulated, lactating Holstein cows were used in a replicated incomplete Latin square design to determine the effects of SARA induction on the ruminal microbiome and epithelium using a SARA induction model. Ruminal contents and epithelial biopsies were collected on d 1 and 6 of each period prior to feeding. Principal coordinate analysis of beta-diversity indicated samples within the liquid fraction separated by day and coincided with an increased relative abundance of genera Prevotella, Ruminococcus, Streptococcus, and Lactobacillus on d 6 (P < 0.06). Phylum Bacteroidetes increased on d 6 (P < 0.01) for SARA cows driven by greater genera Prevotella and YRC22 (P < 0.01). Streptococcus bovis and Succinivibrio dextrinosolvens populations tended to increase on d 6 but were not affected by the severity of acidotic bout. In ruminal epithelium, CLDN1 and CLDN4 expression increased on d 6 (P < 0.03) 24 h after SARA induction, but overall effects on ruminal epithelium were modest. Maternal nutrition provided during mid-gestation may influence skeletal muscle development and long-term metabolism. Three planes of nutrition were provided to cows to address 70% (70%REQ), 100% (REQ), and 130% NRC energy and protein requirements (130%REQ) during mid-gestation. All calf progeny were managed as a single contemporary group and longissimus muscles biopsies were taken on 99, 197, and 392 d of age. The skeletal muscle transcriptome analysis at d 392 indicated over 2,000 co-expressed genes were downregulated in progeny born to 130%REQ-fed compared with REQ-fed dams. These genes were annotated to many lipid-associated pathways including steroid and steroid hormone biosynthesis, sulfur metabolism, retinol metabolism, ketone synthesis and degradation, fat digestion and absorption, and PPAR signaling pathways. Another set of genes (342) was activated in progeny born to 130%REQ-fed compared with 70%REQ-fed dams and correlated negatively with marbling score. These genes were annotated to pathways centered on glycolysis/gluconeogenesis, energy metabolism, and calcium signaling to support increased glycolytic muscle fibers (type 2x) in progeny born to 130%REQ-fed dams. Skeletal muscle miRNA were tightly regulated over time suggesting various roles in postnatal hypertrophy. Maternal plane of nutrition effects (P < 0.1) were observed for miR-376d and miR-381. Results indicate that maternal plane of nutrition has a long-term impact on the skeletal muscle transcriptome and may be linked to effects on meat quality

A cluster analysis of harmony in the McGill Billboard dataset

We set out to perform a cluster analysis of harmonic structures (specifically, chord-to-chord transitions) in the McGill Billboard dataset, to determine whether there is evidence of multiple harmonic grammars and practices in the corpus, and if so, what the optimal division of songs, according to those harmonic grammars, is. We define optimal as providing meaningful, specific information about the harmonic practices of songs in the cluster, but being general enough to be used as a guide to songwriting and predictive listening. We test two hypotheses in our cluster analysis — first that 5–9 clusters would be optimal, based on the work of Walter Everett (2004), and second that 15 clusters would be optimal, based on a set of user-generated genre tags reported by Hendrik Schreiber (2015). We subjected the harmonic structures for each song in the corpus to a K-means cluster analysis. We conclude that the optimal clustering solution is likely to be within the 5–8 cluster range. We also propose that a map of cluster types emerging as the number of clusters increases from one to eight constitutes a greater aid to our understanding of how various harmonic practices, styles, and sub-styles comprise the McGill Billboard dataset

Polyclonal antibodies inhibit growth of key cellulolytic rumen bacterial species

Antibodies targeting specific bacterial species could allow for modification of the rumen microbial population to enhance rumen fermentation. However, there is limited knowledge of targeted antibody effects on rumen bacteria. Therefore, our objective was to develop efficacious polyclonal antibodies to inhibit the growth of targeted cellulolytic bacteria from the rumen. Egg-derived, polyclonal antibodies were developed against pure cultures of Ruminococcus albus 7 (anti-RA7), Ruminococcus albus 8 (anti-RA8), and Fibrobacter succinogenes S85 (anti-FS85). Antibodies were added to a cellobiose-containing growth medium for each of the three targeted species. Antibody efficacy was determined via inoculation time (0 h and 4 h) and dose response. Antibody doses included: 0 (CON), 1.3 × 10−4 (LO), 0.013 (MD), and 1.3 (HI) mg antibody per ml of medium. Each targeted species inoculated at 0 h with HI of their respective antibody had decreased (P &lt; 0.01) final optical density and total acetate concentration after a 52 h growth period when compared with CON or LO. Live/dead stains of R. albus 7 and F. succinogenes S85 dosed at 0 h with HI of their respective antibody indicated a decrease (≥ 96%; P &lt; 0.05) in live bacterial cells during the mid-log phase compared with CON or LO. Addition of HI of anti-FS85 at 0 h in F. succinogenes S85 cultures reduced (P &lt; 0.01) total substrate disappearance over 52 h by at least 48% when compared with CON or LO. Cross-reactivity was assessed by adding HI at 0 h to non-targeted bacterial species. Addition of anti-RA8 or anti-RA7 to F. succinogenes S85 cultures did not affect (P ≥ 0.45) total acetate accumulation after 52 h incubation, indicating that antibodies have less of an inhibitory effect on non-target strains. Addition of anti-FS85 to non-cellulolytic strains did not affect (P ≥ 0.89) OD, substrate disappearance, or total VFA concentrations, providing further evidence of specificity against fiber-degrading bacteria. Western blotting with anti-FS85 indicated selective binding to F. succinogenes S85 proteins. Identification by LC-MS/MS of 8 selected protein spots indicated 7 were outer membrane proteins. Overall, polyclonal antibodies were more efficacious at inhibiting the growth of targeted cellulolytic bacteria than non-targeted bacteria. Validated polyclonal antibodies could serve as an effective approach to modify rumen bacterial populations

