This report is about the implementation of autonomy and control on a water quality measuring unmanned surface vehicle. The project was termed Catfish and involved five teams focusing on different aspects of the initial goal to create an autonomous three-part system; a surface drone, a submerged drone and flying drone. In this iteration of the Catfish project the focus laid on creating the surface drone and submerged drone as the Catfish project will improve over generations of thesis projects. The author of the report was in the Control and Autonomy team and had been tasked with giving the surface drone the autonomy needed to make this project viable. Existing advances made in autonomy was adopted and tested. With the help of estimation algorithms, and sensor fusion, a flight controller navigates the surface drone between a set of GPS waypoints. It is also able to counteract the external forces wind, waves and stream to keep its position. To reach this autonomy four test phases were conducted on a pre-prototype with progressively increased difficult autonomy starting with manual control and ending in advanced autonomy. When the advanced missions were executed the speed and accuracy of two different thruster configurations were examined and the best performing out of the two was implemented on the final prototype the other teams had designed. The project ended with a fully autonomous system that was able to execute all the navigational maneuvers required to operate autonomous water quality measuring missions. / Den här rapporten handlar om implementationen av autonomi och kontroll på en vattenkvalitetsmätande vattenburen drönare. Projektet fick namnet Catfish och blev indelat i fem teams som fokuserade på olika aspekter av ett 3-delsystem; en vattenburen, en undervattens och en flygande drönare. I denna iteration av Catfish projektet fokuserade medlemmarna på att utveckla den vattenburna och undervattens drönaren då projektet kommer fortsätta utvecklas under kommande generationer av Catfish projektrapporter. Författaren av den här rapporten ingick i ett team som hette "Control and Autonomy" och hade i uppgift att installera en autonom intelligens till den vattenburna drönaren för att göra Catfish prototypen användbar. Befintliga framsteg inom forskningsområdet blev granskade och testade. Genom att använda uppskattningsalgoritmer och "sensor fusion" lyckades en "flight controller" navigera drönaren mellan GPS waypoints och även behålla sin position genom att motverka krafterna från vind, vågor och strömmar. För att uppnå denna nivå av autonomi utför en förprototyp fyra test faser av ökad autonomisk svårhetsgrad. Under uppdraget blev hastigheten och precisionen av två olika motoruppsättningar undersöka och den som presterade bäst blev implementerad på den slutgiltig designen som de andra teamen hade utvecklat. Projektet avslutades med att ett fullt autonomt system blev utvecklat som var kapabel till att utföra alla navigationsmanövrar nödvändiga för att genomföra autonoma vattenkvalitetsmätningsuppdrag.

Channel catfish (Ictalurus punctatus) have a broad distribution from Canada to Mexico, suggesting that different strains may have different thermal tolerances. In aquaculture, daily temperature maximums up to 36-40°C and fluctuations of 3-6°C occur, and may be exacerbated by future climate change. To quantify differences in thermal tolerance amongst geographically-distinct channel catfish strains and corresponding hybrid catfish (I. punctatus x [blue catfish] I. furcatus): acute critical thermal maximum (CTmax), and the effects of chronic thermal regimes on growth, survival and differential gene expression were examined. Southern channel catfish had higher CTmax than northern, and channel catfish had higher CTmax than hybrid catfish. Under chronic thermal stress, hybrid catfish had the greatest survival and most consistent growth. Further, northern channel catfish had the greatest magnitude and largest amount of upregulated gene transcripts in response to high temperatures, indicating greater thermal stress. Therefore, catfish thermal tolerance varies by geographic region and species.

Commercial production of catfish is the leading aquaculture industry in the United States. Production in Mississippi, Louisiana, Alabama, and Arkansas representing 96% of the total catfish sales in the USA. In 2017, the USDA-FSIS added testing of generic Escherichia coli and Enterococcus to the sampling of Siluriformes. The incidence of Escherichia coli in fish and seafood has been associated with possible fecal matter contamination. However, this indicator bacteria could also be a part of the natural microflora of catfish ponds where processing plants collect hybrid catfish. Aerobes, Psychrotrophs, Coliforms, Escherichia coli, and Enterobacteriaceae counts among environmental, liquid and fish samples were tested every season and periodically during one day of operation. Generic Escherichia coli counts were greater in late Summer (P ≤ 0.05) for liquid samples (1 log CFU/g) . During the day, Escherichia coli appeared to be more recurrent in the afternoon at the skinning step (P ≤ 0.05).

