Sex determination and genetic management in Nile tilapia using genomic techniques

The PhD research studied two aspects in tilapia, firstly the analysis of sex determination in Nile tilapia (evidence of complex sex-determining systems) and secondly the genetic management of the tilapia species, using different genomic analysis approaches. This research started with the development of two techniques: minimally invasive DNA sampling from fish mucus, which was found to be suitable for standard genotyping and double-digest restriction-site associated DNA sequencing – ddRADseq; and pre-extraction pooling of tissue samples for ddRADseq (BSA-ddRADseq), which was found to be suitable for identifying a locus linked to a trait of interest (sex in this case). The first molecular evidence concerning the sex determination in genetically improved farmed tilapia (GIFT) was described using BSA-ddRADseq. Given the multiple stock origin of GIFT, surprisingly only a single locus (in linkage group 23) was found to be associated with the phenotypic sex across the population. The first evidence of LG23 influence on phenotypic sex in the Stirling population of Nile tilapia was also found. Different combinations of estrogen hormones and high temperature were tested for feminising Nile tilapia: a combined treatment of estrogen hormone and high temperature was found to be more efficient in feminising Nile tilapia than the estrogen alone. A set of species-diagnostic SNP markers were tested which were found to be suitable to distinguish pure species (O. niloticus, O. mossambicus and O. aureus), and these were used to analyse species contribution to GIFT and a selected tilapia hybrid strain. The results of the current research added novel information to our understanding of sex determination in Nile tilapia, which will be helpful in the development of marker-assisted selection in GIFT and other Nile tilapia strains towards the production of all male offspring. The methods developed also have broader applicability in genetic and genomics research

Evaluation of environmental sustainability maxtrix of Deepgen tidal turbine

Tidal energy is a reliable, consistent and abundant source of renewable energy. However, there are many concerns with different tidal energy devices relating to their environmental impacts over the lifetime. It is essential to address these issues by assessing the environmental impacts of these technologies throughout all phases of life cycle. In this context, a cradle to grave life cycle assessment (LCA) study is performed hereby on 1 MW Deepgen tidal turbine. ReCiPe LCA method has been used to evaluate 18 different environmental impacts; i.e., global warming in 100 years horizon, stratospheric ozone depletion, ionising radiation, ozone formation (human health), fine particulate matter formation, ozone formation (terrestrial ecosystems), terrestrial acidification, freshwater eutrophication, marine eutrophication, terrestrial ecotoxicity, freshwater ecotoxicity, marine ecotoxicity, human carcinogenic toxicity, human non-carcinogenic toxicity, land use, mineral resource scarcity, fossil resource scarcity and water consumption. According to the findings, steel, copper and glass fibre reinforced plastic (GFRP) carry the highest contributions across all impact categories. Steel contributes about 30%, on average, across all impact categories; copper contributes significantly to eutrophication and toxicity impacts while GFRP contributes significantly to marine eutrophication. Total global warming emission of the turbine stands at approximately 1 ktCO2 eq which establishes the turbine as a lower GHG impact carrying solution. Findings from the study will serve as a benchmark to deploy more tidal power turbines around the world

New antifriction composites for printing machines based on tool steel grinding waste

In this article, we present research results on the structure and properties of new self-lubricating antifriction composites based on 4H4VMFS tool steel grinding waste with solid lubricant additives. The new composites are designed to work in the friction units of offset cylinders in printing machines at rotation speeds up to 7000 rpm and increased loads up to 5.0 MPa. The developed technology formed composites with a fine-grained heterophase structure with a metal matrix base of tool steel 4H4VMFS regenerated grinding waste, consisting of high-alloy α−solid solution and hard grains of alloying element carbides, as well as evenly distributed CaF2 antiseizure solid lubricant. This structure ensured the formation of composites with favorable functional properties. During the friction process, antiseizure films were formed on the contact surfaces, resulting in a self-lubrication mode. Comparative tests for friction and wear showed significant advantages of the new waste composite compared to cast bronze parts, which are traditionally used in the friction units of offset cylinders of rolled newspaper printing machines. The stable operation of the new composite made it possible to ensure a "wear-free" effect. Studies have shown the importance and prospects of using the wide range of valuable grinding waste in the reproduction cycle to manufacture quality composites. Reuse of such waste would significantly protect the environment from pollution connected with human activity industrial and mitigate negative impacts on ecosystems and the biosphere