High-Precision Inversion of Dynamic Radiography Using Hydrodynamic Features

Radiography is often used to probe complex, evolving density fields in dynamic systems and in so doing gain insight into the underlying physics. This technique has been used in numerous fields including materials science, shock physics, inertial confinement fusion, and other national security applications. In many of these applications, however, complications resulting from noise, scatter, complex beam dynamics, etc. prevent the reconstruction of density from being accurate enough to identify the underlying physics with sufficient confidence. As such, density reconstruction from static/dynamic radiography has typically been limited to identifying discontinuous features such as cracks and voids in a number of these applications. In this work, we propose a fundamentally new approach to reconstructing density from a temporal sequence of radiographic images. Using only the robust features identifiable in radiographs, we combine them with the underlying hydrodynamic equations of motion using a machine learning approach, namely, conditional generative adversarial networks (cGAN), to determine the density fields from a dynamic sequence of radiographs. Next, we seek to further enhance the hydrodynamic consistency of the ML-based density reconstruction through a process of parameter estimation and projection onto a hydrodynamic manifold. In this context, we note that the distance from the hydrodynamic manifold given by the training data to the test data in the parameter space considered both serves as a diagnostic of the robustness of the predictions and serves to augment the training database, with the expectation that the latter will further reduce future density reconstruction errors. Finally, we demonstrate the ability of this method to outperform a traditional radiographic reconstruction in capturing allowable hydrodynamic paths even when relatively small amounts of scatter are present.Comment: Submitted to Optics Expres

A Custom, High-Channel-Count Data Acquisition System for Chemical Species Tomography of Aero-Jet Engine Exhaust Plumes

The fiber-laser imaging of gas turbine exhaust species project aims to provide a video-rate imaging (100 frames/s) diagnostic tool for application to the exhaust plumes of the largest civil aero-jet engines. This remit, enabled by chemical species tomography (CST) currently targeting carbon dioxide (CO 2 ), requires system design that facilitates expansion of multiple parameters. Scalability is needed in order to increase imaging speeds and spatial resolutions and extends the system toward other pertinent gases such as the oxides of nitrogen and sulfur and unburnt hydrocarbons. This paper presents a fully scalable, noninvasive instrument for installation in a commercial engine testing facility, technical challenges having been tackled iteratively through bespoke optical and mechanical design, and it specifically presents the high-speed data acquisition (DAQ) system required. Measurement of gas species concentration is implemented by tunable diode laser absorption with wavelength modulation spectroscopy (TDLAS-WMS) using a custom, high-speed 10-40-MS/s/channel 14-bit DAQ. For CO 2 tomography, the system uses six angular projections of 21 beams each. However, the presented DAQ has capacity for 192 fully parallel 10-Hz-3-MHz differential inputs, achieving a best-case signal-to-noise ratio (SNR) of 56.5 dB prior to filtering. A 12 Ethernet-connected digitization nodes based on field-programmable gate array technology with software control are distributed around a 7-m-diameter mounting “ring.” Hence, the high data rates of 8.96-Gb/s per printed circuit board and 107.52 Gb/s for the whole system can be reduced by using local digital lock-in amplifiers. We believe that this DAQ system is unique in both the TDLAS and CST literatures

Analysis of the Rumen Microbiota of Beef Calves Supplemented During the Suckling Phase

A study was conducted to examine the effects of supplementing beef calves during their suckling phase (popularly known as creep feeding) with supplements that contained or did not contain the enzyme xylanase. Forty-two cow-calf pairs were divided into three groups and assigned to one of three treatments for a period of 105 days, as follows: (1) No supplemental feed for calves (control; CON); (2) Corn and soybean meal-based supplement feed for calves (positive control; PCON); and (3) Same feed regimen as PCON with xylanase added to the supplement (enzyme; ENZ). After 105 days, out of the 42 calves participating in the study, 25 male calves were randomly selected (8 from CON, 9 from PCON, and 8 from ENZ) and samples of their forestomach were collected by esophageal tubing. Immediately after this procedure, all calves were weaned, commingled, and placed in a common post-weaning diet for 4 weeks. At the end of this period, ruminal fluid was once again collected from the same 25 calves. All samples were subjected to DNA extraction and 16S rRNA gene sequencing. At weaning, most of the alpha diversity indexes were greater in CON; however, no differences (P ≥ 0.23) in alpha diversity were observed in samples collected 4 weeks after weaning. Regardless of treatment, 2 phyla – Bacteroidetes and Firmicutes – comprised approximately 80% of the total bacterial abundance of samples collected on both days. At the genus level, an effect of diet (P = 0.02) was observed for Prevotella in the samples collected at weaning; however, no differences were detected in the samples collected 4 weeks after weaning. Calf average daily gain (ADG) during the 105-day creep feeding trial tended (P = 0.09) to be greater in the groups that received supplementation, with the greatest numerical value observed in ENZ. Moreover, there was a positive correlation (ρ = 0.43; P = 0.03) between ADG and abundance of Prevotella, indicating the importance of this bacterial group for ruminants. In summary, most of the significant differences found in this study were detected at weaning, and the majority of them disappeared 4 weeks after the calves were weaned and commingled