Catfish aquaculture is the largest cultured food fish industry in the United States, accounting for approximately $375 million in sales annually, with Mississippi leading the industry with 36,200 surface acres of production. However, infectious diseases such as enteric septicemia of catfish (ESC) are decreasing production efficiencies, creating losses of $40-60 million annually. Live-attenuated oral ESC vaccines are effective in preventing ESC infections, but have not been widely adopted by the catfish industry due to the lack of a system to administer the oral vaccine at the scale seen in commercial catfish production systems. An automated system was developed to administer a dosage of 220.5 ml of a live-attenuated ESC vaccine per kg of catfish feed, adapting commercial catfish feeder design to include a screw conveyor for mixing vaccine and feed in a continuous process, pulse-width modulated spray nozzle control for precise vaccine application, and a programmable automation controller to regulate and monitor system performance. Initial performance evaluations demonstrated system operation within the desired design specifications. System feed rates were determined to be a function of the rotational speed (RPM) of the screw conveyor and to be linear across the operational range. Feed rates were observed to decrease by 45% over dry feed when applying liquid vaccine to the feed stream at the 220.5 ml/kg (100 ml/lb) rate, resulting in a feed rate range of 6.80-34.02 kg/min (15-75 lb/min) (95% CI). Uniform pellet-level vaccine distribution is crucial to efficacy as pellet consumption is directly correlated with fish size, with more criticality in smaller fish fed at low rates. Pellet vaccine concentrations at 6.80, 20.41, and 34.02 ml/kg were highly variable and vaccine application at all rates were observed to be statistically different (less) than the target 220.5ml/kg rate (95% CI), pointing to potential issues with vaccine delivery system configuration or inadequacies in sampling methodology. Further evaluation at the pellet level with live-attenuated vaccine to obtain viable cell counts within individual pellets would provide data necessary to address uniformity of coverage questions more fully and to develop operational protocols that maximize system capabilities and vaccine efficacy.

Since being first reported in the late 1980ies, the Enterobacterium Edwardsiella ictaluri has rose in prevalence to become one of the two most damaging pathogens affecting the channel catfish industry. Despite this significance of the pathogen, understanding of the development of the disease, especially its route of entry into the host and the earlier stages of the infection, is still incomplete. A series of challenges were conducted using bioluminescent E. ictaluri either by infecting fish through immersion or topical application of the bacteria directly on the intact or abraded epithelium. This showed that abraded fish developed septicemia and died faster than non-abraded ones. Furthermore, results from a co-habitation challenge suggested that the bacterium induced septicemia through the skin instead of becoming water-borne. Finally, a histological technique was developed allowing the determination that the bacteria radiated from the initial skin infection site and penetrated deeper into the tissue as the challenge progressed. These results all suggest that site of abrasion on the skin can act as a route of entrance for the pathogen into the fish, a fact never previously reported. Transposon mutagenesis was also performed to construct a library of 1728 mutants. Screening of this library allowed us to identify 16 genes which inactivation lead to a decrease in the bacterium ability to colonize the epithelium or cause mortality. Sequencing of these genes allowed the identification of RstA/B, a regulator of invasion genes in Salmonella enterica Typhimurium, a putative ribonuclease, similar to a Shigella protein regulating the expression of adhesin and a protein that constitutes the second member of a newly discovered adhesin family. Finally, to investigate the development of the infection, fish were infected by bioluminescent E. ictaluri and sampled at various time points. At each time point, nine organs (gills, muscles, intestine, spleen, liver, stomach, heart, head kidney and trunk kidney) were sampled, and their bioluminescence was measured and half of these organs were homogenized, serial diluted, and plate counts determined. This allowed confirmation of a complex disease pathogenesis during ESC involving a period of intense reproduction in the spleen, anterior and posterior kidneys followed by a sharp increase in the levels of bacteria in the blood.

Thesis (Ph.D.)--Mississippi State University. Department of Basic Sciences. / Title from title screen. Includes bibliographical references.