Life cycle environmental sustainability and energy assessment of timber wall construction : a comprehensive overview

This article presents a comprehensive overview of the life cycle environmental and energy assessment for all residential and commercial constructions made of timber walls, globally. The study was carried out based on a systematic literature analysis conducted on the Scopus database. A total of 66 research articles were relevant to timber wall design. Among these, the residential construction sector received more attention than the commercial sector, while the low-rise construction (1–2 stories) gained more attention than high-rise construction (>5 stories). Most of these studies were conducted in Canada, Europe, Malaysia, and the USA. In addition, the end-of-life phase received limited attention compared to upstream phases in most of the studies. We compared all environmental and energy-based life cycle impacts that used “m2” as the functional unit; this group represented 21 research articles. Global warming potential was understandably the most studied life cycle environmental impact category followed by acidification, eutrophication, embodied energy, photochemical oxidation, and abiotic depletion. In terms of global warming impact, the external walls of low-rise buildings emit 18 to 702 kg CO2 kg eq./m2, while the internal walls of the same emit 11 kg CO2 kg eq./m2. In turn, the walls of high-rise buildings carry 114.3 to 227.3 kg CO2 kg eq./m2 in terms of global warming impact. The review highlights variations in timber wall designs and the environmental impact of these variations, together with different system boundaries and varying building lifetimes, as covered in various articles. Finally, a few recommendations have been offered at the end of the article for future researchers of this domain

Local ancestry inference provides insight into Tilapia breeding programmes

Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. It has become increasingly important to keep track of the inheritance of the selected traits under continuous improvement (e.g. growth rate, size at maturity or genetic gender), as selective breeding has also resulted in genes that can hitchhike as part of the process. The goal of this study was to generate a Local Ancestry Interence workflow that harnessed existing tilapia genotyping-by-sequencing studies, such as Double Digest RAD-seq derived Single-Nucleotide Polymorphism markers. We developed a workflow and implemented a suite of tools to resolve the local ancestry of each chromosomal locus based on reference panels of tilapia species of known origin. We used tilapia species, wild populations and breeding programmes to validate our methods. The precision of the pipeline was evaluated on the basis of its ability to identify the genetic makeup of samples of known ancestry. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin

Species composition in the Molobicus hybrid tilapia strain

The “Molobicus” hybrid breeding programme was initiated to improve tilapia growth performance in brackish water. The base population was created by backcrossing F1 Oreochromis niloticus GIFT strains × feral O. mossambicus to O. mossambicus and selective breeding conducted for performance in brackish water with two lines selected in extensive or intensive rearing conditions. A panel of ten diagnostic SNP markers was applied to estimate the species composition at different stages in the Molobicus programme including parental stocks, F1 and seventh generation fish from the selective lines. The O. aureus-specific markers tested revealed zero or negligible contribution from O. aureus to all the groups analysed. Feral O. mossambicus possessed an estimated 0.98 frequency of O. mossambicus-specific alleles, while GIFT samples had an estimated mean frequency of 0.88 O. niloticus-specific alleles. Hybrid F1 GIFT × feral O. mossambicus samples demonstrated close to 50:50 allele frequencies from O. niloticus and O. mossambicus for seven of the eight SNP loci tested. Analysis of the combined seventh generation Molobicus samples revealed a significant excess of O. niloticus alleles in six out of the eight SNPs tested, with this trend being more pronounced in the line selected in intensive culture conditions and showing increased body weight. PCR-based SNP assays such as these can be used to inform on the individual species contribution of fish stocks and provide tools for the genetic management of the tilapia species and future breeding programmes