Photoperiod manipulation is routinely used in the aquaculture industry with the aim to enhance growth by manipulating the timing of reproduction in several commercially important temperate fish species. However, there are clear gaps in our understanding of how photoperiod is perceived by the circadian axis and transmitted to the brain to alter reproduction. Furthermore, due to the wide range of environments inhabited by fish, it is unlikely that one single organization exists. It is therefore believed that comparative studies of temperate species “models” with tropical species such as the African catfish (Clarias gariepinus) that adapted to different environments characterized by weaker light signals can help in such an aim. A number of studies were therefore performed in this PhD project to expand our knowledge on circadian biology and environmental physiological effects in African catfish. The first aim was to characterize the circadian melatonin system in this species (chapter 3). Results clearly showed that the control of melatonin production by the pineal gland was very different in the African catfish as compared to temperate species such as salmon and trout. Indeed, melatonin production appeared to mainly depend on light stimuli perceived by the eyes as opposed to salmonids where light directly perceived by the pineal gland regulates its own melatonin production within photoreceptors. The main evidence was obtained in ophthalmectomised fish that were unable to synthesize and release melatonin into the blood circulation during the dark period. This was the first time that such a decentralized organisation, similar in a way to the mammalian system, was found in any teleost species. In vitro results also supported such findings as African catfish pineal glands in isolation were not able to normally produce melatonin at night as usually seen in all other fish species studied so far. This indirectly suggested that pineal gland photo-sensitivity might be different in this tropical species. Further studies were performed to better determine the amount of light that can be perceived by the African catfish pineal gland depending on light transmittance though the skull (where the pineal gland is located). Surprisingly, it appeared that catfish cranium act as a stronger light filter than in other species resulting in lower light irradiance of the pineal gland. This could explain, although it still needs to be further confirmed, why African catfish photic control of melatonin produced by the pineal would have evolved differently than in temperate species. The work then focused on better characterizing diel melatonin production and endogenous entrainment through exposure to continuous photic regimes (continuous light, LL or darkness, DD) (chapter 4). Daily melatonin profiles of fish exposed to 12L:12D photoperiod (routinely used in indoor systems) confirmed low melatonin production at day (<10 pg/ml) and increase at night (50 pg/ml) as reported in most vertebrate species studied to date. Interestingly, results also showed that melatonin production or suppression can anticipate the change from night to day with basal melatonin levels observed 45 mins prior to the switch on of the light. These observations clearly suggest the involvement of a clock-controlled system of melatonin secretion that is capable of anticipating the next photophase period. Furthermore, when constant light (LL) was applied, day/night melatonin rhythms were abolished as expected due to the constant photic inhibition of AANAT activity (e.g. one of the enzyme responsible for the conversion of serotonin into melatonin). However when fish were exposed to constant darkness (DD), a strong endogenous melatonin rhythm (maintained for at least 4 days and 18 days in catfish and Nile tilapia respectively) was found, demonstrating once again the presence of robust circadian oscillators in this species. The next aim of the doctoral project was then to investigate circadian behaviour of catfish through locomotor activity studies (Chapter 5). African catfish is again a very interesting “model” due to its reported nocturnal activity rhythmicity as compared to most other teleosts species. Locomotor activity is considered as a very useful tool to elucidate the mechanisms of circadian organization in both invertebrates and vertebrates circadian. Results first confirmed the nocturnal activity rhythms in the species. Furthermore, clear circadian endogenous rhythms were observed under constant light (LL) or darkness (DD) during several days before losing rhythmicity. Interestingly, the activity levels varied depending on the stocking density. Finally, the last aim of this project was to test the effects of a range of photoperiodic manipulations on growth performances, sexual development and reproductive performances in African catfish reared from eggs to puberty. Results did not show any differences at the early sages (up to 90 days post hatching) in growth performances nor mortality (high) between control 12L:12D and LL treatments. In contrast, during the juvenile-adult period (from 120 to 360 DPH), significant growth effects were observed, as previously reported in other catfish species, with fish under LL displaying lower growth rate, food consumption and feed conversion efficiency in comparison to most other treatments (12:12, LL, 6:6, 6:18, 12-LL and LL-12) especially 12l:12D. However, no major effects of the photoperiodic treatments were observed with all fish recruited into puberty and developing gonads although differences in the timing of gametogenesis could be observed, especially a delay (circa 2 months) in females exposed to short daylength (6L:18D and 6L:6D). As for egg quality, egg diameter was the only parameter to differ between treatments (slightly larger in egg batch from LL treated females). Overall, none of the photoperiodic regime suppressed maturation in African catfish as opposed to some temperate species. The work carried out during this PhD project clearly advanced our understanding of circadian rhythmicity, light perception and effects of photoperiod on physiology in a tropical species. Future studies are now required to further characterise the circadian system and link it to evolutionary trends within vertebrates.

The purpose of the present study is to present research data on the propagation of the southern spotted channel catfish.

The chemosensory abilities of fishes, are important in order to understand how prey can perceive and avoid predators. Predator-naïve Channel catfish were exposed to four extracts over eight sessions (naïve bass water (NBW), bass that were fed catfish water (BFCW), catfish skin extract (CS), and naïve bass water paired with catfish skin extract (CO)) to determine whether they have an innate predator response to potential chemical cues indicating possible predation risk. Movement was quantified as grid squares crossed, directional changes, and tail beats. Response increased during the first minute following stimulus injection and decreased during the second minute. Channel catfish increased movement upon exposure to stimuli from NBW, CS and CO but not to BFCW. Increased response to bass odor while habituating to catfish skin extract, which presumably contains alarm pheromone, suggests that catfish learned to recognize bass odor without external reinforcement.

The channel catfish, Ictalurus punctatus (Rafinesque), was first introduced into Utah Lake in the summer of 1911, and has since been stocked in the lake on numerous occasions. It has only been in the last few years that the channel catfish has become an important game fish in Utah. As the value of the channel catfish, as a game fish, increased, it has become increasingly important to the state to maintain this species for present and future generations. This study was initiated in 1958 and completed in 19 60, and was financed by the Utah State Department of Fish and Game. Data on certain phases of the channel catfish life history were investigated to provide information to aid in management of this species. The following phases were studied: age and rate of growth; age composition of the population; reproduction success; food habits; movements; and extent of the fishing pressure.