On-line monitoring of particulate processes using digital holography

Digital holography is an effective three’ dimensional imaging technique, with the potential to be used for particle size measurements. A digital hologram can provide reconstructions of volume samples focused at different depths, overcoming the focusing problems encountered by other imaging based techniques. This work explores the potential of digital holography as a tool for online measurement of size and shape of micro particles. The first part of the thesis deals with the development of a technique to obtain 2D information of particles. The system was validated for both spherical and non-spherical (needle shaped) particles. The results from holography are shown to be fully consistent with those from independent techniques such as scanning electron microscopy. While 2D information is sufficient to describe spherical particles, it does not provide accurate information concerning nonspherica1, especially needle- shaped particles. An accurate measurement of the lengths is possible only if the orientation can be unambiguously measured, In order to address this problem, two novel techniques have been developed which simultaneously measure the location, orientation and length of a population of fibers. These have demonstrated by careful validation using single fibers and applied to a fiber population. Finally the technique has been applied to monitor the crystallization of transparent crystals of oxalic acid and measured their growth rate. The results obtained from this work adequately demonstrate the potential of digital holography as a reliable tool for the online monitoring of particulate processes.DOCTOR OF PHILOSOPHY (SCBE

DNA sampling from mucus in the Nile tilapia, Oreochromis niloticus: Minimally invasive sampling for aquaculture-related genetics research

First paragraph: Genotypic information is widely used in the conservation and management of wild fish (Schwartz, Luikart & Waples 2007) and is increasingly valuable in the management of captive populations (e.g. for verification of pedigree or for marker-assisted selection; Perez-Enriquez, Takagi & Taniguchi 1999; Sonesson 2007). Obtaining DNA most commonly involves taking tissue samples from live fish, such as blood or a fin biopsy (Campanella & Smalley 2006), or killing fish (particularly if too small to take biopsy samples: Mirimin, O'Keeffe, Ruggiero, Bolton-Warberg, Vartia & Fitzgerald 2011). Tissue biopsy may have negative impacts on fish, potentially including infection and effects on survival, growth or behaviour (Le Vin, Adam, Tedder, Arnold & Mable 2011); e.g. the adipose fin, commonly removed from salmonids for marking and DNA extraction, is now known to show sexual dimorphism (Hisar, Sönmez, Hisar, Budak & Gültepe 2013) and is thought to function as a flow sensor (Buckland-Nicks, Gillis & Reimchan 2011). In studies on wild fish populations, particularly rare or uncommon species with small body size, it is undesirable to kill large numbers, and this has led to recent publications investigating extraction of DNA from mucus taken from the skin or mouth cavity (Campanella & Smalley 2006; Livia, Antonella, Hovirag, Mauro & Panara 2006; Le Vin etal. 2011; Mirimin etal. 2011; Reid, Kidd & Wilson 2012; de Verdal, Vandeputte, Pepey, Vidal & Chatain 2014). Brush swabbing is one of the less invasive sampling strategies, which is used in a range of other groups of organisms, e.g. humans (Clarke, Prost, Stanton, White, Kaplan & Matisoo-Smith 2014), amphibia (Pidancier, Miquel & Miaud 2003) and molluscs (Henley, Grobler & Neves 2006). The reduced invasiveness of such sampling techniques, and reduced likelihood of impact on the welfare of the fish concerned, also makes them less likely to come under regulations on animal experimentation; swab samples can also be collected without the use of anaesthesia, required under UK regulations for tissue biopsy (Le Vin etal. 2011). Potential drawbacks of such methods may include sample contamination, low DNA quantity or poor quality DNA (Taberlet, Waits & Luikart 1999; Lieber, Berrow, Johnston, Hall, Hall, Gubili, Sims, Jones & Noble 2013)